=============================================================================== About this build: this rebuild has been done as part of reproduce.debian.net where we aim to reproduce Debian binary packages distributed via ftp.debian.org, by rebuilding using the exact same packages as the original build on the buildds, as described in the relevant .buildinfo file from buildinfos.debian.net. For more information please go to https://reproduce.debian.net or join #debian-reproducible on irc.debian.org =============================================================================== Get:1 https://deb.debian.org/debian trixie InRelease [175 kB] Get:2 https://deb.debian.org/debian trixie/main Sources [10.6 MB] Fetched 10.7 MB in 11s (974 kB/s) Reading package lists... 'https://deb.debian.org/debian/pool/main/g/gromacs/gromacs_2025.1-1.dsc' gromacs_2025.1-1.dsc 3277 SHA256:3cf5c33a7f545104cb274e14ba9311bfa69362bf2873218be6967ae4fd7a3ed4 'https://deb.debian.org/debian/pool/main/g/gromacs/gromacs_2025.1.orig-regressiontests.tar.gz' gromacs_2025.1.orig-regressiontests.tar.gz 32653610 SHA256:b38b63f79b23bf4c87dcaf079c49caaa729c7400fa2a4ae8db86514996c8b4de 'https://deb.debian.org/debian/pool/main/g/gromacs/gromacs_2025.1.orig.tar.gz' gromacs_2025.1.orig.tar.gz 44415202 SHA256:0adf621a80fd8043f8defec84ce02811c0cdf42a052232890932d81f25c4d28a 'https://deb.debian.org/debian/pool/main/g/gromacs/gromacs_2025.1-1.debian.tar.xz' gromacs_2025.1-1.debian.tar.xz 37256 SHA256:8c2593924374303fa6d6c534741816678e693dd5e8b386002b5f8a79d6093906 b38b63f79b23bf4c87dcaf079c49caaa729c7400fa2a4ae8db86514996c8b4de gromacs_2025.1.orig-regressiontests.tar.gz 0adf621a80fd8043f8defec84ce02811c0cdf42a052232890932d81f25c4d28a gromacs_2025.1.orig.tar.gz 8c2593924374303fa6d6c534741816678e693dd5e8b386002b5f8a79d6093906 gromacs_2025.1-1.debian.tar.xz 3cf5c33a7f545104cb274e14ba9311bfa69362bf2873218be6967ae4fd7a3ed4 gromacs_2025.1-1.dsc +------------------------------------------------------------------------------+ | Calling debrebuild Wed, 23 Apr 2025 01:57:01 +0000 | +------------------------------------------------------------------------------+ Rebuilding gromacs_2025.1-1_riscv64.buildinfo in /srv/rebuilderd/tmp/rebuilderdLp0KpP/inputs now. + nice /usr/bin/debrebuild --buildresult=/srv/rebuilderd/tmp/rebuilderdLp0KpP/out --builder=sbuild+unshare --cache=/srv/rebuilderd/cache -- /srv/rebuilderd/tmp/rebuilderdLp0KpP/inputs/gromacs_2025.1-1_riscv64.buildinfo /srv/rebuilderd/tmp/rebuilderdLp0KpP/inputs/gromacs_2025.1-1_riscv64.buildinfo containes a GPG signature which has NOT been validated Using defined Build-Path: /build/reproducible-path/gromacs-2025.1 I: verifying dsc... successful! Get:1 http://snapshot.debian.org/archive/debian/20250310T101857Z sid InRelease [205 kB] Get:2 http://snapshot.debian.org/archive/debian/20250315T150632Z sid InRelease [205 kB] Get:3 http://snapshot.debian.org/archive/debian/20250310T101857Z sid/main riscv64 Packages [9731 kB] Get:4 http://snapshot.debian.org/archive/debian/20250315T150632Z sid/main riscv64 Packages [9724 kB] Fetched 19.9 MB in 14s (1453 kB/s) Reading package lists... W: http://snapshot.debian.org/archive/debian/20250310T101857Z/dists/sid/InRelease: Loading /etc/apt/trusted.gpg from deprecated option Dir::Etc::Trusted W: http://snapshot.debian.org/archive/debian/20250315T150632Z/dists/sid/InRelease: Loading /etc/apt/trusted.gpg from deprecated option Dir::Etc::Trusted Get:1 http://snapshot.debian.org/archive/debian/20250310T101857Z sid/main riscv64 cmake riscv64 3.31.6-1 [11.2 MB] Fetched 11.2 MB in 1s (14.8 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmprsmoq5zf/cmake_3.31.6-1_riscv64.deb' Get:1 http://snapshot.debian.org/archive/debian/20250310T101857Z sid/main riscv64 libboost1.83-dev riscv64 1.83.0-4.1+b1 [10.6 MB] Fetched 10.6 MB in 1s (14.8 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpe4btswiz/libboost1.83-dev_1.83.0-4.1+b1_riscv64.deb' Get:1 http://snapshot.debian.org/archive/debian/20250310T101857Z sid/main riscv64 libjsoncpp26 riscv64 1.9.6-3 [78.1 kB] Fetched 78.1 kB in 0s (1030 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpas4hv0s9/libjsoncpp26_1.9.6-3_riscv64.deb' Get:1 http://snapshot.debian.org/archive/debian/20250310T101857Z sid/main riscv64 mpi-default-dev riscv64 1.18 [3376 B] Fetched 3376 B in 0s (49.0 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpaian8ttz/mpi-default-dev_1.18_riscv64.deb' Get:1 http://snapshot.debian.org/archive/debian/20250310T101857Z sid/main riscv64 librhash1 riscv64 1.4.5-1 [145 kB] Fetched 145 kB in 0s (1975 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpwb18i7of/librhash1_1.4.5-1_riscv64.deb' Get:1 http://snapshot.debian.org/archive/debian/20250310T101857Z sid/main riscv64 libatomic1 riscv64 14.2.0-17 [8680 B] Fetched 8680 B in 0s (128 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpr605o93p/libatomic1_14.2.0-17_riscv64.deb' Get:1 http://snapshot.debian.org/archive/debian/20250310T101857Z sid/main riscv64 libmpc3 riscv64 1.3.1-1+b3 [56.7 kB] Fetched 56.7 kB in 0s (836 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp5owgldve/libmpc3_1.3.1-1+b3_riscv64.deb' Get:1 http://snapshot.debian.org/archive/debian/20250310T101857Z sid/main riscv64 libsemanage2 riscv64 3.8-1+b1 [94.9 kB] Fetched 94.9 kB in 0s (1347 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpryxenqkv/libsemanage2_3.8-1+b1_riscv64.deb' Get:1 http://snapshot.debian.org/archive/debian/20250310T101857Z sid/main riscv64 m4 riscv64 1.4.19-7 [296 kB] Fetched 296 kB in 0s (3412 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpadhwjmqf/m4_1.4.19-7_riscv64.deb' Get:1 http://snapshot.debian.org/archive/debian/20250310T101857Z sid/main riscv64 mawk riscv64 1.3.4.20250131-1 [142 kB] Fetched 142 kB in 0s (1845 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpo4ypiqpf/mawk_1.3.4.20250131-1_riscv64.deb' Get:1 http://snapshot.debian.org/archive/debian/20250310T101857Z sid/main riscv64 libitm1 riscv64 14.2.0-17 [25.7 kB] Fetched 25.7 kB in 0s (383 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpwk2o87bo/libitm1_14.2.0-17_riscv64.deb' Get:1 http://snapshot.debian.org/archive/debian/20250310T101857Z sid/main riscv64 libexpat1 riscv64 2.6.4-1 [99.3 kB] Fetched 99.3 kB in 0s (1309 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpz06q8f37/libexpat1_2.6.4-1_riscv64.deb' Get:1 http://snapshot.debian.org/archive/debian/20250310T101857Z sid/main riscv64 cpp riscv64 4:14.2.0-1 [1576 B] Fetched 1576 B in 0s (23.4 kB/s) dpkg-name: info: moved 'cpp_4%3a14.2.0-1_riscv64.deb' to '/srv/rebuilderd/tmp/tmpbo9ffoz_/cpp_14.2.0-1_riscv64.deb' Get:1 http://snapshot.debian.org/archive/debian/20250310T101857Z sid/main riscv64 debhelper all 13.24.1 [920 kB] Fetched 920 kB in 0s (6560 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpr2vjk6z6/debhelper_13.24.1_all.deb' Get:1 http://snapshot.debian.org/archive/debian/20250310T101857Z sid/main riscv64 diffutils riscv64 1:3.10-2 [387 kB] Fetched 387 kB in 0s (4008 kB/s) dpkg-name: info: moved 'diffutils_1%3a3.10-2_riscv64.deb' to '/srv/rebuilderd/tmp/tmpa9zdbi5x/diffutils_3.10-2_riscv64.deb' Get:1 http://snapshot.debian.org/archive/debian/20250310T101857Z sid/main riscv64 libgmp10 riscv64 2:6.3.0+dfsg-3 [558 kB] Fetched 558 kB in 0s (5723 kB/s) dpkg-name: info: moved 'libgmp10_2%3a6.3.0+dfsg-3_riscv64.deb' to '/srv/rebuilderd/tmp/tmpan54ondq/libgmp10_6.3.0+dfsg-3_riscv64.deb' Get:1 http://snapshot.debian.org/archive/debian/20250310T101857Z sid/main riscv64 libfftw3-single3 riscv64 3.3.10-2+b1 [381 kB] Fetched 381 kB in 0s (3981 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpcs_cqjo0/libfftw3-single3_3.3.10-2+b1_riscv64.deb' Get:1 http://snapshot.debian.org/archive/debian/20250310T101857Z sid/main riscv64 libjs-underscore all 1.13.4~dfsg+~1.11.4-3 [116 kB] Fetched 116 kB in 0s (1473 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpi4d4u5rf/libjs-underscore_1.13.4~dfsg+~1.11.4-3_all.deb' Get:1 http://snapshot.debian.org/archive/debian/20250310T101857Z sid/main riscv64 libcap2 riscv64 1:2.75-1 [28.1 kB] Fetched 28.1 kB in 0s (394 kB/s) dpkg-name: info: moved 'libcap2_1%3a2.75-1_riscv64.deb' to '/srv/rebuilderd/tmp/tmpmm822s1c/libcap2_2.75-1_riscv64.deb' Get:1 http://snapshot.debian.org/archive/debian/20250315T150632Z sid/main riscv64 libldap2 riscv64 2.6.9+dfsg-2 [196 kB] Fetched 196 kB in 0s (2329 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp8rsnlx90/libldap2_2.6.9+dfsg-2_riscv64.deb' Get:1 http://snapshot.debian.org/archive/debian/20250310T101857Z sid/main riscv64 libmount1 riscv64 2.40.4-5 [217 kB] Fetched 217 kB in 0s (2581 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpikl1thew/libmount1_2.40.4-5_riscv64.deb' Get:1 http://snapshot.debian.org/archive/debian/20250310T101857Z sid/main riscv64 libzstd1 riscv64 1.5.6+dfsg-2 [355 kB] Fetched 355 kB in 0s (3701 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpdbku8zez/libzstd1_1.5.6+dfsg-2_riscv64.deb' Get:1 http://snapshot.debian.org/archive/debian/20250310T101857Z sid/main riscv64 libpsl5t64 riscv64 0.21.2-1.1+b1 [57.3 kB] Fetched 57.3 kB in 0s (847 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp3gjt7xa4/libpsl5t64_0.21.2-1.1+b1_riscv64.deb' Get:1 http://snapshot.debian.org/archive/debian/20250310T101857Z sid/main riscv64 libk5crypto3 riscv64 1.21.3-4 [99.9 kB] Fetched 99.9 kB in 0s (1423 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp3og_4bw6/libk5crypto3_1.21.3-4_riscv64.deb' Get:1 http://snapshot.debian.org/archive/debian/20250310T101857Z sid/main riscv64 libattr1 riscv64 1:2.5.2-3 [22.9 kB] Fetched 22.9 kB in 0s (349 kB/s) dpkg-name: info: moved 'libattr1_1%3a2.5.2-3_riscv64.deb' to '/srv/rebuilderd/tmp/tmpmfvjypsk/libattr1_2.5.2-3_riscv64.deb' Get:1 http://snapshot.debian.org/archive/debian/20250310T101857Z sid/main riscv64 init-system-helpers all 1.68 [38.7 kB] Fetched 38.7 kB in 0s (572 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpf2_bzvel/init-system-helpers_1.68_all.deb' Get:1 http://snapshot.debian.org/archive/debian/20250310T101857Z sid/main riscv64 libgcc-14-dev riscv64 14.2.0-17 [5213 kB] Fetched 5213 kB in 0s (13.7 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpssbkiz8m/libgcc-14-dev_14.2.0-17_riscv64.deb' Get:1 http://snapshot.debian.org/archive/debian/20250310T101857Z sid/main riscv64 libtinfo6 riscv64 6.5+20250216-2 [347 kB] Fetched 347 kB in 0s (3755 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmppcdfmdw0/libtinfo6_6.5+20250216-2_riscv64.deb' Get:1 http://snapshot.debian.org/archive/debian/20250310T101857Z sid/main riscv64 libpam-modules riscv64 1.7.0-3 [175 kB] Fetched 175 kB in 0s (2351 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpx6qs35f6/libpam-modules_1.7.0-3_riscv64.deb' Get:1 http://snapshot.debian.org/archive/debian/20250310T101857Z sid/main riscv64 libreadline8t64 riscv64 8.2-6 [169 kB] Fetched 169 kB in 0s (2257 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp2l1ury3b/libreadline8t64_8.2-6_riscv64.deb' Get:1 http://snapshot.debian.org/archive/debian/20250310T101857Z sid/main riscv64 libjs-jquery all 3.6.1+dfsg+~3.5.14-1 [326 kB] Fetched 326 kB in 0s (3823 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp3wcoh0km/libjs-jquery_3.6.1+dfsg+~3.5.14-1_all.deb' Get:1 http://snapshot.debian.org/archive/debian/20250310T101857Z sid/main riscv64 libcurl4t64 riscv64 8.12.1-3 [378 kB] Fetched 378 kB in 0s (4219 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmphtptchfg/libcurl4t64_8.12.1-3_riscv64.deb' Get:1 http://snapshot.debian.org/archive/debian/20250310T101857Z sid/main riscv64 libpython3-dev riscv64 3.13.2-2 [10.3 kB] Fetched 10.3 kB in 0s (154 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp64yge8ah/libpython3-dev_3.13.2-2_riscv64.deb' Get:1 http://snapshot.debian.org/archive/debian/20250310T101857Z sid/main riscv64 passwd riscv64 1:4.17.3-1 [1227 kB] Fetched 1227 kB in 0s (7827 kB/s) dpkg-name: info: moved 'passwd_1%3a4.17.3-1_riscv64.deb' to '/srv/rebuilderd/tmp/tmpxzxpt502/passwd_4.17.3-1_riscv64.deb' Get:1 http://snapshot.debian.org/archive/debian/20250315T150632Z sid/main riscv64 libnl-route-3-200 riscv64 3.7.0-1 [183 kB] Fetched 183 kB in 0s (2232 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpppwiwb96/libnl-route-3-200_3.7.0-1_riscv64.deb' Get:1 http://snapshot.debian.org/archive/debian/20250310T101857Z sid/main riscv64 grep riscv64 3.11-4 [430 kB] Fetched 430 kB in 0s (4373 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp5_v8opvy/grep_3.11-4_riscv64.deb' Get:1 http://snapshot.debian.org/archive/debian/20250310T101857Z sid/main riscv64 intltool-debian all 0.35.0+20060710.6 [22.9 kB] Fetched 22.9 kB in 0s (334 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmprgwt3s1z/intltool-debian_0.35.0+20060710.6_all.deb' Get:1 http://snapshot.debian.org/archive/debian/20250310T101857Z sid/main riscv64 hostname riscv64 3.25 [10.7 kB] Fetched 10.7 kB in 0s (158 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmppddj_k_v/hostname_3.25_riscv64.deb' Get:1 http://snapshot.debian.org/archive/debian/20250310T101857Z sid/main riscv64 python3-jaraco.context all 6.0.1-1 [8276 B] Fetched 8276 B in 0s (124 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmphullsymq/python3-jaraco.context_6.0.1-1_all.deb' Get:1 http://snapshot.debian.org/archive/debian/20250310T101857Z sid/main riscv64 libhogweed6t64 riscv64 3.10.1-1 [336 kB] Fetched 336 kB in 0s (3688 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpr_iyj24s/libhogweed6t64_3.10.1-1_riscv64.deb' Get:1 http://snapshot.debian.org/archive/debian/20250310T101857Z sid/main riscv64 libedit2 riscv64 3.1-20250104-1 [92.5 kB] Fetched 92.5 kB in 0s (1218 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp4tasu8si/libedit2_3.1-20250104-1_riscv64.deb' Get:1 http://snapshot.debian.org/archive/debian/20250310T101857Z sid/main riscv64 libibmad5 riscv64 56.0-2 [44.3 kB] Fetched 44.3 kB in 0s (628 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp414xnb50/libibmad5_56.0-2_riscv64.deb' Get:1 http://snapshot.debian.org/archive/debian/20250310T101857Z sid/main riscv64 libgprofng0 riscv64 2.44-3 [718 kB] Fetched 718 kB in 0s (5851 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpqnuhvmwc/libgprofng0_2.44-3_riscv64.deb' Get:1 http://snapshot.debian.org/archive/debian/20250310T101857Z sid/main riscv64 libnghttp2-14 riscv64 1.64.0-1 [77.0 kB] Fetched 77.0 kB in 0s (1062 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp6ua78j_s/libnghttp2-14_1.64.0-1_riscv64.deb' Get:1 http://snapshot.debian.org/archive/debian/20250310T101857Z sid/main riscv64 libpython3.13-minimal riscv64 3.13.2-1 [855 kB] Fetched 855 kB in 0s (6740 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpzuo6dnda/libpython3.13-minimal_3.13.2-1_riscv64.deb' Get:1 http://snapshot.debian.org/archive/debian/20250310T101857Z sid/main riscv64 bsdutils riscv64 1:2.40.4-5 [110 kB] Fetched 110 kB in 0s (1455 kB/s) dpkg-name: info: moved 'bsdutils_1%3a2.40.4-5_riscv64.deb' to '/srv/rebuilderd/tmp/tmpd05rhwfg/bsdutils_2.40.4-5_riscv64.deb' Get:1 http://snapshot.debian.org/archive/debian/20250310T101857Z sid/main riscv64 libfuse3-3 riscv64 3.14.0-10 [88.5 kB] Fetched 88.5 kB in 0s (1192 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpmszh4j0v/libfuse3-3_3.14.0-10_riscv64.deb' Get:1 http://snapshot.debian.org/archive/debian/20250310T101857Z sid/main riscv64 python3-typeguard all 4.4.2-1 [37.3 kB] Fetched 37.3 kB in 0s (539 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmporatv8w7/python3-typeguard_4.4.2-1_all.deb' Get:1 http://snapshot.debian.org/archive/debian/20250310T101857Z sid/main riscv64 libevent-pthreads-2.1-7t64 riscv64 2.1.12-stable-10+b1 [54.1 kB] Fetched 54.1 kB in 0s (740 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpd64nxmdn/libevent-pthreads-2.1-7t64_2.1.12-stable-10+b1_riscv64.deb' Get:1 http://snapshot.debian.org/archive/debian/20250310T101857Z sid/main riscv64 ncurses-base all 6.5+20250216-2 [273 kB] Fetched 273 kB in 0s (3426 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpogn6vsv3/ncurses-base_6.5+20250216-2_all.deb' Get:1 http://snapshot.debian.org/archive/debian/20250310T101857Z sid/main riscv64 libevent-dev riscv64 2.1.12-stable-10+b1 [523 kB] Fetched 523 kB in 0s (4628 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp9r4eqsed/libevent-dev_2.1.12-stable-10+b1_riscv64.deb' Get:1 http://snapshot.debian.org/archive/debian/20250310T101857Z sid/main riscv64 groff-base riscv64 1.23.0-7 [1164 kB] Fetched 1164 kB in 0s (8702 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpe1ax39h4/groff-base_1.23.0-7_riscv64.deb' Get:1 http://snapshot.debian.org/archive/debian/20250310T101857Z sid/main riscv64 libaudit-common all 1:4.0.2-2 [12.7 kB] Fetched 12.7 kB in 0s (186 kB/s) dpkg-name: info: moved 'libaudit-common_1%3a4.0.2-2_all.deb' to '/srv/rebuilderd/tmp/tmpvu8y6sbp/libaudit-common_4.0.2-2_all.deb' Get:1 http://snapshot.debian.org/archive/debian/20250310T101857Z sid/main riscv64 libpython3.13 riscv64 3.13.2-1 [2160 kB] Fetched 2160 kB in 0s (11.2 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmps2r7el_j/libpython3.13_3.13.2-1_riscv64.deb' Get:1 http://snapshot.debian.org/archive/debian/20250310T101857Z sid/main riscv64 libhwloc-dev riscv64 2.12.0-1 [516 kB] Fetched 516 kB in 0s (4801 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpan7pl08y/libhwloc-dev_2.12.0-1_riscv64.deb' Get:1 http://snapshot.debian.org/archive/debian/20250310T101857Z sid/main riscv64 binutils-common riscv64 2.44-3 [2509 kB] Fetched 2509 kB in 0s (10.9 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpcezau0cm/binutils-common_2.44-3_riscv64.deb' Get:1 http://snapshot.debian.org/archive/debian/20250310T101857Z sid/main riscv64 base-passwd riscv64 3.6.6 [53.3 kB] Fetched 53.3 kB in 0s (766 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmppavtb4ld/base-passwd_3.6.6_riscv64.deb' Get:1 http://snapshot.debian.org/archive/debian/20250310T101857Z sid/main riscv64 libibverbs-dev riscv64 56.0-2 [1694 kB] Fetched 1694 kB in 0s (9004 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpwk9n3i7d/libibverbs-dev_56.0-2_riscv64.deb' Get:1 http://snapshot.debian.org/archive/debian/20250310T101857Z sid/main riscv64 libjansson4 riscv64 2.14-2+b3 [40.7 kB] Fetched 40.7 kB in 0s (612 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp3uf9rtjs/libjansson4_2.14-2+b3_riscv64.deb' Get:1 http://snapshot.debian.org/archive/debian/20250310T101857Z sid/main riscv64 libjs-jquery-ui all 1.13.2+dfsg-1 [250 kB] Fetched 250 kB in 0s (3208 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpfkley179/libjs-jquery-ui_1.13.2+dfsg-1_all.deb' Get:1 http://snapshot.debian.org/archive/debian/20250310T101857Z sid/main riscv64 libfftw3-double3 riscv64 3.3.10-2+b1 [378 kB] Fetched 378 kB in 0s (3629 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpth311wz6/libfftw3-double3_3.3.10-2+b1_riscv64.deb' Get:1 http://snapshot.debian.org/archive/debian/20250310T101857Z sid/main riscv64 python3 riscv64 3.13.2-2 [28.1 kB] Fetched 28.1 kB in 0s (399 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmprij_o9l9/python3_3.13.2-2_riscv64.deb' Get:1 http://snapshot.debian.org/archive/debian/20250310T101857Z sid/main riscv64 gcc-riscv64-linux-gnu riscv64 4:14.2.0-1 [1432 B] Fetched 1432 B in 0s (18.8 kB/s) dpkg-name: info: moved 'gcc-riscv64-linux-gnu_4%3a14.2.0-1_riscv64.deb' to '/srv/rebuilderd/tmp/tmp7_fbtco3/gcc-riscv64-linux-gnu_14.2.0-1_riscv64.deb' Get:1 http://snapshot.debian.org/archive/debian/20250310T101857Z sid/main riscv64 libncursesw6 riscv64 6.5+20250216-2 [141 kB] Fetched 141 kB in 0s (1789 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpan2d1qb5/libncursesw6_6.5+20250216-2_riscv64.deb' Get:1 http://snapshot.debian.org/archive/debian/20250310T101857Z sid/main riscv64 libsasl2-2 riscv64 2.1.28+dfsg1-9 [60.9 kB] Fetched 60.9 kB in 0s (818 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmps39ugl_8/libsasl2-2_2.1.28+dfsg1-9_riscv64.deb' Get:1 http://snapshot.debian.org/archive/debian/20250310T101857Z sid/main riscv64 sensible-utils all 0.0.24 [24.8 kB] Fetched 24.8 kB in 0s (365 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp9dhls_cx/sensible-utils_0.0.24_all.deb' Get:1 http://snapshot.debian.org/archive/debian/20250310T101857Z sid/main riscv64 rpcsvc-proto riscv64 1.4.3-1+b2 [62.3 kB] Fetched 62.3 kB in 0s (914 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpwmesmeug/rpcsvc-proto_1.4.3-1+b2_riscv64.deb' Get:1 http://snapshot.debian.org/archive/debian/20250315T150632Z sid/main riscv64 libnl-3-200 riscv64 3.7.0-1 [60.1 kB] Fetched 60.1 kB in 0s (914 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp74piw8q1/libnl-3-200_3.7.0-1_riscv64.deb' Get:1 http://snapshot.debian.org/archive/debian/20250310T101857Z sid/main riscv64 libfftw3-dev riscv64 3.3.10-2+b1 [1492 kB] Fetched 1492 kB in 0s (9260 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp6bolrnmr/libfftw3-dev_3.3.10-2+b1_riscv64.deb' Get:1 http://snapshot.debian.org/archive/debian/20250310T101857Z sid/main riscv64 libmd0 riscv64 1.1.0-2+b1 [37.6 kB] Fetched 37.6 kB in 0s (563 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpaejk4bk0/libmd0_1.1.0-2+b1_riscv64.deb' Get:1 http://snapshot.debian.org/archive/debian/20250310T101857Z sid/main riscv64 libfile-stripnondeterminism-perl all 1.14.1-2 [19.7 kB] Fetched 19.7 kB in 0s (285 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpwg354bnc/libfile-stripnondeterminism-perl_1.14.1-2_all.deb' Get:1 http://snapshot.debian.org/archive/debian/20250310T101857Z sid/main riscv64 cpp-riscv64-linux-gnu riscv64 4:14.2.0-1 [4832 B] Fetched 4832 B in 0s (73.1 kB/s) dpkg-name: info: moved 'cpp-riscv64-linux-gnu_4%3a14.2.0-1_riscv64.deb' to '/srv/rebuilderd/tmp/tmpswdlhkk1/cpp-riscv64-linux-gnu_14.2.0-1_riscv64.deb' Get:1 http://snapshot.debian.org/archive/debian/20250310T101857Z sid/main riscv64 libnuma-dev riscv64 2.0.18-1+b1 [66.1 kB] Fetched 66.1 kB in 0s (987 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmplrl13eyl/libnuma-dev_2.0.18-1+b1_riscv64.deb' Get:1 http://snapshot.debian.org/archive/debian/20250310T101857Z sid/main riscv64 libpython3.13-dev riscv64 3.13.2-1 [14.3 MB] Fetched 14.3 MB in 1s (13.9 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmprksxyy50/libpython3.13-dev_3.13.2-1_riscv64.deb' Get:1 http://snapshot.debian.org/archive/debian/20250310T101857Z sid/main riscv64 patch riscv64 2.7.6-7+b2 [121 kB] Fetched 121 kB in 0s (1715 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp7h9rmo5k/patch_2.7.6-7+b2_riscv64.deb' Get:1 http://snapshot.debian.org/archive/debian/20250310T101857Z sid/main riscv64 python3-minimal riscv64 3.13.2-2 [27.1 kB] Fetched 27.1 kB in 0s (392 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpc5ecj1nj/python3-minimal_3.13.2-2_riscv64.deb' Get:1 http://snapshot.debian.org/archive/debian/20250310T101857Z sid/main riscv64 g++-14-riscv64-linux-gnu riscv64 14.2.0-17 [15.0 MB] Fetched 15.0 MB in 1s (15.4 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp6a2o7wd_/g++-14-riscv64-linux-gnu_14.2.0-17_riscv64.deb' Get:1 http://snapshot.debian.org/archive/debian/20250310T101857Z sid/main riscv64 binutils riscv64 2.44-3 [267 kB] Fetched 267 kB in 0s (3342 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp3ilia45v/binutils_2.44-3_riscv64.deb' Get:1 http://snapshot.debian.org/archive/debian/20250310T101857Z sid/main riscv64 libcbor0.10 riscv64 0.10.2-2 [27.9 kB] Fetched 27.9 kB in 0s (375 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp_fx9v9_a/libcbor0.10_0.10.2-2_riscv64.deb' Get:1 http://snapshot.debian.org/archive/debian/20250310T101857Z sid/main riscv64 binutils-riscv64-linux-gnu riscv64 2.44-3 [856 kB] Fetched 856 kB in 0s (6737 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpik__wk6_/binutils-riscv64-linux-gnu_2.44-3_riscv64.deb' Get:1 http://snapshot.debian.org/archive/debian/20250310T101857Z sid/main riscv64 libgnutls30t64 riscv64 3.8.9-2 [1445 kB] Fetched 1445 kB in 0s (8664 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp6lo75x20/libgnutls30t64_3.8.9-2_riscv64.deb' Get:1 http://snapshot.debian.org/archive/debian/20250310T101857Z sid/main riscv64 dh-autoreconf all 20 [17.1 kB] Fetched 17.1 kB in 0s (252 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmptfliqhl6/dh-autoreconf_20_all.deb' Get:1 http://snapshot.debian.org/archive/debian/20250310T101857Z sid/main riscv64 libnuma1 riscv64 2.0.18-1+b1 [23.4 kB] Fetched 23.4 kB in 0s (354 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp481pqzqx/libnuma1_2.0.18-1+b1_riscv64.deb' Get:1 http://snapshot.debian.org/archive/debian/20250310T101857Z sid/main riscv64 libmuparser2v5 riscv64 2.3.4-1+b1 [140 kB] Fetched 140 kB in 3s (41.4 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpefgfjlrd/libmuparser2v5_2.3.4-1+b1_riscv64.deb' Get:1 http://snapshot.debian.org/archive/debian/20250310T101857Z sid/main riscv64 python3-numpy riscv64 1:2.2.3+ds-5 [3598 kB] Fetched 3598 kB in 0s (12.3 MB/s) dpkg-name: info: moved 'python3-numpy_1%3a2.2.3+ds-5_riscv64.deb' to '/srv/rebuilderd/tmp/tmpq7onvudt/python3-numpy_2.2.3+ds-5_riscv64.deb' Get:1 http://snapshot.debian.org/archive/debian/20250310T101857Z sid/main riscv64 libgomp1 riscv64 14.2.0-17 [131 kB] Fetched 131 kB in 0s (1775 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpgrb89yjj/libgomp1_14.2.0-17_riscv64.deb' Get:1 http://snapshot.debian.org/archive/debian/20250310T101857Z sid/main riscv64 libsepol2 riscv64 3.8-1 [304 kB] Fetched 304 kB in 0s (3437 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpzfhkx0wf/libsepol2_3.8-1_riscv64.deb' Get:1 http://snapshot.debian.org/archive/debian/20250310T101857Z sid/main riscv64 libstdc++6 riscv64 14.2.0-17 [707 kB] Fetched 707 kB in 0s (6400 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp_m63hxn1/libstdc++6_14.2.0-17_riscv64.deb' Get:1 http://snapshot.debian.org/archive/debian/20250310T101857Z sid/main riscv64 libpcre2-8-0 riscv64 10.45-1 [300 kB] Fetched 300 kB in 0s (3392 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpvt0gjrgi/libpcre2-8-0_10.45-1_riscv64.deb' Get:1 http://snapshot.debian.org/archive/debian/20250310T101857Z sid/main riscv64 libx11-data all 2:1.8.10-2 [337 kB] Fetched 337 kB in 0s (3742 kB/s) dpkg-name: info: moved 'libx11-data_2%3a1.8.10-2_all.deb' to '/srv/rebuilderd/tmp/tmpdht1wrpu/libx11-data_1.8.10-2_all.deb' Get:1 http://snapshot.debian.org/archive/debian/20250310T101857Z sid/main riscv64 libpmix2t64 riscv64 5.0.6-5 [647 kB] Fetched 647 kB in 0s (5668 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmprf4t20ga/libpmix2t64_5.0.6-5_riscv64.deb' Get:1 http://snapshot.debian.org/archive/debian/20250310T101857Z sid/main riscv64 libctf-nobfd0 riscv64 2.44-3 [163 kB] Fetched 163 kB in 0s (2185 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpoeymgomx/libctf-nobfd0_2.44-3_riscv64.deb' Get:1 http://snapshot.debian.org/archive/debian/20250310T101857Z sid/main riscv64 media-types all 13.0.0 [29.3 kB] Fetched 29.3 kB in 0s (449 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpdq9_jvap/media-types_13.0.0_all.deb' Get:1 http://snapshot.debian.org/archive/debian/20250310T101857Z sid/main riscv64 libgdbm-compat4t64 riscv64 1.24-2 [50.5 kB] Fetched 50.5 kB in 0s (738 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpkg9pkkxj/libgdbm-compat4t64_1.24-2_riscv64.deb' Get:1 http://snapshot.debian.org/archive/debian/20250310T101857Z sid/main riscv64 ocl-icd-libopencl1 riscv64 2.3.2-1+b2 [39.1 kB] Fetched 39.1 kB in 0s (579 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpcqr1t8rj/ocl-icd-libopencl1_2.3.2-1+b2_riscv64.deb' Get:1 http://snapshot.debian.org/archive/debian/20250310T101857Z sid/main riscv64 pkgconf riscv64 1.8.1-4 [26.1 kB] Fetched 26.1 kB in 0s (379 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpm8_y9z4q/pkgconf_1.8.1-4_riscv64.deb' Get:1 http://snapshot.debian.org/archive/debian/20250310T101857Z sid/main riscv64 sysvinit-utils riscv64 3.14-3 [33.7 kB] Fetched 33.7 kB in 0s (492 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpn2yldqnu/sysvinit-utils_3.14-3_riscv64.deb' Get:1 http://snapshot.debian.org/archive/debian/20250310T101857Z sid/main riscv64 libsqlite3-0 riscv64 3.46.1-2 [905 kB] Fetched 905 kB in 0s (6774 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpczjkjq5d/libsqlite3-0_3.46.1-2_riscv64.deb' Get:1 http://snapshot.debian.org/archive/debian/20250310T101857Z sid/main riscv64 libpython3.13-stdlib riscv64 3.13.2-1 [1942 kB] Fetched 1942 kB in 0s (10.3 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpw25imlvj/libpython3.13-stdlib_3.13.2-1_riscv64.deb' Get:1 http://snapshot.debian.org/archive/debian/20250310T101857Z sid/main riscv64 tar riscv64 1.35+dfsg-3.1 [822 kB] Fetched 822 kB in 0s (6608 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpl0e41p9l/tar_1.35+dfsg-3.1_riscv64.deb' Get:1 http://snapshot.debian.org/archive/debian/20250310T101857Z sid/main riscv64 coreutils riscv64 9.5-1 [2939 kB] Fetched 2939 kB in 0s (11.3 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpt90vl1gs/coreutils_9.5-1_riscv64.deb' Get:1 http://snapshot.debian.org/archive/debian/20250310T101857Z sid/main riscv64 libjs-sphinxdoc all 8.1.3-5 [30.5 kB] Fetched 30.5 kB in 0s (447 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpvby9rsve/libjs-sphinxdoc_8.1.3-5_all.deb' Get:1 http://snapshot.debian.org/archive/debian/20250310T101857Z sid/main riscv64 libffi8 riscv64 3.4.7-1 [21.6 kB] Fetched 21.6 kB in 0s (330 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpsoe7llye/libffi8_3.4.7-1_riscv64.deb' Get:1 http://snapshot.debian.org/archive/debian/20250310T101857Z sid/main riscv64 libevent-openssl-2.1-7t64 riscv64 2.1.12-stable-10+b1 [60.6 kB] Fetched 60.6 kB in 0s (845 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpsd1ydci2/libevent-openssl-2.1-7t64_2.1.12-stable-10+b1_riscv64.deb' Get:1 http://snapshot.debian.org/archive/debian/20250310T101857Z sid/main riscv64 libbz2-1.0 riscv64 1.0.8-6 [40.3 kB] Fetched 40.3 kB in 0s (583 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp7qhqrfp2/libbz2-1.0_1.0.8-6_riscv64.deb' Get:1 http://snapshot.debian.org/archive/debian/20250310T101857Z sid/main riscv64 perl riscv64 5.40.1-2 [267 kB] Fetched 267 kB in 0s (3268 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpdhpjfjd8/perl_5.40.1-2_riscv64.deb' Get:1 http://snapshot.debian.org/archive/debian/20250310T101857Z sid/main riscv64 dash riscv64 0.5.12-12 [101 kB] Fetched 101 kB in 0s (1418 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpvk27zakz/dash_0.5.12-12_riscv64.deb' Get:1 http://snapshot.debian.org/archive/debian/20250310T101857Z sid/main riscv64 libltdl-dev riscv64 2.5.4-4 [188 kB] Fetched 188 kB in 0s (2371 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp4ikf6qie/libltdl-dev_2.5.4-4_riscv64.deb' Get:1 http://snapshot.debian.org/archive/debian/20250310T101857Z sid/main riscv64 dwz riscv64 0.15-1+b3 [114 kB] Fetched 114 kB in 0s (1522 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpnba0hk34/dwz_0.15-1+b3_riscv64.deb' Get:1 http://snapshot.debian.org/archive/debian/20250310T101857Z sid/main riscv64 build-essential riscv64 12.12 [4628 B] Fetched 4628 B in 0s (70.2 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpzla89ey4/build-essential_12.12_riscv64.deb' Get:1 http://snapshot.debian.org/archive/debian/20250310T101857Z sid/main riscv64 libkrb5-3 riscv64 1.21.3-4 [334 kB] Fetched 334 kB in 0s (3697 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp4_x4ak8h/libkrb5-3_1.21.3-4_riscv64.deb' Get:1 http://snapshot.debian.org/archive/debian/20250310T101857Z sid/main riscv64 libnghttp3-9 riscv64 1.8.0-1 [68.5 kB] Fetched 68.5 kB in 0s (1004 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmppog2k0ya/libnghttp3-9_1.8.0-1_riscv64.deb' Get:1 http://snapshot.debian.org/archive/debian/20250315T150632Z sid/main riscv64 libnl-3-dev riscv64 3.7.0-1 [170 kB] Fetched 170 kB in 0s (2328 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp_l0wh0xi/libnl-3-dev_3.7.0-1_riscv64.deb' Get:1 http://snapshot.debian.org/archive/debian/20250310T101857Z sid/main riscv64 g++ riscv64 4:14.2.0-1 [1328 B] Fetched 1328 B in 0s (19.9 kB/s) dpkg-name: info: moved 'g++_4%3a14.2.0-1_riscv64.deb' to '/srv/rebuilderd/tmp/tmpzv71uuj3/g++_14.2.0-1_riscv64.deb' Get:1 http://snapshot.debian.org/archive/debian/20250310T101857Z sid/main riscv64 netbase all 6.4 [12.8 kB] Fetched 12.8 kB in 0s (190 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp6qc_w36a/netbase_6.4_all.deb' Get:1 http://snapshot.debian.org/archive/debian/20250310T101857Z sid/main riscv64 python3-jaraco.functools all 4.1.0-1 [12.0 kB] Fetched 12.0 kB in 0s (166 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmptbc0fvth/python3-jaraco.functools_4.1.0-1_all.deb' Get:1 http://snapshot.debian.org/archive/debian/20250310T101857Z sid/main riscv64 autoconf all 2.72-3 [493 kB] Fetched 493 kB in 0s (4936 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpd536__yi/autoconf_2.72-3_all.deb' Get:1 http://snapshot.debian.org/archive/debian/20250310T101857Z sid/main riscv64 libpciaccess0 riscv64 0.17-3+b3 [51.6 kB] Fetched 51.6 kB in 0s (736 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpnhjo5bmw/libpciaccess0_0.17-3+b3_riscv64.deb' Get:1 http://snapshot.debian.org/archive/debian/20250310T101857Z sid/main riscv64 libsemanage-common all 3.8-1 [7720 B] Fetched 7720 B in 0s (114 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp2bb6v2f6/libsemanage-common_3.8-1_all.deb' Get:1 http://snapshot.debian.org/archive/debian/20250310T101857Z sid/main riscv64 libuchardet0 riscv64 0.0.8-1+b2 [68.8 kB] Fetched 68.8 kB in 0s (942 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp83c869kd/libuchardet0_0.0.8-1+b2_riscv64.deb' Get:1 http://snapshot.debian.org/archive/debian/20250310T101857Z sid/main riscv64 libpmix-dev riscv64 5.0.6-5 [5455 kB] Fetched 5455 kB in 0s (13.7 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpqp6c_wc_/libpmix-dev_5.0.6-5_riscv64.deb' Get:1 http://snapshot.debian.org/archive/debian/20250310T101857Z sid/main riscv64 libxxhash0 riscv64 0.8.3-2 [40.1 kB] Fetched 40.1 kB in 0s (585 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpxqcecce1/libxxhash0_0.8.3-2_riscv64.deb' Get:1 http://snapshot.debian.org/archive/debian/20250310T101857Z sid/main riscv64 pybind11-dev all 2.13.6-2 [205 kB] Fetched 205 kB in 0s (2419 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpjffh4idw/pybind11-dev_2.13.6-2_all.deb' Get:1 http://snapshot.debian.org/archive/debian/20250310T101857Z sid/main riscv64 bzip2 riscv64 1.0.8-6 [40.5 kB] Fetched 40.5 kB in 0s (581 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpcoztetph/bzip2_1.0.8-6_riscv64.deb' Get:1 http://snapshot.debian.org/archive/debian/20250310T101857Z sid/main riscv64 libibumad3 riscv64 56.0-2 [29.4 kB] Fetched 29.4 kB in 0s (397 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp3a2r3467/libibumad3_56.0-2_riscv64.deb' Get:1 http://snapshot.debian.org/archive/debian/20250310T101857Z sid/main riscv64 mpi-default-bin riscv64 1.18 [2580 B] Fetched 2580 B in 0s (36.5 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpz_p47vr2/mpi-default-bin_1.18_riscv64.deb' Downloading dependency 1 of 296: cmake:riscv64=3.31.6-1 Downloading dependency 2 of 296: libboost1.83-dev:riscv64=1.83.0-4.1+b1 Downloading dependency 3 of 296: libjsoncpp26:riscv64=1.9.6-3 Downloading dependency 4 of 296: mpi-default-dev:riscv64=1.18 Downloading dependency 5 of 296: librhash1:riscv64=1.4.5-1 Downloading dependency 6 of 296: libatomic1:riscv64=14.2.0-17 Downloading dependency 7 of 296: libmpc3:riscv64=1.3.1-1+b3 Downloading dependency 8 of 296: libsemanage2:riscv64=3.8-1+b1 Downloading dependency 9 of 296: m4:riscv64=1.4.19-7 Downloading dependency 10 of 296: mawk:riscv64=1.3.4.20250131-1 Downloading dependency 11 of 296: libitm1:riscv64=14.2.0-17 Downloading dependency 12 of 296: libexpat1:riscv64=2.6.4-1 Downloading dependency 13 of 296: cpp:riscv64=4:14.2.0-1 Downloading dependency 14 of 296: debhelper:riscv64=13.24.1 Downloading dependency 15 of 296: diffutils:riscv64=1:3.10-2 Downloading dependency 16 of 296: libgmp10:riscv64=2:6.3.0+dfsg-3 Downloading dependency 17 of 296: libfftw3-single3:riscv64=3.3.10-2+b1 Downloading dependency 18 of 296: libjs-underscore:riscv64=1.13.4~dfsg+~1.11.4-3 Downloading dependency 19 of 296: libcap2:riscv64=1:2.75-1 Downloading dependency 20 of 296: libldap2:riscv64=2.6.9+dfsg-2 Downloading dependency 21 of 296: libmount1:riscv64=2.40.4-5 Downloading dependency 22 of 296: libzstd1:riscv64=1.5.6+dfsg-2 Downloading dependency 23 of 296: libpsl5t64:riscv64=0.21.2-1.1+b1 Downloading dependency 24 of 296: libk5crypto3:riscv64=1.21.3-4 Downloading dependency 25 of 296: libattr1:riscv64=1:2.5.2-3 Downloading dependency 26 of 296: init-system-helpers:riscv64=1.68 Downloading dependency 27 of 296: libgcc-14-dev:riscv64=14.2.0-17 Downloading dependency 28 of 296: libtinfo6:riscv64=6.5+20250216-2 Downloading dependency 29 of 296: libpam-modules:riscv64=1.7.0-3 Downloading dependency 30 of 296: libreadline8t64:riscv64=8.2-6 Downloading dependency 31 of 296: libjs-jquery:riscv64=3.6.1+dfsg+~3.5.14-1 Downloading dependency 32 of 296: libcurl4t64:riscv64=8.12.1-3 Downloading dependency 33 of 296: libpython3-dev:riscv64=3.13.2-2 Downloading dependency 34 of 296: passwd:riscv64=1:4.17.3-1 Downloading dependency 35 of 296: libnl-route-3-200:riscv64=3.7.0-1 Downloading dependency 36 of 296: grep:riscv64=3.11-4 Downloading dependency 37 of 296: intltool-debian:riscv64=0.35.0+20060710.6 Downloading dependency 38 of 296: hostname:riscv64=3.25 Downloading dependency 39 of 296: python3-jaraco.context:riscv64=6.0.1-1 Downloading dependency 40 of 296: libhogweed6t64:riscv64=3.10.1-1 Downloading dependency 41 of 296: libedit2:riscv64=3.1-20250104-1 Downloading dependency 42 of 296: libibmad5:riscv64=56.0-2 Downloading dependency 43 of 296: libgprofng0:riscv64=2.44-3 Downloading dependency 44 of 296: libnghttp2-14:riscv64=1.64.0-1 Downloading dependency 45 of 296: libpython3.13-minimal:riscv64=3.13.2-1 Downloading dependency 46 of 296: bsdutils:riscv64=1:2.40.4-5 Downloading dependency 47 of 296: libfuse3-3:riscv64=3.14.0-10 Downloading dependency 48 of 296: python3-typeguard:riscv64=4.4.2-1 Downloading dependency 49 of 296: libevent-pthreads-2.1-7t64:riscv64=2.1.12-stable-10+b1 Downloading dependency 50 of 296: 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296: libsasl2-2:riscv64=2.1.28+dfsg1-9 Downloading dependency 66 of 296: sensible-utils:riscv64=0.0.24 Downloading dependency 67 of 296: rpcsvc-proto:riscv64=1.4.3-1+b2 Downloading dependency 68 of 296: libnl-3-200:riscv64=3.7.0-1 Downloading dependency 69 of 296: libfftw3-dev:riscv64=3.3.10-2+b1 Downloading dependency 70 of 296: libmd0:riscv64=1.1.0-2+b1 Downloading dependency 71 of 296: libfile-stripnondeterminism-perl:riscv64=1.14.1-2 Downloading dependency 72 of 296: cpp-riscv64-linux-gnu:riscv64=4:14.2.0-1 Downloading dependency 73 of 296: libnuma-dev:riscv64=2.0.18-1+b1 Downloading dependency 74 of 296: libpython3.13-dev:riscv64=3.13.2-1 Downloading dependency 75 of 296: patch:riscv64=2.7.6-7+b2 Downloading dependency 76 of 296: python3-minimal:riscv64=3.13.2-2 Downloading dependency 77 of 296: g++-14-riscv64-linux-gnu:riscv64=14.2.0-17 Downloading dependency 78 of 296: binutils:riscv64=2.44-3 Downloading dependency 79 of 296: libcbor0.10:riscv64=0.10.2-2 Downloading dependency 80 of 296: binutils-riscv64-linux-gnu:riscv64=2.44-3 Downloading dependency 81 of 296: libgnutls30t64:riscv64=3.8.9-2 Downloading dependency 82 of 296: dh-autoreconf:riscv64=20 Downloading dependency 83 of 296: libnuma1:riscv64=2.0.18-1+b1 Downloading dependency 84 of 296: libmuparser2v5:riscv64=2.3.4-1+b1 Downloading dependency 85 of 296: python3-numpy:riscv64=1:2.2.3+ds-5 Downloading dependency 86 of 296: libgomp1:riscv64=14.2.0-17 Downloading dependency 87 of 296: libsepol2:riscv64=3.8-1 Downloading dependency 88 of 296: libstdc++6:riscv64=14.2.0-17 Downloading dependency 89 of 296: libpcre2-8-0:riscv64=10.45-1 Downloading dependency 90 of 296: libx11-data:riscv64=2:1.8.10-2 Downloading dependency 91 of 296: libpmix2t64:riscv64=5.0.6-5 Downloading dependency 92 of 296: libctf-nobfd0:riscv64=2.44-3 Downloading dependency 93 of 296: media-types:riscv64=13.0.0 Downloading dependency 94 of 296: libgdbm-compat4t64:riscv64=1.24-2 Downloading dependency 95 of 296: ocl-icd-libopencl1:riscv64=2.3.2-1+b2 Downloading dependency 96 of 296: pkgconf:riscv64=1.8.1-4 Downloading dependency 97 of 296: sysvinit-utils:riscv64=3.14-3 Downloading dependency 98 of 296: libsqlite3-0:riscv64=3.46.1-2 Downloading dependency 99 of 296: libpython3.13-stdlib:riscv64=3.13.2-1 Downloading dependency 100 of 296: tar:riscv64=1.35+dfsg-3.1 Downloading dependency 101 of 296: coreutils:riscv64=9.5-1 Downloading dependency 102 of 296: libjs-sphinxdoc:riscv64=8.1.3-5 Downloading dependency 103 of 296: libffi8:riscv64=3.4.7-1 Downloading dependency 104 of 296: libevent-openssl-2.1-7t64:riscv64=2.1.12-stable-10+b1 Downloading dependency 105 of 296: libbz2-1.0:riscv64=1.0.8-6 Downloading dependency 106 of 296: perl:riscv64=5.40.1-2 Downloading dependency 107 of 296: dash:riscv64=0.5.12-12 Downloading dependency 108 of 296: libltdl-dev:riscv64=2.5.4-4 Downloading dependency 109 of 296: dwz:riscv64=0.15-1+b3 Downloading dependency 110 of 296: build-essential:riscv64=12.12 Downloading dependency 111 of 296: libkrb5-3:riscv64=1.21.3-4 Downloading dependency 112 of 296: libnghttp3-9:riscv64=1.8.0-1 Downloading dependency 113 of 296: libnl-3-dev:riscv64=3.7.0-1 Downloading dependency 114 of 296: g++:riscv64=4:14.2.0-1 Downloading dependency 115 of 296: netbase:riscv64=6.4 Downloading dependency 116 of 296: python3-jaraco.functools:riscv64=4.1.0-1 Downloading dependency 117 of 296: autoconf:riscv64=2.72-3 Downloading dependency 118 of 296: libpciaccess0:riscv64=0.17-3+b3 Downloading dependency 119 of 296: libsemanage-common:riscv64=3.8-1 Downloading dependency 120 of 296: libuchardet0:riscv64=0.0.8-1+b2 Downloading dependency 121 of 296: libpmix-dev:riscv64=5.0.6-5 Downloading dependency 122 of 296: libxxhash0:riscv64=0.8.3-2 Downloading dependency 123 of 296: pybind11-dev:riscv64=2.13.6-2 Downloading dependency 124 of 296: bzip2:riscv64=1.0.8-6 Downloading dependency 125 of 296: libibumad3:riscv64=56.0-2 Downloading dependency 126 of 296: mpi-default-bin:riscv64=1.18 Downloading dependency 127 of 296: python3-packaging:riscv64=24.2-1Get:1 http://snapshot.debian.org/archive/debian/20250310T101857Z sid/main riscv64 python3-packaging all 24.2-1 [55.3 kB] Fetched 55.3 kB in 0s (799 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp12dkyho0/python3-packaging_24.2-1_all.deb' Get:1 http://snapshot.debian.org/archive/debian/20250310T101857Z sid/main riscv64 libblas3 riscv64 3.12.1-2 [123 kB] Fetched 123 kB in 0s (1504 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmphqx7c8db/libblas3_3.12.1-2_riscv64.deb' Get:1 http://snapshot.debian.org/archive/debian/20250310T101857Z sid/main riscv64 procps riscv64 2:4.0.4-7 [877 kB] Fetched 877 kB in 0s (7582 kB/s) dpkg-name: info: moved 'procps_2%3a4.0.4-7_riscv64.deb' to '/srv/rebuilderd/tmp/tmp96ovqvdh/procps_4.0.4-7_riscv64.deb' Get:1 http://snapshot.debian.org/archive/debian/20250310T101857Z sid/main riscv64 libcc1-0 riscv64 14.2.0-17 [40.3 kB] Fetched 40.3 kB in 0s (599 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpl79msp62/libcc1-0_14.2.0-17_riscv64.deb' Get:1 http://snapshot.debian.org/archive/debian/20250310T101857Z sid/main riscv64 libgcc-s1 riscv64 14.2.0-17 [56.7 kB] Fetched 56.7 kB in 0s (813 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpc2ibem_f/libgcc-s1_14.2.0-17_riscv64.deb' Get:1 http://snapshot.debian.org/archive/debian/20250310T101857Z sid/main riscv64 libevent-extra-2.1-7t64 riscv64 2.1.12-stable-10+b1 [108 kB] Fetched 108 kB in 0s (1509 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp7q5hgqzz/libevent-extra-2.1-7t64_2.1.12-stable-10+b1_riscv64.deb' Get:1 http://snapshot.debian.org/archive/debian/20250310T101857Z sid/main riscv64 python3-numpy-dev riscv64 1:2.2.3+ds-5 [177 kB] Fetched 177 kB in 0s (2460 kB/s) dpkg-name: info: moved 'python3-numpy-dev_1%3a2.2.3+ds-5_riscv64.deb' to '/srv/rebuilderd/tmp/tmp0ov29thj/python3-numpy-dev_2.2.3+ds-5_riscv64.deb' Get:1 http://snapshot.debian.org/archive/debian/20250310T101857Z sid/main riscv64 python3.13 riscv64 3.13.2-1 [745 kB] Fetched 745 kB in 0s (7205 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp_ff_83yw/python3.13_3.13.2-1_riscv64.deb' Get:1 http://snapshot.debian.org/archive/debian/20250310T101857Z sid/main riscv64 python3-iniconfig all 1.1.1-2 [6396 B] Fetched 6396 B in 0s (101 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmppj09bb2b/python3-iniconfig_1.1.1-2_all.deb' Get:1 http://snapshot.debian.org/archive/debian/20250310T101857Z sid/main riscv64 libssl3t64 riscv64 3.4.1-1 [2098 kB] Fetched 2098 kB in 0s (11.2 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpss7ehvbg/libssl3t64_3.4.1-1_riscv64.deb' Get:1 http://snapshot.debian.org/archive/debian/20250310T101857Z sid/main riscv64 file riscv64 1:5.45-3+b1 [43.1 kB] Fetched 43.1 kB in 0s (658 kB/s) dpkg-name: info: moved 'file_1%3a5.45-3+b1_riscv64.deb' to '/srv/rebuilderd/tmp/tmpukzfkf8g/file_5.45-3+b1_riscv64.deb' Get:1 http://snapshot.debian.org/archive/debian/20250310T101857Z sid/main riscv64 automake all 1:1.17-3 [862 kB] Fetched 862 kB in 0s (7050 kB/s) dpkg-name: info: moved 'automake_1%3a1.17-3_all.deb' to '/srv/rebuilderd/tmp/tmpakhjtncv/automake_1.17-3_all.deb' Get:1 http://snapshot.debian.org/archive/debian/20250310T101857Z sid/main riscv64 libgfortran-14-dev riscv64 14.2.0-17 [1089 kB] Fetched 1089 kB in 0s (8983 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp9n9ccv89/libgfortran-14-dev_14.2.0-17_riscv64.deb' Get:1 http://snapshot.debian.org/archive/debian/20250310T101857Z sid/main riscv64 libhwloc15 riscv64 2.12.0-1 [158 kB] Fetched 158 kB in 0s (2098 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpw1wkepcs/libhwloc15_2.12.0-1_riscv64.deb' Get:1 http://snapshot.debian.org/archive/debian/20250310T101857Z sid/main riscv64 python3-more-itertools all 10.6.0-1 [65.3 kB] Fetched 65.3 kB in 0s (954 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp0mfktkul/python3-more-itertools_10.6.0-1_all.deb' Get:1 http://snapshot.debian.org/archive/debian/20250310T101857Z sid/main riscv64 autopoint all 0.23.1-1 [770 kB] Fetched 770 kB in 0s (7074 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpd9j2kjhd/autopoint_0.23.1-1_all.deb' Get:1 http://snapshot.debian.org/archive/debian/20250310T101857Z sid/main riscv64 libmunge2 riscv64 0.5.16-1 [19.9 kB] Fetched 19.9 kB in 0s (305 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpkioz3l1t/libmunge2_0.5.16-1_riscv64.deb' Get:1 http://snapshot.debian.org/archive/debian/20250310T101857Z sid/main riscv64 openssh-client riscv64 1:9.9p2-1 [967 kB] Fetched 967 kB in 0s (7010 kB/s) dpkg-name: info: moved 'openssh-client_1%3a9.9p2-1_riscv64.deb' to '/srv/rebuilderd/tmp/tmp9o8x813b/openssh-client_9.9p2-1_riscv64.deb' Get:1 http://snapshot.debian.org/archive/debian/20250310T101857Z sid/main riscv64 python3-pluggy all 1.5.0-1 [26.9 kB] Fetched 26.9 kB in 0s (417 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpr13bsk6i/python3-pluggy_1.5.0-1_all.deb' Get:1 http://snapshot.debian.org/archive/debian/20250310T101857Z sid/main riscv64 libevent-2.1-7t64 riscv64 2.1.12-stable-10+b1 [182 kB] Fetched 182 kB in 0s (2429 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpf6k090u5/libevent-2.1-7t64_2.1.12-stable-10+b1_riscv64.deb' Get:1 http://snapshot.debian.org/archive/debian/20250310T101857Z sid/main riscv64 libuv1t64 riscv64 1.50.0-2 [154 kB] Fetched 154 kB in 0s (2092 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp7w72zqfy/libuv1t64_1.50.0-2_riscv64.deb' Get:1 http://snapshot.debian.org/archive/debian/20250310T101857Z sid/main riscv64 python3-dev riscv64 3.13.2-2 [26.1 kB] Fetched 26.1 kB in 0s (414 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpr8ozl2rv/python3-dev_3.13.2-2_riscv64.deb' Get:1 http://snapshot.debian.org/archive/debian/20250310T101857Z sid/main riscv64 libpython3-stdlib riscv64 3.13.2-2 [10.1 kB] Fetched 10.1 kB in 0s (157 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpy9i3jl5x/libpython3-stdlib_3.13.2-2_riscv64.deb' Get:1 http://snapshot.debian.org/archive/debian/20250310T101857Z sid/main riscv64 librdmacm1t64 riscv64 56.0-2 [74.0 kB] Fetched 74.0 kB in 0s (1066 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmps2jvetcv/librdmacm1t64_56.0-2_riscv64.deb' Get:1 http://snapshot.debian.org/archive/debian/20250310T101857Z sid/main riscv64 util-linux riscv64 2.40.4-5 [1203 kB] Fetched 1203 kB in 0s (8943 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpgli70yxp/util-linux_2.40.4-5_riscv64.deb' Get:1 http://snapshot.debian.org/archive/debian/20250310T101857Z sid/main riscv64 dpkg riscv64 1.22.18 [1549 kB] Fetched 1549 kB in 0s (10.2 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmphhx940b_/dpkg_1.22.18_riscv64.deb' Get:1 http://snapshot.debian.org/archive/debian/20250310T101857Z sid/main riscv64 liblzma5 riscv64 5.6.4-1 [285 kB] Fetched 285 kB in 0s (3631 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpssjn709a/liblzma5_5.6.4-1_riscv64.deb' Get:1 http://snapshot.debian.org/archive/debian/20250310T101857Z sid/main riscv64 libnettle8t64 riscv64 3.10.1-1 [335 kB] Fetched 335 kB in 0s (3815 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpy9lz5e33/libnettle8t64_3.10.1-1_riscv64.deb' Get:1 http://snapshot.debian.org/archive/debian/20250310T101857Z sid/main riscv64 libdebconfclient0 riscv64 0.277 [10.2 kB] Fetched 10.2 kB in 0s (162 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp13se6y9k/libdebconfclient0_0.277_riscv64.deb' Get:1 http://snapshot.debian.org/archive/debian/20250310T101857Z sid/main riscv64 libpam-modules-bin riscv64 1.7.0-3 [49.0 kB] Fetched 49.0 kB in 0s (762 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpxj8vuhfm/libpam-modules-bin_1.7.0-3_riscv64.deb' Get:1 http://snapshot.debian.org/archive/debian/20250310T101857Z sid/main riscv64 libudev1 riscv64 257.4-1 [151 kB] Fetched 151 kB in 0s (2156 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpyrn5eiu0/libudev1_257.4-1_riscv64.deb' Get:1 http://snapshot.debian.org/archive/debian/20250310T101857Z sid/main riscv64 login.defs all 1:4.17.3-1 [186 kB] Fetched 186 kB in 0s (2567 kB/s) dpkg-name: info: moved 'login.defs_1%3a4.17.3-1_all.deb' to '/srv/rebuilderd/tmp/tmp46hz2psp/login.defs_4.17.3-1_all.deb' Get:1 http://snapshot.debian.org/archive/debian/20250310T101857Z sid/main riscv64 liblsan0 riscv64 14.2.0-17 [1078 kB] Fetched 1078 kB in 0s (8675 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpr4c9rdl4/liblsan0_14.2.0-17_riscv64.deb' Get:1 http://snapshot.debian.org/archive/debian/20250310T101857Z sid/main riscv64 man-db riscv64 2.13.0-1 [1407 kB] Fetched 1407 kB in 0s (9765 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpsrbhiz5q/man-db_2.13.0-1_riscv64.deb' Get:1 http://snapshot.debian.org/archive/debian/20250310T101857Z sid/main riscv64 libmagic-mgc riscv64 1:5.45-3+b1 [314 kB] Fetched 314 kB in 0s (3758 kB/s) dpkg-name: info: moved 'libmagic-mgc_1%3a5.45-3+b1_riscv64.deb' to '/srv/rebuilderd/tmp/tmpvo_jny9n/libmagic-mgc_5.45-3+b1_riscv64.deb' Get:1 http://snapshot.debian.org/archive/debian/20250310T101857Z sid/main riscv64 libpam-runtime all 1.7.0-3 [248 kB] Fetched 248 kB in 0s (3255 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp8zfr5x7h/libpam-runtime_1.7.0-3_all.deb' Get:1 http://snapshot.debian.org/archive/debian/20250310T101857Z sid/main riscv64 libxdmcp6 riscv64 1:1.1.5-1 [28.0 kB] Fetched 28.0 kB in 0s (424 kB/s) dpkg-name: info: moved 'libxdmcp6_1%3a1.1.5-1_riscv64.deb' to '/srv/rebuilderd/tmp/tmp3i3zx_pp/libxdmcp6_1.1.5-1_riscv64.deb' Get:1 http://snapshot.debian.org/archive/debian/20250310T101857Z sid/main riscv64 libkeyutils1 riscv64 1.6.3-4 [9124 B] Fetched 9124 B in 0s (144 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpv4a65ha9/libkeyutils1_1.6.3-4_riscv64.deb' Get:1 http://snapshot.debian.org/archive/debian/20250310T101857Z sid/main riscv64 libblas-dev riscv64 3.12.1-2 [275 kB] Fetched 275 kB in 0s (3306 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpzh6j873e/libblas-dev_3.12.1-2_riscv64.deb' Get:1 http://snapshot.debian.org/archive/debian/20250310T101857Z sid/main riscv64 libmuparser-dev riscv64 2.3.4-1+b1 [33.5 kB] Fetched 33.5 kB in 4s (8359 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpjndzbu_4/libmuparser-dev_2.3.4-1+b1_riscv64.deb' Get:1 http://snapshot.debian.org/archive/debian/20250310T101857Z sid/main riscv64 libssh2-1t64 riscv64 1.11.1-1 [249 kB] Fetched 249 kB in 0s (3157 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp352vsfgv/libssh2-1t64_1.11.1-1_riscv64.deb' Get:1 http://snapshot.debian.org/archive/debian/20250310T101857Z sid/main riscv64 libxnvctrl0 riscv64 535.171.04-1+b2 [14.5 kB] Fetched 14.5 kB in 0s (223 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpihqbe4ad/libxnvctrl0_535.171.04-1+b2_riscv64.deb' Get:1 http://snapshot.debian.org/archive/debian/20250310T101857Z sid/main riscv64 libgfortran5 riscv64 14.2.0-17 [398 kB] Fetched 398 kB in 0s (4467 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpy3b5_2zj/libgfortran5_14.2.0-17_riscv64.deb' Get:1 http://snapshot.debian.org/archive/debian/20250310T101857Z sid/main riscv64 libaudit1 riscv64 1:4.0.2-2+b2 [54.1 kB] Fetched 54.1 kB in 0s (842 kB/s) dpkg-name: info: moved 'libaudit1_1%3a4.0.2-2+b2_riscv64.deb' to '/srv/rebuilderd/tmp/tmp6dxh7nt1/libaudit1_4.0.2-2+b2_riscv64.deb' Get:1 http://snapshot.debian.org/archive/debian/20250310T101857Z sid/main riscv64 lsb-release all 12.1-1 [5912 B] Fetched 5912 B in 0s (87.8 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpusckh41m/lsb-release_12.1-1_all.deb' Get:1 http://snapshot.debian.org/archive/debian/20250310T101857Z sid/main riscv64 libunistring5 riscv64 1.3-1 [474 kB] Fetched 474 kB in 0s (4814 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmptvhvo4m6/libunistring5_1.3-1_riscv64.deb' Get:1 http://snapshot.debian.org/archive/debian/20250310T101857Z sid/main riscv64 python3-pytest all 8.3.5-1 [250 kB] Fetched 250 kB in 0s (3127 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp_jt5m5ue/python3-pytest_8.3.5-1_all.deb' Get:1 http://snapshot.debian.org/archive/debian/20250310T101857Z sid/main riscv64 python3.13-dev riscv64 3.13.2-1 [499 kB] Fetched 499 kB in 0s (5033 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpl7s3bz92/python3.13-dev_3.13.2-1_riscv64.deb' Get:1 http://snapshot.debian.org/archive/debian/20250310T101857Z sid/main riscv64 liblz4-1 riscv64 1.10.0-4 [85.8 kB] Fetched 85.8 kB in 0s (1159 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpvdbrup5q/liblz4-1_1.10.0-4_riscv64.deb' Get:1 http://snapshot.debian.org/archive/debian/20250310T101857Z sid/main riscv64 libblkid1 riscv64 2.40.4-5 [191 kB] Fetched 191 kB in 0s (2302 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpuaq4m3ou/libblkid1_2.40.4-5_riscv64.deb' Get:1 http://snapshot.debian.org/archive/debian/20250310T101857Z sid/main riscv64 libibverbs1 riscv64 56.0-2 [62.5 kB] Fetched 62.5 kB in 0s (822 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp7oaxbvxa/libibverbs1_56.0-2_riscv64.deb' Get:1 http://snapshot.debian.org/archive/debian/20250310T101857Z sid/main riscv64 libopenmpi40 riscv64 5.0.7-1 [2289 kB] Fetched 2289 kB in 0s (10.7 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmppg0x5to_/libopenmpi40_5.0.7-1_riscv64.deb' Get:1 http://snapshot.debian.org/archive/debian/20250310T101857Z sid/main riscv64 libubsan1 riscv64 14.2.0-17 [980 kB] Fetched 980 kB in 0s (8600 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpeofxdvie/libubsan1_14.2.0-17_riscv64.deb' Get:1 http://snapshot.debian.org/archive/debian/20250310T101857Z sid/main riscv64 chrpath riscv64 0.18-1 [14.0 kB] Fetched 14.0 kB in 0s (215 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpmsmvt5s6/chrpath_0.18-1_riscv64.deb' Get:1 http://snapshot.debian.org/archive/debian/20250310T101857Z sid/main riscv64 cpp-14 riscv64 14.2.0-17 [1276 B] Fetched 1276 B in 0s (21.2 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpv2jvyefh/cpp-14_14.2.0-17_riscv64.deb' Get:1 http://snapshot.debian.org/archive/debian/20250310T101857Z sid/main riscv64 liblapack-dev riscv64 3.12.1-2 [11.5 MB] Fetched 11.5 MB in 1s (15.4 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp00kxzel3/liblapack-dev_3.12.1-2_riscv64.deb' Get:1 http://snapshot.debian.org/archive/debian/20250310T101857Z sid/main riscv64 libsasl2-modules-db riscv64 2.1.28+dfsg1-9 [20.5 kB] Fetched 20.5 kB in 0s (322 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp4eeiqmyg/libsasl2-modules-db_2.1.28+dfsg1-9_riscv64.deb' Get:1 http://snapshot.debian.org/archive/debian/20250310T101857Z sid/main riscv64 libicu72 riscv64 72.1-6 [9392 kB] Fetched 9392 kB in 1s (15.7 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp6smccfj1/libicu72_72.1-6_riscv64.deb' Get:1 http://snapshot.debian.org/archive/debian/20250310T101857Z sid/main riscv64 pkgconf-bin riscv64 1.8.1-4 [29.8 kB] Fetched 29.8 kB in 0s (489 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpttfmawhf/pkgconf-bin_1.8.1-4_riscv64.deb' Get:1 http://snapshot.debian.org/archive/debian/20250310T101857Z sid/main riscv64 perl-modules-5.40 all 5.40.1-2 [3017 kB] Fetched 3017 kB in 0s (13.1 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp5k0tk_8m/perl-modules-5.40_5.40.1-2_all.deb' Get:1 http://snapshot.debian.org/archive/debian/20250310T101857Z sid/main riscv64 cpp-14-riscv64-linux-gnu riscv64 14.2.0-17 [14.0 MB] Fetched 14.0 MB in 1s (16.3 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp4220q51b/cpp-14-riscv64-linux-gnu_14.2.0-17_riscv64.deb' Get:1 http://snapshot.debian.org/archive/debian/20250310T101857Z sid/main riscv64 gfortran-14-riscv64-linux-gnu riscv64 14.2.0-17 [14.4 MB] Fetched 14.4 MB in 1s (15.9 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmplgetk7cf/gfortran-14-riscv64-linux-gnu_14.2.0-17_riscv64.deb' Get:1 http://snapshot.debian.org/archive/debian/20250310T101857Z sid/main riscv64 libpipeline1 riscv64 1.5.8-1 [40.3 kB] Fetched 40.3 kB in 0s (616 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmppowo37i4/libpipeline1_1.5.8-1_riscv64.deb' Get:1 http://snapshot.debian.org/archive/debian/20250310T101857Z sid/main riscv64 libc6-dev riscv64 2.41-4 [3129 kB] Fetched 3129 kB in 0s (12.8 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp2xkb0uzh/libc6-dev_2.41-4_riscv64.deb' Get:1 http://snapshot.debian.org/archive/debian/20250310T101857Z sid/main riscv64 libfftw3-bin riscv64 3.3.10-2+b1 [44.9 kB] Fetched 44.9 kB in 0s (664 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpg45g3_at/libfftw3-bin_3.3.10-2+b1_riscv64.deb' Get:1 http://snapshot.debian.org/archive/debian/20250310T101857Z sid/main riscv64 libidn2-0 riscv64 2.3.8-1 [109 kB] Fetched 109 kB in 0s (1521 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpood2hfjn/libidn2-0_2.3.8-1_riscv64.deb' Get:1 http://snapshot.debian.org/archive/debian/20250310T101857Z sid/main riscv64 gettext-base riscv64 0.23.1-1 [243 kB] Fetched 243 kB in 0s (3210 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmptvtio0fo/gettext-base_0.23.1-1_riscv64.deb' Get:1 http://snapshot.debian.org/archive/debian/20250310T101857Z sid/main riscv64 libc6 riscv64 2.41-4 [2465 kB] Fetched 2465 kB in 0s (11.5 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp855o7lgt/libc6_2.41-4_riscv64.deb' Get:1 http://snapshot.debian.org/archive/debian/20250310T101857Z sid/main riscv64 libarchive13t64 riscv64 3.7.4-1.1 [366 kB] Fetched 366 kB in 0s (4320 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpcq2o614z/libarchive13t64_3.7.4-1.1_riscv64.deb' Get:1 http://snapshot.debian.org/archive/debian/20250310T101857Z sid/main riscv64 libdebhelper-perl all 13.24.1 [90.9 kB] Fetched 90.9 kB in 0s (1328 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp_dhww8j2/libdebhelper-perl_13.24.1_all.deb' Get:1 http://snapshot.debian.org/archive/debian/20250310T101857Z sid/main riscv64 libmpfr6 riscv64 4.2.1-1+b2 [659 kB] Fetched 659 kB in 0s (6044 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmppqy8zruo/libmpfr6_4.2.1-1+b2_riscv64.deb' Get:1 http://snapshot.debian.org/archive/debian/20250310T101857Z sid/main riscv64 libsystemd0 riscv64 257.4-1 [467 kB] Fetched 467 kB in 0s (5308 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpu38gpz_u/libsystemd0_257.4-1_riscv64.deb' Get:1 http://snapshot.debian.org/archive/debian/20250310T101857Z sid/main riscv64 libperl5.40 riscv64 5.40.1-2 [3936 kB] Fetched 3936 kB in 0s (12.5 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp5uv2euhg/libperl5.40_5.40.1-2_riscv64.deb' Get:1 http://snapshot.debian.org/archive/debian/20250310T101857Z sid/main riscv64 libelf1t64 riscv64 0.192-4 [194 kB] Fetched 194 kB in 0s (2530 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpr4wv_wum/libelf1t64_0.192-4_riscv64.deb' Get:1 http://snapshot.debian.org/archive/debian/20250310T101857Z sid/main riscv64 librtmp1 riscv64 2.4+20151223.gitfa8646d.1-2+b5 [59.0 kB] Fetched 59.0 kB in 0s (910 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpwi4stkls/librtmp1_2.4+20151223.gitfa8646d.1-2+b5_riscv64.deb' Get:1 http://snapshot.debian.org/archive/debian/20250310T101857Z sid/main riscv64 bsdextrautils riscv64 2.40.4-5 [96.2 kB] Fetched 96.2 kB in 0s (1377 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmphw24saet/bsdextrautils_2.40.4-5_riscv64.deb' Get:1 http://snapshot.debian.org/archive/debian/20250310T101857Z sid/main riscv64 gcc riscv64 4:14.2.0-1 [5132 B] Fetched 5132 B in 0s (85.3 kB/s) dpkg-name: info: moved 'gcc_4%3a14.2.0-1_riscv64.deb' to '/srv/rebuilderd/tmp/tmp9oi6ccq9/gcc_14.2.0-1_riscv64.deb' Get:1 http://snapshot.debian.org/archive/debian/20250310T101857Z sid/main riscv64 libstdc++-14-dev riscv64 14.2.0-17 [5274 kB] Fetched 5274 kB in 0s (14.1 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpt06qzb6a/libstdc++-14-dev_14.2.0-17_riscv64.deb' Get:1 http://snapshot.debian.org/archive/debian/20250310T101857Z sid/main riscv64 python3.13-minimal riscv64 3.13.2-1 [2159 kB] Fetched 2159 kB in 0s (11.4 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp77c9xrbj/python3.13-minimal_3.13.2-1_riscv64.deb' Get:1 http://snapshot.debian.org/archive/debian/20250310T101857Z sid/main riscv64 xz-utils riscv64 5.6.4-1 [554 kB] Fetched 554 kB in 0s (5659 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpq5cfpcc8/xz-utils_5.6.4-1_riscv64.deb' Get:1 http://snapshot.debian.org/archive/debian/20250310T101857Z sid/main riscv64 zlib1g-dev riscv64 1:1.3.dfsg+really1.3.1-1+b1 [978 kB] Fetched 978 kB in 0s (7918 kB/s) dpkg-name: info: moved 'zlib1g-dev_1%3a1.3.dfsg+really1.3.1-1+b1_riscv64.deb' to '/srv/rebuilderd/tmp/tmp7yzh3p7l/zlib1g-dev_1.3.dfsg+really1.3.1-1+b1_riscv64.deb' Get:1 http://snapshot.debian.org/archive/debian/20250310T101857Z sid/main riscv64 autotools-dev all 20220109.1 [51.6 kB] Fetched 51.6 kB in 0s (785 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpvgjt1cyb/autotools-dev_20220109.1_all.deb' Get:1 http://snapshot.debian.org/archive/debian/20250310T101857Z sid/main riscv64 libcap-ng0 riscv64 0.8.5-4+b1 [17.2 kB] Fetched 17.2 kB in 0s (257 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmphvht94pr/libcap-ng0_0.8.5-4+b1_riscv64.deb' Get:1 http://snapshot.debian.org/archive/debian/20250310T101857Z sid/main riscv64 bash-completion all 1:2.16.0-7 [319 kB] Fetched 319 kB in 0s (3545 kB/s) dpkg-name: info: moved 'bash-completion_1%3a2.16.0-7_all.deb' to '/srv/rebuilderd/tmp/tmpogsmvou2/bash-completion_2.16.0-7_all.deb' Get:1 http://snapshot.debian.org/archive/debian/20250310T101857Z sid/main riscv64 libsmartcols1 riscv64 2.40.4-5 [152 kB] Fetched 152 kB in 0s (2002 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpav10vqqv/libsmartcols1_2.40.4-5_riscv64.deb' Get:1 http://snapshot.debian.org/archive/debian/20250310T101857Z sid/main riscv64 openmpi-bin riscv64 5.0.7-1 [192 kB] Fetched 192 kB in 0s (2680 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpr918mwmq/openmpi-bin_5.0.7-1_riscv64.deb' Get:1 http://snapshot.debian.org/archive/debian/20250310T101857Z sid/main riscv64 libasan8 riscv64 14.2.0-17 [2366 kB] Fetched 2366 kB in 0s (11.2 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp9eel_fxo/libasan8_14.2.0-17_riscv64.deb' Get:1 http://snapshot.debian.org/archive/debian/20250310T101857Z sid/main riscv64 sed riscv64 4.9-2 [329 kB] Fetched 329 kB in 0s (3942 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpca4htelp/sed_4.9-2_riscv64.deb' Get:1 http://snapshot.debian.org/archive/debian/20250310T101857Z sid/main riscv64 python3-inflect all 7.3.1-2 [32.4 kB] Fetched 32.4 kB in 0s (480 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp19nux2nf/python3-inflect_7.3.1-2_all.deb' Get:1 http://snapshot.debian.org/archive/debian/20250310T101857Z sid/main riscv64 libexpat1-dev riscv64 2.6.4-1 [286 kB] Fetched 286 kB in 0s (3666 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpsx0j4ysa/libexpat1-dev_2.6.4-1_riscv64.deb' Get:1 http://snapshot.debian.org/archive/debian/20250310T101857Z sid/main riscv64 readline-common all 8.2-6 [69.4 kB] Fetched 69.4 kB in 0s (1060 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpzo6i1wpw/readline-common_8.2-6_all.deb' Get:1 http://snapshot.debian.org/archive/debian/20250310T101857Z sid/main riscv64 dh-strip-nondeterminism all 1.14.1-2 [8620 B] Fetched 8620 B in 0s (128 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp03jck2mg/dh-strip-nondeterminism_1.14.1-2_all.deb' Get:1 http://snapshot.debian.org/archive/debian/20250310T101857Z sid/main riscv64 g++-riscv64-linux-gnu riscv64 4:14.2.0-1 [1196 B] Fetched 1196 B in 0s (18.3 kB/s) dpkg-name: info: moved 'g++-riscv64-linux-gnu_4%3a14.2.0-1_riscv64.deb' to '/srv/rebuilderd/tmp/tmpfxm_fs8n/g++-riscv64-linux-gnu_14.2.0-1_riscv64.deb' Get:1 http://snapshot.debian.org/archive/debian/20250310T101857Z sid/main riscv64 gcc-14-base riscv64 14.2.0-17 [49.1 kB] Fetched 49.1 kB in 0s (731 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp1tn3wyjv/gcc-14-base_14.2.0-17_riscv64.deb' Get:1 http://snapshot.debian.org/archive/debian/20250310T101857Z sid/main riscv64 gfortran-14 riscv64 14.2.0-17 [14.0 kB] Fetched 14.0 kB in 0s (218 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpad3ha0y2/gfortran-14_14.2.0-17_riscv64.deb' Get:1 http://snapshot.debian.org/archive/debian/20250310T101857Z sid/main riscv64 tzdata all 2025a-2 [259 kB] Fetched 259 kB in 0s (3272 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp7uwdxifc/tzdata_2025a-2_all.deb' Get:1 http://snapshot.debian.org/archive/debian/20250310T101857Z sid/main riscv64 adduser all 3.145 [109 kB] Fetched 109 kB in 0s (1571 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmptesbpik5/adduser_3.145_all.deb' Get:1 http://snapshot.debian.org/archive/debian/20250310T101857Z sid/main riscv64 python3-pybind11 all 2.13.6-2 [215 kB] Fetched 215 kB in 0s (2856 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp6b0o1td3/python3-pybind11_2.13.6-2_all.deb' Get:1 http://snapshot.debian.org/archive/debian/20250310T101857Z sid/main riscv64 libc-dev-bin riscv64 2.41-4 [57.6 kB] Fetched 57.6 kB in 0s (882 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpkfh67u3_/libc-dev-bin_2.41-4_riscv64.deb' Get:1 http://snapshot.debian.org/archive/debian/20250310T101857Z sid/main riscv64 libxcb1 riscv64 1.17.0-2+b1 [145 kB] Fetched 145 kB in 0s (1994 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp3jum113e/libxcb1_1.17.0-2+b1_riscv64.deb' Get:1 http://snapshot.debian.org/archive/debian/20250310T101857Z sid/main riscv64 cmake-data all 3.31.6-1 [2268 kB] Fetched 2268 kB in 0s (10.7 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpdji6winj/cmake-data_3.31.6-1_all.deb' Get:1 http://snapshot.debian.org/archive/debian/20250310T101857Z sid/main riscv64 libselinux1 riscv64 3.8-4 [88.0 kB] Fetched 88.0 kB in 0s (1216 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpjr8ivvqu/libselinux1_3.8-4_riscv64.deb' Get:1 http://snapshot.debian.org/archive/debian/20250310T101857Z sid/main riscv64 libxau6 riscv64 1:1.0.11-1 [20.5 kB] Fetched 20.5 kB in 0s (327 kB/s) dpkg-name: info: moved 'libxau6_1%3a1.0.11-1_riscv64.deb' to '/srv/rebuilderd/tmp/tmppu6uh31c/libxau6_1.0.11-1_riscv64.deb' Get:1 http://snapshot.debian.org/archive/debian/20250310T101857Z sid/main riscv64 linux-libc-dev all 6.12.17-1 [2526 kB] Fetched 2526 kB in 0s (10.9 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpv_656mtf/linux-libc-dev_6.12.17-1_all.deb' Get:1 http://snapshot.debian.org/archive/debian/20250315T150632Z sid/main riscv64 libucx0 riscv64 1.18.1+ds-2 [1168 kB] Fetched 1168 kB in 0s (9016 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp0uxhbe8u/libucx0_1.18.1+ds-2_riscv64.deb' Get:1 http://snapshot.debian.org/archive/debian/20250310T101857Z sid/main riscv64 g++-14 riscv64 14.2.0-17 [22.1 kB] Fetched 22.1 kB in 0s (327 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpbmburdp0/g++-14_14.2.0-17_riscv64.deb' Get:1 http://snapshot.debian.org/archive/debian/20250310T101857Z sid/main riscv64 libp11-kit0 riscv64 0.25.5-3 [444 kB] Fetched 444 kB in 0s (4744 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpbqiw0jo8/libp11-kit0_0.25.5-3_riscv64.deb' Get:1 http://snapshot.debian.org/archive/debian/20250310T101857Z sid/main riscv64 gettext riscv64 0.23.1-1 [1682 kB] Fetched 1682 kB in 0s (9672 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpx4peq845/gettext_0.23.1-1_riscv64.deb' Get:1 http://snapshot.debian.org/archive/debian/20250310T101857Z sid/main riscv64 libarchive-zip-perl all 1.68-1 [104 kB] Fetched 104 kB in 0s (1438 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpqhl7ifac/libarchive-zip-perl_1.68-1_all.deb' Get:1 http://snapshot.debian.org/archive/debian/20250310T101857Z sid/main riscv64 libevent-core-2.1-7t64 riscv64 2.1.12-stable-10+b1 [132 kB] Fetched 132 kB in 0s (1780 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp7sogneuf/libevent-core-2.1-7t64_2.1.12-stable-10+b1_riscv64.deb' Get:1 http://snapshot.debian.org/archive/debian/20250310T101857Z sid/main riscv64 dh-python all 6.20250308 [115 kB] Fetched 115 kB in 0s (1656 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpdnslu4be/dh-python_6.20250308_all.deb' Get:1 http://snapshot.debian.org/archive/debian/20250310T101857Z sid/main riscv64 libfabric1 riscv64 1.17.0-3.1 [526 kB] Fetched 526 kB in 0s (5121 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpybs1xnlp/libfabric1_1.17.0-3.1_riscv64.deb' Get:1 http://snapshot.debian.org/archive/debian/20250310T101857Z sid/main riscv64 base-files riscv64 13.7 [72.9 kB] Fetched 72.9 kB in 0s (1072 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp2ci_phn4/base-files_13.7_riscv64.deb' Get:1 http://snapshot.debian.org/archive/debian/20250310T101857Z sid/main riscv64 gcc-14 riscv64 14.2.0-17 [527 kB] Fetched 527 kB in 0s (5080 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp3gi_gjoz/gcc-14_14.2.0-17_riscv64.deb' Get:1 http://snapshot.debian.org/archive/debian/20250310T101857Z sid/main riscv64 libcrypt1 riscv64 1:4.4.38-1 [106 kB] Fetched 106 kB in 0s (1599 kB/s) dpkg-name: info: moved 'libcrypt1_1%3a4.4.38-1_riscv64.deb' to '/srv/rebuilderd/tmp/tmpewtbuqap/libcrypt1_4.4.38-1_riscv64.deb' Get:1 http://snapshot.debian.org/archive/debian/20250310T101857Z sid/main riscv64 libdb5.3t64 riscv64 5.3.28+dfsg2-9 [716 kB] Fetched 716 kB in 0s (6117 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp3_zee4lg/libdb5.3t64_5.3.28+dfsg2-9_riscv64.deb' Get:1 http://snapshot.debian.org/archive/debian/20250310T101857Z sid/main riscv64 libdpkg-perl all 1.22.18 [649 kB] Fetched 649 kB in 0s (6251 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpsyx2hlej/libdpkg-perl_1.22.18_all.deb' Get:1 http://snapshot.debian.org/archive/debian/20250310T101857Z sid/main riscv64 libgssapi-krb5-2 riscv64 1.21.3-4 [142 kB] Fetched 142 kB in 0s (1976 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp6m_bwi9y/libgssapi-krb5-2_1.21.3-4_riscv64.deb' Get:1 http://snapshot.debian.org/archive/debian/20250310T101857Z sid/main riscv64 openssl-provider-legacy riscv64 3.4.1-1 [303 kB] Fetched 303 kB in 0s (3830 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpkfahym2u/openssl-provider-legacy_3.4.1-1_riscv64.deb' Get:1 http://snapshot.debian.org/archive/debian/20250310T101857Z sid/main riscv64 gcc-14-riscv64-linux-gnu riscv64 14.2.0-17 [27.1 MB] Fetched 27.1 MB in 2s (15.6 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpfx412go8/gcc-14-riscv64-linux-gnu_14.2.0-17_riscv64.deb' Get:1 http://snapshot.debian.org/archive/debian/20250310T101857Z sid/main riscv64 libctf0 riscv64 2.44-3 [96.1 kB] Fetched 96.1 kB in 0s (1273 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp_0ztu2so/libctf0_2.44-3_riscv64.deb' Get:1 http://snapshot.debian.org/archive/debian/20250310T101857Z sid/main riscv64 libltdl7 riscv64 2.5.4-4 [415 kB] Fetched 415 kB in 0s (4704 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpycm34jjo/libltdl7_2.5.4-4_riscv64.deb' Get:1 http://snapshot.debian.org/archive/debian/20250310T101857Z sid/main riscv64 libfftw3-long3 riscv64 3.3.10-2+b1 [705 kB] Fetched 705 kB in 0s (6682 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpshxlghav/libfftw3-long3_3.3.10-2+b1_riscv64.deb' Get:1 http://snapshot.debian.org/archive/debian/20250310T101857Z sid/main riscv64 python3-typing-extensions all 4.12.2-2 [73.0 kB] Fetched 73.0 kB in 0s (1044 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpe4lj00ae/python3-typing-extensions_4.12.2-2_all.deb' Get:1 http://snapshot.debian.org/archive/debian/20250310T101857Z sid/main riscv64 python3-pkg-resources all 75.8.0-1 [222 kB] Fetched 222 kB in 0s (2739 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpwopoyplq/python3-pkg-resources_75.8.0-1_all.deb' Downloading dependency 128 of 296: libblas3:riscv64=3.12.1-2 Downloading dependency 129 of 296: procps:riscv64=2:4.0.4-7 Downloading dependency 130 of 296: libcc1-0:riscv64=14.2.0-17 Downloading dependency 131 of 296: libgcc-s1:riscv64=14.2.0-17 Downloading dependency 132 of 296: libevent-extra-2.1-7t64:riscv64=2.1.12-stable-10+b1 Downloading dependency 133 of 296: python3-numpy-dev:riscv64=1:2.2.3+ds-5 Downloading dependency 134 of 296: python3.13:riscv64=3.13.2-1 Downloading dependency 135 of 296: python3-iniconfig:riscv64=1.1.1-2 Downloading dependency 136 of 296: libssl3t64:riscv64=3.4.1-1 Downloading dependency 137 of 296: file:riscv64=1:5.45-3+b1 Downloading dependency 138 of 296: automake:riscv64=1:1.17-3 Downloading dependency 139 of 296: libgfortran-14-dev:riscv64=14.2.0-17 Downloading dependency 140 of 296: libhwloc15:riscv64=2.12.0-1 Downloading dependency 141 of 296: python3-more-itertools:riscv64=10.6.0-1 Downloading dependency 142 of 296: autopoint:riscv64=0.23.1-1 Downloading dependency 143 of 296: libmunge2:riscv64=0.5.16-1 Downloading dependency 144 of 296: openssh-client:riscv64=1:9.9p2-1 Downloading dependency 145 of 296: python3-pluggy:riscv64=1.5.0-1 Downloading dependency 146 of 296: libevent-2.1-7t64:riscv64=2.1.12-stable-10+b1 Downloading dependency 147 of 296: libuv1t64:riscv64=1.50.0-2 Downloading dependency 148 of 296: python3-dev:riscv64=3.13.2-2 Downloading dependency 149 of 296: libpython3-stdlib:riscv64=3.13.2-2 Downloading dependency 150 of 296: librdmacm1t64:riscv64=56.0-2 Downloading dependency 151 of 296: util-linux:riscv64=2.40.4-5 Downloading dependency 152 of 296: dpkg:riscv64=1.22.18 Downloading dependency 153 of 296: liblzma5:riscv64=5.6.4-1 Downloading dependency 154 of 296: libnettle8t64:riscv64=3.10.1-1 Downloading dependency 155 of 296: libdebconfclient0:riscv64=0.277 Downloading dependency 156 of 296: libpam-modules-bin:riscv64=1.7.0-3 Downloading dependency 157 of 296: libudev1:riscv64=257.4-1 Downloading dependency 158 of 296: login.defs:riscv64=1:4.17.3-1 Downloading dependency 159 of 296: liblsan0:riscv64=14.2.0-17 Downloading dependency 160 of 296: man-db:riscv64=2.13.0-1 Downloading dependency 161 of 296: libmagic-mgc:riscv64=1:5.45-3+b1 Downloading dependency 162 of 296: libpam-runtime:riscv64=1.7.0-3 Downloading dependency 163 of 296: libxdmcp6:riscv64=1:1.1.5-1 Downloading dependency 164 of 296: libkeyutils1:riscv64=1.6.3-4 Downloading dependency 165 of 296: libblas-dev:riscv64=3.12.1-2 Downloading dependency 166 of 296: libmuparser-dev:riscv64=2.3.4-1+b1 Downloading dependency 167 of 296: libssh2-1t64:riscv64=1.11.1-1 Downloading dependency 168 of 296: libxnvctrl0:riscv64=535.171.04-1+b2 Downloading dependency 169 of 296: libgfortran5:riscv64=14.2.0-17 Downloading dependency 170 of 296: libaudit1:riscv64=1:4.0.2-2+b2 Downloading dependency 171 of 296: lsb-release:riscv64=12.1-1 Downloading dependency 172 of 296: libunistring5:riscv64=1.3-1 Downloading dependency 173 of 296: python3-pytest:riscv64=8.3.5-1 Downloading dependency 174 of 296: python3.13-dev:riscv64=3.13.2-1 Downloading dependency 175 of 296: liblz4-1:riscv64=1.10.0-4 Downloading dependency 176 of 296: libblkid1:riscv64=2.40.4-5 Downloading dependency 177 of 296: libibverbs1:riscv64=56.0-2 Downloading dependency 178 of 296: libopenmpi40:riscv64=5.0.7-1 Downloading dependency 179 of 296: libubsan1:riscv64=14.2.0-17 Downloading dependency 180 of 296: chrpath:riscv64=0.18-1 Downloading dependency 181 of 296: cpp-14:riscv64=14.2.0-17 Downloading dependency 182 of 296: liblapack-dev:riscv64=3.12.1-2 Downloading dependency 183 of 296: libsasl2-modules-db:riscv64=2.1.28+dfsg1-9 Downloading dependency 184 of 296: libicu72:riscv64=72.1-6 Downloading dependency 185 of 296: pkgconf-bin:riscv64=1.8.1-4 Downloading dependency 186 of 296: perl-modules-5.40:riscv64=5.40.1-2 Downloading dependency 187 of 296: cpp-14-riscv64-linux-gnu:riscv64=14.2.0-17 Downloading dependency 188 of 296: gfortran-14-riscv64-linux-gnu:riscv64=14.2.0-17 Downloading dependency 189 of 296: libpipeline1:riscv64=1.5.8-1 Downloading dependency 190 of 296: libc6-dev:riscv64=2.41-4 Downloading dependency 191 of 296: libfftw3-bin:riscv64=3.3.10-2+b1 Downloading dependency 192 of 296: libidn2-0:riscv64=2.3.8-1 Downloading dependency 193 of 296: gettext-base:riscv64=0.23.1-1 Downloading dependency 194 of 296: libc6:riscv64=2.41-4 Downloading dependency 195 of 296: libarchive13t64:riscv64=3.7.4-1.1 Downloading dependency 196 of 296: libdebhelper-perl:riscv64=13.24.1 Downloading dependency 197 of 296: libmpfr6:riscv64=4.2.1-1+b2 Downloading dependency 198 of 296: libsystemd0:riscv64=257.4-1 Downloading dependency 199 of 296: libperl5.40:riscv64=5.40.1-2 Downloading dependency 200 of 296: libelf1t64:riscv64=0.192-4 Downloading dependency 201 of 296: librtmp1:riscv64=2.4+20151223.gitfa8646d.1-2+b5 Downloading dependency 202 of 296: bsdextrautils:riscv64=2.40.4-5 Downloading dependency 203 of 296: gcc:riscv64=4:14.2.0-1 Downloading dependency 204 of 296: libstdc++-14-dev:riscv64=14.2.0-17 Downloading dependency 205 of 296: python3.13-minimal:riscv64=3.13.2-1 Downloading dependency 206 of 296: xz-utils:riscv64=5.6.4-1 Downloading dependency 207 of 296: zlib1g-dev:riscv64=1:1.3.dfsg+really1.3.1-1+b1 Downloading dependency 208 of 296: autotools-dev:riscv64=20220109.1 Downloading dependency 209 of 296: libcap-ng0:riscv64=0.8.5-4+b1 Downloading dependency 210 of 296: bash-completion:riscv64=1:2.16.0-7 Downloading dependency 211 of 296: libsmartcols1:riscv64=2.40.4-5 Downloading dependency 212 of 296: openmpi-bin:riscv64=5.0.7-1 Downloading dependency 213 of 296: libasan8:riscv64=14.2.0-17 Downloading dependency 214 of 296: sed:riscv64=4.9-2 Downloading dependency 215 of 296: python3-inflect:riscv64=7.3.1-2 Downloading dependency 216 of 296: libexpat1-dev:riscv64=2.6.4-1 Downloading dependency 217 of 296: readline-common:riscv64=8.2-6 Downloading dependency 218 of 296: dh-strip-nondeterminism:riscv64=1.14.1-2 Downloading dependency 219 of 296: g++-riscv64-linux-gnu:riscv64=4:14.2.0-1 Downloading dependency 220 of 296: gcc-14-base:riscv64=14.2.0-17 Downloading dependency 221 of 296: gfortran-14:riscv64=14.2.0-17 Downloading dependency 222 of 296: tzdata:riscv64=2025a-2 Downloading dependency 223 of 296: adduser:riscv64=3.145 Downloading dependency 224 of 296: python3-pybind11:riscv64=2.13.6-2 Downloading dependency 225 of 296: libc-dev-bin:riscv64=2.41-4 Downloading dependency 226 of 296: libxcb1:riscv64=1.17.0-2+b1 Downloading dependency 227 of 296: cmake-data:riscv64=3.31.6-1 Downloading dependency 228 of 296: libselinux1:riscv64=3.8-4 Downloading dependency 229 of 296: libxau6:riscv64=1:1.0.11-1 Downloading dependency 230 of 296: linux-libc-dev:riscv64=6.12.17-1 Downloading dependency 231 of 296: libucx0:riscv64=1.18.1+ds-2 Downloading dependency 232 of 296: g++-14:riscv64=14.2.0-17 Downloading dependency 233 of 296: libp11-kit0:riscv64=0.25.5-3 Downloading dependency 234 of 296: gettext:riscv64=0.23.1-1 Downloading dependency 235 of 296: libarchive-zip-perl:riscv64=1.68-1 Downloading dependency 236 of 296: libevent-core-2.1-7t64:riscv64=2.1.12-stable-10+b1 Downloading dependency 237 of 296: dh-python:riscv64=6.20250308 Downloading dependency 238 of 296: libfabric1:riscv64=1.17.0-3.1 Downloading dependency 239 of 296: base-files:riscv64=13.7 Downloading dependency 240 of 296: gcc-14:riscv64=14.2.0-17 Downloading dependency 241 of 296: libcrypt1:riscv64=1:4.4.38-1 Downloading dependency 242 of 296: libdb5.3t64:riscv64=5.3.28+dfsg2-9 Downloading dependency 243 of 296: libdpkg-perl:riscv64=1.22.18 Downloading dependency 244 of 296: libgssapi-krb5-2:riscv64=1.21.3-4 Downloading dependency 245 of 296: openssl-provider-legacy:riscv64=3.4.1-1 Downloading dependency 246 of 296: gcc-14-riscv64-linux-gnu:riscv64=14.2.0-17 Downloading dependency 247 of 296: libctf0:riscv64=2.44-3 Downloading dependency 248 of 296: libltdl7:riscv64=2.5.4-4 Downloading dependency 249 of 296: libfftw3-long3:riscv64=3.3.10-2+b1 Downloading dependency 250 of 296: python3-typing-extensions:riscv64=4.12.2-2 Downloading dependency 251 of 296: python3-pkg-resources:riscv64=75.8.0-1 Downloading dependency 252 of 296: libcom-err2:riscv64=1.47.2-1Get:1 http://snapshot.debian.org/archive/debian/20250310T101857Z sid/main riscv64 libcom-err2 riscv64 1.47.2-1 [23.7 kB] Fetched 23.7 kB in 0s (370 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpiua6i08m/libcom-err2_1.47.2-1_riscv64.deb' Get:1 http://snapshot.debian.org/archive/debian/20250310T101857Z sid/main riscv64 libuuid1 riscv64 2.40.4-5 [38.7 kB] Fetched 38.7 kB in 0s (600 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpae2bn6o_/libuuid1_2.40.4-5_riscv64.deb' Get:1 http://snapshot.debian.org/archive/debian/20250310T101857Z sid/main riscv64 libsframe1 riscv64 2.44-3 [79.1 kB] Fetched 79.1 kB in 0s (1217 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp1kgtrl2l/libsframe1_2.44-3_riscv64.deb' Get:1 http://snapshot.debian.org/archive/debian/20250310T101857Z sid/main riscv64 openmpi-common all 5.0.7-1 [97.2 kB] Fetched 97.2 kB in 0s (1411 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpxibb6pua/openmpi-common_5.0.7-1_all.deb' Get:1 http://snapshot.debian.org/archive/debian/20250310T101857Z sid/main riscv64 libgdbm6t64 riscv64 1.24-2 [75.9 kB] Fetched 75.9 kB in 0s (1143 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpjjwj8t4q/libgdbm6t64_1.24-2_riscv64.deb' Get:1 http://snapshot.debian.org/archive/debian/20250310T101857Z sid/main riscv64 po-debconf all 1.0.21+nmu1 [248 kB] Fetched 248 kB in 0s (3215 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp690whtwo/po-debconf_1.0.21+nmu1_all.deb' Get:1 http://snapshot.debian.org/archive/debian/20250310T101857Z sid/main riscv64 python3-autocommand all 2.2.2-3 [13.6 kB] Fetched 13.6 kB in 0s (220 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpitcxjxbt/python3-autocommand_2.2.2-3_all.deb' Get:1 http://snapshot.debian.org/archive/debian/20250310T101857Z sid/main riscv64 libisl23 riscv64 0.27-1 [664 kB] Fetched 664 kB in 0s (5765 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpn3ivgfsv/libisl23_0.27-1_riscv64.deb' Get:1 http://snapshot.debian.org/archive/debian/20250310T101857Z sid/main riscv64 libtasn1-6 riscv64 4.20.0-2 [50.6 kB] Fetched 50.6 kB in 0s (746 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmppd42cm49/libtasn1-6_4.20.0-2_riscv64.deb' Get:1 http://snapshot.debian.org/archive/debian/20250310T101857Z sid/main riscv64 liblapack3 riscv64 3.12.1-2 [1993 kB] Fetched 1993 kB in 0s (10.1 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpx1huq316/liblapack3_3.12.1-2_riscv64.deb' Get:1 http://snapshot.debian.org/archive/debian/20250310T101857Z sid/main riscv64 libxext6 riscv64 2:1.3.4-1+b3 [51.7 kB] Fetched 51.7 kB in 0s (755 kB/s) dpkg-name: info: moved 'libxext6_2%3a1.3.4-1+b3_riscv64.deb' to '/srv/rebuilderd/tmp/tmpucipl84b/libxext6_1.3.4-1+b3_riscv64.deb' Get:1 http://snapshot.debian.org/archive/debian/20250310T101857Z sid/main riscv64 libmagic1t64 riscv64 1:5.45-3+b1 [115 kB] Fetched 115 kB in 0s (1509 kB/s) dpkg-name: info: moved 'libmagic1t64_1%3a5.45-3+b1_riscv64.deb' to '/srv/rebuilderd/tmp/tmppcy2moo6/libmagic1t64_5.45-3+b1_riscv64.deb' Get:1 http://snapshot.debian.org/archive/debian/20250310T101857Z sid/main riscv64 libx11-6 riscv64 2:1.8.10-2 [812 kB] Fetched 812 kB in 0s (6423 kB/s) dpkg-name: info: moved 'libx11-6_2%3a1.8.10-2_riscv64.deb' to '/srv/rebuilderd/tmp/tmpcdsrmxmi/libx11-6_1.8.10-2_riscv64.deb' Get:1 http://snapshot.debian.org/archive/debian/20250310T101857Z sid/main riscv64 libxml2 riscv64 2.12.7+dfsg+really2.9.14-0.2+b2 [709 kB] Fetched 709 kB in 0s (5889 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpblfkftst/libxml2_2.12.7+dfsg+really2.9.14-0.2+b2_riscv64.deb' Get:1 http://snapshot.debian.org/archive/debian/20250310T101857Z sid/main riscv64 libcrypt-dev riscv64 1:4.4.38-1 [221 kB] Fetched 221 kB in 0s (2681 kB/s) dpkg-name: info: moved 'libcrypt-dev_1%3a4.4.38-1_riscv64.deb' to '/srv/rebuilderd/tmp/tmpa8jc4b8z/libcrypt-dev_4.4.38-1_riscv64.deb' Get:1 http://snapshot.debian.org/archive/debian/20250310T101857Z sid/main riscv64 libkrb5support0 riscv64 1.21.3-4 [33.8 kB] Fetched 33.8 kB in 0s (489 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmps0guz9zb/libkrb5support0_1.21.3-4_riscv64.deb' Get:1 http://snapshot.debian.org/archive/debian/20250310T101857Z sid/main riscv64 python3-networkx all 3.2.1-5 [13.0 MB] Fetched 13.0 MB in 1s (13.4 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpbekdeytg/python3-networkx_3.2.1-5_all.deb' Get:1 http://snapshot.debian.org/archive/debian/20250310T101857Z sid/main riscv64 libpam0g riscv64 1.7.0-3 [70.0 kB] Fetched 70.0 kB in 0s (1019 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpbuyrobqm/libpam0g_1.7.0-3_riscv64.deb' Get:1 http://snapshot.debian.org/archive/debian/20250310T101857Z sid/main riscv64 architecture-properties riscv64 0.2.6 [2336 B] Fetched 2336 B in 0s (33.4 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpgpi8785x/architecture-properties_0.2.6_riscv64.deb' Get:1 http://snapshot.debian.org/archive/debian/20250310T101857Z sid/main riscv64 dpkg-dev all 1.22.18 [1338 kB] Fetched 1338 kB in 0s (8341 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpkoy4m1dd/dpkg-dev_1.22.18_all.deb' Get:1 http://snapshot.debian.org/archive/debian/20250310T101857Z sid/main riscv64 libhwloc-plugins riscv64 2.12.0-1 [17.5 kB] Fetched 17.5 kB in 0s (235 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmplvmvjd_5/libhwloc-plugins_2.12.0-1_riscv64.deb' Get:1 http://snapshot.debian.org/archive/debian/20250310T101857Z sid/main riscv64 libpkgconf3 riscv64 1.8.1-4 [36.0 kB] Fetched 36.0 kB in 0s (520 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpl3gg9cu9/libpkgconf3_1.8.1-4_riscv64.deb' Get:1 http://snapshot.debian.org/archive/debian/20250315T150632Z sid/main riscv64 python3-mpi4py riscv64 4.0.3-3 [736 kB] Fetched 736 kB in 0s (5431 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp_xs22jlx/python3-mpi4py_4.0.3-3_riscv64.deb' Get:1 http://snapshot.debian.org/archive/debian/20250310T101857Z sid/main riscv64 debianutils riscv64 5.21 [91.5 kB] Fetched 91.5 kB in 0s (1159 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp7xy30crg/debianutils_5.21_riscv64.deb' Get:1 http://snapshot.debian.org/archive/debian/20250310T101857Z sid/main riscv64 libc-bin riscv64 2.41-4 [604 kB] Fetched 604 kB in 0s (5987 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpjdyazejp/libc-bin_2.41-4_riscv64.deb' Get:1 http://snapshot.debian.org/archive/debian/20250310T101857Z sid/main riscv64 findutils riscv64 4.10.0-3 [706 kB] Fetched 706 kB in 0s (6179 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp0vjsfq36/findutils_4.10.0-3_riscv64.deb' Get:1 http://snapshot.debian.org/archive/debian/20250310T101857Z sid/main riscv64 libtool all 2.5.4-4 [539 kB] Fetched 539 kB in 0s (5468 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp00jye2rk/libtool_2.5.4-4_all.deb' Get:1 http://snapshot.debian.org/archive/debian/20250310T101857Z sid/main riscv64 bash riscv64 5.2.37-1.1 [1505 kB] Fetched 1505 kB in 0s (9105 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmptnoj97l2/bash_5.2.37-1.1_riscv64.deb' Get:1 http://snapshot.debian.org/archive/debian/20250310T101857Z sid/main riscv64 libfido2-1 riscv64 1.15.0-1+b1 [83.5 kB] Fetched 83.5 kB in 0s (1129 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmps_o7rksv/libfido2-1_1.15.0-1+b1_riscv64.deb' Get:1 http://snapshot.debian.org/archive/debian/20250310T101857Z sid/main riscv64 libbrotli1 riscv64 1.1.0-2+b7 [358 kB] Fetched 358 kB in 0s (3815 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpc_t6mz0l/libbrotli1_1.1.0-2+b7_riscv64.deb' Get:1 http://snapshot.debian.org/archive/debian/20250310T101857Z sid/main riscv64 libtsan2 riscv64 14.2.0-17 [2242 kB] Fetched 2242 kB in 0s (9995 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpysl068op/libtsan2_14.2.0-17_riscv64.deb' Get:1 http://snapshot.debian.org/archive/debian/20250310T101857Z sid/main riscv64 libbinutils riscv64 2.44-3 [520 kB] Fetched 520 kB in 0s (5375 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpbwe3btch/libbinutils_2.44-3_riscv64.deb' Get:1 http://snapshot.debian.org/archive/debian/20250310T101857Z sid/main riscv64 debconf all 1.5.90 [121 kB] Fetched 121 kB in 0s (1658 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp8drsvs4w/debconf_1.5.90_all.deb' Get:1 http://snapshot.debian.org/archive/debian/20250310T101857Z sid/main riscv64 libacl1 riscv64 2.3.2-2+b1 [32.9 kB] Fetched 32.9 kB in 0s (475 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpjl8t9pa_/libacl1_2.3.2-2+b1_riscv64.deb' Get:1 http://snapshot.debian.org/archive/debian/20250310T101857Z sid/main riscv64 ibverbs-providers riscv64 56.0-2 [388 kB] Fetched 388 kB in 0s (4384 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpf40fb5bo/ibverbs-providers_56.0-2_riscv64.deb' Get:1 http://snapshot.debian.org/archive/debian/20250310T101857Z sid/main riscv64 libbsd0 riscv64 0.12.2-2 [132 kB] Fetched 132 kB in 0s (1841 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpxpgio0sy/libbsd0_0.12.2-2_riscv64.deb' Get:1 http://snapshot.debian.org/archive/debian/20250310T101857Z sid/main riscv64 ncurses-bin riscv64 6.5+20250216-2 [436 kB] Fetched 436 kB in 0s (4361 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpea3uc9w4/ncurses-bin_6.5+20250216-2_riscv64.deb' Get:1 http://snapshot.debian.org/archive/debian/20250310T101857Z sid/main riscv64 libboost-dev riscv64 1.83.0.2+b2 [3832 B] Fetched 3832 B in 0s (56.8 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpkxc2cf0o/libboost-dev_1.83.0.2+b2_riscv64.deb' Get:1 http://snapshot.debian.org/archive/debian/20250310T101857Z sid/main riscv64 zlib1g riscv64 1:1.3.dfsg+really1.3.1-1+b1 [85.7 kB] Fetched 85.7 kB in 0s (1190 kB/s) dpkg-name: info: moved 'zlib1g_1%3a1.3.dfsg+really1.3.1-1+b1_riscv64.deb' to '/srv/rebuilderd/tmp/tmplbma077y/zlib1g_1.3.dfsg+really1.3.1-1+b1_riscv64.deb' Get:1 http://snapshot.debian.org/archive/debian/20250310T101857Z sid/main riscv64 perl-base riscv64 5.40.1-2 [1662 kB] Fetched 1662 kB in 0s (9310 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp3ihuugah/perl-base_5.40.1-2_riscv64.deb' Get:1 http://snapshot.debian.org/archive/debian/20250310T101857Z sid/main riscv64 gzip riscv64 1.13-1 [139 kB] Fetched 139 kB in 0s (1811 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpmn2wrahi/gzip_1.13-1_riscv64.deb' Get:1 http://snapshot.debian.org/archive/debian/20250310T101857Z sid/main riscv64 libproc2-0 riscv64 2:4.0.4-7 [65.4 kB] Fetched 65.4 kB in 0s (913 kB/s) dpkg-name: info: moved 'libproc2-0_2%3a4.0.4-7_riscv64.deb' to '/srv/rebuilderd/tmp/tmpg0hhdp41/libproc2-0_4.0.4-7_riscv64.deb' Get:1 http://snapshot.debian.org/archive/debian/20250310T101857Z sid/main riscv64 libopenmpi-dev riscv64 5.0.7-1 [1089 kB] Fetched 1089 kB in 0s (7525 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp9qdjmnqc/libopenmpi-dev_5.0.7-1_riscv64.deb' Get:1 http://snapshot.debian.org/archive/debian/20250310T101857Z sid/main riscv64 make riscv64 4.4.1-1 [463 kB] Fetched 463 kB in 0s (4189 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp8fch1ojo/make_4.4.1-1_riscv64.deb' Get:1 http://snapshot.debian.org/archive/debian/20250315T150632Z sid/main riscv64 libnl-route-3-dev riscv64 3.7.0-1 [501 kB] Fetched 501 kB in 0s (2706 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpoifuom9h/libnl-route-3-dev_3.7.0-1_riscv64.deb' dpkg-buildpackage: info: source package debootsnap-dummy dpkg-buildpackage: info: source version 1.0 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Equivs Dummy Package Generator dpkg-buildpackage: info: host architecture riscv64 dpkg-source --before-build . debian/rules clean dh clean dh_clean debian/rules binary dh binary dh_update_autotools_config dh_autoreconf create-stamp debian/debhelper-build-stamp dh_prep dh_auto_install --destdir=debian/debootsnap-dummy/ dh_install dh_installdocs dh_installchangelogs dh_perl dh_link dh_strip_nondeterminism dh_compress dh_fixperms dh_missing dh_installdeb dh_gencontrol dh_md5sums dh_builddeb dpkg-deb: building package 'debootsnap-dummy' in '../debootsnap-dummy_1.0_all.deb'. dpkg-genbuildinfo --build=binary -O../debootsnap-dummy_1.0_riscv64.buildinfo dpkg-genchanges --build=binary -O../debootsnap-dummy_1.0_riscv64.changes dpkg-genchanges: info: binary-only upload (no source code included) dpkg-source --after-build . dpkg-buildpackage: info: binary-only upload (no source included) The package has been created. Attention, the package has been created in the /srv/rebuilderd/tmp/tmp5az8mlec/cache directory, not in ".." as indicated by the message above! I: automatically chosen mode: unshare I: chroot architecture riscv64 is equal to the host's architecture I: using /srv/rebuilderd/tmp/mmdebstrap.lYt9sswCCt as tempdir I: running --setup-hook directly: /usr/share/mmdebstrap/hooks/maybe-merged-usr/setup00.sh /srv/rebuilderd/tmp/mmdebstrap.lYt9sswCCt 127.0.0.1 - - [23/Apr/2025 10:11:41] code 404, message File not found 127.0.0.1 - - [23/Apr/2025 10:11:41] "GET /./InRelease HTTP/1.1" 404 - Ign:1 http://localhost:46533 ./ InRelease 127.0.0.1 - - [23/Apr/2025 10:11:41] "GET /./Release HTTP/1.1" 200 - Get:2 http://localhost:46533 ./ Release [462 B] 127.0.0.1 - - [23/Apr/2025 10:11:41] code 404, message File not found 127.0.0.1 - - [23/Apr/2025 10:11:41] "GET /./Release.gpg HTTP/1.1" 404 - Ign:3 http://localhost:46533 ./ Release.gpg 127.0.0.1 - - [23/Apr/2025 10:11:41] "GET /./Packages HTTP/1.1" 200 - Get:4 http://localhost:46533 ./ Packages [369 kB] Fetched 370 kB in 0s (1342 kB/s) Reading package lists... usr-is-merged found but not real -- not running merged-usr setup hook I: skipping apt-get update because it was already run I: downloading packages with apt... 127.0.0.1 - - [23/Apr/2025 10:11:42] "GET /./gcc-14-base_14.2.0-17_riscv64.deb HTTP/1.1" 200 - 127.0.0.1 - - [23/Apr/2025 10:11:42] "GET /./libc6_2.41-4_riscv64.deb HTTP/1.1" 200 - 127.0.0.1 - - [23/Apr/2025 10:11:43] "GET /./libgcc-s1_14.2.0-17_riscv64.deb HTTP/1.1" 200 - 127.0.0.1 - - [23/Apr/2025 10:11:43] "GET /./mawk_1.3.4.20250131-1_riscv64.deb HTTP/1.1" 200 - 127.0.0.1 - - [23/Apr/2025 10:11:43] "GET /./base-files_13.7_riscv64.deb HTTP/1.1" 200 - 127.0.0.1 - - [23/Apr/2025 10:11:43] "GET /./libtinfo6_6.5%2b20250216-2_riscv64.deb HTTP/1.1" 200 - 127.0.0.1 - - [23/Apr/2025 10:11:43] "GET /./debianutils_5.21_riscv64.deb HTTP/1.1" 200 - 127.0.0.1 - - [23/Apr/2025 10:11:43] "GET /./bash_5.2.37-1.1_riscv64.deb HTTP/1.1" 200 - 127.0.0.1 - - [23/Apr/2025 10:11:43] "GET /./libcap2_2.75-1_riscv64.deb HTTP/1.1" 200 - 127.0.0.1 - - [23/Apr/2025 10:11:43] "GET /./libsystemd0_257.4-1_riscv64.deb HTTP/1.1" 200 - 127.0.0.1 - - [23/Apr/2025 10:11:43] "GET /./bsdutils_2.40.4-5_riscv64.deb HTTP/1.1" 200 - 127.0.0.1 - - [23/Apr/2025 10:11:43] "GET /./libacl1_2.3.2-2%2bb1_riscv64.deb HTTP/1.1" 200 - 127.0.0.1 - - [23/Apr/2025 10:11:43] "GET /./libattr1_2.5.2-3_riscv64.deb HTTP/1.1" 200 - 127.0.0.1 - - [23/Apr/2025 10:11:43] "GET /./libgmp10_6.3.0%2bdfsg-3_riscv64.deb HTTP/1.1" 200 - 127.0.0.1 - - [23/Apr/2025 10:11:44] "GET /./libpcre2-8-0_10.45-1_riscv64.deb HTTP/1.1" 200 - 127.0.0.1 - - [23/Apr/2025 10:11:44] "GET /./libselinux1_3.8-4_riscv64.deb HTTP/1.1" 200 - 127.0.0.1 - - [23/Apr/2025 10:11:44] "GET /./libzstd1_1.5.6%2bdfsg-2_riscv64.deb HTTP/1.1" 200 - 127.0.0.1 - - [23/Apr/2025 10:11:44] "GET /./zlib1g_1.3.dfsg%2breally1.3.1-1%2bb1_riscv64.deb HTTP/1.1" 200 - 127.0.0.1 - - [23/Apr/2025 10:11:44] "GET /./libssl3t64_3.4.1-1_riscv64.deb HTTP/1.1" 200 - 127.0.0.1 - - [23/Apr/2025 10:11:44] "GET /./openssl-provider-legacy_3.4.1-1_riscv64.deb HTTP/1.1" 200 - 127.0.0.1 - - [23/Apr/2025 10:11:44] "GET /./coreutils_9.5-1_riscv64.deb HTTP/1.1" 200 - 127.0.0.1 - - [23/Apr/2025 10:11:45] "GET /./dash_0.5.12-12_riscv64.deb HTTP/1.1" 200 - 127.0.0.1 - - [23/Apr/2025 10:11:45] "GET /./diffutils_3.10-2_riscv64.deb HTTP/1.1" 200 - 127.0.0.1 - - [23/Apr/2025 10:11:45] "GET /./libbz2-1.0_1.0.8-6_riscv64.deb HTTP/1.1" 200 - 127.0.0.1 - - [23/Apr/2025 10:11:45] "GET /./liblzma5_5.6.4-1_riscv64.deb HTTP/1.1" 200 - 127.0.0.1 - - [23/Apr/2025 10:11:45] "GET /./libmd0_1.1.0-2%2bb1_riscv64.deb HTTP/1.1" 200 - 127.0.0.1 - - [23/Apr/2025 10:11:45] "GET /./tar_1.35%2bdfsg-3.1_riscv64.deb HTTP/1.1" 200 - 127.0.0.1 - - [23/Apr/2025 10:11:45] "GET /./dpkg_1.22.18_riscv64.deb HTTP/1.1" 200 - 127.0.0.1 - - [23/Apr/2025 10:11:45] "GET /./findutils_4.10.0-3_riscv64.deb HTTP/1.1" 200 - 127.0.0.1 - - [23/Apr/2025 10:11:45] "GET /./grep_3.11-4_riscv64.deb HTTP/1.1" 200 - 127.0.0.1 - - [23/Apr/2025 10:11:45] "GET /./gzip_1.13-1_riscv64.deb HTTP/1.1" 200 - 127.0.0.1 - - [23/Apr/2025 10:11:45] "GET /./hostname_3.25_riscv64.deb HTTP/1.1" 200 - 127.0.0.1 - - [23/Apr/2025 10:11:45] "GET /./ncurses-bin_6.5%2b20250216-2_riscv64.deb HTTP/1.1" 200 - 127.0.0.1 - - [23/Apr/2025 10:11:45] "GET /./libcrypt1_4.4.38-1_riscv64.deb HTTP/1.1" 200 - 127.0.0.1 - - [23/Apr/2025 10:11:45] "GET /./perl-base_5.40.1-2_riscv64.deb HTTP/1.1" 200 - 127.0.0.1 - - [23/Apr/2025 10:11:46] "GET /./sed_4.9-2_riscv64.deb HTTP/1.1" 200 - 127.0.0.1 - - [23/Apr/2025 10:11:46] "GET /./libaudit-common_4.0.2-2_all.deb HTTP/1.1" 200 - 127.0.0.1 - - [23/Apr/2025 10:11:46] "GET /./libcap-ng0_0.8.5-4%2bb1_riscv64.deb HTTP/1.1" 200 - 127.0.0.1 - - [23/Apr/2025 10:11:46] "GET /./libaudit1_4.0.2-2%2bb2_riscv64.deb HTTP/1.1" 200 - 127.0.0.1 - - [23/Apr/2025 10:11:46] "GET /./libdb5.3t64_5.3.28%2bdfsg2-9_riscv64.deb HTTP/1.1" 200 - 127.0.0.1 - - [23/Apr/2025 10:11:46] "GET /./debconf_1.5.90_all.deb HTTP/1.1" 200 - 127.0.0.1 - - [23/Apr/2025 10:11:46] "GET /./libpam0g_1.7.0-3_riscv64.deb HTTP/1.1" 200 - 127.0.0.1 - - [23/Apr/2025 10:11:46] "GET /./libpam-modules-bin_1.7.0-3_riscv64.deb HTTP/1.1" 200 - 127.0.0.1 - - [23/Apr/2025 10:11:46] "GET /./libpam-modules_1.7.0-3_riscv64.deb HTTP/1.1" 200 - 127.0.0.1 - - [23/Apr/2025 10:11:46] "GET /./libpam-runtime_1.7.0-3_all.deb HTTP/1.1" 200 - 127.0.0.1 - - [23/Apr/2025 10:11:46] "GET /./libblkid1_2.40.4-5_riscv64.deb HTTP/1.1" 200 - 127.0.0.1 - - [23/Apr/2025 10:11:46] "GET /./libmount1_2.40.4-5_riscv64.deb HTTP/1.1" 200 - 127.0.0.1 - - [23/Apr/2025 10:11:46] "GET /./libsmartcols1_2.40.4-5_riscv64.deb HTTP/1.1" 200 - 127.0.0.1 - - [23/Apr/2025 10:11:46] "GET /./libudev1_257.4-1_riscv64.deb HTTP/1.1" 200 - 127.0.0.1 - - [23/Apr/2025 10:11:46] "GET /./libuuid1_2.40.4-5_riscv64.deb HTTP/1.1" 200 - 127.0.0.1 - - [23/Apr/2025 10:11:46] "GET /./util-linux_2.40.4-5_riscv64.deb HTTP/1.1" 200 - 127.0.0.1 - - [23/Apr/2025 10:11:46] "GET /./libdebconfclient0_0.277_riscv64.deb HTTP/1.1" 200 - 127.0.0.1 - - [23/Apr/2025 10:11:46] "GET /./base-passwd_3.6.6_riscv64.deb HTTP/1.1" 200 - 127.0.0.1 - - [23/Apr/2025 10:11:46] "GET /./init-system-helpers_1.68_all.deb HTTP/1.1" 200 - 127.0.0.1 - - [23/Apr/2025 10:11:46] "GET /./libc-bin_2.41-4_riscv64.deb HTTP/1.1" 200 - 127.0.0.1 - - [23/Apr/2025 10:11:47] "GET /./ncurses-base_6.5%2b20250216-2_all.deb HTTP/1.1" 200 - 127.0.0.1 - - [23/Apr/2025 10:11:47] "GET /./sysvinit-utils_3.14-3_riscv64.deb HTTP/1.1" 200 - I: extracting archives... I: running --extract-hook directly: /usr/share/mmdebstrap/hooks/maybe-merged-usr/extract00.sh /srv/rebuilderd/tmp/mmdebstrap.lYt9sswCCt 127.0.0.1 - - [23/Apr/2025 10:12:03] code 404, message File not found 127.0.0.1 - - [23/Apr/2025 10:12:03] "GET /./InRelease HTTP/1.1" 404 - Ign:1 http://localhost:46533 ./ InRelease 127.0.0.1 - - [23/Apr/2025 10:12:03] "GET /./Release HTTP/1.1" 304 - Hit:2 http://localhost:46533 ./ Release 127.0.0.1 - - [23/Apr/2025 10:12:03] code 404, message File not found 127.0.0.1 - - [23/Apr/2025 10:12:03] "GET /./Release.gpg HTTP/1.1" 404 - Ign:3 http://localhost:46533 ./ Release.gpg Reading package lists... usr-is-merged found but not real -- not running merged-usr extract hook I: installing essential packages... I: running --essential-hook directly: /usr/share/mmdebstrap/hooks/maybe-merged-usr/essential00.sh /srv/rebuilderd/tmp/mmdebstrap.lYt9sswCCt usr-is-merged was not installed in a previous hook -- not running merged-usr essential hook I: installing remaining packages inside the chroot... 127.0.0.1 - - [23/Apr/2025 10:13:00] "GET /./libpython3.13-minimal_3.13.2-1_riscv64.deb HTTP/1.1" 200 - 127.0.0.1 - - [23/Apr/2025 10:13:00] "GET /./libexpat1_2.6.4-1_riscv64.deb HTTP/1.1" 200 - 127.0.0.1 - - [23/Apr/2025 10:13:00] "GET /./python3.13-minimal_3.13.2-1_riscv64.deb HTTP/1.1" 200 - 127.0.0.1 - - [23/Apr/2025 10:13:00] "GET /./python3-minimal_3.13.2-2_riscv64.deb HTTP/1.1" 200 - 127.0.0.1 - - [23/Apr/2025 10:13:00] "GET /./media-types_13.0.0_all.deb HTTP/1.1" 200 - 127.0.0.1 - - [23/Apr/2025 10:13:00] "GET /./netbase_6.4_all.deb HTTP/1.1" 200 - 127.0.0.1 - - [23/Apr/2025 10:13:00] "GET /./tzdata_2025a-2_all.deb HTTP/1.1" 200 - 127.0.0.1 - - [23/Apr/2025 10:13:00] "GET /./libffi8_3.4.7-1_riscv64.deb HTTP/1.1" 200 - 127.0.0.1 - - [23/Apr/2025 10:13:00] "GET /./libncursesw6_6.5%2b20250216-2_riscv64.deb HTTP/1.1" 200 - 127.0.0.1 - - [23/Apr/2025 10:13:00] "GET /./readline-common_8.2-6_all.deb HTTP/1.1" 200 - 127.0.0.1 - - [23/Apr/2025 10:13:00] "GET /./libreadline8t64_8.2-6_riscv64.deb HTTP/1.1" 200 - 127.0.0.1 - - [23/Apr/2025 10:13:00] "GET /./libsqlite3-0_3.46.1-2_riscv64.deb HTTP/1.1" 200 - 127.0.0.1 - - [23/Apr/2025 10:13:00] "GET /./libpython3.13-stdlib_3.13.2-1_riscv64.deb HTTP/1.1" 200 - 127.0.0.1 - - [23/Apr/2025 10:13:00] "GET /./python3.13_3.13.2-1_riscv64.deb HTTP/1.1" 200 - 127.0.0.1 - - [23/Apr/2025 10:13:01] "GET /./libpython3-stdlib_3.13.2-2_riscv64.deb HTTP/1.1" 200 - 127.0.0.1 - - [23/Apr/2025 10:13:01] "GET /./python3_3.13.2-2_riscv64.deb HTTP/1.1" 200 - 127.0.0.1 - - [23/Apr/2025 10:13:01] "GET /./python3-numpy-dev_2.2.3%2bds-5_riscv64.deb HTTP/1.1" 200 - 127.0.0.1 - - [23/Apr/2025 10:13:01] "GET /./libblas3_3.12.1-2_riscv64.deb HTTP/1.1" 200 - 127.0.0.1 - - [23/Apr/2025 10:13:01] "GET /./libgfortran5_14.2.0-17_riscv64.deb HTTP/1.1" 200 - 127.0.0.1 - - [23/Apr/2025 10:13:01] "GET /./liblapack3_3.12.1-2_riscv64.deb HTTP/1.1" 200 - 127.0.0.1 - - [23/Apr/2025 10:13:01] "GET /./libstdc%2b%2b6_14.2.0-17_riscv64.deb HTTP/1.1" 200 - 127.0.0.1 - - [23/Apr/2025 10:13:01] "GET /./python3-numpy_2.2.3%2bds-5_riscv64.deb HTTP/1.1" 200 - 127.0.0.1 - - [23/Apr/2025 10:13:02] "GET /./login.defs_4.17.3-1_all.deb HTTP/1.1" 200 - 127.0.0.1 - - [23/Apr/2025 10:13:02] "GET /./libbsd0_0.12.2-2_riscv64.deb HTTP/1.1" 200 - 127.0.0.1 - - [23/Apr/2025 10:13:02] "GET /./libsemanage-common_3.8-1_all.deb HTTP/1.1" 200 - 127.0.0.1 - - [23/Apr/2025 10:13:02] "GET /./libsepol2_3.8-1_riscv64.deb HTTP/1.1" 200 - 127.0.0.1 - - [23/Apr/2025 10:13:02] "GET /./libsemanage2_3.8-1%2bb1_riscv64.deb HTTP/1.1" 200 - 127.0.0.1 - - [23/Apr/2025 10:13:02] "GET /./passwd_4.17.3-1_riscv64.deb HTTP/1.1" 200 - 127.0.0.1 - - [23/Apr/2025 10:13:02] "GET /./sensible-utils_0.0.24_all.deb HTTP/1.1" 200 - 127.0.0.1 - - [23/Apr/2025 10:13:02] "GET /./adduser_3.145_all.deb HTTP/1.1" 200 - 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127.0.0.1 - - [23/Apr/2025 10:13:37] "GET /./python3.13-dev_3.13.2-1_riscv64.deb HTTP/1.1" 200 - 127.0.0.1 - - [23/Apr/2025 10:13:37] "GET /./python3-dev_3.13.2-2_riscv64.deb HTTP/1.1" 200 - 127.0.0.1 - - [23/Apr/2025 10:13:37] "GET /./libblas-dev_3.12.1-2_riscv64.deb HTTP/1.1" 200 - 127.0.0.1 - - [23/Apr/2025 10:13:37] "GET /./libmuparser-dev_2.3.4-1%2bb1_riscv64.deb HTTP/1.1" 200 - 127.0.0.1 - - [23/Apr/2025 10:13:37] "GET /./lsb-release_12.1-1_all.deb HTTP/1.1" 200 - 127.0.0.1 - - [23/Apr/2025 10:13:37] "GET /./python3-pytest_8.3.5-1_all.deb HTTP/1.1" 200 - 127.0.0.1 - - [23/Apr/2025 10:13:37] "GET /./liblapack-dev_3.12.1-2_riscv64.deb HTTP/1.1" 200 - 127.0.0.1 - - [23/Apr/2025 10:13:38] "GET /./python3-inflect_7.3.1-2_all.deb HTTP/1.1" 200 - 127.0.0.1 - - [23/Apr/2025 10:13:38] "GET /./python3-pybind11_2.13.6-2_all.deb HTTP/1.1" 200 - 127.0.0.1 - - [23/Apr/2025 10:13:38] "GET /./dh-python_6.20250308_all.deb HTTP/1.1" 200 - 127.0.0.1 - - [23/Apr/2025 10:13:38] "GET /./python3-autocommand_2.2.2-3_all.deb HTTP/1.1" 200 - 127.0.0.1 - - [23/Apr/2025 10:13:38] "GET /./python3-pkg-resources_75.8.0-1_all.deb HTTP/1.1" 200 - 127.0.0.1 - - [23/Apr/2025 10:13:38] "GET /./python3-networkx_3.2.1-5_all.deb HTTP/1.1" 200 - 127.0.0.1 - - [23/Apr/2025 10:13:41] "GET /./python3-mpi4py_4.0.3-3_riscv64.deb HTTP/1.1" 200 - 127.0.0.1 - - [23/Apr/2025 10:13:41] "GET /./libboost-dev_1.83.0.2%2bb2_riscv64.deb HTTP/1.1" 200 - 127.0.0.1 - - [23/Apr/2025 10:13:41] "GET /./debootsnap-dummy_1.0_all.deb HTTP/1.1" 200 - I: running --customize-hook directly: /srv/rebuilderd/tmp/tmp5az8mlec/apt_install.sh /srv/rebuilderd/tmp/mmdebstrap.lYt9sswCCt Reading package lists... Building dependency tree... Reading state information... cmake is already the newest version (3.31.6-1). cmake set to manually installed. libboost1.83-dev is already the newest version (1.83.0-4.1+b1). libboost1.83-dev set to manually installed. libjsoncpp26 is already the newest version (1.9.6-3). libjsoncpp26 set to manually installed. mpi-default-dev is already the newest version (1.18). mpi-default-dev set to manually installed. librhash1 is already the newest version (1.4.5-1). librhash1 set to manually installed. libatomic1 is already the newest version (14.2.0-17). libatomic1 set to manually installed. libmpc3 is already the newest version (1.3.1-1+b3). libmpc3 set to manually installed. libsemanage2 is already the newest version (3.8-1+b1). libsemanage2 set to manually installed. m4 is already the newest version (1.4.19-7). m4 set to manually installed. mawk is already the newest version (1.3.4.20250131-1). libitm1 is already the newest version (14.2.0-17). libitm1 set to manually installed. libexpat1 is already the newest version (2.6.4-1). libexpat1 set to manually installed. cpp is already the newest version (4:14.2.0-1). cpp set to manually installed. debhelper is already the newest version (13.24.1). debhelper set to manually installed. diffutils is already the newest version (1:3.10-2). libgmp10 is already the newest version (2:6.3.0+dfsg-3). libfftw3-single3 is already the newest version (3.3.10-2+b1). libfftw3-single3 set to manually installed. libjs-underscore is already the newest version (1.13.4~dfsg+~1.11.4-3). libjs-underscore set to manually installed. libcap2 is already the newest version (1:2.75-1). libldap2 is already the newest version (2.6.9+dfsg-2). libldap2 set to manually installed. libmount1 is already the newest version (2.40.4-5). libzstd1 is already the newest version (1.5.6+dfsg-2). libpsl5t64 is already the newest version (0.21.2-1.1+b1). libpsl5t64 set to manually installed. libk5crypto3 is already the newest version (1.21.3-4). libk5crypto3 set to manually installed. libattr1 is already the newest version (1:2.5.2-3). init-system-helpers is already the newest version (1.68). libgcc-14-dev is already the newest version (14.2.0-17). libgcc-14-dev set to manually installed. libtinfo6 is already the newest version (6.5+20250216-2). libpam-modules is already the newest version (1.7.0-3). libreadline8t64 is already the newest version (8.2-6). libreadline8t64 set to manually installed. libjs-jquery is already the newest version (3.6.1+dfsg+~3.5.14-1). libjs-jquery set to manually installed. libcurl4t64 is already the newest version (8.12.1-3). libcurl4t64 set to manually installed. libpython3-dev is already the newest version (3.13.2-2). libpython3-dev set to manually installed. passwd is already the newest version (1:4.17.3-1). passwd set to manually installed. libnl-route-3-200 is already the newest version (3.7.0-1). libnl-route-3-200 set to manually installed. grep is already the newest version (3.11-4). intltool-debian is already the newest version (0.35.0+20060710.6). intltool-debian set to manually installed. hostname is already the newest version (3.25). python3-jaraco.context is already the newest version (6.0.1-1). python3-jaraco.context set to manually installed. libhogweed6t64 is already the newest version (3.10.1-1). libhogweed6t64 set to manually installed. libedit2 is already the newest version (3.1-20250104-1). libedit2 set to manually installed. libibmad5 is already the newest version (56.0-2). libibmad5 set to manually installed. libgprofng0 is already the newest version (2.44-3). libgprofng0 set to manually installed. libnghttp2-14 is already the newest version (1.64.0-1). libnghttp2-14 set to manually installed. libpython3.13-minimal is already the newest version (3.13.2-1). libpython3.13-minimal set to manually installed. bsdutils is already the newest version (1:2.40.4-5). libfuse3-3 is already the newest version (3.14.0-10). libfuse3-3 set to manually installed. python3-typeguard is already the newest version (4.4.2-1). python3-typeguard set to manually installed. libevent-pthreads-2.1-7t64 is already the newest version (2.1.12-stable-10+b1). libevent-pthreads-2.1-7t64 set to manually installed. ncurses-base is already the newest version (6.5+20250216-2). libevent-dev is already the newest version (2.1.12-stable-10+b1). libevent-dev set to manually installed. groff-base is already the newest version (1.23.0-7). groff-base set to manually installed. libaudit-common is already the newest version (1:4.0.2-2). libpython3.13 is already the newest version (3.13.2-1). libpython3.13 set to manually installed. libhwloc-dev is already the newest version (2.12.0-1). libhwloc-dev set to manually installed. binutils-common is already the newest version (2.44-3). binutils-common set to manually installed. base-passwd is already the newest version (3.6.6). libibverbs-dev is already the newest version (56.0-2). libibverbs-dev set to manually installed. libjansson4 is already the newest version (2.14-2+b3). libjansson4 set to manually installed. libjs-jquery-ui is already the newest version (1.13.2+dfsg-1). libjs-jquery-ui set to manually installed. libfftw3-double3 is already the newest version (3.3.10-2+b1). libfftw3-double3 set to manually installed. python3 is already the newest version (3.13.2-2). python3 set to manually installed. gcc-riscv64-linux-gnu is already the newest version (4:14.2.0-1). gcc-riscv64-linux-gnu set to manually installed. libncursesw6 is already the newest version (6.5+20250216-2). libncursesw6 set to manually installed. libsasl2-2 is already the newest version (2.1.28+dfsg1-9). libsasl2-2 set to manually installed. sensible-utils is already the newest version (0.0.24). sensible-utils set to manually installed. rpcsvc-proto is already the newest version (1.4.3-1+b2). rpcsvc-proto set to manually installed. libnl-3-200 is already the newest version (3.7.0-1). libnl-3-200 set to manually installed. libfftw3-dev is already the newest version (3.3.10-2+b1). libfftw3-dev set to manually installed. libmd0 is already the newest version (1.1.0-2+b1). libfile-stripnondeterminism-perl is already the newest version (1.14.1-2). libfile-stripnondeterminism-perl set to manually installed. cpp-riscv64-linux-gnu is already the newest version (4:14.2.0-1). cpp-riscv64-linux-gnu set to manually installed. libnuma-dev is already the newest version (2.0.18-1+b1). libnuma-dev set to manually installed. libpython3.13-dev is already the newest version (3.13.2-1). libpython3.13-dev set to manually installed. patch is already the newest version (2.7.6-7+b2). patch set to manually installed. python3-minimal is already the newest version (3.13.2-2). python3-minimal set to manually installed. g++-14-riscv64-linux-gnu is already the newest version (14.2.0-17). g++-14-riscv64-linux-gnu set to manually installed. binutils is already the newest version (2.44-3). binutils set to manually installed. libcbor0.10 is already the newest version (0.10.2-2). libcbor0.10 set to manually installed. binutils-riscv64-linux-gnu is already the newest version (2.44-3). binutils-riscv64-linux-gnu set to manually installed. libgnutls30t64 is already the newest version (3.8.9-2). libgnutls30t64 set to manually installed. dh-autoreconf is already the newest version (20). dh-autoreconf set to manually installed. libnuma1 is already the newest version (2.0.18-1+b1). libnuma1 set to manually installed. libmuparser2v5 is already the newest version (2.3.4-1+b1). libmuparser2v5 set to manually installed. python3-numpy is already the newest version (1:2.2.3+ds-5). python3-numpy set to manually installed. libgomp1 is already the newest version (14.2.0-17). libgomp1 set to manually installed. libsepol2 is already the newest version (3.8-1). libsepol2 set to manually installed. libstdc++6 is already the newest version (14.2.0-17). libstdc++6 set to manually installed. libpcre2-8-0 is already the newest version (10.45-1). libx11-data is already the newest version (2:1.8.10-2). libx11-data set to manually installed. libpmix2t64 is already the newest version (5.0.6-5). libpmix2t64 set to manually installed. libctf-nobfd0 is already the newest version (2.44-3). libctf-nobfd0 set to manually installed. media-types is already the newest version (13.0.0). media-types set to manually installed. libgdbm-compat4t64 is already the newest version (1.24-2). libgdbm-compat4t64 set to manually installed. ocl-icd-libopencl1 is already the newest version (2.3.2-1+b2). ocl-icd-libopencl1 set to manually installed. pkgconf is already the newest version (1.8.1-4). pkgconf set to manually installed. sysvinit-utils is already the newest version (3.14-3). libsqlite3-0 is already the newest version (3.46.1-2). libsqlite3-0 set to manually installed. libpython3.13-stdlib is already the newest version (3.13.2-1). libpython3.13-stdlib set to manually installed. tar is already the newest version (1.35+dfsg-3.1). coreutils is already the newest version (9.5-1). libjs-sphinxdoc is already the newest version (8.1.3-5). libjs-sphinxdoc set to manually installed. libffi8 is already the newest version (3.4.7-1). libffi8 set to manually installed. libevent-openssl-2.1-7t64 is already the newest version (2.1.12-stable-10+b1). libevent-openssl-2.1-7t64 set to manually installed. libbz2-1.0 is already the newest version (1.0.8-6). perl is already the newest version (5.40.1-2). perl set to manually installed. dash is already the newest version (0.5.12-12). libltdl-dev is already the newest version (2.5.4-4). libltdl-dev set to manually installed. dwz is already the newest version (0.15-1+b3). dwz set to manually installed. build-essential is already the newest version (12.12). build-essential set to manually installed. libkrb5-3 is already the newest version (1.21.3-4). libkrb5-3 set to manually installed. libnghttp3-9 is already the newest version (1.8.0-1). libnghttp3-9 set to manually installed. libnl-3-dev is already the newest version (3.7.0-1). libnl-3-dev set to manually installed. g++ is already the newest version (4:14.2.0-1). g++ set to manually installed. netbase is already the newest version (6.4). netbase set to manually installed. python3-jaraco.functools is already the newest version (4.1.0-1). python3-jaraco.functools set to manually installed. autoconf is already the newest version (2.72-3). autoconf set to manually installed. libpciaccess0 is already the newest version (0.17-3+b3). libpciaccess0 set to manually installed. libsemanage-common is already the newest version (3.8-1). libsemanage-common set to manually installed. libuchardet0 is already the newest version (0.0.8-1+b2). libuchardet0 set to manually installed. libpmix-dev is already the newest version (5.0.6-5). libpmix-dev set to manually installed. libxxhash0 is already the newest version (0.8.3-2). libxxhash0 set to manually installed. pybind11-dev is already the newest version (2.13.6-2). pybind11-dev set to manually installed. bzip2 is already the newest version (1.0.8-6). bzip2 set to manually installed. libibumad3 is already the newest version (56.0-2). libibumad3 set to manually installed. mpi-default-bin is already the newest version (1.18). mpi-default-bin set to manually installed. python3-packaging is already the newest version (24.2-1). python3-packaging set to manually installed. libblas3 is already the newest version (3.12.1-2). libblas3 set to manually installed. procps is already the newest version (2:4.0.4-7). procps set to manually installed. libcc1-0 is already the newest version (14.2.0-17). libcc1-0 set to manually installed. libgcc-s1 is already the newest version (14.2.0-17). libevent-extra-2.1-7t64 is already the newest version (2.1.12-stable-10+b1). libevent-extra-2.1-7t64 set to manually installed. python3-numpy-dev is already the newest version (1:2.2.3+ds-5). python3-numpy-dev set to manually installed. python3.13 is already the newest version (3.13.2-1). python3.13 set to manually installed. python3-iniconfig is already the newest version (1.1.1-2). python3-iniconfig set to manually installed. libssl3t64 is already the newest version (3.4.1-1). file is already the newest version (1:5.45-3+b1). file set to manually installed. automake is already the newest version (1:1.17-3). automake set to manually installed. libgfortran-14-dev is already the newest version (14.2.0-17). libgfortran-14-dev set to manually installed. libhwloc15 is already the newest version (2.12.0-1). libhwloc15 set to manually installed. python3-more-itertools is already the newest version (10.6.0-1). python3-more-itertools set to manually installed. autopoint is already the newest version (0.23.1-1). autopoint set to manually installed. libmunge2 is already the newest version (0.5.16-1). libmunge2 set to manually installed. openssh-client is already the newest version (1:9.9p2-1). openssh-client set to manually installed. python3-pluggy is already the newest version (1.5.0-1). python3-pluggy set to manually installed. libevent-2.1-7t64 is already the newest version (2.1.12-stable-10+b1). libevent-2.1-7t64 set to manually installed. libuv1t64 is already the newest version (1.50.0-2). libuv1t64 set to manually installed. python3-dev is already the newest version (3.13.2-2). python3-dev set to manually installed. libpython3-stdlib is already the newest version (3.13.2-2). libpython3-stdlib set to manually installed. librdmacm1t64 is already the newest version (56.0-2). librdmacm1t64 set to manually installed. util-linux is already the newest version (2.40.4-5). dpkg is already the newest version (1.22.18). liblzma5 is already the newest version (5.6.4-1). libnettle8t64 is already the newest version (3.10.1-1). libnettle8t64 set to manually installed. libdebconfclient0 is already the newest version (0.277). libpam-modules-bin is already the newest version (1.7.0-3). libudev1 is already the newest version (257.4-1). login.defs is already the newest version (1:4.17.3-1). login.defs set to manually installed. liblsan0 is already the newest version (14.2.0-17). liblsan0 set to manually installed. man-db is already the newest version (2.13.0-1). man-db set to manually installed. libmagic-mgc is already the newest version (1:5.45-3+b1). libmagic-mgc set to manually installed. libpam-runtime is already the newest version (1.7.0-3). libxdmcp6 is already the newest version (1:1.1.5-1). libxdmcp6 set to manually installed. libkeyutils1 is already the newest version (1.6.3-4). libkeyutils1 set to manually installed. libblas-dev is already the newest version (3.12.1-2). libblas-dev set to manually installed. libmuparser-dev is already the newest version (2.3.4-1+b1). libmuparser-dev set to manually installed. libssh2-1t64 is already the newest version (1.11.1-1). libssh2-1t64 set to manually installed. libxnvctrl0 is already the newest version (535.171.04-1+b2). libxnvctrl0 set to manually installed. libgfortran5 is already the newest version (14.2.0-17). libgfortran5 set to manually installed. libaudit1 is already the newest version (1:4.0.2-2+b2). lsb-release is already the newest version (12.1-1). lsb-release set to manually installed. libunistring5 is already the newest version (1.3-1). libunistring5 set to manually installed. python3-pytest is already the newest version (8.3.5-1). python3-pytest set to manually installed. python3.13-dev is already the newest version (3.13.2-1). python3.13-dev set to manually installed. liblz4-1 is already the newest version (1.10.0-4). liblz4-1 set to manually installed. libblkid1 is already the newest version (2.40.4-5). libibverbs1 is already the newest version (56.0-2). libibverbs1 set to manually installed. libopenmpi40 is already the newest version (5.0.7-1). libopenmpi40 set to manually installed. libubsan1 is already the newest version (14.2.0-17). libubsan1 set to manually installed. chrpath is already the newest version (0.18-1). chrpath set to manually installed. cpp-14 is already the newest version (14.2.0-17). cpp-14 set to manually installed. liblapack-dev is already the newest version (3.12.1-2). liblapack-dev set to manually installed. libsasl2-modules-db is already the newest version (2.1.28+dfsg1-9). libsasl2-modules-db set to manually installed. libicu72 is already the newest version (72.1-6). libicu72 set to manually installed. pkgconf-bin is already the newest version (1.8.1-4). pkgconf-bin set to manually installed. perl-modules-5.40 is already the newest version (5.40.1-2). perl-modules-5.40 set to manually installed. cpp-14-riscv64-linux-gnu is already the newest version (14.2.0-17). cpp-14-riscv64-linux-gnu set to manually installed. gfortran-14-riscv64-linux-gnu is already the newest version (14.2.0-17). gfortran-14-riscv64-linux-gnu set to manually installed. libpipeline1 is already the newest version (1.5.8-1). libpipeline1 set to manually installed. libc6-dev is already the newest version (2.41-4). libc6-dev set to manually installed. libfftw3-bin is already the newest version (3.3.10-2+b1). libfftw3-bin set to manually installed. libidn2-0 is already the newest version (2.3.8-1). libidn2-0 set to manually installed. gettext-base is already the newest version (0.23.1-1). gettext-base set to manually installed. libc6 is already the newest version (2.41-4). libarchive13t64 is already the newest version (3.7.4-1.1). libarchive13t64 set to manually installed. libdebhelper-perl is already the newest version (13.24.1). libdebhelper-perl set to manually installed. libmpfr6 is already the newest version (4.2.1-1+b2). libmpfr6 set to manually installed. libsystemd0 is already the newest version (257.4-1). libperl5.40 is already the newest version (5.40.1-2). libperl5.40 set to manually installed. libelf1t64 is already the newest version (0.192-4). libelf1t64 set to manually installed. librtmp1 is already the newest version (2.4+20151223.gitfa8646d.1-2+b5). librtmp1 set to manually installed. bsdextrautils is already the newest version (2.40.4-5). bsdextrautils set to manually installed. gcc is already the newest version (4:14.2.0-1). gcc set to manually installed. libstdc++-14-dev is already the newest version (14.2.0-17). libstdc++-14-dev set to manually installed. python3.13-minimal is already the newest version (3.13.2-1). python3.13-minimal set to manually installed. xz-utils is already the newest version (5.6.4-1). xz-utils set to manually installed. zlib1g-dev is already the newest version (1:1.3.dfsg+really1.3.1-1+b1). zlib1g-dev set to manually installed. autotools-dev is already the newest version (20220109.1). autotools-dev set to manually installed. libcap-ng0 is already the newest version (0.8.5-4+b1). bash-completion is already the newest version (1:2.16.0-7). bash-completion set to manually installed. libsmartcols1 is already the newest version (2.40.4-5). openmpi-bin is already the newest version (5.0.7-1). openmpi-bin set to manually installed. libasan8 is already the newest version (14.2.0-17). libasan8 set to manually installed. sed is already the newest version (4.9-2). python3-inflect is already the newest version (7.3.1-2). python3-inflect set to manually installed. libexpat1-dev is already the newest version (2.6.4-1). libexpat1-dev set to manually installed. readline-common is already the newest version (8.2-6). readline-common set to manually installed. dh-strip-nondeterminism is already the newest version (1.14.1-2). dh-strip-nondeterminism set to manually installed. g++-riscv64-linux-gnu is already the newest version (4:14.2.0-1). g++-riscv64-linux-gnu set to manually installed. gcc-14-base is already the newest version (14.2.0-17). gfortran-14 is already the newest version (14.2.0-17). gfortran-14 set to manually installed. tzdata is already the newest version (2025a-2). tzdata set to manually installed. adduser is already the newest version (3.145). adduser set to manually installed. python3-pybind11 is already the newest version (2.13.6-2). python3-pybind11 set to manually installed. libc-dev-bin is already the newest version (2.41-4). libc-dev-bin set to manually installed. libxcb1 is already the newest version (1.17.0-2+b1). libxcb1 set to manually installed. cmake-data is already the newest version (3.31.6-1). cmake-data set to manually installed. libselinux1 is already the newest version (3.8-4). libxau6 is already the newest version (1:1.0.11-1). libxau6 set to manually installed. linux-libc-dev is already the newest version (6.12.17-1). linux-libc-dev set to manually installed. libucx0 is already the newest version (1.18.1+ds-2). libucx0 set to manually installed. g++-14 is already the newest version (14.2.0-17). g++-14 set to manually installed. libp11-kit0 is already the newest version (0.25.5-3). libp11-kit0 set to manually installed. gettext is already the newest version (0.23.1-1). gettext set to manually installed. libarchive-zip-perl is already the newest version (1.68-1). libarchive-zip-perl set to manually installed. libevent-core-2.1-7t64 is already the newest version (2.1.12-stable-10+b1). libevent-core-2.1-7t64 set to manually installed. dh-python is already the newest version (6.20250308). dh-python set to manually installed. libfabric1 is already the newest version (1.17.0-3.1). libfabric1 set to manually installed. base-files is already the newest version (13.7). gcc-14 is already the newest version (14.2.0-17). gcc-14 set to manually installed. libcrypt1 is already the newest version (1:4.4.38-1). libdb5.3t64 is already the newest version (5.3.28+dfsg2-9). libdpkg-perl is already the newest version (1.22.18). libdpkg-perl set to manually installed. libgssapi-krb5-2 is already the newest version (1.21.3-4). libgssapi-krb5-2 set to manually installed. openssl-provider-legacy is already the newest version (3.4.1-1). gcc-14-riscv64-linux-gnu is already the newest version (14.2.0-17). gcc-14-riscv64-linux-gnu set to manually installed. libctf0 is already the newest version (2.44-3). libctf0 set to manually installed. libltdl7 is already the newest version (2.5.4-4). libltdl7 set to manually installed. libfftw3-long3 is already the newest version (3.3.10-2+b1). libfftw3-long3 set to manually installed. python3-typing-extensions is already the newest version (4.12.2-2). python3-typing-extensions set to manually installed. python3-pkg-resources is already the newest version (75.8.0-1). python3-pkg-resources set to manually installed. libcom-err2 is already the newest version (1.47.2-1). libcom-err2 set to manually installed. libuuid1 is already the newest version (2.40.4-5). libsframe1 is already the newest version (2.44-3). libsframe1 set to manually installed. openmpi-common is already the newest version (5.0.7-1). openmpi-common set to manually installed. libgdbm6t64 is already the newest version (1.24-2). libgdbm6t64 set to manually installed. po-debconf is already the newest version (1.0.21+nmu1). po-debconf set to manually installed. python3-autocommand is already the newest version (2.2.2-3). python3-autocommand set to manually installed. libisl23 is already the newest version (0.27-1). libisl23 set to manually installed. libtasn1-6 is already the newest version (4.20.0-2). libtasn1-6 set to manually installed. liblapack3 is already the newest version (3.12.1-2). liblapack3 set to manually installed. libxext6 is already the newest version (2:1.3.4-1+b3). libxext6 set to manually installed. libmagic1t64 is already the newest version (1:5.45-3+b1). libmagic1t64 set to manually installed. libx11-6 is already the newest version (2:1.8.10-2). libx11-6 set to manually installed. libxml2 is already the newest version (2.12.7+dfsg+really2.9.14-0.2+b2). libxml2 set to manually installed. libcrypt-dev is already the newest version (1:4.4.38-1). libcrypt-dev set to manually installed. libkrb5support0 is already the newest version (1.21.3-4). libkrb5support0 set to manually installed. python3-networkx is already the newest version (3.2.1-5). python3-networkx set to manually installed. libpam0g is already the newest version (1.7.0-3). architecture-properties is already the newest version (0.2.6). architecture-properties set to manually installed. dpkg-dev is already the newest version (1.22.18). dpkg-dev set to manually installed. libhwloc-plugins is already the newest version (2.12.0-1). libhwloc-plugins set to manually installed. libpkgconf3 is already the newest version (1.8.1-4). libpkgconf3 set to manually installed. python3-mpi4py is already the newest version (4.0.3-3). python3-mpi4py set to manually installed. debianutils is already the newest version (5.21). libc-bin is already the newest version (2.41-4). findutils is already the newest version (4.10.0-3). libtool is already the newest version (2.5.4-4). libtool set to manually installed. bash is already the newest version (5.2.37-1.1). libfido2-1 is already the newest version (1.15.0-1+b1). libfido2-1 set to manually installed. libbrotli1 is already the newest version (1.1.0-2+b7). libbrotli1 set to manually installed. libtsan2 is already the newest version (14.2.0-17). libtsan2 set to manually installed. libbinutils is already the newest version (2.44-3). libbinutils set to manually installed. debconf is already the newest version (1.5.90). libacl1 is already the newest version (2.3.2-2+b1). ibverbs-providers is already the newest version (56.0-2). ibverbs-providers set to manually installed. libbsd0 is already the newest version (0.12.2-2). libbsd0 set to manually installed. ncurses-bin is already the newest version (6.5+20250216-2). libboost-dev is already the newest version (1.83.0.2+b2). libboost-dev set to manually installed. zlib1g is already the newest version (1:1.3.dfsg+really1.3.1-1+b1). perl-base is already the newest version (5.40.1-2). gzip is already the newest version (1.13-1). libproc2-0 is already the newest version (2:4.0.4-7). libproc2-0 set to manually installed. libopenmpi-dev is already the newest version (5.0.7-1). libopenmpi-dev set to manually installed. make is already the newest version (4.4.1-1). make set to manually installed. libnl-route-3-dev is already the newest version (3.7.0-1). libnl-route-3-dev set to manually installed. 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. I: running --customize-hook in shell: sh -c 'chroot "$1" dpkg -r debootsnap-dummy' exec /srv/rebuilderd/tmp/mmdebstrap.lYt9sswCCt (Reading database ... 46062 files and directories currently installed.) Removing debootsnap-dummy (1.0) ... I: running --customize-hook in shell: sh -c 'chroot "$1" dpkg-query --showformat '${binary:Package}=${Version}\n' --show > "$1/pkglist"' exec /srv/rebuilderd/tmp/mmdebstrap.lYt9sswCCt I: running special hook: download /pkglist ./pkglist I: running --customize-hook in shell: sh -c 'rm "$1/pkglist"' exec /srv/rebuilderd/tmp/mmdebstrap.lYt9sswCCt I: running special hook: upload sources.list /etc/apt/sources.list I: waiting for background processes to finish... I: cleaning package lists and apt cache... I: skipping cleanup/reproducible as requested I: creating tarball... I: done I: removing tempdir /srv/rebuilderd/tmp/mmdebstrap.lYt9sswCCt... I: success in 752.1810 seconds Downloading dependency 253 of 296: libuuid1:riscv64=2.40.4-5 Downloading dependency 254 of 296: libsframe1:riscv64=2.44-3 Downloading dependency 255 of 296: openmpi-common:riscv64=5.0.7-1 Downloading dependency 256 of 296: libgdbm6t64:riscv64=1.24-2 Downloading dependency 257 of 296: po-debconf:riscv64=1.0.21+nmu1 Downloading dependency 258 of 296: python3-autocommand:riscv64=2.2.2-3 Downloading dependency 259 of 296: libisl23:riscv64=0.27-1 Downloading dependency 260 of 296: libtasn1-6:riscv64=4.20.0-2 Downloading dependency 261 of 296: liblapack3:riscv64=3.12.1-2 Downloading dependency 262 of 296: libxext6:riscv64=2:1.3.4-1+b3 Downloading dependency 263 of 296: libmagic1t64:riscv64=1:5.45-3+b1 Downloading dependency 264 of 296: libx11-6:riscv64=2:1.8.10-2 Downloading dependency 265 of 296: libxml2:riscv64=2.12.7+dfsg+really2.9.14-0.2+b2 Downloading dependency 266 of 296: libcrypt-dev:riscv64=1:4.4.38-1 Downloading dependency 267 of 296: libkrb5support0:riscv64=1.21.3-4 Downloading dependency 268 of 296: python3-networkx:riscv64=3.2.1-5 Downloading dependency 269 of 296: libpam0g:riscv64=1.7.0-3 Downloading dependency 270 of 296: architecture-properties:riscv64=0.2.6 Downloading dependency 271 of 296: dpkg-dev:riscv64=1.22.18 Downloading dependency 272 of 296: libhwloc-plugins:riscv64=2.12.0-1 Downloading dependency 273 of 296: libpkgconf3:riscv64=1.8.1-4 Downloading dependency 274 of 296: python3-mpi4py:riscv64=4.0.3-3 Downloading dependency 275 of 296: debianutils:riscv64=5.21 Downloading dependency 276 of 296: libc-bin:riscv64=2.41-4 Downloading dependency 277 of 296: findutils:riscv64=4.10.0-3 Downloading dependency 278 of 296: libtool:riscv64=2.5.4-4 Downloading dependency 279 of 296: bash:riscv64=5.2.37-1.1 Downloading dependency 280 of 296: libfido2-1:riscv64=1.15.0-1+b1 Downloading dependency 281 of 296: libbrotli1:riscv64=1.1.0-2+b7 Downloading dependency 282 of 296: libtsan2:riscv64=14.2.0-17 Downloading dependency 283 of 296: libbinutils:riscv64=2.44-3 Downloading dependency 284 of 296: debconf:riscv64=1.5.90 Downloading dependency 285 of 296: libacl1:riscv64=2.3.2-2+b1 Downloading dependency 286 of 296: ibverbs-providers:riscv64=56.0-2 Downloading dependency 287 of 296: libbsd0:riscv64=0.12.2-2 Downloading dependency 288 of 296: ncurses-bin:riscv64=6.5+20250216-2 Downloading dependency 289 of 296: libboost-dev:riscv64=1.83.0.2+b2 Downloading dependency 290 of 296: zlib1g:riscv64=1:1.3.dfsg+really1.3.1-1+b1 Downloading dependency 291 of 296: perl-base:riscv64=5.40.1-2 Downloading dependency 292 of 296: gzip:riscv64=1.13-1 Downloading dependency 293 of 296: libproc2-0:riscv64=2:4.0.4-7 Downloading dependency 294 of 296: libopenmpi-dev:riscv64=5.0.7-1 Downloading dependency 295 of 296: make:riscv64=4.4.1-1 Downloading dependency 296 of 296: libnl-route-3-dev:riscv64=3.7.0-1 env --chdir=/srv/rebuilderd/tmp/rebuilderdLp0KpP/out DEB_BUILD_OPTIONS=parallel=4 LANG=C.UTF-8 LC_COLLATE=C.UTF-8 LC_CTYPE=C.UTF-8 SOURCE_DATE_EPOCH=1741743011 SBUILD_CONFIG=/srv/rebuilderd/tmp/debrebuild8fcwUc/debrebuild.sbuildrc.cjR7DsviUDqX sbuild --build=riscv64 --host=riscv64 --no-source --arch-any --no-arch-all --chroot=/srv/rebuilderd/tmp/debrebuild8fcwUc/debrebuild.tar.nnLnkDHbOC6t --chroot-mode=unshare --dist=unstable --no-run-lintian --no-run-piuparts --no-run-autopkgtest --no-apt-update --no-apt-upgrade --no-apt-distupgrade --verbose --nolog --bd-uninstallable-explainer= --build-path=/build/reproducible-path --dsc-dir=gromacs-2025.1 /srv/rebuilderd/tmp/rebuilderdLp0KpP/inputs/gromacs_2025.1-1.dsc I: consider moving your ~/.sbuildrc to /srv/rebuilderd/.config/sbuild/config.pl The Debian buildds switched to the "unshare" backend and sbuild will default to it in the future. To start using "unshare" add this to your `~/.config/sbuild/config.pl`: $chroot_mode = "unshare"; If you want to keep the old "schroot" mode even in the future, add the following to your `~/.config/sbuild/config.pl`: $chroot_mode = "schroot"; $schroot = "schroot"; sbuild (Debian sbuild) 0.88.5 (01 March 2025) on localhost +==============================================================================+ | gromacs 2025.1-1 (riscv64) Wed, 23 Apr 2025 02:24:14 +0000 | +==============================================================================+ Package: gromacs Version: 2025.1-1 Source Version: 2025.1-1 Distribution: unstable Machine Architecture: riscv64 Host Architecture: riscv64 Build Architecture: riscv64 Build Type: any I: No tarballs found in /srv/rebuilderd/.cache/sbuild I: Unpacking /srv/rebuilderd/tmp/debrebuild8fcwUc/debrebuild.tar.nnLnkDHbOC6t to /srv/rebuilderd/tmp/tmp.sbuild.hc1iiNOIw2... I: Setting up the chroot... I: Creating chroot session... I: Setting up log color... I: Setting up apt archive... +------------------------------------------------------------------------------+ | Fetch source files Wed, 23 Apr 2025 02:27:31 +0000 | +------------------------------------------------------------------------------+ Local sources ------------- /srv/rebuilderd/tmp/rebuilderdLp0KpP/inputs/gromacs_2025.1-1.dsc exists in /srv/rebuilderd/tmp/rebuilderdLp0KpP/inputs; copying to chroot +------------------------------------------------------------------------------+ | Install package build dependencies Wed, 23 Apr 2025 02:28:05 +0000 | +------------------------------------------------------------------------------+ Setup apt archive ----------------- Merged Build-Depends: architecture-is-64-bit, bash-completion, chrpath, cmake (>= 3.13), debhelper-compat (= 13), dh-python, libblas-dev, libboost-dev, libfftw3-dev, libhwloc-dev, liblapack-dev, libmuparser-dev (>= 2.3.4), lsb-release, mpi-default-bin, mpi-default-dev, pkgconf, python3-dev, python3-mpi4py, python3-networkx, python3-numpy, python3-pybind11, python3-pytest, zlib1g-dev, build-essential Filtered Build-Depends: architecture-is-64-bit, bash-completion, chrpath, cmake (>= 3.13), debhelper-compat (= 13), dh-python, libblas-dev, libboost-dev, libfftw3-dev, libhwloc-dev, liblapack-dev, libmuparser-dev (>= 2.3.4), lsb-release, mpi-default-bin, mpi-default-dev, pkgconf, python3-dev, python3-mpi4py, python3-networkx, python3-numpy, python3-pybind11, python3-pytest, zlib1g-dev, build-essential dpkg-deb: building package 'sbuild-build-depends-main-dummy' in '/build/reproducible-path/resolver-XL8dNK/apt_archive/sbuild-build-depends-main-dummy.deb'. Install main build dependencies (apt-based resolver) ---------------------------------------------------- Installing build dependencies +------------------------------------------------------------------------------+ | Check architectures Wed, 23 Apr 2025 02:28:58 +0000 | +------------------------------------------------------------------------------+ Arch check ok (riscv64 included in any all) +------------------------------------------------------------------------------+ | Build environment Wed, 23 Apr 2025 02:29:03 +0000 | +------------------------------------------------------------------------------+ Kernel: Linux 6.12.22-riscv64 #1 SMP Debian 6.12.22-1 (2025-04-10) riscv64 (riscv64) Toolchain package versions: binutils_2.44-3 dpkg-dev_1.22.18 g++-14_14.2.0-17 gcc-14_14.2.0-17 libc6-dev_2.41-4 libstdc++-14-dev_14.2.0-17 libstdc++6_14.2.0-17 linux-libc-dev_6.12.17-1 Package versions: adduser_3.145 architecture-properties_0.2.6 autoconf_2.72-3 automake_1:1.17-3 autopoint_0.23.1-1 autotools-dev_20220109.1 base-files_13.7 base-passwd_3.6.6 bash_5.2.37-1.1 bash-completion_1:2.16.0-7 binutils_2.44-3 binutils-common_2.44-3 binutils-riscv64-linux-gnu_2.44-3 bsdextrautils_2.40.4-5 bsdutils_1:2.40.4-5 build-essential_12.12 bzip2_1.0.8-6 chrpath_0.18-1 cmake_3.31.6-1 cmake-data_3.31.6-1 coreutils_9.5-1 cpp_4:14.2.0-1 cpp-14_14.2.0-17 cpp-14-riscv64-linux-gnu_14.2.0-17 cpp-riscv64-linux-gnu_4:14.2.0-1 dash_0.5.12-12 debconf_1.5.90 debhelper_13.24.1 debianutils_5.21 dh-autoreconf_20 dh-python_6.20250308 dh-strip-nondeterminism_1.14.1-2 diffutils_1:3.10-2 dpkg_1.22.18 dpkg-dev_1.22.18 dwz_0.15-1+b3 file_1:5.45-3+b1 findutils_4.10.0-3 g++_4:14.2.0-1 g++-14_14.2.0-17 g++-14-riscv64-linux-gnu_14.2.0-17 g++-riscv64-linux-gnu_4:14.2.0-1 gcc_4:14.2.0-1 gcc-14_14.2.0-17 gcc-14-base_14.2.0-17 gcc-14-riscv64-linux-gnu_14.2.0-17 gcc-riscv64-linux-gnu_4:14.2.0-1 gettext_0.23.1-1 gettext-base_0.23.1-1 gfortran-14_14.2.0-17 gfortran-14-riscv64-linux-gnu_14.2.0-17 grep_3.11-4 groff-base_1.23.0-7 gzip_1.13-1 hostname_3.25 ibverbs-providers_56.0-2 init-system-helpers_1.68 intltool-debian_0.35.0+20060710.6 libacl1_2.3.2-2+b1 libarchive-zip-perl_1.68-1 libarchive13t64_3.7.4-1.1 libasan8_14.2.0-17 libatomic1_14.2.0-17 libattr1_1:2.5.2-3 libaudit-common_1:4.0.2-2 libaudit1_1:4.0.2-2+b2 libbinutils_2.44-3 libblas-dev_3.12.1-2 libblas3_3.12.1-2 libblkid1_2.40.4-5 libboost-dev_1.83.0.2+b2 libboost1.83-dev_1.83.0-4.1+b1 libbrotli1_1.1.0-2+b7 libbsd0_0.12.2-2 libbz2-1.0_1.0.8-6 libc-bin_2.41-4 libc-dev-bin_2.41-4 libc6_2.41-4 libc6-dev_2.41-4 libcap-ng0_0.8.5-4+b1 libcap2_1:2.75-1 libcbor0.10_0.10.2-2 libcc1-0_14.2.0-17 libcom-err2_1.47.2-1 libcrypt-dev_1:4.4.38-1 libcrypt1_1:4.4.38-1 libctf-nobfd0_2.44-3 libctf0_2.44-3 libcurl4t64_8.12.1-3 libdb5.3t64_5.3.28+dfsg2-9 libdebconfclient0_0.277 libdebhelper-perl_13.24.1 libdpkg-perl_1.22.18 libedit2_3.1-20250104-1 libelf1t64_0.192-4 libevent-2.1-7t64_2.1.12-stable-10+b1 libevent-core-2.1-7t64_2.1.12-stable-10+b1 libevent-dev_2.1.12-stable-10+b1 libevent-extra-2.1-7t64_2.1.12-stable-10+b1 libevent-openssl-2.1-7t64_2.1.12-stable-10+b1 libevent-pthreads-2.1-7t64_2.1.12-stable-10+b1 libexpat1_2.6.4-1 libexpat1-dev_2.6.4-1 libfabric1_1.17.0-3.1 libffi8_3.4.7-1 libfftw3-bin_3.3.10-2+b1 libfftw3-dev_3.3.10-2+b1 libfftw3-double3_3.3.10-2+b1 libfftw3-long3_3.3.10-2+b1 libfftw3-single3_3.3.10-2+b1 libfido2-1_1.15.0-1+b1 libfile-stripnondeterminism-perl_1.14.1-2 libfuse3-3_3.14.0-10 libgcc-14-dev_14.2.0-17 libgcc-s1_14.2.0-17 libgdbm-compat4t64_1.24-2 libgdbm6t64_1.24-2 libgfortran-14-dev_14.2.0-17 libgfortran5_14.2.0-17 libgmp10_2:6.3.0+dfsg-3 libgnutls30t64_3.8.9-2 libgomp1_14.2.0-17 libgprofng0_2.44-3 libgssapi-krb5-2_1.21.3-4 libhogweed6t64_3.10.1-1 libhwloc-dev_2.12.0-1 libhwloc-plugins_2.12.0-1 libhwloc15_2.12.0-1 libibmad5_56.0-2 libibumad3_56.0-2 libibverbs-dev_56.0-2 libibverbs1_56.0-2 libicu72_72.1-6 libidn2-0_2.3.8-1 libisl23_0.27-1 libitm1_14.2.0-17 libjansson4_2.14-2+b3 libjs-jquery_3.6.1+dfsg+~3.5.14-1 libjs-jquery-ui_1.13.2+dfsg-1 libjs-sphinxdoc_8.1.3-5 libjs-underscore_1.13.4~dfsg+~1.11.4-3 libjsoncpp26_1.9.6-3 libk5crypto3_1.21.3-4 libkeyutils1_1.6.3-4 libkrb5-3_1.21.3-4 libkrb5support0_1.21.3-4 liblapack-dev_3.12.1-2 liblapack3_3.12.1-2 libldap2_2.6.9+dfsg-2 liblsan0_14.2.0-17 libltdl-dev_2.5.4-4 libltdl7_2.5.4-4 liblz4-1_1.10.0-4 liblzma5_5.6.4-1 libmagic-mgc_1:5.45-3+b1 libmagic1t64_1:5.45-3+b1 libmd0_1.1.0-2+b1 libmount1_2.40.4-5 libmpc3_1.3.1-1+b3 libmpfr6_4.2.1-1+b2 libmunge2_0.5.16-1 libmuparser-dev_2.3.4-1+b1 libmuparser2v5_2.3.4-1+b1 libncursesw6_6.5+20250216-2 libnettle8t64_3.10.1-1 libnghttp2-14_1.64.0-1 libnghttp3-9_1.8.0-1 libnl-3-200_3.7.0-1 libnl-3-dev_3.7.0-1 libnl-route-3-200_3.7.0-1 libnl-route-3-dev_3.7.0-1 libnuma-dev_2.0.18-1+b1 libnuma1_2.0.18-1+b1 libopenmpi-dev_5.0.7-1 libopenmpi40_5.0.7-1 libp11-kit0_0.25.5-3 libpam-modules_1.7.0-3 libpam-modules-bin_1.7.0-3 libpam-runtime_1.7.0-3 libpam0g_1.7.0-3 libpciaccess0_0.17-3+b3 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libx11-data_2:1.8.10-2 libxau6_1:1.0.11-1 libxcb1_1.17.0-2+b1 libxdmcp6_1:1.1.5-1 libxext6_2:1.3.4-1+b3 libxml2_2.12.7+dfsg+really2.9.14-0.2+b2 libxnvctrl0_535.171.04-1+b2 libxxhash0_0.8.3-2 libzstd1_1.5.6+dfsg-2 linux-libc-dev_6.12.17-1 login.defs_1:4.17.3-1 lsb-release_12.1-1 m4_1.4.19-7 make_4.4.1-1 man-db_2.13.0-1 mawk_1.3.4.20250131-1 media-types_13.0.0 mpi-default-bin_1.18 mpi-default-dev_1.18 ncurses-base_6.5+20250216-2 ncurses-bin_6.5+20250216-2 netbase_6.4 ocl-icd-libopencl1_2.3.2-1+b2 openmpi-bin_5.0.7-1 openmpi-common_5.0.7-1 openssh-client_1:9.9p2-1 openssl-provider-legacy_3.4.1-1 passwd_1:4.17.3-1 patch_2.7.6-7+b2 perl_5.40.1-2 perl-base_5.40.1-2 perl-modules-5.40_5.40.1-2 pkgconf_1.8.1-4 pkgconf-bin_1.8.1-4 po-debconf_1.0.21+nmu1 procps_2:4.0.4-7 pybind11-dev_2.13.6-2 python3_3.13.2-2 python3-autocommand_2.2.2-3 python3-dev_3.13.2-2 python3-inflect_7.3.1-2 python3-iniconfig_1.1.1-2 python3-jaraco.context_6.0.1-1 python3-jaraco.functools_4.1.0-1 python3-minimal_3.13.2-2 python3-more-itertools_10.6.0-1 python3-mpi4py_4.0.3-3 python3-networkx_3.2.1-5 python3-numpy_1:2.2.3+ds-5 python3-numpy-dev_1:2.2.3+ds-5 python3-packaging_24.2-1 python3-pkg-resources_75.8.0-1 python3-pluggy_1.5.0-1 python3-pybind11_2.13.6-2 python3-pytest_8.3.5-1 python3-typeguard_4.4.2-1 python3-typing-extensions_4.12.2-2 python3.13_3.13.2-1 python3.13-dev_3.13.2-1 python3.13-minimal_3.13.2-1 readline-common_8.2-6 rpcsvc-proto_1.4.3-1+b2 sed_4.9-2 sensible-utils_0.0.24 sysvinit-utils_3.14-3 tar_1.35+dfsg-3.1 tzdata_2025a-2 util-linux_2.40.4-5 xz-utils_5.6.4-1 zlib1g_1:1.3.dfsg+really1.3.1-1+b1 zlib1g-dev_1:1.3.dfsg+really1.3.1-1+b1 +------------------------------------------------------------------------------+ | Build Wed, 23 Apr 2025 02:29:04 +0000 | +------------------------------------------------------------------------------+ Unpack source ------------- -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA512 Format: 3.0 (quilt) Source: gromacs Binary: gromacs, gromacs-data, libgromacs10, libgromacs-dev, libnblib-gmx0, libnblib-gmx-dev Architecture: any all Version: 2025.1-1 Maintainer: Debichem Team Uploaders: Nicholas Breen Homepage: https://www.gromacs.org/ Standards-Version: 4.7.0 Vcs-Browser: https://salsa.debian.org/debichem-team/gromacs Vcs-Git: https://salsa.debian.org/debichem-team/gromacs.git Testsuite: autopkgtest Testsuite-Triggers: build-essential, mpi-default-bin, perl Build-Depends: architecture-is-64-bit, bash-completion, chrpath, cmake (>= 3.13), debhelper-compat (= 13), dh-python, libblas-dev, libboost-dev, libfftw3-dev, libhwloc-dev, liblapack-dev, libmuparser-dev (>= 2.3.4), lsb-release, mpi-default-bin, mpi-default-dev, pkgconf, python3-dev, python3-mpi4py, python3-networkx, python3-numpy, python3-pybind11, python3-pytest, zlib1g-dev Build-Depends-Indep: doxygen, furo, ghostscript, graphicsmagick, graphviz, mscgen, python3-pygments, python3-sphinx, python3-sphinx-argparse, python3-sphinx-copybutton, python3-sphinx-inline-tabs, python3-sphinxcontrib.autoprogram, rdfind, symlinks, tex-gyre, texlive-fonts-recommended, texlive-latex-base, texlive-latex-extra Package-List: gromacs deb science optional arch=any gromacs-data deb science optional arch=all libgromacs-dev deb libdevel optional arch=any libgromacs10 deb libs optional arch=any libnblib-gmx-dev deb libdevel optional arch=any libnblib-gmx0 deb libs optional arch=any Checksums-Sha1: 128258464e1a6a0163098b69492ba8dbd36191ea 32653610 gromacs_2025.1.orig-regressiontests.tar.gz 2701b2b12a43c76d017269607161c0c75dc69086 44415202 gromacs_2025.1.orig.tar.gz 10ff82b5727daeb4937d83ba59e9e7c0ee1efdb4 37256 gromacs_2025.1-1.debian.tar.xz Checksums-Sha256: b38b63f79b23bf4c87dcaf079c49caaa729c7400fa2a4ae8db86514996c8b4de 32653610 gromacs_2025.1.orig-regressiontests.tar.gz 0adf621a80fd8043f8defec84ce02811c0cdf42a052232890932d81f25c4d28a 44415202 gromacs_2025.1.orig.tar.gz 8c2593924374303fa6d6c534741816678e693dd5e8b386002b5f8a79d6093906 37256 gromacs_2025.1-1.debian.tar.xz Files: 05315813b1f9f4b31d5531bc01abfaf5 32653610 gromacs_2025.1.orig-regressiontests.tar.gz 16b1eea704c9912b17fc2e9eb6b86e60 44415202 gromacs_2025.1.orig.tar.gz f7fe315bd5ec45e0c60da62c452e83db 37256 gromacs_2025.1-1.debian.tar.xz -----BEGIN PGP SIGNATURE----- iQJGBAEBCgAwFiEEhD5fph5gYziYdtLl7kr9aexlEI8FAmfQ7vQSHG5icmVlbkBk ZWJpYW4ub3JnAAoJEO5K/WnsZRCPCHUP+gOPia8ZXU1AkGhrXgt6lfPFk31ZRNqJ 7O69gN5ASQ8723cyQvRur/yVEG8lWEHjedE2zJlqPex4JO82b8Rbusjs91sUsluj t3e2h5rlSw9dRNn8XL2kND9seet0M1hD5yzCgc7jvKZfRmF2d90aMm0guV+DHFWK VwtQdhk8+sEBAPYpnsAAI2yfWm3oYi84Ef0ETXBdmhGmb9TFRp6uCr6syASpJLt0 XO9Ztly0RmKk63w+sjdaqkexR8urG2gWfEcpw7mEjg2kVBK3KtTohg9E6yRojUAb jO9JpnPFmR2NgS73g1I8NHD+pNEKI1KwAscb006hZU3yjNSpdA4lNW/FeYLprSHX 6ZHOEcf8PFePGS6vmR3tZ4edxhrJthkmqhrZaXmlJK76XZom1yW2WuMRntLYuYKj cGRYwPF5vm4LeJ9ykai4mqJSjKoA18KxT7j4a8/P0QQQhX46i5VwuHAzjCGWHss1 PmWEOegBoIdLr3Mp+oHnaM9FV+Cr9PtQYIhOdjXtlo30yFvvPuKMzXeps1HLyErJ ya0uyPr+13+y1Mm2T1aN+T2aftd9oh9EyrZzjmcCCtlETuzFSVsxjZDaUmh5IqIT Qmrt2qZxHmIdDdox4QpmjPsD43/+877uZ3IPaBdhWmDVJ8XRqbYw1Fbg3jx8Vn6a FdZq3eQAbsoZ =pmmZ -----END PGP SIGNATURE----- dpkg-source: warning: cannot verify inline signature for ./gromacs_2025.1-1.dsc: unsupported subcommand dpkg-source: info: extracting gromacs in /build/reproducible-path/gromacs-2025.1 dpkg-source: info: unpacking gromacs_2025.1.orig.tar.gz dpkg-source: info: unpacking gromacs_2025.1.orig-regressiontests.tar.gz dpkg-source: info: unpacking gromacs_2025.1-1.debian.tar.xz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: applying readme.patch dpkg-source: info: applying copyright-file.patch dpkg-source: info: applying disable-cpuinfotest.patch dpkg-source: info: applying mdrun-test-timeout.patch dpkg-source: info: applying manual-local-mathjax.patch dpkg-source: info: applying mpi-tests-localhost.patch dpkg-source: info: applying manual-image-conversion.patch dpkg-source: info: applying disable-gmxtimingtests.patch dpkg-source: info: applying script-shebang-line.patch Check disk space ---------------- Sufficient free space for build User Environment ---------------- APT_CONFIG=/var/lib/sbuild/apt.conf DEB_BUILD_OPTIONS=parallel=4 HOME=/sbuild-nonexistent LANG=C.UTF-8 LC_ALL=C.UTF-8 LC_COLLATE=C.UTF-8 LC_CTYPE=C.UTF-8 LOGNAME=sbuild PATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games SHELL=/bin/sh SOURCE_DATE_EPOCH=1741743011 USER=sbuild dpkg-buildpackage ----------------- Command: dpkg-buildpackage --sanitize-env -us -uc -B dpkg-buildpackage: info: source package gromacs dpkg-buildpackage: info: source version 2025.1-1 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Nicholas Breen dpkg-source --before-build . dpkg-buildpackage: info: host architecture riscv64 debian/rules clean dh_testdir dh_testroot dh_clean build-basic build-mpi build-manual build/ py3clean admin docs debian/rules binary-arch dh_testdir (mkdir -p build/basic; cd build/basic; cmake \ /build/reproducible-path/gromacs-2025.1 -DCMAKE_VERBOSE_MAKEFILE=ON -DCMAKE_RULE_MESSAGES=OFF -DCMAKE_INSTALL_PREFIX="/usr" -DCMAKE_EXE_LINKER_FLAGS="-Wl,-z,relro -Wl,-z,now" -DCMAKE_SKIP_RPATH=ON -DGMX_EXTERNAL_ZLIB=ON -DGMX_USE_MUPARSER=EXTERNAL -DGMX_VERSION_STRING_OF_FORK="Debian-2025.1-1" -DGMX_GIT_VERSION_INFO=OFF -DGMX_HWLOC=ON -DGMX_SIMD=None -DGMX_MPI=OFF -DGMX_INSTALL_LEGACY_API=ON) -- The C compiler identification is GNU 14.2.0 -- The CXX compiler identification is GNU 14.2.0 -- Detecting C compiler ABI info -- Detecting C compiler ABI info - done -- Check for working C compiler: /usr/bin/cc - skipped -- Detecting C compile features -- Detecting C compile features - done -- Detecting CXX compiler ABI info -- Detecting CXX compiler ABI info - done -- Check for working CXX compiler: /usr/bin/c++ - skipped -- Detecting CXX compile features -- Detecting CXX compile features - done -- Found Python3: /usr/bin/python3 (found suitable version "3.13.2", minimum required is "3.9") found components: Interpreter Development Development.Module Development.Embed -- Found OpenMP_C: -fopenmp (found version "4.5") -- Found OpenMP_CXX: -fopenmp (found version "4.5") -- Found OpenMP: TRUE (found version "4.5") -- Performing Test CFLAGS_WARN_NO_MISSING_FIELD_INITIALIZERS -- Performing Test CFLAGS_WARN_NO_MISSING_FIELD_INITIALIZERS - Success -- Performing Test CFLAGS_EXCESS_PREC -- Performing Test CFLAGS_EXCESS_PREC - Success -- Performing Test CFLAGS_COPT -- Performing Test CFLAGS_COPT - Success -- Performing Test CFLAGS_NOINLINE -- Performing Test CFLAGS_NOINLINE - Success -- Performing Test CXXFLAGS_WARN_NO_MISSING_FIELD_INITIALIZERS -- Performing Test CXXFLAGS_WARN_NO_MISSING_FIELD_INITIALIZERS - Success -- Performing Test CXXFLAGS_EXCESS_PREC -- Performing Test CXXFLAGS_EXCESS_PREC - Success -- Performing Test CXXFLAGS_COPT -- Performing Test CXXFLAGS_COPT - Success -- Performing Test CXXFLAGS_NOINLINE -- Performing Test CXXFLAGS_NOINLINE - Success -- Looking for include file unistd.h -- Looking for include file unistd.h - found -- Looking for include file pwd.h -- Looking for include file pwd.h - found -- Looking for include file dirent.h -- Looking for include file dirent.h - found -- Looking for include file time.h -- Looking for include file time.h - found -- Looking for include file sys/time.h -- Looking for include file sys/time.h - found -- Looking for include file io.h -- Looking for include file io.h - not found -- Looking for include file sched.h -- Looking for include file sched.h - found -- Looking for include file xmmintrin.h -- Looking for include file xmmintrin.h - not found -- Looking for gettimeofday -- Looking for gettimeofday - found -- Looking for sysconf -- Looking for sysconf - found -- Looking for nice -- Looking for nice - found -- Looking for fsync -- Looking for fsync - found -- Looking for _fileno -- Looking for _fileno - not found -- Looking for fileno -- Looking for fileno - found -- Looking for _commit -- Looking for _commit - not found -- Looking for sigaction -- Looking for sigaction - found -- Performing Test HAVE_BUILTIN_CLZ -- Performing Test HAVE_BUILTIN_CLZ - Success -- Performing Test HAVE_BUILTIN_CLZLL -- Performing Test HAVE_BUILTIN_CLZLL - Success -- Looking for clock_gettime in rt -- Looking for clock_gettime in rt - found -- Looking for feenableexcept in m -- Looking for feenableexcept in m - found -- Looking for fedisableexcept in m -- Looking for fedisableexcept in m - found -- Checking for sched.h GNU affinity API -- Performing Test sched_affinity_compile -- Performing Test sched_affinity_compile - Success -- Looking for include file mm_malloc.h -- Looking for include file mm_malloc.h - not found -- Looking for include file malloc.h -- Looking for include file malloc.h - found -- Checking for _mm_malloc() -- Checking for _mm_malloc() - not supported -- Looking for posix_memalign -- Looking for posix_memalign - found -- Looking for memalign -- Looking for memalign - not found -- Torch not found. Neural network potential support will be disabled. -- Using default binary suffix: "" -- Using default library suffix: "" -- Looking for HWLOC -- Looking for hwloc_topology_init -- Looking for hwloc_topology_init - found -- hwloc version: -- Found HWLOC: /lib/riscv64-linux-gnu/libhwloc.so (found suitable version "2.12.0", minimum required is "1.5") -- Performing Test CMAKE_HAVE_LIBC_PTHREAD -- Performing Test CMAKE_HAVE_LIBC_PTHREAD - Success -- Found Threads: TRUE -- Looking for C++ include pthread.h -- Looking for C++ include pthread.h - found -- Performing Test TEST_ATOMICS -- Performing Test TEST_ATOMICS - Success -- Atomic operations found -- Performing Test PTHREAD_SETAFFINITY -- Performing Test PTHREAD_SETAFFINITY - Success -- Found ZLIB: /usr/lib/riscv64-linux-gnu/libz.so (found version "1.3.1") -- Looking for zlibVersion in /usr/lib/riscv64-linux-gnu/libz.so -- Looking for zlibVersion in /usr/lib/riscv64-linux-gnu/libz.so - found -- SIMD instructions disabled -- Performing Test _callconv___vectorcall -- Performing Test _callconv___vectorcall - Failed -- Performing Test _callconv___regcall -- Performing Test _callconv___regcall - Failed -- Performing Test _callconv_ -- Performing Test _callconv_ - Success -- Checking for GCC x86 inline asm -- Checking for GCC x86 inline asm - not supported -- Detected build CPU vendor - RISC-V 64 -- Detected build CPU brand - Unknown CPU brand -- Detected build CPU family - 0 -- Detected build CPU model - 0 -- Detected build CPU stepping - 0 -- Detected build CPU features - -- Checking for 64-bit off_t -- Checking for 64-bit off_t - present -- Checking for fseeko/ftello -- Checking for fseeko/ftello - present -- Checking for SIGUSR1 -- Checking for SIGUSR1 - found -- Checking for pipe support -- Checking for system XDR support -- Checking for system XDR support - not present -- Checking for module 'fftw3f' -- Found fftw3f, version 3.3.10 -- Looking for fftwf_plan_many_dft in /usr/lib/riscv64-linux-gnu/libfftw3f.so -- Looking for fftwf_plan_many_dft in /usr/lib/riscv64-linux-gnu/libfftw3f.so - found -- Looking for fftwf_plan_many_dft_r2c in /usr/lib/riscv64-linux-gnu/libfftw3f.so -- Looking for fftwf_plan_many_dft_r2c in /usr/lib/riscv64-linux-gnu/libfftw3f.so - found -- Looking for fftwf_plan_many_dft_c2r in /usr/lib/riscv64-linux-gnu/libfftw3f.so -- Looking for fftwf_plan_many_dft_c2r in /usr/lib/riscv64-linux-gnu/libfftw3f.so - found -- Looking for fftwf_have_simd_sse in /usr/lib/riscv64-linux-gnu/libfftw3f.so -- Looking for fftwf_have_simd_sse in /usr/lib/riscv64-linux-gnu/libfftw3f.so - not found -- Looking for fftwf_have_sse in /usr/lib/riscv64-linux-gnu/libfftw3f.so -- Looking for fftwf_have_sse in /usr/lib/riscv64-linux-gnu/libfftw3f.so - not found -- Looking for fftwf_have_simd_sse2 in /usr/lib/riscv64-linux-gnu/libfftw3f.so -- Looking for fftwf_have_simd_sse2 in /usr/lib/riscv64-linux-gnu/libfftw3f.so - not found -- Looking for fftwf_have_sse2 in /usr/lib/riscv64-linux-gnu/libfftw3f.so -- Looking for fftwf_have_sse2 in /usr/lib/riscv64-linux-gnu/libfftw3f.so - not found -- Looking for fftwf_have_simd_avx in /usr/lib/riscv64-linux-gnu/libfftw3f.so -- Looking for fftwf_have_simd_avx in /usr/lib/riscv64-linux-gnu/libfftw3f.so - not found -- Looking for fftwf_have_simd_avx2 in /usr/lib/riscv64-linux-gnu/libfftw3f.so -- Looking for fftwf_have_simd_avx2 in /usr/lib/riscv64-linux-gnu/libfftw3f.so - not found -- Looking for fftwf_have_simd_avx2_128 in /usr/lib/riscv64-linux-gnu/libfftw3f.so -- Looking for fftwf_have_simd_avx2_128 in /usr/lib/riscv64-linux-gnu/libfftw3f.so - not found -- Looking for fftwf_have_simd_avx512 in /usr/lib/riscv64-linux-gnu/libfftw3f.so -- Looking for fftwf_have_simd_avx512 in /usr/lib/riscv64-linux-gnu/libfftw3f.so - not found -- Looking for fftwf_have_simd_avx_128_fma in /usr/lib/riscv64-linux-gnu/libfftw3f.so -- Looking for fftwf_have_simd_avx_128_fma in /usr/lib/riscv64-linux-gnu/libfftw3f.so - not found -- Looking for fftwf_have_simd_avx_512 in /usr/lib/riscv64-linux-gnu/libfftw3f.so -- Looking for fftwf_have_simd_avx_512 in /usr/lib/riscv64-linux-gnu/libfftw3f.so - not found -- Looking for fftwf_have_simd_kcvi in /usr/lib/riscv64-linux-gnu/libfftw3f.so -- Looking for fftwf_have_simd_kcvi in /usr/lib/riscv64-linux-gnu/libfftw3f.so - not found -- Looking for fftwf_have_simd_altivec in /usr/lib/riscv64-linux-gnu/libfftw3f.so -- Looking for fftwf_have_simd_altivec in /usr/lib/riscv64-linux-gnu/libfftw3f.so - not found -- Looking for fftwf_have_simd_neon in /usr/lib/riscv64-linux-gnu/libfftw3f.so -- Looking for fftwf_have_simd_neon in /usr/lib/riscv64-linux-gnu/libfftw3f.so - not found -- Looking for fftwf_have_simd_vsx in /usr/lib/riscv64-linux-gnu/libfftw3f.so -- Looking for fftwf_have_simd_vsx in /usr/lib/riscv64-linux-gnu/libfftw3f.so - not found -- Looking for fftwf_have_simd_altivec in /usr/lib/riscv64-linux-gnu/libfftw3f.so -- Looking for fftwf_have_simd_altivec in /usr/lib/riscv64-linux-gnu/libfftw3f.so - not found -- Looking for fftwf_have_altivec in /usr/lib/riscv64-linux-gnu/libfftw3f.so -- Looking for fftwf_have_altivec in /usr/lib/riscv64-linux-gnu/libfftw3f.so - not found -- Using external FFT library - FFTW3 -- Looking for sgemm_ -- Looking for sgemm_ - not found -- Looking for sgemm_ -- Looking for sgemm_ - found -- Found BLAS: /usr/lib/riscv64-linux-gnu/libblas.so -- Looking for cheev_ -- Looking for cheev_ - not found -- Looking for cheev_ -- Looking for cheev_ - found -- Found LAPACK: /usr/lib/riscv64-linux-gnu/liblapack.so;/usr/lib/riscv64-linux-gnu/libblas.so -- Could not convert sample image, ImageMagick convert can not be used. A possible way to fix it can be found here: https://alexvanderbist.com/2018/fixing-imagick-error-unauthorized -- Performing Test HAS_WARNING_EVERYTHING -- Performing Test HAS_WARNING_EVERYTHING - Failed -- Found Python: /usr/bin/python3 (found version "3.13.2") found components: Interpreter -- Performing Test HAVE_NO_DEPRECATED_COPY -- Performing Test HAVE_NO_DEPRECATED_COPY - Success -- Looking for dlopen -- Looking for dlopen - found -- Performing Test HAS_NO_STRINGOP_TRUNCATION -- Performing Test HAS_NO_STRINGOP_TRUNCATION - Success -- Performing Test HAS_WARNING_NO_CAST_FUNCTION_TYPE_STRICT -- Performing Test HAS_WARNING_NO_CAST_FUNCTION_TYPE_STRICT - Success -- Performing Test HAS_NO_UNUSED -- Performing Test HAS_NO_UNUSED - Success -- Performing Test HAS_NO_UNUSED_PARAMETER -- Performing Test HAS_NO_UNUSED_PARAMETER - Success -- Performing Test HAS_NO_MISSING_DECLARATIONS -- Performing Test HAS_NO_MISSING_DECLARATIONS - Success -- Performing Test HAS_NO_NULL_CONVERSIONS -- Performing Test HAS_NO_NULL_CONVERSIONS - Success -- Looking for inttypes.h -- Looking for inttypes.h - found -- Performing Test COMPILER_HAS_HIDDEN_VISIBILITY -- Performing Test COMPILER_HAS_HIDDEN_VISIBILITY - Success -- Performing Test COMPILER_HAS_HIDDEN_INLINE_VISIBILITY -- Performing Test COMPILER_HAS_HIDDEN_INLINE_VISIBILITY - Success -- Performing Test COMPILER_HAS_DEPRECATED_ATTR -- Performing Test COMPILER_HAS_DEPRECATED_ATTR - Success -- Could NOT find Sphinx (missing: SPHINX_EXECUTABLE pygments) (Required is at least version "4.0.0") -- Could NOT find LATEX (missing: LATEX_COMPILER) -- Configuring done (258.9s) -- Generating done (13.0s) -- Build files have been written to: /build/reproducible-path/gromacs-2025.1/build/basic (mkdir -p build/basic-dp; cd build/basic-dp; cmake \ /build/reproducible-path/gromacs-2025.1 -DCMAKE_VERBOSE_MAKEFILE=ON -DCMAKE_RULE_MESSAGES=OFF -DCMAKE_INSTALL_PREFIX="/usr" -DCMAKE_EXE_LINKER_FLAGS="-Wl,-z,relro -Wl,-z,now" -DCMAKE_SKIP_RPATH=ON -DGMX_EXTERNAL_ZLIB=ON -DGMX_USE_MUPARSER=EXTERNAL -DGMX_VERSION_STRING_OF_FORK="Debian-2025.1-1" -DGMX_GIT_VERSION_INFO=OFF -DGMX_HWLOC=ON -DGMX_SIMD=None -DGMX_MPI=OFF -DGMX_DOUBLE=ON) -- The C compiler identification is GNU 14.2.0 -- The CXX compiler identification is GNU 14.2.0 -- Detecting C compiler ABI info -- Detecting C compiler ABI info - done -- Check for working C compiler: /usr/bin/cc - skipped -- Detecting C compile features -- Detecting C compile features - done -- Detecting CXX compiler ABI info -- Detecting CXX compiler ABI info - done -- Check for working CXX compiler: /usr/bin/c++ - skipped -- Detecting CXX compile features -- Detecting CXX compile features - done -- Found Python3: /usr/bin/python3 (found suitable version "3.13.2", minimum required is "3.9") found components: Interpreter Development Development.Module Development.Embed -- Found OpenMP_C: -fopenmp (found version "4.5") -- Found OpenMP_CXX: -fopenmp (found version "4.5") -- Found OpenMP: TRUE (found version "4.5") -- Performing Test CFLAGS_WARN_NO_MISSING_FIELD_INITIALIZERS -- Performing Test CFLAGS_WARN_NO_MISSING_FIELD_INITIALIZERS - Success -- Performing Test CFLAGS_EXCESS_PREC -- Performing Test CFLAGS_EXCESS_PREC - Success -- Performing Test CFLAGS_COPT -- Performing Test CFLAGS_COPT - Success -- Performing Test CFLAGS_NOINLINE -- Performing Test CFLAGS_NOINLINE - Success -- Performing Test CXXFLAGS_WARN_NO_MISSING_FIELD_INITIALIZERS -- Performing Test CXXFLAGS_WARN_NO_MISSING_FIELD_INITIALIZERS - Success -- Performing Test CXXFLAGS_EXCESS_PREC -- Performing Test CXXFLAGS_EXCESS_PREC - Success -- Performing Test CXXFLAGS_COPT -- Performing Test CXXFLAGS_COPT - Success -- Performing Test CXXFLAGS_NOINLINE -- Performing Test CXXFLAGS_NOINLINE - Success -- Looking for include file unistd.h -- Looking for include file unistd.h - found -- Looking for include file pwd.h -- Looking for include file pwd.h - found -- Looking for include file dirent.h -- Looking for include file dirent.h - found -- Looking for include file time.h -- Looking for include file time.h - found -- Looking for include file sys/time.h -- Looking for include file sys/time.h - found -- Looking for include file io.h -- Looking for include file io.h - not found -- Looking for include file sched.h -- Looking for include file sched.h - found -- Looking for include file xmmintrin.h -- Looking for include file xmmintrin.h - not found -- Looking for gettimeofday -- Looking for gettimeofday - found -- Looking for sysconf -- Looking for sysconf - found -- Looking for nice -- Looking for nice - found -- Looking for fsync -- Looking for fsync - found -- Looking for _fileno -- Looking for _fileno - not found -- Looking for fileno -- Looking for fileno - found -- Looking for _commit -- Looking for _commit - not found -- Looking for sigaction -- Looking for sigaction - found -- Performing Test HAVE_BUILTIN_CLZ -- Performing Test HAVE_BUILTIN_CLZ - Success -- Performing Test HAVE_BUILTIN_CLZLL -- Performing Test HAVE_BUILTIN_CLZLL - Success -- Looking for clock_gettime in rt -- Looking for clock_gettime in rt - found -- Looking for feenableexcept in m -- Looking for feenableexcept in m - found -- Looking for fedisableexcept in m -- Looking for fedisableexcept in m - found -- Checking for sched.h GNU affinity API -- Performing Test sched_affinity_compile -- Performing Test sched_affinity_compile - Success -- Looking for include file mm_malloc.h -- Looking for include file mm_malloc.h - not found -- Looking for include file malloc.h -- Looking for include file malloc.h - found -- Checking for _mm_malloc() -- Checking for _mm_malloc() - not supported -- Looking for posix_memalign -- Looking for posix_memalign - found -- Looking for memalign -- Looking for memalign - not found -- Torch not found. Neural network potential support will be disabled. -- Using default binary suffix: "_d" -- Using default library suffix: "_d" -- Looking for HWLOC -- Looking for hwloc_topology_init -- Looking for hwloc_topology_init - found -- hwloc version: -- Found HWLOC: /lib/riscv64-linux-gnu/libhwloc.so (found suitable version "2.12.0", minimum required is "1.5") -- Performing Test CMAKE_HAVE_LIBC_PTHREAD -- Performing Test CMAKE_HAVE_LIBC_PTHREAD - Success -- Found Threads: TRUE -- Looking for C++ include pthread.h -- Looking for C++ include pthread.h - found -- Performing Test TEST_ATOMICS -- Performing Test TEST_ATOMICS - Success -- Atomic operations found -- Performing Test PTHREAD_SETAFFINITY -- Performing Test PTHREAD_SETAFFINITY - Success -- Found ZLIB: /usr/lib/riscv64-linux-gnu/libz.so (found version "1.3.1") -- Looking for zlibVersion in /usr/lib/riscv64-linux-gnu/libz.so -- Looking for zlibVersion in /usr/lib/riscv64-linux-gnu/libz.so - found -- SIMD instructions disabled -- Performing Test _callconv___vectorcall -- Performing Test _callconv___vectorcall - Failed -- Performing Test _callconv___regcall -- Performing Test _callconv___regcall - Failed -- Performing Test _callconv_ -- Performing Test _callconv_ - Success -- Checking for GCC x86 inline asm -- Checking for GCC x86 inline asm - not supported -- Detected build CPU vendor - RISC-V 64 -- Detected build CPU brand - Unknown CPU brand -- Detected build CPU family - 0 -- Detected build CPU model - 0 -- Detected build CPU stepping - 0 -- Detected build CPU features - -- Checking for 64-bit off_t -- Checking for 64-bit off_t - present -- Checking for fseeko/ftello -- Checking for fseeko/ftello - present -- Checking for SIGUSR1 -- Checking for SIGUSR1 - found -- Checking for pipe support -- Checking for system XDR support -- Checking for system XDR support - not present -- Checking for module 'fftw3' -- Found fftw3, version 3.3.10 -- Looking for fftw_plan_many_dft in /usr/lib/riscv64-linux-gnu/libfftw3.so -- Looking for fftw_plan_many_dft in /usr/lib/riscv64-linux-gnu/libfftw3.so - found -- Looking for fftw_plan_many_dft_r2c in /usr/lib/riscv64-linux-gnu/libfftw3.so -- Looking for fftw_plan_many_dft_r2c in /usr/lib/riscv64-linux-gnu/libfftw3.so - found -- Looking for fftw_plan_many_dft_c2r in /usr/lib/riscv64-linux-gnu/libfftw3.so -- Looking for fftw_plan_many_dft_c2r in /usr/lib/riscv64-linux-gnu/libfftw3.so - found -- Looking for fftw_have_simd_sse in /usr/lib/riscv64-linux-gnu/libfftw3.so -- Looking for fftw_have_simd_sse in /usr/lib/riscv64-linux-gnu/libfftw3.so - not found -- Looking for fftw_have_sse in /usr/lib/riscv64-linux-gnu/libfftw3.so -- Looking for fftw_have_sse in /usr/lib/riscv64-linux-gnu/libfftw3.so - not found -- Looking for fftw_have_simd_sse2 in /usr/lib/riscv64-linux-gnu/libfftw3.so -- Looking for fftw_have_simd_sse2 in /usr/lib/riscv64-linux-gnu/libfftw3.so - not found -- Looking for fftw_have_sse2 in /usr/lib/riscv64-linux-gnu/libfftw3.so -- Looking for fftw_have_sse2 in /usr/lib/riscv64-linux-gnu/libfftw3.so - not found -- Looking for fftw_have_simd_avx in /usr/lib/riscv64-linux-gnu/libfftw3.so -- Looking for fftw_have_simd_avx in /usr/lib/riscv64-linux-gnu/libfftw3.so - not found -- Looking for fftw_have_simd_avx2 in /usr/lib/riscv64-linux-gnu/libfftw3.so -- Looking for fftw_have_simd_avx2 in /usr/lib/riscv64-linux-gnu/libfftw3.so - not found -- Looking for fftw_have_simd_avx2_128 in /usr/lib/riscv64-linux-gnu/libfftw3.so -- Looking for fftw_have_simd_avx2_128 in /usr/lib/riscv64-linux-gnu/libfftw3.so - not found -- Looking for fftw_have_simd_avx512 in /usr/lib/riscv64-linux-gnu/libfftw3.so -- Looking for fftw_have_simd_avx512 in /usr/lib/riscv64-linux-gnu/libfftw3.so - not found -- Looking for fftw_have_simd_avx_128_fma in /usr/lib/riscv64-linux-gnu/libfftw3.so -- Looking for fftw_have_simd_avx_128_fma in /usr/lib/riscv64-linux-gnu/libfftw3.so - not found -- Looking for fftw_have_simd_avx_512 in /usr/lib/riscv64-linux-gnu/libfftw3.so -- Looking for fftw_have_simd_avx_512 in /usr/lib/riscv64-linux-gnu/libfftw3.so - not found -- Looking for fftw_have_simd_kcvi in /usr/lib/riscv64-linux-gnu/libfftw3.so -- Looking for fftw_have_simd_kcvi in /usr/lib/riscv64-linux-gnu/libfftw3.so - not found -- Looking for fftw_have_simd_altivec in /usr/lib/riscv64-linux-gnu/libfftw3.so -- Looking for fftw_have_simd_altivec in /usr/lib/riscv64-linux-gnu/libfftw3.so - not found -- Looking for fftw_have_simd_neon in /usr/lib/riscv64-linux-gnu/libfftw3.so -- Looking for fftw_have_simd_neon in /usr/lib/riscv64-linux-gnu/libfftw3.so - not found -- Looking for fftw_have_simd_vsx in /usr/lib/riscv64-linux-gnu/libfftw3.so -- Looking for fftw_have_simd_vsx in /usr/lib/riscv64-linux-gnu/libfftw3.so - not found -- Looking for fftw_have_simd_altivec in /usr/lib/riscv64-linux-gnu/libfftw3.so -- Looking for fftw_have_simd_altivec in /usr/lib/riscv64-linux-gnu/libfftw3.so - not found -- Looking for fftw_have_altivec in /usr/lib/riscv64-linux-gnu/libfftw3.so -- Looking for fftw_have_altivec in /usr/lib/riscv64-linux-gnu/libfftw3.so - not found -- Using external FFT library - FFTW3 -- Looking for sgemm_ -- Looking for sgemm_ - not found -- Looking for sgemm_ -- Looking for sgemm_ - found -- Found BLAS: /usr/lib/riscv64-linux-gnu/libblas.so -- Looking for cheev_ -- Looking for cheev_ - not found -- Looking for cheev_ -- Looking for cheev_ - found -- Found LAPACK: /usr/lib/riscv64-linux-gnu/liblapack.so;/usr/lib/riscv64-linux-gnu/libblas.so -- Could not convert sample image, ImageMagick convert can not be used. A possible way to fix it can be found here: https://alexvanderbist.com/2018/fixing-imagick-error-unauthorized -- Performing Test HAS_WARNING_EVERYTHING -- Performing Test HAS_WARNING_EVERYTHING - Failed -- Found Python: /usr/bin/python3 (found version "3.13.2") found components: Interpreter -- Performing Test HAVE_NO_DEPRECATED_COPY -- Performing Test HAVE_NO_DEPRECATED_COPY - Success -- Looking for dlopen -- Looking for dlopen - found -- Performing Test HAS_NO_STRINGOP_TRUNCATION -- Performing Test HAS_NO_STRINGOP_TRUNCATION - Success -- Performing Test HAS_WARNING_NO_CAST_FUNCTION_TYPE_STRICT -- Performing Test HAS_WARNING_NO_CAST_FUNCTION_TYPE_STRICT - Success -- Performing Test HAS_NO_UNUSED -- Performing Test HAS_NO_UNUSED - Success -- Performing Test HAS_NO_UNUSED_PARAMETER -- Performing Test HAS_NO_UNUSED_PARAMETER - Success -- Performing Test HAS_NO_MISSING_DECLARATIONS -- Performing Test HAS_NO_MISSING_DECLARATIONS - Success -- Performing Test HAS_NO_NULL_CONVERSIONS -- Performing Test HAS_NO_NULL_CONVERSIONS - Success -- Looking for inttypes.h -- Looking for inttypes.h - found -- Performing Test COMPILER_HAS_HIDDEN_VISIBILITY -- Performing Test COMPILER_HAS_HIDDEN_VISIBILITY - Success -- Performing Test COMPILER_HAS_HIDDEN_INLINE_VISIBILITY -- Performing Test COMPILER_HAS_HIDDEN_INLINE_VISIBILITY - Success -- Performing Test COMPILER_HAS_DEPRECATED_ATTR -- Performing Test COMPILER_HAS_DEPRECATED_ATTR - Success -- Could NOT find Sphinx (missing: SPHINX_EXECUTABLE pygments) (Required is at least version "4.0.0") -- Could NOT find LATEX (missing: LATEX_COMPILER) -- Configuring done (259.2s) -- Generating done (11.4s) -- Build files have been written to: /build/reproducible-path/gromacs-2025.1/build/basic-dp (mkdir -p build/mpi; cd build/mpi; CC=/usr/bin/mpicc CXX=/usr/bin/mpicxx cmake \ /build/reproducible-path/gromacs-2025.1 -DCMAKE_VERBOSE_MAKEFILE=ON -DCMAKE_RULE_MESSAGES=OFF -DCMAKE_INSTALL_PREFIX="/usr" -DCMAKE_EXE_LINKER_FLAGS="-Wl,-z,relro -Wl,-z,now" -DCMAKE_SKIP_RPATH=ON -DGMX_EXTERNAL_ZLIB=ON -DGMX_USE_MUPARSER=EXTERNAL -DGMX_VERSION_STRING_OF_FORK="Debian-2025.1-1" -DGMX_GIT_VERSION_INFO=OFF -DGMX_HWLOC=ON -DGMX_SIMD=None -DGMX_MPI=ON -DMPIEXEC="/usr/bin/mpiexec" -DGMXAPI=ON -DGMX_PYTHON_PACKAGE=ON) -- The C compiler identification is GNU 14.2.0 -- The CXX compiler identification is GNU 14.2.0 -- Detecting C compiler ABI info -- Detecting C compiler ABI info - done -- Check for working C compiler: /usr/bin/mpicc - skipped -- Detecting C compile features -- Detecting C compile features - done -- Detecting CXX compiler ABI info -- Detecting CXX compiler ABI info - done -- Check for working CXX compiler: /usr/bin/mpicxx - skipped -- Detecting CXX compile features -- Detecting CXX compile features - done -- Found Python3: /usr/bin/python3 (found suitable version "3.13.2", minimum required is "3.9") found components: Interpreter Development Development.Module Development.Embed -- Found OpenMP_C: -fopenmp (found version "4.5") -- Found OpenMP_CXX: -fopenmp (found version "4.5") -- Found OpenMP: TRUE (found version "4.5") -- Performing Test CFLAGS_WARN_NO_MISSING_FIELD_INITIALIZERS -- Performing Test CFLAGS_WARN_NO_MISSING_FIELD_INITIALIZERS - Success -- Performing Test CFLAGS_EXCESS_PREC -- Performing Test CFLAGS_EXCESS_PREC - Success -- Performing Test CFLAGS_COPT -- Performing Test CFLAGS_COPT - Success -- Performing Test CFLAGS_NOINLINE -- Performing Test CFLAGS_NOINLINE - Success -- Performing Test CXXFLAGS_WARN_NO_MISSING_FIELD_INITIALIZERS -- Performing Test CXXFLAGS_WARN_NO_MISSING_FIELD_INITIALIZERS - Success -- Performing Test CXXFLAGS_EXCESS_PREC -- Performing Test CXXFLAGS_EXCESS_PREC - Success -- Performing Test CXXFLAGS_COPT -- Performing Test CXXFLAGS_COPT - Success -- Performing Test CXXFLAGS_NOINLINE -- Performing Test CXXFLAGS_NOINLINE - Success -- Looking for include file unistd.h -- Looking for include file unistd.h - found -- Looking for include file pwd.h -- Looking for include file pwd.h - found -- Looking for include file dirent.h -- Looking for include file dirent.h - found -- Looking for include file time.h -- Looking for include file time.h - found -- Looking for include file sys/time.h -- Looking for include file sys/time.h - found -- Looking for include file io.h -- Looking for include file io.h - not found -- Looking for include file sched.h -- Looking for include file sched.h - found -- Looking for include file xmmintrin.h -- Looking for include file xmmintrin.h - not found -- Looking for gettimeofday -- Looking for gettimeofday - found -- Looking for sysconf -- Looking for sysconf - found -- Looking for nice -- Looking for nice - found -- Looking for fsync -- Looking for fsync - found -- Looking for _fileno -- Looking for _fileno - not found -- Looking for fileno -- Looking for fileno - found -- Looking for _commit -- Looking for _commit - not found -- Looking for sigaction -- Looking for sigaction - found -- Performing Test HAVE_BUILTIN_CLZ -- Performing Test HAVE_BUILTIN_CLZ - Success -- Performing Test HAVE_BUILTIN_CLZLL -- Performing Test HAVE_BUILTIN_CLZLL - Success -- Looking for clock_gettime in rt -- Looking for clock_gettime in rt - found -- Looking for feenableexcept in m -- Looking for feenableexcept in m - found -- Looking for fedisableexcept in m -- Looking for fedisableexcept in m - found -- Checking for sched.h GNU affinity API -- Performing Test sched_affinity_compile -- Performing Test sched_affinity_compile - Success -- Looking for include file mm_malloc.h -- Looking for include file mm_malloc.h - not found -- Looking for include file malloc.h -- Looking for include file malloc.h - found -- Checking for _mm_malloc() -- Checking for _mm_malloc() - not supported -- Looking for posix_memalign -- Looking for posix_memalign - found -- Looking for memalign -- Looking for memalign - not found -- MPI is not compatible with thread-MPI. Disabling thread-MPI. -- Found MPI_CXX: /usr/bin/mpicxx (found version "3.1") -- Found MPI: TRUE (found version "3.1") found components: CXX -- GROMACS library will use OpenMPI 5.0.7 -- Performing Test HAS_WARNING_NO_OLD_STYLE_CAST -- Performing Test HAS_WARNING_NO_OLD_STYLE_CAST - Success -- Performing Test HAS_WARNING_NO_CAST_QUAL -- Performing Test HAS_WARNING_NO_CAST_QUAL - Success -- Performing Test HAS_WARNING_NO_SUGGEST_OVERRIDE -- Performing Test HAS_WARNING_NO_SUGGEST_OVERRIDE - Success -- Performing Test HAS_WARNING_NO_SUGGEST_DESTRUCTOR_OVERRIDE -- Performing Test HAS_WARNING_NO_SUGGEST_DESTRUCTOR_OVERRIDE - Success -- Performing Test HAS_WARNING_NO_ZERO_AS_NULL_POINTER_CONSTANT -- Performing Test HAS_WARNING_NO_ZERO_AS_NULL_POINTER_CONSTANT - Success -- Torch not found. Neural network potential support will be disabled. -- Using default binary suffix: "_mpi" -- Using default library suffix: "_mpi" -- Looking for HWLOC -- Looking for hwloc_topology_init -- Looking for hwloc_topology_init - found -- hwloc version: -- Found HWLOC: /lib/riscv64-linux-gnu/libhwloc.so (found suitable version "2.12.0", minimum required is "1.5") -- Performing Test CMAKE_HAVE_LIBC_PTHREAD -- Performing Test CMAKE_HAVE_LIBC_PTHREAD - Success -- Found Threads: TRUE -- Looking for C++ include pthread.h -- Looking for C++ include pthread.h - found -- Performing Test TEST_ATOMICS -- Performing Test TEST_ATOMICS - Success -- Atomic operations found -- Performing Test PTHREAD_SETAFFINITY -- Performing Test PTHREAD_SETAFFINITY - Success -- Found ZLIB: /usr/lib/riscv64-linux-gnu/libz.so (found version "1.3.1") -- Looking for zlibVersion in /usr/lib/riscv64-linux-gnu/libz.so -- Looking for zlibVersion in /usr/lib/riscv64-linux-gnu/libz.so - found -- SIMD instructions disabled -- Performing Test _callconv___vectorcall -- Performing Test _callconv___vectorcall - Failed -- Performing Test _callconv___regcall -- Performing Test _callconv___regcall - Failed -- Performing Test _callconv_ -- Performing Test _callconv_ - Success -- Checking for GCC x86 inline asm -- Checking for GCC x86 inline asm - not supported -- Detected build CPU vendor - RISC-V 64 -- Detected build CPU brand - Unknown CPU brand -- Detected build CPU family - 0 -- Detected build CPU model - 0 -- Detected build CPU stepping - 0 -- Detected build CPU features - -- Checking for 64-bit off_t -- Checking for 64-bit off_t - present -- Checking for fseeko/ftello -- Checking for fseeko/ftello - present -- Checking for SIGUSR1 -- Checking for SIGUSR1 - found -- Checking for pipe support -- Checking for system XDR support -- Checking for system XDR support - not present -- Checking for module 'fftw3f' -- Found fftw3f, version 3.3.10 -- Looking for fftwf_plan_many_dft in /usr/lib/riscv64-linux-gnu/libfftw3f.so -- Looking for fftwf_plan_many_dft in /usr/lib/riscv64-linux-gnu/libfftw3f.so - found -- Looking for fftwf_plan_many_dft_r2c in /usr/lib/riscv64-linux-gnu/libfftw3f.so -- Looking for fftwf_plan_many_dft_r2c in /usr/lib/riscv64-linux-gnu/libfftw3f.so - found -- Looking for fftwf_plan_many_dft_c2r in /usr/lib/riscv64-linux-gnu/libfftw3f.so -- Looking for fftwf_plan_many_dft_c2r in /usr/lib/riscv64-linux-gnu/libfftw3f.so - found -- Looking for fftwf_have_simd_sse in /usr/lib/riscv64-linux-gnu/libfftw3f.so -- Looking for fftwf_have_simd_sse in /usr/lib/riscv64-linux-gnu/libfftw3f.so - not found -- Looking for fftwf_have_sse in /usr/lib/riscv64-linux-gnu/libfftw3f.so -- Looking for fftwf_have_sse in /usr/lib/riscv64-linux-gnu/libfftw3f.so - not found -- Looking for fftwf_have_simd_sse2 in /usr/lib/riscv64-linux-gnu/libfftw3f.so -- Looking for fftwf_have_simd_sse2 in /usr/lib/riscv64-linux-gnu/libfftw3f.so - not found -- Looking for fftwf_have_sse2 in /usr/lib/riscv64-linux-gnu/libfftw3f.so -- Looking for fftwf_have_sse2 in /usr/lib/riscv64-linux-gnu/libfftw3f.so - not found -- Looking for fftwf_have_simd_avx in /usr/lib/riscv64-linux-gnu/libfftw3f.so -- Looking for fftwf_have_simd_avx in /usr/lib/riscv64-linux-gnu/libfftw3f.so - not found -- Looking for fftwf_have_simd_avx2 in /usr/lib/riscv64-linux-gnu/libfftw3f.so -- Looking for fftwf_have_simd_avx2 in /usr/lib/riscv64-linux-gnu/libfftw3f.so - not found -- Looking for fftwf_have_simd_avx2_128 in /usr/lib/riscv64-linux-gnu/libfftw3f.so -- Looking for fftwf_have_simd_avx2_128 in /usr/lib/riscv64-linux-gnu/libfftw3f.so - not found -- Looking for fftwf_have_simd_avx512 in /usr/lib/riscv64-linux-gnu/libfftw3f.so -- Looking for fftwf_have_simd_avx512 in /usr/lib/riscv64-linux-gnu/libfftw3f.so - not found -- Looking for fftwf_have_simd_avx_128_fma in /usr/lib/riscv64-linux-gnu/libfftw3f.so -- Looking for fftwf_have_simd_avx_128_fma in /usr/lib/riscv64-linux-gnu/libfftw3f.so - not found -- Looking for fftwf_have_simd_avx_512 in /usr/lib/riscv64-linux-gnu/libfftw3f.so -- Looking for fftwf_have_simd_avx_512 in /usr/lib/riscv64-linux-gnu/libfftw3f.so - not found -- Looking for fftwf_have_simd_kcvi in /usr/lib/riscv64-linux-gnu/libfftw3f.so -- Looking for fftwf_have_simd_kcvi in /usr/lib/riscv64-linux-gnu/libfftw3f.so - not found -- Looking for fftwf_have_simd_altivec in /usr/lib/riscv64-linux-gnu/libfftw3f.so -- Looking for fftwf_have_simd_altivec in /usr/lib/riscv64-linux-gnu/libfftw3f.so - not found -- Looking for fftwf_have_simd_neon in /usr/lib/riscv64-linux-gnu/libfftw3f.so -- Looking for fftwf_have_simd_neon in /usr/lib/riscv64-linux-gnu/libfftw3f.so - not found -- Looking for fftwf_have_simd_vsx in /usr/lib/riscv64-linux-gnu/libfftw3f.so -- Looking for fftwf_have_simd_vsx in /usr/lib/riscv64-linux-gnu/libfftw3f.so - not found -- Looking for fftwf_have_simd_altivec in /usr/lib/riscv64-linux-gnu/libfftw3f.so -- Looking for fftwf_have_simd_altivec in /usr/lib/riscv64-linux-gnu/libfftw3f.so - not found -- Looking for fftwf_have_altivec in /usr/lib/riscv64-linux-gnu/libfftw3f.so -- Looking for fftwf_have_altivec in /usr/lib/riscv64-linux-gnu/libfftw3f.so - not found -- Using external FFT library - FFTW3 -- Looking for sgemm_ -- Looking for sgemm_ - not found -- Looking for sgemm_ -- Looking for sgemm_ - found -- Found BLAS: /usr/lib/riscv64-linux-gnu/libblas.so -- Looking for cheev_ -- Looking for cheev_ - not found -- Looking for cheev_ -- Looking for cheev_ - found -- Found LAPACK: /usr/lib/riscv64-linux-gnu/liblapack.so;/usr/lib/riscv64-linux-gnu/libblas.so -- Could not convert sample image, ImageMagick convert can not be used. A possible way to fix it can be found here: https://alexvanderbist.com/2018/fixing-imagick-error-unauthorized -- Performing Test HAS_WARNING_EVERYTHING -- Performing Test HAS_WARNING_EVERYTHING - Failed -- Found Python: /usr/bin/python3 (found version "3.13.2") found components: Interpreter -- Performing Test HAVE_NO_DEPRECATED_COPY -- Performing Test HAVE_NO_DEPRECATED_COPY - Success -- Looking for dlopen -- Looking for dlopen - found -- Performing Test HAS_NO_STRINGOP_TRUNCATION -- Performing Test HAS_NO_STRINGOP_TRUNCATION - Success -- Performing Test HAS_WARNING_NO_CAST_FUNCTION_TYPE_STRICT -- Performing Test HAS_WARNING_NO_CAST_FUNCTION_TYPE_STRICT - Success -- Performing Test HAS_NO_UNUSED -- Performing Test HAS_NO_UNUSED - Success -- Performing Test HAS_NO_UNUSED_PARAMETER -- Performing Test HAS_NO_UNUSED_PARAMETER - Success -- Performing Test HAS_NO_MISSING_DECLARATIONS -- Performing Test HAS_NO_MISSING_DECLARATIONS - Success -- Performing Test HAS_NO_NULL_CONVERSIONS -- Performing Test HAS_NO_NULL_CONVERSIONS - Success -- Looking for inttypes.h -- Looking for inttypes.h - found -- Performing Test COMPILER_HAS_HIDDEN_VISIBILITY -- Performing Test COMPILER_HAS_HIDDEN_VISIBILITY - Success -- Performing Test COMPILER_HAS_HIDDEN_INLINE_VISIBILITY -- Performing Test COMPILER_HAS_HIDDEN_INLINE_VISIBILITY - Success -- Performing Test COMPILER_HAS_DEPRECATED_ATTR -- Performing Test COMPILER_HAS_DEPRECATED_ATTR - Success -- Performing Test HAS_FLTO -- Performing Test HAS_FLTO - Success -- Configuring Python package for gmxapi version 0.4.0 -- Using /build/reproducible-path/gromacs-2025.1/build/mpi/bin/gmx_mpi from build tree. -- Found pybind11: /usr/include (found version "2.13.6") -- Found Python interpreter: /usr/bin/python3 -- Python site-packages directory is /usr/lib/python./site-packages -- Could NOT find Doxygen (missing: DOXYGEN_EXECUTABLE) Doxygen needs to be installed to generate the C++ documentation -- Performing Test HAVE_NO_IMPLICIT_INT_FLOAT_CONVERSION -- Performing Test HAVE_NO_IMPLICIT_INT_FLOAT_CONVERSION - Success -- Could NOT find Sphinx (missing: SPHINX_EXECUTABLE pygments) (Required is at least version "4.0.0") -- Could NOT find LATEX (missing: LATEX_COMPILER) -- Configuring done (300.1s) -- Generating done (14.0s) -- Build files have been written to: /build/reproducible-path/gromacs-2025.1/build/mpi (mkdir -p build/mpi-dp; cd build/mpi-dp; CC=/usr/bin/mpicc CXX=/usr/bin/mpicxx cmake \ /build/reproducible-path/gromacs-2025.1 -DCMAKE_VERBOSE_MAKEFILE=ON -DCMAKE_RULE_MESSAGES=OFF -DCMAKE_INSTALL_PREFIX="/usr" -DCMAKE_EXE_LINKER_FLAGS="-Wl,-z,relro -Wl,-z,now" -DCMAKE_SKIP_RPATH=ON -DGMX_EXTERNAL_ZLIB=ON -DGMX_USE_MUPARSER=EXTERNAL -DGMX_VERSION_STRING_OF_FORK="Debian-2025.1-1" -DGMX_GIT_VERSION_INFO=OFF -DGMX_HWLOC=ON -DGMX_SIMD=None -DGMX_MPI=ON -DMPIEXEC="/usr/bin/mpiexec" -DGMX_DOUBLE=ON) -- The C compiler identification is GNU 14.2.0 -- The CXX compiler identification is GNU 14.2.0 -- Detecting C compiler ABI info -- Detecting C compiler ABI info - done -- Check for working C compiler: /usr/bin/mpicc - skipped -- Detecting C compile features -- Detecting C compile features - done -- Detecting CXX compiler ABI info -- Detecting CXX compiler ABI info - done -- Check for working CXX compiler: /usr/bin/mpicxx - skipped -- Detecting CXX compile features -- Detecting CXX compile features - done -- Found Python3: /usr/bin/python3 (found suitable version "3.13.2", minimum required is "3.9") found components: Interpreter Development Development.Module Development.Embed -- Found OpenMP_C: -fopenmp (found version "4.5") -- Found OpenMP_CXX: -fopenmp (found version "4.5") -- Found OpenMP: TRUE (found version "4.5") -- Performing Test CFLAGS_WARN_NO_MISSING_FIELD_INITIALIZERS -- Performing Test CFLAGS_WARN_NO_MISSING_FIELD_INITIALIZERS - Success -- Performing Test CFLAGS_EXCESS_PREC -- Performing Test CFLAGS_EXCESS_PREC - Success -- Performing Test CFLAGS_COPT -- Performing Test CFLAGS_COPT - Success -- Performing Test CFLAGS_NOINLINE -- Performing Test CFLAGS_NOINLINE - Success -- Performing Test CXXFLAGS_WARN_NO_MISSING_FIELD_INITIALIZERS -- Performing Test CXXFLAGS_WARN_NO_MISSING_FIELD_INITIALIZERS - Success -- Performing Test CXXFLAGS_EXCESS_PREC -- Performing Test CXXFLAGS_EXCESS_PREC - Success -- Performing Test CXXFLAGS_COPT -- Performing Test CXXFLAGS_COPT - Success -- Performing Test CXXFLAGS_NOINLINE -- Performing Test CXXFLAGS_NOINLINE - Success -- Looking for include file unistd.h -- Looking for include file unistd.h - found -- Looking for include file pwd.h -- Looking for include file pwd.h - found -- Looking for include file dirent.h -- Looking for include file dirent.h - found -- Looking for include file time.h -- Looking for include file time.h - found -- Looking for include file sys/time.h -- Looking for include file sys/time.h - found -- Looking for include file io.h -- Looking for include file io.h - not found -- Looking for include file sched.h -- Looking for include file sched.h - found -- Looking for include file xmmintrin.h -- Looking for include file xmmintrin.h - not found -- Looking for gettimeofday -- Looking for gettimeofday - found -- Looking for sysconf -- Looking for sysconf - found -- Looking for nice -- Looking for nice - found -- Looking for fsync -- Looking for fsync - found -- Looking for _fileno -- Looking for _fileno - not found -- Looking for fileno -- Looking for fileno - found -- Looking for _commit -- Looking for _commit - not found -- Looking for sigaction -- Looking for sigaction - found -- Performing Test HAVE_BUILTIN_CLZ -- Performing Test HAVE_BUILTIN_CLZ - Success -- Performing Test HAVE_BUILTIN_CLZLL -- Performing Test HAVE_BUILTIN_CLZLL - Success -- Looking for clock_gettime in rt -- Looking for clock_gettime in rt - found -- Looking for feenableexcept in m -- Looking for feenableexcept in m - found -- Looking for fedisableexcept in m -- Looking for fedisableexcept in m - found -- Checking for sched.h GNU affinity API -- Performing Test sched_affinity_compile -- Performing Test sched_affinity_compile - Success -- Looking for include file mm_malloc.h -- Looking for include file mm_malloc.h - not found -- Looking for include file malloc.h -- Looking for include file malloc.h - found -- Checking for _mm_malloc() -- Checking for _mm_malloc() - not supported -- Looking for posix_memalign -- Looking for posix_memalign - found -- Looking for memalign -- Looking for memalign - not found -- MPI is not compatible with thread-MPI. Disabling thread-MPI. -- Found MPI_CXX: /usr/bin/mpicxx (found version "3.1") -- Found MPI: TRUE (found version "3.1") found components: CXX -- GROMACS library will use OpenMPI 5.0.7 -- Performing Test HAS_WARNING_NO_OLD_STYLE_CAST -- Performing Test HAS_WARNING_NO_OLD_STYLE_CAST - Success -- Performing Test HAS_WARNING_NO_CAST_QUAL -- Performing Test HAS_WARNING_NO_CAST_QUAL - Success -- Performing Test HAS_WARNING_NO_SUGGEST_OVERRIDE -- Performing Test HAS_WARNING_NO_SUGGEST_OVERRIDE - Success -- Performing Test HAS_WARNING_NO_SUGGEST_DESTRUCTOR_OVERRIDE -- Performing Test HAS_WARNING_NO_SUGGEST_DESTRUCTOR_OVERRIDE - Success -- Performing Test HAS_WARNING_NO_ZERO_AS_NULL_POINTER_CONSTANT -- Performing Test HAS_WARNING_NO_ZERO_AS_NULL_POINTER_CONSTANT - Success -- Torch not found. Neural network potential support will be disabled. -- Using default binary suffix: "_mpi_d" -- Using default library suffix: "_mpi_d" -- Looking for HWLOC -- Looking for hwloc_topology_init -- Looking for hwloc_topology_init - found -- hwloc version: -- Found HWLOC: /lib/riscv64-linux-gnu/libhwloc.so (found suitable version "2.12.0", minimum required is "1.5") -- Performing Test CMAKE_HAVE_LIBC_PTHREAD -- Performing Test CMAKE_HAVE_LIBC_PTHREAD - Success -- Found Threads: TRUE -- Looking for C++ include pthread.h -- Looking for C++ include pthread.h - found -- Performing Test TEST_ATOMICS -- Performing Test TEST_ATOMICS - Success -- Atomic operations found -- Performing Test PTHREAD_SETAFFINITY -- Performing Test PTHREAD_SETAFFINITY - Success -- Found ZLIB: /usr/lib/riscv64-linux-gnu/libz.so (found version "1.3.1") -- Looking for zlibVersion in /usr/lib/riscv64-linux-gnu/libz.so -- Looking for zlibVersion in /usr/lib/riscv64-linux-gnu/libz.so - found -- SIMD instructions disabled -- Performing Test _callconv___vectorcall -- Performing Test _callconv___vectorcall - Failed -- Performing Test _callconv___regcall -- Performing Test _callconv___regcall - Failed -- Performing Test _callconv_ -- Performing Test _callconv_ - Success -- Checking for GCC x86 inline asm -- Checking for GCC x86 inline asm - not supported -- Detected build CPU vendor - RISC-V 64 -- Detected build CPU brand - Unknown CPU brand -- Detected build CPU family - 0 -- Detected build CPU model - 0 -- Detected build CPU stepping - 0 -- Detected build CPU features - -- Checking for 64-bit off_t -- Checking for 64-bit off_t - present -- Checking for fseeko/ftello -- Checking for fseeko/ftello - present -- Checking for SIGUSR1 -- Checking for SIGUSR1 - found -- Checking for pipe support -- Checking for system XDR support -- Checking for system XDR support - not present -- Checking for module 'fftw3' -- Found fftw3, version 3.3.10 -- Looking for fftw_plan_many_dft in /usr/lib/riscv64-linux-gnu/libfftw3.so -- Looking for fftw_plan_many_dft in /usr/lib/riscv64-linux-gnu/libfftw3.so - found -- Looking for fftw_plan_many_dft_r2c in /usr/lib/riscv64-linux-gnu/libfftw3.so -- Looking for fftw_plan_many_dft_r2c in /usr/lib/riscv64-linux-gnu/libfftw3.so - found -- Looking for fftw_plan_many_dft_c2r in /usr/lib/riscv64-linux-gnu/libfftw3.so -- Looking for fftw_plan_many_dft_c2r in /usr/lib/riscv64-linux-gnu/libfftw3.so - found -- Looking for fftw_have_simd_sse in /usr/lib/riscv64-linux-gnu/libfftw3.so -- Looking for fftw_have_simd_sse in /usr/lib/riscv64-linux-gnu/libfftw3.so - not found -- Looking for fftw_have_sse in /usr/lib/riscv64-linux-gnu/libfftw3.so -- Looking for fftw_have_sse in /usr/lib/riscv64-linux-gnu/libfftw3.so - not found -- Looking for fftw_have_simd_sse2 in /usr/lib/riscv64-linux-gnu/libfftw3.so -- Looking for fftw_have_simd_sse2 in /usr/lib/riscv64-linux-gnu/libfftw3.so - not found -- Looking for fftw_have_sse2 in /usr/lib/riscv64-linux-gnu/libfftw3.so -- Looking for fftw_have_sse2 in /usr/lib/riscv64-linux-gnu/libfftw3.so - not found -- Looking for fftw_have_simd_avx in /usr/lib/riscv64-linux-gnu/libfftw3.so -- Looking for fftw_have_simd_avx in /usr/lib/riscv64-linux-gnu/libfftw3.so - not found -- Looking for fftw_have_simd_avx2 in /usr/lib/riscv64-linux-gnu/libfftw3.so -- Looking for fftw_have_simd_avx2 in /usr/lib/riscv64-linux-gnu/libfftw3.so - not found -- Looking for fftw_have_simd_avx2_128 in /usr/lib/riscv64-linux-gnu/libfftw3.so -- Looking for fftw_have_simd_avx2_128 in /usr/lib/riscv64-linux-gnu/libfftw3.so - not found -- Looking for fftw_have_simd_avx512 in /usr/lib/riscv64-linux-gnu/libfftw3.so -- Looking for fftw_have_simd_avx512 in /usr/lib/riscv64-linux-gnu/libfftw3.so - not found -- Looking for fftw_have_simd_avx_128_fma in /usr/lib/riscv64-linux-gnu/libfftw3.so -- Looking for fftw_have_simd_avx_128_fma in /usr/lib/riscv64-linux-gnu/libfftw3.so - not found -- Looking for fftw_have_simd_avx_512 in /usr/lib/riscv64-linux-gnu/libfftw3.so -- Looking for fftw_have_simd_avx_512 in /usr/lib/riscv64-linux-gnu/libfftw3.so - not found -- Looking for fftw_have_simd_kcvi in /usr/lib/riscv64-linux-gnu/libfftw3.so -- Looking for fftw_have_simd_kcvi in /usr/lib/riscv64-linux-gnu/libfftw3.so - not found -- Looking for fftw_have_simd_altivec in /usr/lib/riscv64-linux-gnu/libfftw3.so -- Looking for fftw_have_simd_altivec in /usr/lib/riscv64-linux-gnu/libfftw3.so - not found -- Looking for fftw_have_simd_neon in /usr/lib/riscv64-linux-gnu/libfftw3.so -- Looking for fftw_have_simd_neon in /usr/lib/riscv64-linux-gnu/libfftw3.so - not found -- Looking for fftw_have_simd_vsx in /usr/lib/riscv64-linux-gnu/libfftw3.so -- Looking for fftw_have_simd_vsx in /usr/lib/riscv64-linux-gnu/libfftw3.so - not found -- Looking for fftw_have_simd_altivec in /usr/lib/riscv64-linux-gnu/libfftw3.so -- Looking for fftw_have_simd_altivec in /usr/lib/riscv64-linux-gnu/libfftw3.so - not found -- Looking for fftw_have_altivec in /usr/lib/riscv64-linux-gnu/libfftw3.so -- Looking for fftw_have_altivec in /usr/lib/riscv64-linux-gnu/libfftw3.so - not found -- Using external FFT library - FFTW3 -- Looking for sgemm_ -- Looking for sgemm_ - not found -- Looking for sgemm_ -- Looking for sgemm_ - found -- Found BLAS: /usr/lib/riscv64-linux-gnu/libblas.so -- Looking for cheev_ -- Looking for cheev_ - not found -- Looking for cheev_ -- Looking for cheev_ - found -- Found LAPACK: /usr/lib/riscv64-linux-gnu/liblapack.so;/usr/lib/riscv64-linux-gnu/libblas.so -- Could not convert sample image, ImageMagick convert can not be used. A possible way to fix it can be found here: https://alexvanderbist.com/2018/fixing-imagick-error-unauthorized -- Performing Test HAS_WARNING_EVERYTHING -- Performing Test HAS_WARNING_EVERYTHING - Failed -- Found Python: /usr/bin/python3 (found version "3.13.2") found components: Interpreter -- Performing Test HAVE_NO_DEPRECATED_COPY -- Performing Test HAVE_NO_DEPRECATED_COPY - Success -- Looking for dlopen -- Looking for dlopen - found -- Performing Test HAS_NO_STRINGOP_TRUNCATION -- Performing Test HAS_NO_STRINGOP_TRUNCATION - Success -- Performing Test HAS_WARNING_NO_CAST_FUNCTION_TYPE_STRICT -- Performing Test HAS_WARNING_NO_CAST_FUNCTION_TYPE_STRICT - Success -- Performing Test HAS_NO_UNUSED -- Performing Test HAS_NO_UNUSED - Success -- Performing Test HAS_NO_UNUSED_PARAMETER -- Performing Test HAS_NO_UNUSED_PARAMETER - Success -- Performing Test HAS_NO_MISSING_DECLARATIONS -- Performing Test HAS_NO_MISSING_DECLARATIONS - Success -- Performing Test HAS_NO_NULL_CONVERSIONS -- Performing Test HAS_NO_NULL_CONVERSIONS - Success -- Looking for inttypes.h -- Looking for inttypes.h - found -- Performing Test COMPILER_HAS_HIDDEN_VISIBILITY -- Performing Test COMPILER_HAS_HIDDEN_VISIBILITY - Success -- Performing Test COMPILER_HAS_HIDDEN_INLINE_VISIBILITY -- Performing Test COMPILER_HAS_HIDDEN_INLINE_VISIBILITY - Success -- Performing Test COMPILER_HAS_DEPRECATED_ATTR -- Performing Test COMPILER_HAS_DEPRECATED_ATTR - Success -- Could NOT find Sphinx (missing: SPHINX_EXECUTABLE pygments) (Required is at least version "4.0.0") -- Could NOT find LATEX (missing: LATEX_COMPILER) -- Configuring done (290.7s) -- Generating done (12.7s) -- Build files have been written to: /build/reproducible-path/gromacs-2025.1/build/mpi-dp touch configure-stamp dh_testdir /usr/bin/make -j4 -C build/basic make[1]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/basic' /usr/bin/cmake -S/build/reproducible-path/gromacs-2025.1 -B/build/reproducible-path/gromacs-2025.1/build/basic --check-build-system CMakeFiles/Makefile.cmake 0 /usr/bin/cmake -E cmake_progress_start /build/reproducible-path/gromacs-2025.1/build/basic/CMakeFiles /build/reproducible-path/gromacs-2025.1/build/basic//CMakeFiles/progress.marks /usr/bin/make -f CMakeFiles/Makefile2 all make[2]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/basic' /usr/bin/make -f src/gromacs/selection/CMakeFiles/scanner.dir/build.make src/gromacs/selection/CMakeFiles/scanner.dir/depend /usr/bin/make -f CMakeFiles/release-version-info.dir/build.make CMakeFiles/release-version-info.dir/depend /usr/bin/make -f src/external/rpc_xdr/CMakeFiles/internal_rpc_xdr.dir/build.make src/external/rpc_xdr/CMakeFiles/internal_rpc_xdr.dir/depend make[3]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/basic' cd /build/reproducible-path/gromacs-2025.1/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.1 /build/reproducible-path/gromacs-2025.1/src/gromacs/selection /build/reproducible-path/gromacs-2025.1/build/basic /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/selection /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/selection/CMakeFiles/scanner.dir/DependInfo.cmake "--color=" /usr/bin/make -f src/gromacs/CMakeFiles/thread_mpi.dir/build.make src/gromacs/CMakeFiles/thread_mpi.dir/depend make[3]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/basic' make[3]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/basic' cd /build/reproducible-path/gromacs-2025.1/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.1 /build/reproducible-path/gromacs-2025.1/src/external/rpc_xdr /build/reproducible-path/gromacs-2025.1/build/basic /build/reproducible-path/gromacs-2025.1/build/basic/src/external/rpc_xdr /build/reproducible-path/gromacs-2025.1/build/basic/src/external/rpc_xdr/CMakeFiles/internal_rpc_xdr.dir/DependInfo.cmake "--color=" cd /build/reproducible-path/gromacs-2025.1/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.1 /build/reproducible-path/gromacs-2025.1 /build/reproducible-path/gromacs-2025.1/build/basic /build/reproducible-path/gromacs-2025.1/build/basic /build/reproducible-path/gromacs-2025.1/build/basic/CMakeFiles/release-version-info.dir/DependInfo.cmake "--color=" make[3]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/basic' cd /build/reproducible-path/gromacs-2025.1/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.1 /build/reproducible-path/gromacs-2025.1/src/gromacs /build/reproducible-path/gromacs-2025.1/build/basic /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/CMakeFiles/thread_mpi.dir/DependInfo.cmake "--color=" make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/basic' /usr/bin/make -f CMakeFiles/release-version-info.dir/build.make CMakeFiles/release-version-info.dir/build make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/basic' make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/basic' /usr/bin/make -f src/external/rpc_xdr/CMakeFiles/internal_rpc_xdr.dir/build.make src/external/rpc_xdr/CMakeFiles/internal_rpc_xdr.dir/build /usr/bin/make -f src/gromacs/selection/CMakeFiles/scanner.dir/build.make src/gromacs/selection/CMakeFiles/scanner.dir/build make[3]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/basic' cd /build/reproducible-path/gromacs-2025.1 && /usr/bin/cmake -D PYTHON_EXECUTABLE=/usr/bin/python3 -D PROJECT_VERSION=2025.1-Debian_2025.1_1 -D PROJECT_SOURCE_DIR=/build/reproducible-path/gromacs-2025.1 -D VERSION_CMAKEIN=/build/reproducible-path/gromacs-2025.1/build/basic/VersionInfo-partial.cmake.cmakein -D VERSION_OUT=/build/reproducible-path/gromacs-2025.1/build/basic/VersionInfo.cmake -D VERSION_STRING_OF_FORK=Debian-2025.1-1 -P /build/reproducible-path/gromacs-2025.1/cmake/gmxGenerateVersionInfoWithoutGit.cmake make[3]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/basic' cd /build/reproducible-path/gromacs-2025.1/build/basic/src/external/rpc_xdr && /usr/bin/c++ -DGMX_DOUBLE=0 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -MD -MT src/external/rpc_xdr/CMakeFiles/internal_rpc_xdr.dir/xdr.cpp.o -MF CMakeFiles/internal_rpc_xdr.dir/xdr.cpp.o.d -o CMakeFiles/internal_rpc_xdr.dir/xdr.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/external/rpc_xdr/xdr.cpp make[3]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/basic' cd /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/selection && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic/src/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -Wno-null-conversion -MD -MT src/gromacs/selection/CMakeFiles/scanner.dir/parser.cpp.o -MF CMakeFiles/scanner.dir/parser.cpp.o.d -o CMakeFiles/scanner.dir/parser.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/selection/parser.cpp make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/basic' /usr/bin/make -f src/gromacs/CMakeFiles/thread_mpi.dir/build.make src/gromacs/CMakeFiles/thread_mpi.dir/build make[3]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/basic' cd /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic/src/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -MD -MT src/gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/errhandler.cpp.o -MF CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/errhandler.cpp.o.d -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/errhandler.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/src/errhandler.cpp make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/basic' [ 0%] Built target release-version-info /usr/bin/make -f src/gromacs/CMakeFiles/tng_io_obj.dir/build.make src/gromacs/CMakeFiles/tng_io_obj.dir/depend make[3]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/basic' cd /build/reproducible-path/gromacs-2025.1/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.1 /build/reproducible-path/gromacs-2025.1/src/gromacs /build/reproducible-path/gromacs-2025.1/build/basic /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/CMakeFiles/tng_io_obj.dir/DependInfo.cmake "--color=" make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/basic' /usr/bin/make -f src/gromacs/CMakeFiles/tng_io_obj.dir/build.make src/gromacs/CMakeFiles/tng_io_obj.dir/build make[3]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/basic' cd /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs && /usr/bin/cc -DGMX_DOUBLE=0 -I/build/reproducible-path/gromacs-2025.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.1/build/basic/tng/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -MD -MT src/gromacs/CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/bwlzh.c.o -MF CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/bwlzh.c.o.d -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/bwlzh.c.o -c /build/reproducible-path/gromacs-2025.1/src/external/tng_io/src/compression/bwlzh.c cd /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic/src/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -MD -MT 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/build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic/src/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -MD -MT src/gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/p2p_wait.cpp.o -MF CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/p2p_wait.cpp.o.d -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/p2p_wait.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/src/p2p_wait.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs && 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/build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -MD -MT src/gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/numa_malloc.cpp.o -MF CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/numa_malloc.cpp.o.d -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/numa_malloc.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/src/numa_malloc.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic/src/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -MD -MT src/gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/once.cpp.o -MF CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/once.cpp.o.d -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/once.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/src/once.cpp make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/basic' [ 1%] Built target thread_mpi /usr/bin/make -f src/gromacs/linearalgebra/CMakeFiles/linearalgebra.dir/build.make src/gromacs/linearalgebra/CMakeFiles/linearalgebra.dir/depend make[3]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/basic' cd 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-ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -Wno-null-conversion -MD -MT src/gromacs/selection/CMakeFiles/scanner.dir/scanner.cpp.o -MF CMakeFiles/scanner.dir/scanner.cpp.o.d -o CMakeFiles/scanner.dir/scanner.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/selection/scanner.cpp make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/basic' [ 1%] Built target scanner /usr/bin/make -f src/gromacs/options/CMakeFiles/options.dir/build.make src/gromacs/options/CMakeFiles/options.dir/depend make[3]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/basic' cd /build/reproducible-path/gromacs-2025.1/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.1 /build/reproducible-path/gromacs-2025.1/src/gromacs/options /build/reproducible-path/gromacs-2025.1/build/basic /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/options /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/options/CMakeFiles/options.dir/DependInfo.cmake "--color=" make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/basic' /usr/bin/make -f src/gromacs/options/CMakeFiles/options.dir/build.make src/gromacs/options/CMakeFiles/options.dir/build make[3]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/basic' cd /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/options && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic/src/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -MD -MT src/gromacs/options/CMakeFiles/options.dir/abstractoption.cpp.o -MF CMakeFiles/options.dir/abstractoption.cpp.o.d -o CMakeFiles/options.dir/abstractoption.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/options/abstractoption.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs && /usr/bin/cc -DGMX_DOUBLE=0 -DUSE_STD_INTTYPES_H -I/build/reproducible-path/gromacs-2025.1/src/external/tng_io/include 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-I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic/src/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -MD -MT src/gromacs/options/CMakeFiles/options.dir/abstractsection.cpp.o -MF CMakeFiles/options.dir/abstractsection.cpp.o.d -o CMakeFiles/options.dir/abstractsection.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/options/abstractsection.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/linearalgebra && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY 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-o CMakeFiles/linearalgebra.dir/matrix.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/linearalgebra/matrix.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/options && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic/src/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -MD -MT src/gromacs/options/CMakeFiles/options.dir/basicoptions.cpp.o -MF CMakeFiles/options.dir/basicoptions.cpp.o.d -o CMakeFiles/options.dir/basicoptions.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/options/basicoptions.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/linearalgebra && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/linearalgebra -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-stringop-truncation -MD -MT src/gromacs/linearalgebra/CMakeFiles/linearalgebra.dir/sparsematrix.cpp.o -MF CMakeFiles/linearalgebra.dir/sparsematrix.cpp.o.d -o CMakeFiles/linearalgebra.dir/sparsematrix.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/linearalgebra/sparsematrix.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fopenmp -MD -MT src/gromacs/CMakeFiles/colvars_objlib.dir/__/external/colvars/colvar_neuralnetworkcompute.cpp.o -MF 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/build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fopenmp -MD -MT src/gromacs/CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarbias.cpp.o -MF CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarbias.cpp.o.d -o CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarbias.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/external/colvars/colvarbias.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fopenmp -MD -MT src/gromacs/CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarbias_abf.cpp.o -MF CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarbias_abf.cpp.o.d -o CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarbias_abf.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/external/colvars/colvarbias_abf.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs && /usr/bin/cc -DGMX_DOUBLE=0 -I/build/reproducible-path/gromacs-2025.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.1/build/basic/tng/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -MD -MT src/gromacs/CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/lib/md5.c.o -MF CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/lib/md5.c.o.d -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/lib/md5.c.o -c /build/reproducible-path/gromacs-2025.1/src/external/tng_io/src/lib/md5.c make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/basic' [ 3%] Built target tng_io_obj /usr/bin/make -f src/gromacs/energyanalysis/CMakeFiles/energyanalysis.dir/build.make src/gromacs/energyanalysis/CMakeFiles/energyanalysis.dir/depend make[3]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/basic' cd /build/reproducible-path/gromacs-2025.1/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.1 /build/reproducible-path/gromacs-2025.1/src/gromacs/energyanalysis /build/reproducible-path/gromacs-2025.1/build/basic /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/energyanalysis /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/energyanalysis/CMakeFiles/energyanalysis.dir/DependInfo.cmake "--color=" make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/basic' /usr/bin/make -f 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-Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -MD -MT src/gromacs/energyanalysis/CMakeFiles/energyanalysis.dir/energyterm.cpp.o -MF CMakeFiles/energyanalysis.dir/energyterm.cpp.o.d -o CMakeFiles/energyanalysis.dir/energyterm.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/energyanalysis/energyterm.cpp make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/basic' [ 3%] Built target energyanalysis /usr/bin/make -f src/programs/CMakeFiles/mdrun_objlib.dir/build.make src/programs/CMakeFiles/mdrun_objlib.dir/depend make[3]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/basic' cd /build/reproducible-path/gromacs-2025.1/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.1 /build/reproducible-path/gromacs-2025.1/src/programs /build/reproducible-path/gromacs-2025.1/build/basic /build/reproducible-path/gromacs-2025.1/build/basic/src/programs /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/CMakeFiles/mdrun_objlib.dir/DependInfo.cmake "--color=" make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/basic' /usr/bin/make -f src/programs/CMakeFiles/mdrun_objlib.dir/build.make src/programs/CMakeFiles/mdrun_objlib.dir/build make[3]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/basic' cd /build/reproducible-path/gromacs-2025.1/build/basic/src/programs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic/src/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src 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-fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -MD -MT src/gromacs/options/CMakeFiles/options.dir/behaviorcollection.cpp.o -MF CMakeFiles/options.dir/behaviorcollection.cpp.o.d -o CMakeFiles/options.dir/behaviorcollection.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/options/behaviorcollection.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/options && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic/src/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -MD -MT src/gromacs/options/CMakeFiles/options.dir/filenameoption.cpp.o -MF CMakeFiles/options.dir/filenameoption.cpp.o.d -o CMakeFiles/options.dir/filenameoption.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/options/filenameoption.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fopenmp -MD -MT src/gromacs/CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarbias_alb.cpp.o -MF 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-Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -MD -MT src/programs/CMakeFiles/mdrun_objlib.dir/mdrun/nonbonded_bench.cpp.o -MF CMakeFiles/mdrun_objlib.dir/mdrun/nonbonded_bench.cpp.o.d -o CMakeFiles/mdrun_objlib.dir/mdrun/nonbonded_bench.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/programs/mdrun/nonbonded_bench.cpp make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/basic' [ 3%] Built target mdrun_objlib /usr/bin/make -f src/programs/CMakeFiles/gmx_objlib.dir/build.make src/programs/CMakeFiles/gmx_objlib.dir/depend make[3]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/basic' cd /build/reproducible-path/gromacs-2025.1/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.1 /build/reproducible-path/gromacs-2025.1/src/programs /build/reproducible-path/gromacs-2025.1/build/basic /build/reproducible-path/gromacs-2025.1/build/basic/src/programs /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/CMakeFiles/gmx_objlib.dir/DependInfo.cmake "--color=" make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/basic' /usr/bin/make -f src/programs/CMakeFiles/gmx_objlib.dir/build.make src/programs/CMakeFiles/gmx_objlib.dir/build make[3]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/basic' cd /build/reproducible-path/gromacs-2025.1/build/basic/src/programs && /usr/bin/c++ -DGMX_DOUBLE=0 -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic/src/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -MD -MT src/programs/CMakeFiles/gmx_objlib.dir/gmx.cpp.o -MF CMakeFiles/gmx_objlib.dir/gmx.cpp.o.d -o CMakeFiles/gmx_objlib.dir/gmx.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/programs/gmx.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/options && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic/src/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -MD -MT src/gromacs/options/CMakeFiles/options.dir/filenameoptionmanager.cpp.o -MF CMakeFiles/options.dir/filenameoptionmanager.cpp.o.d -o CMakeFiles/options.dir/filenameoptionmanager.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/options/filenameoptionmanager.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic/src/programs && /usr/bin/c++ -DGMX_DOUBLE=0 -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic/src/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include 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-D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fopenmp -MD -MT src/gromacs/CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarbias_histogram.cpp.o -MF CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarbias_histogram.cpp.o.d -o CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarbias_histogram.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/external/colvars/colvarbias_histogram.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/options && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic/src/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -MD -MT src/gromacs/options/CMakeFiles/options.dir/options.cpp.o -MF CMakeFiles/options.dir/options.cpp.o.d -o CMakeFiles/options.dir/options.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/options/options.cpp make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/basic' [ 3%] Built target gmx_objlib /usr/bin/make -f src/gromacs/pulling/CMakeFiles/pulling.dir/build.make src/gromacs/pulling/CMakeFiles/pulling.dir/depend make[3]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/basic' cd /build/reproducible-path/gromacs-2025.1/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.1 /build/reproducible-path/gromacs-2025.1/src/gromacs/pulling /build/reproducible-path/gromacs-2025.1/build/basic /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/pulling /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/pulling/CMakeFiles/pulling.dir/DependInfo.cmake "--color=" make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/basic' /usr/bin/make -f src/gromacs/pulling/CMakeFiles/pulling.dir/build.make src/gromacs/pulling/CMakeFiles/pulling.dir/build make[3]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/basic' cd /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/pulling && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/pulling/CMakeFiles/pulling.dir/output.cpp.o -MF CMakeFiles/pulling.dir/output.cpp.o.d -o CMakeFiles/pulling.dir/output.cpp.o -c 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/build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fopenmp -MD -MT src/gromacs/CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarbias_meta.cpp.o -MF CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarbias_meta.cpp.o.d -o CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarbias_meta.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/external/colvars/colvarbias_meta.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/options && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic/src/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -MD -MT src/gromacs/options/CMakeFiles/options.dir/optionsvisitor.cpp.o -MF CMakeFiles/options.dir/optionsvisitor.cpp.o.d -o CMakeFiles/options.dir/optionsvisitor.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/options/optionsvisitor.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/pulling && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pulling/include 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-MD -MT src/gromacs/pulling/CMakeFiles/pulling.dir/pull.cpp.o -MF CMakeFiles/pulling.dir/pull.cpp.o.d -o CMakeFiles/pulling.dir/pull.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/pulling/pull.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/options && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic/src/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -MD -MT src/gromacs/options/CMakeFiles/options.dir/timeunitmanager.cpp.o -MF CMakeFiles/options.dir/timeunitmanager.cpp.o.d -o CMakeFiles/options.dir/timeunitmanager.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/options/timeunitmanager.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/options && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic/src/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -MD -MT src/gromacs/options/CMakeFiles/options.dir/treesupport.cpp.o -MF CMakeFiles/options.dir/treesupport.cpp.o.d -o CMakeFiles/options.dir/treesupport.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/options/treesupport.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fopenmp -MD -MT src/gromacs/CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarbias_opes.cpp.o -MF CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarbias_opes.cpp.o.d -o CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarbias_opes.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/external/colvars/colvarbias_opes.cpp make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/basic' [ 5%] Built target options cd /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/pulling && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/linearalgebra/include 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-I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/pulling/CMakeFiles/pulling.dir/transformationcoordinate.cpp.o -MF CMakeFiles/pulling.dir/transformationcoordinate.cpp.o.d -o CMakeFiles/pulling.dir/transformationcoordinate.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/pulling/transformationcoordinate.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fopenmp -MD -MT src/gromacs/CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarcomp.cpp.o -MF CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarcomp.cpp.o.d -o CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarcomp.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/external/colvars/colvarcomp.cpp make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/basic' [ 5%] Built target pulling /usr/bin/make -f src/gromacs/taskassignment/CMakeFiles/taskassignment.dir/build.make src/gromacs/taskassignment/CMakeFiles/taskassignment.dir/depend make[3]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/basic' cd /build/reproducible-path/gromacs-2025.1/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" 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&& /usr/bin/c++ -DGMX_DOUBLE=0 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fopenmp -MD -MT src/gromacs/CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarcomp_angles.cpp.o -MF CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarcomp_angles.cpp.o.d -o CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarcomp_angles.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/external/colvars/colvarcomp_angles.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/taskassignment && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic/src/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include 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-MD -MT src/gromacs/taskassignment/CMakeFiles/taskassignment.dir/taskassignment.cpp.o -MF CMakeFiles/taskassignment.dir/taskassignment.cpp.o.d -o CMakeFiles/taskassignment.dir/taskassignment.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/taskassignment/taskassignment.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/taskassignment && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic/src/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -MD -MT src/gromacs/taskassignment/CMakeFiles/taskassignment.dir/usergpuids.cpp.o -MF CMakeFiles/taskassignment.dir/usergpuids.cpp.o.d -o CMakeFiles/taskassignment.dir/usergpuids.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/taskassignment/usergpuids.cpp /usr/bin/make -f src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/build.make 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/build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/modularsimulator && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -I/build/reproducible-path/gromacs-2025.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.1/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic/src/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -Wno-missing-field-initializers -MD -MT src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/andersentemperaturecoupling.cpp.o -MF CMakeFiles/modularsimulator.dir/andersentemperaturecoupling.cpp.o.d -o CMakeFiles/modularsimulator.dir/andersentemperaturecoupling.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/modularsimulator/andersentemperaturecoupling.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fopenmp -MD -MT src/gromacs/CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarcomp_gpath.cpp.o -MF CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarcomp_gpath.cpp.o.d -o CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarcomp_gpath.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/external/colvars/colvarcomp_gpath.cpp make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/basic' [ 5%] Built target taskassignment cd /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/modularsimulator && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -I/build/reproducible-path/gromacs-2025.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.1/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.1/src/include 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-fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -Wno-missing-field-initializers -MD -MT src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/constraintelement.cpp.o -MF CMakeFiles/modularsimulator.dir/constraintelement.cpp.o.d -o CMakeFiles/modularsimulator.dir/constraintelement.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/modularsimulator/constraintelement.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fopenmp -MD -MT src/gromacs/CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarcomp_protein.cpp.o -MF CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarcomp_protein.cpp.o.d -o 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-I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.1/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/simd/include 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-I/build/reproducible-path/gromacs-2025.1/build/basic/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.1/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/simd/include 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-I/build/reproducible-path/gromacs-2025.1/build/basic/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.1/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/simd/include 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-I/build/reproducible-path/gromacs-2025.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.1/src/external/plumed 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-I/build/reproducible-path/gromacs-2025.1/build/basic/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.1/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/simd/include 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-I/build/reproducible-path/gromacs-2025.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.1/src/external/plumed 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-I/build/reproducible-path/gromacs-2025.1/build/basic/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.1/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/simd/include 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-g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombGeom_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombGeom_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombGeom_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombGeom_VgrpF.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.1/src/include 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-I/build/reproducible-path/gromacs-2025.1/build/basic/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.1/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombLB_VgrpF.cpp.o -MF 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-I/build/reproducible-path/gromacs-2025.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJEwCombGeom_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJEwCombGeom_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJEwCombGeom_F.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJEwCombGeom_F.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.1/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/simd/include 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-g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJEwCombGeom_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJEwCombGeom_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJEwCombGeom_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJEwCombGeom_VgrpF.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.1/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJFSw_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJFSw_F.cpp.o.d -o 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-I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJFSw_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJFSw_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJFSw_VF.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJFSw_VF.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic/src/include -I/build/reproducible-path/gromacs-2025.1/src 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/build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJFSw_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJFSw_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJFSw_VgrpF.cpp.o -c 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-I/build/reproducible-path/gromacs-2025.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJPSw_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJPSw_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJPSw_F.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJPSw_F.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.1/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJPSw_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJPSw_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJPSw_VF.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJPSw_VF.cpp cd 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-I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers 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-I/build/reproducible-path/gromacs-2025.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/gromacs/../external/rpc_xdr -isystem 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-I/build/reproducible-path/gromacs-2025.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJ_VF.cpp.o -MF 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-I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.1/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/taskassignment/include -isystem 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-I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. 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-I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.1/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/taskassignment/include -isystem 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-I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.1/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/taskassignment/include -isystem 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-I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.1/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/taskassignment/include -isystem 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-I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. 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-I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.1/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/taskassignment/include -isystem 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-I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJ_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJ_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJ_F.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJ_F.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.1/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJ_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJ_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJ_VF.cpp.o -c 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-I/build/reproducible-path/gromacs-2025.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJ_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJ_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJ_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJ_VgrpF.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.1/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombGeom_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombGeom_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombGeom_F.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombGeom_F.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.1/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombGeom_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombGeom_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombGeom_VF.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombGeom_VF.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.1/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombGeom_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombGeom_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombGeom_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombGeom_VgrpF.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.1/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombLB_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombLB_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombLB_F.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombLB_F.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.1/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombLB_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombLB_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombLB_VF.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombLB_VF.cpp cd 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-I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers 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src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJEwCombGeom_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJEwCombGeom_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJEwCombGeom_VF.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJEwCombGeom_VF.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.1/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/gromacs/../external/rpc_xdr -isystem 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&& /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.1/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include 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src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJFSw_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJFSw_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJFSw_F.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJFSw_F.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.1/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include 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/build/reproducible-path/gromacs-2025.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJFSw_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJFSw_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJFSw_VF.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJFSw_VF.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.1/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJFSw_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJFSw_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJFSw_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJFSw_VgrpF.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.1/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include 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src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJ_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJ_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJ_F.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJ_F.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.1/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic/api/legacy/include 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-I/build/reproducible-path/gromacs-2025.1/build/basic/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.1/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/simd/include 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-g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombLB_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombLB_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombLB_VF.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombLB_VF.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.1/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/simd/include 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-g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJEwCombGeom_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJEwCombGeom_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJEwCombGeom_F.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJEwCombGeom_F.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.1/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/simd/include 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-I/build/reproducible-path/gromacs-2025.1/build/basic/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.1/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/simd/include 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-fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJFSw_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJFSw_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJFSw_VF.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJFSw_VF.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic/src/include -I/build/reproducible-path/gromacs-2025.1/src 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-I/build/reproducible-path/gromacs-2025.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time 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-I/build/reproducible-path/gromacs-2025.1/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJPSw_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJPSw_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJPSw_VF.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJPSw_VF.cpp cd 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-I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers 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-I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.1/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/taskassignment/include -isystem 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-I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.1/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/taskassignment/include -isystem 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-I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.1/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/taskassignment/include -isystem 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-I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. 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-I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.1/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/taskassignment/include -isystem 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-I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. 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-I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.1/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/taskassignment/include -isystem 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-I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. 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/build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombGeom_F.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.1/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include 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-Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombLB_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombLB_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombLB_F.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombLB_F.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.1/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include 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src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombLB_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombLB_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombLB_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombLB_VgrpF.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.1/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include 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src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJEwCombGeom_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJEwCombGeom_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJEwCombGeom_VF.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJEwCombGeom_VF.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.1/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include 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src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJFSw_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJFSw_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJFSw_F.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJFSw_F.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.1/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic/api/legacy/include 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-I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJ_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJ_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJ_VF.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJ_VF.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.1/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJ_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJ_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJ_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJ_VgrpF.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.1/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_F.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_F.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.1/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_VF.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_VF.cpp cd 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-I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers 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-I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers 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-I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers 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-I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/gromacs/../external/rpc_xdr 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-I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers 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src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJFSw_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJFSw_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJFSw_VF.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJFSw_VF.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.1/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJFSw_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJFSw_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJFSw_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJFSw_VgrpF.cpp cd 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-I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers 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-I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJPSw_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJPSw_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJPSw_VF.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJPSw_VF.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.1/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJPSw_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJPSw_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJPSw_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJPSw_VgrpF.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.1/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/gromacs/../external/rpc_xdr -isystem 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src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJ_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJ_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJ_VF.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJ_VF.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.1/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include 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src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombGeom_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombGeom_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombGeom_F.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombGeom_F.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.1/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include 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src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombGeom_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombGeom_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombGeom_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombGeom_VgrpF.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.1/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include 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src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJEwCombGeom_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJEwCombGeom_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJEwCombGeom_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJEwCombGeom_VgrpF.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.1/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include 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src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJFSw_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJFSw_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJFSw_VF.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJFSw_VF.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.1/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include 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src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJ_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJ_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJ_VF.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJ_VF.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.1/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include 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src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombLB_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombLB_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombLB_VF.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombLB_VF.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.1/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include 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-g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJ_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJ_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJ_F.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJ_F.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic/src/include 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/build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJ_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJ_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJ_VF.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJ_VF.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.1/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include 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-D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJ_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJ_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJ_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJ_VgrpF.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/external/tng_io/include 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/build/reproducible-path/gromacs-2025.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/atomdata.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/atomdata.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/atomdata.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/atomdata.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.1/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/linearalgebra/include 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-fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdlib/membed.cpp.o -MF CMakeFiles/libgromacs.dir/mdlib/membed.cpp.o.d -o CMakeFiles/libgromacs.dir/mdlib/membed.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/mdlib/membed.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.1/build/basic/tng/include 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-isystem /build/reproducible-path/gromacs-2025.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdrun/simulationcontext.cpp.o -MF CMakeFiles/libgromacs.dir/mdrun/simulationcontext.cpp.o.d -o CMakeFiles/libgromacs.dir/mdrun/simulationcontext.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/mdrun/simulationcontext.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic/src/include 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-isystem /build/reproducible-path/gromacs-2025.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdtypes/state_propagator_data_gpu_impl.cpp.o -MF CMakeFiles/libgromacs.dir/mdtypes/state_propagator_data_gpu_impl.cpp.o.d -o CMakeFiles/libgromacs.dir/mdtypes/state_propagator_data_gpu_impl.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/mdtypes/state_propagator_data_gpu_impl.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.1/src/include 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-D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/fileio/checkpoint.cpp.o -MF CMakeFiles/libgromacs.dir/fileio/checkpoint.cpp.o.d -o CMakeFiles/libgromacs.dir/fileio/checkpoint.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/fileio/checkpoint.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.1/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include 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src/gromacs/CMakeFiles/libgromacs.dir/fileio/gmxfio.cpp.o -MF CMakeFiles/libgromacs.dir/fileio/gmxfio.cpp.o.d -o CMakeFiles/libgromacs.dir/fileio/gmxfio.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/fileio/gmxfio.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.1/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/timing/include 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-fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/fileio/gmxfio_xdr.cpp.o -MF CMakeFiles/libgromacs.dir/fileio/gmxfio_xdr.cpp.o.d -o CMakeFiles/libgromacs.dir/fileio/gmxfio_xdr.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/fileio/gmxfio_xdr.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.1/build/basic/tng/include 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-fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/selection/sm_merge.cpp.o -MF CMakeFiles/libgromacs.dir/selection/sm_merge.cpp.o.d -o CMakeFiles/libgromacs.dir/selection/sm_merge.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/selection/sm_merge.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.1/build/basic/tng/include 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-c /build/reproducible-path/gromacs-2025.1/src/gromacs/selection/sm_position.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.1/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pbcutil/include 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-fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/selection/sm_same.cpp.o -MF CMakeFiles/libgromacs.dir/selection/sm_same.cpp.o.d -o CMakeFiles/libgromacs.dir/selection/sm_same.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/selection/sm_same.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.1/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic/api/legacy/include 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-isystem /build/reproducible-path/gromacs-2025.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/selection/sm_simple.cpp.o -MF CMakeFiles/libgromacs.dir/selection/sm_simple.cpp.o.d -o CMakeFiles/libgromacs.dir/selection/sm_simple.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/selection/sm_simple.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.1/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/selection/symrec.cpp.o -MF CMakeFiles/libgromacs.dir/selection/symrec.cpp.o.d -o CMakeFiles/libgromacs.dir/selection/symrec.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/selection/symrec.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs && /usr/bin/cmake -E cmake_link_script CMakeFiles/libgromacs.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,--dependency-file=CMakeFiles/libgromacs.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libgromacs.so.10 -o ../../lib/libgromacs.so.10.0.0 @CMakeFiles/libgromacs.dir/objects1.rsp /lib/riscv64-linux-gnu/libhwloc.so -lrt /usr/lib/riscv64-linux-gnu/libfftw3f.so /usr/lib/riscv64-linux-gnu/libblas.so /usr/lib/riscv64-linux-gnu/liblapack.so /usr/lib/riscv64-linux-gnu/libblas.so /usr/lib/riscv64-linux-gnu/libm.so /usr/lib/riscv64-linux-gnu/liblapack.so /usr/lib/riscv64-linux-gnu/libm.so -lm /usr/lib/riscv64-linux-gnu/libz.so /usr/lib/gcc/riscv64-linux-gnu/14/libgomp.so /lib/riscv64-linux-gnu/libpthread.a /usr/lib/riscv64-linux-gnu/libmuparser.so.2.3.4 -ldl cd /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs && /usr/bin/cmake -E cmake_symlink_library ../../lib/libgromacs.so.10.0.0 ../../lib/libgromacs.so.10 ../../lib/libgromacs.so make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/basic' [ 96%] Built target libgromacs /usr/bin/make -f share/template/CMakeFiles/template.dir/build.make share/template/CMakeFiles/template.dir/depend /usr/bin/make -f api/gmxapi/CMakeFiles/gmxapi.dir/build.make api/gmxapi/CMakeFiles/gmxapi.dir/depend /usr/bin/make -f api/nblib/CMakeFiles/nblib.dir/build.make api/nblib/CMakeFiles/nblib.dir/depend make[3]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/basic' cd /build/reproducible-path/gromacs-2025.1/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.1 /build/reproducible-path/gromacs-2025.1/share/template /build/reproducible-path/gromacs-2025.1/build/basic /build/reproducible-path/gromacs-2025.1/build/basic/share/template /build/reproducible-path/gromacs-2025.1/build/basic/share/template/CMakeFiles/template.dir/DependInfo.cmake "--color=" /usr/bin/make -f src/programs/CMakeFiles/gmx.dir/build.make src/programs/CMakeFiles/gmx.dir/depend make[3]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/basic' cd /build/reproducible-path/gromacs-2025.1/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.1 /build/reproducible-path/gromacs-2025.1/api/gmxapi /build/reproducible-path/gromacs-2025.1/build/basic /build/reproducible-path/gromacs-2025.1/build/basic/api/gmxapi /build/reproducible-path/gromacs-2025.1/build/basic/api/gmxapi/CMakeFiles/gmxapi.dir/DependInfo.cmake "--color=" make[3]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/basic' cd /build/reproducible-path/gromacs-2025.1/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.1 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'/build/reproducible-path/gromacs-2025.1/build/basic' cd /build/reproducible-path/gromacs-2025.1/build/basic/api/nblib && /usr/bin/c++ -DGMX_DOUBLE=0 -DTMPI_USE_VISIBILITY -Dnblib_EXPORTS -I/build/reproducible-path/gromacs-2025.1/api/nblib/include -I/build/reproducible-path/gromacs-2025.1/api/nblib -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic/src/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.1/src -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -Wno-cast-function-type-strict -MD -MT api/nblib/CMakeFiles/nblib.dir/box.cpp.o -MF CMakeFiles/nblib.dir/box.cpp.o.d -o CMakeFiles/nblib.dir/box.cpp.o -c /build/reproducible-path/gromacs-2025.1/api/nblib/box.cpp make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/basic' /usr/bin/make -f share/template/CMakeFiles/template.dir/build.make share/template/CMakeFiles/template.dir/build make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/basic' /usr/bin/make -f src/programs/CMakeFiles/gmx.dir/build.make 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/build/reproducible-path/gromacs-2025.1/api/gmxapi/cpp/context.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic/api/nblib && /usr/bin/c++ -DGMX_DOUBLE=0 -DTMPI_USE_VISIBILITY -Dnblib_EXPORTS -I/build/reproducible-path/gromacs-2025.1/api/nblib/include -I/build/reproducible-path/gromacs-2025.1/api/nblib -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic/src/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include 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/build/reproducible-path/gromacs-2025.1/api/nblib/simulationstate.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic/api/nblib && /usr/bin/c++ -DGMX_DOUBLE=0 -DTMPI_USE_VISIBILITY -Dnblib_EXPORTS -I/build/reproducible-path/gromacs-2025.1/api/nblib/include -I/build/reproducible-path/gromacs-2025.1/api/nblib -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic/src/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include 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-D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -Wno-cast-function-type-strict -MD -MT api/nblib/CMakeFiles/nblib.dir/topology.cpp.o -MF CMakeFiles/nblib.dir/topology.cpp.o.d -o CMakeFiles/nblib.dir/topology.cpp.o -c /build/reproducible-path/gromacs-2025.1/api/nblib/topology.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic/api/nblib && /usr/bin/c++ -DGMX_DOUBLE=0 -DTMPI_USE_VISIBILITY -Dnblib_EXPORTS -I/build/reproducible-path/gromacs-2025.1/api/nblib/include -I/build/reproducible-path/gromacs-2025.1/api/nblib -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic/src/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include 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/build/reproducible-path/gromacs-2025.1/api/nblib/tpr.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic/api/gmxapi && /usr/bin/cmake -E cmake_link_script CMakeFiles/gmxapi.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,--dependency-file=CMakeFiles/gmxapi.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libgmxapi.so.0 -o ../../lib/libgmxapi.so.0.4.0 CMakeFiles/gmxapi.dir/cpp/resourceassignment.cpp.o CMakeFiles/gmxapi.dir/cpp/context.cpp.o CMakeFiles/gmxapi.dir/cpp/exceptions.cpp.o CMakeFiles/gmxapi.dir/cpp/gmxapi.cpp.o CMakeFiles/gmxapi.dir/cpp/md.cpp.o CMakeFiles/gmxapi.dir/cpp/mdmodule.cpp.o CMakeFiles/gmxapi.dir/cpp/mdsignals.cpp.o CMakeFiles/gmxapi.dir/cpp/session.cpp.o CMakeFiles/gmxapi.dir/cpp/status.cpp.o CMakeFiles/gmxapi.dir/cpp/system.cpp.o CMakeFiles/gmxapi.dir/cpp/version.cpp.o CMakeFiles/gmxapi.dir/cpp/workflow.cpp.o CMakeFiles/gmxapi.dir/cpp/tpr.cpp.o ../../lib/libgromacs.so.10.0.0 /usr/lib/riscv64-linux-gnu/libm.so /usr/lib/gcc/riscv64-linux-gnu/14/libgomp.so /lib/riscv64-linux-gnu/libpthread.a cd /build/reproducible-path/gromacs-2025.1/build/basic/api/gmxapi && /usr/bin/cmake -E cmake_symlink_library ../../lib/libgmxapi.so.0.4.0 ../../lib/libgmxapi.so.0 ../../lib/libgmxapi.so make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/basic' [ 98%] Built target gmxapi cd /build/reproducible-path/gromacs-2025.1/build/basic/api/nblib && /usr/bin/c++ -DGMX_DOUBLE=0 -DTMPI_USE_VISIBILITY -Dnblib_EXPORTS -I/build/reproducible-path/gromacs-2025.1/api/nblib/include -I/build/reproducible-path/gromacs-2025.1/api/nblib -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic/src/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include 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api/nblib/CMakeFiles/nblib.dir/virials.cpp.o -MF CMakeFiles/nblib.dir/virials.cpp.o.d -o CMakeFiles/nblib.dir/virials.cpp.o -c /build/reproducible-path/gromacs-2025.1/api/nblib/virials.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic/api/nblib && /usr/bin/c++ -DGMX_DOUBLE=0 -DTMPI_USE_VISIBILITY -Dnblib_EXPORTS -I/build/reproducible-path/gromacs-2025.1/api/nblib/include -I/build/reproducible-path/gromacs-2025.1/api/nblib -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic/src/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pbcutil/include 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-I/build/reproducible-path/gromacs-2025.1/src -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -Wno-cast-function-type-strict -MD -MT api/nblib/CMakeFiles/nblib.dir/listed_forces/transformations.cpp.o -MF CMakeFiles/nblib.dir/listed_forces/transformations.cpp.o.d -o CMakeFiles/nblib.dir/listed_forces/transformations.cpp.o -c /build/reproducible-path/gromacs-2025.1/api/nblib/listed_forces/transformations.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic/api/nblib && /usr/bin/c++ -DGMX_DOUBLE=0 -DTMPI_USE_VISIBILITY -Dnblib_EXPORTS -I/build/reproducible-path/gromacs-2025.1/api/nblib/include -I/build/reproducible-path/gromacs-2025.1/api/nblib -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic/src/include 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-fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,--dependency-file=CMakeFiles/nblib.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libnblib_gmx.so.0 -o ../../lib/libnblib_gmx.so.0.1.0 CMakeFiles/nblib.dir/box.cpp.o CMakeFiles/nblib.dir/gmxcalculatorcpu.cpp.o CMakeFiles/nblib.dir/integrator.cpp.o CMakeFiles/nblib.dir/interactions.cpp.o CMakeFiles/nblib.dir/molecules.cpp.o CMakeFiles/nblib.dir/nbnxmsetuphelpers.cpp.o CMakeFiles/nblib.dir/particlesequencer.cpp.o CMakeFiles/nblib.dir/particletype.cpp.o CMakeFiles/nblib.dir/simulationstate.cpp.o CMakeFiles/nblib.dir/topologyhelpers.cpp.o CMakeFiles/nblib.dir/topology.cpp.o CMakeFiles/nblib.dir/tpr.cpp.o CMakeFiles/nblib.dir/virials.cpp.o CMakeFiles/nblib.dir/listed_forces/calculator.cpp.o CMakeFiles/nblib.dir/listed_forces/transformations.cpp.o CMakeFiles/nblib.dir/listed_forces/conversions.cpp.o CMakeFiles/nblib.dir/listed_forces/convertGmxToNblib.cpp.o CMakeFiles/nblib.dir/util/setup.cpp.o /usr/lib/riscv64-linux-gnu/libm.so ../../lib/libgromacs.so.10.0.0 /usr/lib/riscv64-linux-gnu/libm.so /usr/lib/gcc/riscv64-linux-gnu/14/libgomp.so /lib/riscv64-linux-gnu/libpthread.a /usr/lib/riscv64-linux-gnu/libmuparser.so.2.3.4 cd /build/reproducible-path/gromacs-2025.1/build/basic/api/nblib && /usr/bin/cmake -E cmake_symlink_library ../../lib/libnblib_gmx.so.0.1.0 ../../lib/libnblib_gmx.so.0 ../../lib/libnblib_gmx.so make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/basic' [100%] Built target nblib /usr/bin/make -f api/nblib/samples/CMakeFiles/argon-forces-integration.dir/build.make api/nblib/samples/CMakeFiles/argon-forces-integration.dir/depend /usr/bin/make -f api/nblib/samples/CMakeFiles/methane-water-integration.dir/build.make api/nblib/samples/CMakeFiles/methane-water-integration.dir/depend make[3]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/basic' cd 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"--color=" make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/basic' /usr/bin/make -f api/nblib/samples/CMakeFiles/argon-forces-integration.dir/build.make api/nblib/samples/CMakeFiles/argon-forces-integration.dir/build make[3]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/basic' cd /build/reproducible-path/gromacs-2025.1/build/basic/api/nblib/samples && /usr/bin/c++ -DGMX_DOUBLE=0 -I/build/reproducible-path/gromacs-2025.1/api/nblib/include -I/build/reproducible-path/gromacs-2025.1/api/nblib -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic/api/legacy/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fopenmp -MD -MT api/nblib/samples/CMakeFiles/argon-forces-integration.dir/argon-forces-integration.cpp.o -MF 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../../../bin/argon-forces-integration ../../../lib/libnblib_gmx.so.0.1.0 /usr/lib/riscv64-linux-gnu/libm.so /usr/lib/gcc/riscv64-linux-gnu/14/libgomp.so /lib/riscv64-linux-gnu/libpthread.a -Wl,-rpath-link,/build/reproducible-path/gromacs-2025.1/build/basic/lib make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/basic' [100%] Built target argon-forces-integration cd /build/reproducible-path/gromacs-2025.1/build/basic/api/nblib/samples && /usr/bin/cmake -E cmake_link_script CMakeFiles/methane-water-integration.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/methane-water-integration.dir/link.d "CMakeFiles/methane-water-integration.dir/methane-water-integration.cpp.o" -o ../../../bin/methane-water-integration ../../../lib/libnblib_gmx.so.0.1.0 /usr/lib/riscv64-linux-gnu/libm.so /usr/lib/gcc/riscv64-linux-gnu/14/libgomp.so /lib/riscv64-linux-gnu/libpthread.a -Wl,-rpath-link,/build/reproducible-path/gromacs-2025.1/build/basic/lib make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/basic' [100%] Built target methane-water-integration make[2]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/basic' /usr/bin/cmake -E cmake_progress_start /build/reproducible-path/gromacs-2025.1/build/basic/CMakeFiles 0 make[1]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/basic' /usr/bin/make -j4 -C build/basic-dp make[1]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/basic-dp' /usr/bin/cmake -S/build/reproducible-path/gromacs-2025.1 -B/build/reproducible-path/gromacs-2025.1/build/basic-dp --check-build-system CMakeFiles/Makefile.cmake 0 /usr/bin/cmake -E cmake_progress_start /build/reproducible-path/gromacs-2025.1/build/basic-dp/CMakeFiles 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/usr/bin/make -f src/external/rpc_xdr/CMakeFiles/internal_rpc_xdr.dir/build.make src/external/rpc_xdr/CMakeFiles/internal_rpc_xdr.dir/build make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/basic-dp' /usr/bin/make -f src/gromacs/selection/CMakeFiles/scanner.dir/build.make src/gromacs/selection/CMakeFiles/scanner.dir/build make[3]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/basic-dp' cd /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/external/rpc_xdr && /usr/bin/c++ -DGMX_DOUBLE=1 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -MD -MT src/external/rpc_xdr/CMakeFiles/internal_rpc_xdr.dir/xdr.cpp.o -MF CMakeFiles/internal_rpc_xdr.dir/xdr.cpp.o.d -o CMakeFiles/internal_rpc_xdr.dir/xdr.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/external/rpc_xdr/xdr.cpp make[3]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/basic-dp' cd /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/selection && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -Wno-null-conversion -MD -MT src/gromacs/selection/CMakeFiles/scanner.dir/parser.cpp.o -MF CMakeFiles/scanner.dir/parser.cpp.o.d -o CMakeFiles/scanner.dir/parser.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/selection/parser.cpp make[3]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/basic-dp' cd /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -MD -MT src/gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/errhandler.cpp.o -MF CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/errhandler.cpp.o.d -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/errhandler.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/src/errhandler.cpp make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/basic-dp' [ 0%] Built target release-version-info /usr/bin/make -f src/gromacs/CMakeFiles/tng_io_obj.dir/build.make src/gromacs/CMakeFiles/tng_io_obj.dir/depend make[3]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/basic-dp' cd /build/reproducible-path/gromacs-2025.1/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.1 /build/reproducible-path/gromacs-2025.1/src/gromacs /build/reproducible-path/gromacs-2025.1/build/basic-dp /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/CMakeFiles/tng_io_obj.dir/DependInfo.cmake "--color=" make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/basic-dp' /usr/bin/make -f src/gromacs/CMakeFiles/tng_io_obj.dir/build.make src/gromacs/CMakeFiles/tng_io_obj.dir/build make[3]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/basic-dp' cd /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs && /usr/bin/cc -DGMX_DOUBLE=1 -I/build/reproducible-path/gromacs-2025.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/tng/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -MD -MT 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-MD -MT src/gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/lock.cpp.o -MF CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/lock.cpp.o.d -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/lock.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/src/lock.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/external/rpc_xdr && /usr/bin/c++ -DGMX_DOUBLE=1 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -MD -MT src/external/rpc_xdr/CMakeFiles/internal_rpc_xdr.dir/xdr_stdio.cpp.o -MF CMakeFiles/internal_rpc_xdr.dir/xdr_stdio.cpp.o.d -o CMakeFiles/internal_rpc_xdr.dir/xdr_stdio.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/external/rpc_xdr/xdr_stdio.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -MD -MT src/gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/pthreads.cpp.o -MF CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/pthreads.cpp.o.d -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/pthreads.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/src/pthreads.cpp make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/basic-dp' [ 0%] Built target internal_rpc_xdr cd /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs && 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-I/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -MD -MT src/gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/alltoall.cpp.o -MF CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/alltoall.cpp.o.d -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/alltoall.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/src/alltoall.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs && /usr/bin/cc -DGMX_DOUBLE=1 -I/build/reproducible-path/gromacs-2025.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/tng/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -MD -MT src/gromacs/CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/coder.c.o -MF CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/coder.c.o.d -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/coder.c.o -c /build/reproducible-path/gromacs-2025.1/src/external/tng_io/src/compression/coder.c cd /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs && /usr/bin/cc -DGMX_DOUBLE=1 -I/build/reproducible-path/gromacs-2025.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/tng/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -Wformat 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&& /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -MD -MT src/gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/group.cpp.o -MF CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/group.cpp.o.d -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/group.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/src/group.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -MD -MT src/gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/tmpi_init.cpp.o -MF CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/tmpi_init.cpp.o.d -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/tmpi_init.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/src/tmpi_init.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -MD -MT src/gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/topology.cpp.o -MF CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/topology.cpp.o.d -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/topology.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/src/topology.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -MD -MT src/gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/list.cpp.o -MF CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/list.cpp.o.d -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/list.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/src/list.cpp make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/basic-dp' [ 0%] Built target lmfit_objlib /usr/bin/make -f src/gromacs/CMakeFiles/colvars_objlib.dir/build.make src/gromacs/CMakeFiles/colvars_objlib.dir/depend make[3]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/basic-dp' cd /build/reproducible-path/gromacs-2025.1/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.1 /build/reproducible-path/gromacs-2025.1/src/gromacs /build/reproducible-path/gromacs-2025.1/build/basic-dp /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/CMakeFiles/colvars_objlib.dir/DependInfo.cmake "--color=" make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/basic-dp' /usr/bin/make -f src/gromacs/CMakeFiles/colvars_objlib.dir/build.make src/gromacs/CMakeFiles/colvars_objlib.dir/build make[3]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/basic-dp' cd /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -Wformat 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CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/vals16.c.o.d -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/vals16.c.o -c /build/reproducible-path/gromacs-2025.1/src/external/tng_io/src/compression/vals16.c cd /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs && /usr/bin/cc -DGMX_DOUBLE=1 -I/build/reproducible-path/gromacs-2025.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/tng/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -MD -MT src/gromacs/CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/warnmalloc.c.o -MF CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/warnmalloc.c.o.d -o 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/build/reproducible-path/gromacs-2025.1/src/external/tng_io/src/compression/widemuldiv.c cd /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs && /usr/bin/cc -DGMX_DOUBLE=1 -I/build/reproducible-path/gromacs-2025.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/tng/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -MD -MT src/gromacs/CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/xtc2.c.o -MF CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/xtc2.c.o.d -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/xtc2.c.o -c /build/reproducible-path/gromacs-2025.1/src/external/tng_io/src/compression/xtc2.c cd /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -MD -MT src/gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/scan.cpp.o -MF CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/scan.cpp.o.d -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/scan.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/src/scan.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -MD -MT src/gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/numa_malloc.cpp.o -MF CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/numa_malloc.cpp.o.d -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/numa_malloc.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/src/numa_malloc.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -MD -MT src/gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/once.cpp.o -MF CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/once.cpp.o.d -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/once.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/src/once.cpp make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/basic-dp' [ 1%] Built target thread_mpi cd /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fopenmp -MD -MT src/gromacs/CMakeFiles/colvars_objlib.dir/__/external/colvars/colvar_neuralnetworkcompute.cpp.o -MF CMakeFiles/colvars_objlib.dir/__/external/colvars/colvar_neuralnetworkcompute.cpp.o.d -o CMakeFiles/colvars_objlib.dir/__/external/colvars/colvar_neuralnetworkcompute.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/external/colvars/colvar_neuralnetworkcompute.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs && /usr/bin/cc -DGMX_DOUBLE=1 -I/build/reproducible-path/gromacs-2025.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/tng/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -MD -MT src/gromacs/CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/xtc3.c.o -MF CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/xtc3.c.o.d -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/xtc3.c.o -c /build/reproducible-path/gromacs-2025.1/src/external/tng_io/src/compression/xtc3.c make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/basic-dp' [ 1%] Built target scanner /usr/bin/make -f src/gromacs/linearalgebra/CMakeFiles/linearalgebra.dir/build.make src/gromacs/linearalgebra/CMakeFiles/linearalgebra.dir/depend make[3]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/basic-dp' cd /build/reproducible-path/gromacs-2025.1/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.1 /build/reproducible-path/gromacs-2025.1/src/gromacs/linearalgebra /build/reproducible-path/gromacs-2025.1/build/basic-dp /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/linearalgebra /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/linearalgebra/CMakeFiles/linearalgebra.dir/DependInfo.cmake "--color=" make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/basic-dp' /usr/bin/make -f src/gromacs/linearalgebra/CMakeFiles/linearalgebra.dir/build.make src/gromacs/linearalgebra/CMakeFiles/linearalgebra.dir/build make[3]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/basic-dp' cd /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/linearalgebra && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/linearalgebra -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-stringop-truncation -MD -MT src/gromacs/linearalgebra/CMakeFiles/linearalgebra.dir/eigensolver.cpp.o -MF CMakeFiles/linearalgebra.dir/eigensolver.cpp.o.d -o CMakeFiles/linearalgebra.dir/eigensolver.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/linearalgebra/eigensolver.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/linearalgebra && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/linearalgebra -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-stringop-truncation -MD -MT src/gromacs/linearalgebra/CMakeFiles/linearalgebra.dir/gmx_arpack.cpp.o -MF CMakeFiles/linearalgebra.dir/gmx_arpack.cpp.o.d -o CMakeFiles/linearalgebra.dir/gmx_arpack.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/linearalgebra/gmx_arpack.cpp /usr/bin/make -f src/gromacs/options/CMakeFiles/options.dir/build.make src/gromacs/options/CMakeFiles/options.dir/depend make[3]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/basic-dp' cd /build/reproducible-path/gromacs-2025.1/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.1 /build/reproducible-path/gromacs-2025.1/src/gromacs/options /build/reproducible-path/gromacs-2025.1/build/basic-dp /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/options /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/options/CMakeFiles/options.dir/DependInfo.cmake "--color=" make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/basic-dp' /usr/bin/make -f src/gromacs/options/CMakeFiles/options.dir/build.make src/gromacs/options/CMakeFiles/options.dir/build make[3]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/basic-dp' cd /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/options && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -MD -MT src/gromacs/options/CMakeFiles/options.dir/abstractoption.cpp.o -MF CMakeFiles/options.dir/abstractoption.cpp.o.d -o CMakeFiles/options.dir/abstractoption.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/options/abstractoption.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs && /usr/bin/cc -DGMX_DOUBLE=1 -DUSE_STD_INTTYPES_H -I/build/reproducible-path/gromacs-2025.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/tng/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -MD -MT src/gromacs/CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/lib/tng_io.c.o -MF CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/lib/tng_io.c.o.d -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/lib/tng_io.c.o -c /build/reproducible-path/gromacs-2025.1/src/external/tng_io/src/lib/tng_io.c cd /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/options && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -MD -MT src/gromacs/options/CMakeFiles/options.dir/abstractsection.cpp.o -MF CMakeFiles/options.dir/abstractsection.cpp.o.d -o CMakeFiles/options.dir/abstractsection.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/options/abstractsection.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/options && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -MD -MT src/gromacs/options/CMakeFiles/options.dir/basicoptions.cpp.o -MF CMakeFiles/options.dir/basicoptions.cpp.o.d -o CMakeFiles/options.dir/basicoptions.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/options/basicoptions.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/linearalgebra && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/linearalgebra -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-stringop-truncation -MD -MT src/gromacs/linearalgebra/CMakeFiles/linearalgebra.dir/matrix.cpp.o -MF CMakeFiles/linearalgebra.dir/matrix.cpp.o.d -o CMakeFiles/linearalgebra.dir/matrix.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/linearalgebra/matrix.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/linearalgebra && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/linearalgebra -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-stringop-truncation -MD -MT src/gromacs/linearalgebra/CMakeFiles/linearalgebra.dir/sparsematrix.cpp.o -MF CMakeFiles/linearalgebra.dir/sparsematrix.cpp.o.d -o CMakeFiles/linearalgebra.dir/sparsematrix.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/linearalgebra/sparsematrix.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fopenmp -MD -MT src/gromacs/CMakeFiles/colvars_objlib.dir/__/external/colvars/colvaratoms.cpp.o -MF CMakeFiles/colvars_objlib.dir/__/external/colvars/colvaratoms.cpp.o.d -o CMakeFiles/colvars_objlib.dir/__/external/colvars/colvaratoms.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/external/colvars/colvaratoms.cpp make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/basic-dp' [ 1%] Built target linearalgebra /usr/bin/make -f src/gromacs/energyanalysis/CMakeFiles/energyanalysis.dir/build.make src/gromacs/energyanalysis/CMakeFiles/energyanalysis.dir/depend make[3]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/basic-dp' cd /build/reproducible-path/gromacs-2025.1/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.1 /build/reproducible-path/gromacs-2025.1/src/gromacs/energyanalysis /build/reproducible-path/gromacs-2025.1/build/basic-dp /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/energyanalysis /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/energyanalysis/CMakeFiles/energyanalysis.dir/DependInfo.cmake "--color=" make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/basic-dp' /usr/bin/make -f src/gromacs/energyanalysis/CMakeFiles/energyanalysis.dir/build.make src/gromacs/energyanalysis/CMakeFiles/energyanalysis.dir/build make[3]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/basic-dp' cd /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/energyanalysis && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -I/build/reproducible-path/gromacs-2025.1/src -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -MD -MT src/gromacs/energyanalysis/CMakeFiles/energyanalysis.dir/energyterm.cpp.o -MF CMakeFiles/energyanalysis.dir/energyterm.cpp.o.d -o CMakeFiles/energyanalysis.dir/energyterm.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/energyanalysis/energyterm.cpp make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/basic-dp' [ 1%] Built target energyanalysis cd /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/options && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -MD -MT src/gromacs/options/CMakeFiles/options.dir/behaviorcollection.cpp.o -MF CMakeFiles/options.dir/behaviorcollection.cpp.o.d -o CMakeFiles/options.dir/behaviorcollection.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/options/behaviorcollection.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/options && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -MD -MT src/gromacs/options/CMakeFiles/options.dir/filenameoption.cpp.o -MF CMakeFiles/options.dir/filenameoption.cpp.o.d -o CMakeFiles/options.dir/filenameoption.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/options/filenameoption.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs && /usr/bin/cc -DGMX_DOUBLE=1 -I/build/reproducible-path/gromacs-2025.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/tng/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -MD -MT src/gromacs/CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/lib/md5.c.o -MF CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/lib/md5.c.o.d -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/lib/md5.c.o -c /build/reproducible-path/gromacs-2025.1/src/external/tng_io/src/lib/md5.c make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/basic-dp' [ 3%] Built target tng_io_obj /usr/bin/make -f src/programs/CMakeFiles/mdrun_objlib.dir/build.make src/programs/CMakeFiles/mdrun_objlib.dir/depend make[3]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/basic-dp' cd /build/reproducible-path/gromacs-2025.1/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.1 /build/reproducible-path/gromacs-2025.1/src/programs /build/reproducible-path/gromacs-2025.1/build/basic-dp /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/CMakeFiles/mdrun_objlib.dir/DependInfo.cmake "--color=" make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/basic-dp' /usr/bin/make -f src/programs/CMakeFiles/mdrun_objlib.dir/build.make src/programs/CMakeFiles/mdrun_objlib.dir/build make[3]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/basic-dp' cd /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -MD -MT src/programs/CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o -MF CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o.d -o CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/programs/mdrun/mdrun.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -g -O2 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-I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -MD -MT src/gromacs/options/CMakeFiles/options.dir/filenameoptionmanager.cpp.o -MF CMakeFiles/options.dir/filenameoptionmanager.cpp.o.d -o CMakeFiles/options.dir/filenameoptionmanager.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/options/filenameoptionmanager.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -MD -MT src/programs/CMakeFiles/mdrun_objlib.dir/mdrun/nonbonded_bench.cpp.o -MF CMakeFiles/mdrun_objlib.dir/mdrun/nonbonded_bench.cpp.o.d -o CMakeFiles/mdrun_objlib.dir/mdrun/nonbonded_bench.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/programs/mdrun/nonbonded_bench.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/options && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H 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/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/options && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -MD -MT src/gromacs/options/CMakeFiles/options.dir/optionsassigner.cpp.o -MF CMakeFiles/options.dir/optionsassigner.cpp.o.d -o CMakeFiles/options.dir/optionsassigner.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/options/optionsassigner.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/options && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -MD -MT src/gromacs/options/CMakeFiles/options.dir/optionsection.cpp.o -MF CMakeFiles/options.dir/optionsection.cpp.o.d -o CMakeFiles/options.dir/optionsection.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/options/optionsection.cpp make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/basic-dp' [ 3%] Built target mdrun_objlib /usr/bin/make -f src/programs/CMakeFiles/gmx_objlib.dir/build.make src/programs/CMakeFiles/gmx_objlib.dir/depend make[3]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/basic-dp' cd /build/reproducible-path/gromacs-2025.1/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.1 /build/reproducible-path/gromacs-2025.1/src/programs /build/reproducible-path/gromacs-2025.1/build/basic-dp /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/CMakeFiles/gmx_objlib.dir/DependInfo.cmake "--color=" make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/basic-dp' /usr/bin/make -f src/programs/CMakeFiles/gmx_objlib.dir/build.make src/programs/CMakeFiles/gmx_objlib.dir/build make[3]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/basic-dp' cd /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs && /usr/bin/c++ -DGMX_DOUBLE=1 -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -MD -MT src/programs/CMakeFiles/gmx_objlib.dir/gmx.cpp.o -MF CMakeFiles/gmx_objlib.dir/gmx.cpp.o.d -o CMakeFiles/gmx_objlib.dir/gmx.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/programs/gmx.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/options && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -MD -MT src/gromacs/options/CMakeFiles/options.dir/optionsvisitor.cpp.o -MF CMakeFiles/options.dir/optionsvisitor.cpp.o.d -o CMakeFiles/options.dir/optionsvisitor.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/options/optionsvisitor.cpp /usr/bin/make -f src/gromacs/pulling/CMakeFiles/pulling.dir/build.make src/gromacs/pulling/CMakeFiles/pulling.dir/depend make[3]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/basic-dp' cd /build/reproducible-path/gromacs-2025.1/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.1 /build/reproducible-path/gromacs-2025.1/src/gromacs/pulling /build/reproducible-path/gromacs-2025.1/build/basic-dp /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/pulling /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/pulling/CMakeFiles/pulling.dir/DependInfo.cmake "--color=" make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/basic-dp' /usr/bin/make -f src/gromacs/pulling/CMakeFiles/pulling.dir/build.make src/gromacs/pulling/CMakeFiles/pulling.dir/build make[3]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/basic-dp' cd /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/pulling && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/pulling/CMakeFiles/pulling.dir/output.cpp.o -MF CMakeFiles/pulling.dir/output.cpp.o.d -o CMakeFiles/pulling.dir/output.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/pulling/output.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs && /usr/bin/c++ -DGMX_DOUBLE=1 -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -MD -MT src/programs/CMakeFiles/gmx_objlib.dir/legacymodules.cpp.o -MF CMakeFiles/gmx_objlib.dir/legacymodules.cpp.o.d -o CMakeFiles/gmx_objlib.dir/legacymodules.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/programs/legacymodules.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/options && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -MD -MT src/gromacs/options/CMakeFiles/options.dir/timeunitmanager.cpp.o -MF CMakeFiles/options.dir/timeunitmanager.cpp.o.d -o CMakeFiles/options.dir/timeunitmanager.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/options/timeunitmanager.cpp make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/basic-dp' [ 3%] Built target gmx_objlib cd /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fopenmp -MD -MT src/gromacs/CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarbias_abf.cpp.o -MF CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarbias_abf.cpp.o.d -o CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarbias_abf.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/external/colvars/colvarbias_abf.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/options && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H 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/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fopenmp -MD -MT src/gromacs/CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarbias_abmd.cpp.o -MF CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarbias_abmd.cpp.o.d -o CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarbias_abmd.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/external/colvars/colvarbias_abmd.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/pulling && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/pulling/CMakeFiles/pulling.dir/pull.cpp.o -MF CMakeFiles/pulling.dir/pull.cpp.o.d -o CMakeFiles/pulling.dir/pull.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/pulling/pull.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fopenmp -MD -MT src/gromacs/CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarbias_alb.cpp.o -MF CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarbias_alb.cpp.o.d -o CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarbias_alb.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/external/colvars/colvarbias_alb.cpp make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/basic-dp' [ 5%] Built target options cd /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/pulling && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/pulling/CMakeFiles/pulling.dir/pull_rotation.cpp.o -MF CMakeFiles/pulling.dir/pull_rotation.cpp.o.d -o CMakeFiles/pulling.dir/pull_rotation.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/pulling/pull_rotation.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fopenmp -MD -MT src/gromacs/CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarbias_histogram.cpp.o -MF CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarbias_histogram.cpp.o.d -o CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarbias_histogram.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/external/colvars/colvarbias_histogram.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/pulling && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/pulling/CMakeFiles/pulling.dir/pullcoordexpressionparser.cpp.o -MF CMakeFiles/pulling.dir/pullcoordexpressionparser.cpp.o.d -o CMakeFiles/pulling.dir/pullcoordexpressionparser.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/pulling/pullcoordexpressionparser.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/pulling && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/pulling/CMakeFiles/pulling.dir/pullutil.cpp.o -MF CMakeFiles/pulling.dir/pullutil.cpp.o.d -o CMakeFiles/pulling.dir/pullutil.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/pulling/pullutil.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fopenmp -MD -MT src/gromacs/CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarbias_histogram_reweight_amd.cpp.o -MF CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarbias_histogram_reweight_amd.cpp.o.d -o CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarbias_histogram_reweight_amd.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/external/colvars/colvarbias_histogram_reweight_amd.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/pulling && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/pulling/CMakeFiles/pulling.dir/transformationcoordinate.cpp.o -MF CMakeFiles/pulling.dir/transformationcoordinate.cpp.o.d -o CMakeFiles/pulling.dir/transformationcoordinate.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/pulling/transformationcoordinate.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fopenmp -MD -MT src/gromacs/CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarbias_meta.cpp.o -MF CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarbias_meta.cpp.o.d -o CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarbias_meta.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/external/colvars/colvarbias_meta.cpp make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/basic-dp' [ 5%] Built target pulling cd /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fopenmp -MD -MT src/gromacs/CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarbias_opes.cpp.o -MF CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarbias_opes.cpp.o.d -o CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarbias_opes.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/external/colvars/colvarbias_opes.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fopenmp -MD -MT src/gromacs/CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarbias_restraint.cpp.o -MF CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarbias_restraint.cpp.o.d -o CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarbias_restraint.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/external/colvars/colvarbias_restraint.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fopenmp -MD -MT src/gromacs/CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarcomp.cpp.o -MF CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarcomp.cpp.o.d -o CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarcomp.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/external/colvars/colvarcomp.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fopenmp -MD -MT src/gromacs/CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarcomp_alchlambda.cpp.o -MF CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarcomp_alchlambda.cpp.o.d -o CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarcomp_alchlambda.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/external/colvars/colvarcomp_alchlambda.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fopenmp -MD -MT src/gromacs/CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarcomp_angles.cpp.o -MF CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarcomp_angles.cpp.o.d -o CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarcomp_angles.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/external/colvars/colvarcomp_angles.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fopenmp -MD -MT src/gromacs/CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarcomp_apath.cpp.o -MF CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarcomp_apath.cpp.o.d -o CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarcomp_apath.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/external/colvars/colvarcomp_apath.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fopenmp -MD -MT src/gromacs/CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarcomp_combination.cpp.o -MF CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarcomp_combination.cpp.o.d -o CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarcomp_combination.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/external/colvars/colvarcomp_combination.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fopenmp -MD -MT src/gromacs/CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarcomp_coordnums.cpp.o -MF CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarcomp_coordnums.cpp.o.d -o CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarcomp_coordnums.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/external/colvars/colvarcomp_coordnums.cpp /usr/bin/make -f src/gromacs/taskassignment/CMakeFiles/taskassignment.dir/build.make src/gromacs/taskassignment/CMakeFiles/taskassignment.dir/depend make[3]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/basic-dp' cd /build/reproducible-path/gromacs-2025.1/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.1 /build/reproducible-path/gromacs-2025.1/src/gromacs/taskassignment /build/reproducible-path/gromacs-2025.1/build/basic-dp /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/taskassignment /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/taskassignment/CMakeFiles/taskassignment.dir/DependInfo.cmake "--color=" make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/basic-dp' /usr/bin/make -f src/gromacs/taskassignment/CMakeFiles/taskassignment.dir/build.make src/gromacs/taskassignment/CMakeFiles/taskassignment.dir/build make[3]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/basic-dp' cd /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/taskassignment && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -MD -MT src/gromacs/taskassignment/CMakeFiles/taskassignment.dir/decidegpuusage.cpp.o -MF CMakeFiles/taskassignment.dir/decidegpuusage.cpp.o.d -o CMakeFiles/taskassignment.dir/decidegpuusage.cpp.o -c 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-I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -MD -MT src/gromacs/taskassignment/CMakeFiles/taskassignment.dir/decidesimulationworkload.cpp.o -MF CMakeFiles/taskassignment.dir/decidesimulationworkload.cpp.o.d -o CMakeFiles/taskassignment.dir/decidesimulationworkload.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/taskassignment/decidesimulationworkload.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/taskassignment && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/src/gromacs/taskassignment/include 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/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fopenmp -MD -MT src/gromacs/CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarcomp_protein.cpp.o -MF CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarcomp_protein.cpp.o.d -o CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarcomp_protein.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/external/colvars/colvarcomp_protein.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fopenmp -MD -MT src/gromacs/CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarcomp_rotations.cpp.o -MF CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarcomp_rotations.cpp.o.d -o CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarcomp_rotations.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/external/colvars/colvarcomp_rotations.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/taskassignment && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include 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/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fopenmp -MD -MT src/gromacs/CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarcomp_torchann.cpp.o -MF CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarcomp_torchann.cpp.o.d -o CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarcomp_torchann.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/external/colvars/colvarcomp_torchann.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/taskassignment && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/include 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src/gromacs/taskassignment/CMakeFiles/taskassignment.dir/taskassignment.cpp.o -MF CMakeFiles/taskassignment.dir/taskassignment.cpp.o.d -o CMakeFiles/taskassignment.dir/taskassignment.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/taskassignment/taskassignment.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fopenmp -MD -MT src/gromacs/CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarcomp_volmaps.cpp.o -MF CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarcomp_volmaps.cpp.o.d -o CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarcomp_volmaps.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/external/colvars/colvarcomp_volmaps.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fopenmp -MD -MT src/gromacs/CMakeFiles/colvars_objlib.dir/__/external/colvars/colvardeps.cpp.o -MF CMakeFiles/colvars_objlib.dir/__/external/colvars/colvardeps.cpp.o.d -o CMakeFiles/colvars_objlib.dir/__/external/colvars/colvardeps.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/external/colvars/colvardeps.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fopenmp -MD -MT src/gromacs/CMakeFiles/colvars_objlib.dir/__/external/colvars/colvargrid.cpp.o -MF CMakeFiles/colvars_objlib.dir/__/external/colvars/colvargrid.cpp.o.d -o CMakeFiles/colvars_objlib.dir/__/external/colvars/colvargrid.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/external/colvars/colvargrid.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fopenmp -MD -MT src/gromacs/CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarmodule.cpp.o -MF CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarmodule.cpp.o.d -o CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarmodule.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/external/colvars/colvarmodule.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/taskassignment && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -MD -MT src/gromacs/taskassignment/CMakeFiles/taskassignment.dir/usergpuids.cpp.o -MF CMakeFiles/taskassignment.dir/usergpuids.cpp.o.d -o CMakeFiles/taskassignment.dir/usergpuids.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/taskassignment/usergpuids.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fopenmp -MD -MT src/gromacs/CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarparams.cpp.o -MF CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarparams.cpp.o.d -o CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarparams.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/external/colvars/colvarparams.cpp make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/basic-dp' [ 5%] Built target taskassignment /usr/bin/make -f src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/build.make src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/depend make[3]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/basic-dp' cd /build/reproducible-path/gromacs-2025.1/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.1 /build/reproducible-path/gromacs-2025.1/src/gromacs/modularsimulator /build/reproducible-path/gromacs-2025.1/build/basic-dp /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/modularsimulator /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/DependInfo.cmake "--color=" make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/basic-dp' /usr/bin/make -f 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CMakeFiles/modularsimulator.dir/velocityscalingtemperaturecoupling.cpp.o.d -o CMakeFiles/modularsimulator.dir/velocityscalingtemperaturecoupling.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/modularsimulator/velocityscalingtemperaturecoupling.cpp make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/basic-dp' [ 10%] Built target modularsimulator /usr/bin/make -f src/gromacs/CMakeFiles/libgromacs.dir/build.make src/gromacs/CMakeFiles/libgromacs.dir/depend make[3]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/basic-dp' cd /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs && /usr/bin/cmake -D VERSION_VARIABLES=/build/reproducible-path/gromacs-2025.1/build/basic-dp/VersionInfo.cmake -D VERSION_CMAKEIN=/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/baseversion-gen.cpp.cmakein -D VERSION_OUT=utility/baseversion-gen.cpp -D GMX_SOURCE_DOI= -D GMX_RELEASE_HASH= -D GMX_SOURCE_HASH= -P /build/reproducible-path/gromacs-2025.1/cmake/gmxConfigureVersionInfo.cmake cd /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs && /usr/bin/cmake -E touch utility/baseversion-gen.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.1 /build/reproducible-path/gromacs-2025.1/src/gromacs /build/reproducible-path/gromacs-2025.1/build/basic-dp /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/CMakeFiles/libgromacs.dir/DependInfo.cmake "--color=" make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/basic-dp' /usr/bin/make -f src/gromacs/CMakeFiles/libgromacs.dir/build.make src/gromacs/CMakeFiles/libgromacs.dir/build make[3]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/basic-dp' cd /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include 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src/gromacs/CMakeFiles/libgromacs.dir/utility/alignedallocator.cpp.o -MF CMakeFiles/libgromacs.dir/utility/alignedallocator.cpp.o.d -o CMakeFiles/libgromacs.dir/utility/alignedallocator.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/utility/alignedallocator.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include 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-g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/utility/any.cpp.o -MF CMakeFiles/libgromacs.dir/utility/any.cpp.o.d -o CMakeFiles/libgromacs.dir/utility/any.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/utility/any.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/external/tng_io/include 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/build/reproducible-path/gromacs-2025.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/utility/basenetwork.cpp.o -MF CMakeFiles/libgromacs.dir/utility/basenetwork.cpp.o.d -o CMakeFiles/libgromacs.dir/utility/basenetwork.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/utility/basenetwork.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY 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-fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/utility/binaryinformation.cpp.o -MF CMakeFiles/libgromacs.dir/utility/binaryinformation.cpp.o.d -o CMakeFiles/libgromacs.dir/utility/binaryinformation.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/utility/binaryinformation.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/external/tng_io/include 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/build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJCombGeom_VF.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include 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-D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJCombGeom_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJCombGeom_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJCombGeom_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJCombGeom_VgrpF.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJCombLB_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJCombLB_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJCombLB_F.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJCombLB_F.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJCombLB_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJCombLB_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJCombLB_VF.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJCombLB_VF.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJCombLB_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJCombLB_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJCombLB_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJCombLB_VgrpF.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_F.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_F.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_VF.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_VF.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_VgrpF.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include 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-I/build/reproducible-path/gromacs-2025.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time 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-I/build/reproducible-path/gromacs-2025.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJFSw_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJFSw_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJFSw_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJFSw_VgrpF.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJPSw_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJPSw_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJPSw_F.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJPSw_F.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJPSw_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJPSw_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJPSw_VF.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJPSw_VF.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJPSw_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJPSw_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJPSw_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJPSw_VgrpF.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include 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/build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJ_F.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time 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-I/build/reproducible-path/gromacs-2025.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem 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-I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombGeom_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombGeom_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombGeom_F.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombGeom_F.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombGeom_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombGeom_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombGeom_VF.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombGeom_VF.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 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-I/build/reproducible-path/gromacs-2025.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombGeom_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombGeom_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombGeom_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombGeom_VgrpF.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombLB_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombLB_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombLB_F.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombLB_F.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 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-I/build/reproducible-path/gromacs-2025.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT 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src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJEwCombGeom_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJEwCombGeom_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJEwCombGeom_F.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJEwCombGeom_F.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include 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src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJEwCombGeom_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJEwCombGeom_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJEwCombGeom_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJEwCombGeom_VgrpF.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include 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src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJFSw_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJFSw_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJFSw_VF.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJFSw_VF.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include 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src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJ_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJ_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJ_VF.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJ_VF.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/api/legacy/include 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-Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/linearalgebra/include 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-isystem /build/reproducible-path/gromacs-2025.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJCombLB_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJCombLB_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJCombLB_F.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJCombLB_F.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJCombLB_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJCombLB_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJCombLB_VF.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJCombLB_VF.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJCombLB_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJCombLB_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJCombLB_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJCombLB_VgrpF.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_F.cpp.o -MF 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-isystem /build/reproducible-path/gromacs-2025.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJFSw_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJFSw_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJFSw_F.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJFSw_F.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/linearalgebra/include 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-I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/linearalgebra/include 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-I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/linearalgebra/include 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-isystem /build/reproducible-path/gromacs-2025.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJ_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJ_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJ_F.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJ_F.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/linearalgebra/include 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-isystem /build/reproducible-path/gromacs-2025.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJ_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJ_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJ_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJ_VgrpF.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombGeom_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombGeom_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombGeom_F.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombGeom_F.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.1/src/external/colvars 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-isystem /build/reproducible-path/gromacs-2025.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombLB_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombLB_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombLB_F.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombLB_F.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/linearalgebra/include 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-g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombLB_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombLB_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombLB_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombLB_VgrpF.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJEwCombGeom_F.cpp.o -MF 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-I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJEwCombGeom_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJEwCombGeom_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJEwCombGeom_VF.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJEwCombGeom_VF.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJEwCombGeom_VgrpF.cpp.o -MF 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-I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJFSw_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJFSw_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJFSw_F.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJFSw_F.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJFSw_VF.cpp.o -MF 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-I/build/reproducible-path/gromacs-2025.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJFSw_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJFSw_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJFSw_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJFSw_VgrpF.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJPSw_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJPSw_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJPSw_F.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJPSw_F.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJPSw_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJPSw_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJPSw_VF.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJPSw_VF.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJPSw_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJPSw_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJPSw_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJPSw_VgrpF.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJ_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJ_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJ_F.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJ_F.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJ_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJ_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJ_VF.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJ_VF.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJ_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJ_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJ_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJ_VgrpF.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombGeom_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombGeom_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombGeom_F.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombGeom_F.cpp cd 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-I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombGeom_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombGeom_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombGeom_VF.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombGeom_VF.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombGeom_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombGeom_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombGeom_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombGeom_VgrpF.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombLB_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombLB_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombLB_F.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombLB_F.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombLB_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombLB_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombLB_VF.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombLB_VF.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 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src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJEwCombGeom_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJEwCombGeom_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJEwCombGeom_VF.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJEwCombGeom_VF.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include 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src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJFSw_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJFSw_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJFSw_F.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJFSw_F.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include 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-I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/taskassignment/include -isystem 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-I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. 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-I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombLB_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombLB_F.cpp.o.d -o 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-I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. 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-I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombLB_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombLB_VgrpF.cpp.o.d -o 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-I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_F.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_F.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/taskassignment/include -isystem 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-fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_VgrpF.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/simd/include 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-isystem /build/reproducible-path/gromacs-2025.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJFSw_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJFSw_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJFSw_VF.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJFSw_VF.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJFSw_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJFSw_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJFSw_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJFSw_VgrpF.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJPSw_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJPSw_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJPSw_F.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJPSw_F.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJPSw_VF.cpp.o -MF 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-I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJPSw_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJPSw_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJPSw_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJPSw_VgrpF.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJ_F.cpp.o -MF 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-I/build/reproducible-path/gromacs-2025.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJ_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJ_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJ_VF.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJ_VF.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJ_VgrpF.cpp.o -MF 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-I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombGeom_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombGeom_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombGeom_F.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombGeom_F.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombGeom_VF.cpp.o -MF 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-I/build/reproducible-path/gromacs-2025.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.1/src/external/plumed 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-I/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/simd/include 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-I/build/reproducible-path/gromacs-2025.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.1/src/external/plumed 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-I/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombLB_VgrpF.cpp.o -MF 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-I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.1/src/external/colvars 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-I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJEwCombGeom_VF.cpp.o -MF 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-I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJEwCombGeom_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJEwCombGeom_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJEwCombGeom_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJEwCombGeom_VgrpF.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJFSw_F.cpp.o -MF 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-I/build/reproducible-path/gromacs-2025.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJFSw_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJFSw_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJFSw_VF.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJFSw_VF.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJFSw_VgrpF.cpp.o -MF 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-I/build/reproducible-path/gromacs-2025.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJPSw_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJPSw_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJPSw_F.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJPSw_F.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJPSw_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJPSw_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJPSw_VF.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJPSw_VF.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJPSw_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJPSw_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJPSw_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJPSw_VgrpF.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJ_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJ_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJ_F.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJ_F.cpp cd 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-I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers 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src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_F.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_F.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include 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/build/reproducible-path/gromacs-2025.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_VF.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_VF.cpp cd 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-I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers 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-I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/gromacs/../external/rpc_xdr 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-I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers 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-I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombLB_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombLB_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombLB_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombLB_VgrpF.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_F.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_F.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_VF.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_VF.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_VgrpF.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJFSw_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJFSw_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJFSw_F.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJFSw_F.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJFSw_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJFSw_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJFSw_VF.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJFSw_VF.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJFSw_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJFSw_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJFSw_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJFSw_VgrpF.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers 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-I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/gromacs/../external/rpc_xdr 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-I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers 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-I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJ_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJ_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJ_F.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJ_F.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs && 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-I/build/reproducible-path/gromacs-2025.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJ_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJ_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJ_VF.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJ_VF.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJ_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJ_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJ_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJ_VgrpF.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs && 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-I/build/reproducible-path/gromacs-2025.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombGeom_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombGeom_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombGeom_F.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombGeom_F.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include 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src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombLB_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombLB_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombLB_VF.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombLB_VF.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include 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src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJEwCombGeom_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJEwCombGeom_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJEwCombGeom_F.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJEwCombGeom_F.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include 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src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJFSw_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJFSw_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJFSw_VF.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJFSw_VF.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include 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src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJPSw_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJPSw_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJPSw_F.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJPSw_F.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include 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src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombGeom_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombGeom_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombGeom_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombGeom_VgrpF.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include 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src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombLB_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombLB_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombLB_VF.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombLB_VF.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include 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-I/build/reproducible-path/gromacs-2025.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJEwCombGeom_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJEwCombGeom_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJEwCombGeom_F.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJEwCombGeom_F.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include 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/build/reproducible-path/gromacs-2025.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJEwCombGeom_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJEwCombGeom_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJEwCombGeom_VF.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJEwCombGeom_VF.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs && /usr/bin/c++ 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-I/build/reproducible-path/gromacs-2025.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJEwCombGeom_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJEwCombGeom_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJEwCombGeom_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJEwCombGeom_VgrpF.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJFSw_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJFSw_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJFSw_F.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJFSw_F.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H 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-I/build/reproducible-path/gromacs-2025.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT 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src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJPSw_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJPSw_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJPSw_F.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJPSw_F.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include 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src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJPSw_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJPSw_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJPSw_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJPSw_VgrpF.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include 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-isystem /build/reproducible-path/gromacs-2025.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxpreprocess/genrestr.cpp.o -MF CMakeFiles/libgromacs.dir/gmxpreprocess/genrestr.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxpreprocess/genrestr.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/genrestr.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/include 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-D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdlib/update_constrain_gpu_impl_stubs.cpp.o -MF CMakeFiles/libgromacs.dir/mdlib/update_constrain_gpu_impl_stubs.cpp.o.d -o CMakeFiles/libgromacs.dir/mdlib/update_constrain_gpu_impl_stubs.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/mdlib/update_constrain_gpu_impl_stubs.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/external/tng_io/include 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/build/reproducible-path/gromacs-2025.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdlib/update_vv.cpp.o -MF CMakeFiles/libgromacs.dir/mdlib/update_vv.cpp.o.d -o CMakeFiles/libgromacs.dir/mdlib/update_vv.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/mdlib/update_vv.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/linearalgebra/include 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-fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdlib/updategroupscog.cpp.o -MF CMakeFiles/libgromacs.dir/mdlib/updategroupscog.cpp.o.d -o CMakeFiles/libgromacs.dir/mdlib/updategroupscog.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/mdlib/updategroupscog.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/external/tng_io/include 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/build/reproducible-path/gromacs-2025.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdlib/vcm.cpp.o -MF CMakeFiles/libgromacs.dir/mdlib/vcm.cpp.o.d -o CMakeFiles/libgromacs.dir/mdlib/vcm.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/mdlib/vcm.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS 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src/gromacs/CMakeFiles/libgromacs.dir/mdrunutility/mdmodulesnotifiers.cpp.o -MF CMakeFiles/libgromacs.dir/mdrunutility/mdmodulesnotifiers.cpp.o.d -o CMakeFiles/libgromacs.dir/mdrunutility/mdmodulesnotifiers.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/mdrunutility/mdmodulesnotifiers.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/api/legacy/include 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-isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/selection/sm_same.cpp.o -MF CMakeFiles/libgromacs.dir/selection/sm_same.cpp.o.d -o CMakeFiles/libgromacs.dir/selection/sm_same.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/selection/sm_same.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/selection/sm_simple.cpp.o -MF CMakeFiles/libgromacs.dir/selection/sm_simple.cpp.o.d -o CMakeFiles/libgromacs.dir/selection/sm_simple.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/selection/sm_simple.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/selection/symrec.cpp.o -MF CMakeFiles/libgromacs.dir/selection/symrec.cpp.o.d -o CMakeFiles/libgromacs.dir/selection/symrec.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/selection/symrec.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs && /usr/bin/cmake -E cmake_link_script CMakeFiles/libgromacs.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,--dependency-file=CMakeFiles/libgromacs.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libgromacs_d.so.10 -o ../../lib/libgromacs_d.so.10.0.0 @CMakeFiles/libgromacs.dir/objects1.rsp /lib/riscv64-linux-gnu/libhwloc.so -lrt /usr/lib/riscv64-linux-gnu/libfftw3.so /usr/lib/riscv64-linux-gnu/libblas.so /usr/lib/riscv64-linux-gnu/liblapack.so /usr/lib/riscv64-linux-gnu/libblas.so /usr/lib/riscv64-linux-gnu/libm.so /usr/lib/riscv64-linux-gnu/liblapack.so /usr/lib/riscv64-linux-gnu/libm.so -lm /usr/lib/riscv64-linux-gnu/libz.so /usr/lib/gcc/riscv64-linux-gnu/14/libgomp.so /lib/riscv64-linux-gnu/libpthread.a /usr/lib/riscv64-linux-gnu/libmuparser.so.2.3.4 -ldl cd /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs && /usr/bin/cmake -E cmake_symlink_library ../../lib/libgromacs_d.so.10.0.0 ../../lib/libgromacs_d.so.10 ../../lib/libgromacs_d.so make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/basic-dp' [ 96%] Built target libgromacs /usr/bin/make -f api/gmxapi/CMakeFiles/gmxapi.dir/build.make api/gmxapi/CMakeFiles/gmxapi.dir/depend /usr/bin/make -f api/nblib/CMakeFiles/nblib.dir/build.make api/nblib/CMakeFiles/nblib.dir/depend /usr/bin/make -f src/programs/CMakeFiles/gmx.dir/build.make src/programs/CMakeFiles/gmx.dir/depend make[3]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/basic-dp' cd /build/reproducible-path/gromacs-2025.1/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.1 /build/reproducible-path/gromacs-2025.1/api/gmxapi /build/reproducible-path/gromacs-2025.1/build/basic-dp /build/reproducible-path/gromacs-2025.1/build/basic-dp/api/gmxapi /build/reproducible-path/gromacs-2025.1/build/basic-dp/api/gmxapi/CMakeFiles/gmxapi.dir/DependInfo.cmake "--color=" make[3]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/basic-dp' make[3]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/basic-dp' cd /build/reproducible-path/gromacs-2025.1/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.1 /build/reproducible-path/gromacs-2025.1/src/programs /build/reproducible-path/gromacs-2025.1/build/basic-dp /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/CMakeFiles/gmx.dir/DependInfo.cmake "--color=" cd /build/reproducible-path/gromacs-2025.1/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.1 /build/reproducible-path/gromacs-2025.1/api/nblib /build/reproducible-path/gromacs-2025.1/build/basic-dp /build/reproducible-path/gromacs-2025.1/build/basic-dp/api/nblib /build/reproducible-path/gromacs-2025.1/build/basic-dp/api/nblib/CMakeFiles/nblib.dir/DependInfo.cmake "--color=" make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/basic-dp' /usr/bin/make -f src/programs/CMakeFiles/gmx.dir/build.make src/programs/CMakeFiles/gmx.dir/build make[3]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/basic-dp' cd /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs && /usr/bin/cmake -E cmake_link_script CMakeFiles/gmx.dir/link.txt --verbose=1 make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/basic-dp' /usr/bin/make -f api/nblib/CMakeFiles/nblib.dir/build.make api/nblib/CMakeFiles/nblib.dir/build make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/basic-dp' /usr/bin/make -f api/gmxapi/CMakeFiles/gmxapi.dir/build.make api/gmxapi/CMakeFiles/gmxapi.dir/build make[3]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/basic-dp' cd /build/reproducible-path/gromacs-2025.1/build/basic-dp/api/nblib && /usr/bin/c++ -DGMX_DOUBLE=1 -DTMPI_USE_VISIBILITY -Dnblib_EXPORTS -I/build/reproducible-path/gromacs-2025.1/api/nblib/include -I/build/reproducible-path/gromacs-2025.1/api/nblib -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.1/src -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -Wno-cast-function-type-strict -MD -MT api/nblib/CMakeFiles/nblib.dir/box.cpp.o -MF CMakeFiles/nblib.dir/box.cpp.o.d -o CMakeFiles/nblib.dir/box.cpp.o -c /build/reproducible-path/gromacs-2025.1/api/nblib/box.cpp make[3]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/basic-dp' cd /build/reproducible-path/gromacs-2025.1/build/basic-dp/api/gmxapi && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -Dgmxapi_EXPORTS -I/build/reproducible-path/gromacs-2025.1/api/gmxapi/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/api/gmxapi/include -I/build/reproducible-path/gromacs-2025.1/api/gmxapi/cpp -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT api/gmxapi/CMakeFiles/gmxapi.dir/cpp/resourceassignment.cpp.o -MF CMakeFiles/gmxapi.dir/cpp/resourceassignment.cpp.o.d -o CMakeFiles/gmxapi.dir/cpp/resourceassignment.cpp.o -c /build/reproducible-path/gromacs-2025.1/api/gmxapi/cpp/resourceassignment.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic-dp/api/nblib && /usr/bin/c++ -DGMX_DOUBLE=1 -DTMPI_USE_VISIBILITY -Dnblib_EXPORTS -I/build/reproducible-path/gromacs-2025.1/api/nblib/include -I/build/reproducible-path/gromacs-2025.1/api/nblib -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.1/src -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -Wno-cast-function-type-strict -MD -MT api/nblib/CMakeFiles/nblib.dir/gmxcalculatorcpu.cpp.o -MF CMakeFiles/nblib.dir/gmxcalculatorcpu.cpp.o.d -o CMakeFiles/nblib.dir/gmxcalculatorcpu.cpp.o -c /build/reproducible-path/gromacs-2025.1/api/nblib/gmxcalculatorcpu.cpp /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/gmx.dir/link.d CMakeFiles/gmx_objlib.dir/gmx.cpp.o CMakeFiles/gmx_objlib.dir/legacymodules.cpp.o CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o CMakeFiles/mdrun_objlib.dir/mdrun/nonbonded_bench.cpp.o -o ../../bin/gmx_d ../../lib/libgromacs_d.so.10.0.0 /usr/lib/riscv64-linux-gnu/libm.so /usr/lib/gcc/riscv64-linux-gnu/14/libgomp.so /lib/riscv64-linux-gnu/libpthread.a make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/basic-dp' [ 96%] Built target gmx cd /build/reproducible-path/gromacs-2025.1/build/basic-dp/api/nblib && /usr/bin/c++ -DGMX_DOUBLE=1 -DTMPI_USE_VISIBILITY -Dnblib_EXPORTS -I/build/reproducible-path/gromacs-2025.1/api/nblib/include -I/build/reproducible-path/gromacs-2025.1/api/nblib -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.1/src -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -Wno-cast-function-type-strict -MD -MT api/nblib/CMakeFiles/nblib.dir/integrator.cpp.o -MF CMakeFiles/nblib.dir/integrator.cpp.o.d -o CMakeFiles/nblib.dir/integrator.cpp.o -c /build/reproducible-path/gromacs-2025.1/api/nblib/integrator.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic-dp/api/nblib && /usr/bin/c++ -DGMX_DOUBLE=1 -DTMPI_USE_VISIBILITY -Dnblib_EXPORTS -I/build/reproducible-path/gromacs-2025.1/api/nblib/include -I/build/reproducible-path/gromacs-2025.1/api/nblib -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.1/src -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -Wno-cast-function-type-strict -MD -MT api/nblib/CMakeFiles/nblib.dir/interactions.cpp.o -MF CMakeFiles/nblib.dir/interactions.cpp.o.d -o CMakeFiles/nblib.dir/interactions.cpp.o -c /build/reproducible-path/gromacs-2025.1/api/nblib/interactions.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic-dp/api/gmxapi && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -Dgmxapi_EXPORTS -I/build/reproducible-path/gromacs-2025.1/api/gmxapi/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/api/gmxapi/include -I/build/reproducible-path/gromacs-2025.1/api/gmxapi/cpp 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CMakeFiles/gmxapi.dir/cpp/context.cpp.o -c /build/reproducible-path/gromacs-2025.1/api/gmxapi/cpp/context.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic-dp/api/nblib && /usr/bin/c++ -DGMX_DOUBLE=1 -DTMPI_USE_VISIBILITY -Dnblib_EXPORTS -I/build/reproducible-path/gromacs-2025.1/api/nblib/include -I/build/reproducible-path/gromacs-2025.1/api/nblib -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pulling/include 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-fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -Wno-cast-function-type-strict -MD -MT api/nblib/CMakeFiles/nblib.dir/nbnxmsetuphelpers.cpp.o -MF CMakeFiles/nblib.dir/nbnxmsetuphelpers.cpp.o.d -o CMakeFiles/nblib.dir/nbnxmsetuphelpers.cpp.o -c /build/reproducible-path/gromacs-2025.1/api/nblib/nbnxmsetuphelpers.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic-dp/api/gmxapi && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -Dgmxapi_EXPORTS -I/build/reproducible-path/gromacs-2025.1/api/gmxapi/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/api/gmxapi/include -I/build/reproducible-path/gromacs-2025.1/api/gmxapi/cpp -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.1/src 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-D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT api/gmxapi/CMakeFiles/gmxapi.dir/cpp/gmxapi.cpp.o -MF CMakeFiles/gmxapi.dir/cpp/gmxapi.cpp.o.d -o CMakeFiles/gmxapi.dir/cpp/gmxapi.cpp.o -c /build/reproducible-path/gromacs-2025.1/api/gmxapi/cpp/gmxapi.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic-dp/api/gmxapi && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -Dgmxapi_EXPORTS -I/build/reproducible-path/gromacs-2025.1/api/gmxapi/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/api/gmxapi/include -I/build/reproducible-path/gromacs-2025.1/api/gmxapi/cpp -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT api/gmxapi/CMakeFiles/gmxapi.dir/cpp/md.cpp.o -MF CMakeFiles/gmxapi.dir/cpp/md.cpp.o.d -o CMakeFiles/gmxapi.dir/cpp/md.cpp.o -c /build/reproducible-path/gromacs-2025.1/api/gmxapi/cpp/md.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic-dp/api/nblib && /usr/bin/c++ -DGMX_DOUBLE=1 -DTMPI_USE_VISIBILITY -Dnblib_EXPORTS -I/build/reproducible-path/gromacs-2025.1/api/nblib/include 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-fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -Wno-cast-function-type-strict -MD -MT api/nblib/CMakeFiles/nblib.dir/particlesequencer.cpp.o -MF CMakeFiles/nblib.dir/particlesequencer.cpp.o.d -o CMakeFiles/nblib.dir/particlesequencer.cpp.o -c /build/reproducible-path/gromacs-2025.1/api/nblib/particlesequencer.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic-dp/api/nblib && /usr/bin/c++ -DGMX_DOUBLE=1 -DTMPI_USE_VISIBILITY -Dnblib_EXPORTS -I/build/reproducible-path/gromacs-2025.1/api/nblib/include -I/build/reproducible-path/gromacs-2025.1/api/nblib -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/api/legacy/include 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CMakeFiles/nblib.dir/particletype.cpp.o.d -o CMakeFiles/nblib.dir/particletype.cpp.o -c /build/reproducible-path/gromacs-2025.1/api/nblib/particletype.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic-dp/api/gmxapi && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -Dgmxapi_EXPORTS -I/build/reproducible-path/gromacs-2025.1/api/gmxapi/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/api/gmxapi/include -I/build/reproducible-path/gromacs-2025.1/api/gmxapi/cpp -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT api/gmxapi/CMakeFiles/gmxapi.dir/cpp/mdmodule.cpp.o -MF CMakeFiles/gmxapi.dir/cpp/mdmodule.cpp.o.d -o CMakeFiles/gmxapi.dir/cpp/mdmodule.cpp.o -c /build/reproducible-path/gromacs-2025.1/api/gmxapi/cpp/mdmodule.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic-dp/api/nblib && /usr/bin/c++ -DGMX_DOUBLE=1 -DTMPI_USE_VISIBILITY -Dnblib_EXPORTS -I/build/reproducible-path/gromacs-2025.1/api/nblib/include -I/build/reproducible-path/gromacs-2025.1/api/nblib -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/include 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-fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -Wno-cast-function-type-strict -MD -MT api/nblib/CMakeFiles/nblib.dir/topologyhelpers.cpp.o -MF CMakeFiles/nblib.dir/topologyhelpers.cpp.o.d -o CMakeFiles/nblib.dir/topologyhelpers.cpp.o -c /build/reproducible-path/gromacs-2025.1/api/nblib/topologyhelpers.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic-dp/api/nblib && /usr/bin/c++ -DGMX_DOUBLE=1 -DTMPI_USE_VISIBILITY -Dnblib_EXPORTS -I/build/reproducible-path/gromacs-2025.1/api/nblib/include -I/build/reproducible-path/gromacs-2025.1/api/nblib -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/api/legacy/include 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CMakeFiles/nblib.dir/topology.cpp.o.d -o CMakeFiles/nblib.dir/topology.cpp.o -c /build/reproducible-path/gromacs-2025.1/api/nblib/topology.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic-dp/api/gmxapi && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -Dgmxapi_EXPORTS -I/build/reproducible-path/gromacs-2025.1/api/gmxapi/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/api/gmxapi/include -I/build/reproducible-path/gromacs-2025.1/api/gmxapi/cpp -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT api/gmxapi/CMakeFiles/gmxapi.dir/cpp/session.cpp.o -MF CMakeFiles/gmxapi.dir/cpp/session.cpp.o.d -o CMakeFiles/gmxapi.dir/cpp/session.cpp.o -c /build/reproducible-path/gromacs-2025.1/api/gmxapi/cpp/session.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic-dp/api/nblib && /usr/bin/c++ -DGMX_DOUBLE=1 -DTMPI_USE_VISIBILITY -Dnblib_EXPORTS -I/build/reproducible-path/gromacs-2025.1/api/nblib/include -I/build/reproducible-path/gromacs-2025.1/api/nblib -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/include 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-I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT api/gmxapi/CMakeFiles/gmxapi.dir/cpp/status.cpp.o -MF CMakeFiles/gmxapi.dir/cpp/status.cpp.o.d -o CMakeFiles/gmxapi.dir/cpp/status.cpp.o -c /build/reproducible-path/gromacs-2025.1/api/gmxapi/cpp/status.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic-dp/api/nblib && /usr/bin/c++ -DGMX_DOUBLE=1 -DTMPI_USE_VISIBILITY -Dnblib_EXPORTS -I/build/reproducible-path/gromacs-2025.1/api/nblib/include -I/build/reproducible-path/gromacs-2025.1/api/nblib -I/build/reproducible-path/gromacs-2025.1/src/include 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-fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -Wno-cast-function-type-strict -MD -MT api/nblib/CMakeFiles/nblib.dir/virials.cpp.o -MF CMakeFiles/nblib.dir/virials.cpp.o.d -o CMakeFiles/nblib.dir/virials.cpp.o -c /build/reproducible-path/gromacs-2025.1/api/nblib/virials.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic-dp/api/gmxapi && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -Dgmxapi_EXPORTS -I/build/reproducible-path/gromacs-2025.1/api/gmxapi/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/api/gmxapi/include -I/build/reproducible-path/gromacs-2025.1/api/gmxapi/cpp -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT api/gmxapi/CMakeFiles/gmxapi.dir/cpp/system.cpp.o -MF CMakeFiles/gmxapi.dir/cpp/system.cpp.o.d -o CMakeFiles/gmxapi.dir/cpp/system.cpp.o -c /build/reproducible-path/gromacs-2025.1/api/gmxapi/cpp/system.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic-dp/api/nblib && /usr/bin/c++ -DGMX_DOUBLE=1 -DTMPI_USE_VISIBILITY -Dnblib_EXPORTS -I/build/reproducible-path/gromacs-2025.1/api/nblib/include 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-fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -Wno-cast-function-type-strict -MD -MT api/nblib/CMakeFiles/nblib.dir/listed_forces/calculator.cpp.o -MF CMakeFiles/nblib.dir/listed_forces/calculator.cpp.o.d -o CMakeFiles/nblib.dir/listed_forces/calculator.cpp.o -c /build/reproducible-path/gromacs-2025.1/api/nblib/listed_forces/calculator.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic-dp/api/gmxapi && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -Dgmxapi_EXPORTS -I/build/reproducible-path/gromacs-2025.1/api/gmxapi/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/api/gmxapi/include -I/build/reproducible-path/gromacs-2025.1/api/gmxapi/cpp -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT api/gmxapi/CMakeFiles/gmxapi.dir/cpp/version.cpp.o -MF CMakeFiles/gmxapi.dir/cpp/version.cpp.o.d -o CMakeFiles/gmxapi.dir/cpp/version.cpp.o -c /build/reproducible-path/gromacs-2025.1/api/gmxapi/cpp/version.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic-dp/api/gmxapi && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -Dgmxapi_EXPORTS -I/build/reproducible-path/gromacs-2025.1/api/gmxapi/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/api/gmxapi/include -I/build/reproducible-path/gromacs-2025.1/api/gmxapi/cpp -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT api/gmxapi/CMakeFiles/gmxapi.dir/cpp/workflow.cpp.o -MF CMakeFiles/gmxapi.dir/cpp/workflow.cpp.o.d -o CMakeFiles/gmxapi.dir/cpp/workflow.cpp.o -c /build/reproducible-path/gromacs-2025.1/api/gmxapi/cpp/workflow.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic-dp/api/gmxapi && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -Dgmxapi_EXPORTS -I/build/reproducible-path/gromacs-2025.1/api/gmxapi/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/api/gmxapi/include -I/build/reproducible-path/gromacs-2025.1/api/gmxapi/cpp -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT api/gmxapi/CMakeFiles/gmxapi.dir/cpp/tpr.cpp.o -MF CMakeFiles/gmxapi.dir/cpp/tpr.cpp.o.d -o CMakeFiles/gmxapi.dir/cpp/tpr.cpp.o -c /build/reproducible-path/gromacs-2025.1/api/gmxapi/cpp/tpr.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic-dp/api/nblib && /usr/bin/c++ -DGMX_DOUBLE=1 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-I/build/reproducible-path/gromacs-2025.1/src -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -Wno-cast-function-type-strict -MD -MT api/nblib/CMakeFiles/nblib.dir/listed_forces/transformations.cpp.o -MF CMakeFiles/nblib.dir/listed_forces/transformations.cpp.o.d -o CMakeFiles/nblib.dir/listed_forces/transformations.cpp.o -c /build/reproducible-path/gromacs-2025.1/api/nblib/listed_forces/transformations.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic-dp/api/nblib && /usr/bin/c++ -DGMX_DOUBLE=1 -DTMPI_USE_VISIBILITY -Dnblib_EXPORTS -I/build/reproducible-path/gromacs-2025.1/api/nblib/include -I/build/reproducible-path/gromacs-2025.1/api/nblib -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.1/src -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -Wno-cast-function-type-strict -MD -MT api/nblib/CMakeFiles/nblib.dir/listed_forces/conversions.cpp.o -MF CMakeFiles/nblib.dir/listed_forces/conversions.cpp.o.d -o CMakeFiles/nblib.dir/listed_forces/conversions.cpp.o -c /build/reproducible-path/gromacs-2025.1/api/nblib/listed_forces/conversions.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic-dp/api/gmxapi && /usr/bin/cmake -E cmake_link_script CMakeFiles/gmxapi.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,--dependency-file=CMakeFiles/gmxapi.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libgmxapi_d.so.0 -o ../../lib/libgmxapi_d.so.0.4.0 CMakeFiles/gmxapi.dir/cpp/resourceassignment.cpp.o CMakeFiles/gmxapi.dir/cpp/context.cpp.o CMakeFiles/gmxapi.dir/cpp/exceptions.cpp.o CMakeFiles/gmxapi.dir/cpp/gmxapi.cpp.o CMakeFiles/gmxapi.dir/cpp/md.cpp.o CMakeFiles/gmxapi.dir/cpp/mdmodule.cpp.o CMakeFiles/gmxapi.dir/cpp/mdsignals.cpp.o CMakeFiles/gmxapi.dir/cpp/session.cpp.o CMakeFiles/gmxapi.dir/cpp/status.cpp.o CMakeFiles/gmxapi.dir/cpp/system.cpp.o CMakeFiles/gmxapi.dir/cpp/version.cpp.o CMakeFiles/gmxapi.dir/cpp/workflow.cpp.o CMakeFiles/gmxapi.dir/cpp/tpr.cpp.o ../../lib/libgromacs_d.so.10.0.0 /usr/lib/riscv64-linux-gnu/libm.so /usr/lib/gcc/riscv64-linux-gnu/14/libgomp.so /lib/riscv64-linux-gnu/libpthread.a cd /build/reproducible-path/gromacs-2025.1/build/basic-dp/api/gmxapi && /usr/bin/cmake -E cmake_symlink_library ../../lib/libgmxapi_d.so.0.4.0 ../../lib/libgmxapi_d.so.0 ../../lib/libgmxapi_d.so make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/basic-dp' [ 98%] Built target gmxapi cd /build/reproducible-path/gromacs-2025.1/build/basic-dp/api/nblib && /usr/bin/c++ -DGMX_DOUBLE=1 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-I/build/reproducible-path/gromacs-2025.1/src -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -Wno-cast-function-type-strict -MD -MT api/nblib/CMakeFiles/nblib.dir/listed_forces/convertGmxToNblib.cpp.o -MF CMakeFiles/nblib.dir/listed_forces/convertGmxToNblib.cpp.o.d -o CMakeFiles/nblib.dir/listed_forces/convertGmxToNblib.cpp.o -c /build/reproducible-path/gromacs-2025.1/api/nblib/listed_forces/convertGmxToNblib.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic-dp/api/nblib && /usr/bin/c++ -DGMX_DOUBLE=1 -DTMPI_USE_VISIBILITY -Dnblib_EXPORTS -I/build/reproducible-path/gromacs-2025.1/api/nblib/include -I/build/reproducible-path/gromacs-2025.1/api/nblib -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.1/src -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -Wno-cast-function-type-strict -MD -MT api/nblib/CMakeFiles/nblib.dir/util/setup.cpp.o -MF CMakeFiles/nblib.dir/util/setup.cpp.o.d -o CMakeFiles/nblib.dir/util/setup.cpp.o -c /build/reproducible-path/gromacs-2025.1/api/nblib/util/setup.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic-dp/api/nblib && /usr/bin/cmake -E cmake_link_script CMakeFiles/nblib.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,--dependency-file=CMakeFiles/nblib.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libnblib_gmx.so.0 -o ../../lib/libnblib_gmx.so.0.1.0 CMakeFiles/nblib.dir/box.cpp.o CMakeFiles/nblib.dir/gmxcalculatorcpu.cpp.o CMakeFiles/nblib.dir/integrator.cpp.o CMakeFiles/nblib.dir/interactions.cpp.o CMakeFiles/nblib.dir/molecules.cpp.o CMakeFiles/nblib.dir/nbnxmsetuphelpers.cpp.o CMakeFiles/nblib.dir/particlesequencer.cpp.o CMakeFiles/nblib.dir/particletype.cpp.o CMakeFiles/nblib.dir/simulationstate.cpp.o CMakeFiles/nblib.dir/topologyhelpers.cpp.o CMakeFiles/nblib.dir/topology.cpp.o CMakeFiles/nblib.dir/tpr.cpp.o CMakeFiles/nblib.dir/virials.cpp.o CMakeFiles/nblib.dir/listed_forces/calculator.cpp.o CMakeFiles/nblib.dir/listed_forces/transformations.cpp.o CMakeFiles/nblib.dir/listed_forces/conversions.cpp.o CMakeFiles/nblib.dir/listed_forces/convertGmxToNblib.cpp.o CMakeFiles/nblib.dir/util/setup.cpp.o /usr/lib/riscv64-linux-gnu/libm.so ../../lib/libgromacs_d.so.10.0.0 /usr/lib/riscv64-linux-gnu/libm.so /usr/lib/gcc/riscv64-linux-gnu/14/libgomp.so /lib/riscv64-linux-gnu/libpthread.a /usr/lib/riscv64-linux-gnu/libmuparser.so.2.3.4 cd /build/reproducible-path/gromacs-2025.1/build/basic-dp/api/nblib && /usr/bin/cmake -E cmake_symlink_library ../../lib/libnblib_gmx.so.0.1.0 ../../lib/libnblib_gmx.so.0 ../../lib/libnblib_gmx.so make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/basic-dp' [100%] Built target nblib /usr/bin/make -f api/nblib/samples/CMakeFiles/argon-forces-integration.dir/build.make api/nblib/samples/CMakeFiles/argon-forces-integration.dir/depend /usr/bin/make -f api/nblib/samples/CMakeFiles/methane-water-integration.dir/build.make api/nblib/samples/CMakeFiles/methane-water-integration.dir/depend make[3]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/basic-dp' cd /build/reproducible-path/gromacs-2025.1/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.1 /build/reproducible-path/gromacs-2025.1/api/nblib/samples /build/reproducible-path/gromacs-2025.1/build/basic-dp /build/reproducible-path/gromacs-2025.1/build/basic-dp/api/nblib/samples /build/reproducible-path/gromacs-2025.1/build/basic-dp/api/nblib/samples/CMakeFiles/argon-forces-integration.dir/DependInfo.cmake "--color=" make[3]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/basic-dp' cd /build/reproducible-path/gromacs-2025.1/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.1 /build/reproducible-path/gromacs-2025.1/api/nblib/samples /build/reproducible-path/gromacs-2025.1/build/basic-dp /build/reproducible-path/gromacs-2025.1/build/basic-dp/api/nblib/samples /build/reproducible-path/gromacs-2025.1/build/basic-dp/api/nblib/samples/CMakeFiles/methane-water-integration.dir/DependInfo.cmake "--color=" make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/basic-dp' make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/basic-dp' /usr/bin/make -f api/nblib/samples/CMakeFiles/argon-forces-integration.dir/build.make api/nblib/samples/CMakeFiles/argon-forces-integration.dir/build /usr/bin/make -f api/nblib/samples/CMakeFiles/methane-water-integration.dir/build.make api/nblib/samples/CMakeFiles/methane-water-integration.dir/build make[3]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/basic-dp' cd /build/reproducible-path/gromacs-2025.1/build/basic-dp/api/nblib/samples && /usr/bin/c++ -DGMX_DOUBLE=1 -I/build/reproducible-path/gromacs-2025.1/api/nblib/include -I/build/reproducible-path/gromacs-2025.1/api/nblib -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/api/legacy/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fopenmp -MD -MT api/nblib/samples/CMakeFiles/argon-forces-integration.dir/argon-forces-integration.cpp.o -MF CMakeFiles/argon-forces-integration.dir/argon-forces-integration.cpp.o.d -o CMakeFiles/argon-forces-integration.dir/argon-forces-integration.cpp.o -c /build/reproducible-path/gromacs-2025.1/api/nblib/samples/argon-forces-integration.cpp make[3]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/basic-dp' cd /build/reproducible-path/gromacs-2025.1/build/basic-dp/api/nblib/samples && /usr/bin/c++ -DGMX_DOUBLE=1 -I/build/reproducible-path/gromacs-2025.1/api/nblib/include -I/build/reproducible-path/gromacs-2025.1/api/nblib -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/api/legacy/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fopenmp -MD -MT api/nblib/samples/CMakeFiles/methane-water-integration.dir/methane-water-integration.cpp.o -MF CMakeFiles/methane-water-integration.dir/methane-water-integration.cpp.o.d -o CMakeFiles/methane-water-integration.dir/methane-water-integration.cpp.o -c /build/reproducible-path/gromacs-2025.1/api/nblib/samples/methane-water-integration.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic-dp/api/nblib/samples && /usr/bin/cmake -E cmake_link_script CMakeFiles/argon-forces-integration.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/argon-forces-integration.dir/link.d "CMakeFiles/argon-forces-integration.dir/argon-forces-integration.cpp.o" -o ../../../bin/argon-forces-integration ../../../lib/libnblib_gmx.so.0.1.0 /usr/lib/riscv64-linux-gnu/libm.so /usr/lib/gcc/riscv64-linux-gnu/14/libgomp.so /lib/riscv64-linux-gnu/libpthread.a -Wl,-rpath-link,/build/reproducible-path/gromacs-2025.1/build/basic-dp/lib make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/basic-dp' [100%] Built target 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&& /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/src/testutils/include -I/build/reproducible-path/gromacs-2025.1/src/testutils -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/tinyxml2 -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock/include 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src/gromacs/utility/tests/CMakeFiles/utility-mpi-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/basic' cd /build/reproducible-path/gromacs-2025.1/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.1 /build/reproducible-path/gromacs-2025.1/src/gromacs/utility/tests /build/reproducible-path/gromacs-2025.1/build/basic /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/utility/tests /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/utility/tests/CMakeFiles/utility-mpi-test.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/basic' /usr/bin/make -f src/gromacs/utility/tests/CMakeFiles/utility-mpi-test.dir/build.make src/gromacs/utility/tests/CMakeFiles/utility-mpi-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/basic' cd 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/build/reproducible-path/gromacs-2025.1/src/gromacs/mdlib/tests/constr.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/mdlib/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/mdlib/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/src/testutils/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include 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-DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/mdlib/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/src/testutils/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/timing/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/mdlib/tests/CMakeFiles/mdlib-test.dir/energydrifttracker.cpp.o -MF CMakeFiles/mdlib-test.dir/energydrifttracker.cpp.o.d -o CMakeFiles/mdlib-test.dir/energydrifttracker.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/mdlib/tests/energydrifttracker.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/utility/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/utility/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/src/testutils/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/utility/tests/CMakeFiles/utility-test.dir/cstringutil.cpp.o -MF CMakeFiles/utility-test.dir/cstringutil.cpp.o.d -o CMakeFiles/utility-test.dir/cstringutil.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/utility/tests/cstringutil.cpp /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/nonbonded-fep-test.dir/link.d "CMakeFiles/nonbonded-fep-test.dir/nb_free_energy.cpp.o" "CMakeFiles/nonbonded-fep-test.dir/__/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../../bin/nonbonded-fep-test ../../../../../lib/libtestutils.a ../../../../../lib/libtestutils.a ../../../../../lib/libgromacs.so.10.0.0 /usr/lib/riscv64-linux-gnu/libm.so ../../../../../lib/libgmock.so.1.13.0 ../../../../../lib/libgtest.so.1.13.0 /usr/lib/gcc/riscv64-linux-gnu/14/libgomp.so /lib/riscv64-linux-gnu/libpthread.a /usr/lib/riscv64-linux-gnu/libmuparser.so.2.3.4 make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/basic' [ 66%] Built target nonbonded-fep-test /usr/bin/make -f src/gromacs/applied_forces/awh/tests/CMakeFiles/awh-test.dir/build.make src/gromacs/applied_forces/awh/tests/CMakeFiles/awh-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/basic' cd /build/reproducible-path/gromacs-2025.1/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.1 /build/reproducible-path/gromacs-2025.1/src/gromacs/applied_forces/awh/tests /build/reproducible-path/gromacs-2025.1/build/basic /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/applied_forces/awh/tests /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/applied_forces/awh/tests/CMakeFiles/awh-test.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/basic' /usr/bin/make -f src/gromacs/applied_forces/awh/tests/CMakeFiles/awh-test.dir/build.make src/gromacs/applied_forces/awh/tests/CMakeFiles/awh-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/basic' cd /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/applied_forces/awh/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/applied_forces/awh/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/applied_forces/awh/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/src/testutils/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/applied_forces/awh/tests/CMakeFiles/awh-test.dir/awh_setup.cpp.o -MF CMakeFiles/awh-test.dir/awh_setup.cpp.o.d -o CMakeFiles/awh-test.dir/awh_setup.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/applied_forces/awh/tests/awh_setup.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/mdlib/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/mdlib/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/src/testutils/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/timing/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/mdlib/tests/CMakeFiles/mdlib-test.dir/energyoutput.cpp.o -MF CMakeFiles/mdlib-test.dir/energyoutput.cpp.o.d -o CMakeFiles/mdlib-test.dir/energyoutput.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/mdlib/tests/energyoutput.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/mdlib/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/mdlib/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/src/testutils/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/timing/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/mdlib/tests/CMakeFiles/mdlib-test.dir/expanded.cpp.o -MF CMakeFiles/mdlib-test.dir/expanded.cpp.o.d -o CMakeFiles/mdlib-test.dir/expanded.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/mdlib/tests/expanded.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/utility/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/utility/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/src/testutils/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/utility/tests/CMakeFiles/utility-test.dir/defaultinitializationallocator.cpp.o -MF CMakeFiles/utility-test.dir/defaultinitializationallocator.cpp.o.d -o CMakeFiles/utility-test.dir/defaultinitializationallocator.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/utility/tests/defaultinitializationallocator.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/utility/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/utility/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/src/testutils/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem 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/build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/applied_forces/awh/tests/CMakeFiles/awh-test.dir/biasgrid.cpp.o -MF CMakeFiles/awh-test.dir/biasgrid.cpp.o.d -o CMakeFiles/awh-test.dir/biasgrid.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/applied_forces/awh/tests/biasgrid.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/mdlib/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/mdlib/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/src/testutils/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/timing/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/mdlib/tests/CMakeFiles/mdlib-test.dir/leapfrog.cpp.o -MF CMakeFiles/mdlib-test.dir/leapfrog.cpp.o.d -o CMakeFiles/mdlib-test.dir/leapfrog.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/mdlib/tests/leapfrog.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/mdlib/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/mdlib/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/src/testutils/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/timing/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/mdlib/tests/CMakeFiles/mdlib-test.dir/leapfrogtestdata.cpp.o -MF CMakeFiles/mdlib-test.dir/leapfrogtestdata.cpp.o.d -o CMakeFiles/mdlib-test.dir/leapfrogtestdata.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/mdlib/tests/leapfrogtestdata.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/applied_forces/awh/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/applied_forces/awh/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/applied_forces/awh/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/src/testutils/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/applied_forces/awh/tests/CMakeFiles/awh-test.dir/biassharing.cpp.o -MF CMakeFiles/awh-test.dir/biassharing.cpp.o.d -o CMakeFiles/awh-test.dir/biassharing.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/applied_forces/awh/tests/biassharing.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/utility/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/utility/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/src/testutils/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/utility/tests/CMakeFiles/utility-test.dir/keyvaluetreetransform.cpp.o -MF CMakeFiles/utility-test.dir/keyvaluetreetransform.cpp.o.d -o CMakeFiles/utility-test.dir/keyvaluetreetransform.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/utility/tests/keyvaluetreetransform.cpp /usr/bin/make -f src/gromacs/applied_forces/densityfitting/tests/CMakeFiles/density_fitting_applied_forces-test.dir/build.make src/gromacs/applied_forces/densityfitting/tests/CMakeFiles/density_fitting_applied_forces-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/basic' cd /build/reproducible-path/gromacs-2025.1/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.1 /build/reproducible-path/gromacs-2025.1/src/gromacs/applied_forces/densityfitting/tests /build/reproducible-path/gromacs-2025.1/build/basic /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/applied_forces/densityfitting/tests /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/applied_forces/densityfitting/tests/CMakeFiles/density_fitting_applied_forces-test.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/basic' /usr/bin/make -f src/gromacs/applied_forces/densityfitting/tests/CMakeFiles/density_fitting_applied_forces-test.dir/build.make src/gromacs/applied_forces/densityfitting/tests/CMakeFiles/density_fitting_applied_forces-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/basic' cd /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/applied_forces/densityfitting/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/applied_forces/densityfitting/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/applied_forces/densityfitting/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/src/testutils/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/applied_forces/densityfitting/tests/CMakeFiles/density_fitting_applied_forces-test.dir/densityfitting.cpp.o -MF CMakeFiles/density_fitting_applied_forces-test.dir/densityfitting.cpp.o.d -o CMakeFiles/density_fitting_applied_forces-test.dir/densityfitting.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/applied_forces/densityfitting/tests/densityfitting.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/mdlib/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/mdlib/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/src/testutils/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/timing/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/mdlib/tests/CMakeFiles/mdlib-test.dir/leapfrogtestrunners.cpp.o -MF CMakeFiles/mdlib-test.dir/leapfrogtestrunners.cpp.o.d -o CMakeFiles/mdlib-test.dir/leapfrogtestrunners.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/mdlib/tests/leapfrogtestrunners.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/applied_forces/awh/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/applied_forces/awh/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/applied_forces/awh/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/src/testutils/include 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-DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/applied_forces/awh/tests/CMakeFiles/awh-test.dir/friction_metric.cpp.o -MF CMakeFiles/awh-test.dir/friction_metric.cpp.o.d -o CMakeFiles/awh-test.dir/friction_metric.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/applied_forces/awh/tests/friction_metric.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/utility/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/utility/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/src/testutils/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/utility/tests/CMakeFiles/utility-test.dir/path.cpp.o -MF CMakeFiles/utility-test.dir/path.cpp.o.d -o CMakeFiles/utility-test.dir/path.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/utility/tests/path.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/applied_forces/densityfitting/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/applied_forces/densityfitting/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/applied_forces/densityfitting/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/src/testutils/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic/src/include 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-Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/applied_forces/densityfitting/tests/CMakeFiles/density_fitting_applied_forces-test.dir/__/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/density_fitting_applied_forces-test.dir/__/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/density_fitting_applied_forces-test.dir/__/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/mdlib/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/mdlib/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/src/testutils/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/timing/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/external/muparser 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/usr/bin/cmake -E cmake_link_script CMakeFiles/density_fitting_applied_forces-test.dir/link.txt --verbose=1 cd /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/applied_forces/awh/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/applied_forces/awh/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/applied_forces/awh/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/src/testutils/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/applied_forces/awh/tests/CMakeFiles/awh-test.dir/__/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/awh-test.dir/__/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/awh-test.dir/__/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/mdlib/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/mdlib/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/src/testutils/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/timing/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/mdlib/tests/CMakeFiles/mdlib-test.dir/settletestrunners.cpp.o -MF CMakeFiles/mdlib-test.dir/settletestrunners.cpp.o.d -o CMakeFiles/mdlib-test.dir/settletestrunners.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/mdlib/tests/settletestrunners.cpp /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/density_fitting_applied_forces-test.dir/link.d "CMakeFiles/density_fitting_applied_forces-test.dir/densityfitting.cpp.o" "CMakeFiles/density_fitting_applied_forces-test.dir/densityfittingamplitudelookup.cpp.o" "CMakeFiles/density_fitting_applied_forces-test.dir/densityfittingforceprovider.cpp.o" "CMakeFiles/density_fitting_applied_forces-test.dir/densityfittingoptions.cpp.o" "CMakeFiles/density_fitting_applied_forces-test.dir/__/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../../bin/density_fitting_applied_forces-test ../../../../../lib/libtestutils.a ../../../../../lib/libgromacs.so.10.0.0 ../../../../../lib/libgmock.so.1.13.0 /usr/lib/riscv64-linux-gnu/libm.so /usr/lib/gcc/riscv64-linux-gnu/14/libgomp.so /lib/riscv64-linux-gnu/libpthread.a ../../../../../lib/libgtest.so.1.13.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/basic' [ 67%] Built target density_fitting_applied_forces-test /usr/bin/make -f src/gromacs/applied_forces/qmmm/tests/CMakeFiles/qmmm_applied_forces-test.dir/build.make src/gromacs/applied_forces/qmmm/tests/CMakeFiles/qmmm_applied_forces-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/basic' cd /build/reproducible-path/gromacs-2025.1/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.1 /build/reproducible-path/gromacs-2025.1/src/gromacs/applied_forces/qmmm/tests /build/reproducible-path/gromacs-2025.1/build/basic /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/applied_forces/qmmm/tests /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/applied_forces/qmmm/tests/CMakeFiles/qmmm_applied_forces-test.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/basic' /usr/bin/make -f src/gromacs/applied_forces/qmmm/tests/CMakeFiles/qmmm_applied_forces-test.dir/build.make src/gromacs/applied_forces/qmmm/tests/CMakeFiles/qmmm_applied_forces-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/basic' cd /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/applied_forces/qmmm/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/applied_forces/qmmm/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/src/testutils/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/applied_forces/qmmm/tests/CMakeFiles/qmmm_applied_forces-test.dir/qmmminputgenerator.cpp.o -MF CMakeFiles/qmmm_applied_forces-test.dir/qmmminputgenerator.cpp.o.d -o CMakeFiles/qmmm_applied_forces-test.dir/qmmminputgenerator.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/applied_forces/qmmm/tests/qmmminputgenerator.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/utility/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/utility/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/src/testutils/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/utility/tests/CMakeFiles/utility-test.dir/physicalnodecommunicator.cpp.o -MF CMakeFiles/utility-test.dir/physicalnodecommunicator.cpp.o.d -o CMakeFiles/utility-test.dir/physicalnodecommunicator.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/utility/tests/physicalnodecommunicator.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/applied_forces/awh/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/awh-test.dir/link.txt --verbose=1 cd /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/mdlib/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/mdlib/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/src/testutils/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/timing/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/mdlib/tests/CMakeFiles/mdlib-test.dir/shake.cpp.o -MF CMakeFiles/mdlib-test.dir/shake.cpp.o.d -o CMakeFiles/mdlib-test.dir/shake.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/mdlib/tests/shake.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/utility/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/utility/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/src/testutils/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/utility/tests/CMakeFiles/utility-test.dir/range.cpp.o -MF CMakeFiles/utility-test.dir/range.cpp.o.d -o CMakeFiles/utility-test.dir/range.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/utility/tests/range.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/applied_forces/qmmm/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/applied_forces/qmmm/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/src/testutils/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/applied_forces/qmmm/tests/CMakeFiles/qmmm_applied_forces-test.dir/qmmmtopologypreprocessor.cpp.o -MF CMakeFiles/qmmm_applied_forces-test.dir/qmmmtopologypreprocessor.cpp.o.d -o CMakeFiles/qmmm_applied_forces-test.dir/qmmmtopologypreprocessor.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/applied_forces/qmmm/tests/qmmmtopologypreprocessor.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/utility/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/utility/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/src/testutils/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/utility/tests/CMakeFiles/utility-test.dir/scope_guard.cpp.o -MF CMakeFiles/utility-test.dir/scope_guard.cpp.o.d -o 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/lib/riscv64-linux-gnu/libpthread.a ../../../../../lib/libgtest.so.1.13.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/basic' [ 68%] Built target awh-test /usr/bin/make -f src/gromacs/applied_forces/colvars/tests/CMakeFiles/colvars_applied_forces-test.dir/build.make src/gromacs/applied_forces/colvars/tests/CMakeFiles/colvars_applied_forces-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/basic' cd /build/reproducible-path/gromacs-2025.1/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.1 /build/reproducible-path/gromacs-2025.1/src/gromacs/applied_forces/colvars/tests /build/reproducible-path/gromacs-2025.1/build/basic /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/applied_forces/colvars/tests /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/applied_forces/colvars/tests/CMakeFiles/colvars_applied_forces-test.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/basic' /usr/bin/make -f src/gromacs/applied_forces/colvars/tests/CMakeFiles/colvars_applied_forces-test.dir/build.make src/gromacs/applied_forces/colvars/tests/CMakeFiles/colvars_applied_forces-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/basic' cd /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/applied_forces/colvars/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/applied_forces/colvars/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/applied_forces/colvars/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/src/testutils/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic/src/include 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-DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/utility/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/src/testutils/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/external/muparser -isystem 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-DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/mdlib/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/src/testutils/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include 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-Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/utility/tests/CMakeFiles/utility-test.dir/textreader.cpp.o -MF CMakeFiles/utility-test.dir/textreader.cpp.o.d -o CMakeFiles/utility-test.dir/textreader.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/utility/tests/textreader.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/mdlib/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/mdlib/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/src/testutils/include -I/build/reproducible-path/gromacs-2025.1/src/include 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-Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/qmmm_applied_forces-test.dir/link.d "CMakeFiles/qmmm_applied_forces-test.dir/qmmminputgenerator.cpp.o" "CMakeFiles/qmmm_applied_forces-test.dir/qmmmtopologypreprocessor.cpp.o" "CMakeFiles/qmmm_applied_forces-test.dir/qmmmoptions.cpp.o" "CMakeFiles/qmmm_applied_forces-test.dir/qmmmforceprovider.cpp.o" "CMakeFiles/qmmm_applied_forces-test.dir/qmmm.cpp.o" "CMakeFiles/qmmm_applied_forces-test.dir/__/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../../bin/qmmm_applied_forces-test ../../../../../lib/libtestutils.a ../../../../../lib/libgromacs.so.10.0.0 ../../../../../lib/libgmock.so.1.13.0 /usr/lib/riscv64-linux-gnu/libm.so /usr/lib/gcc/riscv64-linux-gnu/14/libgomp.so /lib/riscv64-linux-gnu/libpthread.a ../../../../../lib/libgtest.so.1.13.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/basic' [ 69%] Built target qmmm_applied_forces-test /usr/bin/make -f src/gromacs/applied_forces/plumed/tests/CMakeFiles/plumed_applied_forces-test.dir/build.make src/gromacs/applied_forces/plumed/tests/CMakeFiles/plumed_applied_forces-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/basic' cd /build/reproducible-path/gromacs-2025.1/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.1 /build/reproducible-path/gromacs-2025.1/src/gromacs/applied_forces/plumed/tests /build/reproducible-path/gromacs-2025.1/build/basic /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/applied_forces/plumed/tests /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/applied_forces/plumed/tests/CMakeFiles/plumed_applied_forces-test.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/basic' /usr/bin/make -f src/gromacs/applied_forces/plumed/tests/CMakeFiles/plumed_applied_forces-test.dir/build.make 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-isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/mdlib/tests/CMakeFiles/mdlib-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/mdlib-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/mdlib-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/testutils/unittest_main.cpp /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/colvars_applied_forces-test.dir/link.d "CMakeFiles/colvars_applied_forces-test.dir/colvars.cpp.o" "CMakeFiles/colvars_applied_forces-test.dir/colvarsoptions.cpp.o" "CMakeFiles/colvars_applied_forces-test.dir/colvarspreprocessor.cpp.o" "CMakeFiles/colvars_applied_forces-test.dir/colvarsforceprovider.cpp.o" "CMakeFiles/colvars_applied_forces-test.dir/__/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../../bin/colvars_applied_forces-test ../../../../../lib/libtestutils.a ../../../../../lib/libgromacs.so.10.0.0 ../../../../../lib/libgmock.so.1.13.0 /usr/lib/riscv64-linux-gnu/libm.so ../../../../../lib/libgtest.so.1.13.0 /usr/lib/gcc/riscv64-linux-gnu/14/libgomp.so /lib/riscv64-linux-gnu/libpthread.a /usr/lib/riscv64-linux-gnu/libmuparser.so.2.3.4 make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/basic' [ 70%] Built target colvars_applied_forces-test /usr/bin/make -f src/gromacs/applied_forces/plumed/tests/CMakeFiles/plumed_md-test.dir/build.make src/gromacs/applied_forces/plumed/tests/CMakeFiles/plumed_md-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/basic' cd /build/reproducible-path/gromacs-2025.1/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.1 /build/reproducible-path/gromacs-2025.1/src/gromacs/applied_forces/plumed/tests /build/reproducible-path/gromacs-2025.1/build/basic /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/applied_forces/plumed/tests /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/applied_forces/plumed/tests/CMakeFiles/plumed_md-test.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/basic' /usr/bin/make -f src/gromacs/applied_forces/plumed/tests/CMakeFiles/plumed_md-test.dir/build.make src/gromacs/applied_forces/plumed/tests/CMakeFiles/plumed_md-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/basic' cd /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/applied_forces/plumed/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/applied_forces/plumed/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/applied_forces/plumed/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/src/testutils/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include 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-Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/applied_forces/plumed/tests/CMakeFiles/plumed_md-test.dir/plumed_md_test.cpp.o -MF CMakeFiles/plumed_md-test.dir/plumed_md_test.cpp.o.d -o CMakeFiles/plumed_md-test.dir/plumed_md_test.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/applied_forces/plumed/tests/plumed_md_test.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/applied_forces/plumed/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/applied_forces/plumed/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/applied_forces/plumed/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/src/testutils/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic/src/include -I/build/reproducible-path/gromacs-2025.1/src 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/build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/applied_forces/plumed/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/plumed_applied_forces-test.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/plumed_applied_forces-test.dir/link.d "CMakeFiles/plumed_applied_forces-test.dir/plumedOptions.cpp.o" "CMakeFiles/plumed_applied_forces-test.dir/__/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../../bin/plumed_applied_forces-test ../../../../../lib/libtestutils.a ../../../../../lib/libgromacs.so.10.0.0 ../../../../../lib/libgmock.so.1.13.0 /usr/lib/riscv64-linux-gnu/libm.so ../../../../../lib/libgtest.so.1.13.0 /usr/lib/gcc/riscv64-linux-gnu/14/libgomp.so /lib/riscv64-linux-gnu/libpthread.a /usr/lib/riscv64-linux-gnu/libmuparser.so.2.3.4 make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/basic' [ 70%] Built target plumed_applied_forces-test /usr/bin/make -f src/gromacs/applied_forces/nnpot/tests/CMakeFiles/nnpot_applied_forces-test.dir/build.make src/gromacs/applied_forces/nnpot/tests/CMakeFiles/nnpot_applied_forces-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/basic' cd /build/reproducible-path/gromacs-2025.1/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.1 /build/reproducible-path/gromacs-2025.1/src/gromacs/applied_forces/nnpot/tests /build/reproducible-path/gromacs-2025.1/build/basic /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/applied_forces/nnpot/tests /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/applied_forces/nnpot/tests/CMakeFiles/nnpot_applied_forces-test.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/basic' /usr/bin/make -f src/gromacs/applied_forces/nnpot/tests/CMakeFiles/nnpot_applied_forces-test.dir/build.make src/gromacs/applied_forces/nnpot/tests/CMakeFiles/nnpot_applied_forces-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/basic' cd /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/applied_forces/nnpot/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/applied_forces/nnpot/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/applied_forces/nnpot/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/src/testutils/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic/src/include 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-ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/applied_forces/nnpot/tests/CMakeFiles/nnpot_applied_forces-test.dir/nnpot.cpp.o -MF CMakeFiles/nnpot_applied_forces-test.dir/nnpot.cpp.o.d -o CMakeFiles/nnpot_applied_forces-test.dir/nnpot.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/applied_forces/nnpot/tests/nnpot.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/applied_forces/nnpot/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/applied_forces/nnpot/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/applied_forces/nnpot/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/src/testutils/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/applied_forces/nnpot/tests/CMakeFiles/nnpot_applied_forces-test.dir/nnpotoptions.cpp.o -MF CMakeFiles/nnpot_applied_forces-test.dir/nnpotoptions.cpp.o.d -o CMakeFiles/nnpot_applied_forces-test.dir/nnpotoptions.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/applied_forces/nnpot/tests/nnpotoptions.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/applied_forces/plumed/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/applied_forces/plumed/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/applied_forces/plumed/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/src/testutils/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/applied_forces/plumed/tests/CMakeFiles/plumed_md-test.dir/plumedTestUtils.cpp.o -MF CMakeFiles/plumed_md-test.dir/plumedTestUtils.cpp.o.d -o CMakeFiles/plumed_md-test.dir/plumedTestUtils.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/applied_forces/plumed/tests/plumedTestUtils.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/applied_forces/plumed/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/applied_forces/plumed/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/applied_forces/plumed/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/src/testutils/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/applied_forces/plumed/tests/CMakeFiles/plumed_md-test.dir/__/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/plumed_md-test.dir/__/__/__/__/testutils/unittest_main.cpp.o.d -o 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../../../../lib/libgromacs.so.10.0.0 ../../../../lib/libgmock.so.1.13.0 /usr/lib/riscv64-linux-gnu/libm.so ../../../../lib/libgtest.so.1.13.0 /usr/lib/gcc/riscv64-linux-gnu/14/libgomp.so /lib/riscv64-linux-gnu/libpthread.a /usr/lib/riscv64-linux-gnu/libmuparser.so.2.3.4 make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/basic' [ 72%] Built target mdlib-test /usr/bin/make -f src/gromacs/applied_forces/tests/CMakeFiles/applied_forces-test.dir/build.make src/gromacs/applied_forces/tests/CMakeFiles/applied_forces-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/basic' cd /build/reproducible-path/gromacs-2025.1/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.1 /build/reproducible-path/gromacs-2025.1/src/gromacs/applied_forces/tests /build/reproducible-path/gromacs-2025.1/build/basic /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/applied_forces/tests /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/applied_forces/tests/CMakeFiles/applied_forces-test.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/basic' /usr/bin/make -f src/gromacs/applied_forces/tests/CMakeFiles/applied_forces-test.dir/build.make src/gromacs/applied_forces/tests/CMakeFiles/applied_forces-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/basic' cd /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/applied_forces/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/applied_forces/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/applied_forces/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/src/testutils/include -I/build/reproducible-path/gromacs-2025.1/src/include 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--verbose=1 cd /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/utility/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/utility/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/src/testutils/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem 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/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/tests/textwriter.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/applied_forces/nnpot/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/applied_forces/nnpot/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/applied_forces/nnpot/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/src/testutils/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic/api/legacy/include 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src/gromacs/applied_forces/nnpot/tests/CMakeFiles/nnpot_applied_forces-test.dir/nnpottopologypreprocessor.cpp.o -MF CMakeFiles/nnpot_applied_forces-test.dir/nnpottopologypreprocessor.cpp.o.d -o CMakeFiles/nnpot_applied_forces-test.dir/nnpottopologypreprocessor.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/applied_forces/nnpot/tests/nnpottopologypreprocessor.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/applied_forces/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/applied_forces/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/applied_forces/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/src/testutils/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic/src/include -I/build/reproducible-path/gromacs-2025.1/src 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/build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/applied_forces/tests/CMakeFiles/applied_forces-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/applied_forces-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/applied_forces-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/utility/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/utility/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/src/testutils/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock/include 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/build/reproducible-path/gromacs-2025.1/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/applied_forces/nnpot/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/applied_forces/nnpot/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/applied_forces/nnpot/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/src/testutils/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic/api/legacy/include 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src/gromacs/applied_forces/nnpot/tests/CMakeFiles/nnpot_applied_forces-test.dir/nnpotforceprovider.cpp.o -MF CMakeFiles/nnpot_applied_forces-test.dir/nnpotforceprovider.cpp.o.d -o CMakeFiles/nnpot_applied_forces-test.dir/nnpotforceprovider.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/applied_forces/nnpot/tests/nnpotforceprovider.cpp /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/plumed_md-test.dir/link.d "CMakeFiles/plumed_md-test.dir/plumed_md_test.cpp.o" "CMakeFiles/plumed_md-test.dir/plumedTestUtils.cpp.o" "CMakeFiles/plumed_md-test.dir/__/__/__/__/testutils/unittest_main.cpp.o" ../../../../programs/CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o ../../../../programs/CMakeFiles/mdrun_objlib.dir/mdrun/nonbonded_bench.cpp.o -o ../../../../../bin/plumed_md-test ../../../../../lib/libtestutils.a ../../../../../lib/libmdrun_test_infrastructure.a -ldl ../../../../../lib/libtestutils.a ../../../../../lib/libgromacs.so.10.0.0 /usr/lib/riscv64-linux-gnu/libm.so /usr/lib/gcc/riscv64-linux-gnu/14/libgomp.so /lib/riscv64-linux-gnu/libpthread.a ../../../../../lib/libgmock.so.1.13.0 ../../../../../lib/libgtest.so.1.13.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/basic' [ 73%] Built target plumed_md-test /usr/bin/make -f src/gromacs/listed_forces/tests/CMakeFiles/listed_forces-test.dir/build.make src/gromacs/listed_forces/tests/CMakeFiles/listed_forces-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/basic' cd /build/reproducible-path/gromacs-2025.1/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.1 /build/reproducible-path/gromacs-2025.1/src/gromacs/listed_forces/tests /build/reproducible-path/gromacs-2025.1/build/basic /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/listed_forces/tests /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/listed_forces/tests/CMakeFiles/listed_forces-test.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/basic' /usr/bin/make -f src/gromacs/listed_forces/tests/CMakeFiles/listed_forces-test.dir/build.make src/gromacs/listed_forces/tests/CMakeFiles/listed_forces-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/basic' cd /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/listed_forces/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/listed_forces/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/listed_forces/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/src/testutils/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pbcutil/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/listed_forces/tests/CMakeFiles/listed_forces-test.dir/bonded.cpp.o -MF CMakeFiles/listed_forces-test.dir/bonded.cpp.o.d -o CMakeFiles/listed_forces-test.dir/bonded.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/listed_forces/tests/bonded.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/utility/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/utility-test.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/applied_forces-test.dir/link.d "CMakeFiles/applied_forces-test.dir/electricfield.cpp.o" "CMakeFiles/applied_forces-test.dir/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../bin/applied_forces-test ../../../../lib/libtestutils.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.10.0.0 /usr/lib/riscv64-linux-gnu/libm.so ../../../../lib/libgmock.so.1.13.0 ../../../../lib/libgtest.so.1.13.0 /usr/lib/gcc/riscv64-linux-gnu/14/libgomp.so /lib/riscv64-linux-gnu/libpthread.a /usr/lib/riscv64-linux-gnu/libmuparser.so.2.3.4 make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/basic' [ 73%] Built target applied_forces-test /usr/bin/make -f src/gromacs/nbnxm/tests/CMakeFiles/nbnxm-test.dir/build.make src/gromacs/nbnxm/tests/CMakeFiles/nbnxm-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/basic' 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-DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/nbnxm/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/src/testutils/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/timing/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem 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/build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/applied_forces/nnpot/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/applied_forces/nnpot/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/applied_forces/nnpot/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/src/testutils/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/applied_forces/nnpot/tests/CMakeFiles/nnpot_applied_forces-test.dir/__/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/nnpot_applied_forces-test.dir/__/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/nnpot_applied_forces-test.dir/__/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/applied_forces/nnpot/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/nnpot_applied_forces-test.dir/link.txt --verbose=1 cd /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/nbnxm/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/nbnxm/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/nbnxm/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/src/testutils/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/timing/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/nbnxm/tests/CMakeFiles/nbnxm-test.dir/kernel_test.cpp.o -MF CMakeFiles/nbnxm-test.dir/kernel_test.cpp.o.d -o CMakeFiles/nbnxm-test.dir/kernel_test.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/tests/kernel_test.cpp /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/nnpot_applied_forces-test.dir/link.d "CMakeFiles/nnpot_applied_forces-test.dir/nnpot.cpp.o" "CMakeFiles/nnpot_applied_forces-test.dir/nnpotoptions.cpp.o" "CMakeFiles/nnpot_applied_forces-test.dir/nnpottopologypreprocessor.cpp.o" "CMakeFiles/nnpot_applied_forces-test.dir/nnpotforceprovider.cpp.o" "CMakeFiles/nnpot_applied_forces-test.dir/__/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../../bin/nnpot_applied_forces-test ../../../../../lib/libtestutils.a ../../../../../lib/libtestutils.a ../../../../../lib/libgromacs.so.10.0.0 /usr/lib/riscv64-linux-gnu/libm.so /usr/lib/gcc/riscv64-linux-gnu/14/libgomp.so /lib/riscv64-linux-gnu/libpthread.a ../../../../../lib/libgmock.so.1.13.0 ../../../../../lib/libgtest.so.1.13.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/basic' [ 74%] Built target nnpot_applied_forces-test /usr/bin/make -f src/gromacs/nbnxm/tests/CMakeFiles/nbnxm-gpu-test.dir/build.make src/gromacs/nbnxm/tests/CMakeFiles/nbnxm-gpu-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/basic' cd /build/reproducible-path/gromacs-2025.1/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.1 /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/tests /build/reproducible-path/gromacs-2025.1/build/basic /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/nbnxm/tests /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/nbnxm/tests/CMakeFiles/nbnxm-gpu-test.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/basic' /usr/bin/make -f src/gromacs/nbnxm/tests/CMakeFiles/nbnxm-gpu-test.dir/build.make src/gromacs/nbnxm/tests/CMakeFiles/nbnxm-gpu-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/basic' cd /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/nbnxm/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/nbnxm/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/nbnxm/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/src/testutils/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/timing/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/nbnxm/tests/CMakeFiles/nbnxm-gpu-test.dir/pairlist.cpp.o -MF CMakeFiles/nbnxm-gpu-test.dir/pairlist.cpp.o.d -o CMakeFiles/nbnxm-gpu-test.dir/pairlist.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/tests/pairlist.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/listed_forces/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/listed_forces/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/listed_forces/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/src/testutils/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pbcutil/include -isystem 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CMakeFiles/listed_forces-test.dir/pairs.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/listed_forces/tests/pairs.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/nbnxm/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/nbnxm/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/nbnxm/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/src/testutils/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/timing/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/nbnxm/tests/CMakeFiles/nbnxm-gpu-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/nbnxm-gpu-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/nbnxm-gpu-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/nbnxm/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/nbnxm-gpu-test.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/nbnxm-gpu-test.dir/link.d "CMakeFiles/nbnxm-gpu-test.dir/pairlist.cpp.o" "CMakeFiles/nbnxm-gpu-test.dir/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../bin/nbnxm-gpu-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.10.0.0 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-I/build/reproducible-path/gromacs-2025.1/src/gromacs/timing/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/nbnxm/tests/CMakeFiles/nbnxm-test.dir/testsystem.cpp.o -MF 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-I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pbcutil/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest -g -O2 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'/build/reproducible-path/gromacs-2025.1/build/basic' cd /build/reproducible-path/gromacs-2025.1/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.1 /build/reproducible-path/gromacs-2025.1/src/gromacs/onlinehelp/tests /build/reproducible-path/gromacs-2025.1/build/basic /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/onlinehelp/tests /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/onlinehelp/tests/CMakeFiles/onlinehelp-test-shared.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/basic' /usr/bin/make -f src/gromacs/onlinehelp/tests/CMakeFiles/onlinehelp-test-shared.dir/build.make src/gromacs/onlinehelp/tests/CMakeFiles/onlinehelp-test-shared.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/basic' cd /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/onlinehelp/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/src/testutils/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -MD -MT src/gromacs/onlinehelp/tests/CMakeFiles/onlinehelp-test-shared.dir/mock_helptopic.cpp.o -MF CMakeFiles/onlinehelp-test-shared.dir/mock_helptopic.cpp.o.d -o CMakeFiles/onlinehelp-test-shared.dir/mock_helptopic.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/onlinehelp/tests/mock_helptopic.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/listed_forces/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/listed_forces-test.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/nbnxm-test.dir/link.d "CMakeFiles/nbnxm-test.dir/exclusions.cpp.o" "CMakeFiles/nbnxm-test.dir/kernel_test.cpp.o" "CMakeFiles/nbnxm-test.dir/kernelsetup.cpp.o" "CMakeFiles/nbnxm-test.dir/simd_energy_accumulator.cpp.o" "CMakeFiles/nbnxm-test.dir/testsystem.cpp.o" "CMakeFiles/nbnxm-test.dir/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../bin/nbnxm-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.10.0.0 ../../../../lib/libgmock.so.1.13.0 /usr/lib/riscv64-linux-gnu/libm.so /usr/lib/gcc/riscv64-linux-gnu/14/libgomp.so /lib/riscv64-linux-gnu/libpthread.a ../../../../lib/libgtest.so.1.13.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/basic' [ 74%] Built target nbnxm-test /usr/bin/make -f src/gromacs/domdec/tests/CMakeFiles/domdec-test.dir/build.make src/gromacs/domdec/tests/CMakeFiles/domdec-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/basic' cd /build/reproducible-path/gromacs-2025.1/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.1 /build/reproducible-path/gromacs-2025.1/src/gromacs/domdec/tests /build/reproducible-path/gromacs-2025.1/build/basic /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/domdec/tests /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/domdec/tests/CMakeFiles/domdec-test.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/basic' /usr/bin/make -f src/gromacs/domdec/tests/CMakeFiles/domdec-test.dir/build.make src/gromacs/domdec/tests/CMakeFiles/domdec-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/basic' cd /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/domdec/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/domdec/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/domdec/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/src/testutils/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/timing/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/domdec/tests/CMakeFiles/domdec-test.dir/hashedmap.cpp.o -MF CMakeFiles/domdec-test.dir/hashedmap.cpp.o.d -o CMakeFiles/domdec-test.dir/hashedmap.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/domdec/tests/hashedmap.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/onlinehelp/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/src/testutils/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock/include -isystem 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/build/reproducible-path/gromacs-2025.1 /build/reproducible-path/gromacs-2025.1/src/gromacs/domdec/tests /build/reproducible-path/gromacs-2025.1/build/basic /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/domdec/tests /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/domdec/tests/CMakeFiles/domdec-mpi-test.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/basic' /usr/bin/make -f src/gromacs/domdec/tests/CMakeFiles/domdec-mpi-test.dir/build.make src/gromacs/domdec/tests/CMakeFiles/domdec-mpi-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/basic' cd /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/domdec/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/domdec/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/domdec/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -DTEST_USES_MPI=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/src/testutils/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/timing/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/domdec/tests/CMakeFiles/domdec-mpi-test.dir/haloexchange_mpi.cpp.o -MF CMakeFiles/domdec-mpi-test.dir/haloexchange_mpi.cpp.o.d -o CMakeFiles/domdec-mpi-test.dir/haloexchange_mpi.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/domdec/tests/haloexchange_mpi.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/domdec/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/domdec/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/domdec/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/src/testutils/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/timing/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/domdec/tests/CMakeFiles/domdec-test.dir/localatomsetmanager.cpp.o -MF CMakeFiles/domdec-test.dir/localatomsetmanager.cpp.o.d -o CMakeFiles/domdec-test.dir/localatomsetmanager.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/domdec/tests/localatomsetmanager.cpp /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/listed_forces-test.dir/link.d "CMakeFiles/listed_forces-test.dir/bonded.cpp.o" "CMakeFiles/listed_forces-test.dir/pairs.cpp.o" "CMakeFiles/listed_forces-test.dir/position_restraints.cpp.o" "CMakeFiles/listed_forces-test.dir/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../bin/listed_forces-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.10.0.0 ../../../../lib/libgmock.so.1.13.0 /usr/lib/riscv64-linux-gnu/libm.so /usr/lib/gcc/riscv64-linux-gnu/14/libgomp.so /lib/riscv64-linux-gnu/libpthread.a ../../../../lib/libgtest.so.1.13.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/basic' [ 75%] Built target listed_forces-test cd /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/domdec/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/domdec/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/domdec/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -DTEST_USES_MPI=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/src/testutils/include -I/build/reproducible-path/gromacs-2025.1/src/include 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/build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/domdec/tests/CMakeFiles/domdec-mpi-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/domdec-mpi-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/domdec-mpi-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/domdec/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/domdec/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/domdec/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/src/testutils/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include 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-MF CMakeFiles/domdec-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/domdec-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/testutils/unittest_main.cpp /usr/bin/make -f src/gromacs/ewald/tests/CMakeFiles/ewald-test.dir/build.make src/gromacs/ewald/tests/CMakeFiles/ewald-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/basic' cd /build/reproducible-path/gromacs-2025.1/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.1 /build/reproducible-path/gromacs-2025.1/src/gromacs/ewald/tests /build/reproducible-path/gromacs-2025.1/build/basic /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/ewald/tests /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/ewald/tests/CMakeFiles/ewald-test.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/basic' /usr/bin/make -f src/gromacs/ewald/tests/CMakeFiles/ewald-test.dir/build.make src/gromacs/ewald/tests/CMakeFiles/ewald-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/basic' cd /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/ewald/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/ewald/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/ewald/tests/Testing/Temporary\" -DTEST_USES_DYNAMIC_REGISTRATION=true -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/src/testutils/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include 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-ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/ewald/tests/CMakeFiles/ewald-test.dir/pmebsplinetest.cpp.o -MF CMakeFiles/ewald-test.dir/pmebsplinetest.cpp.o.d -o CMakeFiles/ewald-test.dir/pmebsplinetest.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/ewald/tests/pmebsplinetest.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/domdec/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/domdec-test.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/utility-test.dir/link.d "CMakeFiles/utility-test.dir/alignedallocator.cpp.o" "CMakeFiles/utility-test.dir/arrayref.cpp.o" "CMakeFiles/utility-test.dir/booltype.cpp.o" "CMakeFiles/utility-test.dir/bitmask32.cpp.o" "CMakeFiles/utility-test.dir/bitmask64.cpp.o" "CMakeFiles/utility-test.dir/bitmask128.cpp.o" "CMakeFiles/utility-test.dir/cstringutil.cpp.o" "CMakeFiles/utility-test.dir/defaultinitializationallocator.cpp.o" "CMakeFiles/utility-test.dir/enumerationhelpers.cpp.o" "CMakeFiles/utility-test.dir/fixedcapacityvector.cpp.o" "CMakeFiles/utility-test.dir/inmemoryserializer.cpp.o" "CMakeFiles/utility-test.dir/keyvaluetreeserializer.cpp.o" "CMakeFiles/utility-test.dir/keyvaluetreetransform.cpp.o" "CMakeFiles/utility-test.dir/listoflists.cpp.o" "CMakeFiles/utility-test.dir/logger.cpp.o" "CMakeFiles/utility-test.dir/message_string_collector.cpp.o" "CMakeFiles/utility-test.dir/path.cpp.o" "CMakeFiles/utility-test.dir/physicalnodecommunicator.cpp.o" "CMakeFiles/utility-test.dir/range.cpp.o" "CMakeFiles/utility-test.dir/scope_guard.cpp.o" "CMakeFiles/utility-test.dir/strconvert.cpp.o" "CMakeFiles/utility-test.dir/stringtoenumvalueconverter.cpp.o" "CMakeFiles/utility-test.dir/stringutil.cpp.o" "CMakeFiles/utility-test.dir/template_mp.cpp.o" "CMakeFiles/utility-test.dir/textreader.cpp.o" "CMakeFiles/utility-test.dir/textwriter.cpp.o" "CMakeFiles/utility-test.dir/typetraits.cpp.o" "CMakeFiles/utility-test.dir/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../bin/utility-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.10.0.0 ../../../../lib/libgmock.so.1.13.0 /usr/lib/riscv64-linux-gnu/libm.so /usr/lib/gcc/riscv64-linux-gnu/14/libgomp.so /lib/riscv64-linux-gnu/libpthread.a ../../../../lib/libgtest.so.1.13.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/basic' [ 76%] Built target utility-test /usr/bin/make -f src/gromacs/fft/tests/CMakeFiles/fft-test.dir/build.make src/gromacs/fft/tests/CMakeFiles/fft-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/basic' cd /build/reproducible-path/gromacs-2025.1/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.1 /build/reproducible-path/gromacs-2025.1/src/gromacs/fft/tests /build/reproducible-path/gromacs-2025.1/build/basic /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/fft/tests /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/fft/tests/CMakeFiles/fft-test.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/basic' /usr/bin/make -f src/gromacs/fft/tests/CMakeFiles/fft-test.dir/build.make src/gromacs/fft/tests/CMakeFiles/fft-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/basic' cd /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/fft/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H 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--verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/domdec-test.dir/link.d "CMakeFiles/domdec-test.dir/hashedmap.cpp.o" "CMakeFiles/domdec-test.dir/localatomsetmanager.cpp.o" "CMakeFiles/domdec-test.dir/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../bin/domdec-test ../../../../lib/libtestutils.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.10.0.0 /usr/lib/riscv64-linux-gnu/libm.so ../../../../lib/libgmock.so.1.13.0 ../../../../lib/libgtest.so.1.13.0 /usr/lib/gcc/riscv64-linux-gnu/14/libgomp.so /lib/riscv64-linux-gnu/libpthread.a /usr/lib/riscv64-linux-gnu/libmuparser.so.2.3.4 make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/basic' [ 76%] Built target domdec-test cd /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/fft/tests && 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'/build/reproducible-path/gromacs-2025.1/build/basic' [ 76%] Built target domdec-mpi-test /usr/bin/make -f src/gromacs/hardware/tests/CMakeFiles/hardware-test.dir/build.make src/gromacs/hardware/tests/CMakeFiles/hardware-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/basic' cd /build/reproducible-path/gromacs-2025.1/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.1 /build/reproducible-path/gromacs-2025.1/src/gromacs/hardware/tests /build/reproducible-path/gromacs-2025.1/build/basic /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/hardware/tests /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/hardware/tests/CMakeFiles/hardware-test.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/basic' /usr/bin/make -f src/gromacs/hardware/tests/CMakeFiles/hardware-test.dir/build.make 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/build/reproducible-path/gromacs-2025.1/src/gromacs/gpu_utils/tests/pinnedmemorychecker.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/gpu_utils/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gpu_utils/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/gpu_utils/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/src/testutils/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic/api/legacy/include 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src/gromacs/gpu_utils/tests/CMakeFiles/gpu_utils-test.dir/device_buffer.cpp.o -MF CMakeFiles/gpu_utils-test.dir/device_buffer.cpp.o.d -o CMakeFiles/gpu_utils-test.dir/device_buffer.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/gpu_utils/tests/device_buffer.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/gpu_utils/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gpu_utils/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/gpu_utils/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/src/testutils/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include 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/build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/gpu_utils/tests/CMakeFiles/gpu_utils-test.dir/hostallocator.cpp.o -MF CMakeFiles/gpu_utils-test.dir/hostallocator.cpp.o.d -o CMakeFiles/gpu_utils-test.dir/hostallocator.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/gpu_utils/tests/hostallocator.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/hardware/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/hardware/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/hardware/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/src/testutils/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/hardware/tests/CMakeFiles/hardware-test.dir/mockhardwaretopology.cpp.o -MF CMakeFiles/hardware-test.dir/mockhardwaretopology.cpp.o.d -o CMakeFiles/hardware-test.dir/mockhardwaretopology.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/hardware/tests/mockhardwaretopology.cpp /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/fft-test.dir/link.d "CMakeFiles/fft-test.dir/fft.cpp.o" "CMakeFiles/fft-test.dir/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../bin/fft-test ../../../../lib/libtestutils.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.10.0.0 /usr/lib/riscv64-linux-gnu/libm.so /usr/lib/gcc/riscv64-linux-gnu/14/libgomp.so /lib/riscv64-linux-gnu/libpthread.a ../../../../lib/libgmock.so.1.13.0 ../../../../lib/libgtest.so.1.13.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/basic' [ 77%] Built target fft-test /usr/bin/make -f src/gromacs/math/tests/CMakeFiles/math-test.dir/build.make src/gromacs/math/tests/CMakeFiles/math-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/basic' cd /build/reproducible-path/gromacs-2025.1/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.1 /build/reproducible-path/gromacs-2025.1/src/gromacs/math/tests /build/reproducible-path/gromacs-2025.1/build/basic 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/build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/math/tests/CMakeFiles/math-test.dir/boxmatrix.cpp.o -MF CMakeFiles/math-test.dir/boxmatrix.cpp.o.d -o CMakeFiles/math-test.dir/boxmatrix.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/math/tests/boxmatrix.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/hardware/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 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-DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/math/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/math/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/src/testutils/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/external/muparser -isystem 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src/gromacs/ewald/tests/CMakeFiles/ewald-test.dir/pmesplinespreadtest.cpp.o -MF CMakeFiles/ewald-test.dir/pmesplinespreadtest.cpp.o.d -o CMakeFiles/ewald-test.dir/pmesplinespreadtest.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/ewald/tests/pmesplinespreadtest.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/hardware/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/hardware/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/hardware/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/src/testutils/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include 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-I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 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"CMakeFiles/hardware-test.dir/device_management.cpp.o" "CMakeFiles/hardware-test.dir/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../bin/hardware-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.10.0.0 ../../../../lib/libgmock.so.1.13.0 /usr/lib/riscv64-linux-gnu/libm.so /usr/lib/gcc/riscv64-linux-gnu/14/libgomp.so /lib/riscv64-linux-gnu/libpthread.a ../../../../lib/libgtest.so.1.13.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/basic' [ 77%] Built target hardware-test /usr/bin/make -f src/gromacs/mdrunutility/tests/CMakeFiles/mdrunutility-test-shared.dir/build.make src/gromacs/mdrunutility/tests/CMakeFiles/mdrunutility-test-shared.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/basic' cd /build/reproducible-path/gromacs-2025.1/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.1 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/build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/mdtypes/tests/CMakeFiles/mdtypes-test.dir/observablesreducer.cpp.o -MF CMakeFiles/mdtypes-test.dir/observablesreducer.cpp.o.d -o CMakeFiles/mdtypes-test.dir/observablesreducer.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/mdtypes/tests/observablesreducer.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/onlinehelp/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/onlinehelp/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/onlinehelp/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/src/testutils/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock -isystem 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-DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/onlinehelp/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/src/testutils/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/onlinehelp/tests/CMakeFiles/onlinehelp-test.dir/helpwritercontext.cpp.o -MF CMakeFiles/onlinehelp-test.dir/helpwritercontext.cpp.o.d -o CMakeFiles/onlinehelp-test.dir/helpwritercontext.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/onlinehelp/tests/helpwritercontext.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/mdspan/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 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&& /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/math/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/math/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/src/testutils/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/external/muparser 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/build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/mdspan/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/mdspan-test.dir/link.txt --verbose=1 cd /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/onlinehelp/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/onlinehelp-test.dir/link.txt --verbose=1 cd /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/mdtypes/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdtypes/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/mdtypes/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/src/testutils/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/mdtypes/tests/CMakeFiles/mdtypes-test.dir/checkpointdata.cpp.o -MF CMakeFiles/mdtypes-test.dir/checkpointdata.cpp.o.d -o CMakeFiles/mdtypes-test.dir/checkpointdata.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/mdtypes/tests/checkpointdata.cpp /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/onlinehelp-test.dir/link.d "CMakeFiles/onlinehelp-test.dir/helpformat.cpp.o" "CMakeFiles/onlinehelp-test.dir/helpmanager.cpp.o" "CMakeFiles/onlinehelp-test.dir/helpwritercontext.cpp.o" "CMakeFiles/onlinehelp-test.dir/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../bin/onlinehelp-test ../../../../lib/libtestutils.a ../../../../lib/libonlinehelp-test-shared.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.10.0.0 /usr/lib/riscv64-linux-gnu/libm.so /usr/lib/gcc/riscv64-linux-gnu/14/libgomp.so /lib/riscv64-linux-gnu/libpthread.a ../../../../lib/libgmock.so.1.13.0 ../../../../lib/libgtest.so.1.13.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/basic' [ 77%] Built target onlinehelp-test /usr/bin/make -f src/gromacs/options/tests/CMakeFiles/options-test.dir/build.make src/gromacs/options/tests/CMakeFiles/options-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/basic' cd /build/reproducible-path/gromacs-2025.1/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.1 /build/reproducible-path/gromacs-2025.1/src/gromacs/options/tests /build/reproducible-path/gromacs-2025.1/build/basic /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/options/tests /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/options/tests/CMakeFiles/options-test.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/basic' /usr/bin/make -f src/gromacs/options/tests/CMakeFiles/options-test.dir/build.make src/gromacs/options/tests/CMakeFiles/options-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/basic' cd /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/options/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/options/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/options/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/src/testutils/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/options/tests/CMakeFiles/options-test.dir/abstractoptionstorage.cpp.o -MF CMakeFiles/options-test.dir/abstractoptionstorage.cpp.o.d -o CMakeFiles/options-test.dir/abstractoptionstorage.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/options/tests/abstractoptionstorage.cpp /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/mdspan-test.dir/link.d "CMakeFiles/mdspan-test.dir/accessor_policy.cpp.o" "CMakeFiles/mdspan-test.dir/extents.cpp.o" "CMakeFiles/mdspan-test.dir/extensions.cpp.o" "CMakeFiles/mdspan-test.dir/layouts.cpp.o" "CMakeFiles/mdspan-test.dir/mdspan.cpp.o" 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/build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/pbcutil/tests /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/pbcutil/tests/CMakeFiles/pbcutil-test.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/basic' /usr/bin/make -f src/gromacs/pbcutil/tests/CMakeFiles/pbcutil-test.dir/build.make src/gromacs/pbcutil/tests/CMakeFiles/pbcutil-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/basic' cd /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/pbcutil/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/pbcutil/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/pbcutil/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/src/testutils/include 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/build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/pbcutil/tests/CMakeFiles/pbcutil-test.dir/com.cpp.o -MF CMakeFiles/pbcutil-test.dir/com.cpp.o.d -o CMakeFiles/pbcutil-test.dir/com.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/pbcutil/tests/com.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/math/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/math/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/math/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/src/testutils/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/math/tests/CMakeFiles/math-test.dir/densityfittingforce.cpp.o -MF CMakeFiles/math-test.dir/densityfittingforce.cpp.o.d -o CMakeFiles/math-test.dir/densityfittingforce.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/math/tests/densityfittingforce.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/math/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H 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-DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/pbcutil/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/src/testutils/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/pbcutil/tests/CMakeFiles/pbcutil-test.dir/mshift.cpp.o -MF CMakeFiles/pbcutil-test.dir/mshift.cpp.o.d -o CMakeFiles/pbcutil-test.dir/mshift.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/pbcutil/tests/mshift.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/math/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 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/build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/math/tests/CMakeFiles/math-test.dir/matrix.cpp.o -MF CMakeFiles/math-test.dir/matrix.cpp.o.d -o CMakeFiles/math-test.dir/matrix.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/math/tests/matrix.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/options/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 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/build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/mdtypes/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdtypes/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/mdtypes/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/src/testutils/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/mdtypes/tests/CMakeFiles/mdtypes-test.dir/multipletimestepping.cpp.o -MF CMakeFiles/mdtypes-test.dir/multipletimestepping.cpp.o.d -o CMakeFiles/mdtypes-test.dir/multipletimestepping.cpp.o -c 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-I/build/reproducible-path/gromacs-2025.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/pbcutil/tests/CMakeFiles/pbcutil-test.dir/pbcenums.cpp.o -MF CMakeFiles/pbcutil-test.dir/pbcenums.cpp.o.d -o CMakeFiles/pbcutil-test.dir/pbcenums.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/pbcutil/tests/pbcenums.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/options/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/options/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/options/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/src/testutils/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/options/tests/CMakeFiles/options-test.dir/filenameoptionmanager.cpp.o -MF CMakeFiles/options-test.dir/filenameoptionmanager.cpp.o.d -o CMakeFiles/options-test.dir/filenameoptionmanager.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/options/tests/filenameoptionmanager.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/pbcutil/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/pbcutil/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/pbcutil/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/src/testutils/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/pbcutil/tests/CMakeFiles/pbcutil-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/pbcutil-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/pbcutil-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/pbcutil/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/pbcutil-test.dir/link.txt --verbose=1 cd /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/math/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/math/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/math/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/src/testutils/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/math/tests/CMakeFiles/math-test.dir/neldermead.cpp.o -MF CMakeFiles/math-test.dir/neldermead.cpp.o.d -o CMakeFiles/math-test.dir/neldermead.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/math/tests/neldermead.cpp /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/pbcutil-test.dir/link.d "CMakeFiles/pbcutil-test.dir/com.cpp.o" "CMakeFiles/pbcutil-test.dir/mshift.cpp.o" "CMakeFiles/pbcutil-test.dir/pbc.cpp.o" "CMakeFiles/pbcutil-test.dir/pbcenums.cpp.o" "CMakeFiles/pbcutil-test.dir/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../bin/pbcutil-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.10.0.0 ../../../../lib/libgmock.so.1.13.0 /usr/lib/riscv64-linux-gnu/libm.so /usr/lib/gcc/riscv64-linux-gnu/14/libgomp.so /lib/riscv64-linux-gnu/libpthread.a ../../../../lib/libgtest.so.1.13.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/basic' [ 80%] Built target pbcutil-test cd /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/options/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/options/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/options/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/src/testutils/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/options/tests/CMakeFiles/options-test.dir/option.cpp.o -MF CMakeFiles/options-test.dir/option.cpp.o.d -o CMakeFiles/options-test.dir/option.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/options/tests/option.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/mdtypes/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdtypes/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/mdtypes/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY 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-DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/options/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/src/testutils/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock/include -isystem 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/build/reproducible-path/gromacs-2025.1/src/gromacs/random/tests/exponentialdistribution.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/math/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/math/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/math/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/src/testutils/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -isystem 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/build/reproducible-path/gromacs-2025.1/src/gromacs/math/tests/paddedvector.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/random/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/random/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/random/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/src/testutils/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -isystem 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../../../../lib/libgtest.so.1.13.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/basic' [ 80%] Built target mdtypes-test cd /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/math/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/math/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/math/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/src/testutils/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic/api/legacy/include 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-I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/random/tests/CMakeFiles/random-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/random-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/random-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/testutils/unittest_main.cpp /usr/bin/make -f src/gromacs/restraint/tests/CMakeFiles/restraintpotential-test.dir/build.make src/gromacs/restraint/tests/CMakeFiles/restraintpotential-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/basic' cd /build/reproducible-path/gromacs-2025.1/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.1 /build/reproducible-path/gromacs-2025.1/src/gromacs/restraint/tests /build/reproducible-path/gromacs-2025.1/build/basic 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/build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/restraint/tests/CMakeFiles/restraintpotential-test.dir/manager.cpp.o -MF CMakeFiles/restraintpotential-test.dir/manager.cpp.o.d -o CMakeFiles/restraintpotential-test.dir/manager.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/restraint/tests/manager.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/random/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/random-test.dir/link.txt --verbose=1 cd /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/options/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H 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'/build/reproducible-path/gromacs-2025.1/build/basic' [ 80%] Built target random-test /usr/bin/make -f src/gromacs/tables/tests/CMakeFiles/table-test.dir/build.make src/gromacs/tables/tests/CMakeFiles/table-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/basic' cd /build/reproducible-path/gromacs-2025.1/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.1 /build/reproducible-path/gromacs-2025.1/src/gromacs/tables/tests /build/reproducible-path/gromacs-2025.1/build/basic /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/tables/tests /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/tables/tests/CMakeFiles/table-test.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/basic' /usr/bin/make -f src/gromacs/tables/tests/CMakeFiles/table-test.dir/build.make src/gromacs/tables/tests/CMakeFiles/table-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/basic' cd /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/tables/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/tables/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/tables/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/src/testutils/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/simd/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/tables/tests/CMakeFiles/table-test.dir/splinetable.cpp.o -MF 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../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.10.0.0 ../../../../lib/libgmock.so.1.13.0 /usr/lib/riscv64-linux-gnu/libm.so /usr/lib/gcc/riscv64-linux-gnu/14/libgomp.so /lib/riscv64-linux-gnu/libpthread.a ../../../../lib/libgtest.so.1.13.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/basic' [ 81%] Built target restraintpotential-test /usr/bin/make -f src/gromacs/taskassignment/tests/CMakeFiles/taskassignment-test.dir/build.make src/gromacs/taskassignment/tests/CMakeFiles/taskassignment-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/basic' cd /build/reproducible-path/gromacs-2025.1/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.1 /build/reproducible-path/gromacs-2025.1/src/gromacs/taskassignment/tests /build/reproducible-path/gromacs-2025.1/build/basic /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/taskassignment/tests 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-DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/taskassignment/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/src/testutils/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/taskassignment/tests/CMakeFiles/taskassignment-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/taskassignment-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/taskassignment-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/options/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/options/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/options/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/src/testutils/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/options/tests/CMakeFiles/options-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/options-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/options-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/taskassignment/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/taskassignment-test.dir/link.txt --verbose=1 cd /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/options/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/options-test.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/taskassignment-test.dir/link.d "CMakeFiles/taskassignment-test.dir/usergpuids.cpp.o" "CMakeFiles/taskassignment-test.dir/__/__/__/testutils/unittest_main.cpp.o" ../CMakeFiles/taskassignment.dir/decidegpuusage.cpp.o ../CMakeFiles/taskassignment.dir/decidesimulationworkload.cpp.o ../CMakeFiles/taskassignment.dir/findallgputasks.cpp.o ../CMakeFiles/taskassignment.dir/reportgpuusage.cpp.o ../CMakeFiles/taskassignment.dir/resourcedivision.cpp.o ../CMakeFiles/taskassignment.dir/taskassignment.cpp.o ../CMakeFiles/taskassignment.dir/usergpuids.cpp.o -o ../../../../bin/taskassignment-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.10.0.0 ../../../../lib/libgmock.so.1.13.0 /usr/lib/riscv64-linux-gnu/libm.so ../../../../lib/libgtest.so.1.13.0 /usr/lib/gcc/riscv64-linux-gnu/14/libgomp.so /lib/riscv64-linux-gnu/libpthread.a /usr/lib/riscv64-linux-gnu/libmuparser.so.2.3.4 make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/basic' [ 81%] Built target taskassignment-test /usr/bin/make -f src/gromacs/timing/tests/CMakeFiles/timing-test.dir/build.make src/gromacs/timing/tests/CMakeFiles/timing-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/basic' cd /build/reproducible-path/gromacs-2025.1/build/basic && /usr/bin/cmake -E cmake_depends "Unix 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-DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/tables/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/tables/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/src/testutils/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/simd/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/tables/tests/CMakeFiles/table-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/table-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/table-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/timing/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/timing/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/timing/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/src/testutils/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/timing/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/timing/tests/CMakeFiles/timing-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/timing-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/timing-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/tables/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/table-test.dir/link.txt --verbose=1 cd /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/timing/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/timing-test.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/timing-test.dir/link.d "CMakeFiles/timing-test.dir/timing.cpp.o" "CMakeFiles/timing-test.dir/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../bin/timing-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.10.0.0 ../../../../lib/libgmock.so.1.13.0 /usr/lib/riscv64-linux-gnu/libm.so /usr/lib/gcc/riscv64-linux-gnu/14/libgomp.so /lib/riscv64-linux-gnu/libpthread.a ../../../../lib/libgtest.so.1.13.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/basic' [ 82%] Built target timing-test /usr/bin/make -f src/gromacs/topology/tests/CMakeFiles/topology-test.dir/build.make src/gromacs/topology/tests/CMakeFiles/topology-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/basic' cd /build/reproducible-path/gromacs-2025.1/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.1 /build/reproducible-path/gromacs-2025.1/src/gromacs/topology/tests /build/reproducible-path/gromacs-2025.1/build/basic /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/topology/tests /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/topology/tests/CMakeFiles/topology-test.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/basic' /usr/bin/make -f src/gromacs/topology/tests/CMakeFiles/topology-test.dir/build.make src/gromacs/topology/tests/CMakeFiles/topology-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/basic' cd /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/topology/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/topology/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/topology/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/src/testutils/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 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../../../../lib/libgtest.so.1.13.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/basic' [ 82%] Built target table-test /usr/bin/make -f src/gromacs/pulling/tests/CMakeFiles/pull-test.dir/build.make src/gromacs/pulling/tests/CMakeFiles/pull-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/basic' cd /build/reproducible-path/gromacs-2025.1/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.1 /build/reproducible-path/gromacs-2025.1/src/gromacs/pulling/tests /build/reproducible-path/gromacs-2025.1/build/basic /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/pulling/tests /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/pulling/tests/CMakeFiles/pull-test.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/basic' /usr/bin/make -f src/gromacs/pulling/tests/CMakeFiles/pull-test.dir/build.make src/gromacs/pulling/tests/CMakeFiles/pull-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/basic' cd /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/pulling/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/pulling/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/pulling/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/src/testutils/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pulling/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/pulling/tests/CMakeFiles/pull-test.dir/pull.cpp.o -MF CMakeFiles/pull-test.dir/pull.cpp.o.d -o CMakeFiles/pull-test.dir/pull.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/pulling/tests/pull.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/pulling/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/pulling/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/pulling/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/src/testutils/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pulling/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/pulling/tests/CMakeFiles/pull-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/pull-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/pull-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/topology/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/topology/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/topology/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/src/testutils/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/topology/tests/CMakeFiles/topology-test.dir/exclusionblocks.cpp.o -MF CMakeFiles/topology-test.dir/exclusionblocks.cpp.o.d -o CMakeFiles/topology-test.dir/exclusionblocks.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/topology/tests/exclusionblocks.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/pulling/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/pull-test.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/pull-test.dir/link.d "CMakeFiles/pull-test.dir/pull.cpp.o" "CMakeFiles/pull-test.dir/__/__/__/testutils/unittest_main.cpp.o" ../CMakeFiles/pulling.dir/output.cpp.o ../CMakeFiles/pulling.dir/pull.cpp.o ../CMakeFiles/pulling.dir/pull_rotation.cpp.o ../CMakeFiles/pulling.dir/pullcoordexpressionparser.cpp.o ../CMakeFiles/pulling.dir/pullutil.cpp.o ../CMakeFiles/pulling.dir/transformationcoordinate.cpp.o -o ../../../../bin/pull-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.10.0.0 ../../../../lib/libgmock.so.1.13.0 /usr/lib/riscv64-linux-gnu/libm.so ../../../../lib/libgtest.so.1.13.0 /usr/lib/gcc/riscv64-linux-gnu/14/libgomp.so /lib/riscv64-linux-gnu/libpthread.a /usr/lib/riscv64-linux-gnu/libmuparser.so.2.3.4 make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/basic' [ 82%] Built target pull-test cd /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/topology/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/topology/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/topology/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/src/testutils/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/topology/tests/CMakeFiles/topology-test.dir/idef.cpp.o -MF CMakeFiles/topology-test.dir/idef.cpp.o.d -o CMakeFiles/topology-test.dir/idef.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/topology/tests/idef.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/topology/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/topology/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/topology/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/src/testutils/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/topology/tests/CMakeFiles/topology-test.dir/index.cpp.o -MF CMakeFiles/topology-test.dir/index.cpp.o.d -o CMakeFiles/topology-test.dir/index.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/topology/tests/index.cpp /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/math-test.dir/link.d "CMakeFiles/math-test.dir/arrayrefwithpadding.cpp.o" "CMakeFiles/math-test.dir/boxmatrix.cpp.o" "CMakeFiles/math-test.dir/complex.cpp.o" "CMakeFiles/math-test.dir/coordinatetransformation.cpp.o" "CMakeFiles/math-test.dir/densityfit.cpp.o" "CMakeFiles/math-test.dir/dofit.cpp.o" "CMakeFiles/math-test.dir/exponentialmovingaverage.cpp.o" "CMakeFiles/math-test.dir/functions.cpp.o" "CMakeFiles/math-test.dir/gausstransform.cpp.o" "CMakeFiles/math-test.dir/densityfittingforce.cpp.o" "CMakeFiles/math-test.dir/invertmatrix.cpp.o" "CMakeFiles/math-test.dir/matrix.cpp.o" "CMakeFiles/math-test.dir/multidimarray.cpp.o" "CMakeFiles/math-test.dir/neldermead.cpp.o" "CMakeFiles/math-test.dir/optimization.cpp.o" "CMakeFiles/math-test.dir/paddedvector.cpp.o" "CMakeFiles/math-test.dir/vectypes.cpp.o" "CMakeFiles/math-test.dir/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../bin/math-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.10.0.0 ../../../../lib/libgmock.so.1.13.0 /usr/lib/riscv64-linux-gnu/libm.so /usr/lib/gcc/riscv64-linux-gnu/14/libgomp.so /lib/riscv64-linux-gnu/libpthread.a ../../../../lib/libgtest.so.1.13.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/basic' [ 83%] Built target math-test cd /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/topology/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/topology/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/topology/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/src/testutils/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/topology/tests/CMakeFiles/topology-test.dir/mtop.cpp.o -MF CMakeFiles/topology-test.dir/mtop.cpp.o.d -o CMakeFiles/topology-test.dir/mtop.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/topology/tests/mtop.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/topology/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/topology/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/topology/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/src/testutils/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/topology/tests/CMakeFiles/topology-test.dir/symtab.cpp.o -MF CMakeFiles/topology-test.dir/symtab.cpp.o.d -o CMakeFiles/topology-test.dir/symtab.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/topology/tests/symtab.cpp /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/options-test.dir/link.d "CMakeFiles/options-test.dir/abstractoptionstorage.cpp.o" "CMakeFiles/options-test.dir/filenameoption.cpp.o" "CMakeFiles/options-test.dir/filenameoptionmanager.cpp.o" "CMakeFiles/options-test.dir/option.cpp.o" "CMakeFiles/options-test.dir/optionsassigner.cpp.o" "CMakeFiles/options-test.dir/repeatingsection.cpp.o" "CMakeFiles/options-test.dir/timeunitmanager.cpp.o" "CMakeFiles/options-test.dir/treesupport.cpp.o" "CMakeFiles/options-test.dir/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../bin/options-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.10.0.0 ../../../../lib/libgmock.so.1.13.0 /usr/lib/riscv64-linux-gnu/libm.so /usr/lib/gcc/riscv64-linux-gnu/14/libgomp.so /lib/riscv64-linux-gnu/libpthread.a ../../../../lib/libgtest.so.1.13.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/basic' [ 83%] Built target options-test /usr/bin/make -f src/gromacs/simd/tests/CMakeFiles/simd-test.dir/build.make 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CMakeFiles/simd-test.dir/bootstrap_loadstore.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/simd/tests/bootstrap_loadstore.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/topology/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/topology/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/topology/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/src/testutils/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic/api/legacy/include 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src/gromacs/topology/tests/CMakeFiles/topology-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/topology-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/topology-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/simd/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/simd/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/simd/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/src/testutils/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include 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-DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/src/testutils/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/simd/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock -isystem 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-DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/simd/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/src/testutils/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/simd/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/simd/tests/CMakeFiles/simd-test.dir/simd_floatingpoint_util.cpp.o -MF CMakeFiles/simd-test.dir/simd_floatingpoint_util.cpp.o.d -o CMakeFiles/simd-test.dir/simd_floatingpoint_util.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/simd/tests/simd_floatingpoint_util.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/simd/tests && /usr/bin/c++ 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/build/reproducible-path/gromacs-2025.1/src/gromacs/simd/tests/simd_math.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/simd/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/simd/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/simd/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/src/testutils/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include 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-I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/simd/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/simd/tests/CMakeFiles/simd-test.dir/simd_vector_operations.cpp.o -MF CMakeFiles/simd-test.dir/simd_vector_operations.cpp.o.d -o CMakeFiles/simd-test.dir/simd_vector_operations.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/simd/tests/simd_vector_operations.cpp /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/topology-test.dir/link.d "CMakeFiles/topology-test.dir/atoms.cpp.o" "CMakeFiles/topology-test.dir/exclusionblocks.cpp.o" "CMakeFiles/topology-test.dir/idef.cpp.o" "CMakeFiles/topology-test.dir/index.cpp.o" "CMakeFiles/topology-test.dir/mtop.cpp.o" "CMakeFiles/topology-test.dir/symtab.cpp.o" "CMakeFiles/topology-test.dir/topsort.cpp.o" "CMakeFiles/topology-test.dir/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../bin/topology-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.10.0.0 ../../../../lib/libgmock.so.1.13.0 /usr/lib/riscv64-linux-gnu/libm.so /usr/lib/gcc/riscv64-linux-gnu/14/libgomp.so /lib/riscv64-linux-gnu/libpthread.a ../../../../lib/libgtest.so.1.13.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/basic' [ 84%] Built target topology-test /usr/bin/make -f src/gromacs/compat/tests/CMakeFiles/compat-test.dir/build.make src/gromacs/compat/tests/CMakeFiles/compat-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/basic' cd /build/reproducible-path/gromacs-2025.1/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.1 /build/reproducible-path/gromacs-2025.1/src/gromacs/compat/tests /build/reproducible-path/gromacs-2025.1/build/basic /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/compat/tests 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-Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/simd/tests/CMakeFiles/simd-test.dir/simd4.cpp.o -MF CMakeFiles/simd-test.dir/simd4.cpp.o.d -o CMakeFiles/simd-test.dir/simd4.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/simd/tests/simd4.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/simd/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/simd/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/simd/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/src/testutils/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/simd/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/simd/tests/CMakeFiles/simd-test.dir/simd4_floatingpoint.cpp.o -MF CMakeFiles/simd-test.dir/simd4_floatingpoint.cpp.o.d -o CMakeFiles/simd-test.dir/simd4_floatingpoint.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/simd/tests/simd4_floatingpoint.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/simd/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/simd/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/simd/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/src/testutils/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic/src/include 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/usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/compat/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/compat/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/src/testutils/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/external/muparser 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src/gromacs/gmxana/tests/CMakeFiles/gmxana-test.dir/build.make src/gromacs/gmxana/tests/CMakeFiles/gmxana-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/basic' cd /build/reproducible-path/gromacs-2025.1/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.1 /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxana/tests /build/reproducible-path/gromacs-2025.1/build/basic /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/gmxana/tests /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/gmxana/tests/CMakeFiles/gmxana-test.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/basic' /usr/bin/make -f src/gromacs/gmxana/tests/CMakeFiles/gmxana-test.dir/build.make src/gromacs/gmxana/tests/CMakeFiles/gmxana-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/basic' cd 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/build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/simd/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/simd-test.dir/link.txt --verbose=1 cd /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/gmxana/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gmxana/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/gmxana/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/src/testutils/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic/api/legacy/include 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-Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/gmxana/tests/CMakeFiles/gmxana-test.dir/gmx_mindist.cpp.o -MF CMakeFiles/gmxana-test.dir/gmx_mindist.cpp.o.d -o CMakeFiles/gmxana-test.dir/gmx_mindist.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxana/tests/gmx_mindist.cpp /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/simd-test.dir/link.d "CMakeFiles/simd-test.dir/base.cpp.o" "CMakeFiles/simd-test.dir/bootstrap_loadstore.cpp.o" "CMakeFiles/simd-test.dir/scalar.cpp.o" "CMakeFiles/simd-test.dir/scalar_util.cpp.o" "CMakeFiles/simd-test.dir/scalar_math.cpp.o" "CMakeFiles/simd-test.dir/simd.cpp.o" "CMakeFiles/simd-test.dir/simd_floatingpoint.cpp.o" "CMakeFiles/simd-test.dir/simd_floatingpoint_util.cpp.o" "CMakeFiles/simd-test.dir/simd_integer.cpp.o" "CMakeFiles/simd-test.dir/simd_math.cpp.o" "CMakeFiles/simd-test.dir/simd_memory.cpp.o" "CMakeFiles/simd-test.dir/simd_vector_operations.cpp.o" "CMakeFiles/simd-test.dir/simd4.cpp.o" "CMakeFiles/simd-test.dir/simd4_floatingpoint.cpp.o" "CMakeFiles/simd-test.dir/simd4_math.cpp.o" "CMakeFiles/simd-test.dir/simd4_vector_operations.cpp.o" "CMakeFiles/simd-test.dir/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../bin/simd-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.10.0.0 ../../../../lib/libgmock.so.1.13.0 /usr/lib/riscv64-linux-gnu/libm.so /usr/lib/gcc/riscv64-linux-gnu/14/libgomp.so /lib/riscv64-linux-gnu/libpthread.a ../../../../lib/libgtest.so.1.13.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/basic' [ 86%] Built target simd-test /usr/bin/make -f src/gromacs/gmxpreprocess/tests/CMakeFiles/gmxpreprocess-test.dir/build.make src/gromacs/gmxpreprocess/tests/CMakeFiles/gmxpreprocess-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/basic' cd /build/reproducible-path/gromacs-2025.1/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.1 /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests /build/reproducible-path/gromacs-2025.1/build/basic /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/gmxpreprocess/tests /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/gmxpreprocess/tests/CMakeFiles/gmxpreprocess-test.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/basic' /usr/bin/make -f src/gromacs/gmxpreprocess/tests/CMakeFiles/gmxpreprocess-test.dir/build.make src/gromacs/gmxpreprocess/tests/CMakeFiles/gmxpreprocess-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/basic' cd /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/gmxpreprocess/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gmxpreprocess/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/src/testutils/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external 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/build/reproducible-path/gromacs-2025.1/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/gmxpreprocess/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gmxpreprocess/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/src/testutils/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include 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src/gromacs/gmxpreprocess/tests/CMakeFiles/pdb2gmx1-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/basic' cd /build/reproducible-path/gromacs-2025.1/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.1 /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests /build/reproducible-path/gromacs-2025.1/build/basic /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/gmxpreprocess/tests /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/gmxpreprocess/tests/CMakeFiles/pdb2gmx1-test.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/basic' /usr/bin/make -f src/gromacs/gmxpreprocess/tests/CMakeFiles/pdb2gmx1-test.dir/build.make src/gromacs/gmxpreprocess/tests/CMakeFiles/pdb2gmx1-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/basic' cd 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-c /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/pdb2gmx.cpp /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/gmxana-test.dir/link.d "CMakeFiles/gmxana-test.dir/entropy.cpp.o" "CMakeFiles/gmxana-test.dir/gmx_chi.cpp.o" "CMakeFiles/gmxana-test.dir/gmx_mindist.cpp.o" "CMakeFiles/gmxana-test.dir/gmx_traj.cpp.o" "CMakeFiles/gmxana-test.dir/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../bin/gmxana-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.10.0.0 ../../../../lib/libgmock.so.1.13.0 /usr/lib/riscv64-linux-gnu/libm.so /usr/lib/gcc/riscv64-linux-gnu/14/libgomp.so /lib/riscv64-linux-gnu/libpthread.a ../../../../lib/libgtest.so.1.13.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/basic' [ 86%] Built target gmxana-test /usr/bin/make -f src/gromacs/gmxpreprocess/tests/CMakeFiles/pdb2gmx2-test.dir/build.make src/gromacs/gmxpreprocess/tests/CMakeFiles/pdb2gmx2-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/basic' cd /build/reproducible-path/gromacs-2025.1/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.1 /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests /build/reproducible-path/gromacs-2025.1/build/basic /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/gmxpreprocess/tests /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/gmxpreprocess/tests/CMakeFiles/pdb2gmx2-test.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/basic' /usr/bin/make -f src/gromacs/gmxpreprocess/tests/CMakeFiles/pdb2gmx2-test.dir/build.make src/gromacs/gmxpreprocess/tests/CMakeFiles/pdb2gmx2-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/basic' cd /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/gmxpreprocess/tests && /usr/bin/c++ -DAMBER=0 -DCHARMM=0 -DGMX_DOUBLE=0 -DGROMOS=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DOPLSAA=0 -DTEST_DATA_PATH=\"src/gromacs/gmxpreprocess/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/src/testutils/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -isystem 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-c /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/pdb2gmx.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/gmxpreprocess/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gmxpreprocess/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/src/testutils/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include 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-MF CMakeFiles/gmxpreprocess-test.dir/gpp_bond_atomtype.cpp.o.d -o CMakeFiles/gmxpreprocess-test.dir/gpp_bond_atomtype.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/gpp_bond_atomtype.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/gmxpreprocess/tests && /usr/bin/c++ -DAMBER=0 -DCHARMM=0 -DGMX_DOUBLE=0 -DGROMOS=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DOPLSAA=1 -DTEST_DATA_PATH=\"src/gromacs/gmxpreprocess/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/src/testutils/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include 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/lib/riscv64-linux-gnu/libpthread.a ../../../../lib/libgtest.so.1.13.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/basic' [ 86%] Built target pdb2gmx1-test /usr/bin/make -f src/gromacs/correlationfunctions/tests/CMakeFiles/correlations-test.dir/build.make src/gromacs/correlationfunctions/tests/CMakeFiles/correlations-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/basic' cd /build/reproducible-path/gromacs-2025.1/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.1 /build/reproducible-path/gromacs-2025.1/src/gromacs/correlationfunctions/tests /build/reproducible-path/gromacs-2025.1/build/basic /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/correlationfunctions/tests /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/correlationfunctions/tests/CMakeFiles/correlations-test.dir/DependInfo.cmake "--color=" make[4]: Leaving directory 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-Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/correlationfunctions/tests/CMakeFiles/correlations-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/correlations-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/correlations-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/correlationfunctions/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/correlations-test.dir/link.txt --verbose=1 cd /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/gmxpreprocess/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gmxpreprocess/tests\" 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-isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/coordinateio/tests/CMakeFiles/coordinateio-test.dir/outputadaptercontainer.cpp.o -MF CMakeFiles/coordinateio-test.dir/outputadaptercontainer.cpp.o.d -o CMakeFiles/coordinateio-test.dir/outputadaptercontainer.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/coordinateio/tests/outputadaptercontainer.cpp /usr/bin/c++ -g -O2 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-Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/gmxpreprocess/tests/CMakeFiles/gmxpreprocess-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/gmxpreprocess-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/gmxpreprocess-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/energyanalysis/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/energyanalysis/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/energyanalysis/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/src/testutils/include 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/build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/energyanalysis/tests/CMakeFiles/energyanalysis-test.dir/legacyenergy.cpp.o -MF CMakeFiles/energyanalysis-test.dir/legacyenergy.cpp.o.d -o CMakeFiles/energyanalysis-test.dir/legacyenergy.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/energyanalysis/tests/legacyenergy.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/gmxpreprocess/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/gmxpreprocess-test.dir/link.txt --verbose=1 cd /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/energyanalysis/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 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/build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -Wno-cast-function-type-strict -MD -MT src/gromacs/fileio/tests/CMakeFiles/fileio-test.dir/filemd5.cpp.o -MF CMakeFiles/fileio-test.dir/filemd5.cpp.o.d -o CMakeFiles/fileio-test.dir/filemd5.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/fileio/tests/filemd5.cpp /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/tool-test-with-leaks.dir/link.d "CMakeFiles/tool-test-with-leaks.dir/convert-tpr-with-leaks.cpp.o" "CMakeFiles/tool-test-with-leaks.dir/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../bin/tool-test-with-leaks ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.10.0.0 ../../../../lib/libgmock.so.1.13.0 /usr/lib/riscv64-linux-gnu/libm.so /usr/lib/gcc/riscv64-linux-gnu/14/libgomp.so /lib/riscv64-linux-gnu/libpthread.a ../../../../lib/libgtest.so.1.13.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/basic' [ 87%] Built target tool-test-with-leaks /usr/bin/make -f src/gromacs/selection/tests/CMakeFiles/selection-test.dir/build.make src/gromacs/selection/tests/CMakeFiles/selection-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/basic' cd /build/reproducible-path/gromacs-2025.1/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.1 /build/reproducible-path/gromacs-2025.1/src/gromacs/selection/tests /build/reproducible-path/gromacs-2025.1/build/basic 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/build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/selection/tests/CMakeFiles/selection-test.dir/indexutil.cpp.o -MF CMakeFiles/selection-test.dir/indexutil.cpp.o.d -o CMakeFiles/selection-test.dir/indexutil.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/selection/tests/indexutil.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/fileio/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/fileio/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/fileio/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY 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/build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/tools/tests/CMakeFiles/tool-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/tool-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/tool-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/tools/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/tool-test.dir/link.txt --verbose=1 cd /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/coordinateio/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/coordinateio/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/coordinateio/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/src/testutils/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/coordinateio/tests/CMakeFiles/coordinateio-test.dir/settimestep.cpp.o -MF CMakeFiles/coordinateio-test.dir/settimestep.cpp.o.d -o CMakeFiles/coordinateio-test.dir/settimestep.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/coordinateio/tests/settimestep.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/selection/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/selection/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/selection/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/src/testutils/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/selection/tests/CMakeFiles/selection-test.dir/poscalc.cpp.o -MF CMakeFiles/selection-test.dir/poscalc.cpp.o.d -o CMakeFiles/selection-test.dir/poscalc.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/selection/tests/poscalc.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/coordinateio/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/coordinateio/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/coordinateio/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/src/testutils/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include 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src/gromacs/coordinateio/tests/CMakeFiles/coordinateio-test.dir/testmodule.cpp.o -MF CMakeFiles/coordinateio-test.dir/testmodule.cpp.o.d -o CMakeFiles/coordinateio-test.dir/testmodule.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/coordinateio/tests/testmodule.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/fileio/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/fileio/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/fileio/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/src/testutils/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include 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-Wno-missing-field-initializers -fopenmp -Wno-cast-function-type-strict -MD -MT src/gromacs/fileio/tests/CMakeFiles/fileio-test.dir/mrcserializer.cpp.o -MF CMakeFiles/fileio-test.dir/mrcserializer.cpp.o.d -o CMakeFiles/fileio-test.dir/mrcserializer.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/fileio/tests/mrcserializer.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/coordinateio/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/coordinateio/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/coordinateio/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/src/testutils/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/coordinateio/tests/CMakeFiles/coordinateio-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/coordinateio-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/coordinateio-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/testutils/unittest_main.cpp /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/tool-test.dir/link.d "CMakeFiles/tool-test.dir/dump.cpp.o" "CMakeFiles/tool-test.dir/helpwriting.cpp.o" "CMakeFiles/tool-test.dir/make_ndx.cpp.o" "CMakeFiles/tool-test.dir/report_methods.cpp.o" "CMakeFiles/tool-test.dir/trjconv.cpp.o" "CMakeFiles/tool-test.dir/convert-tpr.cpp.o" "CMakeFiles/tool-test.dir/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../bin/tool-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.10.0.0 ../../../../lib/libgmock.so.1.13.0 /usr/lib/riscv64-linux-gnu/libm.so /usr/lib/gcc/riscv64-linux-gnu/14/libgomp.so /lib/riscv64-linux-gnu/libpthread.a ../../../../lib/libgtest.so.1.13.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/basic' [ 87%] Built target tool-test /usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-output-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-output-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/basic' cd /build/reproducible-path/gromacs-2025.1/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.1 /build/reproducible-path/gromacs-2025.1/src/programs/mdrun/tests /build/reproducible-path/gromacs-2025.1/build/basic 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-I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-output-test.dir/compressed_x_output.cpp.o -MF CMakeFiles/mdrun-output-test.dir/compressed_x_output.cpp.o.d -o CMakeFiles/mdrun-output-test.dir/compressed_x_output.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/programs/mdrun/tests/compressed_x_output.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/selection/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/selection/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/selection/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/src/testutils/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/selection/tests/CMakeFiles/selection-test.dir/selectioncollection.cpp.o -MF CMakeFiles/selection-test.dir/selectioncollection.cpp.o.d -o CMakeFiles/selection-test.dir/selectioncollection.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/selection/tests/selectioncollection.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/coordinateio/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/coordinateio-test.dir/link.txt --verbose=1 cd /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/fileio/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/fileio/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/fileio/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/src/testutils/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -Wno-cast-function-type-strict -MD -MT src/gromacs/fileio/tests/CMakeFiles/fileio-test.dir/mrcdensitymap.cpp.o -MF CMakeFiles/fileio-test.dir/mrcdensitymap.cpp.o.d -o CMakeFiles/fileio-test.dir/mrcdensitymap.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/fileio/tests/mrcdensitymap.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/src/testutils/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include 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src/programs/mdrun/tests/CMakeFiles/mdrun-output-test.dir/helpwriting.cpp.o -MF CMakeFiles/mdrun-output-test.dir/helpwriting.cpp.o.d -o CMakeFiles/mdrun-output-test.dir/helpwriting.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/programs/mdrun/tests/helpwriting.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/src/testutils/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include 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src/programs/mdrun/tests/CMakeFiles/mdrun-output-test.dir/outputfiles.cpp.o -MF CMakeFiles/mdrun-output-test.dir/outputfiles.cpp.o.d -o CMakeFiles/mdrun-output-test.dir/outputfiles.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/programs/mdrun/tests/outputfiles.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/fileio/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/fileio/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/fileio/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/src/testutils/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -Wno-cast-function-type-strict -MD -MT src/gromacs/fileio/tests/CMakeFiles/fileio-test.dir/mrcdensitymapheader.cpp.o -MF CMakeFiles/fileio-test.dir/mrcdensitymapheader.cpp.o.d -o CMakeFiles/fileio-test.dir/mrcdensitymapheader.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/fileio/tests/mrcdensitymapheader.cpp /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/coordinateio-test.dir/link.d "CMakeFiles/coordinateio-test.dir/builder.cpp.o" "CMakeFiles/coordinateio-test.dir/outputadaptercontainer.cpp.o" "CMakeFiles/coordinateio-test.dir/outputadapters.cpp.o" "CMakeFiles/coordinateio-test.dir/register.cpp.o" "CMakeFiles/coordinateio-test.dir/requirements.cpp.o" "CMakeFiles/coordinateio-test.dir/setatoms.cpp.o" "CMakeFiles/coordinateio-test.dir/setbothtime.cpp.o" "CMakeFiles/coordinateio-test.dir/setstarttime.cpp.o" "CMakeFiles/coordinateio-test.dir/settimestep.cpp.o" "CMakeFiles/coordinateio-test.dir/testmodule.cpp.o" "CMakeFiles/coordinateio-test.dir/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../bin/coordinateio-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.10.0.0 ../../../../lib/libgmock.so.1.13.0 /usr/lib/riscv64-linux-gnu/libm.so /usr/lib/gcc/riscv64-linux-gnu/14/libgomp.so /lib/riscv64-linux-gnu/libpthread.a ../../../../lib/libgtest.so.1.13.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/basic' [ 88%] Built target coordinateio-test /usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-modules-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-modules-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/basic' cd /build/reproducible-path/gromacs-2025.1/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" 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-I/build/reproducible-path/gromacs-2025.1/src/testutils/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-modules-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/mdrun-modules-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/mdrun-modules-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/testutils/unittest_main.cpp /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/mdrun-output-test.dir/link.d "CMakeFiles/mdrun-output-test.dir/compressed_x_output.cpp.o" "CMakeFiles/mdrun-output-test.dir/helpwriting.cpp.o" "CMakeFiles/mdrun-output-test.dir/outputfiles.cpp.o" "CMakeFiles/mdrun-output-test.dir/trajectory_writing.cpp.o" "CMakeFiles/mdrun-output-test.dir/__/__/__/testutils/unittest_main.cpp.o" ../../CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o ../../CMakeFiles/mdrun_objlib.dir/mdrun/nonbonded_bench.cpp.o -o ../../../../bin/mdrun-output-test ../../../../lib/libtestutils.a ../../../../lib/libmdrun_test_infrastructure.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.10.0.0 /usr/lib/riscv64-linux-gnu/libm.so /usr/lib/gcc/riscv64-linux-gnu/14/libgomp.so /lib/riscv64-linux-gnu/libpthread.a ../../../../lib/libgmock.so.1.13.0 ../../../../lib/libgtest.so.1.13.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/basic' [ 88%] Built target mdrun-output-test /usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-io-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-io-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/basic' cd /build/reproducible-path/gromacs-2025.1/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.1 /build/reproducible-path/gromacs-2025.1/src/programs/mdrun/tests /build/reproducible-path/gromacs-2025.1/build/basic /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/CMakeFiles/mdrun-io-test.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/basic' /usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-io-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-io-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/basic' cd 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/build/reproducible-path/gromacs-2025.1/src/programs/mdrun/tests/checkpoint.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/mdrun-modules-test.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/mdrun-modules-test.dir/link.d "CMakeFiles/mdrun-modules-test.dir/densityfittingmodule.cpp.o" "CMakeFiles/mdrun-modules-test.dir/interactiveMD.cpp.o" "CMakeFiles/mdrun-modules-test.dir/mimic.cpp.o" "CMakeFiles/mdrun-modules-test.dir/__/__/__/testutils/unittest_main.cpp.o" ../../CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o ../../CMakeFiles/mdrun_objlib.dir/mdrun/nonbonded_bench.cpp.o -o ../../../../bin/mdrun-modules-test ../../../../lib/libtestutils.a ../../../../lib/libmdrun_test_infrastructure.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.10.0.0 /usr/lib/riscv64-linux-gnu/libm.so /usr/lib/gcc/riscv64-linux-gnu/14/libgomp.so /lib/riscv64-linux-gnu/libpthread.a ../../../../lib/libgmock.so.1.13.0 ../../../../lib/libgtest.so.1.13.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/basic' [ 88%] Built target mdrun-modules-test cd /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/src/testutils/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic/src/include -I/build/reproducible-path/gromacs-2025.1/src 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-DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -Wno-cast-function-type-strict -MD -MT src/gromacs/fileio/tests/CMakeFiles/fileio-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/fileio-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/fileio-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/fileio/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/fileio-test.dir/link.txt --verbose=1 cd /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY 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/build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-io-test.dir/grompp.cpp.o -MF CMakeFiles/mdrun-io-test.dir/grompp.cpp.o.d -o CMakeFiles/mdrun-io-test.dir/grompp.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/programs/mdrun/tests/grompp.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/selection/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/selection/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/selection/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/src/testutils/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock -isystem 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/build/reproducible-path/gromacs-2025.1/src/programs/mdrun/tests/initialconstraints.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/selection/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/selection-test.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/fileio-test.dir/link.d "CMakeFiles/fileio-test.dir/checkpoint.cpp.o" "CMakeFiles/fileio-test.dir/confio.cpp.o" "CMakeFiles/fileio-test.dir/filemd5.cpp.o" "CMakeFiles/fileio-test.dir/filetypes.cpp.o" "CMakeFiles/fileio-test.dir/matio.cpp.o" "CMakeFiles/fileio-test.dir/mrcserializer.cpp.o" "CMakeFiles/fileio-test.dir/mrcdensitymap.cpp.o" "CMakeFiles/fileio-test.dir/mrcdensitymapheader.cpp.o" "CMakeFiles/fileio-test.dir/readinp.cpp.o" "CMakeFiles/fileio-test.dir/timecontrol.cpp.o" "CMakeFiles/fileio-test.dir/fileioxdrserializer.cpp.o" "CMakeFiles/fileio-test.dir/tngio.cpp.o" "CMakeFiles/fileio-test.dir/xvgio.cpp.o" "CMakeFiles/fileio-test.dir/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../bin/fileio-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.10.0.0 ../../../../lib/libgmock.so.1.13.0 /usr/lib/riscv64-linux-gnu/libm.so /usr/lib/gcc/riscv64-linux-gnu/14/libgomp.so /lib/riscv64-linux-gnu/libpthread.a ../../../../lib/libgtest.so.1.13.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/basic' [ 88%] Built target fileio-test /usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/basic' cd /build/reproducible-path/gromacs-2025.1/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.1 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'/build/reproducible-path/gromacs-2025.1/build/basic' cd /build/reproducible-path/gromacs-2025.1/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.1 /build/reproducible-path/gromacs-2025.1/src/programs/mdrun/tests /build/reproducible-path/gromacs-2025.1/build/basic /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/CMakeFiles/mdrun-single-rank-algorithms-test.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/basic' /usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-single-rank-algorithms-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-single-rank-algorithms-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/basic' cd /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests && /usr/bin/c++ 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-c /build/reproducible-path/gromacs-2025.1/src/programs/mdrun/tests/ewaldsurfaceterm.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/src/testutils/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -isystem 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-Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-single-rank-algorithms-test.dir/orires.cpp.o -MF CMakeFiles/mdrun-single-rank-algorithms-test.dir/orires.cpp.o.d -o CMakeFiles/mdrun-single-rank-algorithms-test.dir/orires.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/programs/mdrun/tests/orires.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary\" -DTEST_USES_MPI=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/src/testutils/include -I/build/reproducible-path/gromacs-2025.1/src/include 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Leaving directory '/build/reproducible-path/gromacs-2025.1/build/basic' [ 88%] Built target mdrun-io-test /usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/minimize-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/minimize-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/basic' cd /build/reproducible-path/gromacs-2025.1/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.1 /build/reproducible-path/gromacs-2025.1/src/programs/mdrun/tests /build/reproducible-path/gromacs-2025.1/build/basic /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/CMakeFiles/minimize-test.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/basic' /usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/minimize-test.dir/build.make 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-I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/programs/mdrun/tests/CMakeFiles/minimize-test.dir/minimize.cpp.o -MF CMakeFiles/minimize-test.dir/minimize.cpp.o.d -o CMakeFiles/minimize-test.dir/minimize.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/programs/mdrun/tests/minimize.cpp /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/mdrun-single-rank-algorithms-test.dir/link.d "CMakeFiles/mdrun-single-rank-algorithms-test.dir/dispersion_correction.cpp.o" "CMakeFiles/mdrun-single-rank-algorithms-test.dir/ewaldsurfaceterm.cpp.o" "CMakeFiles/mdrun-single-rank-algorithms-test.dir/orires.cpp.o" "CMakeFiles/mdrun-single-rank-algorithms-test.dir/__/__/__/testutils/unittest_main.cpp.o" ../../CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o ../../CMakeFiles/mdrun_objlib.dir/mdrun/nonbonded_bench.cpp.o -o ../../../../bin/mdrun-single-rank-algorithms-test ../../../../lib/libtestutils.a ../../../../lib/libmdrun_test_infrastructure.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.10.0.0 /usr/lib/riscv64-linux-gnu/libm.so /usr/lib/gcc/riscv64-linux-gnu/14/libgomp.so /lib/riscv64-linux-gnu/libpthread.a ../../../../lib/libgmock.so.1.13.0 ../../../../lib/libgtest.so.1.13.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/basic' [ 88%] Built target mdrun-single-rank-algorithms-test /usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-non-integrator-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-non-integrator-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/basic' cd /build/reproducible-path/gromacs-2025.1/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.1 /build/reproducible-path/gromacs-2025.1/src/programs/mdrun/tests /build/reproducible-path/gromacs-2025.1/build/basic 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/build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-non-integrator-test.dir/nonbonded_bench.cpp.o -MF CMakeFiles/mdrun-non-integrator-test.dir/nonbonded_bench.cpp.o.d -o CMakeFiles/mdrun-non-integrator-test.dir/nonbonded_bench.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/programs/mdrun/tests/nonbonded_bench.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/src/testutils/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock/include -isystem 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'/build/reproducible-path/gromacs-2025.1/build/basic' [ 88%] Built target mdrun-tpi-test cd /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/src/testutils/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -isystem 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'/build/reproducible-path/gromacs-2025.1/build/basic' /usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-multisim-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-multisim-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/basic' cd /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary\" -DTEST_USES_MPI=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/src/testutils/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include 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"CMakeFiles/mdrun-test.dir/constantacceleration.cpp.o" "CMakeFiles/mdrun-test.dir/boxdeformation.cpp.o" "CMakeFiles/mdrun-test.dir/__/__/__/testutils/unittest_main.cpp.o" ../../CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o ../../CMakeFiles/mdrun_objlib.dir/mdrun/nonbonded_bench.cpp.o -o ../../../../bin/mdrun-test ../../../../lib/libtestutils.a ../../../../lib/libmdrun_test_infrastructure.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.10.0.0 /usr/lib/riscv64-linux-gnu/libm.so /usr/lib/gcc/riscv64-linux-gnu/14/libgomp.so /lib/riscv64-linux-gnu/libpthread.a ../../../../lib/libgmock.so.1.13.0 ../../../../lib/libgtest.so.1.13.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/basic' [ 89%] Built target mdrun-test cd /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" 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cmake_link_script CMakeFiles/mdrun-mpi-test.dir/link.txt --verbose=1 cd /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary\" -DTEST_USES_MPI=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/src/testutils/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -isystem 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../../../../lib/libtestutils.a ../../../../lib/libmdrun_test_infrastructure.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.10.0.0 /usr/lib/riscv64-linux-gnu/libm.so /usr/lib/gcc/riscv64-linux-gnu/14/libgomp.so /lib/riscv64-linux-gnu/libpthread.a ../../../../lib/libgmock.so.1.13.0 ../../../../lib/libgtest.so.1.13.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/basic' [ 89%] Built target mdrun-non-integrator-test /usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-multisim-replex-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-multisim-replex-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/basic' cd /build/reproducible-path/gromacs-2025.1/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.1 /build/reproducible-path/gromacs-2025.1/src/programs/mdrun/tests /build/reproducible-path/gromacs-2025.1/build/basic 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-I/build/reproducible-path/gromacs-2025.1/src/testutils/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest/include -isystem 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/build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/mdrun-multisim-test.dir/link.txt --verbose=1 cd /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary\" -DTEST_USES_MPI=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/src/testutils/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic/api/legacy/include 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CMakeFiles/mdrun-multisim-replex-test.dir/replicaexchange.cpp.o.d -o CMakeFiles/mdrun-multisim-replex-test.dir/replicaexchange.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/programs/mdrun/tests/replicaexchange.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary\" -DTEST_USES_MPI=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/src/testutils/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-multisim-replex-equivalence-test.dir/replicaexchange_equivalence.cpp.o -MF CMakeFiles/mdrun-multisim-replex-equivalence-test.dir/replicaexchange_equivalence.cpp.o.d -o CMakeFiles/mdrun-multisim-replex-equivalence-test.dir/replicaexchange_equivalence.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/programs/mdrun/tests/replicaexchange_equivalence.cpp /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/mdrun-mpi-test.dir/link.d "CMakeFiles/mdrun-mpi-test.dir/domain_decomposition.cpp.o" "CMakeFiles/mdrun-mpi-test.dir/mimic.cpp.o" "CMakeFiles/mdrun-mpi-test.dir/__/__/__/testutils/unittest_main.cpp.o" ../../CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o ../../CMakeFiles/mdrun_objlib.dir/mdrun/nonbonded_bench.cpp.o -o ../../../../bin/mdrun-mpi-test ../../../../lib/libtestutils.a ../../../../lib/libmdrun_test_infrastructure.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.10.0.0 /usr/lib/riscv64-linux-gnu/libm.so /usr/lib/gcc/riscv64-linux-gnu/14/libgomp.so /lib/riscv64-linux-gnu/libpthread.a ../../../../lib/libgmock.so.1.13.0 ../../../../lib/libgtest.so.1.13.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/basic' [ 89%] Built target mdrun-mpi-test /usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-mpi-pme-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-mpi-pme-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/basic' cd /build/reproducible-path/gromacs-2025.1/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.1 /build/reproducible-path/gromacs-2025.1/src/programs/mdrun/tests /build/reproducible-path/gromacs-2025.1/build/basic 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"CMakeFiles/mdrun-multisim-test.dir/__/__/__/testutils/unittest_main.cpp.o" ../../CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o ../../CMakeFiles/mdrun_objlib.dir/mdrun/nonbonded_bench.cpp.o -o ../../../../bin/mdrun-multisim-test ../../../../lib/libtestutils.a ../../../../lib/libmdrun_test_infrastructure.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.10.0.0 /usr/lib/riscv64-linux-gnu/libm.so /usr/lib/gcc/riscv64-linux-gnu/14/libgomp.so /lib/riscv64-linux-gnu/libpthread.a ../../../../lib/libgmock.so.1.13.0 ../../../../lib/libgtest.so.1.13.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/basic' [ 90%] Built target mdrun-multisim-test /usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-coordination-basic-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-coordination-basic-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/basic' cd /build/reproducible-path/gromacs-2025.1/build/basic && 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-I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-coordination-basic-test.dir/periodicactions_basic.cpp.o -MF CMakeFiles/mdrun-coordination-basic-test.dir/periodicactions_basic.cpp.o.d -o CMakeFiles/mdrun-coordination-basic-test.dir/periodicactions_basic.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/programs/mdrun/tests/periodicactions_basic.cpp /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/mdrun-multisim-replex-test.dir/link.d "CMakeFiles/mdrun-multisim-replex-test.dir/multisimtest.cpp.o" "CMakeFiles/mdrun-multisim-replex-test.dir/replicaexchange.cpp.o" "CMakeFiles/mdrun-multisim-replex-test.dir/__/__/__/testutils/unittest_main.cpp.o" ../../CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o ../../CMakeFiles/mdrun_objlib.dir/mdrun/nonbonded_bench.cpp.o -o ../../../../bin/mdrun-multisim-replex-test ../../../../lib/libtestutils.a ../../../../lib/libmdrun_test_infrastructure.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.10.0.0 /usr/lib/riscv64-linux-gnu/libm.so /usr/lib/gcc/riscv64-linux-gnu/14/libgomp.so /lib/riscv64-linux-gnu/libpthread.a ../../../../lib/libgmock.so.1.13.0 ../../../../lib/libgtest.so.1.13.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/basic' [ 90%] Built target mdrun-multisim-replex-test /usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-coordination-coupling-test.dir/build.make 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'/build/reproducible-path/gromacs-2025.1/build/basic' [ 91%] Built target mdrun-mpi-pme-test /usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-coordination-constraints-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-coordination-constraints-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/basic' cd /build/reproducible-path/gromacs-2025.1/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.1 /build/reproducible-path/gromacs-2025.1/src/programs/mdrun/tests /build/reproducible-path/gromacs-2025.1/build/basic /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/CMakeFiles/mdrun-coordination-constraints-test.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/basic' /usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-coordination-constraints-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-coordination-constraints-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/basic' cd /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary\" -DTEST_USES_MPI=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/src/testutils/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include 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src/programs/mdrun/tests/CMakeFiles/mdrun-coordination-constraints-test.dir/periodicactions.cpp.o -MF CMakeFiles/mdrun-coordination-constraints-test.dir/periodicactions.cpp.o.d -o CMakeFiles/mdrun-coordination-constraints-test.dir/periodicactions.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/programs/mdrun/tests/periodicactions.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary\" -DTEST_USES_MPI=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/src/testutils/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic/src/include -I/build/reproducible-path/gromacs-2025.1/src 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-DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary\" -DTEST_USES_MPI=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/src/testutils/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-coordination-basic-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/mdrun-coordination-basic-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/mdrun-coordination-basic-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/mdrun-coordination-basic-test.dir/link.txt --verbose=1 cd /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary\" -DTEST_USES_MPI=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/src/testutils/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -isystem 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CMakeFiles/mdrun-coordination-coupling-test.dir/periodicactions_coupling.cpp.o.d -o CMakeFiles/mdrun-coordination-coupling-test.dir/periodicactions_coupling.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/programs/mdrun/tests/periodicactions_coupling.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary\" -DTEST_USES_MPI=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/src/testutils/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include 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-Wno-missing-field-initializers -fopenmp -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-coordination-constraints-test.dir/periodicactions_constraints.cpp.o -MF CMakeFiles/mdrun-coordination-constraints-test.dir/periodicactions_constraints.cpp.o.d -o CMakeFiles/mdrun-coordination-constraints-test.dir/periodicactions_constraints.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/programs/mdrun/tests/periodicactions_constraints.cpp /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/mdrun-multisim-replex-equivalence-test.dir/link.d "CMakeFiles/mdrun-multisim-replex-equivalence-test.dir/multisimtest.cpp.o" "CMakeFiles/mdrun-multisim-replex-equivalence-test.dir/replicaexchange_equivalence.cpp.o" "CMakeFiles/mdrun-multisim-replex-equivalence-test.dir/__/__/__/testutils/unittest_main.cpp.o" ../../CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o ../../CMakeFiles/mdrun_objlib.dir/mdrun/nonbonded_bench.cpp.o -o ../../../../bin/mdrun-multisim-replex-equivalence-test ../../../../lib/libtestutils.a ../../../../lib/libmdrun_test_infrastructure.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.10.0.0 /usr/lib/riscv64-linux-gnu/libm.so /usr/lib/gcc/riscv64-linux-gnu/14/libgomp.so /lib/riscv64-linux-gnu/libpthread.a ../../../../lib/libgmock.so.1.13.0 ../../../../lib/libgtest.so.1.13.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/basic' [ 91%] Built target mdrun-multisim-replex-equivalence-test /usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-fep-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-fep-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/basic' cd /build/reproducible-path/gromacs-2025.1/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.1 /build/reproducible-path/gromacs-2025.1/src/programs/mdrun/tests /build/reproducible-path/gromacs-2025.1/build/basic /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/CMakeFiles/mdrun-fep-test.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/basic' /usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-fep-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-fep-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/basic' cd /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/src/testutils/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-fep-test.dir/expandedensemble.cpp.o -MF CMakeFiles/mdrun-fep-test.dir/expandedensemble.cpp.o.d -o CMakeFiles/mdrun-fep-test.dir/expandedensemble.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/programs/mdrun/tests/expandedensemble.cpp /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/mdrun-coordination-basic-test.dir/link.d "CMakeFiles/mdrun-coordination-basic-test.dir/periodicactions.cpp.o" "CMakeFiles/mdrun-coordination-basic-test.dir/periodicactions_basic.cpp.o" "CMakeFiles/mdrun-coordination-basic-test.dir/__/__/__/testutils/unittest_main.cpp.o" ../../CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o ../../CMakeFiles/mdrun_objlib.dir/mdrun/nonbonded_bench.cpp.o -o ../../../../bin/mdrun-coordination-basic-test ../../../../lib/libtestutils.a ../../../../lib/libmdrun_test_infrastructure.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.10.0.0 /usr/lib/riscv64-linux-gnu/libm.so /usr/lib/gcc/riscv64-linux-gnu/14/libgomp.so /lib/riscv64-linux-gnu/libpthread.a ../../../../lib/libgmock.so.1.13.0 ../../../../lib/libgtest.so.1.13.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/basic' [ 91%] Built target mdrun-coordination-basic-test cd /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/src/testutils/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem 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/build/reproducible-path/gromacs-2025.1/src/programs/mdrun/tests/freeenergy.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary\" -DTEST_USES_MPI=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/src/testutils/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -isystem 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src/programs/mdrun/tests/CMakeFiles/mdrun-coordination-constraints-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/mdrun-coordination-constraints-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/mdrun-coordination-constraints-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/mdrun-coordination-coupling-test.dir/link.txt --verbose=1 cd /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/mdrun-coordination-constraints-test.dir/link.txt --verbose=1 cd /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/src/testutils/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-fep-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/mdrun-fep-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/mdrun-fep-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/testutils/unittest_main.cpp /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/mdrun-coordination-coupling-test.dir/link.d "CMakeFiles/mdrun-coordination-coupling-test.dir/periodicactions.cpp.o" "CMakeFiles/mdrun-coordination-coupling-test.dir/periodicactions_coupling.cpp.o" "CMakeFiles/mdrun-coordination-coupling-test.dir/__/__/__/testutils/unittest_main.cpp.o" ../../CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o ../../CMakeFiles/mdrun_objlib.dir/mdrun/nonbonded_bench.cpp.o -o ../../../../bin/mdrun-coordination-coupling-test ../../../../lib/libtestutils.a ../../../../lib/libmdrun_test_infrastructure.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.10.0.0 /usr/lib/riscv64-linux-gnu/libm.so /usr/lib/gcc/riscv64-linux-gnu/14/libgomp.so /lib/riscv64-linux-gnu/libpthread.a ../../../../lib/libgmock.so.1.13.0 ../../../../lib/libgtest.so.1.13.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/basic' [ 91%] Built target mdrun-coordination-coupling-test /usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-pull-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-pull-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/basic' cd /build/reproducible-path/gromacs-2025.1/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.1 /build/reproducible-path/gromacs-2025.1/src/programs/mdrun/tests /build/reproducible-path/gromacs-2025.1/build/basic /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/CMakeFiles/mdrun-pull-test.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/basic' /usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-pull-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-pull-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/basic' cd /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/src/testutils/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include 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/usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-rotation-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-rotation-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/basic' cd /build/reproducible-path/gromacs-2025.1/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.1 /build/reproducible-path/gromacs-2025.1/src/programs/mdrun/tests /build/reproducible-path/gromacs-2025.1/build/basic /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/CMakeFiles/mdrun-rotation-test.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/basic' /usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-rotation-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-rotation-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/basic' cd /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/src/testutils/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic/api/legacy/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include 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/build/reproducible-path/gromacs-2025.1/src/programs/mdrun/tests/pull_rotation.cpp /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/mdrun-coordination-constraints-test.dir/link.d "CMakeFiles/mdrun-coordination-constraints-test.dir/periodicactions.cpp.o" "CMakeFiles/mdrun-coordination-constraints-test.dir/periodicactions_constraints.cpp.o" "CMakeFiles/mdrun-coordination-constraints-test.dir/__/__/__/testutils/unittest_main.cpp.o" ../../CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o ../../CMakeFiles/mdrun_objlib.dir/mdrun/nonbonded_bench.cpp.o -o ../../../../bin/mdrun-coordination-constraints-test ../../../../lib/libtestutils.a ../../../../lib/libmdrun_test_infrastructure.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.10.0.0 /usr/lib/riscv64-linux-gnu/libm.so /usr/lib/gcc/riscv64-linux-gnu/14/libgomp.so /lib/riscv64-linux-gnu/libpthread.a ../../../../lib/libgmock.so.1.13.0 ../../../../lib/libgtest.so.1.13.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/basic' [ 91%] Built target mdrun-coordination-constraints-test /usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-simulator-comparison-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-simulator-comparison-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/basic' cd /build/reproducible-path/gromacs-2025.1/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.1 /build/reproducible-path/gromacs-2025.1/src/programs/mdrun/tests /build/reproducible-path/gromacs-2025.1/build/basic /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/CMakeFiles/mdrun-simulator-comparison-test.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/basic' /usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-simulator-comparison-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-simulator-comparison-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/basic' cd /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/src/testutils/include -I/build/reproducible-path/gromacs-2025.1/src/include 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-ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-simulator-comparison-test.dir/simulator.cpp.o -MF CMakeFiles/mdrun-simulator-comparison-test.dir/simulator.cpp.o.d -o CMakeFiles/mdrun-simulator-comparison-test.dir/simulator.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/programs/mdrun/tests/simulator.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/mdrun-fep-test.dir/link.txt --verbose=1 cd /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/src/testutils/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-simulator-comparison-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/mdrun-simulator-comparison-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/mdrun-simulator-comparison-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/src/testutils/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic/api/legacy/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-rotation-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/mdrun-rotation-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/mdrun-rotation-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/testutils/unittest_main.cpp /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/mdrun-fep-test.dir/link.d "CMakeFiles/mdrun-fep-test.dir/expandedensemble.cpp.o" "CMakeFiles/mdrun-fep-test.dir/freeenergy.cpp.o" "CMakeFiles/mdrun-fep-test.dir/__/__/__/testutils/unittest_main.cpp.o" ../../CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o ../../CMakeFiles/mdrun_objlib.dir/mdrun/nonbonded_bench.cpp.o -o ../../../../bin/mdrun-fep-test ../../../../lib/libtestutils.a ../../../../lib/libmdrun_test_infrastructure.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.10.0.0 /usr/lib/riscv64-linux-gnu/libm.so /usr/lib/gcc/riscv64-linux-gnu/14/libgomp.so /lib/riscv64-linux-gnu/libpthread.a ../../../../lib/libgmock.so.1.13.0 ../../../../lib/libgtest.so.1.13.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/basic' [ 92%] Built target mdrun-fep-test /usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-vsites-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-vsites-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/basic' cd /build/reproducible-path/gromacs-2025.1/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.1 /build/reproducible-path/gromacs-2025.1/src/programs/mdrun/tests /build/reproducible-path/gromacs-2025.1/build/basic /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/CMakeFiles/mdrun-vsites-test.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/basic' /usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-vsites-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-vsites-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/basic' cd /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary\" -DTEST_USES_MPI=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/src/testutils/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-vsites-test.dir/virtualsites.cpp.o -MF CMakeFiles/mdrun-vsites-test.dir/virtualsites.cpp.o.d -o 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-I/build/reproducible-path/gromacs-2025.1/build/basic/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-pull-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/mdrun-pull-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/mdrun-pull-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/mdrun-pull-test.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/mdrun-rotation-test.dir/link.d "CMakeFiles/mdrun-rotation-test.dir/pull_rotation.cpp.o" "CMakeFiles/mdrun-rotation-test.dir/__/__/__/testutils/unittest_main.cpp.o" ../../CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o ../../CMakeFiles/mdrun_objlib.dir/mdrun/nonbonded_bench.cpp.o -o ../../../../bin/mdrun-rotation-test ../../../../lib/libtestutils.a ../../../../lib/libmdrun_test_infrastructure.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.10.0.0 /usr/lib/riscv64-linux-gnu/libm.so /usr/lib/gcc/riscv64-linux-gnu/14/libgomp.so /lib/riscv64-linux-gnu/libpthread.a ../../../../lib/libgmock.so.1.13.0 ../../../../lib/libgtest.so.1.13.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/basic' [ 93%] Built target mdrun-rotation-test /usr/bin/make -f api/gmxapi/cpp/tests/CMakeFiles/gmxapi-test.dir/build.make api/gmxapi/cpp/tests/CMakeFiles/gmxapi-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/basic' cd /build/reproducible-path/gromacs-2025.1/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.1 /build/reproducible-path/gromacs-2025.1/api/gmxapi/cpp/tests /build/reproducible-path/gromacs-2025.1/build/basic /build/reproducible-path/gromacs-2025.1/build/basic/api/gmxapi/cpp/tests /build/reproducible-path/gromacs-2025.1/build/basic/api/gmxapi/cpp/tests/CMakeFiles/gmxapi-test.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/basic' /usr/bin/make -f api/gmxapi/cpp/tests/CMakeFiles/gmxapi-test.dir/build.make api/gmxapi/cpp/tests/CMakeFiles/gmxapi-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/basic' cd /build/reproducible-path/gromacs-2025.1/build/basic/api/gmxapi/cpp/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"api/gmxapi/cpp/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.1/build/basic/api/gmxapi/cpp/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/src/testutils/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/api/gmxapi/include -I/build/reproducible-path/gromacs-2025.1/build/basic/api/gmxapi/include -I/build/reproducible-path/gromacs-2025.1/api/gmxapi/cpp/tests -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem 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[ 93%] Built target mdrun-simulator-comparison-test /usr/bin/make -f api/gmxapi/cpp/workflow/tests/CMakeFiles/workflow-details-test.dir/build.make api/gmxapi/cpp/workflow/tests/CMakeFiles/workflow-details-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/basic' cd /build/reproducible-path/gromacs-2025.1/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.1 /build/reproducible-path/gromacs-2025.1/api/gmxapi/cpp/workflow/tests /build/reproducible-path/gromacs-2025.1/build/basic /build/reproducible-path/gromacs-2025.1/build/basic/api/gmxapi/cpp/workflow/tests /build/reproducible-path/gromacs-2025.1/build/basic/api/gmxapi/cpp/workflow/tests/CMakeFiles/workflow-details-test.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/basic' /usr/bin/make -f api/gmxapi/cpp/workflow/tests/CMakeFiles/workflow-details-test.dir/build.make 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../../CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o ../../CMakeFiles/mdrun_objlib.dir/mdrun/nonbonded_bench.cpp.o -o ../../../../bin/mdrun-pull-test ../../../../lib/libtestutils.a ../../../../lib/libmdrun_test_infrastructure.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.10.0.0 /usr/lib/riscv64-linux-gnu/libm.so /usr/lib/gcc/riscv64-linux-gnu/14/libgomp.so /lib/riscv64-linux-gnu/libpthread.a ../../../../lib/libgmock.so.1.13.0 ../../../../lib/libgtest.so.1.13.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/basic' [ 93%] Built target mdrun-pull-test /usr/bin/make -f api/nblib/tests/CMakeFiles/nblib-integrator-test.dir/build.make api/nblib/tests/CMakeFiles/nblib-integrator-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/basic' cd /build/reproducible-path/gromacs-2025.1/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.1 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/usr/lib/riscv64-linux-gnu/libm.so /usr/lib/gcc/riscv64-linux-gnu/14/libgomp.so /lib/riscv64-linux-gnu/libpthread.a make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/basic' [ 94%] Built target nblib-integrator-test /usr/bin/make -f api/nblib/tests/CMakeFiles/nblib-integration-test.dir/build.make api/nblib/tests/CMakeFiles/nblib-integration-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/basic' cd /build/reproducible-path/gromacs-2025.1/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.1 /build/reproducible-path/gromacs-2025.1/api/nblib/tests /build/reproducible-path/gromacs-2025.1/build/basic /build/reproducible-path/gromacs-2025.1/build/basic/api/nblib/tests /build/reproducible-path/gromacs-2025.1/build/basic/api/nblib/tests/CMakeFiles/nblib-integration-test.dir/DependInfo.cmake "--color=" make[4]: Leaving directory 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-ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/nblib-tpr-test.dir/link.d "CMakeFiles/nblib-tpr-test.dir/tpr.cpp.o" "CMakeFiles/nblib-tpr-test.dir/__/__/__/src/testutils/unittest_main.cpp.o" -o ../../../bin/nblib-tpr-test ../../../lib/libtestutils.a ../../../lib/libmdrun_test_infrastructure.a ../../../lib/libnblib_test_infrastructure.a ../../../lib/libnblib_gmx.so.0.1.0 ../../../lib/libtestutils.a ../../../lib/libgmock.so.1.13.0 ../../../lib/libgtest.so.1.13.0 ../../../lib/libgromacs.so.10.0.0 /usr/lib/riscv64-linux-gnu/libm.so /usr/lib/gcc/riscv64-linux-gnu/14/libgomp.so /lib/riscv64-linux-gnu/libpthread.a make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/basic' [ 94%] Built target nblib-tpr-test /usr/bin/make -f api/nblib/listed_forces/tests/CMakeFiles/nblib-listed-forces-test.dir/build.make api/nblib/listed_forces/tests/CMakeFiles/nblib-listed-forces-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/basic' cd /build/reproducible-path/gromacs-2025.1/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.1 /build/reproducible-path/gromacs-2025.1/api/nblib/listed_forces/tests /build/reproducible-path/gromacs-2025.1/build/basic /build/reproducible-path/gromacs-2025.1/build/basic/api/nblib/listed_forces/tests /build/reproducible-path/gromacs-2025.1/build/basic/api/nblib/listed_forces/tests/CMakeFiles/nblib-listed-forces-test.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/basic' /usr/bin/make -f api/nblib/listed_forces/tests/CMakeFiles/nblib-listed-forces-test.dir/build.make api/nblib/listed_forces/tests/CMakeFiles/nblib-listed-forces-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/basic' cd /build/reproducible-path/gromacs-2025.1/build/basic/api/nblib/listed_forces/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"api/nblib/listed_forces/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.1/build/basic/api/nblib/listed_forces/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/src/testutils/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/api/nblib/tests -I/build/reproducible-path/gromacs-2025.1/api/nblib/include -I/build/reproducible-path/gromacs-2025.1/api/nblib -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/timing/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT api/nblib/listed_forces/tests/CMakeFiles/nblib-listed-forces-test.dir/bondtypes.cpp.o -MF CMakeFiles/nblib-listed-forces-test.dir/bondtypes.cpp.o.d -o CMakeFiles/nblib-listed-forces-test.dir/bondtypes.cpp.o -c /build/reproducible-path/gromacs-2025.1/api/nblib/listed_forces/tests/bondtypes.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic/api/nblib/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"api/nblib/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.1/build/basic/api/nblib/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/api -I/build/reproducible-path/gromacs-2025.1/src/testutils/include 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/build/reproducible-path/gromacs-2025.1/build/basic/api/gmxapi/cpp/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"api/gmxapi/cpp/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.1/build/basic/api/gmxapi/cpp/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/src/testutils/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/api/gmxapi/include -I/build/reproducible-path/gromacs-2025.1/build/basic/api/gmxapi/include -I/build/reproducible-path/gromacs-2025.1/api/gmxapi/cpp/tests -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT api/gmxapi/cpp/tests/CMakeFiles/gmxapi-test.dir/__/__/__/__/src/testutils/unittest_main.cpp.o -MF 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-I/build/reproducible-path/gromacs-2025.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/api/nblib/tests -I/build/reproducible-path/gromacs-2025.1/api/nblib/include -I/build/reproducible-path/gromacs-2025.1/api/nblib -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/timing/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT api/nblib/listed_forces/tests/CMakeFiles/nblib-listed-forces-test.dir/gmxcalculator.cpp.o -MF CMakeFiles/nblib-listed-forces-test.dir/gmxcalculator.cpp.o.d -o CMakeFiles/nblib-listed-forces-test.dir/gmxcalculator.cpp.o -c /build/reproducible-path/gromacs-2025.1/api/nblib/listed_forces/tests/gmxcalculator.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic/api/gmxapi/cpp/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/gmxapi-test.dir/link.txt --verbose=1 cd /build/reproducible-path/gromacs-2025.1/build/basic/api/nblib/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"api/nblib/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.1/build/basic/api/nblib/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/src/testutils/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/api/nblib/tests -I/build/reproducible-path/gromacs-2025.1/api/nblib/include -I/build/reproducible-path/gromacs-2025.1/api/nblib -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pbcutil/include 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api/nblib/tests/CMakeFiles/nblib-integration-test.dir/simstate.cpp.o -MF CMakeFiles/nblib-integration-test.dir/simstate.cpp.o.d -o CMakeFiles/nblib-integration-test.dir/simstate.cpp.o -c /build/reproducible-path/gromacs-2025.1/api/nblib/tests/simstate.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic/api/nblib/listed_forces/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"api/nblib/listed_forces/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.1/build/basic/api/nblib/listed_forces/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/src/testutils/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include 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-DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.1/build/basic/api/nblib/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/api -I/build/reproducible-path/gromacs-2025.1/src/testutils/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/api/nblib/tests -I/build/reproducible-path/gromacs-2025.1/api/nblib/include -I/build/reproducible-path/gromacs-2025.1/api/nblib -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pbcutil/include 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api/nblib/tests/CMakeFiles/nblib-setup-test.dir/nbnxmsetup.cpp.o -MF CMakeFiles/nblib-setup-test.dir/nbnxmsetup.cpp.o.d -o CMakeFiles/nblib-setup-test.dir/nbnxmsetup.cpp.o -c /build/reproducible-path/gromacs-2025.1/api/nblib/tests/nbnxmsetup.cpp /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/gmxapi-test.dir/link.d "CMakeFiles/gmxapi-test.dir/restraint.cpp.o" "CMakeFiles/gmxapi-test.dir/runner.cpp.o" "CMakeFiles/gmxapi-test.dir/status.cpp.o" "CMakeFiles/gmxapi-test.dir/stopsignaler.cpp.o" "CMakeFiles/gmxapi-test.dir/system.cpp.o" "CMakeFiles/gmxapi-test.dir/version.cpp.o" "CMakeFiles/gmxapi-test.dir/__/__/__/__/src/testutils/unittest_main.cpp.o" ../../../../src/programs/CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o ../../../../src/programs/CMakeFiles/mdrun_objlib.dir/mdrun/nonbonded_bench.cpp.o -o ../../../../bin/gmxapi-test ../../../../lib/libtestutils.a ../../../../lib/libgmxapi.so.0.4.0 ../../../../lib/libmdrun_test_infrastructure.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.10.0.0 /usr/lib/riscv64-linux-gnu/libm.so /usr/lib/gcc/riscv64-linux-gnu/14/libgomp.so /lib/riscv64-linux-gnu/libpthread.a ../../../../lib/libgmock.so.1.13.0 ../../../../lib/libgtest.so.1.13.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/basic' [ 95%] Built target gmxapi-test /usr/bin/make -f api/nblib/util/tests/CMakeFiles/nblib-util-test.dir/build.make api/nblib/util/tests/CMakeFiles/nblib-util-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/basic' cd /build/reproducible-path/gromacs-2025.1/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.1 /build/reproducible-path/gromacs-2025.1/api/nblib/util/tests /build/reproducible-path/gromacs-2025.1/build/basic 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"CMakeFiles/nblib-util-test.dir/traits.cpp.o" "CMakeFiles/nblib-util-test.dir/__/__/__/__/src/testutils/unittest_main.cpp.o" -o ../../../../bin/nblib-util-test ../../../../lib/libtestutils.a ../../../../lib/libnblib_test_infrastructure.a ../../../../lib/libnblib_gmx.so.0.1.0 ../../../../lib/libtestutils.a ../../../../lib/libgmock.so.1.13.0 ../../../../lib/libgtest.so.1.13.0 ../../../../lib/libgromacs.so.10.0.0 /usr/lib/riscv64-linux-gnu/libm.so /usr/lib/gcc/riscv64-linux-gnu/14/libgomp.so /lib/riscv64-linux-gnu/libpthread.a make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/basic' [ 96%] Built target nblib-util-test /usr/bin/make -f src/gromacs/mdrunutility/tests/CMakeFiles/mdrunutility-test.dir/build.make src/gromacs/mdrunutility/tests/CMakeFiles/mdrunutility-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/basic' cd /build/reproducible-path/gromacs-2025.1/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" 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/usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"api/nblib/listed_forces/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.1/build/basic/api/nblib/listed_forces/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/src/testutils/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/api/nblib/tests -I/build/reproducible-path/gromacs-2025.1/api/nblib/include -I/build/reproducible-path/gromacs-2025.1/api/nblib 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-O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT api/nblib/listed_forces/tests/CMakeFiles/nblib-listed-forces-test.dir/kernels.cpp.o -MF CMakeFiles/nblib-listed-forces-test.dir/kernels.cpp.o.d -o CMakeFiles/nblib-listed-forces-test.dir/kernels.cpp.o -c /build/reproducible-path/gromacs-2025.1/api/nblib/listed_forces/tests/kernels.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/commandline/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/commandline/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/commandline/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/src/testutils/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic/src/include 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-Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/commandline/tests/CMakeFiles/commandline-test.dir/cmdlinehelpwriter.cpp.o -MF CMakeFiles/commandline-test.dir/cmdlinehelpwriter.cpp.o.d -o CMakeFiles/commandline-test.dir/cmdlinehelpwriter.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/commandline/tests/cmdlinehelpwriter.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic/api/nblib/listed_forces/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"api/nblib/listed_forces/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.1/build/basic/api/nblib/listed_forces/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/src/testutils/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/api/nblib/tests -I/build/reproducible-path/gromacs-2025.1/api/nblib/include -I/build/reproducible-path/gromacs-2025.1/api/nblib -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/timing/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem 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/build/reproducible-path/gromacs-2025.1/src/gromacs/commandline/tests/cmdlinemodulemanager.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/mdrunutility/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdrunutility/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/mdrunutility/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/src/testutils/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/mdrunutility/tests/CMakeFiles/mdrunutility-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/mdrunutility-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/mdrunutility-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/mdrunutility/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/mdrunutility-test.dir/link.txt --verbose=1 cd /build/reproducible-path/gromacs-2025.1/build/basic/api/nblib/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"api/nblib/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.1/build/basic/api/nblib/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/api -I/build/reproducible-path/gromacs-2025.1/src/testutils/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/api/nblib/tests -I/build/reproducible-path/gromacs-2025.1/api/nblib/include -I/build/reproducible-path/gromacs-2025.1/api/nblib -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT api/nblib/tests/CMakeFiles/nblib-setup-test.dir/virials.cpp.o -MF CMakeFiles/nblib-setup-test.dir/virials.cpp.o.d -o CMakeFiles/nblib-setup-test.dir/virials.cpp.o -c /build/reproducible-path/gromacs-2025.1/api/nblib/tests/virials.cpp /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/mdrunutility-test.dir/link.d "CMakeFiles/mdrunutility-test.dir/mdmodulesnotifier.cpp.o" "CMakeFiles/mdrunutility-test.dir/threadaffinity.cpp.o" "CMakeFiles/mdrunutility-test.dir/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../bin/mdrunutility-test ../../../../lib/libtestutils.a ../../../../lib/libmdrunutility-test-shared.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.10.0.0 /usr/lib/riscv64-linux-gnu/libm.so /usr/lib/gcc/riscv64-linux-gnu/14/libgomp.so /lib/riscv64-linux-gnu/libpthread.a ../../../../lib/libgmock.so.1.13.0 ../../../../lib/libgtest.so.1.13.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/basic' [ 96%] Built target mdrunutility-test /usr/bin/make -f src/gromacs/mdrunutility/tests/CMakeFiles/mdrunutility-mpi-test.dir/build.make src/gromacs/mdrunutility/tests/CMakeFiles/mdrunutility-mpi-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/basic' cd /build/reproducible-path/gromacs-2025.1/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.1 /build/reproducible-path/gromacs-2025.1/src/gromacs/mdrunutility/tests /build/reproducible-path/gromacs-2025.1/build/basic /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/mdrunutility/tests /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/mdrunutility/tests/CMakeFiles/mdrunutility-mpi-test.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/basic' /usr/bin/make -f src/gromacs/mdrunutility/tests/CMakeFiles/mdrunutility-mpi-test.dir/build.make src/gromacs/mdrunutility/tests/CMakeFiles/mdrunutility-mpi-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/basic' cd /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/mdrunutility/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdrunutility/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/mdrunutility/tests/Testing/Temporary\" -DTEST_USES_MPI=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/src/testutils/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem 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/build/reproducible-path/gromacs-2025.1/src/gromacs/mdrunutility/tests/threadaffinity_mpi.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic/api/nblib/listed_forces/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"api/nblib/listed_forces/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.1/build/basic/api/nblib/listed_forces/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/src/testutils/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include 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/build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT api/nblib/listed_forces/tests/CMakeFiles/nblib-listed-forces-test.dir/calculator.cpp.o -MF CMakeFiles/nblib-listed-forces-test.dir/calculator.cpp.o.d -o CMakeFiles/nblib-listed-forces-test.dir/calculator.cpp.o -c /build/reproducible-path/gromacs-2025.1/api/nblib/listed_forces/tests/calculator.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/commandline/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/commandline/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/commandline/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/src/testutils/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock/include -isystem 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-DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"api/nblib/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.1/build/basic/api/nblib/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/api -I/build/reproducible-path/gromacs-2025.1/src/testutils/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/api/nblib/tests -I/build/reproducible-path/gromacs-2025.1/api/nblib/include -I/build/reproducible-path/gromacs-2025.1/api/nblib -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops 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-I/build/reproducible-path/gromacs-2025.1/src/testutils/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/mdrunutility/tests/CMakeFiles/mdrunutility-mpi-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/mdrunutility-mpi-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/mdrunutility-mpi-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/mdrunutility/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/mdrunutility-mpi-test.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -Wformat 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'/build/reproducible-path/gromacs-2025.1/build/basic' cd /build/reproducible-path/gromacs-2025.1/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.1 /build/reproducible-path/gromacs-2025.1/src/gromacs/analysisdata/tests /build/reproducible-path/gromacs-2025.1/build/basic /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/analysisdata/tests /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/analysisdata/tests/CMakeFiles/analysisdata-test.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/basic' /usr/bin/make -f src/gromacs/analysisdata/tests/CMakeFiles/analysisdata-test.dir/build.make src/gromacs/analysisdata/tests/CMakeFiles/analysisdata-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/basic' cd /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/analysisdata/tests && /usr/bin/c++ -DGMX_DOUBLE=0 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-Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT api/nblib/listed_forces/tests/CMakeFiles/nblib-listed-forces-test.dir/conversions.cpp.o -MF CMakeFiles/nblib-listed-forces-test.dir/conversions.cpp.o.d -o CMakeFiles/nblib-listed-forces-test.dir/conversions.cpp.o -c /build/reproducible-path/gromacs-2025.1/api/nblib/listed_forces/tests/conversions.cpp /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/nblib-setup-test.dir/link.d "CMakeFiles/nblib-setup-test.dir/box.cpp.o" "CMakeFiles/nblib-setup-test.dir/interactions.cpp.o" "CMakeFiles/nblib-setup-test.dir/particletype.cpp.o" "CMakeFiles/nblib-setup-test.dir/pbcholder.cpp.o" "CMakeFiles/nblib-setup-test.dir/molecules.cpp.o" "CMakeFiles/nblib-setup-test.dir/nbnxmsetup.cpp.o" "CMakeFiles/nblib-setup-test.dir/topology.cpp.o" "CMakeFiles/nblib-setup-test.dir/virials.cpp.o" "CMakeFiles/nblib-setup-test.dir/__/__/__/src/testutils/unittest_main.cpp.o" -o ../../../bin/nblib-setup-test ../../../lib/libtestutils.a ../../../lib/libmdrun_test_infrastructure.a ../../../lib/libnblib_test_infrastructure.a ../../../lib/libnblib_gmx.so.0.1.0 ../../../lib/libtestutils.a ../../../lib/libgmock.so.1.13.0 ../../../lib/libgtest.so.1.13.0 ../../../lib/libgromacs.so.10.0.0 /usr/lib/riscv64-linux-gnu/libm.so /usr/lib/gcc/riscv64-linux-gnu/14/libgomp.so /lib/riscv64-linux-gnu/libpthread.a make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/basic' [ 97%] Built target nblib-setup-test /usr/bin/make -f src/gromacs/trajectoryanalysis/tests/CMakeFiles/trajectoryanalysis-test.dir/build.make src/gromacs/trajectoryanalysis/tests/CMakeFiles/trajectoryanalysis-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/basic' cd /build/reproducible-path/gromacs-2025.1/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.1 /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests /build/reproducible-path/gromacs-2025.1/build/basic /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/trajectoryanalysis/tests /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/trajectoryanalysis/tests/CMakeFiles/trajectoryanalysis-test.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/basic' /usr/bin/make -f src/gromacs/trajectoryanalysis/tests/CMakeFiles/trajectoryanalysis-test.dir/build.make src/gromacs/trajectoryanalysis/tests/CMakeFiles/trajectoryanalysis-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/basic' cd /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/trajectoryanalysis/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/trajectoryanalysis/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/trajectoryanalysis/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/src/testutils/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem 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/build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/moduletest.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/commandline/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/commandline/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/commandline/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/src/testutils/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -isystem 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-I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/trajectoryanalysis/tests/CMakeFiles/trajectoryanalysis-test.dir/convert_trj.cpp.o -MF CMakeFiles/trajectoryanalysis-test.dir/convert_trj.cpp.o.d -o CMakeFiles/trajectoryanalysis-test.dir/convert_trj.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/convert_trj.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic/api/nblib/listed_forces/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"api/nblib/listed_forces/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.1/build/basic/api/nblib/listed_forces/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/src/testutils/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/api/nblib/tests -I/build/reproducible-path/gromacs-2025.1/api/nblib/include -I/build/reproducible-path/gromacs-2025.1/api/nblib -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/timing/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT api/nblib/listed_forces/tests/CMakeFiles/nblib-listed-forces-test.dir/transformations.cpp.o -MF CMakeFiles/nblib-listed-forces-test.dir/transformations.cpp.o.d -o CMakeFiles/nblib-listed-forces-test.dir/transformations.cpp.o -c /build/reproducible-path/gromacs-2025.1/api/nblib/listed_forces/tests/transformations.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/trajectoryanalysis/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/trajectoryanalysis/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/trajectoryanalysis/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/src/testutils/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/trajectoryanalysis/tests/CMakeFiles/trajectoryanalysis-test.dir/distance.cpp.o -MF CMakeFiles/trajectoryanalysis-test.dir/distance.cpp.o.d -o CMakeFiles/trajectoryanalysis-test.dir/distance.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/distance.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/trajectoryanalysis/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/trajectoryanalysis/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/trajectoryanalysis/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/src/testutils/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/trajectoryanalysis/tests/CMakeFiles/trajectoryanalysis-test.dir/dssp.cpp.o -MF CMakeFiles/trajectoryanalysis-test.dir/dssp.cpp.o.d -o CMakeFiles/trajectoryanalysis-test.dir/dssp.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/dssp.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic/api/nblib/listed_forces/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"api/nblib/listed_forces/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.1/build/basic/api/nblib/listed_forces/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/src/testutils/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/api/nblib/tests -I/build/reproducible-path/gromacs-2025.1/api/nblib/include -I/build/reproducible-path/gromacs-2025.1/api/nblib -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/timing/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT api/nblib/listed_forces/tests/CMakeFiles/nblib-listed-forces-test.dir/__/__/__/__/src/testutils/unittest_main.cpp.o -MF CMakeFiles/nblib-listed-forces-test.dir/__/__/__/__/src/testutils/unittest_main.cpp.o.d -o CMakeFiles/nblib-listed-forces-test.dir/__/__/__/__/src/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/analysisdata/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/analysisdata/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/analysisdata/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/src/testutils/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/analysisdata/tests/CMakeFiles/analysisdata-test.dir/lifetime.cpp.o -MF CMakeFiles/analysisdata-test.dir/lifetime.cpp.o.d -o CMakeFiles/analysisdata-test.dir/lifetime.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/analysisdata/tests/lifetime.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic/api/nblib/listed_forces/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/nblib-listed-forces-test.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/commandline-test.dir/link.d "CMakeFiles/commandline-test.dir/cmdlinehelpmodule.cpp.o" "CMakeFiles/commandline-test.dir/cmdlinehelpwriter.cpp.o" "CMakeFiles/commandline-test.dir/cmdlinemodulemanager.cpp.o" "CMakeFiles/commandline-test.dir/cmdlinemodulemanagertest.cpp.o" "CMakeFiles/commandline-test.dir/cmdlineparser.cpp.o" "CMakeFiles/commandline-test.dir/cmdlineprogramcontext.cpp.o" "CMakeFiles/commandline-test.dir/filenm.cpp.o" "CMakeFiles/commandline-test.dir/pargs.cpp.o" "CMakeFiles/commandline-test.dir/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../bin/commandline-test ../../../../lib/libtestutils.a ../../../../lib/libonlinehelp-test-shared.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.10.0.0 /usr/lib/riscv64-linux-gnu/libm.so /usr/lib/gcc/riscv64-linux-gnu/14/libgomp.so /lib/riscv64-linux-gnu/libpthread.a ../../../../lib/libgmock.so.1.13.0 ../../../../lib/libgtest.so.1.13.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/basic' [ 98%] Built target commandline-test /usr/bin/make -f api/nblib/CMakeFiles/nblib-tests.dir/build.make api/nblib/CMakeFiles/nblib-tests.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/basic' cd /build/reproducible-path/gromacs-2025.1/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.1 /build/reproducible-path/gromacs-2025.1/api/nblib /build/reproducible-path/gromacs-2025.1/build/basic /build/reproducible-path/gromacs-2025.1/build/basic/api/nblib /build/reproducible-path/gromacs-2025.1/build/basic/api/nblib/CMakeFiles/nblib-tests.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/basic' /usr/bin/make -f api/nblib/CMakeFiles/nblib-tests.dir/build.make api/nblib/CMakeFiles/nblib-tests.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/basic' make[4]: Nothing to be done for 'api/nblib/CMakeFiles/nblib-tests.dir/build'. make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/basic' [ 98%] Built target nblib-tests cd /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/trajectoryanalysis/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/trajectoryanalysis/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/trajectoryanalysis/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/src/testutils/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock/include -isystem 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/build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/analysisdata/tests/CMakeFiles/analysisdata-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/analysisdata-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/analysisdata-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/trajectoryanalysis/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/trajectoryanalysis/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/trajectoryanalysis/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/src/testutils/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem 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/build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/freevolume.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/analysisdata/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/analysisdata-test.dir/link.txt --verbose=1 cd /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/trajectoryanalysis/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/trajectoryanalysis/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/trajectoryanalysis/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/src/testutils/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops 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-I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 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"CMakeFiles/nblib-listed-forces-test.dir/typetests.cpp.o" "CMakeFiles/nblib-listed-forces-test.dir/calculator.cpp.o" "CMakeFiles/nblib-listed-forces-test.dir/conversions.cpp.o" "CMakeFiles/nblib-listed-forces-test.dir/shiftforces.cpp.o" "CMakeFiles/nblib-listed-forces-test.dir/transformations.cpp.o" "CMakeFiles/nblib-listed-forces-test.dir/__/__/__/__/src/testutils/unittest_main.cpp.o" -o ../../../../bin/nblib-listed-forces-test ../../../../lib/libtestutils.a ../../../../lib/libnblib_test_infrastructure.a ../../../../lib/libnblib_gmx.so.0.1.0 ../../../../lib/libtestutils.a ../../../../lib/libgmock.so.1.13.0 ../../../../lib/libgtest.so.1.13.0 ../../../../lib/libgromacs.so.10.0.0 /usr/lib/riscv64-linux-gnu/libm.so /usr/lib/gcc/riscv64-linux-gnu/14/libgomp.so /lib/riscv64-linux-gnu/libpthread.a make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/basic' [ 98%] Built target nblib-listed-forces-test cd /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/trajectoryanalysis/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/trajectoryanalysis/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/trajectoryanalysis/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/src/testutils/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/trajectoryanalysis/tests/CMakeFiles/trajectoryanalysis-test.dir/msd.cpp.o -MF CMakeFiles/trajectoryanalysis-test.dir/msd.cpp.o.d -o CMakeFiles/trajectoryanalysis-test.dir/msd.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/msd.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/trajectoryanalysis/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/trajectoryanalysis/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/trajectoryanalysis/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/src/testutils/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -isystem 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CMakeFiles/trajectoryanalysis-test.dir/pairdist.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/pairdist.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/trajectoryanalysis/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/trajectoryanalysis/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/trajectoryanalysis/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/src/testutils/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic/api/legacy/include 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../../../programs/CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o ../../../programs/CMakeFiles/mdrun_objlib.dir/mdrun/nonbonded_bench.cpp.o -o ../../../../bin/trajectoryanalysis-test ../../../../lib/libtestutils.a ../../../../lib/libanalysisdata-test-shared.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.10.0.0 /usr/lib/riscv64-linux-gnu/libm.so /usr/lib/gcc/riscv64-linux-gnu/14/libgomp.so /lib/riscv64-linux-gnu/libpthread.a ../../../../lib/libgmock.so.1.13.0 ../../../../lib/libgtest.so.1.13.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/basic' [100%] Built target trajectoryanalysis-test /usr/bin/make -f CMakeFiles/tests.dir/build.make CMakeFiles/tests.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/basic' cd /build/reproducible-path/gromacs-2025.1/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.1 /build/reproducible-path/gromacs-2025.1 /build/reproducible-path/gromacs-2025.1/build/basic /build/reproducible-path/gromacs-2025.1/build/basic /build/reproducible-path/gromacs-2025.1/build/basic/CMakeFiles/tests.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/basic' /usr/bin/make -f CMakeFiles/tests.dir/build.make CMakeFiles/tests.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/basic' make[4]: Nothing to be done for 'CMakeFiles/tests.dir/build'. make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/basic' [100%] Built target tests make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/basic' /usr/bin/cmake -E cmake_progress_start /build/reproducible-path/gromacs-2025.1/build/basic/CMakeFiles 0 make[2]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/basic' make[1]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/basic' (cd build/basic; LD_LIBRARY_PATH=/build/reproducible-path/gromacs-2025.1/build/basic/lib ctest -V) UpdateCTestConfiguration from :/build/reproducible-path/gromacs-2025.1/build/basic/DartConfiguration.tcl Parse Config file:/build/reproducible-path/gromacs-2025.1/build/basic/DartConfiguration.tcl UpdateCTestConfiguration from :/build/reproducible-path/gromacs-2025.1/build/basic/DartConfiguration.tcl Parse Config file:/build/reproducible-path/gromacs-2025.1/build/basic/DartConfiguration.tcl Test project /build/reproducible-path/gromacs-2025.1/build/basic Constructing a list of tests Done constructing a list of tests Updating test list for fixtures Added 0 tests to meet fixture requirements Checking test dependency graph... Checking test dependency graph end test 1 Start 1: GmxapiExternalInterfaceTests 1: Test command: /build/reproducible-path/gromacs-2025.1/build/basic/bin/gmxapi-test "-ntomp" "2" "--gtest_output=xml:/build/reproducible-path/gromacs-2025.1/build/basic/Testing/Temporary/GmxapiExternalInterfaceTests.xml" 1: Working Directory: /build/reproducible-path/gromacs-2025.1/build/basic/api/gmxapi/cpp/tests 1: Test timeout computed to be: 600 1: [==========] Running 9 tests from 1 test suite. 1: [----------] Global test environment set-up. 1: [----------] 9 tests from GmxApiTest 1: [ RUN ] GmxApiTest.ApiRunnerRestrainedMD 1: Generating 1-4 interactions: fudge = 0.5 1: 1: NOTE 1 [file spc_and_methane.top, line 33]: 1: The bond in molecule-type methane between atoms 1 C and 2 H1 has an 1: estimated oscillational period of 1.1e-02 ps, which is less than 10 times 1: the time step of 2.0e-03 ps. 1: Maybe you forgot to change the constraints mdp option. 1: 1: Number of degrees of freedom in T-Coupling group System is 18.00 1: 1: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/api/gmxapi/cpp/tests/Testing/Temporary/GmxApiTest_ApiRunnerRestrainedMD_input.mdp]: 1: You are using a plain Coulomb cut-off, which might produce artifacts. 1: You might want to consider using PME electrostatics. 1: 1: 1: 1: There were 2 NOTEs 1: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/api/gmxapi/cpp/tests/Testing/Temporary/GmxApiTest_ApiRunnerRestrainedMD.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 1: Changing nstlist from 10 to 25, rlist from 1.057 to 1.183 1: 1: Using 1 MPI thread 1: Using 2 OpenMP threads 1: 1: 1: NOTE: The number of threads is not equal to the number of (logical) cpus 1: and the -pin option is set to auto: will not pin threads to cpus. 1: This can lead to significant performance degradation. 1: Consider using -pin on (and -pinoffset in case you run multiple jobs). 1: starting mdrun 'Water and methane' 1: 2 steps, 0.0 ps. 1: Setting the LD random seed to -4343311 1: 1: Generated 331705 of the 331705 non-bonded parameter combinations 1: 1: Generated 331705 of the 331705 1-4 parameter combinations 1: 1: Excluding 2 bonded neighbours molecule type 'SOL' 1: 1: Excluding 3 bonded neighbours molecule type 'methane' 1: 1: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/spc_and_methane.gro' 1: 1: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 1: 1: Calculated rlist for 1x1 atom pair-list as 1.077 nm, buffer size 0.077 nm 1: 1: Set rlist, assuming 4x4 atom pair-list, to 1.057 nm, buffer size 0.057 nm 1: 1: Note that mdrun will redetermine rlist based on the actual pair-list setup 1: 1: This run will generate roughly 0 Mb of data 1: 1: Writing final coordinates. 1: 1: Core t (s) Wall t (s) (%) 1: Time: 0.050 0.025 197.8 1: (ns/day) (hour/ns) 1: Performance: 19.863 1.208 1: [ OK ] GmxApiTest.ApiRunnerRestrainedMD (4631 ms) 1: [ RUN ] GmxApiTest.RunnerBasicMD 1: Generating 1-4 interactions: fudge = 0.5 1: 1: NOTE 1 [file spc_and_methane.top, line 33]: 1: The bond in molecule-type methane between atoms 1 C and 2 H1 has an 1: estimated oscillational period of 1.1e-02 ps, which is less than 10 times 1: the time step of 2.0e-03 ps. 1: Maybe you forgot to change the constraints mdp option. 1: 1: Number of degrees of freedom in T-Coupling group System is 18.00 1: 1: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/api/gmxapi/cpp/tests/Testing/Temporary/GmxApiTest_RunnerBasicMD_input.mdp]: 1: You are using a plain Coulomb cut-off, which might produce artifacts. 1: You might want to consider using PME electrostatics. 1: 1: 1: 1: There were 2 NOTEs 1: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/api/gmxapi/cpp/tests/Testing/Temporary/GmxApiTest_RunnerBasicMD.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 1: Changing nstlist from 10 to 25, rlist from 1.057 to 1.183 1: 1: Using 1 MPI thread 1: Using 2 OpenMP threads 1: 1: 1: NOTE: The number of threads is not equal to the number of (logical) cpus 1: and the -pin option is set to auto: will not pin threads to cpus. 1: This can lead to significant performance degradation. 1: Consider using -pin on (and -pinoffset in case you run multiple jobs). 1: starting mdrun 'Water and methane' 1: 2 steps, 0.0 ps. 1: Setting the LD random seed to 1609825981 1: 1: Generated 331705 of the 331705 non-bonded parameter combinations 1: 1: Generated 331705 of the 331705 1-4 parameter combinations 1: 1: Excluding 2 bonded neighbours molecule type 'SOL' 1: 1: Excluding 3 bonded neighbours molecule type 'methane' 1: 1: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/spc_and_methane.gro' 1: 1: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 1: 1: Calculated rlist for 1x1 atom pair-list as 1.077 nm, buffer size 0.077 nm 1: 1: Set rlist, assuming 4x4 atom pair-list, to 1.057 nm, buffer size 0.057 nm 1: 1: Note that mdrun will redetermine rlist based on the actual pair-list setup 1: 1: This run will generate roughly 0 Mb of data 1: 1: Writing final coordinates. 1: 1: Core t (s) Wall t (s) (%) 1: Time: 0.050 0.026 197.6 1: (ns/day) (hour/ns) 1: Performance: 19.841 1.210 1: [ OK ] GmxApiTest.RunnerBasicMD (4556 ms) 1: [ RUN ] GmxApiTest.RunnerReinitialize 1: Generating 1-4 interactions: fudge = 0.5 1: 1: NOTE 1 [file spc_and_methane.top, line 33]: 1: The bond in molecule-type methane between atoms 1 C and 2 H1 has an 1: estimated oscillational period of 1.1e-02 ps, which is less than 10 times 1: the time step of 2.0e-03 ps. 1: Maybe you forgot to change the constraints mdp option. 1: 1: Number of degrees of freedom in T-Coupling group System is 18.00 1: 1: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/api/gmxapi/cpp/tests/Testing/Temporary/GmxApiTest_RunnerReinitialize_input.mdp]: 1: You are using a plain Coulomb cut-off, which might produce artifacts. 1: You might want to consider using PME electrostatics. 1: 1: 1: 1: There were 2 NOTEs 1: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/api/gmxapi/cpp/tests/Testing/Temporary/GmxApiTest_RunnerReinitialize.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 1: Changing nstlist from 10 to 25, rlist from 1.057 to 1.183 1: 1: Using 1 MPI thread 1: Using 2 OpenMP threads 1: 1: 1: NOTE: The number of threads is not equal to the number of (logical) cpus 1: and the -pin option is set to auto: will not pin threads to cpus. 1: This can lead to significant performance degradation. 1: Consider using -pin on (and -pinoffset in case you run multiple jobs). 1: starting mdrun 'Water and methane' 1: 20 steps, 0.0 ps. 1: 1: 1: Received the remote INT/TERM signal, stopping within 200 steps 1: 1: Setting the LD random seed to -560300721 1: 1: Generated 331705 of the 331705 non-bonded parameter combinations 1: 1: Generated 331705 of the 331705 1-4 parameter combinations 1: 1: Excluding 2 bonded neighbours molecule type 'SOL' 1: 1: Excluding 3 bonded neighbours molecule type 'methane' 1: 1: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/spc_and_methane.gro' 1: 1: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 1: 1: Calculated rlist for 1x1 atom pair-list as 1.077 nm, buffer size 0.077 nm 1: 1: Set rlist, assuming 4x4 atom pair-list, to 1.057 nm, buffer size 0.057 nm 1: 1: Note that mdrun will redetermine rlist based on the actual pair-list setup 1: 1: This run will generate roughly 0 Mb of data 1: 1: Writing final coordinates. 1: 1: Core t (s) Wall t (s) (%) 1: Time: 0.064 0.032 198.1 1: (ns/day) (hour/ns) 1: Performance: 110.194 0.218 1: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/api/gmxapi/cpp/tests/Testing/Temporary/GmxApiTest_RunnerReinitialize.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 1: Changing nstlist from 10 to 25, rlist from 1.057 to 1.183 1: 1: Using 1 MPI thread 1: Using 2 OpenMP threads 1: 1: 1: NOTE: The number of threads is not equal to the number of (logical) cpus 1: and the -pin option is set to auto: will not pin threads to cpus. 1: This can lead to significant performance degradation. 1: Consider using -pin on (and -pinoffset in case you run multiple jobs). 1: starting mdrun 'Water and methane' 1: 20 steps, 0.0 ps. 1: 1: Writing final coordinates. 1: 1: Core t (s) Wall t (s) (%) 1: Time: 0.060 0.031 198.0 1: (ns/day) (hour/ns) 1: Performance: 116.188 0.207 1: [ OK ] GmxApiTest.RunnerReinitialize (4633 ms) 1: [ RUN ] GmxApiTest.RunnerChainedMD 1: Generating 1-4 interactions: fudge = 0.5 1: 1: NOTE 1 [file spc_and_methane.top, line 33]: 1: The bond in molecule-type methane between atoms 1 C and 2 H1 has an 1: estimated oscillational period of 1.1e-02 ps, which is less than 10 times 1: the time step of 2.0e-03 ps. 1: Maybe you forgot to change the constraints mdp option. 1: 1: Number of degrees of freedom in T-Coupling group System is 18.00 1: 1: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/api/gmxapi/cpp/tests/Testing/Temporary/GmxApiTest_RunnerChainedMD_input.mdp]: 1: You are using a plain Coulomb cut-off, which might produce artifacts. 1: You might want to consider using PME electrostatics. 1: 1: 1: 1: There were 2 NOTEs 1: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/api/gmxapi/cpp/tests/Testing/Temporary/GmxApiTest_RunnerChainedMD.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 1: Changing nstlist from 10 to 25, rlist from 1.057 to 1.183 1: 1: Using 1 MPI thread 1: Using 2 OpenMP threads 1: 1: 1: NOTE: The number of threads is not equal to the number of (logical) cpus 1: and the -pin option is set to auto: will not pin threads to cpus. 1: This can lead to significant performance degradation. 1: Consider using -pin on (and -pinoffset in case you run multiple jobs). 1: starting mdrun 'Water and methane' 1: 2 steps, 0.0 ps. 1: Setting the LD random seed to -4096850 1: 1: Generated 331705 of the 331705 non-bonded parameter combinations 1: 1: Generated 331705 of the 331705 1-4 parameter combinations 1: 1: Excluding 2 bonded neighbours molecule type 'SOL' 1: 1: Excluding 3 bonded neighbours molecule type 'methane' 1: 1: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/spc_and_methane.gro' 1: 1: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 1: 1: Calculated rlist for 1x1 atom pair-list as 1.077 nm, buffer size 0.077 nm 1: 1: Set rlist, assuming 4x4 atom pair-list, to 1.057 nm, buffer size 0.057 nm 1: 1: Note that mdrun will redetermine rlist based on the actual pair-list setup 1: 1: This run will generate roughly 0 Mb of data 1: 1: Writing final coordinates. 1: 1: Core t (s) Wall t (s) (%) 1: Time: 0.039 0.020 197.2 1: (ns/day) (hour/ns) 1: Performance: 25.725 0.933 1: trr version: GMX_trn_file (single precision) 1: 1: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/api/gmxapi/cpp/tests/Testing/Temporary/GmxApiTest_RunnerChainedMD.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 1: Setting nsteps to 4 1: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/api/gmxapi/cpp/tests/Testing/Temporary/GmxApiTest_RunnerChainedMD.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 1: Changing nstlist from 10 to 25, rlist from 1.057 to 1.183 1: 1: Using 1 MPI thread 1: Using 2 OpenMP threads 1: 1: 1: NOTE: The number of threads is not equal to the number of (logical) cpus 1: and the -pin option is set to auto: will not pin threads to cpus. 1: This can lead to significant performance degradation. 1: Consider using -pin on (and -pinoffset in case you run multiple jobs). 1: starting mdrun 'Water and methane' 1: 4 steps, 0.0 ps (continuing from step 2, 0.0 ps). 1: Input file: 1: Run start step 0 1: Run start time 0 ps 1: Step to be made during run 2 1: Runtime for the run 0.00390625 ps 1: Run end step 2 1: Run end time 0.00390625 ps 1: 1: 1: Output file: 1: Run start step 0 1: Run start time 0 ps 1: Step to be made during run 4 1: Runtime for the run 0.0078125 ps 1: Run end step 4 1: Run end time 0.0078125 ps 1: 1: 1: Writing final coordinates. 1: 1: Core t (s) Wall t (s) (%) 1: Time: 0.040 0.020 198.2 1: (ns/day) (hour/ns) 1: Performance: 25.359 0.946 1: 1: [ OK ] GmxApiTest.RunnerChainedMD (4616 ms) 1: [ RUN ] GmxApiTest.Status 1: [ OK ] GmxApiTest.Status (0 ms) 1: [ RUN ] GmxApiTest.ApiRunnerStopSignalClient 1: Generating 1-4 interactions: fudge = 0.5 1: 1: NOTE 1 [file spc_and_methane.top, line 33]: 1: The bond in molecule-type methane between atoms 1 C and 2 H1 has an 1: estimated oscillational period of 1.1e-02 ps, which is less than 10 times 1: the time step of 2.0e-03 ps. 1: Maybe you forgot to change the constraints mdp option. 1: 1: Number of degrees of freedom in T-Coupling group System is 18.00 1: 1: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/api/gmxapi/cpp/tests/Testing/Temporary/GmxApiTest_ApiRunnerStopSignalClient_input.mdp]: 1: You are using a plain Coulomb cut-off, which might produce artifacts. 1: You might want to consider using PME electrostatics. 1: 1: 1: 1: There were 2 NOTEs 1: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/api/gmxapi/cpp/tests/Testing/Temporary/GmxApiTest_ApiRunnerStopSignalClient.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 1: Changing nstlist from 10 to 1, rlist from 1.057 to 1 1: 1: Using 1 MPI thread 1: Using 2 OpenMP threads 1: 1: 1: NOTE: The number of threads is not equal to the number of (logical) cpus 1: and the -pin option is set to auto: will not pin threads to cpus. 1: This can lead to significant performance degradation. 1: Consider using -pin on (and -pinoffset in case you run multiple jobs). 1: starting mdrun 'Water and methane' 1: 4 steps, 0.0 ps. 1: Setting the LD random seed to 1987532109 1: 1: Generated 331705 of the 331705 non-bonded parameter combinations 1: 1: Generated 331705 of the 331705 1-4 parameter combinations 1: 1: Excluding 2 bonded neighbours molecule type 'SOL' 1: 1: Excluding 3 bonded neighbours molecule type 'methane' 1: 1: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/spc_and_methane.gro' 1: 1: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 1: 1: Calculated rlist for 1x1 atom pair-list as 1.077 nm, buffer size 0.077 nm 1: 1: Set rlist, assuming 4x4 atom pair-list, to 1.057 nm, buffer size 0.057 nm 1: 1: Note that mdrun will redetermine rlist based on the actual pair-list setup 1: 1: This run will generate roughly 0 Mb of data 1: 1: Writing final coordinates. 1: 1: Core t (s) Wall t (s) (%) 1: Time: 0.055 0.028 197.7 1: (ns/day) (hour/ns) 1: Performance: 30.458 0.788 1: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/api/gmxapi/cpp/tests/Testing/Temporary/GmxApiTest_ApiRunnerStopSignalClient.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 1: Overriding nsteps with value passed on the command line: 4 steps, 0.00781 ps 1: Changing nstlist from 10 to 1, rlist from 1.057 to 1 1: 1: 1: Using 1 MPI thread 1: Using 2 OpenMP threads 1: 1: 1: NOTE: The number of threads is not equal to the number of (logical) cpus 1: and the -pin option is set to auto: will not pin threads to cpus. 1: This can lead to significant performance degradation. 1: Consider using -pin on (and -pinoffset in case you run multiple jobs). 1: starting mdrun 'Water and methane' 1: 4 steps, 0.0 ps. 1: 1: Core t (s) Wall t (s) (%) 1: Time: 0.045 0.023 195.9 1: (ns/day) (hour/ns) 1: Performance: 14.711 1.631 1: [ OK ] GmxApiTest.ApiRunnerStopSignalClient (4631 ms) 1: [ RUN ] GmxApiTest.SystemConstruction 1: Generating 1-4 interactions: fudge = 0.5 1: 1: NOTE 1 [file spc_and_methane.top, line 33]: 1: The bond in molecule-type methane between atoms 1 C and 2 H1 has an 1: estimated oscillational period of 1.1e-02 ps, which is less than 10 times 1: the time step of 2.0e-03 ps. 1: Maybe you forgot to change the constraints mdp option. 1: 1: Number of degrees of freedom in T-Coupling group System is 18.00 1: 1: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/api/gmxapi/cpp/tests/Testing/Temporary/GmxApiTest_SystemConstruction_input.mdp]: 1: You are using a plain Coulomb cut-off, which might produce artifacts. 1: You might want to consider using PME electrostatics. 1: 1: 1: 1: There were 2 NOTEs 1: Setting the LD random seed to -16795928 1: 1: Generated 331705 of the 331705 non-bonded parameter combinations 1: 1: Generated 331705 of the 331705 1-4 parameter combinations 1: 1: Excluding 2 bonded neighbours molecule type 'SOL' 1: 1: Excluding 3 bonded neighbours molecule type 'methane' 1: 1: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/spc_and_methane.gro' 1: 1: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 1: 1: Calculated rlist for 1x1 atom pair-list as 1.077 nm, buffer size 0.077 nm 1: 1: Set rlist, assuming 4x4 atom pair-list, to 1.057 nm, buffer size 0.057 nm 1: 1: Note that mdrun will redetermine rlist based on the actual pair-list setup 1: 1: This run will generate roughly 0 Mb of data 1: [ OK ] GmxApiTest.SystemConstruction (4472 ms) 1: [ RUN ] GmxApiTest.SaneVersionComparisons 1: [ OK ] GmxApiTest.SaneVersionComparisons (0 ms) 1: [ RUN ] GmxApiTest.VersionNamed0_1_Features 1: [ OK ] GmxApiTest.VersionNamed0_1_Features (0 ms) 1: [----------] 9 tests from GmxApiTest (27543 ms total) 1: 1: [----------] Global test environment tear-down 1: [==========] 9 tests from 1 test suite ran. (27609 ms total) 1: [ PASSED ] 9 tests. 1/92 Test #1: GmxapiExternalInterfaceTests .............. Passed 27.73 sec test 2 Start 2: GmxapiInternalInterfaceTests 2: Test command: /build/reproducible-path/gromacs-2025.1/build/basic/bin/workflow-details-test "-ntomp" "2" "--gtest_output=xml:/build/reproducible-path/gromacs-2025.1/build/basic/Testing/Temporary/GmxapiInternalInterfaceTests.xml" 2: Working Directory: /build/reproducible-path/gromacs-2025.1/build/basic/api/gmxapi/cpp/workflow/tests 2: Test timeout computed to be: 600 2: [==========] Running 2 tests from 1 test suite. 2: [----------] Global test environment set-up. 2: [----------] 2 tests from GmxApiTest 2: [ RUN ] GmxApiTest.BuildApiWorkflowImpl 2: Generating 1-4 interactions: fudge = 0.5 2: 2: NOTE 1 [file spc_and_methane.top, line 33]: 2: The bond in molecule-type methane between atoms 1 C and 2 H1 has an 2: estimated oscillational period of 1.1e-02 ps, which is less than 10 times 2: the time step of 2.0e-03 ps. 2: Maybe you forgot to change the constraints mdp option. 2: 2: Number of degrees of freedom in T-Coupling group System is 18.00 2: 2: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/api/gmxapi/cpp/workflow/tests/Testing/Temporary/GmxApiTest_BuildApiWorkflowImpl_input.mdp]: 2: You are using a plain Coulomb cut-off, which might produce artifacts. 2: You might want to consider using PME electrostatics. 2: 2: 2: 2: There were 2 NOTEs 2: Setting the LD random seed to -75597313 2: 2: Generated 331705 of the 331705 non-bonded parameter combinations 2: 2: Generated 331705 of the 331705 1-4 parameter combinations 2: 2: Excluding 2 bonded neighbours molecule type 'SOL' 2: 2: Excluding 3 bonded neighbours molecule type 'methane' 2: 2: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/spc_and_methane.gro' 2: 2: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 2: 2: Calculated rlist for 1x1 atom pair-list as 1.077 nm, buffer size 0.077 nm 2: 2: Set rlist, assuming 4x4 atom pair-list, to 1.057 nm, buffer size 0.057 nm 2: 2: Note that mdrun will redetermine rlist based on the actual pair-list setup 2: 2: This run will generate roughly 0 Mb of data 2: [ OK ] GmxApiTest.BuildApiWorkflowImpl (4553 ms) 2: [ RUN ] GmxApiTest.CreateApiWorkflow 2: Generating 1-4 interactions: fudge = 0.5 2: 2: NOTE 1 [file spc_and_methane.top, line 33]: 2: The bond in molecule-type methane between atoms 1 C and 2 H1 has an 2: estimated oscillational period of 1.1e-02 ps, which is less than 10 times 2: the time step of 2.0e-03 ps. 2: Maybe you forgot to change the constraints mdp option. 2: 2: Number of degrees of freedom in T-Coupling group System is 18.00 2: 2: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/api/gmxapi/cpp/workflow/tests/Testing/Temporary/GmxApiTest_CreateApiWorkflow_input.mdp]: 2: You are using a plain Coulomb cut-off, which might produce artifacts. 2: You might want to consider using PME electrostatics. 2: 2: 2: 2: There were 2 NOTEs 2: Setting the LD random seed to -540181849 2: 2: Generated 331705 of the 331705 non-bonded parameter combinations 2: 2: Generated 331705 of the 331705 1-4 parameter combinations 2: 2: Excluding 2 bonded neighbours molecule type 'SOL' 2: 2: Excluding 3 bonded neighbours molecule type 'methane' 2: 2: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/spc_and_methane.gro' 2: 2: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 2: 2: Calculated rlist for 1x1 atom pair-list as 1.077 nm, buffer size 0.077 nm 2: 2: Set rlist, assuming 4x4 atom pair-list, to 1.057 nm, buffer size 0.057 nm 2: 2: Note that mdrun will redetermine rlist based on the actual pair-list setup 2: 2: This run will generate roughly 0 Mb of data 2: [ OK ] GmxApiTest.CreateApiWorkflow (4443 ms) 2: [----------] 2 tests from GmxApiTest (8997 ms total) 2: 2: [----------] Global test environment tear-down 2: [==========] 2 tests from 1 test suite ran. (9045 ms total) 2: [ PASSED ] 2 tests. 2/92 Test #2: GmxapiInternalInterfaceTests .............. Passed 9.14 sec test 3 Start 3: NbLibListedForcesTests 3: Test command: /build/reproducible-path/gromacs-2025.1/build/basic/bin/nblib-listed-forces-test "--gtest_output=xml:/build/reproducible-path/gromacs-2025.1/build/basic/Testing/Temporary/NbLibListedForcesTests.xml" 3: Working Directory: /build/reproducible-path/gromacs-2025.1/build/basic/api/nblib/listed_forces/tests 3: Test timeout computed to be: 600 3: [==========] Running 44 tests from 22 test suites. 3: [----------] Global test environment set-up. 3: [----------] 8 tests from NBlibTest 3: [ RUN ] NBlibTest.BondTypesOperatorEqualWorks 3: [ OK ] NBlibTest.BondTypesOperatorEqualWorks (0 ms) 3: [ RUN ] NBlibTest.BondTypesLessThanWorks 3: [ OK ] NBlibTest.BondTypesLessThanWorks (0 ms) 3: [ RUN ] NBlibTest.CanSplitListedWork 3: [ OK ] NBlibTest.CanSplitListedWork (0 ms) 3: [ RUN ] NBlibTest.ListedForceBuffer 3: [ OK ] NBlibTest.ListedForceBuffer (0 ms) 3: [ RUN ] NBlibTest.ListedForceCalculatorCanConstruct 3: [ OK ] NBlibTest.ListedForceCalculatorCanConstruct (0 ms) 3: [ RUN ] NBlibTest.GmxToNblibConversionAllTypes 3: [ OK ] NBlibTest.GmxToNblibConversionAllTypes (0 ms) 3: [ RUN ] NBlibTest.EndToEndListedComparison 3: [ OK ] NBlibTest.EndToEndListedComparison (1 ms) 3: [ RUN ] NBlibTest.shiftForcesAreCorrect 3: [ OK ] NBlibTest.shiftForcesAreCorrect (124 ms) 3: [----------] 8 tests from NBlibTest (127 ms total) 3: 3: [----------] 1 test from Kernels 3: [ RUN ] Kernels.HarmonicScalarKernelCanCompute 3: [ OK ] Kernels.HarmonicScalarKernelCanCompute (0 ms) 3: [----------] 1 test from Kernels (0 ms total) 3: 3: [----------] 1 test from FourCenter 3: [ RUN ] FourCenter.ListedForcesProperDihedralTest 3: [ OK ] FourCenter.ListedForcesProperDihedralTest (1 ms) 3: [----------] 1 test from FourCenter (1 ms total) 3: 3: [----------] 7 tests from ThreeCenter 3: [ RUN ] ThreeCenter.ListedForcesG96AngleTest 3: [ OK ] ThreeCenter.ListedForcesG96AngleTest (0 ms) 3: [ RUN ] ThreeCenter.ListedForcesHarmonicAngleTest 3: [ OK ] ThreeCenter.ListedForcesHarmonicAngleTest (0 ms) 3: [ RUN ] ThreeCenter.ListedForcesLinearAngleTest 3: [ OK ] ThreeCenter.ListedForcesLinearAngleTest (0 ms) 3: [ RUN ] ThreeCenter.ListedForcesCrossBondBondTest 3: [ OK ] ThreeCenter.ListedForcesCrossBondBondTest (0 ms) 3: [ RUN ] ThreeCenter.ListedForcesCrossBondAngleTest 3: [ OK ] ThreeCenter.ListedForcesCrossBondAngleTest (0 ms) 3: [ RUN ] ThreeCenter.ListedForcesQuarticAngleTest 3: [ OK ] ThreeCenter.ListedForcesQuarticAngleTest (0 ms) 3: [ RUN ] ThreeCenter.ListedForcesRestrictedAngleTest 3: [ OK ] ThreeCenter.ListedForcesRestrictedAngleTest (0 ms) 3: [----------] 7 tests from ThreeCenter (5 ms total) 3: 3: [----------] 5 tests from TwoCenter 3: [ RUN ] TwoCenter.ListedForcesHarmonicBondTest 3: [ OK ] TwoCenter.ListedForcesHarmonicBondTest (0 ms) 3: [ RUN ] TwoCenter.ListedForcesG96BondTest 3: [ OK ] TwoCenter.ListedForcesG96BondTest (0 ms) 3: [ RUN ] TwoCenter.ListedForcesCubicBondTest 3: [ OK ] TwoCenter.ListedForcesCubicBondTest (0 ms) 3: [ RUN ] TwoCenter.ListedForcesMorseBondTest 3: [ OK ] TwoCenter.ListedForcesMorseBondTest (0 ms) 3: [ RUN ] TwoCenter.ListedForcesFeneBondTest 3: [ OK ] TwoCenter.ListedForcesFeneBondTest (0 ms) 3: [----------] 5 tests from TwoCenter (3 ms total) 3: 3: [----------] 5 tests from ListedExampleData 3: [ RUN ] ListedExampleData.ComputeHarmonicBondForces 3: [ OK ] ListedExampleData.ComputeHarmonicBondForces (0 ms) 3: [ RUN ] ListedExampleData.ComputeHarmonicBondEnergies 3: [ OK ] ListedExampleData.ComputeHarmonicBondEnergies (0 ms) 3: [ RUN ] ListedExampleData.ComputeHarmonicAngleForces 3: [ OK ] ListedExampleData.ComputeHarmonicAngleForces (0 ms) 3: [ RUN ] ListedExampleData.CanReduceForces 3: [ OK ] ListedExampleData.CanReduceForces (0 ms) 3: [ RUN ] ListedExampleData.CanReduceEnergies 3: [ OK ] ListedExampleData.CanReduceEnergies (0 ms) 3: [----------] 5 tests from ListedExampleData (3 ms total) 3: 3: [----------] 1 test from LinearChainDataFixture 3: [ RUN ] LinearChainDataFixture.Multithreading 3: [ OK ] LinearChainDataFixture.Multithreading (23 ms) 3: [----------] 1 test from LinearChainDataFixture (23 ms total) 3: 3: [----------] 2 tests from ListedShims 3: [ RUN ] ListedShims.ParameterConversion 3: [ OK ] ListedShims.ParameterConversion (0 ms) 3: [ RUN ] ListedShims.GmxToNblibConversion 3: [ OK ] ListedShims.GmxToNblibConversion (0 ms) 3: [----------] 2 tests from ListedShims (0 ms total) 3: 3: [----------] 1 test from CompareEachTypeInNblibAndGmx/NblibGmxListed/0, where TypeParam = nblib::TwoParameterInteraction 3: [ RUN ] CompareEachTypeInNblibAndGmx/NblibGmxListed/0.SameForcesOnBoth 3: [ OK ] CompareEachTypeInNblibAndGmx/NblibGmxListed/0.SameForcesOnBoth (0 ms) 3: [----------] 1 test from CompareEachTypeInNblibAndGmx/NblibGmxListed/0 (0 ms total) 3: 3: [----------] 1 test from CompareEachTypeInNblibAndGmx/NblibGmxListed/1, where TypeParam = nblib::G96BondType 3: [ RUN ] CompareEachTypeInNblibAndGmx/NblibGmxListed/1.SameForcesOnBoth 3: [ OK ] CompareEachTypeInNblibAndGmx/NblibGmxListed/1.SameForcesOnBoth (0 ms) 3: [----------] 1 test from CompareEachTypeInNblibAndGmx/NblibGmxListed/1 (0 ms total) 3: 3: [----------] 1 test from CompareEachTypeInNblibAndGmx/NblibGmxListed/2, where TypeParam = nblib::CubicBondType 3: [ RUN ] CompareEachTypeInNblibAndGmx/NblibGmxListed/2.SameForcesOnBoth 3: [ OK ] CompareEachTypeInNblibAndGmx/NblibGmxListed/2.SameForcesOnBoth (0 ms) 3: [----------] 1 test from CompareEachTypeInNblibAndGmx/NblibGmxListed/2 (0 ms total) 3: 3: [----------] 1 test from CompareEachTypeInNblibAndGmx/NblibGmxListed/3, where TypeParam = nblib::MorseBondType 3: [ RUN ] CompareEachTypeInNblibAndGmx/NblibGmxListed/3.SameForcesOnBoth 3: [ OK ] CompareEachTypeInNblibAndGmx/NblibGmxListed/3.SameForcesOnBoth (0 ms) 3: [----------] 1 test from CompareEachTypeInNblibAndGmx/NblibGmxListed/3 (0 ms total) 3: 3: [----------] 1 test from CompareEachTypeInNblibAndGmx/NblibGmxListed/4, where TypeParam = nblib::TwoParameterInteraction 3: [ RUN ] CompareEachTypeInNblibAndGmx/NblibGmxListed/4.SameForcesOnBoth 3: [ OK ] CompareEachTypeInNblibAndGmx/NblibGmxListed/4.SameForcesOnBoth (0 ms) 3: [----------] 1 test from CompareEachTypeInNblibAndGmx/NblibGmxListed/4 (0 ms total) 3: 3: [----------] 1 test from CompareEachTypeInNblibAndGmx/NblibGmxListed/5, where TypeParam = nblib::AngleInteractionType 3: [ RUN ] CompareEachTypeInNblibAndGmx/NblibGmxListed/5.SameForcesOnBoth 3: [ OK ] CompareEachTypeInNblibAndGmx/NblibGmxListed/5.SameForcesOnBoth (0 ms) 3: [----------] 1 test from CompareEachTypeInNblibAndGmx/NblibGmxListed/5 (0 ms total) 3: 3: [----------] 1 test from CompareEachTypeInNblibAndGmx/NblibGmxListed/6, where TypeParam = nblib::CosineParamAngle 3: [ RUN ] CompareEachTypeInNblibAndGmx/NblibGmxListed/6.SameForcesOnBoth 3: [ OK ] CompareEachTypeInNblibAndGmx/NblibGmxListed/6.SameForcesOnBoth (0 ms) 3: [----------] 1 test from CompareEachTypeInNblibAndGmx/NblibGmxListed/6 (0 ms total) 3: 3: [----------] 1 test from CompareEachTypeInNblibAndGmx/NblibGmxListed/7, where TypeParam = nblib::CosineParamAngle 3: [ RUN ] CompareEachTypeInNblibAndGmx/NblibGmxListed/7.SameForcesOnBoth 3: [ OK ] CompareEachTypeInNblibAndGmx/NblibGmxListed/7.SameForcesOnBoth (0 ms) 3: [----------] 1 test from CompareEachTypeInNblibAndGmx/NblibGmxListed/7 (0 ms total) 3: 3: [----------] 1 test from CompareEachTypeInNblibAndGmx/NblibGmxListed/8, where TypeParam = nblib::TwoParameterInteraction 3: [ RUN ] CompareEachTypeInNblibAndGmx/NblibGmxListed/8.SameForcesOnBoth 3: [ OK ] CompareEachTypeInNblibAndGmx/NblibGmxListed/8.SameForcesOnBoth (0 ms) 3: [----------] 1 test from CompareEachTypeInNblibAndGmx/NblibGmxListed/8 (0 ms total) 3: 3: [----------] 1 test from CompareEachTypeInNblibAndGmx/NblibGmxListed/9, where TypeParam = nblib::QuarticAngle 3: [ RUN ] CompareEachTypeInNblibAndGmx/NblibGmxListed/9.SameForcesOnBoth 3: [ OK ] CompareEachTypeInNblibAndGmx/NblibGmxListed/9.SameForcesOnBoth (0 ms) 3: [----------] 1 test from CompareEachTypeInNblibAndGmx/NblibGmxListed/9 (0 ms total) 3: 3: [----------] 1 test from CompareEachTypeInNblibAndGmx/NblibGmxListed/10, where TypeParam = nblib::CrossBondBond 3: [ RUN ] CompareEachTypeInNblibAndGmx/NblibGmxListed/10.SameForcesOnBoth 3: [ OK ] CompareEachTypeInNblibAndGmx/NblibGmxListed/10.SameForcesOnBoth (0 ms) 3: [----------] 1 test from CompareEachTypeInNblibAndGmx/NblibGmxListed/10 (0 ms total) 3: 3: [----------] 1 test from CompareEachTypeInNblibAndGmx/NblibGmxListed/11, where TypeParam = nblib::CrossBondAngle 3: [ RUN ] CompareEachTypeInNblibAndGmx/NblibGmxListed/11.SameForcesOnBoth 3: [ OK ] CompareEachTypeInNblibAndGmx/NblibGmxListed/11.SameForcesOnBoth (0 ms) 3: [----------] 1 test from CompareEachTypeInNblibAndGmx/NblibGmxListed/11 (0 ms total) 3: 3: [----------] 1 test from CompareEachTypeInNblibAndGmx/NblibGmxListed/12, where TypeParam = nblib::ProperDihedral 3: [ RUN ] CompareEachTypeInNblibAndGmx/NblibGmxListed/12.SameForcesOnBoth 3: [ OK ] CompareEachTypeInNblibAndGmx/NblibGmxListed/12.SameForcesOnBoth (0 ms) 3: [----------] 1 test from CompareEachTypeInNblibAndGmx/NblibGmxListed/12 (0 ms total) 3: 3: [----------] 1 test from ListedTransformations 3: [ RUN ] ListedTransformations.SortInteractionIndices 3: [ OK ] ListedTransformations.SortInteractionIndices (0 ms) 3: [----------] 1 test from ListedTransformations (0 ms total) 3: 3: [----------] Global test environment tear-down 3: [==========] 44 tests from 22 test suites ran. (169 ms total) 3: [ PASSED ] 44 tests. 3/92 Test #3: NbLibListedForcesTests .................... Passed 0.26 sec test 4 Start 4: NbLibSamplesTestArgon 4: Test command: /build/reproducible-path/gromacs-2025.1/build/basic/bin/argon-forces-integration 4: Working Directory: /build/reproducible-path/gromacs-2025.1/build/basic/api/nblib/samples 4: Test timeout computed to be: 1500 4: initial forces on particle 0: x 0.000000 y 0.000000 z 0.000000 4: final forces on particle 0: x -0.412993 y -1.098256 z -0.113191 4: initial position of particle 0: x 0.794000 y 1.439000 z 0.610000 4: final position of particle 0: x 0.789162 y 1.271508 z 0.819867 4/92 Test #4: NbLibSamplesTestArgon ..................... Passed 0.08 sec test 5 Start 5: NbLibSamplesTestMethaneWater 5: Test command: /build/reproducible-path/gromacs-2025.1/build/basic/bin/methane-water-integration 5: Working Directory: /build/reproducible-path/gromacs-2025.1/build/basic/api/nblib/samples 5: Test timeout computed to be: 1500 5: initial position of particle 0: x 0.005000 y 0.600000 z 0.244000 5: final position of particle 9: x 77.358398 y 5.324894 z -80.600098 5/92 Test #5: NbLibSamplesTestMethaneWater .............. Passed 0.09 sec test 6 Start 6: NbLibUtilTests 6: Test command: /build/reproducible-path/gromacs-2025.1/build/basic/bin/nblib-util-test "--gtest_output=xml:/build/reproducible-path/gromacs-2025.1/build/basic/Testing/Temporary/NbLibUtilTests.xml" 6: Working Directory: /build/reproducible-path/gromacs-2025.1/build/basic/api/nblib/util/tests 6: Test timeout computed to be: 30 6: [==========] Running 16 tests from 2 test suites. 6: [----------] Global test environment set-up. 6: [----------] 6 tests from NBlibTest 6: [ RUN ] NBlibTest.isRealValued 6: [ OK ] NBlibTest.isRealValued (0 ms) 6: [ RUN ] NBlibTest.checkNumericValuesHasNan 6: [ OK ] NBlibTest.checkNumericValuesHasNan (0 ms) 6: [ RUN ] NBlibTest.checkNumericValuesHasInf 6: [ OK ] NBlibTest.checkNumericValuesHasInf (0 ms) 6: [ RUN ] NBlibTest.GeneratedVelocitiesAreCorrect 6: Velocities were taken from a Maxwell distribution at 300 K 6: [ OK ] NBlibTest.GeneratedVelocitiesAreCorrect (2 ms) 6: [ RUN ] NBlibTest.generateVelocitySize 6: Velocities were taken from a Maxwell distribution at 300 K 6: [ OK ] NBlibTest.generateVelocitySize (0 ms) 6: [ RUN ] NBlibTest.generateVelocityCheckNumbers 6: Velocities were taken from a Maxwell distribution at 300 K 6: [ OK ] NBlibTest.generateVelocityCheckNumbers (0 ms) 6: [----------] 6 tests from NBlibTest (2 ms total) 6: 6: [----------] 10 tests from NblibTraitsUtils 6: [ RUN ] NblibTraitsUtils.FuseTwo 6: [ OK ] NblibTraitsUtils.FuseTwo (0 ms) 6: [ RUN ] NblibTraitsUtils.Fuse 6: [ OK ] NblibTraitsUtils.Fuse (0 ms) 6: [ RUN ] NblibTraitsUtils.Repeat 6: [ OK ] NblibTraitsUtils.Repeat (0 ms) 6: [ RUN ] NblibTraitsUtils.FindIndexTuple1 6: [ OK ] NblibTraitsUtils.FindIndexTuple1 (0 ms) 6: [ RUN ] NblibTraitsUtils.FindIndexTuple2 6: [ OK ] NblibTraitsUtils.FindIndexTuple2 (0 ms) 6: [ RUN ] NblibTraitsUtils.FindIndexTypeList1 6: [ OK ] NblibTraitsUtils.FindIndexTypeList1 (0 ms) 6: [ RUN ] NblibTraitsUtils.FindIndexTypeList2 6: [ OK ] NblibTraitsUtils.FindIndexTypeList2 (0 ms) 6: [ RUN ] NblibTraitsUtils.Contains 6: [ OK ] NblibTraitsUtils.Contains (0 ms) 6: [ RUN ] NblibTraitsUtils.FindIndexTupleRepeated 6: [ OK ] NblibTraitsUtils.FindIndexTupleRepeated (0 ms) 6: [ RUN ] NblibTraitsUtils.FindIndexTypeListRepeated 6: [ OK ] NblibTraitsUtils.FindIndexTypeListRepeated (0 ms) 6: [----------] 10 tests from NblibTraitsUtils (0 ms total) 6: 6: [----------] Global test environment tear-down 6: [==========] 16 tests from 2 test suites ran. (3 ms total) 6: [ PASSED ] 16 tests. 6/92 Test #6: NbLibUtilTests ............................ Passed 0.08 sec test 7 Start 7: NbLibSetupTests 7: Test command: /build/reproducible-path/gromacs-2025.1/build/basic/bin/nblib-setup-test "--gtest_output=xml:/build/reproducible-path/gromacs-2025.1/build/basic/Testing/Temporary/NbLibSetupTests.xml" 7: Working Directory: /build/reproducible-path/gromacs-2025.1/build/basic/api/nblib/tests 7: Test timeout computed to be: 600 7: [==========] Running 57 tests from 3 test suites. 7: [----------] Global test environment set-up. 7: [----------] 41 tests from NBlibTest 7: [ RUN ] NBlibTest.CubicBoxCannotHaveNaN 7: [ OK ] NBlibTest.CubicBoxCannotHaveNaN (0 ms) 7: [ RUN ] NBlibTest.CubicBoxCannotHaveInf 7: [ OK ] NBlibTest.CubicBoxCannotHaveInf (0 ms) 7: [ RUN ] NBlibTest.RectangularBoxCannotHaveNaN 7: [ OK ] NBlibTest.RectangularBoxCannotHaveNaN (0 ms) 7: [ RUN ] NBlibTest.RectangularBoxCannotHaveInf 7: [ OK ] NBlibTest.RectangularBoxCannotHaveInf (0 ms) 7: [ RUN ] NBlibTest.CubicBoxWorks 7: [ OK ] NBlibTest.CubicBoxWorks (0 ms) 7: [ RUN ] NBlibTest.BoxEqual 7: [ OK ] NBlibTest.BoxEqual (0 ms) 7: [ RUN ] NBlibTest.NonBondedForceParamsCorrect 7: [ OK ] NBlibTest.NonBondedForceParamsCorrect (0 ms) 7: [ RUN ] NBlibTest.CanMergeInteractions 7: [ OK ] NBlibTest.CanMergeInteractions (0 ms) 7: [ RUN ] NBlibTest.ParticleTypeNameCanBeConstructed 7: [ OK ] NBlibTest.ParticleTypeNameCanBeConstructed (0 ms) 7: [ RUN ] NBlibTest.ParticleTypeMassCanBeConstructed 7: [ OK ] NBlibTest.ParticleTypeMassCanBeConstructed (0 ms) 7: [ RUN ] NBlibTest.PbcHolderWorks 7: [ OK ] NBlibTest.PbcHolderWorks (0 ms) 7: [ RUN ] NBlibTest.CanConstructMoleculeWithoutChargeOrResidueName 7: [ OK ] NBlibTest.CanConstructMoleculeWithoutChargeOrResidueName (0 ms) 7: [ RUN ] NBlibTest.CanConstructMoleculeWithChargeWithoutResidueName 7: [ OK ] NBlibTest.CanConstructMoleculeWithChargeWithoutResidueName (0 ms) 7: [ RUN ] NBlibTest.CanConstructMoleculeWithoutChargeWithResidueName 7: [ OK ] NBlibTest.CanConstructMoleculeWithoutChargeWithResidueName (0 ms) 7: [ RUN ] NBlibTest.CanConstructMoleculeWithChargeWithResidueName 7: [ OK ] NBlibTest.CanConstructMoleculeWithChargeWithResidueName (0 ms) 7: [ RUN ] NBlibTest.CanGetNumParticlesInMolecule 7: [ OK ] NBlibTest.CanGetNumParticlesInMolecule (0 ms) 7: [ RUN ] NBlibTest.CanConstructExclusionListFromNames 7: [ OK ] NBlibTest.CanConstructExclusionListFromNames (0 ms) 7: [ RUN ] NBlibTest.CanConstructExclusionListFromNamesAndIndicesMixed 7: [ OK ] NBlibTest.CanConstructExclusionListFromNamesAndIndicesMixed (0 ms) 7: [ RUN ] NBlibTest.AtWorks 7: [ OK ] NBlibTest.AtWorks (0 ms) 7: [ RUN ] NBlibTest.AtThrows 7: [ OK ] NBlibTest.AtThrows (2 ms) 7: [ RUN ] NBlibTest.MoleculeThrowsSameParticleTypeNameDifferentMass 7: [ OK ] NBlibTest.MoleculeThrowsSameParticleTypeNameDifferentMass (0 ms) 7: [ RUN ] NBlibTest.MoleculeDontThrowsSameParticleTypeNameDifferentMass 7: [ OK ] NBlibTest.MoleculeDontThrowsSameParticleTypeNameDifferentMass (0 ms) 7: [ RUN ] NBlibTest.MoleculeNoThrowsSameParticleTypeName 7: [ OK ] NBlibTest.MoleculeNoThrowsSameParticleTypeName (0 ms) 7: [ RUN ] NBlibTest.CanAddInteractions 7: [ OK ] NBlibTest.CanAddInteractions (0 ms) 7: [ RUN ] NBlibTest.CanAddUreyBradley 7: [ OK ] NBlibTest.CanAddUreyBradley (0 ms) 7: [ RUN ] NBlibTest.TopologyHasNumParticles 7: [ OK ] NBlibTest.TopologyHasNumParticles (0 ms) 7: [ RUN ] NBlibTest.TopologyHasCharges 7: [ OK ] NBlibTest.TopologyHasCharges (0 ms) 7: [ RUN ] NBlibTest.TopologyHasMasses 7: [ OK ] NBlibTest.TopologyHasMasses (0 ms) 7: [ RUN ] NBlibTest.TopologyHasParticleTypes 7: [ OK ] NBlibTest.TopologyHasParticleTypes (0 ms) 7: [ RUN ] NBlibTest.TopologyHasParticleTypeIds 7: [ OK ] NBlibTest.TopologyHasParticleTypeIds (0 ms) 7: [ RUN ] NBlibTest.TopologyThrowsIdenticalParticleType 7: [ OK ] NBlibTest.TopologyThrowsIdenticalParticleType (0 ms) 7: [ RUN ] NBlibTest.TopologyHasExclusions 7: [ OK ] NBlibTest.TopologyHasExclusions (0 ms) 7: [ RUN ] NBlibTest.TopologyHasSequencing 7: [ OK ] NBlibTest.TopologyHasSequencing (0 ms) 7: [ RUN ] NBlibTest.TopologyCanAggregateBonds 7: [ OK ] NBlibTest.TopologyCanAggregateBonds (0 ms) 7: [ RUN ] NBlibTest.TopologyCanSequencePairIDs 7: [ OK ] NBlibTest.TopologyCanSequencePairIDs (0 ms) 7: [ RUN ] NBlibTest.TopologySequenceIdThrows 7: No particle O-Atom in residue SOL in molecule SOL found 7: [ OK ] NBlibTest.TopologySequenceIdThrows (0 ms) 7: [ RUN ] NBlibTest.TopologyCanEliminateDuplicateBonds 7: [ OK ] NBlibTest.TopologyCanEliminateDuplicateBonds (0 ms) 7: [ RUN ] NBlibTest.TopologyListedInteractions 7: [ OK ] NBlibTest.TopologyListedInteractions (0 ms) 7: [ RUN ] NBlibTest.TopologyListedInteractionsMultipleTypes 7: [ OK ] NBlibTest.TopologyListedInteractionsMultipleTypes (0 ms) 7: [ RUN ] NBlibTest.TopologyInvalidParticleInInteractionThrows 7: No particle Iron in residue SOL in molecule SOL found 7: [ OK ] NBlibTest.TopologyInvalidParticleInInteractionThrows (0 ms) 7: [ RUN ] NBlibTest.toGmxExclusionBlockWorks 7: [ OK ] NBlibTest.toGmxExclusionBlockWorks (0 ms) 7: [----------] 41 tests from NBlibTest (12 ms total) 7: 7: [----------] 15 tests from NbnxmSetupTest 7: [ RUN ] NbnxmSetupTest.findNumEnergyGroups 7: [ OK ] NbnxmSetupTest.findNumEnergyGroups (0 ms) 7: [ RUN ] NbnxmSetupTest.canTranslateBenchmarkEnumAuto 7: [ OK ] NbnxmSetupTest.canTranslateBenchmarkEnumAuto (0 ms) 7: [ RUN ] NbnxmSetupTest.canTranslateBenchmarkEnumNo 7: [ OK ] NbnxmSetupTest.canTranslateBenchmarkEnumNo (0 ms) 7: [ RUN ] NbnxmSetupTest.canTranslateBenchmarkEnum2XM 7: [ OK ] NbnxmSetupTest.canTranslateBenchmarkEnum2XM (0 ms) 7: [ RUN ] NbnxmSetupTest.canTranslateBenchmarkEnum4XM 7: [ OK ] NbnxmSetupTest.canTranslateBenchmarkEnum4XM (0 ms) 7: [ RUN ] NbnxmSetupTest.CheckKernelSetupThrowsAuto 7: [ OK ] NbnxmSetupTest.CheckKernelSetupThrowsAuto (0 ms) 7: [ RUN ] NbnxmSetupTest.CheckKernelSetupThrowsCount 7: [ OK ] NbnxmSetupTest.CheckKernelSetupThrowsCount (0 ms) 7: [ RUN ] NbnxmSetupTest.canCreateKernelSetupPlain 7: [ OK ] NbnxmSetupTest.canCreateKernelSetupPlain (0 ms) 7: [ RUN ] NbnxmSetupTest.canCreateParticleInfoAllVdv 7: [ OK ] NbnxmSetupTest.canCreateParticleInfoAllVdv (0 ms) 7: [ RUN ] NbnxmSetupTest.ewaldCoeffWorks 7: [ OK ] NbnxmSetupTest.ewaldCoeffWorks (0 ms) 7: [ RUN ] NbnxmSetupTest.updateForcerecWorks 7: [ OK ] NbnxmSetupTest.updateForcerecWorks (0 ms) 7: [ RUN ] NbnxmSetupTest.canCheckKernelSetup 7: [ OK ] NbnxmSetupTest.canCheckKernelSetup (0 ms) 7: [ RUN ] NbnxmSetupTest.cannotCreateKernelSetupCPU2XM 7: [ OK ] NbnxmSetupTest.cannotCreateKernelSetupCPU2XM (0 ms) 7: [ RUN ] NbnxmSetupTest.cannotCreateKernelSetupCPU4XM 7: [ OK ] NbnxmSetupTest.cannotCreateKernelSetupCPU4XM (0 ms) 7: [ RUN ] NbnxmSetupTest.CanCreateNbnxmCPU 7: [ OK ] NbnxmSetupTest.CanCreateNbnxmCPU (0 ms) 7: [----------] 15 tests from NbnxmSetupTest (1 ms total) 7: 7: [----------] 1 test from VirialsTest 7: [ RUN ] VirialsTest.computeVirialTensorWorks 7: [ OK ] VirialsTest.computeVirialTensorWorks (0 ms) 7: [----------] 1 test from VirialsTest (0 ms total) 7: 7: [----------] Global test environment tear-down 7: [==========] 57 tests from 3 test suites ran. (13 ms total) 7: [ PASSED ] 57 tests. 7/92 Test #7: NbLibSetupTests ........................... Passed 0.16 sec test 8 Start 8: NbLibTprTests 8: Test command: /build/reproducible-path/gromacs-2025.1/build/basic/bin/nblib-tpr-test "--gtest_output=xml:/build/reproducible-path/gromacs-2025.1/build/basic/Testing/Temporary/NbLibTprTests.xml" 8: Working Directory: /build/reproducible-path/gromacs-2025.1/build/basic/api/nblib/tests 8: Test timeout computed to be: 30 8: [==========] Running 4 tests from 1 test suite. 8: [----------] Global test environment set-up. 8: [----------] 4 tests from TprReaderTest 8: [ RUN ] TprReaderTest.SimDBTprIsCreated 8: 8: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/api/nblib/tests/Testing/Temporary/TprReaderTest_SimDBTprIsCreated_input.mdp]: 8: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 8: that with the Verlet scheme, nstlist has no effect on the accuracy of 8: your simulation. 8: 8: 8: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/api/nblib/tests/Testing/Temporary/TprReaderTest_SimDBTprIsCreated_input.mdp]: 8: Setting nstcalcenergy (100) equal to nstenergy (4) 8: 8: Number of degrees of freedom in T-Coupling group System is 33.00 8: 8: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/api/nblib/tests/Testing/Temporary/TprReaderTest_SimDBTprIsCreated_input.mdp]: 8: NVE simulation: will use the initial temperature of 68.810 K for 8: determining the Verlet buffer size 8: 8: 8: There were 3 NOTEs 8: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/api/nblib/tests/Testing/Temporary/TprReaderTest_SimDBTprIsCreated.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 8: Generated 1 of the 1 non-bonded parameter combinations 8: 8: Excluding 1 bonded neighbours molecule type 'Argon' 8: 8: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 8: 8: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 8: 8: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 8: 8: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 8: 8: Note that mdrun will redetermine rlist based on the actual pair-list setup 8: 8: This run will generate roughly 0 Mb of data 8: [ OK ] TprReaderTest.SimDBTprIsCreated (38 ms) 8: [ RUN ] TprReaderTest.Spc2Reads 8: 8: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/api/nblib/tests/Testing/Temporary/TprReaderTest_Spc2Reads_input.mdp]: 8: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 8: that with the Verlet scheme, nstlist has no effect on the accuracy of 8: your simulation. 8: 8: 8: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/api/nblib/tests/Testing/Temporary/TprReaderTest_Spc2Reads_input.mdp]: 8: Setting nstcalcenergy (100) equal to nstenergy (4) 8: 8: Generating 1-4 interactions: fudge = 0.5 8: Number of degrees of freedom in T-Coupling group System is 9.00 8: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 8: 8: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/api/nblib/tests/Testing/Temporary/TprReaderTest_Spc2Reads_input.mdp]: 8: NVE simulation: will use the initial temperature of 2573.591 K for 8: determining the Verlet buffer size 8: 8: 8: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic/api/nblib/tests/Testing/Temporary/TprReaderTest_Spc2Reads_input.mdp]: 8: You are using a plain Coulomb cut-off, which might produce artifacts. 8: You might want to consider using PME electrostatics. 8: 8: 8: 8: There were 4 NOTEs 8: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/api/nblib/tests/Testing/Temporary/TprReaderTest_Spc2Reads.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 8: Generated 3 of the 3 non-bonded parameter combinations 8: 8: Generated 3 of the 3 1-4 parameter combinations 8: 8: Excluding 2 bonded neighbours molecule type 'SOL' 8: 8: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/spc2.gro' 8: 8: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 2573.59 K 8: 8: Calculated rlist for 1x1 atom pair-list as 0.906 nm, buffer size 0.206 nm 8: 8: Set rlist, assuming 4x4 atom pair-list, to 0.892 nm, buffer size 0.192 nm 8: 8: Note that mdrun will redetermine rlist based on the actual pair-list setup 8: 8: This run will generate roughly 0 Mb of data 8: [ OK ] TprReaderTest.Spc2Reads (38 ms) 8: [ RUN ] TprReaderTest.ArgonImportedDataIsCorrect 8: 8: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/api/nblib/tests/Testing/Temporary/TprReaderTest_ArgonImportedDataIsCorrect_input.mdp]: 8: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 8: that with the Verlet scheme, nstlist has no effect on the accuracy of 8: your simulation. 8: 8: 8: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/api/nblib/tests/Testing/Temporary/TprReaderTest_ArgonImportedDataIsCorrect_input.mdp]: 8: Setting nstcalcenergy (100) equal to nstenergy (4) 8: 8: Number of degrees of freedom in T-Coupling group System is 33.00 8: 8: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/api/nblib/tests/Testing/Temporary/TprReaderTest_ArgonImportedDataIsCorrect_input.mdp]: 8: NVE simulation: will use the initial temperature of 68.810 K for 8: determining the Verlet buffer size 8: 8: 8: There were 3 NOTEs 8: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/api/nblib/tests/Testing/Temporary/TprReaderTest_ArgonImportedDataIsCorrect.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 8: Generated 1 of the 1 non-bonded parameter combinations 8: 8: Excluding 1 bonded neighbours molecule type 'Argon' 8: 8: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 8: 8: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 8: 8: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 8: 8: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 8: 8: Note that mdrun will redetermine rlist based on the actual pair-list setup 8: 8: This run will generate roughly 0 Mb of data 8: [ OK ] TprReaderTest.ArgonImportedDataIsCorrect (33 ms) 8: [ RUN ] TprReaderTest.FCfromTprDataWorks 8: 8: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/api/nblib/tests/Testing/Temporary/TprReaderTest_FCfromTprDataWorks_input.mdp]: 8: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 8: that with the Verlet scheme, nstlist has no effect on the accuracy of 8: your simulation. 8: 8: 8: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/api/nblib/tests/Testing/Temporary/TprReaderTest_FCfromTprDataWorks_input.mdp]: 8: Setting nstcalcenergy (100) equal to nstenergy (4) 8: 8: Number of degrees of freedom in T-Coupling group System is 33.00 8: 8: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/api/nblib/tests/Testing/Temporary/TprReaderTest_FCfromTprDataWorks_input.mdp]: 8: NVE simulation: will use the initial temperature of 68.810 K for 8: determining the Verlet buffer size 8: 8: 8: There were 3 NOTEs 8: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/api/nblib/tests/Testing/Temporary/TprReaderTest_FCfromTprDataWorks.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 8: Generated 1 of the 1 non-bonded parameter combinations 8: 8: Excluding 1 bonded neighbours molecule type 'Argon' 8: 8: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 8: 8: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 8: 8: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 8: 8: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 8: 8: Note that mdrun will redetermine rlist based on the actual pair-list setup 8: 8: This run will generate roughly 0 Mb of data 8: [ OK ] TprReaderTest.FCfromTprDataWorks (33 ms) 8: [----------] 4 tests from TprReaderTest (144 ms total) 8: 8: [----------] Global test environment tear-down 8: [==========] 4 tests from 1 test suite ran. (194 ms total) 8: [ PASSED ] 4 tests. 8/92 Test #8: NbLibTprTests ............................. Passed 0.28 sec test 9 Start 9: NbLibIntegrationTests 9: Test command: /build/reproducible-path/gromacs-2025.1/build/basic/bin/nblib-integration-test "--gtest_output=xml:/build/reproducible-path/gromacs-2025.1/build/basic/Testing/Temporary/NbLibIntegrationTests.xml" 9: Working Directory: /build/reproducible-path/gromacs-2025.1/build/basic/api/nblib/tests 9: Test timeout computed to be: 600 9: [==========] Running 20 tests from 1 test suite. 9: [----------] Global test environment set-up. 9: [----------] 20 tests from NBlibTest 9: [ RUN ] NBlibTest.GmxForceCalculatorCanCompute 9: [ OK ] NBlibTest.GmxForceCalculatorCanCompute (3 ms) 9: [ RUN ] NBlibTest.ArgonVirialsAreCorrect 9: [ OK ] NBlibTest.ArgonVirialsAreCorrect (4 ms) 9: [ RUN ] NBlibTest.ArgonEnergiesAreCorrect 9: [ OK ] NBlibTest.ArgonEnergiesAreCorrect (3 ms) 9: [ RUN ] NBlibTest.SpcMethanolEnergiesAreCorrect 9: [ OK ] NBlibTest.SpcMethanolEnergiesAreCorrect (3 ms) 9: [ RUN ] NBlibTest.SpcMethanolForcesAreCorrect 9: [ OK ] NBlibTest.SpcMethanolForcesAreCorrect (2 ms) 9: [ RUN ] NBlibTest.ExpectedNumberOfForces 9: [ OK ] NBlibTest.ExpectedNumberOfForces (2 ms) 9: [ RUN ] NBlibTest.CanIntegrateSystem 9: [ OK ] NBlibTest.CanIntegrateSystem (2 ms) 9: [ RUN ] NBlibTest.UpdateChangesForces 9: [ OK ] NBlibTest.UpdateChangesForces (2 ms) 9: [ RUN ] NBlibTest.ArgonOplsaForcesAreCorrect 9: [ OK ] NBlibTest.ArgonOplsaForcesAreCorrect (2 ms) 9: [ RUN ] NBlibTest.ArgonGromos43A1ForcesAreCorrect 9: [ OK ] NBlibTest.ArgonGromos43A1ForcesAreCorrect (1 ms) 9: [ RUN ] NBlibTest.CanConstructSimulationState 9: [ OK ] NBlibTest.CanConstructSimulationState (0 ms) 9: [ RUN ] NBlibTest.SimulationStateThrowsCoordinateNAN 9: [ OK ] NBlibTest.SimulationStateThrowsCoordinateNAN (0 ms) 9: [ RUN ] NBlibTest.SimulationStateThrowsCoordinateINF 9: [ OK ] NBlibTest.SimulationStateThrowsCoordinateINF (0 ms) 9: [ RUN ] NBlibTest.SimulationStateThrowsVelocityNAN 9: [ OK ] NBlibTest.SimulationStateThrowsVelocityNAN (0 ms) 9: [ RUN ] NBlibTest.SimulationStateThrowsVelocityINF 9: [ OK ] NBlibTest.SimulationStateThrowsVelocityINF (0 ms) 9: [ RUN ] NBlibTest.SimulationStateCanMove 9: [ OK ] NBlibTest.SimulationStateCanMove (0 ms) 9: [ RUN ] NBlibTest.SimulationStateCanAssign 9: [ OK ] NBlibTest.SimulationStateCanAssign (0 ms) 9: [ RUN ] NBlibTest.SimulationStateHasBox 9: [ OK ] NBlibTest.SimulationStateHasBox (0 ms) 9: [ RUN ] NBlibTest.SimulationStateHasCorrectCoordinates 9: [ OK ] NBlibTest.SimulationStateHasCorrectCoordinates (0 ms) 9: [ RUN ] NBlibTest.SimulationStateHasCorrectVelocities 9: [ OK ] NBlibTest.SimulationStateHasCorrectVelocities (0 ms) 9: [----------] 20 tests from NBlibTest (36 ms total) 9: 9: [----------] Global test environment tear-down 9: [==========] 20 tests from 1 test suite ran. (37 ms total) 9: [ PASSED ] 20 tests. 9/92 Test #9: NbLibIntegrationTests ..................... Passed 0.12 sec test 10 Start 10: NbLibIntegratorTests 10: Test command: /build/reproducible-path/gromacs-2025.1/build/basic/bin/nblib-integrator-test "--gtest_output=xml:/build/reproducible-path/gromacs-2025.1/build/basic/Testing/Temporary/NbLibIntegratorTests.xml" 10: Working Directory: /build/reproducible-path/gromacs-2025.1/build/basic/api/nblib/tests 10: Test timeout computed to be: 600 10: [==========] Running 1 test from 1 test suite. 10: [----------] Global test environment set-up. 10: [----------] 1 test from NBlibTest 10: [ RUN ] NBlibTest.IntegratorWorks 10: [ OK ] NBlibTest.IntegratorWorks (1 ms) 10: [----------] 1 test from NBlibTest (1 ms total) 10: 10: [----------] Global test environment tear-down 10: [==========] 1 test from 1 test suite ran. (1 ms total) 10: [ PASSED ] 1 test. 10/92 Test #10: NbLibIntegratorTests ...................... Passed 0.08 sec test 11 Start 11: TestUtilsUnitTests 11: Test command: /build/reproducible-path/gromacs-2025.1/build/basic/bin/testutils-test "--gtest_output=xml:/build/reproducible-path/gromacs-2025.1/build/basic/Testing/Temporary/TestUtilsUnitTests.xml" 11: Working Directory: /build/reproducible-path/gromacs-2025.1/build/basic/src/testutils/tests 11: Test timeout computed to be: 30 11: [==========] Running 75 tests from 7 test suites. 11: [----------] Global test environment set-up. 11: [----------] 10 tests from InteractiveTestHelperTest 11: [ RUN ] InteractiveTestHelperTest.ChecksSimpleSession 11: [ OK ] InteractiveTestHelperTest.ChecksSimpleSession (2 ms) 11: [ RUN ] InteractiveTestHelperTest.ChecksSessionWithoutLastNewline 11: [ OK ] InteractiveTestHelperTest.ChecksSessionWithoutLastNewline (1 ms) 11: [ RUN ] InteractiveTestHelperTest.ChecksSessionWithMissingOutput 11: [ OK ] InteractiveTestHelperTest.ChecksSessionWithMissingOutput (1 ms) 11: [ RUN ] InteractiveTestHelperTest.ChecksSessionWithEquivalentOutput 11: [ OK ] InteractiveTestHelperTest.ChecksSessionWithEquivalentOutput (1 ms) 11: [ RUN ] InteractiveTestHelperTest.DetectsIncorrectOutput 11: [ OK ] InteractiveTestHelperTest.DetectsIncorrectOutput (1 ms) 11: [ RUN ] InteractiveTestHelperTest.DetectsMissingOutput 11: [ OK ] InteractiveTestHelperTest.DetectsMissingOutput (1 ms) 11: [ RUN ] InteractiveTestHelperTest.DetectsMissingFinalOutput 11: [ OK ] InteractiveTestHelperTest.DetectsMissingFinalOutput (1 ms) 11: [ RUN ] InteractiveTestHelperTest.DetectsExtraOutput 11: [ OK ] InteractiveTestHelperTest.DetectsExtraOutput (1 ms) 11: [ RUN ] InteractiveTestHelperTest.DetectsMissingInput 11: [ OK ] InteractiveTestHelperTest.DetectsMissingInput (1 ms) 11: [ RUN ] InteractiveTestHelperTest.DetectsExtraInput 11: [ OK ] InteractiveTestHelperTest.DetectsExtraInput (1 ms) 11: [----------] 10 tests from InteractiveTestHelperTest (17 ms total) 11: 11: [----------] 10 tests from NameOfTestFromTupleTest 11: [ RUN ] NameOfTestFromTupleTest.WorksWithEmptyTuple 11: [ OK ] NameOfTestFromTupleTest.WorksWithEmptyTuple (0 ms) 11: [ RUN ] NameOfTestFromTupleTest.WorksWithFormatFunction 11: [ OK ] NameOfTestFromTupleTest.WorksWithFormatFunction (0 ms) 11: [ RUN ] NameOfTestFromTupleTest.WorksWithFormatFunctionOfEnumVariable 11: [ OK ] NameOfTestFromTupleTest.WorksWithFormatFunctionOfEnumVariable (0 ms) 11: [ RUN ] NameOfTestFromTupleTest.RejectsNullptrFormatFunction 11: [ OK ] NameOfTestFromTupleTest.RejectsNullptrFormatFunction (0 ms) 11: [ RUN ] NameOfTestFromTupleTest.WorksWithFormatLambda 11: [ OK ] NameOfTestFromTupleTest.WorksWithFormatLambda (0 ms) 11: [ RUN ] NameOfTestFromTupleTest.WorksWithUseStringFormat 11: [ OK ] NameOfTestFromTupleTest.WorksWithUseStringFormat (0 ms) 11: [ RUN ] NameOfTestFromTupleTest.WorksWithPrefixFormatter 11: [ OK ] NameOfTestFromTupleTest.WorksWithPrefixFormatter (0 ms) 11: [ RUN ] NameOfTestFromTupleTest.WorksWithFormatFunctor 11: [ OK ] NameOfTestFromTupleTest.WorksWithFormatFunctor (0 ms) 11: [ RUN ] NameOfTestFromTupleTest.WorksWithFormatFromEnumerationArray 11: [ OK ] NameOfTestFromTupleTest.WorksWithFormatFromEnumerationArray (0 ms) 11: [ RUN ] NameOfTestFromTupleTest.WorksWithMixtureOfFormatters 11: [ OK ] NameOfTestFromTupleTest.WorksWithMixtureOfFormatters (0 ms) 11: [----------] 10 tests from NameOfTestFromTupleTest (0 ms total) 11: 11: [----------] 3 tests from RefDataFilenameMakerTest 11: [ RUN ] RefDataFilenameMakerTest.WorksWithFormatFunction 11: [ OK ] RefDataFilenameMakerTest.WorksWithFormatFunction (0 ms) 11: [ RUN ] RefDataFilenameMakerTest.WorksWithMixtureOfFormatters 11: [ OK ] RefDataFilenameMakerTest.WorksWithMixtureOfFormatters (0 ms) 11: [ RUN ] RefDataFilenameMakerTest.WorksWithToEmpty 11: [ OK ] RefDataFilenameMakerTest.WorksWithToEmpty (0 ms) 11: [----------] 3 tests from RefDataFilenameMakerTest (0 ms total) 11: 11: [----------] 37 tests from ReferenceDataTest 11: [ RUN ] ReferenceDataTest.HandlesSimpleData 11: [ OK ] ReferenceDataTest.HandlesSimpleData (1 ms) 11: [ RUN ] ReferenceDataTest.HandlesFloatingPointData 11: [ OK ] ReferenceDataTest.HandlesFloatingPointData (0 ms) 11: [ RUN ] ReferenceDataTest.HandlesPresenceChecks 11: [ OK ] ReferenceDataTest.HandlesPresenceChecks (1 ms) 11: [ RUN ] ReferenceDataTest.HandlesStringBlockData 11: [ OK ] ReferenceDataTest.HandlesStringBlockData (0 ms) 11: [ RUN ] ReferenceDataTest.HandlesVectorData 11: [ OK ] ReferenceDataTest.HandlesVectorData (1 ms) 11: [ RUN ] ReferenceDataTest.HandlesSequenceData 11: [ OK ] ReferenceDataTest.HandlesSequenceData (0 ms) 11: [ RUN ] ReferenceDataTest.HandlesSequenceOfCustomData 11: [ OK ] ReferenceDataTest.HandlesSequenceOfCustomData (1 ms) 11: [ RUN ] ReferenceDataTest.CheckSequenceArrayRef 11: [ OK ] ReferenceDataTest.CheckSequenceArrayRef (0 ms) 11: [ RUN ] ReferenceDataTest.CheckSequenceArrayRefHandlesIncorrectData 11: [ OK ] ReferenceDataTest.CheckSequenceArrayRefHandlesIncorrectData (1 ms) 11: [ RUN ] ReferenceDataTest.CheckSequenceArrayRefHandlesSequenceOfCustomData 11: [ OK ] ReferenceDataTest.CheckSequenceArrayRefHandlesSequenceOfCustomData (1 ms) 11: [ RUN ] ReferenceDataTest.HandlesIncorrectData 11: [ OK ] ReferenceDataTest.HandlesIncorrectData (1 ms) 11: [ RUN ] ReferenceDataTest.HandlesIncorrectDataType 11: [ OK ] ReferenceDataTest.HandlesIncorrectDataType (1 ms) 11: [ RUN ] ReferenceDataTest.HandlesMissingData 11: [ OK ] ReferenceDataTest.HandlesMissingData (1 ms) 11: [ RUN ] ReferenceDataTest.HandlesUncheckedData 11: [ OK ] ReferenceDataTest.HandlesUncheckedData (1 ms) 11: [ RUN ] ReferenceDataTest.HandlesUncheckedDataInSequence 11: [ OK ] ReferenceDataTest.HandlesUncheckedDataInSequence (1 ms) 11: [ RUN ] ReferenceDataTest.HandlesUncheckedDataInCompound 11: [ OK ] ReferenceDataTest.HandlesUncheckedDataInCompound (1 ms) 11: [ RUN ] ReferenceDataTest.HandlesAnys 11: [ OK ] ReferenceDataTest.HandlesAnys (0 ms) 11: [ RUN ] ReferenceDataTest.HandlesKeyValueTree 11: [ OK ] ReferenceDataTest.HandlesKeyValueTree (1 ms) 11: [ RUN ] ReferenceDataTest.HandlesKeyValueTreeExtraKey 11: [ OK ] ReferenceDataTest.HandlesKeyValueTreeExtraKey (1 ms) 11: [ RUN ] ReferenceDataTest.HandlesKeyValueTreeMissingKey 11: [ OK ] ReferenceDataTest.HandlesKeyValueTreeMissingKey (1 ms) 11: [ RUN ] ReferenceDataTest.HandlesAnysWithIncorrectValue 11: [ OK ] ReferenceDataTest.HandlesAnysWithIncorrectValue (1 ms) 11: [ RUN ] ReferenceDataTest.HandlesAnysWithIncorrectType 11: [ OK ] ReferenceDataTest.HandlesAnysWithIncorrectType (1 ms) 11: [ RUN ] ReferenceDataTest.HandlesMissingReferenceDataFile 11: [ OK ] ReferenceDataTest.HandlesMissingReferenceDataFile (0 ms) 11: [ RUN ] ReferenceDataTest.HandlesSpecialCharactersInStrings 11: [ OK ] ReferenceDataTest.HandlesSpecialCharactersInStrings (0 ms) 11: [ RUN ] ReferenceDataTest.HandlesStringsWithTextAndWhitespace 11: [ OK ] ReferenceDataTest.HandlesStringsWithTextAndWhitespace (1 ms) 11: [ RUN ] ReferenceDataTest.HandlesEmptyStrings 11: [ OK ] ReferenceDataTest.HandlesEmptyStrings (1 ms) 11: [ RUN ] ReferenceDataTest.HandlesEmbeddedCdataEndTagInTextBlock 11: [ OK ] ReferenceDataTest.HandlesEmbeddedCdataEndTagInTextBlock (1 ms) 11: [ RUN ] ReferenceDataTest.HandlesSequenceItemIndices 11: [ OK ] ReferenceDataTest.HandlesSequenceItemIndices (1 ms) 11: [ RUN ] ReferenceDataTest.HandlesMultipleChecksAgainstSameData 11: [ OK ] ReferenceDataTest.HandlesMultipleChecksAgainstSameData (1 ms) 11: [ RUN ] ReferenceDataTest.HandlesMultipleNullIds 11: [ OK ] ReferenceDataTest.HandlesMultipleNullIds (1 ms) 11: [ RUN ] ReferenceDataTest.HandlesMultipleComparisonsAgainstNullIds 11: [ OK ] ReferenceDataTest.HandlesMultipleComparisonsAgainstNullIds (1 ms) 11: [ RUN ] ReferenceDataTest.HandlesReadingValues 11: [ OK ] ReferenceDataTest.HandlesReadingValues (0 ms) 11: [ RUN ] ReferenceDataTest.HandlesUpdateChangedWithoutChanges 11: [ OK ] ReferenceDataTest.HandlesUpdateChangedWithoutChanges (2 ms) 11: [ RUN ] ReferenceDataTest.HandlesUpdateChangedWithValueChanges 11: [ OK ] ReferenceDataTest.HandlesUpdateChangedWithValueChanges (2 ms) 11: [ RUN ] ReferenceDataTest.HandlesUpdateChangedWithTypeChanges 11: [ OK ] ReferenceDataTest.HandlesUpdateChangedWithTypeChanges (2 ms) 11: [ RUN ] ReferenceDataTest.HandlesUpdateChangedWithCompoundChanges 11: [ OK ] ReferenceDataTest.HandlesUpdateChangedWithCompoundChanges (2 ms) 11: [ RUN ] ReferenceDataTest.HandlesUpdateChangedWithRemovedEntries 11: [ OK ] ReferenceDataTest.HandlesUpdateChangedWithRemovedEntries (2 ms) 11: [----------] 37 tests from ReferenceDataTest (48 ms total) 11: 11: [----------] 7 tests from FloatingPointDifferenceTest 11: [ RUN ] FloatingPointDifferenceTest.HandlesEqualValues 11: [ OK ] FloatingPointDifferenceTest.HandlesEqualValues (0 ms) 11: [ RUN ] FloatingPointDifferenceTest.HandlesFloatValues 11: [ OK ] FloatingPointDifferenceTest.HandlesFloatValues (0 ms) 11: [ RUN ] FloatingPointDifferenceTest.HandlesZerosOfDifferentSign 11: [ OK ] FloatingPointDifferenceTest.HandlesZerosOfDifferentSign (0 ms) 11: [ RUN ] FloatingPointDifferenceTest.HandlesSignComparisonWithZero 11: [ OK ] FloatingPointDifferenceTest.HandlesSignComparisonWithZero (0 ms) 11: [ RUN ] FloatingPointDifferenceTest.HandlesUlpDifferences 11: [ OK ] FloatingPointDifferenceTest.HandlesUlpDifferences (0 ms) 11: [ RUN ] FloatingPointDifferenceTest.HandlesUlpDifferenceAcrossZero 11: [ OK ] FloatingPointDifferenceTest.HandlesUlpDifferenceAcrossZero (0 ms) 11: [ RUN ] FloatingPointDifferenceTest.HandlesNaN 11: [ OK ] FloatingPointDifferenceTest.HandlesNaN (0 ms) 11: [----------] 7 tests from FloatingPointDifferenceTest (0 ms total) 11: 11: [----------] 4 tests from FloatingPointToleranceTest 11: [ RUN ] FloatingPointToleranceTest.UlpTolerance 11: [ OK ] FloatingPointToleranceTest.UlpTolerance (0 ms) 11: [ RUN ] FloatingPointToleranceTest.RelativeToleranceAsFloatingPoint 11: [ OK ] FloatingPointToleranceTest.RelativeToleranceAsFloatingPoint (0 ms) 11: [ RUN ] FloatingPointToleranceTest.RelativeToleranceAsUlp 11: [ OK ] FloatingPointToleranceTest.RelativeToleranceAsUlp (0 ms) 11: [ RUN ] FloatingPointToleranceTest.DefaultFloatTolerance 11: [ OK ] FloatingPointToleranceTest.DefaultFloatTolerance (0 ms) 11: [----------] 4 tests from FloatingPointToleranceTest (0 ms total) 11: 11: [----------] 4 tests from XvgTests 11: [ RUN ] XvgTests.CreateFile 11: [ OK ] XvgTests.CreateFile (2 ms) 11: [ RUN ] XvgTests.CheckMissing 11: [ OK ] XvgTests.CheckMissing (1 ms) 11: [ RUN ] XvgTests.CheckExtra 11: [ OK ] XvgTests.CheckExtra (1 ms) 11: [ RUN ] XvgTests.ReadIncorrect 11: [ OK ] XvgTests.ReadIncorrect (1 ms) 11: [----------] 4 tests from XvgTests (8 ms total) 11: 11: [----------] Global test environment tear-down 11: [==========] 75 tests from 7 test suites ran. (76 ms total) 11: [ PASSED ] 75 tests. 11/92 Test #11: TestUtilsUnitTests ........................ Passed 0.16 sec test 12 Start 12: TestUtilsMpiUnitTests 12: Test command: /build/reproducible-path/gromacs-2025.1/build/basic/bin/testutils-mpi-test "-ntmpi" "2" "--gtest_output=xml:/build/reproducible-path/gromacs-2025.1/build/basic/Testing/Temporary/TestUtilsMpiUnitTests.xml" 12: Working Directory: /build/reproducible-path/gromacs-2025.1/build/basic/src/testutils/tests 12: Test timeout computed to be: 30 12: [==========] Running 1 test from 1 test suite. 12: [----------] Global test environment set-up. 12: [----------] 1 test from MpiSelfTest 12: [ RUN ] MpiSelfTest.Runs 12: [ OK ] MpiSelfTest.Runs (5 ms) 12: [----------] 1 test from MpiSelfTest (5 ms total) 12: 12: [----------] Global test environment tear-down 12: [==========] 1 test from 1 test suite ran. (5 ms total) 12: [ PASSED ] 1 test. 12/92 Test #12: TestUtilsMpiUnitTests ..................... Passed 0.08 sec test 13 Start 13: UtilityUnitTests 13: Test command: /build/reproducible-path/gromacs-2025.1/build/basic/bin/utility-test "--gtest_output=xml:/build/reproducible-path/gromacs-2025.1/build/basic/Testing/Temporary/UtilityUnitTests.xml" 13: Working Directory: /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/utility/tests 13: Test timeout computed to be: 30 13: [==========] Running 420 tests from 65 test suites. 13: [----------] Global test environment set-up. 13: [----------] 6 tests from AllocatorTest/0, where TypeParam = gmx::Allocator 13: [ RUN ] AllocatorTest/0.AllocatorAlignAllocatesWithAlignment 13: [ OK ] AllocatorTest/0.AllocatorAlignAllocatesWithAlignment (0 ms) 13: [ RUN ] AllocatorTest/0.VectorAllocatesAndResizesWithAlignment 13: [ OK ] AllocatorTest/0.VectorAllocatesAndResizesWithAlignment (0 ms) 13: [ RUN ] AllocatorTest/0.VectorAllocatesAndReservesWithAlignment 13: [ OK ] AllocatorTest/0.VectorAllocatesAndReservesWithAlignment (0 ms) 13: [ RUN ] AllocatorTest/0.Move 13: [ OK ] AllocatorTest/0.Move (0 ms) 13: [ RUN ] AllocatorTest/0.StatelessAllocatorUsesNoMemory 13: [ OK ] AllocatorTest/0.StatelessAllocatorUsesNoMemory (0 ms) 13: [ RUN ] AllocatorTest/0.Comparison 13: [ OK ] AllocatorTest/0.Comparison (0 ms) 13: [----------] 6 tests from AllocatorTest/0 (1 ms total) 13: 13: [----------] 6 tests from AllocatorTest/1, where TypeParam = gmx::Allocator 13: [ RUN ] AllocatorTest/1.AllocatorAlignAllocatesWithAlignment 13: [ OK ] AllocatorTest/1.AllocatorAlignAllocatesWithAlignment (0 ms) 13: [ RUN ] AllocatorTest/1.VectorAllocatesAndResizesWithAlignment 13: [ OK ] AllocatorTest/1.VectorAllocatesAndResizesWithAlignment (0 ms) 13: [ RUN ] AllocatorTest/1.VectorAllocatesAndReservesWithAlignment 13: [ OK ] AllocatorTest/1.VectorAllocatesAndReservesWithAlignment (0 ms) 13: [ RUN ] AllocatorTest/1.Move 13: [ OK ] AllocatorTest/1.Move (0 ms) 13: [ RUN ] AllocatorTest/1.StatelessAllocatorUsesNoMemory 13: [ OK ] AllocatorTest/1.StatelessAllocatorUsesNoMemory (0 ms) 13: [ RUN ] AllocatorTest/1.Comparison 13: [ OK ] AllocatorTest/1.Comparison (0 ms) 13: [----------] 6 tests from AllocatorTest/1 (0 ms total) 13: 13: [----------] 6 tests from AllocatorTest/2, where TypeParam = gmx::Allocator 13: [ RUN ] AllocatorTest/2.AllocatorAlignAllocatesWithAlignment 13: [ OK ] AllocatorTest/2.AllocatorAlignAllocatesWithAlignment (0 ms) 13: [ RUN ] AllocatorTest/2.VectorAllocatesAndResizesWithAlignment 13: [ OK ] AllocatorTest/2.VectorAllocatesAndResizesWithAlignment (0 ms) 13: [ RUN ] AllocatorTest/2.VectorAllocatesAndReservesWithAlignment 13: [ OK ] AllocatorTest/2.VectorAllocatesAndReservesWithAlignment (0 ms) 13: [ RUN ] AllocatorTest/2.Move 13: [ OK ] AllocatorTest/2.Move (0 ms) 13: [ RUN ] AllocatorTest/2.StatelessAllocatorUsesNoMemory 13: [ OK ] AllocatorTest/2.StatelessAllocatorUsesNoMemory (0 ms) 13: [ RUN ] AllocatorTest/2.Comparison 13: [ OK ] AllocatorTest/2.Comparison (0 ms) 13: [----------] 6 tests from AllocatorTest/2 (0 ms total) 13: 13: [----------] 6 tests from AllocatorTest/3, where TypeParam = gmx::Allocator 13: [ RUN ] AllocatorTest/3.AllocatorAlignAllocatesWithAlignment 13: [ OK ] AllocatorTest/3.AllocatorAlignAllocatesWithAlignment (0 ms) 13: [ RUN ] AllocatorTest/3.VectorAllocatesAndResizesWithAlignment 13: [ OK ] AllocatorTest/3.VectorAllocatesAndResizesWithAlignment (0 ms) 13: [ RUN ] AllocatorTest/3.VectorAllocatesAndReservesWithAlignment 13: [ OK ] AllocatorTest/3.VectorAllocatesAndReservesWithAlignment (0 ms) 13: [ RUN ] AllocatorTest/3.Move 13: [ OK ] AllocatorTest/3.Move (0 ms) 13: [ RUN ] AllocatorTest/3.StatelessAllocatorUsesNoMemory 13: [ OK ] AllocatorTest/3.StatelessAllocatorUsesNoMemory (0 ms) 13: [ RUN ] AllocatorTest/3.Comparison 13: [ OK ] AllocatorTest/3.Comparison (0 ms) 13: [----------] 6 tests from AllocatorTest/3 (0 ms total) 13: 13: [----------] 6 tests from AllocatorTest/4, where TypeParam = gmx::Allocator, gmx::AlignedAllocationPolicy> 13: [ RUN ] AllocatorTest/4.AllocatorAlignAllocatesWithAlignment 13: [ OK ] AllocatorTest/4.AllocatorAlignAllocatesWithAlignment (0 ms) 13: [ RUN ] AllocatorTest/4.VectorAllocatesAndResizesWithAlignment 13: [ OK ] AllocatorTest/4.VectorAllocatesAndResizesWithAlignment (0 ms) 13: [ RUN ] AllocatorTest/4.VectorAllocatesAndReservesWithAlignment 13: [ OK ] AllocatorTest/4.VectorAllocatesAndReservesWithAlignment (0 ms) 13: [ RUN ] AllocatorTest/4.Move 13: [ OK ] AllocatorTest/4.Move (0 ms) 13: [ RUN ] AllocatorTest/4.StatelessAllocatorUsesNoMemory 13: [ OK ] AllocatorTest/4.StatelessAllocatorUsesNoMemory (0 ms) 13: [ RUN ] AllocatorTest/4.Comparison 13: [ OK ] AllocatorTest/4.Comparison (0 ms) 13: [----------] 6 tests from AllocatorTest/4 (1 ms total) 13: 13: [----------] 6 tests from AllocatorTest/5, where TypeParam = gmx::Allocator, gmx::PageAlignedAllocationPolicy> 13: [ RUN ] AllocatorTest/5.AllocatorAlignAllocatesWithAlignment 13: [ OK ] AllocatorTest/5.AllocatorAlignAllocatesWithAlignment (0 ms) 13: [ RUN ] AllocatorTest/5.VectorAllocatesAndResizesWithAlignment 13: [ OK ] AllocatorTest/5.VectorAllocatesAndResizesWithAlignment (0 ms) 13: [ RUN ] AllocatorTest/5.VectorAllocatesAndReservesWithAlignment 13: [ OK ] AllocatorTest/5.VectorAllocatesAndReservesWithAlignment (0 ms) 13: [ RUN ] AllocatorTest/5.Move 13: [ OK ] AllocatorTest/5.Move (0 ms) 13: [ RUN ] AllocatorTest/5.StatelessAllocatorUsesNoMemory 13: [ OK ] AllocatorTest/5.StatelessAllocatorUsesNoMemory (0 ms) 13: [ RUN ] AllocatorTest/5.Comparison 13: [ OK ] AllocatorTest/5.Comparison (0 ms) 13: [----------] 6 tests from AllocatorTest/5 (1 ms total) 13: 13: [----------] 1 test from AllocatorUntypedTest 13: [ RUN ] AllocatorUntypedTest.Comparison 13: [ OK ] AllocatorUntypedTest.Comparison (0 ms) 13: [----------] 1 test from AllocatorUntypedTest (0 ms total) 13: 13: [----------] 4 tests from EmptyArrayRefTest 13: [ RUN ] EmptyArrayRefTest.IsEmpty 13: [ OK ] EmptyArrayRefTest.IsEmpty (0 ms) 13: [ RUN ] EmptyArrayRefTest.ConstructFromNullptrIsEmpty 13: [ OK ] EmptyArrayRefTest.ConstructFromNullptrIsEmpty (0 ms) 13: [ RUN ] EmptyArrayRefTest.arrayRefFromArrayIsEmptyForNullptr 13: [ OK ] EmptyArrayRefTest.arrayRefFromArrayIsEmptyForNullptr (0 ms) 13: [ RUN ] EmptyArrayRefTest.arrayRefFromArrayIsEmptyForSizeNull 13: [ OK ] EmptyArrayRefTest.arrayRefFromArrayIsEmptyForSizeNull (0 ms) 13: [----------] 4 tests from EmptyArrayRefTest (0 ms total) 13: 13: [----------] 1 test from EmptyConstArrayRefTest 13: [ RUN ] EmptyConstArrayRefTest.IsEmpty 13: [ OK ] EmptyConstArrayRefTest.IsEmpty (0 ms) 13: [----------] 1 test from EmptyConstArrayRefTest (0 ms total) 13: 13: [----------] 9 tests from ArrayRefTest/0, where TypeParam = gmx::ArrayRef 13: [ RUN ] ArrayRefTest/0.MakeWithAssignmentWorks 13: [ OK ] ArrayRefTest/0.MakeWithAssignmentWorks (0 ms) 13: [ RUN ] ArrayRefTest/0.MakeWithNonConstAssignmentWorks 13: [ OK ] ArrayRefTest/0.MakeWithNonConstAssignmentWorks (0 ms) 13: [ RUN ] ArrayRefTest/0.ConstructWithTemplateConstructorWorks 13: [ OK ] ArrayRefTest/0.ConstructWithTemplateConstructorWorks (0 ms) 13: [ RUN ] ArrayRefTest/0.ConstructWithNonConstTemplateConstructorWorks 13: [ OK ] ArrayRefTest/0.ConstructWithNonConstTemplateConstructorWorks (0 ms) 13: [ RUN ] ArrayRefTest/0.ConstructFromPointersWorks 13: [ OK ] ArrayRefTest/0.ConstructFromPointersWorks (0 ms) 13: [ RUN ] ArrayRefTest/0.ConstructFromNonConstPointersWorks 13: [ OK ] ArrayRefTest/0.ConstructFromNonConstPointersWorks (0 ms) 13: [ RUN ] ArrayRefTest/0.ConstructFromVectorWorks 13: [ OK ] ArrayRefTest/0.ConstructFromVectorWorks (0 ms) 13: [ RUN ] ArrayRefTest/0.ConstructFromNonConstVectorWorks 13: [ OK ] ArrayRefTest/0.ConstructFromNonConstVectorWorks (0 ms) 13: [ RUN ] ArrayRefTest/0.ConstructFromStructFieldWithTemplateConstructorWorks 13: [ OK ] ArrayRefTest/0.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms) 13: [----------] 9 tests from ArrayRefTest/0 (0 ms total) 13: 13: [----------] 9 tests from ArrayRefTest/1, where TypeParam = gmx::ArrayRef 13: [ RUN ] ArrayRefTest/1.MakeWithAssignmentWorks 13: [ OK ] ArrayRefTest/1.MakeWithAssignmentWorks (0 ms) 13: [ RUN ] ArrayRefTest/1.MakeWithNonConstAssignmentWorks 13: [ OK ] ArrayRefTest/1.MakeWithNonConstAssignmentWorks (0 ms) 13: [ RUN ] ArrayRefTest/1.ConstructWithTemplateConstructorWorks 13: [ OK ] ArrayRefTest/1.ConstructWithTemplateConstructorWorks (0 ms) 13: [ RUN ] ArrayRefTest/1.ConstructWithNonConstTemplateConstructorWorks 13: [ OK ] ArrayRefTest/1.ConstructWithNonConstTemplateConstructorWorks (0 ms) 13: [ RUN ] ArrayRefTest/1.ConstructFromPointersWorks 13: [ OK ] ArrayRefTest/1.ConstructFromPointersWorks (0 ms) 13: [ RUN ] ArrayRefTest/1.ConstructFromNonConstPointersWorks 13: [ OK ] ArrayRefTest/1.ConstructFromNonConstPointersWorks (0 ms) 13: [ RUN ] ArrayRefTest/1.ConstructFromVectorWorks 13: [ OK ] ArrayRefTest/1.ConstructFromVectorWorks (0 ms) 13: [ RUN ] ArrayRefTest/1.ConstructFromNonConstVectorWorks 13: [ OK ] ArrayRefTest/1.ConstructFromNonConstVectorWorks (0 ms) 13: [ RUN ] ArrayRefTest/1.ConstructFromStructFieldWithTemplateConstructorWorks 13: [ OK ] ArrayRefTest/1.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms) 13: [----------] 9 tests from ArrayRefTest/1 (0 ms total) 13: 13: [----------] 9 tests from ArrayRefTest/2, where TypeParam = gmx::ArrayRef 13: [ RUN ] ArrayRefTest/2.MakeWithAssignmentWorks 13: [ OK ] ArrayRefTest/2.MakeWithAssignmentWorks (0 ms) 13: [ RUN ] ArrayRefTest/2.MakeWithNonConstAssignmentWorks 13: [ OK ] ArrayRefTest/2.MakeWithNonConstAssignmentWorks (0 ms) 13: [ RUN ] ArrayRefTest/2.ConstructWithTemplateConstructorWorks 13: [ OK ] ArrayRefTest/2.ConstructWithTemplateConstructorWorks (0 ms) 13: [ RUN ] ArrayRefTest/2.ConstructWithNonConstTemplateConstructorWorks 13: [ OK ] ArrayRefTest/2.ConstructWithNonConstTemplateConstructorWorks (0 ms) 13: [ RUN ] ArrayRefTest/2.ConstructFromPointersWorks 13: [ OK ] ArrayRefTest/2.ConstructFromPointersWorks (0 ms) 13: [ RUN ] ArrayRefTest/2.ConstructFromNonConstPointersWorks 13: [ OK ] ArrayRefTest/2.ConstructFromNonConstPointersWorks (0 ms) 13: [ RUN ] ArrayRefTest/2.ConstructFromVectorWorks 13: [ OK ] ArrayRefTest/2.ConstructFromVectorWorks (0 ms) 13: [ RUN ] ArrayRefTest/2.ConstructFromNonConstVectorWorks 13: [ OK ] ArrayRefTest/2.ConstructFromNonConstVectorWorks (0 ms) 13: [ RUN ] ArrayRefTest/2.ConstructFromStructFieldWithTemplateConstructorWorks 13: [ OK ] ArrayRefTest/2.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms) 13: [----------] 9 tests from ArrayRefTest/2 (0 ms total) 13: 13: [----------] 9 tests from ArrayRefTest/3, where TypeParam = gmx::ArrayRef 13: [ RUN ] ArrayRefTest/3.MakeWithAssignmentWorks 13: [ OK ] ArrayRefTest/3.MakeWithAssignmentWorks (0 ms) 13: [ RUN ] ArrayRefTest/3.MakeWithNonConstAssignmentWorks 13: [ OK ] ArrayRefTest/3.MakeWithNonConstAssignmentWorks (0 ms) 13: [ RUN ] ArrayRefTest/3.ConstructWithTemplateConstructorWorks 13: [ OK ] ArrayRefTest/3.ConstructWithTemplateConstructorWorks (0 ms) 13: [ RUN ] ArrayRefTest/3.ConstructWithNonConstTemplateConstructorWorks 13: [ OK ] ArrayRefTest/3.ConstructWithNonConstTemplateConstructorWorks (0 ms) 13: [ RUN ] ArrayRefTest/3.ConstructFromPointersWorks 13: [ OK ] ArrayRefTest/3.ConstructFromPointersWorks (0 ms) 13: [ RUN ] ArrayRefTest/3.ConstructFromNonConstPointersWorks 13: [ OK ] ArrayRefTest/3.ConstructFromNonConstPointersWorks (0 ms) 13: [ RUN ] ArrayRefTest/3.ConstructFromVectorWorks 13: [ OK ] ArrayRefTest/3.ConstructFromVectorWorks (0 ms) 13: [ RUN ] ArrayRefTest/3.ConstructFromNonConstVectorWorks 13: [ OK ] ArrayRefTest/3.ConstructFromNonConstVectorWorks (0 ms) 13: [ RUN ] ArrayRefTest/3.ConstructFromStructFieldWithTemplateConstructorWorks 13: [ OK ] ArrayRefTest/3.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms) 13: [----------] 9 tests from ArrayRefTest/3 (0 ms total) 13: 13: [----------] 9 tests from ArrayRefTest/4, where TypeParam = gmx::ArrayRef 13: [ RUN ] ArrayRefTest/4.MakeWithAssignmentWorks 13: [ OK ] ArrayRefTest/4.MakeWithAssignmentWorks (0 ms) 13: [ RUN ] ArrayRefTest/4.MakeWithNonConstAssignmentWorks 13: [ OK ] ArrayRefTest/4.MakeWithNonConstAssignmentWorks (0 ms) 13: [ RUN ] ArrayRefTest/4.ConstructWithTemplateConstructorWorks 13: [ OK ] ArrayRefTest/4.ConstructWithTemplateConstructorWorks (0 ms) 13: [ RUN ] ArrayRefTest/4.ConstructWithNonConstTemplateConstructorWorks 13: [ OK ] ArrayRefTest/4.ConstructWithNonConstTemplateConstructorWorks (0 ms) 13: [ RUN ] ArrayRefTest/4.ConstructFromPointersWorks 13: [ OK ] ArrayRefTest/4.ConstructFromPointersWorks (0 ms) 13: [ RUN ] ArrayRefTest/4.ConstructFromNonConstPointersWorks 13: [ OK ] ArrayRefTest/4.ConstructFromNonConstPointersWorks (0 ms) 13: [ RUN ] ArrayRefTest/4.ConstructFromVectorWorks 13: [ OK ] ArrayRefTest/4.ConstructFromVectorWorks (0 ms) 13: [ RUN ] ArrayRefTest/4.ConstructFromNonConstVectorWorks 13: [ OK ] ArrayRefTest/4.ConstructFromNonConstVectorWorks (0 ms) 13: [ RUN ] ArrayRefTest/4.ConstructFromStructFieldWithTemplateConstructorWorks 13: [ OK ] ArrayRefTest/4.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms) 13: [----------] 9 tests from ArrayRefTest/4 (0 ms total) 13: 13: [----------] 9 tests from ArrayRefTest/5, where TypeParam = gmx::ArrayRef 13: [ RUN ] ArrayRefTest/5.MakeWithAssignmentWorks 13: [ OK ] ArrayRefTest/5.MakeWithAssignmentWorks (0 ms) 13: [ RUN ] ArrayRefTest/5.MakeWithNonConstAssignmentWorks 13: [ OK ] ArrayRefTest/5.MakeWithNonConstAssignmentWorks (0 ms) 13: [ RUN ] ArrayRefTest/5.ConstructWithTemplateConstructorWorks 13: [ OK ] ArrayRefTest/5.ConstructWithTemplateConstructorWorks (0 ms) 13: [ RUN ] ArrayRefTest/5.ConstructWithNonConstTemplateConstructorWorks 13: [ OK ] ArrayRefTest/5.ConstructWithNonConstTemplateConstructorWorks (0 ms) 13: [ RUN ] ArrayRefTest/5.ConstructFromPointersWorks 13: [ OK ] ArrayRefTest/5.ConstructFromPointersWorks (0 ms) 13: [ RUN ] ArrayRefTest/5.ConstructFromNonConstPointersWorks 13: [ OK ] ArrayRefTest/5.ConstructFromNonConstPointersWorks (0 ms) 13: [ RUN ] ArrayRefTest/5.ConstructFromVectorWorks 13: [ OK ] ArrayRefTest/5.ConstructFromVectorWorks (0 ms) 13: [ RUN ] ArrayRefTest/5.ConstructFromNonConstVectorWorks 13: [ OK ] ArrayRefTest/5.ConstructFromNonConstVectorWorks (0 ms) 13: [ RUN ] ArrayRefTest/5.ConstructFromStructFieldWithTemplateConstructorWorks 13: [ OK ] ArrayRefTest/5.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms) 13: [----------] 9 tests from ArrayRefTest/5 (0 ms total) 13: 13: [----------] 9 tests from ArrayRefTest/6, where TypeParam = gmx::ArrayRef 13: [ RUN ] ArrayRefTest/6.MakeWithAssignmentWorks 13: [ OK ] ArrayRefTest/6.MakeWithAssignmentWorks (0 ms) 13: [ RUN ] ArrayRefTest/6.MakeWithNonConstAssignmentWorks 13: [ OK ] ArrayRefTest/6.MakeWithNonConstAssignmentWorks (0 ms) 13: [ RUN ] ArrayRefTest/6.ConstructWithTemplateConstructorWorks 13: [ OK ] ArrayRefTest/6.ConstructWithTemplateConstructorWorks (0 ms) 13: [ RUN ] ArrayRefTest/6.ConstructWithNonConstTemplateConstructorWorks 13: [ OK ] ArrayRefTest/6.ConstructWithNonConstTemplateConstructorWorks (0 ms) 13: [ RUN ] ArrayRefTest/6.ConstructFromPointersWorks 13: [ OK ] ArrayRefTest/6.ConstructFromPointersWorks (0 ms) 13: [ RUN ] ArrayRefTest/6.ConstructFromNonConstPointersWorks 13: [ OK ] ArrayRefTest/6.ConstructFromNonConstPointersWorks (0 ms) 13: [ RUN ] ArrayRefTest/6.ConstructFromVectorWorks 13: [ OK ] ArrayRefTest/6.ConstructFromVectorWorks (0 ms) 13: [ RUN ] ArrayRefTest/6.ConstructFromNonConstVectorWorks 13: [ OK ] ArrayRefTest/6.ConstructFromNonConstVectorWorks (0 ms) 13: [ RUN ] ArrayRefTest/6.ConstructFromStructFieldWithTemplateConstructorWorks 13: [ OK ] ArrayRefTest/6.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms) 13: [----------] 9 tests from ArrayRefTest/6 (0 ms total) 13: 13: [----------] 9 tests from ArrayRefTest/7, where TypeParam = gmx::ArrayRef 13: [ RUN ] ArrayRefTest/7.MakeWithAssignmentWorks 13: [ OK ] ArrayRefTest/7.MakeWithAssignmentWorks (0 ms) 13: [ RUN ] ArrayRefTest/7.MakeWithNonConstAssignmentWorks 13: [ OK ] ArrayRefTest/7.MakeWithNonConstAssignmentWorks (0 ms) 13: [ RUN ] ArrayRefTest/7.ConstructWithTemplateConstructorWorks 13: [ OK ] ArrayRefTest/7.ConstructWithTemplateConstructorWorks (0 ms) 13: [ RUN ] ArrayRefTest/7.ConstructWithNonConstTemplateConstructorWorks 13: [ OK ] ArrayRefTest/7.ConstructWithNonConstTemplateConstructorWorks (0 ms) 13: [ RUN ] ArrayRefTest/7.ConstructFromPointersWorks 13: [ OK ] ArrayRefTest/7.ConstructFromPointersWorks (0 ms) 13: [ RUN ] ArrayRefTest/7.ConstructFromNonConstPointersWorks 13: [ OK ] ArrayRefTest/7.ConstructFromNonConstPointersWorks (0 ms) 13: [ RUN ] ArrayRefTest/7.ConstructFromVectorWorks 13: [ OK ] ArrayRefTest/7.ConstructFromVectorWorks (0 ms) 13: [ RUN ] ArrayRefTest/7.ConstructFromNonConstVectorWorks 13: [ OK ] ArrayRefTest/7.ConstructFromNonConstVectorWorks (0 ms) 13: [ RUN ] ArrayRefTest/7.ConstructFromStructFieldWithTemplateConstructorWorks 13: [ OK ] ArrayRefTest/7.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms) 13: [----------] 9 tests from ArrayRefTest/7 (0 ms total) 13: 13: [----------] 9 tests from ArrayRefTest/8, where TypeParam = gmx::ArrayRef 13: [ RUN ] ArrayRefTest/8.MakeWithAssignmentWorks 13: [ OK ] ArrayRefTest/8.MakeWithAssignmentWorks (0 ms) 13: [ RUN ] ArrayRefTest/8.MakeWithNonConstAssignmentWorks 13: [ OK ] ArrayRefTest/8.MakeWithNonConstAssignmentWorks (0 ms) 13: [ RUN ] ArrayRefTest/8.ConstructWithTemplateConstructorWorks 13: [ OK ] ArrayRefTest/8.ConstructWithTemplateConstructorWorks (0 ms) 13: [ RUN ] ArrayRefTest/8.ConstructWithNonConstTemplateConstructorWorks 13: [ OK ] ArrayRefTest/8.ConstructWithNonConstTemplateConstructorWorks (0 ms) 13: [ RUN ] ArrayRefTest/8.ConstructFromPointersWorks 13: [ OK ] ArrayRefTest/8.ConstructFromPointersWorks (0 ms) 13: [ RUN ] ArrayRefTest/8.ConstructFromNonConstPointersWorks 13: [ OK ] ArrayRefTest/8.ConstructFromNonConstPointersWorks (0 ms) 13: [ RUN ] ArrayRefTest/8.ConstructFromVectorWorks 13: [ OK ] ArrayRefTest/8.ConstructFromVectorWorks (0 ms) 13: [ RUN ] ArrayRefTest/8.ConstructFromNonConstVectorWorks 13: [ OK ] ArrayRefTest/8.ConstructFromNonConstVectorWorks (0 ms) 13: [ RUN ] ArrayRefTest/8.ConstructFromStructFieldWithTemplateConstructorWorks 13: [ OK ] ArrayRefTest/8.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms) 13: [----------] 9 tests from ArrayRefTest/8 (0 ms total) 13: 13: [----------] 9 tests from ArrayRefTest/9, where TypeParam = gmx::ArrayRef 13: [ RUN ] ArrayRefTest/9.MakeWithAssignmentWorks 13: [ OK ] ArrayRefTest/9.MakeWithAssignmentWorks (0 ms) 13: [ RUN ] ArrayRefTest/9.MakeWithNonConstAssignmentWorks 13: [ OK ] ArrayRefTest/9.MakeWithNonConstAssignmentWorks (0 ms) 13: [ RUN ] ArrayRefTest/9.ConstructWithTemplateConstructorWorks 13: [ OK ] ArrayRefTest/9.ConstructWithTemplateConstructorWorks (0 ms) 13: [ RUN ] ArrayRefTest/9.ConstructWithNonConstTemplateConstructorWorks 13: [ OK ] ArrayRefTest/9.ConstructWithNonConstTemplateConstructorWorks (0 ms) 13: [ RUN ] ArrayRefTest/9.ConstructFromPointersWorks 13: [ OK ] ArrayRefTest/9.ConstructFromPointersWorks (0 ms) 13: [ RUN ] ArrayRefTest/9.ConstructFromNonConstPointersWorks 13: [ OK ] ArrayRefTest/9.ConstructFromNonConstPointersWorks (0 ms) 13: [ RUN ] ArrayRefTest/9.ConstructFromVectorWorks 13: [ OK ] ArrayRefTest/9.ConstructFromVectorWorks (0 ms) 13: [ RUN ] ArrayRefTest/9.ConstructFromNonConstVectorWorks 13: [ OK ] ArrayRefTest/9.ConstructFromNonConstVectorWorks (0 ms) 13: [ RUN ] ArrayRefTest/9.ConstructFromStructFieldWithTemplateConstructorWorks 13: [ OK ] ArrayRefTest/9.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms) 13: [----------] 9 tests from ArrayRefTest/9 (0 ms total) 13: 13: [----------] 9 tests from ArrayRefTest/10, where TypeParam = gmx::ArrayRef 13: [ RUN ] ArrayRefTest/10.MakeWithAssignmentWorks 13: [ OK ] ArrayRefTest/10.MakeWithAssignmentWorks (0 ms) 13: [ RUN ] ArrayRefTest/10.MakeWithNonConstAssignmentWorks 13: [ OK ] ArrayRefTest/10.MakeWithNonConstAssignmentWorks (0 ms) 13: [ RUN ] ArrayRefTest/10.ConstructWithTemplateConstructorWorks 13: [ OK ] ArrayRefTest/10.ConstructWithTemplateConstructorWorks (0 ms) 13: [ RUN ] ArrayRefTest/10.ConstructWithNonConstTemplateConstructorWorks 13: [ OK ] ArrayRefTest/10.ConstructWithNonConstTemplateConstructorWorks (0 ms) 13: [ RUN ] ArrayRefTest/10.ConstructFromPointersWorks 13: [ OK ] ArrayRefTest/10.ConstructFromPointersWorks (0 ms) 13: [ RUN ] ArrayRefTest/10.ConstructFromNonConstPointersWorks 13: [ OK ] ArrayRefTest/10.ConstructFromNonConstPointersWorks (0 ms) 13: [ RUN ] ArrayRefTest/10.ConstructFromVectorWorks 13: [ OK ] ArrayRefTest/10.ConstructFromVectorWorks (0 ms) 13: [ RUN ] ArrayRefTest/10.ConstructFromNonConstVectorWorks 13: [ OK ] ArrayRefTest/10.ConstructFromNonConstVectorWorks (0 ms) 13: [ RUN ] ArrayRefTest/10.ConstructFromStructFieldWithTemplateConstructorWorks 13: [ OK ] ArrayRefTest/10.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms) 13: [----------] 9 tests from ArrayRefTest/10 (0 ms total) 13: 13: [----------] 9 tests from ArrayRefTest/11, where TypeParam = gmx::ArrayRef 13: [ RUN ] ArrayRefTest/11.MakeWithAssignmentWorks 13: [ OK ] ArrayRefTest/11.MakeWithAssignmentWorks (0 ms) 13: [ RUN ] ArrayRefTest/11.MakeWithNonConstAssignmentWorks 13: [ OK ] ArrayRefTest/11.MakeWithNonConstAssignmentWorks (0 ms) 13: [ RUN ] ArrayRefTest/11.ConstructWithTemplateConstructorWorks 13: [ OK ] ArrayRefTest/11.ConstructWithTemplateConstructorWorks (0 ms) 13: [ RUN ] ArrayRefTest/11.ConstructWithNonConstTemplateConstructorWorks 13: [ OK ] ArrayRefTest/11.ConstructWithNonConstTemplateConstructorWorks (0 ms) 13: [ RUN ] ArrayRefTest/11.ConstructFromPointersWorks 13: [ OK ] ArrayRefTest/11.ConstructFromPointersWorks (0 ms) 13: [ RUN ] ArrayRefTest/11.ConstructFromNonConstPointersWorks 13: [ OK ] ArrayRefTest/11.ConstructFromNonConstPointersWorks (0 ms) 13: [ RUN ] ArrayRefTest/11.ConstructFromVectorWorks 13: [ OK ] ArrayRefTest/11.ConstructFromVectorWorks (0 ms) 13: [ RUN ] ArrayRefTest/11.ConstructFromNonConstVectorWorks 13: [ OK ] ArrayRefTest/11.ConstructFromNonConstVectorWorks (0 ms) 13: [ RUN ] ArrayRefTest/11.ConstructFromStructFieldWithTemplateConstructorWorks 13: [ OK ] ArrayRefTest/11.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms) 13: [----------] 9 tests from ArrayRefTest/11 (0 ms total) 13: 13: [----------] 9 tests from ArrayRefTest/12, where TypeParam = gmx::ArrayRef 13: [ RUN ] ArrayRefTest/12.MakeWithAssignmentWorks 13: [ OK ] ArrayRefTest/12.MakeWithAssignmentWorks (0 ms) 13: [ RUN ] ArrayRefTest/12.MakeWithNonConstAssignmentWorks 13: [ OK ] ArrayRefTest/12.MakeWithNonConstAssignmentWorks (0 ms) 13: [ RUN ] ArrayRefTest/12.ConstructWithTemplateConstructorWorks 13: [ OK ] ArrayRefTest/12.ConstructWithTemplateConstructorWorks (0 ms) 13: [ RUN ] ArrayRefTest/12.ConstructWithNonConstTemplateConstructorWorks 13: [ OK ] ArrayRefTest/12.ConstructWithNonConstTemplateConstructorWorks (0 ms) 13: [ RUN ] ArrayRefTest/12.ConstructFromPointersWorks 13: [ OK ] ArrayRefTest/12.ConstructFromPointersWorks (0 ms) 13: [ RUN ] ArrayRefTest/12.ConstructFromNonConstPointersWorks 13: [ OK ] ArrayRefTest/12.ConstructFromNonConstPointersWorks (0 ms) 13: [ RUN ] ArrayRefTest/12.ConstructFromVectorWorks 13: [ OK ] ArrayRefTest/12.ConstructFromVectorWorks (0 ms) 13: [ RUN ] ArrayRefTest/12.ConstructFromNonConstVectorWorks 13: [ OK ] ArrayRefTest/12.ConstructFromNonConstVectorWorks (0 ms) 13: [ RUN ] ArrayRefTest/12.ConstructFromStructFieldWithTemplateConstructorWorks 13: [ OK ] ArrayRefTest/12.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms) 13: [----------] 9 tests from ArrayRefTest/12 (0 ms total) 13: 13: [----------] 9 tests from ArrayRefTest/13, where TypeParam = gmx::ArrayRef 13: [ RUN ] ArrayRefTest/13.MakeWithAssignmentWorks 13: [ OK ] ArrayRefTest/13.MakeWithAssignmentWorks (0 ms) 13: [ RUN ] ArrayRefTest/13.MakeWithNonConstAssignmentWorks 13: [ OK ] ArrayRefTest/13.MakeWithNonConstAssignmentWorks (0 ms) 13: [ RUN ] ArrayRefTest/13.ConstructWithTemplateConstructorWorks 13: [ OK ] ArrayRefTest/13.ConstructWithTemplateConstructorWorks (0 ms) 13: [ RUN ] ArrayRefTest/13.ConstructWithNonConstTemplateConstructorWorks 13: [ OK ] ArrayRefTest/13.ConstructWithNonConstTemplateConstructorWorks (0 ms) 13: [ RUN ] ArrayRefTest/13.ConstructFromPointersWorks 13: [ OK ] ArrayRefTest/13.ConstructFromPointersWorks (0 ms) 13: [ RUN ] ArrayRefTest/13.ConstructFromNonConstPointersWorks 13: [ OK ] ArrayRefTest/13.ConstructFromNonConstPointersWorks (0 ms) 13: [ RUN ] ArrayRefTest/13.ConstructFromVectorWorks 13: [ OK ] ArrayRefTest/13.ConstructFromVectorWorks (0 ms) 13: [ RUN ] ArrayRefTest/13.ConstructFromNonConstVectorWorks 13: [ OK ] ArrayRefTest/13.ConstructFromNonConstVectorWorks (0 ms) 13: [ RUN ] ArrayRefTest/13.ConstructFromStructFieldWithTemplateConstructorWorks 13: [ OK ] ArrayRefTest/13.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms) 13: [----------] 9 tests from ArrayRefTest/13 (0 ms total) 13: 13: [----------] 9 tests from ArrayRefTest/14, where TypeParam = gmx::ArrayRef 13: [ RUN ] ArrayRefTest/14.MakeWithAssignmentWorks 13: [ OK ] ArrayRefTest/14.MakeWithAssignmentWorks (0 ms) 13: [ RUN ] ArrayRefTest/14.MakeWithNonConstAssignmentWorks 13: [ OK ] ArrayRefTest/14.MakeWithNonConstAssignmentWorks (0 ms) 13: [ RUN ] ArrayRefTest/14.ConstructWithTemplateConstructorWorks 13: [ OK ] ArrayRefTest/14.ConstructWithTemplateConstructorWorks (0 ms) 13: [ RUN ] ArrayRefTest/14.ConstructWithNonConstTemplateConstructorWorks 13: [ OK ] ArrayRefTest/14.ConstructWithNonConstTemplateConstructorWorks (0 ms) 13: [ RUN ] ArrayRefTest/14.ConstructFromPointersWorks 13: [ OK ] ArrayRefTest/14.ConstructFromPointersWorks (0 ms) 13: [ RUN ] ArrayRefTest/14.ConstructFromNonConstPointersWorks 13: [ OK ] ArrayRefTest/14.ConstructFromNonConstPointersWorks (0 ms) 13: [ RUN ] ArrayRefTest/14.ConstructFromVectorWorks 13: [ OK ] ArrayRefTest/14.ConstructFromVectorWorks (0 ms) 13: [ RUN ] ArrayRefTest/14.ConstructFromNonConstVectorWorks 13: [ OK ] ArrayRefTest/14.ConstructFromNonConstVectorWorks (0 ms) 13: [ RUN ] ArrayRefTest/14.ConstructFromStructFieldWithTemplateConstructorWorks 13: [ OK ] ArrayRefTest/14.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms) 13: [----------] 9 tests from ArrayRefTest/14 (0 ms total) 13: 13: [----------] 9 tests from ArrayRefTest/15, where TypeParam = gmx::ArrayRef 13: [ RUN ] ArrayRefTest/15.MakeWithAssignmentWorks 13: [ OK ] ArrayRefTest/15.MakeWithAssignmentWorks (0 ms) 13: [ RUN ] ArrayRefTest/15.MakeWithNonConstAssignmentWorks 13: [ OK ] ArrayRefTest/15.MakeWithNonConstAssignmentWorks (0 ms) 13: [ RUN ] ArrayRefTest/15.ConstructWithTemplateConstructorWorks 13: [ OK ] ArrayRefTest/15.ConstructWithTemplateConstructorWorks (0 ms) 13: [ RUN ] ArrayRefTest/15.ConstructWithNonConstTemplateConstructorWorks 13: [ OK ] ArrayRefTest/15.ConstructWithNonConstTemplateConstructorWorks (0 ms) 13: [ RUN ] ArrayRefTest/15.ConstructFromPointersWorks 13: [ OK ] ArrayRefTest/15.ConstructFromPointersWorks (0 ms) 13: [ RUN ] ArrayRefTest/15.ConstructFromNonConstPointersWorks 13: [ OK ] ArrayRefTest/15.ConstructFromNonConstPointersWorks (0 ms) 13: [ RUN ] ArrayRefTest/15.ConstructFromVectorWorks 13: [ OK ] ArrayRefTest/15.ConstructFromVectorWorks (0 ms) 13: [ RUN ] ArrayRefTest/15.ConstructFromNonConstVectorWorks 13: [ OK ] ArrayRefTest/15.ConstructFromNonConstVectorWorks (0 ms) 13: [ RUN ] ArrayRefTest/15.ConstructFromStructFieldWithTemplateConstructorWorks 13: [ OK ] ArrayRefTest/15.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms) 13: [----------] 9 tests from ArrayRefTest/15 (0 ms total) 13: 13: [----------] 9 tests from ArrayRefTest/16, where TypeParam = gmx::ArrayRef 13: [ RUN ] ArrayRefTest/16.MakeWithAssignmentWorks 13: [ OK ] ArrayRefTest/16.MakeWithAssignmentWorks (0 ms) 13: [ RUN ] ArrayRefTest/16.MakeWithNonConstAssignmentWorks 13: [ OK ] ArrayRefTest/16.MakeWithNonConstAssignmentWorks (0 ms) 13: [ RUN ] ArrayRefTest/16.ConstructWithTemplateConstructorWorks 13: [ OK ] ArrayRefTest/16.ConstructWithTemplateConstructorWorks (0 ms) 13: [ RUN ] ArrayRefTest/16.ConstructWithNonConstTemplateConstructorWorks 13: [ OK ] ArrayRefTest/16.ConstructWithNonConstTemplateConstructorWorks (0 ms) 13: [ RUN ] ArrayRefTest/16.ConstructFromPointersWorks 13: [ OK ] ArrayRefTest/16.ConstructFromPointersWorks (0 ms) 13: [ RUN ] ArrayRefTest/16.ConstructFromNonConstPointersWorks 13: [ OK ] ArrayRefTest/16.ConstructFromNonConstPointersWorks (0 ms) 13: [ RUN ] ArrayRefTest/16.ConstructFromVectorWorks 13: [ OK ] ArrayRefTest/16.ConstructFromVectorWorks (0 ms) 13: [ RUN ] ArrayRefTest/16.ConstructFromNonConstVectorWorks 13: [ OK ] ArrayRefTest/16.ConstructFromNonConstVectorWorks (0 ms) 13: [ RUN ] ArrayRefTest/16.ConstructFromStructFieldWithTemplateConstructorWorks 13: [ OK ] ArrayRefTest/16.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms) 13: [----------] 9 tests from ArrayRefTest/16 (0 ms total) 13: 13: [----------] 9 tests from ArrayRefTest/17, where TypeParam = gmx::ArrayRef 13: [ RUN ] ArrayRefTest/17.MakeWithAssignmentWorks 13: [ OK ] ArrayRefTest/17.MakeWithAssignmentWorks (0 ms) 13: [ RUN ] ArrayRefTest/17.MakeWithNonConstAssignmentWorks 13: [ OK ] ArrayRefTest/17.MakeWithNonConstAssignmentWorks (0 ms) 13: [ RUN ] ArrayRefTest/17.ConstructWithTemplateConstructorWorks 13: [ OK ] ArrayRefTest/17.ConstructWithTemplateConstructorWorks (0 ms) 13: [ RUN ] ArrayRefTest/17.ConstructWithNonConstTemplateConstructorWorks 13: [ OK ] ArrayRefTest/17.ConstructWithNonConstTemplateConstructorWorks (0 ms) 13: [ RUN ] ArrayRefTest/17.ConstructFromPointersWorks 13: [ OK ] ArrayRefTest/17.ConstructFromPointersWorks (0 ms) 13: [ RUN ] ArrayRefTest/17.ConstructFromNonConstPointersWorks 13: [ OK ] ArrayRefTest/17.ConstructFromNonConstPointersWorks (0 ms) 13: [ RUN ] ArrayRefTest/17.ConstructFromVectorWorks 13: [ OK ] ArrayRefTest/17.ConstructFromVectorWorks (0 ms) 13: [ RUN ] ArrayRefTest/17.ConstructFromNonConstVectorWorks 13: [ OK ] ArrayRefTest/17.ConstructFromNonConstVectorWorks (0 ms) 13: [ RUN ] ArrayRefTest/17.ConstructFromStructFieldWithTemplateConstructorWorks 13: [ OK ] ArrayRefTest/17.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms) 13: [----------] 9 tests from ArrayRefTest/17 (0 ms total) 13: 13: [----------] 9 tests from ArrayRefTest/18, where TypeParam = gmx::ArrayRef 13: [ RUN ] ArrayRefTest/18.MakeWithAssignmentWorks 13: [ OK ] ArrayRefTest/18.MakeWithAssignmentWorks (0 ms) 13: [ RUN ] ArrayRefTest/18.MakeWithNonConstAssignmentWorks 13: [ OK ] ArrayRefTest/18.MakeWithNonConstAssignmentWorks (0 ms) 13: [ RUN ] ArrayRefTest/18.ConstructWithTemplateConstructorWorks 13: [ OK ] ArrayRefTest/18.ConstructWithTemplateConstructorWorks (0 ms) 13: [ RUN ] ArrayRefTest/18.ConstructWithNonConstTemplateConstructorWorks 13: [ OK ] ArrayRefTest/18.ConstructWithNonConstTemplateConstructorWorks (0 ms) 13: [ RUN ] ArrayRefTest/18.ConstructFromPointersWorks 13: [ OK ] ArrayRefTest/18.ConstructFromPointersWorks (0 ms) 13: [ RUN ] ArrayRefTest/18.ConstructFromNonConstPointersWorks 13: [ OK ] ArrayRefTest/18.ConstructFromNonConstPointersWorks (0 ms) 13: [ RUN ] ArrayRefTest/18.ConstructFromVectorWorks 13: [ OK ] ArrayRefTest/18.ConstructFromVectorWorks (0 ms) 13: [ RUN ] ArrayRefTest/18.ConstructFromNonConstVectorWorks 13: [ OK ] ArrayRefTest/18.ConstructFromNonConstVectorWorks (0 ms) 13: [ RUN ] ArrayRefTest/18.ConstructFromStructFieldWithTemplateConstructorWorks 13: [ OK ] ArrayRefTest/18.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms) 13: [----------] 9 tests from ArrayRefTest/18 (0 ms total) 13: 13: [----------] 9 tests from ArrayRefTest/19, where TypeParam = gmx::ArrayRef 13: [ RUN ] ArrayRefTest/19.MakeWithAssignmentWorks 13: [ OK ] ArrayRefTest/19.MakeWithAssignmentWorks (0 ms) 13: [ RUN ] ArrayRefTest/19.MakeWithNonConstAssignmentWorks 13: [ OK ] ArrayRefTest/19.MakeWithNonConstAssignmentWorks (0 ms) 13: [ RUN ] ArrayRefTest/19.ConstructWithTemplateConstructorWorks 13: [ OK ] ArrayRefTest/19.ConstructWithTemplateConstructorWorks (0 ms) 13: [ RUN ] ArrayRefTest/19.ConstructWithNonConstTemplateConstructorWorks 13: [ OK ] ArrayRefTest/19.ConstructWithNonConstTemplateConstructorWorks (0 ms) 13: [ RUN ] ArrayRefTest/19.ConstructFromPointersWorks 13: [ OK ] ArrayRefTest/19.ConstructFromPointersWorks (0 ms) 13: [ RUN ] ArrayRefTest/19.ConstructFromNonConstPointersWorks 13: [ OK ] ArrayRefTest/19.ConstructFromNonConstPointersWorks (0 ms) 13: [ RUN ] ArrayRefTest/19.ConstructFromVectorWorks 13: [ OK ] ArrayRefTest/19.ConstructFromVectorWorks (0 ms) 13: [ RUN ] ArrayRefTest/19.ConstructFromNonConstVectorWorks 13: [ OK ] ArrayRefTest/19.ConstructFromNonConstVectorWorks (0 ms) 13: [ RUN ] ArrayRefTest/19.ConstructFromStructFieldWithTemplateConstructorWorks 13: [ OK ] ArrayRefTest/19.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms) 13: [----------] 9 tests from ArrayRefTest/19 (0 ms total) 13: 13: [----------] 8 tests from BoolType 13: [ RUN ] BoolType.ImplicitConversion 13: [ OK ] BoolType.ImplicitConversion (0 ms) 13: [ RUN ] BoolType.FalseByDefault 13: [ OK ] BoolType.FalseByDefault (0 ms) 13: [ RUN ] BoolType.Assignment 13: [ OK ] BoolType.Assignment (0 ms) 13: [ RUN ] BoolType.Copy 13: [ OK ] BoolType.Copy (0 ms) 13: [ RUN ] BoolType.ArrayRefCanBeCreated 13: [ OK ] BoolType.ArrayRefCanBeCreated (0 ms) 13: [ RUN ] BoolType.CanBeCastToBool 13: [ OK ] BoolType.CanBeCastToBool (0 ms) 13: [ RUN ] BoolType.HasSizeOfBool 13: [ OK ] BoolType.HasSizeOfBool (0 ms) 13: [ RUN ] BoolType.HasAlignmentOfBool 13: [ OK ] BoolType.HasAlignmentOfBool (0 ms) 13: [----------] 8 tests from BoolType (0 ms total) 13: 13: [----------] 4 tests from ArrayRefFromBoolTypeVector 13: [ RUN ] ArrayRefFromBoolTypeVector.CanConstructEmpty 13: [ OK ] ArrayRefFromBoolTypeVector.CanConstructEmpty (0 ms) 13: [ RUN ] ArrayRefFromBoolTypeVector.Works 13: [ OK ] ArrayRefFromBoolTypeVector.Works (0 ms) 13: [ RUN ] ArrayRefFromBoolTypeVector.CanConstructConstEmpty 13: [ OK ] ArrayRefFromBoolTypeVector.CanConstructConstEmpty (0 ms) 13: [ RUN ] ArrayRefFromBoolTypeVector.ConstWorks 13: [ OK ] ArrayRefFromBoolTypeVector.ConstWorks (0 ms) 13: [----------] 4 tests from ArrayRefFromBoolTypeVector (0 ms total) 13: 13: [----------] 7 tests from CStringUtilityTest 13: [ RUN ] CStringUtilityTest.CaseInsensitiveComparison 13: [ OK ] CStringUtilityTest.CaseInsensitiveComparison (0 ms) 13: [ RUN ] CStringUtilityTest.CaseInsensitiveComparisonInLength 13: [ OK ] CStringUtilityTest.CaseInsensitiveComparisonInLength (0 ms) 13: [ RUN ] CStringUtilityTest.strip_comment 13: [ OK ] CStringUtilityTest.strip_comment (0 ms) 13: [ RUN ] CStringUtilityTest.upstring 13: [ OK ] CStringUtilityTest.upstring (0 ms) 13: [ RUN ] CStringUtilityTest.ltrim 13: [ OK ] CStringUtilityTest.ltrim (0 ms) 13: [ RUN ] CStringUtilityTest.rtrim 13: [ OK ] CStringUtilityTest.rtrim (0 ms) 13: [ RUN ] CStringUtilityTest.trim 13: [ OK ] CStringUtilityTest.trim (0 ms) 13: [----------] 7 tests from CStringUtilityTest (0 ms total) 13: 13: [----------] 2 tests from DefaultInitializationAllocator 13: [ RUN ] DefaultInitializationAllocator.PerformsValueInitialization 13: [ OK ] DefaultInitializationAllocator.PerformsValueInitialization (0 ms) 13: [ RUN ] DefaultInitializationAllocator.PerformsNoInitialization 13: [ OK ] DefaultInitializationAllocator.PerformsNoInitialization (0 ms) 13: [----------] 2 tests from DefaultInitializationAllocator (0 ms total) 13: 13: [----------] 4 tests from EnumerationHelpersTest 13: [ RUN ] EnumerationHelpersTest.EnumerationWrapperWorks 13: [ OK ] EnumerationHelpersTest.EnumerationWrapperWorks (0 ms) 13: [ RUN ] EnumerationHelpersTest.EnumerationArrayWorks 13: [ OK ] EnumerationHelpersTest.EnumerationArrayWorks (0 ms) 13: [ RUN ] EnumerationHelpersTest.EnumerationArrayCountIsSafe 13: [ OK ] EnumerationHelpersTest.EnumerationArrayCountIsSafe (0 ms) 13: [ RUN ] EnumerationHelpersTest.ArrayRefOfEnumerationArrayWorks 13: [ OK ] EnumerationHelpersTest.ArrayRefOfEnumerationArrayWorks (0 ms) 13: [----------] 4 tests from EnumerationHelpersTest (0 ms total) 13: 13: [----------] 1 test from EnumClassSuitsEnumerationArray 13: [ RUN ] EnumClassSuitsEnumerationArray.Works 13: [ OK ] EnumClassSuitsEnumerationArray.Works (0 ms) 13: [----------] 1 test from EnumClassSuitsEnumerationArray (0 ms total) 13: 13: [----------] 18 tests from FixedCapacityVectorTest 13: [ RUN ] FixedCapacityVectorTest.IsEmpty 13: [ OK ] FixedCapacityVectorTest.IsEmpty (0 ms) 13: [ RUN ] FixedCapacityVectorTest.ConstructorWorks 13: [ OK ] FixedCapacityVectorTest.ConstructorWorks (0 ms) 13: [ RUN ] FixedCapacityVectorTest.PushWorks 13: [ OK ] FixedCapacityVectorTest.PushWorks (0 ms) 13: [ RUN ] FixedCapacityVectorTest.PopWorks 13: [ OK ] FixedCapacityVectorTest.PopWorks (0 ms) 13: [ RUN ] FixedCapacityVectorTest.ResizeWorks 13: [ OK ] FixedCapacityVectorTest.ResizeWorks (0 ms) 13: [ RUN ] FixedCapacityVectorTest.ClearWorks 13: [ OK ] FixedCapacityVectorTest.ClearWorks (0 ms) 13: [ RUN ] FixedCapacityVectorTest.EmplaceBackWorks 13: [ OK ] FixedCapacityVectorTest.EmplaceBackWorks (0 ms) 13: [ RUN ] FixedCapacityVectorTest.AtThrows 13: [ OK ] FixedCapacityVectorTest.AtThrows (0 ms) 13: [ RUN ] FixedCapacityVectorTest.IteratorWorks 13: [ OK ] FixedCapacityVectorTest.IteratorWorks (0 ms) 13: [ RUN ] FixedCapacityVectorTest.ReverseIteratorWorks 13: [ OK ] FixedCapacityVectorTest.ReverseIteratorWorks (0 ms) 13: [ RUN ] FixedCapacityVectorTest.ZeroCapacityWorks 13: [ OK ] FixedCapacityVectorTest.ZeroCapacityWorks (0 ms) 13: [ RUN ] FixedCapacityVectorTest.CopyConstructorWorks 13: [ OK ] FixedCapacityVectorTest.CopyConstructorWorks (0 ms) 13: [ RUN ] FixedCapacityVectorTest.CopyAssignmentWorks 13: [ OK ] FixedCapacityVectorTest.CopyAssignmentWorks (0 ms) 13: [ RUN ] FixedCapacityVectorTest.MoveConstructorWorks 13: [ OK ] FixedCapacityVectorTest.MoveConstructorWorks (0 ms) 13: [ RUN ] FixedCapacityVectorTest.MoveAssignmentWorks 13: [ OK ] FixedCapacityVectorTest.MoveAssignmentWorks (0 ms) 13: [ RUN ] FixedCapacityVectorTest.ElementAssignmentWorks 13: [ OK ] FixedCapacityVectorTest.ElementAssignmentWorks (0 ms) 13: [ RUN ] FixedCapacityVectorTest.DataWorks 13: [ OK ] FixedCapacityVectorTest.DataWorks (0 ms) 13: [ RUN ] FixedCapacityVectorTest.ConstMethodsWork 13: [ OK ] FixedCapacityVectorTest.ConstMethodsWork (0 ms) 13: [----------] 18 tests from FixedCapacityVectorTest (0 ms total) 13: 13: [----------] 5 tests from InMemorySerializerTest 13: [ RUN ] InMemorySerializerTest.Roundtrip 13: [ OK ] InMemorySerializerTest.Roundtrip (0 ms) 13: [ RUN ] InMemorySerializerTest.RoundtripWithEndianessSwap 13: [ OK ] InMemorySerializerTest.RoundtripWithEndianessSwap (0 ms) 13: [ RUN ] InMemorySerializerTest.SerializerExplicitEndianessSwap 13: [ OK ] InMemorySerializerTest.SerializerExplicitEndianessSwap (0 ms) 13: [ RUN ] InMemorySerializerTest.DeserializerExplicitEndianessSwap 13: [ OK ] InMemorySerializerTest.DeserializerExplicitEndianessSwap (0 ms) 13: [ RUN ] InMemorySerializerTest.SizeIsCorrect 13: [ OK ] InMemorySerializerTest.SizeIsCorrect (0 ms) 13: [----------] 5 tests from InMemorySerializerTest (0 ms total) 13: 13: [----------] 4 tests from KeyValueTreeSerializerTest 13: [ RUN ] KeyValueTreeSerializerTest.EmptyTree 13: [ OK ] KeyValueTreeSerializerTest.EmptyTree (1 ms) 13: [ RUN ] KeyValueTreeSerializerTest.SimpleObject 13: [ OK ] KeyValueTreeSerializerTest.SimpleObject (1 ms) 13: [ RUN ] KeyValueTreeSerializerTest.ObjectWithArrays 13: [ OK ] KeyValueTreeSerializerTest.ObjectWithArrays (0 ms) 13: [ RUN ] KeyValueTreeSerializerTest.ObjectWithObjects 13: [ OK ] KeyValueTreeSerializerTest.ObjectWithObjects (1 ms) 13: [----------] 4 tests from KeyValueTreeSerializerTest (5 ms total) 13: 13: [----------] 7 tests from TreeValueTransformTest 13: [ RUN ] TreeValueTransformTest.SimpleTransforms 13: [ OK ] TreeValueTransformTest.SimpleTransforms (0 ms) 13: [ RUN ] TreeValueTransformTest.SimpleTransformsCaseAndDashInsensitive 13: [ OK ] TreeValueTransformTest.SimpleTransformsCaseAndDashInsensitive (0 ms) 13: [ RUN ] TreeValueTransformTest.SimpleTransformsToObject 13: [ OK ] TreeValueTransformTest.SimpleTransformsToObject (0 ms) 13: [ RUN ] TreeValueTransformTest.ObjectFromString 13: [ OK ] TreeValueTransformTest.ObjectFromString (0 ms) 13: [ RUN ] TreeValueTransformTest.ObjectFromMultipleStrings 13: [ OK ] TreeValueTransformTest.ObjectFromMultipleStrings (0 ms) 13: [ RUN ] TreeValueTransformTest.ScopedTransformRules 13: [ OK ] TreeValueTransformTest.ScopedTransformRules (0 ms) 13: [ RUN ] TreeValueTransformTest.CanAssignUserMultiValue 13: [ OK ] TreeValueTransformTest.CanAssignUserMultiValue (1 ms) 13: [----------] 7 tests from TreeValueTransformTest (6 ms total) 13: 13: [----------] 1 test from TreeValueTransformErrorTest 13: [ RUN ] TreeValueTransformErrorTest.ConversionError 13: [ OK ] TreeValueTransformErrorTest.ConversionError (0 ms) 13: [----------] 1 test from TreeValueTransformErrorTest (0 ms total) 13: 13: [----------] 9 tests from ListOfLists 13: [ RUN ] ListOfLists.EmptyListOfListsWorks 13: [ OK ] ListOfLists.EmptyListOfListsWorks (0 ms) 13: [ RUN ] ListOfLists.AppendWorks 13: [ OK ] ListOfLists.AppendWorks (0 ms) 13: [ RUN ] ListOfLists.EmptyListWorks 13: [ OK ] ListOfLists.EmptyListWorks (0 ms) 13: [ RUN ] ListOfLists.AppendAccessWorks 13: [ OK ] ListOfLists.AppendAccessWorks (0 ms) 13: [ RUN ] ListOfLists.ClearWorks 13: [ OK ] ListOfLists.ClearWorks (0 ms) 13: [ RUN ] ListOfLists.OutOfRangeAccessThrows 13: [ OK ] ListOfLists.OutOfRangeAccessThrows (0 ms) 13: [ RUN ] ListOfLists.FrontAndBackWork 13: [ OK ] ListOfLists.FrontAndBackWork (0 ms) 13: [ RUN ] ListOfLists.ExtractsAndRestores 13: [ OK ] ListOfLists.ExtractsAndRestores (0 ms) 13: [ RUN ] ListOfLists.AppendsListOfListsWithOffset 13: [ OK ] ListOfLists.AppendsListOfListsWithOffset (0 ms) 13: [----------] 9 tests from ListOfLists (0 ms total) 13: 13: [----------] 7 tests from LoggerTest 13: [ RUN ] LoggerTest.EmptyLoggerWorks 13: [ OK ] LoggerTest.EmptyLoggerWorks (0 ms) 13: [ RUN ] LoggerTest.LogsToStream 13: [ OK ] LoggerTest.LogsToStream (3 ms) 13: [ RUN ] LoggerTest.LogsToFile 13: [ OK ] LoggerTest.LogsToFile (2 ms) 13: [ RUN ] LoggerTest.LevelFilteringWorks 13: [ OK ] LoggerTest.LevelFilteringWorks (0 ms) 13: [ RUN ] LoggerTest.LogsToMultipleStreams 13: [ OK ] LoggerTest.LogsToMultipleStreams (0 ms) 13: [ RUN ] LoggerTest.LogsToMultipleFiles 13: [ OK ] LoggerTest.LogsToMultipleFiles (4 ms) 13: [ RUN ] LoggerTest.LogsToStreamAndFile 13: [ OK ] LoggerTest.LogsToStreamAndFile (1 ms) 13: [----------] 7 tests from LoggerTest (13 ms total) 13: 13: [----------] 7 tests from MessageStringCollectorTest 13: [ RUN ] MessageStringCollectorTest.CanAddAndClearMessagesNoContext 13: [ OK ] MessageStringCollectorTest.CanAddAndClearMessagesNoContext (0 ms) 13: [ RUN ] MessageStringCollectorTest.CanAddAndClearMessagesWithContext 13: [ OK ] MessageStringCollectorTest.CanAddAndClearMessagesWithContext (0 ms) 13: [ RUN ] MessageStringCollectorTest.CanAddStringMessages 13: [ OK ] MessageStringCollectorTest.CanAddStringMessages (0 ms) 13: [ RUN ] MessageStringCollectorTest.CanAddCharMessagesConditionally 13: [ OK ] MessageStringCollectorTest.CanAddCharMessagesConditionally (0 ms) 13: [ RUN ] MessageStringCollectorTest.CanAddStringMessagesConditionally 13: [ OK ] MessageStringCollectorTest.CanAddStringMessagesConditionally (0 ms) 13: [ RUN ] MessageStringCollectorTest.CanMoveConstruct 13: [ OK ] MessageStringCollectorTest.CanMoveConstruct (0 ms) 13: [ RUN ] MessageStringCollectorTest.CanMoveAssign 13: [ OK ] MessageStringCollectorTest.CanMoveAssign (0 ms) 13: [----------] 7 tests from MessageStringCollectorTest (0 ms total) 13: 13: [----------] 1 test from PathTest 13: [ RUN ] PathTest.StripSourcePrefixWorks 13: [ OK ] PathTest.StripSourcePrefixWorks (0 ms) 13: [----------] 1 test from PathTest (0 ms total) 13: 13: [----------] 2 tests from PhysicalNodeCommunicatorTest 13: [ RUN ] PhysicalNodeCommunicatorTest.CanConstruct 13: [ OK ] PhysicalNodeCommunicatorTest.CanConstruct (0 ms) 13: [ RUN ] PhysicalNodeCommunicatorTest.CanCallBarrier 13: [ OK ] PhysicalNodeCommunicatorTest.CanCallBarrier (0 ms) 13: [----------] 2 tests from PhysicalNodeCommunicatorTest (0 ms total) 13: 13: [----------] 5 tests from Range 13: [ RUN ] Range.EmptyRangeWorks 13: [ OK ] Range.EmptyRangeWorks (0 ms) 13: [ RUN ] Range.NonEmptyRangeWorks 13: [ OK ] Range.NonEmptyRangeWorks (0 ms) 13: [ RUN ] Range.BeginEnd 13: [ OK ] Range.BeginEnd (0 ms) 13: [ RUN ] Range.IsInRangeWorks 13: [ OK ] Range.IsInRangeWorks (0 ms) 13: [ RUN ] Range.IteratorWorks 13: [ OK ] Range.IteratorWorks (0 ms) 13: [----------] 5 tests from Range (0 ms total) 13: 13: [----------] 3 tests from ScopeGuardTest 13: [ RUN ] ScopeGuardTest.ScopeGuardExecutesCallbackOnExit 13: [ OK ] ScopeGuardTest.ScopeGuardExecutesCallbackOnExit (0 ms) 13: [ RUN ] ScopeGuardTest.ScopeGuardCanFreePointers 13: [ OK ] ScopeGuardTest.ScopeGuardCanFreePointers (0 ms) 13: [ RUN ] ScopeGuardTest.ScopeGuardsCanBeCreatedByHelperFunctions 13: [ OK ] ScopeGuardTest.ScopeGuardsCanBeCreatedByHelperFunctions (0 ms) 13: [----------] 3 tests from ScopeGuardTest (0 ms total) 13: 13: [----------] 7 tests from StringConvert 13: [ RUN ] StringConvert.NoResultFromEptyString 13: [ OK ] StringConvert.NoResultFromEptyString (0 ms) 13: [ RUN ] StringConvert.ThreeFloatsSuccessfully 13: [ OK ] StringConvert.ThreeFloatsSuccessfully (0 ms) 13: [ RUN ] StringConvert.OneIntSucessfully 13: [ OK ] StringConvert.OneIntSucessfully (0 ms) 13: [ RUN ] StringConvert.FloatAsStringToIntArrayThrows 13: [ OK ] StringConvert.FloatAsStringToIntArrayThrows (0 ms) 13: [ RUN ] StringConvert.ThrowsWhenWrongSize 13: [ OK ] StringConvert.ThrowsWhenWrongSize (0 ms) 13: [ RUN ] StringConvert.StringIdentityTransformWithArrayThrows 13: [ OK ] StringConvert.StringIdentityTransformWithArrayThrows (0 ms) 13: [ RUN ] StringConvert.StringIdentityTransformWithArrayOkay 13: [ OK ] StringConvert.StringIdentityTransformWithArrayOkay (0 ms) 13: [----------] 7 tests from StringConvert (0 ms total) 13: 13: [----------] 7 tests from StringToEnumValueConverterTest 13: [ RUN ] StringToEnumValueConverterTest.ExactStringComparisonWorksWithoutStripping 13: [ OK ] StringToEnumValueConverterTest.ExactStringComparisonWorksWithoutStripping (0 ms) 13: [ RUN ] StringToEnumValueConverterTest.CaseInsensitiveStringComparisonWorksWithoutStripping 13: [ OK ] StringToEnumValueConverterTest.CaseInsensitiveStringComparisonWorksWithoutStripping (0 ms) 13: [ RUN ] StringToEnumValueConverterTest.CaseAndDashInsensitiveStringComparisonWorksWithoutStripping 13: [ OK ] StringToEnumValueConverterTest.CaseAndDashInsensitiveStringComparisonWorksWithoutStripping (0 ms) 13: [ RUN ] StringToEnumValueConverterTest.ExactStringComparisonWorksWithStripping 13: [ OK ] StringToEnumValueConverterTest.ExactStringComparisonWorksWithStripping (0 ms) 13: [ RUN ] StringToEnumValueConverterTest.CaseInsensitiveStringComparisonWorksWithStripping 13: [ OK ] StringToEnumValueConverterTest.CaseInsensitiveStringComparisonWorksWithStripping (0 ms) 13: [ RUN ] StringToEnumValueConverterTest.CaseAndDashInsensitiveStringComparisonWorksWithStripping 13: [ OK ] StringToEnumValueConverterTest.CaseAndDashInsensitiveStringComparisonWorksWithStripping (0 ms) 13: [ RUN ] StringToEnumValueConverterTest.CustomConverterWorks 13: [ OK ] StringToEnumValueConverterTest.CustomConverterWorks (0 ms) 13: [----------] 7 tests from StringToEnumValueConverterTest (0 ms total) 13: 13: [----------] 9 tests from StringUtilityTest 13: [ RUN ] StringUtilityTest.StartsWith 13: [ OK ] StringUtilityTest.StartsWith (0 ms) 13: [ RUN ] StringUtilityTest.EndsWith 13: [ OK ] StringUtilityTest.EndsWith (0 ms) 13: [ RUN ] StringUtilityTest.StripSuffixIfPresent 13: [ OK ] StringUtilityTest.StripSuffixIfPresent (0 ms) 13: [ RUN ] StringUtilityTest.StripString 13: [ OK ] StringUtilityTest.StripString (0 ms) 13: [ RUN ] StringUtilityTest.SplitString 13: [ OK ] StringUtilityTest.SplitString (0 ms) 13: [ RUN ] StringUtilityTest.SplitDelimitedString 13: [ OK ] StringUtilityTest.SplitDelimitedString (0 ms) 13: [ RUN ] StringUtilityTest.SplitAndTrimDelimitedString 13: [ OK ] StringUtilityTest.SplitAndTrimDelimitedString (0 ms) 13: [ RUN ] StringUtilityTest.CanCompareCaseInsensitive 13: [ OK ] StringUtilityTest.CanCompareCaseInsensitive (0 ms) 13: [ RUN ] StringUtilityTest.CanCompareCaseInsensitiveInLength 13: [ OK ] StringUtilityTest.CanCompareCaseInsensitiveInLength (0 ms) 13: [----------] 9 tests from StringUtilityTest (0 ms total) 13: 13: [----------] 2 tests from FormatStringTest 13: [ RUN ] FormatStringTest.HandlesBasicFormatting 13: [ OK ] FormatStringTest.HandlesBasicFormatting (0 ms) 13: [ RUN ] FormatStringTest.HandlesLongStrings 13: [ OK ] FormatStringTest.HandlesLongStrings (0 ms) 13: [----------] 2 tests from FormatStringTest (0 ms total) 13: 13: [----------] 1 test from StringFormatterTest 13: [ RUN ] StringFormatterTest.HandlesBasicFormatting 13: [ OK ] StringFormatterTest.HandlesBasicFormatting (0 ms) 13: [----------] 1 test from StringFormatterTest (0 ms total) 13: 13: [----------] 1 test from formatAndJoinTest 13: [ RUN ] formatAndJoinTest.Works 13: [ OK ] formatAndJoinTest.Works (0 ms) 13: [----------] 1 test from formatAndJoinTest (0 ms total) 13: 13: [----------] 1 test from JoinStringsTest 13: [ RUN ] JoinStringsTest.Works 13: [ OK ] JoinStringsTest.Works (0 ms) 13: [----------] 1 test from JoinStringsTest (0 ms total) 13: 13: [----------] 6 tests from ReplaceAllTest 13: [ RUN ] ReplaceAllTest.HandlesEmptyStrings 13: [ OK ] ReplaceAllTest.HandlesEmptyStrings (0 ms) 13: [ RUN ] ReplaceAllTest.HandlesNoMatches 13: [ OK ] ReplaceAllTest.HandlesNoMatches (0 ms) 13: [ RUN ] ReplaceAllTest.HandlesMatchesAtEnds 13: [ OK ] ReplaceAllTest.HandlesMatchesAtEnds (0 ms) 13: [ RUN ] ReplaceAllTest.HandlesMultipleMatches 13: [ OK ] ReplaceAllTest.HandlesMultipleMatches (0 ms) 13: [ RUN ] ReplaceAllTest.HandlesWordBoundaries 13: [ OK ] ReplaceAllTest.HandlesWordBoundaries (0 ms) 13: [ RUN ] ReplaceAllTest.HandlesPossibleRecursiveMatches 13: [ OK ] ReplaceAllTest.HandlesPossibleRecursiveMatches (0 ms) 13: [----------] 6 tests from ReplaceAllTest (0 ms total) 13: 13: [----------] 10 tests from TextLineWrapperTest 13: [ RUN ] TextLineWrapperTest.HandlesEmptyStrings 13: [ OK ] TextLineWrapperTest.HandlesEmptyStrings (0 ms) 13: [ RUN ] TextLineWrapperTest.HandlesTrailingWhitespace 13: [ OK ] TextLineWrapperTest.HandlesTrailingWhitespace (0 ms) 13: [ RUN ] TextLineWrapperTest.HandlesTrailingNewlines 13: [ OK ] TextLineWrapperTest.HandlesTrailingNewlines (0 ms) 13: [ RUN ] TextLineWrapperTest.WrapsCorrectly 13: [ OK ] TextLineWrapperTest.WrapsCorrectly (4 ms) 13: [ RUN ] TextLineWrapperTest.WrapsCorrectlyWithExistingBreaks 13: [ OK ] TextLineWrapperTest.WrapsCorrectlyWithExistingBreaks (0 ms) 13: [ RUN ] TextLineWrapperTest.HandlesIndent 13: [ OK ] TextLineWrapperTest.HandlesIndent (0 ms) 13: [ RUN ] TextLineWrapperTest.HandlesIndentWithEmptyLines 13: [ OK ] TextLineWrapperTest.HandlesIndentWithEmptyLines (8 ms) 13: [ RUN ] TextLineWrapperTest.HandlesHangingIndent 13: [ OK ] TextLineWrapperTest.HandlesHangingIndent (3 ms) 13: [ RUN ] TextLineWrapperTest.HandlesContinuationCharacter 13: [ OK ] TextLineWrapperTest.HandlesContinuationCharacter (0 ms) 13: [ RUN ] TextLineWrapperTest.WrapsCorrectlyWithExtraWhitespace 13: [ OK ] TextLineWrapperTest.WrapsCorrectlyWithExtraWhitespace (3 ms) 13: [----------] 10 tests from TextLineWrapperTest (23 ms total) 13: 13: [----------] 1 test from CompileTimeStringJoin 13: [ RUN ] CompileTimeStringJoin.Works 13: [ OK ] CompileTimeStringJoin.Works (0 ms) 13: [----------] 1 test from CompileTimeStringJoin (0 ms total) 13: 13: [----------] 3 tests from TemplateMPTest 13: [ RUN ] TemplateMPTest.DispatchTemplatedFunctionEnum 13: [ OK ] TemplateMPTest.DispatchTemplatedFunctionEnum (0 ms) 13: [ RUN ] TemplateMPTest.DispatchTemplatedFunctionBool 13: [ OK ] TemplateMPTest.DispatchTemplatedFunctionBool (0 ms) 13: [ RUN ] TemplateMPTest.DispatchTemplatedFunctionEnumBool 13: [ OK ] TemplateMPTest.DispatchTemplatedFunctionEnumBool (0 ms) 13: [----------] 3 tests from TemplateMPTest (0 ms total) 13: 13: [----------] 6 tests from TextWriterTest 13: [ RUN ] TextWriterTest.WritesLines 13: [ OK ] TextWriterTest.WritesLines (0 ms) 13: [ RUN ] TextWriterTest.WritesLinesInParts 13: [ OK ] TextWriterTest.WritesLinesInParts (0 ms) 13: [ RUN ] TextWriterTest.WritesWrappedLines 13: [ OK ] TextWriterTest.WritesWrappedLines (0 ms) 13: [ RUN ] TextWriterTest.WritesLinesInPartsWithWrapper 13: [ OK ] TextWriterTest.WritesLinesInPartsWithWrapper (0 ms) 13: [ RUN ] TextWriterTest.TracksNewlines 13: [ OK ] TextWriterTest.TracksNewlines (0 ms) 13: [ RUN ] TextWriterTest.PreservesTrailingWhitespace 13: [ OK ] TextWriterTest.PreservesTrailingWhitespace (2 ms) 13: [----------] 6 tests from TextWriterTest (5 ms total) 13: 13: [----------] 1 test from TypeTraitsTest 13: [ RUN ] TypeTraitsTest.IsIntegralConstant 13: [ OK ] TypeTraitsTest.IsIntegralConstant (0 ms) 13: [----------] 1 test from TypeTraitsTest (0 ms total) 13: 13: [----------] 6 tests from BitmaskTest32_11/BitmaskTest32 13: [ RUN ] BitmaskTest32_11/BitmaskTest32.SetAndClear/0 13: [ OK ] BitmaskTest32_11/BitmaskTest32.SetAndClear/0 (0 ms) 13: [ RUN ] BitmaskTest32_11/BitmaskTest32.InitBit/0 13: [ OK ] BitmaskTest32_11/BitmaskTest32.InitBit/0 (0 ms) 13: [ RUN ] BitmaskTest32_11/BitmaskTest32.InitLowBits/0 13: [ OK ] BitmaskTest32_11/BitmaskTest32.InitLowBits/0 (0 ms) 13: [ RUN ] BitmaskTest32_11/BitmaskTest32.Disjoint/0 13: [ OK ] BitmaskTest32_11/BitmaskTest32.Disjoint/0 (0 ms) 13: [ RUN ] BitmaskTest32_11/BitmaskTest32.Union/0 13: [ OK ] BitmaskTest32_11/BitmaskTest32.Union/0 (0 ms) 13: [ RUN ] BitmaskTest32_11/BitmaskTest32.ToHex/0 13: [ OK ] BitmaskTest32_11/BitmaskTest32.ToHex/0 (0 ms) 13: [----------] 6 tests from BitmaskTest32_11/BitmaskTest32 (0 ms total) 13: 13: [----------] 12 tests from BitmaskTest64_10_42/BitmaskTest64 13: [ RUN ] BitmaskTest64_10_42/BitmaskTest64.SetAndClear/0 13: [ OK ] BitmaskTest64_10_42/BitmaskTest64.SetAndClear/0 (0 ms) 13: [ RUN ] BitmaskTest64_10_42/BitmaskTest64.SetAndClear/1 13: [ OK ] BitmaskTest64_10_42/BitmaskTest64.SetAndClear/1 (0 ms) 13: [ RUN ] BitmaskTest64_10_42/BitmaskTest64.InitBit/0 13: [ OK ] BitmaskTest64_10_42/BitmaskTest64.InitBit/0 (0 ms) 13: [ RUN ] BitmaskTest64_10_42/BitmaskTest64.InitBit/1 13: [ OK ] BitmaskTest64_10_42/BitmaskTest64.InitBit/1 (0 ms) 13: [ RUN ] BitmaskTest64_10_42/BitmaskTest64.InitLowBits/0 13: [ OK ] BitmaskTest64_10_42/BitmaskTest64.InitLowBits/0 (0 ms) 13: [ RUN ] BitmaskTest64_10_42/BitmaskTest64.InitLowBits/1 13: [ OK ] BitmaskTest64_10_42/BitmaskTest64.InitLowBits/1 (0 ms) 13: [ RUN ] BitmaskTest64_10_42/BitmaskTest64.Disjoint/0 13: [ OK ] BitmaskTest64_10_42/BitmaskTest64.Disjoint/0 (0 ms) 13: [ RUN ] BitmaskTest64_10_42/BitmaskTest64.Disjoint/1 13: [ OK ] BitmaskTest64_10_42/BitmaskTest64.Disjoint/1 (0 ms) 13: [ RUN ] BitmaskTest64_10_42/BitmaskTest64.Union/0 13: [ OK ] BitmaskTest64_10_42/BitmaskTest64.Union/0 (0 ms) 13: [ RUN ] BitmaskTest64_10_42/BitmaskTest64.Union/1 13: [ OK ] BitmaskTest64_10_42/BitmaskTest64.Union/1 (0 ms) 13: [ RUN ] BitmaskTest64_10_42/BitmaskTest64.ToHex/0 13: [ OK ] BitmaskTest64_10_42/BitmaskTest64.ToHex/0 (0 ms) 13: [ RUN ] BitmaskTest64_10_42/BitmaskTest64.ToHex/1 13: [ OK ] BitmaskTest64_10_42/BitmaskTest64.ToHex/1 (0 ms) 13: [----------] 12 tests from BitmaskTest64_10_42/BitmaskTest64 (0 ms total) 13: 13: [----------] 12 tests from BitmaskTest128_9_78/BitmaskTest128 13: [ RUN ] BitmaskTest128_9_78/BitmaskTest128.SetAndClear/0 13: [ OK ] BitmaskTest128_9_78/BitmaskTest128.SetAndClear/0 (0 ms) 13: [ RUN ] BitmaskTest128_9_78/BitmaskTest128.SetAndClear/1 13: [ OK ] BitmaskTest128_9_78/BitmaskTest128.SetAndClear/1 (0 ms) 13: [ RUN ] BitmaskTest128_9_78/BitmaskTest128.InitBit/0 13: [ OK ] BitmaskTest128_9_78/BitmaskTest128.InitBit/0 (0 ms) 13: [ RUN ] BitmaskTest128_9_78/BitmaskTest128.InitBit/1 13: [ OK ] BitmaskTest128_9_78/BitmaskTest128.InitBit/1 (0 ms) 13: [ RUN ] BitmaskTest128_9_78/BitmaskTest128.InitLowBits/0 13: [ OK ] BitmaskTest128_9_78/BitmaskTest128.InitLowBits/0 (0 ms) 13: [ RUN ] BitmaskTest128_9_78/BitmaskTest128.InitLowBits/1 13: [ OK ] BitmaskTest128_9_78/BitmaskTest128.InitLowBits/1 (0 ms) 13: [ RUN ] BitmaskTest128_9_78/BitmaskTest128.Disjoint/0 13: [ OK ] BitmaskTest128_9_78/BitmaskTest128.Disjoint/0 (0 ms) 13: [ RUN ] BitmaskTest128_9_78/BitmaskTest128.Disjoint/1 13: [ OK ] BitmaskTest128_9_78/BitmaskTest128.Disjoint/1 (0 ms) 13: [ RUN ] BitmaskTest128_9_78/BitmaskTest128.Union/0 13: [ OK ] BitmaskTest128_9_78/BitmaskTest128.Union/0 (0 ms) 13: [ RUN ] BitmaskTest128_9_78/BitmaskTest128.Union/1 13: [ OK ] BitmaskTest128_9_78/BitmaskTest128.Union/1 (0 ms) 13: [ RUN ] BitmaskTest128_9_78/BitmaskTest128.ToHex/0 13: [ OK ] BitmaskTest128_9_78/BitmaskTest128.ToHex/0 (0 ms) 13: [ RUN ] BitmaskTest128_9_78/BitmaskTest128.ToHex/1 13: [ OK ] BitmaskTest128_9_78/BitmaskTest128.ToHex/1 (0 ms) 13: [----------] 12 tests from BitmaskTest128_9_78/BitmaskTest128 (0 ms total) 13: 13: [----------] 11 tests from WithInputPaths/PathSearchTest 13: [ RUN ] WithInputPaths/PathSearchTest.SearchOperationsWork/0 13: [ OK ] WithInputPaths/PathSearchTest.SearchOperationsWork/0 (5 ms) 13: [ RUN ] WithInputPaths/PathSearchTest.SearchOperationsWork/1 13: [ OK ] WithInputPaths/PathSearchTest.SearchOperationsWork/1 (0 ms) 13: [ RUN ] WithInputPaths/PathSearchTest.SearchOperationsWork/2 13: [ OK ] WithInputPaths/PathSearchTest.SearchOperationsWork/2 (0 ms) 13: [ RUN ] WithInputPaths/PathSearchTest.SearchOperationsWork/3 13: [ OK ] WithInputPaths/PathSearchTest.SearchOperationsWork/3 (2 ms) 13: [ RUN ] WithInputPaths/PathSearchTest.SearchOperationsWork/4 13: [ OK ] WithInputPaths/PathSearchTest.SearchOperationsWork/4 (1 ms) 13: [ RUN ] WithInputPaths/PathSearchTest.SearchOperationsWork/5 13: [ OK ] WithInputPaths/PathSearchTest.SearchOperationsWork/5 (0 ms) 13: [ RUN ] WithInputPaths/PathSearchTest.SearchOperationsWork/6 13: [ OK ] WithInputPaths/PathSearchTest.SearchOperationsWork/6 (0 ms) 13: [ RUN ] WithInputPaths/PathSearchTest.SearchOperationsWork/7 13: [ OK ] WithInputPaths/PathSearchTest.SearchOperationsWork/7 (0 ms) 13: [ RUN ] WithInputPaths/PathSearchTest.SearchOperationsWork/8 13: [ OK ] WithInputPaths/PathSearchTest.SearchOperationsWork/8 (0 ms) 13: [ RUN ] WithInputPaths/PathSearchTest.SearchOperationsWork/9 13: [ OK ] WithInputPaths/PathSearchTest.SearchOperationsWork/9 (0 ms) 13: [ RUN ] WithInputPaths/PathSearchTest.SearchOperationsWork/10 13: [ OK ] WithInputPaths/PathSearchTest.SearchOperationsWork/10 (0 ms) 13: [----------] 11 tests from WithInputPaths/PathSearchTest (14 ms total) 13: 13: [----------] 7 tests from ParsesLinesDifferently/TextReaderTest 13: [ RUN ] ParsesLinesDifferently/TextReaderTest.UsingDifferentConfigurations/0 13: [ OK ] ParsesLinesDifferently/TextReaderTest.UsingDifferentConfigurations/0 (0 ms) 13: [ RUN ] ParsesLinesDifferently/TextReaderTest.UsingDifferentConfigurations/1 13: [ OK ] ParsesLinesDifferently/TextReaderTest.UsingDifferentConfigurations/1 (0 ms) 13: [ RUN ] ParsesLinesDifferently/TextReaderTest.UsingDifferentConfigurations/2 13: [ OK ] ParsesLinesDifferently/TextReaderTest.UsingDifferentConfigurations/2 (0 ms) 13: [ RUN ] ParsesLinesDifferently/TextReaderTest.UsingDifferentConfigurations/3 13: [ OK ] ParsesLinesDifferently/TextReaderTest.UsingDifferentConfigurations/3 (0 ms) 13: [ RUN ] ParsesLinesDifferently/TextReaderTest.UsingDifferentConfigurations/4 13: [ OK ] ParsesLinesDifferently/TextReaderTest.UsingDifferentConfigurations/4 (0 ms) 13: [ RUN ] ParsesLinesDifferently/TextReaderTest.UsingDifferentConfigurations/5 13: [ OK ] ParsesLinesDifferently/TextReaderTest.UsingDifferentConfigurations/5 (0 ms) 13: [ RUN ] ParsesLinesDifferently/TextReaderTest.UsingDifferentConfigurations/6 13: [ OK ] ParsesLinesDifferently/TextReaderTest.UsingDifferentConfigurations/6 (0 ms) 13: [----------] 7 tests from ParsesLinesDifferently/TextReaderTest (0 ms total) 13: 13: [----------] Global test environment tear-down 13: [==========] 420 tests from 65 test suites ran. (89 ms total) 13: [ PASSED ] 420 tests. 13: 13: YOU HAVE 1 DISABLED TEST 13: 13/92 Test #13: UtilityUnitTests .......................... Passed 0.24 sec test 14 Start 14: UtilityMpiUnitTests 14: Test command: /build/reproducible-path/gromacs-2025.1/build/basic/bin/utility-mpi-test "-ntmpi" "2" "--gtest_output=xml:/build/reproducible-path/gromacs-2025.1/build/basic/Testing/Temporary/UtilityMpiUnitTests.xml" 14: Working Directory: /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/utility/tests 14: Test timeout computed to be: 30 14: [==========] Running 2 tests from 1 test suite. 14: [----------] Global test environment set-up. 14: [----------] 2 tests from PhysicalNodeCommunicatorTest 14: [ RUN ] PhysicalNodeCommunicatorTest.CanConstruct 14: [ OK ] PhysicalNodeCommunicatorTest.CanConstruct (2 ms) 14: [ RUN ] PhysicalNodeCommunicatorTest.CanCallBarrier 14: [ OK ] PhysicalNodeCommunicatorTest.CanCallBarrier (5 ms) 14: [----------] 2 tests from PhysicalNodeCommunicatorTest (8 ms total) 14: 14: [----------] Global test environment tear-down 14: [==========] 2 tests from 1 test suite ran. (8 ms total) 14: [ PASSED ] 2 tests. 14/92 Test #14: UtilityMpiUnitTests ....................... Passed 0.08 sec test 15 Start 15: GmxlibTests 15: Test command: /build/reproducible-path/gromacs-2025.1/build/basic/bin/nonbonded-fep-test "--gtest_output=xml:/build/reproducible-path/gromacs-2025.1/build/basic/Testing/Temporary/GmxlibTests.xml" 15: Working Directory: /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/gmxlib/nonbonded/tests 15: Test timeout computed to be: 30 15: [==========] Running 78 tests from 2 test suites. 15: [----------] Global test environment set-up. 15: [----------] 72 tests from NBInteraction/NonbondedFepTest 15: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/0 15: [ OK ] NBInteraction/NonbondedFepTest.testKernel/0 (2 ms) 15: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/1 15: [ OK ] NBInteraction/NonbondedFepTest.testKernel/1 (1 ms) 15: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/2 15: [ OK ] NBInteraction/NonbondedFepTest.testKernel/2 (1 ms) 15: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/3 15: [ OK ] NBInteraction/NonbondedFepTest.testKernel/3 (1 ms) 15: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/4 15: [ OK ] NBInteraction/NonbondedFepTest.testKernel/4 (1 ms) 15: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/5 15: [ OK ] NBInteraction/NonbondedFepTest.testKernel/5 (1 ms) 15: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/6 15: [ OK ] NBInteraction/NonbondedFepTest.testKernel/6 (1 ms) 15: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/7 15: [ OK ] NBInteraction/NonbondedFepTest.testKernel/7 (1 ms) 15: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/8 15: [ OK ] NBInteraction/NonbondedFepTest.testKernel/8 (1 ms) 15: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/9 15: [ OK ] NBInteraction/NonbondedFepTest.testKernel/9 (1 ms) 15: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/10 15: [ OK ] NBInteraction/NonbondedFepTest.testKernel/10 (1 ms) 15: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/11 15: [ OK ] NBInteraction/NonbondedFepTest.testKernel/11 (1 ms) 15: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/12 15: [ OK ] NBInteraction/NonbondedFepTest.testKernel/12 (1 ms) 15: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/13 15: [ OK ] NBInteraction/NonbondedFepTest.testKernel/13 (0 ms) 15: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/14 15: [ OK ] NBInteraction/NonbondedFepTest.testKernel/14 (0 ms) 15: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/15 15: [ OK ] NBInteraction/NonbondedFepTest.testKernel/15 (0 ms) 15: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/16 15: [ OK ] NBInteraction/NonbondedFepTest.testKernel/16 (0 ms) 15: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/17 15: [ OK ] NBInteraction/NonbondedFepTest.testKernel/17 (0 ms) 15: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/18 15: [ OK ] NBInteraction/NonbondedFepTest.testKernel/18 (0 ms) 15: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/19 15: [ OK ] NBInteraction/NonbondedFepTest.testKernel/19 (0 ms) 15: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/20 15: [ OK ] NBInteraction/NonbondedFepTest.testKernel/20 (0 ms) 15: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/21 15: [ OK ] NBInteraction/NonbondedFepTest.testKernel/21 (0 ms) 15: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/22 15: [ OK ] NBInteraction/NonbondedFepTest.testKernel/22 (0 ms) 15: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/23 15: [ OK ] NBInteraction/NonbondedFepTest.testKernel/23 (0 ms) 15: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/24 15: [ OK ] NBInteraction/NonbondedFepTest.testKernel/24 (3 ms) 15: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/25 15: [ OK ] NBInteraction/NonbondedFepTest.testKernel/25 (1 ms) 15: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/26 15: [ OK ] NBInteraction/NonbondedFepTest.testKernel/26 (1 ms) 15: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/27 15: [ OK ] NBInteraction/NonbondedFepTest.testKernel/27 (1 ms) 15: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/28 15: [ OK ] NBInteraction/NonbondedFepTest.testKernel/28 (1 ms) 15: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/29 15: [ OK ] NBInteraction/NonbondedFepTest.testKernel/29 (1 ms) 15: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/30 15: [ OK ] NBInteraction/NonbondedFepTest.testKernel/30 (1 ms) 15: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/31 15: [ OK ] NBInteraction/NonbondedFepTest.testKernel/31 (1 ms) 15: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/32 15: [ OK ] NBInteraction/NonbondedFepTest.testKernel/32 (1 ms) 15: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/33 15: [ OK ] NBInteraction/NonbondedFepTest.testKernel/33 (1 ms) 15: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/34 15: [ OK ] NBInteraction/NonbondedFepTest.testKernel/34 (1 ms) 15: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/35 15: [ OK ] NBInteraction/NonbondedFepTest.testKernel/35 (1 ms) 15: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/36 15: [ OK ] NBInteraction/NonbondedFepTest.testKernel/36 (1 ms) 15: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/37 15: [ OK ] NBInteraction/NonbondedFepTest.testKernel/37 (1 ms) 15: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/38 15: [ OK ] NBInteraction/NonbondedFepTest.testKernel/38 (0 ms) 15: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/39 15: [ OK ] NBInteraction/NonbondedFepTest.testKernel/39 (1 ms) 15: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/40 15: [ OK ] NBInteraction/NonbondedFepTest.testKernel/40 (0 ms) 15: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/41 15: [ OK ] NBInteraction/NonbondedFepTest.testKernel/41 (0 ms) 15: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/42 15: [ OK ] NBInteraction/NonbondedFepTest.testKernel/42 (0 ms) 15: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/43 15: [ OK ] NBInteraction/NonbondedFepTest.testKernel/43 (1 ms) 15: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/44 15: [ OK ] NBInteraction/NonbondedFepTest.testKernel/44 (0 ms) 15: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/45 15: [ OK ] NBInteraction/NonbondedFepTest.testKernel/45 (1 ms) 15: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/46 15: [ OK ] NBInteraction/NonbondedFepTest.testKernel/46 (7 ms) 15: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/47 15: [ OK ] NBInteraction/NonbondedFepTest.testKernel/47 (1 ms) 15: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/48 15: [ OK ] NBInteraction/NonbondedFepTest.testKernel/48 (0 ms) 15: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/49 15: [ OK ] NBInteraction/NonbondedFepTest.testKernel/49 (0 ms) 15: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/50 15: [ OK ] NBInteraction/NonbondedFepTest.testKernel/50 (1 ms) 15: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/51 15: [ OK ] NBInteraction/NonbondedFepTest.testKernel/51 (1 ms) 15: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/52 15: [ OK ] NBInteraction/NonbondedFepTest.testKernel/52 (1 ms) 15: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/53 15: [ OK ] NBInteraction/NonbondedFepTest.testKernel/53 (1 ms) 15: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/54 15: [ OK ] NBInteraction/NonbondedFepTest.testKernel/54 (1 ms) 15: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/55 15: [ OK ] NBInteraction/NonbondedFepTest.testKernel/55 (1 ms) 15: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/56 15: [ OK ] NBInteraction/NonbondedFepTest.testKernel/56 (0 ms) 15: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/57 15: [ OK ] NBInteraction/NonbondedFepTest.testKernel/57 (1 ms) 15: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/58 15: [ OK ] NBInteraction/NonbondedFepTest.testKernel/58 (0 ms) 15: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/59 15: [ OK ] NBInteraction/NonbondedFepTest.testKernel/59 (0 ms) 15: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/60 15: [ OK ] NBInteraction/NonbondedFepTest.testKernel/60 (1 ms) 15: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/61 15: [ OK ] NBInteraction/NonbondedFepTest.testKernel/61 (1 ms) 15: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/62 15: [ OK ] NBInteraction/NonbondedFepTest.testKernel/62 (1 ms) 15: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/63 15: [ OK ] NBInteraction/NonbondedFepTest.testKernel/63 (1 ms) 15: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/64 15: [ OK ] NBInteraction/NonbondedFepTest.testKernel/64 (1 ms) 15: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/65 15: [ OK ] NBInteraction/NonbondedFepTest.testKernel/65 (1 ms) 15: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/66 15: [ OK ] NBInteraction/NonbondedFepTest.testKernel/66 (1 ms) 15: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/67 15: [ OK ] NBInteraction/NonbondedFepTest.testKernel/67 (1 ms) 15: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/68 15: [ OK ] NBInteraction/NonbondedFepTest.testKernel/68 (1 ms) 15: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/69 15: [ OK ] NBInteraction/NonbondedFepTest.testKernel/69 (1 ms) 15: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/70 15: [ OK ] NBInteraction/NonbondedFepTest.testKernel/70 (1 ms) 15: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/71 15: [ OK ] NBInteraction/NonbondedFepTest.testKernel/71 (1 ms) 15: [----------] 72 tests from NBInteraction/NonbondedFepTest (104 ms total) 15: 15: [----------] 6 tests from NBInteractionShortDistance/NonbondedFepTest 15: [ RUN ] NBInteractionShortDistance/NonbondedFepTest.testKernel/0 15: [ OK ] NBInteractionShortDistance/NonbondedFepTest.testKernel/0 (0 ms) 15: [ RUN ] NBInteractionShortDistance/NonbondedFepTest.testKernel/1 15: [ OK ] NBInteractionShortDistance/NonbondedFepTest.testKernel/1 (0 ms) 15: [ RUN ] NBInteractionShortDistance/NonbondedFepTest.testKernel/2 15: [ OK ] NBInteractionShortDistance/NonbondedFepTest.testKernel/2 (1 ms) 15: [ RUN ] NBInteractionShortDistance/NonbondedFepTest.testKernel/3 15: [ OK ] NBInteractionShortDistance/NonbondedFepTest.testKernel/3 (0 ms) 15: [ RUN ] NBInteractionShortDistance/NonbondedFepTest.testKernel/4 15: [ OK ] NBInteractionShortDistance/NonbondedFepTest.testKernel/4 (0 ms) 15: [ RUN ] NBInteractionShortDistance/NonbondedFepTest.testKernel/5 15: [ OK ] NBInteractionShortDistance/NonbondedFepTest.testKernel/5 (1 ms) 15: [----------] 6 tests from NBInteractionShortDistance/NonbondedFepTest (6 ms total) 15: 15: [----------] Global test environment tear-down 15: [==========] 78 tests from 2 test suites ran. (111 ms total) 15: [ PASSED ] 78 tests. 15/92 Test #15: GmxlibTests ............................... Passed 0.26 sec test 16 Start 16: MdlibUnitTest 16: Test command: /build/reproducible-path/gromacs-2025.1/build/basic/bin/mdlib-test "--gtest_output=xml:/build/reproducible-path/gromacs-2025.1/build/basic/Testing/Temporary/MdlibUnitTest.xml" 16: Working Directory: /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/mdlib/tests 16: Test timeout computed to be: 30 16: [==========] Running 1032 tests from 27 test suites. 16: [----------] Global test environment set-up. 16: [----------] 3 tests from EffectiveAtomDensity 16: [ RUN ] EffectiveAtomDensity.VolumeIndependence 16: [ OK ] EffectiveAtomDensity.VolumeIndependence (0 ms) 16: [ RUN ] EffectiveAtomDensity.WeightingWorks 16: [ OK ] EffectiveAtomDensity.WeightingWorks (0 ms) 16: [ RUN ] EffectiveAtomDensity.LargeValuesHandledWell 16: [ OK ] EffectiveAtomDensity.LargeValuesHandledWell (0 ms) 16: [----------] 3 tests from EffectiveAtomDensity (0 ms total) 16: 16: [----------] 2 tests from AtomNonbondedAndKineticProperties 16: [ RUN ] AtomNonbondedAndKineticProperties.IsAccurate 16: [ OK ] AtomNonbondedAndKineticProperties.IsAccurate (0 ms) 16: [ RUN ] AtomNonbondedAndKineticProperties.ConstraintsWork 16: [ OK ] AtomNonbondedAndKineticProperties.ConstraintsWork (0 ms) 16: [----------] 2 tests from AtomNonbondedAndKineticProperties (0 ms total) 16: 16: [----------] 1 test from VerletBufferConstraintTest 16: [ RUN ] VerletBufferConstraintTest.EqualMasses 16: [ OK ] VerletBufferConstraintTest.EqualMasses (0 ms) 16: [----------] 1 test from VerletBufferConstraintTest (0 ms total) 16: 16: [----------] 1 test from VerletBufferSize 16: [ RUN ] VerletBufferSize.SizeAboveFourIsEquivalent 16: [ OK ] VerletBufferSize.SizeAboveFourIsEquivalent (1 ms) 16: [----------] 1 test from VerletBufferSize (1 ms total) 16: 16: [----------] 6 tests from CalcvirTest 16: [ RUN ] CalcvirTest.CanCalculateVirialAllAtomsInBox 16: [ OK ] CalcvirTest.CanCalculateVirialAllAtomsInBox (7 ms) 16: [ RUN ] CalcvirTest.CanCalculateVirialAllAtomsInBoxScrew 16: [ OK ] CalcvirTest.CanCalculateVirialAllAtomsInBoxScrew (0 ms) 16: [ RUN ] CalcvirTest.CanCalculateVirialAtomsOutOfBoxScrewX 16: [ OK ] CalcvirTest.CanCalculateVirialAtomsOutOfBoxScrewX (1 ms) 16: [ RUN ] CalcvirTest.CanCalculateVirialAtomsOutOfBoxScrewY 16: [ OK ] CalcvirTest.CanCalculateVirialAtomsOutOfBoxScrewY (1 ms) 16: [ RUN ] CalcvirTest.CanCalculateVirialAtomsOutOfBoxScrewZ 16: [ OK ] CalcvirTest.CanCalculateVirialAtomsOutOfBoxScrewZ (1 ms) 16: [ RUN ] CalcvirTest.CanCalculateVirialAtomsOutOfBoxScrewXYZ 16: [ OK ] CalcvirTest.CanCalculateVirialAtomsOutOfBoxScrewXYZ (0 ms) 16: [----------] 6 tests from CalcvirTest (13 ms total) 16: 16: [----------] 2 tests from PrEbinTest 16: [ RUN ] PrEbinTest.HandlesAverages 16: [ OK ] PrEbinTest.HandlesAverages (2 ms) 16: [ RUN ] PrEbinTest.HandlesEmptyAverages 16: [ OK ] PrEbinTest.HandlesEmptyAverages (2 ms) 16: [----------] 2 tests from PrEbinTest (4 ms total) 16: 16: [----------] 3 tests from EnergyDriftTracker 16: [ RUN ] EnergyDriftTracker.emptyWorks 16: [ OK ] EnergyDriftTracker.emptyWorks (0 ms) 16: [ RUN ] EnergyDriftTracker.onePointWorks 16: [ OK ] EnergyDriftTracker.onePointWorks (0 ms) 16: [ RUN ] EnergyDriftTracker.manyPointsWorks 16: [ OK ] EnergyDriftTracker.manyPointsWorks (0 ms) 16: [----------] 3 tests from EnergyDriftTracker (0 ms total) 16: 16: [----------] 4 tests from ShakeTest 16: [ RUN ] ShakeTest.ConstrainsOneBond 16: [ OK ] ShakeTest.ConstrainsOneBond (0 ms) 16: [ RUN ] ShakeTest.ConstrainsTwoDisjointBonds 16: [ OK ] ShakeTest.ConstrainsTwoDisjointBonds (0 ms) 16: [ RUN ] ShakeTest.ConstrainsTwoBondsWithACommonAtom 16: [ OK ] ShakeTest.ConstrainsTwoBondsWithACommonAtom (0 ms) 16: [ RUN ] ShakeTest.ConstrainsThreeBondsWithCommonAtoms 16: [ OK ] ShakeTest.ConstrainsThreeBondsWithCommonAtoms (0 ms) 16: [----------] 4 tests from ShakeTest (0 ms total) 16: 16: [----------] 1 test from NullSignalTest 16: [ RUN ] NullSignalTest.NullSignallerWorks 16: [ OK ] NullSignalTest.NullSignallerWorks (0 ms) 16: [----------] 1 test from NullSignalTest (0 ms total) 16: 16: [----------] 7 tests from SignalTest 16: [ RUN ] SignalTest.NoSignalPropagatesIfNoSignallingTakesPlace 16: [ OK ] SignalTest.NoSignalPropagatesIfNoSignallingTakesPlace (0 ms) 16: [ RUN ] SignalTest.LocalIntraSimSignalPropagatesWhenIntraSimSignalTakesPlace 16: [ OK ] SignalTest.LocalIntraSimSignalPropagatesWhenIntraSimSignalTakesPlace (0 ms) 16: [ RUN ] SignalTest.LocalIntraSimSignalPropagatesWhenInterSimTakesPlace 16: [ OK ] SignalTest.LocalIntraSimSignalPropagatesWhenInterSimTakesPlace (0 ms) 16: [ RUN ] SignalTest.LocalIntraSimSignalPropagatesWhenBothTakePlace 16: [ OK ] SignalTest.LocalIntraSimSignalPropagatesWhenBothTakePlace (0 ms) 16: [ RUN ] SignalTest.NonLocalSignalDoesntPropagateWhenIntraSimSignalTakesPlace 16: [ OK ] SignalTest.NonLocalSignalDoesntPropagateWhenIntraSimSignalTakesPlace (0 ms) 16: [ RUN ] SignalTest.NonLocalSignalPropagatesWhenInterSimSignalTakesPlace 16: [ OK ] SignalTest.NonLocalSignalPropagatesWhenInterSimSignalTakesPlace (0 ms) 16: [ RUN ] SignalTest.NonLocalSignalPropagatesWhenBothTakePlace 16: [ OK ] SignalTest.NonLocalSignalPropagatesWhenBothTakePlace (0 ms) 16: [----------] 7 tests from SignalTest (0 ms total) 16: 16: [----------] 13 tests from UpdateGroupsTest 16: [ RUN ] UpdateGroupsTest.WithEthaneUA 16: [ OK ] UpdateGroupsTest.WithEthaneUA (0 ms) 16: [ RUN ] UpdateGroupsTest.WithMethane 16: [ OK ] UpdateGroupsTest.WithMethane (0 ms) 16: [ RUN ] UpdateGroupsTest.WithEthane 16: [ OK ] UpdateGroupsTest.WithEthane (0 ms) 16: [ RUN ] UpdateGroupsTest.CheckRadiusCalculationAtDifferentTemperaturesWithEthane 16: [ OK ] UpdateGroupsTest.CheckRadiusCalculationAtDifferentTemperaturesWithEthane (0 ms) 16: [ RUN ] UpdateGroupsTest.WithButaneUALogsThatUnsuitableForUpdateGroups 16: [ OK ] UpdateGroupsTest.WithButaneUALogsThatUnsuitableForUpdateGroups (0 ms) 16: [ RUN ] UpdateGroupsTest.WithWaterThreeSite 16: [ OK ] UpdateGroupsTest.WithWaterThreeSite (0 ms) 16: [ RUN ] UpdateGroupsTest.WithWaterFourSite 16: [ OK ] UpdateGroupsTest.WithWaterFourSite (0 ms) 16: [ RUN ] UpdateGroupsTest.WithFourAtomsWithSettle 16: [ OK ] UpdateGroupsTest.WithFourAtomsWithSettle (0 ms) 16: [ RUN ] UpdateGroupsTest.WithWaterFlexAngle 16: [ OK ] UpdateGroupsTest.WithWaterFlexAngle (0 ms) 16: [ RUN ] UpdateGroupsTest.CheckRadiusCalculationAtDifferentTemperaturesWithWaterFlexAngle 16: [ OK ] UpdateGroupsTest.CheckRadiusCalculationAtDifferentTemperaturesWithWaterFlexAngle (0 ms) 16: [ RUN ] UpdateGroupsTest.WithTwoMoltypes 16: [ OK ] UpdateGroupsTest.WithTwoMoltypes (0 ms) 16: [ RUN ] UpdateGroupsTest.LogsWhenSizesAreInvalid 16: [ OK ] UpdateGroupsTest.LogsWhenSizesAreInvalid (1 ms) 16: [ RUN ] UpdateGroupsTest.LogsWhenUpdateGroupsAreNotUseful 16: [ OK ] UpdateGroupsTest.LogsWhenUpdateGroupsAreNotUseful (0 ms) 16: [----------] 13 tests from UpdateGroupsTest (3 ms total) 16: 16: [----------] 1 test from UpdateGroupsCog 16: [ RUN ] UpdateGroupsCog.ComputesCogs 16: [ OK ] UpdateGroupsCog.ComputesCogs (3 ms) 16: [----------] 1 test from UpdateGroupsCog (4 ms total) 16: 16: [----------] 2 tests from WholeMoleculeTransform 16: [ RUN ] WholeMoleculeTransform.MakesMoleculesWhole 16: [ OK ] WholeMoleculeTransform.MakesMoleculesWhole (0 ms) 16: [ RUN ] WholeMoleculeTransform.HandlesReordering 16: [ OK ] WholeMoleculeTransform.HandlesReordering (0 ms) 16: [----------] 2 tests from WholeMoleculeTransform (0 ms total) 16: 16: [----------] 28 tests from WithParameters/ConstraintsTest 16: [ RUN ] WithParameters/ConstraintsTest.SatisfiesConstraints/0 16: [ OK ] WithParameters/ConstraintsTest.SatisfiesConstraints/0 (1 ms) 16: [ RUN ] WithParameters/ConstraintsTest.SatisfiesConstraints/1 16: [ OK ] WithParameters/ConstraintsTest.SatisfiesConstraints/1 (1 ms) 16: [ RUN ] WithParameters/ConstraintsTest.SatisfiesConstraints/2 16: [ OK ] WithParameters/ConstraintsTest.SatisfiesConstraints/2 (1 ms) 16: [ RUN ] WithParameters/ConstraintsTest.SatisfiesConstraints/3 16: [ OK ] WithParameters/ConstraintsTest.SatisfiesConstraints/3 (1 ms) 16: [ RUN ] WithParameters/ConstraintsTest.SatisfiesConstraints/4 16: [ OK ] WithParameters/ConstraintsTest.SatisfiesConstraints/4 (1 ms) 16: [ RUN ] WithParameters/ConstraintsTest.SatisfiesConstraints/5 16: [ OK ] WithParameters/ConstraintsTest.SatisfiesConstraints/5 (1 ms) 16: [ RUN ] WithParameters/ConstraintsTest.SatisfiesConstraints/6 16: [ OK ] WithParameters/ConstraintsTest.SatisfiesConstraints/6 (1 ms) 16: [ RUN ] WithParameters/ConstraintsTest.SatisfiesConstraints/7 16: [ OK ] WithParameters/ConstraintsTest.SatisfiesConstraints/7 (1 ms) 16: [ RUN ] WithParameters/ConstraintsTest.SatisfiesConstraints/8 16: [ OK ] WithParameters/ConstraintsTest.SatisfiesConstraints/8 (1 ms) 16: [ RUN ] WithParameters/ConstraintsTest.SatisfiesConstraints/9 16: [ OK ] WithParameters/ConstraintsTest.SatisfiesConstraints/9 (1 ms) 16: [ RUN ] WithParameters/ConstraintsTest.SatisfiesConstraints/10 16: [ OK ] WithParameters/ConstraintsTest.SatisfiesConstraints/10 (1 ms) 16: [ RUN ] WithParameters/ConstraintsTest.SatisfiesConstraints/11 16: [ OK ] WithParameters/ConstraintsTest.SatisfiesConstraints/11 (2 ms) 16: [ RUN ] WithParameters/ConstraintsTest.SatisfiesConstraints/12 16: [ OK ] WithParameters/ConstraintsTest.SatisfiesConstraints/12 (72 ms) 16: [ RUN ] WithParameters/ConstraintsTest.SatisfiesConstraints/13 16: [ OK ] WithParameters/ConstraintsTest.SatisfiesConstraints/13 (67 ms) 16: [ RUN ] WithParameters/ConstraintsTest.TriangleDetectionWorks/0 16: [ OK ] WithParameters/ConstraintsTest.TriangleDetectionWorks/0 (0 ms) 16: [ RUN ] WithParameters/ConstraintsTest.TriangleDetectionWorks/1 16: [ OK ] WithParameters/ConstraintsTest.TriangleDetectionWorks/1 (0 ms) 16: [ RUN ] WithParameters/ConstraintsTest.TriangleDetectionWorks/2 16: [ OK ] WithParameters/ConstraintsTest.TriangleDetectionWorks/2 (0 ms) 16: [ RUN ] WithParameters/ConstraintsTest.TriangleDetectionWorks/3 16: [ OK ] WithParameters/ConstraintsTest.TriangleDetectionWorks/3 (0 ms) 16: [ RUN ] WithParameters/ConstraintsTest.TriangleDetectionWorks/4 16: [ OK ] WithParameters/ConstraintsTest.TriangleDetectionWorks/4 (0 ms) 16: [ RUN ] WithParameters/ConstraintsTest.TriangleDetectionWorks/5 16: [ OK ] WithParameters/ConstraintsTest.TriangleDetectionWorks/5 (0 ms) 16: [ RUN ] WithParameters/ConstraintsTest.TriangleDetectionWorks/6 16: [ OK ] WithParameters/ConstraintsTest.TriangleDetectionWorks/6 (0 ms) 16: [ RUN ] WithParameters/ConstraintsTest.TriangleDetectionWorks/7 16: [ OK ] WithParameters/ConstraintsTest.TriangleDetectionWorks/7 (0 ms) 16: [ RUN ] WithParameters/ConstraintsTest.TriangleDetectionWorks/8 16: [ OK ] WithParameters/ConstraintsTest.TriangleDetectionWorks/8 (0 ms) 16: [ RUN ] WithParameters/ConstraintsTest.TriangleDetectionWorks/9 16: [ OK ] WithParameters/ConstraintsTest.TriangleDetectionWorks/9 (0 ms) 16: [ RUN ] WithParameters/ConstraintsTest.TriangleDetectionWorks/10 16: [ OK ] WithParameters/ConstraintsTest.TriangleDetectionWorks/10 (0 ms) 16: [ RUN ] WithParameters/ConstraintsTest.TriangleDetectionWorks/11 16: [ OK ] WithParameters/ConstraintsTest.TriangleDetectionWorks/11 (0 ms) 16: [ RUN ] WithParameters/ConstraintsTest.TriangleDetectionWorks/12 16: [ OK ] WithParameters/ConstraintsTest.TriangleDetectionWorks/12 (0 ms) 16: [ RUN ] WithParameters/ConstraintsTest.TriangleDetectionWorks/13 16: [ OK ] WithParameters/ConstraintsTest.TriangleDetectionWorks/13 (0 ms) 16: [----------] 28 tests from WithParameters/ConstraintsTest (179 ms total) 16: 16: [----------] 11 tests from WithParameters/EnergyOutputTest 16: [ RUN ] WithParameters/EnergyOutputTest.CheckOutput/0 16: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/mdlib/tests/Testing/Temporary/WithParameters_EnergyOutputTest_CheckOutput_0.edr as single precision energy file 16: Reading energy frame 0 time 10.100 [ OK ] WithParameters/EnergyOutputTest.CheckOutput/0 (11 ms) 16: [ RUN ] WithParameters/EnergyOutputTest.CheckOutput/1 16: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/mdlib/tests/Testing/Temporary/WithParameters_EnergyOutputTest_CheckOutput_1.edr as single precision energy file 16: Reading energy frame 0 time 10.100 [ OK ] WithParameters/EnergyOutputTest.CheckOutput/1 (6 ms) 16: [ RUN ] WithParameters/EnergyOutputTest.CheckOutput/2 16: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/mdlib/tests/Testing/Temporary/WithParameters_EnergyOutputTest_CheckOutput_2.edr as single precision energy file 16: Reading energy frame 0 time 10.100 [ OK ] WithParameters/EnergyOutputTest.CheckOutput/2 (9 ms) 16: [ RUN ] WithParameters/EnergyOutputTest.CheckOutput/3 16: [ OK ] WithParameters/EnergyOutputTest.CheckOutput/3 (2 ms) 16: [ RUN ] WithParameters/EnergyOutputTest.CheckOutput/4 16: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/mdlib/tests/Testing/Temporary/WithParameters_EnergyOutputTest_CheckOutput_4.edr as single precision energy file 16: Reading energy frame 0 time 10.100 Reading energy frame 1 time 27.500 Reading energy frame 2 time 44.900 Reading energy frame 3 time 62.300 Reading energy frame 4 time 79.700 Reading energy frame 5 time 97.100 Reading energy frame 6 time 114.500 Reading energy frame 7 time 131.900 Reading energy frame 8 time 149.300 Reading energy frame 9 time 166.700 [ OK ] WithParameters/EnergyOutputTest.CheckOutput/4 (39 ms) 16: [ RUN ] WithParameters/EnergyOutputTest.CheckOutput/5 16: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/mdlib/tests/Testing/Temporary/WithParameters_EnergyOutputTest_CheckOutput_5.edr as single precision energy file 16: Reading energy frame 0 time 10.100 [ OK ] WithParameters/EnergyOutputTest.CheckOutput/5 (10 ms) 16: [ RUN ] WithParameters/EnergyOutputTest.CheckOutput/6 16: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/mdlib/tests/Testing/Temporary/WithParameters_EnergyOutputTest_CheckOutput_6.edr as single precision energy file 16: Reading energy frame 0 time 10.100 [ OK ] WithParameters/EnergyOutputTest.CheckOutput/6 (10 ms) 16: [ RUN ] WithParameters/EnergyOutputTest.CheckOutput/7 16: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/mdlib/tests/Testing/Temporary/WithParameters_EnergyOutputTest_CheckOutput_7.edr as single precision energy file 16: Reading energy frame 0 time 10.100 [ OK ] WithParameters/EnergyOutputTest.CheckOutput/7 (10 ms) 16: [ RUN ] WithParameters/EnergyOutputTest.CheckOutput/8 16: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/mdlib/tests/Testing/Temporary/WithParameters_EnergyOutputTest_CheckOutput_8.edr as single precision energy file 16: Reading energy frame 0 time 10.100 [ OK ] WithParameters/EnergyOutputTest.CheckOutput/8 (10 ms) 16: [ RUN ] WithParameters/EnergyOutputTest.CheckOutput/9 16: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/mdlib/tests/Testing/Temporary/WithParameters_EnergyOutputTest_CheckOutput_9.edr as single precision energy file 16: Reading energy frame 0 time 10.100 [ OK ] WithParameters/EnergyOutputTest.CheckOutput/9 (9 ms) 16: [ RUN ] WithParameters/EnergyOutputTest.CheckOutput/10 16: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/mdlib/tests/Testing/Temporary/WithParameters_EnergyOutputTest_CheckOutput_10.edr as single precision energy file 16: Reading energy frame 0 time 10.100 [ OK ] WithParameters/EnergyOutputTest.CheckOutput/10 (10 ms) 16: [----------] 11 tests from WithParameters/EnergyOutputTest (148 ms total) 16: 16: [----------] 24 tests from SimpleTests/CalculateAcceptanceWeightSimple 16: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.UnknownCalculationModeThrows/0 16: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.UnknownCalculationModeThrows/0 (0 ms) 16: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.UnknownCalculationModeThrows/1 16: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.UnknownCalculationModeThrows/1 (0 ms) 16: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.UnknownCalculationModeThrows/2 16: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.UnknownCalculationModeThrows/2 (0 ms) 16: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.UnknownCalculationModeThrows/3 16: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.UnknownCalculationModeThrows/3 (0 ms) 16: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.UnknownCalculationModeThrows/4 16: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.UnknownCalculationModeThrows/4 (0 ms) 16: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.UnknownCalculationModeThrows/5 16: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.UnknownCalculationModeThrows/5 (0 ms) 16: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.UnknownCalculationModeThrows/6 16: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.UnknownCalculationModeThrows/6 (0 ms) 16: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.UnknownCalculationModeThrows/7 16: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.UnknownCalculationModeThrows/7 (0 ms) 16: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.KnownCalculationModeDoesNotThrow/0 16: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.KnownCalculationModeDoesNotThrow/0 (0 ms) 16: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.KnownCalculationModeDoesNotThrow/1 16: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.KnownCalculationModeDoesNotThrow/1 (0 ms) 16: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.KnownCalculationModeDoesNotThrow/2 16: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.KnownCalculationModeDoesNotThrow/2 (0 ms) 16: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.KnownCalculationModeDoesNotThrow/3 16: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.KnownCalculationModeDoesNotThrow/3 (0 ms) 16: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.KnownCalculationModeDoesNotThrow/4 16: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.KnownCalculationModeDoesNotThrow/4 (0 ms) 16: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.KnownCalculationModeDoesNotThrow/5 16: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.KnownCalculationModeDoesNotThrow/5 (0 ms) 16: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.KnownCalculationModeDoesNotThrow/6 16: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.KnownCalculationModeDoesNotThrow/6 (0 ms) 16: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.KnownCalculationModeDoesNotThrow/7 16: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.KnownCalculationModeDoesNotThrow/7 (0 ms) 16: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.BarkerAndMinVarAreIdentical/0 16: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.BarkerAndMinVarAreIdentical/0 (0 ms) 16: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.BarkerAndMinVarAreIdentical/1 16: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.BarkerAndMinVarAreIdentical/1 (0 ms) 16: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.BarkerAndMinVarAreIdentical/2 16: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.BarkerAndMinVarAreIdentical/2 (0 ms) 16: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.BarkerAndMinVarAreIdentical/3 16: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.BarkerAndMinVarAreIdentical/3 (0 ms) 16: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.BarkerAndMinVarAreIdentical/4 16: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.BarkerAndMinVarAreIdentical/4 (0 ms) 16: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.BarkerAndMinVarAreIdentical/5 16: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.BarkerAndMinVarAreIdentical/5 (0 ms) 16: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.BarkerAndMinVarAreIdentical/6 16: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.BarkerAndMinVarAreIdentical/6 (0 ms) 16: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.BarkerAndMinVarAreIdentical/7 16: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.BarkerAndMinVarAreIdentical/7 (0 ms) 16: [----------] 24 tests from SimpleTests/CalculateAcceptanceWeightSimple (2 ms total) 16: 16: [----------] 14 tests from RegressionTests/CalculateAcceptanceWeightRangeRegression 16: [ RUN ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/0 16: [ OK ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/0 (0 ms) 16: [ RUN ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/1 16: [ OK ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/1 (0 ms) 16: [ RUN ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/2 16: [ OK ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/2 (0 ms) 16: [ RUN ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/3 16: [ OK ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/3 (0 ms) 16: [ RUN ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/4 16: [ OK ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/4 (0 ms) 16: [ RUN ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/5 16: [ OK ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/5 (0 ms) 16: [ RUN ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/6 16: [ OK ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/6 (0 ms) 16: [ RUN ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/7 16: [ OK ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/7 (0 ms) 16: [ RUN ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/8 16: [ OK ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/8 (0 ms) 16: [ RUN ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/9 16: [ OK ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/9 (0 ms) 16: [ RUN ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/10 16: [ OK ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/10 (0 ms) 16: [ RUN ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/11 16: [ OK ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/11 (0 ms) 16: [ RUN ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/12 16: [ OK ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/12 (0 ms) 16: [ RUN ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/13 16: [ OK ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/13 (0 ms) 16: [----------] 14 tests from RegressionTests/CalculateAcceptanceWeightRangeRegression (0 ms total) 16: 16: [----------] 23 tests from WithParameters/FreeEnergyParameterTest 16: [ RUN ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/0 16: [ OK ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/0 (0 ms) 16: [ RUN ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/1 16: [ OK ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/1 (0 ms) 16: [ RUN ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/2 16: [ OK ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/2 (0 ms) 16: [ RUN ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/3 16: [ OK ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/3 (0 ms) 16: [ RUN ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/4 16: [ OK ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/4 (0 ms) 16: [ RUN ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/5 16: [ OK ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/5 (0 ms) 16: [ RUN ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/6 16: [ OK ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/6 (0 ms) 16: [ RUN ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/7 16: [ OK ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/7 (0 ms) 16: [ RUN ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/8 16: [ OK ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/8 (0 ms) 16: [ RUN ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/9 16: [ OK ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/9 (0 ms) 16: [ RUN ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/10 16: [ OK ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/10 (0 ms) 16: [ RUN ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/11 16: [ OK ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/11 (0 ms) 16: [ RUN ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/12 16: [ OK ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/12 (0 ms) 16: [ RUN ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/13 16: [ OK ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/13 (0 ms) 16: [ RUN ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/14 16: [ OK ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/14 (0 ms) 16: [ RUN ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/15 16: [ OK ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/15 (0 ms) 16: [ RUN ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/16 16: [ OK ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/16 (0 ms) 16: [ RUN ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/17 16: [ OK ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/17 (0 ms) 16: [ RUN ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/18 16: [ OK ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/18 (0 ms) 16: [ RUN ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/19 16: [ OK ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/19 (0 ms) 16: [ RUN ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/20 16: [ OK ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/20 (0 ms) 16: [ RUN ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/21 16: [ OK ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/21 (0 ms) 16: [ RUN ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/22 16: [ OK ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/22 (0 ms) 16: [----------] 23 tests from WithParameters/FreeEnergyParameterTest (1 ms total) 16: 16: [----------] 17 tests from WithParameters/LangevinTest 16: [ RUN ] WithParameters/LangevinTest.SimpleIntegration/0 16: [ OK ] WithParameters/LangevinTest.SimpleIntegration/0 (1 ms) 16: [ RUN ] WithParameters/LangevinTest.SimpleIntegration/1 16: [ OK ] WithParameters/LangevinTest.SimpleIntegration/1 (0 ms) 16: [ RUN ] WithParameters/LangevinTest.SimpleIntegration/2 16: [ OK ] WithParameters/LangevinTest.SimpleIntegration/2 (0 ms) 16: [ RUN ] WithParameters/LangevinTest.SimpleIntegration/3 16: [ OK ] WithParameters/LangevinTest.SimpleIntegration/3 (0 ms) 16: [ RUN ] WithParameters/LangevinTest.SimpleIntegration/4 16: [ OK ] WithParameters/LangevinTest.SimpleIntegration/4 (0 ms) 16: [ RUN ] WithParameters/LangevinTest.SimpleIntegration/5 16: [ OK ] WithParameters/LangevinTest.SimpleIntegration/5 (0 ms) 16: [ RUN ] WithParameters/LangevinTest.SimpleIntegration/6 16: [ OK ] WithParameters/LangevinTest.SimpleIntegration/6 (0 ms) 16: [ RUN ] WithParameters/LangevinTest.SimpleIntegration/7 16: [ OK ] WithParameters/LangevinTest.SimpleIntegration/7 (0 ms) 16: [ RUN ] WithParameters/LangevinTest.SimpleIntegration/8 16: [ OK ] WithParameters/LangevinTest.SimpleIntegration/8 (0 ms) 16: [ RUN ] WithParameters/LangevinTest.SimpleIntegration/9 16: [ OK ] WithParameters/LangevinTest.SimpleIntegration/9 (0 ms) 16: [ RUN ] WithParameters/LangevinTest.SimpleIntegration/10 16: [ OK ] WithParameters/LangevinTest.SimpleIntegration/10 (0 ms) 16: [ RUN ] WithParameters/LangevinTest.SimpleIntegration/11 16: [ OK ] WithParameters/LangevinTest.SimpleIntegration/11 (0 ms) 16: [ RUN ] WithParameters/LangevinTest.SimpleIntegration/12 16: [ OK ] WithParameters/LangevinTest.SimpleIntegration/12 (1 ms) 16: [ RUN ] WithParameters/LangevinTest.SimpleIntegration/13 16: [ OK ] WithParameters/LangevinTest.SimpleIntegration/13 (1 ms) 16: [ RUN ] WithParameters/LangevinTest.SimpleIntegration/14 16: [ OK ] WithParameters/LangevinTest.SimpleIntegration/14 (1 ms) 16: [ RUN ] WithParameters/LangevinTest.SimpleIntegration/15 16: [ OK ] WithParameters/LangevinTest.SimpleIntegration/15 (1 ms) 16: [ RUN ] WithParameters/LangevinTest.SimpleIntegration/16 16: [ OK ] WithParameters/LangevinTest.SimpleIntegration/16 (1 ms) 16: [----------] 17 tests from WithParameters/LangevinTest (18 ms total) 16: 16: [----------] 16 tests from WithParameters/LeapFrogTest 16: [ RUN ] WithParameters/LeapFrogTest.SimpleIntegration/0 16: [ OK ] WithParameters/LeapFrogTest.SimpleIntegration/0 (0 ms) 16: [ RUN ] WithParameters/LeapFrogTest.SimpleIntegration/1 16: [ OK ] WithParameters/LeapFrogTest.SimpleIntegration/1 (0 ms) 16: [ RUN ] WithParameters/LeapFrogTest.SimpleIntegration/2 16: [ OK ] WithParameters/LeapFrogTest.SimpleIntegration/2 (0 ms) 16: [ RUN ] WithParameters/LeapFrogTest.SimpleIntegration/3 16: [ OK ] WithParameters/LeapFrogTest.SimpleIntegration/3 (0 ms) 16: [ RUN ] WithParameters/LeapFrogTest.SimpleIntegration/4 16: [ OK ] WithParameters/LeapFrogTest.SimpleIntegration/4 (1 ms) 16: [ RUN ] WithParameters/LeapFrogTest.SimpleIntegration/5 16: [ OK ] WithParameters/LeapFrogTest.SimpleIntegration/5 (10 ms) 16: [ RUN ] WithParameters/LeapFrogTest.SimpleIntegration/6 16: [ OK ] WithParameters/LeapFrogTest.SimpleIntegration/6 (32 ms) 16: [ RUN ] WithParameters/LeapFrogTest.SimpleIntegration/7 16: [ OK ] WithParameters/LeapFrogTest.SimpleIntegration/7 (1 ms) 16: [ RUN ] WithParameters/LeapFrogTest.SimpleIntegration/8 16: [ OK ] WithParameters/LeapFrogTest.SimpleIntegration/8 (1 ms) 16: [ RUN ] WithParameters/LeapFrogTest.SimpleIntegration/9 16: [ OK ] WithParameters/LeapFrogTest.SimpleIntegration/9 (1 ms) 16: [ RUN ] WithParameters/LeapFrogTest.SimpleIntegration/10 16: [ OK ] WithParameters/LeapFrogTest.SimpleIntegration/10 (10 ms) 16: [ RUN ] WithParameters/LeapFrogTest.SimpleIntegration/11 16: [ OK ] WithParameters/LeapFrogTest.SimpleIntegration/11 (9 ms) 16: [ RUN ] WithParameters/LeapFrogTest.SimpleIntegration/12 16: [ OK ] WithParameters/LeapFrogTest.SimpleIntegration/12 (9 ms) 16: [ RUN ] WithParameters/LeapFrogTest.SimpleIntegration/13 16: [ OK ] WithParameters/LeapFrogTest.SimpleIntegration/13 (9 ms) 16: [ RUN ] WithParameters/LeapFrogTest.SimpleIntegration/14 16: [ OK ] WithParameters/LeapFrogTest.SimpleIntegration/14 (9 ms) 16: [ RUN ] WithParameters/LeapFrogTest.SimpleIntegration/15 16: [ OK ] WithParameters/LeapFrogTest.SimpleIntegration/15 (10 ms) 16: [----------] 16 tests from WithParameters/LeapFrogTest (129 ms total) 16: 16: [----------] 140 tests from Cubic/ParrRahmTest 16: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_cubic_box_2_5_boxv__100 16: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_cubic_box_2_5_boxv__100 (1 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_cubic_box_2_5_boxv__1 16: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_cubic_box_2_5_boxv__1 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_cubic_box_2_5_boxv__1e_07 16: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_cubic_box_2_5_boxv__1e_07 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_cubic_box_2_5_boxv_0 16: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_cubic_box_2_5_boxv_0 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_cubic_box_2_5_boxv_1e_07 16: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_cubic_box_2_5_boxv_1e_07 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_cubic_box_2_5_boxv_1 16: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_cubic_box_2_5_boxv_1 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_cubic_box_2_5_boxv_100 16: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_cubic_box_2_5_boxv_100 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_cubic_box_10000_boxv__100 16: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_cubic_box_10000_boxv__100 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_cubic_box_10000_boxv__1 16: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_cubic_box_10000_boxv__1 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_cubic_box_10000_boxv__1e_07 16: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_cubic_box_10000_boxv__1e_07 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_cubic_box_10000_boxv_0 16: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_cubic_box_10000_boxv_0 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_cubic_box_10000_boxv_1e_07 16: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_cubic_box_10000_boxv_1e_07 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_cubic_box_10000_boxv_1 16: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_cubic_box_10000_boxv_1 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_cubic_box_10000_boxv_100 16: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_cubic_box_10000_boxv_100 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_cubic_box_2_5_boxv__100 16: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_cubic_box_2_5_boxv__100 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_cubic_box_2_5_boxv__1 16: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_cubic_box_2_5_boxv__1 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_cubic_box_2_5_boxv__1e_07 16: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_cubic_box_2_5_boxv__1e_07 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_cubic_box_2_5_boxv_0 16: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_cubic_box_2_5_boxv_0 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_cubic_box_2_5_boxv_1e_07 16: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_cubic_box_2_5_boxv_1e_07 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_cubic_box_2_5_boxv_1 16: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_cubic_box_2_5_boxv_1 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_cubic_box_2_5_boxv_100 16: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_cubic_box_2_5_boxv_100 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_cubic_box_10000_boxv__100 16: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_cubic_box_10000_boxv__100 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_cubic_box_10000_boxv__1 16: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_cubic_box_10000_boxv__1 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_cubic_box_10000_boxv__1e_07 16: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_cubic_box_10000_boxv__1e_07 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_cubic_box_10000_boxv_0 16: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_cubic_box_10000_boxv_0 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_cubic_box_10000_boxv_1e_07 16: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_cubic_box_10000_boxv_1e_07 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_cubic_box_10000_boxv_1 16: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_cubic_box_10000_boxv_1 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_cubic_box_10000_boxv_100 16: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_cubic_box_10000_boxv_100 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_cubic_box_2_5_boxv__100 16: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_cubic_box_2_5_boxv__100 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_cubic_box_2_5_boxv__1 16: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_cubic_box_2_5_boxv__1 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_cubic_box_2_5_boxv__1e_07 16: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_cubic_box_2_5_boxv__1e_07 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_cubic_box_2_5_boxv_0 16: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_cubic_box_2_5_boxv_0 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_cubic_box_2_5_boxv_1e_07 16: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_cubic_box_2_5_boxv_1e_07 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_cubic_box_2_5_boxv_1 16: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_cubic_box_2_5_boxv_1 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_cubic_box_2_5_boxv_100 16: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_cubic_box_2_5_boxv_100 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_cubic_box_10000_boxv__100 16: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_cubic_box_10000_boxv__100 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_cubic_box_10000_boxv__1 16: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_cubic_box_10000_boxv__1 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_cubic_box_10000_boxv__1e_07 16: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_cubic_box_10000_boxv__1e_07 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_cubic_box_10000_boxv_0 16: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_cubic_box_10000_boxv_0 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_cubic_box_10000_boxv_1e_07 16: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_cubic_box_10000_boxv_1e_07 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_cubic_box_10000_boxv_1 16: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_cubic_box_10000_boxv_1 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_cubic_box_10000_boxv_100 16: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_cubic_box_10000_boxv_100 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_general_shape_cubic_box_2_5_boxv__100 16: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_general_shape_cubic_box_2_5_boxv__100 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_general_shape_cubic_box_2_5_boxv__1 16: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_general_shape_cubic_box_2_5_boxv__1 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_general_shape_cubic_box_2_5_boxv__1e_07 16: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_general_shape_cubic_box_2_5_boxv__1e_07 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_general_shape_cubic_box_2_5_boxv_0 16: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_general_shape_cubic_box_2_5_boxv_0 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_general_shape_cubic_box_2_5_boxv_1e_07 16: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_general_shape_cubic_box_2_5_boxv_1e_07 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_general_shape_cubic_box_2_5_boxv_1 16: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_general_shape_cubic_box_2_5_boxv_1 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_general_shape_cubic_box_2_5_boxv_100 16: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_general_shape_cubic_box_2_5_boxv_100 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_general_shape_cubic_box_10000_boxv__100 16: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_general_shape_cubic_box_10000_boxv__100 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_general_shape_cubic_box_10000_boxv__1 16: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_general_shape_cubic_box_10000_boxv__1 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_general_shape_cubic_box_10000_boxv__1e_07 16: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_general_shape_cubic_box_10000_boxv__1e_07 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_general_shape_cubic_box_10000_boxv_0 16: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_general_shape_cubic_box_10000_boxv_0 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_general_shape_cubic_box_10000_boxv_1e_07 16: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_general_shape_cubic_box_10000_boxv_1e_07 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_general_shape_cubic_box_10000_boxv_1 16: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_general_shape_cubic_box_10000_boxv_1 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_general_shape_cubic_box_10000_boxv_100 16: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_general_shape_cubic_box_10000_boxv_100 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_cubic_box_2_5_boxv__100 16: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_cubic_box_2_5_boxv__100 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_cubic_box_2_5_boxv__1 16: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_cubic_box_2_5_boxv__1 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_cubic_box_2_5_boxv__1e_07 16: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_cubic_box_2_5_boxv__1e_07 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_cubic_box_2_5_boxv_0 16: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_cubic_box_2_5_boxv_0 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_cubic_box_2_5_boxv_1e_07 16: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_cubic_box_2_5_boxv_1e_07 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_cubic_box_2_5_boxv_1 16: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_cubic_box_2_5_boxv_1 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_cubic_box_2_5_boxv_100 16: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_cubic_box_2_5_boxv_100 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_cubic_box_10000_boxv__100 16: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_cubic_box_10000_boxv__100 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_cubic_box_10000_boxv__1 16: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_cubic_box_10000_boxv__1 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_cubic_box_10000_boxv__1e_07 16: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_cubic_box_10000_boxv__1e_07 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_cubic_box_10000_boxv_0 16: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_cubic_box_10000_boxv_0 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_cubic_box_10000_boxv_1e_07 16: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_cubic_box_10000_boxv_1e_07 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_cubic_box_10000_boxv_1 16: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_cubic_box_10000_boxv_1 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_cubic_box_10000_boxv_100 16: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_cubic_box_10000_boxv_100 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_cubic_box_2_5_boxv__100 16: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_cubic_box_2_5_boxv__100 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_cubic_box_2_5_boxv__1 16: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_cubic_box_2_5_boxv__1 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_cubic_box_2_5_boxv__1e_07 16: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_cubic_box_2_5_boxv__1e_07 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_cubic_box_2_5_boxv_0 16: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_cubic_box_2_5_boxv_0 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_cubic_box_2_5_boxv_1e_07 16: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_cubic_box_2_5_boxv_1e_07 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_cubic_box_2_5_boxv_1 16: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_cubic_box_2_5_boxv_1 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_cubic_box_2_5_boxv_100 16: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_cubic_box_2_5_boxv_100 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_cubic_box_10000_boxv__100 16: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_cubic_box_10000_boxv__100 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_cubic_box_10000_boxv__1 16: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_cubic_box_10000_boxv__1 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_cubic_box_10000_boxv__1e_07 16: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_cubic_box_10000_boxv__1e_07 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_cubic_box_10000_boxv_0 16: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_cubic_box_10000_boxv_0 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_cubic_box_10000_boxv_1e_07 16: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_cubic_box_10000_boxv_1e_07 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_cubic_box_10000_boxv_1 16: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_cubic_box_10000_boxv_1 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_cubic_box_10000_boxv_100 16: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_cubic_box_10000_boxv_100 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_cubic_box_2_5_boxv__100 16: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_cubic_box_2_5_boxv__100 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_cubic_box_2_5_boxv__1 16: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_cubic_box_2_5_boxv__1 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_cubic_box_2_5_boxv__1e_07 16: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_cubic_box_2_5_boxv__1e_07 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_cubic_box_2_5_boxv_0 16: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_cubic_box_2_5_boxv_0 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_cubic_box_2_5_boxv_1e_07 16: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_cubic_box_2_5_boxv_1e_07 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_cubic_box_2_5_boxv_1 16: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_cubic_box_2_5_boxv_1 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_cubic_box_2_5_boxv_100 16: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_cubic_box_2_5_boxv_100 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_cubic_box_10000_boxv__100 16: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_cubic_box_10000_boxv__100 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_cubic_box_10000_boxv__1 16: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_cubic_box_10000_boxv__1 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_cubic_box_10000_boxv__1e_07 16: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_cubic_box_10000_boxv__1e_07 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_cubic_box_10000_boxv_0 16: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_cubic_box_10000_boxv_0 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_cubic_box_10000_boxv_1e_07 16: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_cubic_box_10000_boxv_1e_07 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_cubic_box_10000_boxv_1 16: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_cubic_box_10000_boxv_1 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_cubic_box_10000_boxv_100 16: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_cubic_box_10000_boxv_100 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_cubic_box_2_5_boxv__100 16: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_cubic_box_2_5_boxv__100 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_cubic_box_2_5_boxv__1 16: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_cubic_box_2_5_boxv__1 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_cubic_box_2_5_boxv__1e_07 16: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_cubic_box_2_5_boxv__1e_07 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_cubic_box_2_5_boxv_0 16: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_cubic_box_2_5_boxv_0 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_cubic_box_2_5_boxv_1e_07 16: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_cubic_box_2_5_boxv_1e_07 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_cubic_box_2_5_boxv_1 16: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_cubic_box_2_5_boxv_1 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_cubic_box_2_5_boxv_100 16: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_cubic_box_2_5_boxv_100 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_cubic_box_10000_boxv__100 16: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_cubic_box_10000_boxv__100 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_cubic_box_10000_boxv__1 16: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_cubic_box_10000_boxv__1 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_cubic_box_10000_boxv__1e_07 16: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_cubic_box_10000_boxv__1e_07 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_cubic_box_10000_boxv_0 16: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_cubic_box_10000_boxv_0 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_cubic_box_10000_boxv_1e_07 16: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_cubic_box_10000_boxv_1e_07 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_cubic_box_10000_boxv_1 16: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_cubic_box_10000_boxv_1 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_cubic_box_10000_boxv_100 16: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_cubic_box_10000_boxv_100 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_general_shape_cubic_box_2_5_boxv__100 16: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_general_shape_cubic_box_2_5_boxv__100 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_general_shape_cubic_box_2_5_boxv__1 16: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_general_shape_cubic_box_2_5_boxv__1 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_general_shape_cubic_box_2_5_boxv__1e_07 16: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_general_shape_cubic_box_2_5_boxv__1e_07 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_general_shape_cubic_box_2_5_boxv_0 16: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_general_shape_cubic_box_2_5_boxv_0 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_general_shape_cubic_box_2_5_boxv_1e_07 16: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_general_shape_cubic_box_2_5_boxv_1e_07 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_general_shape_cubic_box_2_5_boxv_1 16: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_general_shape_cubic_box_2_5_boxv_1 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_general_shape_cubic_box_2_5_boxv_100 16: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_general_shape_cubic_box_2_5_boxv_100 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_general_shape_cubic_box_10000_boxv__100 16: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_general_shape_cubic_box_10000_boxv__100 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_general_shape_cubic_box_10000_boxv__1 16: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_general_shape_cubic_box_10000_boxv__1 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_general_shape_cubic_box_10000_boxv__1e_07 16: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_general_shape_cubic_box_10000_boxv__1e_07 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_general_shape_cubic_box_10000_boxv_0 16: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_general_shape_cubic_box_10000_boxv_0 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_general_shape_cubic_box_10000_boxv_1e_07 16: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_general_shape_cubic_box_10000_boxv_1e_07 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_general_shape_cubic_box_10000_boxv_1 16: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_general_shape_cubic_box_10000_boxv_1 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_general_shape_cubic_box_10000_boxv_100 16: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_general_shape_cubic_box_10000_boxv_100 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_cubic_box_2_5_boxv__100 16: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_cubic_box_2_5_boxv__100 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_cubic_box_2_5_boxv__1 16: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_cubic_box_2_5_boxv__1 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_cubic_box_2_5_boxv__1e_07 16: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_cubic_box_2_5_boxv__1e_07 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_cubic_box_2_5_boxv_0 16: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_cubic_box_2_5_boxv_0 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_cubic_box_2_5_boxv_1e_07 16: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_cubic_box_2_5_boxv_1e_07 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_cubic_box_2_5_boxv_1 16: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_cubic_box_2_5_boxv_1 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_cubic_box_2_5_boxv_100 16: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_cubic_box_2_5_boxv_100 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_cubic_box_10000_boxv__100 16: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_cubic_box_10000_boxv__100 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_cubic_box_10000_boxv__1 16: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_cubic_box_10000_boxv__1 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_cubic_box_10000_boxv__1e_07 16: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_cubic_box_10000_boxv__1e_07 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_cubic_box_10000_boxv_0 16: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_cubic_box_10000_boxv_0 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_cubic_box_10000_boxv_1e_07 16: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_cubic_box_10000_boxv_1e_07 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_cubic_box_10000_boxv_1 16: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_cubic_box_10000_boxv_1 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_cubic_box_10000_boxv_100 16: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_cubic_box_10000_boxv_100 (0 ms) 16: [----------] 140 tests from Cubic/ParrRahmTest (83 ms total) 16: 16: [----------] 140 tests from Rectilinear/ParrRahmTest 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rect_box_2_5_boxv__100 16: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rect_box_2_5_boxv__100 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rect_box_2_5_boxv__1 16: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rect_box_2_5_boxv__1 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rect_box_2_5_boxv__1e_07 16: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rect_box_2_5_boxv__1e_07 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rect_box_2_5_boxv_0 16: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rect_box_2_5_boxv_0 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rect_box_2_5_boxv_1e_07 16: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rect_box_2_5_boxv_1e_07 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rect_box_2_5_boxv_1 16: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rect_box_2_5_boxv_1 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rect_box_2_5_boxv_100 16: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rect_box_2_5_boxv_100 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rect_box_10000_boxv__100 16: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rect_box_10000_boxv__100 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rect_box_10000_boxv__1 16: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rect_box_10000_boxv__1 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rect_box_10000_boxv__1e_07 16: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rect_box_10000_boxv__1e_07 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rect_box_10000_boxv_0 16: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rect_box_10000_boxv_0 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rect_box_10000_boxv_1e_07 16: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rect_box_10000_boxv_1e_07 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rect_box_10000_boxv_1 16: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rect_box_10000_boxv_1 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rect_box_10000_boxv_100 16: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rect_box_10000_boxv_100 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rect_box_2_5_boxv__100 16: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rect_box_2_5_boxv__100 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rect_box_2_5_boxv__1 16: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rect_box_2_5_boxv__1 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rect_box_2_5_boxv__1e_07 16: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rect_box_2_5_boxv__1e_07 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rect_box_2_5_boxv_0 16: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rect_box_2_5_boxv_0 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rect_box_2_5_boxv_1e_07 16: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rect_box_2_5_boxv_1e_07 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rect_box_2_5_boxv_1 16: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rect_box_2_5_boxv_1 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rect_box_2_5_boxv_100 16: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rect_box_2_5_boxv_100 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rect_box_10000_boxv__100 16: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rect_box_10000_boxv__100 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rect_box_10000_boxv__1 16: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rect_box_10000_boxv__1 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rect_box_10000_boxv__1e_07 16: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rect_box_10000_boxv__1e_07 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rect_box_10000_boxv_0 16: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rect_box_10000_boxv_0 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rect_box_10000_boxv_1e_07 16: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rect_box_10000_boxv_1e_07 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rect_box_10000_boxv_1 16: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rect_box_10000_boxv_1 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rect_box_10000_boxv_100 16: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rect_box_10000_boxv_100 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rect_box_2_5_boxv__100 16: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rect_box_2_5_boxv__100 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rect_box_2_5_boxv__1 16: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rect_box_2_5_boxv__1 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rect_box_2_5_boxv__1e_07 16: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rect_box_2_5_boxv__1e_07 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rect_box_2_5_boxv_0 16: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rect_box_2_5_boxv_0 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rect_box_2_5_boxv_1e_07 16: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rect_box_2_5_boxv_1e_07 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rect_box_2_5_boxv_1 16: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rect_box_2_5_boxv_1 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rect_box_2_5_boxv_100 16: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rect_box_2_5_boxv_100 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rect_box_10000_boxv__100 16: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rect_box_10000_boxv__100 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rect_box_10000_boxv__1 16: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rect_box_10000_boxv__1 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rect_box_10000_boxv__1e_07 16: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rect_box_10000_boxv__1e_07 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rect_box_10000_boxv_0 16: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rect_box_10000_boxv_0 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rect_box_10000_boxv_1e_07 16: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rect_box_10000_boxv_1e_07 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rect_box_10000_boxv_1 16: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rect_box_10000_boxv_1 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rect_box_10000_boxv_100 16: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rect_box_10000_boxv_100 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_general_shape_rect_box_2_5_boxv__100 16: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_general_shape_rect_box_2_5_boxv__100 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_general_shape_rect_box_2_5_boxv__1 16: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_general_shape_rect_box_2_5_boxv__1 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_general_shape_rect_box_2_5_boxv__1e_07 16: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_general_shape_rect_box_2_5_boxv__1e_07 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_general_shape_rect_box_2_5_boxv_0 16: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_general_shape_rect_box_2_5_boxv_0 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_general_shape_rect_box_2_5_boxv_1e_07 16: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_general_shape_rect_box_2_5_boxv_1e_07 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_general_shape_rect_box_2_5_boxv_1 16: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_general_shape_rect_box_2_5_boxv_1 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_general_shape_rect_box_2_5_boxv_100 16: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_general_shape_rect_box_2_5_boxv_100 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_general_shape_rect_box_10000_boxv__100 16: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_general_shape_rect_box_10000_boxv__100 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_general_shape_rect_box_10000_boxv__1 16: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_general_shape_rect_box_10000_boxv__1 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_general_shape_rect_box_10000_boxv__1e_07 16: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_general_shape_rect_box_10000_boxv__1e_07 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_general_shape_rect_box_10000_boxv_0 16: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_general_shape_rect_box_10000_boxv_0 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_general_shape_rect_box_10000_boxv_1e_07 16: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_general_shape_rect_box_10000_boxv_1e_07 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_general_shape_rect_box_10000_boxv_1 16: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_general_shape_rect_box_10000_boxv_1 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_general_shape_rect_box_10000_boxv_100 16: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_general_shape_rect_box_10000_boxv_100 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rect_box_2_5_boxv__100 16: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rect_box_2_5_boxv__100 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rect_box_2_5_boxv__1 16: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rect_box_2_5_boxv__1 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rect_box_2_5_boxv__1e_07 16: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rect_box_2_5_boxv__1e_07 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rect_box_2_5_boxv_0 16: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rect_box_2_5_boxv_0 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rect_box_2_5_boxv_1e_07 16: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rect_box_2_5_boxv_1e_07 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rect_box_2_5_boxv_1 16: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rect_box_2_5_boxv_1 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rect_box_2_5_boxv_100 16: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rect_box_2_5_boxv_100 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rect_box_10000_boxv__100 16: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rect_box_10000_boxv__100 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rect_box_10000_boxv__1 16: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rect_box_10000_boxv__1 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rect_box_10000_boxv__1e_07 16: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rect_box_10000_boxv__1e_07 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rect_box_10000_boxv_0 16: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rect_box_10000_boxv_0 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rect_box_10000_boxv_1e_07 16: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rect_box_10000_boxv_1e_07 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rect_box_10000_boxv_1 16: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rect_box_10000_boxv_1 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rect_box_10000_boxv_100 16: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rect_box_10000_boxv_100 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rect_box_2_5_boxv__100 16: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rect_box_2_5_boxv__100 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rect_box_2_5_boxv__1 16: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rect_box_2_5_boxv__1 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rect_box_2_5_boxv__1e_07 16: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rect_box_2_5_boxv__1e_07 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rect_box_2_5_boxv_0 16: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rect_box_2_5_boxv_0 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rect_box_2_5_boxv_1e_07 16: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rect_box_2_5_boxv_1e_07 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rect_box_2_5_boxv_1 16: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rect_box_2_5_boxv_1 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rect_box_2_5_boxv_100 16: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rect_box_2_5_boxv_100 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rect_box_10000_boxv__100 16: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rect_box_10000_boxv__100 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rect_box_10000_boxv__1 16: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rect_box_10000_boxv__1 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rect_box_10000_boxv__1e_07 16: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rect_box_10000_boxv__1e_07 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rect_box_10000_boxv_0 16: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rect_box_10000_boxv_0 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rect_box_10000_boxv_1e_07 16: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rect_box_10000_boxv_1e_07 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rect_box_10000_boxv_1 16: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rect_box_10000_boxv_1 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rect_box_10000_boxv_100 16: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rect_box_10000_boxv_100 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rect_box_2_5_boxv__100 16: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rect_box_2_5_boxv__100 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rect_box_2_5_boxv__1 16: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rect_box_2_5_boxv__1 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rect_box_2_5_boxv__1e_07 16: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rect_box_2_5_boxv__1e_07 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rect_box_2_5_boxv_0 16: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rect_box_2_5_boxv_0 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rect_box_2_5_boxv_1e_07 16: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rect_box_2_5_boxv_1e_07 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rect_box_2_5_boxv_1 16: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rect_box_2_5_boxv_1 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rect_box_2_5_boxv_100 16: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rect_box_2_5_boxv_100 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rect_box_10000_boxv__100 16: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rect_box_10000_boxv__100 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rect_box_10000_boxv__1 16: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rect_box_10000_boxv__1 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rect_box_10000_boxv__1e_07 16: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rect_box_10000_boxv__1e_07 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rect_box_10000_boxv_0 16: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rect_box_10000_boxv_0 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rect_box_10000_boxv_1e_07 16: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rect_box_10000_boxv_1e_07 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rect_box_10000_boxv_1 16: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rect_box_10000_boxv_1 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rect_box_10000_boxv_100 16: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rect_box_10000_boxv_100 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rect_box_2_5_boxv__100 16: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rect_box_2_5_boxv__100 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rect_box_2_5_boxv__1 16: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rect_box_2_5_boxv__1 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rect_box_2_5_boxv__1e_07 16: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rect_box_2_5_boxv__1e_07 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rect_box_2_5_boxv_0 16: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rect_box_2_5_boxv_0 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rect_box_2_5_boxv_1e_07 16: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rect_box_2_5_boxv_1e_07 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rect_box_2_5_boxv_1 16: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rect_box_2_5_boxv_1 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rect_box_2_5_boxv_100 16: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rect_box_2_5_boxv_100 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rect_box_10000_boxv__100 16: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rect_box_10000_boxv__100 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rect_box_10000_boxv__1 16: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rect_box_10000_boxv__1 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rect_box_10000_boxv__1e_07 16: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rect_box_10000_boxv__1e_07 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rect_box_10000_boxv_0 16: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rect_box_10000_boxv_0 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rect_box_10000_boxv_1e_07 16: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rect_box_10000_boxv_1e_07 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rect_box_10000_boxv_1 16: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rect_box_10000_boxv_1 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rect_box_10000_boxv_100 16: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rect_box_10000_boxv_100 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rect_box_2_5_boxv__100 16: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rect_box_2_5_boxv__100 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rect_box_2_5_boxv__1 16: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rect_box_2_5_boxv__1 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rect_box_2_5_boxv__1e_07 16: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rect_box_2_5_boxv__1e_07 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rect_box_2_5_boxv_0 16: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rect_box_2_5_boxv_0 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rect_box_2_5_boxv_1e_07 16: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rect_box_2_5_boxv_1e_07 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rect_box_2_5_boxv_1 16: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rect_box_2_5_boxv_1 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rect_box_2_5_boxv_100 16: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rect_box_2_5_boxv_100 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rect_box_10000_boxv__100 16: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rect_box_10000_boxv__100 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rect_box_10000_boxv__1 16: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rect_box_10000_boxv__1 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rect_box_10000_boxv__1e_07 16: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rect_box_10000_boxv__1e_07 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rect_box_10000_boxv_0 16: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rect_box_10000_boxv_0 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rect_box_10000_boxv_1e_07 16: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rect_box_10000_boxv_1e_07 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rect_box_10000_boxv_1 16: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rect_box_10000_boxv_1 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rect_box_10000_boxv_100 16: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rect_box_10000_boxv_100 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rect_box_2_5_boxv__100 16: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rect_box_2_5_boxv__100 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rect_box_2_5_boxv__1 16: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rect_box_2_5_boxv__1 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rect_box_2_5_boxv__1e_07 16: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rect_box_2_5_boxv__1e_07 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rect_box_2_5_boxv_0 16: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rect_box_2_5_boxv_0 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rect_box_2_5_boxv_1e_07 16: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rect_box_2_5_boxv_1e_07 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rect_box_2_5_boxv_1 16: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rect_box_2_5_boxv_1 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rect_box_2_5_boxv_100 16: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rect_box_2_5_boxv_100 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rect_box_10000_boxv__100 16: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rect_box_10000_boxv__100 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rect_box_10000_boxv__1 16: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rect_box_10000_boxv__1 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rect_box_10000_boxv__1e_07 16: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rect_box_10000_boxv__1e_07 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rect_box_10000_boxv_0 16: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rect_box_10000_boxv_0 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rect_box_10000_boxv_1e_07 16: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rect_box_10000_boxv_1e_07 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rect_box_10000_boxv_1 16: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rect_box_10000_boxv_1 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rect_box_10000_boxv_100 16: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rect_box_10000_boxv_100 (0 ms) 16: [----------] 140 tests from Rectilinear/ParrRahmTest (85 ms total) 16: 16: [----------] 140 tests from RhombDodecXYSquare/ParrRahmTest 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rds_box_2_5_boxv__100 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rds_box_2_5_boxv__100 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rds_box_2_5_boxv__1 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rds_box_2_5_boxv__1 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rds_box_2_5_boxv__1e_07 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rds_box_2_5_boxv__1e_07 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rds_box_2_5_boxv_0 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rds_box_2_5_boxv_0 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rds_box_2_5_boxv_1e_07 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rds_box_2_5_boxv_1e_07 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rds_box_2_5_boxv_1 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rds_box_2_5_boxv_1 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rds_box_2_5_boxv_100 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rds_box_2_5_boxv_100 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rds_box_10000_boxv__100 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rds_box_10000_boxv__100 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rds_box_10000_boxv__1 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rds_box_10000_boxv__1 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rds_box_10000_boxv__1e_07 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rds_box_10000_boxv__1e_07 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rds_box_10000_boxv_0 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rds_box_10000_boxv_0 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rds_box_10000_boxv_1e_07 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rds_box_10000_boxv_1e_07 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rds_box_10000_boxv_1 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rds_box_10000_boxv_1 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rds_box_10000_boxv_100 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rds_box_10000_boxv_100 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rds_box_2_5_boxv__100 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rds_box_2_5_boxv__100 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rds_box_2_5_boxv__1 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rds_box_2_5_boxv__1 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rds_box_2_5_boxv__1e_07 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rds_box_2_5_boxv__1e_07 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rds_box_2_5_boxv_0 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rds_box_2_5_boxv_0 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rds_box_2_5_boxv_1e_07 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rds_box_2_5_boxv_1e_07 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rds_box_2_5_boxv_1 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rds_box_2_5_boxv_1 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rds_box_2_5_boxv_100 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rds_box_2_5_boxv_100 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rds_box_10000_boxv__100 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rds_box_10000_boxv__100 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rds_box_10000_boxv__1 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rds_box_10000_boxv__1 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rds_box_10000_boxv__1e_07 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rds_box_10000_boxv__1e_07 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rds_box_10000_boxv_0 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rds_box_10000_boxv_0 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rds_box_10000_boxv_1e_07 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rds_box_10000_boxv_1e_07 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rds_box_10000_boxv_1 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rds_box_10000_boxv_1 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rds_box_10000_boxv_100 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rds_box_10000_boxv_100 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rds_box_2_5_boxv__100 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rds_box_2_5_boxv__100 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rds_box_2_5_boxv__1 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rds_box_2_5_boxv__1 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rds_box_2_5_boxv__1e_07 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rds_box_2_5_boxv__1e_07 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rds_box_2_5_boxv_0 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rds_box_2_5_boxv_0 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rds_box_2_5_boxv_1e_07 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rds_box_2_5_boxv_1e_07 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rds_box_2_5_boxv_1 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rds_box_2_5_boxv_1 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rds_box_2_5_boxv_100 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rds_box_2_5_boxv_100 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rds_box_10000_boxv__100 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rds_box_10000_boxv__100 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rds_box_10000_boxv__1 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rds_box_10000_boxv__1 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rds_box_10000_boxv__1e_07 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rds_box_10000_boxv__1e_07 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rds_box_10000_boxv_0 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rds_box_10000_boxv_0 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rds_box_10000_boxv_1e_07 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rds_box_10000_boxv_1e_07 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rds_box_10000_boxv_1 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rds_box_10000_boxv_1 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rds_box_10000_boxv_100 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rds_box_10000_boxv_100 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_general_shape_rds_box_2_5_boxv__100 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_general_shape_rds_box_2_5_boxv__100 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_general_shape_rds_box_2_5_boxv__1 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_general_shape_rds_box_2_5_boxv__1 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_general_shape_rds_box_2_5_boxv__1e_07 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_general_shape_rds_box_2_5_boxv__1e_07 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_general_shape_rds_box_2_5_boxv_0 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_general_shape_rds_box_2_5_boxv_0 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_general_shape_rds_box_2_5_boxv_1e_07 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_general_shape_rds_box_2_5_boxv_1e_07 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_general_shape_rds_box_2_5_boxv_1 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_general_shape_rds_box_2_5_boxv_1 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_general_shape_rds_box_2_5_boxv_100 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_general_shape_rds_box_2_5_boxv_100 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_general_shape_rds_box_10000_boxv__100 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_general_shape_rds_box_10000_boxv__100 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_general_shape_rds_box_10000_boxv__1 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_general_shape_rds_box_10000_boxv__1 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_general_shape_rds_box_10000_boxv__1e_07 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_general_shape_rds_box_10000_boxv__1e_07 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_general_shape_rds_box_10000_boxv_0 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_general_shape_rds_box_10000_boxv_0 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_general_shape_rds_box_10000_boxv_1e_07 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_general_shape_rds_box_10000_boxv_1e_07 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_general_shape_rds_box_10000_boxv_1 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_general_shape_rds_box_10000_boxv_1 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_general_shape_rds_box_10000_boxv_100 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_general_shape_rds_box_10000_boxv_100 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rds_box_2_5_boxv__100 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rds_box_2_5_boxv__100 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rds_box_2_5_boxv__1 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rds_box_2_5_boxv__1 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rds_box_2_5_boxv__1e_07 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rds_box_2_5_boxv__1e_07 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rds_box_2_5_boxv_0 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rds_box_2_5_boxv_0 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rds_box_2_5_boxv_1e_07 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rds_box_2_5_boxv_1e_07 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rds_box_2_5_boxv_1 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rds_box_2_5_boxv_1 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rds_box_2_5_boxv_100 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rds_box_2_5_boxv_100 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rds_box_10000_boxv__100 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rds_box_10000_boxv__100 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rds_box_10000_boxv__1 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rds_box_10000_boxv__1 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rds_box_10000_boxv__1e_07 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rds_box_10000_boxv__1e_07 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rds_box_10000_boxv_0 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rds_box_10000_boxv_0 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rds_box_10000_boxv_1e_07 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rds_box_10000_boxv_1e_07 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rds_box_10000_boxv_1 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rds_box_10000_boxv_1 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rds_box_10000_boxv_100 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rds_box_10000_boxv_100 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rds_box_2_5_boxv__100 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rds_box_2_5_boxv__100 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rds_box_2_5_boxv__1 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rds_box_2_5_boxv__1 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rds_box_2_5_boxv__1e_07 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rds_box_2_5_boxv__1e_07 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rds_box_2_5_boxv_0 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rds_box_2_5_boxv_0 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rds_box_2_5_boxv_1e_07 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rds_box_2_5_boxv_1e_07 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rds_box_2_5_boxv_1 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rds_box_2_5_boxv_1 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rds_box_2_5_boxv_100 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rds_box_2_5_boxv_100 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rds_box_10000_boxv__100 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rds_box_10000_boxv__100 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rds_box_10000_boxv__1 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rds_box_10000_boxv__1 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rds_box_10000_boxv__1e_07 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rds_box_10000_boxv__1e_07 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rds_box_10000_boxv_0 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rds_box_10000_boxv_0 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rds_box_10000_boxv_1e_07 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rds_box_10000_boxv_1e_07 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rds_box_10000_boxv_1 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rds_box_10000_boxv_1 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rds_box_10000_boxv_100 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rds_box_10000_boxv_100 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rds_box_2_5_boxv__100 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rds_box_2_5_boxv__100 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rds_box_2_5_boxv__1 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rds_box_2_5_boxv__1 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rds_box_2_5_boxv__1e_07 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rds_box_2_5_boxv__1e_07 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rds_box_2_5_boxv_0 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rds_box_2_5_boxv_0 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rds_box_2_5_boxv_1e_07 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rds_box_2_5_boxv_1e_07 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rds_box_2_5_boxv_1 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rds_box_2_5_boxv_1 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rds_box_2_5_boxv_100 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rds_box_2_5_boxv_100 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rds_box_10000_boxv__100 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rds_box_10000_boxv__100 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rds_box_10000_boxv__1 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rds_box_10000_boxv__1 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rds_box_10000_boxv__1e_07 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rds_box_10000_boxv__1e_07 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rds_box_10000_boxv_0 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rds_box_10000_boxv_0 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rds_box_10000_boxv_1e_07 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rds_box_10000_boxv_1e_07 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rds_box_10000_boxv_1 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rds_box_10000_boxv_1 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rds_box_10000_boxv_100 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rds_box_10000_boxv_100 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rds_box_2_5_boxv__100 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rds_box_2_5_boxv__100 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rds_box_2_5_boxv__1 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rds_box_2_5_boxv__1 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rds_box_2_5_boxv__1e_07 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rds_box_2_5_boxv__1e_07 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rds_box_2_5_boxv_0 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rds_box_2_5_boxv_0 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rds_box_2_5_boxv_1e_07 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rds_box_2_5_boxv_1e_07 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rds_box_2_5_boxv_1 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rds_box_2_5_boxv_1 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rds_box_2_5_boxv_100 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rds_box_2_5_boxv_100 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rds_box_10000_boxv__100 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rds_box_10000_boxv__100 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rds_box_10000_boxv__1 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rds_box_10000_boxv__1 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rds_box_10000_boxv__1e_07 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rds_box_10000_boxv__1e_07 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rds_box_10000_boxv_0 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rds_box_10000_boxv_0 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rds_box_10000_boxv_1e_07 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rds_box_10000_boxv_1e_07 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rds_box_10000_boxv_1 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rds_box_10000_boxv_1 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rds_box_10000_boxv_100 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rds_box_10000_boxv_100 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rds_box_2_5_boxv__100 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rds_box_2_5_boxv__100 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rds_box_2_5_boxv__1 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rds_box_2_5_boxv__1 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rds_box_2_5_boxv__1e_07 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rds_box_2_5_boxv__1e_07 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rds_box_2_5_boxv_0 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rds_box_2_5_boxv_0 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rds_box_2_5_boxv_1e_07 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rds_box_2_5_boxv_1e_07 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rds_box_2_5_boxv_1 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rds_box_2_5_boxv_1 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rds_box_2_5_boxv_100 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rds_box_2_5_boxv_100 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rds_box_10000_boxv__100 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rds_box_10000_boxv__100 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rds_box_10000_boxv__1 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rds_box_10000_boxv__1 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rds_box_10000_boxv__1e_07 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rds_box_10000_boxv__1e_07 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rds_box_10000_boxv_0 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rds_box_10000_boxv_0 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rds_box_10000_boxv_1e_07 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rds_box_10000_boxv_1e_07 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rds_box_10000_boxv_1 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rds_box_10000_boxv_1 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rds_box_10000_boxv_100 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rds_box_10000_boxv_100 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rds_box_2_5_boxv__100 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rds_box_2_5_boxv__100 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rds_box_2_5_boxv__1 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rds_box_2_5_boxv__1 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rds_box_2_5_boxv__1e_07 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rds_box_2_5_boxv__1e_07 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rds_box_2_5_boxv_0 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rds_box_2_5_boxv_0 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rds_box_2_5_boxv_1e_07 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rds_box_2_5_boxv_1e_07 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rds_box_2_5_boxv_1 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rds_box_2_5_boxv_1 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rds_box_2_5_boxv_100 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rds_box_2_5_boxv_100 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rds_box_10000_boxv__100 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rds_box_10000_boxv__100 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rds_box_10000_boxv__1 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rds_box_10000_boxv__1 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rds_box_10000_boxv__1e_07 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rds_box_10000_boxv__1e_07 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rds_box_10000_boxv_0 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rds_box_10000_boxv_0 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rds_box_10000_boxv_1e_07 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rds_box_10000_boxv_1e_07 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rds_box_10000_boxv_1 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rds_box_10000_boxv_1 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rds_box_10000_boxv_100 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rds_box_10000_boxv_100 (0 ms) 16: [----------] 140 tests from RhombDodecXYSquare/ParrRahmTest (83 ms total) 16: 16: [----------] 140 tests from RhombDodecXYHex/ParrRahmTest 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rdh_box_2_5_boxv__100 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rdh_box_2_5_boxv__100 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rdh_box_2_5_boxv__1 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rdh_box_2_5_boxv__1 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rdh_box_2_5_boxv__1e_07 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rdh_box_2_5_boxv__1e_07 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rdh_box_2_5_boxv_0 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rdh_box_2_5_boxv_0 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rdh_box_2_5_boxv_1e_07 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rdh_box_2_5_boxv_1e_07 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rdh_box_2_5_boxv_1 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rdh_box_2_5_boxv_1 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rdh_box_2_5_boxv_100 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rdh_box_2_5_boxv_100 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rdh_box_10000_boxv__100 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rdh_box_10000_boxv__100 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rdh_box_10000_boxv__1 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rdh_box_10000_boxv__1 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rdh_box_10000_boxv__1e_07 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rdh_box_10000_boxv__1e_07 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rdh_box_10000_boxv_0 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rdh_box_10000_boxv_0 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rdh_box_10000_boxv_1e_07 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rdh_box_10000_boxv_1e_07 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rdh_box_10000_boxv_1 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rdh_box_10000_boxv_1 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rdh_box_10000_boxv_100 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rdh_box_10000_boxv_100 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rdh_box_2_5_boxv__100 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rdh_box_2_5_boxv__100 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rdh_box_2_5_boxv__1 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rdh_box_2_5_boxv__1 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rdh_box_2_5_boxv__1e_07 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rdh_box_2_5_boxv__1e_07 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rdh_box_2_5_boxv_0 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rdh_box_2_5_boxv_0 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rdh_box_2_5_boxv_1e_07 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rdh_box_2_5_boxv_1e_07 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rdh_box_2_5_boxv_1 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rdh_box_2_5_boxv_1 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rdh_box_2_5_boxv_100 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rdh_box_2_5_boxv_100 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rdh_box_10000_boxv__100 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rdh_box_10000_boxv__100 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rdh_box_10000_boxv__1 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rdh_box_10000_boxv__1 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rdh_box_10000_boxv__1e_07 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rdh_box_10000_boxv__1e_07 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rdh_box_10000_boxv_0 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rdh_box_10000_boxv_0 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rdh_box_10000_boxv_1e_07 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rdh_box_10000_boxv_1e_07 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rdh_box_10000_boxv_1 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rdh_box_10000_boxv_1 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rdh_box_10000_boxv_100 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rdh_box_10000_boxv_100 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rdh_box_2_5_boxv__100 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rdh_box_2_5_boxv__100 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rdh_box_2_5_boxv__1 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rdh_box_2_5_boxv__1 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rdh_box_2_5_boxv__1e_07 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rdh_box_2_5_boxv__1e_07 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rdh_box_2_5_boxv_0 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rdh_box_2_5_boxv_0 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rdh_box_2_5_boxv_1e_07 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rdh_box_2_5_boxv_1e_07 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rdh_box_2_5_boxv_1 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rdh_box_2_5_boxv_1 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rdh_box_2_5_boxv_100 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rdh_box_2_5_boxv_100 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rdh_box_10000_boxv__100 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rdh_box_10000_boxv__100 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rdh_box_10000_boxv__1 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rdh_box_10000_boxv__1 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rdh_box_10000_boxv__1e_07 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rdh_box_10000_boxv__1e_07 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rdh_box_10000_boxv_0 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rdh_box_10000_boxv_0 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rdh_box_10000_boxv_1e_07 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rdh_box_10000_boxv_1e_07 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rdh_box_10000_boxv_1 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rdh_box_10000_boxv_1 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rdh_box_10000_boxv_100 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rdh_box_10000_boxv_100 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_general_shape_rdh_box_2_5_boxv__100 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_general_shape_rdh_box_2_5_boxv__100 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_general_shape_rdh_box_2_5_boxv__1 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_general_shape_rdh_box_2_5_boxv__1 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_general_shape_rdh_box_2_5_boxv__1e_07 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_general_shape_rdh_box_2_5_boxv__1e_07 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_general_shape_rdh_box_2_5_boxv_0 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_general_shape_rdh_box_2_5_boxv_0 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_general_shape_rdh_box_2_5_boxv_1e_07 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_general_shape_rdh_box_2_5_boxv_1e_07 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_general_shape_rdh_box_2_5_boxv_1 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_general_shape_rdh_box_2_5_boxv_1 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_general_shape_rdh_box_2_5_boxv_100 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_general_shape_rdh_box_2_5_boxv_100 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_general_shape_rdh_box_10000_boxv__100 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_general_shape_rdh_box_10000_boxv__100 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_general_shape_rdh_box_10000_boxv__1 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_general_shape_rdh_box_10000_boxv__1 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_general_shape_rdh_box_10000_boxv__1e_07 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_general_shape_rdh_box_10000_boxv__1e_07 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_general_shape_rdh_box_10000_boxv_0 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_general_shape_rdh_box_10000_boxv_0 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_general_shape_rdh_box_10000_boxv_1e_07 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_general_shape_rdh_box_10000_boxv_1e_07 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_general_shape_rdh_box_10000_boxv_1 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_general_shape_rdh_box_10000_boxv_1 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_general_shape_rdh_box_10000_boxv_100 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_general_shape_rdh_box_10000_boxv_100 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rdh_box_2_5_boxv__100 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rdh_box_2_5_boxv__100 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rdh_box_2_5_boxv__1 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rdh_box_2_5_boxv__1 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rdh_box_2_5_boxv__1e_07 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rdh_box_2_5_boxv__1e_07 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rdh_box_2_5_boxv_0 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rdh_box_2_5_boxv_0 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rdh_box_2_5_boxv_1e_07 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rdh_box_2_5_boxv_1e_07 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rdh_box_2_5_boxv_1 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rdh_box_2_5_boxv_1 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rdh_box_2_5_boxv_100 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rdh_box_2_5_boxv_100 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rdh_box_10000_boxv__100 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rdh_box_10000_boxv__100 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rdh_box_10000_boxv__1 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rdh_box_10000_boxv__1 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rdh_box_10000_boxv__1e_07 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rdh_box_10000_boxv__1e_07 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rdh_box_10000_boxv_0 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rdh_box_10000_boxv_0 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rdh_box_10000_boxv_1e_07 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rdh_box_10000_boxv_1e_07 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rdh_box_10000_boxv_1 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rdh_box_10000_boxv_1 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rdh_box_10000_boxv_100 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rdh_box_10000_boxv_100 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rdh_box_2_5_boxv__100 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rdh_box_2_5_boxv__100 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rdh_box_2_5_boxv__1 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rdh_box_2_5_boxv__1 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rdh_box_2_5_boxv__1e_07 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rdh_box_2_5_boxv__1e_07 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rdh_box_2_5_boxv_0 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rdh_box_2_5_boxv_0 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rdh_box_2_5_boxv_1e_07 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rdh_box_2_5_boxv_1e_07 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rdh_box_2_5_boxv_1 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rdh_box_2_5_boxv_1 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rdh_box_2_5_boxv_100 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rdh_box_2_5_boxv_100 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rdh_box_10000_boxv__100 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rdh_box_10000_boxv__100 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rdh_box_10000_boxv__1 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rdh_box_10000_boxv__1 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rdh_box_10000_boxv__1e_07 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rdh_box_10000_boxv__1e_07 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rdh_box_10000_boxv_0 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rdh_box_10000_boxv_0 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rdh_box_10000_boxv_1e_07 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rdh_box_10000_boxv_1e_07 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rdh_box_10000_boxv_1 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rdh_box_10000_boxv_1 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rdh_box_10000_boxv_100 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rdh_box_10000_boxv_100 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rdh_box_2_5_boxv__100 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rdh_box_2_5_boxv__100 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rdh_box_2_5_boxv__1 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rdh_box_2_5_boxv__1 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rdh_box_2_5_boxv__1e_07 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rdh_box_2_5_boxv__1e_07 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rdh_box_2_5_boxv_0 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rdh_box_2_5_boxv_0 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rdh_box_2_5_boxv_1e_07 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rdh_box_2_5_boxv_1e_07 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rdh_box_2_5_boxv_1 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rdh_box_2_5_boxv_1 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rdh_box_2_5_boxv_100 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rdh_box_2_5_boxv_100 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rdh_box_10000_boxv__100 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rdh_box_10000_boxv__100 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rdh_box_10000_boxv__1 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rdh_box_10000_boxv__1 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rdh_box_10000_boxv__1e_07 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rdh_box_10000_boxv__1e_07 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rdh_box_10000_boxv_0 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rdh_box_10000_boxv_0 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rdh_box_10000_boxv_1e_07 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rdh_box_10000_boxv_1e_07 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rdh_box_10000_boxv_1 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rdh_box_10000_boxv_1 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rdh_box_10000_boxv_100 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rdh_box_10000_boxv_100 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rdh_box_2_5_boxv__100 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rdh_box_2_5_boxv__100 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rdh_box_2_5_boxv__1 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rdh_box_2_5_boxv__1 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rdh_box_2_5_boxv__1e_07 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rdh_box_2_5_boxv__1e_07 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rdh_box_2_5_boxv_0 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rdh_box_2_5_boxv_0 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rdh_box_2_5_boxv_1e_07 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rdh_box_2_5_boxv_1e_07 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rdh_box_2_5_boxv_1 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rdh_box_2_5_boxv_1 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rdh_box_2_5_boxv_100 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rdh_box_2_5_boxv_100 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rdh_box_10000_boxv__100 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rdh_box_10000_boxv__100 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rdh_box_10000_boxv__1 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rdh_box_10000_boxv__1 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rdh_box_10000_boxv__1e_07 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rdh_box_10000_boxv__1e_07 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rdh_box_10000_boxv_0 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rdh_box_10000_boxv_0 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rdh_box_10000_boxv_1e_07 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rdh_box_10000_boxv_1e_07 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rdh_box_10000_boxv_1 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rdh_box_10000_boxv_1 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rdh_box_10000_boxv_100 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rdh_box_10000_boxv_100 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rdh_box_2_5_boxv__100 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rdh_box_2_5_boxv__100 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rdh_box_2_5_boxv__1 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rdh_box_2_5_boxv__1 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rdh_box_2_5_boxv__1e_07 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rdh_box_2_5_boxv__1e_07 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rdh_box_2_5_boxv_0 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rdh_box_2_5_boxv_0 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rdh_box_2_5_boxv_1e_07 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rdh_box_2_5_boxv_1e_07 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rdh_box_2_5_boxv_1 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rdh_box_2_5_boxv_1 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rdh_box_2_5_boxv_100 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rdh_box_2_5_boxv_100 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rdh_box_10000_boxv__100 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rdh_box_10000_boxv__100 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rdh_box_10000_boxv__1 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rdh_box_10000_boxv__1 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rdh_box_10000_boxv__1e_07 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rdh_box_10000_boxv__1e_07 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rdh_box_10000_boxv_0 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rdh_box_10000_boxv_0 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rdh_box_10000_boxv_1e_07 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rdh_box_10000_boxv_1e_07 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rdh_box_10000_boxv_1 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rdh_box_10000_boxv_1 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rdh_box_10000_boxv_100 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rdh_box_10000_boxv_100 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rdh_box_2_5_boxv__100 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rdh_box_2_5_boxv__100 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rdh_box_2_5_boxv__1 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rdh_box_2_5_boxv__1 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rdh_box_2_5_boxv__1e_07 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rdh_box_2_5_boxv__1e_07 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rdh_box_2_5_boxv_0 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rdh_box_2_5_boxv_0 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rdh_box_2_5_boxv_1e_07 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rdh_box_2_5_boxv_1e_07 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rdh_box_2_5_boxv_1 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rdh_box_2_5_boxv_1 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rdh_box_2_5_boxv_100 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rdh_box_2_5_boxv_100 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rdh_box_10000_boxv__100 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rdh_box_10000_boxv__100 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rdh_box_10000_boxv__1 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rdh_box_10000_boxv__1 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rdh_box_10000_boxv__1e_07 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rdh_box_10000_boxv__1e_07 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rdh_box_10000_boxv_0 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rdh_box_10000_boxv_0 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rdh_box_10000_boxv_1e_07 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rdh_box_10000_boxv_1e_07 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rdh_box_10000_boxv_1 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rdh_box_10000_boxv_1 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rdh_box_10000_boxv_100 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rdh_box_10000_boxv_100 (0 ms) 16: [----------] 140 tests from RhombDodecXYHex/ParrRahmTest (83 ms total) 16: 16: [----------] 140 tests from TruncOct/ParrRahmTest 16: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_to_box_2_5_boxv__100 16: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_to_box_2_5_boxv__100 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_to_box_2_5_boxv__1 16: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_to_box_2_5_boxv__1 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_to_box_2_5_boxv__1e_07 16: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_to_box_2_5_boxv__1e_07 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_to_box_2_5_boxv_0 16: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_to_box_2_5_boxv_0 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_to_box_2_5_boxv_1e_07 16: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_to_box_2_5_boxv_1e_07 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_to_box_2_5_boxv_1 16: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_to_box_2_5_boxv_1 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_to_box_2_5_boxv_100 16: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_to_box_2_5_boxv_100 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_to_box_10000_boxv__100 16: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_to_box_10000_boxv__100 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_to_box_10000_boxv__1 16: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_to_box_10000_boxv__1 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_to_box_10000_boxv__1e_07 16: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_to_box_10000_boxv__1e_07 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_to_box_10000_boxv_0 16: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_to_box_10000_boxv_0 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_to_box_10000_boxv_1e_07 16: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_to_box_10000_boxv_1e_07 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_to_box_10000_boxv_1 16: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_to_box_10000_boxv_1 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_to_box_10000_boxv_100 16: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_to_box_10000_boxv_100 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_to_box_2_5_boxv__100 16: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_to_box_2_5_boxv__100 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_to_box_2_5_boxv__1 16: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_to_box_2_5_boxv__1 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_to_box_2_5_boxv__1e_07 16: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_to_box_2_5_boxv__1e_07 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_to_box_2_5_boxv_0 16: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_to_box_2_5_boxv_0 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_to_box_2_5_boxv_1e_07 16: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_to_box_2_5_boxv_1e_07 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_to_box_2_5_boxv_1 16: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_to_box_2_5_boxv_1 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_to_box_2_5_boxv_100 16: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_to_box_2_5_boxv_100 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_to_box_10000_boxv__100 16: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_to_box_10000_boxv__100 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_to_box_10000_boxv__1 16: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_to_box_10000_boxv__1 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_to_box_10000_boxv__1e_07 16: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_to_box_10000_boxv__1e_07 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_to_box_10000_boxv_0 16: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_to_box_10000_boxv_0 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_to_box_10000_boxv_1e_07 16: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_to_box_10000_boxv_1e_07 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_to_box_10000_boxv_1 16: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_to_box_10000_boxv_1 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_to_box_10000_boxv_100 16: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_to_box_10000_boxv_100 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_to_box_2_5_boxv__100 16: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_to_box_2_5_boxv__100 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_to_box_2_5_boxv__1 16: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_to_box_2_5_boxv__1 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_to_box_2_5_boxv__1e_07 16: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_to_box_2_5_boxv__1e_07 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_to_box_2_5_boxv_0 16: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_to_box_2_5_boxv_0 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_to_box_2_5_boxv_1e_07 16: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_to_box_2_5_boxv_1e_07 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_to_box_2_5_boxv_1 16: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_to_box_2_5_boxv_1 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_to_box_2_5_boxv_100 16: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_to_box_2_5_boxv_100 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_to_box_10000_boxv__100 16: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_to_box_10000_boxv__100 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_to_box_10000_boxv__1 16: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_to_box_10000_boxv__1 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_to_box_10000_boxv__1e_07 16: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_to_box_10000_boxv__1e_07 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_to_box_10000_boxv_0 16: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_to_box_10000_boxv_0 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_to_box_10000_boxv_1e_07 16: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_to_box_10000_boxv_1e_07 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_to_box_10000_boxv_1 16: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_to_box_10000_boxv_1 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_to_box_10000_boxv_100 16: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_to_box_10000_boxv_100 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_general_shape_to_box_2_5_boxv__100 16: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_general_shape_to_box_2_5_boxv__100 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_general_shape_to_box_2_5_boxv__1 16: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_general_shape_to_box_2_5_boxv__1 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_general_shape_to_box_2_5_boxv__1e_07 16: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_general_shape_to_box_2_5_boxv__1e_07 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_general_shape_to_box_2_5_boxv_0 16: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_general_shape_to_box_2_5_boxv_0 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_general_shape_to_box_2_5_boxv_1e_07 16: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_general_shape_to_box_2_5_boxv_1e_07 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_general_shape_to_box_2_5_boxv_1 16: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_general_shape_to_box_2_5_boxv_1 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_general_shape_to_box_2_5_boxv_100 16: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_general_shape_to_box_2_5_boxv_100 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_general_shape_to_box_10000_boxv__100 16: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_general_shape_to_box_10000_boxv__100 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_general_shape_to_box_10000_boxv__1 16: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_general_shape_to_box_10000_boxv__1 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_general_shape_to_box_10000_boxv__1e_07 16: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_general_shape_to_box_10000_boxv__1e_07 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_general_shape_to_box_10000_boxv_0 16: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_general_shape_to_box_10000_boxv_0 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_general_shape_to_box_10000_boxv_1e_07 16: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_general_shape_to_box_10000_boxv_1e_07 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_general_shape_to_box_10000_boxv_1 16: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_general_shape_to_box_10000_boxv_1 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_general_shape_to_box_10000_boxv_100 16: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_general_shape_to_box_10000_boxv_100 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_to_box_2_5_boxv__100 16: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_to_box_2_5_boxv__100 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_to_box_2_5_boxv__1 16: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_to_box_2_5_boxv__1 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_to_box_2_5_boxv__1e_07 16: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_to_box_2_5_boxv__1e_07 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_to_box_2_5_boxv_0 16: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_to_box_2_5_boxv_0 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_to_box_2_5_boxv_1e_07 16: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_to_box_2_5_boxv_1e_07 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_to_box_2_5_boxv_1 16: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_to_box_2_5_boxv_1 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_to_box_2_5_boxv_100 16: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_to_box_2_5_boxv_100 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_to_box_10000_boxv__100 16: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_to_box_10000_boxv__100 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_to_box_10000_boxv__1 16: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_to_box_10000_boxv__1 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_to_box_10000_boxv__1e_07 16: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_to_box_10000_boxv__1e_07 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_to_box_10000_boxv_0 16: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_to_box_10000_boxv_0 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_to_box_10000_boxv_1e_07 16: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_to_box_10000_boxv_1e_07 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_to_box_10000_boxv_1 16: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_to_box_10000_boxv_1 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_to_box_10000_boxv_100 16: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_to_box_10000_boxv_100 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_to_box_2_5_boxv__100 16: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_to_box_2_5_boxv__100 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_to_box_2_5_boxv__1 16: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_to_box_2_5_boxv__1 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_to_box_2_5_boxv__1e_07 16: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_to_box_2_5_boxv__1e_07 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_to_box_2_5_boxv_0 16: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_to_box_2_5_boxv_0 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_to_box_2_5_boxv_1e_07 16: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_to_box_2_5_boxv_1e_07 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_to_box_2_5_boxv_1 16: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_to_box_2_5_boxv_1 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_to_box_2_5_boxv_100 16: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_to_box_2_5_boxv_100 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_to_box_10000_boxv__100 16: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_to_box_10000_boxv__100 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_to_box_10000_boxv__1 16: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_to_box_10000_boxv__1 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_to_box_10000_boxv__1e_07 16: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_to_box_10000_boxv__1e_07 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_to_box_10000_boxv_0 16: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_to_box_10000_boxv_0 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_to_box_10000_boxv_1e_07 16: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_to_box_10000_boxv_1e_07 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_to_box_10000_boxv_1 16: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_to_box_10000_boxv_1 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_to_box_10000_boxv_100 16: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_to_box_10000_boxv_100 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_to_box_2_5_boxv__100 16: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_to_box_2_5_boxv__100 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_to_box_2_5_boxv__1 16: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_to_box_2_5_boxv__1 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_to_box_2_5_boxv__1e_07 16: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_to_box_2_5_boxv__1e_07 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_to_box_2_5_boxv_0 16: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_to_box_2_5_boxv_0 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_to_box_2_5_boxv_1e_07 16: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_to_box_2_5_boxv_1e_07 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_to_box_2_5_boxv_1 16: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_to_box_2_5_boxv_1 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_to_box_2_5_boxv_100 16: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_to_box_2_5_boxv_100 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_to_box_10000_boxv__100 16: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_to_box_10000_boxv__100 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_to_box_10000_boxv__1 16: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_to_box_10000_boxv__1 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_to_box_10000_boxv__1e_07 16: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_to_box_10000_boxv__1e_07 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_to_box_10000_boxv_0 16: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_to_box_10000_boxv_0 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_to_box_10000_boxv_1e_07 16: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_to_box_10000_boxv_1e_07 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_to_box_10000_boxv_1 16: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_to_box_10000_boxv_1 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_to_box_10000_boxv_100 16: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_to_box_10000_boxv_100 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_to_box_2_5_boxv__100 16: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_to_box_2_5_boxv__100 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_to_box_2_5_boxv__1 16: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_to_box_2_5_boxv__1 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_to_box_2_5_boxv__1e_07 16: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_to_box_2_5_boxv__1e_07 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_to_box_2_5_boxv_0 16: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_to_box_2_5_boxv_0 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_to_box_2_5_boxv_1e_07 16: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_to_box_2_5_boxv_1e_07 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_to_box_2_5_boxv_1 16: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_to_box_2_5_boxv_1 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_to_box_2_5_boxv_100 16: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_to_box_2_5_boxv_100 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_to_box_10000_boxv__100 16: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_to_box_10000_boxv__100 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_to_box_10000_boxv__1 16: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_to_box_10000_boxv__1 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_to_box_10000_boxv__1e_07 16: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_to_box_10000_boxv__1e_07 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_to_box_10000_boxv_0 16: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_to_box_10000_boxv_0 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_to_box_10000_boxv_1e_07 16: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_to_box_10000_boxv_1e_07 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_to_box_10000_boxv_1 16: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_to_box_10000_boxv_1 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_to_box_10000_boxv_100 16: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_to_box_10000_boxv_100 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_general_shape_to_box_2_5_boxv__100 16: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_general_shape_to_box_2_5_boxv__100 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_general_shape_to_box_2_5_boxv__1 16: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_general_shape_to_box_2_5_boxv__1 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_general_shape_to_box_2_5_boxv__1e_07 16: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_general_shape_to_box_2_5_boxv__1e_07 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_general_shape_to_box_2_5_boxv_0 16: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_general_shape_to_box_2_5_boxv_0 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_general_shape_to_box_2_5_boxv_1e_07 16: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_general_shape_to_box_2_5_boxv_1e_07 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_general_shape_to_box_2_5_boxv_1 16: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_general_shape_to_box_2_5_boxv_1 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_general_shape_to_box_2_5_boxv_100 16: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_general_shape_to_box_2_5_boxv_100 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_general_shape_to_box_10000_boxv__100 16: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_general_shape_to_box_10000_boxv__100 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_general_shape_to_box_10000_boxv__1 16: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_general_shape_to_box_10000_boxv__1 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_general_shape_to_box_10000_boxv__1e_07 16: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_general_shape_to_box_10000_boxv__1e_07 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_general_shape_to_box_10000_boxv_0 16: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_general_shape_to_box_10000_boxv_0 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_general_shape_to_box_10000_boxv_1e_07 16: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_general_shape_to_box_10000_boxv_1e_07 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_general_shape_to_box_10000_boxv_1 16: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_general_shape_to_box_10000_boxv_1 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_general_shape_to_box_10000_boxv_100 16: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_general_shape_to_box_10000_boxv_100 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_to_box_2_5_boxv__100 16: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_to_box_2_5_boxv__100 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_to_box_2_5_boxv__1 16: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_to_box_2_5_boxv__1 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_to_box_2_5_boxv__1e_07 16: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_to_box_2_5_boxv__1e_07 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_to_box_2_5_boxv_0 16: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_to_box_2_5_boxv_0 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_to_box_2_5_boxv_1e_07 16: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_to_box_2_5_boxv_1e_07 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_to_box_2_5_boxv_1 16: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_to_box_2_5_boxv_1 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_to_box_2_5_boxv_100 16: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_to_box_2_5_boxv_100 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_to_box_10000_boxv__100 16: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_to_box_10000_boxv__100 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_to_box_10000_boxv__1 16: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_to_box_10000_boxv__1 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_to_box_10000_boxv__1e_07 16: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_to_box_10000_boxv__1e_07 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_to_box_10000_boxv_0 16: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_to_box_10000_boxv_0 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_to_box_10000_boxv_1e_07 16: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_to_box_10000_boxv_1e_07 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_to_box_10000_boxv_1 16: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_to_box_10000_boxv_1 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_to_box_10000_boxv_100 16: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_to_box_10000_boxv_100 (0 ms) 16: [----------] 140 tests from TruncOct/ParrRahmTest (80 ms total) 16: 16: [----------] 140 tests from Other/ParrRahmTest 16: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_other_box_2_5_boxv__100 16: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_other_box_2_5_boxv__100 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_other_box_2_5_boxv__1 16: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_other_box_2_5_boxv__1 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_other_box_2_5_boxv__1e_07 16: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_other_box_2_5_boxv__1e_07 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_other_box_2_5_boxv_0 16: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_other_box_2_5_boxv_0 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_other_box_2_5_boxv_1e_07 16: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_other_box_2_5_boxv_1e_07 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_other_box_2_5_boxv_1 16: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_other_box_2_5_boxv_1 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_other_box_2_5_boxv_100 16: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_other_box_2_5_boxv_100 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_other_box_10000_boxv__100 16: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_other_box_10000_boxv__100 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_other_box_10000_boxv__1 16: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_other_box_10000_boxv__1 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_other_box_10000_boxv__1e_07 16: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_other_box_10000_boxv__1e_07 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_other_box_10000_boxv_0 16: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_other_box_10000_boxv_0 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_other_box_10000_boxv_1e_07 16: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_other_box_10000_boxv_1e_07 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_other_box_10000_boxv_1 16: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_other_box_10000_boxv_1 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_other_box_10000_boxv_100 16: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_other_box_10000_boxv_100 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_other_box_2_5_boxv__100 16: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_other_box_2_5_boxv__100 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_other_box_2_5_boxv__1 16: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_other_box_2_5_boxv__1 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_other_box_2_5_boxv__1e_07 16: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_other_box_2_5_boxv__1e_07 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_other_box_2_5_boxv_0 16: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_other_box_2_5_boxv_0 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_other_box_2_5_boxv_1e_07 16: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_other_box_2_5_boxv_1e_07 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_other_box_2_5_boxv_1 16: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_other_box_2_5_boxv_1 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_other_box_2_5_boxv_100 16: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_other_box_2_5_boxv_100 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_other_box_10000_boxv__100 16: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_other_box_10000_boxv__100 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_other_box_10000_boxv__1 16: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_other_box_10000_boxv__1 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_other_box_10000_boxv__1e_07 16: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_other_box_10000_boxv__1e_07 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_other_box_10000_boxv_0 16: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_other_box_10000_boxv_0 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_other_box_10000_boxv_1e_07 16: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_other_box_10000_boxv_1e_07 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_other_box_10000_boxv_1 16: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_other_box_10000_boxv_1 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_other_box_10000_boxv_100 16: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_other_box_10000_boxv_100 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_other_box_2_5_boxv__100 16: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_other_box_2_5_boxv__100 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_other_box_2_5_boxv__1 16: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_other_box_2_5_boxv__1 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_other_box_2_5_boxv__1e_07 16: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_other_box_2_5_boxv__1e_07 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_other_box_2_5_boxv_0 16: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_other_box_2_5_boxv_0 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_other_box_2_5_boxv_1e_07 16: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_other_box_2_5_boxv_1e_07 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_other_box_2_5_boxv_1 16: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_other_box_2_5_boxv_1 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_other_box_2_5_boxv_100 16: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_other_box_2_5_boxv_100 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_other_box_10000_boxv__100 16: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_other_box_10000_boxv__100 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_other_box_10000_boxv__1 16: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_other_box_10000_boxv__1 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_other_box_10000_boxv__1e_07 16: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_other_box_10000_boxv__1e_07 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_other_box_10000_boxv_0 16: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_other_box_10000_boxv_0 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_other_box_10000_boxv_1e_07 16: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_other_box_10000_boxv_1e_07 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_other_box_10000_boxv_1 16: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_other_box_10000_boxv_1 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_other_box_10000_boxv_100 16: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_other_box_10000_boxv_100 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_general_shape_other_box_2_5_boxv__100 16: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_general_shape_other_box_2_5_boxv__100 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_general_shape_other_box_2_5_boxv__1 16: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_general_shape_other_box_2_5_boxv__1 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_general_shape_other_box_2_5_boxv__1e_07 16: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_general_shape_other_box_2_5_boxv__1e_07 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_general_shape_other_box_2_5_boxv_0 16: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_general_shape_other_box_2_5_boxv_0 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_general_shape_other_box_2_5_boxv_1e_07 16: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_general_shape_other_box_2_5_boxv_1e_07 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_general_shape_other_box_2_5_boxv_1 16: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_general_shape_other_box_2_5_boxv_1 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_general_shape_other_box_2_5_boxv_100 16: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_general_shape_other_box_2_5_boxv_100 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_general_shape_other_box_10000_boxv__100 16: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_general_shape_other_box_10000_boxv__100 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_general_shape_other_box_10000_boxv__1 16: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_general_shape_other_box_10000_boxv__1 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_general_shape_other_box_10000_boxv__1e_07 16: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_general_shape_other_box_10000_boxv__1e_07 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_general_shape_other_box_10000_boxv_0 16: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_general_shape_other_box_10000_boxv_0 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_general_shape_other_box_10000_boxv_1e_07 16: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_general_shape_other_box_10000_boxv_1e_07 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_general_shape_other_box_10000_boxv_1 16: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_general_shape_other_box_10000_boxv_1 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_general_shape_other_box_10000_boxv_100 16: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_general_shape_other_box_10000_boxv_100 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_other_box_2_5_boxv__100 16: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_other_box_2_5_boxv__100 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_other_box_2_5_boxv__1 16: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_other_box_2_5_boxv__1 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_other_box_2_5_boxv__1e_07 16: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_other_box_2_5_boxv__1e_07 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_other_box_2_5_boxv_0 16: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_other_box_2_5_boxv_0 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_other_box_2_5_boxv_1e_07 16: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_other_box_2_5_boxv_1e_07 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_other_box_2_5_boxv_1 16: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_other_box_2_5_boxv_1 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_other_box_2_5_boxv_100 16: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_other_box_2_5_boxv_100 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_other_box_10000_boxv__100 16: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_other_box_10000_boxv__100 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_other_box_10000_boxv__1 16: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_other_box_10000_boxv__1 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_other_box_10000_boxv__1e_07 16: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_other_box_10000_boxv__1e_07 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_other_box_10000_boxv_0 16: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_other_box_10000_boxv_0 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_other_box_10000_boxv_1e_07 16: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_other_box_10000_boxv_1e_07 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_other_box_10000_boxv_1 16: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_other_box_10000_boxv_1 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_other_box_10000_boxv_100 16: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_other_box_10000_boxv_100 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_other_box_2_5_boxv__100 16: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_other_box_2_5_boxv__100 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_other_box_2_5_boxv__1 16: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_other_box_2_5_boxv__1 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_other_box_2_5_boxv__1e_07 16: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_other_box_2_5_boxv__1e_07 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_other_box_2_5_boxv_0 16: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_other_box_2_5_boxv_0 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_other_box_2_5_boxv_1e_07 16: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_other_box_2_5_boxv_1e_07 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_other_box_2_5_boxv_1 16: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_other_box_2_5_boxv_1 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_other_box_2_5_boxv_100 16: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_other_box_2_5_boxv_100 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_other_box_10000_boxv__100 16: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_other_box_10000_boxv__100 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_other_box_10000_boxv__1 16: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_other_box_10000_boxv__1 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_other_box_10000_boxv__1e_07 16: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_other_box_10000_boxv__1e_07 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_other_box_10000_boxv_0 16: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_other_box_10000_boxv_0 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_other_box_10000_boxv_1e_07 16: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_other_box_10000_boxv_1e_07 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_other_box_10000_boxv_1 16: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_other_box_10000_boxv_1 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_other_box_10000_boxv_100 16: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_other_box_10000_boxv_100 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_other_box_2_5_boxv__100 16: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_other_box_2_5_boxv__100 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_other_box_2_5_boxv__1 16: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_other_box_2_5_boxv__1 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_other_box_2_5_boxv__1e_07 16: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_other_box_2_5_boxv__1e_07 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_other_box_2_5_boxv_0 16: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_other_box_2_5_boxv_0 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_other_box_2_5_boxv_1e_07 16: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_other_box_2_5_boxv_1e_07 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_other_box_2_5_boxv_1 16: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_other_box_2_5_boxv_1 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_other_box_2_5_boxv_100 16: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_other_box_2_5_boxv_100 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_other_box_10000_boxv__100 16: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_other_box_10000_boxv__100 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_other_box_10000_boxv__1 16: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_other_box_10000_boxv__1 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_other_box_10000_boxv__1e_07 16: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_other_box_10000_boxv__1e_07 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_other_box_10000_boxv_0 16: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_other_box_10000_boxv_0 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_other_box_10000_boxv_1e_07 16: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_other_box_10000_boxv_1e_07 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_other_box_10000_boxv_1 16: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_other_box_10000_boxv_1 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_other_box_10000_boxv_100 16: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_other_box_10000_boxv_100 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_other_box_2_5_boxv__100 16: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_other_box_2_5_boxv__100 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_other_box_2_5_boxv__1 16: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_other_box_2_5_boxv__1 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_other_box_2_5_boxv__1e_07 16: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_other_box_2_5_boxv__1e_07 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_other_box_2_5_boxv_0 16: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_other_box_2_5_boxv_0 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_other_box_2_5_boxv_1e_07 16: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_other_box_2_5_boxv_1e_07 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_other_box_2_5_boxv_1 16: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_other_box_2_5_boxv_1 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_other_box_2_5_boxv_100 16: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_other_box_2_5_boxv_100 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_other_box_10000_boxv__100 16: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_other_box_10000_boxv__100 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_other_box_10000_boxv__1 16: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_other_box_10000_boxv__1 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_other_box_10000_boxv__1e_07 16: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_other_box_10000_boxv__1e_07 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_other_box_10000_boxv_0 16: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_other_box_10000_boxv_0 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_other_box_10000_boxv_1e_07 16: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_other_box_10000_boxv_1e_07 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_other_box_10000_boxv_1 16: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_other_box_10000_boxv_1 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_other_box_10000_boxv_100 16: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_other_box_10000_boxv_100 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_general_shape_other_box_2_5_boxv__100 16: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_general_shape_other_box_2_5_boxv__100 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_general_shape_other_box_2_5_boxv__1 16: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_general_shape_other_box_2_5_boxv__1 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_general_shape_other_box_2_5_boxv__1e_07 16: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_general_shape_other_box_2_5_boxv__1e_07 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_general_shape_other_box_2_5_boxv_0 16: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_general_shape_other_box_2_5_boxv_0 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_general_shape_other_box_2_5_boxv_1e_07 16: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_general_shape_other_box_2_5_boxv_1e_07 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_general_shape_other_box_2_5_boxv_1 16: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_general_shape_other_box_2_5_boxv_1 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_general_shape_other_box_2_5_boxv_100 16: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_general_shape_other_box_2_5_boxv_100 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_general_shape_other_box_10000_boxv__100 16: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_general_shape_other_box_10000_boxv__100 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_general_shape_other_box_10000_boxv__1 16: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_general_shape_other_box_10000_boxv__1 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_general_shape_other_box_10000_boxv__1e_07 16: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_general_shape_other_box_10000_boxv__1e_07 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_general_shape_other_box_10000_boxv_0 16: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_general_shape_other_box_10000_boxv_0 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_general_shape_other_box_10000_boxv_1e_07 16: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_general_shape_other_box_10000_boxv_1e_07 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_general_shape_other_box_10000_boxv_1 16: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_general_shape_other_box_10000_boxv_1 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_general_shape_other_box_10000_boxv_100 16: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_general_shape_other_box_10000_boxv_100 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_other_box_2_5_boxv__100 16: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_other_box_2_5_boxv__100 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_other_box_2_5_boxv__1 16: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_other_box_2_5_boxv__1 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_other_box_2_5_boxv__1e_07 16: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_other_box_2_5_boxv__1e_07 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_other_box_2_5_boxv_0 16: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_other_box_2_5_boxv_0 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_other_box_2_5_boxv_1e_07 16: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_other_box_2_5_boxv_1e_07 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_other_box_2_5_boxv_1 16: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_other_box_2_5_boxv_1 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_other_box_2_5_boxv_100 16: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_other_box_2_5_boxv_100 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_other_box_10000_boxv__100 16: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_other_box_10000_boxv__100 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_other_box_10000_boxv__1 16: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_other_box_10000_boxv__1 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_other_box_10000_boxv__1e_07 16: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_other_box_10000_boxv__1e_07 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_other_box_10000_boxv_0 16: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_other_box_10000_boxv_0 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_other_box_10000_boxv_1e_07 16: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_other_box_10000_boxv_1e_07 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_other_box_10000_boxv_1 16: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_other_box_10000_boxv_1 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_other_box_10000_boxv_100 16: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_other_box_10000_boxv_100 (0 ms) 16: [----------] 140 tests from Other/ParrRahmTest (79 ms total) 16: 16: [----------] 13 tests from WithParameters/SettleTest 16: [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/0 16: [ OK ] WithParameters/SettleTest.SatisfiesConstraints/0 (1 ms) 16: [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/1 16: [ OK ] WithParameters/SettleTest.SatisfiesConstraints/1 (0 ms) 16: [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/2 16: [ OK ] WithParameters/SettleTest.SatisfiesConstraints/2 (1 ms) 16: [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/3 16: [ OK ] WithParameters/SettleTest.SatisfiesConstraints/3 (1 ms) 16: [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/4 16: [ OK ] WithParameters/SettleTest.SatisfiesConstraints/4 (1 ms) 16: [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/5 16: [ OK ] WithParameters/SettleTest.SatisfiesConstraints/5 (2 ms) 16: [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/6 16: [ OK ] WithParameters/SettleTest.SatisfiesConstraints/6 (2 ms) 16: [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/7 16: [ OK ] WithParameters/SettleTest.SatisfiesConstraints/7 (3 ms) 16: [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/8 16: [ OK ] WithParameters/SettleTest.SatisfiesConstraints/8 (7 ms) 16: [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/9 16: [ OK ] WithParameters/SettleTest.SatisfiesConstraints/9 (3 ms) 16: [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/10 16: [ OK ] WithParameters/SettleTest.SatisfiesConstraints/10 (3 ms) 16: [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/11 16: [ OK ] WithParameters/SettleTest.SatisfiesConstraints/11 (6 ms) 16: [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/12 16: [ OK ] WithParameters/SettleTest.SatisfiesConstraints/12 (6 ms) 16: [----------] 13 tests from WithParameters/SettleTest (50 ms total) 16: 16: [----------] Global test environment tear-down 16: [==========] 1032 tests from 27 test suites ran. (1056 ms total) 16: [ PASSED ] 1032 tests. 16/92 Test #16: MdlibUnitTest ............................. Passed 1.69 sec test 17 Start 17: AwhTest 17: Test command: /build/reproducible-path/gromacs-2025.1/build/basic/bin/awh-test "--gtest_output=xml:/build/reproducible-path/gromacs-2025.1/build/basic/Testing/Temporary/AwhTest.xml" 17: Working Directory: /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/applied_forces/awh/tests 17: Test timeout computed to be: 30 17: [==========] Running 27 tests from 10 test suites. 17: [----------] Global test environment set-up. 17: [----------] 3 tests from SerializationTest 17: [ RUN ] SerializationTest.CanSerializeDimParams 17: [ OK ] SerializationTest.CanSerializeDimParams (0 ms) 17: [ RUN ] SerializationTest.CanSerializeBiasParams 17: [ OK ] SerializationTest.CanSerializeBiasParams (0 ms) 17: [ RUN ] SerializationTest.CanSerializeAwhParams 17: [ OK ] SerializationTest.CanSerializeAwhParams (0 ms) 17: [----------] 3 tests from SerializationTest (0 ms total) 17: 17: [----------] 1 test from BiasTest 17: [ RUN ] BiasTest.DetectsCovering 17: [ OK ] BiasTest.DetectsCovering (6 ms) 17: [----------] 1 test from BiasTest (6 ms total) 17: 17: [----------] 1 test from biasGridTest 17: [ RUN ] biasGridTest.neighborhood 17: [ OK ] biasGridTest.neighborhood (9 ms) 17: [----------] 1 test from biasGridTest (9 ms total) 17: 17: [----------] 2 tests from BiasSharingTest 17: [ RUN ] BiasSharingTest.SharingWorks 17: [ OK ] BiasSharingTest.SharingWorks (57 ms) 17: [ RUN ] BiasSharingTest.SharingScalingByMetricWorks 17: [ OK ] BiasSharingTest.SharingScalingByMetricWorks (47 ms) 17: [----------] 2 tests from BiasSharingTest (105 ms total) 17: 17: [----------] 2 tests from BiasFepLambdaStateTest 17: [ RUN ] BiasFepLambdaStateTest.DetectsCovering 17: [ OK ] BiasFepLambdaStateTest.DetectsCovering (25 ms) 17: [ RUN ] BiasFepLambdaStateTest.DetectsLargeNegativeForeignEnergy 17: [ OK ] BiasFepLambdaStateTest.DetectsLargeNegativeForeignEnergy (0 ms) 17: [----------] 2 tests from BiasFepLambdaStateTest (26 ms total) 17: 17: [----------] 8 tests from WithParameters/BiasTest 17: [ RUN ] WithParameters/BiasTest.ForcesBiasPmfWeightSum/0 17: [ OK ] WithParameters/BiasTest.ForcesBiasPmfWeightSum/0 (4 ms) 17: [ RUN ] WithParameters/BiasTest.ForcesBiasPmfWeightSum/1 17: [ OK ] WithParameters/BiasTest.ForcesBiasPmfWeightSum/1 (3 ms) 17: [ RUN ] WithParameters/BiasTest.ForcesBiasPmfWeightSum/2 17: [ OK ] WithParameters/BiasTest.ForcesBiasPmfWeightSum/2 (3 ms) 17: [ RUN ] WithParameters/BiasTest.ForcesBiasPmfWeightSum/3 17: [ OK ] WithParameters/BiasTest.ForcesBiasPmfWeightSum/3 (3 ms) 17: [ RUN ] WithParameters/BiasTest.ForcesBiasPmfWeightSum/4 17: [ OK ] WithParameters/BiasTest.ForcesBiasPmfWeightSum/4 (3 ms) 17: [ RUN ] WithParameters/BiasTest.ForcesBiasPmfWeightSum/5 17: [ OK ] WithParameters/BiasTest.ForcesBiasPmfWeightSum/5 (4 ms) 17: [ RUN ] WithParameters/BiasTest.ForcesBiasPmfWeightSum/6 17: [ OK ] WithParameters/BiasTest.ForcesBiasPmfWeightSum/6 (3 ms) 17: [ RUN ] WithParameters/BiasTest.ForcesBiasPmfWeightSum/7 17: [ OK ] WithParameters/BiasTest.ForcesBiasPmfWeightSum/7 (3 ms) 17: [----------] 8 tests from WithParameters/BiasTest (34 ms total) 17: 17: [----------] 2 tests from WithParameters/BiasStateTest 17: [ RUN ] WithParameters/BiasStateTest.InitializesFromFile/0 17: [ OK ] WithParameters/BiasStateTest.InitializesFromFile/0 (1 ms) 17: [ RUN ] WithParameters/BiasStateTest.InitializesFromFile/1 17: [ OK ] WithParameters/BiasStateTest.InitializesFromFile/1 (1 ms) 17: [----------] 2 tests from WithParameters/BiasStateTest (3 ms total) 17: 17: [----------] 1 test from WithParameters/UserInputTest 17: [ RUN ] WithParameters/UserInputTest.ParsesUser3DInput/0 17: [ OK ] WithParameters/UserInputTest.ParsesUser3DInput/0 (2 ms) 17: [----------] 1 test from WithParameters/UserInputTest (2 ms total) 17: 17: [----------] 4 tests from WithParameters/BiasFepLambdaStateTest 17: [ RUN ] WithParameters/BiasFepLambdaStateTest.ForcesBiasPmf/0 17: [ OK ] WithParameters/BiasFepLambdaStateTest.ForcesBiasPmf/0 (53 ms) 17: [ RUN ] WithParameters/BiasFepLambdaStateTest.ForcesBiasPmf/1 17: [ OK ] WithParameters/BiasFepLambdaStateTest.ForcesBiasPmf/1 (53 ms) 17: [ RUN ] WithParameters/BiasFepLambdaStateTest.ForcesBiasPmf/2 17: [ OK ] WithParameters/BiasFepLambdaStateTest.ForcesBiasPmf/2 (53 ms) 17: [ RUN ] WithParameters/BiasFepLambdaStateTest.ForcesBiasPmf/3 17: [ OK ] WithParameters/BiasFepLambdaStateTest.ForcesBiasPmf/3 (48 ms) 17: [----------] 4 tests from WithParameters/BiasFepLambdaStateTest (218 ms total) 17: 17: [----------] 3 tests from WithParameters/FrictionMetricTest 17: [ RUN ] WithParameters/FrictionMetricTest.FrictionMetric/0 17: [ OK ] WithParameters/FrictionMetricTest.FrictionMetric/0 (1 ms) 17: [ RUN ] WithParameters/FrictionMetricTest.FrictionMetric/1 17: [ OK ] WithParameters/FrictionMetricTest.FrictionMetric/1 (8 ms) 17: [ RUN ] WithParameters/FrictionMetricTest.FrictionMetric/2 17: [ OK ] WithParameters/FrictionMetricTest.FrictionMetric/2 (186 ms) 17: [----------] 3 tests from WithParameters/FrictionMetricTest (217 ms total) 17: 17: [----------] Global test environment tear-down 17: [==========] 27 tests from 10 test suites ran. (626 ms total) 17: [ PASSED ] 27 tests. 17/92 Test #17: AwhTest ................................... Passed 0.71 sec test 18 Start 18: DensityFittingAppliedForcesUnitTest 18: Test command: /build/reproducible-path/gromacs-2025.1/build/basic/bin/density_fitting_applied_forces-test "--gtest_output=xml:/build/reproducible-path/gromacs-2025.1/build/basic/Testing/Temporary/DensityFittingAppliedForcesUnitTest.xml" 18: Working Directory: /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/applied_forces/densityfitting/tests 18: Test timeout computed to be: 30 18: [==========] Running 18 tests from 4 test suites. 18: [----------] Global test environment set-up. 18: [----------] 2 tests from DensityFittingTest 18: [ RUN ] DensityFittingTest.ForceProviderLackingInputThrows 18: [ OK ] DensityFittingTest.ForceProviderLackingInputThrows (1 ms) 18: [ RUN ] DensityFittingTest.SingleAtom 18: [ OK ] DensityFittingTest.SingleAtom (2 ms) 18: [----------] 2 tests from DensityFittingTest (4 ms total) 18: 18: [----------] 7 tests from DensityFittingAmplitudeLookupTest 18: [ RUN ] DensityFittingAmplitudeLookupTest.Unity 18: [ OK ] DensityFittingAmplitudeLookupTest.Unity (0 ms) 18: [ RUN ] DensityFittingAmplitudeLookupTest.Charge 18: [ OK ] DensityFittingAmplitudeLookupTest.Charge (0 ms) 18: [ RUN ] DensityFittingAmplitudeLookupTest.Masses 18: [ OK ] DensityFittingAmplitudeLookupTest.Masses (0 ms) 18: [ RUN ] DensityFittingAmplitudeLookupTest.CanCopyAssign 18: [ OK ] DensityFittingAmplitudeLookupTest.CanCopyAssign (0 ms) 18: [ RUN ] DensityFittingAmplitudeLookupTest.CanCopyConstruct 18: [ OK ] DensityFittingAmplitudeLookupTest.CanCopyConstruct (0 ms) 18: [ RUN ] DensityFittingAmplitudeLookupTest.CanMoveAssign 18: [ OK ] DensityFittingAmplitudeLookupTest.CanMoveAssign (0 ms) 18: [ RUN ] DensityFittingAmplitudeLookupTest.CanMoveConstruct 18: [ OK ] DensityFittingAmplitudeLookupTest.CanMoveConstruct (0 ms) 18: [----------] 7 tests from DensityFittingAmplitudeLookupTest (0 ms total) 18: 18: [----------] 1 test from DensityFittingForceProviderState 18: [ RUN ] DensityFittingForceProviderState.RoundTripSaving 18: [ OK ] DensityFittingForceProviderState.RoundTripSaving (0 ms) 18: [----------] 1 test from DensityFittingForceProviderState (0 ms total) 18: 18: [----------] 8 tests from DensityFittingOptionsTest 18: [ RUN ] DensityFittingOptionsTest.DefaultParameters 18: [ OK ] DensityFittingOptionsTest.DefaultParameters (0 ms) 18: [ RUN ] DensityFittingOptionsTest.OptionSetsActive 18: [ OK ] DensityFittingOptionsTest.OptionSetsActive (0 ms) 18: [ RUN ] DensityFittingOptionsTest.OutputNoDefaultValuesWhenInactive 18: [ OK ] DensityFittingOptionsTest.OutputNoDefaultValuesWhenInactive (0 ms) 18: [ RUN ] DensityFittingOptionsTest.OutputDefaultValuesWhenActive 18: [ OK ] DensityFittingOptionsTest.OutputDefaultValuesWhenActive (1 ms) 18: [ RUN ] DensityFittingOptionsTest.CanConvertGroupStringToIndexGroup 18: [ OK ] DensityFittingOptionsTest.CanConvertGroupStringToIndexGroup (0 ms) 18: [ RUN ] DensityFittingOptionsTest.InternalsToKvt 18: [ OK ] DensityFittingOptionsTest.InternalsToKvt (0 ms) 18: [ RUN ] DensityFittingOptionsTest.KvtToInternal 18: [ OK ] DensityFittingOptionsTest.KvtToInternal (0 ms) 18: [ RUN ] DensityFittingOptionsTest.RoundTripForInternalsIsIdempotent 18: [ OK ] DensityFittingOptionsTest.RoundTripForInternalsIsIdempotent (0 ms) 18: [----------] 8 tests from DensityFittingOptionsTest (5 ms total) 18: 18: [----------] Global test environment tear-down 18: [==========] 18 tests from 4 test suites ran. (10 ms total) 18: [ PASSED ] 18 tests. 18/92 Test #18: DensityFittingAppliedForcesUnitTest ....... Passed 0.08 sec test 19 Start 19: QMMMAppliedForcesUnitTest 19: Test command: /build/reproducible-path/gromacs-2025.1/build/basic/bin/qmmm_applied_forces-test "--gtest_output=xml:/build/reproducible-path/gromacs-2025.1/build/basic/Testing/Temporary/QMMMAppliedForcesUnitTest.xml" 19: Working Directory: /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/applied_forces/qmmm/tests 19: Test timeout computed to be: 30 19: [==========] Running 21 tests from 5 test suites. 19: [----------] Global test environment set-up. 19: [----------] 3 tests from QMMMInputGeneratorTest 19: [ RUN ] QMMMInputGeneratorTest.CanConstruct 19: [ OK ] QMMMInputGeneratorTest.CanConstruct (0 ms) 19: [ RUN ] QMMMInputGeneratorTest.TwoWatersPBENoLink 19: [ OK ] QMMMInputGeneratorTest.TwoWatersPBENoLink (1 ms) 19: [ RUN ] QMMMInputGeneratorTest.TwoWatersPBEWithLink 19: [ OK ] QMMMInputGeneratorTest.TwoWatersPBEWithLink (0 ms) 19: [----------] 3 tests from QMMMInputGeneratorTest (2 ms total) 19: 19: [----------] 7 tests from QMMMTopologyPreprocessorTest 19: [ RUN ] QMMMTopologyPreprocessorTest.CanConstruct 19: [ OK ] QMMMTopologyPreprocessorTest.CanConstruct (0 ms) 19: [ RUN ] QMMMTopologyPreprocessorTest.FourWatersFirstQMNoLink 19: 19: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary/QMMMTopologyPreprocessorTest_FourWatersFirstQMNoLink_4water.mdp]: 19: For a correct single-point energy evaluation with nsteps = 0, use 19: continuation = yes to avoid constraining the input coordinates. 19: 19: Generating 1-4 interactions: fudge = 0.5 19: Number of degrees of freedom in T-Coupling group rest is 21.00 19: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 19: 19: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary/QMMMTopologyPreprocessorTest_FourWatersFirstQMNoLink_4water.mdp]: 19: NVE simulation with an initial temperature of zero: will use a Verlet 19: buffer of 10%. Check your energy drift! 19: 19: 19: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary/QMMMTopologyPreprocessorTest_FourWatersFirstQMNoLink_4water.mdp]: 19: You are using a plain Coulomb cut-off, which might produce artifacts. 19: You might want to consider using PME electrostatics. 19: 19: 19: 19: There were 3 NOTEs 19: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary/QMMMTopologyPreprocessorTest_FourWatersFirstQMNoLink_4water.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 19: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary/QMMMTopologyPreprocessorTest_FourWatersFirstQMNoLink_4water.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 19: Setting the LD random seed to -816095370 19: 19: Generated 10 of the 10 non-bonded parameter combinations 19: 19: Generated 10 of the 10 1-4 parameter combinations 19: 19: Excluding 2 bonded neighbours molecule type 'SOL' 19: 19: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/4water.gro', all velocities are zero 19: Analysing residue names: 19: There are: 4 Water residues 19: 19: This run will generate roughly 0 Mb of data 19: [ OK ] QMMMTopologyPreprocessorTest.FourWatersFirstQMNoLink (29 ms) 19: [ RUN ] QMMMTopologyPreprocessorTest.FourWatersSeondAndForthQMNoLink 19: 19: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary/QMMMTopologyPreprocessorTest_FourWatersSeondAndForthQMNoLink_4water.mdp]: 19: For a correct single-point energy evaluation with nsteps = 0, use 19: continuation = yes to avoid constraining the input coordinates. 19: 19: Generating 1-4 interactions: fudge = 0.5 19: Number of degrees of freedom in T-Coupling group rest is 21.00 19: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 19: 19: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary/QMMMTopologyPreprocessorTest_FourWatersSeondAndForthQMNoLink_4water.mdp]: 19: NVE simulation with an initial temperature of zero: will use a Verlet 19: buffer of 10%. Check your energy drift! 19: 19: 19: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary/QMMMTopologyPreprocessorTest_FourWatersSeondAndForthQMNoLink_4water.mdp]: 19: You are using a plain Coulomb cut-off, which might produce artifacts. 19: You might want to consider using PME electrostatics. 19: 19: 19: 19: There were 3 NOTEs 19: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary/QMMMTopologyPreprocessorTest_FourWatersSeondAndForthQMNoLink_4water.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 19: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary/QMMMTopologyPreprocessorTest_FourWatersSeondAndForthQMNoLink_4water.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 19: Setting the LD random seed to -681771025 19: 19: Generated 10 of the 10 non-bonded parameter combinations 19: 19: Generated 10 of the 10 1-4 parameter combinations 19: 19: Excluding 2 bonded neighbours molecule type 'SOL' 19: 19: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/4water.gro', all velocities are zero 19: Analysing residue names: 19: There are: 4 Water residues 19: 19: This run will generate roughly 0 Mb of data 19: [ OK ] QMMMTopologyPreprocessorTest.FourWatersSeondAndForthQMNoLink (27 ms) 19: [ RUN ] QMMMTopologyPreprocessorTest.FourWatersFirstQMWithLink 19: 19: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary/QMMMTopologyPreprocessorTest_FourWatersFirstQMWithLink_4water.mdp]: 19: For a correct single-point energy evaluation with nsteps = 0, use 19: continuation = yes to avoid constraining the input coordinates. 19: 19: Generating 1-4 interactions: fudge = 0.5 19: Number of degrees of freedom in T-Coupling group rest is 21.00 19: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 19: 19: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary/QMMMTopologyPreprocessorTest_FourWatersFirstQMWithLink_4water.mdp]: 19: NVE simulation with an initial temperature of zero: will use a Verlet 19: buffer of 10%. Check your energy drift! 19: 19: 19: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary/QMMMTopologyPreprocessorTest_FourWatersFirstQMWithLink_4water.mdp]: 19: You are using a plain Coulomb cut-off, which might produce artifacts. 19: You might want to consider using PME electrostatics. 19: 19: 19: 19: There were 3 NOTEs 19: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary/QMMMTopologyPreprocessorTest_FourWatersFirstQMWithLink_4water.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 19: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary/QMMMTopologyPreprocessorTest_FourWatersFirstQMWithLink_4water.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 19: Setting the LD random seed to -1093273681 19: 19: Generated 10 of the 10 non-bonded parameter combinations 19: 19: Generated 10 of the 10 1-4 parameter combinations 19: 19: Excluding 2 bonded neighbours molecule type 'SOL' 19: 19: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/4water.gro', all velocities are zero 19: Analysing residue names: 19: There are: 4 Water residues 19: 19: This run will generate roughly 0 Mb of data 19: [ OK ] QMMMTopologyPreprocessorTest.FourWatersFirstQMWithLink (26 ms) 19: [ RUN ] QMMMTopologyPreprocessorTest.AlanineDipeptideWithLinksNoConstraints 19: 19: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary/QMMMTopologyPreprocessorTest_AlanineDipeptideWithLinksNoConstraints_alanine_vacuo.mdp]: 19: For a correct single-point energy evaluation with nsteps = 0, use 19: continuation = yes to avoid constraining the input coordinates. 19: 19: Generating 1-4 interactions: fudge = 0.5 19: Number of degrees of freedom in T-Coupling group rest is 63.00 19: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 19: 19: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary/QMMMTopologyPreprocessorTest_AlanineDipeptideWithLinksNoConstraints_alanine_vacuo.mdp]: 19: NVE simulation: will use the initial temperature of 129.093 K for 19: determining the Verlet buffer size 19: 19: 19: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary/QMMMTopologyPreprocessorTest_AlanineDipeptideWithLinksNoConstraints_alanine_vacuo.mdp]: 19: You are using a plain Coulomb cut-off, which might produce artifacts. 19: You might want to consider using PME electrostatics. 19: 19: 19: 19: There were 3 NOTEs 19: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary/QMMMTopologyPreprocessorTest_AlanineDipeptideWithLinksNoConstraints_alanine_vacuo.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 19: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary/QMMMTopologyPreprocessorTest_AlanineDipeptideWithLinksNoConstraints_alanine_vacuo.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 19: Setting the LD random seed to -285215160 19: 19: Generated 2145 of the 2145 non-bonded parameter combinations 19: 19: Generated 2145 of the 2145 1-4 parameter combinations 19: 19: Excluding 3 bonded neighbours molecule type 'ALANINEDIPEPTIDE' 19: 19: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/alanine_vacuo.gro' 19: Analysing residue names: 19: There are: 3 Protein residues 19: Analysing Protein... 19: 19: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 129.093 K 19: 19: Calculated rlist for 1x1 atom pair-list as 1.021 nm, buffer size 0.021 nm 19: 19: Set rlist, assuming 4x4 atom pair-list, to 1.013 nm, buffer size 0.013 nm 19: 19: Note that mdrun will redetermine rlist based on the actual pair-list setup 19: 19: This run will generate roughly 0 Mb of data 19: [ OK ] QMMMTopologyPreprocessorTest.AlanineDipeptideWithLinksNoConstraints (84 ms) 19: [ RUN ] QMMMTopologyPreprocessorTest.AlanineDipeptideWithLinksWithConstraints 19: 19: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary/QMMMTopologyPreprocessorTest_AlanineDipeptideWithLinksWithConstraints_alanine_vacuo.mdp]: 19: For a correct single-point energy evaluation with nsteps = 0, use 19: continuation = yes to avoid constraining the input coordinates. 19: 19: Generating 1-4 interactions: fudge = 0.5 19: 19: NOTE 2 [file unknown]: 19: You are using constraints on all bonds, whereas the forcefield has been 19: parametrized only with constraints involving hydrogen atoms. We suggest 19: using constraints = h-bonds instead, this will also improve performance. 19: 19: 19: NOTE 3 [file unknown]: 19: For energy conservation with LINCS, lincs_iter should be 2 or larger. 19: 19: 19: Number of degrees of freedom in T-Coupling group rest is 42.00 19: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 19: 19: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary/QMMMTopologyPreprocessorTest_AlanineDipeptideWithLinksWithConstraints_alanine_vacuo.mdp]: 19: NVE simulation: will use the initial temperature of 193.640 K for 19: determining the Verlet buffer size 19: 19: 19: NOTE 5 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary/QMMMTopologyPreprocessorTest_AlanineDipeptideWithLinksWithConstraints_alanine_vacuo.mdp]: 19: You are using a plain Coulomb cut-off, which might produce artifacts. 19: You might want to consider using PME electrostatics. 19: 19: 19: 19: There were 5 NOTEs 19: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary/QMMMTopologyPreprocessorTest_AlanineDipeptideWithLinksWithConstraints_alanine_vacuo.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 19: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary/QMMMTopologyPreprocessorTest_AlanineDipeptideWithLinksWithConstraints_alanine_vacuo.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 19: Setting the LD random seed to 1574801919 19: 19: Generated 2145 of the 2145 non-bonded parameter combinations 19: 19: Generated 2145 of the 2145 1-4 parameter combinations 19: 19: Excluding 3 bonded neighbours molecule type 'ALANINEDIPEPTIDE' 19: 19: turning all bonds into constraints... 19: 19: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/alanine_vacuo.gro' 19: Analysing residue names: 19: There are: 3 Protein residues 19: Analysing Protein... 19: 19: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 193.64 K 19: 19: Calculated rlist for 1x1 atom pair-list as 1.023 nm, buffer size 0.023 nm 19: 19: Set rlist, assuming 4x4 atom pair-list, to 1.015 nm, buffer size 0.015 nm 19: 19: Note that mdrun will redetermine rlist based on the actual pair-list setup 19: 19: This run will generate roughly 0 Mb of data 19: [ OK ] QMMMTopologyPreprocessorTest.AlanineDipeptideWithLinksWithConstraints (95 ms) 19: [ RUN ] QMMMTopologyPreprocessorTest.RemovingQMVsites 19: 19: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary/QMMMTopologyPreprocessorTest_RemovingQMVsites_vsite_test.mdp]: 19: For a correct single-point energy evaluation with nsteps = 0, use 19: continuation = yes to avoid constraining the input coordinates. 19: 19: Number of degrees of freedom in T-Coupling group rest is 45.00 19: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 19: 19: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary/QMMMTopologyPreprocessorTest_RemovingQMVsites_vsite_test.mdp]: 19: NVE simulation with an initial temperature of zero: will use a Verlet 19: buffer of 10%. Check your energy drift! 19: 19: 19: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary/QMMMTopologyPreprocessorTest_RemovingQMVsites_vsite_test.mdp]: 19: You are using a plain Coulomb cut-off, which might produce artifacts. 19: You might want to consider using PME electrostatics. 19: 19: 19: 19: There were 3 NOTEs 19: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary/QMMMTopologyPreprocessorTest_RemovingQMVsites_vsite_test.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 19: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary/QMMMTopologyPreprocessorTest_RemovingQMVsites_vsite_test.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 19: Setting the LD random seed to -805393921 19: 19: Generated 3 of the 6 non-bonded parameter combinations 19: 19: Excluding 3 bonded neighbours molecule type 'VSTEST' 19: 19: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/vsite_test.gro', all velocities are zero 19: 19: Cleaning up constraints and constant bonded interactions with virtual sites 19: Analysing residue names: 19: There are: 1 Other residues 19: Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups... 19: 19: This run will generate roughly 0 Mb of data 19: [ OK ] QMMMTopologyPreprocessorTest.RemovingQMVsites (31 ms) 19: [----------] 7 tests from QMMMTopologyPreprocessorTest (297 ms total) 19: 19: [----------] 9 tests from QMMMOptionsTest 19: [ RUN ] QMMMOptionsTest.DefaultParameters 19: [ OK ] QMMMOptionsTest.DefaultParameters (0 ms) 19: [ RUN ] QMMMOptionsTest.OptionSetsActive 19: [ OK ] QMMMOptionsTest.OptionSetsActive (0 ms) 19: [ RUN ] QMMMOptionsTest.OutputNoDefaultValuesWhenInactive 19: [ OK ] QMMMOptionsTest.OutputNoDefaultValuesWhenInactive (0 ms) 19: [ RUN ] QMMMOptionsTest.OutputDefaultValuesWhenActive 19: [ OK ] QMMMOptionsTest.OutputDefaultValuesWhenActive (0 ms) 19: [ RUN ] QMMMOptionsTest.CanConvertGroupStringToIndexGroup 19: [ OK ] QMMMOptionsTest.CanConvertGroupStringToIndexGroup (0 ms) 19: [ RUN ] QMMMOptionsTest.NoQMGroupConvertGroupStringToIndexGroup 19: [ OK ] QMMMOptionsTest.NoQMGroupConvertGroupStringToIndexGroup (0 ms) 19: [ RUN ] QMMMOptionsTest.EmptyQMGroupConvertGroupStringToIndexGroup 19: [ OK ] QMMMOptionsTest.EmptyQMGroupConvertGroupStringToIndexGroup (0 ms) 19: [ RUN ] QMMMOptionsTest.InternalsToKvtAndBack 19: [ OK ] QMMMOptionsTest.InternalsToKvtAndBack (0 ms) 19: [ RUN ] QMMMOptionsTest.CP2KInputProcessing 19: [ OK ] QMMMOptionsTest.CP2KInputProcessing (2 ms) 19: [----------] 9 tests from QMMMOptionsTest (7 ms total) 19: 19: [----------] 1 test from QMMMForceProviderTest 19: [ RUN ] QMMMForceProviderTest.CanConstructOrNot 19: [ OK ] QMMMForceProviderTest.CanConstructOrNot (0 ms) 19: [----------] 1 test from QMMMForceProviderTest (0 ms total) 19: 19: [----------] 1 test from QMMMTest 19: [ RUN ] QMMMTest.ForceProviderLackingInputThrows 19: [ OK ] QMMMTest.ForceProviderLackingInputThrows (0 ms) 19: [----------] 1 test from QMMMTest (0 ms total) 19: 19: [----------] Global test environment tear-down 19: [==========] 21 tests from 5 test suites ran. (307 ms total) 19: [ PASSED ] 21 tests. 19/92 Test #19: QMMMAppliedForcesUnitTest ................. Passed 0.38 sec test 20 Start 20: ColvarsAppliedForcesUnitTest 20: Test command: /build/reproducible-path/gromacs-2025.1/build/basic/bin/colvars_applied_forces-test "--gtest_output=xml:/build/reproducible-path/gromacs-2025.1/build/basic/Testing/Temporary/ColvarsAppliedForcesUnitTest.xml" 20: Working Directory: /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/applied_forces/colvars/tests 20: Test timeout computed to be: 30 20: [==========] Running 16 tests from 4 test suites. 20: [----------] Global test environment set-up. 20: [----------] 1 test from ColvarsTest 20: [ RUN ] ColvarsTest.ForceProviderLackingInputThrows 20: [ OK ] ColvarsTest.ForceProviderLackingInputThrows (0 ms) 20: [----------] 1 test from ColvarsTest (0 ms total) 20: 20: [----------] 6 tests from ColvarsOptionsTest 20: [ RUN ] ColvarsOptionsTest.OutputNoDefaultValuesWhenInactive 20: [ OK ] ColvarsOptionsTest.OutputNoDefaultValuesWhenInactive (2 ms) 20: [ RUN ] ColvarsOptionsTest.OutputDefaultValuesWhenActive 20: [ OK ] ColvarsOptionsTest.OutputDefaultValuesWhenActive (1 ms) 20: [ RUN ] ColvarsOptionsTest.OutputValuesWhenActive 20: [ OK ] ColvarsOptionsTest.OutputValuesWhenActive (1 ms) 20: [ RUN ] ColvarsOptionsTest.OptionSetsActive 20: [ OK ] ColvarsOptionsTest.OptionSetsActive (0 ms) 20: [ RUN ] ColvarsOptionsTest.InternalsToKvtAndBack 20: 20: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsOptionsTest_InternalsToKvtAndBack_4water.mdp]: 20: For a correct single-point energy evaluation with nsteps = 0, use 20: continuation = yes to avoid constraining the input coordinates. 20: 20: Generating 1-4 interactions: fudge = 0.5 20: Number of degrees of freedom in T-Coupling group rest is 21.00 20: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 20: 20: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsOptionsTest_InternalsToKvtAndBack_4water.mdp]: 20: NVE simulation with an initial temperature of zero: will use a Verlet 20: buffer of 10%. Check your energy drift! 20: 20: 20: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsOptionsTest_InternalsToKvtAndBack_4water.mdp]: 20: You are using a plain Coulomb cut-off, which might produce artifacts. 20: You might want to consider using PME electrostatics. 20: 20: 20: 20: There were 3 NOTEs 20: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsOptionsTest_InternalsToKvtAndBack_4water.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 20: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsOptionsTest_InternalsToKvtAndBack_4water.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 20: Setting the LD random seed to -572606465 20: 20: Generated 10 of the 10 non-bonded parameter combinations 20: 20: Generated 10 of the 10 1-4 parameter combinations 20: 20: Excluding 2 bonded neighbours molecule type 'SOL' 20: 20: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/4water.gro', all velocities are zero 20: Analysing residue names: 20: There are: 4 Water residues 20: 20: This run will generate roughly 0 Mb of data 20: [ OK ] ColvarsOptionsTest.InternalsToKvtAndBack (40 ms) 20: [ RUN ] ColvarsOptionsTest.RetrieveEdrFilename 20: [ OK ] ColvarsOptionsTest.RetrieveEdrFilename (0 ms) 20: [----------] 6 tests from ColvarsOptionsTest (45 ms total) 20: 20: [----------] 4 tests from ColvarsPreProcessorTest 20: [ RUN ] ColvarsPreProcessorTest.CanConstructColvarsPreProcess 20: 20: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsPreProcessorTest_CanConstructColvarsPreProcess_4water.mdp]: 20: For a correct single-point energy evaluation with nsteps = 0, use 20: continuation = yes to avoid constraining the input coordinates. 20: 20: Generating 1-4 interactions: fudge = 0.5 20: Number of degrees of freedom in T-Coupling group rest is 21.00 20: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 20: 20: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsPreProcessorTest_CanConstructColvarsPreProcess_4water.mdp]: 20: NVE simulation with an initial temperature of zero: will use a Verlet 20: buffer of 10%. Check your energy drift! 20: 20: 20: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsPreProcessorTest_CanConstructColvarsPreProcess_4water.mdp]: 20: You are using a plain Coulomb cut-off, which might produce artifacts. 20: You might want to consider using PME electrostatics. 20: 20: 20: 20: There were 3 NOTEs 20: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsPreProcessorTest_CanConstructColvarsPreProcess_4water.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 20: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsPreProcessorTest_CanConstructColvarsPreProcess_4water.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 20: Setting the LD random seed to -1292537873 20: 20: Generated 10 of the 10 non-bonded parameter combinations 20: 20: Generated 10 of the 10 1-4 parameter combinations 20: 20: Excluding 2 bonded neighbours molecule type 'SOL' 20: 20: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/4water.gro', all velocities are zero 20: Analysing residue names: 20: There are: 4 Water residues 20: 20: This run will generate roughly 0 Mb of data 20: [ OK ] ColvarsPreProcessorTest.CanConstructColvarsPreProcess (31 ms) 20: [ RUN ] ColvarsPreProcessorTest.CheckValuesFourWaters 20: 20: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsPreProcessorTest_CheckValuesFourWaters_4water.mdp]: 20: For a correct single-point energy evaluation with nsteps = 0, use 20: continuation = yes to avoid constraining the input coordinates. 20: 20: Generating 1-4 interactions: fudge = 0.5 20: Number of degrees of freedom in T-Coupling group rest is 21.00 20: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 20: 20: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsPreProcessorTest_CheckValuesFourWaters_4water.mdp]: 20: NVE simulation with an initial temperature of zero: will use a Verlet 20: buffer of 10%. Check your energy drift! 20: 20: 20: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsPreProcessorTest_CheckValuesFourWaters_4water.mdp]: 20: You are using a plain Coulomb cut-off, which might produce artifacts. 20: You might want to consider using PME electrostatics. 20: 20: 20: 20: There were 3 NOTEs 20: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsPreProcessorTest_CheckValuesFourWaters_4water.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 20: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsPreProcessorTest_CheckValuesFourWaters_4water.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 20: Setting the LD random seed to -19969261 20: 20: Generated 10 of the 10 non-bonded parameter combinations 20: 20: Generated 10 of the 10 1-4 parameter combinations 20: 20: Excluding 2 bonded neighbours molecule type 'SOL' 20: 20: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/4water.gro', all velocities are zero 20: Analysing residue names: 20: There are: 4 Water residues 20: 20: This run will generate roughly 0 Mb of data 20: [ OK ] ColvarsPreProcessorTest.CheckValuesFourWaters (40 ms) 20: [ RUN ] ColvarsPreProcessorTest.CheckNestedInputFiles 20: 20: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsPreProcessorTest_CheckNestedInputFiles_4water.mdp]: 20: For a correct single-point energy evaluation with nsteps = 0, use 20: continuation = yes to avoid constraining the input coordinates. 20: 20: Generating 1-4 interactions: fudge = 0.5 20: Number of degrees of freedom in T-Coupling group rest is 21.00 20: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 20: 20: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsPreProcessorTest_CheckNestedInputFiles_4water.mdp]: 20: NVE simulation with an initial temperature of zero: will use a Verlet 20: buffer of 10%. Check your energy drift! 20: 20: 20: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsPreProcessorTest_CheckNestedInputFiles_4water.mdp]: 20: You are using a plain Coulomb cut-off, which might produce artifacts. 20: You might want to consider using PME electrostatics. 20: 20: 20: 20: There were 3 NOTEs 20: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsPreProcessorTest_CheckNestedInputFiles_4water.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 20: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsPreProcessorTest_CheckNestedInputFiles_4water.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 20: Setting the LD random seed to -69492839 20: 20: Generated 10 of the 10 non-bonded parameter combinations 20: 20: Generated 10 of the 10 1-4 parameter combinations 20: 20: Excluding 2 bonded neighbours molecule type 'SOL' 20: 20: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/4water.gro', all velocities are zero 20: Analysing residue names: 20: There are: 4 Water residues 20: 20: This run will generate roughly 0 Mb of data 20: [ OK ] ColvarsPreProcessorTest.CheckNestedInputFiles (40 ms) 20: [ RUN ] ColvarsPreProcessorTest.WrongColvarsInput 20: 20: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsPreProcessorTest_WrongColvarsInput_4water.mdp]: 20: For a correct single-point energy evaluation with nsteps = 0, use 20: continuation = yes to avoid constraining the input coordinates. 20: 20: Generating 1-4 interactions: fudge = 0.5 20: Number of degrees of freedom in T-Coupling group rest is 21.00 20: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 20: 20: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsPreProcessorTest_WrongColvarsInput_4water.mdp]: 20: NVE simulation with an initial temperature of zero: will use a Verlet 20: buffer of 10%. Check your energy drift! 20: 20: 20: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsPreProcessorTest_WrongColvarsInput_4water.mdp]: 20: You are using a plain Coulomb cut-off, which might produce artifacts. 20: You might want to consider using PME electrostatics. 20: 20: 20: 20: There were 3 NOTEs 20: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsPreProcessorTest_WrongColvarsInput_4water.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 20: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsPreProcessorTest_WrongColvarsInput_4water.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 20: Setting the LD random seed to 2009062389 20: 20: Generated 10 of the 10 non-bonded parameter combinations 20: 20: Generated 10 of the 10 1-4 parameter combinations 20: 20: Excluding 2 bonded neighbours molecule type 'SOL' 20: 20: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/4water.gro', all velocities are zero 20: Analysing residue names: 20: There are: 4 Water residues 20: 20: This run will generate roughly 0 Mb of data 20: [ OK ] ColvarsPreProcessorTest.WrongColvarsInput (33 ms) 20: [----------] 4 tests from ColvarsPreProcessorTest (147 ms total) 20: 20: [----------] 5 tests from ColvarsForceProviderTest 20: [ RUN ] ColvarsForceProviderTest.CanConstructOrNot 20: [ OK ] ColvarsForceProviderTest.CanConstructOrNot (3 ms) 20: [ RUN ] ColvarsForceProviderTest.SimpleInputs 20: 20: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsForceProviderTest_SimpleInputs_4water.mdp]: 20: For a correct single-point energy evaluation with nsteps = 0, use 20: continuation = yes to avoid constraining the input coordinates. 20: 20: Generating 1-4 interactions: fudge = 0.5 20: Number of degrees of freedom in T-Coupling group rest is 21.00 20: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 20: 20: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsForceProviderTest_SimpleInputs_4water.mdp]: 20: NVE simulation with an initial temperature of zero: will use a Verlet 20: buffer of 10%. Check your energy drift! 20: 20: 20: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsForceProviderTest_SimpleInputs_4water.mdp]: 20: You are using a plain Coulomb cut-off, which might produce artifacts. 20: You might want to consider using PME electrostatics. 20: 20: 20: 20: There were 3 NOTEs 20: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsForceProviderTest_SimpleInputs_4water.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 20: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsForceProviderTest_SimpleInputs_4water.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 20: Setting the LD random seed to 2100276095 20: 20: Generated 10 of the 10 non-bonded parameter combinations 20: 20: Generated 10 of the 10 1-4 parameter combinations 20: 20: Excluding 2 bonded neighbours molecule type 'SOL' 20: 20: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/4water.gro', all velocities are zero 20: Analysing residue names: 20: There are: 4 Water residues 20: 20: This run will generate roughly 0 Mb of data 20: [ OK ] ColvarsForceProviderTest.SimpleInputs (38 ms) 20: [ RUN ] ColvarsForceProviderTest.WrongColvarsInput 20: 20: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsForceProviderTest_WrongColvarsInput_4water.mdp]: 20: For a correct single-point energy evaluation with nsteps = 0, use 20: continuation = yes to avoid constraining the input coordinates. 20: 20: Generating 1-4 interactions: fudge = 0.5 20: Number of degrees of freedom in T-Coupling group rest is 21.00 20: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 20: 20: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsForceProviderTest_WrongColvarsInput_4water.mdp]: 20: NVE simulation with an initial temperature of zero: will use a Verlet 20: buffer of 10%. Check your energy drift! 20: 20: 20: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsForceProviderTest_WrongColvarsInput_4water.mdp]: 20: You are using a plain Coulomb cut-off, which might produce artifacts. 20: You might want to consider using PME electrostatics. 20: 20: 20: 20: There were 3 NOTEs 20: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsForceProviderTest_WrongColvarsInput_4water.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 20: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsForceProviderTest_WrongColvarsInput_4water.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 20: Setting the LD random seed to -1207969793 20: 20: Generated 10 of the 10 non-bonded parameter combinations 20: 20: Generated 10 of the 10 1-4 parameter combinations 20: 20: Excluding 2 bonded neighbours molecule type 'SOL' 20: 20: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/4water.gro', all velocities are zero 20: Analysing residue names: 20: There are: 4 Water residues 20: 20: This run will generate roughly 0 Mb of data 20: [ OK ] ColvarsForceProviderTest.WrongColvarsInput (35 ms) 20: [ RUN ] ColvarsForceProviderTest.CalculateForces4water 20: 20: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsForceProviderTest_CalculateForces4water_4water.mdp]: 20: For a correct single-point energy evaluation with nsteps = 0, use 20: continuation = yes to avoid constraining the input coordinates. 20: 20: Generating 1-4 interactions: fudge = 0.5 20: Number of degrees of freedom in T-Coupling group rest is 21.00 20: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 20: 20: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsForceProviderTest_CalculateForces4water_4water.mdp]: 20: NVE simulation with an initial temperature of zero: will use a Verlet 20: buffer of 10%. Check your energy drift! 20: 20: 20: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsForceProviderTest_CalculateForces4water_4water.mdp]: 20: You are using a plain Coulomb cut-off, which might produce artifacts. 20: You might want to consider using PME electrostatics. 20: 20: 20: 20: There were 3 NOTEs 20: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsForceProviderTest_CalculateForces4water_4water.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 20: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsForceProviderTest_CalculateForces4water_4water.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 20: Setting the LD random seed to 1468005823 20: 20: Generated 10 of the 10 non-bonded parameter combinations 20: 20: Generated 10 of the 10 1-4 parameter combinations 20: 20: Excluding 2 bonded neighbours molecule type 'SOL' 20: 20: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/4water.gro', all velocities are zero 20: Analysing residue names: 20: There are: 4 Water residues 20: 20: This run will generate roughly 0 Mb of data 20: [ OK ] ColvarsForceProviderTest.CalculateForces4water (47 ms) 20: [ RUN ] ColvarsForceProviderTest.CalculateForcesAlanine 20: 20: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsForceProviderTest_CalculateForcesAlanine_ala.mdp]: 20: For a correct single-point energy evaluation with nsteps = 0, use 20: continuation = yes to avoid constraining the input coordinates. 20: 20: Generating 1-4 interactions: fudge = 0.5 20: Number of degrees of freedom in T-Coupling group rest is 66.00 20: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 20: 20: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsForceProviderTest_CalculateForcesAlanine_ala.mdp]: 20: NVE simulation: will use the initial temperature of 300.368 K for 20: determining the Verlet buffer size 20: 20: 20: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsForceProviderTest_CalculateForcesAlanine_ala.mdp]: 20: You are using a plain Coulomb cut-off, which might produce artifacts. 20: You might want to consider using PME electrostatics. 20: 20: 20: 20: There were 3 NOTEs 20: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsForceProviderTest_CalculateForcesAlanine_ala.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 20: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsForceProviderTest_CalculateForcesAlanine_ala.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 20: Setting the LD random seed to -409994764 20: 20: Generated 2211 of the 2211 non-bonded parameter combinations 20: 20: Generated 2211 of the 2211 1-4 parameter combinations 20: 20: Excluding 3 bonded neighbours molecule type 'Protein_chain_A' 20: 20: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/ala.gro' 20: Analysing residue names: 20: There are: 2 Protein residues 20: Analysing Protein... 20: 20: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 300.368 K 20: 20: Calculated rlist for 1x1 atom pair-list as 1.048 nm, buffer size 0.048 nm 20: 20: Set rlist, assuming 4x4 atom pair-list, to 1.036 nm, buffer size 0.036 nm 20: 20: Note that mdrun will redetermine rlist based on the actual pair-list setup 20: 20: This run will generate roughly 0 Mb of data 20: [ OK ] ColvarsForceProviderTest.CalculateForcesAlanine (118 ms) 20: [----------] 5 tests from ColvarsForceProviderTest (244 ms total) 20: 20: [----------] Global test environment tear-down 20: [==========] 16 tests from 4 test suites ran. (438 ms total) 20: [ PASSED ] 16 tests. 20/92 Test #20: ColvarsAppliedForcesUnitTest .............. Passed 0.52 sec test 21 Start 21: PlumedAppliedForcesUnitTests 21: Test command: /build/reproducible-path/gromacs-2025.1/build/basic/bin/plumed_applied_forces-test "--gtest_output=xml:/build/reproducible-path/gromacs-2025.1/build/basic/Testing/Temporary/PlumedAppliedForcesUnitTests.xml" 21: Working Directory: /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/applied_forces/plumed/tests 21: Test timeout computed to be: 30 21: [==========] Running 8 tests from 1 test suite. 21: [----------] Global test environment set-up. 21: [----------] 8 tests from PlumedOptionsTest 21: [ RUN ] PlumedOptionsTest.defaultConstructor 21: [ OK ] PlumedOptionsTest.defaultConstructor (1 ms) 21: [ RUN ] PlumedOptionsTest.setTimeStep 21: [ OK ] PlumedOptionsTest.setTimeStep (0 ms) 21: [ RUN ] PlumedOptionsTest.setStartingBehavior 21: [ OK ] PlumedOptionsTest.setStartingBehavior (0 ms) 21: [ RUN ] PlumedOptionsTest.setPlumedFile 21: [ OK ] PlumedOptionsTest.setPlumedFile (0 ms) 21: [ RUN ] PlumedOptionsTest.setPlumedFileNotSet 21: [ OK ] PlumedOptionsTest.setPlumedFileNotSet (0 ms) 21: [ RUN ] PlumedOptionsTest.setEnsembleTemperature_data 21: [ OK ] PlumedOptionsTest.setEnsembleTemperature_data (0 ms) 21: [ RUN ] PlumedOptionsTest.setEnsembleTemperature_notConstant 21: [ OK ] PlumedOptionsTest.setEnsembleTemperature_notConstant (0 ms) 21: [ RUN ] PlumedOptionsTest.setTopology 21: 21: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/applied_forces/plumed/tests/Testing/Temporary/PlumedOptionsTest_setTopology_4water.mdp]: 21: For a correct single-point energy evaluation with nsteps = 0, use 21: continuation = yes to avoid constraining the input coordinates. 21: 21: Generating 1-4 interactions: fudge = 0.5 21: Number of degrees of freedom in T-Coupling group rest is 21.00 21: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 21: 21: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/applied_forces/plumed/tests/Testing/Temporary/PlumedOptionsTest_setTopology_4water.mdp]: 21: NVE simulation with an initial temperature of zero: will use a Verlet 21: buffer of 10%. Check your energy drift! 21: 21: 21: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/applied_forces/plumed/tests/Testing/Temporary/PlumedOptionsTest_setTopology_4water.mdp]: 21: You are using a plain Coulomb cut-off, which might produce artifacts. 21: You might want to consider using PME electrostatics. 21: 21: 21: 21: There were 3 NOTEs 21: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/applied_forces/plumed/tests/Testing/Temporary/PlumedOptionsTest_setTopology_4water.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 21: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/applied_forces/plumed/tests/Testing/Temporary/PlumedOptionsTest_setTopology_4water.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 21: 21: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/applied_forces/plumed/tests/Testing/Temporary/PlumedOptionsTest_setTopology_angles1.mdp]: 21: For a correct single-point energy evaluation with nsteps = 0, use 21: continuation = yes to avoid constraining the input coordinates. 21: 21: 21: NOTE 2 [file angles1.top, line 72]: 21: In moleculetype 'butane' 4 atoms are not bound by a potential or 21: constraint to any other atom in the same moleculetype. Although 21: technically this might not cause issues in a simulation, this often means 21: that the user forgot to add a bond/potential/constraint or put multiple 21: molecules in the same moleculetype definition by mistake. Run with -v to 21: get information for each atom. 21: 21: Number of degrees of freedom in T-Coupling group rest is 9.00 21: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 21: 21: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/applied_forces/plumed/tests/Testing/Temporary/PlumedOptionsTest_setTopology_angles1.mdp]: 21: NVE simulation: will use the initial temperature of 238.919 K for 21: determining the Verlet buffer size 21: 21: 21: There were 3 NOTEs 21: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/applied_forces/plumed/tests/Testing/Temporary/PlumedOptionsTest_setTopology_angles1.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 21: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/applied_forces/plumed/tests/Testing/Temporary/PlumedOptionsTest_setTopology_angles1.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 21: 21: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/applied_forces/plumed/tests/Testing/Temporary/PlumedOptionsTest_setTopology_argon5832.mdp]: 21: For a correct single-point energy evaluation with nsteps = 0, use 21: continuation = yes to avoid constraining the input coordinates. 21: 21: Number of degrees of freedom in T-Coupling group rest is 17493.00 21: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 21: 21: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/applied_forces/plumed/tests/Testing/Temporary/PlumedOptionsTest_setTopology_argon5832.mdp]: 21: NVE simulation: will use the initial temperature of 67.983 K for 21: determining the Verlet buffer size 21: 21: 21: There were 2 NOTEs 21: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/applied_forces/plumed/tests/Testing/Temporary/PlumedOptionsTest_setTopology_argon5832.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 21: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/applied_forces/plumed/tests/Testing/Temporary/PlumedOptionsTest_setTopology_argon5832.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 21: 21: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/applied_forces/plumed/tests/Testing/Temporary/PlumedOptionsTest_setTopology_argon4.mdp]: 21: For a correct single-point energy evaluation with nsteps = 0, use 21: continuation = yes to avoid constraining the input coordinates. 21: 21: Number of degrees of freedom in T-Coupling group rest is 9.00 21: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 21: 21: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/applied_forces/plumed/tests/Testing/Temporary/PlumedOptionsTest_setTopology_argon4.mdp]: 21: NVE simulation with an initial temperature of zero: will use a Verlet 21: buffer of 10%. Check your energy drift! 21: 21: 21: There were 2 NOTEs 21: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/applied_forces/plumed/tests/Testing/Temporary/PlumedOptionsTest_setTopology_argon4.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 21: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/applied_forces/plumed/tests/Testing/Temporary/PlumedOptionsTest_setTopology_argon4.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 21: 21: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/applied_forces/plumed/tests/Testing/Temporary/PlumedOptionsTest_setTopology_dipoles.mdp]: 21: For a correct single-point energy evaluation with nsteps = 0, use 21: continuation = yes to avoid constraining the input coordinates. 21: 21: Number of degrees of freedom in T-Coupling group rest is 9.00 21: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 21: 21: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/applied_forces/plumed/tests/Testing/Temporary/PlumedOptionsTest_setTopology_dipoles.mdp]: 21: NVE simulation with an initial temperature of zero: will use a Verlet 21: buffer of 10%. Check your energy drift! 21: 21: 21: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/applied_forces/plumed/tests/Testing/Temporary/PlumedOptionsTest_setTopology_dipoles.mdp]: 21: You are using a plain Coulomb cut-off, which might produce artifacts. 21: You might want to consider using PME electrostatics. 21: 21: 21: 21: There were 3 NOTEs 21: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/applied_forces/plumed/tests/Testing/Temporary/PlumedOptionsTest_setTopology_dipoles.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 21: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/applied_forces/plumed/tests/Testing/Temporary/PlumedOptionsTest_setTopology_dipoles.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 21: 21: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/applied_forces/plumed/tests/Testing/Temporary/PlumedOptionsTest_setTopology_spc_and_methane.mdp]: 21: For a correct single-point energy evaluation with nsteps = 0, use 21: continuation = yes to avoid constraining the input coordinates. 21: 21: Generating 1-4 interactions: fudge = 0.5 21: Number of degrees of freedom in T-Coupling group rest is 18.00 21: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 21: 21: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/applied_forces/plumed/tests/Testing/Temporary/PlumedOptionsTest_setTopology_spc_and_methane.mdp]: 21: NVE simulation: will use the initial temperature of 135.187 K for 21: determining the Verlet buffer size 21: 21: 21: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/applied_forces/plumed/tests/Testing/Temporary/PlumedOptionsTest_setTopology_spc_and_methane.mdp]: 21: You are using a plain Coulomb cut-off, which might produce artifacts. 21: You might want to consider using PME electrostatics. 21: 21: 21: 21: There were 3 NOTEs 21: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/applied_forces/plumed/tests/Testing/Temporary/PlumedOptionsTest_setTopology_spc_and_methane.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 21: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/applied_forces/plumed/tests/Testing/Temporary/PlumedOptionsTest_setTopology_spc_and_methane.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 21: Setting the LD random seed to -336081097 21: 21: Generated 10 of the 10 non-bonded parameter combinations 21: 21: Generated 10 of the 10 1-4 parameter combinations 21: 21: Excluding 2 bonded neighbours molecule type 'SOL' 21: 21: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/4water.gro', all velocities are zero 21: Analysing residue names: 21: There are: 4 Water residues 21: 21: This run will generate roughly 0 Mb of data 21: Setting the LD random seed to 2034225005 21: 21: Generated 3 of the 3 non-bonded parameter combinations 21: 21: Excluding 3 bonded neighbours molecule type 'butane' 21: 21: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/angles1.gro' 21: Analysing residue names: 21: There are: 1 Other residues 21: Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups... 21: 21: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 238.919 K 21: 21: Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm 21: 21: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm 21: 21: Note that mdrun will redetermine rlist based on the actual pair-list setup 21: 21: This run will generate roughly 0 Mb of data 21: Setting the LD random seed to 1270340334 21: 21: Generated 1 of the 1 non-bonded parameter combinations 21: 21: Excluding 1 bonded neighbours molecule type 'Argon' 21: 21: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon5832.gro' 21: Analysing residue names: 21: There are: 5832 Other residues 21: Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups... 21: 21: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 67.9831 K 21: 21: Calculated rlist for 1x1 atom pair-list as 1.001 nm, buffer size 0.001 nm 21: 21: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm 21: 21: Note that mdrun will redetermine rlist based on the actual pair-list setup 21: 21: This run will generate roughly 0 Mb of data 21: Setting the LD random seed to -538346630 21: 21: Generated 1 of the 1 non-bonded parameter combinations 21: 21: Excluding 1 bonded neighbours molecule type 'ArgonA' 21: 21: Excluding 1 bonded neighbours molecule type 'ArgonB' 21: 21: Excluding 1 bonded neighbours molecule type 'ArgonC' 21: 21: Excluding 1 bonded neighbours molecule type 'ArgonD' 21: 21: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon4.gro', all velocities are zero 21: Analysing residue names: 21: There are: 4 Other residues 21: Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups... 21: 21: This run will generate roughly 0 Mb of data 21: Setting the LD random seed to -1645257993 21: 21: Generated 1 of the 1 non-bonded parameter combinations 21: 21: Excluding 1 bonded neighbours molecule type 'Dipole' 21: 21: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/dipoles.gro', all velocities are zero 21: Analysing residue names: 21: There are: 2 Other residues 21: Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups... 21: 21: This run will generate roughly 0 Mb of data 21: Setting the LD random seed to -835714 21: 21: Generated 331705 of the 331705 non-bonded parameter combinations 21: 21: Generated 331705 of the 331705 1-4 parameter combinations 21: 21: Excluding 2 bonded neighbours molecule type 'SOL' 21: 21: Excluding 3 bonded neighbours molecule type 'methane' 21: 21: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/spc_and_methane.gro' 21: Analysing residue names: 21: There are: 1 Water residues 21: There are: 1 Other residues 21: Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups... 21: 21: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 135.187 K 21: 21: Calculated rlist for 1x1 atom pair-list as 1.020 nm, buffer size 0.020 nm 21: 21: Set rlist, assuming 4x4 atom pair-list, to 1.013 nm, buffer size 0.013 nm 21: 21: Note that mdrun will redetermine rlist based on the actual pair-list setup 21: 21: This run will generate roughly 0 Mb of data 21: [ OK ] PlumedOptionsTest.setTopology (4748 ms) 21: [----------] 8 tests from PlumedOptionsTest (4753 ms total) 21: 21: [----------] Global test environment tear-down 21: [==========] 8 tests from 1 test suite ran. (4753 ms total) 21: [ PASSED ] 8 tests. 21/92 Test #21: PlumedAppliedForcesUnitTests .............. Passed 4.85 sec test 22 Start 22: PlumedMDTests 22: Test command: /build/reproducible-path/gromacs-2025.1/build/basic/bin/plumed_md-test "--gtest_output=xml:/build/reproducible-path/gromacs-2025.1/build/basic/Testing/Temporary/PlumedMDTests.xml" 22: Working Directory: /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/applied_forces/plumed/tests 22: Test timeout computed to be: 600 22: [==========] Running 2 tests from 1 test suite. 22: [----------] Global test environment set-up. 22: [----------] 2 tests from SimplePlumedMD/PlumedRun 22: [ RUN ] SimplePlumedMD/PlumedRun.PlumedSees/0 22: ./src/gromacs/applied_forces/plumed/tests/plumed_md_test.cpp:92: Skipped 22: The GMX_TEST_PLUMED_KERNEL_IS_AVAILABLE environment variable is not set, and the PLUMED kernel was not found. 22: [ SKIPPED ] SimplePlumedMD/PlumedRun.PlumedSees/0 (0 ms) 22: [ RUN ] SimplePlumedMD/PlumedRun.PlumedDoes/0 22: ./src/gromacs/applied_forces/plumed/tests/plumed_md_test.cpp:92: Skipped 22: The GMX_TEST_PLUMED_KERNEL_IS_AVAILABLE environment variable is not set, and the PLUMED kernel was not found. 22: [ SKIPPED ] SimplePlumedMD/PlumedRun.PlumedDoes/0 (0 ms) 22: [----------] 2 tests from SimplePlumedMD/PlumedRun (1 ms total) 22: 22: [----------] Global test environment tear-down 22: [==========] 2 tests from 1 test suite ran. (55 ms total) 22: [ PASSED ] 0 tests. 22: [ SKIPPED ] 2 tests, listed below: 22: [ SKIPPED ] SimplePlumedMD/PlumedRun.PlumedSees/0 22: [ SKIPPED ] SimplePlumedMD/PlumedRun.PlumedDoes/0 22/92 Test #22: PlumedMDTests ............................. Passed 0.14 sec test 23 Start 23: NNPotAppliedForcesUnitTest 23: Test command: /build/reproducible-path/gromacs-2025.1/build/basic/bin/nnpot_applied_forces-test "--gtest_output=xml:/build/reproducible-path/gromacs-2025.1/build/basic/Testing/Temporary/NNPotAppliedForcesUnitTest.xml" 23: Working Directory: /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/applied_forces/nnpot/tests 23: Test timeout computed to be: 30 23: [==========] Running 12 tests from 4 test suites. 23: [----------] Global test environment set-up. 23: [----------] 1 test from NNPotTest 23: [ RUN ] NNPotTest.ForceProviderLackingInputThrows 23: [ OK ] NNPotTest.ForceProviderLackingInputThrows (0 ms) 23: [----------] 1 test from NNPotTest (1 ms total) 23: 23: [----------] 5 tests from NNPotOptionsTest 23: [ RUN ] NNPotOptionsTest.DefaultParameters 23: [ OK ] NNPotOptionsTest.DefaultParameters (5 ms) 23: [ RUN ] NNPotOptionsTest.OptionSetsActive 23: [ OK ] NNPotOptionsTest.OptionSetsActive (0 ms) 23: [ RUN ] NNPotOptionsTest.OutputNoDefaultValuesWhenInactive 23: [ OK ] NNPotOptionsTest.OutputNoDefaultValuesWhenInactive (0 ms) 23: [ RUN ] NNPotOptionsTest.OutputDefaultValuesWhenActive 23: [ OK ] NNPotOptionsTest.OutputDefaultValuesWhenActive (1 ms) 23: [ RUN ] NNPotOptionsTest.InternalsToKvtAndBack 23: [ OK ] NNPotOptionsTest.InternalsToKvtAndBack (0 ms) 23: [----------] 5 tests from NNPotOptionsTest (9 ms total) 23: 23: [----------] 5 tests from NNPotTopologyPreprocessorTest 23: [ RUN ] NNPotTopologyPreprocessorTest.CanConstruct 23: [ OK ] NNPotTopologyPreprocessorTest.CanConstruct (0 ms) 23: [ RUN ] NNPotTopologyPreprocessorTest.FourWatersFirstInQMRegion 23: 23: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/applied_forces/nnpot/tests/Testing/Temporary/NNPotTopologyPreprocessorTest_FourWatersFirstInQMRegion_4water.mdp]: 23: For a correct single-point energy evaluation with nsteps = 0, use 23: continuation = yes to avoid constraining the input coordinates. 23: 23: Generating 1-4 interactions: fudge = 0.5 23: Number of degrees of freedom in T-Coupling group rest is 21.00 23: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 23: 23: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/applied_forces/nnpot/tests/Testing/Temporary/NNPotTopologyPreprocessorTest_FourWatersFirstInQMRegion_4water.mdp]: 23: NVE simulation with an initial temperature of zero: will use a Verlet 23: buffer of 10%. Check your energy drift! 23: 23: 23: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/applied_forces/nnpot/tests/Testing/Temporary/NNPotTopologyPreprocessorTest_FourWatersFirstInQMRegion_4water.mdp]: 23: You are using a plain Coulomb cut-off, which might produce artifacts. 23: You might want to consider using PME electrostatics. 23: 23: 23: 23: There were 3 NOTEs 23: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/applied_forces/nnpot/tests/Testing/Temporary/NNPotTopologyPreprocessorTest_FourWatersFirstInQMRegion_4water.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 23: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/applied_forces/nnpot/tests/Testing/Temporary/NNPotTopologyPreprocessorTest_FourWatersFirstInQMRegion_4water.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 23: Setting the LD random seed to 1055276510 23: 23: Generated 10 of the 10 non-bonded parameter combinations 23: 23: Generated 10 of the 10 1-4 parameter combinations 23: 23: Excluding 2 bonded neighbours molecule type 'SOL' 23: 23: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/4water.gro', all velocities are zero 23: Analysing residue names: 23: There are: 4 Water residues 23: 23: This run will generate roughly 0 Mb of data 23: [ OK ] NNPotTopologyPreprocessorTest.FourWatersFirstInQMRegion (32 ms) 23: [ RUN ] NNPotTopologyPreprocessorTest.FourWatersSecondAndFourthInQMRegion 23: 23: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/applied_forces/nnpot/tests/Testing/Temporary/NNPotTopologyPreprocessorTest_FourWatersSecondAndFourthInQMRegion_4water.mdp]: 23: For a correct single-point energy evaluation with nsteps = 0, use 23: continuation = yes to avoid constraining the input coordinates. 23: 23: Generating 1-4 interactions: fudge = 0.5 23: Number of degrees of freedom in T-Coupling group rest is 21.00 23: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 23: 23: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/applied_forces/nnpot/tests/Testing/Temporary/NNPotTopologyPreprocessorTest_FourWatersSecondAndFourthInQMRegion_4water.mdp]: 23: NVE simulation with an initial temperature of zero: will use a Verlet 23: buffer of 10%. Check your energy drift! 23: 23: 23: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/applied_forces/nnpot/tests/Testing/Temporary/NNPotTopologyPreprocessorTest_FourWatersSecondAndFourthInQMRegion_4water.mdp]: 23: You are using a plain Coulomb cut-off, which might produce artifacts. 23: You might want to consider using PME electrostatics. 23: 23: 23: 23: There were 3 NOTEs 23: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/applied_forces/nnpot/tests/Testing/Temporary/NNPotTopologyPreprocessorTest_FourWatersSecondAndFourthInQMRegion_4water.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 23: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/applied_forces/nnpot/tests/Testing/Temporary/NNPotTopologyPreprocessorTest_FourWatersSecondAndFourthInQMRegion_4water.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 23: Setting the LD random seed to -1402013761 23: 23: Generated 10 of the 10 non-bonded parameter combinations 23: 23: Generated 10 of the 10 1-4 parameter combinations 23: 23: Excluding 2 bonded neighbours molecule type 'SOL' 23: 23: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/4water.gro', all velocities are zero 23: Analysing residue names: 23: There are: 4 Water residues 23: 23: This run will generate roughly 0 Mb of data 23: [ OK ] NNPotTopologyPreprocessorTest.FourWatersSecondAndFourthInQMRegion (30 ms) 23: [ RUN ] NNPotTopologyPreprocessorTest.AlanineDipeptideWithLinkAtomsNoConstraints 23: 23: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/applied_forces/nnpot/tests/Testing/Temporary/NNPotTopologyPreprocessorTest_AlanineDipeptideWithLinkAtomsNoConstraints_alanine_vacuo.mdp]: 23: For a correct single-point energy evaluation with nsteps = 0, use 23: continuation = yes to avoid constraining the input coordinates. 23: 23: Generating 1-4 interactions: fudge = 0.5 23: Number of degrees of freedom in T-Coupling group rest is 63.00 23: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 23: 23: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/applied_forces/nnpot/tests/Testing/Temporary/NNPotTopologyPreprocessorTest_AlanineDipeptideWithLinkAtomsNoConstraints_alanine_vacuo.mdp]: 23: NVE simulation: will use the initial temperature of 129.093 K for 23: determining the Verlet buffer size 23: 23: 23: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/applied_forces/nnpot/tests/Testing/Temporary/NNPotTopologyPreprocessorTest_AlanineDipeptideWithLinkAtomsNoConstraints_alanine_vacuo.mdp]: 23: You are using a plain Coulomb cut-off, which might produce artifacts. 23: You might want to consider using PME electrostatics. 23: 23: 23: 23: There were 3 NOTEs 23: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/applied_forces/nnpot/tests/Testing/Temporary/NNPotTopologyPreprocessorTest_AlanineDipeptideWithLinkAtomsNoConstraints_alanine_vacuo.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 23: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/applied_forces/nnpot/tests/Testing/Temporary/NNPotTopologyPreprocessorTest_AlanineDipeptideWithLinkAtomsNoConstraints_alanine_vacuo.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 23: Setting the LD random seed to -437267201 23: 23: Generated 2145 of the 2145 non-bonded parameter combinations 23: 23: Generated 2145 of the 2145 1-4 parameter combinations 23: 23: Excluding 3 bonded neighbours molecule type 'ALANINEDIPEPTIDE' 23: 23: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/alanine_vacuo.gro' 23: Analysing residue names: 23: There are: 3 Protein residues 23: Analysing Protein... 23: 23: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 129.093 K 23: 23: Calculated rlist for 1x1 atom pair-list as 1.021 nm, buffer size 0.021 nm 23: 23: Set rlist, assuming 4x4 atom pair-list, to 1.013 nm, buffer size 0.013 nm 23: 23: Note that mdrun will redetermine rlist based on the actual pair-list setup 23: 23: This run will generate roughly 0 Mb of data 23: [ OK ] NNPotTopologyPreprocessorTest.AlanineDipeptideWithLinkAtomsNoConstraints (90 ms) 23: [ RUN ] NNPotTopologyPreprocessorTest.AlanineDipeptideWithLinkAtomsWithConstraints 23: 23: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/applied_forces/nnpot/tests/Testing/Temporary/NNPotTopologyPreprocessorTest_AlanineDipeptideWithLinkAtomsWithConstraints_alanine_vacuo.mdp]: 23: For a correct single-point energy evaluation with nsteps = 0, use 23: continuation = yes to avoid constraining the input coordinates. 23: 23: Generating 1-4 interactions: fudge = 0.5 23: 23: NOTE 2 [file unknown]: 23: You are using constraints on all bonds, whereas the forcefield has been 23: parametrized only with constraints involving hydrogen atoms. We suggest 23: using constraints = h-bonds instead, this will also improve performance. 23: 23: 23: NOTE 3 [file unknown]: 23: For energy conservation with LINCS, lincs_iter should be 2 or larger. 23: 23: 23: Number of degrees of freedom in T-Coupling group rest is 42.00 23: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 23: 23: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/applied_forces/nnpot/tests/Testing/Temporary/NNPotTopologyPreprocessorTest_AlanineDipeptideWithLinkAtomsWithConstraints_alanine_vacuo.mdp]: 23: NVE simulation: will use the initial temperature of 193.640 K for 23: determining the Verlet buffer size 23: 23: 23: NOTE 5 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/applied_forces/nnpot/tests/Testing/Temporary/NNPotTopologyPreprocessorTest_AlanineDipeptideWithLinkAtomsWithConstraints_alanine_vacuo.mdp]: 23: You are using a plain Coulomb cut-off, which might produce artifacts. 23: You might want to consider using PME electrostatics. 23: 23: 23: 23: There were 5 NOTEs 23: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/applied_forces/nnpot/tests/Testing/Temporary/NNPotTopologyPreprocessorTest_AlanineDipeptideWithLinkAtomsWithConstraints_alanine_vacuo.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 23: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/applied_forces/nnpot/tests/Testing/Temporary/NNPotTopologyPreprocessorTest_AlanineDipeptideWithLinkAtomsWithConstraints_alanine_vacuo.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 23: Setting the LD random seed to 888893111 23: 23: Generated 2145 of the 2145 non-bonded parameter combinations 23: 23: Generated 2145 of the 2145 1-4 parameter combinations 23: 23: Excluding 3 bonded neighbours molecule type 'ALANINEDIPEPTIDE' 23: 23: turning all bonds into constraints... 23: 23: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/alanine_vacuo.gro' 23: Analysing residue names: 23: There are: 3 Protein residues 23: Analysing Protein... 23: 23: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 193.64 K 23: 23: Calculated rlist for 1x1 atom pair-list as 1.023 nm, buffer size 0.023 nm 23: 23: Set rlist, assuming 4x4 atom pair-list, to 1.015 nm, buffer size 0.015 nm 23: 23: Note that mdrun will redetermine rlist based on the actual pair-list setup 23: 23: This run will generate roughly 0 Mb of data 23: [ OK ] NNPotTopologyPreprocessorTest.AlanineDipeptideWithLinkAtomsWithConstraints (99 ms) 23: [----------] 5 tests from NNPotTopologyPreprocessorTest (252 ms total) 23: 23: [----------] 1 test from NNPotForceProviderTest 23: [ RUN ] NNPotForceProviderTest.CanConstruct 23: [ OK ] NNPotForceProviderTest.CanConstruct (0 ms) 23: [----------] 1 test from NNPotForceProviderTest (0 ms total) 23: 23: [----------] Global test environment tear-down 23: [==========] 12 tests from 4 test suites ran. (263 ms total) 23: [ PASSED ] 12 tests. 23/92 Test #23: NNPotAppliedForcesUnitTest ................ Passed 0.40 sec test 24 Start 24: AppliedForcesUnitTest 24: Test command: /build/reproducible-path/gromacs-2025.1/build/basic/bin/applied_forces-test "--gtest_output=xml:/build/reproducible-path/gromacs-2025.1/build/basic/Testing/Temporary/AppliedForcesUnitTest.xml" 24: Working Directory: /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/applied_forces/tests 24: Test timeout computed to be: 30 24: [==========] Running 3 tests from 1 test suite. 24: [----------] Global test environment set-up. 24: [----------] 3 tests from ElectricFieldTest 24: [ RUN ] ElectricFieldTest.Static 24: [ OK ] ElectricFieldTest.Static (0 ms) 24: [ RUN ] ElectricFieldTest.Oscillating 24: [ OK ] ElectricFieldTest.Oscillating (0 ms) 24: [ RUN ] ElectricFieldTest.Pulsed 24: [ OK ] ElectricFieldTest.Pulsed (0 ms) 24: [----------] 3 tests from ElectricFieldTest (1 ms total) 24: 24: [----------] Global test environment tear-down 24: [==========] 3 tests from 1 test suite ran. (1 ms total) 24: [ PASSED ] 3 tests. 24/92 Test #24: AppliedForcesUnitTest ..................... Passed 0.09 sec test 25 Start 25: ListedForcesTest 25: Test command: /build/reproducible-path/gromacs-2025.1/build/basic/bin/listed_forces-test "--gtest_output=xml:/build/reproducible-path/gromacs-2025.1/build/basic/Testing/Temporary/ListedForcesTest.xml" 25: Working Directory: /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/listed_forces/tests 25: Test timeout computed to be: 30 25: [==========] Running 132 tests from 9 test suites. 25: [----------] Global test environment set-up. 25: [----------] 24 tests from Bond/ListedForcesTest 25: [ RUN ] Bond/ListedForcesTest.Ifunc/0 25: [ OK ] Bond/ListedForcesTest.Ifunc/0 (1 ms) 25: [ RUN ] Bond/ListedForcesTest.Ifunc/1 25: [ OK ] Bond/ListedForcesTest.Ifunc/1 (1 ms) 25: [ RUN ] Bond/ListedForcesTest.Ifunc/2 25: [ OK ] Bond/ListedForcesTest.Ifunc/2 (1 ms) 25: [ RUN ] Bond/ListedForcesTest.Ifunc/3 25: [ OK ] Bond/ListedForcesTest.Ifunc/3 (2 ms) 25: [ RUN ] Bond/ListedForcesTest.Ifunc/4 25: [ OK ] Bond/ListedForcesTest.Ifunc/4 (2 ms) 25: [ RUN ] Bond/ListedForcesTest.Ifunc/5 25: [ OK ] Bond/ListedForcesTest.Ifunc/5 (1 ms) 25: [ RUN ] Bond/ListedForcesTest.Ifunc/6 25: [ OK ] Bond/ListedForcesTest.Ifunc/6 (1 ms) 25: [ RUN ] Bond/ListedForcesTest.Ifunc/7 25: [ OK ] Bond/ListedForcesTest.Ifunc/7 (0 ms) 25: [ RUN ] Bond/ListedForcesTest.Ifunc/8 25: [ OK ] Bond/ListedForcesTest.Ifunc/8 (0 ms) 25: [ RUN ] Bond/ListedForcesTest.Ifunc/9 25: [ OK ] Bond/ListedForcesTest.Ifunc/9 (1 ms) 25: [ RUN ] Bond/ListedForcesTest.Ifunc/10 25: [ OK ] Bond/ListedForcesTest.Ifunc/10 (1 ms) 25: [ RUN ] Bond/ListedForcesTest.Ifunc/11 25: [ OK ] Bond/ListedForcesTest.Ifunc/11 (1 ms) 25: [ RUN ] Bond/ListedForcesTest.Ifunc/12 25: [ OK ] Bond/ListedForcesTest.Ifunc/12 (0 ms) 25: [ RUN ] Bond/ListedForcesTest.Ifunc/13 25: [ OK ] Bond/ListedForcesTest.Ifunc/13 (0 ms) 25: [ RUN ] Bond/ListedForcesTest.Ifunc/14 25: [ OK ] Bond/ListedForcesTest.Ifunc/14 (0 ms) 25: [ RUN ] Bond/ListedForcesTest.Ifunc/15 25: [ OK ] Bond/ListedForcesTest.Ifunc/15 (1 ms) 25: [ RUN ] Bond/ListedForcesTest.Ifunc/16 25: [ OK ] Bond/ListedForcesTest.Ifunc/16 (1 ms) 25: [ RUN ] Bond/ListedForcesTest.Ifunc/17 25: [ OK ] Bond/ListedForcesTest.Ifunc/17 (1 ms) 25: [ RUN ] Bond/ListedForcesTest.Ifunc/18 25: [ OK ] Bond/ListedForcesTest.Ifunc/18 (0 ms) 25: [ RUN ] Bond/ListedForcesTest.Ifunc/19 25: [ OK ] Bond/ListedForcesTest.Ifunc/19 (0 ms) 25: [ RUN ] Bond/ListedForcesTest.Ifunc/20 25: [ OK ] Bond/ListedForcesTest.Ifunc/20 (0 ms) 25: [ RUN ] Bond/ListedForcesTest.Ifunc/21 25: [ OK ] Bond/ListedForcesTest.Ifunc/21 (0 ms) 25: [ RUN ] Bond/ListedForcesTest.Ifunc/22 25: [ OK ] Bond/ListedForcesTest.Ifunc/22 (0 ms) 25: [ RUN ] Bond/ListedForcesTest.Ifunc/23 25: [ OK ] Bond/ListedForcesTest.Ifunc/23 (0 ms) 25: [----------] 24 tests from Bond/ListedForcesTest (36 ms total) 25: 25: [----------] 33 tests from Angle/ListedForcesTest 25: [ RUN ] Angle/ListedForcesTest.Ifunc/0 25: [ OK ] Angle/ListedForcesTest.Ifunc/0 (1 ms) 25: [ RUN ] Angle/ListedForcesTest.Ifunc/1 25: [ OK ] Angle/ListedForcesTest.Ifunc/1 (0 ms) 25: [ RUN ] Angle/ListedForcesTest.Ifunc/2 25: [ OK ] Angle/ListedForcesTest.Ifunc/2 (0 ms) 25: [ RUN ] Angle/ListedForcesTest.Ifunc/3 25: [ OK ] Angle/ListedForcesTest.Ifunc/3 (1 ms) 25: [ RUN ] Angle/ListedForcesTest.Ifunc/4 25: [ OK ] Angle/ListedForcesTest.Ifunc/4 (1 ms) 25: [ RUN ] Angle/ListedForcesTest.Ifunc/5 25: [ OK ] Angle/ListedForcesTest.Ifunc/5 (1 ms) 25: [ RUN ] Angle/ListedForcesTest.Ifunc/6 25: [ OK ] Angle/ListedForcesTest.Ifunc/6 (1 ms) 25: [ RUN ] Angle/ListedForcesTest.Ifunc/7 25: [ OK ] Angle/ListedForcesTest.Ifunc/7 (0 ms) 25: [ RUN ] Angle/ListedForcesTest.Ifunc/8 25: [ OK ] Angle/ListedForcesTest.Ifunc/8 (1 ms) 25: [ RUN ] Angle/ListedForcesTest.Ifunc/9 25: [ OK ] Angle/ListedForcesTest.Ifunc/9 (1 ms) 25: [ RUN ] Angle/ListedForcesTest.Ifunc/10 25: [ OK ] Angle/ListedForcesTest.Ifunc/10 (1 ms) 25: [ RUN ] Angle/ListedForcesTest.Ifunc/11 25: [ OK ] Angle/ListedForcesTest.Ifunc/11 (1 ms) 25: [ RUN ] Angle/ListedForcesTest.Ifunc/12 25: [ OK ] Angle/ListedForcesTest.Ifunc/12 (0 ms) 25: [ RUN ] Angle/ListedForcesTest.Ifunc/13 25: [ OK ] Angle/ListedForcesTest.Ifunc/13 (0 ms) 25: [ RUN ] Angle/ListedForcesTest.Ifunc/14 25: [ OK ] Angle/ListedForcesTest.Ifunc/14 (0 ms) 25: [ RUN ] Angle/ListedForcesTest.Ifunc/15 25: [ OK ] Angle/ListedForcesTest.Ifunc/15 (1 ms) 25: [ RUN ] Angle/ListedForcesTest.Ifunc/16 25: [ OK ] Angle/ListedForcesTest.Ifunc/16 (1 ms) 25: [ RUN ] Angle/ListedForcesTest.Ifunc/17 25: [ OK ] Angle/ListedForcesTest.Ifunc/17 (1 ms) 25: [ RUN ] Angle/ListedForcesTest.Ifunc/18 25: [ OK ] Angle/ListedForcesTest.Ifunc/18 (1 ms) 25: [ RUN ] Angle/ListedForcesTest.Ifunc/19 25: [ OK ] Angle/ListedForcesTest.Ifunc/19 (0 ms) 25: [ RUN ] Angle/ListedForcesTest.Ifunc/20 25: [ OK ] Angle/ListedForcesTest.Ifunc/20 (0 ms) 25: [ RUN ] Angle/ListedForcesTest.Ifunc/21 25: [ OK ] Angle/ListedForcesTest.Ifunc/21 (0 ms) 25: [ RUN ] Angle/ListedForcesTest.Ifunc/22 25: [ OK ] Angle/ListedForcesTest.Ifunc/22 (0 ms) 25: [ RUN ] Angle/ListedForcesTest.Ifunc/23 25: [ OK ] Angle/ListedForcesTest.Ifunc/23 (1 ms) 25: [ RUN ] Angle/ListedForcesTest.Ifunc/24 25: [ OK ] Angle/ListedForcesTest.Ifunc/24 (0 ms) 25: [ RUN ] Angle/ListedForcesTest.Ifunc/25 25: [ OK ] Angle/ListedForcesTest.Ifunc/25 (0 ms) 25: [ RUN ] Angle/ListedForcesTest.Ifunc/26 25: [ OK ] Angle/ListedForcesTest.Ifunc/26 (0 ms) 25: [ RUN ] Angle/ListedForcesTest.Ifunc/27 25: [ OK ] Angle/ListedForcesTest.Ifunc/27 (1 ms) 25: [ RUN ] Angle/ListedForcesTest.Ifunc/28 25: [ OK ] Angle/ListedForcesTest.Ifunc/28 (1 ms) 25: [ RUN ] Angle/ListedForcesTest.Ifunc/29 25: [ OK ] Angle/ListedForcesTest.Ifunc/29 (1 ms) 25: [ RUN ] Angle/ListedForcesTest.Ifunc/30 25: [ OK ] Angle/ListedForcesTest.Ifunc/30 (0 ms) 25: [ RUN ] Angle/ListedForcesTest.Ifunc/31 25: [ OK ] Angle/ListedForcesTest.Ifunc/31 (0 ms) 25: [ RUN ] Angle/ListedForcesTest.Ifunc/32 25: [ OK ] Angle/ListedForcesTest.Ifunc/32 (0 ms) 25: [----------] 33 tests from Angle/ListedForcesTest (44 ms total) 25: 25: [----------] 18 tests from Dihedral/ListedForcesTest 25: [ RUN ] Dihedral/ListedForcesTest.Ifunc/0 25: [ OK ] Dihedral/ListedForcesTest.Ifunc/0 (1 ms) 25: [ RUN ] Dihedral/ListedForcesTest.Ifunc/1 25: [ OK ] Dihedral/ListedForcesTest.Ifunc/1 (1 ms) 25: [ RUN ] Dihedral/ListedForcesTest.Ifunc/2 25: [ OK ] Dihedral/ListedForcesTest.Ifunc/2 (1 ms) 25: [ RUN ] Dihedral/ListedForcesTest.Ifunc/3 25: [ OK ] Dihedral/ListedForcesTest.Ifunc/3 (0 ms) 25: [ RUN ] Dihedral/ListedForcesTest.Ifunc/4 25: [ OK ] Dihedral/ListedForcesTest.Ifunc/4 (1 ms) 25: [ RUN ] Dihedral/ListedForcesTest.Ifunc/5 25: [ OK ] Dihedral/ListedForcesTest.Ifunc/5 (1 ms) 25: [ RUN ] Dihedral/ListedForcesTest.Ifunc/6 25: [ OK ] Dihedral/ListedForcesTest.Ifunc/6 (0 ms) 25: [ RUN ] Dihedral/ListedForcesTest.Ifunc/7 25: [ OK ] Dihedral/ListedForcesTest.Ifunc/7 (1 ms) 25: [ RUN ] Dihedral/ListedForcesTest.Ifunc/8 25: [ OK ] Dihedral/ListedForcesTest.Ifunc/8 (0 ms) 25: [ RUN ] Dihedral/ListedForcesTest.Ifunc/9 25: [ OK ] Dihedral/ListedForcesTest.Ifunc/9 (1 ms) 25: [ RUN ] Dihedral/ListedForcesTest.Ifunc/10 25: [ OK ] Dihedral/ListedForcesTest.Ifunc/10 (1 ms) 25: [ RUN ] Dihedral/ListedForcesTest.Ifunc/11 25: [ OK ] Dihedral/ListedForcesTest.Ifunc/11 (1 ms) 25: [ RUN ] Dihedral/ListedForcesTest.Ifunc/12 25: [ OK ] Dihedral/ListedForcesTest.Ifunc/12 (1 ms) 25: [ RUN ] Dihedral/ListedForcesTest.Ifunc/13 25: [ OK ] Dihedral/ListedForcesTest.Ifunc/13 (1 ms) 25: [ RUN ] Dihedral/ListedForcesTest.Ifunc/14 25: [ OK ] Dihedral/ListedForcesTest.Ifunc/14 (1 ms) 25: [ RUN ] Dihedral/ListedForcesTest.Ifunc/15 25: [ OK ] Dihedral/ListedForcesTest.Ifunc/15 (0 ms) 25: [ RUN ] Dihedral/ListedForcesTest.Ifunc/16 25: [ OK ] Dihedral/ListedForcesTest.Ifunc/16 (0 ms) 25: [ RUN ] Dihedral/ListedForcesTest.Ifunc/17 25: [ OK ] Dihedral/ListedForcesTest.Ifunc/17 (0 ms) 25: [----------] 18 tests from Dihedral/ListedForcesTest (26 ms total) 25: 25: [----------] 12 tests from Polarize/ListedForcesTest 25: [ RUN ] Polarize/ListedForcesTest.Ifunc/0 25: [ OK ] Polarize/ListedForcesTest.Ifunc/0 (1 ms) 25: [ RUN ] Polarize/ListedForcesTest.Ifunc/1 25: [ OK ] Polarize/ListedForcesTest.Ifunc/1 (0 ms) 25: [ RUN ] Polarize/ListedForcesTest.Ifunc/2 25: [ OK ] Polarize/ListedForcesTest.Ifunc/2 (0 ms) 25: [ RUN ] Polarize/ListedForcesTest.Ifunc/3 25: [ OK ] Polarize/ListedForcesTest.Ifunc/3 (0 ms) 25: [ RUN ] Polarize/ListedForcesTest.Ifunc/4 25: [ OK ] Polarize/ListedForcesTest.Ifunc/4 (1 ms) 25: [ RUN ] Polarize/ListedForcesTest.Ifunc/5 25: [ OK ] Polarize/ListedForcesTest.Ifunc/5 (0 ms) 25: [ RUN ] Polarize/ListedForcesTest.Ifunc/6 25: [ OK ] Polarize/ListedForcesTest.Ifunc/6 (0 ms) 25: [ RUN ] Polarize/ListedForcesTest.Ifunc/7 25: [ OK ] Polarize/ListedForcesTest.Ifunc/7 (0 ms) 25: [ RUN ] Polarize/ListedForcesTest.Ifunc/8 25: [ OK ] Polarize/ListedForcesTest.Ifunc/8 (1 ms) 25: [ RUN ] Polarize/ListedForcesTest.Ifunc/9 25: [ OK ] Polarize/ListedForcesTest.Ifunc/9 (1 ms) 25: [ RUN ] Polarize/ListedForcesTest.Ifunc/10 25: [ OK ] Polarize/ListedForcesTest.Ifunc/10 (1 ms) 25: [ RUN ] Polarize/ListedForcesTest.Ifunc/11 25: [ OK ] Polarize/ListedForcesTest.Ifunc/11 (1 ms) 25: [----------] 12 tests from Polarize/ListedForcesTest (14 ms total) 25: 25: [----------] 18 tests from Restraints/ListedForcesTest 25: [ RUN ] Restraints/ListedForcesTest.Ifunc/0 25: [ OK ] Restraints/ListedForcesTest.Ifunc/0 (1 ms) 25: [ RUN ] Restraints/ListedForcesTest.Ifunc/1 25: [ OK ] Restraints/ListedForcesTest.Ifunc/1 (1 ms) 25: [ RUN ] Restraints/ListedForcesTest.Ifunc/2 25: [ OK ] Restraints/ListedForcesTest.Ifunc/2 (1 ms) 25: [ RUN ] Restraints/ListedForcesTest.Ifunc/3 25: [ OK ] Restraints/ListedForcesTest.Ifunc/3 (1 ms) 25: [ RUN ] Restraints/ListedForcesTest.Ifunc/4 25: [ OK ] Restraints/ListedForcesTest.Ifunc/4 (0 ms) 25: [ RUN ] Restraints/ListedForcesTest.Ifunc/5 25: [ OK ] Restraints/ListedForcesTest.Ifunc/5 (0 ms) 25: [ RUN ] Restraints/ListedForcesTest.Ifunc/6 25: [ OK ] Restraints/ListedForcesTest.Ifunc/6 (1 ms) 25: [ RUN ] Restraints/ListedForcesTest.Ifunc/7 25: [ OK ] Restraints/ListedForcesTest.Ifunc/7 (1 ms) 25: [ RUN ] Restraints/ListedForcesTest.Ifunc/8 25: [ OK ] Restraints/ListedForcesTest.Ifunc/8 (1 ms) 25: [ RUN ] Restraints/ListedForcesTest.Ifunc/9 25: [ OK ] Restraints/ListedForcesTest.Ifunc/9 (1 ms) 25: [ RUN ] Restraints/ListedForcesTest.Ifunc/10 25: [ OK ] Restraints/ListedForcesTest.Ifunc/10 (0 ms) 25: [ RUN ] Restraints/ListedForcesTest.Ifunc/11 25: [ OK ] Restraints/ListedForcesTest.Ifunc/11 (0 ms) 25: [ RUN ] Restraints/ListedForcesTest.Ifunc/12 25: [ OK ] Restraints/ListedForcesTest.Ifunc/12 (0 ms) 25: [ RUN ] Restraints/ListedForcesTest.Ifunc/13 25: [ OK ] Restraints/ListedForcesTest.Ifunc/13 (2 ms) 25: [ RUN ] Restraints/ListedForcesTest.Ifunc/14 25: [ OK ] Restraints/ListedForcesTest.Ifunc/14 (1 ms) 25: [ RUN ] Restraints/ListedForcesTest.Ifunc/15 25: [ OK ] Restraints/ListedForcesTest.Ifunc/15 (3 ms) 25: [ RUN ] Restraints/ListedForcesTest.Ifunc/16 25: [ OK ] Restraints/ListedForcesTest.Ifunc/16 (2 ms) 25: [ RUN ] Restraints/ListedForcesTest.Ifunc/17 25: [ OK ] Restraints/ListedForcesTest.Ifunc/17 (2 ms) 25: [----------] 18 tests from Restraints/ListedForcesTest (31 ms total) 25: 25: [----------] 3 tests from BondZeroLength/ListedForcesTest 25: [ RUN ] BondZeroLength/ListedForcesTest.Ifunc/0 25: [ OK ] BondZeroLength/ListedForcesTest.Ifunc/0 (2 ms) 25: [ RUN ] BondZeroLength/ListedForcesTest.Ifunc/1 25: [ OK ] BondZeroLength/ListedForcesTest.Ifunc/1 (1 ms) 25: [ RUN ] BondZeroLength/ListedForcesTest.Ifunc/2 25: [ OK ] BondZeroLength/ListedForcesTest.Ifunc/2 (0 ms) 25: [----------] 3 tests from BondZeroLength/ListedForcesTest (4 ms total) 25: 25: [----------] 3 tests from AngleZero/ListedForcesTest 25: [ RUN ] AngleZero/ListedForcesTest.Ifunc/0 25: [ OK ] AngleZero/ListedForcesTest.Ifunc/0 (0 ms) 25: [ RUN ] AngleZero/ListedForcesTest.Ifunc/1 25: [ OK ] AngleZero/ListedForcesTest.Ifunc/1 (0 ms) 25: [ RUN ] AngleZero/ListedForcesTest.Ifunc/2 25: [ OK ] AngleZero/ListedForcesTest.Ifunc/2 (0 ms) 25: [----------] 3 tests from AngleZero/ListedForcesTest (2 ms total) 25: 25: [----------] 12 tests from 14Interaction/ListedForcesPairsTest 25: [ RUN ] 14Interaction/ListedForcesPairsTest.Ifunc/0 25: [ OK ] 14Interaction/ListedForcesPairsTest.Ifunc/0 (2 ms) 25: [ RUN ] 14Interaction/ListedForcesPairsTest.Ifunc/1 25: [ OK ] 14Interaction/ListedForcesPairsTest.Ifunc/1 (2 ms) 25: [ RUN ] 14Interaction/ListedForcesPairsTest.Ifunc/2 25: [ OK ] 14Interaction/ListedForcesPairsTest.Ifunc/2 (2 ms) 25: [ RUN ] 14Interaction/ListedForcesPairsTest.Ifunc/3 25: [ OK ] 14Interaction/ListedForcesPairsTest.Ifunc/3 (0 ms) 25: [ RUN ] 14Interaction/ListedForcesPairsTest.Ifunc/4 25: [ OK ] 14Interaction/ListedForcesPairsTest.Ifunc/4 (0 ms) 25: [ RUN ] 14Interaction/ListedForcesPairsTest.Ifunc/5 25: [ OK ] 14Interaction/ListedForcesPairsTest.Ifunc/5 (0 ms) 25: [ RUN ] 14Interaction/ListedForcesPairsTest.Ifunc/6 25: [ OK ] 14Interaction/ListedForcesPairsTest.Ifunc/6 (0 ms) 25: [ RUN ] 14Interaction/ListedForcesPairsTest.Ifunc/7 25: [ OK ] 14Interaction/ListedForcesPairsTest.Ifunc/7 (0 ms) 25: [ RUN ] 14Interaction/ListedForcesPairsTest.Ifunc/8 25: [ OK ] 14Interaction/ListedForcesPairsTest.Ifunc/8 (0 ms) 25: [ RUN ] 14Interaction/ListedForcesPairsTest.Ifunc/9 25: [ OK ] 14Interaction/ListedForcesPairsTest.Ifunc/9 (0 ms) 25: [ RUN ] 14Interaction/ListedForcesPairsTest.Ifunc/10 25: [ OK ] 14Interaction/ListedForcesPairsTest.Ifunc/10 (0 ms) 25: [ RUN ] 14Interaction/ListedForcesPairsTest.Ifunc/11 25: [ OK ] 14Interaction/ListedForcesPairsTest.Ifunc/11 (0 ms) 25: [----------] 12 tests from 14Interaction/ListedForcesPairsTest (17 ms total) 25: 25: [----------] 9 tests from PosResBasicTest/PositionRestraintsTest 25: [ RUN ] PosResBasicTest/PositionRestraintsTest.BasicPosResNoFreeEnergy/0 25: [ OK ] PosResBasicTest/PositionRestraintsTest.BasicPosResNoFreeEnergy/0 (0 ms) 25: [ RUN ] PosResBasicTest/PositionRestraintsTest.BasicPosResNoFreeEnergy/1 25: [ OK ] PosResBasicTest/PositionRestraintsTest.BasicPosResNoFreeEnergy/1 (0 ms) 25: [ RUN ] PosResBasicTest/PositionRestraintsTest.BasicPosResNoFreeEnergy/2 25: [ OK ] PosResBasicTest/PositionRestraintsTest.BasicPosResNoFreeEnergy/2 (0 ms) 25: [ RUN ] PosResBasicTest/PositionRestraintsTest.BasicPosResNoFreeEnergy/3 25: [ OK ] PosResBasicTest/PositionRestraintsTest.BasicPosResNoFreeEnergy/3 (0 ms) 25: [ RUN ] PosResBasicTest/PositionRestraintsTest.BasicPosResNoFreeEnergy/4 25: [ OK ] PosResBasicTest/PositionRestraintsTest.BasicPosResNoFreeEnergy/4 (0 ms) 25: [ RUN ] PosResBasicTest/PositionRestraintsTest.BasicPosResNoFreeEnergy/5 25: [ OK ] PosResBasicTest/PositionRestraintsTest.BasicPosResNoFreeEnergy/5 (0 ms) 25: [ RUN ] PosResBasicTest/PositionRestraintsTest.BasicPosResNoFreeEnergy/6 25: [ OK ] PosResBasicTest/PositionRestraintsTest.BasicPosResNoFreeEnergy/6 (0 ms) 25: [ RUN ] PosResBasicTest/PositionRestraintsTest.BasicPosResNoFreeEnergy/7 25: [ OK ] PosResBasicTest/PositionRestraintsTest.BasicPosResNoFreeEnergy/7 (0 ms) 25: [ RUN ] PosResBasicTest/PositionRestraintsTest.BasicPosResNoFreeEnergy/8 25: [ OK ] PosResBasicTest/PositionRestraintsTest.BasicPosResNoFreeEnergy/8 (0 ms) 25: [----------] 9 tests from PosResBasicTest/PositionRestraintsTest (7 ms total) 25: 25: [----------] Global test environment tear-down 25: [==========] 132 tests from 9 test suites ran. (187 ms total) 25: [ PASSED ] 132 tests. 25/92 Test #25: ListedForcesTest .......................... Passed 0.31 sec test 26 Start 26: NbnxmTests 26: Test command: /build/reproducible-path/gromacs-2025.1/build/basic/bin/nbnxm-test "--gtest_output=xml:/build/reproducible-path/gromacs-2025.1/build/basic/Testing/Temporary/NbnxmTests.xml" 26: Working Directory: /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/nbnxm/tests 26: Test timeout computed to be: 30 26: [==========] Running 380 tests from 3 test suites. 26: [----------] Global test environment set-up. 26: [----------] 18 tests from KernelSetupTest 26: [ RUN ] KernelSetupTest.getCoulombKernelTypeRF 26: [ OK ] KernelSetupTest.getCoulombKernelTypeRF (0 ms) 26: [ RUN ] KernelSetupTest.getCoulombKernelTypeCut 26: [ OK ] KernelSetupTest.getCoulombKernelTypeCut (0 ms) 26: [ RUN ] KernelSetupTest.getCoulombKernelTypeTable 26: [ OK ] KernelSetupTest.getCoulombKernelTypeTable (0 ms) 26: [ RUN ] KernelSetupTest.getCoulombKernelTypeTableTwin 26: [ OK ] KernelSetupTest.getCoulombKernelTypeTableTwin (0 ms) 26: [ RUN ] KernelSetupTest.getCoulombKernelTypeEwald 26: [ OK ] KernelSetupTest.getCoulombKernelTypeEwald (0 ms) 26: [ RUN ] KernelSetupTest.getCoulombKernelTypeEwaldTwin 26: [ OK ] KernelSetupTest.getCoulombKernelTypeEwaldTwin (0 ms) 26: [ RUN ] KernelSetupTest.getVdwKernelTypeLjCutCombGeomNone 26: [ OK ] KernelSetupTest.getVdwKernelTypeLjCutCombGeomNone (0 ms) 26: [ RUN ] KernelSetupTest.getVdwKernelTypeLjCutCombGeomPotShift 26: [ OK ] KernelSetupTest.getVdwKernelTypeLjCutCombGeomPotShift (0 ms) 26: [ RUN ] KernelSetupTest.getVdwKernelTypeLjCutCombLBNone 26: [ OK ] KernelSetupTest.getVdwKernelTypeLjCutCombLBNone (0 ms) 26: [ RUN ] KernelSetupTest.getVdwKernelTypeLjCutCombLBPotShift 26: [ OK ] KernelSetupTest.getVdwKernelTypeLjCutCombLBPotShift (0 ms) 26: [ RUN ] KernelSetupTest.getVdwKernelTypeLjCutCombNoneNone 26: [ OK ] KernelSetupTest.getVdwKernelTypeLjCutCombNoneNone (0 ms) 26: [ RUN ] KernelSetupTest.getVdwKernelTypeLjCutCombNonePotShift 26: [ OK ] KernelSetupTest.getVdwKernelTypeLjCutCombNonePotShift (0 ms) 26: [ RUN ] KernelSetupTest.getVdwKernelTypeLjCutThrows 26: [ OK ] KernelSetupTest.getVdwKernelTypeLjCutThrows (0 ms) 26: [ RUN ] KernelSetupTest.getVdwKernelTypeLjCutForceSwitch 26: [ OK ] KernelSetupTest.getVdwKernelTypeLjCutForceSwitch (0 ms) 26: [ RUN ] KernelSetupTest.getVdwKernelTypePmeGeom 26: [ OK ] KernelSetupTest.getVdwKernelTypePmeGeom (0 ms) 26: [ RUN ] KernelSetupTest.getVdwKernelTypePmeNone 26: [ OK ] KernelSetupTest.getVdwKernelTypePmeNone (0 ms) 26: [ RUN ] KernelSetupTest.getVdwKernelTypeLjCutPotSwitch 26: [ OK ] KernelSetupTest.getVdwKernelTypeLjCutPotSwitch (0 ms) 26: [ RUN ] KernelSetupTest.getVdwKernelTypeAllCountThrows 26: [ OK ] KernelSetupTest.getVdwKernelTypeAllCountThrows (0 ms) 26: [----------] 18 tests from KernelSetupTest (1 ms total) 26: 26: [----------] 2 tests from WithParameters/CpuListDiagonalExclusionsTest 26: [ RUN ] WithParameters/CpuListDiagonalExclusionsTest.CheckMask/0 26: [ OK ] WithParameters/CpuListDiagonalExclusionsTest.CheckMask/0 (0 ms) 26: [ RUN ] WithParameters/CpuListDiagonalExclusionsTest.CheckMask/1 26: [ OK ] WithParameters/CpuListDiagonalExclusionsTest.CheckMask/1 (0 ms) 26: [----------] 2 tests from WithParameters/CpuListDiagonalExclusionsTest (0 ms total) 26: 26: [----------] 360 tests from Combinations/NbnxmKernelTest 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombReactionField_VdwCutCombGeom 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:540: Skipped 26: There are no combination rule versions of the plain-C kernel 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombReactionField_VdwCutCombGeom (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombReactionField_VdwCutCombGeom 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:540: Skipped 26: There are no combination rule versions of the plain-C kernel 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombReactionField_VdwCutCombGeom (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwCutCombGeom 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:540: Skipped 26: There are no combination rule versions of the plain-C kernel 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwCutCombGeom (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombReactionField_VdwCutCombLB 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:540: Skipped 26: There are no combination rule versions of the plain-C kernel 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombReactionField_VdwCutCombLB (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombReactionField_VdwCutCombLB 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:540: Skipped 26: There are no combination rule versions of the plain-C kernel 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombReactionField_VdwCutCombLB (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwCutCombLB 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:540: Skipped 26: There are no combination rule versions of the plain-C kernel 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwCutCombLB (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombReactionField_VdwCutCombNone 26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombReactionField_VdwCutCombNone (23 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombReactionField_VdwCutCombNone 26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombReactionField_VdwCutCombNone (20 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwCutCombNone 26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwCutCombNone (21 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombReactionField_VdwForceSwitch 26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombReactionField_VdwForceSwitch (23 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombReactionField_VdwForceSwitch 26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombReactionField_VdwForceSwitch (22 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwForceSwitch 26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwForceSwitch (21 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombReactionField_VdwPotSwitch 26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombReactionField_VdwPotSwitch (23 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombReactionField_VdwPotSwitch 26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombReactionField_VdwPotSwitch (22 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwPotSwitch 26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwPotSwitch (22 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombReactionField_VdwEwaldCombGeom 26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombReactionField_VdwEwaldCombGeom (23 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombReactionField_VdwEwaldCombGeom 26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombReactionField_VdwEwaldCombGeom (22 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwEwaldCombGeom 26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwEwaldCombGeom (22 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombEwald_VdwCutCombGeom 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 26: Analytical Ewald is not implemented for the plain-C kernel, skip this test 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombEwald_VdwCutCombGeom (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombEwald_VdwCutCombGeom 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 26: Analytical Ewald is not implemented for the plain-C kernel, skip this test 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombEwald_VdwCutCombGeom (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombEwald_VdwCutCombGeom 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 26: Analytical Ewald is not implemented for the plain-C kernel, skip this test 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombEwald_VdwCutCombGeom (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombEwald_VdwCutCombLB 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 26: Analytical Ewald is not implemented for the plain-C kernel, skip this test 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombEwald_VdwCutCombLB (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombEwald_VdwCutCombLB 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 26: Analytical Ewald is not implemented for the plain-C kernel, skip this test 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombEwald_VdwCutCombLB (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombEwald_VdwCutCombLB 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 26: Analytical Ewald is not implemented for the plain-C kernel, skip this test 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombEwald_VdwCutCombLB (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombEwald_VdwCutCombNone 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 26: Analytical Ewald is not implemented for the plain-C kernel, skip this test 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombEwald_VdwCutCombNone (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombEwald_VdwCutCombNone 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 26: Analytical Ewald is not implemented for the plain-C kernel, skip this test 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombEwald_VdwCutCombNone (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombEwald_VdwCutCombNone 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 26: Analytical Ewald is not implemented for the plain-C kernel, skip this test 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombEwald_VdwCutCombNone (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombEwald_VdwForceSwitch 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 26: Analytical Ewald is not implemented for the plain-C kernel, skip this test 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombEwald_VdwForceSwitch (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombEwald_VdwForceSwitch 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 26: Analytical Ewald is not implemented for the plain-C kernel, skip this test 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombEwald_VdwForceSwitch (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombEwald_VdwForceSwitch 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 26: Analytical Ewald is not implemented for the plain-C kernel, skip this test 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombEwald_VdwForceSwitch (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombEwald_VdwPotSwitch 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 26: Analytical Ewald is not implemented for the plain-C kernel, skip this test 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombEwald_VdwPotSwitch (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombEwald_VdwPotSwitch 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 26: Analytical Ewald is not implemented for the plain-C kernel, skip this test 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombEwald_VdwPotSwitch (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombEwald_VdwPotSwitch 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 26: Analytical Ewald is not implemented for the plain-C kernel, skip this test 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombEwald_VdwPotSwitch (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombEwald_VdwEwaldCombGeom 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 26: Analytical Ewald is not implemented for the plain-C kernel, skip this test 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombEwald_VdwEwaldCombGeom (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombEwald_VdwEwaldCombGeom 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 26: Analytical Ewald is not implemented for the plain-C kernel, skip this test 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombEwald_VdwEwaldCombGeom (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombEwald_VdwEwaldCombGeom 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 26: Analytical Ewald is not implemented for the plain-C kernel, skip this test 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombEwald_VdwEwaldCombGeom (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombEwaldTwin_VdwCutCombGeom 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 26: Analytical Ewald is not implemented for the plain-C kernel, skip this test 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombEwaldTwin_VdwCutCombGeom (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombEwaldTwin_VdwCutCombGeom 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 26: Analytical Ewald is not implemented for the plain-C kernel, skip this test 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombEwaldTwin_VdwCutCombGeom (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombGeom 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 26: Analytical Ewald is not implemented for the plain-C kernel, skip this test 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombGeom (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombEwaldTwin_VdwCutCombLB 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 26: Analytical Ewald is not implemented for the plain-C kernel, skip this test 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombEwaldTwin_VdwCutCombLB (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombEwaldTwin_VdwCutCombLB 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 26: Analytical Ewald is not implemented for the plain-C kernel, skip this test 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombEwaldTwin_VdwCutCombLB (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombLB 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 26: Analytical Ewald is not implemented for the plain-C kernel, skip this test 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombLB (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombEwaldTwin_VdwCutCombNone 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 26: Analytical Ewald is not implemented for the plain-C kernel, skip this test 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombEwaldTwin_VdwCutCombNone (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombEwaldTwin_VdwCutCombNone 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 26: Analytical Ewald is not implemented for the plain-C kernel, skip this test 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombEwaldTwin_VdwCutCombNone (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombNone 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 26: Analytical Ewald is not implemented for the plain-C kernel, skip this test 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombNone (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombEwaldTwin_VdwForceSwitch 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 26: Analytical Ewald is not implemented for the plain-C kernel, skip this test 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombEwaldTwin_VdwForceSwitch (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombEwaldTwin_VdwForceSwitch 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 26: Analytical Ewald is not implemented for the plain-C kernel, skip this test 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombEwaldTwin_VdwForceSwitch (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwForceSwitch 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 26: Analytical Ewald is not implemented for the plain-C kernel, skip this test 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwForceSwitch (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombEwaldTwin_VdwPotSwitch 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 26: Analytical Ewald is not implemented for the plain-C kernel, skip this test 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombEwaldTwin_VdwPotSwitch (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombEwaldTwin_VdwPotSwitch 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 26: Analytical Ewald is not implemented for the plain-C kernel, skip this test 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombEwaldTwin_VdwPotSwitch (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwPotSwitch 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 26: Analytical Ewald is not implemented for the plain-C kernel, skip this test 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwPotSwitch (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombEwaldTwin_VdwEwaldCombGeom 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 26: Analytical Ewald is not implemented for the plain-C kernel, skip this test 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombEwaldTwin_VdwEwaldCombGeom (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombEwaldTwin_VdwEwaldCombGeom 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 26: Analytical Ewald is not implemented for the plain-C kernel, skip this test 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombEwaldTwin_VdwEwaldCombGeom (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwEwaldCombGeom 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 26: Analytical Ewald is not implemented for the plain-C kernel, skip this test 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwEwaldCombGeom (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_NoEnergies_CoulombEwald_VdwCutCombGeom 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:540: Skipped 26: There are no combination rule versions of the plain-C kernel 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_NoEnergies_CoulombEwald_VdwCutCombGeom (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_Energies_CoulombEwald_VdwCutCombGeom 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:540: Skipped 26: There are no combination rule versions of the plain-C kernel 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_Energies_CoulombEwald_VdwCutCombGeom (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_ThreeEnergyGroups_CoulombEwald_VdwCutCombGeom 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:540: Skipped 26: There are no combination rule versions of the plain-C kernel 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_ThreeEnergyGroups_CoulombEwald_VdwCutCombGeom (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_NoEnergies_CoulombEwald_VdwCutCombLB 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:540: Skipped 26: There are no combination rule versions of the plain-C kernel 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_NoEnergies_CoulombEwald_VdwCutCombLB (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_Energies_CoulombEwald_VdwCutCombLB 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:540: Skipped 26: There are no combination rule versions of the plain-C kernel 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_Energies_CoulombEwald_VdwCutCombLB (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_ThreeEnergyGroups_CoulombEwald_VdwCutCombLB 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:540: Skipped 26: There are no combination rule versions of the plain-C kernel 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_ThreeEnergyGroups_CoulombEwald_VdwCutCombLB (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_NoEnergies_CoulombEwald_VdwCutCombNone 26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_NoEnergies_CoulombEwald_VdwCutCombNone (22 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_Energies_CoulombEwald_VdwCutCombNone 26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_Energies_CoulombEwald_VdwCutCombNone (22 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_ThreeEnergyGroups_CoulombEwald_VdwCutCombNone 26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_ThreeEnergyGroups_CoulombEwald_VdwCutCombNone (23 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_NoEnergies_CoulombEwald_VdwForceSwitch 26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_NoEnergies_CoulombEwald_VdwForceSwitch (24 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_Energies_CoulombEwald_VdwForceSwitch 26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_Energies_CoulombEwald_VdwForceSwitch (22 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_ThreeEnergyGroups_CoulombEwald_VdwForceSwitch 26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_ThreeEnergyGroups_CoulombEwald_VdwForceSwitch (21 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_NoEnergies_CoulombEwald_VdwPotSwitch 26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_NoEnergies_CoulombEwald_VdwPotSwitch (22 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_Energies_CoulombEwald_VdwPotSwitch 26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_Energies_CoulombEwald_VdwPotSwitch (22 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_ThreeEnergyGroups_CoulombEwald_VdwPotSwitch 26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_ThreeEnergyGroups_CoulombEwald_VdwPotSwitch (22 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_NoEnergies_CoulombEwald_VdwEwaldCombGeom 26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_NoEnergies_CoulombEwald_VdwEwaldCombGeom (24 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_Energies_CoulombEwald_VdwEwaldCombGeom 26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_Energies_CoulombEwald_VdwEwaldCombGeom (23 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_ThreeEnergyGroups_CoulombEwald_VdwEwaldCombGeom 26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_ThreeEnergyGroups_CoulombEwald_VdwEwaldCombGeom (23 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_NoEnergies_CoulombEwaldTwin_VdwCutCombGeom 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:540: Skipped 26: There are no combination rule versions of the plain-C kernel 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_NoEnergies_CoulombEwaldTwin_VdwCutCombGeom (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_Energies_CoulombEwaldTwin_VdwCutCombGeom 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:540: Skipped 26: There are no combination rule versions of the plain-C kernel 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_Energies_CoulombEwaldTwin_VdwCutCombGeom (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombGeom 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:540: Skipped 26: There are no combination rule versions of the plain-C kernel 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombGeom (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_NoEnergies_CoulombEwaldTwin_VdwCutCombLB 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:540: Skipped 26: There are no combination rule versions of the plain-C kernel 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_NoEnergies_CoulombEwaldTwin_VdwCutCombLB (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_Energies_CoulombEwaldTwin_VdwCutCombLB 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:540: Skipped 26: There are no combination rule versions of the plain-C kernel 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_Energies_CoulombEwaldTwin_VdwCutCombLB (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombLB 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:540: Skipped 26: There are no combination rule versions of the plain-C kernel 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombLB (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_NoEnergies_CoulombEwaldTwin_VdwCutCombNone 26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_NoEnergies_CoulombEwaldTwin_VdwCutCombNone (21 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_Energies_CoulombEwaldTwin_VdwCutCombNone 26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_Energies_CoulombEwaldTwin_VdwCutCombNone (21 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombNone 26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombNone (22 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_NoEnergies_CoulombEwaldTwin_VdwForceSwitch 26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_NoEnergies_CoulombEwaldTwin_VdwForceSwitch (23 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_Energies_CoulombEwaldTwin_VdwForceSwitch 26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_Energies_CoulombEwaldTwin_VdwForceSwitch (21 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwForceSwitch 26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwForceSwitch (22 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_NoEnergies_CoulombEwaldTwin_VdwPotSwitch 26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_NoEnergies_CoulombEwaldTwin_VdwPotSwitch (23 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_Energies_CoulombEwaldTwin_VdwPotSwitch 26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_Energies_CoulombEwaldTwin_VdwPotSwitch (22 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwPotSwitch 26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwPotSwitch (22 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_NoEnergies_CoulombEwaldTwin_VdwEwaldCombGeom 26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_NoEnergies_CoulombEwaldTwin_VdwEwaldCombGeom (23 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_Energies_CoulombEwaldTwin_VdwEwaldCombGeom 26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_Energies_CoulombEwaldTwin_VdwEwaldCombGeom (24 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwEwaldCombGeom 26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwEwaldCombGeom (24 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombReactionField_VdwCutCombGeom 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:540: Skipped 26: There are no combination rule versions of the plain-C kernel 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombReactionField_VdwCutCombGeom (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombReactionField_VdwCutCombGeom 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:540: Skipped 26: There are no combination rule versions of the plain-C kernel 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombReactionField_VdwCutCombGeom (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwCutCombGeom 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:540: Skipped 26: There are no combination rule versions of the plain-C kernel 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwCutCombGeom (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombReactionField_VdwCutCombLB 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:540: Skipped 26: There are no combination rule versions of the plain-C kernel 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombReactionField_VdwCutCombLB (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombReactionField_VdwCutCombLB 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:540: Skipped 26: There are no combination rule versions of the plain-C kernel 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombReactionField_VdwCutCombLB (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwCutCombLB 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:540: Skipped 26: There are no combination rule versions of the plain-C kernel 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwCutCombLB (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombReactionField_VdwCutCombNone 26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombReactionField_VdwCutCombNone (19 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombReactionField_VdwCutCombNone 26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombReactionField_VdwCutCombNone (19 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwCutCombNone 26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwCutCombNone (19 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombReactionField_VdwForceSwitch 26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombReactionField_VdwForceSwitch (19 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombReactionField_VdwForceSwitch 26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombReactionField_VdwForceSwitch (20 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwForceSwitch 26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwForceSwitch (19 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombReactionField_VdwPotSwitch 26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombReactionField_VdwPotSwitch (20 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombReactionField_VdwPotSwitch 26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombReactionField_VdwPotSwitch (21 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwPotSwitch 26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwPotSwitch (20 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombReactionField_VdwEwaldCombGeom 26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombReactionField_VdwEwaldCombGeom (22 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombReactionField_VdwEwaldCombGeom 26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombReactionField_VdwEwaldCombGeom (22 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwEwaldCombGeom 26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwEwaldCombGeom (22 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombEwald_VdwCutCombGeom 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 26: Analytical Ewald is not implemented for the plain-C kernel, skip this test 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombEwald_VdwCutCombGeom (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombEwald_VdwCutCombGeom 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 26: Analytical Ewald is not implemented for the plain-C kernel, skip this test 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombEwald_VdwCutCombGeom (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombEwald_VdwCutCombGeom 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 26: Analytical Ewald is not implemented for the plain-C kernel, skip this test 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombEwald_VdwCutCombGeom (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombEwald_VdwCutCombLB 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 26: Analytical Ewald is not implemented for the plain-C kernel, skip this test 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombEwald_VdwCutCombLB (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombEwald_VdwCutCombLB 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 26: Analytical Ewald is not implemented for the plain-C kernel, skip this test 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombEwald_VdwCutCombLB (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombEwald_VdwCutCombLB 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 26: Analytical Ewald is not implemented for the plain-C kernel, skip this test 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombEwald_VdwCutCombLB (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombEwald_VdwCutCombNone 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 26: Analytical Ewald is not implemented for the plain-C kernel, skip this test 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombEwald_VdwCutCombNone (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombEwald_VdwCutCombNone 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 26: Analytical Ewald is not implemented for the plain-C kernel, skip this test 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombEwald_VdwCutCombNone (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombEwald_VdwCutCombNone 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 26: Analytical Ewald is not implemented for the plain-C kernel, skip this test 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombEwald_VdwCutCombNone (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombEwald_VdwForceSwitch 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 26: Analytical Ewald is not implemented for the plain-C kernel, skip this test 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombEwald_VdwForceSwitch (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombEwald_VdwForceSwitch 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 26: Analytical Ewald is not implemented for the plain-C kernel, skip this test 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombEwald_VdwForceSwitch (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombEwald_VdwForceSwitch 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 26: Analytical Ewald is not implemented for the plain-C kernel, skip this test 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombEwald_VdwForceSwitch (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombEwald_VdwPotSwitch 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 26: Analytical Ewald is not implemented for the plain-C kernel, skip this test 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombEwald_VdwPotSwitch (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombEwald_VdwPotSwitch 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 26: Analytical Ewald is not implemented for the plain-C kernel, skip this test 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombEwald_VdwPotSwitch (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombEwald_VdwPotSwitch 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 26: Analytical Ewald is not implemented for the plain-C kernel, skip this test 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombEwald_VdwPotSwitch (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombEwald_VdwEwaldCombGeom 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 26: Analytical Ewald is not implemented for the plain-C kernel, skip this test 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombEwald_VdwEwaldCombGeom (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombEwald_VdwEwaldCombGeom 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 26: Analytical Ewald is not implemented for the plain-C kernel, skip this test 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombEwald_VdwEwaldCombGeom (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombEwald_VdwEwaldCombGeom 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 26: Analytical Ewald is not implemented for the plain-C kernel, skip this test 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombEwald_VdwEwaldCombGeom (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombEwaldTwin_VdwCutCombGeom 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 26: Analytical Ewald is not implemented for the plain-C kernel, skip this test 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombEwaldTwin_VdwCutCombGeom (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombEwaldTwin_VdwCutCombGeom 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 26: Analytical Ewald is not implemented for the plain-C kernel, skip this test 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombEwaldTwin_VdwCutCombGeom (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombGeom 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 26: Analytical Ewald is not implemented for the plain-C kernel, skip this test 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombGeom (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombEwaldTwin_VdwCutCombLB 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 26: Analytical Ewald is not implemented for the plain-C kernel, skip this test 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombEwaldTwin_VdwCutCombLB (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombEwaldTwin_VdwCutCombLB 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 26: Analytical Ewald is not implemented for the plain-C kernel, skip this test 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombEwaldTwin_VdwCutCombLB (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombLB 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 26: Analytical Ewald is not implemented for the plain-C kernel, skip this test 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombLB (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombEwaldTwin_VdwCutCombNone 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 26: Analytical Ewald is not implemented for the plain-C kernel, skip this test 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombEwaldTwin_VdwCutCombNone (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombEwaldTwin_VdwCutCombNone 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 26: Analytical Ewald is not implemented for the plain-C kernel, skip this test 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombEwaldTwin_VdwCutCombNone (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombNone 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 26: Analytical Ewald is not implemented for the plain-C kernel, skip this test 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombNone (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombEwaldTwin_VdwForceSwitch 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 26: Analytical Ewald is not implemented for the plain-C kernel, skip this test 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombEwaldTwin_VdwForceSwitch (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombEwaldTwin_VdwForceSwitch 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 26: Analytical Ewald is not implemented for the plain-C kernel, skip this test 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombEwaldTwin_VdwForceSwitch (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwForceSwitch 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 26: Analytical Ewald is not implemented for the plain-C kernel, skip this test 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwForceSwitch (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombEwaldTwin_VdwPotSwitch 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 26: Analytical Ewald is not implemented for the plain-C kernel, skip this test 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombEwaldTwin_VdwPotSwitch (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombEwaldTwin_VdwPotSwitch 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 26: Analytical Ewald is not implemented for the plain-C kernel, skip this test 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombEwaldTwin_VdwPotSwitch (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwPotSwitch 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 26: Analytical Ewald is not implemented for the plain-C kernel, skip this test 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwPotSwitch (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombEwaldTwin_VdwEwaldCombGeom 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 26: Analytical Ewald is not implemented for the plain-C kernel, skip this test 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombEwaldTwin_VdwEwaldCombGeom (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombEwaldTwin_VdwEwaldCombGeom 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 26: Analytical Ewald is not implemented for the plain-C kernel, skip this test 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombEwaldTwin_VdwEwaldCombGeom (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwEwaldCombGeom 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 26: Analytical Ewald is not implemented for the plain-C kernel, skip this test 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwEwaldCombGeom (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_NoEnergies_CoulombEwald_VdwCutCombGeom 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:540: Skipped 26: There are no combination rule versions of the plain-C kernel 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_NoEnergies_CoulombEwald_VdwCutCombGeom (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_Energies_CoulombEwald_VdwCutCombGeom 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:540: Skipped 26: There are no combination rule versions of the plain-C kernel 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_Energies_CoulombEwald_VdwCutCombGeom (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_ThreeEnergyGroups_CoulombEwald_VdwCutCombGeom 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:540: Skipped 26: There are no combination rule versions of the plain-C kernel 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_ThreeEnergyGroups_CoulombEwald_VdwCutCombGeom (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_NoEnergies_CoulombEwald_VdwCutCombLB 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:540: Skipped 26: There are no combination rule versions of the plain-C kernel 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_NoEnergies_CoulombEwald_VdwCutCombLB (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_Energies_CoulombEwald_VdwCutCombLB 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:540: Skipped 26: There are no combination rule versions of the plain-C kernel 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_Energies_CoulombEwald_VdwCutCombLB (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_ThreeEnergyGroups_CoulombEwald_VdwCutCombLB 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:540: Skipped 26: There are no combination rule versions of the plain-C kernel 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_ThreeEnergyGroups_CoulombEwald_VdwCutCombLB (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_NoEnergies_CoulombEwald_VdwCutCombNone 26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_NoEnergies_CoulombEwald_VdwCutCombNone (22 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_Energies_CoulombEwald_VdwCutCombNone 26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_Energies_CoulombEwald_VdwCutCombNone (22 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_ThreeEnergyGroups_CoulombEwald_VdwCutCombNone 26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_ThreeEnergyGroups_CoulombEwald_VdwCutCombNone (20 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_NoEnergies_CoulombEwald_VdwForceSwitch 26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_NoEnergies_CoulombEwald_VdwForceSwitch (21 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_Energies_CoulombEwald_VdwForceSwitch 26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_Energies_CoulombEwald_VdwForceSwitch (21 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_ThreeEnergyGroups_CoulombEwald_VdwForceSwitch 26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_ThreeEnergyGroups_CoulombEwald_VdwForceSwitch (20 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_NoEnergies_CoulombEwald_VdwPotSwitch 26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_NoEnergies_CoulombEwald_VdwPotSwitch (22 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_Energies_CoulombEwald_VdwPotSwitch 26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_Energies_CoulombEwald_VdwPotSwitch (24 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_ThreeEnergyGroups_CoulombEwald_VdwPotSwitch 26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_ThreeEnergyGroups_CoulombEwald_VdwPotSwitch (24 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_NoEnergies_CoulombEwald_VdwEwaldCombGeom 26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_NoEnergies_CoulombEwald_VdwEwaldCombGeom (26 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_Energies_CoulombEwald_VdwEwaldCombGeom 26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_Energies_CoulombEwald_VdwEwaldCombGeom (25 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_ThreeEnergyGroups_CoulombEwald_VdwEwaldCombGeom 26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_ThreeEnergyGroups_CoulombEwald_VdwEwaldCombGeom (25 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_NoEnergies_CoulombEwaldTwin_VdwCutCombGeom 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:540: Skipped 26: There are no combination rule versions of the plain-C kernel 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_NoEnergies_CoulombEwaldTwin_VdwCutCombGeom (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_Energies_CoulombEwaldTwin_VdwCutCombGeom 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:540: Skipped 26: There are no combination rule versions of the plain-C kernel 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_Energies_CoulombEwaldTwin_VdwCutCombGeom (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombGeom 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:540: Skipped 26: There are no combination rule versions of the plain-C kernel 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombGeom (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_NoEnergies_CoulombEwaldTwin_VdwCutCombLB 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:540: Skipped 26: There are no combination rule versions of the plain-C kernel 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_NoEnergies_CoulombEwaldTwin_VdwCutCombLB (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_Energies_CoulombEwaldTwin_VdwCutCombLB 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:540: Skipped 26: There are no combination rule versions of the plain-C kernel 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_Energies_CoulombEwaldTwin_VdwCutCombLB (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombLB 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:540: Skipped 26: There are no combination rule versions of the plain-C kernel 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombLB (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_NoEnergies_CoulombEwaldTwin_VdwCutCombNone 26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_NoEnergies_CoulombEwaldTwin_VdwCutCombNone (22 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_Energies_CoulombEwaldTwin_VdwCutCombNone 26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_Energies_CoulombEwaldTwin_VdwCutCombNone (22 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombNone 26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombNone (22 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_NoEnergies_CoulombEwaldTwin_VdwForceSwitch 26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_NoEnergies_CoulombEwaldTwin_VdwForceSwitch (23 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_Energies_CoulombEwaldTwin_VdwForceSwitch 26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_Energies_CoulombEwaldTwin_VdwForceSwitch (23 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwForceSwitch 26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwForceSwitch (23 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_NoEnergies_CoulombEwaldTwin_VdwPotSwitch 26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_NoEnergies_CoulombEwaldTwin_VdwPotSwitch (23 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_Energies_CoulombEwaldTwin_VdwPotSwitch 26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_Energies_CoulombEwaldTwin_VdwPotSwitch (24 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwPotSwitch 26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwPotSwitch (23 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_NoEnergies_CoulombEwaldTwin_VdwEwaldCombGeom 26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_NoEnergies_CoulombEwaldTwin_VdwEwaldCombGeom (26 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_Energies_CoulombEwaldTwin_VdwEwaldCombGeom 26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_Energies_CoulombEwaldTwin_VdwEwaldCombGeom (26 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwEwaldCombGeom 26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwEwaldCombGeom (26 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_NoEnergies_CoulombReactionField_VdwCutCombGeom 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:514: Skipped 26: Cannot test or generate data for 4xN kernels without suitable SIMD support 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_NoEnergies_CoulombReactionField_VdwCutCombGeom (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_Energies_CoulombReactionField_VdwCutCombGeom 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:514: Skipped 26: Cannot test or generate data for 4xN kernels without suitable SIMD support 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_Energies_CoulombReactionField_VdwCutCombGeom (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwCutCombGeom 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:514: Skipped 26: Cannot test or generate data for 4xN kernels without suitable SIMD support 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwCutCombGeom (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_NoEnergies_CoulombReactionField_VdwCutCombLB 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:514: Skipped 26: Cannot test or generate data for 4xN kernels without suitable SIMD support 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_NoEnergies_CoulombReactionField_VdwCutCombLB (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_Energies_CoulombReactionField_VdwCutCombLB 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:514: Skipped 26: Cannot test or generate data for 4xN kernels without suitable SIMD support 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_Energies_CoulombReactionField_VdwCutCombLB (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwCutCombLB 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:514: Skipped 26: Cannot test or generate data for 4xN kernels without suitable SIMD support 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwCutCombLB (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_NoEnergies_CoulombReactionField_VdwCutCombNone 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:514: Skipped 26: Cannot test or generate data for 4xN kernels without suitable SIMD support 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_NoEnergies_CoulombReactionField_VdwCutCombNone (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_Energies_CoulombReactionField_VdwCutCombNone 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:514: Skipped 26: Cannot test or generate data for 4xN kernels without suitable SIMD support 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_Energies_CoulombReactionField_VdwCutCombNone (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwCutCombNone 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:514: Skipped 26: Cannot test or generate data for 4xN kernels without suitable SIMD support 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwCutCombNone (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_NoEnergies_CoulombReactionField_VdwForceSwitch 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:514: Skipped 26: Cannot test or generate data for 4xN kernels without suitable SIMD support 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_NoEnergies_CoulombReactionField_VdwForceSwitch (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_Energies_CoulombReactionField_VdwForceSwitch 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:514: Skipped 26: Cannot test or generate data for 4xN kernels without suitable SIMD support 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_Energies_CoulombReactionField_VdwForceSwitch (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwForceSwitch 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:514: Skipped 26: Cannot test or generate data for 4xN kernels without suitable SIMD support 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwForceSwitch (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_NoEnergies_CoulombReactionField_VdwPotSwitch 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:514: Skipped 26: Cannot test or generate data for 4xN kernels without suitable SIMD support 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_NoEnergies_CoulombReactionField_VdwPotSwitch (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_Energies_CoulombReactionField_VdwPotSwitch 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:514: Skipped 26: Cannot test or generate data for 4xN kernels without suitable SIMD support 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_Energies_CoulombReactionField_VdwPotSwitch (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwPotSwitch 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:514: Skipped 26: Cannot test or generate data for 4xN kernels without suitable SIMD support 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwPotSwitch (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_NoEnergies_CoulombReactionField_VdwEwaldCombGeom 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:514: Skipped 26: Cannot test or generate data for 4xN kernels without suitable SIMD support 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_NoEnergies_CoulombReactionField_VdwEwaldCombGeom (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_Energies_CoulombReactionField_VdwEwaldCombGeom 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:514: Skipped 26: Cannot test or generate data for 4xN kernels without suitable SIMD support 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_Energies_CoulombReactionField_VdwEwaldCombGeom (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwEwaldCombGeom 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:514: Skipped 26: Cannot test or generate data for 4xN kernels without suitable SIMD support 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwEwaldCombGeom (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_NoEnergies_CoulombEwald_VdwCutCombGeom 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:514: Skipped 26: Cannot test or generate data for 4xN kernels without suitable SIMD support 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_NoEnergies_CoulombEwald_VdwCutCombGeom (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_Energies_CoulombEwald_VdwCutCombGeom 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:514: Skipped 26: Cannot test or generate data for 4xN kernels without suitable SIMD support 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_Energies_CoulombEwald_VdwCutCombGeom (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_ThreeEnergyGroups_CoulombEwald_VdwCutCombGeom 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:514: Skipped 26: Cannot test or generate data for 4xN kernels without suitable SIMD support 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_ThreeEnergyGroups_CoulombEwald_VdwCutCombGeom (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_NoEnergies_CoulombEwald_VdwCutCombLB 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:514: Skipped 26: Cannot test or generate data for 4xN kernels without suitable SIMD support 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_NoEnergies_CoulombEwald_VdwCutCombLB (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_Energies_CoulombEwald_VdwCutCombLB 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:514: Skipped 26: Cannot test or generate data for 4xN kernels without suitable SIMD support 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_Energies_CoulombEwald_VdwCutCombLB (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_ThreeEnergyGroups_CoulombEwald_VdwCutCombLB 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:514: Skipped 26: Cannot test or generate data for 4xN kernels without suitable SIMD support 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_ThreeEnergyGroups_CoulombEwald_VdwCutCombLB (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_NoEnergies_CoulombEwald_VdwCutCombNone 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:514: Skipped 26: Cannot test or generate data for 4xN kernels without suitable SIMD support 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_NoEnergies_CoulombEwald_VdwCutCombNone (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_Energies_CoulombEwald_VdwCutCombNone 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:514: Skipped 26: Cannot test or generate data for 4xN kernels without suitable SIMD support 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_Energies_CoulombEwald_VdwCutCombNone (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_ThreeEnergyGroups_CoulombEwald_VdwCutCombNone 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:514: Skipped 26: Cannot test or generate data for 4xN kernels without suitable SIMD support 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_ThreeEnergyGroups_CoulombEwald_VdwCutCombNone (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_NoEnergies_CoulombEwald_VdwForceSwitch 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:514: Skipped 26: Cannot test or generate data for 4xN kernels without suitable SIMD support 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_NoEnergies_CoulombEwald_VdwForceSwitch (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_Energies_CoulombEwald_VdwForceSwitch 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:514: Skipped 26: Cannot test or generate data for 4xN kernels without suitable SIMD support 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_Energies_CoulombEwald_VdwForceSwitch (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_ThreeEnergyGroups_CoulombEwald_VdwForceSwitch 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:514: Skipped 26: Cannot test or generate data for 4xN kernels without suitable SIMD support 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_ThreeEnergyGroups_CoulombEwald_VdwForceSwitch (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_NoEnergies_CoulombEwald_VdwPotSwitch 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:514: Skipped 26: Cannot test or generate data for 4xN kernels without suitable SIMD support 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_NoEnergies_CoulombEwald_VdwPotSwitch (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_Energies_CoulombEwald_VdwPotSwitch 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:514: Skipped 26: Cannot test or generate data for 4xN kernels without suitable SIMD support 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_Energies_CoulombEwald_VdwPotSwitch (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_ThreeEnergyGroups_CoulombEwald_VdwPotSwitch 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:514: Skipped 26: Cannot test or generate data for 4xN kernels without suitable SIMD support 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_ThreeEnergyGroups_CoulombEwald_VdwPotSwitch (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_NoEnergies_CoulombEwald_VdwEwaldCombGeom 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:514: Skipped 26: Cannot test or generate data for 4xN kernels without suitable SIMD support 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_NoEnergies_CoulombEwald_VdwEwaldCombGeom (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_Energies_CoulombEwald_VdwEwaldCombGeom 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:514: Skipped 26: Cannot test or generate data for 4xN kernels without suitable SIMD support 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_Energies_CoulombEwald_VdwEwaldCombGeom (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_ThreeEnergyGroups_CoulombEwald_VdwEwaldCombGeom 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:514: Skipped 26: Cannot test or generate data for 4xN kernels without suitable SIMD support 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_ThreeEnergyGroups_CoulombEwald_VdwEwaldCombGeom (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_NoEnergies_CoulombEwaldTwin_VdwCutCombGeom 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:514: Skipped 26: Cannot test or generate data for 4xN kernels without suitable SIMD support 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_NoEnergies_CoulombEwaldTwin_VdwCutCombGeom (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_Energies_CoulombEwaldTwin_VdwCutCombGeom 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:514: Skipped 26: Cannot test or generate data for 4xN kernels without suitable SIMD support 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_Energies_CoulombEwaldTwin_VdwCutCombGeom (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombGeom 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:514: Skipped 26: Cannot test or generate data for 4xN kernels without suitable SIMD support 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombGeom (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_NoEnergies_CoulombEwaldTwin_VdwCutCombLB 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:514: Skipped 26: Cannot test or generate data for 4xN kernels without suitable SIMD support 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_NoEnergies_CoulombEwaldTwin_VdwCutCombLB (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_Energies_CoulombEwaldTwin_VdwCutCombLB 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:514: Skipped 26: Cannot test or generate data for 4xN kernels without suitable SIMD support 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_Energies_CoulombEwaldTwin_VdwCutCombLB (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombLB 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:514: Skipped 26: Cannot test or generate data for 4xN kernels without suitable SIMD support 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombLB (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_NoEnergies_CoulombEwaldTwin_VdwCutCombNone 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:514: Skipped 26: Cannot test or generate data for 4xN kernels without suitable SIMD support 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_NoEnergies_CoulombEwaldTwin_VdwCutCombNone (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_Energies_CoulombEwaldTwin_VdwCutCombNone 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:514: Skipped 26: Cannot test or generate data for 4xN kernels without suitable SIMD support 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_Energies_CoulombEwaldTwin_VdwCutCombNone (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombNone 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:514: Skipped 26: Cannot test or generate data for 4xN kernels without suitable SIMD support 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombNone (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_NoEnergies_CoulombEwaldTwin_VdwForceSwitch 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:514: Skipped 26: Cannot test or generate data for 4xN kernels without suitable SIMD support 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_NoEnergies_CoulombEwaldTwin_VdwForceSwitch (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_Energies_CoulombEwaldTwin_VdwForceSwitch 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:514: Skipped 26: Cannot test or generate data for 4xN kernels without suitable SIMD support 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_Energies_CoulombEwaldTwin_VdwForceSwitch (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwForceSwitch 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:514: Skipped 26: Cannot test or generate data for 4xN kernels without suitable SIMD support 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwForceSwitch (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_NoEnergies_CoulombEwaldTwin_VdwPotSwitch 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:514: Skipped 26: Cannot test or generate data for 4xN kernels without suitable SIMD support 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_NoEnergies_CoulombEwaldTwin_VdwPotSwitch (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_Energies_CoulombEwaldTwin_VdwPotSwitch 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:514: Skipped 26: Cannot test or generate data for 4xN kernels without suitable SIMD support 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_Energies_CoulombEwaldTwin_VdwPotSwitch (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwPotSwitch 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:514: Skipped 26: Cannot test or generate data for 4xN kernels without suitable SIMD support 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwPotSwitch (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_NoEnergies_CoulombEwaldTwin_VdwEwaldCombGeom 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:514: Skipped 26: Cannot test or generate data for 4xN kernels without suitable SIMD support 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_NoEnergies_CoulombEwaldTwin_VdwEwaldCombGeom (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_Energies_CoulombEwaldTwin_VdwEwaldCombGeom 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:514: Skipped 26: Cannot test or generate data for 4xN kernels without suitable SIMD support 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_Energies_CoulombEwaldTwin_VdwEwaldCombGeom (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwEwaldCombGeom 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:514: Skipped 26: Cannot test or generate data for 4xN kernels without suitable SIMD support 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwEwaldCombGeom (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_NoEnergies_CoulombEwald_VdwCutCombGeom 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:514: Skipped 26: Cannot test or generate data for 4xN kernels without suitable SIMD support 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_NoEnergies_CoulombEwald_VdwCutCombGeom (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_Energies_CoulombEwald_VdwCutCombGeom 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:514: Skipped 26: Cannot test or generate data for 4xN kernels without suitable SIMD support 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_Energies_CoulombEwald_VdwCutCombGeom (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_ThreeEnergyGroups_CoulombEwald_VdwCutCombGeom 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:514: Skipped 26: Cannot test or generate data for 4xN kernels without suitable SIMD support 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_ThreeEnergyGroups_CoulombEwald_VdwCutCombGeom (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_NoEnergies_CoulombEwald_VdwCutCombLB 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:514: Skipped 26: Cannot test or generate data for 4xN kernels without suitable SIMD support 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_NoEnergies_CoulombEwald_VdwCutCombLB (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_Energies_CoulombEwald_VdwCutCombLB 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:514: Skipped 26: Cannot test or generate data for 4xN kernels without suitable SIMD support 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_Energies_CoulombEwald_VdwCutCombLB (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_ThreeEnergyGroups_CoulombEwald_VdwCutCombLB 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:514: Skipped 26: Cannot test or generate data for 4xN kernels without suitable SIMD support 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_ThreeEnergyGroups_CoulombEwald_VdwCutCombLB (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_NoEnergies_CoulombEwald_VdwCutCombNone 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:514: Skipped 26: Cannot test or generate data for 4xN kernels without suitable SIMD support 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_NoEnergies_CoulombEwald_VdwCutCombNone (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_Energies_CoulombEwald_VdwCutCombNone 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:514: Skipped 26: Cannot test or generate data for 4xN kernels without suitable SIMD support 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_Energies_CoulombEwald_VdwCutCombNone (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_ThreeEnergyGroups_CoulombEwald_VdwCutCombNone 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:514: Skipped 26: Cannot test or generate data for 4xN kernels without suitable SIMD support 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_ThreeEnergyGroups_CoulombEwald_VdwCutCombNone (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_NoEnergies_CoulombEwald_VdwForceSwitch 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:514: Skipped 26: Cannot test or generate data for 4xN kernels without suitable SIMD support 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_NoEnergies_CoulombEwald_VdwForceSwitch (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_Energies_CoulombEwald_VdwForceSwitch 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:514: Skipped 26: Cannot test or generate data for 4xN kernels without suitable SIMD support 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_Energies_CoulombEwald_VdwForceSwitch (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_ThreeEnergyGroups_CoulombEwald_VdwForceSwitch 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:514: Skipped 26: Cannot test or generate data for 4xN kernels without suitable SIMD support 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_ThreeEnergyGroups_CoulombEwald_VdwForceSwitch (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_NoEnergies_CoulombEwald_VdwPotSwitch 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:514: Skipped 26: Cannot test or generate data for 4xN kernels without suitable SIMD support 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_NoEnergies_CoulombEwald_VdwPotSwitch (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_Energies_CoulombEwald_VdwPotSwitch 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:514: Skipped 26: Cannot test or generate data for 4xN kernels without suitable SIMD support 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_Energies_CoulombEwald_VdwPotSwitch (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_ThreeEnergyGroups_CoulombEwald_VdwPotSwitch 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:514: Skipped 26: Cannot test or generate data for 4xN kernels without suitable SIMD support 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_ThreeEnergyGroups_CoulombEwald_VdwPotSwitch (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_NoEnergies_CoulombEwald_VdwEwaldCombGeom 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:514: Skipped 26: Cannot test or generate data for 4xN kernels without suitable SIMD support 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_NoEnergies_CoulombEwald_VdwEwaldCombGeom (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_Energies_CoulombEwald_VdwEwaldCombGeom 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:514: Skipped 26: Cannot test or generate data for 4xN kernels without suitable SIMD support 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_Energies_CoulombEwald_VdwEwaldCombGeom (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_ThreeEnergyGroups_CoulombEwald_VdwEwaldCombGeom 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:514: Skipped 26: Cannot test or generate data for 4xN kernels without suitable SIMD support 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_ThreeEnergyGroups_CoulombEwald_VdwEwaldCombGeom (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_NoEnergies_CoulombEwaldTwin_VdwCutCombGeom 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:514: Skipped 26: Cannot test or generate data for 4xN kernels without suitable SIMD support 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_NoEnergies_CoulombEwaldTwin_VdwCutCombGeom (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_Energies_CoulombEwaldTwin_VdwCutCombGeom 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:514: Skipped 26: Cannot test or generate data for 4xN kernels without suitable SIMD support 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_Energies_CoulombEwaldTwin_VdwCutCombGeom (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombGeom 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:514: Skipped 26: Cannot test or generate data for 4xN kernels without suitable SIMD support 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombGeom (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_NoEnergies_CoulombEwaldTwin_VdwCutCombLB 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:514: Skipped 26: Cannot test or generate data for 4xN kernels without suitable SIMD support 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_NoEnergies_CoulombEwaldTwin_VdwCutCombLB (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_Energies_CoulombEwaldTwin_VdwCutCombLB 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:514: Skipped 26: Cannot test or generate data for 4xN kernels without suitable SIMD support 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_Energies_CoulombEwaldTwin_VdwCutCombLB (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombLB 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:514: Skipped 26: Cannot test or generate data for 4xN kernels without suitable SIMD support 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombLB (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_NoEnergies_CoulombEwaldTwin_VdwCutCombNone 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:514: Skipped 26: Cannot test or generate data for 4xN kernels without suitable SIMD support 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_NoEnergies_CoulombEwaldTwin_VdwCutCombNone (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_Energies_CoulombEwaldTwin_VdwCutCombNone 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:514: Skipped 26: Cannot test or generate data for 4xN kernels without suitable SIMD support 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_Energies_CoulombEwaldTwin_VdwCutCombNone (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombNone 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:514: Skipped 26: Cannot test or generate data for 4xN kernels without suitable SIMD support 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombNone (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_NoEnergies_CoulombEwaldTwin_VdwForceSwitch 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:514: Skipped 26: Cannot test or generate data for 4xN kernels without suitable SIMD support 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_NoEnergies_CoulombEwaldTwin_VdwForceSwitch (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_Energies_CoulombEwaldTwin_VdwForceSwitch 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:514: Skipped 26: Cannot test or generate data for 4xN kernels without suitable SIMD support 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_Energies_CoulombEwaldTwin_VdwForceSwitch (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwForceSwitch 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:514: Skipped 26: Cannot test or generate data for 4xN kernels without suitable SIMD support 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwForceSwitch (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_NoEnergies_CoulombEwaldTwin_VdwPotSwitch 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:514: Skipped 26: Cannot test or generate data for 4xN kernels without suitable SIMD support 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_NoEnergies_CoulombEwaldTwin_VdwPotSwitch (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_Energies_CoulombEwaldTwin_VdwPotSwitch 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:514: Skipped 26: Cannot test or generate data for 4xN kernels without suitable SIMD support 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_Energies_CoulombEwaldTwin_VdwPotSwitch (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwPotSwitch 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:514: Skipped 26: Cannot test or generate data for 4xN kernels without suitable SIMD support 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwPotSwitch (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_NoEnergies_CoulombEwaldTwin_VdwEwaldCombGeom 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:514: Skipped 26: Cannot test or generate data for 4xN kernels without suitable SIMD support 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_NoEnergies_CoulombEwaldTwin_VdwEwaldCombGeom (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_Energies_CoulombEwaldTwin_VdwEwaldCombGeom 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:514: Skipped 26: Cannot test or generate data for 4xN kernels without suitable SIMD support 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_Energies_CoulombEwaldTwin_VdwEwaldCombGeom (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwEwaldCombGeom 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:514: Skipped 26: Cannot test or generate data for 4xN kernels without suitable SIMD support 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwEwaldCombGeom (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombReactionField_VdwCutCombGeom 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped 26: Cannot test or generate data for 2xNN kernels without suitable SIMD support 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombReactionField_VdwCutCombGeom (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombReactionField_VdwCutCombGeom 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped 26: Cannot test or generate data for 2xNN kernels without suitable SIMD support 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombReactionField_VdwCutCombGeom (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwCutCombGeom 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped 26: Cannot test or generate data for 2xNN kernels without suitable SIMD support 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwCutCombGeom (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombReactionField_VdwCutCombLB 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped 26: Cannot test or generate data for 2xNN kernels without suitable SIMD support 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombReactionField_VdwCutCombLB (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombReactionField_VdwCutCombLB 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped 26: Cannot test or generate data for 2xNN kernels without suitable SIMD support 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombReactionField_VdwCutCombLB (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwCutCombLB 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped 26: Cannot test or generate data for 2xNN kernels without suitable SIMD support 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwCutCombLB (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombReactionField_VdwCutCombNone 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped 26: Cannot test or generate data for 2xNN kernels without suitable SIMD support 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombReactionField_VdwCutCombNone (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombReactionField_VdwCutCombNone 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped 26: Cannot test or generate data for 2xNN kernels without suitable SIMD support 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombReactionField_VdwCutCombNone (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwCutCombNone 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped 26: Cannot test or generate data for 2xNN kernels without suitable SIMD support 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwCutCombNone (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombReactionField_VdwForceSwitch 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped 26: Cannot test or generate data for 2xNN kernels without suitable SIMD support 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombReactionField_VdwForceSwitch (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombReactionField_VdwForceSwitch 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped 26: Cannot test or generate data for 2xNN kernels without suitable SIMD support 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombReactionField_VdwForceSwitch (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwForceSwitch 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped 26: Cannot test or generate data for 2xNN kernels without suitable SIMD support 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwForceSwitch (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombReactionField_VdwPotSwitch 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped 26: Cannot test or generate data for 2xNN kernels without suitable SIMD support 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombReactionField_VdwPotSwitch (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombReactionField_VdwPotSwitch 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped 26: Cannot test or generate data for 2xNN kernels without suitable SIMD support 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombReactionField_VdwPotSwitch (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwPotSwitch 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped 26: Cannot test or generate data for 2xNN kernels without suitable SIMD support 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwPotSwitch (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombReactionField_VdwEwaldCombGeom 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped 26: Cannot test or generate data for 2xNN kernels without suitable SIMD support 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombReactionField_VdwEwaldCombGeom (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombReactionField_VdwEwaldCombGeom 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped 26: Cannot test or generate data for 2xNN kernels without suitable SIMD support 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombReactionField_VdwEwaldCombGeom (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwEwaldCombGeom 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped 26: Cannot test or generate data for 2xNN kernels without suitable SIMD support 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwEwaldCombGeom (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombEwald_VdwCutCombGeom 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped 26: Cannot test or generate data for 2xNN kernels without suitable SIMD support 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombEwald_VdwCutCombGeom (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombEwald_VdwCutCombGeom 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped 26: Cannot test or generate data for 2xNN kernels without suitable SIMD support 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombEwald_VdwCutCombGeom (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombEwald_VdwCutCombGeom 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped 26: Cannot test or generate data for 2xNN kernels without suitable SIMD support 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombEwald_VdwCutCombGeom (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombEwald_VdwCutCombLB 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped 26: Cannot test or generate data for 2xNN kernels without suitable SIMD support 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombEwald_VdwCutCombLB (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombEwald_VdwCutCombLB 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped 26: Cannot test or generate data for 2xNN kernels without suitable SIMD support 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombEwald_VdwCutCombLB (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombEwald_VdwCutCombLB 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped 26: Cannot test or generate data for 2xNN kernels without suitable SIMD support 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombEwald_VdwCutCombLB (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombEwald_VdwCutCombNone 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped 26: Cannot test or generate data for 2xNN kernels without suitable SIMD support 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombEwald_VdwCutCombNone (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombEwald_VdwCutCombNone 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped 26: Cannot test or generate data for 2xNN kernels without suitable SIMD support 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombEwald_VdwCutCombNone (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombEwald_VdwCutCombNone 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped 26: Cannot test or generate data for 2xNN kernels without suitable SIMD support 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombEwald_VdwCutCombNone (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombEwald_VdwForceSwitch 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped 26: Cannot test or generate data for 2xNN kernels without suitable SIMD support 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombEwald_VdwForceSwitch (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombEwald_VdwForceSwitch 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped 26: Cannot test or generate data for 2xNN kernels without suitable SIMD support 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombEwald_VdwForceSwitch (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombEwald_VdwForceSwitch 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped 26: Cannot test or generate data for 2xNN kernels without suitable SIMD support 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombEwald_VdwForceSwitch (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombEwald_VdwPotSwitch 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped 26: Cannot test or generate data for 2xNN kernels without suitable SIMD support 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombEwald_VdwPotSwitch (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombEwald_VdwPotSwitch 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped 26: Cannot test or generate data for 2xNN kernels without suitable SIMD support 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombEwald_VdwPotSwitch (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombEwald_VdwPotSwitch 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped 26: Cannot test or generate data for 2xNN kernels without suitable SIMD support 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombEwald_VdwPotSwitch (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombEwald_VdwEwaldCombGeom 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped 26: Cannot test or generate data for 2xNN kernels without suitable SIMD support 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombEwald_VdwEwaldCombGeom (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombEwald_VdwEwaldCombGeom 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped 26: Cannot test or generate data for 2xNN kernels without suitable SIMD support 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombEwald_VdwEwaldCombGeom (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombEwald_VdwEwaldCombGeom 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped 26: Cannot test or generate data for 2xNN kernels without suitable SIMD support 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombEwald_VdwEwaldCombGeom (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombEwaldTwin_VdwCutCombGeom 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped 26: Cannot test or generate data for 2xNN kernels without suitable SIMD support 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombEwaldTwin_VdwCutCombGeom (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombEwaldTwin_VdwCutCombGeom 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped 26: Cannot test or generate data for 2xNN kernels without suitable SIMD support 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombEwaldTwin_VdwCutCombGeom (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombGeom 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped 26: Cannot test or generate data for 2xNN kernels without suitable SIMD support 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombGeom (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombEwaldTwin_VdwCutCombLB 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped 26: Cannot test or generate data for 2xNN kernels without suitable SIMD support 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombEwaldTwin_VdwCutCombLB (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombEwaldTwin_VdwCutCombLB 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped 26: Cannot test or generate data for 2xNN kernels without suitable SIMD support 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombEwaldTwin_VdwCutCombLB (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombLB 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped 26: Cannot test or generate data for 2xNN kernels without suitable SIMD support 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombLB (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombEwaldTwin_VdwCutCombNone 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped 26: Cannot test or generate data for 2xNN kernels without suitable SIMD support 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombEwaldTwin_VdwCutCombNone (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombEwaldTwin_VdwCutCombNone 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped 26: Cannot test or generate data for 2xNN kernels without suitable SIMD support 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombEwaldTwin_VdwCutCombNone (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombNone 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped 26: Cannot test or generate data for 2xNN kernels without suitable SIMD support 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombNone (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombEwaldTwin_VdwForceSwitch 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped 26: Cannot test or generate data for 2xNN kernels without suitable SIMD support 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombEwaldTwin_VdwForceSwitch (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombEwaldTwin_VdwForceSwitch 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped 26: Cannot test or generate data for 2xNN kernels without suitable SIMD support 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombEwaldTwin_VdwForceSwitch (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwForceSwitch 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped 26: Cannot test or generate data for 2xNN kernels without suitable SIMD support 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwForceSwitch (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombEwaldTwin_VdwPotSwitch 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped 26: Cannot test or generate data for 2xNN kernels without suitable SIMD support 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombEwaldTwin_VdwPotSwitch (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombEwaldTwin_VdwPotSwitch 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped 26: Cannot test or generate data for 2xNN kernels without suitable SIMD support 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombEwaldTwin_VdwPotSwitch (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwPotSwitch 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped 26: Cannot test or generate data for 2xNN kernels without suitable SIMD support 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwPotSwitch (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombEwaldTwin_VdwEwaldCombGeom 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped 26: Cannot test or generate data for 2xNN kernels without suitable SIMD support 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombEwaldTwin_VdwEwaldCombGeom (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombEwaldTwin_VdwEwaldCombGeom 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped 26: Cannot test or generate data for 2xNN kernels without suitable SIMD support 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombEwaldTwin_VdwEwaldCombGeom (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwEwaldCombGeom 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped 26: Cannot test or generate data for 2xNN kernels without suitable SIMD support 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwEwaldCombGeom (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_NoEnergies_CoulombEwald_VdwCutCombGeom 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped 26: Cannot test or generate data for 2xNN kernels without suitable SIMD support 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_NoEnergies_CoulombEwald_VdwCutCombGeom (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_Energies_CoulombEwald_VdwCutCombGeom 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped 26: Cannot test or generate data for 2xNN kernels without suitable SIMD support 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_Energies_CoulombEwald_VdwCutCombGeom (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_ThreeEnergyGroups_CoulombEwald_VdwCutCombGeom 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped 26: Cannot test or generate data for 2xNN kernels without suitable SIMD support 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_ThreeEnergyGroups_CoulombEwald_VdwCutCombGeom (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_NoEnergies_CoulombEwald_VdwCutCombLB 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped 26: Cannot test or generate data for 2xNN kernels without suitable SIMD support 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_NoEnergies_CoulombEwald_VdwCutCombLB (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_Energies_CoulombEwald_VdwCutCombLB 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped 26: Cannot test or generate data for 2xNN kernels without suitable SIMD support 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_Energies_CoulombEwald_VdwCutCombLB (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_ThreeEnergyGroups_CoulombEwald_VdwCutCombLB 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped 26: Cannot test or generate data for 2xNN kernels without suitable SIMD support 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_ThreeEnergyGroups_CoulombEwald_VdwCutCombLB (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_NoEnergies_CoulombEwald_VdwCutCombNone 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped 26: Cannot test or generate data for 2xNN kernels without suitable SIMD support 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_NoEnergies_CoulombEwald_VdwCutCombNone (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_Energies_CoulombEwald_VdwCutCombNone 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped 26: Cannot test or generate data for 2xNN kernels without suitable SIMD support 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_Energies_CoulombEwald_VdwCutCombNone (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_ThreeEnergyGroups_CoulombEwald_VdwCutCombNone 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped 26: Cannot test or generate data for 2xNN kernels without suitable SIMD support 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_ThreeEnergyGroups_CoulombEwald_VdwCutCombNone (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_NoEnergies_CoulombEwald_VdwForceSwitch 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped 26: Cannot test or generate data for 2xNN kernels without suitable SIMD support 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_NoEnergies_CoulombEwald_VdwForceSwitch (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_Energies_CoulombEwald_VdwForceSwitch 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped 26: Cannot test or generate data for 2xNN kernels without suitable SIMD support 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_Energies_CoulombEwald_VdwForceSwitch (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_ThreeEnergyGroups_CoulombEwald_VdwForceSwitch 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped 26: Cannot test or generate data for 2xNN kernels without suitable SIMD support 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_ThreeEnergyGroups_CoulombEwald_VdwForceSwitch (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_NoEnergies_CoulombEwald_VdwPotSwitch 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped 26: Cannot test or generate data for 2xNN kernels without suitable SIMD support 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_NoEnergies_CoulombEwald_VdwPotSwitch (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_Energies_CoulombEwald_VdwPotSwitch 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped 26: Cannot test or generate data for 2xNN kernels without suitable SIMD support 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_Energies_CoulombEwald_VdwPotSwitch (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_ThreeEnergyGroups_CoulombEwald_VdwPotSwitch 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped 26: Cannot test or generate data for 2xNN kernels without suitable SIMD support 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_ThreeEnergyGroups_CoulombEwald_VdwPotSwitch (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_NoEnergies_CoulombEwald_VdwEwaldCombGeom 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped 26: Cannot test or generate data for 2xNN kernels without suitable SIMD support 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_NoEnergies_CoulombEwald_VdwEwaldCombGeom (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_Energies_CoulombEwald_VdwEwaldCombGeom 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped 26: Cannot test or generate data for 2xNN kernels without suitable SIMD support 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_Energies_CoulombEwald_VdwEwaldCombGeom (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_ThreeEnergyGroups_CoulombEwald_VdwEwaldCombGeom 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped 26: Cannot test or generate data for 2xNN kernels without suitable SIMD support 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_ThreeEnergyGroups_CoulombEwald_VdwEwaldCombGeom (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_NoEnergies_CoulombEwaldTwin_VdwCutCombGeom 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped 26: Cannot test or generate data for 2xNN kernels without suitable SIMD support 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_NoEnergies_CoulombEwaldTwin_VdwCutCombGeom (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_Energies_CoulombEwaldTwin_VdwCutCombGeom 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped 26: Cannot test or generate data for 2xNN kernels without suitable SIMD support 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_Energies_CoulombEwaldTwin_VdwCutCombGeom (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombGeom 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped 26: Cannot test or generate data for 2xNN kernels without suitable SIMD support 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombGeom (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_NoEnergies_CoulombEwaldTwin_VdwCutCombLB 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped 26: Cannot test or generate data for 2xNN kernels without suitable SIMD support 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_NoEnergies_CoulombEwaldTwin_VdwCutCombLB (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_Energies_CoulombEwaldTwin_VdwCutCombLB 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped 26: Cannot test or generate data for 2xNN kernels without suitable SIMD support 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_Energies_CoulombEwaldTwin_VdwCutCombLB (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombLB 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped 26: Cannot test or generate data for 2xNN kernels without suitable SIMD support 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombLB (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_NoEnergies_CoulombEwaldTwin_VdwCutCombNone 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped 26: Cannot test or generate data for 2xNN kernels without suitable SIMD support 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_NoEnergies_CoulombEwaldTwin_VdwCutCombNone (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_Energies_CoulombEwaldTwin_VdwCutCombNone 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped 26: Cannot test or generate data for 2xNN kernels without suitable SIMD support 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_Energies_CoulombEwaldTwin_VdwCutCombNone (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombNone 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped 26: Cannot test or generate data for 2xNN kernels without suitable SIMD support 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombNone (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_NoEnergies_CoulombEwaldTwin_VdwForceSwitch 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped 26: Cannot test or generate data for 2xNN kernels without suitable SIMD support 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_NoEnergies_CoulombEwaldTwin_VdwForceSwitch (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_Energies_CoulombEwaldTwin_VdwForceSwitch 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped 26: Cannot test or generate data for 2xNN kernels without suitable SIMD support 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_Energies_CoulombEwaldTwin_VdwForceSwitch (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwForceSwitch 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped 26: Cannot test or generate data for 2xNN kernels without suitable SIMD support 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwForceSwitch (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_NoEnergies_CoulombEwaldTwin_VdwPotSwitch 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped 26: Cannot test or generate data for 2xNN kernels without suitable SIMD support 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_NoEnergies_CoulombEwaldTwin_VdwPotSwitch (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_Energies_CoulombEwaldTwin_VdwPotSwitch 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped 26: Cannot test or generate data for 2xNN kernels without suitable SIMD support 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_Energies_CoulombEwaldTwin_VdwPotSwitch (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwPotSwitch 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped 26: Cannot test or generate data for 2xNN kernels without suitable SIMD support 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwPotSwitch (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_NoEnergies_CoulombEwaldTwin_VdwEwaldCombGeom 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped 26: Cannot test or generate data for 2xNN kernels without suitable SIMD support 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_NoEnergies_CoulombEwaldTwin_VdwEwaldCombGeom (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_Energies_CoulombEwaldTwin_VdwEwaldCombGeom 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped 26: Cannot test or generate data for 2xNN kernels without suitable SIMD support 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_Energies_CoulombEwaldTwin_VdwEwaldCombGeom (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwEwaldCombGeom 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped 26: Cannot test or generate data for 2xNN kernels without suitable SIMD support 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwEwaldCombGeom (0 ms) 26: [----------] 360 tests from Combinations/NbnxmKernelTest (1801 ms total) 26: 26: [----------] Global test environment tear-down 26: [==========] 380 tests from 3 test suites ran. (1804 ms total) 26: [ PASSED ] 92 tests. 26: [ SKIPPED ] 288 tests, listed below: 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombReactionField_VdwCutCombGeom 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombReactionField_VdwCutCombGeom 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwCutCombGeom 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombReactionField_VdwCutCombLB 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombReactionField_VdwCutCombLB 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwCutCombLB 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombEwald_VdwCutCombGeom 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombEwald_VdwCutCombGeom 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombEwald_VdwCutCombGeom 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombEwald_VdwCutCombLB 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombEwald_VdwCutCombLB 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombEwald_VdwCutCombLB 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombEwald_VdwCutCombNone 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombEwald_VdwCutCombNone 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombEwald_VdwCutCombNone 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombEwald_VdwForceSwitch 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombEwald_VdwForceSwitch 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombEwald_VdwForceSwitch 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombEwald_VdwPotSwitch 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombEwald_VdwPotSwitch 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombEwald_VdwPotSwitch 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombEwald_VdwEwaldCombGeom 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombEwald_VdwEwaldCombGeom 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombEwald_VdwEwaldCombGeom 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombEwaldTwin_VdwCutCombGeom 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombEwaldTwin_VdwCutCombGeom 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombGeom 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombEwaldTwin_VdwCutCombLB 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombEwaldTwin_VdwCutCombLB 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombLB 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombEwaldTwin_VdwCutCombNone 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombEwaldTwin_VdwCutCombNone 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombNone 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombEwaldTwin_VdwForceSwitch 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombEwaldTwin_VdwForceSwitch 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwForceSwitch 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombEwaldTwin_VdwPotSwitch 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombEwaldTwin_VdwPotSwitch 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwPotSwitch 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombEwaldTwin_VdwEwaldCombGeom 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombEwaldTwin_VdwEwaldCombGeom 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwEwaldCombGeom 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_NoEnergies_CoulombEwald_VdwCutCombGeom 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_Energies_CoulombEwald_VdwCutCombGeom 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_ThreeEnergyGroups_CoulombEwald_VdwCutCombGeom 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_NoEnergies_CoulombEwald_VdwCutCombLB 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_Energies_CoulombEwald_VdwCutCombLB 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_ThreeEnergyGroups_CoulombEwald_VdwCutCombLB 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_NoEnergies_CoulombEwaldTwin_VdwCutCombGeom 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_Energies_CoulombEwaldTwin_VdwCutCombGeom 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombGeom 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_NoEnergies_CoulombEwaldTwin_VdwCutCombLB 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_Energies_CoulombEwaldTwin_VdwCutCombLB 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombLB 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombReactionField_VdwCutCombGeom 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombReactionField_VdwCutCombGeom 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwCutCombGeom 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombReactionField_VdwCutCombLB 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombReactionField_VdwCutCombLB 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwCutCombLB 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombEwald_VdwCutCombGeom 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombEwald_VdwCutCombGeom 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombEwald_VdwCutCombGeom 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombEwald_VdwCutCombLB 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombEwald_VdwCutCombLB 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombEwald_VdwCutCombLB 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombEwald_VdwCutCombNone 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombEwald_VdwCutCombNone 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombEwald_VdwCutCombNone 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombEwald_VdwForceSwitch 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombEwald_VdwForceSwitch 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombEwald_VdwForceSwitch 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombEwald_VdwPotSwitch 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombEwald_VdwPotSwitch 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombEwald_VdwPotSwitch 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombEwald_VdwEwaldCombGeom 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombEwald_VdwEwaldCombGeom 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombEwald_VdwEwaldCombGeom 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombEwaldTwin_VdwCutCombGeom 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombEwaldTwin_VdwCutCombGeom 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombGeom 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombEwaldTwin_VdwCutCombLB 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombEwaldTwin_VdwCutCombLB 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombLB 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombEwaldTwin_VdwCutCombNone 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombEwaldTwin_VdwCutCombNone 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombNone 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombEwaldTwin_VdwForceSwitch 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombEwaldTwin_VdwForceSwitch 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwForceSwitch 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombEwaldTwin_VdwPotSwitch 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombEwaldTwin_VdwPotSwitch 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwPotSwitch 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombEwaldTwin_VdwEwaldCombGeom 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombEwaldTwin_VdwEwaldCombGeom 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwEwaldCombGeom 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_NoEnergies_CoulombEwald_VdwCutCombGeom 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_Energies_CoulombEwald_VdwCutCombGeom 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_ThreeEnergyGroups_CoulombEwald_VdwCutCombGeom 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_NoEnergies_CoulombEwald_VdwCutCombLB 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_Energies_CoulombEwald_VdwCutCombLB 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_ThreeEnergyGroups_CoulombEwald_VdwCutCombLB 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_NoEnergies_CoulombEwaldTwin_VdwCutCombGeom 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_Energies_CoulombEwaldTwin_VdwCutCombGeom 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombGeom 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_NoEnergies_CoulombEwaldTwin_VdwCutCombLB 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_Energies_CoulombEwaldTwin_VdwCutCombLB 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombLB 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_NoEnergies_CoulombReactionField_VdwCutCombGeom 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_Energies_CoulombReactionField_VdwCutCombGeom 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwCutCombGeom 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_NoEnergies_CoulombReactionField_VdwCutCombLB 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_Energies_CoulombReactionField_VdwCutCombLB 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwCutCombLB 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_NoEnergies_CoulombReactionField_VdwCutCombNone 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_Energies_CoulombReactionField_VdwCutCombNone 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwCutCombNone 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_NoEnergies_CoulombReactionField_VdwForceSwitch 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_Energies_CoulombReactionField_VdwForceSwitch 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwForceSwitch 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_NoEnergies_CoulombReactionField_VdwPotSwitch 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_Energies_CoulombReactionField_VdwPotSwitch 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwPotSwitch 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_NoEnergies_CoulombReactionField_VdwEwaldCombGeom 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_Energies_CoulombReactionField_VdwEwaldCombGeom 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwEwaldCombGeom 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_NoEnergies_CoulombEwald_VdwCutCombGeom 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_Energies_CoulombEwald_VdwCutCombGeom 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_ThreeEnergyGroups_CoulombEwald_VdwCutCombGeom 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_NoEnergies_CoulombEwald_VdwCutCombLB 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_Energies_CoulombEwald_VdwCutCombLB 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_ThreeEnergyGroups_CoulombEwald_VdwCutCombLB 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_NoEnergies_CoulombEwald_VdwCutCombNone 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_Energies_CoulombEwald_VdwCutCombNone 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_ThreeEnergyGroups_CoulombEwald_VdwCutCombNone 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_NoEnergies_CoulombEwald_VdwForceSwitch 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_Energies_CoulombEwald_VdwForceSwitch 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_ThreeEnergyGroups_CoulombEwald_VdwForceSwitch 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_NoEnergies_CoulombEwald_VdwPotSwitch 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_Energies_CoulombEwald_VdwPotSwitch 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_ThreeEnergyGroups_CoulombEwald_VdwPotSwitch 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_NoEnergies_CoulombEwald_VdwEwaldCombGeom 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_Energies_CoulombEwald_VdwEwaldCombGeom 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_ThreeEnergyGroups_CoulombEwald_VdwEwaldCombGeom 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_NoEnergies_CoulombEwaldTwin_VdwCutCombGeom 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_Energies_CoulombEwaldTwin_VdwCutCombGeom 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombGeom 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_NoEnergies_CoulombEwaldTwin_VdwCutCombLB 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_Energies_CoulombEwaldTwin_VdwCutCombLB 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombLB 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_NoEnergies_CoulombEwaldTwin_VdwCutCombNone 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_Energies_CoulombEwaldTwin_VdwCutCombNone 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombNone 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_NoEnergies_CoulombEwaldTwin_VdwForceSwitch 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_Energies_CoulombEwaldTwin_VdwForceSwitch 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwForceSwitch 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_NoEnergies_CoulombEwaldTwin_VdwPotSwitch 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_Energies_CoulombEwaldTwin_VdwPotSwitch 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwPotSwitch 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_NoEnergies_CoulombEwaldTwin_VdwEwaldCombGeom 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_Energies_CoulombEwaldTwin_VdwEwaldCombGeom 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwEwaldCombGeom 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_NoEnergies_CoulombEwald_VdwCutCombGeom 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_Energies_CoulombEwald_VdwCutCombGeom 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_ThreeEnergyGroups_CoulombEwald_VdwCutCombGeom 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_NoEnergies_CoulombEwald_VdwCutCombLB 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_Energies_CoulombEwald_VdwCutCombLB 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_ThreeEnergyGroups_CoulombEwald_VdwCutCombLB 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_NoEnergies_CoulombEwald_VdwCutCombNone 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_Energies_CoulombEwald_VdwCutCombNone 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_ThreeEnergyGroups_CoulombEwald_VdwCutCombNone 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_NoEnergies_CoulombEwald_VdwForceSwitch 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_Energies_CoulombEwald_VdwForceSwitch 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_ThreeEnergyGroups_CoulombEwald_VdwForceSwitch 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_NoEnergies_CoulombEwald_VdwPotSwitch 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_Energies_CoulombEwald_VdwPotSwitch 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_ThreeEnergyGroups_CoulombEwald_VdwPotSwitch 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_NoEnergies_CoulombEwald_VdwEwaldCombGeom 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_Energies_CoulombEwald_VdwEwaldCombGeom 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_ThreeEnergyGroups_CoulombEwald_VdwEwaldCombGeom 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_NoEnergies_CoulombEwaldTwin_VdwCutCombGeom 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_Energies_CoulombEwaldTwin_VdwCutCombGeom 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombGeom 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_NoEnergies_CoulombEwaldTwin_VdwCutCombLB 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_Energies_CoulombEwaldTwin_VdwCutCombLB 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombLB 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_NoEnergies_CoulombEwaldTwin_VdwCutCombNone 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_Energies_CoulombEwaldTwin_VdwCutCombNone 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombNone 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_NoEnergies_CoulombEwaldTwin_VdwForceSwitch 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_Energies_CoulombEwaldTwin_VdwForceSwitch 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwForceSwitch 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_NoEnergies_CoulombEwaldTwin_VdwPotSwitch 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_Energies_CoulombEwaldTwin_VdwPotSwitch 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwPotSwitch 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_NoEnergies_CoulombEwaldTwin_VdwEwaldCombGeom 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_Energies_CoulombEwaldTwin_VdwEwaldCombGeom 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwEwaldCombGeom 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombReactionField_VdwCutCombGeom 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombReactionField_VdwCutCombGeom 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwCutCombGeom 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombReactionField_VdwCutCombLB 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombReactionField_VdwCutCombLB 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwCutCombLB 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombReactionField_VdwCutCombNone 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombReactionField_VdwCutCombNone 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwCutCombNone 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombReactionField_VdwForceSwitch 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombReactionField_VdwForceSwitch 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwForceSwitch 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombReactionField_VdwPotSwitch 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombReactionField_VdwPotSwitch 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwPotSwitch 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombReactionField_VdwEwaldCombGeom 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombReactionField_VdwEwaldCombGeom 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwEwaldCombGeom 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombEwald_VdwCutCombGeom 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombEwald_VdwCutCombGeom 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombEwald_VdwCutCombGeom 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombEwald_VdwCutCombLB 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombEwald_VdwCutCombLB 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombEwald_VdwCutCombLB 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombEwald_VdwCutCombNone 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombEwald_VdwCutCombNone 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombEwald_VdwCutCombNone 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombEwald_VdwForceSwitch 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombEwald_VdwForceSwitch 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombEwald_VdwForceSwitch 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombEwald_VdwPotSwitch 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombEwald_VdwPotSwitch 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombEwald_VdwPotSwitch 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombEwald_VdwEwaldCombGeom 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombEwald_VdwEwaldCombGeom 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombEwald_VdwEwaldCombGeom 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombEwaldTwin_VdwCutCombGeom 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombEwaldTwin_VdwCutCombGeom 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombGeom 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombEwaldTwin_VdwCutCombLB 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombEwaldTwin_VdwCutCombLB 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombLB 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombEwaldTwin_VdwCutCombNone 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombEwaldTwin_VdwCutCombNone 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombNone 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombEwaldTwin_VdwForceSwitch 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombEwaldTwin_VdwForceSwitch 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwForceSwitch 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombEwaldTwin_VdwPotSwitch 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombEwaldTwin_VdwPotSwitch 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwPotSwitch 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombEwaldTwin_VdwEwaldCombGeom 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombEwaldTwin_VdwEwaldCombGeom 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwEwaldCombGeom 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_NoEnergies_CoulombEwald_VdwCutCombGeom 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_Energies_CoulombEwald_VdwCutCombGeom 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_ThreeEnergyGroups_CoulombEwald_VdwCutCombGeom 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_NoEnergies_CoulombEwald_VdwCutCombLB 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_Energies_CoulombEwald_VdwCutCombLB 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_ThreeEnergyGroups_CoulombEwald_VdwCutCombLB 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_NoEnergies_CoulombEwald_VdwCutCombNone 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_Energies_CoulombEwald_VdwCutCombNone 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_ThreeEnergyGroups_CoulombEwald_VdwCutCombNone 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_NoEnergies_CoulombEwald_VdwForceSwitch 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_Energies_CoulombEwald_VdwForceSwitch 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_ThreeEnergyGroups_CoulombEwald_VdwForceSwitch 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_NoEnergies_CoulombEwald_VdwPotSwitch 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_Energies_CoulombEwald_VdwPotSwitch 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_ThreeEnergyGroups_CoulombEwald_VdwPotSwitch 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_NoEnergies_CoulombEwald_VdwEwaldCombGeom 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_Energies_CoulombEwald_VdwEwaldCombGeom 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_ThreeEnergyGroups_CoulombEwald_VdwEwaldCombGeom 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_NoEnergies_CoulombEwaldTwin_VdwCutCombGeom 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_Energies_CoulombEwaldTwin_VdwCutCombGeom 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombGeom 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_NoEnergies_CoulombEwaldTwin_VdwCutCombLB 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_Energies_CoulombEwaldTwin_VdwCutCombLB 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombLB 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_NoEnergies_CoulombEwaldTwin_VdwCutCombNone 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_Energies_CoulombEwaldTwin_VdwCutCombNone 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombNone 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_NoEnergies_CoulombEwaldTwin_VdwForceSwitch 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_Energies_CoulombEwaldTwin_VdwForceSwitch 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwForceSwitch 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_NoEnergies_CoulombEwaldTwin_VdwPotSwitch 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_Energies_CoulombEwaldTwin_VdwPotSwitch 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwPotSwitch 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_NoEnergies_CoulombEwaldTwin_VdwEwaldCombGeom 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_Energies_CoulombEwaldTwin_VdwEwaldCombGeom 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwEwaldCombGeom 26/92 Test #26: NbnxmTests ................................ Passed 2.02 sec test 27 Start 27: NbnxmGpuTests 27: Test command: /build/reproducible-path/gromacs-2025.1/build/basic/bin/nbnxm-gpu-test "--gtest_output=xml:/build/reproducible-path/gromacs-2025.1/build/basic/Testing/Temporary/NbnxmGpuTests.xml" 27: Working Directory: /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/nbnxm/tests 27: Test timeout computed to be: 30 27: [==========] Running 0 tests from 0 test suites. 27: [==========] 0 tests from 0 test suites ran. (0 ms total) 27: [ PASSED ] 0 tests. 27/92 Test #27: NbnxmGpuTests ............................. Passed 0.12 sec test 28 Start 28: CommandLineUnitTests 28: Test command: /build/reproducible-path/gromacs-2025.1/build/basic/bin/commandline-test "--gtest_output=xml:/build/reproducible-path/gromacs-2025.1/build/basic/Testing/Temporary/CommandLineUnitTests.xml" 28: Working Directory: /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/commandline/tests 28: Test timeout computed to be: 30 28: [==========] Running 60 tests from 7 test suites. 28: [----------] Global test environment set-up. 28: [----------] 3 tests from CommandLineHelpModuleTest 28: [ RUN ] CommandLineHelpModuleTest.PrintsGeneralHelp 28: [ OK ] CommandLineHelpModuleTest.PrintsGeneralHelp (4 ms) 28: [ RUN ] CommandLineHelpModuleTest.PrintsHelpOnTopic 28: [ OK ] CommandLineHelpModuleTest.PrintsHelpOnTopic (2 ms) 28: [ RUN ] CommandLineHelpModuleTest.ExportsHelp 28: [ OK ] CommandLineHelpModuleTest.ExportsHelp (6 ms) 28: [----------] 3 tests from CommandLineHelpModuleTest (13 ms total) 28: 28: [----------] 7 tests from CommandLineHelpWriterTest 28: [ RUN ] CommandLineHelpWriterTest.HandlesOptionTypes 28: [ OK ] CommandLineHelpWriterTest.HandlesOptionTypes (4 ms) 28: [ RUN ] CommandLineHelpWriterTest.HandlesDefaultValuesFromVariables 28: [ OK ] CommandLineHelpWriterTest.HandlesDefaultValuesFromVariables (2 ms) 28: [ RUN ] CommandLineHelpWriterTest.HandlesLongFileOptions 28: [ OK ] CommandLineHelpWriterTest.HandlesLongFileOptions (2 ms) 28: [ RUN ] CommandLineHelpWriterTest.HandlesLongOptions 28: [ OK ] CommandLineHelpWriterTest.HandlesLongOptions (1 ms) 28: [ RUN ] CommandLineHelpWriterTest.HandlesOptionGroups 28: [ OK ] CommandLineHelpWriterTest.HandlesOptionGroups (1 ms) 28: [ RUN ] CommandLineHelpWriterTest.HandlesHelpText 28: [ OK ] CommandLineHelpWriterTest.HandlesHelpText (1 ms) 28: [ RUN ] CommandLineHelpWriterTest.HandlesKnownIssues 28: [ OK ] CommandLineHelpWriterTest.HandlesKnownIssues (0 ms) 28: [----------] 7 tests from CommandLineHelpWriterTest (14 ms total) 28: 28: [----------] 6 tests from CommandLineModuleManagerTest 28: [ RUN ] CommandLineModuleManagerTest.RunsModule 28: [ OK ] CommandLineModuleManagerTest.RunsModule (0 ms) 28: [ RUN ] CommandLineModuleManagerTest.RunsModuleHelp 28: [ OK ] CommandLineModuleManagerTest.RunsModuleHelp (0 ms) 28: [ RUN ] CommandLineModuleManagerTest.RunsModuleHelpAfterQuiet 28: [ OK ] CommandLineModuleManagerTest.RunsModuleHelpAfterQuiet (0 ms) 28: [ RUN ] CommandLineModuleManagerTest.RunsModuleHelpWithDashH 28: [ OK ] CommandLineModuleManagerTest.RunsModuleHelpWithDashH (0 ms) 28: [ RUN ] CommandLineModuleManagerTest.RunsModuleHelpWithDashHWithSingleModule 28: [ OK ] CommandLineModuleManagerTest.RunsModuleHelpWithDashHWithSingleModule (0 ms) 28: [ RUN ] CommandLineModuleManagerTest.HandlesConflictingBinaryAndModuleNames 28: [ OK ] CommandLineModuleManagerTest.HandlesConflictingBinaryAndModuleNames (0 ms) 28: [----------] 6 tests from CommandLineModuleManagerTest (3 ms total) 28: 28: [----------] 13 tests from CommandLineParserTest 28: [ RUN ] CommandLineParserTest.HandlesSingleValues 28: [ OK ] CommandLineParserTest.HandlesSingleValues (0 ms) 28: [ RUN ] CommandLineParserTest.HandlesBooleanWithoutArgument 28: [ OK ] CommandLineParserTest.HandlesBooleanWithoutArgument (0 ms) 28: [ RUN ] CommandLineParserTest.HandlesBooleanAsNoWithoutArgument 28: [ OK ] CommandLineParserTest.HandlesBooleanAsNoWithoutArgument (0 ms) 28: [ RUN ] CommandLineParserTest.ThrowsWithBooleanAsNoWithArgument 28: [ OK ] CommandLineParserTest.ThrowsWithBooleanAsNoWithArgument (0 ms) 28: [ RUN ] CommandLineParserTest.HandlesNegativeNumbers 28: [ OK ] CommandLineParserTest.HandlesNegativeNumbers (0 ms) 28: [ RUN ] CommandLineParserTest.HandlesString 28: [ OK ] CommandLineParserTest.HandlesString (0 ms) 28: [ RUN ] CommandLineParserTest.RejectsStringWithMultipleValues 28: [ OK ] CommandLineParserTest.RejectsStringWithMultipleValues (0 ms) 28: [ RUN ] CommandLineParserTest.HandlesDoubleDashOptionPrefix 28: [ OK ] CommandLineParserTest.HandlesDoubleDashOptionPrefix (0 ms) 28: [ RUN ] CommandLineParserTest.HandlesOptionsStartingWithNumbers 28: [ OK ] CommandLineParserTest.HandlesOptionsStartingWithNumbers (0 ms) 28: [ RUN ] CommandLineParserTest.HandlesSkipUnknown 28: [ OK ] CommandLineParserTest.HandlesSkipUnknown (0 ms) 28: [ RUN ] CommandLineParserTest.RejectsPositionalArgumentsByDefault 28: [ OK ] CommandLineParserTest.RejectsPositionalArgumentsByDefault (0 ms) 28: [ RUN ] CommandLineParserTest.CanAllowPositionalArguments 28: [ OK ] CommandLineParserTest.CanAllowPositionalArguments (0 ms) 28: [ RUN ] CommandLineParserTest.CannotHavePositionalArgumentsAfterOptions 28: [ OK ] CommandLineParserTest.CannotHavePositionalArgumentsAfterOptions (0 ms) 28: [----------] 13 tests from CommandLineParserTest (3 ms total) 28: 28: [----------] 6 tests from CommandLineProgramContextTest 28: [ RUN ] CommandLineProgramContextTest.FindsBinaryWithAbsolutePath 28: [ OK ] CommandLineProgramContextTest.FindsBinaryWithAbsolutePath (0 ms) 28: [ RUN ] CommandLineProgramContextTest.FindsBinaryWithRelativePath 28: [ OK ] CommandLineProgramContextTest.FindsBinaryWithRelativePath (0 ms) 28: [ RUN ] CommandLineProgramContextTest.FindsBinaryFromPath 28: [ OK ] CommandLineProgramContextTest.FindsBinaryFromPath (0 ms) 28: [ RUN ] CommandLineProgramContextTest.FindsBinaryFromCurrentDirectory 28: [ OK ] CommandLineProgramContextTest.FindsBinaryFromCurrentDirectory (0 ms) 28: [ RUN ] CommandLineProgramContextTest.FindsBinaryFromAbsoluteSymLink 28: [ OK ] CommandLineProgramContextTest.FindsBinaryFromAbsoluteSymLink (0 ms) 28: [ RUN ] CommandLineProgramContextTest.FindsBinaryFromRelativeSymLink 28: [ OK ] CommandLineProgramContextTest.FindsBinaryFromRelativeSymLink (0 ms) 28: [----------] 6 tests from CommandLineProgramContextTest (1 ms total) 28: 28: [----------] 3 tests from OutputNamesTest 28: [ RUN ] OutputNamesTest.CanBeSuffixed 28: [ OK ] OutputNamesTest.CanBeSuffixed (0 ms) 28: [ RUN ] OutputNamesTest.HasSuffixFromNoAppend 28: [ OK ] OutputNamesTest.HasSuffixFromNoAppend (0 ms) 28: [ RUN ] OutputNamesTest.CanHavePartNumberAdded 28: [ OK ] OutputNamesTest.CanHavePartNumberAdded (0 ms) 28: [----------] 3 tests from OutputNamesTest (0 ms total) 28: 28: [----------] 22 tests from ParseCommonArgsTest 28: [ RUN ] ParseCommonArgsTest.ParsesIntegerArgs 28: [ OK ] ParseCommonArgsTest.ParsesIntegerArgs (0 ms) 28: [ RUN ] ParseCommonArgsTest.ParsesInt64Args 28: [ OK ] ParseCommonArgsTest.ParsesInt64Args (0 ms) 28: [ RUN ] ParseCommonArgsTest.ParsesRealArgs 28: [ OK ] ParseCommonArgsTest.ParsesRealArgs (0 ms) 28: [ RUN ] ParseCommonArgsTest.ParsesStringArgs 28: [ OK ] ParseCommonArgsTest.ParsesStringArgs (0 ms) 28: [ RUN ] ParseCommonArgsTest.ParsesBooleanArgs 28: [ OK ] ParseCommonArgsTest.ParsesBooleanArgs (0 ms) 28: [ RUN ] ParseCommonArgsTest.ParsesBooleanArgsToValuesOfSuitableEnum 28: [ OK ] ParseCommonArgsTest.ParsesBooleanArgsToValuesOfSuitableEnum (0 ms) 28: [ RUN ] ParseCommonArgsTest.ParsesVectorArgs 28: [ OK ] ParseCommonArgsTest.ParsesVectorArgs (0 ms) 28: [ RUN ] ParseCommonArgsTest.ParsesTimeArgs 28: [ OK ] ParseCommonArgsTest.ParsesTimeArgs (0 ms) 28: [ RUN ] ParseCommonArgsTest.ParsesTimeArgsWithTimeUnit 28: [ OK ] ParseCommonArgsTest.ParsesTimeArgsWithTimeUnit (0 ms) 28: [ RUN ] ParseCommonArgsTest.ParsesEnumArgs 28: [ OK ] ParseCommonArgsTest.ParsesEnumArgs (0 ms) 28: [ RUN ] ParseCommonArgsTest.ParsesFileArgs 28: [ OK ] ParseCommonArgsTest.ParsesFileArgs (0 ms) 28: [ RUN ] ParseCommonArgsTest.ParsesFileArgsWithDefaults 28: [ OK ] ParseCommonArgsTest.ParsesFileArgsWithDefaults (0 ms) 28: [ RUN ] ParseCommonArgsTest.ParsesFileArgsWithDefaultFileName 28: [ OK ] ParseCommonArgsTest.ParsesFileArgsWithDefaultFileName (0 ms) 28: [ RUN ] ParseCommonArgsTest.ParseFileArgsWithCustomDefaultExtension 28: [ OK ] ParseCommonArgsTest.ParseFileArgsWithCustomDefaultExtension (0 ms) 28: [ RUN ] ParseCommonArgsTest.HandlesNonExistentInputFiles 28: [ OK ] ParseCommonArgsTest.HandlesNonExistentInputFiles (0 ms) 28: [ RUN ] ParseCommonArgsTest.HandlesNonExistentOptionalInputFiles 28: [ OK ] ParseCommonArgsTest.HandlesNonExistentOptionalInputFiles (0 ms) 28: [ RUN ] ParseCommonArgsTest.AcceptsNonExistentInputFilesIfSpecified 28: [ OK ] ParseCommonArgsTest.AcceptsNonExistentInputFilesIfSpecified (0 ms) 28: [ RUN ] ParseCommonArgsTest.HandlesCompressedFiles 28: [ OK ] ParseCommonArgsTest.HandlesCompressedFiles (1 ms) 28: [ RUN ] ParseCommonArgsTest.AcceptsUnknownTrajectoryExtension 28: Value is /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/commandline/tests/Testing/Temporary/ParseCommonArgsTest_AcceptsUnknownTrajectoryExtension.foo 28: [ OK ] ParseCommonArgsTest.AcceptsUnknownTrajectoryExtension (0 ms) 28: [ RUN ] ParseCommonArgsTest.CompletesExtensionFromExistingFile 28: [ OK ] ParseCommonArgsTest.CompletesExtensionFromExistingFile (3 ms) 28: [ RUN ] ParseCommonArgsTest.CompletesExtensionFromExistingFileWithDefaultFileName 28: [ OK ] ParseCommonArgsTest.CompletesExtensionFromExistingFileWithDefaultFileName (3 ms) 28: [ RUN ] ParseCommonArgsTest.CanKeepUnknownArgs 28: [ OK ] ParseCommonArgsTest.CanKeepUnknownArgs (0 ms) 28: [----------] 22 tests from ParseCommonArgsTest (15 ms total) 28: 28: [----------] Global test environment tear-down 28: [==========] 60 tests from 7 test suites ran. (53 ms total) 28: [ PASSED ] 60 tests. 28/92 Test #28: CommandLineUnitTests ...................... Passed 0.14 sec test 29 Start 29: DomDecTests 29: Test command: /build/reproducible-path/gromacs-2025.1/build/basic/bin/domdec-test "--gtest_output=xml:/build/reproducible-path/gromacs-2025.1/build/basic/Testing/Temporary/DomDecTests.xml" 29: Working Directory: /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/domdec/tests 29: Test timeout computed to be: 30 29: [==========] Running 9 tests from 2 test suites. 29: [----------] Global test environment set-up. 29: [----------] 7 tests from HashedMap 29: [ RUN ] HashedMap.InsertsFinds 29: [ OK ] HashedMap.InsertsFinds (0 ms) 29: [ RUN ] HashedMap.NegativeKeysWork 29: [ OK ] HashedMap.NegativeKeysWork (0 ms) 29: [ RUN ] HashedMap.InsertsErases 29: [ OK ] HashedMap.InsertsErases (0 ms) 29: [ RUN ] HashedMap.InsertsOrAssigns 29: [ OK ] HashedMap.InsertsOrAssigns (0 ms) 29: [ RUN ] HashedMap.Clears 29: [ OK ] HashedMap.Clears (0 ms) 29: [ RUN ] HashedMap.LinkedEntries 29: [ OK ] HashedMap.LinkedEntries (0 ms) 29: [ RUN ] HashedMap.ResizesTable 29: [ OK ] HashedMap.ResizesTable (0 ms) 29: [----------] 7 tests from HashedMap (0 ms total) 29: 29: [----------] 2 tests from LocalAtomSetManager 29: [ RUN ] LocalAtomSetManager.CanAddEmptyLocalAtomSet 29: [ OK ] LocalAtomSetManager.CanAddEmptyLocalAtomSet (0 ms) 29: [ RUN ] LocalAtomSetManager.CanAddandReadLocalAtomSetIndices 29: [ OK ] LocalAtomSetManager.CanAddandReadLocalAtomSetIndices (0 ms) 29: [----------] 2 tests from LocalAtomSetManager (0 ms total) 29: 29: [----------] Global test environment tear-down 29: [==========] 9 tests from 2 test suites ran. (0 ms total) 29: [ PASSED ] 9 tests. 29/92 Test #29: DomDecTests ............................... Passed 0.09 sec test 30 Start 30: DomDecMpiTests 30: Test command: /build/reproducible-path/gromacs-2025.1/build/basic/bin/domdec-mpi-test "-ntmpi" "4" "--gtest_output=xml:/build/reproducible-path/gromacs-2025.1/build/basic/Testing/Temporary/DomDecMpiTests.xml" 30: Working Directory: /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/domdec/tests 30: Test timeout computed to be: 30 30: [==========] Running 4 tests from 1 test suite. 30: [----------] Global test environment set-up. 30: [----------] 4 tests from HaloExchangeTest 30: [ RUN ] HaloExchangeTest.Coordinates1dHaloWith1Pulse 30: [ OK ] HaloExchangeTest.Coordinates1dHaloWith1Pulse (7 ms) 30: [ RUN ] HaloExchangeTest.Coordinates1dHaloWith2Pulses 30: [ OK ] HaloExchangeTest.Coordinates1dHaloWith2Pulses (47 ms) 30: [ RUN ] HaloExchangeTest.Coordinates2dHaloWith1PulseInEachDim 30: [ OK ] HaloExchangeTest.Coordinates2dHaloWith1PulseInEachDim (20 ms) 30: [ RUN ] HaloExchangeTest.Coordinates2dHaloWith2PulsesInDim1 30: [ OK ] HaloExchangeTest.Coordinates2dHaloWith2PulsesInDim1 (35 ms) 30: [----------] 4 tests from HaloExchangeTest (111 ms total) 30: 30: [----------] Global test environment tear-down 30: [==========] 4 tests from 1 test suite ran. (111 ms total) 30: [ PASSED ] 4 tests. 30/92 Test #30: DomDecMpiTests ............................ Passed 0.24 sec test 31 Start 31: EwaldUnitTests 31: Test command: /build/reproducible-path/gromacs-2025.1/build/basic/bin/ewald-test "--gtest_output=xml:/build/reproducible-path/gromacs-2025.1/build/basic/Testing/Temporary/EwaldUnitTests.xml" 31: Working Directory: /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/ewald/tests 31: Test timeout computed to be: 30 31: [==========] Running 407 tests from 9 test suites. 31: [----------] Global test environment set-up. 31: [----------] 6 tests from SeparatePmeRanksPermittedTest 31: [ RUN ] SeparatePmeRanksPermittedTest.ZeroPmeDisableReasons 31: [ OK ] SeparatePmeRanksPermittedTest.ZeroPmeDisableReasons (0 ms) 31: [ RUN ] SeparatePmeRanksPermittedTest.CanBeDisabled 31: [ OK ] SeparatePmeRanksPermittedTest.CanBeDisabled (0 ms) 31: [ RUN ] SeparatePmeRanksPermittedTest.OneDisableReasonFlag 31: [ OK ] SeparatePmeRanksPermittedTest.OneDisableReasonFlag (0 ms) 31: [ RUN ] SeparatePmeRanksPermittedTest.OneDisableReasonText 31: [ OK ] SeparatePmeRanksPermittedTest.OneDisableReasonText (0 ms) 31: [ RUN ] SeparatePmeRanksPermittedTest.TwoDisableReasonText 31: [ OK ] SeparatePmeRanksPermittedTest.TwoDisableReasonText (0 ms) 31: [ RUN ] SeparatePmeRanksPermittedTest.EmptyDisableReasonText 31: [ OK ] SeparatePmeRanksPermittedTest.EmptyDisableReasonText (0 ms) 31: [----------] 6 tests from SeparatePmeRanksPermittedTest (0 ms total) 31: 31: [----------] 108 tests from Pme_SplineAndSpreadTest 31: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_16_12_14_system_1_atom_spline 31: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_16_12_14_system_1_atom_spline (8 ms) 31: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_16_12_14_system_1_atom_spread 31: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_16_12_14_system_1_atom_spread (2 ms) 31: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_16_12_14_system_1_atom_fused spline and spread 31: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_16_12_14_system_1_atom_fused spline and spread (2 ms) 31: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_16_12_14_system_2_atoms_spline 31: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_16_12_14_system_2_atoms_spline (2 ms) 31: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_16_12_14_system_2_atoms_spread 31: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_16_12_14_system_2_atoms_spread (2 ms) 31: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_16_12_14_system_2_atoms_fused spline and spread 31: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_16_12_14_system_2_atoms_fused spline and spread (2 ms) 31: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_16_12_14_system_13_atoms_spline 31: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_16_12_14_system_13_atoms_spline (8 ms) 31: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_16_12_14_system_13_atoms_spread 31: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_16_12_14_system_13_atoms_spread (8 ms) 31: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_16_12_14_system_13_atoms_fused spline and spread 31: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_16_12_14_system_13_atoms_fused spline and spread (9 ms) 31: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_19_17_11_system_1_atom_spline 31: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_19_17_11_system_1_atom_spline (6 ms) 31: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_19_17_11_system_1_atom_spread 31: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_19_17_11_system_1_atom_spread (2 ms) 31: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_19_17_11_system_1_atom_fused spline and spread 31: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_19_17_11_system_1_atom_fused spline and spread (2 ms) 31: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_19_17_11_system_2_atoms_spline 31: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_19_17_11_system_2_atoms_spline (2 ms) 31: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_19_17_11_system_2_atoms_spread 31: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_19_17_11_system_2_atoms_spread (2 ms) 31: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_19_17_11_system_2_atoms_fused spline and spread 31: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_19_17_11_system_2_atoms_fused spline and spread (2 ms) 31: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_19_17_11_system_13_atoms_spline 31: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_19_17_11_system_13_atoms_spline (8 ms) 31: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_19_17_11_system_13_atoms_spread 31: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_19_17_11_system_13_atoms_spread (9 ms) 31: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_19_17_11_system_13_atoms_fused spline and spread 31: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_19_17_11_system_13_atoms_fused spline and spread (10 ms) 31: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_16_12_14_system_1_atom_spline 31: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_16_12_14_system_1_atom_spline (3 ms) 31: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_16_12_14_system_1_atom_spread 31: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_16_12_14_system_1_atom_spread (2 ms) 31: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_16_12_14_system_1_atom_fused spline and spread 31: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_16_12_14_system_1_atom_fused spline and spread (2 ms) 31: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_16_12_14_system_2_atoms_spline 31: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_16_12_14_system_2_atoms_spline (3 ms) 31: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_16_12_14_system_2_atoms_spread 31: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_16_12_14_system_2_atoms_spread (3 ms) 31: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_16_12_14_system_2_atoms_fused spline and spread 31: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_16_12_14_system_2_atoms_fused spline and spread (3 ms) 31: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_16_12_14_system_13_atoms_spline 31: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_16_12_14_system_13_atoms_spline (12 ms) 31: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_16_12_14_system_13_atoms_spread 31: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_16_12_14_system_13_atoms_spread (11 ms) 31: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_16_12_14_system_13_atoms_fused spline and spread 31: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_16_12_14_system_13_atoms_fused spline and spread (13 ms) 31: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_19_17_11_system_1_atom_spline 31: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_19_17_11_system_1_atom_spline (3 ms) 31: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_19_17_11_system_1_atom_spread 31: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_19_17_11_system_1_atom_spread (3 ms) 31: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_19_17_11_system_1_atom_fused spline and spread 31: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_19_17_11_system_1_atom_fused spline and spread (3 ms) 31: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_19_17_11_system_2_atoms_spline 31: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_19_17_11_system_2_atoms_spline (3 ms) 31: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_19_17_11_system_2_atoms_spread 31: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_19_17_11_system_2_atoms_spread (3 ms) 31: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_19_17_11_system_2_atoms_fused spline and spread 31: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_19_17_11_system_2_atoms_fused spline and spread (4 ms) 31: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_19_17_11_system_13_atoms_spline 31: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_19_17_11_system_13_atoms_spline (13 ms) 31: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_19_17_11_system_13_atoms_spread 31: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_19_17_11_system_13_atoms_spread (14 ms) 31: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_19_17_11_system_13_atoms_fused spline and spread 31: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_19_17_11_system_13_atoms_fused spline and spread (15 ms) 31: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_16_12_14_system_1_atom_spline 31: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_16_12_14_system_1_atom_spline (4 ms) 31: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_16_12_14_system_1_atom_spread 31: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_16_12_14_system_1_atom_spread (3 ms) 31: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_16_12_14_system_1_atom_fused spline and spread 31: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_16_12_14_system_1_atom_fused spline and spread (3 ms) 31: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_16_12_14_system_2_atoms_spline 31: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_16_12_14_system_2_atoms_spline (3 ms) 31: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_16_12_14_system_2_atoms_spread 31: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_16_12_14_system_2_atoms_spread (4 ms) 31: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_16_12_14_system_2_atoms_fused spline and spread 31: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_16_12_14_system_2_atoms_fused spline and spread (4 ms) 31: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_16_12_14_system_13_atoms_spline 31: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_16_12_14_system_13_atoms_spline (18 ms) 31: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_16_12_14_system_13_atoms_spread 31: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_16_12_14_system_13_atoms_spread (20 ms) 31: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_16_12_14_system_13_atoms_fused spline and spread 31: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_16_12_14_system_13_atoms_fused spline and spread (18 ms) 31: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_19_17_11_system_1_atom_spline 31: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_19_17_11_system_1_atom_spline (4 ms) 31: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_19_17_11_system_1_atom_spread 31: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_19_17_11_system_1_atom_spread (4 ms) 31: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_19_17_11_system_1_atom_fused spline and spread 31: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_19_17_11_system_1_atom_fused spline and spread (4 ms) 31: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_19_17_11_system_2_atoms_spline 31: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_19_17_11_system_2_atoms_spline (7 ms) 31: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_19_17_11_system_2_atoms_spread 31: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_19_17_11_system_2_atoms_spread (5 ms) 31: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_19_17_11_system_2_atoms_fused spline and spread 31: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_19_17_11_system_2_atoms_fused spline and spread (5 ms) 31: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_19_17_11_system_13_atoms_spline 31: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_19_17_11_system_13_atoms_spline (16 ms) 31: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_19_17_11_system_13_atoms_spread 31: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_19_17_11_system_13_atoms_spread (23 ms) 31: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_19_17_11_system_13_atoms_fused spline and spread 31: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_19_17_11_system_13_atoms_fused spline and spread (21 ms) 31: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_16_12_14_system_1_atom_spline 31: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_16_12_14_system_1_atom_spline (2 ms) 31: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_16_12_14_system_1_atom_spread 31: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_16_12_14_system_1_atom_spread (2 ms) 31: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_16_12_14_system_1_atom_fused spline and spread 31: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_16_12_14_system_1_atom_fused spline and spread (1 ms) 31: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_16_12_14_system_2_atoms_spline 31: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_16_12_14_system_2_atoms_spline (2 ms) 31: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_16_12_14_system_2_atoms_spread 31: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_16_12_14_system_2_atoms_spread (2 ms) 31: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_16_12_14_system_2_atoms_fused spline and spread 31: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_16_12_14_system_2_atoms_fused spline and spread (2 ms) 31: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_16_12_14_system_13_atoms_spline 31: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_16_12_14_system_13_atoms_spline (7 ms) 31: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_16_12_14_system_13_atoms_spread 31: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_16_12_14_system_13_atoms_spread (7 ms) 31: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_16_12_14_system_13_atoms_fused spline and spread 31: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_16_12_14_system_13_atoms_fused spline and spread (8 ms) 31: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_19_17_11_system_1_atom_spline 31: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_19_17_11_system_1_atom_spline (2 ms) 31: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_19_17_11_system_1_atom_spread 31: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_19_17_11_system_1_atom_spread (1 ms) 31: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_19_17_11_system_1_atom_fused spline and spread 31: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_19_17_11_system_1_atom_fused spline and spread (2 ms) 31: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_19_17_11_system_2_atoms_spline 31: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_19_17_11_system_2_atoms_spline (2 ms) 31: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_19_17_11_system_2_atoms_spread 31: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_19_17_11_system_2_atoms_spread (2 ms) 31: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_19_17_11_system_2_atoms_fused spline and spread 31: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_19_17_11_system_2_atoms_fused spline and spread (2 ms) 31: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_19_17_11_system_13_atoms_spline 31: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_19_17_11_system_13_atoms_spline (8 ms) 31: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_19_17_11_system_13_atoms_spread 31: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_19_17_11_system_13_atoms_spread (8 ms) 31: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_19_17_11_system_13_atoms_fused spline and spread 31: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_19_17_11_system_13_atoms_fused spline and spread (8 ms) 31: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_16_12_14_system_1_atom_spline 31: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_16_12_14_system_1_atom_spline (2 ms) 31: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_16_12_14_system_1_atom_spread 31: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_16_12_14_system_1_atom_spread (2 ms) 31: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_16_12_14_system_1_atom_fused spline and spread 31: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_16_12_14_system_1_atom_fused spline and spread (2 ms) 31: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_16_12_14_system_2_atoms_spline 31: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_16_12_14_system_2_atoms_spline (3 ms) 31: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_16_12_14_system_2_atoms_spread 31: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_16_12_14_system_2_atoms_spread (3 ms) 31: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_16_12_14_system_2_atoms_fused spline and spread 31: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_16_12_14_system_2_atoms_fused spline and spread (3 ms) 31: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_16_12_14_system_13_atoms_spline 31: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_16_12_14_system_13_atoms_spline (10 ms) 31: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_16_12_14_system_13_atoms_spread 31: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_16_12_14_system_13_atoms_spread (11 ms) 31: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_16_12_14_system_13_atoms_fused spline and spread 31: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_16_12_14_system_13_atoms_fused spline and spread (11 ms) 31: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_19_17_11_system_1_atom_spline 31: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_19_17_11_system_1_atom_spline (3 ms) 31: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_19_17_11_system_1_atom_spread 31: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_19_17_11_system_1_atom_spread (2 ms) 31: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_19_17_11_system_1_atom_fused spline and spread 31: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_19_17_11_system_1_atom_fused spline and spread (2 ms) 31: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_19_17_11_system_2_atoms_spline 31: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_19_17_11_system_2_atoms_spline (3 ms) 31: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_19_17_11_system_2_atoms_spread 31: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_19_17_11_system_2_atoms_spread (3 ms) 31: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_19_17_11_system_2_atoms_fused spline and spread 31: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_19_17_11_system_2_atoms_fused spline and spread (4 ms) 31: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_19_17_11_system_13_atoms_spline 31: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_19_17_11_system_13_atoms_spline (11 ms) 31: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_19_17_11_system_13_atoms_spread 31: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_19_17_11_system_13_atoms_spread (13 ms) 31: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_19_17_11_system_13_atoms_fused spline and spread 31: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_19_17_11_system_13_atoms_fused spline and spread (14 ms) 31: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_16_12_14_system_1_atom_spline 31: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_16_12_14_system_1_atom_spline (3 ms) 31: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_16_12_14_system_1_atom_spread 31: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_16_12_14_system_1_atom_spread (3 ms) 31: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_16_12_14_system_1_atom_fused spline and spread 31: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_16_12_14_system_1_atom_fused spline and spread (3 ms) 31: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_16_12_14_system_2_atoms_spline 31: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_16_12_14_system_2_atoms_spline (5 ms) 31: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_16_12_14_system_2_atoms_spread 31: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_16_12_14_system_2_atoms_spread (6 ms) 31: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_16_12_14_system_2_atoms_fused spline and spread 31: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_16_12_14_system_2_atoms_fused spline and spread (6 ms) 31: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_16_12_14_system_13_atoms_spline 31: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_16_12_14_system_13_atoms_spline (15 ms) 31: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_16_12_14_system_13_atoms_spread 31: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_16_12_14_system_13_atoms_spread (16 ms) 31: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_16_12_14_system_13_atoms_fused spline and spread 31: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_16_12_14_system_13_atoms_fused spline and spread (17 ms) 31: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_19_17_11_system_1_atom_spline 31: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_19_17_11_system_1_atom_spline (4 ms) 31: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_19_17_11_system_1_atom_spread 31: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_19_17_11_system_1_atom_spread (3 ms) 31: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_19_17_11_system_1_atom_fused spline and spread 31: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_19_17_11_system_1_atom_fused spline and spread (3 ms) 31: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_19_17_11_system_2_atoms_spline 31: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_19_17_11_system_2_atoms_spline (4 ms) 31: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_19_17_11_system_2_atoms_spread 31: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_19_17_11_system_2_atoms_spread (6 ms) 31: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_19_17_11_system_2_atoms_fused spline and spread 31: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_19_17_11_system_2_atoms_fused spline and spread (5 ms) 31: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_19_17_11_system_13_atoms_spline 31: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_19_17_11_system_13_atoms_spline (15 ms) 31: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_19_17_11_system_13_atoms_spread 31: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_19_17_11_system_13_atoms_spread (20 ms) 31: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_19_17_11_system_13_atoms_fused spline and spread 31: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_19_17_11_system_13_atoms_fused spline and spread (19 ms) 31: [----------] 108 tests from Pme_SplineAndSpreadTest (838 ms total) 31: 31: [----------] 64 tests from Pme_SolveTest 31: [ RUN ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ 31: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 31: Test is being skipped because: 31: CPU PME solve does not implement XYZ grid ordering 31: 31: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ (0 ms) 31: [ RUN ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy 31: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 31: Test is being skipped because: 31: CPU PME solve does not implement XYZ grid ordering 31: 31: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy (0 ms) 31: [ RUN ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_ 31: [ OK ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_ (4 ms) 31: [ RUN ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_energy 31: [ OK ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_energy (2 ms) 31: [ RUN ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ 31: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 31: Test is being skipped because: 31: CPU PME solve does not implement XYZ grid ordering 31: 31: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ (0 ms) 31: [ RUN ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy 31: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 31: Test is being skipped because: 31: CPU PME solve does not implement XYZ grid ordering 31: 31: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy (0 ms) 31: [ RUN ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_ 31: [ OK ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_ (3 ms) 31: [ RUN ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_energy 31: [ OK ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_energy (3 ms) 31: [ RUN ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ 31: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 31: Test is being skipped because: 31: CPU PME solve does not implement XYZ grid ordering 31: 31: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ (0 ms) 31: [ RUN ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy 31: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 31: Test is being skipped because: 31: CPU PME solve does not implement XYZ grid ordering 31: 31: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy (0 ms) 31: [ RUN ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_ 31: [ OK ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_ (2 ms) 31: [ RUN ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_energy 31: [ OK ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_energy (2 ms) 31: [ RUN ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ 31: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 31: Test is being skipped because: 31: CPU PME solve does not implement XYZ grid ordering 31: 31: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ (0 ms) 31: [ RUN ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy 31: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 31: Test is being skipped because: 31: CPU PME solve does not implement XYZ grid ordering 31: 31: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy (0 ms) 31: [ RUN ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_ 31: [ OK ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_ (3 ms) 31: [ RUN ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_energy 31: [ OK ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_energy (3 ms) 31: [ RUN ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ 31: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 31: Test is being skipped because: 31: CPU PME solve does not implement XYZ grid ordering 31: 31: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ (0 ms) 31: [ RUN ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy 31: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 31: Test is being skipped because: 31: CPU PME solve does not implement XYZ grid ordering 31: 31: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy (0 ms) 31: [ RUN ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_ 31: [ OK ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_ (6 ms) 31: [ RUN ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_energy 31: [ OK ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_energy (1 ms) 31: [ RUN ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ 31: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 31: Test is being skipped because: 31: CPU PME solve does not implement XYZ grid ordering 31: 31: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ (0 ms) 31: [ RUN ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy 31: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 31: Test is being skipped because: 31: CPU PME solve does not implement XYZ grid ordering 31: 31: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy (0 ms) 31: [ RUN ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_ 31: [ OK ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_ (2 ms) 31: [ RUN ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_energy 31: [ OK ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_energy (2 ms) 31: [ RUN ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ 31: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 31: Test is being skipped because: 31: CPU PME solve does not implement XYZ grid ordering 31: 31: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ (0 ms) 31: [ RUN ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy 31: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 31: Test is being skipped because: 31: CPU PME solve does not implement XYZ grid ordering 31: 31: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy (0 ms) 31: [ RUN ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_ 31: [ OK ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_ (1 ms) 31: [ RUN ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_energy 31: [ OK ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_energy (1 ms) 31: [ RUN ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ 31: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 31: Test is being skipped because: 31: CPU PME solve does not implement XYZ grid ordering 31: 31: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ (0 ms) 31: [ RUN ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy 31: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 31: Test is being skipped because: 31: CPU PME solve does not implement XYZ grid ordering 31: 31: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy (0 ms) 31: [ RUN ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_ 31: [ OK ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_ (2 ms) 31: [ RUN ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_energy 31: [ OK ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_energy (2 ms) 31: [ RUN ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ 31: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 31: Test is being skipped because: 31: CPU PME solve does not implement XYZ grid ordering 31: 31: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ (0 ms) 31: [ RUN ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy 31: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 31: Test is being skipped because: 31: CPU PME solve does not implement XYZ grid ordering 31: 31: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy (0 ms) 31: [ RUN ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_ 31: [ OK ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_ (2 ms) 31: [ RUN ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_energy 31: [ OK ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_energy (2 ms) 31: [ RUN ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ 31: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 31: Test is being skipped because: 31: CPU PME solve does not implement XYZ grid ordering 31: 31: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ (0 ms) 31: [ RUN ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy 31: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 31: Test is being skipped because: 31: CPU PME solve does not implement XYZ grid ordering 31: 31: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy (0 ms) 31: [ RUN ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_ 31: [ OK ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_ (3 ms) 31: [ RUN ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_energy 31: [ OK ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_energy (3 ms) 31: [ RUN ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ 31: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 31: Test is being skipped because: 31: CPU PME solve does not implement XYZ grid ordering 31: 31: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ (0 ms) 31: [ RUN ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy 31: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 31: Test is being skipped because: 31: CPU PME solve does not implement XYZ grid ordering 31: 31: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy (0 ms) 31: [ RUN ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_ 31: [ OK ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_ (2 ms) 31: [ RUN ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_energy 31: [ OK ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_energy (2 ms) 31: [ RUN ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ 31: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 31: Test is being skipped because: 31: CPU PME solve does not implement XYZ grid ordering 31: 31: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ (0 ms) 31: [ RUN ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy 31: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 31: Test is being skipped because: 31: CPU PME solve does not implement XYZ grid ordering 31: 31: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy (0 ms) 31: [ RUN ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_ 31: [ OK ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_ (5 ms) 31: [ RUN ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_energy 31: [ OK ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_energy (4 ms) 31: [ RUN ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ 31: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 31: Test is being skipped because: 31: CPU PME solve does not implement XYZ grid ordering 31: 31: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ (0 ms) 31: [ RUN ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy 31: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 31: Test is being skipped because: 31: CPU PME solve does not implement XYZ grid ordering 31: 31: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy (0 ms) 31: [ RUN ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_ 31: [ OK ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_ (4 ms) 31: [ RUN ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_energy 31: [ OK ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_energy (1 ms) 31: [ RUN ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ 31: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 31: Test is being skipped because: 31: CPU PME solve does not implement XYZ grid ordering 31: 31: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ (0 ms) 31: [ RUN ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy 31: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 31: Test is being skipped because: 31: CPU PME solve does not implement XYZ grid ordering 31: 31: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy (0 ms) 31: [ RUN ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_ 31: [ OK ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_ (3 ms) 31: [ RUN ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_energy 31: [ OK ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_energy (2 ms) 31: [ RUN ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ 31: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 31: Test is being skipped because: 31: CPU PME solve does not implement XYZ grid ordering 31: 31: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ (0 ms) 31: [ RUN ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy 31: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 31: Test is being skipped because: 31: CPU PME solve does not implement XYZ grid ordering 31: 31: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy (0 ms) 31: [ RUN ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_ 31: [ OK ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_ (1 ms) 31: [ RUN ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_energy 31: [ OK ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_energy (1 ms) 31: [ RUN ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ 31: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 31: Test is being skipped because: 31: CPU PME solve does not implement XYZ grid ordering 31: 31: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ (0 ms) 31: [ RUN ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy 31: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 31: Test is being skipped because: 31: CPU PME solve does not implement XYZ grid ordering 31: 31: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy (0 ms) 31: [ RUN ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_ 31: [ OK ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_ (3 ms) 31: [ RUN ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_energy 31: [ OK ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_energy (2 ms) 31: [----------] 64 tests from Pme_SolveTest (101 ms total) 31: 31: [----------] 32 tests from PmeDiffEwaldQ_SolveTest 31: [ RUN ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_ 31: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 31: Test is being skipped because: 31: CPU PME solve does not implement XYZ grid ordering 31: 31: [ SKIPPED ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_ (0 ms) 31: [ RUN ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_energy 31: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 31: Test is being skipped because: 31: CPU PME solve does not implement XYZ grid ordering 31: 31: [ SKIPPED ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_energy (0 ms) 31: [ RUN ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_YZX_ 31: [ OK ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_YZX_ (2 ms) 31: [ RUN ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_YZX_energy 31: [ OK ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_YZX_energy (6 ms) 31: [ RUN ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_ 31: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 31: Test is being skipped because: 31: CPU PME solve does not implement XYZ grid ordering 31: 31: [ SKIPPED ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_ (0 ms) 31: [ RUN ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_energy 31: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 31: Test is being skipped because: 31: CPU PME solve does not implement XYZ grid ordering 31: 31: [ SKIPPED ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_energy (0 ms) 31: [ RUN ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_YZX_ 31: [ OK ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_YZX_ (2 ms) 31: [ RUN ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_YZX_energy 31: [ OK ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_YZX_energy (2 ms) 31: [ RUN ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_ 31: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 31: Test is being skipped because: 31: CPU PME solve does not implement XYZ grid ordering 31: 31: [ SKIPPED ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_ (0 ms) 31: [ RUN ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_energy 31: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 31: Test is being skipped because: 31: CPU PME solve does not implement XYZ grid ordering 31: 31: [ SKIPPED ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_energy (0 ms) 31: [ RUN ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_YZX_ 31: [ OK ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_YZX_ (2 ms) 31: [ RUN ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_YZX_energy 31: [ OK ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_YZX_energy (1 ms) 31: [ RUN ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_ 31: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 31: Test is being skipped because: 31: CPU PME solve does not implement XYZ grid ordering 31: 31: [ SKIPPED ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_ (0 ms) 31: [ RUN ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_energy 31: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 31: Test is being skipped because: 31: CPU PME solve does not implement XYZ grid ordering 31: 31: [ SKIPPED ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_energy (0 ms) 31: [ RUN ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_YZX_ 31: [ OK ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_YZX_ (2 ms) 31: [ RUN ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_YZX_energy 31: [ OK ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_YZX_energy (1 ms) 31: [ RUN ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_ 31: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 31: Test is being skipped because: 31: CPU PME solve does not implement XYZ grid ordering 31: 31: [ SKIPPED ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_ (0 ms) 31: [ RUN ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_energy 31: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 31: Test is being skipped because: 31: CPU PME solve does not implement XYZ grid ordering 31: 31: [ SKIPPED ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_energy (0 ms) 31: [ RUN ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_YZX_ 31: [ OK ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_YZX_ (2 ms) 31: [ RUN ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_YZX_energy 31: [ OK ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_YZX_energy (2 ms) 31: [ RUN ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_ 31: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 31: Test is being skipped because: 31: CPU PME solve does not implement XYZ grid ordering 31: 31: [ SKIPPED ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_ (0 ms) 31: [ RUN ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_energy 31: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 31: Test is being skipped because: 31: CPU PME solve does not implement XYZ grid ordering 31: 31: [ SKIPPED ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_energy (0 ms) 31: [ RUN ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_YZX_ 31: [ OK ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_YZX_ (2 ms) 31: [ RUN ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_YZX_energy 31: [ OK ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_YZX_energy (2 ms) 31: [ RUN ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_ 31: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 31: Test is being skipped because: 31: CPU PME solve does not implement XYZ grid ordering 31: 31: [ SKIPPED ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_ (0 ms) 31: [ RUN ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_energy 31: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 31: Test is being skipped because: 31: CPU PME solve does not implement XYZ grid ordering 31: 31: [ SKIPPED ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_energy (0 ms) 31: [ RUN ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_YZX_ 31: [ OK ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_YZX_ (1 ms) 31: [ RUN ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_YZX_energy 31: [ OK ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_YZX_energy (1 ms) 31: [ RUN ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_ 31: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 31: Test is being skipped because: 31: CPU PME solve does not implement XYZ grid ordering 31: 31: [ SKIPPED ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_ (0 ms) 31: [ RUN ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_energy 31: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 31: Test is being skipped because: 31: CPU PME solve does not implement XYZ grid ordering 31: 31: [ SKIPPED ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_energy (0 ms) 31: [ RUN ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_YZX_ 31: [ OK ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_YZX_ (1 ms) 31: [ RUN ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_YZX_energy 31: [ OK ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_YZX_energy (1 ms) 31: [----------] 32 tests from PmeDiffEwaldQ_SolveTest (42 ms total) 31: 31: [----------] 32 tests from PmeDiffEwaldLJ_SolveTest 31: [ RUN ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_ 31: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 31: Test is being skipped because: 31: CPU PME solve does not implement XYZ grid ordering 31: 31: [ SKIPPED ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_ (0 ms) 31: [ RUN ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_energy 31: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 31: Test is being skipped because: 31: CPU PME solve does not implement XYZ grid ordering 31: 31: [ SKIPPED ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_energy (0 ms) 31: [ RUN ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_YZX_ 31: [ OK ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_YZX_ (4 ms) 31: [ RUN ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_YZX_energy 31: [ OK ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_YZX_energy (5 ms) 31: [ RUN ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_ 31: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 31: Test is being skipped because: 31: CPU PME solve does not implement XYZ grid ordering 31: 31: [ SKIPPED ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_ (0 ms) 31: [ RUN ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_energy 31: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 31: Test is being skipped because: 31: CPU PME solve does not implement XYZ grid ordering 31: 31: [ SKIPPED ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_energy (0 ms) 31: [ RUN ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_YZX_ 31: [ OK ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_YZX_ (4 ms) 31: [ RUN ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_YZX_energy 31: [ OK ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_YZX_energy (3 ms) 31: [ RUN ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_ 31: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 31: Test is being skipped because: 31: CPU PME solve does not implement XYZ grid ordering 31: 31: [ SKIPPED ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_ (0 ms) 31: [ RUN ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_energy 31: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 31: Test is being skipped because: 31: CPU PME solve does not implement XYZ grid ordering 31: 31: [ SKIPPED ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_energy (0 ms) 31: [ RUN ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_YZX_ 31: [ OK ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_YZX_ (2 ms) 31: [ RUN ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_YZX_energy 31: [ OK ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_YZX_energy (2 ms) 31: [ RUN ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_ 31: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 31: Test is being skipped because: 31: CPU PME solve does not implement XYZ grid ordering 31: 31: [ SKIPPED ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_ (0 ms) 31: [ RUN ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_energy 31: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 31: Test is being skipped because: 31: CPU PME solve does not implement XYZ grid ordering 31: 31: [ SKIPPED ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_energy (0 ms) 31: [ RUN ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_YZX_ 31: [ OK ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_YZX_ (2 ms) 31: [ RUN ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_YZX_energy 31: [ OK ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_YZX_energy (2 ms) 31: [ RUN ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_ 31: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 31: Test is being skipped because: 31: CPU PME solve does not implement XYZ grid ordering 31: 31: [ SKIPPED ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_ (0 ms) 31: [ RUN ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_energy 31: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 31: Test is being skipped because: 31: CPU PME solve does not implement XYZ grid ordering 31: 31: [ SKIPPED ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_energy (0 ms) 31: [ RUN ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_YZX_ 31: [ OK ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_YZX_ (4 ms) 31: [ RUN ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_YZX_energy 31: [ OK ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_YZX_energy (3 ms) 31: [ RUN ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_ 31: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 31: Test is being skipped because: 31: CPU PME solve does not implement XYZ grid ordering 31: 31: [ SKIPPED ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_ (0 ms) 31: [ RUN ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_energy 31: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 31: Test is being skipped because: 31: CPU PME solve does not implement XYZ grid ordering 31: 31: [ SKIPPED ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_energy (0 ms) 31: [ RUN ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_YZX_ 31: [ OK ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_YZX_ (4 ms) 31: [ RUN ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_YZX_energy 31: [ OK ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_YZX_energy (3 ms) 31: [ RUN ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_ 31: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 31: Test is being skipped because: 31: CPU PME solve does not implement XYZ grid ordering 31: 31: [ SKIPPED ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_ (0 ms) 31: [ RUN ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_energy 31: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 31: Test is being skipped because: 31: CPU PME solve does not implement XYZ grid ordering 31: 31: [ SKIPPED ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_energy (0 ms) 31: [ RUN ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_YZX_ 31: [ OK ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_YZX_ (2 ms) 31: [ RUN ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_YZX_energy 31: [ OK ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_YZX_energy (2 ms) 31: [ RUN ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_ 31: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 31: Test is being skipped because: 31: CPU PME solve does not implement XYZ grid ordering 31: 31: [ SKIPPED ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_ (0 ms) 31: [ RUN ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_energy 31: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 31: Test is being skipped because: 31: CPU PME solve does not implement XYZ grid ordering 31: 31: [ SKIPPED ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_energy (0 ms) 31: [ RUN ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_YZX_ 31: [ OK ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_YZX_ (2 ms) 31: [ RUN ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_YZX_energy 31: [ OK ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_YZX_energy (2 ms) 31: [----------] 32 tests from PmeDiffEwaldLJ_SolveTest (56 ms total) 31: 31: [----------] 64 tests from PmeDiffEps_SolveTest 31: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ 31: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 31: Test is being skipped because: 31: CPU PME solve does not implement XYZ grid ordering 31: 31: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ (0 ms) 31: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy 31: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 31: Test is being skipped because: 31: CPU PME solve does not implement XYZ grid ordering 31: 31: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy (0 ms) 31: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_ 31: [ OK ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_ (2 ms) 31: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_energy 31: [ OK ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_energy (2 ms) 31: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ 31: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 31: Test is being skipped because: 31: CPU PME solve does not implement XYZ grid ordering 31: 31: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ (0 ms) 31: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy 31: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 31: Test is being skipped because: 31: CPU PME solve does not implement XYZ grid ordering 31: 31: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy (0 ms) 31: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_ 31: [ OK ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_ (11 ms) 31: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_energy 31: [ OK ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_energy (3 ms) 31: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ 31: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 31: Test is being skipped because: 31: CPU PME solve does not implement XYZ grid ordering 31: 31: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ (0 ms) 31: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy 31: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 31: Test is being skipped because: 31: CPU PME solve does not implement XYZ grid ordering 31: 31: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy (0 ms) 31: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_ 31: [ OK ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_ (2 ms) 31: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_energy 31: [ OK ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_energy (2 ms) 31: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ 31: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 31: Test is being skipped because: 31: CPU PME solve does not implement XYZ grid ordering 31: 31: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ (0 ms) 31: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy 31: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 31: Test is being skipped because: 31: CPU PME solve does not implement XYZ grid ordering 31: 31: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy (0 ms) 31: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_ 31: [ OK ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_ (3 ms) 31: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_energy 31: [ OK ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_energy (3 ms) 31: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ 31: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 31: Test is being skipped because: 31: CPU PME solve does not implement XYZ grid ordering 31: 31: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ (0 ms) 31: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy 31: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 31: Test is being skipped because: 31: CPU PME solve does not implement XYZ grid ordering 31: 31: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy (0 ms) 31: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_ 31: [ OK ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_ (1 ms) 31: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_energy 31: [ OK ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_energy (1 ms) 31: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ 31: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 31: Test is being skipped because: 31: CPU PME solve does not implement XYZ grid ordering 31: 31: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ (0 ms) 31: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy 31: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 31: Test is being skipped because: 31: CPU PME solve does not implement XYZ grid ordering 31: 31: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy (0 ms) 31: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_ 31: [ OK ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_ (2 ms) 31: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_energy 31: [ OK ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_energy (2 ms) 31: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ 31: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 31: Test is being skipped because: 31: CPU PME solve does not implement XYZ grid ordering 31: 31: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ (0 ms) 31: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy 31: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 31: Test is being skipped because: 31: CPU PME solve does not implement XYZ grid ordering 31: 31: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy (0 ms) 31: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_ 31: [ OK ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_ (2 ms) 31: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_energy 31: [ OK ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_energy (1 ms) 31: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ 31: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 31: Test is being skipped because: 31: CPU PME solve does not implement XYZ grid ordering 31: 31: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ (0 ms) 31: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy 31: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 31: Test is being skipped because: 31: CPU PME solve does not implement XYZ grid ordering 31: 31: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy (0 ms) 31: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_ 31: [ OK ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_ (2 ms) 31: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_energy 31: [ OK ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_energy (2 ms) 31: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ 31: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 31: Test is being skipped because: 31: CPU PME solve does not implement XYZ grid ordering 31: 31: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ (0 ms) 31: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy 31: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 31: Test is being skipped because: 31: CPU PME solve does not implement XYZ grid ordering 31: 31: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy (0 ms) 31: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_ 31: [ OK ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_ (2 ms) 31: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_energy 31: [ OK ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_energy (2 ms) 31: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ 31: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 31: Test is being skipped because: 31: CPU PME solve does not implement XYZ grid ordering 31: 31: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ (0 ms) 31: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy 31: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 31: Test is being skipped because: 31: CPU PME solve does not implement XYZ grid ordering 31: 31: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy (0 ms) 31: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_ 31: [ OK ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_ (4 ms) 31: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_energy 31: [ OK ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_energy (3 ms) 31: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ 31: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 31: Test is being skipped because: 31: CPU PME solve does not implement XYZ grid ordering 31: 31: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ (0 ms) 31: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy 31: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 31: Test is being skipped because: 31: CPU PME solve does not implement XYZ grid ordering 31: 31: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy (0 ms) 31: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_ 31: [ OK ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_ (13 ms) 31: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_energy 31: [ OK ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_energy (2 ms) 31: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ 31: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 31: Test is being skipped because: 31: CPU PME solve does not implement XYZ grid ordering 31: 31: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ (0 ms) 31: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy 31: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 31: Test is being skipped because: 31: CPU PME solve does not implement XYZ grid ordering 31: 31: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy (0 ms) 31: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_ 31: [ OK ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_ (4 ms) 31: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_energy 31: [ OK ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_energy (3 ms) 31: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ 31: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 31: Test is being skipped because: 31: CPU PME solve does not implement XYZ grid ordering 31: 31: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ (0 ms) 31: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy 31: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 31: Test is being skipped because: 31: CPU PME solve does not implement XYZ grid ordering 31: 31: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy (0 ms) 31: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_ 31: [ OK ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_ (2 ms) 31: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_energy 31: [ OK ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_energy (1 ms) 31: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ 31: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 31: Test is being skipped because: 31: CPU PME solve does not implement XYZ grid ordering 31: 31: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ (0 ms) 31: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy 31: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 31: Test is being skipped because: 31: CPU PME solve does not implement XYZ grid ordering 31: 31: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy (0 ms) 31: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_ 31: [ OK ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_ (3 ms) 31: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_energy 31: [ OK ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_energy (2 ms) 31: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ 31: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 31: Test is being skipped because: 31: CPU PME solve does not implement XYZ grid ordering 31: 31: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ (0 ms) 31: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy 31: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 31: Test is being skipped because: 31: CPU PME solve does not implement XYZ grid ordering 31: 31: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy (0 ms) 31: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_ 31: [ OK ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_ (1 ms) 31: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_energy 31: [ OK ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_energy (1 ms) 31: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ 31: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 31: Test is being skipped because: 31: CPU PME solve does not implement XYZ grid ordering 31: 31: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ (0 ms) 31: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy 31: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 31: Test is being skipped because: 31: CPU PME solve does not implement XYZ grid ordering 31: 31: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy (0 ms) 31: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_ 31: [ OK ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_ (2 ms) 31: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_energy 31: [ OK ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_energy (2 ms) 31: [----------] 64 tests from PmeDiffEps_SolveTest (113 ms total) 31: 31: [----------] 72 tests from Pme_GatherTest 31: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_3_grid_16_12_14_gridvalues_first_system_1_atom 31: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_3_grid_16_12_14_gridvalues_first_system_1_atom (2 ms) 31: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_3_grid_16_12_14_gridvalues_first_system_2_atoms 31: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_3_grid_16_12_14_gridvalues_first_system_2_atoms (1 ms) 31: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_3_grid_16_12_14_gridvalues_first_system_13_atoms 31: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_3_grid_16_12_14_gridvalues_first_system_13_atoms (1 ms) 31: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_3_grid_16_12_14_gridvalues_second_system_1_atom 31: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_3_grid_16_12_14_gridvalues_second_system_1_atom (1 ms) 31: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_3_grid_16_12_14_gridvalues_second_system_2_atoms 31: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_3_grid_16_12_14_gridvalues_second_system_2_atoms (1 ms) 31: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_3_grid_16_12_14_gridvalues_second_system_13_atoms 31: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_3_grid_16_12_14_gridvalues_second_system_13_atoms (1 ms) 31: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_3_grid_13_15_11_gridvalues_first_system_1_atom 31: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_3_grid_13_15_11_gridvalues_first_system_1_atom (1 ms) 31: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_3_grid_13_15_11_gridvalues_first_system_2_atoms 31: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_3_grid_13_15_11_gridvalues_first_system_2_atoms (1 ms) 31: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_3_grid_13_15_11_gridvalues_first_system_13_atoms 31: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_3_grid_13_15_11_gridvalues_first_system_13_atoms (1 ms) 31: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_3_grid_13_15_11_gridvalues_second_system_1_atom 31: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_3_grid_13_15_11_gridvalues_second_system_1_atom (1 ms) 31: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_3_grid_13_15_11_gridvalues_second_system_2_atoms 31: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_3_grid_13_15_11_gridvalues_second_system_2_atoms (1 ms) 31: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_3_grid_13_15_11_gridvalues_second_system_13_atoms 31: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_3_grid_13_15_11_gridvalues_second_system_13_atoms (2 ms) 31: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_4_grid_16_12_14_gridvalues_first_system_1_atom 31: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_4_grid_16_12_14_gridvalues_first_system_1_atom (1 ms) 31: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_4_grid_16_12_14_gridvalues_first_system_2_atoms 31: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_4_grid_16_12_14_gridvalues_first_system_2_atoms (1 ms) 31: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_4_grid_16_12_14_gridvalues_first_system_13_atoms 31: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_4_grid_16_12_14_gridvalues_first_system_13_atoms (1 ms) 31: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_4_grid_16_12_14_gridvalues_second_system_1_atom 31: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_4_grid_16_12_14_gridvalues_second_system_1_atom (1 ms) 31: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_4_grid_16_12_14_gridvalues_second_system_2_atoms 31: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_4_grid_16_12_14_gridvalues_second_system_2_atoms (1 ms) 31: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_4_grid_16_12_14_gridvalues_second_system_13_atoms 31: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_4_grid_16_12_14_gridvalues_second_system_13_atoms (1 ms) 31: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_4_grid_13_15_11_gridvalues_first_system_1_atom 31: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_4_grid_13_15_11_gridvalues_first_system_1_atom (1 ms) 31: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_4_grid_13_15_11_gridvalues_first_system_2_atoms 31: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_4_grid_13_15_11_gridvalues_first_system_2_atoms (1 ms) 31: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_4_grid_13_15_11_gridvalues_first_system_13_atoms 31: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_4_grid_13_15_11_gridvalues_first_system_13_atoms (1 ms) 31: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_4_grid_13_15_11_gridvalues_second_system_1_atom 31: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_4_grid_13_15_11_gridvalues_second_system_1_atom (1 ms) 31: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_4_grid_13_15_11_gridvalues_second_system_2_atoms 31: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_4_grid_13_15_11_gridvalues_second_system_2_atoms (1 ms) 31: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_4_grid_13_15_11_gridvalues_second_system_13_atoms 31: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_4_grid_13_15_11_gridvalues_second_system_13_atoms (1 ms) 31: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_5_grid_16_12_14_gridvalues_first_system_1_atom 31: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_5_grid_16_12_14_gridvalues_first_system_1_atom (1 ms) 31: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_5_grid_16_12_14_gridvalues_first_system_2_atoms 31: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_5_grid_16_12_14_gridvalues_first_system_2_atoms (1 ms) 31: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_5_grid_16_12_14_gridvalues_first_system_13_atoms 31: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_5_grid_16_12_14_gridvalues_first_system_13_atoms (1 ms) 31: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_5_grid_16_12_14_gridvalues_second_system_1_atom 31: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_5_grid_16_12_14_gridvalues_second_system_1_atom (1 ms) 31: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_5_grid_16_12_14_gridvalues_second_system_2_atoms 31: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_5_grid_16_12_14_gridvalues_second_system_2_atoms (1 ms) 31: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_5_grid_16_12_14_gridvalues_second_system_13_atoms 31: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_5_grid_16_12_14_gridvalues_second_system_13_atoms (1 ms) 31: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_5_grid_13_15_11_gridvalues_first_system_1_atom 31: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_5_grid_13_15_11_gridvalues_first_system_1_atom (1 ms) 31: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_5_grid_13_15_11_gridvalues_first_system_2_atoms 31: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_5_grid_13_15_11_gridvalues_first_system_2_atoms (1 ms) 31: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_5_grid_13_15_11_gridvalues_first_system_13_atoms 31: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_5_grid_13_15_11_gridvalues_first_system_13_atoms (1 ms) 31: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_5_grid_13_15_11_gridvalues_second_system_1_atom 31: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_5_grid_13_15_11_gridvalues_second_system_1_atom (1 ms) 31: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_5_grid_13_15_11_gridvalues_second_system_2_atoms 31: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_5_grid_13_15_11_gridvalues_second_system_2_atoms (1 ms) 31: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_5_grid_13_15_11_gridvalues_second_system_13_atoms 31: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_5_grid_13_15_11_gridvalues_second_system_13_atoms (1 ms) 31: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_3_grid_16_12_14_gridvalues_first_system_1_atom 31: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_3_grid_16_12_14_gridvalues_first_system_1_atom (1 ms) 31: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_3_grid_16_12_14_gridvalues_first_system_2_atoms 31: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_3_grid_16_12_14_gridvalues_first_system_2_atoms (1 ms) 31: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_3_grid_16_12_14_gridvalues_first_system_13_atoms 31: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_3_grid_16_12_14_gridvalues_first_system_13_atoms (2 ms) 31: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_3_grid_16_12_14_gridvalues_second_system_1_atom 31: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_3_grid_16_12_14_gridvalues_second_system_1_atom (1 ms) 31: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_3_grid_16_12_14_gridvalues_second_system_2_atoms 31: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_3_grid_16_12_14_gridvalues_second_system_2_atoms (1 ms) 31: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_3_grid_16_12_14_gridvalues_second_system_13_atoms 31: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_3_grid_16_12_14_gridvalues_second_system_13_atoms (1 ms) 31: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_3_grid_13_15_11_gridvalues_first_system_1_atom 31: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_3_grid_13_15_11_gridvalues_first_system_1_atom (1 ms) 31: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_3_grid_13_15_11_gridvalues_first_system_2_atoms 31: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_3_grid_13_15_11_gridvalues_first_system_2_atoms (1 ms) 31: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_3_grid_13_15_11_gridvalues_first_system_13_atoms 31: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_3_grid_13_15_11_gridvalues_first_system_13_atoms (2 ms) 31: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_3_grid_13_15_11_gridvalues_second_system_1_atom 31: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_3_grid_13_15_11_gridvalues_second_system_1_atom (1 ms) 31: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_3_grid_13_15_11_gridvalues_second_system_2_atoms 31: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_3_grid_13_15_11_gridvalues_second_system_2_atoms (1 ms) 31: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_3_grid_13_15_11_gridvalues_second_system_13_atoms 31: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_3_grid_13_15_11_gridvalues_second_system_13_atoms (1 ms) 31: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_4_grid_16_12_14_gridvalues_first_system_1_atom 31: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_4_grid_16_12_14_gridvalues_first_system_1_atom (1 ms) 31: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_4_grid_16_12_14_gridvalues_first_system_2_atoms 31: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_4_grid_16_12_14_gridvalues_first_system_2_atoms (1 ms) 31: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_4_grid_16_12_14_gridvalues_first_system_13_atoms 31: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_4_grid_16_12_14_gridvalues_first_system_13_atoms (1 ms) 31: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_4_grid_16_12_14_gridvalues_second_system_1_atom 31: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_4_grid_16_12_14_gridvalues_second_system_1_atom (1 ms) 31: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_4_grid_16_12_14_gridvalues_second_system_2_atoms 31: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_4_grid_16_12_14_gridvalues_second_system_2_atoms (1 ms) 31: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_4_grid_16_12_14_gridvalues_second_system_13_atoms 31: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_4_grid_16_12_14_gridvalues_second_system_13_atoms (1 ms) 31: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_4_grid_13_15_11_gridvalues_first_system_1_atom 31: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_4_grid_13_15_11_gridvalues_first_system_1_atom (1 ms) 31: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_4_grid_13_15_11_gridvalues_first_system_2_atoms 31: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_4_grid_13_15_11_gridvalues_first_system_2_atoms (1 ms) 31: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_4_grid_13_15_11_gridvalues_first_system_13_atoms 31: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_4_grid_13_15_11_gridvalues_first_system_13_atoms (1 ms) 31: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_4_grid_13_15_11_gridvalues_second_system_1_atom 31: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_4_grid_13_15_11_gridvalues_second_system_1_atom (14 ms) 31: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_4_grid_13_15_11_gridvalues_second_system_2_atoms 31: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_4_grid_13_15_11_gridvalues_second_system_2_atoms (1 ms) 31: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_4_grid_13_15_11_gridvalues_second_system_13_atoms 31: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_4_grid_13_15_11_gridvalues_second_system_13_atoms (2 ms) 31: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_5_grid_16_12_14_gridvalues_first_system_1_atom 31: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_5_grid_16_12_14_gridvalues_first_system_1_atom (1 ms) 31: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_5_grid_16_12_14_gridvalues_first_system_2_atoms 31: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_5_grid_16_12_14_gridvalues_first_system_2_atoms (1 ms) 31: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_5_grid_16_12_14_gridvalues_first_system_13_atoms 31: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_5_grid_16_12_14_gridvalues_first_system_13_atoms (2 ms) 31: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_5_grid_16_12_14_gridvalues_second_system_1_atom 31: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_5_grid_16_12_14_gridvalues_second_system_1_atom (1 ms) 31: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_5_grid_16_12_14_gridvalues_second_system_2_atoms 31: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_5_grid_16_12_14_gridvalues_second_system_2_atoms (1 ms) 31: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_5_grid_16_12_14_gridvalues_second_system_13_atoms 31: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_5_grid_16_12_14_gridvalues_second_system_13_atoms (1 ms) 31: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_5_grid_13_15_11_gridvalues_first_system_1_atom 31: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_5_grid_13_15_11_gridvalues_first_system_1_atom (1 ms) 31: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_5_grid_13_15_11_gridvalues_first_system_2_atoms 31: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_5_grid_13_15_11_gridvalues_first_system_2_atoms (1 ms) 31: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_5_grid_13_15_11_gridvalues_first_system_13_atoms 31: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_5_grid_13_15_11_gridvalues_first_system_13_atoms (2 ms) 31: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_5_grid_13_15_11_gridvalues_second_system_1_atom 31: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_5_grid_13_15_11_gridvalues_second_system_1_atom (1 ms) 31: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_5_grid_13_15_11_gridvalues_second_system_2_atoms 31: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_5_grid_13_15_11_gridvalues_second_system_2_atoms (1 ms) 31: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_5_grid_13_15_11_gridvalues_second_system_13_atoms 31: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_5_grid_13_15_11_gridvalues_second_system_13_atoms (1 ms) 31: [----------] 72 tests from Pme_GatherTest (140 ms total) 31: 31: [----------] 5 tests from InsaneInput/PmeBSplineModuliFailureTest 31: [ RUN ] InsaneInput/PmeBSplineModuliFailureTest.Throws/0 31: [ OK ] InsaneInput/PmeBSplineModuliFailureTest.Throws/0 (0 ms) 31: [ RUN ] InsaneInput/PmeBSplineModuliFailureTest.Throws/1 31: [ OK ] InsaneInput/PmeBSplineModuliFailureTest.Throws/1 (0 ms) 31: [ RUN ] InsaneInput/PmeBSplineModuliFailureTest.Throws/2 31: [ OK ] InsaneInput/PmeBSplineModuliFailureTest.Throws/2 (0 ms) 31: [ RUN ] InsaneInput/PmeBSplineModuliFailureTest.Throws/3 31: [ OK ] InsaneInput/PmeBSplineModuliFailureTest.Throws/3 (9 ms) 31: [ RUN ] InsaneInput/PmeBSplineModuliFailureTest.Throws/4 31: [ OK ] InsaneInput/PmeBSplineModuliFailureTest.Throws/4 (0 ms) 31: [----------] 5 tests from InsaneInput/PmeBSplineModuliFailureTest (11 ms total) 31: 31: [----------] 24 tests from SaneInput1/PmeBSplineModuliCorrectnessTest 31: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/0 31: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/0 (13 ms) 31: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/1 31: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/1 (11 ms) 31: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/2 31: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/2 (10 ms) 31: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/3 31: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/3 (10 ms) 31: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/4 31: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/4 (10 ms) 31: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/5 31: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/5 (11 ms) 31: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/6 31: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/6 (12 ms) 31: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/7 31: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/7 (13 ms) 31: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/8 31: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/8 (13 ms) 31: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/9 31: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/9 (11 ms) 31: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/10 31: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/10 (11 ms) 31: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/11 31: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/11 (13 ms) 31: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/12 31: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/12 (22 ms) 31: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/13 31: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/13 (10 ms) 31: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/14 31: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/14 (11 ms) 31: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/15 31: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/15 (10 ms) 31: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/16 31: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/16 (10 ms) 31: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/17 31: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/17 (10 ms) 31: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/18 31: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/18 (11 ms) 31: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/19 31: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/19 (10 ms) 31: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/20 31: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/20 (11 ms) 31: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/21 31: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/21 (11 ms) 31: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/22 31: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/22 (11 ms) 31: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/23 31: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/23 (11 ms) 31: [----------] 24 tests from SaneInput1/PmeBSplineModuliCorrectnessTest (300 ms total) 31: 31: [----------] Global test environment tear-down 31: [==========] 407 tests from 9 test suites ran. (1605 ms total) 31: [ PASSED ] 311 tests. 31: [ SKIPPED ] 96 tests, listed below: 31: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ 31: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy 31: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ 31: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy 31: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ 31: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy 31: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ 31: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy 31: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ 31: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy 31: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ 31: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy 31: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ 31: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy 31: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ 31: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy 31: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ 31: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy 31: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ 31: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy 31: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ 31: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy 31: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ 31: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy 31: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ 31: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy 31: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ 31: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy 31: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ 31: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy 31: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ 31: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy 31: [ SKIPPED ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_ 31: [ SKIPPED ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_energy 31: [ SKIPPED ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_ 31: [ SKIPPED ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_energy 31: [ SKIPPED ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_ 31: [ SKIPPED ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_energy 31: [ SKIPPED ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_ 31: [ SKIPPED ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_energy 31: [ SKIPPED ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_ 31: [ SKIPPED ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_energy 31: [ SKIPPED ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_ 31: [ SKIPPED ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_energy 31: [ SKIPPED ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_ 31: [ SKIPPED ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_energy 31: [ SKIPPED ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_ 31: [ SKIPPED ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_energy 31: [ SKIPPED ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_ 31: [ SKIPPED ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_energy 31: [ SKIPPED ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_ 31: [ SKIPPED ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_energy 31: [ SKIPPED ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_ 31: [ SKIPPED ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_energy 31: [ SKIPPED ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_ 31: [ SKIPPED ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_energy 31: [ SKIPPED ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_ 31: [ SKIPPED ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_energy 31: [ SKIPPED ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_ 31: [ SKIPPED ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_energy 31: [ SKIPPED ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_ 31: [ SKIPPED ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_energy 31: [ SKIPPED ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_ 31: [ SKIPPED ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_energy 31: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ 31: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy 31: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ 31: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy 31: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ 31: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy 31: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ 31: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy 31: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ 31: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy 31: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ 31: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy 31: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ 31: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy 31: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ 31: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy 31: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ 31: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy 31: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ 31: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy 31: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ 31: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy 31: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ 31: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy 31: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ 31: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy 31: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ 31: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy 31: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ 31: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy 31: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ 31: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy 31/92 Test #31: EwaldUnitTests ............................ Passed 1.82 sec test 32 Start 32: FFTUnitTests 32: Test command: /build/reproducible-path/gromacs-2025.1/build/basic/bin/fft-test "--gtest_output=xml:/build/reproducible-path/gromacs-2025.1/build/basic/Testing/Temporary/FFTUnitTests.xml" 32: Working Directory: /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/fft/tests 32: Test timeout computed to be: 1920 32: [==========] Running 15 tests from 4 test suites. 32: [----------] Global test environment set-up. 32: [----------] 2 tests from ManyFFTTest 32: [ RUN ] ManyFFTTest.Complex1DLength48Multi5Test 32: [ OK ] ManyFFTTest.Complex1DLength48Multi5Test (21 ms) 32: [ RUN ] ManyFFTTest.Real1DLength48Multi5Test 32: [ OK ] ManyFFTTest.Real1DLength48Multi5Test (30 ms) 32: [----------] 2 tests from ManyFFTTest (56 ms total) 32: 32: [----------] 1 test from FFTTest 32: [ RUN ] FFTTest.Real2DLength18_15Test 32: [ OK ] FFTTest.Real2DLength18_15Test (10 ms) 32: [----------] 1 test from FFTTest (11 ms total) 32: 32: [----------] 10 tests from 7_8_25_36_60/FFTTest1D 32: [ RUN ] 7_8_25_36_60/FFTTest1D.Complex/0 32: [ OK ] 7_8_25_36_60/FFTTest1D.Complex/0 (2 ms) 32: [ RUN ] 7_8_25_36_60/FFTTest1D.Complex/1 32: [ OK ] 7_8_25_36_60/FFTTest1D.Complex/1 (2 ms) 32: [ RUN ] 7_8_25_36_60/FFTTest1D.Complex/2 32: [ OK ] 7_8_25_36_60/FFTTest1D.Complex/2 (3 ms) 32: [ RUN ] 7_8_25_36_60/FFTTest1D.Complex/3 32: [ OK ] 7_8_25_36_60/FFTTest1D.Complex/3 (6 ms) 32: [ RUN ] 7_8_25_36_60/FFTTest1D.Complex/4 32: [ OK ] 7_8_25_36_60/FFTTest1D.Complex/4 (6 ms) 32: [ RUN ] 7_8_25_36_60/FFTTest1D.Real/0 32: [ OK ] 7_8_25_36_60/FFTTest1D.Real/0 (2 ms) 32: [ RUN ] 7_8_25_36_60/FFTTest1D.Real/1 32: [ OK ] 7_8_25_36_60/FFTTest1D.Real/1 (2 ms) 32: [ RUN ] 7_8_25_36_60/FFTTest1D.Real/2 32: [ OK ] 7_8_25_36_60/FFTTest1D.Real/2 (2 ms) 32: [ RUN ] 7_8_25_36_60/FFTTest1D.Real/3 32: [ OK ] 7_8_25_36_60/FFTTest1D.Real/3 (17 ms) 32: [ RUN ] 7_8_25_36_60/FFTTest1D.Real/4 32: [ OK ] 7_8_25_36_60/FFTTest1D.Real/4 (26 ms) 32: [----------] 10 tests from 7_8_25_36_60/FFTTest1D (75 ms total) 32: 32: [----------] 2 tests from Works/ParameterizedFFTTest3D 32: [ RUN ] Works/ParameterizedFFTTest3D.RunsOnHost/5_6_9 32: [ OK ] Works/ParameterizedFFTTest3D.RunsOnHost/5_6_9 (6 ms) 32: [ RUN ] Works/ParameterizedFFTTest3D.RunsOnHost/5_5_10 32: [ OK ] Works/ParameterizedFFTTest3D.RunsOnHost/5_5_10 (6 ms) 32: [----------] 2 tests from Works/ParameterizedFFTTest3D (14 ms total) 32: 32: [----------] Global test environment tear-down 32: [==========] 15 tests from 4 test suites ran. (158 ms total) 32: [ PASSED ] 15 tests. 32/92 Test #32: FFTUnitTests .............................. Passed 0.29 sec test 33 Start 33: GpuUtilsUnitTests 33: Test command: /build/reproducible-path/gromacs-2025.1/build/basic/bin/gpu_utils-test "--gtest_output=xml:/build/reproducible-path/gromacs-2025.1/build/basic/Testing/Temporary/GpuUtilsUnitTests.xml" 33: Working Directory: /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/gpu_utils/tests 33: Test timeout computed to be: 30 33: [==========] Running 67 tests from 22 test suites. 33: [----------] Global test environment set-up. 33: [----------] 2 tests from ClfftInitializer 33: [ RUN ] ClfftInitializer.SingleInitializationWorks 33: [ OK ] ClfftInitializer.SingleInitializationWorks (0 ms) 33: [ RUN ] ClfftInitializer.TwoInitializationsWork 33: [ OK ] ClfftInitializer.TwoInitializationsWork (0 ms) 33: [----------] 2 tests from ClfftInitializer (0 ms total) 33: 33: [----------] 1 test from DevicesAvailable 33: [ RUN ] DevicesAvailable.ShouldBeAbleToRunOnDevice 33: [ OK ] DevicesAvailable.ShouldBeAbleToRunOnDevice (0 ms) 33: [----------] 1 test from DevicesAvailable (0 ms total) 33: 33: [----------] 1 test from DeviceStreamManagerTest 33: [ RUN ] DeviceStreamManagerTest.CorrectStreamsAreReturnedOnNonbondedDevice 33: [ OK ] DeviceStreamManagerTest.CorrectStreamsAreReturnedOnNonbondedDevice (0 ms) 33: [----------] 1 test from DeviceStreamManagerTest (0 ms total) 33: 33: [----------] 2 tests from HostAllocatorTest/0, where TypeParam = int 33: [ RUN ] HostAllocatorTest/0.EmptyMemoryAlwaysWorks 33: [ OK ] HostAllocatorTest/0.EmptyMemoryAlwaysWorks (0 ms) 33: [ RUN ] HostAllocatorTest/0.StatefulAllocatorUsesMemory 33: [ OK ] HostAllocatorTest/0.StatefulAllocatorUsesMemory (0 ms) 33: [----------] 2 tests from HostAllocatorTest/0 (0 ms total) 33: 33: [----------] 2 tests from HostAllocatorTest/1, where TypeParam = float 33: [ RUN ] HostAllocatorTest/1.EmptyMemoryAlwaysWorks 33: [ OK ] HostAllocatorTest/1.EmptyMemoryAlwaysWorks (0 ms) 33: [ RUN ] HostAllocatorTest/1.StatefulAllocatorUsesMemory 33: [ OK ] HostAllocatorTest/1.StatefulAllocatorUsesMemory (0 ms) 33: [----------] 2 tests from HostAllocatorTest/1 (0 ms total) 33: 33: [----------] 2 tests from HostAllocatorTest/2, where TypeParam = gmx::BasicVector 33: [ RUN ] HostAllocatorTest/2.EmptyMemoryAlwaysWorks 33: [ OK ] HostAllocatorTest/2.EmptyMemoryAlwaysWorks (0 ms) 33: [ RUN ] HostAllocatorTest/2.StatefulAllocatorUsesMemory 33: [ OK ] HostAllocatorTest/2.StatefulAllocatorUsesMemory (0 ms) 33: [----------] 2 tests from HostAllocatorTest/2 (0 ms total) 33: 33: [----------] 2 tests from HostAllocatorTest/3, where TypeParam = gmx::test::MoveOnly 33: [ RUN ] HostAllocatorTest/3.EmptyMemoryAlwaysWorks 33: [ OK ] HostAllocatorTest/3.EmptyMemoryAlwaysWorks (0 ms) 33: [ RUN ] HostAllocatorTest/3.StatefulAllocatorUsesMemory 33: [ OK ] HostAllocatorTest/3.StatefulAllocatorUsesMemory (0 ms) 33: [----------] 2 tests from HostAllocatorTest/3 (0 ms total) 33: 33: [----------] 3 tests from HostAllocatorTestCopyable/0, where TypeParam = int 33: [ RUN ] HostAllocatorTestCopyable/0.VectorsWithDefaultHostAllocatorAlwaysWorks 33: [ OK ] HostAllocatorTestCopyable/0.VectorsWithDefaultHostAllocatorAlwaysWorks (0 ms) 33: [ RUN ] HostAllocatorTestCopyable/0.TransfersWithoutPinningWork 33: [ OK ] HostAllocatorTestCopyable/0.TransfersWithoutPinningWork (0 ms) 33: [ RUN ] HostAllocatorTestCopyable/0.FillInputAlsoWorksAfterCallingReserve 33: [ OK ] HostAllocatorTestCopyable/0.FillInputAlsoWorksAfterCallingReserve (0 ms) 33: [----------] 3 tests from HostAllocatorTestCopyable/0 (0 ms total) 33: 33: [----------] 3 tests from HostAllocatorTestCopyable/1, where TypeParam = float 33: [ RUN ] HostAllocatorTestCopyable/1.VectorsWithDefaultHostAllocatorAlwaysWorks 33: [ OK ] HostAllocatorTestCopyable/1.VectorsWithDefaultHostAllocatorAlwaysWorks (0 ms) 33: [ RUN ] HostAllocatorTestCopyable/1.TransfersWithoutPinningWork 33: [ OK ] HostAllocatorTestCopyable/1.TransfersWithoutPinningWork (0 ms) 33: [ RUN ] HostAllocatorTestCopyable/1.FillInputAlsoWorksAfterCallingReserve 33: [ OK ] HostAllocatorTestCopyable/1.FillInputAlsoWorksAfterCallingReserve (0 ms) 33: [----------] 3 tests from HostAllocatorTestCopyable/1 (0 ms total) 33: 33: [----------] 3 tests from HostAllocatorTestCopyable/2, where TypeParam = gmx::BasicVector 33: [ RUN ] HostAllocatorTestCopyable/2.VectorsWithDefaultHostAllocatorAlwaysWorks 33: [ OK ] HostAllocatorTestCopyable/2.VectorsWithDefaultHostAllocatorAlwaysWorks (0 ms) 33: [ RUN ] HostAllocatorTestCopyable/2.TransfersWithoutPinningWork 33: [ OK ] HostAllocatorTestCopyable/2.TransfersWithoutPinningWork (0 ms) 33: [ RUN ] HostAllocatorTestCopyable/2.FillInputAlsoWorksAfterCallingReserve 33: [ OK ] HostAllocatorTestCopyable/2.FillInputAlsoWorksAfterCallingReserve (0 ms) 33: [----------] 3 tests from HostAllocatorTestCopyable/2 (0 ms total) 33: 33: [----------] 5 tests from HostAllocatorTestNoMem/0, where TypeParam = int 33: [ RUN ] HostAllocatorTestNoMem/0.CreateVector 33: [ OK ] HostAllocatorTestNoMem/0.CreateVector (0 ms) 33: [ RUN ] HostAllocatorTestNoMem/0.MoveAssignment 33: [ OK ] HostAllocatorTestNoMem/0.MoveAssignment (0 ms) 33: [ RUN ] HostAllocatorTestNoMem/0.MoveConstruction 33: [ OK ] HostAllocatorTestNoMem/0.MoveConstruction (0 ms) 33: [ RUN ] HostAllocatorTestNoMem/0.Swap 33: [ OK ] HostAllocatorTestNoMem/0.Swap (0 ms) 33: [ RUN ] HostAllocatorTestNoMem/0.Comparison 33: [ OK ] HostAllocatorTestNoMem/0.Comparison (0 ms) 33: [----------] 5 tests from HostAllocatorTestNoMem/0 (0 ms total) 33: 33: [----------] 5 tests from HostAllocatorTestNoMem/1, where TypeParam = float 33: [ RUN ] HostAllocatorTestNoMem/1.CreateVector 33: [ OK ] HostAllocatorTestNoMem/1.CreateVector (0 ms) 33: [ RUN ] HostAllocatorTestNoMem/1.MoveAssignment 33: [ OK ] HostAllocatorTestNoMem/1.MoveAssignment (0 ms) 33: [ RUN ] HostAllocatorTestNoMem/1.MoveConstruction 33: [ OK ] HostAllocatorTestNoMem/1.MoveConstruction (0 ms) 33: [ RUN ] HostAllocatorTestNoMem/1.Swap 33: [ OK ] HostAllocatorTestNoMem/1.Swap (0 ms) 33: [ RUN ] HostAllocatorTestNoMem/1.Comparison 33: [ OK ] HostAllocatorTestNoMem/1.Comparison (0 ms) 33: [----------] 5 tests from HostAllocatorTestNoMem/1 (0 ms total) 33: 33: [----------] 5 tests from HostAllocatorTestNoMem/2, where TypeParam = gmx::BasicVector 33: [ RUN ] HostAllocatorTestNoMem/2.CreateVector 33: [ OK ] HostAllocatorTestNoMem/2.CreateVector (0 ms) 33: [ RUN ] HostAllocatorTestNoMem/2.MoveAssignment 33: [ OK ] HostAllocatorTestNoMem/2.MoveAssignment (0 ms) 33: [ RUN ] HostAllocatorTestNoMem/2.MoveConstruction 33: [ OK ] HostAllocatorTestNoMem/2.MoveConstruction (0 ms) 33: [ RUN ] HostAllocatorTestNoMem/2.Swap 33: [ OK ] HostAllocatorTestNoMem/2.Swap (0 ms) 33: [ RUN ] HostAllocatorTestNoMem/2.Comparison 33: [ OK ] HostAllocatorTestNoMem/2.Comparison (0 ms) 33: [----------] 5 tests from HostAllocatorTestNoMem/2 (0 ms total) 33: 33: [----------] 5 tests from HostAllocatorTestNoMem/3, where TypeParam = gmx::test::MoveOnly 33: [ RUN ] HostAllocatorTestNoMem/3.CreateVector 33: [ OK ] HostAllocatorTestNoMem/3.CreateVector (0 ms) 33: [ RUN ] HostAllocatorTestNoMem/3.MoveAssignment 33: [ OK ] HostAllocatorTestNoMem/3.MoveAssignment (0 ms) 33: [ RUN ] HostAllocatorTestNoMem/3.MoveConstruction 33: [ OK ] HostAllocatorTestNoMem/3.MoveConstruction (0 ms) 33: [ RUN ] HostAllocatorTestNoMem/3.Swap 33: [ OK ] HostAllocatorTestNoMem/3.Swap (0 ms) 33: [ RUN ] HostAllocatorTestNoMem/3.Comparison 33: [ OK ] HostAllocatorTestNoMem/3.Comparison (0 ms) 33: [----------] 5 tests from HostAllocatorTestNoMem/3 (0 ms total) 33: 33: [----------] 3 tests from HostAllocatorTestNoMemCopyable/0, where TypeParam = int 33: [ RUN ] HostAllocatorTestNoMemCopyable/0.CopyAssignment 33: [ OK ] HostAllocatorTestNoMemCopyable/0.CopyAssignment (0 ms) 33: [ RUN ] HostAllocatorTestNoMemCopyable/0.CopyConstruction 33: [ OK ] HostAllocatorTestNoMemCopyable/0.CopyConstruction (0 ms) 33: [ RUN ] HostAllocatorTestNoMemCopyable/0.CopyConstructionOfStructHoldingAHostVectorDoesNotCopyTheAllocator 33: [ OK ] HostAllocatorTestNoMemCopyable/0.CopyConstructionOfStructHoldingAHostVectorDoesNotCopyTheAllocator (0 ms) 33: [----------] 3 tests from HostAllocatorTestNoMemCopyable/0 (0 ms total) 33: 33: [----------] 3 tests from HostAllocatorTestNoMemCopyable/1, where TypeParam = float 33: [ RUN ] HostAllocatorTestNoMemCopyable/1.CopyAssignment 33: [ OK ] HostAllocatorTestNoMemCopyable/1.CopyAssignment (0 ms) 33: [ RUN ] HostAllocatorTestNoMemCopyable/1.CopyConstruction 33: [ OK ] HostAllocatorTestNoMemCopyable/1.CopyConstruction (0 ms) 33: [ RUN ] HostAllocatorTestNoMemCopyable/1.CopyConstructionOfStructHoldingAHostVectorDoesNotCopyTheAllocator 33: [ OK ] HostAllocatorTestNoMemCopyable/1.CopyConstructionOfStructHoldingAHostVectorDoesNotCopyTheAllocator (0 ms) 33: [----------] 3 tests from HostAllocatorTestNoMemCopyable/1 (0 ms total) 33: 33: [----------] 3 tests from HostAllocatorTestNoMemCopyable/2, where TypeParam = gmx::BasicVector 33: [ RUN ] HostAllocatorTestNoMemCopyable/2.CopyAssignment 33: [ OK ] HostAllocatorTestNoMemCopyable/2.CopyAssignment (0 ms) 33: [ RUN ] HostAllocatorTestNoMemCopyable/2.CopyConstruction 33: [ OK ] HostAllocatorTestNoMemCopyable/2.CopyConstruction (0 ms) 33: [ RUN ] HostAllocatorTestNoMemCopyable/2.CopyConstructionOfStructHoldingAHostVectorDoesNotCopyTheAllocator 33: [ OK ] HostAllocatorTestNoMemCopyable/2.CopyConstructionOfStructHoldingAHostVectorDoesNotCopyTheAllocator (0 ms) 33: [----------] 3 tests from HostAllocatorTestNoMemCopyable/2 (0 ms total) 33: 33: [----------] 1 test from HostAllocatorUntypedTest 33: [ RUN ] HostAllocatorUntypedTest.Comparison 33: [ OK ] HostAllocatorUntypedTest.Comparison (0 ms) 33: [----------] 1 test from HostAllocatorUntypedTest (0 ms total) 33: 33: [----------] 4 tests from AllocatorTest/0, where TypeParam = gmx::Allocator 33: [ RUN ] AllocatorTest/0.AllocatorAlignAllocatesWithAlignment 33: [ OK ] AllocatorTest/0.AllocatorAlignAllocatesWithAlignment (0 ms) 33: [ RUN ] AllocatorTest/0.VectorAllocatesAndResizesWithAlignment 33: [ OK ] AllocatorTest/0.VectorAllocatesAndResizesWithAlignment (0 ms) 33: [ RUN ] AllocatorTest/0.VectorAllocatesAndReservesWithAlignment 33: [ OK ] AllocatorTest/0.VectorAllocatesAndReservesWithAlignment (0 ms) 33: [ RUN ] AllocatorTest/0.Move 33: [ OK ] AllocatorTest/0.Move (0 ms) 33: [----------] 4 tests from AllocatorTest/0 (0 ms total) 33: 33: [----------] 4 tests from AllocatorTest/1, where TypeParam = gmx::Allocator 33: [ RUN ] AllocatorTest/1.AllocatorAlignAllocatesWithAlignment 33: [ OK ] AllocatorTest/1.AllocatorAlignAllocatesWithAlignment (0 ms) 33: [ RUN ] AllocatorTest/1.VectorAllocatesAndResizesWithAlignment 33: [ OK ] AllocatorTest/1.VectorAllocatesAndResizesWithAlignment (0 ms) 33: [ RUN ] AllocatorTest/1.VectorAllocatesAndReservesWithAlignment 33: [ OK ] AllocatorTest/1.VectorAllocatesAndReservesWithAlignment (0 ms) 33: [ RUN ] AllocatorTest/1.Move 33: [ OK ] AllocatorTest/1.Move (0 ms) 33: [----------] 4 tests from AllocatorTest/1 (0 ms total) 33: 33: [----------] 4 tests from AllocatorTest/2, where TypeParam = gmx::Allocator, gmx::HostAllocationPolicy> 33: [ RUN ] AllocatorTest/2.AllocatorAlignAllocatesWithAlignment 33: [ OK ] AllocatorTest/2.AllocatorAlignAllocatesWithAlignment (0 ms) 33: [ RUN ] AllocatorTest/2.VectorAllocatesAndResizesWithAlignment 33: [ OK ] AllocatorTest/2.VectorAllocatesAndResizesWithAlignment (1 ms) 33: [ RUN ] AllocatorTest/2.VectorAllocatesAndReservesWithAlignment 33: [ OK ] AllocatorTest/2.VectorAllocatesAndReservesWithAlignment (0 ms) 33: [ RUN ] AllocatorTest/2.Move 33: [ OK ] AllocatorTest/2.Move (0 ms) 33: [----------] 4 tests from AllocatorTest/2 (1 ms total) 33: 33: [----------] 4 tests from AllocatorTest/3, where TypeParam = gmx::Allocator 33: [ RUN ] AllocatorTest/3.AllocatorAlignAllocatesWithAlignment 33: [ OK ] AllocatorTest/3.AllocatorAlignAllocatesWithAlignment (0 ms) 33: [ RUN ] AllocatorTest/3.VectorAllocatesAndResizesWithAlignment 33: [ OK ] AllocatorTest/3.VectorAllocatesAndResizesWithAlignment (0 ms) 33: [ RUN ] AllocatorTest/3.VectorAllocatesAndReservesWithAlignment 33: [ OK ] AllocatorTest/3.VectorAllocatesAndReservesWithAlignment (0 ms) 33: [ RUN ] AllocatorTest/3.Move 33: [ OK ] AllocatorTest/3.Move (0 ms) 33: [----------] 4 tests from AllocatorTest/3 (0 ms total) 33: 33: [----------] Global test environment tear-down 33: [==========] 67 tests from 22 test suites ran. (5 ms total) 33: [ PASSED ] 67 tests. 33/92 Test #33: GpuUtilsUnitTests ......................... Passed 0.14 sec test 34 Start 34: HardwareUnitTests 34: Test command: /build/reproducible-path/gromacs-2025.1/build/basic/bin/hardware-test "--gtest_output=xml:/build/reproducible-path/gromacs-2025.1/build/basic/Testing/Temporary/HardwareUnitTests.xml" 34: Working Directory: /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/hardware/tests 34: Test timeout computed to be: 30 34: [==========] Running 22 tests from 10 test suites. 34: [----------] Global test environment set-up. 34: [----------] 1 test from CpuInfoTest 34: [ RUN ] CpuInfoTest.SupportLevel 34: [ OK ] CpuInfoTest.SupportLevel (0 ms) 34: [----------] 1 test from CpuInfoTest (0 ms total) 34: 34: [----------] 4 tests from HardwareTopologyTest 34: [ RUN ] HardwareTopologyTest.Execute 34: [ OK ] HardwareTopologyTest.Execute (48 ms) 34: [ RUN ] HardwareTopologyTest.HwlocExecute 34: [ OK ] HardwareTopologyTest.HwlocExecute (46 ms) 34: [ RUN ] HardwareTopologyTest.ProcessorSelfconsistency 34: [ OK ] HardwareTopologyTest.ProcessorSelfconsistency (47 ms) 34: [ RUN ] HardwareTopologyTest.NumaCacheSelfconsistency 34: [ OK ] HardwareTopologyTest.NumaCacheSelfconsistency (46 ms) 34: [----------] 4 tests from HardwareTopologyTest (190 ms total) 34: 34: [----------] 1 test from DevicesManagerTest 34: [ RUN ] DevicesManagerTest.Serialization 34: [ OK ] DevicesManagerTest.Serialization (0 ms) 34: [ DISABLED ] DevicesManagerTest.DISABLED_DetectsUuid 34: [----------] 1 test from DevicesManagerTest (0 ms total) 34: 34: [----------] 1 test from UuidStringTest 34: [ RUN ] UuidStringTest.Works 34: [ OK ] UuidStringTest.Works (0 ms) 34: [----------] 1 test from UuidStringTest (0 ms total) 34: 34: [----------] 5 tests from XeonE52620/MockHardwareTopologyTest 34: [ RUN ] XeonE52620/MockHardwareTopologyTest.DetectsHardware/0 34: [ OK ] XeonE52620/MockHardwareTopologyTest.DetectsHardware/0 (11 ms) 34: [ RUN ] XeonE52620/MockHardwareTopologyTest.DetectsHardware/1 34: [ OK ] XeonE52620/MockHardwareTopologyTest.DetectsHardware/1 (4 ms) 34: [ RUN ] XeonE52620/MockHardwareTopologyTest.DetectsHardware/2 34: [ OK ] XeonE52620/MockHardwareTopologyTest.DetectsHardware/2 (4 ms) 34: [ RUN ] XeonE52620/MockHardwareTopologyTest.DetectsHardware/3 34: [ OK ] XeonE52620/MockHardwareTopologyTest.DetectsHardware/3 (4 ms) 34: [ RUN ] XeonE52620/MockHardwareTopologyTest.DetectsHardware/4 34: [ OK ] XeonE52620/MockHardwareTopologyTest.DetectsHardware/4 (4 ms) 34: [----------] 5 tests from XeonE52620/MockHardwareTopologyTest (32 ms total) 34: 34: [----------] 5 tests from Xeon4116/MockHardwareTopologyTest 34: [ RUN ] Xeon4116/MockHardwareTopologyTest.DetectsHardware/0 34: [ OK ] Xeon4116/MockHardwareTopologyTest.DetectsHardware/0 (12 ms) 34: [ RUN ] Xeon4116/MockHardwareTopologyTest.DetectsHardware/1 34: [ OK ] Xeon4116/MockHardwareTopologyTest.DetectsHardware/1 (4 ms) 34: [ RUN ] Xeon4116/MockHardwareTopologyTest.DetectsHardware/2 34: [ OK ] Xeon4116/MockHardwareTopologyTest.DetectsHardware/2 (4 ms) 34: [ RUN ] Xeon4116/MockHardwareTopologyTest.DetectsHardware/3 34: [ OK ] Xeon4116/MockHardwareTopologyTest.DetectsHardware/3 (3 ms) 34: [ RUN ] Xeon4116/MockHardwareTopologyTest.DetectsHardware/4 34: [ OK ] Xeon4116/MockHardwareTopologyTest.DetectsHardware/4 (4 ms) 34: [----------] 5 tests from Xeon4116/MockHardwareTopologyTest (32 ms total) 34: 34: [----------] 2 tests from Core12900K/MockHardwareTopologyTest 34: [ RUN ] Core12900K/MockHardwareTopologyTest.DetectsHardware/0 34: [ OK ] Core12900K/MockHardwareTopologyTest.DetectsHardware/0 (6 ms) 34: [ RUN ] Core12900K/MockHardwareTopologyTest.DetectsHardware/1 34: [ OK ] Core12900K/MockHardwareTopologyTest.DetectsHardware/1 (6 ms) 34: [----------] 2 tests from Core12900K/MockHardwareTopologyTest (15 ms total) 34: 34: [----------] 1 test from Core12900K/MockHardwareTopologySpecialSystemTest 34: [ RUN ] Core12900K/MockHardwareTopologySpecialSystemTest.DetectsHardware/0 34: [ OK ] Core12900K/MockHardwareTopologySpecialSystemTest.DetectsHardware/0 (15 ms) 34: [----------] 1 test from Core12900K/MockHardwareTopologySpecialSystemTest (16 ms total) 34: 34: [----------] 1 test from Power9/MockHardwareTopologySpecialSystemTest 34: [ RUN ] Power9/MockHardwareTopologySpecialSystemTest.DetectsHardware/0 34: [ OK ] Power9/MockHardwareTopologySpecialSystemTest.DetectsHardware/0 (25 ms) 34: [----------] 1 test from Power9/MockHardwareTopologySpecialSystemTest (26 ms total) 34: 34: [----------] 1 test from A64fx/MockHardwareTopologySpecialSystemTest 34: [ RUN ] A64fx/MockHardwareTopologySpecialSystemTest.DetectsHardware/0 34: [ OK ] A64fx/MockHardwareTopologySpecialSystemTest.DetectsHardware/0 (39 ms) 34: [----------] 1 test from A64fx/MockHardwareTopologySpecialSystemTest (41 ms total) 34: 34: [----------] Global test environment tear-down 34: [==========] 22 tests from 10 test suites ran. (356 ms total) 34: [ PASSED ] 22 tests. 34: 34: YOU HAVE 1 DISABLED TEST 34: 34/92 Test #34: HardwareUnitTests ......................... Passed 0.44 sec test 35 Start 35: MathUnitTests 35: Test command: /build/reproducible-path/gromacs-2025.1/build/basic/bin/math-test "--gtest_output=xml:/build/reproducible-path/gromacs-2025.1/build/basic/Testing/Temporary/MathUnitTests.xml" 35: Working Directory: /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/math/tests 35: Test timeout computed to be: 30 35: [==========] Running 328 tests from 41 test suites. 35: [----------] Global test environment set-up. 35: [----------] 1 test from EmptyArrayRefWithPaddingTest 35: [ RUN ] EmptyArrayRefWithPaddingTest.IsEmpty 35: [ OK ] EmptyArrayRefWithPaddingTest.IsEmpty (0 ms) 35: [----------] 1 test from EmptyArrayRefWithPaddingTest (0 ms total) 35: 35: [----------] 1 test from EmptyConstArrayRefWithPaddingTest 35: [ RUN ] EmptyConstArrayRefWithPaddingTest.IsEmpty 35: [ OK ] EmptyConstArrayRefWithPaddingTest.IsEmpty (0 ms) 35: [----------] 1 test from EmptyConstArrayRefWithPaddingTest (0 ms total) 35: 35: [----------] 2 tests from ArrayRefWithPaddingTest/0, where TypeParam = gmx::ArrayRefWithPadding 35: [ RUN ] ArrayRefWithPaddingTest/0.AssignFromPaddedVectorWorks 35: [ OK ] ArrayRefWithPaddingTest/0.AssignFromPaddedVectorWorks (0 ms) 35: [ RUN ] ArrayRefWithPaddingTest/0.ConstructFromPointersWorks 35: [ OK ] ArrayRefWithPaddingTest/0.ConstructFromPointersWorks (0 ms) 35: [----------] 2 tests from ArrayRefWithPaddingTest/0 (0 ms total) 35: 35: [----------] 2 tests from ArrayRefWithPaddingTest/1, where TypeParam = gmx::ArrayRefWithPadding 35: [ RUN ] ArrayRefWithPaddingTest/1.AssignFromPaddedVectorWorks 35: [ OK ] ArrayRefWithPaddingTest/1.AssignFromPaddedVectorWorks (0 ms) 35: [ RUN ] ArrayRefWithPaddingTest/1.ConstructFromPointersWorks 35: [ OK ] ArrayRefWithPaddingTest/1.ConstructFromPointersWorks (0 ms) 35: [----------] 2 tests from ArrayRefWithPaddingTest/1 (0 ms total) 35: 35: [----------] 2 tests from ArrayRefWithPaddingTest/2, where TypeParam = gmx::ArrayRefWithPadding 35: [ RUN ] ArrayRefWithPaddingTest/2.AssignFromPaddedVectorWorks 35: [ OK ] ArrayRefWithPaddingTest/2.AssignFromPaddedVectorWorks (0 ms) 35: [ RUN ] ArrayRefWithPaddingTest/2.ConstructFromPointersWorks 35: [ OK ] ArrayRefWithPaddingTest/2.ConstructFromPointersWorks (0 ms) 35: [----------] 2 tests from ArrayRefWithPaddingTest/2 (0 ms total) 35: 35: [----------] 2 tests from InvertBoxMatrixTest 35: [ RUN ] InvertBoxMatrixTest.IdentityIsImpotent 35: [ OK ] InvertBoxMatrixTest.IdentityIsImpotent (0 ms) 35: [ RUN ] InvertBoxMatrixTest.ComputesInverseInPlace 35: [ OK ] InvertBoxMatrixTest.ComputesInverseInPlace (0 ms) 35: [----------] 2 tests from InvertBoxMatrixTest (0 ms total) 35: 35: [----------] 8 tests from ComplexNumberTest 35: [ RUN ] ComplexNumberTest.RealComplexMultiply 35: [ OK ] ComplexNumberTest.RealComplexMultiply (2 ms) 35: [ RUN ] ComplexNumberTest.RealComplexExp 35: [ OK ] ComplexNumberTest.RealComplexExp (0 ms) 35: [ RUN ] ComplexNumberTest.ComplexAdd 35: [ OK ] ComplexNumberTest.ComplexAdd (1 ms) 35: [ RUN ] ComplexNumberTest.ComplexSubtract 35: [ OK ] ComplexNumberTest.ComplexSubtract (1 ms) 35: [ RUN ] ComplexNumberTest.ComplexMultiply 35: [ OK ] ComplexNumberTest.ComplexMultiply (0 ms) 35: [ RUN ] ComplexNumberTest.ComplexDivision 35: [ OK ] ComplexNumberTest.ComplexDivision (0 ms) 35: [ RUN ] ComplexNumberTest.ComplexConjugate 35: [ OK ] ComplexNumberTest.ComplexConjugate (0 ms) 35: [ RUN ] ComplexNumberTest.ComplexAbs2 35: [ OK ] ComplexNumberTest.ComplexAbs2 (0 ms) 35: [----------] 8 tests from ComplexNumberTest (9 ms total) 35: 35: [----------] 11 tests from TranslateAndScaleTest 35: [ RUN ] TranslateAndScaleTest.identityTransformation 35: [ OK ] TranslateAndScaleTest.identityTransformation (0 ms) 35: [ RUN ] TranslateAndScaleTest.translationWithIdentityScaling 35: [ OK ] TranslateAndScaleTest.translationWithIdentityScaling (0 ms) 35: [ RUN ] TranslateAndScaleTest.scalingWithZeroTranslation 35: [ OK ] TranslateAndScaleTest.scalingWithZeroTranslation (0 ms) 35: [ RUN ] TranslateAndScaleTest.translationAndScalingNonTrivial 35: [ OK ] TranslateAndScaleTest.translationAndScalingNonTrivial (0 ms) 35: [ RUN ] TranslateAndScaleTest.translationAndScalingNonTrivialSingeVector 35: [ OK ] TranslateAndScaleTest.translationAndScalingNonTrivialSingeVector (0 ms) 35: [ RUN ] TranslateAndScaleTest.scalingIdentity 35: [ OK ] TranslateAndScaleTest.scalingIdentity (0 ms) 35: [ RUN ] TranslateAndScaleTest.scalingNonTrivial 35: [ OK ] TranslateAndScaleTest.scalingNonTrivial (0 ms) 35: [ RUN ] TranslateAndScaleTest.scalingNonTrivialSingleVector 35: [ OK ] TranslateAndScaleTest.scalingNonTrivialSingleVector (0 ms) 35: [ RUN ] TranslateAndScaleTest.scalingInverseNoZero 35: [ OK ] TranslateAndScaleTest.scalingInverseNoZero (0 ms) 35: [ RUN ] TranslateAndScaleTest.scalingInverseWithOneScaleDimensionZero 35: [ OK ] TranslateAndScaleTest.scalingInverseWithOneScaleDimensionZero (0 ms) 35: [ RUN ] TranslateAndScaleTest.scalingInverseWithOneScaleDimensionZeroSingleVector 35: [ OK ] TranslateAndScaleTest.scalingInverseWithOneScaleDimensionZeroSingleVector (0 ms) 35: [----------] 11 tests from TranslateAndScaleTest (0 ms total) 35: 35: [----------] 3 tests from AffineTransformationTest 35: [ RUN ] AffineTransformationTest.identityTransformYieldsSameVectors 35: [ OK ] AffineTransformationTest.identityTransformYieldsSameVectors (0 ms) 35: [ RUN ] AffineTransformationTest.applyTransformationToVectors 35: [ OK ] AffineTransformationTest.applyTransformationToVectors (0 ms) 35: [ RUN ] AffineTransformationTest.retrieveGradient 35: [ OK ] AffineTransformationTest.retrieveGradient (0 ms) 35: [----------] 3 tests from AffineTransformationTest (0 ms total) 35: 35: [----------] 14 tests from DensitySimilarityTest 35: [ RUN ] DensitySimilarityTest.InnerProductIsCorrect 35: [ OK ] DensitySimilarityTest.InnerProductIsCorrect (0 ms) 35: [ RUN ] DensitySimilarityTest.InnerProductGradientIsCorrect 35: [ OK ] DensitySimilarityTest.InnerProductGradientIsCorrect (0 ms) 35: [ RUN ] DensitySimilarityTest.GradientThrowsIfDensitiesDontMatch 35: [ OK ] DensitySimilarityTest.GradientThrowsIfDensitiesDontMatch (0 ms) 35: [ RUN ] DensitySimilarityTest.SimilarityThrowsIfDensitiesDontMatch 35: [ OK ] DensitySimilarityTest.SimilarityThrowsIfDensitiesDontMatch (0 ms) 35: [ RUN ] DensitySimilarityTest.CopiedMeasureInnerProductIsCorrect 35: [ OK ] DensitySimilarityTest.CopiedMeasureInnerProductIsCorrect (0 ms) 35: [ RUN ] DensitySimilarityTest.RelativeEntropyOfSameDensityIsZero 35: [ OK ] DensitySimilarityTest.RelativeEntropyOfSameDensityIsZero (0 ms) 35: [ RUN ] DensitySimilarityTest.RelativeEntropyIsCorrect 35: [ OK ] DensitySimilarityTest.RelativeEntropyIsCorrect (0 ms) 35: [ RUN ] DensitySimilarityTest.RelativeEntropyGradientIsCorrect 35: [ OK ] DensitySimilarityTest.RelativeEntropyGradientIsCorrect (3 ms) 35: [ RUN ] DensitySimilarityTest.CrossCorrelationIsOne 35: [ OK ] DensitySimilarityTest.CrossCorrelationIsOne (295 ms) 35: [ RUN ] DensitySimilarityTest.CrossCorrelationIsMinusOneWhenAntiCorrelated 35: [ OK ] DensitySimilarityTest.CrossCorrelationIsMinusOneWhenAntiCorrelated (305 ms) 35: [ RUN ] DensitySimilarityTest.CrossCorrelationGradientIsZeroWhenCorrelated 35: [ OK ] DensitySimilarityTest.CrossCorrelationGradientIsZeroWhenCorrelated (13 ms) 35: [ RUN ] DensitySimilarityTest.CrossCorrelationGradientIsCorrect 35: [ OK ] DensitySimilarityTest.CrossCorrelationGradientIsCorrect (1 ms) 35: [ RUN ] DensitySimilarityTest.NormalizationCorrect 35: [ OK ] DensitySimilarityTest.NormalizationCorrect (0 ms) 35: [ RUN ] DensitySimilarityTest.NormalizationAllNonPositive 35: [ OK ] DensitySimilarityTest.NormalizationAllNonPositive (0 ms) 35: [----------] 14 tests from DensitySimilarityTest (620 ms total) 35: 35: [----------] 6 tests from StructureSimilarityTest 35: [ RUN ] StructureSimilarityTest.StructureComparedToSelfHasZeroRMSD 35: [ OK ] StructureSimilarityTest.StructureComparedToSelfHasZeroRMSD (0 ms) 35: [ RUN ] StructureSimilarityTest.StructureComparedToSelfHasZeroRho 35: [ OK ] StructureSimilarityTest.StructureComparedToSelfHasZeroRho (0 ms) 35: [ RUN ] StructureSimilarityTest.YieldsCorrectRMSD 35: [ OK ] StructureSimilarityTest.YieldsCorrectRMSD (0 ms) 35: [ RUN ] StructureSimilarityTest.YieldsCorrectRho 35: [ OK ] StructureSimilarityTest.YieldsCorrectRho (0 ms) 35: [ RUN ] StructureSimilarityTest.YieldsCorrectRMSDWithIndex 35: [ OK ] StructureSimilarityTest.YieldsCorrectRMSDWithIndex (0 ms) 35: [ RUN ] StructureSimilarityTest.YieldsCorrectRhoWidthIndex 35: [ OK ] StructureSimilarityTest.YieldsCorrectRhoWidthIndex (0 ms) 35: [----------] 6 tests from StructureSimilarityTest (0 ms total) 35: 35: [----------] 8 tests from ExponentialMovingAverage 35: [ RUN ] ExponentialMovingAverage.ThrowsWhenLagTimeIsZero 35: [ OK ] ExponentialMovingAverage.ThrowsWhenLagTimeIsZero (0 ms) 35: [ RUN ] ExponentialMovingAverage.ThrowsWhenLagTimeIsNegative 35: [ OK ] ExponentialMovingAverage.ThrowsWhenLagTimeIsNegative (0 ms) 35: [ RUN ] ExponentialMovingAverage.LagTimeOneYieldsInstantaneousValue 35: [ OK ] ExponentialMovingAverage.LagTimeOneYieldsInstantaneousValue (0 ms) 35: [ RUN ] ExponentialMovingAverage.YieldsCorrectValue 35: [ OK ] ExponentialMovingAverage.YieldsCorrectValue (0 ms) 35: [ RUN ] ExponentialMovingAverage.SetAverageCorrectly 35: [ OK ] ExponentialMovingAverage.SetAverageCorrectly (0 ms) 35: [ RUN ] ExponentialMovingAverage.DeterminesCorrectlyIfIncreasing 35: [ OK ] ExponentialMovingAverage.DeterminesCorrectlyIfIncreasing (0 ms) 35: [ RUN ] ExponentialMovingAverage.InverseLagTimeCorrect 35: [ OK ] ExponentialMovingAverage.InverseLagTimeCorrect (0 ms) 35: [ RUN ] ExponentialMovingAverage.RoundTripAsKeyValueTree 35: [ OK ] ExponentialMovingAverage.RoundTripAsKeyValueTree (0 ms) 35: [----------] 8 tests from ExponentialMovingAverage (0 ms total) 35: 35: [----------] 21 tests from FunctionTest 35: [ RUN ] FunctionTest.StaticLog2 35: [ OK ] FunctionTest.StaticLog2 (0 ms) 35: [ RUN ] FunctionTest.Log2I32Bit 35: [ OK ] FunctionTest.Log2I32Bit (0 ms) 35: [ RUN ] FunctionTest.Log2I64Bit 35: [ OK ] FunctionTest.Log2I64Bit (0 ms) 35: [ RUN ] FunctionTest.GreatestCommonDivisor 35: [ OK ] FunctionTest.GreatestCommonDivisor (0 ms) 35: [ RUN ] FunctionTest.InvsqrtFloat 35: [ OK ] FunctionTest.InvsqrtFloat (0 ms) 35: [ RUN ] FunctionTest.InvsqrtDouble 35: [ OK ] FunctionTest.InvsqrtDouble (0 ms) 35: [ RUN ] FunctionTest.InvsqrtInteger 35: [ OK ] FunctionTest.InvsqrtInteger (0 ms) 35: [ RUN ] FunctionTest.InvcbrtFloat 35: [ OK ] FunctionTest.InvcbrtFloat (0 ms) 35: [ RUN ] FunctionTest.InvcbrtDouble 35: [ OK ] FunctionTest.InvcbrtDouble (0 ms) 35: [ RUN ] FunctionTest.InvcbrtInteger 35: [ OK ] FunctionTest.InvcbrtInteger (0 ms) 35: [ RUN ] FunctionTest.SixthrootFloat 35: [ OK ] FunctionTest.SixthrootFloat (0 ms) 35: [ RUN ] FunctionTest.SixthrootDouble 35: [ OK ] FunctionTest.SixthrootDouble (0 ms) 35: [ RUN ] FunctionTest.SixthrootInteger 35: [ OK ] FunctionTest.SixthrootInteger (0 ms) 35: [ RUN ] FunctionTest.InvsixthrootFloat 35: [ OK ] FunctionTest.InvsixthrootFloat (0 ms) 35: [ RUN ] FunctionTest.InvsixthrootDouble 35: [ OK ] FunctionTest.InvsixthrootDouble (0 ms) 35: [ RUN ] FunctionTest.InvsixthrootInteger 35: [ OK ] FunctionTest.InvsixthrootInteger (0 ms) 35: [ RUN ] FunctionTest.Powers 35: [ OK ] FunctionTest.Powers (0 ms) 35: [ RUN ] FunctionTest.ErfInvFloat 35: [ OK ] FunctionTest.ErfInvFloat (0 ms) 35: [ RUN ] FunctionTest.ErfInvDouble 35: [ OK ] FunctionTest.ErfInvDouble (0 ms) 35: [ RUN ] FunctionTest.ErfAndErfInvAreInversesFloat 35: [ OK ] FunctionTest.ErfAndErfInvAreInversesFloat (0 ms) 35: [ RUN ] FunctionTest.ErfAndErfInvAreInversesDouble 35: [ OK ] FunctionTest.ErfAndErfInvAreInversesDouble (0 ms) 35: [----------] 21 tests from FunctionTest (12 ms total) 35: 35: [----------] 2 tests from FunctionTestIntegerTypes/0, where TypeParam = signed char 35: [ RUN ] FunctionTestIntegerTypes/0.IsPowerOfTwo 35: [ OK ] FunctionTestIntegerTypes/0.IsPowerOfTwo (0 ms) 35: [ RUN ] FunctionTestIntegerTypes/0.DivideRoundUp 35: [ OK ] FunctionTestIntegerTypes/0.DivideRoundUp (0 ms) 35: [----------] 2 tests from FunctionTestIntegerTypes/0 (0 ms total) 35: 35: [----------] 2 tests from FunctionTestIntegerTypes/1, where TypeParam = unsigned char 35: [ RUN ] FunctionTestIntegerTypes/1.IsPowerOfTwo 35: [ OK ] FunctionTestIntegerTypes/1.IsPowerOfTwo (0 ms) 35: [ RUN ] FunctionTestIntegerTypes/1.DivideRoundUp 35: [ OK ] FunctionTestIntegerTypes/1.DivideRoundUp (0 ms) 35: [----------] 2 tests from FunctionTestIntegerTypes/1 (0 ms total) 35: 35: [----------] 2 tests from FunctionTestIntegerTypes/2, where TypeParam = short 35: [ RUN ] FunctionTestIntegerTypes/2.IsPowerOfTwo 35: [ OK ] FunctionTestIntegerTypes/2.IsPowerOfTwo (0 ms) 35: [ RUN ] FunctionTestIntegerTypes/2.DivideRoundUp 35: [ OK ] FunctionTestIntegerTypes/2.DivideRoundUp (0 ms) 35: [----------] 2 tests from FunctionTestIntegerTypes/2 (0 ms total) 35: 35: [----------] 2 tests from FunctionTestIntegerTypes/3, where TypeParam = unsigned short 35: [ RUN ] FunctionTestIntegerTypes/3.IsPowerOfTwo 35: [ OK ] FunctionTestIntegerTypes/3.IsPowerOfTwo (0 ms) 35: [ RUN ] FunctionTestIntegerTypes/3.DivideRoundUp 35: [ OK ] FunctionTestIntegerTypes/3.DivideRoundUp (0 ms) 35: [----------] 2 tests from FunctionTestIntegerTypes/3 (0 ms total) 35: 35: [----------] 2 tests from FunctionTestIntegerTypes/4, where TypeParam = int 35: [ RUN ] FunctionTestIntegerTypes/4.IsPowerOfTwo 35: [ OK ] FunctionTestIntegerTypes/4.IsPowerOfTwo (0 ms) 35: [ RUN ] FunctionTestIntegerTypes/4.DivideRoundUp 35: [ OK ] FunctionTestIntegerTypes/4.DivideRoundUp (0 ms) 35: [----------] 2 tests from FunctionTestIntegerTypes/4 (0 ms total) 35: 35: [----------] 2 tests from FunctionTestIntegerTypes/5, where TypeParam = unsigned int 35: [ RUN ] FunctionTestIntegerTypes/5.IsPowerOfTwo 35: [ OK ] FunctionTestIntegerTypes/5.IsPowerOfTwo (0 ms) 35: [ RUN ] FunctionTestIntegerTypes/5.DivideRoundUp 35: [ OK ] FunctionTestIntegerTypes/5.DivideRoundUp (0 ms) 35: [----------] 2 tests from FunctionTestIntegerTypes/5 (0 ms total) 35: 35: [----------] 2 tests from FunctionTestIntegerTypes/6, where TypeParam = long 35: [ RUN ] FunctionTestIntegerTypes/6.IsPowerOfTwo 35: [ OK ] FunctionTestIntegerTypes/6.IsPowerOfTwo (0 ms) 35: [ RUN ] FunctionTestIntegerTypes/6.DivideRoundUp 35: [ OK ] FunctionTestIntegerTypes/6.DivideRoundUp (0 ms) 35: [----------] 2 tests from FunctionTestIntegerTypes/6 (0 ms total) 35: 35: [----------] 2 tests from FunctionTestIntegerTypes/7, where TypeParam = unsigned long 35: [ RUN ] FunctionTestIntegerTypes/7.IsPowerOfTwo 35: [ OK ] FunctionTestIntegerTypes/7.IsPowerOfTwo (0 ms) 35: [ RUN ] FunctionTestIntegerTypes/7.DivideRoundUp 35: [ OK ] FunctionTestIntegerTypes/7.DivideRoundUp (0 ms) 35: [----------] 2 tests from FunctionTestIntegerTypes/7 (0 ms total) 35: 35: [----------] 4 tests from GaussianOn1DLattice 35: [ RUN ] GaussianOn1DLattice.sumsCloseToOne 35: [ OK ] GaussianOn1DLattice.sumsCloseToOne (0 ms) 35: [ RUN ] GaussianOn1DLattice.isCorrect 35: [ OK ] GaussianOn1DLattice.isCorrect (0 ms) 35: [ RUN ] GaussianOn1DLattice.complementaryAmplitudesSumToZero 35: [ OK ] GaussianOn1DLattice.complementaryAmplitudesSumToZero (0 ms) 35: [ RUN ] GaussianOn1DLattice.doesNotOverflowForLargeRange 35: [ OK ] GaussianOn1DLattice.doesNotOverflowForLargeRange (0 ms) 35: [----------] 4 tests from GaussianOn1DLattice (0 ms total) 35: 35: [----------] 9 tests from GaussTransformTest 35: [ RUN ] GaussTransformTest.isZeroUponConstruction 35: [ OK ] GaussTransformTest.isZeroUponConstruction (0 ms) 35: [ RUN ] GaussTransformTest.isZeroAddingZeroAmplitudeGauss 35: [ OK ] GaussTransformTest.isZeroAddingZeroAmplitudeGauss (0 ms) 35: [ RUN ] GaussTransformTest.isZeroAfterSettingZero 35: [ OK ] GaussTransformTest.isZeroAfterSettingZero (0 ms) 35: [ RUN ] GaussTransformTest.isZeroWhenOutsideRangeinX 35: [ OK ] GaussTransformTest.isZeroWhenOutsideRangeinX (0 ms) 35: [ RUN ] GaussTransformTest.isZeroWhenOutsideRangeinY 35: [ OK ] GaussTransformTest.isZeroWhenOutsideRangeinY (0 ms) 35: [ RUN ] GaussTransformTest.isZeroWhenOutsideRangeinZ 35: [ OK ] GaussTransformTest.isZeroWhenOutsideRangeinZ (0 ms) 35: [ RUN ] GaussTransformTest.complementaryGaussAddToZero 35: [ OK ] GaussTransformTest.complementaryGaussAddToZero (0 ms) 35: [ RUN ] GaussTransformTest.centerGaussianInCubeHasExpectedValues 35: [ OK ] GaussTransformTest.centerGaussianInCubeHasExpectedValues (0 ms) 35: [ RUN ] GaussTransformTest.view 35: [ OK ] GaussTransformTest.view (0 ms) 35: [----------] 9 tests from GaussTransformTest (0 ms total) 35: 35: [----------] 3 tests from DensityFittingForce 35: [ RUN ] DensityFittingForce.isZeroWhenMatchingDensity 35: [ OK ] DensityFittingForce.isZeroWhenMatchingDensity (0 ms) 35: [ RUN ] DensityFittingForce.isZeroWhenMismatchingSameAllDirections 35: [ OK ] DensityFittingForce.isZeroWhenMismatchingSameAllDirections (0 ms) 35: [ RUN ] DensityFittingForce.pullsTowardsDerivative 35: [ OK ] DensityFittingForce.pullsTowardsDerivative (0 ms) 35: [----------] 3 tests from DensityFittingForce (0 ms total) 35: 35: [----------] 2 tests from InvertMatrixTest 35: [ RUN ] InvertMatrixTest.IdentityIsImpotent 35: [ OK ] InvertMatrixTest.IdentityIsImpotent (0 ms) 35: [ RUN ] InvertMatrixTest.ComputesInverse 35: [ OK ] InvertMatrixTest.ComputesInverse (0 ms) 35: [----------] 2 tests from InvertMatrixTest (0 ms total) 35: 35: [----------] 22 tests from MatrixTest 35: [ RUN ] MatrixTest.canSetFromArray 35: [ OK ] MatrixTest.canSetFromArray (0 ms) 35: [ RUN ] MatrixTest.canSetStaticallyFromList 35: [ OK ] MatrixTest.canSetStaticallyFromList (0 ms) 35: [ RUN ] MatrixTest.canConstructAndFill 35: [ OK ] MatrixTest.canConstructAndFill (0 ms) 35: [ RUN ] MatrixTest.canSetValues 35: [ OK ] MatrixTest.canSetValues (0 ms) 35: [ RUN ] MatrixTest.canCopyAssign 35: [ OK ] MatrixTest.canCopyAssign (0 ms) 35: [ RUN ] MatrixTest.canSwap 35: [ OK ] MatrixTest.canSwap (0 ms) 35: [ RUN ] MatrixTest.staticMultiDimArrayExtent 35: [ OK ] MatrixTest.staticMultiDimArrayExtent (0 ms) 35: [ RUN ] MatrixTest.canAddMatrix 35: [ OK ] MatrixTest.canAddMatrix (0 ms) 35: [ RUN ] MatrixTest.canSubstractMatrix 35: [ OK ] MatrixTest.canSubstractMatrix (0 ms) 35: [ RUN ] MatrixTest.canNegateMatrix 35: [ OK ] MatrixTest.canNegateMatrix (0 ms) 35: [ RUN ] MatrixTest.determinantWorks 35: [ OK ] MatrixTest.determinantWorks (0 ms) 35: [ RUN ] MatrixTest.noninvertableDeterminantIsZero 35: [ OK ] MatrixTest.noninvertableDeterminantIsZero (0 ms) 35: [ RUN ] MatrixTest.determinantOfDiagonalMatrix 35: [ OK ] MatrixTest.determinantOfDiagonalMatrix (0 ms) 35: [ RUN ] MatrixTest.traceWorks 35: [ OK ] MatrixTest.traceWorks (0 ms) 35: [ RUN ] MatrixTest.transposeWorks 35: [ OK ] MatrixTest.transposeWorks (0 ms) 35: [ RUN ] MatrixTest.transposeOfSymmetricMatrix 35: [ OK ] MatrixTest.transposeOfSymmetricMatrix (0 ms) 35: [ RUN ] MatrixTest.canCreateFromLegacyMatrix 35: [ OK ] MatrixTest.canCreateFromLegacyMatrix (0 ms) 35: [ RUN ] MatrixTest.canFillLegacyMatrix 35: [ OK ] MatrixTest.canFillLegacyMatrix (0 ms) 35: [ RUN ] MatrixTest.IdentityMatrix 35: [ OK ] MatrixTest.IdentityMatrix (0 ms) 35: [ RUN ] MatrixTest.MatrixMatrixInnerProduct 35: [ OK ] MatrixTest.MatrixMatrixInnerProduct (0 ms) 35: [ RUN ] MatrixTest.MatrixMatrixMultiplication 35: [ OK ] MatrixTest.MatrixMatrixMultiplication (0 ms) 35: [ RUN ] MatrixTest.MatrixVectorMultiplication 35: [ OK ] MatrixTest.MatrixVectorMultiplication (0 ms) 35: [----------] 22 tests from MatrixTest (0 ms total) 35: 35: [----------] 25 tests from MultiDimArrayTest 35: [ RUN ] MultiDimArrayTest.canConstructAndFillStatic 35: [ OK ] MultiDimArrayTest.canConstructAndFillStatic (0 ms) 35: [ RUN ] MultiDimArrayTest.canConstructAndFillDynamic 35: [ OK ] MultiDimArrayTest.canConstructAndFillDynamic (0 ms) 35: [ RUN ] MultiDimArrayTest.canSetValuesInStatic 35: [ OK ] MultiDimArrayTest.canSetValuesInStatic (0 ms) 35: [ RUN ] MultiDimArrayTest.canSetValuesInDynamic 35: [ OK ] MultiDimArrayTest.canSetValuesInDynamic (0 ms) 35: [ RUN ] MultiDimArrayTest.canMoveConstructStatic 35: [ OK ] MultiDimArrayTest.canMoveConstructStatic (0 ms) 35: [ RUN ] MultiDimArrayTest.canMoveConstructDynamic 35: [ OK ] MultiDimArrayTest.canMoveConstructDynamic (0 ms) 35: [ RUN ] MultiDimArrayTest.canMoveAssignStatic 35: [ OK ] MultiDimArrayTest.canMoveAssignStatic (0 ms) 35: [ RUN ] MultiDimArrayTest.canMoveAssignDynamic 35: [ OK ] MultiDimArrayTest.canMoveAssignDynamic (0 ms) 35: [ RUN ] MultiDimArrayTest.canCopyConstructStatic 35: [ OK ] MultiDimArrayTest.canCopyConstructStatic (0 ms) 35: [ RUN ] MultiDimArrayTest.canCopyConstructDynamic 35: [ OK ] MultiDimArrayTest.canCopyConstructDynamic (0 ms) 35: [ RUN ] MultiDimArrayTest.canCopyAssignStatic 35: [ OK ] MultiDimArrayTest.canCopyAssignStatic (0 ms) 35: [ RUN ] MultiDimArrayTest.canCopyAssignDynamic 35: [ OK ] MultiDimArrayTest.canCopyAssignDynamic (0 ms) 35: [ RUN ] MultiDimArrayTest.canSwapStatic 35: [ OK ] MultiDimArrayTest.canSwapStatic (0 ms) 35: [ RUN ] MultiDimArrayTest.canSwapDynamic 35: [ OK ] MultiDimArrayTest.canSwapDynamic (0 ms) 35: [ RUN ] MultiDimArrayTest.staticMultiDimArrayExtent 35: [ OK ] MultiDimArrayTest.staticMultiDimArrayExtent (0 ms) 35: [ RUN ] MultiDimArrayTest.dynamicMultiDimArrayExtent 35: [ OK ] MultiDimArrayTest.dynamicMultiDimArrayExtent (0 ms) 35: [ RUN ] MultiDimArrayTest.dynamicMultiDimArrayResizesToCorrectExtent 35: [ OK ] MultiDimArrayTest.dynamicMultiDimArrayResizesToCorrectExtent (0 ms) 35: [ RUN ] MultiDimArrayTest.dynamicMultiDimArrayResizeAndSetValue 35: [ OK ] MultiDimArrayTest.dynamicMultiDimArrayResizeAndSetValue (0 ms) 35: [ RUN ] MultiDimArrayTest.staticMultiDimArrayFromArray 35: [ OK ] MultiDimArrayTest.staticMultiDimArrayFromArray (0 ms) 35: [ RUN ] MultiDimArrayTest.conversionToView 35: [ OK ] MultiDimArrayTest.conversionToView (0 ms) 35: [ RUN ] MultiDimArrayTest.conversionToConstView 35: [ OK ] MultiDimArrayTest.conversionToConstView (0 ms) 35: [ RUN ] MultiDimArrayTest.viewBegin 35: [ OK ] MultiDimArrayTest.viewBegin (0 ms) 35: [ RUN ] MultiDimArrayTest.viewEnd 35: [ OK ] MultiDimArrayTest.viewEnd (0 ms) 35: [ RUN ] MultiDimArrayTest.constViewConstBegin 35: [ OK ] MultiDimArrayTest.constViewConstBegin (0 ms) 35: [ RUN ] MultiDimArrayTest.constViewConstEnd 35: [ OK ] MultiDimArrayTest.constViewConstEnd (0 ms) 35: [----------] 25 tests from MultiDimArrayTest (0 ms total) 35: 35: [----------] 4 tests from MultiDimArrayToMdSpanTest 35: [ RUN ] MultiDimArrayToMdSpanTest.convertsToMdSpan 35: [ OK ] MultiDimArrayToMdSpanTest.convertsToMdSpan (0 ms) 35: [ RUN ] MultiDimArrayToMdSpanTest.constArrayToMdSpan 35: [ OK ] MultiDimArrayToMdSpanTest.constArrayToMdSpan (0 ms) 35: [ RUN ] MultiDimArrayToMdSpanTest.nonConstArrayToConstMdSpan 35: [ OK ] MultiDimArrayToMdSpanTest.nonConstArrayToConstMdSpan (0 ms) 35: [ RUN ] MultiDimArrayToMdSpanTest.implicitConversionToMdSpan 35: [ OK ] MultiDimArrayToMdSpanTest.implicitConversionToMdSpan (0 ms) 35: [----------] 4 tests from MultiDimArrayToMdSpanTest (0 ms total) 35: 35: [----------] 9 tests from NelderMeadSimplexTest 35: [ RUN ] NelderMeadSimplexTest.BestVertex 35: [ OK ] NelderMeadSimplexTest.BestVertex (0 ms) 35: [ RUN ] NelderMeadSimplexTest.WorstVertex 35: [ OK ] NelderMeadSimplexTest.WorstVertex (0 ms) 35: [ RUN ] NelderMeadSimplexTest.SecondWorstValue 35: [ OK ] NelderMeadSimplexTest.SecondWorstValue (0 ms) 35: [ RUN ] NelderMeadSimplexTest.ReflectionPoint 35: [ OK ] NelderMeadSimplexTest.ReflectionPoint (0 ms) 35: [ RUN ] NelderMeadSimplexTest.EvaluateExpansionPoint 35: [ OK ] NelderMeadSimplexTest.EvaluateExpansionPoint (0 ms) 35: [ RUN ] NelderMeadSimplexTest.EvaluateContractionPoint 35: [ OK ] NelderMeadSimplexTest.EvaluateContractionPoint (0 ms) 35: [ RUN ] NelderMeadSimplexTest.SwapOutWorst 35: [ OK ] NelderMeadSimplexTest.SwapOutWorst (0 ms) 35: [ RUN ] NelderMeadSimplexTest.ShrinkSimplexPointsExceptBest 35: [ OK ] NelderMeadSimplexTest.ShrinkSimplexPointsExceptBest (0 ms) 35: [ RUN ] NelderMeadSimplexTest.OrientedLength 35: [ OK ] NelderMeadSimplexTest.OrientedLength (0 ms) 35: [----------] 9 tests from NelderMeadSimplexTest (0 ms total) 35: 35: [----------] 2 tests from NelderMead 35: [ RUN ] NelderMead.Optimizes2DFunctionCorrectly 35: [ OK ] NelderMead.Optimizes2DFunctionCorrectly (169 ms) 35: [ RUN ] NelderMead.Optimizes3DFunctorCorrectly 35: [ OK ] NelderMead.Optimizes3DFunctorCorrectly (1 ms) 35: [----------] 2 tests from NelderMead (170 ms total) 35: 35: [----------] 11 tests from PaddedVectorTest/0, where TypeParam = std::allocator 35: [ RUN ] PaddedVectorTest/0.DefaultConstructorWorks 35: [ OK ] PaddedVectorTest/0.DefaultConstructorWorks (0 ms) 35: [ RUN ] PaddedVectorTest/0.ResizeWorks 35: [ OK ] PaddedVectorTest/0.ResizeWorks (0 ms) 35: [ RUN ] PaddedVectorTest/0.ReserveWorks 35: [ OK ] PaddedVectorTest/0.ReserveWorks (0 ms) 35: [ RUN ] PaddedVectorTest/0.ReserveWorksTheSameAsNoReserve 35: [ OK ] PaddedVectorTest/0.ReserveWorksTheSameAsNoReserve (0 ms) 35: [ RUN ] PaddedVectorTest/0.MoveConstructorWorks 35: [ OK ] PaddedVectorTest/0.MoveConstructorWorks (0 ms) 35: [ RUN ] PaddedVectorTest/0.MoveConstructorWithAllocatorWorks 35: [ OK ] PaddedVectorTest/0.MoveConstructorWithAllocatorWorks (0 ms) 35: [ RUN ] PaddedVectorTest/0.MoveAssignmentWorks 35: [ OK ] PaddedVectorTest/0.MoveAssignmentWorks (0 ms) 35: [ RUN ] PaddedVectorTest/0.ArrayRefConversionsAreIdentical 35: [ OK ] PaddedVectorTest/0.ArrayRefConversionsAreIdentical (0 ms) 35: [ RUN ] PaddedVectorTest/0.CanCopyAssign 35: [ OK ] PaddedVectorTest/0.CanCopyAssign (0 ms) 35: [ RUN ] PaddedVectorTest/0.CanMoveAssign 35: [ OK ] PaddedVectorTest/0.CanMoveAssign (0 ms) 35: [ RUN ] PaddedVectorTest/0.CanSwap 35: [ OK ] PaddedVectorTest/0.CanSwap (0 ms) 35: [----------] 11 tests from PaddedVectorTest/0 (0 ms total) 35: 35: [----------] 11 tests from PaddedVectorTest/1, where TypeParam = std::allocator 35: [ RUN ] PaddedVectorTest/1.DefaultConstructorWorks 35: [ OK ] PaddedVectorTest/1.DefaultConstructorWorks (0 ms) 35: [ RUN ] PaddedVectorTest/1.ResizeWorks 35: [ OK ] PaddedVectorTest/1.ResizeWorks (0 ms) 35: [ RUN ] PaddedVectorTest/1.ReserveWorks 35: [ OK ] PaddedVectorTest/1.ReserveWorks (0 ms) 35: [ RUN ] PaddedVectorTest/1.ReserveWorksTheSameAsNoReserve 35: [ OK ] PaddedVectorTest/1.ReserveWorksTheSameAsNoReserve (0 ms) 35: [ RUN ] PaddedVectorTest/1.MoveConstructorWorks 35: [ OK ] PaddedVectorTest/1.MoveConstructorWorks (0 ms) 35: [ RUN ] PaddedVectorTest/1.MoveConstructorWithAllocatorWorks 35: [ OK ] PaddedVectorTest/1.MoveConstructorWithAllocatorWorks (0 ms) 35: [ RUN ] PaddedVectorTest/1.MoveAssignmentWorks 35: [ OK ] PaddedVectorTest/1.MoveAssignmentWorks (0 ms) 35: [ RUN ] PaddedVectorTest/1.ArrayRefConversionsAreIdentical 35: [ OK ] PaddedVectorTest/1.ArrayRefConversionsAreIdentical (0 ms) 35: [ RUN ] PaddedVectorTest/1.CanCopyAssign 35: [ OK ] PaddedVectorTest/1.CanCopyAssign (0 ms) 35: [ RUN ] PaddedVectorTest/1.CanMoveAssign 35: [ OK ] PaddedVectorTest/1.CanMoveAssign (0 ms) 35: [ RUN ] PaddedVectorTest/1.CanSwap 35: [ OK ] PaddedVectorTest/1.CanSwap (0 ms) 35: [----------] 11 tests from PaddedVectorTest/1 (0 ms total) 35: 35: [----------] 11 tests from PaddedVectorTest/2, where TypeParam = std::allocator 35: [ RUN ] PaddedVectorTest/2.DefaultConstructorWorks 35: [ OK ] PaddedVectorTest/2.DefaultConstructorWorks (0 ms) 35: [ RUN ] PaddedVectorTest/2.ResizeWorks 35: [ OK ] PaddedVectorTest/2.ResizeWorks (0 ms) 35: [ RUN ] PaddedVectorTest/2.ReserveWorks 35: [ OK ] PaddedVectorTest/2.ReserveWorks (0 ms) 35: [ RUN ] PaddedVectorTest/2.ReserveWorksTheSameAsNoReserve 35: [ OK ] PaddedVectorTest/2.ReserveWorksTheSameAsNoReserve (0 ms) 35: [ RUN ] PaddedVectorTest/2.MoveConstructorWorks 35: [ OK ] PaddedVectorTest/2.MoveConstructorWorks (0 ms) 35: [ RUN ] PaddedVectorTest/2.MoveConstructorWithAllocatorWorks 35: [ OK ] PaddedVectorTest/2.MoveConstructorWithAllocatorWorks (0 ms) 35: [ RUN ] PaddedVectorTest/2.MoveAssignmentWorks 35: [ OK ] PaddedVectorTest/2.MoveAssignmentWorks (0 ms) 35: [ RUN ] PaddedVectorTest/2.ArrayRefConversionsAreIdentical 35: [ OK ] PaddedVectorTest/2.ArrayRefConversionsAreIdentical (0 ms) 35: [ RUN ] PaddedVectorTest/2.CanCopyAssign 35: [ OK ] PaddedVectorTest/2.CanCopyAssign (0 ms) 35: [ RUN ] PaddedVectorTest/2.CanMoveAssign 35: [ OK ] PaddedVectorTest/2.CanMoveAssign (0 ms) 35: [ RUN ] PaddedVectorTest/2.CanSwap 35: [ OK ] PaddedVectorTest/2.CanSwap (0 ms) 35: [----------] 11 tests from PaddedVectorTest/2 (0 ms total) 35: 35: [----------] 11 tests from PaddedVectorTest/3, where TypeParam = std::allocator > 35: [ RUN ] PaddedVectorTest/3.DefaultConstructorWorks 35: [ OK ] PaddedVectorTest/3.DefaultConstructorWorks (0 ms) 35: [ RUN ] PaddedVectorTest/3.ResizeWorks 35: [ OK ] PaddedVectorTest/3.ResizeWorks (0 ms) 35: [ RUN ] PaddedVectorTest/3.ReserveWorks 35: [ OK ] PaddedVectorTest/3.ReserveWorks (0 ms) 35: [ RUN ] PaddedVectorTest/3.ReserveWorksTheSameAsNoReserve 35: [ OK ] PaddedVectorTest/3.ReserveWorksTheSameAsNoReserve (0 ms) 35: [ RUN ] PaddedVectorTest/3.MoveConstructorWorks 35: [ OK ] PaddedVectorTest/3.MoveConstructorWorks (0 ms) 35: [ RUN ] PaddedVectorTest/3.MoveConstructorWithAllocatorWorks 35: [ OK ] PaddedVectorTest/3.MoveConstructorWithAllocatorWorks (0 ms) 35: [ RUN ] PaddedVectorTest/3.MoveAssignmentWorks 35: [ OK ] PaddedVectorTest/3.MoveAssignmentWorks (0 ms) 35: [ RUN ] PaddedVectorTest/3.ArrayRefConversionsAreIdentical 35: [ OK ] PaddedVectorTest/3.ArrayRefConversionsAreIdentical (0 ms) 35: [ RUN ] PaddedVectorTest/3.CanCopyAssign 35: [ OK ] PaddedVectorTest/3.CanCopyAssign (0 ms) 35: [ RUN ] PaddedVectorTest/3.CanMoveAssign 35: [ OK ] PaddedVectorTest/3.CanMoveAssign (0 ms) 35: [ RUN ] PaddedVectorTest/3.CanSwap 35: [ OK ] PaddedVectorTest/3.CanSwap (0 ms) 35: [----------] 11 tests from PaddedVectorTest/3 (0 ms total) 35: 35: [----------] 11 tests from PaddedVectorTest/4, where TypeParam = std::allocator > 35: [ RUN ] PaddedVectorTest/4.DefaultConstructorWorks 35: [ OK ] PaddedVectorTest/4.DefaultConstructorWorks (0 ms) 35: [ RUN ] PaddedVectorTest/4.ResizeWorks 35: [ OK ] PaddedVectorTest/4.ResizeWorks (0 ms) 35: [ RUN ] PaddedVectorTest/4.ReserveWorks 35: [ OK ] PaddedVectorTest/4.ReserveWorks (0 ms) 35: [ RUN ] PaddedVectorTest/4.ReserveWorksTheSameAsNoReserve 35: [ OK ] PaddedVectorTest/4.ReserveWorksTheSameAsNoReserve (0 ms) 35: [ RUN ] PaddedVectorTest/4.MoveConstructorWorks 35: [ OK ] PaddedVectorTest/4.MoveConstructorWorks (0 ms) 35: [ RUN ] PaddedVectorTest/4.MoveConstructorWithAllocatorWorks 35: [ OK ] PaddedVectorTest/4.MoveConstructorWithAllocatorWorks (0 ms) 35: [ RUN ] PaddedVectorTest/4.MoveAssignmentWorks 35: [ OK ] PaddedVectorTest/4.MoveAssignmentWorks (0 ms) 35: [ RUN ] PaddedVectorTest/4.ArrayRefConversionsAreIdentical 35: [ OK ] PaddedVectorTest/4.ArrayRefConversionsAreIdentical (0 ms) 35: [ RUN ] PaddedVectorTest/4.CanCopyAssign 35: [ OK ] PaddedVectorTest/4.CanCopyAssign (0 ms) 35: [ RUN ] PaddedVectorTest/4.CanMoveAssign 35: [ OK ] PaddedVectorTest/4.CanMoveAssign (0 ms) 35: [ RUN ] PaddedVectorTest/4.CanSwap 35: [ OK ] PaddedVectorTest/4.CanSwap (0 ms) 35: [----------] 11 tests from PaddedVectorTest/4 (0 ms total) 35: 35: [----------] 11 tests from PaddedVectorTest/5, where TypeParam = gmx::Allocator 35: [ RUN ] PaddedVectorTest/5.DefaultConstructorWorks 35: [ OK ] PaddedVectorTest/5.DefaultConstructorWorks (0 ms) 35: [ RUN ] PaddedVectorTest/5.ResizeWorks 35: [ OK ] PaddedVectorTest/5.ResizeWorks (0 ms) 35: [ RUN ] PaddedVectorTest/5.ReserveWorks 35: [ OK ] PaddedVectorTest/5.ReserveWorks (0 ms) 35: [ RUN ] PaddedVectorTest/5.ReserveWorksTheSameAsNoReserve 35: [ OK ] PaddedVectorTest/5.ReserveWorksTheSameAsNoReserve (0 ms) 35: [ RUN ] PaddedVectorTest/5.MoveConstructorWorks 35: [ OK ] PaddedVectorTest/5.MoveConstructorWorks (0 ms) 35: [ RUN ] PaddedVectorTest/5.MoveConstructorWithAllocatorWorks 35: [ OK ] PaddedVectorTest/5.MoveConstructorWithAllocatorWorks (0 ms) 35: [ RUN ] PaddedVectorTest/5.MoveAssignmentWorks 35: [ OK ] PaddedVectorTest/5.MoveAssignmentWorks (0 ms) 35: [ RUN ] PaddedVectorTest/5.ArrayRefConversionsAreIdentical 35: [ OK ] PaddedVectorTest/5.ArrayRefConversionsAreIdentical (0 ms) 35: [ RUN ] PaddedVectorTest/5.CanCopyAssign 35: [ OK ] PaddedVectorTest/5.CanCopyAssign (0 ms) 35: [ RUN ] PaddedVectorTest/5.CanMoveAssign 35: [ OK ] PaddedVectorTest/5.CanMoveAssign (0 ms) 35: [ RUN ] PaddedVectorTest/5.CanSwap 35: [ OK ] PaddedVectorTest/5.CanSwap (0 ms) 35: [----------] 11 tests from PaddedVectorTest/5 (0 ms total) 35: 35: [----------] 11 tests from PaddedVectorTest/6, where TypeParam = gmx::Allocator 35: [ RUN ] PaddedVectorTest/6.DefaultConstructorWorks 35: [ OK ] PaddedVectorTest/6.DefaultConstructorWorks (0 ms) 35: [ RUN ] PaddedVectorTest/6.ResizeWorks 35: [ OK ] PaddedVectorTest/6.ResizeWorks (0 ms) 35: [ RUN ] PaddedVectorTest/6.ReserveWorks 35: [ OK ] PaddedVectorTest/6.ReserveWorks (0 ms) 35: [ RUN ] PaddedVectorTest/6.ReserveWorksTheSameAsNoReserve 35: [ OK ] PaddedVectorTest/6.ReserveWorksTheSameAsNoReserve (0 ms) 35: [ RUN ] PaddedVectorTest/6.MoveConstructorWorks 35: [ OK ] PaddedVectorTest/6.MoveConstructorWorks (0 ms) 35: [ RUN ] PaddedVectorTest/6.MoveConstructorWithAllocatorWorks 35: [ OK ] PaddedVectorTest/6.MoveConstructorWithAllocatorWorks (0 ms) 35: [ RUN ] PaddedVectorTest/6.MoveAssignmentWorks 35: [ OK ] PaddedVectorTest/6.MoveAssignmentWorks (0 ms) 35: [ RUN ] PaddedVectorTest/6.ArrayRefConversionsAreIdentical 35: [ OK ] PaddedVectorTest/6.ArrayRefConversionsAreIdentical (0 ms) 35: [ RUN ] PaddedVectorTest/6.CanCopyAssign 35: [ OK ] PaddedVectorTest/6.CanCopyAssign (0 ms) 35: [ RUN ] PaddedVectorTest/6.CanMoveAssign 35: [ OK ] PaddedVectorTest/6.CanMoveAssign (0 ms) 35: [ RUN ] PaddedVectorTest/6.CanSwap 35: [ OK ] PaddedVectorTest/6.CanSwap (0 ms) 35: [----------] 11 tests from PaddedVectorTest/6 (0 ms total) 35: 35: [----------] 11 tests from PaddedVectorTest/7, where TypeParam = gmx::Allocator 35: [ RUN ] PaddedVectorTest/7.DefaultConstructorWorks 35: [ OK ] PaddedVectorTest/7.DefaultConstructorWorks (0 ms) 35: [ RUN ] PaddedVectorTest/7.ResizeWorks 35: [ OK ] PaddedVectorTest/7.ResizeWorks (0 ms) 35: [ RUN ] PaddedVectorTest/7.ReserveWorks 35: [ OK ] PaddedVectorTest/7.ReserveWorks (0 ms) 35: [ RUN ] PaddedVectorTest/7.ReserveWorksTheSameAsNoReserve 35: [ OK ] PaddedVectorTest/7.ReserveWorksTheSameAsNoReserve (0 ms) 35: [ RUN ] PaddedVectorTest/7.MoveConstructorWorks 35: [ OK ] PaddedVectorTest/7.MoveConstructorWorks (0 ms) 35: [ RUN ] PaddedVectorTest/7.MoveConstructorWithAllocatorWorks 35: [ OK ] PaddedVectorTest/7.MoveConstructorWithAllocatorWorks (0 ms) 35: [ RUN ] PaddedVectorTest/7.MoveAssignmentWorks 35: [ OK ] PaddedVectorTest/7.MoveAssignmentWorks (0 ms) 35: [ RUN ] PaddedVectorTest/7.ArrayRefConversionsAreIdentical 35: [ OK ] PaddedVectorTest/7.ArrayRefConversionsAreIdentical (0 ms) 35: [ RUN ] PaddedVectorTest/7.CanCopyAssign 35: [ OK ] PaddedVectorTest/7.CanCopyAssign (0 ms) 35: [ RUN ] PaddedVectorTest/7.CanMoveAssign 35: [ OK ] PaddedVectorTest/7.CanMoveAssign (0 ms) 35: [ RUN ] PaddedVectorTest/7.CanSwap 35: [ OK ] PaddedVectorTest/7.CanSwap (0 ms) 35: [----------] 11 tests from PaddedVectorTest/7 (0 ms total) 35: 35: [----------] 11 tests from PaddedVectorTest/8, where TypeParam = gmx::Allocator, gmx::AlignedAllocationPolicy> 35: [ RUN ] PaddedVectorTest/8.DefaultConstructorWorks 35: [ OK ] PaddedVectorTest/8.DefaultConstructorWorks (0 ms) 35: [ RUN ] PaddedVectorTest/8.ResizeWorks 35: [ OK ] PaddedVectorTest/8.ResizeWorks (0 ms) 35: [ RUN ] PaddedVectorTest/8.ReserveWorks 35: [ OK ] PaddedVectorTest/8.ReserveWorks (0 ms) 35: [ RUN ] PaddedVectorTest/8.ReserveWorksTheSameAsNoReserve 35: [ OK ] PaddedVectorTest/8.ReserveWorksTheSameAsNoReserve (0 ms) 35: [ RUN ] PaddedVectorTest/8.MoveConstructorWorks 35: [ OK ] PaddedVectorTest/8.MoveConstructorWorks (0 ms) 35: [ RUN ] PaddedVectorTest/8.MoveConstructorWithAllocatorWorks 35: [ OK ] PaddedVectorTest/8.MoveConstructorWithAllocatorWorks (0 ms) 35: [ RUN ] PaddedVectorTest/8.MoveAssignmentWorks 35: [ OK ] PaddedVectorTest/8.MoveAssignmentWorks (0 ms) 35: [ RUN ] PaddedVectorTest/8.ArrayRefConversionsAreIdentical 35: [ OK ] PaddedVectorTest/8.ArrayRefConversionsAreIdentical (0 ms) 35: [ RUN ] PaddedVectorTest/8.CanCopyAssign 35: [ OK ] PaddedVectorTest/8.CanCopyAssign (0 ms) 35: [ RUN ] PaddedVectorTest/8.CanMoveAssign 35: [ OK ] PaddedVectorTest/8.CanMoveAssign (0 ms) 35: [ RUN ] PaddedVectorTest/8.CanSwap 35: [ OK ] PaddedVectorTest/8.CanSwap (0 ms) 35: [----------] 11 tests from PaddedVectorTest/8 (0 ms total) 35: 35: [----------] 11 tests from PaddedVectorTest/9, where TypeParam = gmx::Allocator, gmx::AlignedAllocationPolicy> 35: [ RUN ] PaddedVectorTest/9.DefaultConstructorWorks 35: [ OK ] PaddedVectorTest/9.DefaultConstructorWorks (0 ms) 35: [ RUN ] PaddedVectorTest/9.ResizeWorks 35: [ OK ] PaddedVectorTest/9.ResizeWorks (0 ms) 35: [ RUN ] PaddedVectorTest/9.ReserveWorks 35: [ OK ] PaddedVectorTest/9.ReserveWorks (0 ms) 35: [ RUN ] PaddedVectorTest/9.ReserveWorksTheSameAsNoReserve 35: [ OK ] PaddedVectorTest/9.ReserveWorksTheSameAsNoReserve (0 ms) 35: [ RUN ] PaddedVectorTest/9.MoveConstructorWorks 35: [ OK ] PaddedVectorTest/9.MoveConstructorWorks (0 ms) 35: [ RUN ] PaddedVectorTest/9.MoveConstructorWithAllocatorWorks 35: [ OK ] PaddedVectorTest/9.MoveConstructorWithAllocatorWorks (0 ms) 35: [ RUN ] PaddedVectorTest/9.MoveAssignmentWorks 35: [ OK ] PaddedVectorTest/9.MoveAssignmentWorks (0 ms) 35: [ RUN ] PaddedVectorTest/9.ArrayRefConversionsAreIdentical 35: [ OK ] PaddedVectorTest/9.ArrayRefConversionsAreIdentical (0 ms) 35: [ RUN ] PaddedVectorTest/9.CanCopyAssign 35: [ OK ] PaddedVectorTest/9.CanCopyAssign (0 ms) 35: [ RUN ] PaddedVectorTest/9.CanMoveAssign 35: [ OK ] PaddedVectorTest/9.CanMoveAssign (0 ms) 35: [ RUN ] PaddedVectorTest/9.CanSwap 35: [ OK ] PaddedVectorTest/9.CanSwap (0 ms) 35: [----------] 11 tests from PaddedVectorTest/9 (0 ms total) 35: 35: [----------] 41 tests from RVecTest 35: [ RUN ] RVecTest.CanBeStoredInVector 35: [ OK ] RVecTest.CanBeStoredInVector (0 ms) 35: [ RUN ] RVecTest.ConvertsImplicitlyFrom_rvec 35: [ OK ] RVecTest.ConvertsImplicitlyFrom_rvec (0 ms) 35: [ RUN ] RVecTest.ConvertsImplicitlyTo_rvec 35: [ OK ] RVecTest.ConvertsImplicitlyTo_rvec (0 ms) 35: [ RUN ] RVecTest.WorksAsMutable_rvec 35: [ OK ] RVecTest.WorksAsMutable_rvec (0 ms) 35: [ RUN ] RVecTest.WorksAs_rvec_Array 35: [ OK ] RVecTest.WorksAs_rvec_Array (0 ms) 35: [ RUN ] RVecTest.ComparesEqual 35: [ OK ] RVecTest.ComparesEqual (0 ms) 35: [ RUN ] RVecTest.ComparesUnequal 35: [ OK ] RVecTest.ComparesUnequal (0 ms) 35: [ RUN ] RVecTest.CanAddRVecToRvec 35: [ OK ] RVecTest.CanAddRVecToRvec (0 ms) 35: [ RUN ] RVecTest.CanAddAssignRVecToRvec 35: [ OK ] RVecTest.CanAddAssignRVecToRvec (0 ms) 35: [ RUN ] RVecTest.CanSubtractRVecFromRvec 35: [ OK ] RVecTest.CanSubtractRVecFromRvec (0 ms) 35: [ RUN ] RVecTest.CanSubtractAssignRVecFromRvec 35: [ OK ] RVecTest.CanSubtractAssignRVecFromRvec (0 ms) 35: [ RUN ] RVecTest.CanDotProductRVecByRvec 35: [ OK ] RVecTest.CanDotProductRVecByRvec (0 ms) 35: [ RUN ] RVecTest.CanCrossProductRVecByRvec 35: [ OK ] RVecTest.CanCrossProductRVecByRvec (0 ms) 35: [ RUN ] RVecTest.CanDivideRVecInplace 35: [ OK ] RVecTest.CanDivideRVecInplace (0 ms) 35: [ RUN ] RVecTest.CanScaleRVec 35: [ OK ] RVecTest.CanScaleRVec (0 ms) 35: [ RUN ] RVecTest.CanDivideRVec 35: [ OK ] RVecTest.CanDivideRVec (0 ms) 35: [ RUN ] RVecTest.CanDoUnitvFromRVec 35: [ OK ] RVecTest.CanDoUnitvFromRVec (0 ms) 35: [ RUN ] RVecTest.CanSqLengthOfRVec 35: [ OK ] RVecTest.CanSqLengthOfRVec (0 ms) 35: [ RUN ] RVecTest.CanLengthOfRVec 35: [ OK ] RVecTest.CanLengthOfRVec (0 ms) 35: [ RUN ] RVecTest.CanCastToRVec 35: [ OK ] RVecTest.CanCastToRVec (0 ms) 35: [ RUN ] RVecTest.CanCastToDVec 35: [ OK ] RVecTest.CanCastToDVec (0 ms) 35: [ RUN ] RVecTest.CanLeftScalarMultiply 35: [ OK ] RVecTest.CanLeftScalarMultiply (0 ms) 35: [ RUN ] RVecTest.CanRightScalarMultiply 35: [ OK ] RVecTest.CanRightScalarMultiply (0 ms) 35: [ RUN ] RVecTest.CanGetUnitvFromRVec 35: [ OK ] RVecTest.CanGetUnitvFromRVec (0 ms) 35: [ RUN ] RVecTest.CanGetSqLengthOfRVec 35: [ OK ] RVecTest.CanGetSqLengthOfRVec (0 ms) 35: [ RUN ] RVecTest.CanGetLengthOfRVec 35: [ OK ] RVecTest.CanGetLengthOfRVec (0 ms) 35: [ RUN ] RVecTest.CanDoCrossProductOfRVec 35: [ OK ] RVecTest.CanDoCrossProductOfRVec (0 ms) 35: [ RUN ] RVecTest.CanDoDotProductOfRVec 35: [ OK ] RVecTest.CanDoDotProductOfRVec (0 ms) 35: [ RUN ] RVecTest.CanScaleByVector 35: [ OK ] RVecTest.CanScaleByVector (0 ms) 35: [ RUN ] RVecTest.CanNegate 35: [ OK ] RVecTest.CanNegate (0 ms) 35: [ RUN ] RVecTest.asIVec 35: [ OK ] RVecTest.asIVec (0 ms) 35: [ RUN ] RVecTest.elementWiseMin 35: [ OK ] RVecTest.elementWiseMin (0 ms) 35: [ RUN ] RVecTest.elementWiseMax 35: [ OK ] RVecTest.elementWiseMax (0 ms) 35: [ RUN ] RVecTest.WorksAs_dvec_Reference 35: [ OK ] RVecTest.WorksAs_dvec_Reference (0 ms) 35: [ RUN ] RVecTest.WorksAs_ivec_Reference 35: [ OK ] RVecTest.WorksAs_ivec_Reference (0 ms) 35: [ RUN ] RVecTest.WorksAs_rvec_Reference 35: [ OK ] RVecTest.WorksAs_rvec_Reference (0 ms) 35: [ RUN ] RVecTest.CopyConstructorWorks 35: [ OK ] RVecTest.CopyConstructorWorks (0 ms) 35: [ RUN ] RVecTest.CopyAssignmentWorks 35: [ OK ] RVecTest.CopyAssignmentWorks (0 ms) 35: [ RUN ] RVecTest.MoveConstructorWorks 35: [ OK ] RVecTest.MoveConstructorWorks (0 ms) 35: [ RUN ] RVecTest.MoveAssignmentWorks 35: [ OK ] RVecTest.MoveAssignmentWorks (0 ms) 35: [ RUN ] RVecTest.UsableInConstexpr 35: [ OK ] RVecTest.UsableInConstexpr (0 ms) 35: [----------] 41 tests from RVecTest (1 ms total) 35: 35: [----------] Global test environment tear-down 35: [==========] 328 tests from 41 test suites ran. (826 ms total) 35: [ PASSED ] 328 tests. 35/92 Test #35: MathUnitTests ............................. Passed 0.96 sec test 36 Start 36: MdrunUtilityUnitTests 36: Test command: /build/reproducible-path/gromacs-2025.1/build/basic/bin/mdrunutility-test "--gtest_output=xml:/build/reproducible-path/gromacs-2025.1/build/basic/Testing/Temporary/MdrunUtilityUnitTests.xml" 36: Working Directory: /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/mdrunutility/tests 36: Test timeout computed to be: 30 36: [==========] Running 21 tests from 2 test suites. 36: [----------] Global test environment set-up. 36: [----------] 4 tests from MDModulesNotifierTest 36: [ RUN ] MDModulesNotifierTest.AddConsumer 36: [ OK ] MDModulesNotifierTest.AddConsumer (0 ms) 36: [ RUN ] MDModulesNotifierTest.AddConsumerWithPointerParameter 36: [ OK ] MDModulesNotifierTest.AddConsumerWithPointerParameter (0 ms) 36: [ RUN ] MDModulesNotifierTest.AddTwoDifferentConsumers 36: [ OK ] MDModulesNotifierTest.AddTwoDifferentConsumers (0 ms) 36: [ RUN ] MDModulesNotifierTest.AddConsumerOfTwoResources 36: [ OK ] MDModulesNotifierTest.AddConsumerOfTwoResources (0 ms) 36: [----------] 4 tests from MDModulesNotifierTest (0 ms total) 36: 36: [----------] 17 tests from ThreadAffinityTest 36: [ RUN ] ThreadAffinityTest.DoesNothingWhenDisabled 36: [ OK ] ThreadAffinityTest.DoesNothingWhenDisabled (0 ms) 36: [ RUN ] ThreadAffinityTest.DoesNothingWhenNotSupported 36: [ OK ] ThreadAffinityTest.DoesNothingWhenNotSupported (0 ms) 36: [ RUN ] ThreadAffinityTest.DoesNothingWithAutoAndTooFewUserSetThreads 36: [ OK ] ThreadAffinityTest.DoesNothingWithAutoAndTooFewUserSetThreads (1 ms) 36: [ RUN ] ThreadAffinityTest.DoesNothingWithAutoAndTooManyUserSetThreads 36: [ OK ] ThreadAffinityTest.DoesNothingWithAutoAndTooManyUserSetThreads (0 ms) 36: [ RUN ] ThreadAffinityTest.DoesNothingWithAutoAndTooManyAutoSetThreads 36: [ OK ] ThreadAffinityTest.DoesNothingWithAutoAndTooManyAutoSetThreads (0 ms) 36: [ RUN ] ThreadAffinityTest.DoesNothingWithUnknownHardware 36: [ OK ] ThreadAffinityTest.DoesNothingWithUnknownHardware (0 ms) 36: [ RUN ] ThreadAffinityTest.DoesNothingWithTooManyThreads 36: [ OK ] ThreadAffinityTest.DoesNothingWithTooManyThreads (0 ms) 36: [ RUN ] ThreadAffinityTest.DoesNothingWithTooLargeOffset 36: [ OK ] ThreadAffinityTest.DoesNothingWithTooLargeOffset (2 ms) 36: [ RUN ] ThreadAffinityTest.DoesNothingWithTooLargeStride 36: [ OK ] ThreadAffinityTest.DoesNothingWithTooLargeStride (0 ms) 36: [ RUN ] ThreadAffinityTest.PinsSingleThreadWithAuto 36: [ OK ] ThreadAffinityTest.PinsSingleThreadWithAuto (0 ms) 36: [ RUN ] ThreadAffinityTest.PinsSingleThreadWhenForced 36: [ OK ] ThreadAffinityTest.PinsSingleThreadWhenForced (0 ms) 36: [ RUN ] ThreadAffinityTest.PinsSingleThreadWithOffsetWhenForced 36: [ OK ] ThreadAffinityTest.PinsSingleThreadWithOffsetWhenForced (1 ms) 36: [ RUN ] ThreadAffinityTest.HandlesPinningFailureWithSingleThread 36: NOTE: Affinity setting failed. 36: [ OK ] ThreadAffinityTest.HandlesPinningFailureWithSingleThread (0 ms) 36: [ RUN ] ThreadAffinityTest.PinsMultipleThreadsWithAuto 36: [ OK ] ThreadAffinityTest.PinsMultipleThreadsWithAuto (4 ms) 36: [ RUN ] ThreadAffinityTest.PinsMultipleThreadsWithStrideWhenForced 36: [ OK ] ThreadAffinityTest.PinsMultipleThreadsWithStrideWhenForced (1 ms) 36: [ RUN ] ThreadAffinityTest.PinsWithAutoAndFewerAutoSetThreads 36: [ OK ] ThreadAffinityTest.PinsWithAutoAndFewerAutoSetThreads (2 ms) 36: [ RUN ] ThreadAffinityTest.HandlesPinningFailureWithOneThreadFailing 36: NOTE: Affinity setting for 1/2 threads failed. 36: [ OK ] ThreadAffinityTest.HandlesPinningFailureWithOneThreadFailing (3 ms) 36: [----------] 17 tests from ThreadAffinityTest (23 ms total) 36: 36: [----------] Global test environment tear-down 36: [==========] 21 tests from 2 test suites ran. (23 ms total) 36: [ PASSED ] 21 tests. 36/92 Test #36: MdrunUtilityUnitTests ..................... Passed 0.10 sec test 37 Start 37: MdrunUtilityMpiUnitTests 37: Test command: /build/reproducible-path/gromacs-2025.1/build/basic/bin/mdrunutility-mpi-test "-ntmpi" "4" "--gtest_output=xml:/build/reproducible-path/gromacs-2025.1/build/basic/Testing/Temporary/MdrunUtilityMpiUnitTests.xml" 37: Working Directory: /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/mdrunutility/tests 37: Test timeout computed to be: 30 37: [==========] Running 13 tests from 2 test suites. 37: [----------] Global test environment set-up. 37: [----------] 6 tests from ThreadAffinityMultiRankTest 37: [ RUN ] ThreadAffinityMultiRankTest.PinsWholeNode 37: [ OK ] ThreadAffinityMultiRankTest.PinsWholeNode (105 ms) 37: [ RUN ] ThreadAffinityMultiRankTest.PinsWithOffsetAndStride 37: [ OK ] ThreadAffinityMultiRankTest.PinsWithOffsetAndStride (101 ms) 37: [ RUN ] ThreadAffinityMultiRankTest.PinsTwoNodes 37: [ OK ] ThreadAffinityMultiRankTest.PinsTwoNodes (88 ms) 37: [ RUN ] ThreadAffinityMultiRankTest.DoesNothingWhenDisabled 37: [ OK ] ThreadAffinityMultiRankTest.DoesNothingWhenDisabled (33 ms) 37: [ RUN ] ThreadAffinityMultiRankTest.HandlesTooManyThreadsWithAuto 37: [ OK ] ThreadAffinityMultiRankTest.HandlesTooManyThreadsWithAuto (79 ms) 37: [ RUN ] ThreadAffinityMultiRankTest.HandlesTooManyThreadsWithForce 37: [ OK ] ThreadAffinityMultiRankTest.HandlesTooManyThreadsWithForce (92 ms) 37: [----------] 6 tests from ThreadAffinityMultiRankTest (501 ms total) 37: 37: [----------] 7 tests from ThreadAffinityHeterogeneousNodesTest 37: [ RUN ] ThreadAffinityHeterogeneousNodesTest.PinsOnMainOnly 37: [ OK ] ThreadAffinityHeterogeneousNodesTest.PinsOnMainOnly (49 ms) 37: [ RUN ] ThreadAffinityHeterogeneousNodesTest.PinsOnNonMainOnly 37: [ OK ] ThreadAffinityHeterogeneousNodesTest.PinsOnNonMainOnly (19 ms) 37: [ RUN ] ThreadAffinityHeterogeneousNodesTest.HandlesUnknownHardwareOnNonMain 37: [ OK ] ThreadAffinityHeterogeneousNodesTest.HandlesUnknownHardwareOnNonMain (48 ms) 37: [ RUN ] ThreadAffinityHeterogeneousNodesTest.PinsAutomaticallyOnMainOnly 37: [ OK ] ThreadAffinityHeterogeneousNodesTest.PinsAutomaticallyOnMainOnly (91 ms) 37: [ RUN ] ThreadAffinityHeterogeneousNodesTest.PinsAutomaticallyOnNonMainOnly 37: [ OK ] ThreadAffinityHeterogeneousNodesTest.PinsAutomaticallyOnNonMainOnly (87 ms) 37: [ RUN ] ThreadAffinityHeterogeneousNodesTest.HandlesInvalidOffsetOnNonMainOnly 37: [ OK ] ThreadAffinityHeterogeneousNodesTest.HandlesInvalidOffsetOnNonMainOnly (83 ms) 37: [ RUN ] ThreadAffinityHeterogeneousNodesTest.HandlesInvalidStrideOnNonMainOnly 37: [ OK ] ThreadAffinityHeterogeneousNodesTest.HandlesInvalidStrideOnNonMainOnly (87 ms) 37: [----------] 7 tests from ThreadAffinityHeterogeneousNodesTest (466 ms total) 37: 37: [----------] Global test environment tear-down 37: [==========] 13 tests from 2 test suites ran. (968 ms total) 37: [ PASSED ] 13 tests. 37/92 Test #37: MdrunUtilityMpiUnitTests .................. Passed 1.05 sec test 38 Start 38: MDSpanTests 38: Test command: /build/reproducible-path/gromacs-2025.1/build/basic/bin/mdspan-test "--gtest_output=xml:/build/reproducible-path/gromacs-2025.1/build/basic/Testing/Temporary/MDSpanTests.xml" 38: Working Directory: /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/mdspan/tests 38: Test timeout computed to be: 30 38: [==========] Running 32 tests from 7 test suites. 38: [----------] Global test environment set-up. 38: [----------] 4 tests from BasicAccessorPolicy 38: [ RUN ] BasicAccessorPolicy.Decay 38: [ OK ] BasicAccessorPolicy.Decay (0 ms) 38: [ RUN ] BasicAccessorPolicy.Access 38: [ OK ] BasicAccessorPolicy.Access (0 ms) 38: [ RUN ] BasicAccessorPolicy.Offset 38: [ OK ] BasicAccessorPolicy.Offset (0 ms) 38: [ RUN ] BasicAccessorPolicy.CopyAccessor 38: [ OK ] BasicAccessorPolicy.CopyAccessor (0 ms) 38: [----------] 4 tests from BasicAccessorPolicy (0 ms total) 38: 38: [----------] 4 tests from ExtentsTest 38: [ RUN ] ExtentsTest.Construction 38: [ OK ] ExtentsTest.Construction (0 ms) 38: [ RUN ] ExtentsTest.PurelyStatic 38: [ OK ] ExtentsTest.PurelyStatic (0 ms) 38: [ RUN ] ExtentsTest.RankNought 38: [ OK ] ExtentsTest.RankNought (0 ms) 38: [ RUN ] ExtentsTest.Assignment 38: [ OK ] ExtentsTest.Assignment (0 ms) 38: [----------] 4 tests from ExtentsTest (0 ms total) 38: 38: [----------] 8 tests from MdSpanExtension 38: [ RUN ] MdSpanExtension.SlicingAllStatic 38: [ OK ] MdSpanExtension.SlicingAllStatic (0 ms) 38: [ RUN ] MdSpanExtension.SlicingDynamic 38: [ OK ] MdSpanExtension.SlicingDynamic (0 ms) 38: [ RUN ] MdSpanExtension.SlicingAllStatic3D 38: [ OK ] MdSpanExtension.SlicingAllStatic3D (0 ms) 38: [ RUN ] MdSpanExtension.SlicingEqualsView3D 38: [ OK ] MdSpanExtension.SlicingEqualsView3D (0 ms) 38: [ RUN ] MdSpanExtension.additionWorks 38: [ OK ] MdSpanExtension.additionWorks (0 ms) 38: [ RUN ] MdSpanExtension.subtractionWorks 38: [ OK ] MdSpanExtension.subtractionWorks (0 ms) 38: [ RUN ] MdSpanExtension.multiplicationWorks 38: [ OK ] MdSpanExtension.multiplicationWorks (0 ms) 38: [ RUN ] MdSpanExtension.divisionWorks 38: [ OK ] MdSpanExtension.divisionWorks (0 ms) 38: [----------] 8 tests from MdSpanExtension (0 ms total) 38: 38: [----------] 3 tests from LayoutTests 38: [ RUN ] LayoutTests.LayoutRightConstruction 38: [ OK ] LayoutTests.LayoutRightConstruction (0 ms) 38: [ RUN ] LayoutTests.LayoutRightProperties 38: [ OK ] LayoutTests.LayoutRightProperties (0 ms) 38: [ RUN ] LayoutTests.LayoutRightOperator 38: [ OK ] LayoutTests.LayoutRightOperator (0 ms) 38: [----------] 3 tests from LayoutTests (0 ms total) 38: 38: [----------] 1 test from MdSpanTest 38: [ RUN ] MdSpanTest.MdSpanWrapsBasicMdSpanCorrectly 38: [ OK ] MdSpanTest.MdSpanWrapsBasicMdSpanCorrectly (0 ms) 38: [----------] 1 test from MdSpanTest (0 ms total) 38: 38: [----------] 6 tests from MdSpanTest/0, where TypeParam = gmx::basic_mdspan, gmx::layout_right, gmx::accessor_basic > 38: [ RUN ] MdSpanTest/0.Rank 38: [ OK ] MdSpanTest/0.Rank (0 ms) 38: [ RUN ] MdSpanTest/0.DynamicRank 38: [ OK ] MdSpanTest/0.DynamicRank (0 ms) 38: [ RUN ] MdSpanTest/0.Extents 38: [ OK ] MdSpanTest/0.Extents (0 ms) 38: [ RUN ] MdSpanTest/0.Strides 38: [ OK ] MdSpanTest/0.Strides (0 ms) 38: [ RUN ] MdSpanTest/0.Properties 38: [ OK ] MdSpanTest/0.Properties (0 ms) 38: [ RUN ] MdSpanTest/0.Operator 38: [ OK ] MdSpanTest/0.Operator (0 ms) 38: [----------] 6 tests from MdSpanTest/0 (0 ms total) 38: 38: [----------] 6 tests from MdSpanTest/1, where TypeParam = gmx::basic_mdspan, gmx::layout_right, gmx::accessor_basic > 38: [ RUN ] MdSpanTest/1.Rank 38: [ OK ] MdSpanTest/1.Rank (0 ms) 38: [ RUN ] MdSpanTest/1.DynamicRank 38: [ OK ] MdSpanTest/1.DynamicRank (0 ms) 38: [ RUN ] MdSpanTest/1.Extents 38: [ OK ] MdSpanTest/1.Extents (0 ms) 38: [ RUN ] MdSpanTest/1.Strides 38: [ OK ] MdSpanTest/1.Strides (0 ms) 38: [ RUN ] MdSpanTest/1.Properties 38: [ OK ] MdSpanTest/1.Properties (0 ms) 38: [ RUN ] MdSpanTest/1.Operator 38: [ OK ] MdSpanTest/1.Operator (0 ms) 38: [----------] 6 tests from MdSpanTest/1 (0 ms total) 38: 38: [----------] Global test environment tear-down 38: [==========] 32 tests from 7 test suites ran. (1 ms total) 38: [ PASSED ] 32 tests. 38/92 Test #38: MDSpanTests ............................... Passed 0.08 sec test 39 Start 39: MdtypesUnitTest 39: Test command: /build/reproducible-path/gromacs-2025.1/build/basic/bin/mdtypes-test "--gtest_output=xml:/build/reproducible-path/gromacs-2025.1/build/basic/Testing/Temporary/MdtypesUnitTest.xml" 39: Working Directory: /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/mdtypes/tests 39: Test timeout computed to be: 30 39: [==========] Running 97 tests from 7 test suites. 39: [----------] Global test environment set-up. 39: [----------] 4 tests from ForeingLambdaTermsDhdl 39: [ RUN ] ForeingLambdaTermsDhdl.RateCheckWorks 39: [ OK ] ForeingLambdaTermsDhdl.RateCheckWorks (0 ms) 39: [ RUN ] ForeingLambdaTermsDhdl.AllLinear 39: [ OK ] ForeingLambdaTermsDhdl.AllLinear (0 ms) 39: [ RUN ] ForeingLambdaTermsDhdl.AllLinearNegative 39: [ OK ] ForeingLambdaTermsDhdl.AllLinearNegative (0 ms) 39: [ RUN ] ForeingLambdaTermsDhdl.SeparateVdwCoul 39: [ OK ] ForeingLambdaTermsDhdl.SeparateVdwCoul (0 ms) 39: [----------] 4 tests from ForeingLambdaTermsDhdl (0 ms total) 39: 39: [----------] 4 tests from ObservablesReducerTest 39: [ RUN ] ObservablesReducerTest.CanMoveAssign 39: [ OK ] ObservablesReducerTest.CanMoveAssign (0 ms) 39: [ RUN ] ObservablesReducerTest.CanMoveConstruct 39: [ OK ] ObservablesReducerTest.CanMoveConstruct (0 ms) 39: [ RUN ] ObservablesReducerTest.CanBuildAndUseWithNoSubscribers 39: [ OK ] ObservablesReducerTest.CanBuildAndUseWithNoSubscribers (0 ms) 39: [ RUN ] ObservablesReducerTest.CanBuildAndUseWithOneSubscriber 39: [ OK ] ObservablesReducerTest.CanBuildAndUseWithOneSubscriber (0 ms) 39: [----------] 4 tests from ObservablesReducerTest (0 ms total) 39: 39: [----------] 2 tests from CheckpointDataTest 39: [ RUN ] CheckpointDataTest.SingleDataTest 39: [ OK ] CheckpointDataTest.SingleDataTest (11 ms) 39: [ RUN ] CheckpointDataTest.MultiDataTest 39: [ OK ] CheckpointDataTest.MultiDataTest (67 ms) 39: [----------] 2 tests from CheckpointDataTest (79 ms total) 39: 39: [----------] 7 tests from ForceBuffers 39: [ RUN ] ForceBuffers.ConstructsUnpinned 39: [ OK ] ForceBuffers.ConstructsUnpinned (0 ms) 39: [ RUN ] ForceBuffers.ConstructsPinned 39: [ OK ] ForceBuffers.ConstructsPinned (0 ms) 39: [ RUN ] ForceBuffers.ConstructsEmpty 39: [ OK ] ForceBuffers.ConstructsEmpty (0 ms) 39: [ RUN ] ForceBuffers.ResizeWorks 39: [ OK ] ForceBuffers.ResizeWorks (0 ms) 39: [ RUN ] ForceBuffers.PaddingWorks 39: [ OK ] ForceBuffers.PaddingWorks (0 ms) 39: [ RUN ] ForceBuffers.CopyWorks 39: [ OK ] ForceBuffers.CopyWorks (0 ms) 39: [ RUN ] ForceBuffers.CopyDoesNotPin 39: [ OK ] ForceBuffers.CopyDoesNotPin (0 ms) 39: [----------] 7 tests from ForceBuffers (0 ms total) 39: 39: [----------] 5 tests from MultipleTimeStepping 39: [ RUN ] MultipleTimeStepping.ChecksNumLevels 39: [ OK ] MultipleTimeStepping.ChecksNumLevels (0 ms) 39: [ RUN ] MultipleTimeStepping.SelectsForceGroups 39: [ OK ] MultipleTimeStepping.SelectsForceGroups (0 ms) 39: [ RUN ] MultipleTimeStepping.ChecksStepFactor 39: [ OK ] MultipleTimeStepping.ChecksStepFactor (0 ms) 39: [ RUN ] MultipleTimeStepping.ChecksPmeIsAtLastLevel 39: [ OK ] MultipleTimeStepping.ChecksPmeIsAtLastLevel (0 ms) 39: [ RUN ] MultipleTimeStepping.ChecksIntegrator 39: [ OK ] MultipleTimeStepping.ChecksIntegrator (0 ms) 39: [----------] 5 tests from MultipleTimeStepping (0 ms total) 39: 39: [----------] 60 tests from WithVariousSubscriberCounts/ObservablesReducerIntegrationTest 39: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseSimply/numSubscribers0numRanks1 39: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseSimply/numSubscribers0numRanks1 (0 ms) 39: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseSimply/numSubscribers0numRanks2 39: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseSimply/numSubscribers0numRanks2 (0 ms) 39: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseSimply/numSubscribers0numRanks3 39: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseSimply/numSubscribers0numRanks3 (0 ms) 39: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseSimply/numSubscribers1numRanks1 39: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseSimply/numSubscribers1numRanks1 (0 ms) 39: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseSimply/numSubscribers1numRanks2 39: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseSimply/numSubscribers1numRanks2 (0 ms) 39: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseSimply/numSubscribers1numRanks3 39: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseSimply/numSubscribers1numRanks3 (0 ms) 39: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseSimply/numSubscribers2numRanks1 39: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseSimply/numSubscribers2numRanks1 (0 ms) 39: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseSimply/numSubscribers2numRanks2 39: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseSimply/numSubscribers2numRanks2 (0 ms) 39: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseSimply/numSubscribers2numRanks3 39: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseSimply/numSubscribers2numRanks3 (0 ms) 39: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseSimply/numSubscribers3numRanks1 39: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseSimply/numSubscribers3numRanks1 (0 ms) 39: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseSimply/numSubscribers3numRanks2 39: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseSimply/numSubscribers3numRanks2 (0 ms) 39: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseSimply/numSubscribers3numRanks3 39: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseSimply/numSubscribers3numRanks3 (0 ms) 39: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseOverMultipleSteps/numSubscribers0numRanks1 39: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseOverMultipleSteps/numSubscribers0numRanks1 (0 ms) 39: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseOverMultipleSteps/numSubscribers0numRanks2 39: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseOverMultipleSteps/numSubscribers0numRanks2 (0 ms) 39: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseOverMultipleSteps/numSubscribers0numRanks3 39: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseOverMultipleSteps/numSubscribers0numRanks3 (0 ms) 39: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseOverMultipleSteps/numSubscribers1numRanks1 39: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseOverMultipleSteps/numSubscribers1numRanks1 (0 ms) 39: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseOverMultipleSteps/numSubscribers1numRanks2 39: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseOverMultipleSteps/numSubscribers1numRanks2 (0 ms) 39: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseOverMultipleSteps/numSubscribers1numRanks3 39: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseOverMultipleSteps/numSubscribers1numRanks3 (0 ms) 39: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseOverMultipleSteps/numSubscribers2numRanks1 39: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseOverMultipleSteps/numSubscribers2numRanks1 (0 ms) 39: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseOverMultipleSteps/numSubscribers2numRanks2 39: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseOverMultipleSteps/numSubscribers2numRanks2 (0 ms) 39: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseOverMultipleSteps/numSubscribers2numRanks3 39: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseOverMultipleSteps/numSubscribers2numRanks3 (0 ms) 39: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseOverMultipleSteps/numSubscribers3numRanks1 39: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseOverMultipleSteps/numSubscribers3numRanks1 (0 ms) 39: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseOverMultipleSteps/numSubscribers3numRanks2 39: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseOverMultipleSteps/numSubscribers3numRanks2 (0 ms) 39: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseOverMultipleSteps/numSubscribers3numRanks3 39: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseOverMultipleSteps/numSubscribers3numRanks3 (0 ms) 39: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWithoutAllNeedingReduction/numSubscribers0numRanks1 39: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWithoutAllNeedingReduction/numSubscribers0numRanks1 (0 ms) 39: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWithoutAllNeedingReduction/numSubscribers0numRanks2 39: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWithoutAllNeedingReduction/numSubscribers0numRanks2 (0 ms) 39: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWithoutAllNeedingReduction/numSubscribers0numRanks3 39: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWithoutAllNeedingReduction/numSubscribers0numRanks3 (0 ms) 39: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWithoutAllNeedingReduction/numSubscribers1numRanks1 39: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWithoutAllNeedingReduction/numSubscribers1numRanks1 (0 ms) 39: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWithoutAllNeedingReduction/numSubscribers1numRanks2 39: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWithoutAllNeedingReduction/numSubscribers1numRanks2 (0 ms) 39: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWithoutAllNeedingReduction/numSubscribers1numRanks3 39: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWithoutAllNeedingReduction/numSubscribers1numRanks3 (0 ms) 39: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWithoutAllNeedingReduction/numSubscribers2numRanks1 39: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWithoutAllNeedingReduction/numSubscribers2numRanks1 (0 ms) 39: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWithoutAllNeedingReduction/numSubscribers2numRanks2 39: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWithoutAllNeedingReduction/numSubscribers2numRanks2 (0 ms) 39: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWithoutAllNeedingReduction/numSubscribers2numRanks3 39: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWithoutAllNeedingReduction/numSubscribers2numRanks3 (0 ms) 39: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWithoutAllNeedingReduction/numSubscribers3numRanks1 39: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWithoutAllNeedingReduction/numSubscribers3numRanks1 (0 ms) 39: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWithoutAllNeedingReduction/numSubscribers3numRanks2 39: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWithoutAllNeedingReduction/numSubscribers3numRanks2 (0 ms) 39: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWithoutAllNeedingReduction/numSubscribers3numRanks3 39: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWithoutAllNeedingReduction/numSubscribers3numRanks3 (0 ms) 39: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenASubscriberUsesEventually/numSubscribers0numRanks1 39: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenASubscriberUsesEventually/numSubscribers0numRanks1 (0 ms) 39: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenASubscriberUsesEventually/numSubscribers0numRanks2 39: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenASubscriberUsesEventually/numSubscribers0numRanks2 (0 ms) 39: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenASubscriberUsesEventually/numSubscribers0numRanks3 39: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenASubscriberUsesEventually/numSubscribers0numRanks3 (0 ms) 39: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenASubscriberUsesEventually/numSubscribers1numRanks1 39: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenASubscriberUsesEventually/numSubscribers1numRanks1 (0 ms) 39: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenASubscriberUsesEventually/numSubscribers1numRanks2 39: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenASubscriberUsesEventually/numSubscribers1numRanks2 (0 ms) 39: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenASubscriberUsesEventually/numSubscribers1numRanks3 39: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenASubscriberUsesEventually/numSubscribers1numRanks3 (0 ms) 39: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenASubscriberUsesEventually/numSubscribers2numRanks1 39: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenASubscriberUsesEventually/numSubscribers2numRanks1 (0 ms) 39: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenASubscriberUsesEventually/numSubscribers2numRanks2 39: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenASubscriberUsesEventually/numSubscribers2numRanks2 (0 ms) 39: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenASubscriberUsesEventually/numSubscribers2numRanks3 39: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenASubscriberUsesEventually/numSubscribers2numRanks3 (0 ms) 39: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenASubscriberUsesEventually/numSubscribers3numRanks1 39: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenASubscriberUsesEventually/numSubscribers3numRanks1 (0 ms) 39: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenASubscriberUsesEventually/numSubscribers3numRanks2 39: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenASubscriberUsesEventually/numSubscribers3numRanks2 (0 ms) 39: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenASubscriberUsesEventually/numSubscribers3numRanks3 39: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenASubscriberUsesEventually/numSubscribers3numRanks3 (0 ms) 39: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenAllSubscribersUseEventually/numSubscribers0numRanks1 39: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenAllSubscribersUseEventually/numSubscribers0numRanks1 (0 ms) 39: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenAllSubscribersUseEventually/numSubscribers0numRanks2 39: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenAllSubscribersUseEventually/numSubscribers0numRanks2 (0 ms) 39: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenAllSubscribersUseEventually/numSubscribers0numRanks3 39: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenAllSubscribersUseEventually/numSubscribers0numRanks3 (0 ms) 39: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenAllSubscribersUseEventually/numSubscribers1numRanks1 39: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenAllSubscribersUseEventually/numSubscribers1numRanks1 (0 ms) 39: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenAllSubscribersUseEventually/numSubscribers1numRanks2 39: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenAllSubscribersUseEventually/numSubscribers1numRanks2 (0 ms) 39: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenAllSubscribersUseEventually/numSubscribers1numRanks3 39: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenAllSubscribersUseEventually/numSubscribers1numRanks3 (0 ms) 39: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenAllSubscribersUseEventually/numSubscribers2numRanks1 39: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenAllSubscribersUseEventually/numSubscribers2numRanks1 (0 ms) 39: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenAllSubscribersUseEventually/numSubscribers2numRanks2 39: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenAllSubscribersUseEventually/numSubscribers2numRanks2 (0 ms) 39: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenAllSubscribersUseEventually/numSubscribers2numRanks3 39: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenAllSubscribersUseEventually/numSubscribers2numRanks3 (0 ms) 39: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenAllSubscribersUseEventually/numSubscribers3numRanks1 39: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenAllSubscribersUseEventually/numSubscribers3numRanks1 (0 ms) 39: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenAllSubscribersUseEventually/numSubscribers3numRanks2 39: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenAllSubscribersUseEventually/numSubscribers3numRanks2 (0 ms) 39: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenAllSubscribersUseEventually/numSubscribers3numRanks3 39: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenAllSubscribersUseEventually/numSubscribers3numRanks3 (0 ms) 39: [----------] 60 tests from WithVariousSubscriberCounts/ObservablesReducerIntegrationTest (9 ms total) 39: 39: [----------] 15 tests from ChecksStepInterval/MtsIntervalTest 39: [ RUN ] ChecksStepInterval/MtsIntervalTest.Works/0 39: [ OK ] ChecksStepInterval/MtsIntervalTest.Works/0 (0 ms) 39: [ RUN ] ChecksStepInterval/MtsIntervalTest.Works/1 39: [ OK ] ChecksStepInterval/MtsIntervalTest.Works/1 (0 ms) 39: [ RUN ] ChecksStepInterval/MtsIntervalTest.Works/2 39: [ OK ] ChecksStepInterval/MtsIntervalTest.Works/2 (0 ms) 39: [ RUN ] ChecksStepInterval/MtsIntervalTest.Works/3 39: [ OK ] ChecksStepInterval/MtsIntervalTest.Works/3 (0 ms) 39: [ RUN ] ChecksStepInterval/MtsIntervalTest.Works/4 39: [ OK ] ChecksStepInterval/MtsIntervalTest.Works/4 (0 ms) 39: [ RUN ] ChecksStepInterval/MtsIntervalTest.Works/5 39: [ OK ] ChecksStepInterval/MtsIntervalTest.Works/5 (0 ms) 39: [ RUN ] ChecksStepInterval/MtsIntervalTest.Works/6 39: [ OK ] ChecksStepInterval/MtsIntervalTest.Works/6 (0 ms) 39: [ RUN ] ChecksStepInterval/MtsIntervalTest.Works/7 39: [ OK ] ChecksStepInterval/MtsIntervalTest.Works/7 (0 ms) 39: [ RUN ] ChecksStepInterval/MtsIntervalTest.Works/8 39: [ OK ] ChecksStepInterval/MtsIntervalTest.Works/8 (0 ms) 39: [ RUN ] ChecksStepInterval/MtsIntervalTest.Works/9 39: [ OK ] ChecksStepInterval/MtsIntervalTest.Works/9 (0 ms) 39: [ RUN ] ChecksStepInterval/MtsIntervalTest.Works/10 39: [ OK ] ChecksStepInterval/MtsIntervalTest.Works/10 (0 ms) 39: [ RUN ] ChecksStepInterval/MtsIntervalTest.Works/11 39: [ OK ] ChecksStepInterval/MtsIntervalTest.Works/11 (0 ms) 39: [ RUN ] ChecksStepInterval/MtsIntervalTest.Works/12 39: [ OK ] ChecksStepInterval/MtsIntervalTest.Works/12 (0 ms) 39: [ RUN ] ChecksStepInterval/MtsIntervalTest.Works/13 39: [ OK ] ChecksStepInterval/MtsIntervalTest.Works/13 (0 ms) 39: [ RUN ] ChecksStepInterval/MtsIntervalTest.Works/14 39: [ OK ] ChecksStepInterval/MtsIntervalTest.Works/14 (0 ms) 39: [----------] 15 tests from ChecksStepInterval/MtsIntervalTest (0 ms total) 39: 39: [----------] Global test environment tear-down 39: [==========] 97 tests from 7 test suites ran. (91 ms total) 39: [ PASSED ] 97 tests. 39/92 Test #39: MdtypesUnitTest ........................... Passed 0.18 sec test 40 Start 40: OnlineHelpUnitTests 40: Test command: /build/reproducible-path/gromacs-2025.1/build/basic/bin/onlinehelp-test "--gtest_output=xml:/build/reproducible-path/gromacs-2025.1/build/basic/Testing/Temporary/OnlineHelpUnitTests.xml" 40: Working Directory: /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/onlinehelp/tests 40: Test timeout computed to be: 30 40: [==========] Running 22 tests from 4 test suites. 40: [----------] Global test environment set-up. 40: [----------] 6 tests from TextTableFormatterTest 40: [ RUN ] TextTableFormatterTest.HandlesBasicCase 40: [ OK ] TextTableFormatterTest.HandlesBasicCase (2 ms) 40: [ RUN ] TextTableFormatterTest.HandlesEmptyColumnTitles 40: [ OK ] TextTableFormatterTest.HandlesEmptyColumnTitles (1 ms) 40: [ RUN ] TextTableFormatterTest.HandlesIndentation 40: [ OK ] TextTableFormatterTest.HandlesIndentation (0 ms) 40: [ RUN ] TextTableFormatterTest.HandlesOverflowingLines 40: [ OK ] TextTableFormatterTest.HandlesOverflowingLines (0 ms) 40: [ RUN ] TextTableFormatterTest.HandlesLastColumnFolding 40: [ OK ] TextTableFormatterTest.HandlesLastColumnFolding (0 ms) 40: [ RUN ] TextTableFormatterTest.HandlesEmptyColumns 40: [ OK ] TextTableFormatterTest.HandlesEmptyColumns (0 ms) 40: [----------] 6 tests from TextTableFormatterTest (6 ms total) 40: 40: [----------] 3 tests from HelpManagerTest 40: [ RUN ] HelpManagerTest.HandlesRootTopic 40: [ OK ] HelpManagerTest.HandlesRootTopic (0 ms) 40: [ RUN ] HelpManagerTest.HandlesSubTopics 40: [ OK ] HelpManagerTest.HandlesSubTopics (0 ms) 40: [ RUN ] HelpManagerTest.HandlesInvalidTopics 40: [ OK ] HelpManagerTest.HandlesInvalidTopics (0 ms) 40: [----------] 3 tests from HelpManagerTest (1 ms total) 40: 40: [----------] 2 tests from HelpTopicFormattingTest 40: [ RUN ] HelpTopicFormattingTest.FormatsSimpleTopic 40: [ OK ] HelpTopicFormattingTest.FormatsSimpleTopic (1 ms) 40: [ RUN ] HelpTopicFormattingTest.FormatsCompositeTopicWithSubTopics 40: [ OK ] HelpTopicFormattingTest.FormatsCompositeTopicWithSubTopics (1 ms) 40: [----------] 2 tests from HelpTopicFormattingTest (3 ms total) 40: 40: [----------] 11 tests from HelpWriterContextTest 40: [ RUN ] HelpWriterContextTest.FormatsParagraphs 40: [ OK ] HelpWriterContextTest.FormatsParagraphs (0 ms) 40: [ RUN ] HelpWriterContextTest.FormatsRstStyleParagraphs 40: [ OK ] HelpWriterContextTest.FormatsRstStyleParagraphs (0 ms) 40: [ RUN ] HelpWriterContextTest.CleansUpExtraWhitespace 40: [ OK ] HelpWriterContextTest.CleansUpExtraWhitespace (0 ms) 40: [ RUN ] HelpWriterContextTest.FormatsLiteralText 40: [ OK ] HelpWriterContextTest.FormatsLiteralText (1 ms) 40: [ RUN ] HelpWriterContextTest.FormatsLiteralTextAtBeginning 40: [ OK ] HelpWriterContextTest.FormatsLiteralTextAtBeginning (1 ms) 40: [ RUN ] HelpWriterContextTest.FormatsLiteralTextWithIndentation 40: [ OK ] HelpWriterContextTest.FormatsLiteralTextWithIndentation (0 ms) 40: [ RUN ] HelpWriterContextTest.FormatsBulletList 40: [ OK ] HelpWriterContextTest.FormatsBulletList (0 ms) 40: [ RUN ] HelpWriterContextTest.FormatsEnumeratedList 40: [ OK ] HelpWriterContextTest.FormatsEnumeratedList (0 ms) 40: [ RUN ] HelpWriterContextTest.FormatsSimpleTable 40: [ OK ] HelpWriterContextTest.FormatsSimpleTable (1 ms) 40: [ RUN ] HelpWriterContextTest.FormatsGridTable 40: [ OK ] HelpWriterContextTest.FormatsGridTable (1 ms) 40: [ RUN ] HelpWriterContextTest.FormatsTitles 40: [ OK ] HelpWriterContextTest.FormatsTitles (1 ms) 40: [----------] 11 tests from HelpWriterContextTest (12 ms total) 40: 40: [----------] Global test environment tear-down 40: [==========] 22 tests from 4 test suites ran. (24 ms total) 40: [ PASSED ] 22 tests. 40/92 Test #40: OnlineHelpUnitTests ....................... Passed 0.10 sec test 41 Start 41: OptionsUnitTests 41: Test command: /build/reproducible-path/gromacs-2025.1/build/basic/bin/options-test "--gtest_output=xml:/build/reproducible-path/gromacs-2025.1/build/basic/Testing/Temporary/OptionsUnitTests.xml" 41: Working Directory: /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/options/tests 41: Test timeout computed to be: 30 41: [==========] Running 112 tests from 18 test suites. 41: [----------] Global test environment set-up. 41: [----------] 5 tests from AbstractOptionStorageTest 41: [ RUN ] AbstractOptionStorageTest.HandlesSetInFinish 41: [ OK ] AbstractOptionStorageTest.HandlesSetInFinish (0 ms) 41: [ RUN ] AbstractOptionStorageTest.HandlesValueRemoval 41: [ OK ] AbstractOptionStorageTest.HandlesValueRemoval (0 ms) 41: [ RUN ] AbstractOptionStorageTest.HandlesValueAddition 41: [ OK ] AbstractOptionStorageTest.HandlesValueAddition (0 ms) 41: [ RUN ] AbstractOptionStorageTest.HandlesTooManyValueAddition 41: [ OK ] AbstractOptionStorageTest.HandlesTooManyValueAddition (0 ms) 41: [ RUN ] AbstractOptionStorageTest.AllowsEmptyValues 41: [ OK ] AbstractOptionStorageTest.AllowsEmptyValues (0 ms) 41: [----------] 5 tests from AbstractOptionStorageTest (2 ms total) 41: 41: [----------] 10 tests from FileNameOptionTest 41: [ RUN ] FileNameOptionTest.HandlesRequiredDefaultValueWithoutExtension 41: [ OK ] FileNameOptionTest.HandlesRequiredDefaultValueWithoutExtension (0 ms) 41: [ RUN ] FileNameOptionTest.HandlesRequiredOptionWithoutValue 41: [ OK ] FileNameOptionTest.HandlesRequiredOptionWithoutValue (0 ms) 41: [ RUN ] FileNameOptionTest.HandlesOptionalUnsetOption 41: [ OK ] FileNameOptionTest.HandlesOptionalUnsetOption (0 ms) 41: [ RUN ] FileNameOptionTest.HandlesOptionalDefaultValueWithoutExtension 41: [ OK ] FileNameOptionTest.HandlesOptionalDefaultValueWithoutExtension (0 ms) 41: [ RUN ] FileNameOptionTest.HandlesRequiredCustomDefaultExtension 41: [ OK ] FileNameOptionTest.HandlesRequiredCustomDefaultExtension (0 ms) 41: [ RUN ] FileNameOptionTest.HandlesOptionalCustomDefaultExtension 41: [ OK ] FileNameOptionTest.HandlesOptionalCustomDefaultExtension (0 ms) 41: [ RUN ] FileNameOptionTest.GivesErrorOnUnknownFileSuffix 41: [ OK ] FileNameOptionTest.GivesErrorOnUnknownFileSuffix (0 ms) 41: [ RUN ] FileNameOptionTest.GivesErrorOnInvalidFileSuffix 41: [ OK ] FileNameOptionTest.GivesErrorOnInvalidFileSuffix (0 ms) 41: [ RUN ] FileNameOptionTest.HandlesRequiredCsvValueWithoutExtension 41: [ OK ] FileNameOptionTest.HandlesRequiredCsvValueWithoutExtension (0 ms) 41: [ RUN ] FileNameOptionTest.HandlesRequiredCsvOptionWithoutValue 41: [ OK ] FileNameOptionTest.HandlesRequiredCsvOptionWithoutValue (0 ms) 41: [----------] 10 tests from FileNameOptionTest (1 ms total) 41: 41: [----------] 16 tests from FileNameOptionManagerTest 41: [ RUN ] FileNameOptionManagerTest.AddsMissingExtension 41: [ OK ] FileNameOptionManagerTest.AddsMissingExtension (0 ms) 41: [ RUN ] FileNameOptionManagerTest.AddsMissingCustomDefaultExtension 41: [ OK ] FileNameOptionManagerTest.AddsMissingCustomDefaultExtension (0 ms) 41: [ RUN ] FileNameOptionManagerTest.GivesErrorOnMissingInputFile 41: [ OK ] FileNameOptionManagerTest.GivesErrorOnMissingInputFile (4 ms) 41: [ RUN ] FileNameOptionManagerTest.GivesErrorOnMissingGenericInputFile 41: [ OK ] FileNameOptionManagerTest.GivesErrorOnMissingGenericInputFile (0 ms) 41: [ RUN ] FileNameOptionManagerTest.GivesErrorOnMissingDefaultInputFile 41: [ OK ] FileNameOptionManagerTest.GivesErrorOnMissingDefaultInputFile (0 ms) 41: [ RUN ] FileNameOptionManagerTest.GivesErrorOnMissingRequiredInputFile 41: [ OK ] FileNameOptionManagerTest.GivesErrorOnMissingRequiredInputFile (0 ms) 41: [ RUN ] FileNameOptionManagerTest.AcceptsMissingInputFileIfSpecified 41: [ OK ] FileNameOptionManagerTest.AcceptsMissingInputFileIfSpecified (0 ms) 41: [ RUN ] FileNameOptionManagerTest.AcceptsMissingDefaultInputFileIfSpecified 41: [ OK ] FileNameOptionManagerTest.AcceptsMissingDefaultInputFileIfSpecified (0 ms) 41: [ RUN ] FileNameOptionManagerTest.AcceptsMissingRequiredInputFileIfSpecified 41: [ OK ] FileNameOptionManagerTest.AcceptsMissingRequiredInputFileIfSpecified (0 ms) 41: [ RUN ] FileNameOptionManagerTest.AddsMissingExtensionBasedOnExistingFile 41: [ OK ] FileNameOptionManagerTest.AddsMissingExtensionBasedOnExistingFile (0 ms) 41: [ RUN ] FileNameOptionManagerTest.AddsMissingExtensionForRequiredDefaultNameBasedOnExistingFile 41: [ OK ] FileNameOptionManagerTest.AddsMissingExtensionForRequiredDefaultNameBasedOnExistingFile (0 ms) 41: [ RUN ] FileNameOptionManagerTest.AddsMissingExtensionForOptionalDefaultNameBasedOnExistingFile 41: [ OK ] FileNameOptionManagerTest.AddsMissingExtensionForOptionalDefaultNameBasedOnExistingFile (0 ms) 41: [ RUN ] FileNameOptionManagerTest.AddsMissingExtensionForRequiredFromDefaultNameOptionBasedOnExistingFile 41: [ OK ] FileNameOptionManagerTest.AddsMissingExtensionForRequiredFromDefaultNameOptionBasedOnExistingFile (0 ms) 41: [ RUN ] FileNameOptionManagerTest.AddsMissingExtensionForOptionalFromDefaultNameOptionBasedOnExistingFile 41: [ OK ] FileNameOptionManagerTest.AddsMissingExtensionForOptionalFromDefaultNameOptionBasedOnExistingFile (0 ms) 41: [ RUN ] FileNameOptionManagerTest.DefaultNameOptionWorksWithoutInputChecking 41: [ OK ] FileNameOptionManagerTest.DefaultNameOptionWorksWithoutInputChecking (0 ms) 41: [ RUN ] FileNameOptionManagerTest.AcceptsCompressedInputFile 41: [ OK ] FileNameOptionManagerTest.AcceptsCompressedInputFile (0 ms) 41: [----------] 16 tests from FileNameOptionManagerTest (6 ms total) 41: 41: [----------] 1 test from OptionsTest 41: [ RUN ] OptionsTest.FailsOnNonsafeStorage 41: [ OK ] OptionsTest.FailsOnNonsafeStorage (0 ms) 41: [----------] 1 test from OptionsTest (0 ms total) 41: 41: [----------] 9 tests from OptionsAssignerTest 41: [ RUN ] OptionsAssignerTest.HandlesMissingRequiredParameter 41: [ OK ] OptionsAssignerTest.HandlesMissingRequiredParameter (0 ms) 41: [ RUN ] OptionsAssignerTest.HandlesRequiredParameterWithDefaultValue 41: [ OK ] OptionsAssignerTest.HandlesRequiredParameterWithDefaultValue (0 ms) 41: [ RUN ] OptionsAssignerTest.HandlesInvalidMultipleParameter 41: [ OK ] OptionsAssignerTest.HandlesInvalidMultipleParameter (0 ms) 41: [ RUN ] OptionsAssignerTest.HandlesMultipleParameter 41: [ OK ] OptionsAssignerTest.HandlesMultipleParameter (0 ms) 41: [ RUN ] OptionsAssignerTest.HandlesMissingValue 41: [ OK ] OptionsAssignerTest.HandlesMissingValue (0 ms) 41: [ RUN ] OptionsAssignerTest.HandlesExtraValue 41: [ OK ] OptionsAssignerTest.HandlesExtraValue (0 ms) 41: [ RUN ] OptionsAssignerTest.HandlesGroups 41: [ OK ] OptionsAssignerTest.HandlesGroups (0 ms) 41: [ RUN ] OptionsAssignerTest.HandlesSections 41: [ OK ] OptionsAssignerTest.HandlesSections (0 ms) 41: [ RUN ] OptionsAssignerTest.HandlesMultipleSources 41: [ OK ] OptionsAssignerTest.HandlesMultipleSources (0 ms) 41: [----------] 9 tests from OptionsAssignerTest (1 ms total) 41: 41: [----------] 4 tests from OptionsAssignerBooleanTest 41: [ RUN ] OptionsAssignerBooleanTest.StoresYesValue 41: [ OK ] OptionsAssignerBooleanTest.StoresYesValue (0 ms) 41: [ RUN ] OptionsAssignerBooleanTest.SetsBooleanWithoutExplicitValue 41: [ OK ] OptionsAssignerBooleanTest.SetsBooleanWithoutExplicitValue (0 ms) 41: [ RUN ] OptionsAssignerBooleanTest.ClearsBooleanWithPrefixNo 41: [ OK ] OptionsAssignerBooleanTest.ClearsBooleanWithPrefixNo (0 ms) 41: [ RUN ] OptionsAssignerBooleanTest.HandlesBooleanWithPrefixAndValue 41: [ OK ] OptionsAssignerBooleanTest.HandlesBooleanWithPrefixAndValue (0 ms) 41: [----------] 4 tests from OptionsAssignerBooleanTest (3 ms total) 41: 41: [----------] 13 tests from OptionsAssignerIntegerTest 41: [ RUN ] OptionsAssignerIntegerTest.StoresSingleValue 41: [ OK ] OptionsAssignerIntegerTest.StoresSingleValue (0 ms) 41: [ RUN ] OptionsAssignerIntegerTest.HandlesEmptyValue 41: [ OK ] OptionsAssignerIntegerTest.HandlesEmptyValue (0 ms) 41: [ RUN ] OptionsAssignerIntegerTest.HandlesInvalidValue 41: [ OK ] OptionsAssignerIntegerTest.HandlesInvalidValue (0 ms) 41: [ RUN ] OptionsAssignerIntegerTest.HandlesOverflow 41: [ OK ] OptionsAssignerIntegerTest.HandlesOverflow (0 ms) 41: [ RUN ] OptionsAssignerIntegerTest.StoresDefaultValue 41: [ OK ] OptionsAssignerIntegerTest.StoresDefaultValue (0 ms) 41: [ RUN ] OptionsAssignerIntegerTest.StoresDefaultValueIfSet 41: [ OK ] OptionsAssignerIntegerTest.StoresDefaultValueIfSet (0 ms) 41: [ RUN ] OptionsAssignerIntegerTest.HandlesDefaultValueIfSetWhenNotSet 41: [ OK ] OptionsAssignerIntegerTest.HandlesDefaultValueIfSetWhenNotSet (0 ms) 41: [ RUN ] OptionsAssignerIntegerTest.HandlesBothDefaultValues 41: [ OK ] OptionsAssignerIntegerTest.HandlesBothDefaultValues (0 ms) 41: [ RUN ] OptionsAssignerIntegerTest.StoresToVector 41: [ OK ] OptionsAssignerIntegerTest.StoresToVector (0 ms) 41: [ RUN ] OptionsAssignerIntegerTest.HandlesVectors 41: [ OK ] OptionsAssignerIntegerTest.HandlesVectors (0 ms) 41: [ RUN ] OptionsAssignerIntegerTest.HandlesVectorFromSingleValue 41: [ OK ] OptionsAssignerIntegerTest.HandlesVectorFromSingleValue (0 ms) 41: [ RUN ] OptionsAssignerIntegerTest.HandlesVectorsWithDefaultValue 41: [ OK ] OptionsAssignerIntegerTest.HandlesVectorsWithDefaultValue (0 ms) 41: [ RUN ] OptionsAssignerIntegerTest.HandlesVectorsWithDefaultValueWithInvalidAssignment 41: [ OK ] OptionsAssignerIntegerTest.HandlesVectorsWithDefaultValueWithInvalidAssignment (0 ms) 41: [----------] 13 tests from OptionsAssignerIntegerTest (1 ms total) 41: 41: [----------] 5 tests from OptionsAssignerDoubleTest 41: [ RUN ] OptionsAssignerDoubleTest.StoresSingleValue 41: [ OK ] OptionsAssignerDoubleTest.StoresSingleValue (0 ms) 41: [ RUN ] OptionsAssignerDoubleTest.StoresValueFromFloat 41: [ OK ] OptionsAssignerDoubleTest.StoresValueFromFloat (0 ms) 41: [ RUN ] OptionsAssignerDoubleTest.HandlesEmptyValue 41: [ OK ] OptionsAssignerDoubleTest.HandlesEmptyValue (0 ms) 41: [ RUN ] OptionsAssignerDoubleTest.HandlesPreSetScaleValue 41: [ OK ] OptionsAssignerDoubleTest.HandlesPreSetScaleValue (0 ms) 41: [ RUN ] OptionsAssignerDoubleTest.HandlesPostSetScaleValue 41: [ OK ] OptionsAssignerDoubleTest.HandlesPostSetScaleValue (0 ms) 41: [----------] 5 tests from OptionsAssignerDoubleTest (0 ms total) 41: 41: [----------] 9 tests from OptionsAssignerStringTest 41: [ RUN ] OptionsAssignerStringTest.StoresSingleValue 41: [ OK ] OptionsAssignerStringTest.StoresSingleValue (0 ms) 41: [ RUN ] OptionsAssignerStringTest.HandlesEnumValue 41: [ OK ] OptionsAssignerStringTest.HandlesEnumValue (0 ms) 41: [ RUN ] OptionsAssignerStringTest.HandlesEnumValueFromNullTerminatedArray 41: [ OK ] OptionsAssignerStringTest.HandlesEnumValueFromNullTerminatedArray (0 ms) 41: [ RUN ] OptionsAssignerStringTest.HandlesIncorrectEnumValue 41: [ OK ] OptionsAssignerStringTest.HandlesIncorrectEnumValue (0 ms) 41: [ RUN ] OptionsAssignerStringTest.CompletesEnumValue 41: [ OK ] OptionsAssignerStringTest.CompletesEnumValue (0 ms) 41: [ RUN ] OptionsAssignerStringTest.HandlesEnumWithNoValue 41: [ OK ] OptionsAssignerStringTest.HandlesEnumWithNoValue (0 ms) 41: [ RUN ] OptionsAssignerStringTest.HandlesEnumDefaultValue 41: [ OK ] OptionsAssignerStringTest.HandlesEnumDefaultValue (0 ms) 41: [ RUN ] OptionsAssignerStringTest.HandlesEnumDefaultValueFromVariable 41: [ OK ] OptionsAssignerStringTest.HandlesEnumDefaultValueFromVariable (0 ms) 41: [ RUN ] OptionsAssignerStringTest.HandlesEnumDefaultValueFromVector 41: [ OK ] OptionsAssignerStringTest.HandlesEnumDefaultValueFromVector (0 ms) 41: [----------] 9 tests from OptionsAssignerStringTest (0 ms total) 41: 41: [----------] 6 tests from OptionsAssignerEnumTest 41: [ RUN ] OptionsAssignerEnumTest.StoresSingleValue 41: [ OK ] OptionsAssignerEnumTest.StoresSingleValue (0 ms) 41: [ RUN ] OptionsAssignerEnumTest.StoresVectorValues 41: [ OK ] OptionsAssignerEnumTest.StoresVectorValues (0 ms) 41: [ RUN ] OptionsAssignerEnumTest.HandlesInitialValueOutOfRange 41: [ OK ] OptionsAssignerEnumTest.HandlesInitialValueOutOfRange (0 ms) 41: [ RUN ] OptionsAssignerEnumTest.HandlesEnumDefaultValue 41: [ OK ] OptionsAssignerEnumTest.HandlesEnumDefaultValue (0 ms) 41: [ RUN ] OptionsAssignerEnumTest.HandlesEnumDefaultValueFromVariable 41: [ OK ] OptionsAssignerEnumTest.HandlesEnumDefaultValueFromVariable (0 ms) 41: [ RUN ] OptionsAssignerEnumTest.HandlesEnumDefaultValueFromVector 41: [ OK ] OptionsAssignerEnumTest.HandlesEnumDefaultValueFromVector (0 ms) 41: [----------] 6 tests from OptionsAssignerEnumTest (0 ms total) 41: 41: [----------] 8 tests from RepeatingOptionSectionTest 41: [ RUN ] RepeatingOptionSectionTest.HandlesNoInstance 41: [ OK ] RepeatingOptionSectionTest.HandlesNoInstance (0 ms) 41: [ RUN ] RepeatingOptionSectionTest.HandlesNoInstanceWithRequiredOption 41: [ OK ] RepeatingOptionSectionTest.HandlesNoInstanceWithRequiredOption (0 ms) 41: [ RUN ] RepeatingOptionSectionTest.HandlesSingleInstance 41: [ OK ] RepeatingOptionSectionTest.HandlesSingleInstance (0 ms) 41: [ RUN ] RepeatingOptionSectionTest.HandlesDefaultValue 41: [ OK ] RepeatingOptionSectionTest.HandlesDefaultValue (0 ms) 41: [ RUN ] RepeatingOptionSectionTest.HandlesTwoInstances 41: [ OK ] RepeatingOptionSectionTest.HandlesTwoInstances (0 ms) 41: [ RUN ] RepeatingOptionSectionTest.HandlesUnsetOptionWithImplicitDefault 41: [ OK ] RepeatingOptionSectionTest.HandlesUnsetOptionWithImplicitDefault (0 ms) 41: [ RUN ] RepeatingOptionSectionTest.HandlesUnsetOptionWithExplicitDefault 41: [ OK ] RepeatingOptionSectionTest.HandlesUnsetOptionWithExplicitDefault (0 ms) 41: [ RUN ] RepeatingOptionSectionTest.HandlesNestedSections 41: [ OK ] RepeatingOptionSectionTest.HandlesNestedSections (0 ms) 41: [----------] 8 tests from RepeatingOptionSectionTest (0 ms total) 41: 41: [----------] 1 test from TimeUnitManagerTest 41: [ RUN ] TimeUnitManagerTest.BasicOperations 41: [ OK ] TimeUnitManagerTest.BasicOperations (0 ms) 41: [----------] 1 test from TimeUnitManagerTest (0 ms total) 41: 41: [----------] 4 tests from TimeUnitBehaviorTest 41: [ RUN ] TimeUnitBehaviorTest.ScalesAssignedOptionValue 41: [ OK ] TimeUnitBehaviorTest.ScalesAssignedOptionValue (0 ms) 41: [ RUN ] TimeUnitBehaviorTest.DoesNotScaleDefaultValues 41: [ OK ] TimeUnitBehaviorTest.DoesNotScaleDefaultValues (0 ms) 41: [ RUN ] TimeUnitBehaviorTest.ScalesUserInputWithMultipleSources 41: [ OK ] TimeUnitBehaviorTest.ScalesUserInputWithMultipleSources (0 ms) 41: [ RUN ] TimeUnitBehaviorTest.TimeUnitOptionWorks 41: [ OK ] TimeUnitBehaviorTest.TimeUnitOptionWorks (0 ms) 41: [----------] 4 tests from TimeUnitBehaviorTest (0 ms total) 41: 41: [----------] 2 tests from TreeValueSupportAssignTest 41: [ RUN ] TreeValueSupportAssignTest.AssignsFromTree 41: [ OK ] TreeValueSupportAssignTest.AssignsFromTree (0 ms) 41: [ RUN ] TreeValueSupportAssignTest.AssignsFromTreeWithArrays 41: [ OK ] TreeValueSupportAssignTest.AssignsFromTreeWithArrays (0 ms) 41: [----------] 2 tests from TreeValueSupportAssignTest (0 ms total) 41: 41: [----------] 1 test from TreeValueSupportAssignErrorTest 41: [ RUN ] TreeValueSupportAssignErrorTest.HandlesInvalidValue 41: [ OK ] TreeValueSupportAssignErrorTest.HandlesInvalidValue (0 ms) 41: [----------] 1 test from TreeValueSupportAssignErrorTest (0 ms total) 41: 41: [----------] 5 tests from TreeValueSupportCheckTest 41: [ RUN ] TreeValueSupportCheckTest.HandlesEmpty 41: [ OK ] TreeValueSupportCheckTest.HandlesEmpty (0 ms) 41: [ RUN ] TreeValueSupportCheckTest.HandlesMatchingTree 41: [ OK ] TreeValueSupportCheckTest.HandlesMatchingTree (0 ms) 41: [ RUN ] TreeValueSupportCheckTest.HandlesSmallerTree1 41: [ OK ] TreeValueSupportCheckTest.HandlesSmallerTree1 (0 ms) 41: [ RUN ] TreeValueSupportCheckTest.HandlesSmallerTree2 41: [ OK ] TreeValueSupportCheckTest.HandlesSmallerTree2 (0 ms) 41: [ RUN ] TreeValueSupportCheckTest.DetectsExtraValue 41: [ OK ] TreeValueSupportCheckTest.DetectsExtraValue (0 ms) 41: [----------] 5 tests from TreeValueSupportCheckTest (0 ms total) 41: 41: [----------] 6 tests from TreeValueSupportAdjustTest 41: [ RUN ] TreeValueSupportAdjustTest.FillsDefaultValues 41: [ OK ] TreeValueSupportAdjustTest.FillsDefaultValues (1 ms) 41: [ RUN ] TreeValueSupportAdjustTest.FillsDefaultVectorValues 41: [ OK ] TreeValueSupportAdjustTest.FillsDefaultVectorValues (5 ms) 41: [ RUN ] TreeValueSupportAdjustTest.FillsDefaultObjectValues 41: [ OK ] TreeValueSupportAdjustTest.FillsDefaultObjectValues (4 ms) 41: [ RUN ] TreeValueSupportAdjustTest.NormalizesValues 41: [ OK ] TreeValueSupportAdjustTest.NormalizesValues (1 ms) 41: [ RUN ] TreeValueSupportAdjustTest.MergesDefaultValues 41: [ OK ] TreeValueSupportAdjustTest.MergesDefaultValues (1 ms) 41: [ RUN ] TreeValueSupportAdjustTest.OrdersValues 41: [ OK ] TreeValueSupportAdjustTest.OrdersValues (1 ms) 41: [----------] 6 tests from TreeValueSupportAdjustTest (15 ms total) 41: 41: [----------] 7 tests from TreeValueSupportTest 41: [ RUN ] TreeValueSupportTest.SupportsBooleanOption 41: [ OK ] TreeValueSupportTest.SupportsBooleanOption (1 ms) 41: [ RUN ] TreeValueSupportTest.SupportsIntegerOption 41: [ OK ] TreeValueSupportTest.SupportsIntegerOption (1 ms) 41: [ RUN ] TreeValueSupportTest.SupportsInt64Option 41: [ OK ] TreeValueSupportTest.SupportsInt64Option (0 ms) 41: [ RUN ] TreeValueSupportTest.SupportsStringOption 41: [ OK ] TreeValueSupportTest.SupportsStringOption (0 ms) 41: [ RUN ] TreeValueSupportTest.SupportsFloatOption 41: [ OK ] TreeValueSupportTest.SupportsFloatOption (0 ms) 41: [ RUN ] TreeValueSupportTest.SupportsDoubleOption 41: [ OK ] TreeValueSupportTest.SupportsDoubleOption (0 ms) 41: [ RUN ] TreeValueSupportTest.SupportsEnumOption 41: [ OK ] TreeValueSupportTest.SupportsEnumOption (0 ms) 41: [----------] 7 tests from TreeValueSupportTest (6 ms total) 41: 41: [----------] Global test environment tear-down 41: [==========] 112 tests from 18 test suites ran. (43 ms total) 41: [ PASSED ] 112 tests. 41/92 Test #41: OptionsUnitTests .......................... Passed 0.14 sec test 42 Start 42: PbcutilUnitTest 42: Test command: /build/reproducible-path/gromacs-2025.1/build/basic/bin/pbcutil-test "--gtest_output=xml:/build/reproducible-path/gromacs-2025.1/build/basic/Testing/Temporary/PbcutilUnitTest.xml" 42: Working Directory: /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/pbcutil/tests 42: Test timeout computed to be: 30 42: [==========] Running 36 tests from 5 test suites. 42: [----------] Global test environment set-up. 42: [----------] 1 test from ShiftTest 42: [ RUN ] ShiftTest.CoordinateShiftWorks 42: [ OK ] ShiftTest.CoordinateShiftWorks (0 ms) 42: [----------] 1 test from ShiftTest (0 ms total) 42: 42: [----------] 2 tests from MShift 42: [ RUN ] MShift.shiftsAndUnshifts 42: [ OK ] MShift.shiftsAndUnshifts (0 ms) 42: [ RUN ] MShift.shiftsAndUnshiftsSelf 42: [ OK ] MShift.shiftsAndUnshiftsSelf (0 ms) 42: [----------] 2 tests from MShift (1 ms total) 42: 42: [----------] 4 tests from PbcTest 42: [ RUN ] PbcTest.CalcShiftsWorks 42: [ OK ] PbcTest.CalcShiftsWorks (2 ms) 42: [ RUN ] PbcTest.PutAtomsInCubicBoxAlreadyInBox 42: [ OK ] PbcTest.PutAtomsInCubicBoxAlreadyInBox (0 ms) 42: [ RUN ] PbcTest.PutAtomsInCubicBoxFromOutsideBox 42: [ OK ] PbcTest.PutAtomsInCubicBoxFromOutsideBox (0 ms) 42: [ RUN ] PbcTest.PutAtomsInTriclinicBoxFromOutsideBox 42: [ OK ] PbcTest.PutAtomsInTriclinicBoxFromOutsideBox (0 ms) 42: [----------] 4 tests from PbcTest (3 ms total) 42: 42: [----------] 2 tests from PbcEnumsTest 42: [ RUN ] PbcEnumsTest.CenteringTypeNamesAreCorrect 42: [ OK ] PbcEnumsTest.CenteringTypeNamesAreCorrect (0 ms) 42: [ RUN ] PbcEnumsTest.UnitCellTypeNamesAreCorrect 42: [ OK ] PbcEnumsTest.UnitCellTypeNamesAreCorrect (0 ms) 42: [----------] 2 tests from PbcEnumsTest (0 ms total) 42: 42: [----------] 27 tests from CorrectCoordinates/COMInPlaceTest 42: [ RUN ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/0 42: [ OK ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/0 (1 ms) 42: [ RUN ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/1 42: [ OK ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/1 (1 ms) 42: [ RUN ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/2 42: [ OK ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/2 (1 ms) 42: [ RUN ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/3 42: [ OK ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/3 (1 ms) 42: [ RUN ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/4 42: [ OK ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/4 (1 ms) 42: [ RUN ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/5 42: [ OK ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/5 (1 ms) 42: [ RUN ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/6 42: [ OK ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/6 (1 ms) 42: [ RUN ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/7 42: [ OK ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/7 (1 ms) 42: [ RUN ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/8 42: [ OK ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/8 (1 ms) 42: [ RUN ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/9 42: [ OK ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/9 (1 ms) 42: [ RUN ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/10 42: [ OK ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/10 (1 ms) 42: [ RUN ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/11 42: [ OK ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/11 (1 ms) 42: [ RUN ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/12 42: [ OK ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/12 (1 ms) 42: [ RUN ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/13 42: [ OK ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/13 (1 ms) 42: [ RUN ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/14 42: [ OK ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/14 (1 ms) 42: [ RUN ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/15 42: [ OK ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/15 (1 ms) 42: [ RUN ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/16 42: [ OK ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/16 (1 ms) 42: [ RUN ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/17 42: [ OK ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/17 (1 ms) 42: [ RUN ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/18 42: [ OK ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/18 (1 ms) 42: [ RUN ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/19 42: [ OK ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/19 (1 ms) 42: [ RUN ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/20 42: [ OK ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/20 (1 ms) 42: [ RUN ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/21 42: [ OK ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/21 (1 ms) 42: [ RUN ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/22 42: [ OK ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/22 (1 ms) 42: [ RUN ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/23 42: [ OK ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/23 (1 ms) 42: [ RUN ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/24 42: [ OK ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/24 (1 ms) 42: [ RUN ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/25 42: [ OK ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/25 (1 ms) 42: [ RUN ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/26 42: [ OK ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/26 (1 ms) 42: [----------] 27 tests from CorrectCoordinates/COMInPlaceTest (38 ms total) 42: 42: [----------] Global test environment tear-down 42: [==========] 36 tests from 5 test suites ran. (43 ms total) 42: [ PASSED ] 36 tests. 42/92 Test #42: PbcutilUnitTest ........................... Passed 0.12 sec test 43 Start 43: RandomUnitTests 43: Test command: /build/reproducible-path/gromacs-2025.1/build/basic/bin/random-test "--gtest_output=xml:/build/reproducible-path/gromacs-2025.1/build/basic/Testing/Temporary/RandomUnitTests.xml" 43: Working Directory: /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/random/tests 43: Test timeout computed to be: 30 43: [==========] Running 44 tests from 10 test suites. 43: [----------] Global test environment set-up. 43: [----------] 4 tests from ExponentialDistributionTest 43: [ RUN ] ExponentialDistributionTest.Output 43: [ OK ] ExponentialDistributionTest.Output (1 ms) 43: [ RUN ] ExponentialDistributionTest.Logical 43: [ OK ] ExponentialDistributionTest.Logical (0 ms) 43: [ RUN ] ExponentialDistributionTest.Reset 43: [ OK ] ExponentialDistributionTest.Reset (0 ms) 43: [ RUN ] ExponentialDistributionTest.AltParam 43: [ OK ] ExponentialDistributionTest.AltParam (0 ms) 43: [----------] 4 tests from ExponentialDistributionTest (1 ms total) 43: 43: [----------] 4 tests from GammaDistributionTest 43: [ RUN ] GammaDistributionTest.Output 43: [ OK ] GammaDistributionTest.Output (0 ms) 43: [ RUN ] GammaDistributionTest.Logical 43: [ OK ] GammaDistributionTest.Logical (0 ms) 43: [ RUN ] GammaDistributionTest.Reset 43: [ OK ] GammaDistributionTest.Reset (0 ms) 43: [ RUN ] GammaDistributionTest.AltParam 43: [ OK ] GammaDistributionTest.AltParam (0 ms) 43: [----------] 4 tests from GammaDistributionTest (1 ms total) 43: 43: [----------] 4 tests from NormalDistributionTest 43: [ RUN ] NormalDistributionTest.Output 43: [ OK ] NormalDistributionTest.Output (1 ms) 43: [ RUN ] NormalDistributionTest.Logical 43: [ OK ] NormalDistributionTest.Logical (0 ms) 43: [ RUN ] NormalDistributionTest.Reset 43: [ OK ] NormalDistributionTest.Reset (0 ms) 43: [ RUN ] NormalDistributionTest.AltParam 43: [ OK ] NormalDistributionTest.AltParam (0 ms) 43: [----------] 4 tests from NormalDistributionTest (1 ms total) 43: 43: [----------] 1 test from SeedTest 43: [ RUN ] SeedTest.makeRandomSeed 43: [ OK ] SeedTest.makeRandomSeed (0 ms) 43: [----------] 1 test from SeedTest (0 ms total) 43: 43: [----------] 6 tests from TabulatedNormalDistributionTest 43: [ RUN ] TabulatedNormalDistributionTest.Output14 43: [ OK ] TabulatedNormalDistributionTest.Output14 (0 ms) 43: [ RUN ] TabulatedNormalDistributionTest.Output16 43: [ OK ] TabulatedNormalDistributionTest.Output16 (0 ms) 43: [ RUN ] TabulatedNormalDistributionTest.OutputDouble14 43: [ OK ] TabulatedNormalDistributionTest.OutputDouble14 (0 ms) 43: [ RUN ] TabulatedNormalDistributionTest.Logical 43: [ OK ] TabulatedNormalDistributionTest.Logical (0 ms) 43: [ RUN ] TabulatedNormalDistributionTest.Reset 43: [ OK ] TabulatedNormalDistributionTest.Reset (0 ms) 43: [ RUN ] TabulatedNormalDistributionTest.AltParam 43: [ OK ] TabulatedNormalDistributionTest.AltParam (0 ms) 43: [----------] 6 tests from TabulatedNormalDistributionTest (2 ms total) 43: 43: [----------] 1 test from TabulatedNormalDistributionTableTest 43: [ RUN ] TabulatedNormalDistributionTableTest.HasValidProperties 43: [ OK ] TabulatedNormalDistributionTableTest.HasValidProperties (3 ms) 43: [----------] 1 test from TabulatedNormalDistributionTableTest (3 ms total) 43: 43: [----------] 6 tests from ThreeFry2x64Test 43: [ RUN ] ThreeFry2x64Test.Logical 43: [ OK ] ThreeFry2x64Test.Logical (0 ms) 43: [ RUN ] ThreeFry2x64Test.InternalCounterSequence 43: [ OK ] ThreeFry2x64Test.InternalCounterSequence (1 ms) 43: [ RUN ] ThreeFry2x64Test.Reseed 43: [ OK ] ThreeFry2x64Test.Reseed (0 ms) 43: [ RUN ] ThreeFry2x64Test.Discard 43: [ OK ] ThreeFry2x64Test.Discard (0 ms) 43: [ RUN ] ThreeFry2x64Test.InvalidCounter 43: [ OK ] ThreeFry2x64Test.InvalidCounter (0 ms) 43: [ RUN ] ThreeFry2x64Test.ExhaustInternalCounter 43: [ OK ] ThreeFry2x64Test.ExhaustInternalCounter (0 ms) 43: [----------] 6 tests from ThreeFry2x64Test (1 ms total) 43: 43: [----------] 4 tests from UniformIntDistributionTest 43: [ RUN ] UniformIntDistributionTest.Output 43: [ OK ] UniformIntDistributionTest.Output (0 ms) 43: [ RUN ] UniformIntDistributionTest.Logical 43: [ OK ] UniformIntDistributionTest.Logical (0 ms) 43: [ RUN ] UniformIntDistributionTest.Reset 43: [ OK ] UniformIntDistributionTest.Reset (0 ms) 43: [ RUN ] UniformIntDistributionTest.AltParam 43: [ OK ] UniformIntDistributionTest.AltParam (0 ms) 43: [----------] 4 tests from UniformIntDistributionTest (0 ms total) 43: 43: [----------] 5 tests from UniformRealDistributionTest 43: [ RUN ] UniformRealDistributionTest.GenerateCanonical 43: [ OK ] UniformRealDistributionTest.GenerateCanonical (0 ms) 43: [ RUN ] UniformRealDistributionTest.Output 43: [ OK ] UniformRealDistributionTest.Output (0 ms) 43: [ RUN ] UniformRealDistributionTest.Logical 43: [ OK ] UniformRealDistributionTest.Logical (0 ms) 43: [ RUN ] UniformRealDistributionTest.Reset 43: [ OK ] UniformRealDistributionTest.Reset (0 ms) 43: [ RUN ] UniformRealDistributionTest.AltParam 43: [ OK ] UniformRealDistributionTest.AltParam (0 ms) 43: [----------] 5 tests from UniformRealDistributionTest (1 ms total) 43: 43: [----------] 9 tests from KnownAnswersTest/ThreeFry2x64Test 43: [ RUN ] KnownAnswersTest/ThreeFry2x64Test.Default/0 43: [ OK ] KnownAnswersTest/ThreeFry2x64Test.Default/0 (0 ms) 43: [ RUN ] KnownAnswersTest/ThreeFry2x64Test.Default/1 43: [ OK ] KnownAnswersTest/ThreeFry2x64Test.Default/1 (0 ms) 43: [ RUN ] KnownAnswersTest/ThreeFry2x64Test.Default/2 43: [ OK ] KnownAnswersTest/ThreeFry2x64Test.Default/2 (1 ms) 43: [ RUN ] KnownAnswersTest/ThreeFry2x64Test.Fast/0 43: [ OK ] KnownAnswersTest/ThreeFry2x64Test.Fast/0 (0 ms) 43: [ RUN ] KnownAnswersTest/ThreeFry2x64Test.Fast/1 43: [ OK ] KnownAnswersTest/ThreeFry2x64Test.Fast/1 (0 ms) 43: [ RUN ] KnownAnswersTest/ThreeFry2x64Test.Fast/2 43: [ OK ] KnownAnswersTest/ThreeFry2x64Test.Fast/2 (1 ms) 43: [ RUN ] KnownAnswersTest/ThreeFry2x64Test.Using40Rounds/0 43: [ OK ] KnownAnswersTest/ThreeFry2x64Test.Using40Rounds/0 (0 ms) 43: [ RUN ] KnownAnswersTest/ThreeFry2x64Test.Using40Rounds/1 43: [ OK ] KnownAnswersTest/ThreeFry2x64Test.Using40Rounds/1 (0 ms) 43: [ RUN ] KnownAnswersTest/ThreeFry2x64Test.Using40Rounds/2 43: [ OK ] KnownAnswersTest/ThreeFry2x64Test.Using40Rounds/2 (0 ms) 43: [----------] 9 tests from KnownAnswersTest/ThreeFry2x64Test (7 ms total) 43: 43: [----------] Global test environment tear-down 43: [==========] 44 tests from 10 test suites ran. (22 ms total) 43: [ PASSED ] 44 tests. 43/92 Test #43: RandomUnitTests ........................... Passed 0.12 sec test 44 Start 44: RestraintTests 44: Test command: /build/reproducible-path/gromacs-2025.1/build/basic/bin/restraintpotential-test "--gtest_output=xml:/build/reproducible-path/gromacs-2025.1/build/basic/Testing/Temporary/RestraintTests.xml" 44: Working Directory: /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/restraint/tests 44: Test timeout computed to be: 30 44: [==========] Running 1 test from 1 test suite. 44: [----------] Global test environment set-up. 44: [----------] 1 test from RestraintManager 44: [ RUN ] RestraintManager.restraintList 44: [ OK ] RestraintManager.restraintList (0 ms) 44: [----------] 1 test from RestraintManager (0 ms total) 44: 44: [----------] Global test environment tear-down 44: [==========] 1 test from 1 test suite ran. (1 ms total) 44: [ PASSED ] 1 test. 44/92 Test #44: RestraintTests ............................ Passed 0.08 sec test 45 Start 45: TableUnitTests 45: Test command: /build/reproducible-path/gromacs-2025.1/build/basic/bin/table-test "--gtest_output=xml:/build/reproducible-path/gromacs-2025.1/build/basic/Testing/Temporary/TableUnitTests.xml" 45: Working Directory: /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/tables/tests 45: Test timeout computed to be: 30 45: [==========] Running 16 tests from 2 test suites. 45: [----------] Global test environment set-up. 45: [----------] 8 tests from SplineTableTest/0, where TypeParam = gmx::QuadraticSplineTable 45: [ RUN ] SplineTableTest/0.HandlesIncorrectInput 45: [ OK ] SplineTableTest/0.HandlesIncorrectInput (5 ms) 45: [ RUN ] SplineTableTest/0.Sinc 45: [ OK ] SplineTableTest/0.Sinc (3 ms) 45: [ RUN ] SplineTableTest/0.LJ12 45: [ OK ] SplineTableTest/0.LJ12 (63 ms) 45: [ RUN ] SplineTableTest/0.PmeCorrection 45: [ OK ] SplineTableTest/0.PmeCorrection (7 ms) 45: [ RUN ] SplineTableTest/0.HandlesIncorrectNumericalInput 45: [ OK ] SplineTableTest/0.HandlesIncorrectNumericalInput (1 ms) 45: [ RUN ] SplineTableTest/0.NumericalInputPmeCorr 45: [ OK ] SplineTableTest/0.NumericalInputPmeCorr (6 ms) 45: [ RUN ] SplineTableTest/0.TwoFunctions 45: [ OK ] SplineTableTest/0.TwoFunctions (129 ms) 45: [ RUN ] SplineTableTest/0.ThreeFunctions 45: [ OK ] SplineTableTest/0.ThreeFunctions (170 ms) 45: [----------] 8 tests from SplineTableTest/0 (389 ms total) 45: 45: [----------] 8 tests from SplineTableTest/1, where TypeParam = gmx::CubicSplineTable 45: [ RUN ] SplineTableTest/1.HandlesIncorrectInput 45: [ OK ] SplineTableTest/1.HandlesIncorrectInput (5 ms) 45: [ RUN ] SplineTableTest/1.Sinc 45: [ OK ] SplineTableTest/1.Sinc (3 ms) 45: [ RUN ] SplineTableTest/1.LJ12 45: [ OK ] SplineTableTest/1.LJ12 (8 ms) 45: [ RUN ] SplineTableTest/1.PmeCorrection 45: [ OK ] SplineTableTest/1.PmeCorrection (7 ms) 45: [ RUN ] SplineTableTest/1.HandlesIncorrectNumericalInput 45: [ OK ] SplineTableTest/1.HandlesIncorrectNumericalInput (1 ms) 45: [ RUN ] SplineTableTest/1.NumericalInputPmeCorr 45: [ OK ] SplineTableTest/1.NumericalInputPmeCorr (6 ms) 45: [ RUN ] SplineTableTest/1.TwoFunctions 45: [ OK ] SplineTableTest/1.TwoFunctions (16 ms) 45: [ RUN ] SplineTableTest/1.ThreeFunctions 45: [ OK ] SplineTableTest/1.ThreeFunctions (19 ms) 45: [----------] 8 tests from SplineTableTest/1 (69 ms total) 45: 45: [----------] Global test environment tear-down 45: [==========] 16 tests from 2 test suites ran. (459 ms total) 45: [ PASSED ] 16 tests. 45/92 Test #45: TableUnitTests ............................ Passed 0.54 sec test 46 Start 46: TaskAssignmentUnitTests 46: Test command: /build/reproducible-path/gromacs-2025.1/build/basic/bin/taskassignment-test "--gtest_output=xml:/build/reproducible-path/gromacs-2025.1/build/basic/Testing/Temporary/TaskAssignmentUnitTests.xml" 46: Working Directory: /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/taskassignment/tests 46: Test timeout computed to be: 30 46: [==========] Running 3 tests from 2 test suites. 46: [----------] Global test environment set-up. 46: [----------] 2 tests from UserTaskAssignmentStringHandlingTest 46: [ RUN ] UserTaskAssignmentStringHandlingTest.ParsingAndReconstructionWork 46: [ OK ] UserTaskAssignmentStringHandlingTest.ParsingAndReconstructionWork (0 ms) 46: [ RUN ] UserTaskAssignmentStringHandlingTest.EmptyStringCanBeValid 46: [ OK ] UserTaskAssignmentStringHandlingTest.EmptyStringCanBeValid (0 ms) 46: [----------] 2 tests from UserTaskAssignmentStringHandlingTest (0 ms total) 46: 46: [----------] 1 test from GpuIdAndAssignmentStringHandlingTest 46: [ RUN ] GpuIdAndAssignmentStringHandlingTest.InvalidInputsThrow 46: [ OK ] GpuIdAndAssignmentStringHandlingTest.InvalidInputsThrow (2 ms) 46: [----------] 1 test from GpuIdAndAssignmentStringHandlingTest (2 ms total) 46: 46: [----------] Global test environment tear-down 46: [==========] 3 tests from 2 test suites ran. (2 ms total) 46: [ PASSED ] 3 tests. 46/92 Test #46: TaskAssignmentUnitTests ................... Passed 0.07 sec test 47 Start 47: GmxTimingTests 47: Test command: /build/reproducible-path/gromacs-2025.1/build/basic/bin/timing-test "--gtest_output=xml:/build/reproducible-path/gromacs-2025.1/build/basic/Testing/Temporary/GmxTimingTests.xml" 47: Working Directory: /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/timing/tests 47: Test timeout computed to be: 30 47: [==========] Running 6 tests from 1 test suite. 47: [----------] Global test environment set-up. 47: [----------] 6 tests from TimingTest 47: [ RUN ] TimingTest.ElementCountingWorks 47: [ OK ] TimingTest.ElementCountingWorks (0 ms) 47: [ RUN ] TimingTest.ElementNoCountingWorks 47: [ OK ] TimingTest.ElementNoCountingWorks (0 ms) 47: [ RUN ] TimingTest.SubElementCountingWorks 47: [ OK ] TimingTest.SubElementCountingWorks (0 ms) 47: [ RUN ] TimingTest.SubElementNoCountingWorks 47: [ OK ] TimingTest.SubElementNoCountingWorks (0 ms) 47: [ RUN ] TimingTest.RunWallCycle 47: [ OK ] TimingTest.RunWallCycle (1 ms) 47: [ RUN ] TimingTest.RunWallCycleSub 47: [ OK ] TimingTest.RunWallCycleSub (0 ms) 47: [----------] 6 tests from TimingTest (1 ms total) 47: 47: [----------] Global test environment tear-down 47: [==========] 6 tests from 1 test suite ran. (1 ms total) 47: [ PASSED ] 6 tests. 47/92 Test #47: GmxTimingTests ............................ Passed 0.08 sec test 48 Start 48: TopologyTest 48: Test command: /build/reproducible-path/gromacs-2025.1/build/basic/bin/topology-test "--gtest_output=xml:/build/reproducible-path/gromacs-2025.1/build/basic/Testing/Temporary/TopologyTest.xml" 48: Working Directory: /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/topology/tests 48: Test timeout computed to be: 30 48: [==========] Running 153 tests from 10 test suites. 48: [----------] Global test environment set-up. 48: [----------] 3 tests from PdbAtomEntryTest 48: [ RUN ] PdbAtomEntryTest.CanCreateBasicEntry 48: [ OK ] PdbAtomEntryTest.CanCreateBasicEntry (0 ms) 48: [ RUN ] PdbAtomEntryTest.CanCreateEntryWithOccupAndBfac 48: [ OK ] PdbAtomEntryTest.CanCreateEntryWithOccupAndBfac (0 ms) 48: [ RUN ] PdbAtomEntryTest.CanCreateFullEntry 48: [ OK ] PdbAtomEntryTest.CanCreateFullEntry (0 ms) 48: [----------] 3 tests from PdbAtomEntryTest (0 ms total) 48: 48: [----------] 3 tests from ExclusionBlockTest 48: [ RUN ] ExclusionBlockTest.ConvertBlockAToExclusionBlocks 48: [ OK ] ExclusionBlockTest.ConvertBlockAToExclusionBlocks (0 ms) 48: [ RUN ] ExclusionBlockTest.ConvertExclusionBlockToBlocka 48: [ OK ] ExclusionBlockTest.ConvertExclusionBlockToBlocka (0 ms) 48: [ RUN ] ExclusionBlockTest.MergeExclusions 48: [ OK ] ExclusionBlockTest.MergeExclusions (0 ms) 48: [----------] 3 tests from ExclusionBlockTest (0 ms total) 48: 48: [----------] 6 tests from InteractionListTest 48: [ RUN ] InteractionListTest.EmptyWorks 48: [ OK ] InteractionListTest.EmptyWorks (0 ms) 48: [ RUN ] InteractionListTest.CanAddInteractionArray 48: [ OK ] InteractionListTest.CanAddInteractionArray (0 ms) 48: [ RUN ] InteractionListTest.CanAddInteractionArrayMultipleAtoms 48: [ OK ] InteractionListTest.CanAddInteractionArrayMultipleAtoms (0 ms) 48: [ RUN ] InteractionListTest.CanAddInteractionPointer 48: [ OK ] InteractionListTest.CanAddInteractionPointer (0 ms) 48: [ RUN ] InteractionListTest.CanAddListToOtherList 48: [ OK ] InteractionListTest.CanAddListToOtherList (0 ms) 48: [ RUN ] InteractionListTest.ClearingWorks 48: [ OK ] InteractionListTest.ClearingWorks (0 ms) 48: [----------] 6 tests from InteractionListTest (0 ms total) 48: 48: [----------] 3 tests from IndexTest 48: [ RUN ] IndexTest.AnalyseWorksDefaultGroups 48: 48: WARNING: Masses and atomic (Van der Waals) radii will be guessed 48: based on residue and atom names, since they could not be 48: definitively assigned from the information in your input 48: files. These guessed numbers might deviate from the mass 48: and radius of the atom type. Please check the output 48: files if necessary. Note, that this functionality may 48: be removed in a future GROMACS version. Please, consider 48: using another file format for your input. 48: 48: [ OK ] IndexTest.AnalyseWorksDefaultGroups (25 ms) 48: [ RUN ] IndexTest.WriteIndexWorks 48: 48: WARNING: Masses and atomic (Van der Waals) radii will be guessed 48: based on residue and atom names, since they could not be 48: definitively assigned from the information in your input 48: files. These guessed numbers might deviate from the mass 48: and radius of the atom type. Please check the output 48: files if necessary. Note, that this functionality may 48: be removed in a future GROMACS version. Please, consider 48: using another file format for your input. 48: 48: [ OK ] IndexTest.WriteIndexWorks (17 ms) 48: [ RUN ] IndexTest.WriteAndReadIndexWorks 48: 48: WARNING: Masses and atomic (Van der Waals) radii will be guessed 48: based on residue and atom names, since they could not be 48: definitively assigned from the information in your input 48: files. These guessed numbers might deviate from the mass 48: and radius of the atom type. Please check the output 48: files if necessary. Note, that this functionality may 48: be removed in a future GROMACS version. Please, consider 48: using another file format for your input. 48: 48: [ OK ] IndexTest.WriteAndReadIndexWorks (19 ms) 48: [----------] 3 tests from IndexTest (64 ms total) 48: 48: [----------] 4 tests from MtopTest 48: [ RUN ] MtopTest.RangeBasedLoop 48: [ OK ] MtopTest.RangeBasedLoop (0 ms) 48: [ RUN ] MtopTest.Operators 48: [ OK ] MtopTest.Operators (0 ms) 48: [ RUN ] MtopTest.CanFindResidueStartAndEndAtoms 48: [ OK ] MtopTest.CanFindResidueStartAndEndAtoms (0 ms) 48: [ RUN ] MtopTest.CanSortPerturbedInteractionsCorrectly 48: [ OK ] MtopTest.CanSortPerturbedInteractionsCorrectly (0 ms) 48: [----------] 4 tests from MtopTest (0 ms total) 48: 48: [----------] 2 tests from IListRangeTest 48: [ RUN ] IListRangeTest.RangeBasedLoopWorks 48: [ OK ] IListRangeTest.RangeBasedLoopWorks (0 ms) 48: [ RUN ] IListRangeTest.RangeBasedLoopWithIntermolecularInteraction 48: [ OK ] IListRangeTest.RangeBasedLoopWithIntermolecularInteraction (0 ms) 48: [----------] 2 tests from IListRangeTest (0 ms total) 48: 48: [----------] 13 tests from StringTableTest 48: [ RUN ] StringTableTest.AddSingleEntry 48: [ OK ] StringTableTest.AddSingleEntry (1 ms) 48: [ RUN ] StringTableTest.CanAccessWithAt 48: [ OK ] StringTableTest.CanAccessWithAt (1 ms) 48: [ RUN ] StringTableTest.CanAccessWithBracket 48: [ OK ] StringTableTest.CanAccessWithBracket (1 ms) 48: [ RUN ] StringTableTest.ThrowsOutOfRange 48: [ OK ] StringTableTest.ThrowsOutOfRange (1 ms) 48: [ RUN ] StringTableTest.StringCompareIsCorrect 48: [ OK ] StringTableTest.StringCompareIsCorrect (1 ms) 48: [ RUN ] StringTableTest.AddTwoDistinctEntries 48: [ OK ] StringTableTest.AddTwoDistinctEntries (1 ms) 48: [ RUN ] StringTableTest.TryToAddDuplicates 48: [ OK ] StringTableTest.TryToAddDuplicates (1 ms) 48: [ RUN ] StringTableTest.AddLargeNumberOfEntries 48: [ OK ] StringTableTest.AddLargeNumberOfEntries (1 ms) 48: [ RUN ] StringTableTest.NoDuplicatesInLargeTable 48: [ OK ] StringTableTest.NoDuplicatesInLargeTable (1 ms) 48: [ RUN ] StringTableTest.CanWriteToBuffer 48: [ OK ] StringTableTest.CanWriteToBuffer (0 ms) 48: [ RUN ] StringTableTest.Roundtrip 48: [ OK ] StringTableTest.Roundtrip (0 ms) 48: [ RUN ] StringTableTest.RoundtripWithCorrectStringIndices 48: [ OK ] StringTableTest.RoundtripWithCorrectStringIndices (0 ms) 48: [ RUN ] StringTableTest.CanCopyToLegacyTable 48: [ OK ] StringTableTest.CanCopyToLegacyTable (0 ms) 48: [----------] 13 tests from StringTableTest (13 ms total) 48: 48: [----------] 6 tests from LegacySymtabTest 48: [ RUN ] LegacySymtabTest.EmptyOnOpen 48: [ OK ] LegacySymtabTest.EmptyOnOpen (0 ms) 48: [ RUN ] LegacySymtabTest.AddSingleEntry 48: [ OK ] LegacySymtabTest.AddSingleEntry (0 ms) 48: [ RUN ] LegacySymtabTest.AddTwoDistinctEntries 48: [ OK ] LegacySymtabTest.AddTwoDistinctEntries (0 ms) 48: [ RUN ] LegacySymtabTest.TryToAddDuplicates 48: [ OK ] LegacySymtabTest.TryToAddDuplicates (0 ms) 48: [ RUN ] LegacySymtabTest.AddLargeNumberOfEntries 48: [ OK ] LegacySymtabTest.AddLargeNumberOfEntries (0 ms) 48: [ RUN ] LegacySymtabTest.NoDuplicatesInLargeTable 48: [ OK ] LegacySymtabTest.NoDuplicatesInLargeTable (0 ms) 48: [----------] 6 tests from LegacySymtabTest (2 ms total) 48: 48: [----------] 5 tests from TopSortTest 48: [ RUN ] TopSortTest.WorksOnEmptyIdef 48: [ OK ] TopSortTest.WorksOnEmptyIdef (0 ms) 48: [ RUN ] TopSortTest.WorksOnIdefWithNoPerturbedInteraction 48: [ OK ] TopSortTest.WorksOnIdefWithNoPerturbedInteraction (0 ms) 48: [ RUN ] TopSortTest.WorksOnIdefWithPerturbedInteractions 48: [ OK ] TopSortTest.WorksOnIdefWithPerturbedInteractions (0 ms) 48: [ RUN ] TopSortTest.SortsIdefWithPerturbedInteractions 48: [ OK ] TopSortTest.SortsIdefWithPerturbedInteractions (0 ms) 48: [ RUN ] TopSortTest.SortsMoreComplexIdefWithPerturbedInteractions 48: [ OK ] TopSortTest.SortsMoreComplexIdefWithPerturbedInteractions (0 ms) 48: [----------] 5 tests from TopSortTest (0 ms total) 48: 48: [----------] 108 tests from BuildsValidDataStructure/SimulationParticleTest 48: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/0 48: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/0 (0 ms) 48: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/1 48: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/1 (0 ms) 48: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/2 48: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/2 (0 ms) 48: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/3 48: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/3 (0 ms) 48: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/4 48: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/4 (0 ms) 48: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/5 48: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/5 (0 ms) 48: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/6 48: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/6 (0 ms) 48: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/7 48: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/7 (0 ms) 48: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/8 48: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/8 (0 ms) 48: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/9 48: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/9 (0 ms) 48: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/10 48: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/10 (0 ms) 48: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/11 48: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/11 (0 ms) 48: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/12 48: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/12 (0 ms) 48: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/13 48: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/13 (0 ms) 48: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/14 48: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/14 (0 ms) 48: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/15 48: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/15 (0 ms) 48: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/16 48: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/16 (0 ms) 48: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/17 48: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/17 (0 ms) 48: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/18 48: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/18 (0 ms) 48: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/19 48: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/19 (0 ms) 48: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/20 48: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/20 (0 ms) 48: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/21 48: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/21 (0 ms) 48: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/22 48: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/22 (1 ms) 48: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/23 48: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/23 (0 ms) 48: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/24 48: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/24 (0 ms) 48: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/25 48: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/25 (0 ms) 48: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/26 48: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/26 (0 ms) 48: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/27 48: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/27 (0 ms) 48: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/28 48: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/28 (0 ms) 48: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/29 48: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/29 (0 ms) 48: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/30 48: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/30 (0 ms) 48: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/31 48: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/31 (0 ms) 48: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/32 48: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/32 (0 ms) 48: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/33 48: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/33 (0 ms) 48: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/34 48: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/34 (0 ms) 48: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/35 48: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/35 (0 ms) 48: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/36 48: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/36 (0 ms) 48: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/37 48: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/37 (0 ms) 48: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/38 48: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/38 (0 ms) 48: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/39 48: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/39 (0 ms) 48: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/40 48: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/40 (0 ms) 48: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/41 48: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/41 (0 ms) 48: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/42 48: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/42 (0 ms) 48: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/43 48: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/43 (0 ms) 48: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/44 48: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/44 (0 ms) 48: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/45 48: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/45 (0 ms) 48: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/46 48: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/46 (0 ms) 48: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/47 48: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/47 (0 ms) 48: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/48 48: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/48 (0 ms) 48: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/49 48: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/49 (0 ms) 48: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/50 48: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/50 (0 ms) 48: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/51 48: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/51 (0 ms) 48: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/52 48: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/52 (0 ms) 48: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/53 48: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/53 (0 ms) 48: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/0 48: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/0 (0 ms) 48: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/1 48: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/1 (0 ms) 48: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/2 48: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/2 (0 ms) 48: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/3 48: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/3 (0 ms) 48: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/4 48: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/4 (0 ms) 48: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/5 48: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/5 (0 ms) 48: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/6 48: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/6 (0 ms) 48: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/7 48: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/7 (0 ms) 48: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/8 48: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/8 (0 ms) 48: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/9 48: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/9 (0 ms) 48: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/10 48: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/10 (0 ms) 48: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/11 48: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/11 (0 ms) 48: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/12 48: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/12 (0 ms) 48: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/13 48: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/13 (0 ms) 48: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/14 48: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/14 (0 ms) 48: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/15 48: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/15 (0 ms) 48: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/16 48: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/16 (0 ms) 48: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/17 48: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/17 (0 ms) 48: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/18 48: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/18 (0 ms) 48: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/19 48: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/19 (0 ms) 48: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/20 48: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/20 (0 ms) 48: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/21 48: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/21 (0 ms) 48: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/22 48: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/22 (0 ms) 48: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/23 48: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/23 (0 ms) 48: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/24 48: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/24 (0 ms) 48: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/25 48: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/25 (0 ms) 48: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/26 48: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/26 (0 ms) 48: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/27 48: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/27 (0 ms) 48: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/28 48: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/28 (0 ms) 48: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/29 48: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/29 (0 ms) 48: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/30 48: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/30 (0 ms) 48: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/31 48: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/31 (0 ms) 48: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/32 48: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/32 (0 ms) 48: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/33 48: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/33 (0 ms) 48: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/34 48: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/34 (0 ms) 48: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/35 48: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/35 (0 ms) 48: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/36 48: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/36 (0 ms) 48: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/37 48: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/37 (0 ms) 48: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/38 48: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/38 (0 ms) 48: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/39 48: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/39 (0 ms) 48: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/40 48: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/40 (0 ms) 48: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/41 48: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/41 (0 ms) 48: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/42 48: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/42 (0 ms) 48: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/43 48: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/43 (0 ms) 48: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/44 48: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/44 (0 ms) 48: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/45 48: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/45 (0 ms) 48: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/46 48: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/46 (0 ms) 48: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/47 48: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/47 (0 ms) 48: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/48 48: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/48 (0 ms) 48: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/49 48: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/49 (0 ms) 48: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/50 48: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/50 (0 ms) 48: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/51 48: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/51 (0 ms) 48: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/52 48: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/52 (0 ms) 48: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/53 48: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/53 (0 ms) 48: [----------] 108 tests from BuildsValidDataStructure/SimulationParticleTest (88 ms total) 48: 48: [----------] Global test environment tear-down 48: [==========] 153 tests from 10 test suites ran. (170 ms total) 48: [ PASSED ] 153 tests. 48: 48: YOU HAVE 1 DISABLED TEST 48: 48/92 Test #48: TopologyTest .............................. Passed 0.27 sec test 49 Start 49: PullTest 49: Test command: /build/reproducible-path/gromacs-2025.1/build/basic/bin/pull-test "--gtest_output=xml:/build/reproducible-path/gromacs-2025.1/build/basic/Testing/Temporary/PullTest.xml" 49: Working Directory: /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/pulling/tests 49: Test timeout computed to be: 30 49: [==========] Running 10 tests from 1 test suite. 49: [----------] Global test environment set-up. 49: [----------] 10 tests from PullTest 49: [ RUN ] PullTest.MaxPullDistanceXyzScrewBox 49: [ OK ] PullTest.MaxPullDistanceXyzScrewBox (0 ms) 49: [ RUN ] PullTest.MaxPullDistanceXyzCubicBox 49: [ OK ] PullTest.MaxPullDistanceXyzCubicBox (0 ms) 49: [ RUN ] PullTest.MaxPullDistanceXyzTricBox 49: [ OK ] PullTest.MaxPullDistanceXyzTricBox (0 ms) 49: [ RUN ] PullTest.MaxPullDistanceXyzLongBox 49: [ OK ] PullTest.MaxPullDistanceXyzLongBox (0 ms) 49: [ RUN ] PullTest.MaxPullDistanceXySkewedBox 49: [ OK ] PullTest.MaxPullDistanceXySkewedBox (0 ms) 49: [ RUN ] PullTest.TransformationCoordSimple 49: [ OK ] PullTest.TransformationCoordSimple (0 ms) 49: [ RUN ] PullTest.TransformationCoordAdvanced 49: [ OK ] PullTest.TransformationCoordAdvanced (0 ms) 49: [ RUN ] PullTest.TransformationCoordTime 49: [ OK ] PullTest.TransformationCoordTime (0 ms) 49: [ RUN ] PullTest.TransformationCoordTimeNotAllowed 49: [ OK ] PullTest.TransformationCoordTimeNotAllowed (0 ms) 49: [ RUN ] PullTest.TransformationCoordDummyExpression 49: [ OK ] PullTest.TransformationCoordDummyExpression (0 ms) 49: [----------] 10 tests from PullTest (3 ms total) 49: 49: [----------] Global test environment tear-down 49: [==========] 10 tests from 1 test suite ran. (3 ms total) 49: [ PASSED ] 10 tests. 49/92 Test #49: PullTest .................................. Passed 0.08 sec test 50 Start 50: SimdUnitTests 50: Test command: /build/reproducible-path/gromacs-2025.1/build/basic/bin/simd-test "--gtest_output=xml:/build/reproducible-path/gromacs-2025.1/build/basic/Testing/Temporary/SimdUnitTests.xml" 50: Working Directory: /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/simd/tests 50: Test timeout computed to be: 30 50: [==========] Running 86 tests from 3 test suites. 50: [----------] Global test environment set-up. 50: [----------] 41 tests from SimdScalarTest 50: [ RUN ] SimdScalarTest.load 50: [ OK ] SimdScalarTest.load (0 ms) 50: [ RUN ] SimdScalarTest.loadU 50: [ OK ] SimdScalarTest.loadU (0 ms) 50: [ RUN ] SimdScalarTest.store 50: [ OK ] SimdScalarTest.store (0 ms) 50: [ RUN ] SimdScalarTest.storeU 50: [ OK ] SimdScalarTest.storeU (0 ms) 50: [ RUN ] SimdScalarTest.setZero 50: [ OK ] SimdScalarTest.setZero (0 ms) 50: [ RUN ] SimdScalarTest.andNot 50: [ OK ] SimdScalarTest.andNot (0 ms) 50: [ RUN ] SimdScalarTest.fma 50: [ OK ] SimdScalarTest.fma (0 ms) 50: [ RUN ] SimdScalarTest.fms 50: [ OK ] SimdScalarTest.fms (0 ms) 50: [ RUN ] SimdScalarTest.fnma 50: [ OK ] SimdScalarTest.fnma (0 ms) 50: [ RUN ] SimdScalarTest.fnms 50: [ OK ] SimdScalarTest.fnms (0 ms) 50: [ RUN ] SimdScalarTest.maskAdd 50: [ OK ] SimdScalarTest.maskAdd (0 ms) 50: [ RUN ] SimdScalarTest.maskzMul 50: [ OK ] SimdScalarTest.maskzMul (0 ms) 50: [ RUN ] SimdScalarTest.maskzFma 50: [ OK ] SimdScalarTest.maskzFma (0 ms) 50: [ RUN ] SimdScalarTest.abs 50: [ OK ] SimdScalarTest.abs (0 ms) 50: [ RUN ] SimdScalarTest.max 50: [ OK ] SimdScalarTest.max (0 ms) 50: [ RUN ] SimdScalarTest.min 50: [ OK ] SimdScalarTest.min (0 ms) 50: [ RUN ] SimdScalarTest.round 50: [ OK ] SimdScalarTest.round (0 ms) 50: [ RUN ] SimdScalarTest.trunc 50: [ OK ] SimdScalarTest.trunc (0 ms) 50: [ RUN ] SimdScalarTest.reduce 50: [ OK ] SimdScalarTest.reduce (0 ms) 50: [ RUN ] SimdScalarTest.testBits 50: [ OK ] SimdScalarTest.testBits (0 ms) 50: [ RUN ] SimdScalarTest.anyTrue 50: [ OK ] SimdScalarTest.anyTrue (0 ms) 50: [ RUN ] SimdScalarTest.selectByMask 50: [ OK ] SimdScalarTest.selectByMask (0 ms) 50: [ RUN ] SimdScalarTest.selectByNotMask 50: [ OK ] SimdScalarTest.selectByNotMask (0 ms) 50: [ RUN ] SimdScalarTest.blend 50: [ OK ] SimdScalarTest.blend (0 ms) 50: [ RUN ] SimdScalarTest.cvtR2I 50: [ OK ] SimdScalarTest.cvtR2I (0 ms) 50: [ RUN ] SimdScalarTest.cvttR2I 50: [ OK ] SimdScalarTest.cvttR2I (0 ms) 50: [ RUN ] SimdScalarTest.cvtI2R 50: [ OK ] SimdScalarTest.cvtI2R (0 ms) 50: [ RUN ] SimdScalarTest.cvtF2D 50: [ OK ] SimdScalarTest.cvtF2D (0 ms) 50: [ RUN ] SimdScalarTest.cvtD2D 50: [ OK ] SimdScalarTest.cvtD2D (0 ms) 50: [ RUN ] SimdScalarTest.loadI 50: [ OK ] SimdScalarTest.loadI (0 ms) 50: [ RUN ] SimdScalarTest.loadUI 50: [ OK ] SimdScalarTest.loadUI (0 ms) 50: [ RUN ] SimdScalarTest.storeI 50: [ OK ] SimdScalarTest.storeI (0 ms) 50: [ RUN ] SimdScalarTest.storeUI 50: [ OK ] SimdScalarTest.storeUI (0 ms) 50: [ RUN ] SimdScalarTest.andNotI 50: [ OK ] SimdScalarTest.andNotI (0 ms) 50: [ RUN ] SimdScalarTest.testBitsI 50: [ OK ] SimdScalarTest.testBitsI (0 ms) 50: [ RUN ] SimdScalarTest.selectByMaskI 50: [ OK ] SimdScalarTest.selectByMaskI (0 ms) 50: [ RUN ] SimdScalarTest.selectByNotMaskI 50: [ OK ] SimdScalarTest.selectByNotMaskI (0 ms) 50: [ RUN ] SimdScalarTest.blendI 50: [ OK ] SimdScalarTest.blendI (0 ms) 50: [ RUN ] SimdScalarTest.cvtB2IB 50: [ OK ] SimdScalarTest.cvtB2IB (0 ms) 50: [ RUN ] SimdScalarTest.cvtIB2B 50: [ OK ] SimdScalarTest.cvtIB2B (0 ms) 50: [ RUN ] SimdScalarTest.expandScalarsToTriplets 50: [ OK ] SimdScalarTest.expandScalarsToTriplets (0 ms) 50: [----------] 41 tests from SimdScalarTest (3 ms total) 50: 50: [----------] 8 tests from SimdScalarUtilTest 50: [ RUN ] SimdScalarUtilTest.gatherLoadTranspose 50: [ OK ] SimdScalarUtilTest.gatherLoadTranspose (0 ms) 50: [ RUN ] SimdScalarUtilTest.gatherLoadUTranspose 50: [ OK ] SimdScalarUtilTest.gatherLoadUTranspose (0 ms) 50: [ RUN ] SimdScalarUtilTest.transposeScatterStoreU 50: [ OK ] SimdScalarUtilTest.transposeScatterStoreU (0 ms) 50: [ RUN ] SimdScalarUtilTest.transposeScatterIncrU 50: [ OK ] SimdScalarUtilTest.transposeScatterIncrU (0 ms) 50: [ RUN ] SimdScalarUtilTest.transposeScatterDecrU 50: [ OK ] SimdScalarUtilTest.transposeScatterDecrU (0 ms) 50: [ RUN ] SimdScalarUtilTest.gatherLoadBySimdIntTranspose 50: [ OK ] SimdScalarUtilTest.gatherLoadBySimdIntTranspose (0 ms) 50: [ RUN ] SimdScalarUtilTest.gatherLoadUBySimdIntTranspose 50: [ OK ] SimdScalarUtilTest.gatherLoadUBySimdIntTranspose (0 ms) 50: [ RUN ] SimdScalarUtilTest.reduceIncr4ReturnSum 50: [ OK ] SimdScalarUtilTest.reduceIncr4ReturnSum (0 ms) 50: [----------] 8 tests from SimdScalarUtilTest (0 ms total) 50: 50: [----------] 37 tests from SimdScalarMathTest 50: [ RUN ] SimdScalarMathTest.copysign 50: [ OK ] SimdScalarMathTest.copysign (0 ms) 50: [ RUN ] SimdScalarMathTest.invsqrtPair 50: [ OK ] SimdScalarMathTest.invsqrtPair (0 ms) 50: [ RUN ] SimdScalarMathTest.inv 50: [ OK ] SimdScalarMathTest.inv (0 ms) 50: [ RUN ] SimdScalarMathTest.maskzInvsqrt 50: [ OK ] SimdScalarMathTest.maskzInvsqrt (0 ms) 50: [ RUN ] SimdScalarMathTest.log 50: [ OK ] SimdScalarMathTest.log (0 ms) 50: [ RUN ] SimdScalarMathTest.exp2 50: [ OK ] SimdScalarMathTest.exp2 (0 ms) 50: [ RUN ] SimdScalarMathTest.exp 50: [ OK ] SimdScalarMathTest.exp (0 ms) 50: [ RUN ] SimdScalarMathTest.erf 50: [ OK ] SimdScalarMathTest.erf (0 ms) 50: [ RUN ] SimdScalarMathTest.erfc 50: [ OK ] SimdScalarMathTest.erfc (0 ms) 50: [ RUN ] SimdScalarMathTest.sincos 50: [ OK ] SimdScalarMathTest.sincos (0 ms) 50: [ RUN ] SimdScalarMathTest.sin 50: [ OK ] SimdScalarMathTest.sin (0 ms) 50: [ RUN ] SimdScalarMathTest.cos 50: [ OK ] SimdScalarMathTest.cos (0 ms) 50: [ RUN ] SimdScalarMathTest.tan 50: [ OK ] SimdScalarMathTest.tan (0 ms) 50: [ RUN ] SimdScalarMathTest.asin 50: [ OK ] SimdScalarMathTest.asin (0 ms) 50: [ RUN ] SimdScalarMathTest.acos 50: [ OK ] SimdScalarMathTest.acos (0 ms) 50: [ RUN ] SimdScalarMathTest.atan 50: [ OK ] SimdScalarMathTest.atan (0 ms) 50: [ RUN ] SimdScalarMathTest.atan2 50: [ OK ] SimdScalarMathTest.atan2 (0 ms) 50: [ RUN ] SimdScalarMathTest.pmeForceCorrection 50: [ OK ] SimdScalarMathTest.pmeForceCorrection (0 ms) 50: [ RUN ] SimdScalarMathTest.pmePotentialCorrection 50: [ OK ] SimdScalarMathTest.pmePotentialCorrection (0 ms) 50: [ RUN ] SimdScalarMathTest.invsqrtPairSingleAccuracy 50: [ OK ] SimdScalarMathTest.invsqrtPairSingleAccuracy (0 ms) 50: [ RUN ] SimdScalarMathTest.invSingleAccuracy 50: [ OK ] SimdScalarMathTest.invSingleAccuracy (0 ms) 50: [ RUN ] SimdScalarMathTest.maskzInvsqrtSingleAccuracy 50: [ OK ] SimdScalarMathTest.maskzInvsqrtSingleAccuracy (0 ms) 50: [ RUN ] SimdScalarMathTest.logSingleAccuracy 50: [ OK ] SimdScalarMathTest.logSingleAccuracy (0 ms) 50: [ RUN ] SimdScalarMathTest.exp2SingleAccuracy 50: [ OK ] SimdScalarMathTest.exp2SingleAccuracy (0 ms) 50: [ RUN ] SimdScalarMathTest.expSingleAccuracy 50: [ OK ] SimdScalarMathTest.expSingleAccuracy (0 ms) 50: [ RUN ] SimdScalarMathTest.erfSingleAccuracy 50: [ OK ] SimdScalarMathTest.erfSingleAccuracy (0 ms) 50: [ RUN ] SimdScalarMathTest.erfcSingleAccuracy 50: [ OK ] SimdScalarMathTest.erfcSingleAccuracy (0 ms) 50: [ RUN ] SimdScalarMathTest.sincosSingleAccuracy 50: [ OK ] SimdScalarMathTest.sincosSingleAccuracy (0 ms) 50: [ RUN ] SimdScalarMathTest.sinSingleAccuracy 50: [ OK ] SimdScalarMathTest.sinSingleAccuracy (0 ms) 50: [ RUN ] SimdScalarMathTest.cosSingleAccuracy 50: [ OK ] SimdScalarMathTest.cosSingleAccuracy (0 ms) 50: [ RUN ] SimdScalarMathTest.tanSingleAccuracy 50: [ OK ] SimdScalarMathTest.tanSingleAccuracy (0 ms) 50: [ RUN ] SimdScalarMathTest.asinSingleAccuracy 50: [ OK ] SimdScalarMathTest.asinSingleAccuracy (0 ms) 50: [ RUN ] SimdScalarMathTest.acosSingleAccuracy 50: [ OK ] SimdScalarMathTest.acosSingleAccuracy (0 ms) 50: [ RUN ] SimdScalarMathTest.atanSingleAccuracy 50: [ OK ] SimdScalarMathTest.atanSingleAccuracy (0 ms) 50: [ RUN ] SimdScalarMathTest.atan2SingleAccuracy 50: [ OK ] SimdScalarMathTest.atan2SingleAccuracy (0 ms) 50: [ RUN ] SimdScalarMathTest.pmeForceCorrectionSingleAccuracy 50: [ OK ] SimdScalarMathTest.pmeForceCorrectionSingleAccuracy (0 ms) 50: [ RUN ] SimdScalarMathTest.pmePotentialCorrectionSingleAccuracy 50: [ OK ] SimdScalarMathTest.pmePotentialCorrectionSingleAccuracy (0 ms) 50: [----------] 37 tests from SimdScalarMathTest (2 ms total) 50: 50: [----------] Global test environment tear-down 50: [==========] 86 tests from 3 test suites ran. (6 ms total) 50: [ PASSED ] 86 tests. 50/92 Test #50: SimdUnitTests ............................. Passed 0.10 sec test 51 Start 51: CompatibilityHelpersTests 51: Test command: /build/reproducible-path/gromacs-2025.1/build/basic/bin/compat-test "--gtest_output=xml:/build/reproducible-path/gromacs-2025.1/build/basic/Testing/Temporary/CompatibilityHelpersTests.xml" 51: Working Directory: /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/compat/tests 51: Test timeout computed to be: 30 51: [==========] Running 9 tests from 6 test suites. 51: [----------] Global test environment set-up. 51: [----------] 4 tests from TemplateMPTest 51: [ RUN ] TemplateMPTest.MpWithIndexInt 51: [ OK ] TemplateMPTest.MpWithIndexInt (0 ms) 51: [ RUN ] TemplateMPTest.MpWithIndexIntBad 51: [ OK ] TemplateMPTest.MpWithIndexIntBad (0 ms) 51: [ RUN ] TemplateMPTest.MpWithIndexBool 51: [ OK ] TemplateMPTest.MpWithIndexBool (0 ms) 51: [ RUN ] TemplateMPTest.MpWithIndexEnum 51: [ OK ] TemplateMPTest.MpWithIndexEnum (0 ms) 51: [----------] 4 tests from TemplateMPTest (0 ms total) 51: 51: [----------] 1 test from NotNullConstruction 51: [ RUN ] NotNullConstruction.Works 51: [ OK ] NotNullConstruction.Works (0 ms) 51: [----------] 1 test from NotNullConstruction (0 ms total) 51: 51: [----------] 1 test from NotNullCasting 51: [ RUN ] NotNullCasting.Works 51: [ OK ] NotNullCasting.Works (0 ms) 51: [----------] 1 test from NotNullCasting (0 ms total) 51: 51: [----------] 1 test from NotNullAssignment 51: [ RUN ] NotNullAssignment.Works 51: [ OK ] NotNullAssignment.Works (0 ms) 51: [----------] 1 test from NotNullAssignment (0 ms total) 51: 51: [----------] 1 test from MakeNotNull 51: [ RUN ] MakeNotNull.Works 51: [ OK ] MakeNotNull.Works (0 ms) 51: [----------] 1 test from MakeNotNull (0 ms total) 51: 51: [----------] 1 test from NotNull 51: [ RUN ] NotNull.WorksInContainers 51: [ OK ] NotNull.WorksInContainers (0 ms) 51: [----------] 1 test from NotNull (0 ms total) 51: 51: [----------] Global test environment tear-down 51: [==========] 9 tests from 6 test suites ran. (1 ms total) 51: [ PASSED ] 9 tests. 51/92 Test #51: CompatibilityHelpersTests ................. Passed 0.08 sec test 52 Start 52: GmxAnaTest 52: Test command: /build/reproducible-path/gromacs-2025.1/build/basic/bin/gmxana-test "--gtest_output=xml:/build/reproducible-path/gromacs-2025.1/build/basic/Testing/Temporary/GmxAnaTest.xml" 52: Working Directory: /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/gmxana/tests 52: Test timeout computed to be: 600 52: [==========] Running 31 tests from 4 test suites. 52: [----------] Global test environment set-up. 52: [----------] 7 tests from Entropy 52: [ RUN ] Entropy.Schlitter_300_NoLinear 52: [ OK ] Entropy.Schlitter_300_NoLinear (2 ms) 52: [ RUN ] Entropy.Schlitter_300_Linear 52: [ OK ] Entropy.Schlitter_300_Linear (1 ms) 52: [ RUN ] Entropy.QuasiHarmonic_300_NoLinear 52: [ OK ] Entropy.QuasiHarmonic_300_NoLinear (1 ms) 52: [ RUN ] Entropy.QuasiHarmonic_200_NoLinear 52: [ OK ] Entropy.QuasiHarmonic_200_NoLinear (0 ms) 52: [ RUN ] Entropy.QuasiHarmonic_200_Linear 52: [ OK ] Entropy.QuasiHarmonic_200_Linear (0 ms) 52: [ RUN ] Entropy.EntropyCompare_200_Linear 52: [ OK ] Entropy.EntropyCompare_200_Linear (0 ms) 52: [ RUN ] Entropy.EntropyCompare_300_Linear 52: [ OK ] Entropy.EntropyCompare_300_Linear (0 ms) 52: [----------] 7 tests from Entropy (7 ms total) 52: 52: [----------] 2 tests from GmxChiTest 52: [ RUN ] GmxChiTest.gmxchiWorksWithAll 52: Analyzing from residue 1 to residue 11 52: 10 residues with dihedrals found 52: 46 dihedrals found 52: Reading frames from gro file 'First 10 residues from 1AKI t= 0.00000 step= 0', 156 atoms. 52: Reading frame 0 time 0.000 Reading frame 1 time 0.020 Reading frame 2 time 0.040 Last frame 2 time 0.040 52: j after resetting (nr. active dihedrals) = 46 52: Printing phiLYS1.xvg Printing phiVAL2.xvg Printing phiPHE3.xvg Printing phiGLY4.xvg Printing phiARG5.xvg Printing phiCYS6.xvg Printing phiGLU7.xvg Printing phiLEU8.xvg Printing phiALA9.xvg Printing phiALA10.xvg Printing psiLYS1.xvg Printing psiVAL2.xvg Printing psiPHE3.xvg Printing psiGLY4.xvg Printing psiARG5.xvg Printing psiCYS6.xvg Printing psiGLU7.xvg Printing psiLEU8.xvg Printing psiALA9.xvg Printing psiALA10.xvg Printing omegaVAL2.xvg Printing omegaPHE3.xvg Printing omegaGLY4.xvg Printing omegaARG5.xvg Printing omegaCYS6.xvg Printing omegaGLU7.xvg Printing omegaLEU8.xvg Printing omegaALA9.xvg Printing omegaALA10.xvg Printing chi1LYS1.xvg Printing chi1VAL2.xvg Printing chi1PHE3.xvg Printing chi1ARG5.xvg Printing chi1CYS6.xvg Printing chi1GLU7.xvg Printing chi1LEU8.xvg Printing chi2LYS1.xvg Printing chi2PHE3.xvg Printing chi2ARG5.xvg Printing chi2GLU7.xvg Printing chi2LEU8.xvg Printing chi3LYS1.xvg Printing chi3ARG5.xvg Printing chi3GLU7.xvg Printing chi4LYS1.xvg Printing chi4ARG5.xvg 52: Now calculating transitions... 52: Total number of transitions: 0 52: Now printing out transitions and OPs... 52: Now printing out rotamer occupancies... 52: Now calculating Chi product trajectories... 52: Printing chiproductLYS1.xvg and histo-chiprodLYS1.xvg Printing chiproductVAL2.xvg and histo-chiprodVAL2.xvg Printing chiproductPHE3.xvg and histo-chiprodPHE3.xvg Printing chiproductARG5.xvg and histo-chiprodARG5.xvg Printing chiproductCYS6.xvg and histo-chiprodCYS6.xvg Printing chiproductGLU7.xvg and histo-chiprodGLU7.xvg Printing chiproductLEU8.xvg and histo-chiprodLEU8.xvg 52: [ OK ] GmxChiTest.gmxchiWorksWithAll (5278 ms) 52: [ RUN ] GmxChiTest.gmxchiWorksWithr0AndrN 52: Analyzing from residue 2 to residue 6 52: 5 residues with dihedrals found 52: 23 dihedrals found 52: Reading frames from gro file 'First 10 residues from 1AKI t= 0.00000 step= 0', 156 atoms. 52: Reading frame 0 time 0.000 Reading frame 1 time 0.020 Reading frame 2 time 0.040 Last frame 2 time 0.040 52: j after resetting (nr. active dihedrals) = 23 52: Printing phiVAL2.xvg Printing phiPHE3.xvg Printing phiGLY4.xvg Printing phiARG5.xvg Printing phiCYS6.xvg Printing psiVAL2.xvg Printing psiPHE3.xvg Printing psiGLY4.xvg Printing psiARG5.xvg Printing psiCYS6.xvg Printing omegaVAL2.xvg Printing omegaPHE3.xvg Printing omegaGLY4.xvg Printing omegaARG5.xvg Printing omegaCYS6.xvg Printing chi1VAL2.xvg Printing chi1PHE3.xvg Printing chi1ARG5.xvg Printing chi1CYS6.xvg Printing chi2PHE3.xvg Printing chi2ARG5.xvg Printing chi3ARG5.xvg Printing chi4ARG5.xvg 52: Now calculating transitions... 52: Total number of transitions: 0 52: Now printing out transitions and OPs... 52: Now printing out rotamer occupancies... 52: Now calculating Chi product trajectories... 52: Printing chiproductVAL2.xvg and histo-chiprodVAL2.xvg Printing chiproductPHE3.xvg and histo-chiprodPHE3.xvg Printing chiproductARG5.xvg and histo-chiprodARG5.xvg Printing chiproductCYS6.xvg and histo-chiprodCYS6.xvg 52: [ OK ] GmxChiTest.gmxchiWorksWithr0AndrN (2520 ms) 52: [----------] 2 tests from GmxChiTest (8897 ms total) 52: 52: [----------] 10 tests from MindistTest 52: [ RUN ] MindistTest.mindistWorksWithSingleAtoms 52: Group 0 ( atom1) has 1 elements 52: Group 1 ( atom2) has 1 elements 52: Group 2 ( atom3) has 1 elements 52: Group 3 ( atoms12) has 2 elements 52: Group 4 ( atoms23) has 2 elements 52: Group 5 ( atoms123) has 3 elements 52: Select a group: Select a group: Reading frames from gro file 'mindist_beads', 3 atoms. 52: Reading frame 0 time 0.000 Last frame 0 time 0.000 52: Selected 0: 'atom1' 52: Selected 1: 'atom2' 52: [ OK ] MindistTest.mindistWorksWithSingleAtoms (56 ms) 52: [ RUN ] MindistTest.mindistWorksWithMultipleAtoms 52: Group 0 ( atom1) has 1 elements 52: Group 1 ( atom2) has 1 elements 52: Group 2 ( atom3) has 1 elements 52: Group 3 ( atoms12) has 2 elements 52: Group 4 ( atoms23) has 2 elements 52: Group 5 ( atoms123) has 3 elements 52: Select a group: Select a group: Reading frames from gro file 'mindist_beads', 3 atoms. 52: Reading frame 0 time 0.000 Last frame 0 time 0.000 52: Selected 2: 'atom3' 52: Selected 3: 'atoms12' 52: [ OK ] MindistTest.mindistWorksWithMultipleAtoms (6 ms) 52: [ RUN ] MindistTest.mindistDoesNotPickUpContacts 52: Group 0 ( atom1) has 1 elements 52: Group 1 ( atom2) has 1 elements 52: Group 2 ( atom3) has 1 elements 52: Group 3 ( atoms12) has 2 elements 52: Group 4 ( atoms23) has 2 elements 52: Group 5 ( atoms123) has 3 elements 52: Select a group: Select a group: Reading frames from gro file 'mindist_beads', 3 atoms. 52: Reading frame 0 time 0.000 Last frame 0 time 0.000 52: Selected 0: 'atom1' 52: Selected 1: 'atom2' 52: [ OK ] MindistTest.mindistDoesNotPickUpContacts (6 ms) 52: [ RUN ] MindistTest.mindistPicksUpContacts 52: Group 0 ( atom1) has 1 elements 52: Group 1 ( atom2) has 1 elements 52: Group 2 ( atom3) has 1 elements 52: Group 3 ( atoms12) has 2 elements 52: Group 4 ( atoms23) has 2 elements 52: Group 5 ( atoms123) has 3 elements 52: Select a group: Select a group: Reading frames from gro file 'mindist_beads', 3 atoms. 52: Reading frame 0 time 0.000 Last frame 0 time 0.000 52: Selected 0: 'atom1' 52: Selected 1: 'atom2' 52: [ OK ] MindistTest.mindistPicksUpContacts (6 ms) 52: [ RUN ] MindistTest.ngWorks 52: Group 0 ( atom1) has 1 elements 52: Group 1 ( atom2) has 1 elements 52: Group 2 ( atom3) has 1 elements 52: Group 3 ( atoms12) has 2 elements 52: Group 4 ( atoms23) has 2 elements 52: Group 5 ( atoms123) has 3 elements 52: Select a group: Select a group: Select a group: Reading frames from gro file 'mindist_beads', 3 atoms. 52: Reading frame 0 time 0.000 Last frame 0 time 0.000 52: Selected 0: 'atom1' 52: Selected 1: 'atom2' 52: Selected 2: 'atom3' 52: [ OK ] MindistTest.ngWorks (5 ms) 52: [ RUN ] MindistTest.groupWorks 52: Group 0 ( atom1) has 1 elements 52: Group 1 ( atom2) has 1 elements 52: Group 2 ( atom3) has 1 elements 52: Group 3 ( atoms12) has 2 elements 52: Group 4 ( atoms23) has 2 elements 52: Group 5 ( atoms123) has 3 elements 52: Select a group: Select a group: Reading frames from gro file 'mindist_beads', 3 atoms. 52: Reading frame 0 time 0.000 Last frame 0 time 0.000 52: Selected 3: 'atoms12' 52: Selected 2: 'atom3' 52: [ OK ] MindistTest.groupWorks (6 ms) 52: [ RUN ] MindistTest.maxDistWorks 52: Group 0 ( atom1) has 1 elements 52: Group 1 ( atom2) has 1 elements 52: Group 2 ( atom3) has 1 elements 52: Group 3 ( atoms12) has 2 elements 52: Group 4 ( atoms23) has 2 elements 52: Group 5 ( atoms123) has 3 elements 52: Select a group: Select a group: Reading frames from gro file 'mindist_beads', 3 atoms. 52: Reading frame 0 time 0.000 Last frame 0 time 0.000 52: Selected 2: 'atom3' 52: Selected 3: 'atoms12' 52: [ OK ] MindistTest.maxDistWorks (6 ms) 52: [ RUN ] MindistTest.noPbcWorks 52: Group 0 ( atom1) has 1 elements 52: Group 1 ( atom2) has 1 elements 52: Group 2 ( atom3) has 1 elements 52: Group 3 ( atoms12) has 2 elements 52: Group 4 ( atoms23) has 2 elements 52: Group 5 ( atoms123) has 3 elements 52: Select a group: Select a group: Reading frames from gro file 'mindist_beads', 3 atoms. 52: Reading frame 0 time 0.000 Last frame 0 time 0.000 52: Selected 0: 'atom1' 52: Selected 1: 'atom2' 52: [ OK ] MindistTest.noPbcWorks (5 ms) 52: [ RUN ] MindistTest.resPerTimeWorks 52: Group 0 ( atom1) has 1 elements 52: Group 1 ( atom2) has 1 elements 52: Group 2 ( atom3) has 1 elements 52: Group 3 ( atoms12) has 2 elements 52: Group 4 ( atoms23) has 2 elements 52: Group 5 ( atoms123) has 3 elements 52: Select a group: Select a group: Reading frames from gro file 'mindist_beads', 3 atoms. 52: Reading frame 0 time 0.000 Last frame 0 time 0.000 52: Selected 3: 'atoms12' 52: Selected 2: 'atom3' 52: [ OK ] MindistTest.resPerTimeWorks (6 ms) 52: [ RUN ] MindistTest.matrixWorks 52: Group 0 ( atom1) has 1 elements 52: Group 1 ( atom2) has 1 elements 52: Group 2 ( atom3) has 1 elements 52: Group 3 ( atoms12) has 2 elements 52: Group 4 ( atoms23) has 2 elements 52: Group 5 ( atoms123) has 3 elements 52: Select a group: Reading frames from gro file 'mindist_beads', 3 atoms. 52: Reading frame 0 time 0.000 Last frame 0 time 0.000 52: Selected 5: 'atoms123' 52: Special case: making distance matrix between all atoms in group atoms123 52: [ OK ] MindistTest.matrixWorks (6 ms) 52: [----------] 10 tests from MindistTest (114 ms total) 52: 52: [----------] 12 tests from NoFatalErrorWhenWritingFrom/GmxTraj 52: [ RUN ] NoFatalErrorWhenWritingFrom/GmxTraj.WithDifferentInputFormats/0 52: Group 0 ( System) has 6 elements 52: Group 1 ( Water) has 6 elements 52: Group 2 ( SOL) has 6 elements 52: Select a group: trr version: GMX_trn_file (single precision) 52: Reading frame 0 time 0.000 Reading frame 1 time 1.000 Last frame 1 time 1.000 52: Selected 0: 'System' 52: [ OK ] NoFatalErrorWhenWritingFrom/GmxTraj.WithDifferentInputFormats/0 (7 ms) 52: [ RUN ] NoFatalErrorWhenWritingFrom/GmxTraj.WithDifferentInputFormats/1 52: Group 0 ( System) has 6 elements 52: Group 1 ( Water) has 6 elements 52: Group 2 ( SOL) has 6 elements 52: Select a group: Reading frame 0 time 0.000 Reading frame 1 time 1.000 Last frame 1 time 1.000 52: Selected 0: 'System' 52: [ OK ] NoFatalErrorWhenWritingFrom/GmxTraj.WithDifferentInputFormats/1 (8 ms) 52: [ RUN ] NoFatalErrorWhenWritingFrom/GmxTraj.WithDifferentInputFormats/2 52: Group 0 ( System) has 6 elements 52: Group 1 ( Water) has 6 elements 52: Group 2 ( SOL) has 6 elements 52: Select a group: Reading frames from gro file 'Generated by trjconv t= 0.00000 step= 0', 6 atoms. 52: Reading frame 0 time 0.000 Reading frame 1 time 1.000 Last frame 1 time 1.000 52: Selected 0: 'System' 52: [ OK ] NoFatalErrorWhenWritingFrom/GmxTraj.WithDifferentInputFormats/2 (8 ms) 52: [ RUN ] NoFatalErrorWhenWritingFrom/GmxTraj.WithDifferentInputFormats/3 52: Group 0 ( System) has 6 elements 52: Group 1 ( Water) has 6 elements 52: Group 2 ( SOL) has 6 elements 52: Select a group: Reading frames from pdb file Reading frame 0 time 0.000 'Generated by trjconv t= 1.00000 step= 1', 6 atoms 52: Reading frame 1 time 1.000 Last frame 1 time 1.000 52: Selected 0: 'System' 52: [ OK ] NoFatalErrorWhenWritingFrom/GmxTraj.WithDifferentInputFormats/3 (8 ms) 52: [ RUN ] NoFatalErrorWhenWritingFrom/GmxTraj.WithDifferentInputFormats/4 52: Group 0 ( System) has 6 elements 52: Group 1 ( Water) has 6 elements 52: Group 2 ( SOL) has 6 elements 52: Select a group: Reading frame 0 time 0.000 Reading frame 1 time 1.000 Last frame 1 time 1.000 52: Selected 0: 'System' 52: [ OK ] NoFatalErrorWhenWritingFrom/GmxTraj.WithDifferentInputFormats/4 (8 ms) 52: [ RUN ] NoFatalErrorWhenWritingFrom/GmxTraj.WithDifferentInputFormats/5 52: Group 0 ( System) has 6 elements 52: Group 1 ( Water) has 6 elements 52: Group 2 ( SOL) has 6 elements 52: Select a group: Reading frame 0 time 0.000 Reading frame 1 time 1.000 Last frame 1 time 1.000 52: Selected 0: 'System' 52: [ OK ] NoFatalErrorWhenWritingFrom/GmxTraj.WithDifferentInputFormats/5 (9 ms) 52: [ RUN ] NoFatalErrorWhenWritingFrom/GmxTraj.RotationalKineticEnergy/0 52: Group 0 ( System) has 6 elements 52: Group 1 ( Water) has 6 elements 52: Group 2 ( SOL) has 6 elements 52: Select a group: Reading frame 0 time 0.000 52: WARNING: If there are molecules in the input trajectory file 52: that are broken across periodic boundaries, they 52: cannot be made whole (or treated as whole) without 52: you providing a run input file. 52: 52: Reading frame 1 time 1.000 Last frame 1 time 1.000 52: 52: WARNING: Masses and atomic (Van der Waals) radii will be guessed 52: based on residue and atom names, since they could not be 52: definitively assigned from the information in your input 52: files. These guessed numbers might deviate from the mass 52: and radius of the atom type. Please check the output 52: files if necessary. Note, that this functionality may 52: be removed in a future GROMACS version. Please, consider 52: using another file format for your input. 52: 52: Selected 0: 'System' 52: [ OK ] NoFatalErrorWhenWritingFrom/GmxTraj.RotationalKineticEnergy/0 (13 ms) 52: [ RUN ] NoFatalErrorWhenWritingFrom/GmxTraj.RotationalKineticEnergy/1 52: Group 0 ( System) has 6 elements 52: Group 1 ( Water) has 6 elements 52: Group 2 ( SOL) has 6 elements 52: Select a group: Reading frame 0 time 0.000 52: WARNING: If there are molecules in the input trajectory file 52: that are broken across periodic boundaries, they 52: cannot be made whole (or treated as whole) without 52: you providing a run input file. 52: 52: Reading frame 1 time 1.000 Last frame 1 time 1.000 52: 52: WARNING: Masses and atomic (Van der Waals) radii will be guessed 52: based on residue and atom names, since they could not be 52: definitively assigned from the information in your input 52: files. These guessed numbers might deviate from the mass 52: and radius of the atom type. Please check the output 52: files if necessary. Note, that this functionality may 52: be removed in a future GROMACS version. Please, consider 52: using another file format for your input. 52: 52: Selected 0: 'System' 52: [ OK ] NoFatalErrorWhenWritingFrom/GmxTraj.RotationalKineticEnergy/1 (14 ms) 52: [ RUN ] NoFatalErrorWhenWritingFrom/GmxTraj.RotationalKineticEnergy/2 52: Group 0 ( System) has 6 elements 52: Group 1 ( Water) has 6 elements 52: Group 2 ( SOL) has 6 elements 52: Select a group: Reading frames from gro file 'Generated by trjconv t= 0.00000 step= 0', 6 atoms. 52: Reading frame 0 time 0.000 52: WARNING: If there are molecules in the input trajectory file 52: that are broken across periodic boundaries, they 52: cannot be made whole (or treated as whole) without 52: you providing a run input file. 52: 52: Reading frame 1 time 1.000 Last frame 1 time 1.000 52: 52: WARNING: Masses and atomic (Van der Waals) radii will be guessed 52: based on residue and atom names, since they could not be 52: definitively assigned from the information in your input 52: files. These guessed numbers might deviate from the mass 52: and radius of the atom type. Please check the output 52: files if necessary. Note, that this functionality may 52: be removed in a future GROMACS version. Please, consider 52: using another file format for your input. 52: 52: Selected 0: 'System' 52: [ OK ] NoFatalErrorWhenWritingFrom/GmxTraj.RotationalKineticEnergy/2 (12 ms) 52: [ RUN ] NoFatalErrorWhenWritingFrom/GmxTraj.RotationalKineticEnergy/3 52: Group 0 ( System) has 6 elements 52: Group 1 ( Water) has 6 elements 52: Group 2 ( SOL) has 6 elements 52: Select a group: Reading frames from pdb file Reading frame 0 time 0.000 52: WARNING: If there are molecules in the input trajectory file 52: that are broken across periodic boundaries, they 52: cannot be made whole (or treated as whole) without 52: you providing a run input file. 52: 52: 'Generated by trjconv t= 1.00000 step= 1', 6 atoms 52: Reading frame 1 time 1.000 Last frame 1 time 1.000 52: 52: WARNING: Masses and atomic (Van der Waals) radii will be guessed 52: based on residue and atom names, since they could not be 52: definitively assigned from the information in your input 52: files. These guessed numbers might deviate from the mass 52: and radius of the atom type. Please check the output 52: files if necessary. Note, that this functionality may 52: be removed in a future GROMACS version. Please, consider 52: using another file format for your input. 52: 52: Selected 0: 'System' 52: [ OK ] NoFatalErrorWhenWritingFrom/GmxTraj.RotationalKineticEnergy/3 (12 ms) 52: [ RUN ] NoFatalErrorWhenWritingFrom/GmxTraj.RotationalKineticEnergy/4 52: Group 0 ( System) has 6 elements 52: Group 1 ( Water) has 6 elements 52: Group 2 ( SOL) has 6 elements 52: Select a group: Reading frame 0 time 0.000 52: WARNING: If there are molecules in the input trajectory file 52: that are broken across periodic boundaries, they 52: cannot be made whole (or treated as whole) without 52: you providing a run input file. 52: 52: Reading frame 1 time 1.000 Last frame 1 time 1.000 52: 52: WARNING: Masses and atomic (Van der Waals) radii will be guessed 52: based on residue and atom names, since they could not be 52: definitively assigned from the information in your input 52: files. These guessed numbers might deviate from the mass 52: and radius of the atom type. Please check the output 52: files if necessary. Note, that this functionality may 52: be removed in a future GROMACS version. Please, consider 52: using another file format for your input. 52: 52: Selected 0: 'System' 52: [ OK ] NoFatalErrorWhenWritingFrom/GmxTraj.RotationalKineticEnergy/4 (13 ms) 52: [ RUN ] NoFatalErrorWhenWritingFrom/GmxTraj.RotationalKineticEnergy/5 52: Group 0 ( System) has 6 elements 52: Group 1 ( Water) has 6 elements 52: Group 2 ( SOL) has 6 elements 52: Select a group: Reading frame 0 time 0.000 52: WARNING: If there are molecules in the input trajectory file 52: that are broken across periodic boundaries, they 52: cannot be made whole (or treated as whole) without 52: you providing a run input file. 52: 52: Reading frame 1 time 1.000 Last frame 1 time 1.000 52: 52: WARNING: Masses and atomic (Van der Waals) radii will be guessed 52: based on residue and atom names, since they could not be 52: definitively assigned from the information in your input 52: files. These guessed numbers might deviate from the mass 52: and radius of the atom type. Please check the output 52: files if necessary. Note, that this functionality may 52: be removed in a future GROMACS version. Please, consider 52: using another file format for your input. 52: 52: Selected 0: 'System' 52: [ OK ] NoFatalErrorWhenWritingFrom/GmxTraj.RotationalKineticEnergy/5 (13 ms) 52: [----------] 12 tests from NoFatalErrorWhenWritingFrom/GmxTraj (131 ms total) 52: 52: [----------] Global test environment tear-down 52: [==========] 31 tests from 4 test suites ran. (9150 ms total) 52: [ PASSED ] 31 tests. 52/92 Test #52: GmxAnaTest ................................ Passed 9.26 sec test 53 Start 53: GmxPreprocessTests 53: Test command: /build/reproducible-path/gromacs-2025.1/build/basic/bin/gmxpreprocess-test "--gtest_output=xml:/build/reproducible-path/gromacs-2025.1/build/basic/Testing/Temporary/GmxPreprocessTests.xml" 53: Working Directory: /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/gmxpreprocess/tests 53: Test timeout computed to be: 1920 53: [==========] Running 260 tests from 16 test suites. 53: [----------] Global test environment set-up. 53: [----------] 1 test from ConvertInteractionsTest 53: [ RUN ] ConvertInteractionsTest.DoingNothingWorks 53: [ OK ] ConvertInteractionsTest.DoingNothingWorks (0 ms) 53: [----------] 1 test from ConvertInteractionsTest (0 ms total) 53: 53: [----------] 4 tests from GenconfTest 53: [ RUN ] GenconfTest.nbox_Works 53: [ OK ] GenconfTest.nbox_Works (4 ms) 53: [ RUN ] GenconfTest.nbox_norenumber_Works 53: [ OK ] GenconfTest.nbox_norenumber_Works (3 ms) 53: [ RUN ] GenconfTest.nbox_dist_Works 53: [ OK ] GenconfTest.nbox_dist_Works (4 ms) 53: [ RUN ] GenconfTest.nbox_rot_Works 53: center of geometry: 1.733667, 1.477000, 0.905167 53: center of geometry: 1.733667, 1.477000, 0.905167 53: center of geometry: 1.733667, 1.477000, 0.905167 53: center of geometry: 1.733667, 1.477000, 0.905167 53: center of geometry: 1.733667, 1.477000, 0.905167 53: center of geometry: 1.733667, 1.477000, 0.905167 53: center of geometry: 1.733667, 1.477000, 0.905167 53: center of geometry: 1.733667, 1.477000, 0.905167 53: center of geometry: 1.733667, 1.477000, 0.905167 53: center of geometry: 1.733667, 1.477000, 0.905167 53: center of geometry: 1.733667, 1.477000, 0.905167 53: center of geometry: 1.733667, 1.477000, 0.905167 53: [ OK ] GenconfTest.nbox_rot_Works (4 ms) 53: [----------] 4 tests from GenconfTest (16 ms total) 53: 53: [----------] 2 tests from GenionTest 53: [ RUN ] GenionTest.HighConcentrationIonPlacement 53: 53: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GenionTest_HighConcentrationIonPlacement_input.mdp]: 53: rlist is equal to rvdw and/or rcoulomb: there is no explicit Verlet 53: buffer. The cluster pair list does have a buffering effect, but choosing 53: a larger rlist might be necessary for good energy conservation. 53: 53: 53: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GenionTest_HighConcentrationIonPlacement_input.mdp]: 53: verlet-buffer-pressure-tolerance is ignored when verlet-buffer-tolerance 53: < 0 53: 53: 53: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GenionTest_HighConcentrationIonPlacement_input.mdp]: 53: For a correct single-point energy evaluation with nsteps = 0, use 53: continuation = yes to avoid constraining the input coordinates. 53: 53: Generating 1-4 interactions: fudge = 0.5 53: Number of degrees of freedom in T-Coupling group rest is 1308.00 53: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 53: 53: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GenionTest_HighConcentrationIonPlacement_input.mdp]: 53: You are using a plain Coulomb cut-off, which might produce artifacts. 53: You might want to consider using PME electrostatics. 53: 53: 53: 53: There were 4 NOTEs 53: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GenionTest_HighConcentrationIonPlacement_spc216_with_methane.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 53: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GenionTest_HighConcentrationIonPlacement_spc216_with_methane.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 53: Group 0 ( System) has 653 elements 53: Group 1 ( Water) has 648 elements 53: Group 2 ( SOL) has 648 elements 53: Group 3 ( non-Water) has 5 elements 53: Group 4 ( Other) has 5 elements 53: Group 5 ( METH) has 5 elements 53: Select a group: Number of (3-atomic) solvent molecules: 216 53: Using random seed 1997. 53: Replacing solvent molecule 56 (atom 168) with NA 53: Replacing solvent molecule 120 (atom 360) with NA 53: Replacing solvent molecule 182 (atom 546) with NA 53: Replacing solvent molecule 71 (atom 213) with NA 53: Replacing solvent molecule 189 (atom 567) with CL 53: Replacing solvent molecule 54 (atom 162) with CL 53: Replacing solvent molecule 155 (atom 465) with CL 53: Replacing solvent molecule 99 (atom 297) with CL 53: 53: Setting the LD random seed to -20980129 53: 53: Generated 331705 of the 331705 non-bonded parameter combinations 53: 53: Generated 331705 of the 331705 1-4 parameter combinations 53: 53: Excluding 2 bonded neighbours molecule type 'SOL' 53: 53: Excluding 3 bonded neighbours molecule type 'methane' 53: 53: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/spc216_with_methane.gro' 53: Analysing residue names: 53: There are: 216 Water residues 53: There are: 1 Other residues 53: Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups... 53: 53: This run will generate roughly 0 Mb of data 53: Will try to add 4 NA ions and 4 CL ions. 53: Select a continuous group of solvent molecules 53: Selected 1: 'Water' 53: [ OK ] GenionTest.HighConcentrationIonPlacement (4596 ms) 53: [ RUN ] GenionTest.NoIonPlacement 53: 53: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GenionTest_NoIonPlacement_input.mdp]: 53: rlist is equal to rvdw and/or rcoulomb: there is no explicit Verlet 53: buffer. The cluster pair list does have a buffering effect, but choosing 53: a larger rlist might be necessary for good energy conservation. 53: 53: 53: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GenionTest_NoIonPlacement_input.mdp]: 53: verlet-buffer-pressure-tolerance is ignored when verlet-buffer-tolerance 53: < 0 53: 53: 53: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GenionTest_NoIonPlacement_input.mdp]: 53: For a correct single-point energy evaluation with nsteps = 0, use 53: continuation = yes to avoid constraining the input coordinates. 53: 53: Generating 1-4 interactions: fudge = 0.5 53: Number of degrees of freedom in T-Coupling group rest is 1308.00 53: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 53: 53: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GenionTest_NoIonPlacement_input.mdp]: 53: You are using a plain Coulomb cut-off, which might produce artifacts. 53: You might want to consider using PME electrostatics. 53: 53: 53: 53: There were 4 NOTEs 53: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GenionTest_NoIonPlacement_spc216_with_methane.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 53: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GenionTest_NoIonPlacement_spc216_with_methane.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 53: No ions to add, will just copy input configuration. 53: Setting the LD random seed to -1610647658 53: 53: Generated 331705 of the 331705 non-bonded parameter combinations 53: 53: Generated 331705 of the 331705 1-4 parameter combinations 53: 53: Excluding 2 bonded neighbours molecule type 'SOL' 53: 53: Excluding 3 bonded neighbours molecule type 'methane' 53: 53: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/spc216_with_methane.gro' 53: Analysing residue names: 53: There are: 216 Water residues 53: There are: 1 Other residues 53: Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups... 53: 53: This run will generate roughly 0 Mb of data 53: [ OK ] GenionTest.NoIonPlacement (4341 ms) 53: [----------] 2 tests from GenionTest (8938 ms total) 53: 53: [----------] 1 test from GenRestrTest 53: [ RUN ] GenRestrTest.SimpleRestraintsGenerated 53: 53: Reading structure file 53: Group 0 ( System) has 156 elements 53: Group 1 ( Protein) has 156 elements 53: Group 2 ( Protein-H) has 75 elements 53: Group 3 ( C-alpha) has 10 elements 53: Group 4 ( Backbone) has 30 elements 53: Group 5 ( MainChain) has 40 elements 53: Group 6 ( MainChain+Cb) has 49 elements 53: Group 7 ( MainChain+H) has 52 elements 53: Group 8 ( SideChain) has 104 elements 53: Group 9 ( SideChain-H) has 35 elements 53: Select a group: Select group to position restrain 53: Selected 3: 'C-alpha' 53: [ OK ] GenRestrTest.SimpleRestraintsGenerated (13 ms) 53: [----------] 1 test from GenRestrTest (13 ms total) 53: 53: [----------] 9 tests from PreprocessingAtomTypesTest 53: [ RUN ] PreprocessingAtomTypesTest.EmptyOnCreate 53: [ OK ] PreprocessingAtomTypesTest.EmptyOnCreate (0 ms) 53: [ RUN ] PreprocessingAtomTypesTest.IndexOutOfRangeInvalid 53: [ OK ] PreprocessingAtomTypesTest.IndexOutOfRangeInvalid (0 ms) 53: [ RUN ] PreprocessingAtomTypesTest.AddTypeWorks 53: [ OK ] PreprocessingAtomTypesTest.AddTypeWorks (0 ms) 53: [ RUN ] PreprocessingAtomTypesTest.AddMultipleTypesWorks 53: [ OK ] PreprocessingAtomTypesTest.AddMultipleTypesWorks (0 ms) 53: [ RUN ] PreprocessingAtomTypesTest.CannotAddDuplicateEntry 53: [ OK ] PreprocessingAtomTypesTest.CannotAddDuplicateEntry (0 ms) 53: [ RUN ] PreprocessingAtomTypesTest.CorrectNameFound 53: [ OK ] PreprocessingAtomTypesTest.CorrectNameFound (0 ms) 53: [ RUN ] PreprocessingAtomTypesTest.WrongNameNotFound 53: [ OK ] PreprocessingAtomTypesTest.WrongNameNotFound (0 ms) 53: [ RUN ] PreprocessingAtomTypesTest.CorrectNameFromTypeNumber 53: [ OK ] PreprocessingAtomTypesTest.CorrectNameFromTypeNumber (0 ms) 53: [ RUN ] PreprocessingAtomTypesTest.NoNameFromIncorrectTypeNumber 53: [ OK ] PreprocessingAtomTypesTest.NoNameFromIncorrectTypeNumber (0 ms) 53: [----------] 9 tests from PreprocessingAtomTypesTest (0 ms total) 53: 53: [----------] 10 tests from PreprocessingBondAtomTypeTest 53: [ RUN ] PreprocessingBondAtomTypeTest.EmptyOnCreate 53: [ OK ] PreprocessingBondAtomTypeTest.EmptyOnCreate (0 ms) 53: [ RUN ] PreprocessingBondAtomTypeTest.IndexOutOfRangeInvalid 53: [ OK ] PreprocessingBondAtomTypeTest.IndexOutOfRangeInvalid (0 ms) 53: [ RUN ] PreprocessingBondAtomTypeTest.AddTypeWorks 53: [ OK ] PreprocessingBondAtomTypeTest.AddTypeWorks (0 ms) 53: [ RUN ] PreprocessingBondAtomTypeTest.AddMultipleTypesWorks 53: [ OK ] PreprocessingBondAtomTypeTest.AddMultipleTypesWorks (0 ms) 53: [ RUN ] PreprocessingBondAtomTypeTest.CannotAddDuplicateEntry 53: [ OK ] PreprocessingBondAtomTypeTest.CannotAddDuplicateEntry (0 ms) 53: [ RUN ] PreprocessingBondAtomTypeTest.ReturnsCorrectIndexOnDuplicateType 53: [ OK ] PreprocessingBondAtomTypeTest.ReturnsCorrectIndexOnDuplicateType (0 ms) 53: [ RUN ] PreprocessingBondAtomTypeTest.CorrectNameFound 53: [ OK ] PreprocessingBondAtomTypeTest.CorrectNameFound (0 ms) 53: [ RUN ] PreprocessingBondAtomTypeTest.WrongNameNotFound 53: [ OK ] PreprocessingBondAtomTypeTest.WrongNameNotFound (0 ms) 53: [ RUN ] PreprocessingBondAtomTypeTest.CorrectNameFromTypeNumber 53: [ OK ] PreprocessingBondAtomTypeTest.CorrectNameFromTypeNumber (0 ms) 53: [ RUN ] PreprocessingBondAtomTypeTest.NoNameFromIncorrectTypeNumber 53: [ OK ] PreprocessingBondAtomTypeTest.NoNameFromIncorrectTypeNumber (0 ms) 53: [----------] 10 tests from PreprocessingBondAtomTypeTest (0 ms total) 53: 53: [----------] 3 tests from GromppDirectiveTest 53: [ RUN ] GromppDirectiveTest.edgeCaseAtomTypeNames 53: Ignoring obsolete mdp entry 'title' 53: Generating 1-4 interactions: fudge = 0.5 53: 53: NOTE 1 [file directives.top, line 59]: 53: In moleculetype 'A' 2 atoms are not bound by a potential or constraint to 53: any other atom in the same moleculetype. Although technically this might 53: not cause issues in a simulation, this often means that the user forgot 53: to add a bond/potential/constraint or put multiple molecules in the same 53: moleculetype definition by mistake. Run with -v to get information for 53: each atom. 53: 53: Number of degrees of freedom in T-Coupling group rest is 9.00 53: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 53: 53: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GromppDirectiveTest_edgeCaseAtomTypeNames_directives.mdp]: 53: NVE simulation: will use the initial temperature of 300.000 K for 53: determining the Verlet buffer size 53: 53: 53: There were 2 NOTEs 53: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GromppDirectiveTest_edgeCaseAtomTypeNames_directives.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 53: Setting the LD random seed to -437534737 53: 53: Generated 10 of the 10 non-bonded parameter combinations 53: 53: Generated 10 of the 10 1-4 parameter combinations 53: 53: Excluding 0 bonded neighbours molecule type 'A' 53: 53: Setting gen_seed to -1707164289 53: 53: Velocities were taken from a Maxwell distribution at 300 K 53: Analysing residue names: 53: There are: 1 Other residues 53: Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups... 53: 53: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 300 K 53: 53: Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm 53: 53: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm 53: 53: Note that mdrun will redetermine rlist based on the actual pair-list setup 53: 53: This run will generate roughly 0 Mb of data 53: [ OK ] GromppDirectiveTest.edgeCaseAtomTypeNames (31 ms) 53: [ RUN ] GromppDirectiveTest.NoteOnDihedralNotSumToZero 53: Ignoring obsolete mdp entry 'title' 53: Generating 1-4 interactions: fudge = 0.5 53: 53: NOTE 1 [file directives.top, line 59]: 53: 1 dihedrals with function type 3 (Ryckaert-Bellemans or Fourier) have 53: coefficients that do not sum to zero. This does not affect the simulation 53: and can be ignored, unless you are comparing potential energy values with 53: other force field ports and/or MD software. 53: First such dihedral in molecule A, involving atoms 0 2 1 3 53: 53: 53: NOTE 2 [file directives.top, line 59]: 53: In moleculetype 'A' 2 atoms are not bound by a potential or constraint to 53: any other atom in the same moleculetype. Although technically this might 53: not cause issues in a simulation, this often means that the user forgot 53: to add a bond/potential/constraint or put multiple molecules in the same 53: moleculetype definition by mistake. Run with -v to get information for 53: each atom. 53: 53: Number of degrees of freedom in T-Coupling group rest is 9.00 53: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 53: 53: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GromppDirectiveTest_NoteOnDihedralNotSumToZero_directives.mdp]: 53: NVE simulation: will use the initial temperature of 300.000 K for 53: determining the Verlet buffer size 53: 53: 53: There were 3 NOTEs 53: Setting the LD random seed to 2137895615 53: 53: Generated 10 of the 10 non-bonded parameter combinations 53: 53: Generated 10 of the 10 1-4 parameter combinations 53: 53: Excluding 0 bonded neighbours molecule type 'A' 53: 53: Setting gen_seed to -613548033 53: 53: Velocities were taken from a Maxwell distribution at 300 K 53: Analysing residue names: 53: There are: 1 Other residues 53: Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups... 53: 53: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 300 K 53: 53: Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm 53: 53: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm 53: 53: Note that mdrun will redetermine rlist based on the actual pair-list setup 53: 53: This run will generate roughly 0 Mb of data 53: [ OK ] GromppDirectiveTest.NoteOnDihedralNotSumToZero (29 ms) 53: [ RUN ] GromppDirectiveTest.WarnOnDihedralSumDifferentForFreeEnergy 53: Setting the LD random seed to 1534742487 53: 53: Generated 10 of the 10 non-bonded parameter combinations 53: 53: Generated 10 of the 10 1-4 parameter combinations 53: 53: Excluding 0 bonded neighbours molecule type 'A' 53: 53: Setting gen_seed to -407012362 53: 53: Velocities were taken from a Maxwell distribution at 300 K 53: Analysing residue names: 53: There are: 1 Other residues 53: Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups... 53: 53: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 300 K 53: 53: Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm 53: 53: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm 53: 53: Note that mdrun will redetermine rlist based on the actual pair-list setup 53: 53: This run will generate roughly 0 Mb of data 53: [ OK ] GromppDirectiveTest.WarnOnDihedralSumDifferentForFreeEnergy (56 ms) 53: [----------] 3 tests from GromppDirectiveTest (117 ms total) 53: 53: [----------] 6 tests from InsertMoleculesTest 53: [ RUN ] InsertMoleculesTest.InsertsMoleculesIntoExistingConfiguration 53: Reading solute configuration 53: Initialising inter-atomic distances... 53: 53: WARNING: Masses and atomic (Van der Waals) radii will be guessed 53: based on residue and atom names, since they could not be 53: definitively assigned from the information in your input 53: files. These guessed numbers might deviate from the mass 53: and radius of the atom type. Please check the output 53: files if necessary. Note, that this functionality may 53: be removed in a future GROMACS version. Please, consider 53: using another file format for your input. 53: 53: NOTE: From version 5.0 gmxpreprocess-test uses the Van der Waals radii 53: from the source below. This means the results may be different 53: compared to previous GROMACS versions. 53: 53: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 53: A. Bondi 53: van der Waals Volumes and Radii 53: J. Phys. Chem. (1964) 53: DOI: 10.1021/j100785a001 53: -------- -------- --- Thank You --- -------- -------- 53: 53: Using random seed 1997 53: Try 1 success (now 8 atoms)! 53: 53: Added 1 molecules (out of 1 requested) 53: Writing generated configuration to /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/InsertMoleculesTest_InsertsMoleculesIntoExistingConfiguration_out.gro 53: 53: Output configuration contains 8 atoms in 4 residues 53: [ OK ] InsertMoleculesTest.InsertsMoleculesIntoExistingConfiguration (11 ms) 53: [ RUN ] InsertMoleculesTest.InsertsMoleculesIntoEmptyBox 53: Initialising inter-atomic distances... 53: 53: WARNING: Masses and atomic (Van der Waals) radii will be guessed 53: based on residue and atom names, since they could not be 53: definitively assigned from the information in your input 53: files. These guessed numbers might deviate from the mass 53: and radius of the atom type. Please check the output 53: files if necessary. Note, that this functionality may 53: be removed in a future GROMACS version. Please, consider 53: using another file format for your input. 53: 53: NOTE: From version 5.0 gmxpreprocess-test uses the Van der Waals radii 53: from the source below. This means the results may be different 53: compared to previous GROMACS versions. 53: 53: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 53: A. Bondi 53: van der Waals Volumes and Radii 53: J. Phys. Chem. (1964) 53: DOI: 10.1021/j100785a001 53: -------- -------- --- Thank You --- -------- -------- 53: 53: Using random seed 1997 53: Try 1 success (now 2 atoms)! 53: Try 2 success (now 4 atoms)! 53: Try 3 success (now 6 atoms)! 53: Try 4 success (now 8 atoms)! 53: Try 5 success (now 10 atoms)! 53: 53: Added 5 molecules (out of 5 requested) 53: Writing generated configuration to /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/InsertMoleculesTest_InsertsMoleculesIntoEmptyBox_out.gro 53: 53: Output configuration contains 10 atoms in 10 residues 53: [ OK ] InsertMoleculesTest.InsertsMoleculesIntoEmptyBox (10 ms) 53: [ RUN ] InsertMoleculesTest.InsertsMoleculesIntoEmptyBoxConcentration 53: Initialising inter-atomic distances... 53: 53: WARNING: Masses and atomic (Van der Waals) radii will be guessed 53: based on residue and atom names, since they could not be 53: definitively assigned from the information in your input 53: files. These guessed numbers might deviate from the mass 53: and radius of the atom type. Please check the output 53: files if necessary. Note, that this functionality may 53: be removed in a future GROMACS version. Please, consider 53: using another file format for your input. 53: 53: NOTE: From version 5.0 gmxpreprocess-test uses the Van der Waals radii 53: from the source below. This means the results may be different 53: compared to previous GROMACS versions. 53: 53: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 53: A. Bondi 53: van der Waals Volumes and Radii 53: J. Phys. Chem. (1964) 53: DOI: 10.1021/j100785a001 53: -------- -------- --- Thank You --- -------- -------- 53: 53: Using random seed 1997 53: Try 1 success (now 2 atoms)! 53: Try 2 success (now 4 atoms)! 53: Try 3 success (now 6 atoms)! 53: Try 4 success (now 8 atoms)! 53: Try 5 success (now 10 atoms)! 53: 53: Added 5 molecules (out of 5 requested) 53: Writing generated configuration to /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/InsertMoleculesTest_InsertsMoleculesIntoEmptyBoxConcentration_out.gro 53: 53: Output configuration contains 10 atoms in 10 residues 53: [ OK ] InsertMoleculesTest.InsertsMoleculesIntoEmptyBoxConcentration (11 ms) 53: [ RUN ] InsertMoleculesTest.InsertsMoleculesIntoEnlargedBox 53: Reading solute configuration 53: Initialising inter-atomic distances... 53: 53: WARNING: Masses and atomic (Van der Waals) radii will be guessed 53: based on residue and atom names, since they could not be 53: definitively assigned from the information in your input 53: files. These guessed numbers might deviate from the mass 53: and radius of the atom type. Please check the output 53: files if necessary. Note, that this functionality may 53: be removed in a future GROMACS version. Please, consider 53: using another file format for your input. 53: 53: NOTE: From version 5.0 gmxpreprocess-test uses the Van der Waals radii 53: from the source below. This means the results may be different 53: compared to previous GROMACS versions. 53: 53: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 53: A. Bondi 53: van der Waals Volumes and Radii 53: J. Phys. Chem. (1964) 53: DOI: 10.1021/j100785a001 53: -------- -------- --- Thank You --- -------- -------- 53: 53: Using random seed 1997 53: Try 1 success (now 8 atoms)! 53: Try 2 success (now 10 atoms)! 53: 53: Added 2 molecules (out of 2 requested) 53: Writing generated configuration to /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/InsertMoleculesTest_InsertsMoleculesIntoEnlargedBox_out.gro 53: 53: Output configuration contains 10 atoms in 4 residues 53: [ OK ] InsertMoleculesTest.InsertsMoleculesIntoEnlargedBox (9 ms) 53: [ RUN ] InsertMoleculesTest.InsertsMoleculesWithReplacement 53: Reading solute configuration 53: Initialising inter-atomic distances... 53: 53: WARNING: Masses and atomic (Van der Waals) radii will be guessed 53: based on residue and atom names, since they could not be 53: definitively assigned from the information in your input 53: files. These guessed numbers might deviate from the mass 53: and radius of the atom type. Please check the output 53: files if necessary. Note, that this functionality may 53: be removed in a future GROMACS version. Please, consider 53: using another file format for your input. 53: 53: NOTE: From version 5.0 gmxpreprocess-test uses the Van der Waals radii 53: from the source below. This means the results may be different 53: compared to previous GROMACS versions. 53: 53: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 53: A. Bondi 53: van der Waals Volumes and Radii 53: J. Phys. Chem. (1964) 53: DOI: 10.1021/j100785a001 53: -------- -------- --- Thank You --- -------- -------- 53: 53: Using random seed 1997 53: Try 1 success (now 650 atoms)! 53: Try 2 success (now 652 atoms)! 53: Try 3 success (now 654 atoms)! 53: Try 4 success (now 656 atoms)! 53: 53: Added 4 molecules (out of 4 requested) 53: Replaced 8 residues (24 atoms) 53: Writing generated configuration to /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/InsertMoleculesTest_InsertsMoleculesWithReplacement_out.gro 53: 53: Output configuration contains 632 atoms in 212 residues 53: [ OK ] InsertMoleculesTest.InsertsMoleculesWithReplacement (29 ms) 53: [ RUN ] InsertMoleculesTest.InsertsMoleculesIntoFixedPositions 53: Initialising inter-atomic distances... 53: 53: WARNING: Masses and atomic (Van der Waals) radii will be guessed 53: based on residue and atom names, since they could not be 53: definitively assigned from the information in your input 53: files. These guessed numbers might deviate from the mass 53: and radius of the atom type. Please check the output 53: files if necessary. Note, that this functionality may 53: be removed in a future GROMACS version. Please, consider 53: using another file format for your input. 53: 53: NOTE: From version 5.0 gmxpreprocess-test uses the Van der Waals radii 53: from the source below. This means the results may be different 53: compared to previous GROMACS versions. 53: 53: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 53: A. Bondi 53: van der Waals Volumes and Radii 53: J. Phys. Chem. (1964) 53: DOI: 10.1021/j100785a001 53: -------- -------- --- Thank You --- -------- -------- 53: 53: Using random seed 1997 53: Read 4 positions from file /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/InsertMoleculesTest_InsertsMoleculesIntoFixedPositions_5.dat 53: 53: Try 1 success (now 2 atoms)! 53: Try 2 success (now 4 atoms)! 53: Try 3 Try 4 Try 5 Try 6 Try 7 Try 8 Try 9 Try 10 Try 11 Try 12 skipped position (0.990, 2.010, 3.000) 53: Try 13 success (now 6 atoms)! 53: 53: Added 3 molecules (out of 4 requested) 53: Writing generated configuration to /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/InsertMoleculesTest_InsertsMoleculesIntoFixedPositions_out.gro 53: 53: Output configuration contains 6 atoms in 3 residues 53: [ OK ] InsertMoleculesTest.InsertsMoleculesIntoFixedPositions (10 ms) 53: [----------] 6 tests from InsertMoleculesTest (84 ms total) 53: 53: [----------] 3 tests from MassRepartitioning 53: [ RUN ] MassRepartitioning.ValidCaseWorks 53: The smallest mass in the system is 2, setting the minimum mass to 6 53: [ OK ] MassRepartitioning.ValidCaseWorks (0 ms) 53: [ RUN ] MassRepartitioning.UnboundGivesWarning 53: 53: WARNING 1 [file unknown]: 53: The are 1 atoms that have a mass below the mass repartitioning limit but 53: are not bound. These masses cannot be repartitioned. 53: 53: The smallest mass in the system is 2, setting the minimum mass to 6 53: [ OK ] MassRepartitioning.UnboundGivesWarning (0 ms) 53: [ RUN ] MassRepartitioning.LightPartnerGivesError 53: 53: ERROR 1 [file unknown]: 53: Light atoms are bound to at least one atom that has a too low mass for 53: repartitioning 53: 53: The smallest mass in the system is 2, setting the minimum mass to 6 53: [ OK ] MassRepartitioning.LightPartnerGivesError (0 ms) 53: [----------] 3 tests from MassRepartitioning (0 ms total) 53: 53: [----------] 35 tests from GetIrTest 53: [ RUN ] GetIrTest.HandlesDifferentKindsOfMdpLines 53: Ignoring obsolete mdp entry 'title' 53: Replacing old mdp entry 'xtc_grps' by 'compressed-x-grps' 53: 53: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_HandlesDifferentKindsOfMdpLines_input.mdp]: 53: For a correct single-point energy evaluation with nsteps = 0, use 53: continuation = yes to avoid constraining the input coordinates. 53: 53: [ OK ] GetIrTest.HandlesDifferentKindsOfMdpLines (23 ms) 53: [ RUN ] GetIrTest.RejectsNonCommentLineWithNoEquals 53: [ OK ] GetIrTest.RejectsNonCommentLineWithNoEquals (32 ms) 53: [ RUN ] GetIrTest.AcceptsKeyWithoutValue 53: 53: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_AcceptsKeyWithoutValue_input.mdp]: 53: For a correct single-point energy evaluation with nsteps = 0, use 53: continuation = yes to avoid constraining the input coordinates. 53: 53: [ OK ] GetIrTest.AcceptsKeyWithoutValue (23 ms) 53: [ RUN ] GetIrTest.RejectsValueWithoutKey 53: [ OK ] GetIrTest.RejectsValueWithoutKey (35 ms) 53: [ RUN ] GetIrTest.RejectsEmptyKeyAndEmptyValue 53: [ OK ] GetIrTest.RejectsEmptyKeyAndEmptyValue (35 ms) 53: [ RUN ] GetIrTest.AcceptsDefineParametersWithValuesIncludingAssignment 53: 53: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_AcceptsDefineParametersWithValuesIncludingAssignment_input.mdp]: 53: For a correct single-point energy evaluation with nsteps = 0, use 53: continuation = yes to avoid constraining the input coordinates. 53: 53: [ OK ] GetIrTest.AcceptsDefineParametersWithValuesIncludingAssignment (22 ms) 53: [ RUN ] GetIrTest.AcceptsEmptyLines 53: 53: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_AcceptsEmptyLines_input.mdp]: 53: For a correct single-point energy evaluation with nsteps = 0, use 53: continuation = yes to avoid constraining the input coordinates. 53: 53: [ OK ] GetIrTest.AcceptsEmptyLines (24 ms) 53: [ RUN ] GetIrTest.MtsCheckNstcalcenergy 53: 53: ERROR 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_MtsCheckNstcalcenergy_input.mdp]: 53: With MTS, nstcalcenergy = 5 should be a multiple of mts-factor = 2 53: 53: 53: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_MtsCheckNstcalcenergy_input.mdp]: 53: For a correct single-point energy evaluation with nsteps = 0, use 53: continuation = yes to avoid constraining the input coordinates. 53: 53: [ OK ] GetIrTest.MtsCheckNstcalcenergy (17 ms) 53: [ RUN ] GetIrTest.MtsCheckNstenergy 53: 53: ERROR 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_MtsCheckNstenergy_input.mdp]: 53: With MTS, nstenergy = 5 should be a multiple of mts-factor = 2 53: 53: 53: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_MtsCheckNstenergy_input.mdp]: 53: Setting nstcalcenergy (100) equal to nstenergy (5) 53: 53: 53: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_MtsCheckNstenergy_input.mdp]: 53: For a correct single-point energy evaluation with nsteps = 0, use 53: continuation = yes to avoid constraining the input coordinates. 53: 53: [ OK ] GetIrTest.MtsCheckNstenergy (18 ms) 53: [ RUN ] GetIrTest.MtsCheckNstpcouple 53: 53: ERROR 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_MtsCheckNstpcouple_input.mdp, line 7]: 53: Pressure coupling incorrect number of values (I need exactly 1) 53: 53: 53: ERROR 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_MtsCheckNstpcouple_input.mdp, line 7]: 53: Pressure coupling incorrect number of values (I need exactly 1) 53: 53: 53: ERROR 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_MtsCheckNstpcouple_input.mdp]: 53: With multiple time stepping, nstpcouple should be a multiple of 53: mts-factor 53: 53: 53: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_MtsCheckNstpcouple_input.mdp]: 53: For a correct single-point energy evaluation with nsteps = 0, use 53: continuation = yes to avoid constraining the input coordinates. 53: 53: 53: ERROR 4 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_MtsCheckNstpcouple_input.mdp]: 53: The Berendsen barostat does not generate any strictly correct ensemble, 53: and should not be used for new production simulations (in our opinion). 53: We recommend using the C-rescale barostat instead. 53: 53: 53: ERROR 5 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_MtsCheckNstpcouple_input.mdp]: 53: compressibility must be > 0 when using pressure coupling Berendsen 53: 53: 53: [ OK ] GetIrTest.MtsCheckNstpcouple (20 ms) 53: [ RUN ] GetIrTest.MtsCheckNstdhdl 53: 53: ERROR 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_MtsCheckNstdhdl_input.mdp]: 53: With MTS, nstdhdl = 5 should be a multiple of mts-factor = 2 53: 53: 53: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_MtsCheckNstdhdl_input.mdp]: 53: Setting nstcalcenergy (100) equal to nstdhdl (5) 53: 53: 53: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_MtsCheckNstdhdl_input.mdp]: 53: For a correct single-point energy evaluation with nsteps = 0, use 53: continuation = yes to avoid constraining the input coordinates. 53: 53: 53: ERROR 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_MtsCheckNstdhdl_input.mdp]: 53: Lambda state must be set, either with init-lambda-state or with 53: init-lambda 53: 53: [ OK ] GetIrTest.MtsCheckNstdhdl (17 ms) 53: [ RUN ] GetIrTest.MtsCheckSDNotSupported 53: 53: ERROR 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_MtsCheckSDNotSupported_input.mdp]: 53: Multiple time stepping is only supported with integrator md 53: 53: 53: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_MtsCheckSDNotSupported_input.mdp]: 53: For a correct single-point energy evaluation with nsteps = 0, use 53: continuation = yes to avoid constraining the input coordinates. 53: 53: [ OK ] GetIrTest.MtsCheckSDNotSupported (18 ms) 53: [ RUN ] GetIrTest.AcceptsElectricField 53: 53: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_AcceptsElectricField_input.mdp]: 53: For a correct single-point energy evaluation with nsteps = 0, use 53: continuation = yes to avoid constraining the input coordinates. 53: 53: [ OK ] GetIrTest.AcceptsElectricField (23 ms) 53: [ RUN ] GetIrTest.AcceptsElectricFieldPulsed 53: 53: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_AcceptsElectricFieldPulsed_input.mdp]: 53: For a correct single-point energy evaluation with nsteps = 0, use 53: continuation = yes to avoid constraining the input coordinates. 53: 53: [ OK ] GetIrTest.AcceptsElectricFieldPulsed (23 ms) 53: [ RUN ] GetIrTest.AcceptsElectricFieldOscillating 53: 53: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_AcceptsElectricFieldOscillating_input.mdp]: 53: For a correct single-point energy evaluation with nsteps = 0, use 53: continuation = yes to avoid constraining the input coordinates. 53: 53: [ OK ] GetIrTest.AcceptsElectricFieldOscillating (24 ms) 53: [ RUN ] GetIrTest.RejectsDuplicateOldAndNewKeys 53: [ OK ] GetIrTest.RejectsDuplicateOldAndNewKeys (10 ms) 53: [ RUN ] GetIrTest.AcceptsImplicitSolventNo 53: 53: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_AcceptsImplicitSolventNo_input.mdp]: 53: For a correct single-point energy evaluation with nsteps = 0, use 53: continuation = yes to avoid constraining the input coordinates. 53: 53: [ OK ] GetIrTest.AcceptsImplicitSolventNo (28 ms) 53: [ RUN ] GetIrTest.RejectsImplicitSolventYes 53: [ OK ] GetIrTest.RejectsImplicitSolventYes (38 ms) 53: [ RUN ] GetIrTest.AcceptsMimic 53: 53: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_AcceptsMimic_input.mdp]: 53: For a correct single-point energy evaluation with nsteps = 0, use 53: continuation = yes to avoid constraining the input coordinates. 53: 53: [ OK ] GetIrTest.AcceptsMimic (24 ms) 53: [ RUN ] GetIrTest.AcceptsTransformationCoord 53: 53: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_AcceptsTransformationCoord_input.mdp, line 11]: 53: pull-coord2 has a non-zero force constant and is also referenced in 53: pull-coord1-expression. Make sure that this is intended. In most use 53: cases, the pull coordinates referenced by a transformation coordinate 53: should have their force constant set to zero. 53: 53: 53: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_AcceptsTransformationCoord_input.mdp]: 53: For a correct single-point energy evaluation with nsteps = 0, use 53: continuation = yes to avoid constraining the input coordinates. 53: 53: [ OK ] GetIrTest.AcceptsTransformationCoord (23 ms) 53: [ RUN ] GetIrTest.InvalidTransformationCoordWithConstraint 53: 53: ERROR 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_InvalidTransformationCoordWithConstraint_input.mdp, line 7]: 53: pull-coord1 cannot have type 'constraint' and geometry 'transformation' 53: 53: 53: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_InvalidTransformationCoordWithConstraint_input.mdp]: 53: For a correct single-point energy evaluation with nsteps = 0, use 53: continuation = yes to avoid constraining the input coordinates. 53: 53: [ OK ] GetIrTest.InvalidTransformationCoordWithConstraint (19 ms) 53: [ RUN ] GetIrTest.InvalidPullCoordWithConstraintInTransformationExpression 53: 53: ERROR 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_InvalidPullCoordWithConstraintInTransformationExpression_input.mdp, line 10]: 53: pull-coord2 can not use pull-coord1 in the transformation since this is a 53: constraint 53: 53: 53: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_InvalidPullCoordWithConstraintInTransformationExpression_input.mdp]: 53: For a correct single-point energy evaluation with nsteps = 0, use 53: continuation = yes to avoid constraining the input coordinates. 53: 53: [ OK ] GetIrTest.InvalidPullCoordWithConstraintInTransformationExpression (21 ms) 53: [ RUN ] GetIrTest.InvalidTransformationCoordDxValue 53: 53: ERROR 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_InvalidTransformationCoordDxValue_input.mdp, line 7]: 53: pull-coord1-dx cannot be set to zero for pull coordinate of geometry 53: 'transformation' 53: 53: 53: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_InvalidTransformationCoordDxValue_input.mdp]: 53: For a correct single-point energy evaluation with nsteps = 0, use 53: continuation = yes to avoid constraining the input coordinates. 53: 53: [ OK ] GetIrTest.InvalidTransformationCoordDxValue (19 ms) 53: [ RUN ] GetIrTest.MissingTransformationCoordExpression 53: 53: ERROR 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_MissingTransformationCoordExpression_input.mdp, line 5]: 53: pull-coord1-expression not set for pull coordinate of geometry 53: 'transformation' 53: 53: 53: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_MissingTransformationCoordExpression_input.mdp]: 53: For a correct single-point energy evaluation with nsteps = 0, use 53: continuation = yes to avoid constraining the input coordinates. 53: 53: [ OK ] GetIrTest.MissingTransformationCoordExpression (20 ms) 53: [ RUN ] GetIrTest.lambdaOverOneCheck_SC_And_ExactlyAsManyStep 53: [ OK ] GetIrTest.lambdaOverOneCheck_SC_And_ExactlyAsManyStep (17 ms) 53: [ RUN ] GetIrTest.lambdaOverOneCheck_SC_And_ExactlyAsManyStep_negativeDelta 53: [ OK ] GetIrTest.lambdaOverOneCheck_SC_And_ExactlyAsManyStep_negativeDelta (17 ms) 53: [ RUN ] GetIrTest.lambdaOverOneCheck_NoSC_And_ExactlyAsManyStep 53: [ OK ] GetIrTest.lambdaOverOneCheck_NoSC_And_ExactlyAsManyStep (16 ms) 53: [ RUN ] GetIrTest.lambdaOverOneCheck_NoSC_And_ExactlyAsManyStep_negativeDelta 53: [ OK ] GetIrTest.lambdaOverOneCheck_NoSC_And_ExactlyAsManyStep_negativeDelta (17 ms) 53: [ RUN ] GetIrTest.lambdaOverOneCheck_SC_And_OneStepTooMuch 53: 53: ERROR 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_lambdaOverOneCheck_SC_And_OneStepTooMuch_input.mdp]: 53: With init-lambda = 0 and delta_lambda = 1e-05 and no explicit input, 53: coul-lambdas and vdw-lambdas will be greater than 1 after step 100000 of 53: in total 100001 steps. This is not compatible with using soft-core 53: potentials. 53: 53: 53: [ OK ] GetIrTest.lambdaOverOneCheck_SC_And_OneStepTooMuch (17 ms) 53: [ RUN ] GetIrTest.lambdaOverOneCheck_SC_And_OneStepTooMuch_negativeDelta 53: 53: ERROR 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_lambdaOverOneCheck_SC_And_OneStepTooMuch_negativeDelta_input.mdp]: 53: With init-lambda = 1 and delta_lambda = -1e-05, the lambda components 53: won't change anymore after step 100000 until the end of the simulation 53: after 100001 steps. 53: 53: 53: [ OK ] GetIrTest.lambdaOverOneCheck_SC_And_OneStepTooMuch_negativeDelta (17 ms) 53: [ RUN ] GetIrTest.lambdaOverOneCheck_NoSC_And_OneStepTooMuch_negativeDelta 53: 53: ERROR 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_lambdaOverOneCheck_NoSC_And_OneStepTooMuch_negativeDelta_input.mdp]: 53: With init-lambda = 1 and delta_lambda = -1e-05, the lambda components 53: won't change anymore after step 100000 until the end of the simulation 53: after 100001 steps. 53: 53: 53: [ OK ] GetIrTest.lambdaOverOneCheck_NoSC_And_OneStepTooMuch_negativeDelta (17 ms) 53: [ RUN ] GetIrTest.lambdaOverOneCheck_LambdaVector_And_OneStepTooMuch 53: 53: ERROR 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_lambdaOverOneCheck_LambdaVector_And_OneStepTooMuch_input.mdp]: 53: With init-lambda-state = 0 and delta_lambda = 1e-05, the lambda 53: components won't change anymore after step 100000 until the end of the 53: simulation after 100001 steps. 53: 53: 53: [ OK ] GetIrTest.lambdaOverOneCheck_LambdaVector_And_OneStepTooMuch (18 ms) 53: [ RUN ] GetIrTest.lambdaOverOneCheck_LambdaVector_And_OneStepTooMuch_negativeDelta 53: 53: ERROR 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_lambdaOverOneCheck_LambdaVector_And_OneStepTooMuch_negativeDelta_input.mdp]: 53: With init-lambda-state = 2 and delta_lambda = -1e-05, the lambda 53: components won't change anymore after step 100000 until the end of the 53: simulation after 100001 steps. 53: 53: 53: [ OK ] GetIrTest.lambdaOverOneCheck_LambdaVector_And_OneStepTooMuch_negativeDelta (17 ms) 53: [ RUN ] GetIrTest.lambdaOverOneCheck_LambdaVector_And_ExactlyAsManyStep 53: [ OK ] GetIrTest.lambdaOverOneCheck_LambdaVector_And_ExactlyAsManyStep (16 ms) 53: [ RUN ] GetIrTest.lambdaOverOneCheck_LambdaVector_And_ExactlyAsManyStep_negativeDelta 53: [ OK ] GetIrTest.lambdaOverOneCheck_LambdaVector_And_ExactlyAsManyStep_negativeDelta (16 ms) 53: [----------] 35 tests from GetIrTest (761 ms total) 53: 53: [----------] 6 tests from SolvateTest 53: [ RUN ] SolvateTest.cs_box_Works 53: Reading solvent configuration 53: 53: Initialising inter-atomic distances... 53: 53: WARNING: Masses and atomic (Van der Waals) radii will be guessed 53: based on residue and atom names, since they could not be 53: definitively assigned from the information in your input 53: files. These guessed numbers might deviate from the mass 53: and radius of the atom type. Please check the output 53: files if necessary. Note, that this functionality may 53: be removed in a future GROMACS version. Please, consider 53: using another file format for your input. 53: 53: NOTE: From version 5.0 gmxpreprocess-test uses the Van der Waals radii 53: from the source below. This means the results may be different 53: compared to previous GROMACS versions. 53: 53: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 53: A. Bondi 53: van der Waals Volumes and Radii 53: J. Phys. Chem. (1964) 53: DOI: 10.1021/j100785a001 53: -------- -------- --- Thank You --- -------- -------- 53: 53: Generating solvent configuration 53: Will generate new solvent configuration of 1x1x1 boxes 53: Solvent box contains 270 atoms in 90 residues 53: Removed 129 solvent atoms due to solvent-solvent overlap 53: Sorting configuration 53: Found 1 molecule type: 53: SOL ( 3 atoms): 47 residues 53: Generated solvent containing 141 atoms in 47 residues 53: Writing generated configuration to /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/SolvateTest_cs_box_Works_out.gro 53: 53: Output configuration contains 141 atoms in 47 residues 53: Volume : 1.331 (nm^3) 53: Density : 1056.36 (g/l) 53: Number of solvent molecules: 47 53: 53: [ OK ] SolvateTest.cs_box_Works (22 ms) 53: [ RUN ] SolvateTest.cs_cp_Works 53: Reading solute configuration 53: Reading solvent configuration 53: 53: Initialising inter-atomic distances... 53: 53: WARNING: Masses and atomic (Van der Waals) radii will be guessed 53: based on residue and atom names, since they could not be 53: definitively assigned from the information in your input 53: files. These guessed numbers might deviate from the mass 53: and radius of the atom type. Please check the output 53: files if necessary. Note, that this functionality may 53: be removed in a future GROMACS version. Please, consider 53: using another file format for your input. 53: 53: NOTE: From version 5.0 gmxpreprocess-test uses the Van der Waals radii 53: from the source below. This means the results may be different 53: compared to previous GROMACS versions. 53: 53: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 53: A. Bondi 53: van der Waals Volumes and Radii 53: J. Phys. Chem. (1964) 53: DOI: 10.1021/j100785a001 53: -------- -------- --- Thank You --- -------- -------- 53: 53: Generating solvent configuration 53: Will generate new solvent configuration of 2x2x2 boxes 53: Solvent box contains 3660 atoms in 1220 residues 53: Removed 987 solvent atoms due to solvent-solvent overlap 53: Removed 15 solvent atoms due to solute-solvent overlap 53: Sorting configuration 53: Found 1 molecule type: 53: SOL ( 3 atoms): 886 residues 53: Generated solvent containing 2658 atoms in 886 residues 53: Writing generated configuration to /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/SolvateTest_cs_cp_Works_out.gro 53: 53: Output configuration contains 2664 atoms in 888 residues 53: Volume : 27.2709 (nm^3) 53: Density : 974.777 (g/l) 53: Number of solvent molecules: 886 53: 53: [ OK ] SolvateTest.cs_cp_Works (103 ms) 53: [ RUN ] SolvateTest.cs_cp_p_Works 53: Reading solute configuration 53: Reading solvent configuration 53: 53: Initialising inter-atomic distances... 53: 53: WARNING: Masses and atomic (Van der Waals) radii will be guessed 53: based on residue and atom names, since they could not be 53: definitively assigned from the information in your input 53: files. These guessed numbers might deviate from the mass 53: and radius of the atom type. Please check the output 53: files if necessary. Note, that this functionality may 53: be removed in a future GROMACS version. Please, consider 53: using another file format for your input. 53: 53: NOTE: From version 5.0 gmxpreprocess-test uses the Van der Waals radii 53: from the source below. This means the results may be different 53: compared to previous GROMACS versions. 53: 53: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 53: A. Bondi 53: van der Waals Volumes and Radii 53: J. Phys. Chem. (1964) 53: DOI: 10.1021/j100785a001 53: -------- -------- --- Thank You --- -------- -------- 53: 53: Generating solvent configuration 53: Will generate new solvent configuration of 2x2x2 boxes 53: Solvent box contains 3660 atoms in 1220 residues 53: Removed 987 solvent atoms due to solvent-solvent overlap 53: Removed 15 solvent atoms due to solute-solvent overlap 53: Sorting configuration 53: Found 1 molecule type: 53: SOL ( 3 atoms): 886 residues 53: Generated solvent containing 2658 atoms in 886 residues 53: Writing generated configuration to /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/SolvateTest_cs_cp_p_Works_out.gro 53: 53: Output configuration contains 2664 atoms in 888 residues 53: Volume : 27.2709 (nm^3) 53: Density : 974.777 (g/l) 53: Number of solvent molecules: 886 53: 53: Processing topology 53: Adding line for 886 solvent molecules with resname (SOL) to topology file (/build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/SolvateTest_cs_cp_p_Works_spc-and-methanol.top) 53: [ OK ] SolvateTest.cs_cp_p_Works (113 ms) 53: [ RUN ] SolvateTest.shell_Works 53: Reading solute configuration 53: Reading solvent configuration 53: 53: Initialising inter-atomic distances... 53: 53: WARNING: Masses and atomic (Van der Waals) radii will be guessed 53: based on residue and atom names, since they could not be 53: definitively assigned from the information in your input 53: files. These guessed numbers might deviate from the mass 53: and radius of the atom type. Please check the output 53: files if necessary. Note, that this functionality may 53: be removed in a future GROMACS version. Please, consider 53: using another file format for your input. 53: 53: NOTE: From version 5.0 gmxpreprocess-test uses the Van der Waals radii 53: from the source below. This means the results may be different 53: compared to previous GROMACS versions. 53: 53: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 53: A. Bondi 53: van der Waals Volumes and Radii 53: J. Phys. Chem. (1964) 53: DOI: 10.1021/j100785a001 53: -------- -------- --- Thank You --- -------- -------- 53: 53: Generating solvent configuration 53: Will generate new solvent configuration of 2x2x2 boxes 53: Solvent box contains 3660 atoms in 1220 residues 53: Removed 987 solvent atoms due to solvent-solvent overlap 53: Removed 1902 solvent atoms more than 1.000000 nm from solute. 53: Removed 15 solvent atoms due to solute-solvent overlap 53: Sorting configuration 53: Found 1 molecule type: 53: SOL ( 3 atoms): 252 residues 53: Generated solvent containing 756 atoms in 252 residues 53: Writing generated configuration to /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/SolvateTest_shell_Works_out.gro 53: 53: Output configuration contains 762 atoms in 254 residues 53: Volume : 27.2709 (nm^3) 53: Density : 279.3 (g/l) 53: Number of solvent molecules: 252 53: 53: [ OK ] SolvateTest.shell_Works (71 ms) 53: [ RUN ] SolvateTest.update_Topology_Works 53: Reading solute configuration 53: Reading solvent configuration 53: 53: Initialising inter-atomic distances... 53: 53: WARNING: Masses and atomic (Van der Waals) radii will be guessed 53: based on residue and atom names, since they could not be 53: definitively assigned from the information in your input 53: files. These guessed numbers might deviate from the mass 53: and radius of the atom type. Please check the output 53: files if necessary. Note, that this functionality may 53: be removed in a future GROMACS version. Please, consider 53: using another file format for your input. 53: 53: NOTE: From version 5.0 gmxpreprocess-test uses the Van der Waals radii 53: from the source below. This means the results may be different 53: compared to previous GROMACS versions. 53: 53: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 53: A. Bondi 53: van der Waals Volumes and Radii 53: J. Phys. Chem. (1964) 53: DOI: 10.1021/j100785a001 53: -------- -------- --- Thank You --- -------- -------- 53: 53: Generating solvent configuration 53: Will generate new solvent configuration of 3x3x3 boxes 53: Solvent box contains 14952 atoms in 4984 residues 53: Removed 2787 solvent atoms due to solvent-solvent overlap 53: Removed 30 solvent atoms due to solute-solvent overlap 53: Sorting configuration 53: Found 2 different molecule types: 53: HOH ( 3 atoms): 1876 residues 53: SOL ( 3 atoms): 2169 residues 53: Generated solvent containing 0 atoms in 0 residues 53: Writing generated configuration to /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/SolvateTest_update_Topology_Works_out.gro 53: 53: Output configuration contains 12141 atoms in 4047 residues 53: Volume : 125 (nm^3) 53: Density : 968.963 (g/l) 53: Number of solvent molecules: 4045 53: 53: Processing topology 53: Adding line for 1876 solvent molecules with resname (HOH) to topology file (/build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/SolvateTest_update_Topology_Works_simple.top) 53: Adding line for 2169 solvent molecules with resname (SOL) to topology file (/build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/SolvateTest_update_Topology_Works_simple.top) 53: [ OK ] SolvateTest.update_Topology_Works (429 ms) 53: [ RUN ] SolvateTest.cs_pdb_big_box_Works 53: Reading solvent configuration 53: 53: Initialising inter-atomic distances... 53: 53: WARNING: Masses and atomic (Van der Waals) radii will be guessed 53: based on residue and atom names, since they could not be 53: definitively assigned from the information in your input 53: files. These guessed numbers might deviate from the mass 53: and radius of the atom type. Please check the output 53: files if necessary. Note, that this functionality may 53: be removed in a future GROMACS version. Please, consider 53: using another file format for your input. 53: 53: NOTE: From version 5.0 gmxpreprocess-test uses the Van der Waals radii 53: from the source below. This means the results may be different 53: compared to previous GROMACS versions. 53: 53: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 53: A. Bondi 53: van der Waals Volumes and Radii 53: J. Phys. Chem. (1964) 53: DOI: 10.1021/j100785a001 53: -------- -------- --- Thank You --- -------- -------- 53: 53: Generating solvent configuration 53: Will generate new solvent configuration of 2x2x2 boxes 53: Solvent box contains 1218 atoms in 406 residues 53: Removed 555 solvent atoms due to solvent-solvent overlap 53: Sorting configuration 53: Found 1 molecule type: 53: SOL ( 3 atoms): 221 residues 53: Generated solvent containing 663 atoms in 221 residues 53: Writing generated configuration to /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/SolvateTest_cs_pdb_big_box_Works_out.gro 53: 53: Output configuration contains 663 atoms in 221 residues 53: Volume : 8 (nm^3) 53: Density : 826.409 (g/l) 53: Number of solvent molecules: 221 53: 53: [ OK ] SolvateTest.cs_pdb_big_box_Works (45 ms) 53: [----------] 6 tests from SolvateTest (786 ms total) 53: 53: [----------] 1 test from TopDirTests 53: [ RUN ] TopDirTests.NamesArrayHasCorrectSize 53: [ OK ] TopDirTests.NamesArrayHasCorrectSize (0 ms) 53: [----------] 1 test from TopDirTests (0 ms total) 53: 53: [----------] 95 tests from InteractionFunctionKind/ConvertInteractionsTest 53: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Bond 53: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/Bond (0 ms) 53: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/G96Bond 53: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/G96Bond (0 ms) 53: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Morse 53: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/Morse (0 ms) 53: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Cubic_Bonds 53: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/Cubic_Bonds (0 ms) 53: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Connect_Bonds 53: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/Connect_Bonds (0 ms) 53: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Harmonic_Pot_ 53: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/Harmonic_Pot_ (0 ms) 53: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/FENE_Bonds 53: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/FENE_Bonds (0 ms) 53: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Tab__Bonds 53: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/Tab__Bonds (0 ms) 53: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Tab__Bonds_NC 53: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/Tab__Bonds_NC (0 ms) 53: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Restraint_Pot_ 53: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/Restraint_Pot_ (0 ms) 53: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Angle 53: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/Angle (0 ms) 53: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/G96Angle 53: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/G96Angle (0 ms) 53: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Restr__Angles 53: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/Restr__Angles (0 ms) 53: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Lin__Angle 53: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/Lin__Angle (0 ms) 53: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Bond_Cross 53: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/Bond_Cross (0 ms) 53: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/BA_Cross 53: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/BA_Cross (0 ms) 53: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/U_B 53: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/U_B (0 ms) 53: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Quartic_Angles 53: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/Quartic_Angles (0 ms) 53: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Tab__Angles 53: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/Tab__Angles (0 ms) 53: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Proper_Dih_ 53: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/Proper_Dih_ (0 ms) 53: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Ryckaert_Bell_ 53: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/Ryckaert_Bell_ (0 ms) 53: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Restr__Dih_ 53: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/Restr__Dih_ (0 ms) 53: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/CBT_Dih_ 53: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/CBT_Dih_ (0 ms) 53: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Fourier_Dih_ 53: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/Fourier_Dih_ (0 ms) 53: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Improper_Dih_ 53: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/Improper_Dih_ (0 ms) 53: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Per__Imp__Dih_ 53: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/Per__Imp__Dih_ (0 ms) 53: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Tab__Dih_ 53: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/Tab__Dih_ (0 ms) 53: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/CMAP_Dih_ 53: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/CMAP_Dih_ (0 ms) 53: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/GB_1_2_Pol_ 53: ./src/gromacs/gmxpreprocess/tests/convparm.cpp:132: Skipped 53: Skipping interaction type that does not represent a interaction with parameters converted in grompp 53: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/GB_1_2_Pol_ (0 ms) 53: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/GB_1_3_Pol_ 53: ./src/gromacs/gmxpreprocess/tests/convparm.cpp:132: Skipped 53: Skipping interaction type that does not represent a interaction with parameters converted in grompp 53: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/GB_1_3_Pol_ (0 ms) 53: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/GB_1_4_Pol_ 53: ./src/gromacs/gmxpreprocess/tests/convparm.cpp:132: Skipped 53: Skipping interaction type that does not represent a interaction with parameters converted in grompp 53: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/GB_1_4_Pol_ (0 ms) 53: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/GB_Polariz_ 53: ./src/gromacs/gmxpreprocess/tests/convparm.cpp:132: Skipped 53: Skipping interaction type that does not represent a interaction with parameters converted in grompp 53: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/GB_Polariz_ (0 ms) 53: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Nonpolar_Sol_ 53: ./src/gromacs/gmxpreprocess/tests/convparm.cpp:132: Skipped 53: Skipping interaction type that does not represent a interaction with parameters converted in grompp 53: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/Nonpolar_Sol_ (0 ms) 53: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/LJ_14 53: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/LJ_14 (0 ms) 53: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Coulomb_14 53: ./src/gromacs/gmxpreprocess/tests/convparm.cpp:132: Skipped 53: Skipping interaction type that does not represent a interaction with parameters converted in grompp 53: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/Coulomb_14 (0 ms) 53: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/LJC_14_q 53: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/LJC_14_q (0 ms) 53: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/LJC_Pairs_NB 53: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/LJC_Pairs_NB (0 ms) 53: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/LJ__SR_ 53: ./src/gromacs/gmxpreprocess/tests/convparm.cpp:132: Skipped 53: Skipping interaction type that does not represent a interaction with parameters converted in grompp 53: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/LJ__SR_ (0 ms) 53: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Buck_ham__SR_ 53: ./src/gromacs/gmxpreprocess/tests/convparm.cpp:132: Skipped 53: Skipping interaction type that does not represent a interaction with parameters converted in grompp 53: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/Buck_ham__SR_ (0 ms) 53: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/LJ 53: ./src/gromacs/gmxpreprocess/tests/convparm.cpp:132: Skipped 53: Skipping interaction type that does not represent a interaction with parameters converted in grompp 53: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/LJ (0 ms) 53: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/B_ham 53: ./src/gromacs/gmxpreprocess/tests/convparm.cpp:132: Skipped 53: Skipping interaction type that does not represent a interaction with parameters converted in grompp 53: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/B_ham (0 ms) 53: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Disper__corr_ 53: ./src/gromacs/gmxpreprocess/tests/convparm.cpp:132: Skipped 53: Skipping interaction type that does not represent a interaction with parameters converted in grompp 53: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/Disper__corr_ (0 ms) 53: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Coulomb__SR_ 53: ./src/gromacs/gmxpreprocess/tests/convparm.cpp:132: Skipped 53: Skipping interaction type that does not represent a interaction with parameters converted in grompp 53: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/Coulomb__SR_ (0 ms) 53: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Coul 53: ./src/gromacs/gmxpreprocess/tests/convparm.cpp:132: Skipped 53: Skipping interaction type that does not represent a interaction with parameters converted in grompp 53: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/Coul (0 ms) 53: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/RF_excl_ 53: ./src/gromacs/gmxpreprocess/tests/convparm.cpp:132: Skipped 53: Skipping interaction type that does not represent a interaction with parameters converted in grompp 53: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/RF_excl_ (0 ms) 53: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Coul__recip_ 53: ./src/gromacs/gmxpreprocess/tests/convparm.cpp:132: Skipped 53: Skipping interaction type that does not represent a interaction with parameters converted in grompp 53: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/Coul__recip_ (0 ms) 53: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/LJ_recip_ 53: ./src/gromacs/gmxpreprocess/tests/convparm.cpp:132: Skipped 53: Skipping interaction type that does not represent a interaction with parameters converted in grompp 53: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/LJ_recip_ (0 ms) 53: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/DPD 53: ./src/gromacs/gmxpreprocess/tests/convparm.cpp:132: Skipped 53: Skipping interaction type that does not represent a interaction with parameters converted in grompp 53: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/DPD (0 ms) 53: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Polarization 53: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/Polarization (0 ms) 53: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Water_Pol_ 53: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/Water_Pol_ (0 ms) 53: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Thole_Pol_ 53: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/Thole_Pol_ (0 ms) 53: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Anharm__Pol_ 53: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/Anharm__Pol_ (0 ms) 53: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Position_Rest_ 53: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/Position_Rest_ (0 ms) 53: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Flat_b__P_R_ 53: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/Flat_b__P_R_ (0 ms) 53: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Dis__Rest_ 53: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/Dis__Rest_ (0 ms) 53: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/D_R_Viol___nm_ 53: ./src/gromacs/gmxpreprocess/tests/convparm.cpp:132: Skipped 53: Skipping interaction type that does not represent a interaction with parameters converted in grompp 53: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/D_R_Viol___nm_ (0 ms) 53: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Orient__Rest_ 53: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/Orient__Rest_ (0 ms) 53: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Ori__R__RMSD 53: ./src/gromacs/gmxpreprocess/tests/convparm.cpp:132: Skipped 53: Skipping interaction type that does not represent a interaction with parameters converted in grompp 53: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/Ori__R__RMSD (0 ms) 53: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Angle_Rest_ 53: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/Angle_Rest_ (0 ms) 53: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Angle_Rest__Z 53: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/Angle_Rest__Z (0 ms) 53: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Dih__Rest_ 53: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/Dih__Rest_ (0 ms) 53: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Dih__Rest__Vi_ 53: ./src/gromacs/gmxpreprocess/tests/convparm.cpp:132: Skipped 53: Skipping interaction type that does not represent a interaction with parameters converted in grompp 53: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/Dih__Rest__Vi_ (0 ms) 53: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Constraint 53: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/Constraint (0 ms) 53: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Constr__No_Co_ 53: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/Constr__No_Co_ (0 ms) 53: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Settle 53: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/Settle (0 ms) 53: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Virtual_site_1 53: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/Virtual_site_1 (0 ms) 53: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Virtual_site_2 53: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/Virtual_site_2 (0 ms) 53: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Virt__site_2fd 53: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/Virt__site_2fd (0 ms) 53: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Virtual_site_3 53: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/Virtual_site_3 (0 ms) 53: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Virt__site_3fd 53: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/Virt__site_3fd (0 ms) 53: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Vir__site_3fad 53: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/Vir__site_3fad (0 ms) 53: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Vir__site_3out 53: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/Vir__site_3out (0 ms) 53: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Virt__site_4fd 53: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/Virt__site_4fd (0 ms) 53: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Vir__site_4fdn 53: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/Vir__site_4fdn (0 ms) 53: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Virtual_site_N 53: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/Virtual_site_N (0 ms) 53: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/COM_Pull_En_ 53: ./src/gromacs/gmxpreprocess/tests/convparm.cpp:132: Skipped 53: Skipping interaction type that does not represent a interaction with parameters converted in grompp 53: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/COM_Pull_En_ (0 ms) 53: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Dens__fitting 53: ./src/gromacs/gmxpreprocess/tests/convparm.cpp:132: Skipped 53: Skipping interaction type that does not represent a interaction with parameters converted in grompp 53: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/Dens__fitting (0 ms) 53: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Quantum_En_ 53: ./src/gromacs/gmxpreprocess/tests/convparm.cpp:132: Skipped 53: Skipping interaction type that does not represent a interaction with parameters converted in grompp 53: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/Quantum_En_ (0 ms) 53: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/NN_Potential 53: ./src/gromacs/gmxpreprocess/tests/convparm.cpp:132: Skipped 53: Skipping interaction type that does not represent a interaction with parameters converted in grompp 53: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/NN_Potential (0 ms) 53: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Potential 53: ./src/gromacs/gmxpreprocess/tests/convparm.cpp:132: Skipped 53: Skipping interaction type that does not represent a interaction with parameters converted in grompp 53: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/Potential (0 ms) 53: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Kinetic_En_ 53: ./src/gromacs/gmxpreprocess/tests/convparm.cpp:132: Skipped 53: Skipping interaction type that does not represent a interaction with parameters converted in grompp 53: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/Kinetic_En_ (0 ms) 53: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Total_Energy 53: ./src/gromacs/gmxpreprocess/tests/convparm.cpp:132: Skipped 53: Skipping interaction type that does not represent a interaction with parameters converted in grompp 53: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/Total_Energy (0 ms) 53: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Conserved_En_ 53: ./src/gromacs/gmxpreprocess/tests/convparm.cpp:132: Skipped 53: Skipping interaction type that does not represent a interaction with parameters converted in grompp 53: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/Conserved_En_ (0 ms) 53: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Temperature 53: ./src/gromacs/gmxpreprocess/tests/convparm.cpp:132: Skipped 53: Skipping interaction type that does not represent a interaction with parameters converted in grompp 53: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/Temperature (0 ms) 53: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Vir__Temp_ 53: ./src/gromacs/gmxpreprocess/tests/convparm.cpp:132: Skipped 53: Skipping interaction type that does not represent a interaction with parameters converted in grompp 53: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/Vir__Temp_ (0 ms) 53: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Pres__DC 53: ./src/gromacs/gmxpreprocess/tests/convparm.cpp:132: Skipped 53: Skipping interaction type that does not represent a interaction with parameters converted in grompp 53: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/Pres__DC (0 ms) 53: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Pressure 53: ./src/gromacs/gmxpreprocess/tests/convparm.cpp:132: Skipped 53: Skipping interaction type that does not represent a interaction with parameters converted in grompp 53: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/Pressure (0 ms) 53: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/dH_dl_constr_ 53: ./src/gromacs/gmxpreprocess/tests/convparm.cpp:132: Skipped 53: Skipping interaction type that does not represent a interaction with parameters converted in grompp 53: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/dH_dl_constr_ (0 ms) 53: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/dVremain_dl 53: ./src/gromacs/gmxpreprocess/tests/convparm.cpp:132: Skipped 53: Skipping interaction type that does not represent a interaction with parameters converted in grompp 53: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/dVremain_dl (0 ms) 53: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/dEkin_dl 53: ./src/gromacs/gmxpreprocess/tests/convparm.cpp:132: Skipped 53: Skipping interaction type that does not represent a interaction with parameters converted in grompp 53: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/dEkin_dl (0 ms) 53: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/dVcoul_dl 53: ./src/gromacs/gmxpreprocess/tests/convparm.cpp:132: Skipped 53: Skipping interaction type that does not represent a interaction with parameters converted in grompp 53: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/dVcoul_dl (0 ms) 53: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/dVvdw_dl 53: ./src/gromacs/gmxpreprocess/tests/convparm.cpp:132: Skipped 53: Skipping interaction type that does not represent a interaction with parameters converted in grompp 53: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/dVvdw_dl (0 ms) 53: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/dVbonded_dl 53: ./src/gromacs/gmxpreprocess/tests/convparm.cpp:132: Skipped 53: Skipping interaction type that does not represent a interaction with parameters converted in grompp 53: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/dVbonded_dl (0 ms) 53: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/dVrestraint_dl 53: ./src/gromacs/gmxpreprocess/tests/convparm.cpp:132: Skipped 53: Skipping interaction type that does not represent a interaction with parameters converted in grompp 53: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/dVrestraint_dl (0 ms) 53: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/dVtemp_dl 53: ./src/gromacs/gmxpreprocess/tests/convparm.cpp:132: Skipped 53: Skipping interaction type that does not represent a interaction with parameters converted in grompp 53: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/dVtemp_dl (0 ms) 53: [----------] 95 tests from InteractionFunctionKind/ConvertInteractionsTest (11 ms total) 53: 53: [----------] 45 tests from SinglePeptideFragments/EditconfTest 53: [ RUN ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFile/0 53: Note that major changes are planned in future for editconf, to improve usability and utility. 53: Read 252 atoms 53: Volume: 338.104 nm^3, corresponds to roughly 152100 electrons 53: No velocities found 53: [ OK ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFile/0 (30 ms) 53: [ RUN ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFile/1 53: Note that major changes are planned in future for editconf, to improve usability and utility. 53: Read 252 atoms 53: Volume: 338.104 nm^3, corresponds to roughly 152100 electrons 53: No velocities found 53: [ OK ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFile/1 (19 ms) 53: [ RUN ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFile/2 53: Note that major changes are planned in future for editconf, to improve usability and utility. 53: Read 252 atoms 53: Volume: 338.104 nm^3, corresponds to roughly 152100 electrons 53: No velocities found 53: [ OK ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFile/2 (20 ms) 53: [ RUN ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFile/3 53: Note that major changes are planned in future for editconf, to improve usability and utility. 53: Read 252 atoms 53: Volume: 338.104 nm^3, corresponds to roughly 152100 electrons 53: No velocities found 53: [ OK ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFile/3 (14 ms) 53: [ RUN ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFile/4 53: Note that major changes are planned in future for editconf, to improve usability and utility. 53: Read 252 atoms 53: Volume: 338.104 nm^3, corresponds to roughly 152100 electrons 53: No velocities found 53: [ OK ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFile/4 (11 ms) 53: [ RUN ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFile/5 53: Note that major changes are planned in future for editconf, to improve usability and utility. 53: Read 252 atoms 53: Volume: 338.104 nm^3, corresponds to roughly 152100 electrons 53: No velocities found 53: [ OK ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFile/5 (12 ms) 53: [ RUN ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFile/6 53: Note that major changes are planned in future for editconf, to improve usability and utility. 53: Read 252 atoms 53: Volume: 338.104 nm^3, corresponds to roughly 152100 electrons 53: No velocities found 53: [ OK ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFile/6 (16 ms) 53: [ RUN ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFile/7 53: Note that major changes are planned in future for editconf, to improve usability and utility. 53: Read 252 atoms 53: Volume: 338.104 nm^3, corresponds to roughly 152100 electrons 53: No velocities found 53: [ OK ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFile/7 (13 ms) 53: [ RUN ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFile/8 53: Note that major changes are planned in future for editconf, to improve usability and utility. 53: Read 252 atoms 53: Volume: 338.104 nm^3, corresponds to roughly 152100 electrons 53: No velocities found 53: [ OK ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFile/8 (14 ms) 53: [ RUN ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFileUsingIndexGroup/0 53: 53: Select a group for output: 53: Group 0 ( two_residues) has 23 elements 53: There is one group in the index 53: Note that major changes are planned in future for editconf, to improve usability and utility. 53: Read 252 atoms 53: Volume: 338.104 nm^3, corresponds to roughly 152100 electrons 53: No velocities found 53: [ OK ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFileUsingIndexGroup/0 (18 ms) 53: [ RUN ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFileUsingIndexGroup/1 53: 53: Select a group for output: 53: Group 0 ( two_residues) has 23 elements 53: There is one group in the index 53: Note that major changes are planned in future for editconf, to improve usability and utility. 53: Read 252 atoms 53: Volume: 338.104 nm^3, corresponds to roughly 152100 electrons 53: No velocities found 53: [ OK ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFileUsingIndexGroup/1 (17 ms) 53: [ RUN ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFileUsingIndexGroup/2 53: 53: Select a group for output: 53: Group 0 ( two_residues) has 23 elements 53: There is one group in the index 53: Note that major changes are planned in future for editconf, to improve usability and utility. 53: Read 252 atoms 53: Volume: 338.104 nm^3, corresponds to roughly 152100 electrons 53: No velocities found 53: [ OK ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFileUsingIndexGroup/2 (16 ms) 53: [ RUN ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFileUsingIndexGroup/3 53: 53: Select a group for output: 53: Group 0 ( two_residues) has 23 elements 53: There is one group in the index 53: Note that major changes are planned in future for editconf, to improve usability and utility. 53: Read 252 atoms 53: Volume: 338.104 nm^3, corresponds to roughly 152100 electrons 53: No velocities found 53: [ OK ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFileUsingIndexGroup/3 (9 ms) 53: [ RUN ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFileUsingIndexGroup/4 53: 53: Select a group for output: 53: Group 0 ( two_residues) has 23 elements 53: There is one group in the index 53: Note that major changes are planned in future for editconf, to improve usability and utility. 53: Read 252 atoms 53: Volume: 338.104 nm^3, corresponds to roughly 152100 electrons 53: No velocities found 53: [ OK ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFileUsingIndexGroup/4 (8 ms) 53: [ RUN ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFileUsingIndexGroup/5 53: 53: Select a group for output: 53: Group 0 ( two_residues) has 23 elements 53: There is one group in the index 53: Note that major changes are planned in future for editconf, to improve usability and utility. 53: Read 252 atoms 53: Volume: 338.104 nm^3, corresponds to roughly 152100 electrons 53: No velocities found 53: [ OK ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFileUsingIndexGroup/5 (8 ms) 53: [ RUN ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFileUsingIndexGroup/6 53: 53: Select a group for output: 53: Group 0 ( two_residues) has 23 elements 53: There is one group in the index 53: Note that major changes are planned in future for editconf, to improve usability and utility. 53: Read 252 atoms 53: Volume: 338.104 nm^3, corresponds to roughly 152100 electrons 53: No velocities found 53: [ OK ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFileUsingIndexGroup/6 (11 ms) 53: [ RUN ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFileUsingIndexGroup/7 53: 53: Select a group for output: 53: Group 0 ( two_residues) has 23 elements 53: There is one group in the index 53: Note that major changes are planned in future for editconf, to improve usability and utility. 53: Read 252 atoms 53: Volume: 338.104 nm^3, corresponds to roughly 152100 electrons 53: No velocities found 53: [ OK ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFileUsingIndexGroup/7 (11 ms) 53: [ RUN ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFileUsingIndexGroup/8 53: 53: Select a group for output: 53: Group 0 ( two_residues) has 23 elements 53: There is one group in the index 53: Note that major changes are planned in future for editconf, to improve usability and utility. 53: Read 252 atoms 53: Volume: 338.104 nm^3, corresponds to roughly 152100 electrons 53: No velocities found 53: [ OK ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFileUsingIndexGroup/8 (11 ms) 53: [ RUN ] SinglePeptideFragments/EditconfTest.HandlesCenter/0 53: Note that major changes are planned in future for editconf, to improve usability and utility. 53: Read 252 atoms 53: Volume: 338.104 nm^3, corresponds to roughly 152100 electrons 53: No velocities found 53: system size : 2.004 1.472 1.704 (nm) 53: center : 3.816 1.632 0.195 (nm) 53: box vectors : 8.056 5.637 7.445 (nm) 53: box angles : 90.00 90.00 90.00 (degrees) 53: box volume : 338.10 (nm^3) 53: shift : 0.212 1.187 3.527 (nm) 53: new center : 4.028 2.819 3.723 (nm) 53: [ OK ] SinglePeptideFragments/EditconfTest.HandlesCenter/0 (21 ms) 53: [ RUN ] SinglePeptideFragments/EditconfTest.HandlesCenter/1 53: Note that major changes are planned in future for editconf, to improve usability and utility. 53: Read 252 atoms 53: Volume: 338.104 nm^3, corresponds to roughly 152100 electrons 53: No velocities found 53: system size : 2.004 1.472 1.704 (nm) 53: center : 3.816 1.632 0.195 (nm) 53: box vectors : 8.056 5.637 7.445 (nm) 53: box angles : 90.00 90.00 90.00 (degrees) 53: box volume : 338.10 (nm^3) 53: shift : 0.212 1.187 3.527 (nm) 53: new center : 4.028 2.819 3.723 (nm) 53: [ OK ] SinglePeptideFragments/EditconfTest.HandlesCenter/1 (19 ms) 53: [ RUN ] SinglePeptideFragments/EditconfTest.HandlesCenter/2 53: Note that major changes are planned in future for editconf, to improve usability and utility. 53: Read 252 atoms 53: Volume: 338.104 nm^3, corresponds to roughly 152100 electrons 53: No velocities found 53: system size : 2.004 1.472 1.704 (nm) 53: center : 3.816 1.632 0.195 (nm) 53: box vectors : 8.056 5.637 7.445 (nm) 53: box angles : 90.00 90.00 90.00 (degrees) 53: box volume : 338.10 (nm^3) 53: shift : 0.212 1.187 3.527 (nm) 53: new center : 4.028 2.819 3.723 (nm) 53: [ OK ] SinglePeptideFragments/EditconfTest.HandlesCenter/2 (19 ms) 53: [ RUN ] SinglePeptideFragments/EditconfTest.HandlesCenter/3 53: Note that major changes are planned in future for editconf, to improve usability and utility. 53: Read 252 atoms 53: Volume: 338.104 nm^3, corresponds to roughly 152100 electrons 53: No velocities found 53: system size : 2.004 1.472 1.704 (nm) 53: center : 3.816 1.632 0.195 (nm) 53: box vectors : 8.056 5.637 7.445 (nm) 53: box angles : 90.00 90.00 90.00 (degrees) 53: box volume : 338.10 (nm^3) 53: shift : 0.212 1.187 3.527 (nm) 53: new center : 4.028 2.819 3.723 (nm) 53: [ OK ] SinglePeptideFragments/EditconfTest.HandlesCenter/3 (13 ms) 53: [ RUN ] SinglePeptideFragments/EditconfTest.HandlesCenter/4 53: Note that major changes are planned in future for editconf, to improve usability and utility. 53: Read 252 atoms 53: Volume: 338.104 nm^3, corresponds to roughly 152100 electrons 53: No velocities found 53: system size : 2.004 1.472 1.704 (nm) 53: center : 3.816 1.632 0.195 (nm) 53: box vectors : 8.056 5.637 7.445 (nm) 53: box angles : 90.00 90.00 90.00 (degrees) 53: box volume : 338.10 (nm^3) 53: shift : 0.212 1.187 3.527 (nm) 53: new center : 4.028 2.819 3.723 (nm) 53: [ OK ] SinglePeptideFragments/EditconfTest.HandlesCenter/4 (10 ms) 53: [ RUN ] SinglePeptideFragments/EditconfTest.HandlesCenter/5 53: Note that major changes are planned in future for editconf, to improve usability and utility. 53: Read 252 atoms 53: Volume: 338.104 nm^3, corresponds to roughly 152100 electrons 53: No velocities found 53: system size : 2.004 1.472 1.704 (nm) 53: center : 3.816 1.632 0.195 (nm) 53: box vectors : 8.056 5.637 7.445 (nm) 53: box angles : 90.00 90.00 90.00 (degrees) 53: box volume : 338.10 (nm^3) 53: shift : 0.212 1.187 3.527 (nm) 53: new center : 4.028 2.819 3.723 (nm) 53: [ OK ] SinglePeptideFragments/EditconfTest.HandlesCenter/5 (11 ms) 53: [ RUN ] SinglePeptideFragments/EditconfTest.HandlesCenter/6 53: Note that major changes are planned in future for editconf, to improve usability and utility. 53: Read 252 atoms 53: Volume: 338.104 nm^3, corresponds to roughly 152100 electrons 53: No velocities found 53: system size : 2.004 1.472 1.704 (nm) 53: center : 3.816 1.632 0.195 (nm) 53: box vectors : 8.056 5.637 7.445 (nm) 53: box angles : 90.00 90.00 90.00 (degrees) 53: box volume : 338.10 (nm^3) 53: shift : 0.212 1.187 3.527 (nm) 53: new center : 4.028 2.819 3.723 (nm) 53: [ OK ] SinglePeptideFragments/EditconfTest.HandlesCenter/6 (15 ms) 53: [ RUN ] SinglePeptideFragments/EditconfTest.HandlesCenter/7 53: Note that major changes are planned in future for editconf, to improve usability and utility. 53: Read 252 atoms 53: Volume: 338.104 nm^3, corresponds to roughly 152100 electrons 53: No velocities found 53: system size : 2.004 1.472 1.704 (nm) 53: center : 3.816 1.632 0.195 (nm) 53: box vectors : 8.056 5.637 7.445 (nm) 53: box angles : 90.00 90.00 90.00 (degrees) 53: box volume : 338.10 (nm^3) 53: shift : 0.212 1.187 3.527 (nm) 53: new center : 4.028 2.819 3.723 (nm) 53: [ OK ] SinglePeptideFragments/EditconfTest.HandlesCenter/7 (13 ms) 53: [ RUN ] SinglePeptideFragments/EditconfTest.HandlesCenter/8 53: Note that major changes are planned in future for editconf, to improve usability and utility. 53: Read 252 atoms 53: Volume: 338.104 nm^3, corresponds to roughly 152100 electrons 53: No velocities found 53: system size : 2.004 1.472 1.704 (nm) 53: center : 3.816 1.632 0.195 (nm) 53: box vectors : 8.056 5.637 7.445 (nm) 53: box angles : 90.00 90.00 90.00 (degrees) 53: box volume : 338.10 (nm^3) 53: shift : 0.212 1.187 3.527 (nm) 53: new center : 4.028 2.819 3.723 (nm) 53: [ OK ] SinglePeptideFragments/EditconfTest.HandlesCenter/8 (13 ms) 53: [ RUN ] SinglePeptideFragments/EditconfTest.HandlesCenterAndDiameter/0 53: Note that major changes are planned in future for editconf, to improve usability and utility. 53: Read 252 atoms 53: Volume: 338.104 nm^3, corresponds to roughly 152100 electrons 53: No velocities found 53: system size : 2.004 1.472 1.704 (nm) 53: center : 3.816 1.632 0.195 (nm) 53: box vectors : 8.056 5.637 7.445 (nm) 53: box angles : 90.00 90.00 90.00 (degrees) 53: box volume : 338.10 (nm^3) 53: shift : -0.814 1.104 2.657 (nm) 53: new center : 3.002 2.736 2.852 (nm) 53: new box vectors : 6.004 5.472 5.704 (nm) 53: new box angles : 90.00 90.00 90.00 (degrees) 53: new box volume : 187.42 (nm^3) 53: 53: WARNING: No boxtype specified - distance condition applied in each dimension. 53: If the molecule rotates the actual distance will be smaller. You might want 53: to use a cubic box instead, or why not try a dodecahedron today? 53: [ OK ] SinglePeptideFragments/EditconfTest.HandlesCenterAndDiameter/0 (21 ms) 53: [ RUN ] SinglePeptideFragments/EditconfTest.HandlesCenterAndDiameter/1 53: Note that major changes are planned in future for editconf, to improve usability and utility. 53: Read 252 atoms 53: Volume: 338.104 nm^3, corresponds to roughly 152100 electrons 53: No velocities found 53: system size : 2.004 1.472 1.704 (nm) 53: center : 3.816 1.632 0.195 (nm) 53: box vectors : 8.056 5.637 7.445 (nm) 53: box angles : 90.00 90.00 90.00 (degrees) 53: box volume : 338.10 (nm^3) 53: shift : -0.814 1.104 2.657 (nm) 53: new center : 3.002 2.736 2.852 (nm) 53: new box vectors : 6.004 5.472 5.704 (nm) 53: new box angles : 90.00 90.00 90.00 (degrees) 53: new box volume : 187.42 (nm^3) 53: 53: WARNING: No boxtype specified - distance condition applied in each dimension. 53: If the molecule rotates the actual distance will be smaller. You might want 53: to use a cubic box instead, or why not try a dodecahedron today? 53: [ OK ] SinglePeptideFragments/EditconfTest.HandlesCenterAndDiameter/1 (18 ms) 53: [ RUN ] SinglePeptideFragments/EditconfTest.HandlesCenterAndDiameter/2 53: Note that major changes are planned in future for editconf, to improve usability and utility. 53: Read 252 atoms 53: Volume: 338.104 nm^3, corresponds to roughly 152100 electrons 53: No velocities found 53: system size : 2.004 1.472 1.704 (nm) 53: center : 3.816 1.632 0.195 (nm) 53: box vectors : 8.056 5.637 7.445 (nm) 53: box angles : 90.00 90.00 90.00 (degrees) 53: box volume : 338.10 (nm^3) 53: shift : -0.814 1.104 2.657 (nm) 53: new center : 3.002 2.736 2.852 (nm) 53: new box vectors : 6.004 5.472 5.704 (nm) 53: new box angles : 90.00 90.00 90.00 (degrees) 53: new box volume : 187.42 (nm^3) 53: 53: WARNING: No boxtype specified - distance condition applied in each dimension. 53: If the molecule rotates the actual distance will be smaller. You might want 53: to use a cubic box instead, or why not try a dodecahedron today? 53: [ OK ] SinglePeptideFragments/EditconfTest.HandlesCenterAndDiameter/2 (19 ms) 53: [ RUN ] SinglePeptideFragments/EditconfTest.HandlesCenterAndDiameter/3 53: Note that major changes are planned in future for editconf, to improve usability and utility. 53: Read 252 atoms 53: Volume: 338.104 nm^3, corresponds to roughly 152100 electrons 53: No velocities found 53: system size : 2.004 1.472 1.704 (nm) 53: center : 3.816 1.632 0.195 (nm) 53: box vectors : 8.056 5.637 7.445 (nm) 53: box angles : 90.00 90.00 90.00 (degrees) 53: box volume : 338.10 (nm^3) 53: shift : -0.814 1.104 2.657 (nm) 53: new center : 3.002 2.736 2.852 (nm) 53: new box vectors : 6.004 5.472 5.704 (nm) 53: new box angles : 90.00 90.00 90.00 (degrees) 53: new box volume : 187.40 (nm^3) 53: 53: WARNING: No boxtype specified - distance condition applied in each dimension. 53: If the molecule rotates the actual distance will be smaller. You might want 53: to use a cubic box instead, or why not try a dodecahedron today? 53: [ OK ] SinglePeptideFragments/EditconfTest.HandlesCenterAndDiameter/3 (13 ms) 53: [ RUN ] SinglePeptideFragments/EditconfTest.HandlesCenterAndDiameter/4 53: Note that major changes are planned in future for editconf, to improve usability and utility. 53: Read 252 atoms 53: Volume: 338.104 nm^3, corresponds to roughly 152100 electrons 53: No velocities found 53: system size : 2.004 1.472 1.704 (nm) 53: center : 3.816 1.632 0.195 (nm) 53: box vectors : 8.056 5.637 7.445 (nm) 53: box angles : 90.00 90.00 90.00 (degrees) 53: box volume : 338.10 (nm^3) 53: shift : -0.814 1.104 2.657 (nm) 53: new center : 3.002 2.736 2.852 (nm) 53: new box vectors : 6.004 5.472 5.704 (nm) 53: new box angles : 90.00 90.00 90.00 (degrees) 53: new box volume : 187.40 (nm^3) 53: 53: WARNING: No boxtype specified - distance condition applied in each dimension. 53: If the molecule rotates the actual distance will be smaller. You might want 53: to use a cubic box instead, or why not try a dodecahedron today? 53: [ OK ] SinglePeptideFragments/EditconfTest.HandlesCenterAndDiameter/4 (10 ms) 53: [ RUN ] SinglePeptideFragments/EditconfTest.HandlesCenterAndDiameter/5 53: Note that major changes are planned in future for editconf, to improve usability and utility. 53: Read 252 atoms 53: Volume: 338.104 nm^3, corresponds to roughly 152100 electrons 53: No velocities found 53: system size : 2.004 1.472 1.704 (nm) 53: center : 3.816 1.632 0.195 (nm) 53: box vectors : 8.056 5.637 7.445 (nm) 53: box angles : 90.00 90.00 90.00 (degrees) 53: box volume : 338.10 (nm^3) 53: shift : -0.814 1.104 2.657 (nm) 53: new center : 3.002 2.736 2.852 (nm) 53: new box vectors : 6.004 5.472 5.704 (nm) 53: new box angles : 90.00 90.00 90.00 (degrees) 53: new box volume : 187.40 (nm^3) 53: 53: WARNING: No boxtype specified - distance condition applied in each dimension. 53: If the molecule rotates the actual distance will be smaller. You might want 53: to use a cubic box instead, or why not try a dodecahedron today? 53: [ OK ] SinglePeptideFragments/EditconfTest.HandlesCenterAndDiameter/5 (11 ms) 53: [ RUN ] SinglePeptideFragments/EditconfTest.HandlesCenterAndDiameter/6 53: Note that major changes are planned in future for editconf, to improve usability and utility. 53: Read 252 atoms 53: Volume: 338.104 nm^3, corresponds to roughly 152100 electrons 53: No velocities found 53: system size : 2.004 1.472 1.704 (nm) 53: center : 3.816 1.632 0.195 (nm) 53: box vectors : 8.056 5.637 7.445 (nm) 53: box angles : 90.00 90.00 90.00 (degrees) 53: box volume : 338.10 (nm^3) 53: shift : -0.814 1.104 2.657 (nm) 53: new center : 3.002 2.736 2.852 (nm) 53: new box vectors : 6.004 5.472 5.704 (nm) 53: new box angles : 90.00 90.00 90.00 (degrees) 53: new box volume : 187.40 (nm^3) 53: 53: WARNING: No boxtype specified - distance condition applied in each dimension. 53: If the molecule rotates the actual distance will be smaller. You might want 53: to use a cubic box instead, or why not try a dodecahedron today? 53: [ OK ] SinglePeptideFragments/EditconfTest.HandlesCenterAndDiameter/6 (15 ms) 53: [ RUN ] SinglePeptideFragments/EditconfTest.HandlesCenterAndDiameter/7 53: Note that major changes are planned in future for editconf, to improve usability and utility. 53: Read 252 atoms 53: Volume: 338.104 nm^3, corresponds to roughly 152100 electrons 53: No velocities found 53: system size : 2.004 1.472 1.704 (nm) 53: center : 3.816 1.632 0.195 (nm) 53: box vectors : 8.056 5.637 7.445 (nm) 53: box angles : 90.00 90.00 90.00 (degrees) 53: box volume : 338.10 (nm^3) 53: shift : -0.814 1.104 2.657 (nm) 53: new center : 3.002 2.736 2.852 (nm) 53: new box vectors : 6.004 5.472 5.704 (nm) 53: new box angles : 90.00 90.00 90.00 (degrees) 53: new box volume : 187.40 (nm^3) 53: 53: WARNING: No boxtype specified - distance condition applied in each dimension. 53: If the molecule rotates the actual distance will be smaller. You might want 53: to use a cubic box instead, or why not try a dodecahedron today? 53: [ OK ] SinglePeptideFragments/EditconfTest.HandlesCenterAndDiameter/7 (13 ms) 53: [ RUN ] SinglePeptideFragments/EditconfTest.HandlesCenterAndDiameter/8 53: Note that major changes are planned in future for editconf, to improve usability and utility. 53: Read 252 atoms 53: Volume: 338.104 nm^3, corresponds to roughly 152100 electrons 53: No velocities found 53: system size : 2.004 1.472 1.704 (nm) 53: center : 3.816 1.632 0.195 (nm) 53: box vectors : 8.056 5.637 7.445 (nm) 53: box angles : 90.00 90.00 90.00 (degrees) 53: box volume : 338.10 (nm^3) 53: shift : -0.814 1.104 2.657 (nm) 53: new center : 3.002 2.736 2.852 (nm) 53: new box vectors : 6.004 5.472 5.704 (nm) 53: new box angles : 90.00 90.00 90.00 (degrees) 53: new box volume : 187.40 (nm^3) 53: 53: WARNING: No boxtype specified - distance condition applied in each dimension. 53: If the molecule rotates the actual distance will be smaller. You might want 53: to use a cubic box instead, or why not try a dodecahedron today? 53: [ OK ] SinglePeptideFragments/EditconfTest.HandlesCenterAndDiameter/8 (13 ms) 53: [ RUN ] SinglePeptideFragments/EditconfTest.HandlesBothNoCenterAndDiameter/0 53: Note that major changes are planned in future for editconf, to improve usability and utility. 53: Read 252 atoms 53: Volume: 338.104 nm^3, corresponds to roughly 152100 electrons 53: No velocities found 53: system size : 2.004 1.472 1.704 (nm) 53: center : 3.816 1.632 0.195 (nm) 53: box vectors : 8.056 5.637 7.445 (nm) 53: box angles : 90.00 90.00 90.00 (degrees) 53: box volume : 338.10 (nm^3) 53: new center : 3.816 1.632 0.195 (nm) 53: new box vectors : 5.004 4.472 4.704 (nm) 53: new box angles : 90.00 90.00 90.00 (degrees) 53: new box volume : 105.28 (nm^3) 53: 53: WARNING: No boxtype specified - distance condition applied in each dimension. 53: If the molecule rotates the actual distance will be smaller. You might want 53: to use a cubic box instead, or why not try a dodecahedron today? 53: [ OK ] SinglePeptideFragments/EditconfTest.HandlesBothNoCenterAndDiameter/0 (20 ms) 53: [ RUN ] SinglePeptideFragments/EditconfTest.HandlesBothNoCenterAndDiameter/1 53: Note that major changes are planned in future for editconf, to improve usability and utility. 53: Read 252 atoms 53: Volume: 338.104 nm^3, corresponds to roughly 152100 electrons 53: No velocities found 53: system size : 2.004 1.472 1.704 (nm) 53: center : 3.816 1.632 0.195 (nm) 53: box vectors : 8.056 5.637 7.445 (nm) 53: box angles : 90.00 90.00 90.00 (degrees) 53: box volume : 338.10 (nm^3) 53: new center : 3.816 1.632 0.195 (nm) 53: new box vectors : 5.004 4.472 4.704 (nm) 53: new box angles : 90.00 90.00 90.00 (degrees) 53: new box volume : 105.28 (nm^3) 53: 53: WARNING: No boxtype specified - distance condition applied in each dimension. 53: If the molecule rotates the actual distance will be smaller. You might want 53: to use a cubic box instead, or why not try a dodecahedron today? 53: [ OK ] SinglePeptideFragments/EditconfTest.HandlesBothNoCenterAndDiameter/1 (18 ms) 53: [ RUN ] SinglePeptideFragments/EditconfTest.HandlesBothNoCenterAndDiameter/2 53: Note that major changes are planned in future for editconf, to improve usability and utility. 53: Read 252 atoms 53: Volume: 338.104 nm^3, corresponds to roughly 152100 electrons 53: No velocities found 53: system size : 2.004 1.472 1.704 (nm) 53: center : 3.816 1.632 0.195 (nm) 53: box vectors : 8.056 5.637 7.445 (nm) 53: box angles : 90.00 90.00 90.00 (degrees) 53: box volume : 338.10 (nm^3) 53: new center : 3.816 1.632 0.195 (nm) 53: new box vectors : 5.004 4.472 4.704 (nm) 53: new box angles : 90.00 90.00 90.00 (degrees) 53: new box volume : 105.28 (nm^3) 53: 53: WARNING: No boxtype specified - distance condition applied in each dimension. 53: If the molecule rotates the actual distance will be smaller. You might want 53: to use a cubic box instead, or why not try a dodecahedron today? 53: [ OK ] SinglePeptideFragments/EditconfTest.HandlesBothNoCenterAndDiameter/2 (19 ms) 53: [ RUN ] SinglePeptideFragments/EditconfTest.HandlesBothNoCenterAndDiameter/3 53: Note that major changes are planned in future for editconf, to improve usability and utility. 53: Read 252 atoms 53: Volume: 338.104 nm^3, corresponds to roughly 152100 electrons 53: No velocities found 53: system size : 2.004 1.472 1.704 (nm) 53: center : 3.816 1.632 0.195 (nm) 53: box vectors : 8.056 5.637 7.445 (nm) 53: box angles : 90.00 90.00 90.00 (degrees) 53: box volume : 338.10 (nm^3) 53: new center : 3.816 1.632 0.195 (nm) 53: new box vectors : 5.004 4.472 4.704 (nm) 53: new box angles : 90.00 90.00 90.00 (degrees) 53: new box volume : 105.27 (nm^3) 53: 53: WARNING: No boxtype specified - distance condition applied in each dimension. 53: If the molecule rotates the actual distance will be smaller. You might want 53: to use a cubic box instead, or why not try a dodecahedron today? 53: [ OK ] SinglePeptideFragments/EditconfTest.HandlesBothNoCenterAndDiameter/3 (12 ms) 53: [ RUN ] SinglePeptideFragments/EditconfTest.HandlesBothNoCenterAndDiameter/4 53: Note that major changes are planned in future for editconf, to improve usability and utility. 53: Read 252 atoms 53: Volume: 338.104 nm^3, corresponds to roughly 152100 electrons 53: No velocities found 53: system size : 2.004 1.472 1.704 (nm) 53: center : 3.816 1.632 0.195 (nm) 53: box vectors : 8.056 5.637 7.445 (nm) 53: box angles : 90.00 90.00 90.00 (degrees) 53: box volume : 338.10 (nm^3) 53: new center : 3.816 1.632 0.195 (nm) 53: new box vectors : 5.004 4.472 4.704 (nm) 53: new box angles : 90.00 90.00 90.00 (degrees) 53: new box volume : 105.27 (nm^3) 53: 53: WARNING: No boxtype specified - distance condition applied in each dimension. 53: If the molecule rotates the actual distance will be smaller. You might want 53: to use a cubic box instead, or why not try a dodecahedron today? 53: [ OK ] SinglePeptideFragments/EditconfTest.HandlesBothNoCenterAndDiameter/4 (10 ms) 53: [ RUN ] SinglePeptideFragments/EditconfTest.HandlesBothNoCenterAndDiameter/5 53: Note that major changes are planned in future for editconf, to improve usability and utility. 53: Read 252 atoms 53: Volume: 338.104 nm^3, corresponds to roughly 152100 electrons 53: No velocities found 53: system size : 2.004 1.472 1.704 (nm) 53: center : 3.816 1.632 0.195 (nm) 53: box vectors : 8.056 5.637 7.445 (nm) 53: box angles : 90.00 90.00 90.00 (degrees) 53: box volume : 338.10 (nm^3) 53: new center : 3.816 1.632 0.195 (nm) 53: new box vectors : 5.004 4.472 4.704 (nm) 53: new box angles : 90.00 90.00 90.00 (degrees) 53: new box volume : 105.27 (nm^3) 53: 53: WARNING: No boxtype specified - distance condition applied in each dimension. 53: If the molecule rotates the actual distance will be smaller. You might want 53: to use a cubic box instead, or why not try a dodecahedron today? 53: [ OK ] SinglePeptideFragments/EditconfTest.HandlesBothNoCenterAndDiameter/5 (12 ms) 53: [ RUN ] SinglePeptideFragments/EditconfTest.HandlesBothNoCenterAndDiameter/6 53: Note that major changes are planned in future for editconf, to improve usability and utility. 53: Read 252 atoms 53: Volume: 338.104 nm^3, corresponds to roughly 152100 electrons 53: No velocities found 53: system size : 2.004 1.472 1.704 (nm) 53: center : 3.816 1.632 0.195 (nm) 53: box vectors : 8.056 5.637 7.445 (nm) 53: box angles : 90.00 90.00 90.00 (degrees) 53: box volume : 338.10 (nm^3) 53: new center : 3.816 1.632 0.195 (nm) 53: new box vectors : 5.004 4.472 4.704 (nm) 53: new box angles : 90.00 90.00 90.00 (degrees) 53: new box volume : 105.27 (nm^3) 53: 53: WARNING: No boxtype specified - distance condition applied in each dimension. 53: If the molecule rotates the actual distance will be smaller. You might want 53: to use a cubic box instead, or why not try a dodecahedron today? 53: [ OK ] SinglePeptideFragments/EditconfTest.HandlesBothNoCenterAndDiameter/6 (16 ms) 53: [ RUN ] SinglePeptideFragments/EditconfTest.HandlesBothNoCenterAndDiameter/7 53: Note that major changes are planned in future for editconf, to improve usability and utility. 53: Read 252 atoms 53: Volume: 338.104 nm^3, corresponds to roughly 152100 electrons 53: No velocities found 53: system size : 2.004 1.472 1.704 (nm) 53: center : 3.816 1.632 0.195 (nm) 53: box vectors : 8.056 5.637 7.445 (nm) 53: box angles : 90.00 90.00 90.00 (degrees) 53: box volume : 338.10 (nm^3) 53: new center : 3.816 1.632 0.195 (nm) 53: new box vectors : 5.004 4.472 4.704 (nm) 53: new box angles : 90.00 90.00 90.00 (degrees) 53: new box volume : 105.27 (nm^3) 53: 53: WARNING: No boxtype specified - distance condition applied in each dimension. 53: If the molecule rotates the actual distance will be smaller. You might want 53: to use a cubic box instead, or why not try a dodecahedron today? 53: [ OK ] SinglePeptideFragments/EditconfTest.HandlesBothNoCenterAndDiameter/7 (13 ms) 53: [ RUN ] SinglePeptideFragments/EditconfTest.HandlesBothNoCenterAndDiameter/8 53: Note that major changes are planned in future for editconf, to improve usability and utility. 53: Read 252 atoms 53: Volume: 338.104 nm^3, corresponds to roughly 152100 electrons 53: No velocities found 53: system size : 2.004 1.472 1.704 (nm) 53: center : 3.816 1.632 0.195 (nm) 53: box vectors : 8.056 5.637 7.445 (nm) 53: box angles : 90.00 90.00 90.00 (degrees) 53: box volume : 338.10 (nm^3) 53: new center : 3.816 1.632 0.195 (nm) 53: new box vectors : 5.004 4.472 4.704 (nm) 53: new box angles : 90.00 90.00 90.00 (degrees) 53: new box volume : 105.27 (nm^3) 53: 53: WARNING: No boxtype specified - distance condition applied in each dimension. 53: If the molecule rotates the actual distance will be smaller. You might want 53: to use a cubic box instead, or why not try a dodecahedron today? 53: [ OK ] SinglePeptideFragments/EditconfTest.HandlesBothNoCenterAndDiameter/8 (14 ms) 53: [----------] 45 tests from SinglePeptideFragments/EditconfTest (689 ms total) 53: 53: [----------] 16 tests from CorrectVelocity/MaxwellTest 53: [ RUN ] CorrectVelocity/MaxwellTest.CreationWorks/0 53: [ OK ] CorrectVelocity/MaxwellTest.CreationWorks/0 (4 ms) 53: [ RUN ] CorrectVelocity/MaxwellTest.CreationWorks/1 53: [ OK ] CorrectVelocity/MaxwellTest.CreationWorks/1 (7 ms) 53: [ RUN ] CorrectVelocity/MaxwellTest.CreationWorks/2 53: [ OK ] CorrectVelocity/MaxwellTest.CreationWorks/2 (4 ms) 53: [ RUN ] CorrectVelocity/MaxwellTest.CreationWorks/3 53: [ OK ] CorrectVelocity/MaxwellTest.CreationWorks/3 (7 ms) 53: [ RUN ] CorrectVelocity/MaxwellTest.CreationWorks/4 53: [ OK ] CorrectVelocity/MaxwellTest.CreationWorks/4 (4 ms) 53: [ RUN ] CorrectVelocity/MaxwellTest.CreationWorks/5 53: [ OK ] CorrectVelocity/MaxwellTest.CreationWorks/5 (7 ms) 53: [ RUN ] CorrectVelocity/MaxwellTest.CreationWorks/6 53: [ OK ] CorrectVelocity/MaxwellTest.CreationWorks/6 (4 ms) 53: [ RUN ] CorrectVelocity/MaxwellTest.CreationWorks/7 53: [ OK ] CorrectVelocity/MaxwellTest.CreationWorks/7 (7 ms) 53: [ RUN ] CorrectVelocity/MaxwellTest.CreationWorks/8 53: [ OK ] CorrectVelocity/MaxwellTest.CreationWorks/8 (4 ms) 53: [ RUN ] CorrectVelocity/MaxwellTest.CreationWorks/9 53: [ OK ] CorrectVelocity/MaxwellTest.CreationWorks/9 (7 ms) 53: [ RUN ] CorrectVelocity/MaxwellTest.CreationWorks/10 53: [ OK ] CorrectVelocity/MaxwellTest.CreationWorks/10 (4 ms) 53: [ RUN ] CorrectVelocity/MaxwellTest.CreationWorks/11 53: [ OK ] CorrectVelocity/MaxwellTest.CreationWorks/11 (7 ms) 53: [ RUN ] CorrectVelocity/MaxwellTest.CreationWorks/12 53: [ OK ] CorrectVelocity/MaxwellTest.CreationWorks/12 (4 ms) 53: [ RUN ] CorrectVelocity/MaxwellTest.CreationWorks/13 53: [ OK ] CorrectVelocity/MaxwellTest.CreationWorks/13 (7 ms) 53: [ RUN ] CorrectVelocity/MaxwellTest.CreationWorks/14 53: [ OK ] CorrectVelocity/MaxwellTest.CreationWorks/14 (4 ms) 53: [ RUN ] CorrectVelocity/MaxwellTest.CreationWorks/15 53: [ OK ] CorrectVelocity/MaxwellTest.CreationWorks/15 (7 ms) 53: [----------] 16 tests from CorrectVelocity/MaxwellTest (110 ms total) 53: 53: [----------] 23 tests from CMAPDefinesAndErrors/GromppDirectiveTest 53: [ RUN ] CMAPDefinesAndErrors/GromppDirectiveTest.AcceptValidAndErrorOnInvalidCMAP/0 53: Setting the LD random seed to 2143272383 53: 53: Generated 3 of the 3 non-bonded parameter combinations 53: 53: Generated 3 of the 3 1-4 parameter combinations 53: [ OK ] CMAPDefinesAndErrors/GromppDirectiveTest.AcceptValidAndErrorOnInvalidCMAP/0 (42 ms) 53: [ RUN ] CMAPDefinesAndErrors/GromppDirectiveTest.AcceptValidAndErrorOnInvalidCMAP/1 53: Setting the LD random seed to -338329731 53: [ OK ] CMAPDefinesAndErrors/GromppDirectiveTest.AcceptValidAndErrorOnInvalidCMAP/1 (40 ms) 53: [ RUN ] CMAPDefinesAndErrors/GromppDirectiveTest.AcceptValidAndErrorOnInvalidCMAP/2 53: Ignoring obsolete mdp entry 'title' 53: Generating 1-4 interactions: fudge = 0.5 53: 53: NOTE 1 [file directives-cmap.top, line 114]: 53: In moleculetype 'A' 5 atoms are not bound by a potential or constraint to 53: any other atom in the same moleculetype. Although technically this might 53: not cause issues in a simulation, this often means that the user forgot 53: to add a bond/potential/constraint or put multiple molecules in the same 53: moleculetype definition by mistake. Run with -v to get information for 53: each atom. 53: 53: Number of degrees of freedom in T-Coupling group rest is 12.00 53: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 53: 53: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/CMAPDefinesAndErrors_GromppDirectiveTest_AcceptValidAndErrorOnInvalidCMAP_2_directives-cmap.mdp]: 53: NVE simulation: will use the initial temperature of 300.000 K for 53: determining the Verlet buffer size 53: 53: 53: There were 2 NOTEs 53: Setting the LD random seed to -9061065 53: 53: Generated 3 of the 3 non-bonded parameter combinations 53: 53: Generated 3 of the 3 1-4 parameter combinations 53: 53: Excluding 0 bonded neighbours molecule type 'A' 53: 53: Setting gen_seed to -202924815 53: 53: Velocities were taken from a Maxwell distribution at 300 K 53: Analysing residue names: 53: There are: 1 Other residues 53: Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups... 53: 53: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 300 K 53: 53: Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm 53: 53: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm 53: 53: Note that mdrun will redetermine rlist based on the actual pair-list setup 53: 53: This run will generate roughly 0 Mb of data 53: [ OK ] CMAPDefinesAndErrors/GromppDirectiveTest.AcceptValidAndErrorOnInvalidCMAP/2 (30 ms) 53: [ RUN ] CMAPDefinesAndErrors/GromppDirectiveTest.AcceptValidAndErrorOnInvalidCMAP/3 53: Ignoring obsolete mdp entry 'title' 53: Generating 1-4 interactions: fudge = 0.5 53: 53: NOTE 1 [file directives-cmap.top, line 114]: 53: In moleculetype 'A' 5 atoms are not bound by a potential or constraint to 53: any other atom in the same moleculetype. Although technically this might 53: not cause issues in a simulation, this often means that the user forgot 53: to add a bond/potential/constraint or put multiple molecules in the same 53: moleculetype definition by mistake. Run with -v to get information for 53: each atom. 53: 53: Number of degrees of freedom in T-Coupling group rest is 12.00 53: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 53: 53: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/CMAPDefinesAndErrors_GromppDirectiveTest_AcceptValidAndErrorOnInvalidCMAP_3_directives-cmap.mdp]: 53: NVE simulation: will use the initial temperature of 300.000 K for 53: determining the Verlet buffer size 53: 53: 53: There were 2 NOTEs 53: Setting the LD random seed to -1351473185 53: 53: Generated 3 of the 3 non-bonded parameter combinations 53: 53: Generated 3 of the 3 1-4 parameter combinations 53: 53: Excluding 0 bonded neighbours molecule type 'A' 53: 53: Setting gen_seed to -1342769281 53: 53: Velocities were taken from a Maxwell distribution at 300 K 53: Analysing residue names: 53: There are: 1 Other residues 53: Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups... 53: 53: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 300 K 53: 53: Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm 53: 53: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm 53: 53: Note that mdrun will redetermine rlist based on the actual pair-list setup 53: 53: This run will generate roughly 0 Mb of data 53: [ OK ] CMAPDefinesAndErrors/GromppDirectiveTest.AcceptValidAndErrorOnInvalidCMAP/3 (30 ms) 53: [ RUN ] CMAPDefinesAndErrors/GromppDirectiveTest.AcceptValidAndErrorOnInvalidCMAP/4 53: Ignoring obsolete mdp entry 'title' 53: Generating 1-4 interactions: fudge = 0.5 53: 53: NOTE 1 [file directives-cmap.top, line 114]: 53: In moleculetype 'A' 5 atoms are not bound by a potential or constraint to 53: any other atom in the same moleculetype. Although technically this might 53: not cause issues in a simulation, this often means that the user forgot 53: to add a bond/potential/constraint or put multiple molecules in the same 53: moleculetype definition by mistake. Run with -v to get information for 53: each atom. 53: 53: Number of degrees of freedom in T-Coupling group rest is 12.00 53: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 53: 53: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/CMAPDefinesAndErrors_GromppDirectiveTest_AcceptValidAndErrorOnInvalidCMAP_4_directives-cmap.mdp]: 53: NVE simulation: will use the initial temperature of 300.000 K for 53: determining the Verlet buffer size 53: 53: 53: There were 2 NOTEs 53: Setting the LD random seed to 233549599 53: 53: Generated 3 of the 3 non-bonded parameter combinations 53: 53: Generated 3 of the 3 1-4 parameter combinations 53: 53: Excluding 0 bonded neighbours molecule type 'A' 53: 53: Setting gen_seed to -1797341187 53: 53: Velocities were taken from a Maxwell distribution at 300 K 53: Analysing residue names: 53: There are: 1 Other residues 53: Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups... 53: 53: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 300 K 53: 53: Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm 53: 53: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm 53: 53: Note that mdrun will redetermine rlist based on the actual pair-list setup 53: 53: This run will generate roughly 0 Mb of data 53: [ OK ] CMAPDefinesAndErrors/GromppDirectiveTest.AcceptValidAndErrorOnInvalidCMAP/4 (30 ms) 53: [ RUN ] CMAPDefinesAndErrors/GromppDirectiveTest.AcceptValidAndErrorOnInvalidCMAP/5 53: Ignoring obsolete mdp entry 'title' 53: Generating 1-4 interactions: fudge = 0.5 53: 53: NOTE 1 [file directives-cmap.top, line 114]: 53: In moleculetype 'A' 5 atoms are not bound by a potential or constraint to 53: any other atom in the same moleculetype. Although technically this might 53: not cause issues in a simulation, this often means that the user forgot 53: to add a bond/potential/constraint or put multiple molecules in the same 53: moleculetype definition by mistake. Run with -v to get information for 53: each atom. 53: 53: Number of degrees of freedom in T-Coupling group rest is 12.00 53: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 53: 53: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/CMAPDefinesAndErrors_GromppDirectiveTest_AcceptValidAndErrorOnInvalidCMAP_5_directives-cmap.mdp]: 53: NVE simulation: will use the initial temperature of 300.000 K for 53: determining the Verlet buffer size 53: 53: 53: There were 2 NOTEs 53: Setting the LD random seed to -1091076953 53: 53: Generated 3 of the 3 non-bonded parameter combinations 53: 53: Generated 3 of the 3 1-4 parameter combinations 53: 53: Excluding 0 bonded neighbours molecule type 'A' 53: 53: Setting gen_seed to -772284545 53: 53: Velocities were taken from a Maxwell distribution at 300 K 53: Analysing residue names: 53: There are: 1 Other residues 53: Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups... 53: 53: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 300 K 53: 53: Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm 53: 53: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm 53: 53: Note that mdrun will redetermine rlist based on the actual pair-list setup 53: 53: This run will generate roughly 0 Mb of data 53: [ OK ] CMAPDefinesAndErrors/GromppDirectiveTest.AcceptValidAndErrorOnInvalidCMAP/5 (30 ms) 53: [ RUN ] CMAPDefinesAndErrors/GromppDirectiveTest.AcceptValidAndErrorOnInvalidCMAP/6 53: Setting the LD random seed to -277943210 53: [ OK ] CMAPDefinesAndErrors/GromppDirectiveTest.AcceptValidAndErrorOnInvalidCMAP/6 (49 ms) 53: [ RUN ] CMAPDefinesAndErrors/GromppDirectiveTest.AcceptValidAndErrorOnInvalidCMAP/7 53: Setting the LD random seed to -805314577 53: 53: Generated 3 of the 3 non-bonded parameter combinations 53: 53: Generated 3 of the 3 1-4 parameter combinations 53: 53: Excluding 0 bonded neighbours molecule type 'A' 53: 53: Setting gen_seed to 1997799283 53: 53: Velocities were taken from a Maxwell distribution at 300 K 53: [ OK ] CMAPDefinesAndErrors/GromppDirectiveTest.AcceptValidAndErrorOnInvalidCMAP/7 (43 ms) 53: [ RUN ] CMAPDefinesAndErrors/GromppDirectiveTest.AcceptValidAndErrorOnInvalidCMAP/8 53: Setting the LD random seed to 1576205439 53: [ OK ] CMAPDefinesAndErrors/GromppDirectiveTest.AcceptValidAndErrorOnInvalidCMAP/8 (39 ms) 53: [ RUN ] CMAPDefinesAndErrors/GromppDirectiveTest.AcceptValidAndErrorOnInvalidCMAP/9 53: Setting the LD random seed to -1862637189 53: 53: Generated 3 of the 3 non-bonded parameter combinations 53: 53: Generated 3 of the 3 1-4 parameter combinations 53: 53: Excluding 0 bonded neighbours molecule type 'A' 53: 53: Setting gen_seed to -419561602 53: 53: Velocities were taken from a Maxwell distribution at 300 K 53: [ OK ] CMAPDefinesAndErrors/GromppDirectiveTest.AcceptValidAndErrorOnInvalidCMAP/9 (43 ms) 53: [ RUN ] CMAPDefinesAndErrors/GromppDirectiveTest.AcceptValidAndErrorOnInvalidCMAP/10 53: Setting the LD random seed to -67634945 53: 53: Generated 3 of the 3 non-bonded parameter combinations 53: 53: Generated 3 of the 3 1-4 parameter combinations 53: 53: Excluding 0 bonded neighbours molecule type 'A' 53: 53: Setting gen_seed to -805316614 53: 53: Velocities were taken from a Maxwell distribution at 300 K 53: [ OK ] CMAPDefinesAndErrors/GromppDirectiveTest.AcceptValidAndErrorOnInvalidCMAP/10 (47 ms) 53: [ RUN ] CMAPDefinesAndErrors/GromppDirectiveTest.AcceptValidAndErrorOnInvalidCMAP/11 53: Setting the LD random seed to 717192626 53: 53: Generated 3 of the 3 non-bonded parameter combinations 53: 53: Generated 3 of the 3 1-4 parameter combinations 53: 53: Excluding 0 bonded neighbours molecule type 'A' 53: 53: Setting gen_seed to 1073143679 53: 53: Velocities were taken from a Maxwell distribution at 300 K 53: [ OK ] CMAPDefinesAndErrors/GromppDirectiveTest.AcceptValidAndErrorOnInvalidCMAP/11 (42 ms) 53: [ RUN ] CMAPDefinesAndErrors/GromppDirectiveTest.AcceptValidAndErrorOnInvalidCMAP/12 53: Setting the LD random seed to -285349425 53: 53: Generated 3 of the 3 non-bonded parameter combinations 53: 53: Generated 3 of the 3 1-4 parameter combinations 53: 53: Excluding 0 bonded neighbours molecule type 'A' 53: 53: Setting gen_seed to -1711300609 53: 53: Velocities were taken from a Maxwell distribution at 300 K 53: [ OK ] CMAPDefinesAndErrors/GromppDirectiveTest.AcceptValidAndErrorOnInvalidCMAP/12 (46 ms) 53: [ RUN ] CMAPDefinesAndErrors/GromppDirectiveTest.AcceptValidAndErrorOnInvalidCMAP/13 53: Setting the LD random seed to -33865729 53: 53: Generated 3 of the 3 non-bonded parameter combinations 53: 53: Generated 3 of the 3 1-4 parameter combinations 53: 53: Excluding 0 bonded neighbours molecule type 'A' 53: 53: Setting gen_seed to 2112880441 53: 53: Velocities were taken from a Maxwell distribution at 300 K 53: [ OK ] CMAPDefinesAndErrors/GromppDirectiveTest.AcceptValidAndErrorOnInvalidCMAP/13 (41 ms) 53: [ RUN ] CMAPDefinesAndErrors/GromppDirectiveTest.AcceptValidAndErrorOnInvalidCMAP/14 53: Setting the LD random seed to -131265 53: 53: Generated 3 of the 3 non-bonded parameter combinations 53: 53: Generated 3 of the 3 1-4 parameter combinations 53: 53: Excluding 0 bonded neighbours molecule type 'A' 53: 53: Setting gen_seed to -1074266115 53: 53: Velocities were taken from a Maxwell distribution at 300 K 53: [ OK ] CMAPDefinesAndErrors/GromppDirectiveTest.AcceptValidAndErrorOnInvalidCMAP/14 (42 ms) 53: [ RUN ] CMAPDefinesAndErrors/GromppDirectiveTest.AcceptValidAndErrorOnInvalidCMAP/15 53: Setting the LD random seed to -71603338 53: 53: Generated 3 of the 3 non-bonded parameter combinations 53: 53: Generated 3 of the 3 1-4 parameter combinations 53: 53: Excluding 0 bonded neighbours molecule type 'A' 53: 53: Setting gen_seed to -6292264 53: 53: Velocities were taken from a Maxwell distribution at 300 K 53: [ OK ] CMAPDefinesAndErrors/GromppDirectiveTest.AcceptValidAndErrorOnInvalidCMAP/15 (42 ms) 53: [ RUN ] CMAPDefinesAndErrors/GromppDirectiveTest.AcceptValidAndErrorOnInvalidCMAP/16 53: Ignoring obsolete mdp entry 'title' 53: Generating 1-4 interactions: fudge = 0.5 53: 53: NOTE 1 [file directives-cmap.top, line 114]: 53: In moleculetype 'A' 5 atoms are not bound by a potential or constraint to 53: any other atom in the same moleculetype. Although technically this might 53: not cause issues in a simulation, this often means that the user forgot 53: to add a bond/potential/constraint or put multiple molecules in the same 53: moleculetype definition by mistake. Run with -v to get information for 53: each atom. 53: 53: Number of degrees of freedom in T-Coupling group rest is 12.00 53: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 53: 53: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/CMAPDefinesAndErrors_GromppDirectiveTest_AcceptValidAndErrorOnInvalidCMAP_16_directives-cmap.mdp]: 53: NVE simulation: will use the initial temperature of 300.000 K for 53: determining the Verlet buffer size 53: 53: 53: There were 2 NOTEs 53: Setting the LD random seed to 1536945871 53: 53: Generated 3 of the 3 non-bonded parameter combinations 53: 53: Generated 3 of the 3 1-4 parameter combinations 53: 53: Excluding 0 bonded neighbours molecule type 'A' 53: 53: Setting gen_seed to -26216993 53: 53: Velocities were taken from a Maxwell distribution at 300 K 53: Analysing residue names: 53: There are: 1 Other residues 53: Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups... 53: 53: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 300 K 53: 53: Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm 53: 53: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm 53: 53: Note that mdrun will redetermine rlist based on the actual pair-list setup 53: 53: This run will generate roughly 0 Mb of data 53: [ OK ] CMAPDefinesAndErrors/GromppDirectiveTest.AcceptValidAndErrorOnInvalidCMAP/16 (31 ms) 53: [ RUN ] CMAPDefinesAndErrors/GromppDirectiveTest.AcceptValidAndErrorOnInvalidCMAP/17 53: Ignoring obsolete mdp entry 'title' 53: Generating 1-4 interactions: fudge = 0.5 53: 53: NOTE 1 [file directives-cmap.top, line 114]: 53: In moleculetype 'A' 5 atoms are not bound by a potential or constraint to 53: any other atom in the same moleculetype. Although technically this might 53: not cause issues in a simulation, this often means that the user forgot 53: to add a bond/potential/constraint or put multiple molecules in the same 53: moleculetype definition by mistake. Run with -v to get information for 53: each atom. 53: 53: Number of degrees of freedom in T-Coupling group rest is 12.00 53: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 53: 53: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/CMAPDefinesAndErrors_GromppDirectiveTest_AcceptValidAndErrorOnInvalidCMAP_17_directives-cmap.mdp]: 53: NVE simulation: will use the initial temperature of 300.000 K for 53: determining the Verlet buffer size 53: 53: 53: There were 2 NOTEs 53: Setting the LD random seed to 1061025775 53: 53: Generated 3 of the 3 non-bonded parameter combinations 53: 53: Generated 3 of the 3 1-4 parameter combinations 53: 53: Excluding 0 bonded neighbours molecule type 'A' 53: 53: Setting gen_seed to -1361474 53: 53: Velocities were taken from a Maxwell distribution at 300 K 53: Analysing residue names: 53: There are: 1 Other residues 53: Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups... 53: 53: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 300 K 53: 53: Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm 53: 53: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm 53: 53: Note that mdrun will redetermine rlist based on the actual pair-list setup 53: 53: This run will generate roughly 0 Mb of data 53: [ OK ] CMAPDefinesAndErrors/GromppDirectiveTest.AcceptValidAndErrorOnInvalidCMAP/17 (31 ms) 53: [ RUN ] CMAPDefinesAndErrors/GromppDirectiveTest.AcceptValidAndErrorOnInvalidCMAP/18 53: Setting the LD random seed to -1347846806 53: 53: Generated 3 of the 3 non-bonded parameter combinations 53: 53: Generated 3 of the 3 1-4 parameter combinations 53: [ OK ] CMAPDefinesAndErrors/GromppDirectiveTest.AcceptValidAndErrorOnInvalidCMAP/18 (39 ms) 53: [ RUN ] CMAPDefinesAndErrors/GromppDirectiveTest.AcceptValidAndErrorOnInvalidCMAP/19 53: Setting the LD random seed to -19103779 53: 53: Generated 3 of the 3 non-bonded parameter combinations 53: 53: Generated 3 of the 3 1-4 parameter combinations 53: 53: Excluding 0 bonded neighbours molecule type 'A' 53: 53: Setting gen_seed to -579159237 53: 53: Velocities were taken from a Maxwell distribution at 300 K 53: Analysing residue names: 53: There are: 1 Other residues 53: Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups... 53: 53: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 300 K 53: 53: Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm 53: 53: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm 53: 53: Note that mdrun will redetermine rlist based on the actual pair-list setup 53: 53: This run will generate roughly 0 Mb of data 53: [ OK ] CMAPDefinesAndErrors/GromppDirectiveTest.AcceptValidAndErrorOnInvalidCMAP/19 (43 ms) 53: [ RUN ] CMAPDefinesAndErrors/GromppDirectiveTest.AcceptValidAndErrorOnInvalidCMAP/20 53: Setting the LD random seed to -720898 53: 53: Generated 3 of the 3 non-bonded parameter combinations 53: 53: Generated 3 of the 3 1-4 parameter combinations 53: [ OK ] CMAPDefinesAndErrors/GromppDirectiveTest.AcceptValidAndErrorOnInvalidCMAP/20 (38 ms) 53: [ RUN ] CMAPDefinesAndErrors/GromppDirectiveTest.AcceptValidAndErrorOnInvalidCMAP/21 53: Ignoring obsolete mdp entry 'title' 53: Generating 1-4 interactions: fudge = 0.5 53: 53: NOTE 1 [file directives-cmap.top, line 114]: 53: In moleculetype 'A' 5 atoms are not bound by a potential or constraint to 53: any other atom in the same moleculetype. Although technically this might 53: not cause issues in a simulation, this often means that the user forgot 53: to add a bond/potential/constraint or put multiple molecules in the same 53: moleculetype definition by mistake. Run with -v to get information for 53: each atom. 53: 53: Number of degrees of freedom in T-Coupling group rest is 12.00 53: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 53: 53: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/CMAPDefinesAndErrors_GromppDirectiveTest_AcceptValidAndErrorOnInvalidCMAP_21_directives-cmap.mdp]: 53: NVE simulation: will use the initial temperature of 300.000 K for 53: determining the Verlet buffer size 53: 53: 53: There were 2 NOTEs 53: Setting the LD random seed to 1056809949 53: 53: Generated 3 of the 3 non-bonded parameter combinations 53: 53: Generated 3 of the 3 1-4 parameter combinations 53: 53: Excluding 0 bonded neighbours molecule type 'A' 53: 53: Setting gen_seed to 1055899379 53: 53: Velocities were taken from a Maxwell distribution at 300 K 53: Analysing residue names: 53: There are: 1 Other residues 53: Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups... 53: 53: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 300 K 53: 53: Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm 53: 53: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm 53: 53: Note that mdrun will redetermine rlist based on the actual pair-list setup 53: 53: This run will generate roughly 0 Mb of data 53: [ OK ] CMAPDefinesAndErrors/GromppDirectiveTest.AcceptValidAndErrorOnInvalidCMAP/21 (30 ms) 53: [ RUN ] CMAPDefinesAndErrors/GromppDirectiveTest.AcceptValidAndErrorOnInvalidCMAP/22 53: Setting the LD random seed to -33690625 53: 53: Generated 3 of the 3 non-bonded parameter combinations 53: 53: Generated 3 of the 3 1-4 parameter combinations 53: [ OK ] CMAPDefinesAndErrors/GromppDirectiveTest.AcceptValidAndErrorOnInvalidCMAP/22 (39 ms) 53: [----------] 23 tests from CMAPDefinesAndErrors/GromppDirectiveTest (900 ms total) 53: 53: [----------] Global test environment tear-down 53: [==========] 260 tests from 16 test suites ran. (12433 ms total) 53: [ PASSED ] 220 tests. 53: [ SKIPPED ] 40 tests, listed below: 53: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/GB_1_2_Pol_ 53: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/GB_1_3_Pol_ 53: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/GB_1_4_Pol_ 53: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/GB_Polariz_ 53: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/Nonpolar_Sol_ 53: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/Coulomb_14 53: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/LJ__SR_ 53: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/Buck_ham__SR_ 53: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/LJ 53: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/B_ham 53: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/Disper__corr_ 53: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/Coulomb__SR_ 53: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/Coul 53: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/RF_excl_ 53: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/Coul__recip_ 53: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/LJ_recip_ 53: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/DPD 53: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/D_R_Viol___nm_ 53: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/Ori__R__RMSD 53: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/Dih__Rest__Vi_ 53: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/COM_Pull_En_ 53: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/Dens__fitting 53: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/Quantum_En_ 53: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/NN_Potential 53: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/Potential 53: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/Kinetic_En_ 53: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/Total_Energy 53: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/Conserved_En_ 53: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/Temperature 53: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/Vir__Temp_ 53: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/Pres__DC 53: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/Pressure 53: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/dH_dl_constr_ 53: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/dVremain_dl 53: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/dEkin_dl 53: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/dVcoul_dl 53: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/dVvdw_dl 53: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/dVbonded_dl 53: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/dVrestraint_dl 53: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/dVtemp_dl 53/92 Test #53: GmxPreprocessTests ........................ Passed 12.55 sec test 54 Start 54: Pdb2gmx1Test 54: Test command: /build/reproducible-path/gromacs-2025.1/build/basic/bin/pdb2gmx1-test "--gtest_output=xml:/build/reproducible-path/gromacs-2025.1/build/basic/Testing/Temporary/Pdb2gmx1Test.xml" 54: Working Directory: /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/gmxpreprocess/tests 54: Test timeout computed to be: 1920 54: [==========] Running 30 tests from 1 test suite. 54: [----------] Global test environment set-up. 54: [----------] 30 tests from Oplsaa/Pdb2gmxTest 54: [ RUN ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip3p_vsite_none_id_or_ter_merge_no_Apdb_format_gro_match_file 54: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/oplsaa.ff/aminoacids.r2b 54: All occupancies are one 54: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/oplsaa.ff/atomtypes.atp 54: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/oplsaa.ff/aminoacids.rtp 54: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/oplsaa.ff/aminoacids.hdb 54: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/oplsaa.ff/aminoacids.n.tdb 54: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/oplsaa.ff/aminoacids.c.tdb 54: Analysing hydrogen-bonding network for automated assignment of histidine 54: protonation. 25 donors and 23 acceptors were found. 54: There are 41 hydrogen bonds 54: Will use HISE for residue 8 54: 9 out of 9 lines of specbond.dat converted successfully 54: Special Atom Distance matrix: 54: CYS3 HIS8 54: SG9 NE251 54: HIS8 NE251 1.055 54: MET12 SD83 0.763 0.990 54: Before cleaning: 653 pairs 54: Before cleaning: 663 dihedrals 54: Using the Oplsaa force field in directory oplsaa.ff 54: 54: going to rename oplsaa.ff/aminoacids.r2b 54: Reading /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/A.pdb... 54: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms 54: 54: Analyzing pdb file 54: Splitting chemical chains based on TER records or chain id changing. 54: 54: There are 1 chains and 0 blocks of water and 16 residues with 128 atoms 54: 54: chain #res #atoms 54: 54: 1 ' ' 16 128 54: 54: All occupancies are one 54: 54: Reading residue database... (Oplsaa) 54: 54: Processing chain 1 (128 atoms, 16 residues) 54: 54: Identified residue ALA2 as a starting terminus. 54: 54: Identified residue SER17 as a ending terminus. 54: Start terminus ALA-2: NH3+ 54: End terminus SER-17: COO- 54: 54: Checking for duplicate atoms.... 54: 54: Generating any missing hydrogen atoms and/or adding termini. 54: 54: Now there are 16 residues with 252 atoms 54: 54: Making bonds... 54: 54: Number of bonds was 254, now 254 54: 54: Generating angles, dihedrals and pairs... 54: 54: Making cmap torsions... 54: 54: There are 663 dihedrals, 51 impropers, 457 angles 54: 650 pairs, 254 bonds and 0 virtual sites 54: 54: Total mass 1846.112 a.m.u. 54: 54: Total charge -0.000 e 54: 54: Writing topology 54: 54: Writing coordinate file... 54: 54: --------- PLEASE NOTE ------------ 54: 54: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/A.pdb. 54: 54: The Oplsaa force field and the tip3p water model are used. 54: 54: --------- ETON ESAELP ------------ 54: [ OK ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip3p_vsite_none_id_or_ter_merge_no_Apdb_format_gro_match_file (212 ms) 54: [ RUN ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip3p_vsite_none_id_or_ter_merge_no_Bpdb_format_gro_match_file 54: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/oplsaa.ff/aminoacids.r2b 54: All occupancies are one 54: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/oplsaa.ff/atomtypes.atp 54: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/oplsaa.ff/aminoacids.rtp 54: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/oplsaa.ff/aminoacids.hdb 54: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/oplsaa.ff/aminoacids.n.tdb 54: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/oplsaa.ff/aminoacids.c.tdb 54: Analysing hydrogen-bonding network for automated assignment of histidine 54: protonation. 30 donors and 22 acceptors were found. 54: There are 36 hydrogen bonds 54: Will use HISE for residue 29 54: Will use HISE for residue 32 54: 9 out of 9 lines of specbond.dat converted successfully 54: Special Atom Distance matrix: 54: CYS27 HIS29 54: SG90 NE2111 54: HIS29 NE2111 0.987 54: HIS32 NE2135 1.590 1.155 54: Before cleaning: 748 pairs 54: Before cleaning: 778 dihedrals 54: Using the Oplsaa force field in directory oplsaa.ff 54: 54: going to rename oplsaa.ff/aminoacids.r2b 54: Reading /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/B.pdb... 54: Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms 54: 54: Analyzing pdb file 54: Splitting chemical chains based on TER records or chain id changing. 54: 54: There are 1 chains and 0 blocks of water and 16 residues with 149 atoms 54: 54: chain #res #atoms 54: 54: 1 ' ' 16 149 54: 54: All occupancies are one 54: 54: Reading residue database... (Oplsaa) 54: 54: Processing chain 1 (149 atoms, 16 residues) 54: 54: Replaced 1 residue named GLUH to the default GLU. Use interactive selection of protonated residues if that is what you need. 54: 54: Identified residue THR18 as a starting terminus. 54: 54: Identified residue PHE33 as a ending terminus. 54: Start terminus THR-18: NH3+ 54: End terminus PHE-33: COO- 54: 54: Checking for duplicate atoms.... 54: 54: Generating any missing hydrogen atoms and/or adding termini. 54: 54: Now there are 16 residues with 281 atoms 54: 54: Making bonds... 54: 54: Number of bonds was 290, now 290 54: 54: Generating angles, dihedrals and pairs... 54: 54: Making cmap torsions... 54: 54: There are 778 dihedrals, 72 impropers, 516 angles 54: 736 pairs, 290 bonds and 0 virtual sites 54: 54: Total mass 2088.357 a.m.u. 54: 54: Total charge 1.000 e 54: 54: Writing topology 54: 54: Writing coordinate file... 54: 54: --------- PLEASE NOTE ------------ 54: 54: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/B.pdb. 54: 54: The Oplsaa force field and the tip3p water model are used. 54: 54: --------- ETON ESAELP ------------ 54: [ OK ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip3p_vsite_none_id_or_ter_merge_no_Bpdb_format_gro_match_file (227 ms) 54: [ RUN ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip3p_vsite_none_id_or_ter_merge_no_Cpdb_format_gro_match_file 54: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/oplsaa.ff/aminoacids.r2b 54: All occupancies are one 54: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/oplsaa.ff/atomtypes.atp 54: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/oplsaa.ff/aminoacids.rtp 54: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/oplsaa.ff/aminoacids.hdb 54: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/oplsaa.ff/aminoacids.n.tdb 54: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/oplsaa.ff/aminoacids.c.tdb 54: Analysing hydrogen-bonding network for automated assignment of histidine 54: protonation. 22 donors and 22 acceptors were found. 54: There are 26 hydrogen bonds 54: Will use HISE for residue 45 54: 9 out of 9 lines of specbond.dat converted successfully 54: Special Atom Distance matrix: 54: HIS45 54: NE295 54: MET46 SD102 1.078 54: Before cleaning: 676 pairs 54: Before cleaning: 696 dihedrals 54: Using the Oplsaa force field in directory oplsaa.ff 54: 54: going to rename oplsaa.ff/aminoacids.r2b 54: Reading /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/C.pdb... 54: Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms 54: 54: Analyzing pdb file 54: Splitting chemical chains based on TER records or chain id changing. 54: 54: There are 1 chains and 0 blocks of water and 16 residues with 132 atoms 54: 54: chain #res #atoms 54: 54: 1 ' ' 16 132 54: 54: All occupancies are one 54: 54: Reading residue database... (Oplsaa) 54: 54: Processing chain 1 (132 atoms, 16 residues) 54: 54: Identified residue ALA34 as a starting terminus. 54: 54: Identified residue ALA49 as a ending terminus. 54: Start terminus ALA-34: NH3+ 54: End terminus ALA-49: COO- 54: 54: Checking for duplicate atoms.... 54: 54: Generating any missing hydrogen atoms and/or adding termini. 54: 54: Now there are 16 residues with 255 atoms 54: 54: Making bonds... 54: 54: Number of bonds was 261, now 261 54: 54: Generating angles, dihedrals and pairs... 54: 54: Making cmap torsions... 54: 54: There are 696 dihedrals, 56 impropers, 472 angles 54: 667 pairs, 261 bonds and 0 virtual sites 54: 54: Total mass 1861.128 a.m.u. 54: 54: Total charge -1.000 e 54: 54: Writing topology 54: 54: Writing coordinate file... 54: 54: --------- PLEASE NOTE ------------ 54: 54: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/C.pdb. 54: 54: The Oplsaa force field and the tip3p water model are used. 54: 54: --------- ETON ESAELP ------------ 54: [ OK ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip3p_vsite_none_id_or_ter_merge_no_Cpdb_format_gro_match_file (208 ms) 54: [ RUN ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip3p_vsite_none_id_or_ter_merge_no_Dpdb_format_gro_match_file 54: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/oplsaa.ff/aminoacids.r2b 54: All occupancies are one 54: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/oplsaa.ff/atomtypes.atp 54: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/oplsaa.ff/aminoacids.rtp 54: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/oplsaa.ff/aminoacids.hdb 54: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/oplsaa.ff/aminoacids.n.tdb 54: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/oplsaa.ff/aminoacids.c.tdb 54: Analysing hydrogen-bonding network for automated assignment of histidine 54: protonation. 22 donors and 21 acceptors were found. 54: There are 30 hydrogen bonds 54: Will use HISE for residue 60 54: 9 out of 9 lines of specbond.dat converted successfully 54: Special Atom Distance matrix: 54: HIS60 54: NE285 54: CYS62 SG98 0.803 54: Before cleaning: 603 pairs 54: Before cleaning: 618 dihedrals 54: Using the Oplsaa force field in directory oplsaa.ff 54: 54: going to rename oplsaa.ff/aminoacids.r2b 54: Reading /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/D.pdb... 54: Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms 54: 54: Analyzing pdb file 54: Splitting chemical chains based on TER records or chain id changing. 54: 54: There are 1 chains and 0 blocks of water and 16 residues with 117 atoms 54: 54: chain #res #atoms 54: 54: 1 ' ' 16 117 54: 54: All occupancies are one 54: 54: Reading residue database... (Oplsaa) 54: 54: Processing chain 1 (117 atoms, 16 residues) 54: 54: Replaced 1 residue named ASPH to the default ASP. Use interactive selection of protonated residues if that is what you need. 54: 54: Identified residue LYS50 as a starting terminus. 54: 54: Identified residue PRO65 as a ending terminus. 54: Start terminus LYS-50: NH3+ 54: End terminus PRO-65: PRO-COO- 54: 54: Checking for duplicate atoms.... 54: 54: Generating any missing hydrogen atoms and/or adding termini. 54: 54: Now there are 16 residues with 228 atoms 54: 54: Making bonds... 54: 54: Number of bonds was 232, now 232 54: 54: Generating angles, dihedrals and pairs... 54: 54: Making cmap torsions... 54: 54: There are 618 dihedrals, 48 impropers, 419 angles 54: 597 pairs, 232 bonds and 0 virtual sites 54: 54: Total mass 1662.883 a.m.u. 54: 54: Total charge -0.000 e 54: 54: Writing topology 54: 54: Writing coordinate file... 54: 54: --------- PLEASE NOTE ------------ 54: 54: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/D.pdb. 54: 54: The Oplsaa force field and the tip3p water model are used. 54: 54: --------- ETON ESAELP ------------ 54: [ OK ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip3p_vsite_none_id_or_ter_merge_no_Dpdb_format_gro_match_file (195 ms) 54: [ RUN ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip3p_vsite_none_id_or_ter_merge_no_Epdb_format_gro_match_file 54: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/oplsaa.ff/aminoacids.r2b 54: All occupancies are one 54: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/oplsaa.ff/atomtypes.atp 54: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/oplsaa.ff/aminoacids.rtp 54: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/oplsaa.ff/aminoacids.hdb 54: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/oplsaa.ff/aminoacids.n.tdb 54: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/oplsaa.ff/aminoacids.c.tdb 54: Analysing hydrogen-bonding network for automated assignment of histidine 54: protonation. 89 donors and 98 acceptors were found. 54: There are 129 hydrogen bonds 54: Will use HISE for residue 31 54: Will use HISE for residue 51 54: 9 out of 9 lines of specbond.dat converted successfully 54: Special Atom Distance matrix: 54: CYS25 HIS31 HIS51 54: SG14 NE264 NE2226 54: HIS31 NE264 1.921 54: HIS51 NE2226 1.498 2.650 54: CYS80 SG477 0.207 1.984 1.570 54: Linking CYS-25 SG-14 and CYS-80 SG-477... 54: Before cleaning: 2499 pairs 54: Before cleaning: 2524 dihedrals 54: Using the Oplsaa force field in directory oplsaa.ff 54: 54: going to rename oplsaa.ff/aminoacids.r2b 54: Reading /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/E.pdb... 54: Read 'This is a fragment of 2d4f for testing a disulfide bridge', 488 atoms 54: 54: Analyzing pdb file 54: Splitting chemical chains based on TER records or chain id changing. 54: 54: There are 1 chains and 0 blocks of water and 58 residues with 488 atoms 54: 54: chain #res #atoms 54: 54: 1 'A' 58 488 54: 54: All occupancies are one 54: 54: Reading residue database... (Oplsaa) 54: 54: Processing chain 1 'A' (488 atoms, 58 residues) 54: 54: Identified residue ASN24 as a starting terminus. 54: 54: Identified residue ARG81 as a ending terminus. 54: Start terminus ASN-24: NH3+ 54: End terminus ARG-81: COO- 54: 54: Checking for duplicate atoms.... 54: 54: Generating any missing hydrogen atoms and/or adding termini. 54: 54: Now there are 58 residues with 936 atoms 54: 54: Making bonds... 54: 54: Number of bonds was 951, now 951 54: 54: Generating angles, dihedrals and pairs... 54: 54: Making cmap torsions... 54: 54: There are 2524 dihedrals, 208 impropers, 1704 angles 54: 2469 pairs, 951 bonds and 0 virtual sites 54: 54: Total mass 6908.578 a.m.u. 54: 54: Total charge -6.000 e 54: 54: Writing topology 54: 54: Writing coordinate file... 54: 54: --------- PLEASE NOTE ------------ 54: 54: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/E.pdb. 54: 54: The Oplsaa force field and the tip3p water model are used. 54: 54: --------- ETON ESAELP ------------ 54: [ OK ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip3p_vsite_none_id_or_ter_merge_no_Epdb_format_gro_match_file (635 ms) 54: [ RUN ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip3p_vsite_h_id_or_ter_merge_no_Apdb_format_gro_match_file 54: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/oplsaa.ff/aminoacids.r2b 54: All occupancies are one 54: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/oplsaa.ff/atomtypes.atp 54: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/oplsaa.ff/aminoacids.rtp 54: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/oplsaa.ff/aminoacids.hdb 54: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/oplsaa.ff/aminoacids.n.tdb 54: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/oplsaa.ff/aminoacids.c.tdb 54: Analysing hydrogen-bonding network for automated assignment of histidine 54: protonation. 25 donors and 23 acceptors were found. 54: There are 41 hydrogen bonds 54: Will use HISE for residue 8 54: 9 out of 9 lines of specbond.dat converted successfully 54: Special Atom Distance matrix: 54: CYS3 HIS8 54: SG9 NE251 54: HIS8 NE251 1.055 54: MET12 SD83 0.763 0.990 54: Marked 124 virtual sites 54: Added 16 dummy masses 54: Added 26 new constraints 54: Before cleaning: 653 pairs 54: Before cleaning: 663 dihedrals 54: Using the Oplsaa force field in directory oplsaa.ff 54: 54: going to rename oplsaa.ff/aminoacids.r2b 54: Reading /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/A.pdb... 54: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms 54: 54: Analyzing pdb file 54: Splitting chemical chains based on TER records or chain id changing. 54: 54: There are 1 chains and 0 blocks of water and 16 residues with 128 atoms 54: 54: chain #res #atoms 54: 54: 1 ' ' 16 128 54: 54: All occupancies are one 54: 54: Reading residue database... (Oplsaa) 54: 54: Processing chain 1 (128 atoms, 16 residues) 54: 54: Identified residue ALA2 as a starting terminus. 54: 54: Identified residue SER17 as a ending terminus. 54: Start terminus ALA-2: NH3+ 54: End terminus SER-17: COO- 54: 54: Checking for duplicate atoms.... 54: 54: Generating any missing hydrogen atoms and/or adding termini. 54: 54: Now there are 16 residues with 252 atoms 54: 54: Making bonds... 54: 54: Number of bonds was 254, now 254 54: 54: Generating angles, dihedrals and pairs... 54: 54: Making cmap torsions... 54: 54: There are 663 dihedrals, 51 impropers, 457 angles 54: 650 pairs, 254 bonds and 130 virtual sites 54: 54: Total mass 1846.112 a.m.u. 54: 54: Total charge -0.000 e 54: 54: Writing topology 54: 54: Writing coordinate file... 54: 54: --------- PLEASE NOTE ------------ 54: 54: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/A.pdb. 54: 54: The Oplsaa force field and the tip3p water model are used. 54: 54: --------- ETON ESAELP ------------ 54: [ OK ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip3p_vsite_h_id_or_ter_merge_no_Apdb_format_gro_match_file (228 ms) 54: [ RUN ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip3p_vsite_h_id_or_ter_merge_no_Bpdb_format_gro_match_file 54: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/oplsaa.ff/aminoacids.r2b 54: All occupancies are one 54: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/oplsaa.ff/atomtypes.atp 54: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/oplsaa.ff/aminoacids.rtp 54: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/oplsaa.ff/aminoacids.hdb 54: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/oplsaa.ff/aminoacids.n.tdb 54: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/oplsaa.ff/aminoacids.c.tdb 54: Analysing hydrogen-bonding network for automated assignment of histidine 54: protonation. 30 donors and 22 acceptors were found. 54: There are 36 hydrogen bonds 54: Will use HISE for residue 29 54: Will use HISE for residue 32 54: 9 out of 9 lines of specbond.dat converted successfully 54: Special Atom Distance matrix: 54: CYS27 HIS29 54: SG90 NE2111 54: HIS29 NE2111 0.987 54: HIS32 NE2135 1.590 1.155 54: Marked 132 virtual sites 54: Added 10 dummy masses 54: Added 19 new constraints 54: Before cleaning: 748 pairs 54: Before cleaning: 778 dihedrals 54: Using the Oplsaa force field in directory oplsaa.ff 54: 54: going to rename oplsaa.ff/aminoacids.r2b 54: Reading /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/B.pdb... 54: Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms 54: 54: Analyzing pdb file 54: Splitting chemical chains based on TER records or chain id changing. 54: 54: There are 1 chains and 0 blocks of water and 16 residues with 149 atoms 54: 54: chain #res #atoms 54: 54: 1 ' ' 16 149 54: 54: All occupancies are one 54: 54: Reading residue database... (Oplsaa) 54: 54: Processing chain 1 (149 atoms, 16 residues) 54: 54: Replaced 1 residue named GLUH to the default GLU. Use interactive selection of protonated residues if that is what you need. 54: 54: Identified residue THR18 as a starting terminus. 54: 54: Identified residue PHE33 as a ending terminus. 54: Start terminus THR-18: NH3+ 54: End terminus PHE-33: COO- 54: 54: Checking for duplicate atoms.... 54: 54: Generating any missing hydrogen atoms and/or adding termini. 54: 54: Now there are 16 residues with 281 atoms 54: 54: Making bonds... 54: 54: Number of bonds was 290, now 290 54: 54: Generating angles, dihedrals and pairs... 54: 54: Making cmap torsions... 54: 54: There are 778 dihedrals, 72 impropers, 516 angles 54: 736 pairs, 290 bonds and 133 virtual sites 54: 54: Total mass 2088.357 a.m.u. 54: 54: Total charge 1.000 e 54: 54: Writing topology 54: 54: Writing coordinate file... 54: 54: --------- PLEASE NOTE ------------ 54: 54: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/B.pdb. 54: 54: The Oplsaa force field and the tip3p water model are used. 54: 54: --------- ETON ESAELP ------------ 54: [ OK ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip3p_vsite_h_id_or_ter_merge_no_Bpdb_format_gro_match_file (253 ms) 54: [ RUN ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip3p_vsite_h_id_or_ter_merge_no_Cpdb_format_gro_match_file 54: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/oplsaa.ff/aminoacids.r2b 54: All occupancies are one 54: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/oplsaa.ff/atomtypes.atp 54: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/oplsaa.ff/aminoacids.rtp 54: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/oplsaa.ff/aminoacids.hdb 54: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/oplsaa.ff/aminoacids.n.tdb 54: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/oplsaa.ff/aminoacids.c.tdb 54: Analysing hydrogen-bonding network for automated assignment of histidine 54: protonation. 22 donors and 22 acceptors were found. 54: There are 26 hydrogen bonds 54: Will use HISE for residue 45 54: 9 out of 9 lines of specbond.dat converted successfully 54: Special Atom Distance matrix: 54: HIS45 54: NE295 54: MET46 SD102 1.078 54: Marked 123 virtual sites 54: Added 22 dummy masses 54: Added 35 new constraints 54: Before cleaning: 676 pairs 54: Before cleaning: 696 dihedrals 54: Using the Oplsaa force field in directory oplsaa.ff 54: 54: going to rename oplsaa.ff/aminoacids.r2b 54: Reading /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/C.pdb... 54: Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms 54: 54: Analyzing pdb file 54: Splitting chemical chains based on TER records or chain id changing. 54: 54: There are 1 chains and 0 blocks of water and 16 residues with 132 atoms 54: 54: chain #res #atoms 54: 54: 1 ' ' 16 132 54: 54: All occupancies are one 54: 54: Reading residue database... (Oplsaa) 54: 54: Processing chain 1 (132 atoms, 16 residues) 54: 54: Identified residue ALA34 as a starting terminus. 54: 54: Identified residue ALA49 as a ending terminus. 54: Start terminus ALA-34: NH3+ 54: End terminus ALA-49: COO- 54: 54: Checking for duplicate atoms.... 54: 54: Generating any missing hydrogen atoms and/or adding termini. 54: 54: Now there are 16 residues with 255 atoms 54: 54: Making bonds... 54: 54: Number of bonds was 261, now 261 54: 54: Generating angles, dihedrals and pairs... 54: 54: Making cmap torsions... 54: 54: There are 696 dihedrals, 56 impropers, 472 angles 54: 667 pairs, 261 bonds and 132 virtual sites 54: 54: Total mass 1861.128 a.m.u. 54: 54: Total charge -1.000 e 54: 54: Writing topology 54: 54: Writing coordinate file... 54: 54: --------- PLEASE NOTE ------------ 54: 54: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/C.pdb. 54: 54: The Oplsaa force field and the tip3p water model are used. 54: 54: --------- ETON ESAELP ------------ 54: [ OK ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip3p_vsite_h_id_or_ter_merge_no_Cpdb_format_gro_match_file (228 ms) 54: [ RUN ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip3p_vsite_h_id_or_ter_merge_no_Dpdb_format_gro_match_file 54: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/oplsaa.ff/aminoacids.r2b 54: All occupancies are one 54: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/oplsaa.ff/atomtypes.atp 54: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/oplsaa.ff/aminoacids.rtp 54: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/oplsaa.ff/aminoacids.hdb 54: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/oplsaa.ff/aminoacids.n.tdb 54: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/oplsaa.ff/aminoacids.c.tdb 54: Analysing hydrogen-bonding network for automated assignment of histidine 54: protonation. 22 donors and 21 acceptors were found. 54: There are 30 hydrogen bonds 54: Will use HISE for residue 60 54: 9 out of 9 lines of specbond.dat converted successfully 54: Special Atom Distance matrix: 54: HIS60 54: NE285 54: CYS62 SG98 0.803 54: Marked 111 virtual sites 54: Added 18 dummy masses 54: Added 31 new constraints 54: Before cleaning: 603 pairs 54: Before cleaning: 618 dihedrals 54: Using the Oplsaa force field in directory oplsaa.ff 54: 54: going to rename oplsaa.ff/aminoacids.r2b 54: Reading /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/D.pdb... 54: Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms 54: 54: Analyzing pdb file 54: Splitting chemical chains based on TER records or chain id changing. 54: 54: There are 1 chains and 0 blocks of water and 16 residues with 117 atoms 54: 54: chain #res #atoms 54: 54: 1 ' ' 16 117 54: 54: All occupancies are one 54: 54: Reading residue database... (Oplsaa) 54: 54: Processing chain 1 (117 atoms, 16 residues) 54: 54: Replaced 1 residue named ASPH to the default ASP. Use interactive selection of protonated residues if that is what you need. 54: 54: Identified residue LYS50 as a starting terminus. 54: 54: Identified residue PRO65 as a ending terminus. 54: Start terminus LYS-50: NH3+ 54: End terminus PRO-65: PRO-COO- 54: 54: Checking for duplicate atoms.... 54: 54: Generating any missing hydrogen atoms and/or adding termini. 54: 54: Now there are 16 residues with 228 atoms 54: 54: Making bonds... 54: 54: Number of bonds was 232, now 232 54: 54: Generating angles, dihedrals and pairs... 54: 54: Making cmap torsions... 54: 54: There are 618 dihedrals, 48 impropers, 419 angles 54: 597 pairs, 232 bonds and 116 virtual sites 54: 54: Total mass 1662.883 a.m.u. 54: 54: Total charge -0.000 e 54: 54: Writing topology 54: 54: Writing coordinate file... 54: 54: --------- PLEASE NOTE ------------ 54: 54: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/D.pdb. 54: 54: The Oplsaa force field and the tip3p water model are used. 54: 54: --------- ETON ESAELP ------------ 54: [ OK ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip3p_vsite_h_id_or_ter_merge_no_Dpdb_format_gro_match_file (203 ms) 54: [ RUN ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip3p_vsite_h_id_or_ter_merge_no_Epdb_format_gro_match_file 54: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/oplsaa.ff/aminoacids.r2b 54: All occupancies are one 54: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/oplsaa.ff/atomtypes.atp 54: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/oplsaa.ff/aminoacids.rtp 54: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/oplsaa.ff/aminoacids.hdb 54: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/oplsaa.ff/aminoacids.n.tdb 54: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/oplsaa.ff/aminoacids.c.tdb 54: Analysing hydrogen-bonding network for automated assignment of histidine 54: protonation. 89 donors and 98 acceptors were found. 54: There are 129 hydrogen bonds 54: Will use HISE for residue 31 54: Will use HISE for residue 51 54: 9 out of 9 lines of specbond.dat converted successfully 54: Special Atom Distance matrix: 54: CYS25 HIS31 HIS51 54: SG14 NE264 NE2226 54: HIS31 NE264 1.921 54: HIS51 NE2226 1.498 2.650 54: CYS80 SG477 0.207 1.984 1.570 54: Linking CYS-25 SG-14 and CYS-80 SG-477... 54: Marked 447 virtual sites 54: Added 58 dummy masses 54: Added 101 new constraints 54: Before cleaning: 2499 pairs 54: Before cleaning: 2524 dihedrals 54: Using the Oplsaa force field in directory oplsaa.ff 54: 54: going to rename oplsaa.ff/aminoacids.r2b 54: Reading /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/E.pdb... 54: Read 'This is a fragment of 2d4f for testing a disulfide bridge', 488 atoms 54: 54: Analyzing pdb file 54: Splitting chemical chains based on TER records or chain id changing. 54: 54: There are 1 chains and 0 blocks of water and 58 residues with 488 atoms 54: 54: chain #res #atoms 54: 54: 1 'A' 58 488 54: 54: All occupancies are one 54: 54: Reading residue database... (Oplsaa) 54: 54: Processing chain 1 'A' (488 atoms, 58 residues) 54: 54: Identified residue ASN24 as a starting terminus. 54: 54: Identified residue ARG81 as a ending terminus. 54: Start terminus ASN-24: NH3+ 54: End terminus ARG-81: COO- 54: 54: Checking for duplicate atoms.... 54: 54: Generating any missing hydrogen atoms and/or adding termini. 54: 54: Now there are 58 residues with 936 atoms 54: 54: Making bonds... 54: 54: Number of bonds was 951, now 951 54: 54: Generating angles, dihedrals and pairs... 54: 54: Making cmap torsions... 54: 54: There are 2524 dihedrals, 208 impropers, 1704 angles 54: 2469 pairs, 951 bonds and 462 virtual sites 54: 54: Total mass 6908.578 a.m.u. 54: 54: Total charge -6.000 e 54: 54: Writing topology 54: 54: Writing coordinate file... 54: 54: --------- PLEASE NOTE ------------ 54: 54: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/E.pdb. 54: 54: The Oplsaa force field and the tip3p water model are used. 54: 54: --------- ETON ESAELP ------------ 54: [ OK ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip3p_vsite_h_id_or_ter_merge_no_Epdb_format_gro_match_file (692 ms) 54: [ RUN ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip4p_vsite_none_id_or_ter_merge_no_Apdb_format_gro_match_file 54: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/oplsaa.ff/aminoacids.r2b 54: All occupancies are one 54: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/oplsaa.ff/atomtypes.atp 54: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/oplsaa.ff/aminoacids.rtp 54: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/oplsaa.ff/aminoacids.hdb 54: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/oplsaa.ff/aminoacids.n.tdb 54: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/oplsaa.ff/aminoacids.c.tdb 54: Analysing hydrogen-bonding network for automated assignment of histidine 54: protonation. 25 donors and 23 acceptors were found. 54: There are 41 hydrogen bonds 54: Will use HISE for residue 8 54: 9 out of 9 lines of specbond.dat converted successfully 54: Special Atom Distance matrix: 54: CYS3 HIS8 54: SG9 NE251 54: HIS8 NE251 1.055 54: MET12 SD83 0.763 0.990 54: Before cleaning: 653 pairs 54: Before cleaning: 663 dihedrals 54: Using the Oplsaa force field in directory oplsaa.ff 54: 54: going to rename oplsaa.ff/aminoacids.r2b 54: Reading /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/A.pdb... 54: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms 54: 54: Analyzing pdb file 54: Splitting chemical chains based on TER records or chain id changing. 54: 54: There are 1 chains and 0 blocks of water and 16 residues with 128 atoms 54: 54: chain #res #atoms 54: 54: 1 ' ' 16 128 54: 54: All occupancies are one 54: 54: Reading residue database... (Oplsaa) 54: 54: Processing chain 1 (128 atoms, 16 residues) 54: 54: Identified residue ALA2 as a starting terminus. 54: 54: Identified residue SER17 as a ending terminus. 54: Start terminus ALA-2: NH3+ 54: End terminus SER-17: COO- 54: 54: Checking for duplicate atoms.... 54: 54: Generating any missing hydrogen atoms and/or adding termini. 54: 54: Now there are 16 residues with 252 atoms 54: 54: Making bonds... 54: 54: Number of bonds was 254, now 254 54: 54: Generating angles, dihedrals and pairs... 54: 54: Making cmap torsions... 54: 54: There are 663 dihedrals, 51 impropers, 457 angles 54: 650 pairs, 254 bonds and 0 virtual sites 54: 54: Total mass 1846.112 a.m.u. 54: 54: Total charge -0.000 e 54: 54: Writing topology 54: 54: Writing coordinate file... 54: 54: --------- PLEASE NOTE ------------ 54: 54: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/A.pdb. 54: 54: The Oplsaa force field and the tip4p water model are used. 54: 54: --------- ETON ESAELP ------------ 54: [ OK ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip4p_vsite_none_id_or_ter_merge_no_Apdb_format_gro_match_file (211 ms) 54: [ RUN ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip4p_vsite_none_id_or_ter_merge_no_Bpdb_format_gro_match_file 54: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/oplsaa.ff/aminoacids.r2b 54: All occupancies are one 54: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/oplsaa.ff/atomtypes.atp 54: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/oplsaa.ff/aminoacids.rtp 54: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/oplsaa.ff/aminoacids.hdb 54: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/oplsaa.ff/aminoacids.n.tdb 54: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/oplsaa.ff/aminoacids.c.tdb 54: Analysing hydrogen-bonding network for automated assignment of histidine 54: protonation. 30 donors and 22 acceptors were found. 54: There are 36 hydrogen bonds 54: Will use HISE for residue 29 54: Will use HISE for residue 32 54: 9 out of 9 lines of specbond.dat converted successfully 54: Special Atom Distance matrix: 54: CYS27 HIS29 54: SG90 NE2111 54: HIS29 NE2111 0.987 54: HIS32 NE2135 1.590 1.155 54: Before cleaning: 748 pairs 54: Before cleaning: 778 dihedrals 54: Using the Oplsaa force field in directory oplsaa.ff 54: 54: going to rename oplsaa.ff/aminoacids.r2b 54: Reading /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/B.pdb... 54: Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms 54: 54: Analyzing pdb file 54: Splitting chemical chains based on TER records or chain id changing. 54: 54: There are 1 chains and 0 blocks of water and 16 residues with 149 atoms 54: 54: chain #res #atoms 54: 54: 1 ' ' 16 149 54: 54: All occupancies are one 54: 54: Reading residue database... (Oplsaa) 54: 54: Processing chain 1 (149 atoms, 16 residues) 54: 54: Replaced 1 residue named GLUH to the default GLU. Use interactive selection of protonated residues if that is what you need. 54: 54: Identified residue THR18 as a starting terminus. 54: 54: Identified residue PHE33 as a ending terminus. 54: Start terminus THR-18: NH3+ 54: End terminus PHE-33: COO- 54: 54: Checking for duplicate atoms.... 54: 54: Generating any missing hydrogen atoms and/or adding termini. 54: 54: Now there are 16 residues with 281 atoms 54: 54: Making bonds... 54: 54: Number of bonds was 290, now 290 54: 54: Generating angles, dihedrals and pairs... 54: 54: Making cmap torsions... 54: 54: There are 778 dihedrals, 72 impropers, 516 angles 54: 736 pairs, 290 bonds and 0 virtual sites 54: 54: Total mass 2088.357 a.m.u. 54: 54: Total charge 1.000 e 54: 54: Writing topology 54: 54: Writing coordinate file... 54: 54: --------- PLEASE NOTE ------------ 54: 54: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/B.pdb. 54: 54: The Oplsaa force field and the tip4p water model are used. 54: 54: --------- ETON ESAELP ------------ 54: [ OK ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip4p_vsite_none_id_or_ter_merge_no_Bpdb_format_gro_match_file (219 ms) 54: [ RUN ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip4p_vsite_none_id_or_ter_merge_no_Cpdb_format_gro_match_file 54: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/oplsaa.ff/aminoacids.r2b 54: All occupancies are one 54: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/oplsaa.ff/atomtypes.atp 54: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/oplsaa.ff/aminoacids.rtp 54: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/oplsaa.ff/aminoacids.hdb 54: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/oplsaa.ff/aminoacids.n.tdb 54: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/oplsaa.ff/aminoacids.c.tdb 54: Analysing hydrogen-bonding network for automated assignment of histidine 54: protonation. 22 donors and 22 acceptors were found. 54: There are 26 hydrogen bonds 54: Will use HISE for residue 45 54: 9 out of 9 lines of specbond.dat converted successfully 54: Special Atom Distance matrix: 54: HIS45 54: NE295 54: MET46 SD102 1.078 54: Before cleaning: 676 pairs 54: Before cleaning: 696 dihedrals 54: Using the Oplsaa force field in directory oplsaa.ff 54: 54: going to rename oplsaa.ff/aminoacids.r2b 54: Reading /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/C.pdb... 54: Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms 54: 54: Analyzing pdb file 54: Splitting chemical chains based on TER records or chain id changing. 54: 54: There are 1 chains and 0 blocks of water and 16 residues with 132 atoms 54: 54: chain #res #atoms 54: 54: 1 ' ' 16 132 54: 54: All occupancies are one 54: 54: Reading residue database... (Oplsaa) 54: 54: Processing chain 1 (132 atoms, 16 residues) 54: 54: Identified residue ALA34 as a starting terminus. 54: 54: Identified residue ALA49 as a ending terminus. 54: Start terminus ALA-34: NH3+ 54: End terminus ALA-49: COO- 54: 54: Checking for duplicate atoms.... 54: 54: Generating any missing hydrogen atoms and/or adding termini. 54: 54: Now there are 16 residues with 255 atoms 54: 54: Making bonds... 54: 54: Number of bonds was 261, now 261 54: 54: Generating angles, dihedrals and pairs... 54: 54: Making cmap torsions... 54: 54: There are 696 dihedrals, 56 impropers, 472 angles 54: 667 pairs, 261 bonds and 0 virtual sites 54: 54: Total mass 1861.128 a.m.u. 54: 54: Total charge -1.000 e 54: 54: Writing topology 54: 54: Writing coordinate file... 54: 54: --------- PLEASE NOTE ------------ 54: 54: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/C.pdb. 54: 54: The Oplsaa force field and the tip4p water model are used. 54: 54: --------- ETON ESAELP ------------ 54: [ OK ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip4p_vsite_none_id_or_ter_merge_no_Cpdb_format_gro_match_file (217 ms) 54: [ RUN ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip4p_vsite_none_id_or_ter_merge_no_Dpdb_format_gro_match_file 54: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/oplsaa.ff/aminoacids.r2b 54: All occupancies are one 54: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/oplsaa.ff/atomtypes.atp 54: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/oplsaa.ff/aminoacids.rtp 54: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/oplsaa.ff/aminoacids.hdb 54: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/oplsaa.ff/aminoacids.n.tdb 54: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/oplsaa.ff/aminoacids.c.tdb 54: Analysing hydrogen-bonding network for automated assignment of histidine 54: protonation. 22 donors and 21 acceptors were found. 54: There are 30 hydrogen bonds 54: Will use HISE for residue 60 54: 9 out of 9 lines of specbond.dat converted successfully 54: Special Atom Distance matrix: 54: HIS60 54: NE285 54: CYS62 SG98 0.803 54: Before cleaning: 603 pairs 54: Before cleaning: 618 dihedrals 54: Using the Oplsaa force field in directory oplsaa.ff 54: 54: going to rename oplsaa.ff/aminoacids.r2b 54: Reading /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/D.pdb... 54: Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms 54: 54: Analyzing pdb file 54: Splitting chemical chains based on TER records or chain id changing. 54: 54: There are 1 chains and 0 blocks of water and 16 residues with 117 atoms 54: 54: chain #res #atoms 54: 54: 1 ' ' 16 117 54: 54: All occupancies are one 54: 54: Reading residue database... (Oplsaa) 54: 54: Processing chain 1 (117 atoms, 16 residues) 54: 54: Replaced 1 residue named ASPH to the default ASP. Use interactive selection of protonated residues if that is what you need. 54: 54: Identified residue LYS50 as a starting terminus. 54: 54: Identified residue PRO65 as a ending terminus. 54: Start terminus LYS-50: NH3+ 54: End terminus PRO-65: PRO-COO- 54: 54: Checking for duplicate atoms.... 54: 54: Generating any missing hydrogen atoms and/or adding termini. 54: 54: Now there are 16 residues with 228 atoms 54: 54: Making bonds... 54: 54: Number of bonds was 232, now 232 54: 54: Generating angles, dihedrals and pairs... 54: 54: Making cmap torsions... 54: 54: There are 618 dihedrals, 48 impropers, 419 angles 54: 597 pairs, 232 bonds and 0 virtual sites 54: 54: Total mass 1662.883 a.m.u. 54: 54: Total charge -0.000 e 54: 54: Writing topology 54: 54: Writing coordinate file... 54: 54: --------- PLEASE NOTE ------------ 54: 54: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/D.pdb. 54: 54: The Oplsaa force field and the tip4p water model are used. 54: 54: --------- ETON ESAELP ------------ 54: [ OK ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip4p_vsite_none_id_or_ter_merge_no_Dpdb_format_gro_match_file (207 ms) 54: [ RUN ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip4p_vsite_none_id_or_ter_merge_no_Epdb_format_gro_match_file 54: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/oplsaa.ff/aminoacids.r2b 54: All occupancies are one 54: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/oplsaa.ff/atomtypes.atp 54: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/oplsaa.ff/aminoacids.rtp 54: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/oplsaa.ff/aminoacids.hdb 54: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/oplsaa.ff/aminoacids.n.tdb 54: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/oplsaa.ff/aminoacids.c.tdb 54: Analysing hydrogen-bonding network for automated assignment of histidine 54: protonation. 89 donors and 98 acceptors were found. 54: There are 129 hydrogen bonds 54: Will use HISE for residue 31 54: Will use HISE for residue 51 54: 9 out of 9 lines of specbond.dat converted successfully 54: Special Atom Distance matrix: 54: CYS25 HIS31 HIS51 54: SG14 NE264 NE2226 54: HIS31 NE264 1.921 54: HIS51 NE2226 1.498 2.650 54: CYS80 SG477 0.207 1.984 1.570 54: Linking CYS-25 SG-14 and CYS-80 SG-477... 54: Before cleaning: 2499 pairs 54: Before cleaning: 2524 dihedrals 54: Using the Oplsaa force field in directory oplsaa.ff 54: 54: going to rename oplsaa.ff/aminoacids.r2b 54: Reading /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/E.pdb... 54: Read 'This is a fragment of 2d4f for testing a disulfide bridge', 488 atoms 54: 54: Analyzing pdb file 54: Splitting chemical chains based on TER records or chain id changing. 54: 54: There are 1 chains and 0 blocks of water and 58 residues with 488 atoms 54: 54: chain #res #atoms 54: 54: 1 'A' 58 488 54: 54: All occupancies are one 54: 54: Reading residue database... (Oplsaa) 54: 54: Processing chain 1 'A' (488 atoms, 58 residues) 54: 54: Identified residue ASN24 as a starting terminus. 54: 54: Identified residue ARG81 as a ending terminus. 54: Start terminus ASN-24: NH3+ 54: End terminus ARG-81: COO- 54: 54: Checking for duplicate atoms.... 54: 54: Generating any missing hydrogen atoms and/or adding termini. 54: 54: Now there are 58 residues with 936 atoms 54: 54: Making bonds... 54: 54: Number of bonds was 951, now 951 54: 54: Generating angles, dihedrals and pairs... 54: 54: Making cmap torsions... 54: 54: There are 2524 dihedrals, 208 impropers, 1704 angles 54: 2469 pairs, 951 bonds and 0 virtual sites 54: 54: Total mass 6908.578 a.m.u. 54: 54: Total charge -6.000 e 54: 54: Writing topology 54: 54: Writing coordinate file... 54: 54: --------- PLEASE NOTE ------------ 54: 54: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/E.pdb. 54: 54: The Oplsaa force field and the tip4p water model are used. 54: 54: --------- ETON ESAELP ------------ 54: [ OK ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip4p_vsite_none_id_or_ter_merge_no_Epdb_format_gro_match_file (624 ms) 54: [ RUN ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip4p_vsite_h_id_or_ter_merge_no_Apdb_format_gro_match_file 54: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/oplsaa.ff/aminoacids.r2b 54: All occupancies are one 54: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/oplsaa.ff/atomtypes.atp 54: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/oplsaa.ff/aminoacids.rtp 54: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/oplsaa.ff/aminoacids.hdb 54: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/oplsaa.ff/aminoacids.n.tdb 54: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/oplsaa.ff/aminoacids.c.tdb 54: Analysing hydrogen-bonding network for automated assignment of histidine 54: protonation. 25 donors and 23 acceptors were found. 54: There are 41 hydrogen bonds 54: Will use HISE for residue 8 54: 9 out of 9 lines of specbond.dat converted successfully 54: Special Atom Distance matrix: 54: CYS3 HIS8 54: SG9 NE251 54: HIS8 NE251 1.055 54: MET12 SD83 0.763 0.990 54: Marked 124 virtual sites 54: Added 16 dummy masses 54: Added 26 new constraints 54: Before cleaning: 653 pairs 54: Before cleaning: 663 dihedrals 54: Using the Oplsaa force field in directory oplsaa.ff 54: 54: going to rename oplsaa.ff/aminoacids.r2b 54: Reading /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/A.pdb... 54: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms 54: 54: Analyzing pdb file 54: Splitting chemical chains based on TER records or chain id changing. 54: 54: There are 1 chains and 0 blocks of water and 16 residues with 128 atoms 54: 54: chain #res #atoms 54: 54: 1 ' ' 16 128 54: 54: All occupancies are one 54: 54: Reading residue database... (Oplsaa) 54: 54: Processing chain 1 (128 atoms, 16 residues) 54: 54: Identified residue ALA2 as a starting terminus. 54: 54: Identified residue SER17 as a ending terminus. 54: Start terminus ALA-2: NH3+ 54: End terminus SER-17: COO- 54: 54: Checking for duplicate atoms.... 54: 54: Generating any missing hydrogen atoms and/or adding termini. 54: 54: Now there are 16 residues with 252 atoms 54: 54: Making bonds... 54: 54: Number of bonds was 254, now 254 54: 54: Generating angles, dihedrals and pairs... 54: 54: Making cmap torsions... 54: 54: There are 663 dihedrals, 51 impropers, 457 angles 54: 650 pairs, 254 bonds and 130 virtual sites 54: 54: Total mass 1846.112 a.m.u. 54: 54: Total charge -0.000 e 54: 54: Writing topology 54: 54: Writing coordinate file... 54: 54: --------- PLEASE NOTE ------------ 54: 54: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/A.pdb. 54: 54: The Oplsaa force field and the tip4p water model are used. 54: 54: --------- ETON ESAELP ------------ 54: [ OK ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip4p_vsite_h_id_or_ter_merge_no_Apdb_format_gro_match_file (226 ms) 54: [ RUN ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip4p_vsite_h_id_or_ter_merge_no_Bpdb_format_gro_match_file 54: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/oplsaa.ff/aminoacids.r2b 54: All occupancies are one 54: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/oplsaa.ff/atomtypes.atp 54: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/oplsaa.ff/aminoacids.rtp 54: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/oplsaa.ff/aminoacids.hdb 54: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/oplsaa.ff/aminoacids.n.tdb 54: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/oplsaa.ff/aminoacids.c.tdb 54: Analysing hydrogen-bonding network for automated assignment of histidine 54: protonation. 30 donors and 22 acceptors were found. 54: There are 36 hydrogen bonds 54: Will use HISE for residue 29 54: Will use HISE for residue 32 54: 9 out of 9 lines of specbond.dat converted successfully 54: Special Atom Distance matrix: 54: CYS27 HIS29 54: SG90 NE2111 54: HIS29 NE2111 0.987 54: HIS32 NE2135 1.590 1.155 54: Marked 132 virtual sites 54: Added 10 dummy masses 54: Added 19 new constraints 54: Before cleaning: 748 pairs 54: Before cleaning: 778 dihedrals 54: Using the Oplsaa force field in directory oplsaa.ff 54: 54: going to rename oplsaa.ff/aminoacids.r2b 54: Reading /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/B.pdb... 54: Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms 54: 54: Analyzing pdb file 54: Splitting chemical chains based on TER records or chain id changing. 54: 54: There are 1 chains and 0 blocks of water and 16 residues with 149 atoms 54: 54: chain #res #atoms 54: 54: 1 ' ' 16 149 54: 54: All occupancies are one 54: 54: Reading residue database... (Oplsaa) 54: 54: Processing chain 1 (149 atoms, 16 residues) 54: 54: Replaced 1 residue named GLUH to the default GLU. Use interactive selection of protonated residues if that is what you need. 54: 54: Identified residue THR18 as a starting terminus. 54: 54: Identified residue PHE33 as a ending terminus. 54: Start terminus THR-18: NH3+ 54: End terminus PHE-33: COO- 54: 54: Checking for duplicate atoms.... 54: 54: Generating any missing hydrogen atoms and/or adding termini. 54: 54: Now there are 16 residues with 281 atoms 54: 54: Making bonds... 54: 54: Number of bonds was 290, now 290 54: 54: Generating angles, dihedrals and pairs... 54: 54: Making cmap torsions... 54: 54: There are 778 dihedrals, 72 impropers, 516 angles 54: 736 pairs, 290 bonds and 133 virtual sites 54: 54: Total mass 2088.357 a.m.u. 54: 54: Total charge 1.000 e 54: 54: Writing topology 54: 54: Writing coordinate file... 54: 54: --------- PLEASE NOTE ------------ 54: 54: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/B.pdb. 54: 54: The Oplsaa force field and the tip4p water model are used. 54: 54: --------- ETON ESAELP ------------ 54: [ OK ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip4p_vsite_h_id_or_ter_merge_no_Bpdb_format_gro_match_file (253 ms) 54: [ RUN ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip4p_vsite_h_id_or_ter_merge_no_Cpdb_format_gro_match_file 54: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/oplsaa.ff/aminoacids.r2b 54: All occupancies are one 54: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/oplsaa.ff/atomtypes.atp 54: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/oplsaa.ff/aminoacids.rtp 54: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/oplsaa.ff/aminoacids.hdb 54: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/oplsaa.ff/aminoacids.n.tdb 54: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/oplsaa.ff/aminoacids.c.tdb 54: Analysing hydrogen-bonding network for automated assignment of histidine 54: protonation. 22 donors and 22 acceptors were found. 54: There are 26 hydrogen bonds 54: Will use HISE for residue 45 54: 9 out of 9 lines of specbond.dat converted successfully 54: Special Atom Distance matrix: 54: HIS45 54: NE295 54: MET46 SD102 1.078 54: Marked 123 virtual sites 54: Added 22 dummy masses 54: Added 35 new constraints 54: Before cleaning: 676 pairs 54: Before cleaning: 696 dihedrals 54: Using the Oplsaa force field in directory oplsaa.ff 54: 54: going to rename oplsaa.ff/aminoacids.r2b 54: Reading /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/C.pdb... 54: Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms 54: 54: Analyzing pdb file 54: Splitting chemical chains based on TER records or chain id changing. 54: 54: There are 1 chains and 0 blocks of water and 16 residues with 132 atoms 54: 54: chain #res #atoms 54: 54: 1 ' ' 16 132 54: 54: All occupancies are one 54: 54: Reading residue database... (Oplsaa) 54: 54: Processing chain 1 (132 atoms, 16 residues) 54: 54: Identified residue ALA34 as a starting terminus. 54: 54: Identified residue ALA49 as a ending terminus. 54: Start terminus ALA-34: NH3+ 54: End terminus ALA-49: COO- 54: 54: Checking for duplicate atoms.... 54: 54: Generating any missing hydrogen atoms and/or adding termini. 54: 54: Now there are 16 residues with 255 atoms 54: 54: Making bonds... 54: 54: Number of bonds was 261, now 261 54: 54: Generating angles, dihedrals and pairs... 54: 54: Making cmap torsions... 54: 54: There are 696 dihedrals, 56 impropers, 472 angles 54: 667 pairs, 261 bonds and 132 virtual sites 54: 54: Total mass 1861.128 a.m.u. 54: 54: Total charge -1.000 e 54: 54: Writing topology 54: 54: Writing coordinate file... 54: 54: --------- PLEASE NOTE ------------ 54: 54: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/C.pdb. 54: 54: The Oplsaa force field and the tip4p water model are used. 54: 54: --------- ETON ESAELP ------------ 54: [ OK ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip4p_vsite_h_id_or_ter_merge_no_Cpdb_format_gro_match_file (237 ms) 54: [ RUN ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip4p_vsite_h_id_or_ter_merge_no_Dpdb_format_gro_match_file 54: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/oplsaa.ff/aminoacids.r2b 54: All occupancies are one 54: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/oplsaa.ff/atomtypes.atp 54: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/oplsaa.ff/aminoacids.rtp 54: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/oplsaa.ff/aminoacids.hdb 54: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/oplsaa.ff/aminoacids.n.tdb 54: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/oplsaa.ff/aminoacids.c.tdb 54: Analysing hydrogen-bonding network for automated assignment of histidine 54: protonation. 22 donors and 21 acceptors were found. 54: There are 30 hydrogen bonds 54: Will use HISE for residue 60 54: 9 out of 9 lines of specbond.dat converted successfully 54: Special Atom Distance matrix: 54: HIS60 54: NE285 54: CYS62 SG98 0.803 54: Marked 111 virtual sites 54: Added 18 dummy masses 54: Added 31 new constraints 54: Before cleaning: 603 pairs 54: Before cleaning: 618 dihedrals 54: Using the Oplsaa force field in directory oplsaa.ff 54: 54: going to rename oplsaa.ff/aminoacids.r2b 54: Reading /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/D.pdb... 54: Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms 54: 54: Analyzing pdb file 54: Splitting chemical chains based on TER records or chain id changing. 54: 54: There are 1 chains and 0 blocks of water and 16 residues with 117 atoms 54: 54: chain #res #atoms 54: 54: 1 ' ' 16 117 54: 54: All occupancies are one 54: 54: Reading residue database... (Oplsaa) 54: 54: Processing chain 1 (117 atoms, 16 residues) 54: 54: Replaced 1 residue named ASPH to the default ASP. Use interactive selection of protonated residues if that is what you need. 54: 54: Identified residue LYS50 as a starting terminus. 54: 54: Identified residue PRO65 as a ending terminus. 54: Start terminus LYS-50: NH3+ 54: End terminus PRO-65: PRO-COO- 54: 54: Checking for duplicate atoms.... 54: 54: Generating any missing hydrogen atoms and/or adding termini. 54: 54: Now there are 16 residues with 228 atoms 54: 54: Making bonds... 54: 54: Number of bonds was 232, now 232 54: 54: Generating angles, dihedrals and pairs... 54: 54: Making cmap torsions... 54: 54: There are 618 dihedrals, 48 impropers, 419 angles 54: 597 pairs, 232 bonds and 116 virtual sites 54: 54: Total mass 1662.883 a.m.u. 54: 54: Total charge -0.000 e 54: 54: Writing topology 54: 54: Writing coordinate file... 54: 54: --------- PLEASE NOTE ------------ 54: 54: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/D.pdb. 54: 54: The Oplsaa force field and the tip4p water model are used. 54: 54: --------- ETON ESAELP ------------ 54: [ OK ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip4p_vsite_h_id_or_ter_merge_no_Dpdb_format_gro_match_file (207 ms) 54: [ RUN ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip4p_vsite_h_id_or_ter_merge_no_Epdb_format_gro_match_file 54: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/oplsaa.ff/aminoacids.r2b 54: All occupancies are one 54: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/oplsaa.ff/atomtypes.atp 54: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/oplsaa.ff/aminoacids.rtp 54: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/oplsaa.ff/aminoacids.hdb 54: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/oplsaa.ff/aminoacids.n.tdb 54: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/oplsaa.ff/aminoacids.c.tdb 54: Analysing hydrogen-bonding network for automated assignment of histidine 54: protonation. 89 donors and 98 acceptors were found. 54: There are 129 hydrogen bonds 54: Will use HISE for residue 31 54: Will use HISE for residue 51 54: 9 out of 9 lines of specbond.dat converted successfully 54: Special Atom Distance matrix: 54: CYS25 HIS31 HIS51 54: SG14 NE264 NE2226 54: HIS31 NE264 1.921 54: HIS51 NE2226 1.498 2.650 54: CYS80 SG477 0.207 1.984 1.570 54: Linking CYS-25 SG-14 and CYS-80 SG-477... 54: Marked 447 virtual sites 54: Added 58 dummy masses 54: Added 101 new constraints 54: Before cleaning: 2499 pairs 54: Before cleaning: 2524 dihedrals 54: Using the Oplsaa force field in directory oplsaa.ff 54: 54: going to rename oplsaa.ff/aminoacids.r2b 54: Reading /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/E.pdb... 54: Read 'This is a fragment of 2d4f for testing a disulfide bridge', 488 atoms 54: 54: Analyzing pdb file 54: Splitting chemical chains based on TER records or chain id changing. 54: 54: There are 1 chains and 0 blocks of water and 58 residues with 488 atoms 54: 54: chain #res #atoms 54: 54: 1 'A' 58 488 54: 54: All occupancies are one 54: 54: Reading residue database... (Oplsaa) 54: 54: Processing chain 1 'A' (488 atoms, 58 residues) 54: 54: Identified residue ASN24 as a starting terminus. 54: 54: Identified residue ARG81 as a ending terminus. 54: Start terminus ASN-24: NH3+ 54: End terminus ARG-81: COO- 54: 54: Checking for duplicate atoms.... 54: 54: Generating any missing hydrogen atoms and/or adding termini. 54: 54: Now there are 58 residues with 936 atoms 54: 54: Making bonds... 54: 54: Number of bonds was 951, now 951 54: 54: Generating angles, dihedrals and pairs... 54: 54: Making cmap torsions... 54: 54: There are 2524 dihedrals, 208 impropers, 1704 angles 54: 2469 pairs, 951 bonds and 462 virtual sites 54: 54: Total mass 6908.578 a.m.u. 54: 54: Total charge -6.000 e 54: 54: Writing topology 54: 54: Writing coordinate file... 54: 54: --------- PLEASE NOTE ------------ 54: 54: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/E.pdb. 54: 54: The Oplsaa force field and the tip4p water model are used. 54: 54: --------- ETON ESAELP ------------ 54: [ OK ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip4p_vsite_h_id_or_ter_merge_no_Epdb_format_gro_match_file (684 ms) 54: [ RUN ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip5p_vsite_none_id_or_ter_merge_no_Apdb_format_gro_match_file 54: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/oplsaa.ff/aminoacids.r2b 54: All occupancies are one 54: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/oplsaa.ff/atomtypes.atp 54: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/oplsaa.ff/aminoacids.rtp 54: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/oplsaa.ff/aminoacids.hdb 54: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/oplsaa.ff/aminoacids.n.tdb 54: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/oplsaa.ff/aminoacids.c.tdb 54: Analysing hydrogen-bonding network for automated assignment of histidine 54: protonation. 25 donors and 23 acceptors were found. 54: There are 41 hydrogen bonds 54: Will use HISE for residue 8 54: 9 out of 9 lines of specbond.dat converted successfully 54: Special Atom Distance matrix: 54: CYS3 HIS8 54: SG9 NE251 54: HIS8 NE251 1.055 54: MET12 SD83 0.763 0.990 54: Before cleaning: 653 pairs 54: Before cleaning: 663 dihedrals 54: Using the Oplsaa force field in directory oplsaa.ff 54: 54: going to rename oplsaa.ff/aminoacids.r2b 54: Reading /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/A.pdb... 54: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms 54: 54: Analyzing pdb file 54: Splitting chemical chains based on TER records or chain id changing. 54: 54: There are 1 chains and 0 blocks of water and 16 residues with 128 atoms 54: 54: chain #res #atoms 54: 54: 1 ' ' 16 128 54: 54: All occupancies are one 54: 54: Reading residue database... (Oplsaa) 54: 54: Processing chain 1 (128 atoms, 16 residues) 54: 54: Identified residue ALA2 as a starting terminus. 54: 54: Identified residue SER17 as a ending terminus. 54: Start terminus ALA-2: NH3+ 54: End terminus SER-17: COO- 54: 54: Checking for duplicate atoms.... 54: 54: Generating any missing hydrogen atoms and/or adding termini. 54: 54: Now there are 16 residues with 252 atoms 54: 54: Making bonds... 54: 54: Number of bonds was 254, now 254 54: 54: Generating angles, dihedrals and pairs... 54: 54: Making cmap torsions... 54: 54: There are 663 dihedrals, 51 impropers, 457 angles 54: 650 pairs, 254 bonds and 0 virtual sites 54: 54: Total mass 1846.112 a.m.u. 54: 54: Total charge -0.000 e 54: 54: Writing topology 54: 54: Writing coordinate file... 54: 54: --------- PLEASE NOTE ------------ 54: 54: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/A.pdb. 54: 54: The Oplsaa force field and the tip5p water model are used. 54: 54: --------- ETON ESAELP ------------ 54: [ OK ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip5p_vsite_none_id_or_ter_merge_no_Apdb_format_gro_match_file (210 ms) 54: [ RUN ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip5p_vsite_none_id_or_ter_merge_no_Bpdb_format_gro_match_file 54: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/oplsaa.ff/aminoacids.r2b 54: All occupancies are one 54: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/oplsaa.ff/atomtypes.atp 54: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/oplsaa.ff/aminoacids.rtp 54: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/oplsaa.ff/aminoacids.hdb 54: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/oplsaa.ff/aminoacids.n.tdb 54: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/oplsaa.ff/aminoacids.c.tdb 54: Analysing hydrogen-bonding network for automated assignment of histidine 54: protonation. 30 donors and 22 acceptors were found. 54: There are 36 hydrogen bonds 54: Will use HISE for residue 29 54: Will use HISE for residue 32 54: 9 out of 9 lines of specbond.dat converted successfully 54: Special Atom Distance matrix: 54: CYS27 HIS29 54: SG90 NE2111 54: HIS29 NE2111 0.987 54: HIS32 NE2135 1.590 1.155 54: Before cleaning: 748 pairs 54: Before cleaning: 778 dihedrals 54: Using the Oplsaa force field in directory oplsaa.ff 54: 54: going to rename oplsaa.ff/aminoacids.r2b 54: Reading /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/B.pdb... 54: Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms 54: 54: Analyzing pdb file 54: Splitting chemical chains based on TER records or chain id changing. 54: 54: There are 1 chains and 0 blocks of water and 16 residues with 149 atoms 54: 54: chain #res #atoms 54: 54: 1 ' ' 16 149 54: 54: All occupancies are one 54: 54: Reading residue database... (Oplsaa) 54: 54: Processing chain 1 (149 atoms, 16 residues) 54: 54: Replaced 1 residue named GLUH to the default GLU. Use interactive selection of protonated residues if that is what you need. 54: 54: Identified residue THR18 as a starting terminus. 54: 54: Identified residue PHE33 as a ending terminus. 54: Start terminus THR-18: NH3+ 54: End terminus PHE-33: COO- 54: 54: Checking for duplicate atoms.... 54: 54: Generating any missing hydrogen atoms and/or adding termini. 54: 54: Now there are 16 residues with 281 atoms 54: 54: Making bonds... 54: 54: Number of bonds was 290, now 290 54: 54: Generating angles, dihedrals and pairs... 54: 54: Making cmap torsions... 54: 54: There are 778 dihedrals, 72 impropers, 516 angles 54: 736 pairs, 290 bonds and 0 virtual sites 54: 54: Total mass 2088.357 a.m.u. 54: 54: Total charge 1.000 e 54: 54: Writing topology 54: 54: Writing coordinate file... 54: 54: --------- PLEASE NOTE ------------ 54: 54: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/B.pdb. 54: 54: The Oplsaa force field and the tip5p water model are used. 54: 54: --------- ETON ESAELP ------------ 54: [ OK ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip5p_vsite_none_id_or_ter_merge_no_Bpdb_format_gro_match_file (231 ms) 54: [ RUN ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip5p_vsite_none_id_or_ter_merge_no_Cpdb_format_gro_match_file 54: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/oplsaa.ff/aminoacids.r2b 54: All occupancies are one 54: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/oplsaa.ff/atomtypes.atp 54: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/oplsaa.ff/aminoacids.rtp 54: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/oplsaa.ff/aminoacids.hdb 54: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/oplsaa.ff/aminoacids.n.tdb 54: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/oplsaa.ff/aminoacids.c.tdb 54: Analysing hydrogen-bonding network for automated assignment of histidine 54: protonation. 22 donors and 22 acceptors were found. 54: There are 26 hydrogen bonds 54: Will use HISE for residue 45 54: 9 out of 9 lines of specbond.dat converted successfully 54: Special Atom Distance matrix: 54: HIS45 54: NE295 54: MET46 SD102 1.078 54: Before cleaning: 676 pairs 54: Before cleaning: 696 dihedrals 54: Using the Oplsaa force field in directory oplsaa.ff 54: 54: going to rename oplsaa.ff/aminoacids.r2b 54: Reading /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/C.pdb... 54: Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms 54: 54: Analyzing pdb file 54: Splitting chemical chains based on TER records or chain id changing. 54: 54: There are 1 chains and 0 blocks of water and 16 residues with 132 atoms 54: 54: chain #res #atoms 54: 54: 1 ' ' 16 132 54: 54: All occupancies are one 54: 54: Reading residue database... (Oplsaa) 54: 54: Processing chain 1 (132 atoms, 16 residues) 54: 54: Identified residue ALA34 as a starting terminus. 54: 54: Identified residue ALA49 as a ending terminus. 54: Start terminus ALA-34: NH3+ 54: End terminus ALA-49: COO- 54: 54: Checking for duplicate atoms.... 54: 54: Generating any missing hydrogen atoms and/or adding termini. 54: 54: Now there are 16 residues with 255 atoms 54: 54: Making bonds... 54: 54: Number of bonds was 261, now 261 54: 54: Generating angles, dihedrals and pairs... 54: 54: Making cmap torsions... 54: 54: There are 696 dihedrals, 56 impropers, 472 angles 54: 667 pairs, 261 bonds and 0 virtual sites 54: 54: Total mass 1861.128 a.m.u. 54: 54: Total charge -1.000 e 54: 54: Writing topology 54: 54: Writing coordinate file... 54: 54: --------- PLEASE NOTE ------------ 54: 54: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/C.pdb. 54: 54: The Oplsaa force field and the tip5p water model are used. 54: 54: --------- ETON ESAELP ------------ 54: [ OK ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip5p_vsite_none_id_or_ter_merge_no_Cpdb_format_gro_match_file (220 ms) 54: [ RUN ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip5p_vsite_none_id_or_ter_merge_no_Dpdb_format_gro_match_file 54: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/oplsaa.ff/aminoacids.r2b 54: All occupancies are one 54: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/oplsaa.ff/atomtypes.atp 54: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/oplsaa.ff/aminoacids.rtp 54: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/oplsaa.ff/aminoacids.hdb 54: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/oplsaa.ff/aminoacids.n.tdb 54: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/oplsaa.ff/aminoacids.c.tdb 54: Analysing hydrogen-bonding network for automated assignment of histidine 54: protonation. 22 donors and 21 acceptors were found. 54: There are 30 hydrogen bonds 54: Will use HISE for residue 60 54: 9 out of 9 lines of specbond.dat converted successfully 54: Special Atom Distance matrix: 54: HIS60 54: NE285 54: CYS62 SG98 0.803 54: Before cleaning: 603 pairs 54: Before cleaning: 618 dihedrals 54: Using the Oplsaa force field in directory oplsaa.ff 54: 54: going to rename oplsaa.ff/aminoacids.r2b 54: Reading /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/D.pdb... 54: Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms 54: 54: Analyzing pdb file 54: Splitting chemical chains based on TER records or chain id changing. 54: 54: There are 1 chains and 0 blocks of water and 16 residues with 117 atoms 54: 54: chain #res #atoms 54: 54: 1 ' ' 16 117 54: 54: All occupancies are one 54: 54: Reading residue database... (Oplsaa) 54: 54: Processing chain 1 (117 atoms, 16 residues) 54: 54: Replaced 1 residue named ASPH to the default ASP. Use interactive selection of protonated residues if that is what you need. 54: 54: Identified residue LYS50 as a starting terminus. 54: 54: Identified residue PRO65 as a ending terminus. 54: Start terminus LYS-50: NH3+ 54: End terminus PRO-65: PRO-COO- 54: 54: Checking for duplicate atoms.... 54: 54: Generating any missing hydrogen atoms and/or adding termini. 54: 54: Now there are 16 residues with 228 atoms 54: 54: Making bonds... 54: 54: Number of bonds was 232, now 232 54: 54: Generating angles, dihedrals and pairs... 54: 54: Making cmap torsions... 54: 54: There are 618 dihedrals, 48 impropers, 419 angles 54: 597 pairs, 232 bonds and 0 virtual sites 54: 54: Total mass 1662.883 a.m.u. 54: 54: Total charge -0.000 e 54: 54: Writing topology 54: 54: Writing coordinate file... 54: 54: --------- PLEASE NOTE ------------ 54: 54: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/D.pdb. 54: 54: The Oplsaa force field and the tip5p water model are used. 54: 54: --------- ETON ESAELP ------------ 54: [ OK ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip5p_vsite_none_id_or_ter_merge_no_Dpdb_format_gro_match_file (199 ms) 54: [ RUN ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip5p_vsite_none_id_or_ter_merge_no_Epdb_format_gro_match_file 54: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/oplsaa.ff/aminoacids.r2b 54: All occupancies are one 54: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/oplsaa.ff/atomtypes.atp 54: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/oplsaa.ff/aminoacids.rtp 54: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/oplsaa.ff/aminoacids.hdb 54: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/oplsaa.ff/aminoacids.n.tdb 54: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/oplsaa.ff/aminoacids.c.tdb 54: Analysing hydrogen-bonding network for automated assignment of histidine 54: protonation. 89 donors and 98 acceptors were found. 54: There are 129 hydrogen bonds 54: Will use HISE for residue 31 54: Will use HISE for residue 51 54: 9 out of 9 lines of specbond.dat converted successfully 54: Special Atom Distance matrix: 54: CYS25 HIS31 HIS51 54: SG14 NE264 NE2226 54: HIS31 NE264 1.921 54: HIS51 NE2226 1.498 2.650 54: CYS80 SG477 0.207 1.984 1.570 54: Linking CYS-25 SG-14 and CYS-80 SG-477... 54: Before cleaning: 2499 pairs 54: Before cleaning: 2524 dihedrals 54: Using the Oplsaa force field in directory oplsaa.ff 54: 54: going to rename oplsaa.ff/aminoacids.r2b 54: Reading /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/E.pdb... 54: Read 'This is a fragment of 2d4f for testing a disulfide bridge', 488 atoms 54: 54: Analyzing pdb file 54: Splitting chemical chains based on TER records or chain id changing. 54: 54: There are 1 chains and 0 blocks of water and 58 residues with 488 atoms 54: 54: chain #res #atoms 54: 54: 1 'A' 58 488 54: 54: All occupancies are one 54: 54: Reading residue database... (Oplsaa) 54: 54: Processing chain 1 'A' (488 atoms, 58 residues) 54: 54: Identified residue ASN24 as a starting terminus. 54: 54: Identified residue ARG81 as a ending terminus. 54: Start terminus ASN-24: NH3+ 54: End terminus ARG-81: COO- 54: 54: Checking for duplicate atoms.... 54: 54: Generating any missing hydrogen atoms and/or adding termini. 54: 54: Now there are 58 residues with 936 atoms 54: 54: Making bonds... 54: 54: Number of bonds was 951, now 951 54: 54: Generating angles, dihedrals and pairs... 54: 54: Making cmap torsions... 54: 54: There are 2524 dihedrals, 208 impropers, 1704 angles 54: 2469 pairs, 951 bonds and 0 virtual sites 54: 54: Total mass 6908.578 a.m.u. 54: 54: Total charge -6.000 e 54: 54: Writing topology 54: 54: Writing coordinate file... 54: 54: --------- PLEASE NOTE ------------ 54: 54: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/E.pdb. 54: 54: The Oplsaa force field and the tip5p water model are used. 54: 54: --------- ETON ESAELP ------------ 54: [ OK ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip5p_vsite_none_id_or_ter_merge_no_Epdb_format_gro_match_file (603 ms) 54: [ RUN ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip5p_vsite_h_id_or_ter_merge_no_Apdb_format_gro_match_file 54: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/oplsaa.ff/aminoacids.r2b 54: All occupancies are one 54: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/oplsaa.ff/atomtypes.atp 54: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/oplsaa.ff/aminoacids.rtp 54: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/oplsaa.ff/aminoacids.hdb 54: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/oplsaa.ff/aminoacids.n.tdb 54: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/oplsaa.ff/aminoacids.c.tdb 54: Analysing hydrogen-bonding network for automated assignment of histidine 54: protonation. 25 donors and 23 acceptors were found. 54: There are 41 hydrogen bonds 54: Will use HISE for residue 8 54: 9 out of 9 lines of specbond.dat converted successfully 54: Special Atom Distance matrix: 54: CYS3 HIS8 54: SG9 NE251 54: HIS8 NE251 1.055 54: MET12 SD83 0.763 0.990 54: Marked 124 virtual sites 54: Added 16 dummy masses 54: Added 26 new constraints 54: Before cleaning: 653 pairs 54: Before cleaning: 663 dihedrals 54: Using the Oplsaa force field in directory oplsaa.ff 54: 54: going to rename oplsaa.ff/aminoacids.r2b 54: Reading /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/A.pdb... 54: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms 54: 54: Analyzing pdb file 54: Splitting chemical chains based on TER records or chain id changing. 54: 54: There are 1 chains and 0 blocks of water and 16 residues with 128 atoms 54: 54: chain #res #atoms 54: 54: 1 ' ' 16 128 54: 54: All occupancies are one 54: 54: Reading residue database... (Oplsaa) 54: 54: Processing chain 1 (128 atoms, 16 residues) 54: 54: Identified residue ALA2 as a starting terminus. 54: 54: Identified residue SER17 as a ending terminus. 54: Start terminus ALA-2: NH3+ 54: End terminus SER-17: COO- 54: 54: Checking for duplicate atoms.... 54: 54: Generating any missing hydrogen atoms and/or adding termini. 54: 54: Now there are 16 residues with 252 atoms 54: 54: Making bonds... 54: 54: Number of bonds was 254, now 254 54: 54: Generating angles, dihedrals and pairs... 54: 54: Making cmap torsions... 54: 54: There are 663 dihedrals, 51 impropers, 457 angles 54: 650 pairs, 254 bonds and 130 virtual sites 54: 54: Total mass 1846.112 a.m.u. 54: 54: Total charge -0.000 e 54: 54: Writing topology 54: 54: Writing coordinate file... 54: 54: --------- PLEASE NOTE ------------ 54: 54: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/A.pdb. 54: 54: The Oplsaa force field and the tip5p water model are used. 54: 54: --------- ETON ESAELP ------------ 54: [ OK ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip5p_vsite_h_id_or_ter_merge_no_Apdb_format_gro_match_file (221 ms) 54: [ RUN ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip5p_vsite_h_id_or_ter_merge_no_Bpdb_format_gro_match_file 54: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/oplsaa.ff/aminoacids.r2b 54: All occupancies are one 54: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/oplsaa.ff/atomtypes.atp 54: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/oplsaa.ff/aminoacids.rtp 54: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/oplsaa.ff/aminoacids.hdb 54: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/oplsaa.ff/aminoacids.n.tdb 54: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/oplsaa.ff/aminoacids.c.tdb 54: Analysing hydrogen-bonding network for automated assignment of histidine 54: protonation. 30 donors and 22 acceptors were found. 54: There are 36 hydrogen bonds 54: Will use HISE for residue 29 54: Will use HISE for residue 32 54: 9 out of 9 lines of specbond.dat converted successfully 54: Special Atom Distance matrix: 54: CYS27 HIS29 54: SG90 NE2111 54: HIS29 NE2111 0.987 54: HIS32 NE2135 1.590 1.155 54: Marked 132 virtual sites 54: Added 10 dummy masses 54: Added 19 new constraints 54: Before cleaning: 748 pairs 54: Before cleaning: 778 dihedrals 54: Using the Oplsaa force field in directory oplsaa.ff 54: 54: going to rename oplsaa.ff/aminoacids.r2b 54: Reading /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/B.pdb... 54: Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms 54: 54: Analyzing pdb file 54: Splitting chemical chains based on TER records or chain id changing. 54: 54: There are 1 chains and 0 blocks of water and 16 residues with 149 atoms 54: 54: chain #res #atoms 54: 54: 1 ' ' 16 149 54: 54: All occupancies are one 54: 54: Reading residue database... (Oplsaa) 54: 54: Processing chain 1 (149 atoms, 16 residues) 54: 54: Replaced 1 residue named GLUH to the default GLU. Use interactive selection of protonated residues if that is what you need. 54: 54: Identified residue THR18 as a starting terminus. 54: 54: Identified residue PHE33 as a ending terminus. 54: Start terminus THR-18: NH3+ 54: End terminus PHE-33: COO- 54: 54: Checking for duplicate atoms.... 54: 54: Generating any missing hydrogen atoms and/or adding termini. 54: 54: Now there are 16 residues with 281 atoms 54: 54: Making bonds... 54: 54: Number of bonds was 290, now 290 54: 54: Generating angles, dihedrals and pairs... 54: 54: Making cmap torsions... 54: 54: There are 778 dihedrals, 72 impropers, 516 angles 54: 736 pairs, 290 bonds and 133 virtual sites 54: 54: Total mass 2088.357 a.m.u. 54: 54: Total charge 1.000 e 54: 54: Writing topology 54: 54: Writing coordinate file... 54: 54: --------- PLEASE NOTE ------------ 54: 54: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/B.pdb. 54: 54: The Oplsaa force field and the tip5p water model are used. 54: 54: --------- ETON ESAELP ------------ 54: [ OK ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip5p_vsite_h_id_or_ter_merge_no_Bpdb_format_gro_match_file (248 ms) 54: [ RUN ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip5p_vsite_h_id_or_ter_merge_no_Cpdb_format_gro_match_file 54: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/oplsaa.ff/aminoacids.r2b 54: All occupancies are one 54: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/oplsaa.ff/atomtypes.atp 54: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/oplsaa.ff/aminoacids.rtp 54: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/oplsaa.ff/aminoacids.hdb 54: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/oplsaa.ff/aminoacids.n.tdb 54: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/oplsaa.ff/aminoacids.c.tdb 54: Analysing hydrogen-bonding network for automated assignment of histidine 54: protonation. 22 donors and 22 acceptors were found. 54: There are 26 hydrogen bonds 54: Will use HISE for residue 45 54: 9 out of 9 lines of specbond.dat converted successfully 54: Special Atom Distance matrix: 54: HIS45 54: NE295 54: MET46 SD102 1.078 54: Marked 123 virtual sites 54: Added 22 dummy masses 54: Added 35 new constraints 54: Before cleaning: 676 pairs 54: Before cleaning: 696 dihedrals 54: Using the Oplsaa force field in directory oplsaa.ff 54: 54: going to rename oplsaa.ff/aminoacids.r2b 54: Reading /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/C.pdb... 54: Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms 54: 54: Analyzing pdb file 54: Splitting chemical chains based on TER records or chain id changing. 54: 54: There are 1 chains and 0 blocks of water and 16 residues with 132 atoms 54: 54: chain #res #atoms 54: 54: 1 ' ' 16 132 54: 54: All occupancies are one 54: 54: Reading residue database... (Oplsaa) 54: 54: Processing chain 1 (132 atoms, 16 residues) 54: 54: Identified residue ALA34 as a starting terminus. 54: 54: Identified residue ALA49 as a ending terminus. 54: Start terminus ALA-34: NH3+ 54: End terminus ALA-49: COO- 54: 54: Checking for duplicate atoms.... 54: 54: Generating any missing hydrogen atoms and/or adding termini. 54: 54: Now there are 16 residues with 255 atoms 54: 54: Making bonds... 54: 54: Number of bonds was 261, now 261 54: 54: Generating angles, dihedrals and pairs... 54: 54: Making cmap torsions... 54: 54: There are 696 dihedrals, 56 impropers, 472 angles 54: 667 pairs, 261 bonds and 132 virtual sites 54: 54: Total mass 1861.128 a.m.u. 54: 54: Total charge -1.000 e 54: 54: Writing topology 54: 54: Writing coordinate file... 54: 54: --------- PLEASE NOTE ------------ 54: 54: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/C.pdb. 54: 54: The Oplsaa force field and the tip5p water model are used. 54: 54: --------- ETON ESAELP ------------ 54: [ OK ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip5p_vsite_h_id_or_ter_merge_no_Cpdb_format_gro_match_file (232 ms) 54: [ RUN ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip5p_vsite_h_id_or_ter_merge_no_Dpdb_format_gro_match_file 54: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/oplsaa.ff/aminoacids.r2b 54: All occupancies are one 54: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/oplsaa.ff/atomtypes.atp 54: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/oplsaa.ff/aminoacids.rtp 54: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/oplsaa.ff/aminoacids.hdb 54: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/oplsaa.ff/aminoacids.n.tdb 54: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/oplsaa.ff/aminoacids.c.tdb 54: Analysing hydrogen-bonding network for automated assignment of histidine 54: protonation. 22 donors and 21 acceptors were found. 54: There are 30 hydrogen bonds 54: Will use HISE for residue 60 54: 9 out of 9 lines of specbond.dat converted successfully 54: Special Atom Distance matrix: 54: HIS60 54: NE285 54: CYS62 SG98 0.803 54: Marked 111 virtual sites 54: Added 18 dummy masses 54: Added 31 new constraints 54: Before cleaning: 603 pairs 54: Before cleaning: 618 dihedrals 54: Using the Oplsaa force field in directory oplsaa.ff 54: 54: going to rename oplsaa.ff/aminoacids.r2b 54: Reading /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/D.pdb... 54: Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms 54: 54: Analyzing pdb file 54: Splitting chemical chains based on TER records or chain id changing. 54: 54: There are 1 chains and 0 blocks of water and 16 residues with 117 atoms 54: 54: chain #res #atoms 54: 54: 1 ' ' 16 117 54: 54: All occupancies are one 54: 54: Reading residue database... (Oplsaa) 54: 54: Processing chain 1 (117 atoms, 16 residues) 54: 54: Replaced 1 residue named ASPH to the default ASP. Use interactive selection of protonated residues if that is what you need. 54: 54: Identified residue LYS50 as a starting terminus. 54: 54: Identified residue PRO65 as a ending terminus. 54: Start terminus LYS-50: NH3+ 54: End terminus PRO-65: PRO-COO- 54: 54: Checking for duplicate atoms.... 54: 54: Generating any missing hydrogen atoms and/or adding termini. 54: 54: Now there are 16 residues with 228 atoms 54: 54: Making bonds... 54: 54: Number of bonds was 232, now 232 54: 54: Generating angles, dihedrals and pairs... 54: 54: Making cmap torsions... 54: 54: There are 618 dihedrals, 48 impropers, 419 angles 54: 597 pairs, 232 bonds and 116 virtual sites 54: 54: Total mass 1662.883 a.m.u. 54: 54: Total charge -0.000 e 54: 54: Writing topology 54: 54: Writing coordinate file... 54: 54: --------- PLEASE NOTE ------------ 54: 54: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/D.pdb. 54: 54: The Oplsaa force field and the tip5p water model are used. 54: 54: --------- ETON ESAELP ------------ 54: [ OK ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip5p_vsite_h_id_or_ter_merge_no_Dpdb_format_gro_match_file (204 ms) 54: [ RUN ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip5p_vsite_h_id_or_ter_merge_no_Epdb_format_gro_match_file 54: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/oplsaa.ff/aminoacids.r2b 54: All occupancies are one 54: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/oplsaa.ff/atomtypes.atp 54: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/oplsaa.ff/aminoacids.rtp 54: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/oplsaa.ff/aminoacids.hdb 54: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/oplsaa.ff/aminoacids.n.tdb 54: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/oplsaa.ff/aminoacids.c.tdb 54: Analysing hydrogen-bonding network for automated assignment of histidine 54: protonation. 89 donors and 98 acceptors were found. 54: There are 129 hydrogen bonds 54: Will use HISE for residue 31 54: Will use HISE for residue 51 54: 9 out of 9 lines of specbond.dat converted successfully 54: Special Atom Distance matrix: 54: CYS25 HIS31 HIS51 54: SG14 NE264 NE2226 54: HIS31 NE264 1.921 54: HIS51 NE2226 1.498 2.650 54: CYS80 SG477 0.207 1.984 1.570 54: Linking CYS-25 SG-14 and CYS-80 SG-477... 54: Marked 447 virtual sites 54: Added 58 dummy masses 54: Added 101 new constraints 54: Before cleaning: 2499 pairs 54: Before cleaning: 2524 dihedrals 54: Using the Oplsaa force field in directory oplsaa.ff 54: 54: going to rename oplsaa.ff/aminoacids.r2b 54: Reading /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/E.pdb... 54: Read 'This is a fragment of 2d4f for testing a disulfide bridge', 488 atoms 54: 54: Analyzing pdb file 54: Splitting chemical chains based on TER records or chain id changing. 54: 54: There are 1 chains and 0 blocks of water and 58 residues with 488 atoms 54: 54: chain #res #atoms 54: 54: 1 'A' 58 488 54: 54: All occupancies are one 54: 54: Reading residue database... (Oplsaa) 54: 54: Processing chain 1 'A' (488 atoms, 58 residues) 54: 54: Identified residue ASN24 as a starting terminus. 54: 54: Identified residue ARG81 as a ending terminus. 54: Start terminus ASN-24: NH3+ 54: End terminus ARG-81: COO- 54: 54: Checking for duplicate atoms.... 54: 54: Generating any missing hydrogen atoms and/or adding termini. 54: 54: Now there are 58 residues with 936 atoms 54: 54: Making bonds... 54: 54: Number of bonds was 951, now 951 54: 54: Generating angles, dihedrals and pairs... 54: 54: Making cmap torsions... 54: 54: There are 2524 dihedrals, 208 impropers, 1704 angles 54: 2469 pairs, 951 bonds and 462 virtual sites 54: 54: Total mass 6908.578 a.m.u. 54: 54: Total charge -6.000 e 54: 54: Writing topology 54: 54: Writing coordinate file... 54: 54: --------- PLEASE NOTE ------------ 54: 54: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/E.pdb. 54: 54: The Oplsaa force field and the tip5p water model are used. 54: 54: --------- ETON ESAELP ------------ 54: [ OK ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip5p_vsite_h_id_or_ter_merge_no_Epdb_format_gro_match_file (693 ms) 54: [----------] 30 tests from Oplsaa/Pdb2gmxTest (9251 ms total) 54: 54: [----------] Global test environment tear-down 54: [==========] 30 tests from 1 test suite ran. (9251 ms total) 54: [ PASSED ] 30 tests. 54/92 Test #54: Pdb2gmx1Test .............................. Passed 9.34 sec test 55 Start 55: Pdb2gmx2Test 55: Test command: /build/reproducible-path/gromacs-2025.1/build/basic/bin/pdb2gmx2-test "--gtest_output=xml:/build/reproducible-path/gromacs-2025.1/build/basic/Testing/Temporary/Pdb2gmx2Test.xml" 55: Working Directory: /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/gmxpreprocess/tests 55: Test timeout computed to be: 1920 55: [==========] Running 40 tests from 2 test suites. 55: [----------] Global test environment set-up. 55: [----------] 20 tests from G43a1/Pdb2gmxTest 55: [ RUN ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spc_vsite_none_id_or_ter_merge_no_Apdb_format_gro_match_file 55: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos43a1.ff/aminoacids.r2b 55: All occupancies are one 55: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos43a1.ff/atomtypes.atp 55: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos43a1.ff/aminoacids.rtp 55: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos43a1.ff/aminoacids.hdb 55: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos43a1.ff/aminoacids.n.tdb 55: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos43a1.ff/aminoacids.c.tdb 55: Analysing hydrogen-bonding network for automated assignment of histidine 55: protonation. 25 donors and 23 acceptors were found. 55: There are 41 hydrogen bonds 55: Will use HISE for residue 8 55: 9 out of 9 lines of specbond.dat converted successfully 55: Special Atom Distance matrix: 55: CYS3 HIS8 55: SG9 NE251 55: HIS8 NE251 1.055 55: MET12 SD83 0.763 0.990 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: WARNING: Residue 1 named ALA of a molecule in the input file was mapped 55: to an entry in the topology database, but the atom H used in 55: an interaction of type angle in that entry is not found in the 55: input file. Perhaps your atom and/or residue naming needs to be 55: fixed. 55: 55: 55: 55: WARNING: WARNING: Residue 16 named SER of a molecule in the input file was mapped 55: to an entry in the topology database, but the atom O used in 55: an interaction of type angle in that entry is not found in the 55: input file. Perhaps your atom and/or residue naming needs to be 55: fixed. 55: 55: 55: Before cleaning: 267 pairs 55: Before cleaning: 305 dihedrals 55: Using the Gromos43a1 force field in directory gromos43a1.ff 55: 55: going to rename gromos43a1.ff/aminoacids.r2b 55: Reading /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/A.pdb... 55: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms 55: 55: Analyzing pdb file 55: Splitting chemical chains based on TER records or chain id changing. 55: 55: There are 1 chains and 0 blocks of water and 16 residues with 128 atoms 55: 55: chain #res #atoms 55: 55: 1 ' ' 16 128 55: 55: All occupancies are one 55: 55: Reading residue database... (Gromos43a1) 55: 55: Processing chain 1 (128 atoms, 16 residues) 55: 55: Identified residue ALA2 as a starting terminus. 55: 55: Identified residue SER17 as a ending terminus. 55: Start terminus ALA-2: NH3+ 55: End terminus SER-17: COO- 55: 55: Checking for duplicate atoms.... 55: 55: Generating any missing hydrogen atoms and/or adding termini. 55: 55: Now there are 16 residues with 165 atoms 55: 55: Making bonds... 55: 55: Number of bonds was 172, now 167 55: 55: Generating angles, dihedrals and pairs... 55: 55: Making cmap torsions... 55: 55: There are 90 dihedrals, 77 impropers, 241 angles 55: 267 pairs, 167 bonds and 0 virtual sites 55: 55: Total mass 1846.116 a.m.u. 55: 55: Total charge 0.000 e 55: 55: Writing topology 55: 55: Writing coordinate file... 55: 55: --------- PLEASE NOTE ------------ 55: 55: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/A.pdb. 55: 55: The Gromos43a1 force field and the spc water model are used. 55: 55: --------- ETON ESAELP ------------ 55: [ OK ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spc_vsite_none_id_or_ter_merge_no_Apdb_format_gro_match_file (248 ms) 55: [ RUN ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spc_vsite_none_id_or_ter_merge_no_Bpdb_format_gro_match_file 55: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos43a1.ff/aminoacids.r2b 55: All occupancies are one 55: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos43a1.ff/atomtypes.atp 55: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos43a1.ff/aminoacids.rtp 55: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos43a1.ff/aminoacids.hdb 55: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos43a1.ff/aminoacids.n.tdb 55: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos43a1.ff/aminoacids.c.tdb 55: Analysing hydrogen-bonding network for automated assignment of histidine 55: protonation. 30 donors and 22 acceptors were found. 55: There are 36 hydrogen bonds 55: Will use HISE for residue 29 55: Will use HISE for residue 32 55: 9 out of 9 lines of specbond.dat converted successfully 55: Special Atom Distance matrix: 55: CYS27 HIS29 55: SG90 NE2111 55: HIS29 NE2111 0.987 55: HIS32 NE2135 1.590 1.155 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: WARNING: Residue 1 named THR of a molecule in the input file was mapped 55: to an entry in the topology database, but the atom H used in 55: an interaction of type angle in that entry is not found in the 55: input file. Perhaps your atom and/or residue naming needs to be 55: fixed. 55: 55: 55: 55: WARNING: WARNING: Residue 16 named PHE of a molecule in the input file was mapped 55: to an entry in the topology database, but the atom O used in 55: an interaction of type angle in that entry is not found in the 55: input file. Perhaps your atom and/or residue naming needs to be 55: fixed. 55: 55: 55: Before cleaning: 273 pairs 55: Before cleaning: 429 dihedrals 55: Using the Gromos43a1 force field in directory gromos43a1.ff 55: 55: going to rename gromos43a1.ff/aminoacids.r2b 55: Reading /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/B.pdb... 55: Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms 55: 55: Analyzing pdb file 55: Splitting chemical chains based on TER records or chain id changing. 55: 55: There are 1 chains and 0 blocks of water and 16 residues with 149 atoms 55: 55: chain #res #atoms 55: 55: 1 ' ' 16 149 55: 55: All occupancies are one 55: 55: Reading residue database... (Gromos43a1) 55: 55: Processing chain 1 (149 atoms, 16 residues) 55: 55: Replaced 1 residue named GLUH to the default GLU. Use interactive selection of protonated residues if that is what you need. 55: 55: Identified residue THR18 as a starting terminus. 55: 55: Identified residue PHE33 as a ending terminus. 55: Start terminus THR-18: NH3+ 55: End terminus PHE-33: COO- 55: 55: Checking for duplicate atoms.... 55: 55: Generating any missing hydrogen atoms and/or adding termini. 55: 55: Now there are 16 residues with 202 atoms 55: 55: Making bonds... 55: 55: Number of bonds was 216, now 211 55: 55: Generating angles, dihedrals and pairs... 55: 55: Making cmap torsions... 55: 55: There are 93 dihedrals, 134 impropers, 316 angles 55: 273 pairs, 211 bonds and 0 virtual sites 55: 55: Total mass 2088.361 a.m.u. 55: 55: Total charge 1.000 e 55: 55: Writing topology 55: 55: Writing coordinate file... 55: 55: --------- PLEASE NOTE ------------ 55: 55: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/B.pdb. 55: 55: The Gromos43a1 force field and the spc water model are used. 55: 55: --------- ETON ESAELP ------------ 55: [ OK ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spc_vsite_none_id_or_ter_merge_no_Bpdb_format_gro_match_file (268 ms) 55: [ RUN ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spc_vsite_none_id_or_ter_merge_no_Cpdb_format_gro_match_file 55: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos43a1.ff/aminoacids.r2b 55: All occupancies are one 55: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos43a1.ff/atomtypes.atp 55: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos43a1.ff/aminoacids.rtp 55: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos43a1.ff/aminoacids.hdb 55: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos43a1.ff/aminoacids.n.tdb 55: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos43a1.ff/aminoacids.c.tdb 55: Analysing hydrogen-bonding network for automated assignment of histidine 55: protonation. 22 donors and 22 acceptors were found. 55: There are 26 hydrogen bonds 55: Will use HISE for residue 45 55: 9 out of 9 lines of specbond.dat converted successfully 55: Special Atom Distance matrix: 55: HIS45 55: NE295 55: MET46 SD102 1.078 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: WARNING: Residue 1 named ALA of a molecule in the input file was mapped 55: to an entry in the topology database, but the atom H used in 55: an interaction of type angle in that entry is not found in the 55: input file. Perhaps your atom and/or residue naming needs to be 55: fixed. 55: 55: 55: 55: WARNING: WARNING: Residue 16 named ALA of a molecule in the input file was mapped 55: to an entry in the topology database, but the atom O used in 55: an interaction of type angle in that entry is not found in the 55: input file. Perhaps your atom and/or residue naming needs to be 55: fixed. 55: 55: 55: Before cleaning: 242 pairs 55: Before cleaning: 349 dihedrals 55: Using the Gromos43a1 force field in directory gromos43a1.ff 55: 55: going to rename gromos43a1.ff/aminoacids.r2b 55: Reading /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/C.pdb... 55: Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms 55: 55: Analyzing pdb file 55: Splitting chemical chains based on TER records or chain id changing. 55: 55: There are 1 chains and 0 blocks of water and 16 residues with 132 atoms 55: 55: chain #res #atoms 55: 55: 1 ' ' 16 132 55: 55: All occupancies are one 55: 55: Reading residue database... (Gromos43a1) 55: 55: Processing chain 1 (132 atoms, 16 residues) 55: 55: Identified residue ALA34 as a starting terminus. 55: 55: Identified residue ALA49 as a ending terminus. 55: Start terminus ALA-34: NH3+ 55: End terminus ALA-49: COO- 55: 55: Checking for duplicate atoms.... 55: 55: Generating any missing hydrogen atoms and/or adding termini. 55: 55: Now there are 16 residues with 168 atoms 55: 55: Making bonds... 55: 55: Number of bonds was 179, now 174 55: 55: Generating angles, dihedrals and pairs... 55: 55: Making cmap torsions... 55: 55: There are 81 dihedrals, 102 impropers, 260 angles 55: 242 pairs, 174 bonds and 0 virtual sites 55: 55: Total mass 1861.132 a.m.u. 55: 55: Total charge -1.000 e 55: 55: Writing topology 55: 55: Writing coordinate file... 55: 55: --------- PLEASE NOTE ------------ 55: 55: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/C.pdb. 55: 55: The Gromos43a1 force field and the spc water model are used. 55: 55: --------- ETON ESAELP ------------ 55: [ OK ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spc_vsite_none_id_or_ter_merge_no_Cpdb_format_gro_match_file (242 ms) 55: [ RUN ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spc_vsite_none_id_or_ter_merge_no_Dpdb_format_gro_match_file 55: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos43a1.ff/aminoacids.r2b 55: All occupancies are one 55: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos43a1.ff/atomtypes.atp 55: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos43a1.ff/aminoacids.rtp 55: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos43a1.ff/aminoacids.hdb 55: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos43a1.ff/aminoacids.n.tdb 55: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos43a1.ff/aminoacids.c.tdb 55: Analysing hydrogen-bonding network for automated assignment of histidine 55: protonation. 22 donors and 21 acceptors were found. 55: There are 30 hydrogen bonds 55: Will use HISE for residue 60 55: 9 out of 9 lines of specbond.dat converted successfully 55: Special Atom Distance matrix: 55: HIS60 55: NE285 55: CYS62 SG98 0.803 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: WARNING: Residue 1 named LYS of a molecule in the input file was mapped 55: to an entry in the topology database, but the atom H used in 55: an interaction of type angle in that entry is not found in the 55: input file. Perhaps your atom and/or residue naming needs to be 55: fixed. 55: 55: 55: 55: WARNING: WARNING: Residue 16 named PRO of a molecule in the input file was mapped 55: to an entry in the topology database, but the atom O used in 55: an interaction of type angle in that entry is not found in the 55: input file. Perhaps your atom and/or residue naming needs to be 55: fixed. 55: 55: 55: Before cleaning: 232 pairs 55: Before cleaning: 299 dihedrals 55: Using the Gromos43a1 force field in directory gromos43a1.ff 55: 55: going to rename gromos43a1.ff/aminoacids.r2b 55: Reading /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/D.pdb... 55: Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms 55: 55: Analyzing pdb file 55: Splitting chemical chains based on TER records or chain id changing. 55: 55: There are 1 chains and 0 blocks of water and 16 residues with 117 atoms 55: 55: chain #res #atoms 55: 55: 1 ' ' 16 117 55: 55: All occupancies are one 55: 55: Reading residue database... (Gromos43a1) 55: 55: Processing chain 1 (117 atoms, 16 residues) 55: 55: Replaced 1 residue named ASPH to the default ASP. Use interactive selection of protonated residues if that is what you need. 55: 55: Identified residue LYS50 as a starting terminus. 55: 55: Identified residue PRO65 as a ending terminus. 55: Start terminus LYS-50: NH3+ 55: End terminus PRO-65: COO- 55: 55: Checking for duplicate atoms.... 55: 55: Generating any missing hydrogen atoms and/or adding termini. 55: 55: Now there are 16 residues with 150 atoms 55: 55: Making bonds... 55: 55: Number of bonds was 159, now 154 55: 55: Generating angles, dihedrals and pairs... 55: 55: Making cmap torsions... 55: 55: There are 78 dihedrals, 80 impropers, 227 angles 55: 232 pairs, 154 bonds and 0 virtual sites 55: 55: Total mass 1662.887 a.m.u. 55: 55: Total charge 0.000 e 55: 55: Writing topology 55: 55: Writing coordinate file... 55: 55: --------- PLEASE NOTE ------------ 55: 55: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/D.pdb. 55: 55: The Gromos43a1 force field and the spc water model are used. 55: 55: --------- ETON ESAELP ------------ 55: [ OK ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spc_vsite_none_id_or_ter_merge_no_Dpdb_format_gro_match_file (228 ms) 55: [ RUN ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spc_vsite_none_id_or_ter_merge_no_Epdb_format_gro_match_file 55: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos43a1.ff/aminoacids.r2b 55: All occupancies are one 55: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos43a1.ff/atomtypes.atp 55: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos43a1.ff/aminoacids.rtp 55: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos43a1.ff/aminoacids.hdb 55: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos43a1.ff/aminoacids.n.tdb 55: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos43a1.ff/aminoacids.c.tdb 55: Analysing hydrogen-bonding network for automated assignment of histidine 55: protonation. 89 donors and 98 acceptors were found. 55: There are 129 hydrogen bonds 55: Will use HISE for residue 31 55: Will use HISE for residue 51 55: 9 out of 9 lines of specbond.dat converted successfully 55: Special Atom Distance matrix: 55: CYS25 HIS31 HIS51 55: SG14 NE264 NE2226 55: HIS31 NE264 1.921 55: HIS51 NE2226 1.498 2.650 55: CYS80 SG477 0.207 1.984 1.570 55: Linking CYS-25 SG-14 and CYS-80 SG-477... 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: WARNING: Residue 1 named ASN of a molecule in the input file was mapped 55: to an entry in the topology database, but the atom H used in 55: an interaction of type angle in that entry is not found in the 55: input file. Perhaps your atom and/or residue naming needs to be 55: fixed. 55: 55: 55: 55: WARNING: WARNING: Residue 58 named ARG of a molecule in the input file was mapped 55: to an entry in the topology database, but the atom O used in 55: an interaction of type angle in that entry is not found in the 55: input file. Perhaps your atom and/or residue naming needs to be 55: fixed. 55: 55: 55: Before cleaning: 972 pairs 55: Before cleaning: 1256 dihedrals 55: Using the Gromos43a1 force field in directory gromos43a1.ff 55: 55: going to rename gromos43a1.ff/aminoacids.r2b 55: Reading /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/E.pdb... 55: Read 'This is a fragment of 2d4f for testing a disulfide bridge', 488 atoms 55: 55: Analyzing pdb file 55: Splitting chemical chains based on TER records or chain id changing. 55: 55: There are 1 chains and 0 blocks of water and 58 residues with 488 atoms 55: 55: chain #res #atoms 55: 55: 1 'A' 58 488 55: 55: All occupancies are one 55: 55: Reading residue database... (Gromos43a1) 55: 55: Processing chain 1 'A' (488 atoms, 58 residues) 55: 55: Identified residue ASN24 as a starting terminus. 55: 55: Identified residue ARG81 as a ending terminus. 55: Start terminus ASN-24: NH3+ 55: End terminus ARG-81: COO- 55: 55: Checking for duplicate atoms.... 55: 55: Generating any missing hydrogen atoms and/or adding termini. 55: 55: Now there are 58 residues with 635 atoms 55: 55: Making bonds... 55: 55: Number of bonds was 655, now 650 55: 55: Generating angles, dihedrals and pairs... 55: 55: Making cmap torsions... 55: 55: There are 321 dihedrals, 350 impropers, 955 angles 55: 972 pairs, 650 bonds and 0 virtual sites 55: 55: Total mass 6908.582 a.m.u. 55: 55: Total charge -6.000 e 55: 55: Writing topology 55: 55: Writing coordinate file... 55: 55: --------- PLEASE NOTE ------------ 55: 55: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/E.pdb. 55: 55: The Gromos43a1 force field and the spc water model are used. 55: 55: --------- ETON ESAELP ------------ 55: [ OK ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spc_vsite_none_id_or_ter_merge_no_Epdb_format_gro_match_file (486 ms) 55: [ RUN ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spc_vsite_h_id_or_ter_merge_no_Apdb_format_gro_match_file 55: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos43a1.ff/aminoacids.r2b 55: All occupancies are one 55: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos43a1.ff/atomtypes.atp 55: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos43a1.ff/aminoacids.rtp 55: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos43a1.ff/aminoacids.hdb 55: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos43a1.ff/aminoacids.n.tdb 55: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos43a1.ff/aminoacids.c.tdb 55: Analysing hydrogen-bonding network for automated assignment of histidine 55: protonation. 25 donors and 23 acceptors were found. 55: There are 41 hydrogen bonds 55: Will use HISE for residue 8 55: 9 out of 9 lines of specbond.dat converted successfully 55: Special Atom Distance matrix: 55: CYS3 HIS8 55: SG9 NE251 55: HIS8 NE251 1.055 55: MET12 SD83 0.763 0.990 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: Marked 37 virtual sites 55: Added 4 dummy masses 55: Added 8 new constraints 55: 55: WARNING: WARNING: Residue 1 named ALA of a molecule in the input file was mapped 55: to an entry in the topology database, but the atom H used in 55: an interaction of type angle in that entry is not found in the 55: input file. Perhaps your atom and/or residue naming needs to be 55: fixed. 55: 55: 55: 55: WARNING: WARNING: Residue 16 named SER of a molecule in the input file was mapped 55: to an entry in the topology database, but the atom O used in 55: an interaction of type angle in that entry is not found in the 55: input file. Perhaps your atom and/or residue naming needs to be 55: fixed. 55: 55: 55: Before cleaning: 267 pairs 55: Before cleaning: 305 dihedrals 55: Using the Gromos43a1 force field in directory gromos43a1.ff 55: 55: going to rename gromos43a1.ff/aminoacids.r2b 55: Reading /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/A.pdb... 55: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms 55: 55: Analyzing pdb file 55: Splitting chemical chains based on TER records or chain id changing. 55: 55: There are 1 chains and 0 blocks of water and 16 residues with 128 atoms 55: 55: chain #res #atoms 55: 55: 1 ' ' 16 128 55: 55: All occupancies are one 55: 55: Reading residue database... (Gromos43a1) 55: 55: Processing chain 1 (128 atoms, 16 residues) 55: 55: Identified residue ALA2 as a starting terminus. 55: 55: Identified residue SER17 as a ending terminus. 55: Start terminus ALA-2: NH3+ 55: End terminus SER-17: COO- 55: 55: Checking for duplicate atoms.... 55: 55: Generating any missing hydrogen atoms and/or adding termini. 55: 55: Now there are 16 residues with 165 atoms 55: 55: Making bonds... 55: 55: Number of bonds was 172, now 167 55: 55: Generating angles, dihedrals and pairs... 55: 55: Making cmap torsions... 55: 55: There are 90 dihedrals, 77 impropers, 241 angles 55: 267 pairs, 167 bonds and 37 virtual sites 55: 55: Total mass 1846.116 a.m.u. 55: 55: Total charge 0.000 e 55: 55: Writing topology 55: 55: Writing coordinate file... 55: 55: --------- PLEASE NOTE ------------ 55: 55: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/A.pdb. 55: 55: The Gromos43a1 force field and the spc water model are used. 55: 55: --------- ETON ESAELP ------------ 55: [ OK ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spc_vsite_h_id_or_ter_merge_no_Apdb_format_gro_match_file (241 ms) 55: [ RUN ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spc_vsite_h_id_or_ter_merge_no_Bpdb_format_gro_match_file 55: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos43a1.ff/aminoacids.r2b 55: All occupancies are one 55: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos43a1.ff/atomtypes.atp 55: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos43a1.ff/aminoacids.rtp 55: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos43a1.ff/aminoacids.hdb 55: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos43a1.ff/aminoacids.n.tdb 55: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos43a1.ff/aminoacids.c.tdb 55: Analysing hydrogen-bonding network for automated assignment of histidine 55: protonation. 30 donors and 22 acceptors were found. 55: There are 36 hydrogen bonds 55: Will use HISE for residue 29 55: Will use HISE for residue 32 55: 9 out of 9 lines of specbond.dat converted successfully 55: Special Atom Distance matrix: 55: CYS27 HIS29 55: SG90 NE2111 55: HIS29 NE2111 0.987 55: HIS32 NE2135 1.590 1.155 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: Marked 53 virtual sites 55: Added 4 dummy masses 55: Added 10 new constraints 55: 55: WARNING: WARNING: Residue 1 named THR of a molecule in the input file was mapped 55: to an entry in the topology database, but the atom H used in 55: an interaction of type angle in that entry is not found in the 55: input file. Perhaps your atom and/or residue naming needs to be 55: fixed. 55: 55: 55: 55: WARNING: WARNING: Residue 16 named PHE of a molecule in the input file was mapped 55: to an entry in the topology database, but the atom O used in 55: an interaction of type angle in that entry is not found in the 55: input file. Perhaps your atom and/or residue naming needs to be 55: fixed. 55: 55: 55: Before cleaning: 273 pairs 55: Before cleaning: 429 dihedrals 55: Using the Gromos43a1 force field in directory gromos43a1.ff 55: 55: going to rename gromos43a1.ff/aminoacids.r2b 55: Reading /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/B.pdb... 55: Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms 55: 55: Analyzing pdb file 55: Splitting chemical chains based on TER records or chain id changing. 55: 55: There are 1 chains and 0 blocks of water and 16 residues with 149 atoms 55: 55: chain #res #atoms 55: 55: 1 ' ' 16 149 55: 55: All occupancies are one 55: 55: Reading residue database... (Gromos43a1) 55: 55: Processing chain 1 (149 atoms, 16 residues) 55: 55: Replaced 1 residue named GLUH to the default GLU. Use interactive selection of protonated residues if that is what you need. 55: 55: Identified residue THR18 as a starting terminus. 55: 55: Identified residue PHE33 as a ending terminus. 55: Start terminus THR-18: NH3+ 55: End terminus PHE-33: COO- 55: 55: Checking for duplicate atoms.... 55: 55: Generating any missing hydrogen atoms and/or adding termini. 55: 55: Now there are 16 residues with 202 atoms 55: 55: Making bonds... 55: 55: Number of bonds was 216, now 211 55: 55: Generating angles, dihedrals and pairs... 55: 55: Making cmap torsions... 55: 55: There are 93 dihedrals, 134 impropers, 316 angles 55: 273 pairs, 211 bonds and 51 virtual sites 55: 55: Total mass 2088.361 a.m.u. 55: 55: Total charge 1.000 e 55: 55: Writing topology 55: 55: Writing coordinate file... 55: 55: --------- PLEASE NOTE ------------ 55: 55: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/B.pdb. 55: 55: The Gromos43a1 force field and the spc water model are used. 55: 55: --------- ETON ESAELP ------------ 55: [ OK ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spc_vsite_h_id_or_ter_merge_no_Bpdb_format_gro_match_file (263 ms) 55: [ RUN ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spc_vsite_h_id_or_ter_merge_no_Cpdb_format_gro_match_file 55: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos43a1.ff/aminoacids.r2b 55: All occupancies are one 55: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos43a1.ff/atomtypes.atp 55: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos43a1.ff/aminoacids.rtp 55: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos43a1.ff/aminoacids.hdb 55: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos43a1.ff/aminoacids.n.tdb 55: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos43a1.ff/aminoacids.c.tdb 55: Analysing hydrogen-bonding network for automated assignment of histidine 55: protonation. 22 donors and 22 acceptors were found. 55: There are 26 hydrogen bonds 55: Will use HISE for residue 45 55: 9 out of 9 lines of specbond.dat converted successfully 55: Special Atom Distance matrix: 55: HIS45 55: NE295 55: MET46 SD102 1.078 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: Marked 36 virtual sites 55: Added 4 dummy masses 55: Added 8 new constraints 55: 55: WARNING: WARNING: Residue 1 named ALA of a molecule in the input file was mapped 55: to an entry in the topology database, but the atom H used in 55: an interaction of type angle in that entry is not found in the 55: input file. Perhaps your atom and/or residue naming needs to be 55: fixed. 55: 55: 55: 55: WARNING: WARNING: Residue 16 named ALA of a molecule in the input file was mapped 55: to an entry in the topology database, but the atom O used in 55: an interaction of type angle in that entry is not found in the 55: input file. Perhaps your atom and/or residue naming needs to be 55: fixed. 55: 55: 55: Before cleaning: 242 pairs 55: Before cleaning: 349 dihedrals 55: Using the Gromos43a1 force field in directory gromos43a1.ff 55: 55: going to rename gromos43a1.ff/aminoacids.r2b 55: Reading /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/C.pdb... 55: Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms 55: 55: Analyzing pdb file 55: Splitting chemical chains based on TER records or chain id changing. 55: 55: There are 1 chains and 0 blocks of water and 16 residues with 132 atoms 55: 55: chain #res #atoms 55: 55: 1 ' ' 16 132 55: 55: All occupancies are one 55: 55: Reading residue database... (Gromos43a1) 55: 55: Processing chain 1 (132 atoms, 16 residues) 55: 55: Identified residue ALA34 as a starting terminus. 55: 55: Identified residue ALA49 as a ending terminus. 55: Start terminus ALA-34: NH3+ 55: End terminus ALA-49: COO- 55: 55: Checking for duplicate atoms.... 55: 55: Generating any missing hydrogen atoms and/or adding termini. 55: 55: Now there are 16 residues with 168 atoms 55: 55: Making bonds... 55: 55: Number of bonds was 179, now 174 55: 55: Generating angles, dihedrals and pairs... 55: 55: Making cmap torsions... 55: 55: There are 81 dihedrals, 102 impropers, 260 angles 55: 242 pairs, 174 bonds and 36 virtual sites 55: 55: Total mass 1861.132 a.m.u. 55: 55: Total charge -1.000 e 55: 55: Writing topology 55: 55: Writing coordinate file... 55: 55: --------- PLEASE NOTE ------------ 55: 55: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/C.pdb. 55: 55: The Gromos43a1 force field and the spc water model are used. 55: 55: --------- ETON ESAELP ------------ 55: [ OK ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spc_vsite_h_id_or_ter_merge_no_Cpdb_format_gro_match_file (262 ms) 55: [ RUN ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spc_vsite_h_id_or_ter_merge_no_Dpdb_format_gro_match_file 55: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos43a1.ff/aminoacids.r2b 55: All occupancies are one 55: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos43a1.ff/atomtypes.atp 55: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos43a1.ff/aminoacids.rtp 55: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos43a1.ff/aminoacids.hdb 55: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos43a1.ff/aminoacids.n.tdb 55: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos43a1.ff/aminoacids.c.tdb 55: Analysing hydrogen-bonding network for automated assignment of histidine 55: protonation. 22 donors and 21 acceptors were found. 55: There are 30 hydrogen bonds 55: Will use HISE for residue 60 55: 9 out of 9 lines of specbond.dat converted successfully 55: Special Atom Distance matrix: 55: HIS60 55: NE285 55: CYS62 SG98 0.803 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: Marked 33 virtual sites 55: Added 4 dummy masses 55: Added 10 new constraints 55: 55: WARNING: WARNING: Residue 1 named LYS of a molecule in the input file was mapped 55: to an entry in the topology database, but the atom H used in 55: an interaction of type angle in that entry is not found in the 55: input file. Perhaps your atom and/or residue naming needs to be 55: fixed. 55: 55: 55: 55: WARNING: WARNING: Residue 16 named PRO of a molecule in the input file was mapped 55: to an entry in the topology database, but the atom O used in 55: an interaction of type angle in that entry is not found in the 55: input file. Perhaps your atom and/or residue naming needs to be 55: fixed. 55: 55: 55: Before cleaning: 232 pairs 55: Before cleaning: 299 dihedrals 55: Using the Gromos43a1 force field in directory gromos43a1.ff 55: 55: going to rename gromos43a1.ff/aminoacids.r2b 55: Reading /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/D.pdb... 55: Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms 55: 55: Analyzing pdb file 55: Splitting chemical chains based on TER records or chain id changing. 55: 55: There are 1 chains and 0 blocks of water and 16 residues with 117 atoms 55: 55: chain #res #atoms 55: 55: 1 ' ' 16 117 55: 55: All occupancies are one 55: 55: Reading residue database... (Gromos43a1) 55: 55: Processing chain 1 (117 atoms, 16 residues) 55: 55: Replaced 1 residue named ASPH to the default ASP. Use interactive selection of protonated residues if that is what you need. 55: 55: Identified residue LYS50 as a starting terminus. 55: 55: Identified residue PRO65 as a ending terminus. 55: Start terminus LYS-50: NH3+ 55: End terminus PRO-65: COO- 55: 55: Checking for duplicate atoms.... 55: 55: Generating any missing hydrogen atoms and/or adding termini. 55: 55: Now there are 16 residues with 150 atoms 55: 55: Making bonds... 55: 55: Number of bonds was 159, now 154 55: 55: Generating angles, dihedrals and pairs... 55: 55: Making cmap torsions... 55: 55: There are 78 dihedrals, 80 impropers, 227 angles 55: 232 pairs, 154 bonds and 31 virtual sites 55: 55: Total mass 1662.887 a.m.u. 55: 55: Total charge 0.000 e 55: 55: Writing topology 55: 55: Writing coordinate file... 55: 55: --------- PLEASE NOTE ------------ 55: 55: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/D.pdb. 55: 55: The Gromos43a1 force field and the spc water model are used. 55: 55: --------- ETON ESAELP ------------ 55: [ OK ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spc_vsite_h_id_or_ter_merge_no_Dpdb_format_gro_match_file (341 ms) 55: [ RUN ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spc_vsite_h_id_or_ter_merge_no_Epdb_format_gro_match_file 55: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos43a1.ff/aminoacids.r2b 55: All occupancies are one 55: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos43a1.ff/atomtypes.atp 55: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos43a1.ff/aminoacids.rtp 55: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos43a1.ff/aminoacids.hdb 55: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos43a1.ff/aminoacids.n.tdb 55: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos43a1.ff/aminoacids.c.tdb 55: Analysing hydrogen-bonding network for automated assignment of histidine 55: protonation. 89 donors and 98 acceptors were found. 55: There are 129 hydrogen bonds 55: Will use HISE for residue 31 55: Will use HISE for residue 51 55: 9 out of 9 lines of specbond.dat converted successfully 55: Special Atom Distance matrix: 55: CYS25 HIS31 HIS51 55: SG14 NE264 NE2226 55: HIS31 NE264 1.921 55: HIS51 NE2226 1.498 2.650 55: CYS80 SG477 0.207 1.984 1.570 55: Linking CYS-25 SG-14 and CYS-80 SG-477... 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: Marked 146 virtual sites 55: Added 10 dummy masses 55: Added 29 new constraints 55: 55: WARNING: WARNING: Residue 1 named ASN of a molecule in the input file was mapped 55: to an entry in the topology database, but the atom H used in 55: an interaction of type angle in that entry is not found in the 55: input file. Perhaps your atom and/or residue naming needs to be 55: fixed. 55: 55: 55: 55: WARNING: WARNING: Residue 58 named ARG of a molecule in the input file was mapped 55: to an entry in the topology database, but the atom O used in 55: an interaction of type angle in that entry is not found in the 55: input file. Perhaps your atom and/or residue naming needs to be 55: fixed. 55: 55: 55: Before cleaning: 972 pairs 55: Before cleaning: 1256 dihedrals 55: Using the Gromos43a1 force field in directory gromos43a1.ff 55: 55: going to rename gromos43a1.ff/aminoacids.r2b 55: Reading /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/E.pdb... 55: Read 'This is a fragment of 2d4f for testing a disulfide bridge', 488 atoms 55: 55: Analyzing pdb file 55: Splitting chemical chains based on TER records or chain id changing. 55: 55: There are 1 chains and 0 blocks of water and 58 residues with 488 atoms 55: 55: chain #res #atoms 55: 55: 1 'A' 58 488 55: 55: All occupancies are one 55: 55: Reading residue database... (Gromos43a1) 55: 55: Processing chain 1 'A' (488 atoms, 58 residues) 55: 55: Identified residue ASN24 as a starting terminus. 55: 55: Identified residue ARG81 as a ending terminus. 55: Start terminus ASN-24: NH3+ 55: End terminus ARG-81: COO- 55: 55: Checking for duplicate atoms.... 55: 55: Generating any missing hydrogen atoms and/or adding termini. 55: 55: Now there are 58 residues with 635 atoms 55: 55: Making bonds... 55: 55: Number of bonds was 655, now 650 55: 55: Generating angles, dihedrals and pairs... 55: 55: Making cmap torsions... 55: 55: There are 321 dihedrals, 350 impropers, 955 angles 55: 972 pairs, 650 bonds and 137 virtual sites 55: 55: Total mass 6908.582 a.m.u. 55: 55: Total charge -6.000 e 55: 55: Writing topology 55: 55: Writing coordinate file... 55: 55: --------- PLEASE NOTE ------------ 55: 55: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/E.pdb. 55: 55: The Gromos43a1 force field and the spc water model are used. 55: 55: --------- ETON ESAELP ------------ 55: [ OK ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spc_vsite_h_id_or_ter_merge_no_Epdb_format_gro_match_file (561 ms) 55: [ RUN ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spce_vsite_none_id_or_ter_merge_no_Apdb_format_gro_match_file 55: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos43a1.ff/aminoacids.r2b 55: All occupancies are one 55: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos43a1.ff/atomtypes.atp 55: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos43a1.ff/aminoacids.rtp 55: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos43a1.ff/aminoacids.hdb 55: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos43a1.ff/aminoacids.n.tdb 55: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos43a1.ff/aminoacids.c.tdb 55: Analysing hydrogen-bonding network for automated assignment of histidine 55: protonation. 25 donors and 23 acceptors were found. 55: There are 41 hydrogen bonds 55: Will use HISE for residue 8 55: 9 out of 9 lines of specbond.dat converted successfully 55: Special Atom Distance matrix: 55: CYS3 HIS8 55: SG9 NE251 55: HIS8 NE251 1.055 55: MET12 SD83 0.763 0.990 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: WARNING: Residue 1 named ALA of a molecule in the input file was mapped 55: to an entry in the topology database, but the atom H used in 55: an interaction of type angle in that entry is not found in the 55: input file. Perhaps your atom and/or residue naming needs to be 55: fixed. 55: 55: 55: 55: WARNING: WARNING: Residue 16 named SER of a molecule in the input file was mapped 55: to an entry in the topology database, but the atom O used in 55: an interaction of type angle in that entry is not found in the 55: input file. Perhaps your atom and/or residue naming needs to be 55: fixed. 55: 55: 55: Before cleaning: 267 pairs 55: Before cleaning: 305 dihedrals 55: Using the Gromos43a1 force field in directory gromos43a1.ff 55: 55: going to rename gromos43a1.ff/aminoacids.r2b 55: Reading /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/A.pdb... 55: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms 55: 55: Analyzing pdb file 55: Splitting chemical chains based on TER records or chain id changing. 55: 55: There are 1 chains and 0 blocks of water and 16 residues with 128 atoms 55: 55: chain #res #atoms 55: 55: 1 ' ' 16 128 55: 55: All occupancies are one 55: 55: Reading residue database... (Gromos43a1) 55: 55: Processing chain 1 (128 atoms, 16 residues) 55: 55: Identified residue ALA2 as a starting terminus. 55: 55: Identified residue SER17 as a ending terminus. 55: Start terminus ALA-2: NH3+ 55: End terminus SER-17: COO- 55: 55: Checking for duplicate atoms.... 55: 55: Generating any missing hydrogen atoms and/or adding termini. 55: 55: Now there are 16 residues with 165 atoms 55: 55: Making bonds... 55: 55: Number of bonds was 172, now 167 55: 55: Generating angles, dihedrals and pairs... 55: 55: Making cmap torsions... 55: 55: There are 90 dihedrals, 77 impropers, 241 angles 55: 267 pairs, 167 bonds and 0 virtual sites 55: 55: Total mass 1846.116 a.m.u. 55: 55: Total charge 0.000 e 55: 55: Writing topology 55: 55: Writing coordinate file... 55: 55: --------- PLEASE NOTE ------------ 55: 55: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/A.pdb. 55: 55: The Gromos43a1 force field and the spce water model are used. 55: 55: --------- ETON ESAELP ------------ 55: [ OK ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spce_vsite_none_id_or_ter_merge_no_Apdb_format_gro_match_file (303 ms) 55: [ RUN ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spce_vsite_none_id_or_ter_merge_no_Bpdb_format_gro_match_file 55: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos43a1.ff/aminoacids.r2b 55: All occupancies are one 55: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos43a1.ff/atomtypes.atp 55: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos43a1.ff/aminoacids.rtp 55: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos43a1.ff/aminoacids.hdb 55: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos43a1.ff/aminoacids.n.tdb 55: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos43a1.ff/aminoacids.c.tdb 55: Analysing hydrogen-bonding network for automated assignment of histidine 55: protonation. 30 donors and 22 acceptors were found. 55: There are 36 hydrogen bonds 55: Will use HISE for residue 29 55: Will use HISE for residue 32 55: 9 out of 9 lines of specbond.dat converted successfully 55: Special Atom Distance matrix: 55: CYS27 HIS29 55: SG90 NE2111 55: HIS29 NE2111 0.987 55: HIS32 NE2135 1.590 1.155 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: WARNING: Residue 1 named THR of a molecule in the input file was mapped 55: to an entry in the topology database, but the atom H used in 55: an interaction of type angle in that entry is not found in the 55: input file. Perhaps your atom and/or residue naming needs to be 55: fixed. 55: 55: 55: 55: WARNING: WARNING: Residue 16 named PHE of a molecule in the input file was mapped 55: to an entry in the topology database, but the atom O used in 55: an interaction of type angle in that entry is not found in the 55: input file. Perhaps your atom and/or residue naming needs to be 55: fixed. 55: 55: 55: Before cleaning: 273 pairs 55: Before cleaning: 429 dihedrals 55: Using the Gromos43a1 force field in directory gromos43a1.ff 55: 55: going to rename gromos43a1.ff/aminoacids.r2b 55: Reading /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/B.pdb... 55: Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms 55: 55: Analyzing pdb file 55: Splitting chemical chains based on TER records or chain id changing. 55: 55: There are 1 chains and 0 blocks of water and 16 residues with 149 atoms 55: 55: chain #res #atoms 55: 55: 1 ' ' 16 149 55: 55: All occupancies are one 55: 55: Reading residue database... (Gromos43a1) 55: 55: Processing chain 1 (149 atoms, 16 residues) 55: 55: Replaced 1 residue named GLUH to the default GLU. Use interactive selection of protonated residues if that is what you need. 55: 55: Identified residue THR18 as a starting terminus. 55: 55: Identified residue PHE33 as a ending terminus. 55: Start terminus THR-18: NH3+ 55: End terminus PHE-33: COO- 55: 55: Checking for duplicate atoms.... 55: 55: Generating any missing hydrogen atoms and/or adding termini. 55: 55: Now there are 16 residues with 202 atoms 55: 55: Making bonds... 55: 55: Number of bonds was 216, now 211 55: 55: Generating angles, dihedrals and pairs... 55: 55: Making cmap torsions... 55: 55: There are 93 dihedrals, 134 impropers, 316 angles 55: 273 pairs, 211 bonds and 0 virtual sites 55: 55: Total mass 2088.361 a.m.u. 55: 55: Total charge 1.000 e 55: 55: Writing topology 55: 55: Writing coordinate file... 55: 55: --------- PLEASE NOTE ------------ 55: 55: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/B.pdb. 55: 55: The Gromos43a1 force field and the spce water model are used. 55: 55: --------- ETON ESAELP ------------ 55: [ OK ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spce_vsite_none_id_or_ter_merge_no_Bpdb_format_gro_match_file (358 ms) 55: [ RUN ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spce_vsite_none_id_or_ter_merge_no_Cpdb_format_gro_match_file 55: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos43a1.ff/aminoacids.r2b 55: All occupancies are one 55: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos43a1.ff/atomtypes.atp 55: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos43a1.ff/aminoacids.rtp 55: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos43a1.ff/aminoacids.hdb 55: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos43a1.ff/aminoacids.n.tdb 55: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos43a1.ff/aminoacids.c.tdb 55: Analysing hydrogen-bonding network for automated assignment of histidine 55: protonation. 22 donors and 22 acceptors were found. 55: There are 26 hydrogen bonds 55: Will use HISE for residue 45 55: 9 out of 9 lines of specbond.dat converted successfully 55: Special Atom Distance matrix: 55: HIS45 55: NE295 55: MET46 SD102 1.078 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: WARNING: Residue 1 named ALA of a molecule in the input file was mapped 55: to an entry in the topology database, but the atom H used in 55: an interaction of type angle in that entry is not found in the 55: input file. Perhaps your atom and/or residue naming needs to be 55: fixed. 55: 55: 55: 55: WARNING: WARNING: Residue 16 named ALA of a molecule in the input file was mapped 55: to an entry in the topology database, but the atom O used in 55: an interaction of type angle in that entry is not found in the 55: input file. Perhaps your atom and/or residue naming needs to be 55: fixed. 55: 55: 55: Before cleaning: 242 pairs 55: Before cleaning: 349 dihedrals 55: Using the Gromos43a1 force field in directory gromos43a1.ff 55: 55: going to rename gromos43a1.ff/aminoacids.r2b 55: Reading /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/C.pdb... 55: Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms 55: 55: Analyzing pdb file 55: Splitting chemical chains based on TER records or chain id changing. 55: 55: There are 1 chains and 0 blocks of water and 16 residues with 132 atoms 55: 55: chain #res #atoms 55: 55: 1 ' ' 16 132 55: 55: All occupancies are one 55: 55: Reading residue database... (Gromos43a1) 55: 55: Processing chain 1 (132 atoms, 16 residues) 55: 55: Identified residue ALA34 as a starting terminus. 55: 55: Identified residue ALA49 as a ending terminus. 55: Start terminus ALA-34: NH3+ 55: End terminus ALA-49: COO- 55: 55: Checking for duplicate atoms.... 55: 55: Generating any missing hydrogen atoms and/or adding termini. 55: 55: Now there are 16 residues with 168 atoms 55: 55: Making bonds... 55: 55: Number of bonds was 179, now 174 55: 55: Generating angles, dihedrals and pairs... 55: 55: Making cmap torsions... 55: 55: There are 81 dihedrals, 102 impropers, 260 angles 55: 242 pairs, 174 bonds and 0 virtual sites 55: 55: Total mass 1861.132 a.m.u. 55: 55: Total charge -1.000 e 55: 55: Writing topology 55: 55: Writing coordinate file... 55: 55: --------- PLEASE NOTE ------------ 55: 55: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/C.pdb. 55: 55: The Gromos43a1 force field and the spce water model are used. 55: 55: --------- ETON ESAELP ------------ 55: [ OK ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spce_vsite_none_id_or_ter_merge_no_Cpdb_format_gro_match_file (257 ms) 55: [ RUN ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spce_vsite_none_id_or_ter_merge_no_Dpdb_format_gro_match_file 55: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos43a1.ff/aminoacids.r2b 55: All occupancies are one 55: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos43a1.ff/atomtypes.atp 55: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos43a1.ff/aminoacids.rtp 55: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos43a1.ff/aminoacids.hdb 55: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos43a1.ff/aminoacids.n.tdb 55: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos43a1.ff/aminoacids.c.tdb 55: Analysing hydrogen-bonding network for automated assignment of histidine 55: protonation. 22 donors and 21 acceptors were found. 55: There are 30 hydrogen bonds 55: Will use HISE for residue 60 55: 9 out of 9 lines of specbond.dat converted successfully 55: Special Atom Distance matrix: 55: HIS60 55: NE285 55: CYS62 SG98 0.803 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: WARNING: Residue 1 named LYS of a molecule in the input file was mapped 55: to an entry in the topology database, but the atom H used in 55: an interaction of type angle in that entry is not found in the 55: input file. Perhaps your atom and/or residue naming needs to be 55: fixed. 55: 55: 55: 55: WARNING: WARNING: Residue 16 named PRO of a molecule in the input file was mapped 55: to an entry in the topology database, but the atom O used in 55: an interaction of type angle in that entry is not found in the 55: input file. Perhaps your atom and/or residue naming needs to be 55: fixed. 55: 55: 55: Before cleaning: 232 pairs 55: Before cleaning: 299 dihedrals 55: Using the Gromos43a1 force field in directory gromos43a1.ff 55: 55: going to rename gromos43a1.ff/aminoacids.r2b 55: Reading /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/D.pdb... 55: Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms 55: 55: Analyzing pdb file 55: Splitting chemical chains based on TER records or chain id changing. 55: 55: There are 1 chains and 0 blocks of water and 16 residues with 117 atoms 55: 55: chain #res #atoms 55: 55: 1 ' ' 16 117 55: 55: All occupancies are one 55: 55: Reading residue database... (Gromos43a1) 55: 55: Processing chain 1 (117 atoms, 16 residues) 55: 55: Replaced 1 residue named ASPH to the default ASP. Use interactive selection of protonated residues if that is what you need. 55: 55: Identified residue LYS50 as a starting terminus. 55: 55: Identified residue PRO65 as a ending terminus. 55: Start terminus LYS-50: NH3+ 55: End terminus PRO-65: COO- 55: 55: Checking for duplicate atoms.... 55: 55: Generating any missing hydrogen atoms and/or adding termini. 55: 55: Now there are 16 residues with 150 atoms 55: 55: Making bonds... 55: 55: Number of bonds was 159, now 154 55: 55: Generating angles, dihedrals and pairs... 55: 55: Making cmap torsions... 55: 55: There are 78 dihedrals, 80 impropers, 227 angles 55: 232 pairs, 154 bonds and 0 virtual sites 55: 55: Total mass 1662.887 a.m.u. 55: 55: Total charge 0.000 e 55: 55: Writing topology 55: 55: Writing coordinate file... 55: 55: --------- PLEASE NOTE ------------ 55: 55: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/D.pdb. 55: 55: The Gromos43a1 force field and the spce water model are used. 55: 55: --------- ETON ESAELP ------------ 55: [ OK ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spce_vsite_none_id_or_ter_merge_no_Dpdb_format_gro_match_file (244 ms) 55: [ RUN ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spce_vsite_none_id_or_ter_merge_no_Epdb_format_gro_match_file 55: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos43a1.ff/aminoacids.r2b 55: All occupancies are one 55: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos43a1.ff/atomtypes.atp 55: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos43a1.ff/aminoacids.rtp 55: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos43a1.ff/aminoacids.hdb 55: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos43a1.ff/aminoacids.n.tdb 55: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos43a1.ff/aminoacids.c.tdb 55: Analysing hydrogen-bonding network for automated assignment of histidine 55: protonation. 89 donors and 98 acceptors were found. 55: There are 129 hydrogen bonds 55: Will use HISE for residue 31 55: Will use HISE for residue 51 55: 9 out of 9 lines of specbond.dat converted successfully 55: Special Atom Distance matrix: 55: CYS25 HIS31 HIS51 55: SG14 NE264 NE2226 55: HIS31 NE264 1.921 55: HIS51 NE2226 1.498 2.650 55: CYS80 SG477 0.207 1.984 1.570 55: Linking CYS-25 SG-14 and CYS-80 SG-477... 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: WARNING: Residue 1 named ASN of a molecule in the input file was mapped 55: to an entry in the topology database, but the atom H used in 55: an interaction of type angle in that entry is not found in the 55: input file. Perhaps your atom and/or residue naming needs to be 55: fixed. 55: 55: 55: 55: WARNING: WARNING: Residue 58 named ARG of a molecule in the input file was mapped 55: to an entry in the topology database, but the atom O used in 55: an interaction of type angle in that entry is not found in the 55: input file. Perhaps your atom and/or residue naming needs to be 55: fixed. 55: 55: 55: Before cleaning: 972 pairs 55: Before cleaning: 1256 dihedrals 55: Using the Gromos43a1 force field in directory gromos43a1.ff 55: 55: going to rename gromos43a1.ff/aminoacids.r2b 55: Reading /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/E.pdb... 55: Read 'This is a fragment of 2d4f for testing a disulfide bridge', 488 atoms 55: 55: Analyzing pdb file 55: Splitting chemical chains based on TER records or chain id changing. 55: 55: There are 1 chains and 0 blocks of water and 58 residues with 488 atoms 55: 55: chain #res #atoms 55: 55: 1 'A' 58 488 55: 55: All occupancies are one 55: 55: Reading residue database... (Gromos43a1) 55: 55: Processing chain 1 'A' (488 atoms, 58 residues) 55: 55: Identified residue ASN24 as a starting terminus. 55: 55: Identified residue ARG81 as a ending terminus. 55: Start terminus ASN-24: NH3+ 55: End terminus ARG-81: COO- 55: 55: Checking for duplicate atoms.... 55: 55: Generating any missing hydrogen atoms and/or adding termini. 55: 55: Now there are 58 residues with 635 atoms 55: 55: Making bonds... 55: 55: Number of bonds was 655, now 650 55: 55: Generating angles, dihedrals and pairs... 55: 55: Making cmap torsions... 55: 55: There are 321 dihedrals, 350 impropers, 955 angles 55: 972 pairs, 650 bonds and 0 virtual sites 55: 55: Total mass 6908.582 a.m.u. 55: 55: Total charge -6.000 e 55: 55: Writing topology 55: 55: Writing coordinate file... 55: 55: --------- PLEASE NOTE ------------ 55: 55: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/E.pdb. 55: 55: The Gromos43a1 force field and the spce water model are used. 55: 55: --------- ETON ESAELP ------------ 55: [ OK ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spce_vsite_none_id_or_ter_merge_no_Epdb_format_gro_match_file (504 ms) 55: [ RUN ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spce_vsite_h_id_or_ter_merge_no_Apdb_format_gro_match_file 55: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos43a1.ff/aminoacids.r2b 55: All occupancies are one 55: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos43a1.ff/atomtypes.atp 55: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos43a1.ff/aminoacids.rtp 55: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos43a1.ff/aminoacids.hdb 55: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos43a1.ff/aminoacids.n.tdb 55: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos43a1.ff/aminoacids.c.tdb 55: Analysing hydrogen-bonding network for automated assignment of histidine 55: protonation. 25 donors and 23 acceptors were found. 55: There are 41 hydrogen bonds 55: Will use HISE for residue 8 55: 9 out of 9 lines of specbond.dat converted successfully 55: Special Atom Distance matrix: 55: CYS3 HIS8 55: SG9 NE251 55: HIS8 NE251 1.055 55: MET12 SD83 0.763 0.990 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: Marked 37 virtual sites 55: Added 4 dummy masses 55: Added 8 new constraints 55: 55: WARNING: WARNING: Residue 1 named ALA of a molecule in the input file was mapped 55: to an entry in the topology database, but the atom H used in 55: an interaction of type angle in that entry is not found in the 55: input file. Perhaps your atom and/or residue naming needs to be 55: fixed. 55: 55: 55: 55: WARNING: WARNING: Residue 16 named SER of a molecule in the input file was mapped 55: to an entry in the topology database, but the atom O used in 55: an interaction of type angle in that entry is not found in the 55: input file. Perhaps your atom and/or residue naming needs to be 55: fixed. 55: 55: 55: Before cleaning: 267 pairs 55: Before cleaning: 305 dihedrals 55: Using the Gromos43a1 force field in directory gromos43a1.ff 55: 55: going to rename gromos43a1.ff/aminoacids.r2b 55: Reading /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/A.pdb... 55: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms 55: 55: Analyzing pdb file 55: Splitting chemical chains based on TER records or chain id changing. 55: 55: There are 1 chains and 0 blocks of water and 16 residues with 128 atoms 55: 55: chain #res #atoms 55: 55: 1 ' ' 16 128 55: 55: All occupancies are one 55: 55: Reading residue database... (Gromos43a1) 55: 55: Processing chain 1 (128 atoms, 16 residues) 55: 55: Identified residue ALA2 as a starting terminus. 55: 55: Identified residue SER17 as a ending terminus. 55: Start terminus ALA-2: NH3+ 55: End terminus SER-17: COO- 55: 55: Checking for duplicate atoms.... 55: 55: Generating any missing hydrogen atoms and/or adding termini. 55: 55: Now there are 16 residues with 165 atoms 55: 55: Making bonds... 55: 55: Number of bonds was 172, now 167 55: 55: Generating angles, dihedrals and pairs... 55: 55: Making cmap torsions... 55: 55: There are 90 dihedrals, 77 impropers, 241 angles 55: 267 pairs, 167 bonds and 37 virtual sites 55: 55: Total mass 1846.116 a.m.u. 55: 55: Total charge 0.000 e 55: 55: Writing topology 55: 55: Writing coordinate file... 55: 55: --------- PLEASE NOTE ------------ 55: 55: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/A.pdb. 55: 55: The Gromos43a1 force field and the spce water model are used. 55: 55: --------- ETON ESAELP ------------ 55: [ OK ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spce_vsite_h_id_or_ter_merge_no_Apdb_format_gro_match_file (262 ms) 55: [ RUN ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spce_vsite_h_id_or_ter_merge_no_Bpdb_format_gro_match_file 55: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos43a1.ff/aminoacids.r2b 55: All occupancies are one 55: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos43a1.ff/atomtypes.atp 55: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos43a1.ff/aminoacids.rtp 55: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos43a1.ff/aminoacids.hdb 55: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos43a1.ff/aminoacids.n.tdb 55: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos43a1.ff/aminoacids.c.tdb 55: Analysing hydrogen-bonding network for automated assignment of histidine 55: protonation. 30 donors and 22 acceptors were found. 55: There are 36 hydrogen bonds 55: Will use HISE for residue 29 55: Will use HISE for residue 32 55: 9 out of 9 lines of specbond.dat converted successfully 55: Special Atom Distance matrix: 55: CYS27 HIS29 55: SG90 NE2111 55: HIS29 NE2111 0.987 55: HIS32 NE2135 1.590 1.155 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: Marked 53 virtual sites 55: Added 4 dummy masses 55: Added 10 new constraints 55: 55: WARNING: WARNING: Residue 1 named THR of a molecule in the input file was mapped 55: to an entry in the topology database, but the atom H used in 55: an interaction of type angle in that entry is not found in the 55: input file. Perhaps your atom and/or residue naming needs to be 55: fixed. 55: 55: 55: 55: WARNING: WARNING: Residue 16 named PHE of a molecule in the input file was mapped 55: to an entry in the topology database, but the atom O used in 55: an interaction of type angle in that entry is not found in the 55: input file. Perhaps your atom and/or residue naming needs to be 55: fixed. 55: 55: 55: Before cleaning: 273 pairs 55: Before cleaning: 429 dihedrals 55: Using the Gromos43a1 force field in directory gromos43a1.ff 55: 55: going to rename gromos43a1.ff/aminoacids.r2b 55: Reading /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/B.pdb... 55: Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms 55: 55: Analyzing pdb file 55: Splitting chemical chains based on TER records or chain id changing. 55: 55: There are 1 chains and 0 blocks of water and 16 residues with 149 atoms 55: 55: chain #res #atoms 55: 55: 1 ' ' 16 149 55: 55: All occupancies are one 55: 55: Reading residue database... (Gromos43a1) 55: 55: Processing chain 1 (149 atoms, 16 residues) 55: 55: Replaced 1 residue named GLUH to the default GLU. Use interactive selection of protonated residues if that is what you need. 55: 55: Identified residue THR18 as a starting terminus. 55: 55: Identified residue PHE33 as a ending terminus. 55: Start terminus THR-18: NH3+ 55: End terminus PHE-33: COO- 55: 55: Checking for duplicate atoms.... 55: 55: Generating any missing hydrogen atoms and/or adding termini. 55: 55: Now there are 16 residues with 202 atoms 55: 55: Making bonds... 55: 55: Number of bonds was 216, now 211 55: 55: Generating angles, dihedrals and pairs... 55: 55: Making cmap torsions... 55: 55: There are 93 dihedrals, 134 impropers, 316 angles 55: 273 pairs, 211 bonds and 51 virtual sites 55: 55: Total mass 2088.361 a.m.u. 55: 55: Total charge 1.000 e 55: 55: Writing topology 55: 55: Writing coordinate file... 55: 55: --------- PLEASE NOTE ------------ 55: 55: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/B.pdb. 55: 55: The Gromos43a1 force field and the spce water model are used. 55: 55: --------- ETON ESAELP ------------ 55: [ OK ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spce_vsite_h_id_or_ter_merge_no_Bpdb_format_gro_match_file (261 ms) 55: [ RUN ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spce_vsite_h_id_or_ter_merge_no_Cpdb_format_gro_match_file 55: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos43a1.ff/aminoacids.r2b 55: All occupancies are one 55: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos43a1.ff/atomtypes.atp 55: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos43a1.ff/aminoacids.rtp 55: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos43a1.ff/aminoacids.hdb 55: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos43a1.ff/aminoacids.n.tdb 55: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos43a1.ff/aminoacids.c.tdb 55: Analysing hydrogen-bonding network for automated assignment of histidine 55: protonation. 22 donors and 22 acceptors were found. 55: There are 26 hydrogen bonds 55: Will use HISE for residue 45 55: 9 out of 9 lines of specbond.dat converted successfully 55: Special Atom Distance matrix: 55: HIS45 55: NE295 55: MET46 SD102 1.078 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: Marked 36 virtual sites 55: Added 4 dummy masses 55: Added 8 new constraints 55: 55: WARNING: WARNING: Residue 1 named ALA of a molecule in the input file was mapped 55: to an entry in the topology database, but the atom H used in 55: an interaction of type angle in that entry is not found in the 55: input file. Perhaps your atom and/or residue naming needs to be 55: fixed. 55: 55: 55: 55: WARNING: WARNING: Residue 16 named ALA of a molecule in the input file was mapped 55: to an entry in the topology database, but the atom O used in 55: an interaction of type angle in that entry is not found in the 55: input file. Perhaps your atom and/or residue naming needs to be 55: fixed. 55: 55: 55: Before cleaning: 242 pairs 55: Before cleaning: 349 dihedrals 55: Using the Gromos43a1 force field in directory gromos43a1.ff 55: 55: going to rename gromos43a1.ff/aminoacids.r2b 55: Reading /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/C.pdb... 55: Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms 55: 55: Analyzing pdb file 55: Splitting chemical chains based on TER records or chain id changing. 55: 55: There are 1 chains and 0 blocks of water and 16 residues with 132 atoms 55: 55: chain #res #atoms 55: 55: 1 ' ' 16 132 55: 55: All occupancies are one 55: 55: Reading residue database... (Gromos43a1) 55: 55: Processing chain 1 (132 atoms, 16 residues) 55: 55: Identified residue ALA34 as a starting terminus. 55: 55: Identified residue ALA49 as a ending terminus. 55: Start terminus ALA-34: NH3+ 55: End terminus ALA-49: COO- 55: 55: Checking for duplicate atoms.... 55: 55: Generating any missing hydrogen atoms and/or adding termini. 55: 55: Now there are 16 residues with 168 atoms 55: 55: Making bonds... 55: 55: Number of bonds was 179, now 174 55: 55: Generating angles, dihedrals and pairs... 55: 55: Making cmap torsions... 55: 55: There are 81 dihedrals, 102 impropers, 260 angles 55: 242 pairs, 174 bonds and 36 virtual sites 55: 55: Total mass 1861.132 a.m.u. 55: 55: Total charge -1.000 e 55: 55: Writing topology 55: 55: Writing coordinate file... 55: 55: --------- PLEASE NOTE ------------ 55: 55: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/C.pdb. 55: 55: The Gromos43a1 force field and the spce water model are used. 55: 55: --------- ETON ESAELP ------------ 55: [ OK ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spce_vsite_h_id_or_ter_merge_no_Cpdb_format_gro_match_file (241 ms) 55: [ RUN ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spce_vsite_h_id_or_ter_merge_no_Dpdb_format_gro_match_file 55: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos43a1.ff/aminoacids.r2b 55: All occupancies are one 55: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos43a1.ff/atomtypes.atp 55: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos43a1.ff/aminoacids.rtp 55: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos43a1.ff/aminoacids.hdb 55: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos43a1.ff/aminoacids.n.tdb 55: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos43a1.ff/aminoacids.c.tdb 55: Analysing hydrogen-bonding network for automated assignment of histidine 55: protonation. 22 donors and 21 acceptors were found. 55: There are 30 hydrogen bonds 55: Will use HISE for residue 60 55: 9 out of 9 lines of specbond.dat converted successfully 55: Special Atom Distance matrix: 55: HIS60 55: NE285 55: CYS62 SG98 0.803 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: Marked 33 virtual sites 55: Added 4 dummy masses 55: Added 10 new constraints 55: 55: WARNING: WARNING: Residue 1 named LYS of a molecule in the input file was mapped 55: to an entry in the topology database, but the atom H used in 55: an interaction of type angle in that entry is not found in the 55: input file. Perhaps your atom and/or residue naming needs to be 55: fixed. 55: 55: 55: 55: WARNING: WARNING: Residue 16 named PRO of a molecule in the input file was mapped 55: to an entry in the topology database, but the atom O used in 55: an interaction of type angle in that entry is not found in the 55: input file. Perhaps your atom and/or residue naming needs to be 55: fixed. 55: 55: 55: Before cleaning: 232 pairs 55: Before cleaning: 299 dihedrals 55: Using the Gromos43a1 force field in directory gromos43a1.ff 55: 55: going to rename gromos43a1.ff/aminoacids.r2b 55: Reading /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/D.pdb... 55: Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms 55: 55: Analyzing pdb file 55: Splitting chemical chains based on TER records or chain id changing. 55: 55: There are 1 chains and 0 blocks of water and 16 residues with 117 atoms 55: 55: chain #res #atoms 55: 55: 1 ' ' 16 117 55: 55: All occupancies are one 55: 55: Reading residue database... (Gromos43a1) 55: 55: Processing chain 1 (117 atoms, 16 residues) 55: 55: Replaced 1 residue named ASPH to the default ASP. Use interactive selection of protonated residues if that is what you need. 55: 55: Identified residue LYS50 as a starting terminus. 55: 55: Identified residue PRO65 as a ending terminus. 55: Start terminus LYS-50: NH3+ 55: End terminus PRO-65: COO- 55: 55: Checking for duplicate atoms.... 55: 55: Generating any missing hydrogen atoms and/or adding termini. 55: 55: Now there are 16 residues with 150 atoms 55: 55: Making bonds... 55: 55: Number of bonds was 159, now 154 55: 55: Generating angles, dihedrals and pairs... 55: 55: Making cmap torsions... 55: 55: There are 78 dihedrals, 80 impropers, 227 angles 55: 232 pairs, 154 bonds and 31 virtual sites 55: 55: Total mass 1662.887 a.m.u. 55: 55: Total charge 0.000 e 55: 55: Writing topology 55: 55: Writing coordinate file... 55: 55: --------- PLEASE NOTE ------------ 55: 55: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/D.pdb. 55: 55: The Gromos43a1 force field and the spce water model are used. 55: 55: --------- ETON ESAELP ------------ 55: [ OK ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spce_vsite_h_id_or_ter_merge_no_Dpdb_format_gro_match_file (240 ms) 55: [ RUN ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spce_vsite_h_id_or_ter_merge_no_Epdb_format_gro_match_file 55: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos43a1.ff/aminoacids.r2b 55: All occupancies are one 55: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos43a1.ff/atomtypes.atp 55: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos43a1.ff/aminoacids.rtp 55: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos43a1.ff/aminoacids.hdb 55: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos43a1.ff/aminoacids.n.tdb 55: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos43a1.ff/aminoacids.c.tdb 55: Analysing hydrogen-bonding network for automated assignment of histidine 55: protonation. 89 donors and 98 acceptors were found. 55: There are 129 hydrogen bonds 55: Will use HISE for residue 31 55: Will use HISE for residue 51 55: 9 out of 9 lines of specbond.dat converted successfully 55: Special Atom Distance matrix: 55: CYS25 HIS31 HIS51 55: SG14 NE264 NE2226 55: HIS31 NE264 1.921 55: HIS51 NE2226 1.498 2.650 55: CYS80 SG477 0.207 1.984 1.570 55: Linking CYS-25 SG-14 and CYS-80 SG-477... 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: Marked 146 virtual sites 55: Added 10 dummy masses 55: Added 29 new constraints 55: 55: WARNING: WARNING: Residue 1 named ASN of a molecule in the input file was mapped 55: to an entry in the topology database, but the atom H used in 55: an interaction of type angle in that entry is not found in the 55: input file. Perhaps your atom and/or residue naming needs to be 55: fixed. 55: 55: 55: 55: WARNING: WARNING: Residue 58 named ARG of a molecule in the input file was mapped 55: to an entry in the topology database, but the atom O used in 55: an interaction of type angle in that entry is not found in the 55: input file. Perhaps your atom and/or residue naming needs to be 55: fixed. 55: 55: 55: Before cleaning: 972 pairs 55: Before cleaning: 1256 dihedrals 55: Using the Gromos43a1 force field in directory gromos43a1.ff 55: 55: going to rename gromos43a1.ff/aminoacids.r2b 55: Reading /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/E.pdb... 55: Read 'This is a fragment of 2d4f for testing a disulfide bridge', 488 atoms 55: 55: Analyzing pdb file 55: Splitting chemical chains based on TER records or chain id changing. 55: 55: There are 1 chains and 0 blocks of water and 58 residues with 488 atoms 55: 55: chain #res #atoms 55: 55: 1 'A' 58 488 55: 55: All occupancies are one 55: 55: Reading residue database... (Gromos43a1) 55: 55: Processing chain 1 'A' (488 atoms, 58 residues) 55: 55: Identified residue ASN24 as a starting terminus. 55: 55: Identified residue ARG81 as a ending terminus. 55: Start terminus ASN-24: NH3+ 55: End terminus ARG-81: COO- 55: 55: Checking for duplicate atoms.... 55: 55: Generating any missing hydrogen atoms and/or adding termini. 55: 55: Now there are 58 residues with 635 atoms 55: 55: Making bonds... 55: 55: Number of bonds was 655, now 650 55: 55: Generating angles, dihedrals and pairs... 55: 55: Making cmap torsions... 55: 55: There are 321 dihedrals, 350 impropers, 955 angles 55: 972 pairs, 650 bonds and 137 virtual sites 55: 55: Total mass 6908.582 a.m.u. 55: 55: Total charge -6.000 e 55: 55: Writing topology 55: 55: Writing coordinate file... 55: 55: --------- PLEASE NOTE ------------ 55: 55: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/E.pdb. 55: 55: The Gromos43a1 force field and the spce water model are used. 55: 55: --------- ETON ESAELP ------------ 55: [ OK ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spce_vsite_h_id_or_ter_merge_no_Epdb_format_gro_match_file (530 ms) 55: [----------] 20 tests from G43a1/Pdb2gmxTest (6351 ms total) 55: 55: [----------] 20 tests from G53a6/Pdb2gmxTest 55: [ RUN ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spc_vsite_none_id_or_ter_merge_no_Apdb_format_gro_match_file 55: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos53a6.ff/aminoacids.r2b 55: All occupancies are one 55: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos53a6.ff/atomtypes.atp 55: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos53a6.ff/aminoacids.rtp 55: 55: Using default: removing proper dihedrals found on the same bond as a proper dihedral 55: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos53a6.ff/aminoacids.hdb 55: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos53a6.ff/aminoacids.n.tdb 55: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos53a6.ff/aminoacids.c.tdb 55: Analysing hydrogen-bonding network for automated assignment of histidine 55: protonation. 25 donors and 23 acceptors were found. 55: There are 41 hydrogen bonds 55: Will use HISE for residue 8 55: 9 out of 9 lines of specbond.dat converted successfully 55: Special Atom Distance matrix: 55: CYS3 HIS8 55: SG9 NE251 55: HIS8 NE251 1.055 55: MET12 SD83 0.763 0.990 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: WARNING: Residue 1 named ALA of a molecule in the input file was mapped 55: to an entry in the topology database, but the atom H used in 55: an interaction of type angle in that entry is not found in the 55: input file. Perhaps your atom and/or residue naming needs to be 55: fixed. 55: 55: 55: 55: WARNING: WARNING: Residue 16 named SER of a molecule in the input file was mapped 55: to an entry in the topology database, but the atom O used in 55: an interaction of type angle in that entry is not found in the 55: input file. Perhaps your atom and/or residue naming needs to be 55: fixed. 55: 55: 55: Before cleaning: 267 pairs 55: Before cleaning: 312 dihedrals 55: Using the Gromos53a6 force field in directory gromos53a6.ff 55: 55: going to rename gromos53a6.ff/aminoacids.r2b 55: Reading /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/A.pdb... 55: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms 55: 55: Analyzing pdb file 55: Splitting chemical chains based on TER records or chain id changing. 55: 55: There are 1 chains and 0 blocks of water and 16 residues with 128 atoms 55: 55: chain #res #atoms 55: 55: 1 ' ' 16 128 55: 55: All occupancies are one 55: 55: Reading residue database... (Gromos53a6) 55: 55: Using default: not generating all possible dihedrals 55: 55: Using default: excluding 3 bonded neighbors 55: 55: Using default: generating 1,4 H--H interactions 55: 55: Using default: removing proper dihedrals found on the same bond as a proper dihedral 55: 55: Processing chain 1 (128 atoms, 16 residues) 55: 55: Identified residue ALA2 as a starting terminus. 55: 55: Identified residue SER17 as a ending terminus. 55: Start terminus ALA-2: NH3+ 55: End terminus SER-17: COO- 55: 55: Checking for duplicate atoms.... 55: 55: Generating any missing hydrogen atoms and/or adding termini. 55: 55: Now there are 16 residues with 167 atoms 55: 55: Making bonds... 55: 55: Number of bonds was 174, now 169 55: 55: Generating angles, dihedrals and pairs... 55: 55: Making cmap torsions... 55: 55: There are 90 dihedrals, 79 impropers, 245 angles 55: 267 pairs, 169 bonds and 0 virtual sites 55: 55: Total mass 1846.116 a.m.u. 55: 55: Total charge -0.000 e 55: 55: Writing topology 55: 55: Writing coordinate file... 55: 55: --------- PLEASE NOTE ------------ 55: 55: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/A.pdb. 55: 55: The Gromos53a6 force field and the spc water model are used. 55: 55: --------- ETON ESAELP ------------ 55: [ OK ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spc_vsite_none_id_or_ter_merge_no_Apdb_format_gro_match_file (266 ms) 55: [ RUN ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spc_vsite_none_id_or_ter_merge_no_Bpdb_format_gro_match_file 55: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos53a6.ff/aminoacids.r2b 55: All occupancies are one 55: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos53a6.ff/atomtypes.atp 55: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos53a6.ff/aminoacids.rtp 55: 55: Using default: removing proper dihedrals found on the same bond as a proper dihedral 55: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos53a6.ff/aminoacids.hdb 55: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos53a6.ff/aminoacids.n.tdb 55: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos53a6.ff/aminoacids.c.tdb 55: Analysing hydrogen-bonding network for automated assignment of histidine 55: protonation. 30 donors and 22 acceptors were found. 55: There are 36 hydrogen bonds 55: Will use HISE for residue 29 55: Will use HISE for residue 32 55: 9 out of 9 lines of specbond.dat converted successfully 55: Special Atom Distance matrix: 55: CYS27 HIS29 55: SG90 NE2111 55: HIS29 NE2111 0.987 55: HIS32 NE2135 1.590 1.155 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: WARNING: Residue 1 named THR of a molecule in the input file was mapped 55: to an entry in the topology database, but the atom H used in 55: an interaction of type angle in that entry is not found in the 55: input file. Perhaps your atom and/or residue naming needs to be 55: fixed. 55: 55: 55: 55: WARNING: WARNING: Residue 16 named PHE of a molecule in the input file was mapped 55: to an entry in the topology database, but the atom O used in 55: an interaction of type angle in that entry is not found in the 55: input file. Perhaps your atom and/or residue naming needs to be 55: fixed. 55: 55: 55: Before cleaning: 273 pairs 55: Before cleaning: 443 dihedrals 55: Using the Gromos53a6 force field in directory gromos53a6.ff 55: 55: going to rename gromos53a6.ff/aminoacids.r2b 55: Reading /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/B.pdb... 55: Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms 55: 55: Analyzing pdb file 55: Splitting chemical chains based on TER records or chain id changing. 55: 55: There are 1 chains and 0 blocks of water and 16 residues with 149 atoms 55: 55: chain #res #atoms 55: 55: 1 ' ' 16 149 55: 55: All occupancies are one 55: 55: Reading residue database... (Gromos53a6) 55: 55: Using default: not generating all possible dihedrals 55: 55: Using default: excluding 3 bonded neighbors 55: 55: Using default: generating 1,4 H--H interactions 55: 55: Using default: removing proper dihedrals found on the same bond as a proper dihedral 55: 55: Processing chain 1 (149 atoms, 16 residues) 55: 55: Replaced 1 residue named GLUH to the default GLU. Use interactive selection of protonated residues if that is what you need. 55: 55: Identified residue THR18 as a starting terminus. 55: 55: Identified residue PHE33 as a ending terminus. 55: Start terminus THR-18: NH3+ 55: End terminus PHE-33: COO- 55: 55: Checking for duplicate atoms.... 55: 55: Generating any missing hydrogen atoms and/or adding termini. 55: 55: Now there are 16 residues with 206 atoms 55: 55: Making bonds... 55: 55: Number of bonds was 220, now 215 55: 55: Generating angles, dihedrals and pairs... 55: 55: Making cmap torsions... 55: 55: There are 93 dihedrals, 138 impropers, 324 angles 55: 273 pairs, 215 bonds and 0 virtual sites 55: 55: Total mass 2088.361 a.m.u. 55: 55: Total charge 1.000 e 55: 55: Writing topology 55: 55: Writing coordinate file... 55: 55: --------- PLEASE NOTE ------------ 55: 55: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/B.pdb. 55: 55: The Gromos53a6 force field and the spc water model are used. 55: 55: --------- ETON ESAELP ------------ 55: [ OK ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spc_vsite_none_id_or_ter_merge_no_Bpdb_format_gro_match_file (305 ms) 55: [ RUN ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spc_vsite_none_id_or_ter_merge_no_Cpdb_format_gro_match_file 55: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos53a6.ff/aminoacids.r2b 55: All occupancies are one 55: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos53a6.ff/atomtypes.atp 55: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos53a6.ff/aminoacids.rtp 55: 55: Using default: removing proper dihedrals found on the same bond as a proper dihedral 55: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos53a6.ff/aminoacids.hdb 55: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos53a6.ff/aminoacids.n.tdb 55: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos53a6.ff/aminoacids.c.tdb 55: Analysing hydrogen-bonding network for automated assignment of histidine 55: protonation. 22 donors and 22 acceptors were found. 55: There are 26 hydrogen bonds 55: Will use HISE for residue 45 55: 9 out of 9 lines of specbond.dat converted successfully 55: Special Atom Distance matrix: 55: HIS45 55: NE295 55: MET46 SD102 1.078 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: WARNING: Residue 1 named ALA of a molecule in the input file was mapped 55: to an entry in the topology database, but the atom H used in 55: an interaction of type angle in that entry is not found in the 55: input file. Perhaps your atom and/or residue naming needs to be 55: fixed. 55: 55: 55: 55: WARNING: WARNING: Residue 16 named ALA of a molecule in the input file was mapped 55: to an entry in the topology database, but the atom O used in 55: an interaction of type angle in that entry is not found in the 55: input file. Perhaps your atom and/or residue naming needs to be 55: fixed. 55: 55: 55: Before cleaning: 242 pairs 55: Before cleaning: 356 dihedrals 55: Using the Gromos53a6 force field in directory gromos53a6.ff 55: 55: going to rename gromos53a6.ff/aminoacids.r2b 55: Reading /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/C.pdb... 55: Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms 55: 55: Analyzing pdb file 55: Splitting chemical chains based on TER records or chain id changing. 55: 55: There are 1 chains and 0 blocks of water and 16 residues with 132 atoms 55: 55: chain #res #atoms 55: 55: 1 ' ' 16 132 55: 55: All occupancies are one 55: 55: Reading residue database... (Gromos53a6) 55: 55: Using default: not generating all possible dihedrals 55: 55: Using default: excluding 3 bonded neighbors 55: 55: Using default: generating 1,4 H--H interactions 55: 55: Using default: removing proper dihedrals found on the same bond as a proper dihedral 55: 55: Processing chain 1 (132 atoms, 16 residues) 55: 55: Identified residue ALA34 as a starting terminus. 55: 55: Identified residue ALA49 as a ending terminus. 55: Start terminus ALA-34: NH3+ 55: End terminus ALA-49: COO- 55: 55: Checking for duplicate atoms.... 55: 55: Generating any missing hydrogen atoms and/or adding termini. 55: 55: Now there are 16 residues with 170 atoms 55: 55: Making bonds... 55: 55: Number of bonds was 181, now 176 55: 55: Generating angles, dihedrals and pairs... 55: 55: Making cmap torsions... 55: 55: There are 81 dihedrals, 104 impropers, 264 angles 55: 242 pairs, 176 bonds and 0 virtual sites 55: 55: Total mass 1861.132 a.m.u. 55: 55: Total charge -1.000 e 55: 55: Writing topology 55: 55: Writing coordinate file... 55: 55: --------- PLEASE NOTE ------------ 55: 55: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/C.pdb. 55: 55: The Gromos53a6 force field and the spc water model are used. 55: 55: --------- ETON ESAELP ------------ 55: [ OK ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spc_vsite_none_id_or_ter_merge_no_Cpdb_format_gro_match_file (283 ms) 55: [ RUN ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spc_vsite_none_id_or_ter_merge_no_Dpdb_format_gro_match_file 55: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos53a6.ff/aminoacids.r2b 55: All occupancies are one 55: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos53a6.ff/atomtypes.atp 55: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos53a6.ff/aminoacids.rtp 55: 55: Using default: removing proper dihedrals found on the same bond as a proper dihedral 55: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos53a6.ff/aminoacids.hdb 55: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos53a6.ff/aminoacids.n.tdb 55: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos53a6.ff/aminoacids.c.tdb 55: Analysing hydrogen-bonding network for automated assignment of histidine 55: protonation. 22 donors and 21 acceptors were found. 55: There are 30 hydrogen bonds 55: Will use HISE for residue 60 55: 9 out of 9 lines of specbond.dat converted successfully 55: Special Atom Distance matrix: 55: HIS60 55: NE285 55: CYS62 SG98 0.803 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: WARNING: Residue 1 named LYS of a molecule in the input file was mapped 55: to an entry in the topology database, but the atom H used in 55: an interaction of type angle in that entry is not found in the 55: input file. Perhaps your atom and/or residue naming needs to be 55: fixed. 55: 55: 55: 55: WARNING: WARNING: Residue 16 named PRO of a molecule in the input file was mapped 55: to an entry in the topology database, but the atom O used in 55: an interaction of type angle in that entry is not found in the 55: input file. Perhaps your atom and/or residue naming needs to be 55: fixed. 55: 55: 55: Before cleaning: 232 pairs 55: Before cleaning: 306 dihedrals 55: Using the Gromos53a6 force field in directory gromos53a6.ff 55: 55: going to rename gromos53a6.ff/aminoacids.r2b 55: Reading /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/D.pdb... 55: Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms 55: 55: Analyzing pdb file 55: Splitting chemical chains based on TER records or chain id changing. 55: 55: There are 1 chains and 0 blocks of water and 16 residues with 117 atoms 55: 55: chain #res #atoms 55: 55: 1 ' ' 16 117 55: 55: All occupancies are one 55: 55: Reading residue database... (Gromos53a6) 55: 55: Using default: not generating all possible dihedrals 55: 55: Using default: excluding 3 bonded neighbors 55: 55: Using default: generating 1,4 H--H interactions 55: 55: Using default: removing proper dihedrals found on the same bond as a proper dihedral 55: 55: Processing chain 1 (117 atoms, 16 residues) 55: 55: Replaced 1 residue named ASPH to the default ASP. Use interactive selection of protonated residues if that is what you need. 55: 55: Identified residue LYS50 as a starting terminus. 55: 55: Identified residue PRO65 as a ending terminus. 55: Start terminus LYS-50: NH3+ 55: End terminus PRO-65: COO- 55: 55: Checking for duplicate atoms.... 55: 55: Generating any missing hydrogen atoms and/or adding termini. 55: 55: Now there are 16 residues with 152 atoms 55: 55: Making bonds... 55: 55: Number of bonds was 161, now 156 55: 55: Generating angles, dihedrals and pairs... 55: 55: Making cmap torsions... 55: 55: There are 78 dihedrals, 82 impropers, 231 angles 55: 232 pairs, 156 bonds and 0 virtual sites 55: 55: Total mass 1662.887 a.m.u. 55: 55: Total charge -0.000 e 55: 55: Writing topology 55: 55: Writing coordinate file... 55: 55: --------- PLEASE NOTE ------------ 55: 55: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/D.pdb. 55: 55: The Gromos53a6 force field and the spc water model are used. 55: 55: --------- ETON ESAELP ------------ 55: [ OK ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spc_vsite_none_id_or_ter_merge_no_Dpdb_format_gro_match_file (272 ms) 55: [ RUN ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spc_vsite_none_id_or_ter_merge_no_Epdb_format_gro_match_file 55: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos53a6.ff/aminoacids.r2b 55: All occupancies are one 55: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos53a6.ff/atomtypes.atp 55: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos53a6.ff/aminoacids.rtp 55: 55: Using default: removing proper dihedrals found on the same bond as a proper dihedral 55: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos53a6.ff/aminoacids.hdb 55: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos53a6.ff/aminoacids.n.tdb 55: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos53a6.ff/aminoacids.c.tdb 55: Analysing hydrogen-bonding network for automated assignment of histidine 55: protonation. 89 donors and 98 acceptors were found. 55: There are 129 hydrogen bonds 55: Will use HISE for residue 31 55: Will use HISE for residue 51 55: 9 out of 9 lines of specbond.dat converted successfully 55: Special Atom Distance matrix: 55: CYS25 HIS31 HIS51 55: SG14 NE264 NE2226 55: HIS31 NE264 1.921 55: HIS51 NE2226 1.498 2.650 55: CYS80 SG477 0.207 1.984 1.570 55: Linking CYS-25 SG-14 and CYS-80 SG-477... 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: WARNING: Residue 1 named ASN of a molecule in the input file was mapped 55: to an entry in the topology database, but the atom H used in 55: an interaction of type angle in that entry is not found in the 55: input file. Perhaps your atom and/or residue naming needs to be 55: fixed. 55: 55: 55: 55: WARNING: WARNING: Residue 58 named ARG of a molecule in the input file was mapped 55: to an entry in the topology database, but the atom O used in 55: an interaction of type angle in that entry is not found in the 55: input file. Perhaps your atom and/or residue naming needs to be 55: fixed. 55: 55: 55: Before cleaning: 972 pairs 55: Before cleaning: 1270 dihedrals 55: Using the Gromos53a6 force field in directory gromos53a6.ff 55: 55: going to rename gromos53a6.ff/aminoacids.r2b 55: Reading /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/E.pdb... 55: Read 'This is a fragment of 2d4f for testing a disulfide bridge', 488 atoms 55: 55: Analyzing pdb file 55: Splitting chemical chains based on TER records or chain id changing. 55: 55: There are 1 chains and 0 blocks of water and 58 residues with 488 atoms 55: 55: chain #res #atoms 55: 55: 1 'A' 58 488 55: 55: All occupancies are one 55: 55: Reading residue database... (Gromos53a6) 55: 55: Using default: not generating all possible dihedrals 55: 55: Using default: excluding 3 bonded neighbors 55: 55: Using default: generating 1,4 H--H interactions 55: 55: Using default: removing proper dihedrals found on the same bond as a proper dihedral 55: 55: Processing chain 1 'A' (488 atoms, 58 residues) 55: 55: Identified residue ASN24 as a starting terminus. 55: 55: Identified residue ARG81 as a ending terminus. 55: Start terminus ASN-24: NH3+ 55: End terminus ARG-81: COO- 55: 55: Checking for duplicate atoms.... 55: 55: Generating any missing hydrogen atoms and/or adding termini. 55: 55: Now there are 58 residues with 639 atoms 55: 55: Making bonds... 55: 55: Number of bonds was 659, now 654 55: 55: Generating angles, dihedrals and pairs... 55: 55: Making cmap torsions... 55: 55: There are 321 dihedrals, 354 impropers, 963 angles 55: 972 pairs, 654 bonds and 0 virtual sites 55: 55: Total mass 6908.582 a.m.u. 55: 55: Total charge -6.000 e 55: 55: Writing topology 55: 55: Writing coordinate file... 55: 55: --------- PLEASE NOTE ------------ 55: 55: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/E.pdb. 55: 55: The Gromos53a6 force field and the spc water model are used. 55: 55: --------- ETON ESAELP ------------ 55: [ OK ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spc_vsite_none_id_or_ter_merge_no_Epdb_format_gro_match_file (511 ms) 55: [ RUN ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spc_vsite_h_id_or_ter_merge_no_Apdb_format_gro_match_file 55: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos53a6.ff/aminoacids.r2b 55: All occupancies are one 55: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos53a6.ff/atomtypes.atp 55: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos53a6.ff/aminoacids.rtp 55: 55: Using default: removing proper dihedrals found on the same bond as a proper dihedral 55: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos53a6.ff/aminoacids.hdb 55: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos53a6.ff/aminoacids.n.tdb 55: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos53a6.ff/aminoacids.c.tdb 55: Analysing hydrogen-bonding network for automated assignment of histidine 55: protonation. 25 donors and 23 acceptors were found. 55: There are 41 hydrogen bonds 55: Will use HISE for residue 8 55: 9 out of 9 lines of specbond.dat converted successfully 55: Special Atom Distance matrix: 55: CYS3 HIS8 55: SG9 NE251 55: HIS8 NE251 1.055 55: MET12 SD83 0.763 0.990 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: Marked 39 virtual sites 55: Added 4 dummy masses 55: Added 8 new constraints 55: 55: WARNING: WARNING: Residue 1 named ALA of a molecule in the input file was mapped 55: to an entry in the topology database, but the atom H used in 55: an interaction of type angle in that entry is not found in the 55: input file. Perhaps your atom and/or residue naming needs to be 55: fixed. 55: 55: 55: 55: WARNING: WARNING: Residue 16 named SER of a molecule in the input file was mapped 55: to an entry in the topology database, but the atom O used in 55: an interaction of type angle in that entry is not found in the 55: input file. Perhaps your atom and/or residue naming needs to be 55: fixed. 55: 55: 55: Before cleaning: 267 pairs 55: Before cleaning: 312 dihedrals 55: Using the Gromos53a6 force field in directory gromos53a6.ff 55: 55: going to rename gromos53a6.ff/aminoacids.r2b 55: Reading /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/A.pdb... 55: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms 55: 55: Analyzing pdb file 55: Splitting chemical chains based on TER records or chain id changing. 55: 55: There are 1 chains and 0 blocks of water and 16 residues with 128 atoms 55: 55: chain #res #atoms 55: 55: 1 ' ' 16 128 55: 55: All occupancies are one 55: 55: Reading residue database... (Gromos53a6) 55: 55: Using default: not generating all possible dihedrals 55: 55: Using default: excluding 3 bonded neighbors 55: 55: Using default: generating 1,4 H--H interactions 55: 55: Using default: removing proper dihedrals found on the same bond as a proper dihedral 55: 55: Processing chain 1 (128 atoms, 16 residues) 55: 55: Identified residue ALA2 as a starting terminus. 55: 55: Identified residue SER17 as a ending terminus. 55: Start terminus ALA-2: NH3+ 55: End terminus SER-17: COO- 55: 55: Checking for duplicate atoms.... 55: 55: Generating any missing hydrogen atoms and/or adding termini. 55: 55: Now there are 16 residues with 167 atoms 55: 55: Making bonds... 55: 55: Number of bonds was 174, now 169 55: 55: Generating angles, dihedrals and pairs... 55: 55: Making cmap torsions... 55: 55: There are 90 dihedrals, 79 impropers, 245 angles 55: 267 pairs, 169 bonds and 39 virtual sites 55: 55: Total mass 1846.116 a.m.u. 55: 55: Total charge -0.000 e 55: 55: Writing topology 55: 55: Writing coordinate file... 55: 55: --------- PLEASE NOTE ------------ 55: 55: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/A.pdb. 55: 55: The Gromos53a6 force field and the spc water model are used. 55: 55: --------- ETON ESAELP ------------ 55: [ OK ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spc_vsite_h_id_or_ter_merge_no_Apdb_format_gro_match_file (310 ms) 55: [ RUN ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spc_vsite_h_id_or_ter_merge_no_Bpdb_format_gro_match_file 55: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos53a6.ff/aminoacids.r2b 55: All occupancies are one 55: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos53a6.ff/atomtypes.atp 55: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos53a6.ff/aminoacids.rtp 55: 55: Using default: removing proper dihedrals found on the same bond as a proper dihedral 55: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos53a6.ff/aminoacids.hdb 55: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos53a6.ff/aminoacids.n.tdb 55: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos53a6.ff/aminoacids.c.tdb 55: Analysing hydrogen-bonding network for automated assignment of histidine 55: protonation. 30 donors and 22 acceptors were found. 55: There are 36 hydrogen bonds 55: Will use HISE for residue 29 55: Will use HISE for residue 32 55: 9 out of 9 lines of specbond.dat converted successfully 55: Special Atom Distance matrix: 55: CYS27 HIS29 55: SG90 NE2111 55: HIS29 NE2111 0.987 55: HIS32 NE2135 1.590 1.155 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: Marked 57 virtual sites 55: Added 4 dummy masses 55: Added 10 new constraints 55: 55: WARNING: WARNING: Residue 1 named THR of a molecule in the input file was mapped 55: to an entry in the topology database, but the atom H used in 55: an interaction of type angle in that entry is not found in the 55: input file. Perhaps your atom and/or residue naming needs to be 55: fixed. 55: 55: 55: 55: WARNING: WARNING: Residue 16 named PHE of a molecule in the input file was mapped 55: to an entry in the topology database, but the atom O used in 55: an interaction of type angle in that entry is not found in the 55: input file. Perhaps your atom and/or residue naming needs to be 55: fixed. 55: 55: 55: Before cleaning: 273 pairs 55: Before cleaning: 443 dihedrals 55: Using the Gromos53a6 force field in directory gromos53a6.ff 55: 55: going to rename gromos53a6.ff/aminoacids.r2b 55: Reading /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/B.pdb... 55: Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms 55: 55: Analyzing pdb file 55: Splitting chemical chains based on TER records or chain id changing. 55: 55: There are 1 chains and 0 blocks of water and 16 residues with 149 atoms 55: 55: chain #res #atoms 55: 55: 1 ' ' 16 149 55: 55: All occupancies are one 55: 55: Reading residue database... (Gromos53a6) 55: 55: Using default: not generating all possible dihedrals 55: 55: Using default: excluding 3 bonded neighbors 55: 55: Using default: generating 1,4 H--H interactions 55: 55: Using default: removing proper dihedrals found on the same bond as a proper dihedral 55: 55: Processing chain 1 (149 atoms, 16 residues) 55: 55: Replaced 1 residue named GLUH to the default GLU. Use interactive selection of protonated residues if that is what you need. 55: 55: Identified residue THR18 as a starting terminus. 55: 55: Identified residue PHE33 as a ending terminus. 55: Start terminus THR-18: NH3+ 55: End terminus PHE-33: COO- 55: 55: Checking for duplicate atoms.... 55: 55: Generating any missing hydrogen atoms and/or adding termini. 55: 55: Now there are 16 residues with 206 atoms 55: 55: Making bonds... 55: 55: Number of bonds was 220, now 215 55: 55: Generating angles, dihedrals and pairs... 55: 55: Making cmap torsions... 55: 55: There are 93 dihedrals, 138 impropers, 324 angles 55: 273 pairs, 215 bonds and 55 virtual sites 55: 55: Total mass 2088.361 a.m.u. 55: 55: Total charge 1.000 e 55: 55: Writing topology 55: 55: Writing coordinate file... 55: 55: --------- PLEASE NOTE ------------ 55: 55: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/B.pdb. 55: 55: The Gromos53a6 force field and the spc water model are used. 55: 55: --------- ETON ESAELP ------------ 55: [ OK ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spc_vsite_h_id_or_ter_merge_no_Bpdb_format_gro_match_file (299 ms) 55: [ RUN ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spc_vsite_h_id_or_ter_merge_no_Cpdb_format_gro_match_file 55: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos53a6.ff/aminoacids.r2b 55: All occupancies are one 55: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos53a6.ff/atomtypes.atp 55: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos53a6.ff/aminoacids.rtp 55: 55: Using default: removing proper dihedrals found on the same bond as a proper dihedral 55: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos53a6.ff/aminoacids.hdb 55: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos53a6.ff/aminoacids.n.tdb 55: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos53a6.ff/aminoacids.c.tdb 55: Analysing hydrogen-bonding network for automated assignment of histidine 55: protonation. 22 donors and 22 acceptors were found. 55: There are 26 hydrogen bonds 55: Will use HISE for residue 45 55: 9 out of 9 lines of specbond.dat converted successfully 55: Special Atom Distance matrix: 55: HIS45 55: NE295 55: MET46 SD102 1.078 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: Marked 38 virtual sites 55: Added 4 dummy masses 55: Added 8 new constraints 55: 55: WARNING: WARNING: Residue 1 named ALA of a molecule in the input file was mapped 55: to an entry in the topology database, but the atom H used in 55: an interaction of type angle in that entry is not found in the 55: input file. Perhaps your atom and/or residue naming needs to be 55: fixed. 55: 55: 55: 55: WARNING: WARNING: Residue 16 named ALA of a molecule in the input file was mapped 55: to an entry in the topology database, but the atom O used in 55: an interaction of type angle in that entry is not found in the 55: input file. Perhaps your atom and/or residue naming needs to be 55: fixed. 55: 55: 55: Before cleaning: 242 pairs 55: Before cleaning: 356 dihedrals 55: Using the Gromos53a6 force field in directory gromos53a6.ff 55: 55: going to rename gromos53a6.ff/aminoacids.r2b 55: Reading /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/C.pdb... 55: Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms 55: 55: Analyzing pdb file 55: Splitting chemical chains based on TER records or chain id changing. 55: 55: There are 1 chains and 0 blocks of water and 16 residues with 132 atoms 55: 55: chain #res #atoms 55: 55: 1 ' ' 16 132 55: 55: All occupancies are one 55: 55: Reading residue database... (Gromos53a6) 55: 55: Using default: not generating all possible dihedrals 55: 55: Using default: excluding 3 bonded neighbors 55: 55: Using default: generating 1,4 H--H interactions 55: 55: Using default: removing proper dihedrals found on the same bond as a proper dihedral 55: 55: Processing chain 1 (132 atoms, 16 residues) 55: 55: Identified residue ALA34 as a starting terminus. 55: 55: Identified residue ALA49 as a ending terminus. 55: Start terminus ALA-34: NH3+ 55: End terminus ALA-49: COO- 55: 55: Checking for duplicate atoms.... 55: 55: Generating any missing hydrogen atoms and/or adding termini. 55: 55: Now there are 16 residues with 170 atoms 55: 55: Making bonds... 55: 55: Number of bonds was 181, now 176 55: 55: Generating angles, dihedrals and pairs... 55: 55: Making cmap torsions... 55: 55: There are 81 dihedrals, 104 impropers, 264 angles 55: 242 pairs, 176 bonds and 38 virtual sites 55: 55: Total mass 1861.132 a.m.u. 55: 55: Total charge -1.000 e 55: 55: Writing topology 55: 55: Writing coordinate file... 55: 55: --------- PLEASE NOTE ------------ 55: 55: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/C.pdb. 55: 55: The Gromos53a6 force field and the spc water model are used. 55: 55: --------- ETON ESAELP ------------ 55: [ OK ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spc_vsite_h_id_or_ter_merge_no_Cpdb_format_gro_match_file (305 ms) 55: [ RUN ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spc_vsite_h_id_or_ter_merge_no_Dpdb_format_gro_match_file 55: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos53a6.ff/aminoacids.r2b 55: All occupancies are one 55: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos53a6.ff/atomtypes.atp 55: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos53a6.ff/aminoacids.rtp 55: 55: Using default: removing proper dihedrals found on the same bond as a proper dihedral 55: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos53a6.ff/aminoacids.hdb 55: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos53a6.ff/aminoacids.n.tdb 55: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos53a6.ff/aminoacids.c.tdb 55: Analysing hydrogen-bonding network for automated assignment of histidine 55: protonation. 22 donors and 21 acceptors were found. 55: There are 30 hydrogen bonds 55: Will use HISE for residue 60 55: 9 out of 9 lines of specbond.dat converted successfully 55: Special Atom Distance matrix: 55: HIS60 55: NE285 55: CYS62 SG98 0.803 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: Marked 35 virtual sites 55: Added 4 dummy masses 55: Added 10 new constraints 55: 55: WARNING: WARNING: Residue 1 named LYS of a molecule in the input file was mapped 55: to an entry in the topology database, but the atom H used in 55: an interaction of type angle in that entry is not found in the 55: input file. Perhaps your atom and/or residue naming needs to be 55: fixed. 55: 55: 55: 55: WARNING: WARNING: Residue 16 named PRO of a molecule in the input file was mapped 55: to an entry in the topology database, but the atom O used in 55: an interaction of type angle in that entry is not found in the 55: input file. Perhaps your atom and/or residue naming needs to be 55: fixed. 55: 55: 55: Before cleaning: 232 pairs 55: Before cleaning: 306 dihedrals 55: Using the Gromos53a6 force field in directory gromos53a6.ff 55: 55: going to rename gromos53a6.ff/aminoacids.r2b 55: Reading /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/D.pdb... 55: Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms 55: 55: Analyzing pdb file 55: Splitting chemical chains based on TER records or chain id changing. 55: 55: There are 1 chains and 0 blocks of water and 16 residues with 117 atoms 55: 55: chain #res #atoms 55: 55: 1 ' ' 16 117 55: 55: All occupancies are one 55: 55: Reading residue database... (Gromos53a6) 55: 55: Using default: not generating all possible dihedrals 55: 55: Using default: excluding 3 bonded neighbors 55: 55: Using default: generating 1,4 H--H interactions 55: 55: Using default: removing proper dihedrals found on the same bond as a proper dihedral 55: 55: Processing chain 1 (117 atoms, 16 residues) 55: 55: Replaced 1 residue named ASPH to the default ASP. Use interactive selection of protonated residues if that is what you need. 55: 55: Identified residue LYS50 as a starting terminus. 55: 55: Identified residue PRO65 as a ending terminus. 55: Start terminus LYS-50: NH3+ 55: End terminus PRO-65: COO- 55: 55: Checking for duplicate atoms.... 55: 55: Generating any missing hydrogen atoms and/or adding termini. 55: 55: Now there are 16 residues with 152 atoms 55: 55: Making bonds... 55: 55: Number of bonds was 161, now 156 55: 55: Generating angles, dihedrals and pairs... 55: 55: Making cmap torsions... 55: 55: There are 78 dihedrals, 82 impropers, 231 angles 55: 232 pairs, 156 bonds and 33 virtual sites 55: 55: Total mass 1662.887 a.m.u. 55: 55: Total charge -0.000 e 55: 55: Writing topology 55: 55: Writing coordinate file... 55: 55: --------- PLEASE NOTE ------------ 55: 55: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/D.pdb. 55: 55: The Gromos53a6 force field and the spc water model are used. 55: 55: --------- ETON ESAELP ------------ 55: [ OK ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spc_vsite_h_id_or_ter_merge_no_Dpdb_format_gro_match_file (317 ms) 55: [ RUN ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spc_vsite_h_id_or_ter_merge_no_Epdb_format_gro_match_file 55: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos53a6.ff/aminoacids.r2b 55: All occupancies are one 55: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos53a6.ff/atomtypes.atp 55: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos53a6.ff/aminoacids.rtp 55: 55: Using default: removing proper dihedrals found on the same bond as a proper dihedral 55: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos53a6.ff/aminoacids.hdb 55: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos53a6.ff/aminoacids.n.tdb 55: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos53a6.ff/aminoacids.c.tdb 55: Analysing hydrogen-bonding network for automated assignment of histidine 55: protonation. 89 donors and 98 acceptors were found. 55: There are 129 hydrogen bonds 55: Will use HISE for residue 31 55: Will use HISE for residue 51 55: 9 out of 9 lines of specbond.dat converted successfully 55: Special Atom Distance matrix: 55: CYS25 HIS31 HIS51 55: SG14 NE264 NE2226 55: HIS31 NE264 1.921 55: HIS51 NE2226 1.498 2.650 55: CYS80 SG477 0.207 1.984 1.570 55: Linking CYS-25 SG-14 and CYS-80 SG-477... 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: Marked 150 virtual sites 55: Added 10 dummy masses 55: Added 29 new constraints 55: 55: WARNING: WARNING: Residue 1 named ASN of a molecule in the input file was mapped 55: to an entry in the topology database, but the atom H used in 55: an interaction of type angle in that entry is not found in the 55: input file. Perhaps your atom and/or residue naming needs to be 55: fixed. 55: 55: 55: 55: WARNING: WARNING: Residue 58 named ARG of a molecule in the input file was mapped 55: to an entry in the topology database, but the atom O used in 55: an interaction of type angle in that entry is not found in the 55: input file. Perhaps your atom and/or residue naming needs to be 55: fixed. 55: 55: 55: Before cleaning: 972 pairs 55: Before cleaning: 1270 dihedrals 55: Using the Gromos53a6 force field in directory gromos53a6.ff 55: 55: going to rename gromos53a6.ff/aminoacids.r2b 55: Reading /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/E.pdb... 55: Read 'This is a fragment of 2d4f for testing a disulfide bridge', 488 atoms 55: 55: Analyzing pdb file 55: Splitting chemical chains based on TER records or chain id changing. 55: 55: There are 1 chains and 0 blocks of water and 58 residues with 488 atoms 55: 55: chain #res #atoms 55: 55: 1 'A' 58 488 55: 55: All occupancies are one 55: 55: Reading residue database... (Gromos53a6) 55: 55: Using default: not generating all possible dihedrals 55: 55: Using default: excluding 3 bonded neighbors 55: 55: Using default: generating 1,4 H--H interactions 55: 55: Using default: removing proper dihedrals found on the same bond as a proper dihedral 55: 55: Processing chain 1 'A' (488 atoms, 58 residues) 55: 55: Identified residue ASN24 as a starting terminus. 55: 55: Identified residue ARG81 as a ending terminus. 55: Start terminus ASN-24: NH3+ 55: End terminus ARG-81: COO- 55: 55: Checking for duplicate atoms.... 55: 55: Generating any missing hydrogen atoms and/or adding termini. 55: 55: Now there are 58 residues with 639 atoms 55: 55: Making bonds... 55: 55: Number of bonds was 659, now 654 55: 55: Generating angles, dihedrals and pairs... 55: 55: Making cmap torsions... 55: 55: There are 321 dihedrals, 354 impropers, 963 angles 55: 972 pairs, 654 bonds and 141 virtual sites 55: 55: Total mass 6908.582 a.m.u. 55: 55: Total charge -6.000 e 55: 55: Writing topology 55: 55: Writing coordinate file... 55: 55: --------- PLEASE NOTE ------------ 55: 55: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/E.pdb. 55: 55: The Gromos53a6 force field and the spc water model are used. 55: 55: --------- ETON ESAELP ------------ 55: [ OK ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spc_vsite_h_id_or_ter_merge_no_Epdb_format_gro_match_file (623 ms) 55: [ RUN ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spce_vsite_none_id_or_ter_merge_no_Apdb_format_gro_match_file 55: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos53a6.ff/aminoacids.r2b 55: All occupancies are one 55: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos53a6.ff/atomtypes.atp 55: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos53a6.ff/aminoacids.rtp 55: 55: Using default: removing proper dihedrals found on the same bond as a proper dihedral 55: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos53a6.ff/aminoacids.hdb 55: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos53a6.ff/aminoacids.n.tdb 55: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos53a6.ff/aminoacids.c.tdb 55: Analysing hydrogen-bonding network for automated assignment of histidine 55: protonation. 25 donors and 23 acceptors were found. 55: There are 41 hydrogen bonds 55: Will use HISE for residue 8 55: 9 out of 9 lines of specbond.dat converted successfully 55: Special Atom Distance matrix: 55: CYS3 HIS8 55: SG9 NE251 55: HIS8 NE251 1.055 55: MET12 SD83 0.763 0.990 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: WARNING: Residue 1 named ALA of a molecule in the input file was mapped 55: to an entry in the topology database, but the atom H used in 55: an interaction of type angle in that entry is not found in the 55: input file. Perhaps your atom and/or residue naming needs to be 55: fixed. 55: 55: 55: 55: WARNING: WARNING: Residue 16 named SER of a molecule in the input file was mapped 55: to an entry in the topology database, but the atom O used in 55: an interaction of type angle in that entry is not found in the 55: input file. Perhaps your atom and/or residue naming needs to be 55: fixed. 55: 55: 55: Before cleaning: 267 pairs 55: Before cleaning: 312 dihedrals 55: Using the Gromos53a6 force field in directory gromos53a6.ff 55: 55: going to rename gromos53a6.ff/aminoacids.r2b 55: Reading /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/A.pdb... 55: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms 55: 55: Analyzing pdb file 55: Splitting chemical chains based on TER records or chain id changing. 55: 55: There are 1 chains and 0 blocks of water and 16 residues with 128 atoms 55: 55: chain #res #atoms 55: 55: 1 ' ' 16 128 55: 55: All occupancies are one 55: 55: Reading residue database... (Gromos53a6) 55: 55: Using default: not generating all possible dihedrals 55: 55: Using default: excluding 3 bonded neighbors 55: 55: Using default: generating 1,4 H--H interactions 55: 55: Using default: removing proper dihedrals found on the same bond as a proper dihedral 55: 55: Processing chain 1 (128 atoms, 16 residues) 55: 55: Identified residue ALA2 as a starting terminus. 55: 55: Identified residue SER17 as a ending terminus. 55: Start terminus ALA-2: NH3+ 55: End terminus SER-17: COO- 55: 55: Checking for duplicate atoms.... 55: 55: Generating any missing hydrogen atoms and/or adding termini. 55: 55: Now there are 16 residues with 167 atoms 55: 55: Making bonds... 55: 55: Number of bonds was 174, now 169 55: 55: Generating angles, dihedrals and pairs... 55: 55: Making cmap torsions... 55: 55: There are 90 dihedrals, 79 impropers, 245 angles 55: 267 pairs, 169 bonds and 0 virtual sites 55: 55: Total mass 1846.116 a.m.u. 55: 55: Total charge -0.000 e 55: 55: Writing topology 55: 55: Writing coordinate file... 55: 55: --------- PLEASE NOTE ------------ 55: 55: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/A.pdb. 55: 55: The Gromos53a6 force field and the spce water model are used. 55: 55: --------- ETON ESAELP ------------ 55: [ OK ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spce_vsite_none_id_or_ter_merge_no_Apdb_format_gro_match_file (295 ms) 55: [ RUN ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spce_vsite_none_id_or_ter_merge_no_Bpdb_format_gro_match_file 55: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos53a6.ff/aminoacids.r2b 55: All occupancies are one 55: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos53a6.ff/atomtypes.atp 55: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos53a6.ff/aminoacids.rtp 55: 55: Using default: removing proper dihedrals found on the same bond as a proper dihedral 55: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos53a6.ff/aminoacids.hdb 55: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos53a6.ff/aminoacids.n.tdb 55: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos53a6.ff/aminoacids.c.tdb 55: Analysing hydrogen-bonding network for automated assignment of histidine 55: protonation. 30 donors and 22 acceptors were found. 55: There are 36 hydrogen bonds 55: Will use HISE for residue 29 55: Will use HISE for residue 32 55: 9 out of 9 lines of specbond.dat converted successfully 55: Special Atom Distance matrix: 55: CYS27 HIS29 55: SG90 NE2111 55: HIS29 NE2111 0.987 55: HIS32 NE2135 1.590 1.155 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: WARNING: Residue 1 named THR of a molecule in the input file was mapped 55: to an entry in the topology database, but the atom H used in 55: an interaction of type angle in that entry is not found in the 55: input file. Perhaps your atom and/or residue naming needs to be 55: fixed. 55: 55: 55: 55: WARNING: WARNING: Residue 16 named PHE of a molecule in the input file was mapped 55: to an entry in the topology database, but the atom O used in 55: an interaction of type angle in that entry is not found in the 55: input file. Perhaps your atom and/or residue naming needs to be 55: fixed. 55: 55: 55: Before cleaning: 273 pairs 55: Before cleaning: 443 dihedrals 55: Using the Gromos53a6 force field in directory gromos53a6.ff 55: 55: going to rename gromos53a6.ff/aminoacids.r2b 55: Reading /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/B.pdb... 55: Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms 55: 55: Analyzing pdb file 55: Splitting chemical chains based on TER records or chain id changing. 55: 55: There are 1 chains and 0 blocks of water and 16 residues with 149 atoms 55: 55: chain #res #atoms 55: 55: 1 ' ' 16 149 55: 55: All occupancies are one 55: 55: Reading residue database... (Gromos53a6) 55: 55: Using default: not generating all possible dihedrals 55: 55: Using default: excluding 3 bonded neighbors 55: 55: Using default: generating 1,4 H--H interactions 55: 55: Using default: removing proper dihedrals found on the same bond as a proper dihedral 55: 55: Processing chain 1 (149 atoms, 16 residues) 55: 55: Replaced 1 residue named GLUH to the default GLU. Use interactive selection of protonated residues if that is what you need. 55: 55: Identified residue THR18 as a starting terminus. 55: 55: Identified residue PHE33 as a ending terminus. 55: Start terminus THR-18: NH3+ 55: End terminus PHE-33: COO- 55: 55: Checking for duplicate atoms.... 55: 55: Generating any missing hydrogen atoms and/or adding termini. 55: 55: Now there are 16 residues with 206 atoms 55: 55: Making bonds... 55: 55: Number of bonds was 220, now 215 55: 55: Generating angles, dihedrals and pairs... 55: 55: Making cmap torsions... 55: 55: There are 93 dihedrals, 138 impropers, 324 angles 55: 273 pairs, 215 bonds and 0 virtual sites 55: 55: Total mass 2088.361 a.m.u. 55: 55: Total charge 1.000 e 55: 55: Writing topology 55: 55: Writing coordinate file... 55: 55: --------- PLEASE NOTE ------------ 55: 55: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/B.pdb. 55: 55: The Gromos53a6 force field and the spce water model are used. 55: 55: --------- ETON ESAELP ------------ 55: [ OK ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spce_vsite_none_id_or_ter_merge_no_Bpdb_format_gro_match_file (348 ms) 55: [ RUN ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spce_vsite_none_id_or_ter_merge_no_Cpdb_format_gro_match_file 55: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos53a6.ff/aminoacids.r2b 55: All occupancies are one 55: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos53a6.ff/atomtypes.atp 55: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos53a6.ff/aminoacids.rtp 55: 55: Using default: removing proper dihedrals found on the same bond as a proper dihedral 55: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos53a6.ff/aminoacids.hdb 55: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos53a6.ff/aminoacids.n.tdb 55: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos53a6.ff/aminoacids.c.tdb 55: Analysing hydrogen-bonding network for automated assignment of histidine 55: protonation. 22 donors and 22 acceptors were found. 55: There are 26 hydrogen bonds 55: Will use HISE for residue 45 55: 9 out of 9 lines of specbond.dat converted successfully 55: Special Atom Distance matrix: 55: HIS45 55: NE295 55: MET46 SD102 1.078 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: WARNING: Residue 1 named ALA of a molecule in the input file was mapped 55: to an entry in the topology database, but the atom H used in 55: an interaction of type angle in that entry is not found in the 55: input file. Perhaps your atom and/or residue naming needs to be 55: fixed. 55: 55: 55: 55: WARNING: WARNING: Residue 16 named ALA of a molecule in the input file was mapped 55: to an entry in the topology database, but the atom O used in 55: an interaction of type angle in that entry is not found in the 55: input file. Perhaps your atom and/or residue naming needs to be 55: fixed. 55: 55: 55: Before cleaning: 242 pairs 55: Before cleaning: 356 dihedrals 55: Using the Gromos53a6 force field in directory gromos53a6.ff 55: 55: going to rename gromos53a6.ff/aminoacids.r2b 55: Reading /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/C.pdb... 55: Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms 55: 55: Analyzing pdb file 55: Splitting chemical chains based on TER records or chain id changing. 55: 55: There are 1 chains and 0 blocks of water and 16 residues with 132 atoms 55: 55: chain #res #atoms 55: 55: 1 ' ' 16 132 55: 55: All occupancies are one 55: 55: Reading residue database... (Gromos53a6) 55: 55: Using default: not generating all possible dihedrals 55: 55: Using default: excluding 3 bonded neighbors 55: 55: Using default: generating 1,4 H--H interactions 55: 55: Using default: removing proper dihedrals found on the same bond as a proper dihedral 55: 55: Processing chain 1 (132 atoms, 16 residues) 55: 55: Identified residue ALA34 as a starting terminus. 55: 55: Identified residue ALA49 as a ending terminus. 55: Start terminus ALA-34: NH3+ 55: End terminus ALA-49: COO- 55: 55: Checking for duplicate atoms.... 55: 55: Generating any missing hydrogen atoms and/or adding termini. 55: 55: Now there are 16 residues with 170 atoms 55: 55: Making bonds... 55: 55: Number of bonds was 181, now 176 55: 55: Generating angles, dihedrals and pairs... 55: 55: Making cmap torsions... 55: 55: There are 81 dihedrals, 104 impropers, 264 angles 55: 242 pairs, 176 bonds and 0 virtual sites 55: 55: Total mass 1861.132 a.m.u. 55: 55: Total charge -1.000 e 55: 55: Writing topology 55: 55: Writing coordinate file... 55: 55: --------- PLEASE NOTE ------------ 55: 55: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/C.pdb. 55: 55: The Gromos53a6 force field and the spce water model are used. 55: 55: --------- ETON ESAELP ------------ 55: [ OK ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spce_vsite_none_id_or_ter_merge_no_Cpdb_format_gro_match_file (285 ms) 55: [ RUN ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spce_vsite_none_id_or_ter_merge_no_Dpdb_format_gro_match_file 55: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos53a6.ff/aminoacids.r2b 55: All occupancies are one 55: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos53a6.ff/atomtypes.atp 55: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos53a6.ff/aminoacids.rtp 55: 55: Using default: removing proper dihedrals found on the same bond as a proper dihedral 55: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos53a6.ff/aminoacids.hdb 55: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos53a6.ff/aminoacids.n.tdb 55: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos53a6.ff/aminoacids.c.tdb 55: Analysing hydrogen-bonding network for automated assignment of histidine 55: protonation. 22 donors and 21 acceptors were found. 55: There are 30 hydrogen bonds 55: Will use HISE for residue 60 55: 9 out of 9 lines of specbond.dat converted successfully 55: Special Atom Distance matrix: 55: HIS60 55: NE285 55: CYS62 SG98 0.803 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: WARNING: Residue 1 named LYS of a molecule in the input file was mapped 55: to an entry in the topology database, but the atom H used in 55: an interaction of type angle in that entry is not found in the 55: input file. Perhaps your atom and/or residue naming needs to be 55: fixed. 55: 55: 55: 55: WARNING: WARNING: Residue 16 named PRO of a molecule in the input file was mapped 55: to an entry in the topology database, but the atom O used in 55: an interaction of type angle in that entry is not found in the 55: input file. Perhaps your atom and/or residue naming needs to be 55: fixed. 55: 55: 55: Before cleaning: 232 pairs 55: Before cleaning: 306 dihedrals 55: Using the Gromos53a6 force field in directory gromos53a6.ff 55: 55: going to rename gromos53a6.ff/aminoacids.r2b 55: Reading /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/D.pdb... 55: Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms 55: 55: Analyzing pdb file 55: Splitting chemical chains based on TER records or chain id changing. 55: 55: There are 1 chains and 0 blocks of water and 16 residues with 117 atoms 55: 55: chain #res #atoms 55: 55: 1 ' ' 16 117 55: 55: All occupancies are one 55: 55: Reading residue database... (Gromos53a6) 55: 55: Using default: not generating all possible dihedrals 55: 55: Using default: excluding 3 bonded neighbors 55: 55: Using default: generating 1,4 H--H interactions 55: 55: Using default: removing proper dihedrals found on the same bond as a proper dihedral 55: 55: Processing chain 1 (117 atoms, 16 residues) 55: 55: Replaced 1 residue named ASPH to the default ASP. Use interactive selection of protonated residues if that is what you need. 55: 55: Identified residue LYS50 as a starting terminus. 55: 55: Identified residue PRO65 as a ending terminus. 55: Start terminus LYS-50: NH3+ 55: End terminus PRO-65: COO- 55: 55: Checking for duplicate atoms.... 55: 55: Generating any missing hydrogen atoms and/or adding termini. 55: 55: Now there are 16 residues with 152 atoms 55: 55: Making bonds... 55: 55: Number of bonds was 161, now 156 55: 55: Generating angles, dihedrals and pairs... 55: 55: Making cmap torsions... 55: 55: There are 78 dihedrals, 82 impropers, 231 angles 55: 232 pairs, 156 bonds and 0 virtual sites 55: 55: Total mass 1662.887 a.m.u. 55: 55: Total charge -0.000 e 55: 55: Writing topology 55: 55: Writing coordinate file... 55: 55: --------- PLEASE NOTE ------------ 55: 55: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/D.pdb. 55: 55: The Gromos53a6 force field and the spce water model are used. 55: 55: --------- ETON ESAELP ------------ 55: [ OK ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spce_vsite_none_id_or_ter_merge_no_Dpdb_format_gro_match_file (292 ms) 55: [ RUN ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spce_vsite_none_id_or_ter_merge_no_Epdb_format_gro_match_file 55: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos53a6.ff/aminoacids.r2b 55: All occupancies are one 55: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos53a6.ff/atomtypes.atp 55: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos53a6.ff/aminoacids.rtp 55: 55: Using default: removing proper dihedrals found on the same bond as a proper dihedral 55: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos53a6.ff/aminoacids.hdb 55: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos53a6.ff/aminoacids.n.tdb 55: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos53a6.ff/aminoacids.c.tdb 55: Analysing hydrogen-bonding network for automated assignment of histidine 55: protonation. 89 donors and 98 acceptors were found. 55: There are 129 hydrogen bonds 55: Will use HISE for residue 31 55: Will use HISE for residue 51 55: 9 out of 9 lines of specbond.dat converted successfully 55: Special Atom Distance matrix: 55: CYS25 HIS31 HIS51 55: SG14 NE264 NE2226 55: HIS31 NE264 1.921 55: HIS51 NE2226 1.498 2.650 55: CYS80 SG477 0.207 1.984 1.570 55: Linking CYS-25 SG-14 and CYS-80 SG-477... 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: WARNING: Residue 1 named ASN of a molecule in the input file was mapped 55: to an entry in the topology database, but the atom H used in 55: an interaction of type angle in that entry is not found in the 55: input file. Perhaps your atom and/or residue naming needs to be 55: fixed. 55: 55: 55: 55: WARNING: WARNING: Residue 58 named ARG of a molecule in the input file was mapped 55: to an entry in the topology database, but the atom O used in 55: an interaction of type angle in that entry is not found in the 55: input file. Perhaps your atom and/or residue naming needs to be 55: fixed. 55: 55: 55: Before cleaning: 972 pairs 55: Before cleaning: 1270 dihedrals 55: Using the Gromos53a6 force field in directory gromos53a6.ff 55: 55: going to rename gromos53a6.ff/aminoacids.r2b 55: Reading /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/E.pdb... 55: Read 'This is a fragment of 2d4f for testing a disulfide bridge', 488 atoms 55: 55: Analyzing pdb file 55: Splitting chemical chains based on TER records or chain id changing. 55: 55: There are 1 chains and 0 blocks of water and 58 residues with 488 atoms 55: 55: chain #res #atoms 55: 55: 1 'A' 58 488 55: 55: All occupancies are one 55: 55: Reading residue database... (Gromos53a6) 55: 55: Using default: not generating all possible dihedrals 55: 55: Using default: excluding 3 bonded neighbors 55: 55: Using default: generating 1,4 H--H interactions 55: 55: Using default: removing proper dihedrals found on the same bond as a proper dihedral 55: 55: Processing chain 1 'A' (488 atoms, 58 residues) 55: 55: Identified residue ASN24 as a starting terminus. 55: 55: Identified residue ARG81 as a ending terminus. 55: Start terminus ASN-24: NH3+ 55: End terminus ARG-81: COO- 55: 55: Checking for duplicate atoms.... 55: 55: Generating any missing hydrogen atoms and/or adding termini. 55: 55: Now there are 58 residues with 639 atoms 55: 55: Making bonds... 55: 55: Number of bonds was 659, now 654 55: 55: Generating angles, dihedrals and pairs... 55: 55: Making cmap torsions... 55: 55: There are 321 dihedrals, 354 impropers, 963 angles 55: 972 pairs, 654 bonds and 0 virtual sites 55: 55: Total mass 6908.582 a.m.u. 55: 55: Total charge -6.000 e 55: 55: Writing topology 55: 55: Writing coordinate file... 55: 55: --------- PLEASE NOTE ------------ 55: 55: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/E.pdb. 55: 55: The Gromos53a6 force field and the spce water model are used. 55: 55: --------- ETON ESAELP ------------ 55: [ OK ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spce_vsite_none_id_or_ter_merge_no_Epdb_format_gro_match_file (501 ms) 55: [ RUN ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spce_vsite_h_id_or_ter_merge_no_Apdb_format_gro_match_file 55: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos53a6.ff/aminoacids.r2b 55: All occupancies are one 55: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos53a6.ff/atomtypes.atp 55: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos53a6.ff/aminoacids.rtp 55: 55: Using default: removing proper dihedrals found on the same bond as a proper dihedral 55: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos53a6.ff/aminoacids.hdb 55: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos53a6.ff/aminoacids.n.tdb 55: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos53a6.ff/aminoacids.c.tdb 55: Analysing hydrogen-bonding network for automated assignment of histidine 55: protonation. 25 donors and 23 acceptors were found. 55: There are 41 hydrogen bonds 55: Will use HISE for residue 8 55: 9 out of 9 lines of specbond.dat converted successfully 55: Special Atom Distance matrix: 55: CYS3 HIS8 55: SG9 NE251 55: HIS8 NE251 1.055 55: MET12 SD83 0.763 0.990 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: Marked 39 virtual sites 55: Added 4 dummy masses 55: Added 8 new constraints 55: 55: WARNING: WARNING: Residue 1 named ALA of a molecule in the input file was mapped 55: to an entry in the topology database, but the atom H used in 55: an interaction of type angle in that entry is not found in the 55: input file. Perhaps your atom and/or residue naming needs to be 55: fixed. 55: 55: 55: 55: WARNING: WARNING: Residue 16 named SER of a molecule in the input file was mapped 55: to an entry in the topology database, but the atom O used in 55: an interaction of type angle in that entry is not found in the 55: input file. Perhaps your atom and/or residue naming needs to be 55: fixed. 55: 55: 55: Before cleaning: 267 pairs 55: Before cleaning: 312 dihedrals 55: Using the Gromos53a6 force field in directory gromos53a6.ff 55: 55: going to rename gromos53a6.ff/aminoacids.r2b 55: Reading /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/A.pdb... 55: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms 55: 55: Analyzing pdb file 55: Splitting chemical chains based on TER records or chain id changing. 55: 55: There are 1 chains and 0 blocks of water and 16 residues with 128 atoms 55: 55: chain #res #atoms 55: 55: 1 ' ' 16 128 55: 55: All occupancies are one 55: 55: Reading residue database... (Gromos53a6) 55: 55: Using default: not generating all possible dihedrals 55: 55: Using default: excluding 3 bonded neighbors 55: 55: Using default: generating 1,4 H--H interactions 55: 55: Using default: removing proper dihedrals found on the same bond as a proper dihedral 55: 55: Processing chain 1 (128 atoms, 16 residues) 55: 55: Identified residue ALA2 as a starting terminus. 55: 55: Identified residue SER17 as a ending terminus. 55: Start terminus ALA-2: NH3+ 55: End terminus SER-17: COO- 55: 55: Checking for duplicate atoms.... 55: 55: Generating any missing hydrogen atoms and/or adding termini. 55: 55: Now there are 16 residues with 167 atoms 55: 55: Making bonds... 55: 55: Number of bonds was 174, now 169 55: 55: Generating angles, dihedrals and pairs... 55: 55: Making cmap torsions... 55: 55: There are 90 dihedrals, 79 impropers, 245 angles 55: 267 pairs, 169 bonds and 39 virtual sites 55: 55: Total mass 1846.116 a.m.u. 55: 55: Total charge -0.000 e 55: 55: Writing topology 55: 55: Writing coordinate file... 55: 55: --------- PLEASE NOTE ------------ 55: 55: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/A.pdb. 55: 55: The Gromos53a6 force field and the spce water model are used. 55: 55: --------- ETON ESAELP ------------ 55: [ OK ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spce_vsite_h_id_or_ter_merge_no_Apdb_format_gro_match_file (298 ms) 55: [ RUN ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spce_vsite_h_id_or_ter_merge_no_Bpdb_format_gro_match_file 55: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos53a6.ff/aminoacids.r2b 55: All occupancies are one 55: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos53a6.ff/atomtypes.atp 55: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos53a6.ff/aminoacids.rtp 55: 55: Using default: removing proper dihedrals found on the same bond as a proper dihedral 55: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos53a6.ff/aminoacids.hdb 55: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos53a6.ff/aminoacids.n.tdb 55: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos53a6.ff/aminoacids.c.tdb 55: Analysing hydrogen-bonding network for automated assignment of histidine 55: protonation. 30 donors and 22 acceptors were found. 55: There are 36 hydrogen bonds 55: Will use HISE for residue 29 55: Will use HISE for residue 32 55: 9 out of 9 lines of specbond.dat converted successfully 55: Special Atom Distance matrix: 55: CYS27 HIS29 55: SG90 NE2111 55: HIS29 NE2111 0.987 55: HIS32 NE2135 1.590 1.155 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: Marked 57 virtual sites 55: Added 4 dummy masses 55: Added 10 new constraints 55: 55: WARNING: WARNING: Residue 1 named THR of a molecule in the input file was mapped 55: to an entry in the topology database, but the atom H used in 55: an interaction of type angle in that entry is not found in the 55: input file. Perhaps your atom and/or residue naming needs to be 55: fixed. 55: 55: 55: 55: WARNING: WARNING: Residue 16 named PHE of a molecule in the input file was mapped 55: to an entry in the topology database, but the atom O used in 55: an interaction of type angle in that entry is not found in the 55: input file. Perhaps your atom and/or residue naming needs to be 55: fixed. 55: 55: 55: Before cleaning: 273 pairs 55: Before cleaning: 443 dihedrals 55: Using the Gromos53a6 force field in directory gromos53a6.ff 55: 55: going to rename gromos53a6.ff/aminoacids.r2b 55: Reading /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/B.pdb... 55: Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms 55: 55: Analyzing pdb file 55: Splitting chemical chains based on TER records or chain id changing. 55: 55: There are 1 chains and 0 blocks of water and 16 residues with 149 atoms 55: 55: chain #res #atoms 55: 55: 1 ' ' 16 149 55: 55: All occupancies are one 55: 55: Reading residue database... (Gromos53a6) 55: 55: Using default: not generating all possible dihedrals 55: 55: Using default: excluding 3 bonded neighbors 55: 55: Using default: generating 1,4 H--H interactions 55: 55: Using default: removing proper dihedrals found on the same bond as a proper dihedral 55: 55: Processing chain 1 (149 atoms, 16 residues) 55: 55: Replaced 1 residue named GLUH to the default GLU. Use interactive selection of protonated residues if that is what you need. 55: 55: Identified residue THR18 as a starting terminus. 55: 55: Identified residue PHE33 as a ending terminus. 55: Start terminus THR-18: NH3+ 55: End terminus PHE-33: COO- 55: 55: Checking for duplicate atoms.... 55: 55: Generating any missing hydrogen atoms and/or adding termini. 55: 55: Now there are 16 residues with 206 atoms 55: 55: Making bonds... 55: 55: Number of bonds was 220, now 215 55: 55: Generating angles, dihedrals and pairs... 55: 55: Making cmap torsions... 55: 55: There are 93 dihedrals, 138 impropers, 324 angles 55: 273 pairs, 215 bonds and 55 virtual sites 55: 55: Total mass 2088.361 a.m.u. 55: 55: Total charge 1.000 e 55: 55: Writing topology 55: 55: Writing coordinate file... 55: 55: --------- PLEASE NOTE ------------ 55: 55: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/B.pdb. 55: 55: The Gromos53a6 force field and the spce water model are used. 55: 55: --------- ETON ESAELP ------------ 55: [ OK ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spce_vsite_h_id_or_ter_merge_no_Bpdb_format_gro_match_file (290 ms) 55: [ RUN ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spce_vsite_h_id_or_ter_merge_no_Cpdb_format_gro_match_file 55: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos53a6.ff/aminoacids.r2b 55: All occupancies are one 55: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos53a6.ff/atomtypes.atp 55: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos53a6.ff/aminoacids.rtp 55: 55: Using default: removing proper dihedrals found on the same bond as a proper dihedral 55: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos53a6.ff/aminoacids.hdb 55: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos53a6.ff/aminoacids.n.tdb 55: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos53a6.ff/aminoacids.c.tdb 55: Analysing hydrogen-bonding network for automated assignment of histidine 55: protonation. 22 donors and 22 acceptors were found. 55: There are 26 hydrogen bonds 55: Will use HISE for residue 45 55: 9 out of 9 lines of specbond.dat converted successfully 55: Special Atom Distance matrix: 55: HIS45 55: NE295 55: MET46 SD102 1.078 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: Marked 38 virtual sites 55: Added 4 dummy masses 55: Added 8 new constraints 55: 55: WARNING: WARNING: Residue 1 named ALA of a molecule in the input file was mapped 55: to an entry in the topology database, but the atom H used in 55: an interaction of type angle in that entry is not found in the 55: input file. Perhaps your atom and/or residue naming needs to be 55: fixed. 55: 55: 55: 55: WARNING: WARNING: Residue 16 named ALA of a molecule in the input file was mapped 55: to an entry in the topology database, but the atom O used in 55: an interaction of type angle in that entry is not found in the 55: input file. Perhaps your atom and/or residue naming needs to be 55: fixed. 55: 55: 55: Before cleaning: 242 pairs 55: Before cleaning: 356 dihedrals 55: Using the Gromos53a6 force field in directory gromos53a6.ff 55: 55: going to rename gromos53a6.ff/aminoacids.r2b 55: Reading /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/C.pdb... 55: Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms 55: 55: Analyzing pdb file 55: Splitting chemical chains based on TER records or chain id changing. 55: 55: There are 1 chains and 0 blocks of water and 16 residues with 132 atoms 55: 55: chain #res #atoms 55: 55: 1 ' ' 16 132 55: 55: All occupancies are one 55: 55: Reading residue database... (Gromos53a6) 55: 55: Using default: not generating all possible dihedrals 55: 55: Using default: excluding 3 bonded neighbors 55: 55: Using default: generating 1,4 H--H interactions 55: 55: Using default: removing proper dihedrals found on the same bond as a proper dihedral 55: 55: Processing chain 1 (132 atoms, 16 residues) 55: 55: Identified residue ALA34 as a starting terminus. 55: 55: Identified residue ALA49 as a ending terminus. 55: Start terminus ALA-34: NH3+ 55: End terminus ALA-49: COO- 55: 55: Checking for duplicate atoms.... 55: 55: Generating any missing hydrogen atoms and/or adding termini. 55: 55: Now there are 16 residues with 170 atoms 55: 55: Making bonds... 55: 55: Number of bonds was 181, now 176 55: 55: Generating angles, dihedrals and pairs... 55: 55: Making cmap torsions... 55: 55: There are 81 dihedrals, 104 impropers, 264 angles 55: 242 pairs, 176 bonds and 38 virtual sites 55: 55: Total mass 1861.132 a.m.u. 55: 55: Total charge -1.000 e 55: 55: Writing topology 55: 55: Writing coordinate file... 55: 55: --------- PLEASE NOTE ------------ 55: 55: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/C.pdb. 55: 55: The Gromos53a6 force field and the spce water model are used. 55: 55: --------- ETON ESAELP ------------ 55: [ OK ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spce_vsite_h_id_or_ter_merge_no_Cpdb_format_gro_match_file (280 ms) 55: [ RUN ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spce_vsite_h_id_or_ter_merge_no_Dpdb_format_gro_match_file 55: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos53a6.ff/aminoacids.r2b 55: All occupancies are one 55: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos53a6.ff/atomtypes.atp 55: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos53a6.ff/aminoacids.rtp 55: 55: Using default: removing proper dihedrals found on the same bond as a proper dihedral 55: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos53a6.ff/aminoacids.hdb 55: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos53a6.ff/aminoacids.n.tdb 55: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos53a6.ff/aminoacids.c.tdb 55: Analysing hydrogen-bonding network for automated assignment of histidine 55: protonation. 22 donors and 21 acceptors were found. 55: There are 30 hydrogen bonds 55: Will use HISE for residue 60 55: 9 out of 9 lines of specbond.dat converted successfully 55: Special Atom Distance matrix: 55: HIS60 55: NE285 55: CYS62 SG98 0.803 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: Marked 35 virtual sites 55: Added 4 dummy masses 55: Added 10 new constraints 55: 55: WARNING: WARNING: Residue 1 named LYS of a molecule in the input file was mapped 55: to an entry in the topology database, but the atom H used in 55: an interaction of type angle in that entry is not found in the 55: input file. Perhaps your atom and/or residue naming needs to be 55: fixed. 55: 55: 55: 55: WARNING: WARNING: Residue 16 named PRO of a molecule in the input file was mapped 55: to an entry in the topology database, but the atom O used in 55: an interaction of type angle in that entry is not found in the 55: input file. Perhaps your atom and/or residue naming needs to be 55: fixed. 55: 55: 55: Before cleaning: 232 pairs 55: Before cleaning: 306 dihedrals 55: Using the Gromos53a6 force field in directory gromos53a6.ff 55: 55: going to rename gromos53a6.ff/aminoacids.r2b 55: Reading /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/D.pdb... 55: Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms 55: 55: Analyzing pdb file 55: Splitting chemical chains based on TER records or chain id changing. 55: 55: There are 1 chains and 0 blocks of water and 16 residues with 117 atoms 55: 55: chain #res #atoms 55: 55: 1 ' ' 16 117 55: 55: All occupancies are one 55: 55: Reading residue database... (Gromos53a6) 55: 55: Using default: not generating all possible dihedrals 55: 55: Using default: excluding 3 bonded neighbors 55: 55: Using default: generating 1,4 H--H interactions 55: 55: Using default: removing proper dihedrals found on the same bond as a proper dihedral 55: 55: Processing chain 1 (117 atoms, 16 residues) 55: 55: Replaced 1 residue named ASPH to the default ASP. Use interactive selection of protonated residues if that is what you need. 55: 55: Identified residue LYS50 as a starting terminus. 55: 55: Identified residue PRO65 as a ending terminus. 55: Start terminus LYS-50: NH3+ 55: End terminus PRO-65: COO- 55: 55: Checking for duplicate atoms.... 55: 55: Generating any missing hydrogen atoms and/or adding termini. 55: 55: Now there are 16 residues with 152 atoms 55: 55: Making bonds... 55: 55: Number of bonds was 161, now 156 55: 55: Generating angles, dihedrals and pairs... 55: 55: Making cmap torsions... 55: 55: There are 78 dihedrals, 82 impropers, 231 angles 55: 232 pairs, 156 bonds and 33 virtual sites 55: 55: Total mass 1662.887 a.m.u. 55: 55: Total charge -0.000 e 55: 55: Writing topology 55: 55: Writing coordinate file... 55: 55: --------- PLEASE NOTE ------------ 55: 55: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/D.pdb. 55: 55: The Gromos53a6 force field and the spce water model are used. 55: 55: --------- ETON ESAELP ------------ 55: [ OK ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spce_vsite_h_id_or_ter_merge_no_Dpdb_format_gro_match_file (267 ms) 55: [ RUN ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spce_vsite_h_id_or_ter_merge_no_Epdb_format_gro_match_file 55: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos53a6.ff/aminoacids.r2b 55: All occupancies are one 55: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos53a6.ff/atomtypes.atp 55: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos53a6.ff/aminoacids.rtp 55: 55: Using default: removing proper dihedrals found on the same bond as a proper dihedral 55: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos53a6.ff/aminoacids.hdb 55: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos53a6.ff/aminoacids.n.tdb 55: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos53a6.ff/aminoacids.c.tdb 55: Analysing hydrogen-bonding network for automated assignment of histidine 55: protonation. 89 donors and 98 acceptors were found. 55: There are 129 hydrogen bonds 55: Will use HISE for residue 31 55: Will use HISE for residue 51 55: 9 out of 9 lines of specbond.dat converted successfully 55: Special Atom Distance matrix: 55: CYS25 HIS31 HIS51 55: SG14 NE264 NE2226 55: HIS31 NE264 1.921 55: HIS51 NE2226 1.498 2.650 55: CYS80 SG477 0.207 1.984 1.570 55: Linking CYS-25 SG-14 and CYS-80 SG-477... 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: Marked 150 virtual sites 55: Added 10 dummy masses 55: Added 29 new constraints 55: 55: WARNING: WARNING: Residue 1 named ASN of a molecule in the input file was mapped 55: to an entry in the topology database, but the atom H used in 55: an interaction of type angle in that entry is not found in the 55: input file. Perhaps your atom and/or residue naming needs to be 55: fixed. 55: 55: 55: 55: WARNING: WARNING: Residue 58 named ARG of a molecule in the input file was mapped 55: to an entry in the topology database, but the atom O used in 55: an interaction of type angle in that entry is not found in the 55: input file. Perhaps your atom and/or residue naming needs to be 55: fixed. 55: 55: 55: Before cleaning: 972 pairs 55: Before cleaning: 1270 dihedrals 55: Using the Gromos53a6 force field in directory gromos53a6.ff 55: 55: going to rename gromos53a6.ff/aminoacids.r2b 55: Reading /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/E.pdb... 55: Read 'This is a fragment of 2d4f for testing a disulfide bridge', 488 atoms 55: 55: Analyzing pdb file 55: Splitting chemical chains based on TER records or chain id changing. 55: 55: There are 1 chains and 0 blocks of water and 58 residues with 488 atoms 55: 55: chain #res #atoms 55: 55: 1 'A' 58 488 55: 55: All occupancies are one 55: 55: Reading residue database... (Gromos53a6) 55: 55: Using default: not generating all possible dihedrals 55: 55: Using default: excluding 3 bonded neighbors 55: 55: Using default: generating 1,4 H--H interactions 55: 55: Using default: removing proper dihedrals found on the same bond as a proper dihedral 55: 55: Processing chain 1 'A' (488 atoms, 58 residues) 55: 55: Identified residue ASN24 as a starting terminus. 55: 55: Identified residue ARG81 as a ending terminus. 55: Start terminus ASN-24: NH3+ 55: End terminus ARG-81: COO- 55: 55: Checking for duplicate atoms.... 55: 55: Generating any missing hydrogen atoms and/or adding termini. 55: 55: Now there are 58 residues with 639 atoms 55: 55: Making bonds... 55: 55: Number of bonds was 659, now 654 55: 55: Generating angles, dihedrals and pairs... 55: 55: Making cmap torsions... 55: 55: There are 321 dihedrals, 354 impropers, 963 angles 55: 972 pairs, 654 bonds and 141 virtual sites 55: 55: Total mass 6908.582 a.m.u. 55: 55: Total charge -6.000 e 55: 55: Writing topology 55: 55: Writing coordinate file... 55: 55: --------- PLEASE NOTE ------------ 55: 55: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/E.pdb. 55: 55: The Gromos53a6 force field and the spce water model are used. 55: 55: --------- ETON ESAELP ------------ 55: [ OK ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spce_vsite_h_id_or_ter_merge_no_Epdb_format_gro_match_file (550 ms) 55: [----------] 20 tests from G53a6/Pdb2gmxTest (6917 ms total) 55: 55: [----------] Global test environment tear-down 55: [==========] 40 tests from 2 test suites ran. (13268 ms total) 55: [ PASSED ] 40 tests. 55/92 Test #55: Pdb2gmx2Test .............................. Passed 13.36 sec test 56 Start 56: Pdb2gmx3Test 56: Test command: /build/reproducible-path/gromacs-2025.1/build/basic/bin/pdb2gmx3-test "--gtest_output=xml:/build/reproducible-path/gromacs-2025.1/build/basic/Testing/Temporary/Pdb2gmx3Test.xml" 56: Working Directory: /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/gmxpreprocess/tests 56: Test timeout computed to be: 1920 56: [==========] Running 39 tests from 6 test suites. 56: [----------] Global test environment set-up. 56: [----------] 10 tests from Amber/Pdb2gmxTest 56: [ RUN ] Amber/Pdb2gmxTest.Runs/ff_amber99sbildn_tip3p_vsite_none_id_or_ter_merge_no_Apdb_format_gro_match_file 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/amber99sb-ildn.ff/aminoacids.r2b 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/amber99sb-ildn.ff/dna.r2b 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/amber99sb-ildn.ff/rna.r2b 56: All occupancies are one 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/amber99sb-ildn.ff/atomtypes.atp 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/amber99sb-ildn.ff/aminoacids.rtp 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/amber99sb-ildn.ff/dna.rtp 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/amber99sb-ildn.ff/rna.rtp 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/amber99sb-ildn.ff/aminoacids.hdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/amber99sb-ildn.ff/dna.hdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/amber99sb-ildn.ff/rna.hdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/amber99sb-ildn.ff/aminoacids.n.tdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/amber99sb-ildn.ff/aminoacids.c.tdb 56: Analysing hydrogen-bonding network for automated assignment of histidine 56: protonation. 25 donors and 23 acceptors were found. 56: There are 41 hydrogen bonds 56: Will use HISE for residue 8 56: 9 out of 9 lines of specbond.dat converted successfully 56: Special Atom Distance matrix: 56: CYS3 HIS8 56: SG9 NE251 56: HIS8 NE251 1.055 56: MET12 SD83 0.763 0.990 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/amber99sb-ildn.ff/aminoacids.arn 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/amber99sb-ildn.ff/dna.arn 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/amber99sb-ildn.ff/rna.arn 56: Before cleaning: 653 pairs 56: Before cleaning: 691 dihedrals 56: Using the Amber99sb-ildn force field in directory amber99sb-ildn.ff 56: 56: going to rename amber99sb-ildn.ff/aminoacids.r2b 56: 56: going to rename amber99sb-ildn.ff/dna.r2b 56: 56: going to rename amber99sb-ildn.ff/rna.r2b 56: Reading /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/A.pdb... 56: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms 56: 56: Analyzing pdb file 56: Splitting chemical chains based on TER records or chain id changing. 56: 56: There are 1 chains and 0 blocks of water and 16 residues with 128 atoms 56: 56: chain #res #atoms 56: 56: 1 ' ' 16 128 56: 56: All occupancies are one 56: 56: Reading residue database... (Amber99sb-ildn) 56: 56: Processing chain 1 (128 atoms, 16 residues) 56: 56: Identified residue ALA2 as a starting terminus. 56: 56: Identified residue SER17 as a ending terminus. 56: 56: Checking for duplicate atoms.... 56: 56: Generating any missing hydrogen atoms and/or adding termini. 56: 56: Now there are 16 residues with 252 atoms 56: 56: Making bonds... 56: 56: Number of bonds was 255, now 254 56: 56: Generating angles, dihedrals and pairs... 56: 56: Making cmap torsions... 56: 56: There are 691 dihedrals, 51 impropers, 457 angles 56: 650 pairs, 254 bonds and 0 virtual sites 56: 56: Total mass 1846.132 a.m.u. 56: 56: Total charge 0.000 e 56: 56: Writing topology 56: 56: Writing coordinate file... 56: 56: --------- PLEASE NOTE ------------ 56: 56: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/A.pdb. 56: 56: The Amber99sb-ildn force field and the tip3p water model are used. 56: 56: --------- ETON ESAELP ------------ 56: [ OK ] Amber/Pdb2gmxTest.Runs/ff_amber99sbildn_tip3p_vsite_none_id_or_ter_merge_no_Apdb_format_gro_match_file (330 ms) 56: [ RUN ] Amber/Pdb2gmxTest.Runs/ff_amber99sbildn_tip3p_vsite_none_id_or_ter_merge_no_Bpdb_format_gro_match_file 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/amber99sb-ildn.ff/aminoacids.r2b 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/amber99sb-ildn.ff/dna.r2b 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/amber99sb-ildn.ff/rna.r2b 56: All occupancies are one 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/amber99sb-ildn.ff/atomtypes.atp 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/amber99sb-ildn.ff/aminoacids.rtp 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/amber99sb-ildn.ff/dna.rtp 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/amber99sb-ildn.ff/rna.rtp 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/amber99sb-ildn.ff/aminoacids.hdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/amber99sb-ildn.ff/dna.hdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/amber99sb-ildn.ff/rna.hdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/amber99sb-ildn.ff/aminoacids.n.tdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/amber99sb-ildn.ff/aminoacids.c.tdb 56: Analysing hydrogen-bonding network for automated assignment of histidine 56: protonation. 30 donors and 22 acceptors were found. 56: There are 36 hydrogen bonds 56: Will use HISE for residue 29 56: Will use HISE for residue 32 56: 9 out of 9 lines of specbond.dat converted successfully 56: Special Atom Distance matrix: 56: CYS27 HIS29 56: SG90 NE2111 56: HIS29 NE2111 0.987 56: HIS32 NE2135 1.590 1.155 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/amber99sb-ildn.ff/aminoacids.arn 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/amber99sb-ildn.ff/dna.arn 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/amber99sb-ildn.ff/rna.arn 56: Before cleaning: 748 pairs 56: Before cleaning: 788 dihedrals 56: Using the Amber99sb-ildn force field in directory amber99sb-ildn.ff 56: 56: going to rename amber99sb-ildn.ff/aminoacids.r2b 56: 56: going to rename amber99sb-ildn.ff/dna.r2b 56: 56: going to rename amber99sb-ildn.ff/rna.r2b 56: Reading /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/B.pdb... 56: Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms 56: 56: Analyzing pdb file 56: Splitting chemical chains based on TER records or chain id changing. 56: 56: There are 1 chains and 0 blocks of water and 16 residues with 149 atoms 56: 56: chain #res #atoms 56: 56: 1 ' ' 16 149 56: 56: All occupancies are one 56: 56: Reading residue database... (Amber99sb-ildn) 56: 56: Processing chain 1 (149 atoms, 16 residues) 56: 56: Replaced 1 residue named GLUH to the default GLU. Use interactive selection of protonated residues if that is what you need. 56: 56: Identified residue THR18 as a starting terminus. 56: 56: Identified residue PHE33 as a ending terminus. 56: 56: Checking for duplicate atoms.... 56: 56: Generating any missing hydrogen atoms and/or adding termini. 56: 56: Now there are 16 residues with 281 atoms 56: 56: Making bonds... 56: 56: Number of bonds was 291, now 290 56: 56: Generating angles, dihedrals and pairs... 56: 56: Making cmap torsions... 56: 56: There are 788 dihedrals, 72 impropers, 516 angles 56: 736 pairs, 290 bonds and 0 virtual sites 56: 56: Total mass 2088.366 a.m.u. 56: 56: Total charge 1.000 e 56: 56: Writing topology 56: 56: Writing coordinate file... 56: 56: --------- PLEASE NOTE ------------ 56: 56: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/B.pdb. 56: 56: The Amber99sb-ildn force field and the tip3p water model are used. 56: 56: --------- ETON ESAELP ------------ 56: [ OK ] Amber/Pdb2gmxTest.Runs/ff_amber99sbildn_tip3p_vsite_none_id_or_ter_merge_no_Bpdb_format_gro_match_file (315 ms) 56: [ RUN ] Amber/Pdb2gmxTest.Runs/ff_amber99sbildn_tip3p_vsite_none_id_or_ter_merge_no_Cpdb_format_gro_match_file 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/amber99sb-ildn.ff/aminoacids.r2b 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/amber99sb-ildn.ff/dna.r2b 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/amber99sb-ildn.ff/rna.r2b 56: All occupancies are one 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/amber99sb-ildn.ff/atomtypes.atp 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/amber99sb-ildn.ff/aminoacids.rtp 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/amber99sb-ildn.ff/dna.rtp 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/amber99sb-ildn.ff/rna.rtp 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/amber99sb-ildn.ff/aminoacids.hdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/amber99sb-ildn.ff/dna.hdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/amber99sb-ildn.ff/rna.hdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/amber99sb-ildn.ff/aminoacids.n.tdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/amber99sb-ildn.ff/aminoacids.c.tdb 56: Analysing hydrogen-bonding network for automated assignment of histidine 56: protonation. 22 donors and 22 acceptors were found. 56: There are 26 hydrogen bonds 56: Will use HISE for residue 45 56: 9 out of 9 lines of specbond.dat converted successfully 56: Special Atom Distance matrix: 56: HIS45 56: NE295 56: MET46 SD102 1.078 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/amber99sb-ildn.ff/aminoacids.arn 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/amber99sb-ildn.ff/dna.arn 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/amber99sb-ildn.ff/rna.arn 56: Before cleaning: 676 pairs 56: Before cleaning: 727 dihedrals 56: Using the Amber99sb-ildn force field in directory amber99sb-ildn.ff 56: 56: going to rename amber99sb-ildn.ff/aminoacids.r2b 56: 56: going to rename amber99sb-ildn.ff/dna.r2b 56: 56: going to rename amber99sb-ildn.ff/rna.r2b 56: Reading /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/C.pdb... 56: Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms 56: 56: Analyzing pdb file 56: Splitting chemical chains based on TER records or chain id changing. 56: 56: There are 1 chains and 0 blocks of water and 16 residues with 132 atoms 56: 56: chain #res #atoms 56: 56: 1 ' ' 16 132 56: 56: All occupancies are one 56: 56: Reading residue database... (Amber99sb-ildn) 56: 56: Processing chain 1 (132 atoms, 16 residues) 56: 56: Identified residue ALA34 as a starting terminus. 56: 56: Identified residue ALA49 as a ending terminus. 56: 56: Checking for duplicate atoms.... 56: 56: Generating any missing hydrogen atoms and/or adding termini. 56: 56: Now there are 16 residues with 255 atoms 56: 56: Making bonds... 56: 56: Number of bonds was 262, now 261 56: 56: Generating angles, dihedrals and pairs... 56: 56: Making cmap torsions... 56: 56: There are 727 dihedrals, 56 impropers, 472 angles 56: 667 pairs, 261 bonds and 0 virtual sites 56: 56: Total mass 1861.124 a.m.u. 56: 56: Total charge -1.000 e 56: 56: Writing topology 56: 56: Writing coordinate file... 56: 56: --------- PLEASE NOTE ------------ 56: 56: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/C.pdb. 56: 56: The Amber99sb-ildn force field and the tip3p water model are used. 56: 56: --------- ETON ESAELP ------------ 56: [ OK ] Amber/Pdb2gmxTest.Runs/ff_amber99sbildn_tip3p_vsite_none_id_or_ter_merge_no_Cpdb_format_gro_match_file (301 ms) 56: [ RUN ] Amber/Pdb2gmxTest.Runs/ff_amber99sbildn_tip3p_vsite_none_id_or_ter_merge_no_Dpdb_format_gro_match_file 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/amber99sb-ildn.ff/aminoacids.r2b 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/amber99sb-ildn.ff/dna.r2b 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/amber99sb-ildn.ff/rna.r2b 56: All occupancies are one 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/amber99sb-ildn.ff/atomtypes.atp 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/amber99sb-ildn.ff/aminoacids.rtp 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/amber99sb-ildn.ff/dna.rtp 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/amber99sb-ildn.ff/rna.rtp 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/amber99sb-ildn.ff/aminoacids.hdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/amber99sb-ildn.ff/dna.hdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/amber99sb-ildn.ff/rna.hdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/amber99sb-ildn.ff/aminoacids.n.tdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/amber99sb-ildn.ff/aminoacids.c.tdb 56: Analysing hydrogen-bonding network for automated assignment of histidine 56: protonation. 22 donors and 21 acceptors were found. 56: There are 30 hydrogen bonds 56: Will use HISE for residue 60 56: 9 out of 9 lines of specbond.dat converted successfully 56: Special Atom Distance matrix: 56: HIS60 56: NE285 56: CYS62 SG98 0.803 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/amber99sb-ildn.ff/aminoacids.arn 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/amber99sb-ildn.ff/dna.arn 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/amber99sb-ildn.ff/rna.arn 56: Before cleaning: 603 pairs 56: Before cleaning: 634 dihedrals 56: Using the Amber99sb-ildn force field in directory amber99sb-ildn.ff 56: 56: going to rename amber99sb-ildn.ff/aminoacids.r2b 56: 56: going to rename amber99sb-ildn.ff/dna.r2b 56: 56: going to rename amber99sb-ildn.ff/rna.r2b 56: Reading /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/D.pdb... 56: Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms 56: 56: Analyzing pdb file 56: Splitting chemical chains based on TER records or chain id changing. 56: 56: There are 1 chains and 0 blocks of water and 16 residues with 117 atoms 56: 56: chain #res #atoms 56: 56: 1 ' ' 16 117 56: 56: All occupancies are one 56: 56: Reading residue database... (Amber99sb-ildn) 56: 56: Processing chain 1 (117 atoms, 16 residues) 56: 56: Replaced 1 residue named ASPH to the default ASP. Use interactive selection of protonated residues if that is what you need. 56: 56: Identified residue LYS50 as a starting terminus. 56: 56: Identified residue PRO65 as a ending terminus. 56: 56: Checking for duplicate atoms.... 56: 56: Generating any missing hydrogen atoms and/or adding termini. 56: 56: Now there are 16 residues with 228 atoms 56: 56: Making bonds... 56: 56: Number of bonds was 233, now 232 56: 56: Generating angles, dihedrals and pairs... 56: 56: Making cmap torsions... 56: 56: There are 634 dihedrals, 48 impropers, 419 angles 56: 597 pairs, 232 bonds and 0 virtual sites 56: 56: Total mass 1662.888 a.m.u. 56: 56: Total charge -0.000 e 56: 56: Writing topology 56: 56: Writing coordinate file... 56: 56: --------- PLEASE NOTE ------------ 56: 56: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/D.pdb. 56: 56: The Amber99sb-ildn force field and the tip3p water model are used. 56: 56: --------- ETON ESAELP ------------ 56: [ OK ] Amber/Pdb2gmxTest.Runs/ff_amber99sbildn_tip3p_vsite_none_id_or_ter_merge_no_Dpdb_format_gro_match_file (283 ms) 56: [ RUN ] Amber/Pdb2gmxTest.Runs/ff_amber99sbildn_tip3p_vsite_none_id_or_ter_merge_no_Epdb_format_gro_match_file 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/amber99sb-ildn.ff/aminoacids.r2b 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/amber99sb-ildn.ff/dna.r2b 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/amber99sb-ildn.ff/rna.r2b 56: All occupancies are one 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/amber99sb-ildn.ff/atomtypes.atp 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/amber99sb-ildn.ff/aminoacids.rtp 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/amber99sb-ildn.ff/dna.rtp 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/amber99sb-ildn.ff/rna.rtp 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/amber99sb-ildn.ff/aminoacids.hdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/amber99sb-ildn.ff/dna.hdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/amber99sb-ildn.ff/rna.hdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/amber99sb-ildn.ff/aminoacids.n.tdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/amber99sb-ildn.ff/aminoacids.c.tdb 56: Analysing hydrogen-bonding network for automated assignment of histidine 56: protonation. 89 donors and 98 acceptors were found. 56: There are 129 hydrogen bonds 56: Will use HISE for residue 31 56: Will use HISE for residue 51 56: 9 out of 9 lines of specbond.dat converted successfully 56: Special Atom Distance matrix: 56: CYS25 HIS31 HIS51 56: SG14 NE264 NE2226 56: HIS31 NE264 1.921 56: HIS51 NE2226 1.498 2.650 56: CYS80 SG477 0.207 1.984 1.570 56: Linking CYS-25 SG-14 and CYS-80 SG-477... 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/amber99sb-ildn.ff/aminoacids.arn 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/amber99sb-ildn.ff/dna.arn 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/amber99sb-ildn.ff/rna.arn 56: Before cleaning: 2499 pairs 56: Before cleaning: 2631 dihedrals 56: Using the Amber99sb-ildn force field in directory amber99sb-ildn.ff 56: 56: going to rename amber99sb-ildn.ff/aminoacids.r2b 56: 56: going to rename amber99sb-ildn.ff/dna.r2b 56: 56: going to rename amber99sb-ildn.ff/rna.r2b 56: Reading /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/E.pdb... 56: Read 'This is a fragment of 2d4f for testing a disulfide bridge', 488 atoms 56: 56: Analyzing pdb file 56: Splitting chemical chains based on TER records or chain id changing. 56: 56: There are 1 chains and 0 blocks of water and 58 residues with 488 atoms 56: 56: chain #res #atoms 56: 56: 1 'A' 58 488 56: 56: All occupancies are one 56: 56: Reading residue database... (Amber99sb-ildn) 56: 56: Processing chain 1 'A' (488 atoms, 58 residues) 56: 56: Identified residue ASN24 as a starting terminus. 56: 56: Identified residue ARG81 as a ending terminus. 56: 56: Checking for duplicate atoms.... 56: 56: Generating any missing hydrogen atoms and/or adding termini. 56: 56: Now there are 58 residues with 936 atoms 56: 56: Making bonds... 56: 56: Number of bonds was 952, now 951 56: 56: Generating angles, dihedrals and pairs... 56: 56: Making cmap torsions... 56: 56: There are 2631 dihedrals, 208 impropers, 1704 angles 56: 2469 pairs, 951 bonds and 0 virtual sites 56: 56: Total mass 6908.576 a.m.u. 56: 56: Total charge -6.000 e 56: 56: Writing topology 56: 56: Writing coordinate file... 56: 56: --------- PLEASE NOTE ------------ 56: 56: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/E.pdb. 56: 56: The Amber99sb-ildn force field and the tip3p water model are used. 56: 56: --------- ETON ESAELP ------------ 56: [ OK ] Amber/Pdb2gmxTest.Runs/ff_amber99sbildn_tip3p_vsite_none_id_or_ter_merge_no_Epdb_format_gro_match_file (759 ms) 56: [ RUN ] Amber/Pdb2gmxTest.Runs/ff_amber99sbildn_tip3p_vsite_h_id_or_ter_merge_no_Apdb_format_gro_match_file 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/amber99sb-ildn.ff/aminoacids.r2b 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/amber99sb-ildn.ff/dna.r2b 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/amber99sb-ildn.ff/rna.r2b 56: All occupancies are one 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/amber99sb-ildn.ff/atomtypes.atp 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/amber99sb-ildn.ff/aminoacids.rtp 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/amber99sb-ildn.ff/dna.rtp 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/amber99sb-ildn.ff/rna.rtp 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/amber99sb-ildn.ff/aminoacids.hdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/amber99sb-ildn.ff/dna.hdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/amber99sb-ildn.ff/rna.hdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/amber99sb-ildn.ff/aminoacids.n.tdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/amber99sb-ildn.ff/aminoacids.c.tdb 56: Analysing hydrogen-bonding network for automated assignment of histidine 56: protonation. 25 donors and 23 acceptors were found. 56: There are 41 hydrogen bonds 56: Will use HISE for residue 8 56: 9 out of 9 lines of specbond.dat converted successfully 56: Special Atom Distance matrix: 56: CYS3 HIS8 56: SG9 NE251 56: HIS8 NE251 1.055 56: MET12 SD83 0.763 0.990 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/amber99sb-ildn.ff/aminoacids.arn 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/amber99sb-ildn.ff/dna.arn 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/amber99sb-ildn.ff/rna.arn 56: Marked 124 virtual sites 56: Added 16 dummy masses 56: Added 26 new constraints 56: Before cleaning: 653 pairs 56: Before cleaning: 691 dihedrals 56: Using the Amber99sb-ildn force field in directory amber99sb-ildn.ff 56: 56: going to rename amber99sb-ildn.ff/aminoacids.r2b 56: 56: going to rename amber99sb-ildn.ff/dna.r2b 56: 56: going to rename amber99sb-ildn.ff/rna.r2b 56: Reading /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/A.pdb... 56: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms 56: 56: Analyzing pdb file 56: Splitting chemical chains based on TER records or chain id changing. 56: 56: There are 1 chains and 0 blocks of water and 16 residues with 128 atoms 56: 56: chain #res #atoms 56: 56: 1 ' ' 16 128 56: 56: All occupancies are one 56: 56: Reading residue database... (Amber99sb-ildn) 56: 56: Processing chain 1 (128 atoms, 16 residues) 56: 56: Identified residue ALA2 as a starting terminus. 56: 56: Identified residue SER17 as a ending terminus. 56: 56: Checking for duplicate atoms.... 56: 56: Generating any missing hydrogen atoms and/or adding termini. 56: 56: Now there are 16 residues with 252 atoms 56: 56: Making bonds... 56: 56: Number of bonds was 255, now 254 56: 56: Generating angles, dihedrals and pairs... 56: 56: Making cmap torsions... 56: 56: There are 691 dihedrals, 51 impropers, 457 angles 56: 650 pairs, 254 bonds and 130 virtual sites 56: 56: Total mass 1846.132 a.m.u. 56: 56: Total charge 0.000 e 56: 56: Writing topology 56: 56: Writing coordinate file... 56: 56: --------- PLEASE NOTE ------------ 56: 56: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/A.pdb. 56: 56: The Amber99sb-ildn force field and the tip3p water model are used. 56: 56: --------- ETON ESAELP ------------ 56: [ OK ] Amber/Pdb2gmxTest.Runs/ff_amber99sbildn_tip3p_vsite_h_id_or_ter_merge_no_Apdb_format_gro_match_file (340 ms) 56: [ RUN ] Amber/Pdb2gmxTest.Runs/ff_amber99sbildn_tip3p_vsite_h_id_or_ter_merge_no_Bpdb_format_gro_match_file 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/amber99sb-ildn.ff/aminoacids.r2b 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/amber99sb-ildn.ff/dna.r2b 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/amber99sb-ildn.ff/rna.r2b 56: All occupancies are one 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/amber99sb-ildn.ff/atomtypes.atp 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/amber99sb-ildn.ff/aminoacids.rtp 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/amber99sb-ildn.ff/dna.rtp 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/amber99sb-ildn.ff/rna.rtp 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/amber99sb-ildn.ff/aminoacids.hdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/amber99sb-ildn.ff/dna.hdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/amber99sb-ildn.ff/rna.hdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/amber99sb-ildn.ff/aminoacids.n.tdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/amber99sb-ildn.ff/aminoacids.c.tdb 56: Analysing hydrogen-bonding network for automated assignment of histidine 56: protonation. 30 donors and 22 acceptors were found. 56: There are 36 hydrogen bonds 56: Will use HISE for residue 29 56: Will use HISE for residue 32 56: 9 out of 9 lines of specbond.dat converted successfully 56: Special Atom Distance matrix: 56: CYS27 HIS29 56: SG90 NE2111 56: HIS29 NE2111 0.987 56: HIS32 NE2135 1.590 1.155 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/amber99sb-ildn.ff/aminoacids.arn 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/amber99sb-ildn.ff/dna.arn 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/amber99sb-ildn.ff/rna.arn 56: Marked 132 virtual sites 56: Added 10 dummy masses 56: Added 19 new constraints 56: Before cleaning: 748 pairs 56: Before cleaning: 788 dihedrals 56: Using the Amber99sb-ildn force field in directory amber99sb-ildn.ff 56: 56: going to rename amber99sb-ildn.ff/aminoacids.r2b 56: 56: going to rename amber99sb-ildn.ff/dna.r2b 56: 56: going to rename amber99sb-ildn.ff/rna.r2b 56: Reading /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/B.pdb... 56: Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms 56: 56: Analyzing pdb file 56: Splitting chemical chains based on TER records or chain id changing. 56: 56: There are 1 chains and 0 blocks of water and 16 residues with 149 atoms 56: 56: chain #res #atoms 56: 56: 1 ' ' 16 149 56: 56: All occupancies are one 56: 56: Reading residue database... (Amber99sb-ildn) 56: 56: Processing chain 1 (149 atoms, 16 residues) 56: 56: Replaced 1 residue named GLUH to the default GLU. Use interactive selection of protonated residues if that is what you need. 56: 56: Identified residue THR18 as a starting terminus. 56: 56: Identified residue PHE33 as a ending terminus. 56: 56: Checking for duplicate atoms.... 56: 56: Generating any missing hydrogen atoms and/or adding termini. 56: 56: Now there are 16 residues with 281 atoms 56: 56: Making bonds... 56: 56: Number of bonds was 291, now 290 56: 56: Generating angles, dihedrals and pairs... 56: 56: Making cmap torsions... 56: 56: There are 788 dihedrals, 72 impropers, 516 angles 56: 736 pairs, 290 bonds and 133 virtual sites 56: 56: Total mass 2088.366 a.m.u. 56: 56: Total charge 1.000 e 56: 56: Writing topology 56: 56: Writing coordinate file... 56: 56: --------- PLEASE NOTE ------------ 56: 56: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/B.pdb. 56: 56: The Amber99sb-ildn force field and the tip3p water model are used. 56: 56: --------- ETON ESAELP ------------ 56: [ OK ] Amber/Pdb2gmxTest.Runs/ff_amber99sbildn_tip3p_vsite_h_id_or_ter_merge_no_Bpdb_format_gro_match_file (321 ms) 56: [ RUN ] Amber/Pdb2gmxTest.Runs/ff_amber99sbildn_tip3p_vsite_h_id_or_ter_merge_no_Cpdb_format_gro_match_file 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/amber99sb-ildn.ff/aminoacids.r2b 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/amber99sb-ildn.ff/dna.r2b 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/amber99sb-ildn.ff/rna.r2b 56: All occupancies are one 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/amber99sb-ildn.ff/atomtypes.atp 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/amber99sb-ildn.ff/aminoacids.rtp 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/amber99sb-ildn.ff/dna.rtp 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/amber99sb-ildn.ff/rna.rtp 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/amber99sb-ildn.ff/aminoacids.hdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/amber99sb-ildn.ff/dna.hdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/amber99sb-ildn.ff/rna.hdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/amber99sb-ildn.ff/aminoacids.n.tdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/amber99sb-ildn.ff/aminoacids.c.tdb 56: Analysing hydrogen-bonding network for automated assignment of histidine 56: protonation. 22 donors and 22 acceptors were found. 56: There are 26 hydrogen bonds 56: Will use HISE for residue 45 56: 9 out of 9 lines of specbond.dat converted successfully 56: Special Atom Distance matrix: 56: HIS45 56: NE295 56: MET46 SD102 1.078 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/amber99sb-ildn.ff/aminoacids.arn 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/amber99sb-ildn.ff/dna.arn 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/amber99sb-ildn.ff/rna.arn 56: Marked 123 virtual sites 56: Added 22 dummy masses 56: Added 35 new constraints 56: Before cleaning: 676 pairs 56: Before cleaning: 727 dihedrals 56: Using the Amber99sb-ildn force field in directory amber99sb-ildn.ff 56: 56: going to rename amber99sb-ildn.ff/aminoacids.r2b 56: 56: going to rename amber99sb-ildn.ff/dna.r2b 56: 56: going to rename amber99sb-ildn.ff/rna.r2b 56: Reading /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/C.pdb... 56: Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms 56: 56: Analyzing pdb file 56: Splitting chemical chains based on TER records or chain id changing. 56: 56: There are 1 chains and 0 blocks of water and 16 residues with 132 atoms 56: 56: chain #res #atoms 56: 56: 1 ' ' 16 132 56: 56: All occupancies are one 56: 56: Reading residue database... (Amber99sb-ildn) 56: 56: Processing chain 1 (132 atoms, 16 residues) 56: 56: Identified residue ALA34 as a starting terminus. 56: 56: Identified residue ALA49 as a ending terminus. 56: 56: Checking for duplicate atoms.... 56: 56: Generating any missing hydrogen atoms and/or adding termini. 56: 56: Now there are 16 residues with 255 atoms 56: 56: Making bonds... 56: 56: Number of bonds was 262, now 261 56: 56: Generating angles, dihedrals and pairs... 56: 56: Making cmap torsions... 56: 56: There are 727 dihedrals, 56 impropers, 472 angles 56: 667 pairs, 261 bonds and 132 virtual sites 56: 56: Total mass 1861.124 a.m.u. 56: 56: Total charge -1.000 e 56: 56: Writing topology 56: 56: Writing coordinate file... 56: 56: --------- PLEASE NOTE ------------ 56: 56: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/C.pdb. 56: 56: The Amber99sb-ildn force field and the tip3p water model are used. 56: 56: --------- ETON ESAELP ------------ 56: [ OK ] Amber/Pdb2gmxTest.Runs/ff_amber99sbildn_tip3p_vsite_h_id_or_ter_merge_no_Cpdb_format_gro_match_file (323 ms) 56: [ RUN ] Amber/Pdb2gmxTest.Runs/ff_amber99sbildn_tip3p_vsite_h_id_or_ter_merge_no_Dpdb_format_gro_match_file 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/amber99sb-ildn.ff/aminoacids.r2b 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/amber99sb-ildn.ff/dna.r2b 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/amber99sb-ildn.ff/rna.r2b 56: All occupancies are one 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/amber99sb-ildn.ff/atomtypes.atp 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/amber99sb-ildn.ff/aminoacids.rtp 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/amber99sb-ildn.ff/dna.rtp 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/amber99sb-ildn.ff/rna.rtp 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/amber99sb-ildn.ff/aminoacids.hdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/amber99sb-ildn.ff/dna.hdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/amber99sb-ildn.ff/rna.hdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/amber99sb-ildn.ff/aminoacids.n.tdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/amber99sb-ildn.ff/aminoacids.c.tdb 56: Analysing hydrogen-bonding network for automated assignment of histidine 56: protonation. 22 donors and 21 acceptors were found. 56: There are 30 hydrogen bonds 56: Will use HISE for residue 60 56: 9 out of 9 lines of specbond.dat converted successfully 56: Special Atom Distance matrix: 56: HIS60 56: NE285 56: CYS62 SG98 0.803 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/amber99sb-ildn.ff/aminoacids.arn 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/amber99sb-ildn.ff/dna.arn 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/amber99sb-ildn.ff/rna.arn 56: Marked 111 virtual sites 56: Added 18 dummy masses 56: Added 31 new constraints 56: Before cleaning: 603 pairs 56: Before cleaning: 634 dihedrals 56: Using the Amber99sb-ildn force field in directory amber99sb-ildn.ff 56: 56: going to rename amber99sb-ildn.ff/aminoacids.r2b 56: 56: going to rename amber99sb-ildn.ff/dna.r2b 56: 56: going to rename amber99sb-ildn.ff/rna.r2b 56: Reading /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/D.pdb... 56: Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms 56: 56: Analyzing pdb file 56: Splitting chemical chains based on TER records or chain id changing. 56: 56: There are 1 chains and 0 blocks of water and 16 residues with 117 atoms 56: 56: chain #res #atoms 56: 56: 1 ' ' 16 117 56: 56: All occupancies are one 56: 56: Reading residue database... (Amber99sb-ildn) 56: 56: Processing chain 1 (117 atoms, 16 residues) 56: 56: Replaced 1 residue named ASPH to the default ASP. Use interactive selection of protonated residues if that is what you need. 56: 56: Identified residue LYS50 as a starting terminus. 56: 56: Identified residue PRO65 as a ending terminus. 56: 56: Checking for duplicate atoms.... 56: 56: Generating any missing hydrogen atoms and/or adding termini. 56: 56: Now there are 16 residues with 228 atoms 56: 56: Making bonds... 56: 56: Number of bonds was 233, now 232 56: 56: Generating angles, dihedrals and pairs... 56: 56: Making cmap torsions... 56: 56: There are 634 dihedrals, 48 impropers, 419 angles 56: 597 pairs, 232 bonds and 116 virtual sites 56: 56: Total mass 1662.888 a.m.u. 56: 56: Total charge -0.000 e 56: 56: Writing topology 56: 56: Writing coordinate file... 56: 56: --------- PLEASE NOTE ------------ 56: 56: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/D.pdb. 56: 56: The Amber99sb-ildn force field and the tip3p water model are used. 56: 56: --------- ETON ESAELP ------------ 56: [ OK ] Amber/Pdb2gmxTest.Runs/ff_amber99sbildn_tip3p_vsite_h_id_or_ter_merge_no_Dpdb_format_gro_match_file (303 ms) 56: [ RUN ] Amber/Pdb2gmxTest.Runs/ff_amber99sbildn_tip3p_vsite_h_id_or_ter_merge_no_Epdb_format_gro_match_file 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/amber99sb-ildn.ff/aminoacids.r2b 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/amber99sb-ildn.ff/dna.r2b 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/amber99sb-ildn.ff/rna.r2b 56: All occupancies are one 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/amber99sb-ildn.ff/atomtypes.atp 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/amber99sb-ildn.ff/aminoacids.rtp 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/amber99sb-ildn.ff/dna.rtp 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/amber99sb-ildn.ff/rna.rtp 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/amber99sb-ildn.ff/aminoacids.hdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/amber99sb-ildn.ff/dna.hdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/amber99sb-ildn.ff/rna.hdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/amber99sb-ildn.ff/aminoacids.n.tdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/amber99sb-ildn.ff/aminoacids.c.tdb 56: Analysing hydrogen-bonding network for automated assignment of histidine 56: protonation. 89 donors and 98 acceptors were found. 56: There are 129 hydrogen bonds 56: Will use HISE for residue 31 56: Will use HISE for residue 51 56: 9 out of 9 lines of specbond.dat converted successfully 56: Special Atom Distance matrix: 56: CYS25 HIS31 HIS51 56: SG14 NE264 NE2226 56: HIS31 NE264 1.921 56: HIS51 NE2226 1.498 2.650 56: CYS80 SG477 0.207 1.984 1.570 56: Linking CYS-25 SG-14 and CYS-80 SG-477... 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/amber99sb-ildn.ff/aminoacids.arn 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/amber99sb-ildn.ff/dna.arn 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/amber99sb-ildn.ff/rna.arn 56: Marked 447 virtual sites 56: Added 58 dummy masses 56: Added 101 new constraints 56: Before cleaning: 2499 pairs 56: Before cleaning: 2631 dihedrals 56: Using the Amber99sb-ildn force field in directory amber99sb-ildn.ff 56: 56: going to rename amber99sb-ildn.ff/aminoacids.r2b 56: 56: going to rename amber99sb-ildn.ff/dna.r2b 56: 56: going to rename amber99sb-ildn.ff/rna.r2b 56: Reading /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/E.pdb... 56: Read 'This is a fragment of 2d4f for testing a disulfide bridge', 488 atoms 56: 56: Analyzing pdb file 56: Splitting chemical chains based on TER records or chain id changing. 56: 56: There are 1 chains and 0 blocks of water and 58 residues with 488 atoms 56: 56: chain #res #atoms 56: 56: 1 'A' 58 488 56: 56: All occupancies are one 56: 56: Reading residue database... (Amber99sb-ildn) 56: 56: Processing chain 1 'A' (488 atoms, 58 residues) 56: 56: Identified residue ASN24 as a starting terminus. 56: 56: Identified residue ARG81 as a ending terminus. 56: 56: Checking for duplicate atoms.... 56: 56: Generating any missing hydrogen atoms and/or adding termini. 56: 56: Now there are 58 residues with 936 atoms 56: 56: Making bonds... 56: 56: Number of bonds was 952, now 951 56: 56: Generating angles, dihedrals and pairs... 56: 56: Making cmap torsions... 56: 56: There are 2631 dihedrals, 208 impropers, 1704 angles 56: 2469 pairs, 951 bonds and 462 virtual sites 56: 56: Total mass 6908.576 a.m.u. 56: 56: Total charge -6.000 e 56: 56: Writing topology 56: 56: Writing coordinate file... 56: 56: --------- PLEASE NOTE ------------ 56: 56: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/E.pdb. 56: 56: The Amber99sb-ildn force field and the tip3p water model are used. 56: 56: --------- ETON ESAELP ------------ 56: [ OK ] Amber/Pdb2gmxTest.Runs/ff_amber99sbildn_tip3p_vsite_h_id_or_ter_merge_no_Epdb_format_gro_match_file (844 ms) 56: [----------] 10 tests from Amber/Pdb2gmxTest (4132 ms total) 56: 56: [----------] 1 test from AmberTip4p/Pdb2gmxTest 56: [ RUN ] AmberTip4p/Pdb2gmxTest.Runs/ff_amber99sbildn_tip4p_vsite_none_id_or_ter_merge_no_tip4ppdb_format_gro_match_full 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/amber99sb-ildn.ff/aminoacids.r2b 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/amber99sb-ildn.ff/dna.r2b 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/amber99sb-ildn.ff/rna.r2b 56: All occupancies are one 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/amber99sb-ildn.ff/atomtypes.atp 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/amber99sb-ildn.ff/aminoacids.rtp 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/amber99sb-ildn.ff/dna.rtp 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/amber99sb-ildn.ff/rna.rtp 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/amber99sb-ildn.ff/aminoacids.hdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/amber99sb-ildn.ff/dna.hdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/amber99sb-ildn.ff/rna.hdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/amber99sb-ildn.ff/aminoacids.n.tdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/amber99sb-ildn.ff/aminoacids.c.tdb 56: 9 out of 9 lines of specbond.dat converted successfully 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/amber99sb-ildn.ff/aminoacids.arn 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/amber99sb-ildn.ff/dna.arn 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/amber99sb-ildn.ff/rna.arn 56: Using the Amber99sb-ildn force field in directory amber99sb-ildn.ff 56: 56: going to rename amber99sb-ildn.ff/aminoacids.r2b 56: 56: going to rename amber99sb-ildn.ff/dna.r2b 56: 56: going to rename amber99sb-ildn.ff/rna.r2b 56: Reading /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/tip4p.pdb... 56: Read 'TIP4p ice to test that MW is handled correctly', 4 atoms 56: 56: Analyzing pdb file 56: Splitting chemical chains based on TER records or chain id changing. 56: 56: There are 0 chains and 1 blocks of water and 2 residues with 4 atoms 56: 56: chain #res #atoms 56: 56: 1 ' ' 2 4 (only water) 56: 56: All occupancies are one 56: 56: Reading residue database... (Amber99sb-ildn) 56: 56: Processing chain 1 (4 atoms, 2 residues) 56: 56: Problem with chain definition, or missing terminal residues. This chain does not appear to contain a recognized chain molecule. If this is incorrect, you can edit residuetypes.dat to modify the behavior. 56: 56: Checking for duplicate atoms.... 56: 56: Generating any missing hydrogen atoms and/or adding termini. 56: 56: Now there are 2 residues with 8 atoms 56: 56: Making bonds... 56: 56: Number of bonds was 4, now 4 56: 56: Generating angles, dihedrals and pairs... 56: 56: Making cmap torsions... 56: 56: There are 0 dihedrals, 0 impropers, 2 angles 56: 0 pairs, 4 bonds and 0 virtual sites 56: 56: Total mass 36.032 a.m.u. 56: 56: Total charge 0.000 e 56: 56: Writing coordinate file... 56: 56: --------- PLEASE NOTE ------------ 56: 56: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/tip4p.pdb. 56: 56: The Amber99sb-ildn force field and the tip4p water model are used. 56: 56: --------- ETON ESAELP ------------ 56: [ OK ] AmberTip4p/Pdb2gmxTest.Runs/ff_amber99sbildn_tip4p_vsite_none_id_or_ter_merge_no_tip4ppdb_format_gro_match_full (137 ms) 56: [----------] 1 test from AmberTip4p/Pdb2gmxTest (137 ms total) 56: 56: [----------] 12 tests from Charmm/Pdb2gmxTest 56: [ RUN ] Charmm/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_or_ter_merge_no_Apdb_format_gro_match_file 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/aminoacids.r2b 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/rna.r2b 56: All occupancies are one 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/atomtypes.atp 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/aminoacids.rtp 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/dna.rtp 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/lipids.rtp 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/rna.rtp 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/aminoacids.hdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/dna.hdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/lipids.hdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/rna.hdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/aminoacids.n.tdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/dna.n.tdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/rna.n.tdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/aminoacids.c.tdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/dna.c.tdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/rna.c.tdb 56: Analysing hydrogen-bonding network for automated assignment of histidine 56: protonation. 25 donors and 23 acceptors were found. 56: There are 41 hydrogen bonds 56: Will use HISE for residue 8 56: 9 out of 9 lines of specbond.dat converted successfully 56: Special Atom Distance matrix: 56: CYS3 HIS8 56: SG9 NE251 56: HIS8 NE251 1.055 56: MET12 SD83 0.763 0.990 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/aminoacids.arn 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/dna.arn 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/rna.arn 56: Before cleaning: 653 pairs 56: Before cleaning: 663 dihedrals 56: Using the Charmm27 force field in directory charmm27.ff 56: 56: going to rename charmm27.ff/aminoacids.r2b 56: 56: going to rename charmm27.ff/rna.r2b 56: Reading /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/A.pdb... 56: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms 56: 56: Analyzing pdb file 56: Splitting chemical chains based on TER records or chain id changing. 56: 56: There are 1 chains and 0 blocks of water and 16 residues with 128 atoms 56: 56: chain #res #atoms 56: 56: 1 ' ' 16 128 56: 56: All occupancies are one 56: 56: Reading residue database... (Charmm27) 56: 56: Processing chain 1 (128 atoms, 16 residues) 56: 56: Identified residue ALA2 as a starting terminus. 56: 56: Identified residue SER17 as a ending terminus. 56: Start terminus ALA-2: NH3+ 56: End terminus SER-17: COO- 56: 56: Checking for duplicate atoms.... 56: 56: Generating any missing hydrogen atoms and/or adding termini. 56: 56: Now there are 16 residues with 252 atoms 56: 56: Making bonds... 56: 56: Number of bonds was 254, now 254 56: 56: Generating angles, dihedrals and pairs... 56: 56: Making cmap torsions... 56: 56: There are 14 cmap torsion pairs 56: 56: There are 663 dihedrals, 48 impropers, 457 angles 56: 650 pairs, 254 bonds and 0 virtual sites 56: 56: Total mass 1846.115 a.m.u. 56: 56: Total charge 0.000 e 56: 56: Writing topology 56: 56: Writing coordinate file... 56: 56: --------- PLEASE NOTE ------------ 56: 56: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/A.pdb. 56: 56: The Charmm27 force field and the tip3p water model are used. 56: 56: --------- ETON ESAELP ------------ 56: [ OK ] Charmm/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_or_ter_merge_no_Apdb_format_gro_match_file (294 ms) 56: [ RUN ] Charmm/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_or_ter_merge_no_Bpdb_format_gro_match_file 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/aminoacids.r2b 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/rna.r2b 56: All occupancies are one 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/atomtypes.atp 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/aminoacids.rtp 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/dna.rtp 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/lipids.rtp 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/rna.rtp 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/aminoacids.hdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/dna.hdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/lipids.hdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/rna.hdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/aminoacids.n.tdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/dna.n.tdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/rna.n.tdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/aminoacids.c.tdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/dna.c.tdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/rna.c.tdb 56: Analysing hydrogen-bonding network for automated assignment of histidine 56: protonation. 30 donors and 22 acceptors were found. 56: There are 36 hydrogen bonds 56: Will use HISE for residue 29 56: Will use HISE for residue 32 56: 9 out of 9 lines of specbond.dat converted successfully 56: Special Atom Distance matrix: 56: CYS27 HIS29 56: SG90 NE2111 56: HIS29 NE2111 0.987 56: HIS32 NE2135 1.590 1.155 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/aminoacids.arn 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/dna.arn 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/rna.arn 56: Before cleaning: 748 pairs 56: Before cleaning: 778 dihedrals 56: Using the Charmm27 force field in directory charmm27.ff 56: 56: going to rename charmm27.ff/aminoacids.r2b 56: 56: going to rename charmm27.ff/rna.r2b 56: Reading /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/B.pdb... 56: Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms 56: 56: Analyzing pdb file 56: Splitting chemical chains based on TER records or chain id changing. 56: 56: There are 1 chains and 0 blocks of water and 16 residues with 149 atoms 56: 56: chain #res #atoms 56: 56: 1 ' ' 16 149 56: 56: All occupancies are one 56: 56: Reading residue database... (Charmm27) 56: 56: Processing chain 1 (149 atoms, 16 residues) 56: 56: Replaced 1 residue named GLUH to the default GLU. Use interactive selection of protonated residues if that is what you need. 56: 56: Identified residue THR18 as a starting terminus. 56: 56: Identified residue PHE33 as a ending terminus. 56: Start terminus THR-18: NH3+ 56: End terminus PHE-33: COO- 56: 56: Checking for duplicate atoms.... 56: 56: Generating any missing hydrogen atoms and/or adding termini. 56: 56: Now there are 16 residues with 281 atoms 56: 56: Making bonds... 56: 56: Number of bonds was 290, now 290 56: 56: Generating angles, dihedrals and pairs... 56: 56: Making cmap torsions... 56: 56: There are 14 cmap torsion pairs 56: 56: There are 778 dihedrals, 49 impropers, 516 angles 56: 736 pairs, 290 bonds and 0 virtual sites 56: 56: Total mass 2088.361 a.m.u. 56: 56: Total charge 1.000 e 56: 56: Writing topology 56: 56: Writing coordinate file... 56: 56: --------- PLEASE NOTE ------------ 56: 56: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/B.pdb. 56: 56: The Charmm27 force field and the tip3p water model are used. 56: 56: --------- ETON ESAELP ------------ 56: [ OK ] Charmm/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_or_ter_merge_no_Bpdb_format_gro_match_file (280 ms) 56: [ RUN ] Charmm/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_or_ter_merge_no_Cpdb_format_gro_match_file 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/aminoacids.r2b 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/rna.r2b 56: All occupancies are one 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/atomtypes.atp 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/aminoacids.rtp 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/dna.rtp 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/lipids.rtp 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/rna.rtp 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/aminoacids.hdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/dna.hdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/lipids.hdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/rna.hdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/aminoacids.n.tdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/dna.n.tdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/rna.n.tdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/aminoacids.c.tdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/dna.c.tdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/rna.c.tdb 56: Analysing hydrogen-bonding network for automated assignment of histidine 56: protonation. 22 donors and 22 acceptors were found. 56: There are 26 hydrogen bonds 56: Will use HISE for residue 45 56: 9 out of 9 lines of specbond.dat converted successfully 56: Special Atom Distance matrix: 56: HIS45 56: NE295 56: MET46 SD102 1.078 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/aminoacids.arn 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/dna.arn 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/rna.arn 56: Before cleaning: 676 pairs 56: Before cleaning: 696 dihedrals 56: Using the Charmm27 force field in directory charmm27.ff 56: 56: going to rename charmm27.ff/aminoacids.r2b 56: 56: going to rename charmm27.ff/rna.r2b 56: Reading /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/C.pdb... 56: Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms 56: 56: Analyzing pdb file 56: Splitting chemical chains based on TER records or chain id changing. 56: 56: There are 1 chains and 0 blocks of water and 16 residues with 132 atoms 56: 56: chain #res #atoms 56: 56: 1 ' ' 16 132 56: 56: All occupancies are one 56: 56: Reading residue database... (Charmm27) 56: 56: Processing chain 1 (132 atoms, 16 residues) 56: 56: Identified residue ALA34 as a starting terminus. 56: 56: Identified residue ALA49 as a ending terminus. 56: Start terminus ALA-34: NH3+ 56: End terminus ALA-49: COO- 56: 56: Checking for duplicate atoms.... 56: 56: Generating any missing hydrogen atoms and/or adding termini. 56: 56: Now there are 16 residues with 255 atoms 56: 56: Making bonds... 56: 56: Number of bonds was 261, now 261 56: 56: Generating angles, dihedrals and pairs... 56: 56: Making cmap torsions... 56: 56: There are 14 cmap torsion pairs 56: 56: There are 696 dihedrals, 39 impropers, 472 angles 56: 667 pairs, 261 bonds and 0 virtual sites 56: 56: Total mass 1861.130 a.m.u. 56: 56: Total charge -1.000 e 56: 56: Writing topology 56: 56: Writing coordinate file... 56: 56: --------- PLEASE NOTE ------------ 56: 56: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/C.pdb. 56: 56: The Charmm27 force field and the tip3p water model are used. 56: 56: --------- ETON ESAELP ------------ 56: [ OK ] Charmm/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_or_ter_merge_no_Cpdb_format_gro_match_file (265 ms) 56: [ RUN ] Charmm/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_or_ter_merge_no_Dpdb_format_gro_match_file 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/aminoacids.r2b 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/rna.r2b 56: All occupancies are one 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/atomtypes.atp 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/aminoacids.rtp 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/dna.rtp 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/lipids.rtp 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/rna.rtp 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/aminoacids.hdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/dna.hdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/lipids.hdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/rna.hdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/aminoacids.n.tdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/dna.n.tdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/rna.n.tdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/aminoacids.c.tdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/dna.c.tdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/rna.c.tdb 56: Analysing hydrogen-bonding network for automated assignment of histidine 56: protonation. 22 donors and 21 acceptors were found. 56: There are 30 hydrogen bonds 56: Will use HISE for residue 60 56: 9 out of 9 lines of specbond.dat converted successfully 56: Special Atom Distance matrix: 56: HIS60 56: NE285 56: CYS62 SG98 0.803 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/aminoacids.arn 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/dna.arn 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/rna.arn 56: Before cleaning: 603 pairs 56: Before cleaning: 618 dihedrals 56: Using the Charmm27 force field in directory charmm27.ff 56: 56: going to rename charmm27.ff/aminoacids.r2b 56: 56: going to rename charmm27.ff/rna.r2b 56: Reading /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/D.pdb... 56: Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms 56: 56: Analyzing pdb file 56: Splitting chemical chains based on TER records or chain id changing. 56: 56: There are 1 chains and 0 blocks of water and 16 residues with 117 atoms 56: 56: chain #res #atoms 56: 56: 1 ' ' 16 117 56: 56: All occupancies are one 56: 56: Reading residue database... (Charmm27) 56: 56: Processing chain 1 (117 atoms, 16 residues) 56: 56: Replaced 1 residue named ASPH to the default ASP. Use interactive selection of protonated residues if that is what you need. 56: 56: Identified residue LYS50 as a starting terminus. 56: 56: Identified residue PRO65 as a ending terminus. 56: Start terminus LYS-50: NH3+ 56: End terminus PRO-65: COO- 56: 56: Checking for duplicate atoms.... 56: 56: Generating any missing hydrogen atoms and/or adding termini. 56: 56: Now there are 16 residues with 228 atoms 56: 56: Making bonds... 56: 56: Number of bonds was 232, now 232 56: 56: Generating angles, dihedrals and pairs... 56: 56: Making cmap torsions... 56: 56: There are 14 cmap torsion pairs 56: 56: There are 618 dihedrals, 38 impropers, 419 angles 56: 597 pairs, 232 bonds and 0 virtual sites 56: 56: Total mass 1662.885 a.m.u. 56: 56: Total charge 0.000 e 56: 56: Writing topology 56: 56: Writing coordinate file... 56: 56: --------- PLEASE NOTE ------------ 56: 56: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/D.pdb. 56: 56: The Charmm27 force field and the tip3p water model are used. 56: 56: --------- ETON ESAELP ------------ 56: [ OK ] Charmm/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_or_ter_merge_no_Dpdb_format_gro_match_file (247 ms) 56: [ RUN ] Charmm/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_or_ter_merge_no_Epdb_format_gro_match_file 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/aminoacids.r2b 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/rna.r2b 56: All occupancies are one 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/atomtypes.atp 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/aminoacids.rtp 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/dna.rtp 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/lipids.rtp 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/rna.rtp 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/aminoacids.hdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/dna.hdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/lipids.hdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/rna.hdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/aminoacids.n.tdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/dna.n.tdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/rna.n.tdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/aminoacids.c.tdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/dna.c.tdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/rna.c.tdb 56: Analysing hydrogen-bonding network for automated assignment of histidine 56: protonation. 89 donors and 98 acceptors were found. 56: There are 129 hydrogen bonds 56: Will use HISE for residue 31 56: Will use HISE for residue 51 56: 9 out of 9 lines of specbond.dat converted successfully 56: Special Atom Distance matrix: 56: CYS25 HIS31 HIS51 56: SG14 NE264 NE2226 56: HIS31 NE264 1.921 56: HIS51 NE2226 1.498 2.650 56: CYS80 SG477 0.207 1.984 1.570 56: Linking CYS-25 SG-14 and CYS-80 SG-477... 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/aminoacids.arn 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/dna.arn 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/rna.arn 56: Before cleaning: 2499 pairs 56: Before cleaning: 2524 dihedrals 56: Using the Charmm27 force field in directory charmm27.ff 56: 56: going to rename charmm27.ff/aminoacids.r2b 56: 56: going to rename charmm27.ff/rna.r2b 56: Reading /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/E.pdb... 56: Read 'This is a fragment of 2d4f for testing a disulfide bridge', 488 atoms 56: 56: Analyzing pdb file 56: Splitting chemical chains based on TER records or chain id changing. 56: 56: There are 1 chains and 0 blocks of water and 58 residues with 488 atoms 56: 56: chain #res #atoms 56: 56: 1 'A' 58 488 56: 56: All occupancies are one 56: 56: Reading residue database... (Charmm27) 56: 56: Processing chain 1 'A' (488 atoms, 58 residues) 56: 56: Identified residue ASN24 as a starting terminus. 56: 56: Identified residue ARG81 as a ending terminus. 56: Start terminus ASN-24: NH3+ 56: End terminus ARG-81: COO- 56: 56: Checking for duplicate atoms.... 56: 56: Generating any missing hydrogen atoms and/or adding termini. 56: 56: Now there are 58 residues with 936 atoms 56: 56: Making bonds... 56: 56: Number of bonds was 951, now 951 56: 56: Generating angles, dihedrals and pairs... 56: 56: Making cmap torsions... 56: 56: There are 56 cmap torsion pairs 56: 56: There are 2524 dihedrals, 149 impropers, 1704 angles 56: 2469 pairs, 951 bonds and 0 virtual sites 56: 56: Total mass 6908.566 a.m.u. 56: 56: Total charge -6.000 e 56: 56: Writing topology 56: 56: Writing coordinate file... 56: 56: --------- PLEASE NOTE ------------ 56: 56: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/E.pdb. 56: 56: The Charmm27 force field and the tip3p water model are used. 56: 56: --------- ETON ESAELP ------------ 56: [ OK ] Charmm/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_or_ter_merge_no_Epdb_format_gro_match_file (669 ms) 56: [ RUN ] Charmm/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_or_ter_merge_no_monomerpdb_format_gro_match_file 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/aminoacids.r2b 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/rna.r2b 56: All occupancies are one 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/atomtypes.atp 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/aminoacids.rtp 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/dna.rtp 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/lipids.rtp 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/rna.rtp 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/aminoacids.hdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/dna.hdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/lipids.hdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/rna.hdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/aminoacids.n.tdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/dna.n.tdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/rna.n.tdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/aminoacids.c.tdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/dna.c.tdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/rna.c.tdb 56: 9 out of 9 lines of specbond.dat converted successfully 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/aminoacids.arn 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/dna.arn 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/rna.arn 56: Before cleaning: 39 pairs 56: Before cleaning: 39 dihedrals 56: Using the Charmm27 force field in directory charmm27.ff 56: 56: going to rename charmm27.ff/aminoacids.r2b 56: 56: going to rename charmm27.ff/rna.r2b 56: Reading /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/monomer.pdb... 56: Read 'GLU', 9 atoms 56: 56: Analyzing pdb file 56: Splitting chemical chains based on TER records or chain id changing. 56: 56: There are 1 chains and 0 blocks of water and 1 residues with 9 atoms 56: 56: chain #res #atoms 56: 56: 1 'X' 1 9 56: 56: All occupancies are one 56: 56: Reading residue database... (Charmm27) 56: 56: Processing chain 1 'X' (9 atoms, 1 residues) 56: 56: Identified residue GLU1 as a starting terminus. 56: 56: Identified residue GLU1 as a ending terminus. 56: Start terminus GLU-1: NH3+ 56: End terminus GLU-1: COO- 56: 56: Checking for duplicate atoms.... 56: 56: Generating any missing hydrogen atoms and/or adding termini. 56: 56: Now there are 1 residues with 18 atoms 56: 56: Making bonds... 56: 56: Number of bonds was 17, now 17 56: 56: Generating angles, dihedrals and pairs... 56: 56: Making cmap torsions... 56: 56: There are 39 dihedrals, 2 impropers, 30 angles 56: 39 pairs, 17 bonds and 0 virtual sites 56: 56: Total mass 146.123 a.m.u. 56: 56: Total charge -1.000 e 56: 56: Writing topology 56: 56: Writing coordinate file... 56: 56: --------- PLEASE NOTE ------------ 56: 56: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/monomer.pdb. 56: 56: The Charmm27 force field and the tip3p water model are used. 56: 56: --------- ETON ESAELP ------------ 56: [ OK ] Charmm/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_or_ter_merge_no_monomerpdb_format_gro_match_file (126 ms) 56: [ RUN ] Charmm/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_h_id_or_ter_merge_no_Apdb_format_gro_match_file 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/aminoacids.r2b 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/rna.r2b 56: All occupancies are one 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/atomtypes.atp 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/aminoacids.rtp 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/dna.rtp 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/lipids.rtp 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/rna.rtp 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/aminoacids.hdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/dna.hdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/lipids.hdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/rna.hdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/aminoacids.n.tdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/dna.n.tdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/rna.n.tdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/aminoacids.c.tdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/dna.c.tdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/rna.c.tdb 56: Analysing hydrogen-bonding network for automated assignment of histidine 56: protonation. 25 donors and 23 acceptors were found. 56: There are 41 hydrogen bonds 56: Will use HISE for residue 8 56: 9 out of 9 lines of specbond.dat converted successfully 56: Special Atom Distance matrix: 56: CYS3 HIS8 56: SG9 NE251 56: HIS8 NE251 1.055 56: MET12 SD83 0.763 0.990 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/aminoacids.arn 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/dna.arn 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/rna.arn 56: Marked 124 virtual sites 56: Added 16 dummy masses 56: Added 26 new constraints 56: Before cleaning: 653 pairs 56: Before cleaning: 663 dihedrals 56: Using the Charmm27 force field in directory charmm27.ff 56: 56: going to rename charmm27.ff/aminoacids.r2b 56: 56: going to rename charmm27.ff/rna.r2b 56: Reading /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/A.pdb... 56: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms 56: 56: Analyzing pdb file 56: Splitting chemical chains based on TER records or chain id changing. 56: 56: There are 1 chains and 0 blocks of water and 16 residues with 128 atoms 56: 56: chain #res #atoms 56: 56: 1 ' ' 16 128 56: 56: All occupancies are one 56: 56: Reading residue database... (Charmm27) 56: 56: Processing chain 1 (128 atoms, 16 residues) 56: 56: Identified residue ALA2 as a starting terminus. 56: 56: Identified residue SER17 as a ending terminus. 56: Start terminus ALA-2: NH3+ 56: End terminus SER-17: COO- 56: 56: Checking for duplicate atoms.... 56: 56: Generating any missing hydrogen atoms and/or adding termini. 56: 56: Now there are 16 residues with 252 atoms 56: 56: Making bonds... 56: 56: Number of bonds was 254, now 254 56: 56: Generating angles, dihedrals and pairs... 56: 56: Making cmap torsions... 56: 56: There are 14 cmap torsion pairs 56: 56: There are 663 dihedrals, 48 impropers, 457 angles 56: 650 pairs, 254 bonds and 130 virtual sites 56: 56: Total mass 1846.115 a.m.u. 56: 56: Total charge 0.000 e 56: 56: Writing topology 56: 56: Writing coordinate file... 56: 56: --------- PLEASE NOTE ------------ 56: 56: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/A.pdb. 56: 56: The Charmm27 force field and the tip3p water model are used. 56: 56: --------- ETON ESAELP ------------ 56: [ OK ] Charmm/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_h_id_or_ter_merge_no_Apdb_format_gro_match_file (283 ms) 56: [ RUN ] Charmm/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_h_id_or_ter_merge_no_Bpdb_format_gro_match_file 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/aminoacids.r2b 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/rna.r2b 56: All occupancies are one 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/atomtypes.atp 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/aminoacids.rtp 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/dna.rtp 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/lipids.rtp 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/rna.rtp 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/aminoacids.hdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/dna.hdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/lipids.hdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/rna.hdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/aminoacids.n.tdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/dna.n.tdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/rna.n.tdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/aminoacids.c.tdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/dna.c.tdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/rna.c.tdb 56: Analysing hydrogen-bonding network for automated assignment of histidine 56: protonation. 30 donors and 22 acceptors were found. 56: There are 36 hydrogen bonds 56: Will use HISE for residue 29 56: Will use HISE for residue 32 56: 9 out of 9 lines of specbond.dat converted successfully 56: Special Atom Distance matrix: 56: CYS27 HIS29 56: SG90 NE2111 56: HIS29 NE2111 0.987 56: HIS32 NE2135 1.590 1.155 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/aminoacids.arn 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/dna.arn 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/rna.arn 56: Marked 132 virtual sites 56: Added 10 dummy masses 56: Added 19 new constraints 56: Before cleaning: 748 pairs 56: Before cleaning: 778 dihedrals 56: Using the Charmm27 force field in directory charmm27.ff 56: 56: going to rename charmm27.ff/aminoacids.r2b 56: 56: going to rename charmm27.ff/rna.r2b 56: Reading /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/B.pdb... 56: Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms 56: 56: Analyzing pdb file 56: Splitting chemical chains based on TER records or chain id changing. 56: 56: There are 1 chains and 0 blocks of water and 16 residues with 149 atoms 56: 56: chain #res #atoms 56: 56: 1 ' ' 16 149 56: 56: All occupancies are one 56: 56: Reading residue database... (Charmm27) 56: 56: Processing chain 1 (149 atoms, 16 residues) 56: 56: Replaced 1 residue named GLUH to the default GLU. Use interactive selection of protonated residues if that is what you need. 56: 56: Identified residue THR18 as a starting terminus. 56: 56: Identified residue PHE33 as a ending terminus. 56: Start terminus THR-18: NH3+ 56: End terminus PHE-33: COO- 56: 56: Checking for duplicate atoms.... 56: 56: Generating any missing hydrogen atoms and/or adding termini. 56: 56: Now there are 16 residues with 281 atoms 56: 56: Making bonds... 56: 56: Number of bonds was 290, now 290 56: 56: Generating angles, dihedrals and pairs... 56: 56: Making cmap torsions... 56: 56: There are 14 cmap torsion pairs 56: 56: There are 778 dihedrals, 49 impropers, 516 angles 56: 736 pairs, 290 bonds and 133 virtual sites 56: 56: Total mass 2088.361 a.m.u. 56: 56: Total charge 1.000 e 56: 56: Writing topology 56: 56: Writing coordinate file... 56: 56: --------- PLEASE NOTE ------------ 56: 56: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/B.pdb. 56: 56: The Charmm27 force field and the tip3p water model are used. 56: 56: --------- ETON ESAELP ------------ 56: [ OK ] Charmm/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_h_id_or_ter_merge_no_Bpdb_format_gro_match_file (296 ms) 56: [ RUN ] Charmm/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_h_id_or_ter_merge_no_Cpdb_format_gro_match_file 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/aminoacids.r2b 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/rna.r2b 56: All occupancies are one 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/atomtypes.atp 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/aminoacids.rtp 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/dna.rtp 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/lipids.rtp 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/rna.rtp 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/aminoacids.hdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/dna.hdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/lipids.hdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/rna.hdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/aminoacids.n.tdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/dna.n.tdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/rna.n.tdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/aminoacids.c.tdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/dna.c.tdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/rna.c.tdb 56: Analysing hydrogen-bonding network for automated assignment of histidine 56: protonation. 22 donors and 22 acceptors were found. 56: There are 26 hydrogen bonds 56: Will use HISE for residue 45 56: 9 out of 9 lines of specbond.dat converted successfully 56: Special Atom Distance matrix: 56: HIS45 56: NE295 56: MET46 SD102 1.078 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/aminoacids.arn 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/dna.arn 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/rna.arn 56: Marked 123 virtual sites 56: Added 22 dummy masses 56: Added 35 new constraints 56: Before cleaning: 676 pairs 56: Before cleaning: 696 dihedrals 56: Using the Charmm27 force field in directory charmm27.ff 56: 56: going to rename charmm27.ff/aminoacids.r2b 56: 56: going to rename charmm27.ff/rna.r2b 56: Reading /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/C.pdb... 56: Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms 56: 56: Analyzing pdb file 56: Splitting chemical chains based on TER records or chain id changing. 56: 56: There are 1 chains and 0 blocks of water and 16 residues with 132 atoms 56: 56: chain #res #atoms 56: 56: 1 ' ' 16 132 56: 56: All occupancies are one 56: 56: Reading residue database... (Charmm27) 56: 56: Processing chain 1 (132 atoms, 16 residues) 56: 56: Identified residue ALA34 as a starting terminus. 56: 56: Identified residue ALA49 as a ending terminus. 56: Start terminus ALA-34: NH3+ 56: End terminus ALA-49: COO- 56: 56: Checking for duplicate atoms.... 56: 56: Generating any missing hydrogen atoms and/or adding termini. 56: 56: Now there are 16 residues with 255 atoms 56: 56: Making bonds... 56: 56: Number of bonds was 261, now 261 56: 56: Generating angles, dihedrals and pairs... 56: 56: Making cmap torsions... 56: 56: There are 14 cmap torsion pairs 56: 56: There are 696 dihedrals, 39 impropers, 472 angles 56: 667 pairs, 261 bonds and 132 virtual sites 56: 56: Total mass 1861.130 a.m.u. 56: 56: Total charge -1.000 e 56: 56: Writing topology 56: 56: Writing coordinate file... 56: 56: --------- PLEASE NOTE ------------ 56: 56: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/C.pdb. 56: 56: The Charmm27 force field and the tip3p water model are used. 56: 56: --------- ETON ESAELP ------------ 56: [ OK ] Charmm/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_h_id_or_ter_merge_no_Cpdb_format_gro_match_file (279 ms) 56: [ RUN ] Charmm/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_h_id_or_ter_merge_no_Dpdb_format_gro_match_file 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/aminoacids.r2b 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/rna.r2b 56: All occupancies are one 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/atomtypes.atp 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/aminoacids.rtp 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/dna.rtp 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/lipids.rtp 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/rna.rtp 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/aminoacids.hdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/dna.hdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/lipids.hdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/rna.hdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/aminoacids.n.tdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/dna.n.tdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/rna.n.tdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/aminoacids.c.tdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/dna.c.tdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/rna.c.tdb 56: Analysing hydrogen-bonding network for automated assignment of histidine 56: protonation. 22 donors and 21 acceptors were found. 56: There are 30 hydrogen bonds 56: Will use HISE for residue 60 56: 9 out of 9 lines of specbond.dat converted successfully 56: Special Atom Distance matrix: 56: HIS60 56: NE285 56: CYS62 SG98 0.803 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/aminoacids.arn 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/dna.arn 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/rna.arn 56: Marked 111 virtual sites 56: Added 18 dummy masses 56: Added 31 new constraints 56: Before cleaning: 603 pairs 56: Before cleaning: 618 dihedrals 56: Using the Charmm27 force field in directory charmm27.ff 56: 56: going to rename charmm27.ff/aminoacids.r2b 56: 56: going to rename charmm27.ff/rna.r2b 56: Reading /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/D.pdb... 56: Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms 56: 56: Analyzing pdb file 56: Splitting chemical chains based on TER records or chain id changing. 56: 56: There are 1 chains and 0 blocks of water and 16 residues with 117 atoms 56: 56: chain #res #atoms 56: 56: 1 ' ' 16 117 56: 56: All occupancies are one 56: 56: Reading residue database... (Charmm27) 56: 56: Processing chain 1 (117 atoms, 16 residues) 56: 56: Replaced 1 residue named ASPH to the default ASP. Use interactive selection of protonated residues if that is what you need. 56: 56: Identified residue LYS50 as a starting terminus. 56: 56: Identified residue PRO65 as a ending terminus. 56: Start terminus LYS-50: NH3+ 56: End terminus PRO-65: COO- 56: 56: Checking for duplicate atoms.... 56: 56: Generating any missing hydrogen atoms and/or adding termini. 56: 56: Now there are 16 residues with 228 atoms 56: 56: Making bonds... 56: 56: Number of bonds was 232, now 232 56: 56: Generating angles, dihedrals and pairs... 56: 56: Making cmap torsions... 56: 56: There are 14 cmap torsion pairs 56: 56: There are 618 dihedrals, 38 impropers, 419 angles 56: 597 pairs, 232 bonds and 116 virtual sites 56: 56: Total mass 1662.885 a.m.u. 56: 56: Total charge 0.000 e 56: 56: Writing topology 56: 56: Writing coordinate file... 56: 56: --------- PLEASE NOTE ------------ 56: 56: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/D.pdb. 56: 56: The Charmm27 force field and the tip3p water model are used. 56: 56: --------- ETON ESAELP ------------ 56: [ OK ] Charmm/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_h_id_or_ter_merge_no_Dpdb_format_gro_match_file (275 ms) 56: [ RUN ] Charmm/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_h_id_or_ter_merge_no_Epdb_format_gro_match_file 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/aminoacids.r2b 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/rna.r2b 56: All occupancies are one 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/atomtypes.atp 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/aminoacids.rtp 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/dna.rtp 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/lipids.rtp 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/rna.rtp 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/aminoacids.hdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/dna.hdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/lipids.hdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/rna.hdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/aminoacids.n.tdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/dna.n.tdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/rna.n.tdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/aminoacids.c.tdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/dna.c.tdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/rna.c.tdb 56: Analysing hydrogen-bonding network for automated assignment of histidine 56: protonation. 89 donors and 98 acceptors were found. 56: There are 129 hydrogen bonds 56: Will use HISE for residue 31 56: Will use HISE for residue 51 56: 9 out of 9 lines of specbond.dat converted successfully 56: Special Atom Distance matrix: 56: CYS25 HIS31 HIS51 56: SG14 NE264 NE2226 56: HIS31 NE264 1.921 56: HIS51 NE2226 1.498 2.650 56: CYS80 SG477 0.207 1.984 1.570 56: Linking CYS-25 SG-14 and CYS-80 SG-477... 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/aminoacids.arn 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/dna.arn 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/rna.arn 56: Marked 447 virtual sites 56: Added 58 dummy masses 56: Added 101 new constraints 56: Before cleaning: 2499 pairs 56: Before cleaning: 2524 dihedrals 56: Using the Charmm27 force field in directory charmm27.ff 56: 56: going to rename charmm27.ff/aminoacids.r2b 56: 56: going to rename charmm27.ff/rna.r2b 56: Reading /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/E.pdb... 56: Read 'This is a fragment of 2d4f for testing a disulfide bridge', 488 atoms 56: 56: Analyzing pdb file 56: Splitting chemical chains based on TER records or chain id changing. 56: 56: There are 1 chains and 0 blocks of water and 58 residues with 488 atoms 56: 56: chain #res #atoms 56: 56: 1 'A' 58 488 56: 56: All occupancies are one 56: 56: Reading residue database... (Charmm27) 56: 56: Processing chain 1 'A' (488 atoms, 58 residues) 56: 56: Identified residue ASN24 as a starting terminus. 56: 56: Identified residue ARG81 as a ending terminus. 56: Start terminus ASN-24: NH3+ 56: End terminus ARG-81: COO- 56: 56: Checking for duplicate atoms.... 56: 56: Generating any missing hydrogen atoms and/or adding termini. 56: 56: Now there are 58 residues with 936 atoms 56: 56: Making bonds... 56: 56: Number of bonds was 951, now 951 56: 56: Generating angles, dihedrals and pairs... 56: 56: Making cmap torsions... 56: 56: There are 56 cmap torsion pairs 56: 56: There are 2524 dihedrals, 149 impropers, 1704 angles 56: 2469 pairs, 951 bonds and 462 virtual sites 56: 56: Total mass 6908.566 a.m.u. 56: 56: Total charge -6.000 e 56: 56: Writing topology 56: 56: Writing coordinate file... 56: 56: --------- PLEASE NOTE ------------ 56: 56: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/E.pdb. 56: 56: The Charmm27 force field and the tip3p water model are used. 56: 56: --------- ETON ESAELP ------------ 56: [ OK ] Charmm/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_h_id_or_ter_merge_no_Epdb_format_gro_match_file (770 ms) 56: [ RUN ] Charmm/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_h_id_or_ter_merge_no_monomerpdb_format_gro_match_file 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/aminoacids.r2b 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/rna.r2b 56: All occupancies are one 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/atomtypes.atp 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/aminoacids.rtp 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/dna.rtp 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/lipids.rtp 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/rna.rtp 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/aminoacids.hdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/dna.hdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/lipids.hdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/rna.hdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/aminoacids.n.tdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/dna.n.tdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/rna.n.tdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/aminoacids.c.tdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/dna.c.tdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/rna.c.tdb 56: 9 out of 9 lines of specbond.dat converted successfully 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/aminoacids.arn 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/dna.arn 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/rna.arn 56: Marked 8 virtual sites 56: Added 2 dummy masses 56: Added 3 new constraints 56: Before cleaning: 39 pairs 56: Before cleaning: 39 dihedrals 56: Using the Charmm27 force field in directory charmm27.ff 56: 56: going to rename charmm27.ff/aminoacids.r2b 56: 56: going to rename charmm27.ff/rna.r2b 56: Reading /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/monomer.pdb... 56: Read 'GLU', 9 atoms 56: 56: Analyzing pdb file 56: Splitting chemical chains based on TER records or chain id changing. 56: 56: There are 1 chains and 0 blocks of water and 1 residues with 9 atoms 56: 56: chain #res #atoms 56: 56: 1 'X' 1 9 56: 56: All occupancies are one 56: 56: Reading residue database... (Charmm27) 56: 56: Processing chain 1 'X' (9 atoms, 1 residues) 56: 56: Identified residue GLU1 as a starting terminus. 56: 56: Identified residue GLU1 as a ending terminus. 56: Start terminus GLU-1: NH3+ 56: End terminus GLU-1: COO- 56: 56: Checking for duplicate atoms.... 56: 56: Generating any missing hydrogen atoms and/or adding termini. 56: 56: Now there are 1 residues with 18 atoms 56: 56: Making bonds... 56: 56: Number of bonds was 17, now 17 56: 56: Generating angles, dihedrals and pairs... 56: 56: Making cmap torsions... 56: 56: There are 39 dihedrals, 2 impropers, 30 angles 56: 39 pairs, 17 bonds and 9 virtual sites 56: 56: Total mass 146.123 a.m.u. 56: 56: Total charge -1.000 e 56: 56: Writing topology 56: 56: Writing coordinate file... 56: 56: --------- PLEASE NOTE ------------ 56: 56: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/monomer.pdb. 56: 56: The Charmm27 force field and the tip3p water model are used. 56: 56: --------- ETON ESAELP ------------ 56: [ OK ] Charmm/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_h_id_or_ter_merge_no_monomerpdb_format_gro_match_file (138 ms) 56: [----------] 12 tests from Charmm/Pdb2gmxTest (3932 ms total) 56: 56: [----------] 8 tests from ChainSep/Pdb2gmxTest 56: [ RUN ] ChainSep/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_merge_all_chainTerpdb_format_gro_match_file 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/aminoacids.r2b 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/rna.r2b 56: All occupancies are one 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/atomtypes.atp 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/aminoacids.rtp 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/dna.rtp 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/lipids.rtp 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/rna.rtp 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/aminoacids.hdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/dna.hdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/lipids.hdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/rna.hdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/aminoacids.n.tdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/dna.n.tdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/rna.n.tdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/aminoacids.c.tdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/dna.c.tdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/rna.c.tdb 56: Analysing hydrogen-bonding network for automated assignment of histidine 56: protonation. 25 donors and 23 acceptors were found. 56: There are 41 hydrogen bonds 56: Will use HISE for residue 8 56: 9 out of 9 lines of specbond.dat converted successfully 56: Special Atom Distance matrix: 56: CYS3 HIS8 56: SG9 NE251 56: HIS8 NE251 1.055 56: MET12 SD83 0.763 0.990 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/aminoacids.arn 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/dna.arn 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/rna.arn 56: Before cleaning: 651 pairs 56: Before cleaning: 661 dihedrals 56: Using the Charmm27 force field in directory charmm27.ff 56: 56: going to rename charmm27.ff/aminoacids.r2b 56: 56: going to rename charmm27.ff/rna.r2b 56: Reading /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/chainTer.pdb... 56: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 127 atoms 56: 56: Analyzing pdb file 56: Splitting chemical chains based on changing chain id only (ignoring TER records). 56: 56: Merged chains into joint molecule definitions at 2 places. 56: 56: There are 1 chains and 0 blocks of water and 16 residues with 127 atoms 56: 56: chain #res #atoms 56: 56: 1 'A' 16 127 56: 56: All occupancies are one 56: 56: Reading residue database... (Charmm27) 56: 56: Processing chain 1 'A' (127 atoms, 16 residues) 56: 56: Identified residue ALA2 as a starting terminus. 56: 56: Identified residue GLU5 as a ending terminus. 56: 56: Identified residue PHE6 as a starting terminus. 56: 56: Identified residue MET12 as a ending terminus. 56: 56: Identified residue ASN13 as a starting terminus. 56: 56: Identified residue SER17 as a ending terminus. 56: Start terminus ALA-2: NH3+ 56: End terminus GLU-5: COO- 56: Start terminus PHE-6: NH3+ 56: End terminus MET-12: COO- 56: Start terminus ASN-13: NH3+ 56: End terminus SER-17: COO- 56: 56: Checking for duplicate atoms.... 56: 56: Generating any missing hydrogen atoms and/or adding termini. 56: 56: Now there are 16 residues with 258 atoms 56: 56: Making bonds... 56: 56: Number of bonds was 258, now 258 56: 56: Generating angles, dihedrals and pairs... 56: 56: Making cmap torsions... 56: 56: There are 10 cmap torsion pairs 56: 56: There are 661 dihedrals, 46 impropers, 463 angles 56: 648 pairs, 258 bonds and 0 virtual sites 56: 56: Total mass 1882.146 a.m.u. 56: 56: Total charge 0.000 e 56: 56: Writing topology 56: 56: Writing coordinate file... 56: 56: --------- PLEASE NOTE ------------ 56: 56: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/chainTer.pdb. 56: 56: The Charmm27 force field and the tip3p water model are used. 56: 56: --------- ETON ESAELP ------------ 56: [ OK ] ChainSep/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_merge_all_chainTerpdb_format_gro_match_file (261 ms) 56: [ RUN ] ChainSep/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_merge_no_chainTerpdb_format_gro_match_file 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/aminoacids.r2b 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/rna.r2b 56: All occupancies are one 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/atomtypes.atp 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/aminoacids.rtp 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/dna.rtp 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/lipids.rtp 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/rna.rtp 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/aminoacids.hdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/dna.hdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/lipids.hdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/rna.hdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/aminoacids.n.tdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/dna.n.tdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/rna.n.tdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/aminoacids.c.tdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/dna.c.tdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/rna.c.tdb 56: 9 out of 9 lines of specbond.dat converted successfully 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/aminoacids.arn 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/dna.arn 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/rna.arn 56: Before cleaning: 123 pairs 56: Before cleaning: 123 dihedrals 56: Analysing hydrogen-bonding network for automated assignment of histidine 56: protonation. 10 donors and 7 acceptors were found. 56: There are 7 hydrogen bonds 56: Will use HISE for residue 8 56: 9 out of 9 lines of specbond.dat converted successfully 56: Special Atom Distance matrix: 56: HIS8 56: NE223 56: MET12 SD55 0.990 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/aminoacids.arn 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/dna.arn 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/rna.arn 56: Before cleaning: 317 pairs 56: Before cleaning: 322 dihedrals 56: 9 out of 9 lines of specbond.dat converted successfully 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/aminoacids.arn 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/dna.arn 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/rna.arn 56: Before cleaning: 211 pairs 56: Before cleaning: 216 dihedrals 56: Using the Charmm27 force field in directory charmm27.ff 56: 56: going to rename charmm27.ff/aminoacids.r2b 56: 56: going to rename charmm27.ff/rna.r2b 56: Reading /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/chainTer.pdb... 56: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 127 atoms 56: 56: Analyzing pdb file 56: Splitting chemical chains based on changing chain id only (ignoring TER records). 56: 56: There are 3 chains and 0 blocks of water and 16 residues with 127 atoms 56: 56: chain #res #atoms 56: 56: 1 'A' 4 28 56: 56: 2 'B' 7 58 56: 56: 3 'C' 5 41 56: 56: All occupancies are one 56: 56: Reading residue database... (Charmm27) 56: 56: Processing chain 1 'A' (28 atoms, 4 residues) 56: 56: Identified residue ALA2 as a starting terminus. 56: 56: Identified residue GLU5 as a ending terminus. 56: Start terminus ALA-2: NH3+ 56: End terminus GLU-5: COO- 56: 56: Checking for duplicate atoms.... 56: 56: Generating any missing hydrogen atoms and/or adding termini. 56: 56: Now there are 4 residues with 51 atoms 56: Chain time... 56: 56: Making bonds... 56: 56: Number of bonds was 50, now 50 56: 56: Generating angles, dihedrals and pairs... 56: 56: Making cmap torsions... 56: 56: There are 2 cmap torsion pairs 56: 56: There are 123 dihedrals, 9 impropers, 88 angles 56: 123 pairs, 50 bonds and 0 virtual sites 56: 56: Total mass 434.421 a.m.u. 56: 56: Total charge -2.000 e 56: 56: Writing topology 56: 56: Processing chain 2 'B' (58 atoms, 7 residues) 56: 56: Identified residue PHE6 as a starting terminus. 56: 56: Identified residue MET12 as a ending terminus. 56: Start terminus PHE-6: NH3+ 56: End terminus MET-12: COO- 56: 56: Checking for duplicate atoms.... 56: 56: Generating any missing hydrogen atoms and/or adding termini. 56: 56: Now there are 7 residues with 124 atoms 56: Chain time... 56: 56: Making bonds... 56: 56: Number of bonds was 125, now 125 56: 56: Generating angles, dihedrals and pairs... 56: 56: Making cmap torsions... 56: 56: There are 5 cmap torsion pairs 56: 56: There are 322 dihedrals, 19 impropers, 227 angles 56: 314 pairs, 125 bonds and 0 virtual sites 56: 56: Total mass 846.083 a.m.u. 56: 56: Total charge 1.000 e 56: 56: Writing topology 56: 56: Processing chain 3 'C' (41 atoms, 5 residues) 56: 56: Identified residue ASN13 as a starting terminus. 56: 56: Identified residue SER17 as a ending terminus. 56: Start terminus ASN-13: NH3+ 56: End terminus SER-17: COO- 56: 56: Checking for duplicate atoms.... 56: 56: Generating any missing hydrogen atoms and/or adding termini. 56: 56: Now there are 5 residues with 83 atoms 56: Chain time... 56: 56: Making bonds... 56: 56: Number of bonds was 83, now 83 56: 56: Generating angles, dihedrals and pairs... 56: 56: Making cmap torsions... 56: 56: There are 3 cmap torsion pairs 56: 56: There are 216 dihedrals, 18 impropers, 148 angles 56: 211 pairs, 83 bonds and 0 virtual sites 56: 56: Total mass 601.643 a.m.u. 56: 56: Total charge 1.000 e 56: 56: Writing topology 56: 56: Including chain 1 in system: 51 atoms 4 residues 56: 56: Including chain 2 in system: 124 atoms 7 residues 56: 56: Including chain 3 in system: 83 atoms 5 residues 56: 56: Now there are 258 atoms and 16 residues 56: 56: Total mass in system 1882.146 a.m.u. 56: 56: Total charge in system 0.000 e 56: 56: Writing coordinate file... 56: 56: --------- PLEASE NOTE ------------ 56: 56: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/chainTer.pdb. 56: 56: The Charmm27 force field and the tip3p water model are used. 56: 56: --------- ETON ESAELP ------------ 56: [ OK ] ChainSep/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_merge_no_chainTerpdb_format_gro_match_file (213 ms) 56: [ RUN ] ChainSep/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_ter_merge_all_chainTerpdb_format_gro_match_file 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/aminoacids.r2b 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/rna.r2b 56: All occupancies are one 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/atomtypes.atp 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/aminoacids.rtp 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/dna.rtp 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/lipids.rtp 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/rna.rtp 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/aminoacids.hdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/dna.hdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/lipids.hdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/rna.hdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/aminoacids.n.tdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/dna.n.tdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/rna.n.tdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/aminoacids.c.tdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/dna.c.tdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/rna.c.tdb 56: Analysing hydrogen-bonding network for automated assignment of histidine 56: protonation. 25 donors and 23 acceptors were found. 56: There are 41 hydrogen bonds 56: Will use HISE for residue 8 56: 9 out of 9 lines of specbond.dat converted successfully 56: Special Atom Distance matrix: 56: CYS3 HIS8 56: SG9 NE251 56: HIS8 NE251 1.055 56: MET12 SD83 0.763 0.990 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/aminoacids.arn 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/dna.arn 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/rna.arn 56: Before cleaning: 651 pairs 56: Before cleaning: 661 dihedrals 56: Using the Charmm27 force field in directory charmm27.ff 56: 56: going to rename charmm27.ff/aminoacids.r2b 56: 56: going to rename charmm27.ff/rna.r2b 56: Reading /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/chainTer.pdb... 56: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 127 atoms 56: 56: Analyzing pdb file 56: Splitting chemical chains based on TER records only (ignoring chain id). 56: 56: Merged chains into joint molecule definitions at 2 places. 56: 56: There are 1 chains and 0 blocks of water and 16 residues with 127 atoms 56: 56: chain #res #atoms 56: 56: 1 'A' 16 127 56: 56: All occupancies are one 56: 56: Reading residue database... (Charmm27) 56: 56: Processing chain 1 'A' (127 atoms, 16 residues) 56: 56: Identified residue ALA2 as a starting terminus. 56: 56: Identified residue ILE9 as a ending terminus. 56: 56: Identified residue LYS10 as a starting terminus. 56: 56: Identified residue MET12 as a ending terminus. 56: 56: Identified residue ASN13 as a starting terminus. 56: 56: Identified residue SER17 as a ending terminus. 56: Start terminus ALA-2: NH3+ 56: End terminus ILE-9: COO- 56: Start terminus LYS-10: NH3+ 56: End terminus MET-12: COO- 56: Start terminus ASN-13: NH3+ 56: End terminus SER-17: COO- 56: 56: Checking for duplicate atoms.... 56: 56: Generating any missing hydrogen atoms and/or adding termini. 56: 56: Now there are 16 residues with 258 atoms 56: 56: Making bonds... 56: 56: Number of bonds was 258, now 258 56: 56: Generating angles, dihedrals and pairs... 56: 56: Making cmap torsions... 56: 56: There are 10 cmap torsion pairs 56: 56: There are 661 dihedrals, 46 impropers, 463 angles 56: 648 pairs, 258 bonds and 0 virtual sites 56: 56: Total mass 1882.146 a.m.u. 56: 56: Total charge 0.000 e 56: 56: Writing topology 56: 56: Writing coordinate file... 56: 56: --------- PLEASE NOTE ------------ 56: 56: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/chainTer.pdb. 56: 56: The Charmm27 force field and the tip3p water model are used. 56: 56: --------- ETON ESAELP ------------ 56: [ OK ] ChainSep/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_ter_merge_all_chainTerpdb_format_gro_match_file (257 ms) 56: [ RUN ] ChainSep/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_ter_merge_no_chainTerpdb_format_gro_match_file 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/aminoacids.r2b 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/rna.r2b 56: All occupancies are one 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/atomtypes.atp 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/aminoacids.rtp 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/dna.rtp 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/lipids.rtp 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/rna.rtp 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/aminoacids.hdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/dna.hdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/lipids.hdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/rna.hdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/aminoacids.n.tdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/dna.n.tdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/rna.n.tdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/aminoacids.c.tdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/dna.c.tdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/rna.c.tdb 56: Analysing hydrogen-bonding network for automated assignment of histidine 56: protonation. 10 donors and 12 acceptors were found. 56: There are 13 hydrogen bonds 56: Will use HISE for residue 8 56: 9 out of 9 lines of specbond.dat converted successfully 56: Special Atom Distance matrix: 56: CYS3 56: SG9 56: HIS8 NE251 1.055 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/aminoacids.arn 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/dna.arn 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/rna.arn 56: Before cleaning: 288 pairs 56: Before cleaning: 293 dihedrals 56: 9 out of 9 lines of specbond.dat converted successfully 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/aminoacids.arn 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/dna.arn 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/rna.arn 56: Before cleaning: 152 pairs 56: Before cleaning: 152 dihedrals 56: 9 out of 9 lines of specbond.dat converted successfully 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/aminoacids.arn 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/dna.arn 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/rna.arn 56: Before cleaning: 211 pairs 56: Before cleaning: 216 dihedrals 56: Using the Charmm27 force field in directory charmm27.ff 56: 56: going to rename charmm27.ff/aminoacids.r2b 56: 56: going to rename charmm27.ff/rna.r2b 56: Reading /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/chainTer.pdb... 56: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 127 atoms 56: 56: Analyzing pdb file 56: Splitting chemical chains based on TER records only (ignoring chain id). 56: 56: There are 3 chains and 0 blocks of water and 16 residues with 127 atoms 56: 56: chain #res #atoms 56: 56: 1 'A' 8 61 56: 56: 2 'B' 3 25 56: 56: 3 'C' 5 41 56: 56: All occupancies are one 56: 56: Reading residue database... (Charmm27) 56: 56: Processing chain 1 'A' (61 atoms, 8 residues) 56: 56: Identified residue ALA2 as a starting terminus. 56: 56: Identified residue ILE9 as a ending terminus. 56: Start terminus ALA-2: NH3+ 56: End terminus ILE-9: COO- 56: 56: Checking for duplicate atoms.... 56: 56: Generating any missing hydrogen atoms and/or adding termini. 56: 56: Now there are 8 residues with 114 atoms 56: Chain time... 56: 56: Making bonds... 56: 56: Number of bonds was 115, now 115 56: 56: Generating angles, dihedrals and pairs... 56: 56: Making cmap torsions... 56: 56: There are 6 cmap torsion pairs 56: 56: There are 293 dihedrals, 23 impropers, 203 angles 56: 285 pairs, 115 bonds and 0 virtual sites 56: 56: Total mass 888.952 a.m.u. 56: 56: Total charge -2.000 e 56: 56: Writing topology 56: 56: Processing chain 2 'B' (25 atoms, 3 residues) 56: 56: Identified residue LYS10 as a starting terminus. 56: 56: Identified residue MET12 as a ending terminus. 56: Start terminus LYS-10: NH3+ 56: End terminus MET-12: COO- 56: 56: Checking for duplicate atoms.... 56: 56: Generating any missing hydrogen atoms and/or adding termini. 56: 56: Now there are 3 residues with 61 atoms 56: Chain time... 56: 56: Making bonds... 56: 56: Number of bonds was 60, now 60 56: 56: Generating angles, dihedrals and pairs... 56: 56: Making cmap torsions... 56: 56: There are 1 cmap torsion pairs 56: 56: There are 152 dihedrals, 5 impropers, 112 angles 56: 152 pairs, 60 bonds and 0 virtual sites 56: 56: Total mass 391.552 a.m.u. 56: 56: Total charge 1.000 e 56: 56: Writing topology 56: 56: Processing chain 3 'C' (41 atoms, 5 residues) 56: 56: Identified residue ASN13 as a starting terminus. 56: 56: Identified residue SER17 as a ending terminus. 56: Start terminus ASN-13: NH3+ 56: End terminus SER-17: COO- 56: 56: Checking for duplicate atoms.... 56: 56: Generating any missing hydrogen atoms and/or adding termini. 56: 56: Now there are 5 residues with 83 atoms 56: Chain time... 56: 56: Making bonds... 56: 56: Number of bonds was 83, now 83 56: 56: Generating angles, dihedrals and pairs... 56: 56: Making cmap torsions... 56: 56: There are 3 cmap torsion pairs 56: 56: There are 216 dihedrals, 18 impropers, 148 angles 56: 211 pairs, 83 bonds and 0 virtual sites 56: 56: Total mass 601.643 a.m.u. 56: 56: Total charge 1.000 e 56: 56: Writing topology 56: 56: Including chain 1 in system: 114 atoms 8 residues 56: 56: Including chain 2 in system: 61 atoms 3 residues 56: 56: Including chain 3 in system: 83 atoms 5 residues 56: 56: Now there are 258 atoms and 16 residues 56: 56: Total mass in system 1882.146 a.m.u. 56: 56: Total charge in system 0.000 e 56: 56: Writing coordinate file... 56: 56: --------- PLEASE NOTE ------------ 56: 56: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/chainTer.pdb. 56: 56: The Charmm27 force field and the tip3p water model are used. 56: 56: --------- ETON ESAELP ------------ 56: [ OK ] ChainSep/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_ter_merge_no_chainTerpdb_format_gro_match_file (210 ms) 56: [ RUN ] ChainSep/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_or_ter_merge_all_chainTerpdb_format_gro_match_file 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/aminoacids.r2b 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/rna.r2b 56: All occupancies are one 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/atomtypes.atp 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/aminoacids.rtp 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/dna.rtp 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/lipids.rtp 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/rna.rtp 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/aminoacids.hdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/dna.hdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/lipids.hdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/rna.hdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/aminoacids.n.tdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/dna.n.tdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/rna.n.tdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/aminoacids.c.tdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/dna.c.tdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/rna.c.tdb 56: Analysing hydrogen-bonding network for automated assignment of histidine 56: protonation. 25 donors and 23 acceptors were found. 56: There are 41 hydrogen bonds 56: Will use HISE for residue 8 56: 9 out of 9 lines of specbond.dat converted successfully 56: Special Atom Distance matrix: 56: CYS3 HIS8 56: SG9 NE251 56: HIS8 NE251 1.055 56: MET12 SD83 0.763 0.990 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/aminoacids.arn 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/dna.arn 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/rna.arn 56: Before cleaning: 650 pairs 56: Before cleaning: 660 dihedrals 56: Using the Charmm27 force field in directory charmm27.ff 56: 56: going to rename charmm27.ff/aminoacids.r2b 56: 56: going to rename charmm27.ff/rna.r2b 56: Reading /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/chainTer.pdb... 56: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 127 atoms 56: 56: Analyzing pdb file 56: Splitting chemical chains based on TER records or chain id changing. 56: 56: Merged chains into joint molecule definitions at 3 places. 56: 56: There are 1 chains and 0 blocks of water and 16 residues with 127 atoms 56: 56: chain #res #atoms 56: 56: 1 'A' 16 127 56: 56: All occupancies are one 56: 56: Reading residue database... (Charmm27) 56: 56: Processing chain 1 'A' (127 atoms, 16 residues) 56: 56: Identified residue ALA2 as a starting terminus. 56: 56: Identified residue GLU5 as a ending terminus. 56: 56: Identified residue PHE6 as a starting terminus. 56: 56: Identified residue ILE9 as a ending terminus. 56: 56: Identified residue LYS10 as a starting terminus. 56: 56: Identified residue MET12 as a ending terminus. 56: 56: Identified residue ASN13 as a starting terminus. 56: 56: Identified residue SER17 as a ending terminus. 56: Start terminus ALA-2: NH3+ 56: End terminus GLU-5: COO- 56: Start terminus PHE-6: NH3+ 56: End terminus ILE-9: COO- 56: Start terminus LYS-10: NH3+ 56: End terminus MET-12: COO- 56: Start terminus ASN-13: NH3+ 56: End terminus SER-17: COO- 56: 56: Checking for duplicate atoms.... 56: 56: Generating any missing hydrogen atoms and/or adding termini. 56: 56: Now there are 16 residues with 261 atoms 56: 56: Making bonds... 56: 56: Number of bonds was 260, now 260 56: 56: Generating angles, dihedrals and pairs... 56: 56: Making cmap torsions... 56: 56: There are 8 cmap torsion pairs 56: 56: There are 660 dihedrals, 45 impropers, 466 angles 56: 647 pairs, 260 bonds and 0 virtual sites 56: 56: Total mass 1900.162 a.m.u. 56: 56: Total charge 0.000 e 56: 56: Writing topology 56: 56: Writing coordinate file... 56: 56: --------- PLEASE NOTE ------------ 56: 56: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/chainTer.pdb. 56: 56: The Charmm27 force field and the tip3p water model are used. 56: 56: --------- ETON ESAELP ------------ 56: [ OK ] ChainSep/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_or_ter_merge_all_chainTerpdb_format_gro_match_file (261 ms) 56: [ RUN ] ChainSep/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_or_ter_merge_no_chainTerpdb_format_gro_match_file 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/aminoacids.r2b 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/rna.r2b 56: Chain identifier 'B' is used in two non-sequential blocks. They will be treated as separate chains unless you reorder your file. 56: 56: All occupancies are one 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/atomtypes.atp 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/aminoacids.rtp 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/dna.rtp 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/lipids.rtp 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/rna.rtp 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/aminoacids.hdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/dna.hdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/lipids.hdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/rna.hdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/aminoacids.n.tdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/dna.n.tdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/rna.n.tdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/aminoacids.c.tdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/dna.c.tdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/rna.c.tdb 56: 9 out of 9 lines of specbond.dat converted successfully 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/aminoacids.arn 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/dna.arn 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/rna.arn 56: Before cleaning: 123 pairs 56: Before cleaning: 123 dihedrals 56: Analysing hydrogen-bonding network for automated assignment of histidine 56: protonation. 6 donors and 4 acceptors were found. 56: There are 3 hydrogen bonds 56: Will use HISE for residue 8 56: 9 out of 9 lines of specbond.dat converted successfully 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/aminoacids.arn 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/dna.arn 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/rna.arn 56: Before cleaning: 164 pairs 56: Before cleaning: 169 dihedrals 56: 9 out of 9 lines of specbond.dat converted successfully 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/aminoacids.arn 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/dna.arn 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/rna.arn 56: Before cleaning: 152 pairs 56: Before cleaning: 152 dihedrals 56: 9 out of 9 lines of specbond.dat converted successfully 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/aminoacids.arn 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/dna.arn 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/rna.arn 56: Before cleaning: 211 pairs 56: Before cleaning: 216 dihedrals 56: Using the Charmm27 force field in directory charmm27.ff 56: 56: going to rename charmm27.ff/aminoacids.r2b 56: 56: going to rename charmm27.ff/rna.r2b 56: Reading /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/chainTer.pdb... 56: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 127 atoms 56: 56: Analyzing pdb file 56: Splitting chemical chains based on TER records or chain id changing. 56: 56: Chain identifier 'B' is used in two non-sequential blocks. They will be treated as separate chains unless you reorder your file. 56: 56: There are 4 chains and 0 blocks of water and 16 residues with 127 atoms 56: 56: chain #res #atoms 56: 56: 1 'A' 4 28 56: 56: 2 'B' 4 33 56: 56: 3 'B' 3 25 56: 56: 4 'C' 5 41 56: 56: All occupancies are one 56: 56: Reading residue database... (Charmm27) 56: 56: Processing chain 1 'A' (28 atoms, 4 residues) 56: 56: Identified residue ALA2 as a starting terminus. 56: 56: Identified residue GLU5 as a ending terminus. 56: Start terminus ALA-2: NH3+ 56: End terminus GLU-5: COO- 56: 56: Checking for duplicate atoms.... 56: 56: Generating any missing hydrogen atoms and/or adding termini. 56: 56: Now there are 4 residues with 51 atoms 56: Chain time... 56: 56: Making bonds... 56: 56: Number of bonds was 50, now 50 56: 56: Generating angles, dihedrals and pairs... 56: 56: Making cmap torsions... 56: 56: There are 2 cmap torsion pairs 56: 56: There are 123 dihedrals, 9 impropers, 88 angles 56: 123 pairs, 50 bonds and 0 virtual sites 56: 56: Total mass 434.421 a.m.u. 56: 56: Total charge -2.000 e 56: 56: Writing topology 56: 56: Processing chain 2 'B' (33 atoms, 4 residues) 56: 56: Identified residue PHE6 as a starting terminus. 56: 56: Identified residue ILE9 as a ending terminus. 56: Start terminus PHE-6: NH3+ 56: End terminus ILE-9: COO- 56: 56: Checking for duplicate atoms.... 56: 56: Generating any missing hydrogen atoms and/or adding termini. 56: 56: Now there are 4 residues with 66 atoms 56: Chain time... 56: 56: Making bonds... 56: 56: Number of bonds was 67, now 67 56: 56: Generating angles, dihedrals and pairs... 56: 56: Making cmap torsions... 56: 56: There are 2 cmap torsion pairs 56: 56: There are 169 dihedrals, 13 impropers, 118 angles 56: 161 pairs, 67 bonds and 0 virtual sites 56: 56: Total mass 472.547 a.m.u. 56: 56: Total charge 0.000 e 56: 56: Writing topology 56: 56: Processing chain 3 'B' (25 atoms, 3 residues) 56: 56: Identified residue LYS10 as a starting terminus. 56: 56: Identified residue MET12 as a ending terminus. 56: Start terminus LYS-10: NH3+ 56: End terminus MET-12: COO- 56: 56: Checking for duplicate atoms.... 56: 56: Generating any missing hydrogen atoms and/or adding termini. 56: 56: Now there are 3 residues with 61 atoms 56: Chain time... 56: 56: Making bonds... 56: 56: Number of bonds was 60, now 60 56: 56: Generating angles, dihedrals and pairs... 56: 56: Making cmap torsions... 56: 56: There are 1 cmap torsion pairs 56: 56: There are 152 dihedrals, 5 impropers, 112 angles 56: 152 pairs, 60 bonds and 0 virtual sites 56: 56: Total mass 391.552 a.m.u. 56: 56: Total charge 1.000 e 56: 56: Writing topology 56: 56: Processing chain 4 'C' (41 atoms, 5 residues) 56: 56: Identified residue ASN13 as a starting terminus. 56: 56: Identified residue SER17 as a ending terminus. 56: Start terminus ASN-13: NH3+ 56: End terminus SER-17: COO- 56: 56: Checking for duplicate atoms.... 56: 56: Generating any missing hydrogen atoms and/or adding termini. 56: 56: Now there are 5 residues with 83 atoms 56: Chain time... 56: 56: Making bonds... 56: 56: Number of bonds was 83, now 83 56: 56: Generating angles, dihedrals and pairs... 56: 56: Making cmap torsions... 56: 56: There are 3 cmap torsion pairs 56: 56: There are 216 dihedrals, 18 impropers, 148 angles 56: 211 pairs, 83 bonds and 0 virtual sites 56: 56: Total mass 601.643 a.m.u. 56: 56: Total charge 1.000 e 56: 56: Writing topology 56: 56: Including chain 1 in system: 51 atoms 4 residues 56: 56: Including chain 2 in system: 66 atoms 4 residues 56: 56: Including chain 3 in system: 61 atoms 3 residues 56: 56: Including chain 4 in system: 83 atoms 5 residues 56: 56: Now there are 261 atoms and 16 residues 56: 56: Total mass in system 1900.162 a.m.u. 56: 56: Total charge in system 0.000 e 56: 56: Writing coordinate file... 56: 56: --------- PLEASE NOTE ------------ 56: 56: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/chainTer.pdb. 56: 56: The Charmm27 force field and the tip3p water model are used. 56: 56: --------- ETON ESAELP ------------ 56: [ OK ] ChainSep/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_or_ter_merge_no_chainTerpdb_format_gro_match_file (225 ms) 56: [ RUN ] ChainSep/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_and_ter_merge_all_chainTerpdb_format_gro_match_file 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/aminoacids.r2b 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/rna.r2b 56: All occupancies are one 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/atomtypes.atp 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/aminoacids.rtp 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/dna.rtp 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/lipids.rtp 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/rna.rtp 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/aminoacids.hdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/dna.hdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/lipids.hdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/rna.hdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/aminoacids.n.tdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/dna.n.tdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/rna.n.tdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/aminoacids.c.tdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/dna.c.tdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/rna.c.tdb 56: Analysing hydrogen-bonding network for automated assignment of histidine 56: protonation. 25 donors and 23 acceptors were found. 56: There are 41 hydrogen bonds 56: Will use HISE for residue 8 56: 9 out of 9 lines of specbond.dat converted successfully 56: Special Atom Distance matrix: 56: CYS3 HIS8 56: SG9 NE251 56: HIS8 NE251 1.055 56: MET12 SD83 0.763 0.990 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/aminoacids.arn 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/dna.arn 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/rna.arn 56: Before cleaning: 652 pairs 56: Before cleaning: 662 dihedrals 56: Using the Charmm27 force field in directory charmm27.ff 56: 56: going to rename charmm27.ff/aminoacids.r2b 56: 56: going to rename charmm27.ff/rna.r2b 56: Reading /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/chainTer.pdb... 56: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 127 atoms 56: 56: Analyzing pdb file 56: Splitting chemical chains based on TER records and chain id changing. 56: 56: Merged chains into joint molecule definitions at 1 places. 56: 56: There are 1 chains and 0 blocks of water and 16 residues with 127 atoms 56: 56: chain #res #atoms 56: 56: 1 'A' 16 127 56: 56: All occupancies are one 56: 56: Reading residue database... (Charmm27) 56: 56: Processing chain 1 'A' (127 atoms, 16 residues) 56: 56: Identified residue ALA2 as a starting terminus. 56: 56: Identified residue MET12 as a ending terminus. 56: 56: Identified residue ASN13 as a starting terminus. 56: 56: Identified residue SER17 as a ending terminus. 56: Start terminus ALA-2: NH3+ 56: End terminus MET-12: COO- 56: Start terminus ASN-13: NH3+ 56: End terminus SER-17: COO- 56: 56: Checking for duplicate atoms.... 56: 56: Generating any missing hydrogen atoms and/or adding termini. 56: 56: Now there are 16 residues with 255 atoms 56: 56: Making bonds... 56: 56: Number of bonds was 256, now 256 56: 56: Generating angles, dihedrals and pairs... 56: 56: Making cmap torsions... 56: 56: There are 12 cmap torsion pairs 56: 56: There are 662 dihedrals, 47 impropers, 460 angles 56: 649 pairs, 256 bonds and 0 virtual sites 56: 56: Total mass 1864.131 a.m.u. 56: 56: Total charge 0.000 e 56: 56: Writing topology 56: 56: Writing coordinate file... 56: 56: --------- PLEASE NOTE ------------ 56: 56: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/chainTer.pdb. 56: 56: The Charmm27 force field and the tip3p water model are used. 56: 56: --------- ETON ESAELP ------------ 56: [ OK ] ChainSep/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_and_ter_merge_all_chainTerpdb_format_gro_match_file (271 ms) 56: [ RUN ] ChainSep/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_and_ter_merge_no_chainTerpdb_format_gro_match_file 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/aminoacids.r2b 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/rna.r2b 56: All occupancies are one 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/atomtypes.atp 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/aminoacids.rtp 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/dna.rtp 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/lipids.rtp 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/rna.rtp 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/aminoacids.hdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/dna.hdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/lipids.hdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/rna.hdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/aminoacids.n.tdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/dna.n.tdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/rna.n.tdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/aminoacids.c.tdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/dna.c.tdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/rna.c.tdb 56: Analysing hydrogen-bonding network for automated assignment of histidine 56: protonation. 14 donors and 15 acceptors were found. 56: There are 20 hydrogen bonds 56: Will use HISE for residue 8 56: 9 out of 9 lines of specbond.dat converted successfully 56: Special Atom Distance matrix: 56: CYS3 HIS8 56: SG9 NE251 56: HIS8 NE251 1.055 56: MET12 SD83 0.763 0.990 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/aminoacids.arn 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/dna.arn 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/rna.arn 56: Before cleaning: 441 pairs 56: Before cleaning: 446 dihedrals 56: 9 out of 9 lines of specbond.dat converted successfully 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/aminoacids.arn 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/dna.arn 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/rna.arn 56: Before cleaning: 211 pairs 56: Before cleaning: 216 dihedrals 56: Using the Charmm27 force field in directory charmm27.ff 56: 56: going to rename charmm27.ff/aminoacids.r2b 56: 56: going to rename charmm27.ff/rna.r2b 56: Reading /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/chainTer.pdb... 56: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 127 atoms 56: 56: Analyzing pdb file 56: Splitting chemical chains based on TER records and chain id changing. 56: 56: There are 2 chains and 0 blocks of water and 16 residues with 127 atoms 56: 56: chain #res #atoms 56: 56: 1 'A' 11 86 56: 56: 2 'C' 5 41 56: 56: All occupancies are one 56: 56: Reading residue database... (Charmm27) 56: 56: Processing chain 1 'A' (86 atoms, 11 residues) 56: 56: Identified residue ALA2 as a starting terminus. 56: 56: Identified residue MET12 as a ending terminus. 56: Start terminus ALA-2: NH3+ 56: End terminus MET-12: COO- 56: 56: Checking for duplicate atoms.... 56: 56: Generating any missing hydrogen atoms and/or adding termini. 56: 56: Now there are 11 residues with 172 atoms 56: Chain time... 56: 56: Making bonds... 56: 56: Number of bonds was 173, now 173 56: 56: Generating angles, dihedrals and pairs... 56: 56: Making cmap torsions... 56: 56: There are 9 cmap torsion pairs 56: 56: There are 446 dihedrals, 29 impropers, 312 angles 56: 438 pairs, 173 bonds and 0 virtual sites 56: 56: Total mass 1262.488 a.m.u. 56: 56: Total charge -1.000 e 56: 56: Writing topology 56: 56: Processing chain 2 'C' (41 atoms, 5 residues) 56: 56: Identified residue ASN13 as a starting terminus. 56: 56: Identified residue SER17 as a ending terminus. 56: Start terminus ASN-13: NH3+ 56: End terminus SER-17: COO- 56: 56: Checking for duplicate atoms.... 56: 56: Generating any missing hydrogen atoms and/or adding termini. 56: 56: Now there are 5 residues with 83 atoms 56: Chain time... 56: 56: Making bonds... 56: 56: Number of bonds was 83, now 83 56: 56: Generating angles, dihedrals and pairs... 56: 56: Making cmap torsions... 56: 56: There are 3 cmap torsion pairs 56: 56: There are 216 dihedrals, 18 impropers, 148 angles 56: 211 pairs, 83 bonds and 0 virtual sites 56: 56: Total mass 601.643 a.m.u. 56: 56: Total charge 1.000 e 56: 56: Writing topology 56: 56: Including chain 1 in system: 172 atoms 11 residues 56: 56: Including chain 2 in system: 83 atoms 5 residues 56: 56: Now there are 255 atoms and 16 residues 56: 56: Total mass in system 1864.131 a.m.u. 56: 56: Total charge in system 0.000 e 56: 56: Writing coordinate file... 56: 56: --------- PLEASE NOTE ------------ 56: 56: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/chainTer.pdb. 56: 56: The Charmm27 force field and the tip3p water model are used. 56: 56: --------- ETON ESAELP ------------ 56: [ OK ] ChainSep/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_and_ter_merge_no_chainTerpdb_format_gro_match_file (210 ms) 56: [----------] 8 tests from ChainSep/Pdb2gmxTest (1912 ms total) 56: 56: [----------] 4 tests from ChainChanges/Pdb2gmxTest 56: [ RUN ] ChainChanges/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_merge_no_fragmentspdb_format_pdb_match_file 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/aminoacids.r2b 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/rna.r2b 56: All occupancies are one 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/atomtypes.atp 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/aminoacids.rtp 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/dna.rtp 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/lipids.rtp 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/rna.rtp 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/aminoacids.hdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/dna.hdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/lipids.hdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/rna.hdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/aminoacids.n.tdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/dna.n.tdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/rna.n.tdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/aminoacids.c.tdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/dna.c.tdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/rna.c.tdb 56: 9 out of 9 lines of specbond.dat converted successfully 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/aminoacids.arn 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/dna.arn 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/rna.arn 56: Before cleaning: 83 pairs 56: Before cleaning: 83 dihedrals 56: 9 out of 9 lines of specbond.dat converted successfully 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/aminoacids.arn 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/dna.arn 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/rna.arn 56: Before cleaning: 145 pairs 56: Before cleaning: 150 dihedrals 56: Using the Charmm27 force field in directory charmm27.ff 56: 56: going to rename charmm27.ff/aminoacids.r2b 56: 56: going to rename charmm27.ff/rna.r2b 56: Reading /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/fragments.pdb... 56: Read 'Fragments of peptides and ions', 47 atoms 56: 56: Analyzing pdb file 56: Splitting chemical chains based on changing chain id only (ignoring TER records). 56: 56: There are 2 chains and 0 blocks of water and 6 residues with 47 atoms 56: 56: chain #res #atoms 56: 56: 1 'A' 3 19 56: 56: 2 'B' 3 28 56: 56: All occupancies are one 56: 56: Reading residue database... (Charmm27) 56: 56: Processing chain 1 'A' (19 atoms, 3 residues) 56: 56: Identified residue ALA2 as a starting terminus. 56: 56: Identified residue ASP4 as a ending terminus. 56: Start terminus ALA-2: NH3+ 56: End terminus ASP-4: COO- 56: 56: Checking for duplicate atoms.... 56: 56: Generating any missing hydrogen atoms and/or adding termini. 56: 56: Now there are 3 residues with 36 atoms 56: Chain time... 56: 56: Making bonds... 56: 56: Number of bonds was 35, now 35 56: 56: Generating angles, dihedrals and pairs... 56: 56: Making cmap torsions... 56: 56: There are 1 cmap torsion pairs 56: 56: There are 83 dihedrals, 6 impropers, 61 angles 56: 83 pairs, 35 bonds and 0 virtual sites 56: 56: Total mass 306.314 a.m.u. 56: 56: Total charge -1.000 e 56: 56: Writing topology 56: 56: Processing chain 2 'B' (28 atoms, 3 residues) 56: 56: Identified residue THR18 as a starting terminus. 56: 56: Identified residue TRP20 as a ending terminus. 56: Start terminus THR-18: NH3+ 56: End terminus TRP-20: COO- 56: 56: Checking for duplicate atoms.... 56: 56: Generating any missing hydrogen atoms and/or adding termini. 56: 56: Now there are 3 residues with 57 atoms 56: Chain time... 56: 56: Making bonds... 56: 56: Number of bonds was 58, now 58 56: 56: Generating angles, dihedrals and pairs... 56: 56: Making cmap torsions... 56: 56: There are 1 cmap torsion pairs 56: 56: There are 150 dihedrals, 5 impropers, 103 angles 56: 142 pairs, 58 bonds and 0 virtual sites 56: 56: Total mass 404.468 a.m.u. 56: 56: Total charge -0.000 e 56: 56: Writing topology 56: 56: Including chain 1 in system: 36 atoms 3 residues 56: 56: Including chain 2 in system: 57 atoms 3 residues 56: 56: Now there are 93 atoms and 6 residues 56: 56: Total mass in system 710.782 a.m.u. 56: 56: Total charge in system -1.000 e 56: 56: Writing coordinate file... 56: 56: --------- PLEASE NOTE ------------ 56: 56: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/fragments.pdb. 56: 56: The Charmm27 force field and the tip3p water model are used. 56: 56: --------- ETON ESAELP ------------ 56: [ OK ] ChainChanges/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_merge_no_fragmentspdb_format_pdb_match_file (157 ms) 56: [ RUN ] ChainChanges/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_ter_merge_no_fragmentspdb_format_pdb_match_file 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/aminoacids.r2b 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/rna.r2b 56: All occupancies are one 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/atomtypes.atp 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/aminoacids.rtp 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/dna.rtp 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/lipids.rtp 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/rna.rtp 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/aminoacids.hdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/dna.hdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/lipids.hdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/rna.hdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/aminoacids.n.tdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/dna.n.tdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/rna.n.tdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/aminoacids.c.tdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/dna.c.tdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/rna.c.tdb 56: 9 out of 9 lines of specbond.dat converted successfully 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/aminoacids.arn 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/dna.arn 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/rna.arn 56: Before cleaning: 83 pairs 56: Before cleaning: 83 dihedrals 56: 9 out of 9 lines of specbond.dat converted successfully 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/aminoacids.arn 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/dna.arn 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/rna.arn 56: Before cleaning: 145 pairs 56: Before cleaning: 150 dihedrals 56: Using the Charmm27 force field in directory charmm27.ff 56: 56: going to rename charmm27.ff/aminoacids.r2b 56: 56: going to rename charmm27.ff/rna.r2b 56: Reading /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/fragments.pdb... 56: Read 'Fragments of peptides and ions', 47 atoms 56: 56: Analyzing pdb file 56: Splitting chemical chains based on TER records only (ignoring chain id). 56: 56: There are 2 chains and 0 blocks of water and 6 residues with 47 atoms 56: 56: chain #res #atoms 56: 56: 1 'A' 3 19 56: 56: 2 'B' 3 28 56: 56: All occupancies are one 56: 56: Reading residue database... (Charmm27) 56: 56: Processing chain 1 'A' (19 atoms, 3 residues) 56: 56: Identified residue ALA2 as a starting terminus. 56: 56: Identified residue ASP4 as a ending terminus. 56: Start terminus ALA-2: NH3+ 56: End terminus ASP-4: COO- 56: 56: Checking for duplicate atoms.... 56: 56: Generating any missing hydrogen atoms and/or adding termini. 56: 56: Now there are 3 residues with 36 atoms 56: Chain time... 56: 56: Making bonds... 56: 56: Number of bonds was 35, now 35 56: 56: Generating angles, dihedrals and pairs... 56: 56: Making cmap torsions... 56: 56: There are 1 cmap torsion pairs 56: 56: There are 83 dihedrals, 6 impropers, 61 angles 56: 83 pairs, 35 bonds and 0 virtual sites 56: 56: Total mass 306.314 a.m.u. 56: 56: Total charge -1.000 e 56: 56: Writing topology 56: 56: Processing chain 2 'B' (28 atoms, 3 residues) 56: 56: Identified residue THR18 as a starting terminus. 56: 56: Identified residue TRP20 as a ending terminus. 56: Start terminus THR-18: NH3+ 56: End terminus TRP-20: COO- 56: 56: Checking for duplicate atoms.... 56: 56: Generating any missing hydrogen atoms and/or adding termini. 56: 56: Now there are 3 residues with 57 atoms 56: Chain time... 56: 56: Making bonds... 56: 56: Number of bonds was 58, now 58 56: 56: Generating angles, dihedrals and pairs... 56: 56: Making cmap torsions... 56: 56: There are 1 cmap torsion pairs 56: 56: There are 150 dihedrals, 5 impropers, 103 angles 56: 142 pairs, 58 bonds and 0 virtual sites 56: 56: Total mass 404.468 a.m.u. 56: 56: Total charge -0.000 e 56: 56: Writing topology 56: 56: Including chain 1 in system: 36 atoms 3 residues 56: 56: Including chain 2 in system: 57 atoms 3 residues 56: 56: Now there are 93 atoms and 6 residues 56: 56: Total mass in system 710.782 a.m.u. 56: 56: Total charge in system -1.000 e 56: 56: Writing coordinate file... 56: 56: --------- PLEASE NOTE ------------ 56: 56: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/fragments.pdb. 56: 56: The Charmm27 force field and the tip3p water model are used. 56: 56: --------- ETON ESAELP ------------ 56: [ OK ] ChainChanges/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_ter_merge_no_fragmentspdb_format_pdb_match_file (162 ms) 56: [ RUN ] ChainChanges/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_or_ter_merge_no_fragmentspdb_format_pdb_match_file 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/aminoacids.r2b 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/rna.r2b 56: All occupancies are one 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/atomtypes.atp 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/aminoacids.rtp 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/dna.rtp 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/lipids.rtp 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/rna.rtp 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/aminoacids.hdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/dna.hdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/lipids.hdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/rna.hdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/aminoacids.n.tdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/dna.n.tdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/rna.n.tdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/aminoacids.c.tdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/dna.c.tdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/rna.c.tdb 56: 9 out of 9 lines of specbond.dat converted successfully 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/aminoacids.arn 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/dna.arn 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/rna.arn 56: Before cleaning: 83 pairs 56: Before cleaning: 83 dihedrals 56: 9 out of 9 lines of specbond.dat converted successfully 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/aminoacids.arn 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/dna.arn 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/rna.arn 56: Before cleaning: 145 pairs 56: Before cleaning: 150 dihedrals 56: Using the Charmm27 force field in directory charmm27.ff 56: 56: going to rename charmm27.ff/aminoacids.r2b 56: 56: going to rename charmm27.ff/rna.r2b 56: Reading /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/fragments.pdb... 56: Read 'Fragments of peptides and ions', 47 atoms 56: 56: Analyzing pdb file 56: Splitting chemical chains based on TER records or chain id changing. 56: 56: There are 2 chains and 0 blocks of water and 6 residues with 47 atoms 56: 56: chain #res #atoms 56: 56: 1 'A' 3 19 56: 56: 2 'B' 3 28 56: 56: All occupancies are one 56: 56: Reading residue database... (Charmm27) 56: 56: Processing chain 1 'A' (19 atoms, 3 residues) 56: 56: Identified residue ALA2 as a starting terminus. 56: 56: Identified residue ASP4 as a ending terminus. 56: Start terminus ALA-2: NH3+ 56: End terminus ASP-4: COO- 56: 56: Checking for duplicate atoms.... 56: 56: Generating any missing hydrogen atoms and/or adding termini. 56: 56: Now there are 3 residues with 36 atoms 56: Chain time... 56: 56: Making bonds... 56: 56: Number of bonds was 35, now 35 56: 56: Generating angles, dihedrals and pairs... 56: 56: Making cmap torsions... 56: 56: There are 1 cmap torsion pairs 56: 56: There are 83 dihedrals, 6 impropers, 61 angles 56: 83 pairs, 35 bonds and 0 virtual sites 56: 56: Total mass 306.314 a.m.u. 56: 56: Total charge -1.000 e 56: 56: Writing topology 56: 56: Processing chain 2 'B' (28 atoms, 3 residues) 56: 56: Identified residue THR18 as a starting terminus. 56: 56: Identified residue TRP20 as a ending terminus. 56: Start terminus THR-18: NH3+ 56: End terminus TRP-20: COO- 56: 56: Checking for duplicate atoms.... 56: 56: Generating any missing hydrogen atoms and/or adding termini. 56: 56: Now there are 3 residues with 57 atoms 56: Chain time... 56: 56: Making bonds... 56: 56: Number of bonds was 58, now 58 56: 56: Generating angles, dihedrals and pairs... 56: 56: Making cmap torsions... 56: 56: There are 1 cmap torsion pairs 56: 56: There are 150 dihedrals, 5 impropers, 103 angles 56: 142 pairs, 58 bonds and 0 virtual sites 56: 56: Total mass 404.468 a.m.u. 56: 56: Total charge -0.000 e 56: 56: Writing topology 56: 56: Including chain 1 in system: 36 atoms 3 residues 56: 56: Including chain 2 in system: 57 atoms 3 residues 56: 56: Now there are 93 atoms and 6 residues 56: 56: Total mass in system 710.782 a.m.u. 56: 56: Total charge in system -1.000 e 56: 56: Writing coordinate file... 56: 56: --------- PLEASE NOTE ------------ 56: 56: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/fragments.pdb. 56: 56: The Charmm27 force field and the tip3p water model are used. 56: 56: --------- ETON ESAELP ------------ 56: [ OK ] ChainChanges/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_or_ter_merge_no_fragmentspdb_format_pdb_match_file (160 ms) 56: [ RUN ] ChainChanges/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_and_ter_merge_no_fragmentspdb_format_pdb_match_file 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/aminoacids.r2b 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/rna.r2b 56: All occupancies are one 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/atomtypes.atp 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/aminoacids.rtp 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/dna.rtp 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/lipids.rtp 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/rna.rtp 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/aminoacids.hdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/dna.hdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/lipids.hdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/rna.hdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/aminoacids.n.tdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/dna.n.tdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/rna.n.tdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/aminoacids.c.tdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/dna.c.tdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/rna.c.tdb 56: 9 out of 9 lines of specbond.dat converted successfully 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/aminoacids.arn 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/dna.arn 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/rna.arn 56: Before cleaning: 83 pairs 56: Before cleaning: 83 dihedrals 56: 9 out of 9 lines of specbond.dat converted successfully 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/aminoacids.arn 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/dna.arn 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/rna.arn 56: Before cleaning: 145 pairs 56: Before cleaning: 150 dihedrals 56: Using the Charmm27 force field in directory charmm27.ff 56: 56: going to rename charmm27.ff/aminoacids.r2b 56: 56: going to rename charmm27.ff/rna.r2b 56: Reading /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/fragments.pdb... 56: Read 'Fragments of peptides and ions', 47 atoms 56: 56: Analyzing pdb file 56: Splitting chemical chains based on TER records and chain id changing. 56: 56: There are 2 chains and 0 blocks of water and 6 residues with 47 atoms 56: 56: chain #res #atoms 56: 56: 1 'A' 3 19 56: 56: 2 'B' 3 28 56: 56: All occupancies are one 56: 56: Reading residue database... (Charmm27) 56: 56: Processing chain 1 'A' (19 atoms, 3 residues) 56: 56: Identified residue ALA2 as a starting terminus. 56: 56: Identified residue ASP4 as a ending terminus. 56: Start terminus ALA-2: NH3+ 56: End terminus ASP-4: COO- 56: 56: Checking for duplicate atoms.... 56: 56: Generating any missing hydrogen atoms and/or adding termini. 56: 56: Now there are 3 residues with 36 atoms 56: Chain time... 56: 56: Making bonds... 56: 56: Number of bonds was 35, now 35 56: 56: Generating angles, dihedrals and pairs... 56: 56: Making cmap torsions... 56: 56: There are 1 cmap torsion pairs 56: 56: There are 83 dihedrals, 6 impropers, 61 angles 56: 83 pairs, 35 bonds and 0 virtual sites 56: 56: Total mass 306.314 a.m.u. 56: 56: Total charge -1.000 e 56: 56: Writing topology 56: 56: Processing chain 2 'B' (28 atoms, 3 residues) 56: 56: Identified residue THR18 as a starting terminus. 56: 56: Identified residue TRP20 as a ending terminus. 56: Start terminus THR-18: NH3+ 56: End terminus TRP-20: COO- 56: 56: Checking for duplicate atoms.... 56: 56: Generating any missing hydrogen atoms and/or adding termini. 56: 56: Now there are 3 residues with 57 atoms 56: Chain time... 56: 56: Making bonds... 56: 56: Number of bonds was 58, now 58 56: 56: Generating angles, dihedrals and pairs... 56: 56: Making cmap torsions... 56: 56: There are 1 cmap torsion pairs 56: 56: There are 150 dihedrals, 5 impropers, 103 angles 56: 142 pairs, 58 bonds and 0 virtual sites 56: 56: Total mass 404.468 a.m.u. 56: 56: Total charge -0.000 e 56: 56: Writing topology 56: 56: Including chain 1 in system: 36 atoms 3 residues 56: 56: Including chain 2 in system: 57 atoms 3 residues 56: 56: Now there are 93 atoms and 6 residues 56: 56: Total mass in system 710.782 a.m.u. 56: 56: Total charge in system -1.000 e 56: 56: Writing coordinate file... 56: 56: --------- PLEASE NOTE ------------ 56: 56: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/fragments.pdb. 56: 56: The Charmm27 force field and the tip3p water model are used. 56: 56: --------- ETON ESAELP ------------ 56: [ OK ] ChainChanges/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_and_ter_merge_no_fragmentspdb_format_pdb_match_file (159 ms) 56: [----------] 4 tests from ChainChanges/Pdb2gmxTest (641 ms total) 56: 56: [----------] 4 tests from Cyclic/Pdb2gmxTest 56: [ RUN ] Cyclic/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_or_ter_merge_no_cycrnapdb_format_gro_match_file 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/aminoacids.r2b 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/rna.r2b 56: WARNING: all CONECT records are ignored 56: Chain identifier 'Q' is used in two non-sequential blocks. They will be treated as separate chains unless you reorder your file. 56: 56: All occupancies are one 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/atomtypes.atp 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/aminoacids.rtp 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/dna.rtp 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/lipids.rtp 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/rna.rtp 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/aminoacids.hdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/dna.hdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/lipids.hdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/rna.hdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/aminoacids.n.tdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/dna.n.tdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/rna.n.tdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/aminoacids.c.tdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/dna.c.tdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/rna.c.tdb 56: 9 out of 9 lines of specbond.dat converted successfully 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/aminoacids.arn 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/dna.arn 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/rna.arn 56: Before cleaning: 6040 pairs 56: Before cleaning: 6605 dihedrals 56: 9 out of 9 lines of specbond.dat converted successfully 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/aminoacids.arn 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/dna.arn 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/rna.arn 56: Before cleaning: 6040 pairs 56: Before cleaning: 6605 dihedrals 56: 9 out of 9 lines of specbond.dat converted successfully 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/aminoacids.arn 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/dna.arn 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/rna.arn 56: 9 out of 9 lines of specbond.dat converted successfully 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/aminoacids.arn 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/dna.arn 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/rna.arn 56: 9 out of 9 lines of specbond.dat converted successfully 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/aminoacids.arn 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/dna.arn 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/rna.arn 56: Using the Charmm27 force field in directory charmm27.ff 56: 56: going to rename charmm27.ff/aminoacids.r2b 56: 56: going to rename charmm27.ff/rna.r2b 56: Reading /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/cyc-rna.pdb... 56: Read 'L1 RIBOZYME RNA LIGASE', 3087 atoms 56: 56: Analyzing pdb file 56: Splitting chemical chains based on TER records or chain id changing. 56: 56: Chain identifier 'Q' is used in two non-sequential blocks. They will be treated as separate chains unless you reorder your file. 56: 56: Moved all the water blocks to the end 56: 56: There are 3 chains and 2 blocks of water and 175 residues with 3087 atoms 56: 56: chain #res #atoms 56: 56: 1 'P' 71 1527 56: 56: 2 'Q' 71 1527 56: 56: 3 'Q' 7 7 56: 56: 4 ' ' 10 10 (only water) 56: 56: 5 ' ' 16 16 (only water) 56: 56: All occupancies are one 56: 56: Reading residue database... (Charmm27) 56: 56: Processing chain 1 'P' (1527 atoms, 71 residues) 56: 56: Identified residue G1 as a starting terminus. 56: 56: Identified residue U71 as a ending terminus. 56: 56: Checking for duplicate atoms.... 56: 56: Generating any missing hydrogen atoms and/or adding termini. 56: 56: Now there are 71 residues with 2297 atoms 56: Chain time... 56: 56: Making bonds... 56: 56: Number of bonds was 2481, now 2481 56: 56: Generating angles, dihedrals and pairs... 56: 56: Making cmap torsions... 56: 56: There are 6605 dihedrals, 183 impropers, 4434 angles 56: 5827 pairs, 2481 bonds and 0 virtual sites 56: 56: Total mass 22984.514 a.m.u. 56: 56: Total charge -71.000 e 56: 56: Writing topology 56: 56: Processing chain 2 'Q' (1527 atoms, 71 residues) 56: 56: Identified residue G1 as a starting terminus. 56: 56: Identified residue U71 as a ending terminus. 56: 56: Checking for duplicate atoms.... 56: 56: Generating any missing hydrogen atoms and/or adding termini. 56: 56: Now there are 71 residues with 2297 atoms 56: Chain time... 56: 56: Making bonds... 56: 56: Number of bonds was 2481, now 2481 56: 56: Generating angles, dihedrals and pairs... 56: 56: Making cmap torsions... 56: 56: There are 6605 dihedrals, 183 impropers, 4434 angles 56: 5827 pairs, 2481 bonds and 0 virtual sites 56: 56: Total mass 22984.514 a.m.u. 56: 56: Total charge -71.000 e 56: 56: Writing topology 56: 56: Processing chain 3 'Q' (7 atoms, 7 residues) 56: 56: Residue MG72 has type 'Ion', assuming it is not linked into a chain. 56: 56: Residue MG73 has type 'Ion', assuming it is not linked into a chain. 56: 56: Residue MG74 has type 'Ion', assuming it is not linked into a chain. 56: 56: Residue MG75 has type 'Ion', assuming it is not linked into a chain. 56: 56: Residue MG76 has type 'Ion', assuming it is not linked into a chain. 56: 56: Disabling further notes about ions. 56: 56: Problem with chain definition, or missing terminal residues. This chain does not appear to contain a recognized chain molecule. If this is incorrect, you can edit residuetypes.dat to modify the behavior. 56: 56: Checking for duplicate atoms.... 56: 56: Generating any missing hydrogen atoms and/or adding termini. 56: 56: Now there are 7 residues with 7 atoms 56: Chain time... 56: 56: Making bonds... 56: 56: No bonds 56: 56: Generating angles, dihedrals and pairs... 56: 56: Making cmap torsions... 56: 56: There are 0 dihedrals, 0 impropers, 0 angles 56: 0 pairs, 0 bonds and 0 virtual sites 56: 56: Total mass 170.135 a.m.u. 56: 56: Total charge 14.000 e 56: 56: Writing topology 56: 56: Processing chain 4 (10 atoms, 10 residues) 56: 56: Problem with chain definition, or missing terminal residues. This chain does not appear to contain a recognized chain molecule. If this is incorrect, you can edit residuetypes.dat to modify the behavior. 56: 56: Checking for duplicate atoms.... 56: 56: Generating any missing hydrogen atoms and/or adding termini. 56: 56: Now there are 10 residues with 30 atoms 56: 56: Making bonds... 56: 56: Number of bonds was 30, now 30 56: 56: Generating angles, dihedrals and pairs... 56: 56: Making cmap torsions... 56: 56: There are 0 dihedrals, 0 impropers, 30 angles 56: 0 pairs, 30 bonds and 0 virtual sites 56: 56: Total mass 180.154 a.m.u. 56: 56: Total charge 0.000 e 56: 56: Processing chain 5 (16 atoms, 16 residues) 56: 56: Problem with chain definition, or missing terminal residues. This chain does not appear to contain a recognized chain molecule. If this is incorrect, you can edit residuetypes.dat to modify the behavior. 56: 56: Checking for duplicate atoms.... 56: 56: Generating any missing hydrogen atoms and/or adding termini. 56: 56: Now there are 16 residues with 48 atoms 56: 56: Making bonds... 56: 56: Number of bonds was 48, now 48 56: 56: Generating angles, dihedrals and pairs... 56: 56: Making cmap torsions... 56: 56: There are 0 dihedrals, 0 impropers, 48 angles 56: 0 pairs, 48 bonds and 0 virtual sites 56: 56: Total mass 288.246 a.m.u. 56: 56: Total charge 0.000 e 56: 56: Including chain 1 in system: 2297 atoms 71 residues 56: 56: Including chain 2 in system: 2297 atoms 71 residues 56: 56: Including chain 3 in system: 7 atoms 7 residues 56: 56: Including chain 4 in system: 30 atoms 10 residues 56: 56: Including chain 5 in system: 48 atoms 16 residues 56: 56: Now there are 4679 atoms and 175 residues 56: 56: Total mass in system 46607.562 a.m.u. 56: 56: Total charge in system -128.000 e 56: 56: Writing coordinate file... 56: 56: --------- PLEASE NOTE ------------ 56: 56: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/cyc-rna.pdb. 56: 56: The Charmm27 force field and the tip3p water model are used. 56: 56: --------- ETON ESAELP ------------ 56: [ OK ] Cyclic/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_or_ter_merge_no_cycrnapdb_format_gro_match_file (2704 ms) 56: [ RUN ] Cyclic/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_or_ter_merge_no_cycprotpdb_format_gro_match_file 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/aminoacids.r2b 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/rna.r2b 56: All occupancies are one 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/atomtypes.atp 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/aminoacids.rtp 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/dna.rtp 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/lipids.rtp 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/rna.rtp 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/aminoacids.hdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/dna.hdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/lipids.hdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/rna.hdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/aminoacids.n.tdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/dna.n.tdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/rna.n.tdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/aminoacids.c.tdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/dna.c.tdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/rna.c.tdb 56: 9 out of 9 lines of specbond.dat converted successfully 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/aminoacids.arn 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/dna.arn 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/rna.arn 56: Before cleaning: 2325 pairs 56: Before cleaning: 2325 dihedrals 56: Using the Charmm27 force field in directory charmm27.ff 56: 56: going to rename charmm27.ff/aminoacids.r2b 56: 56: going to rename charmm27.ff/rna.r2b 56: Reading /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/cyc-prot.pdb... 56: Read 'CARNOCYCLIN-A', 413 atoms 56: 56: Analyzing pdb file 56: Splitting chemical chains based on TER records or chain id changing. 56: 56: There are 1 chains and 0 blocks of water and 60 residues with 413 atoms 56: 56: chain #res #atoms 56: 56: 1 'A' 60 413 56: 56: All occupancies are one 56: 56: Reading residue database... (Charmm27) 56: 56: Processing chain 1 'A' (413 atoms, 60 residues) 56: 56: Identified residue LEU1 as a starting terminus. 56: 56: Identified residue LEU60 as a ending terminus. 56: 56: Checking for duplicate atoms.... 56: 56: Generating any missing hydrogen atoms and/or adding termini. 56: 56: Now there are 60 residues with 878 atoms 56: 56: Making bonds... 56: 56: Number of bonds was 880, now 880 56: 56: Generating angles, dihedrals and pairs... 56: 56: Making cmap torsions... 56: 56: There are 60 cmap torsion pairs 56: 56: There are 2325 dihedrals, 137 impropers, 1614 angles 56: 2319 pairs, 880 bonds and 0 virtual sites 56: 56: Total mass 5866.087 a.m.u. 56: 56: Total charge 4.000 e 56: 56: Writing topology 56: 56: Writing coordinate file... 56: 56: --------- PLEASE NOTE ------------ 56: 56: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/cyc-prot.pdb. 56: 56: The Charmm27 force field and the tip3p water model are used. 56: 56: --------- ETON ESAELP ------------ 56: [ OK ] Cyclic/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_or_ter_merge_no_cycprotpdb_format_gro_match_file (630 ms) 56: [ RUN ] Cyclic/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_or_ter_merge_all_cycrnapdb_format_gro_match_file 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/aminoacids.r2b 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/rna.r2b 56: WARNING: all CONECT records are ignored 56: All occupancies are one 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/atomtypes.atp 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/aminoacids.rtp 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/dna.rtp 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/lipids.rtp 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/rna.rtp 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/aminoacids.hdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/dna.hdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/lipids.hdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/rna.hdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/aminoacids.n.tdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/dna.n.tdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/rna.n.tdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/aminoacids.c.tdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/dna.c.tdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/rna.c.tdb 56: 9 out of 9 lines of specbond.dat converted successfully 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/aminoacids.arn 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/dna.arn 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/rna.arn 56: Before cleaning: 12080 pairs 56: Before cleaning: 13210 dihedrals 56: 9 out of 9 lines of specbond.dat converted successfully 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/aminoacids.arn 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/dna.arn 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/rna.arn 56: 9 out of 9 lines of specbond.dat converted successfully 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/aminoacids.arn 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/dna.arn 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/rna.arn 56: Using the Charmm27 force field in directory charmm27.ff 56: 56: going to rename charmm27.ff/aminoacids.r2b 56: 56: going to rename charmm27.ff/rna.r2b 56: Reading /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/cyc-rna.pdb... 56: Read 'L1 RIBOZYME RNA LIGASE', 3087 atoms 56: 56: Analyzing pdb file 56: Splitting chemical chains based on TER records or chain id changing. 56: 56: Moved all the water blocks to the end 56: 56: Merged chains into joint molecule definitions at 2 places. 56: 56: There are 1 chains and 2 blocks of water and 175 residues with 3087 atoms 56: 56: chain #res #atoms 56: 56: 1 'P' 149 3061 56: 56: 2 ' ' 10 10 (only water) 56: 56: 3 ' ' 16 16 (only water) 56: 56: All occupancies are one 56: 56: Reading residue database... (Charmm27) 56: 56: Processing chain 1 'P' (3061 atoms, 149 residues) 56: 56: Identified residue G1 as a starting terminus. 56: 56: Identified residue U71 as a ending terminus. 56: 56: Identified residue G1 as a starting terminus. 56: 56: Identified residue U71 as a ending terminus. 56: 56: Residue MG72 has type 'Ion', assuming it is not linked into a chain. 56: 56: Residue MG73 has type 'Ion', assuming it is not linked into a chain. 56: 56: Residue MG74 has type 'Ion', assuming it is not linked into a chain. 56: 56: Residue MG75 has type 'Ion', assuming it is not linked into a chain. 56: 56: Residue MG76 has type 'Ion', assuming it is not linked into a chain. 56: 56: Disabling further notes about ions. 56: 56: Checking for duplicate atoms.... 56: 56: Generating any missing hydrogen atoms and/or adding termini. 56: 56: Now there are 149 residues with 4601 atoms 56: 56: Making bonds... 56: 56: Number of bonds was 4962, now 4962 56: 56: Generating angles, dihedrals and pairs... 56: 56: Making cmap torsions... 56: 56: There are 13210 dihedrals, 366 impropers, 8868 angles 56: 11654 pairs, 4962 bonds and 0 virtual sites 56: 56: Total mass 46139.162 a.m.u. 56: 56: Total charge -128.000 e 56: 56: Writing topology 56: 56: Processing chain 2 (10 atoms, 10 residues) 56: 56: Problem with chain definition, or missing terminal residues. This chain does not appear to contain a recognized chain molecule. If this is incorrect, you can edit residuetypes.dat to modify the behavior. 56: 56: Checking for duplicate atoms.... 56: 56: Generating any missing hydrogen atoms and/or adding termini. 56: 56: Now there are 10 residues with 30 atoms 56: 56: Making bonds... 56: 56: Number of bonds was 30, now 30 56: 56: Generating angles, dihedrals and pairs... 56: 56: Making cmap torsions... 56: 56: There are 0 dihedrals, 0 impropers, 30 angles 56: 0 pairs, 30 bonds and 0 virtual sites 56: 56: Total mass 180.154 a.m.u. 56: 56: Total charge 0.000 e 56: 56: Processing chain 3 (16 atoms, 16 residues) 56: 56: Problem with chain definition, or missing terminal residues. This chain does not appear to contain a recognized chain molecule. If this is incorrect, you can edit residuetypes.dat to modify the behavior. 56: 56: Checking for duplicate atoms.... 56: 56: Generating any missing hydrogen atoms and/or adding termini. 56: 56: Now there are 16 residues with 48 atoms 56: 56: Making bonds... 56: 56: Number of bonds was 48, now 48 56: 56: Generating angles, dihedrals and pairs... 56: 56: Making cmap torsions... 56: 56: There are 0 dihedrals, 0 impropers, 48 angles 56: 0 pairs, 48 bonds and 0 virtual sites 56: 56: Total mass 288.246 a.m.u. 56: 56: Total charge 0.000 e 56: 56: Including chain 1 in system: 4601 atoms 149 residues 56: 56: Including chain 2 in system: 30 atoms 10 residues 56: 56: Including chain 3 in system: 48 atoms 16 residues 56: 56: Now there are 4679 atoms and 175 residues 56: 56: Total mass in system 46607.562 a.m.u. 56: 56: Total charge in system -128.000 e 56: 56: Writing coordinate file... 56: 56: --------- PLEASE NOTE ------------ 56: 56: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/cyc-rna.pdb. 56: 56: The Charmm27 force field and the tip3p water model are used. 56: 56: --------- ETON ESAELP ------------ 56: [ OK ] Cyclic/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_or_ter_merge_all_cycrnapdb_format_gro_match_file (4310 ms) 56: [ RUN ] Cyclic/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_or_ter_merge_all_cycprotpdb_format_gro_match_file 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/aminoacids.r2b 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/rna.r2b 56: All occupancies are one 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/atomtypes.atp 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/aminoacids.rtp 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/dna.rtp 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/lipids.rtp 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/rna.rtp 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/aminoacids.hdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/dna.hdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/lipids.hdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/rna.hdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/aminoacids.n.tdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/dna.n.tdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/rna.n.tdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/aminoacids.c.tdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/dna.c.tdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/rna.c.tdb 56: 9 out of 9 lines of specbond.dat converted successfully 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/aminoacids.arn 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/dna.arn 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/rna.arn 56: Before cleaning: 2325 pairs 56: Before cleaning: 2325 dihedrals 56: Using the Charmm27 force field in directory charmm27.ff 56: 56: going to rename charmm27.ff/aminoacids.r2b 56: 56: going to rename charmm27.ff/rna.r2b 56: Reading /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/cyc-prot.pdb... 56: Read 'CARNOCYCLIN-A', 413 atoms 56: 56: Analyzing pdb file 56: Splitting chemical chains based on TER records or chain id changing. 56: 56: There are 1 chains and 0 blocks of water and 60 residues with 413 atoms 56: 56: chain #res #atoms 56: 56: 1 'A' 60 413 56: 56: All occupancies are one 56: 56: Reading residue database... (Charmm27) 56: 56: Processing chain 1 'A' (413 atoms, 60 residues) 56: 56: Identified residue LEU1 as a starting terminus. 56: 56: Identified residue LEU60 as a ending terminus. 56: 56: Checking for duplicate atoms.... 56: 56: Generating any missing hydrogen atoms and/or adding termini. 56: 56: Now there are 60 residues with 878 atoms 56: 56: Making bonds... 56: 56: Number of bonds was 880, now 880 56: 56: Generating angles, dihedrals and pairs... 56: 56: Making cmap torsions... 56: 56: There are 60 cmap torsion pairs 56: 56: There are 2325 dihedrals, 137 impropers, 1614 angles 56: 2319 pairs, 880 bonds and 0 virtual sites 56: 56: Total mass 5866.087 a.m.u. 56: 56: Total charge 4.000 e 56: 56: Writing topology 56: 56: Writing coordinate file... 56: 56: --------- PLEASE NOTE ------------ 56: 56: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/cyc-prot.pdb. 56: 56: The Charmm27 force field and the tip3p water model are used. 56: 56: --------- ETON ESAELP ------------ 56: [ OK ] Cyclic/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_or_ter_merge_all_cycprotpdb_format_gro_match_file (658 ms) 56: [----------] 4 tests from Cyclic/Pdb2gmxTest (8311 ms total) 56: 56: [----------] Global test environment tear-down 56: [==========] 39 tests from 6 test suites ran. (19067 ms total) 56: [ PASSED ] 39 tests. 56/92 Test #56: Pdb2gmx3Test .............................. Passed 19.16 sec test 57 Start 57: CorrelationsTest 57: Test command: /build/reproducible-path/gromacs-2025.1/build/basic/bin/correlations-test "--gtest_output=xml:/build/reproducible-path/gromacs-2025.1/build/basic/Testing/Temporary/CorrelationsTest.xml" 57: Working Directory: /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/correlationfunctions/tests 57: Test timeout computed to be: 30 57: [==========] Running 21 tests from 3 test suites. 57: [----------] Global test environment set-up. 57: [----------] 10 tests from AutocorrTest 57: [ RUN ] AutocorrTest.EacNormal 57: [ OK ] AutocorrTest.EacNormal (17 ms) 57: [ RUN ] AutocorrTest.EacNoNormalize 57: [ OK ] AutocorrTest.EacNoNormalize (9 ms) 57: [ RUN ] AutocorrTest.EacCos 57: [ OK ] AutocorrTest.EacCos (16 ms) 57: [ RUN ] AutocorrTest.EacVector 57: [ OK ] AutocorrTest.EacVector (24 ms) 57: [ RUN ] AutocorrTest.EacRcross 57: [ OK ] AutocorrTest.EacRcross (7 ms) 57: [ RUN ] AutocorrTest.EacP0 57: [ OK ] AutocorrTest.EacP0 (24 ms) 57: [ RUN ] AutocorrTest.EacP1 57: [ OK ] AutocorrTest.EacP1 (24 ms) 57: [ RUN ] AutocorrTest.EacP2 57: [ OK ] AutocorrTest.EacP2 (44 ms) 57: [ RUN ] AutocorrTest.EacP3 57: [ OK ] AutocorrTest.EacP3 (29 ms) 57: [ RUN ] AutocorrTest.EacP4 57: [ OK ] AutocorrTest.EacP4 (27 ms) 57: [----------] 10 tests from AutocorrTest (234 ms total) 57: 57: [----------] 10 tests from ExpfitTest 57: [ RUN ] ExpfitTest.EffnEXP1 57: [ OK ] ExpfitTest.EffnEXP1 (6 ms) 57: [ RUN ] ExpfitTest.EffnEXP2 57: [ OK ] ExpfitTest.EffnEXP2 (9 ms) 57: [ RUN ] ExpfitTest.EffnEXPEXP 57: [ OK ] ExpfitTest.EffnEXPEXP (17 ms) 57: [ RUN ] ExpfitTest.EffnEXP5 57: [ OK ] ExpfitTest.EffnEXP5 (41 ms) 57: [ RUN ] ExpfitTest.EffnEXP7 57: [ OK ] ExpfitTest.EffnEXP7 (33 ms) 57: [ RUN ] ExpfitTest.EffnEXP9 57: [ OK ] ExpfitTest.EffnEXP9 (155 ms) 57: [ RUN ] ExpfitTest.EffnERF 57: [ OK ] ExpfitTest.EffnERF (22 ms) 57: [ RUN ] ExpfitTest.EffnERREST 57: [ OK ] ExpfitTest.EffnERREST (29 ms) 57: [ RUN ] ExpfitTest.EffnVAC 57: [ OK ] ExpfitTest.EffnVAC (60 ms) 57: [ RUN ] ExpfitTest.EffnPRES 57: [ OK ] ExpfitTest.EffnPRES (94 ms) 57: [----------] 10 tests from ExpfitTest (472 ms total) 57: 57: [----------] 1 test from ManyAutocorrelationTest 57: [ RUN ] ManyAutocorrelationTest.Empty 57: [ OK ] ManyAutocorrelationTest.Empty (0 ms) 57: [----------] 1 test from ManyAutocorrelationTest (0 ms total) 57: 57: [----------] Global test environment tear-down 57: [==========] 21 tests from 3 test suites ran. (740 ms total) 57: [ PASSED ] 21 tests. 57/92 Test #57: CorrelationsTest .......................... Passed 0.82 sec test 58 Start 58: AnalysisDataUnitTests 58: Test command: /build/reproducible-path/gromacs-2025.1/build/basic/bin/analysisdata-test "--gtest_output=xml:/build/reproducible-path/gromacs-2025.1/build/basic/Testing/Temporary/AnalysisDataUnitTests.xml" 58: Working Directory: /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/analysisdata/tests 58: Test timeout computed to be: 30 58: [==========] Running 69 tests from 14 test suites. 58: [----------] Global test environment set-up. 58: [----------] 3 tests from AnalysisDataInitializationTest 58: [ RUN ] AnalysisDataInitializationTest.BasicInitialization 58: [ OK ] AnalysisDataInitializationTest.BasicInitialization (0 ms) 58: [ RUN ] AnalysisDataInitializationTest.ChecksMultiColumnModules 58: [ OK ] AnalysisDataInitializationTest.ChecksMultiColumnModules (0 ms) 58: [ RUN ] AnalysisDataInitializationTest.ChecksMultipointModules 58: [ OK ] AnalysisDataInitializationTest.ChecksMultipointModules (0 ms) 58: [----------] 3 tests from AnalysisDataInitializationTest (0 ms total) 58: 58: [----------] 8 tests from AnalysisDataCommonTest/0, where TypeParam = gmx::test::(anonymous namespace)::SimpleInputData 58: [ RUN ] AnalysisDataCommonTest/0.CallsModuleCorrectly 58: [ OK ] AnalysisDataCommonTest/0.CallsModuleCorrectly (3 ms) 58: [ RUN ] AnalysisDataCommonTest/0.CallsParallelModuleCorrectly 58: [ OK ] AnalysisDataCommonTest/0.CallsParallelModuleCorrectly (2 ms) 58: [ RUN ] AnalysisDataCommonTest/0.CallsMixedModulesCorrectly 58: [ OK ] AnalysisDataCommonTest/0.CallsMixedModulesCorrectly (1 ms) 58: [ RUN ] AnalysisDataCommonTest/0.CallsColumnModuleCorrectly 58: [ OK ] AnalysisDataCommonTest/0.CallsColumnModuleCorrectly (1 ms) 58: [ RUN ] AnalysisDataCommonTest/0.CallsModuleCorrectlyWithOutOfOrderFrames 58: [ OK ] AnalysisDataCommonTest/0.CallsModuleCorrectlyWithOutOfOrderFrames (2 ms) 58: [ RUN ] AnalysisDataCommonTest/0.FullStorageWorks 58: [ OK ] AnalysisDataCommonTest/0.FullStorageWorks (1 ms) 58: [ RUN ] AnalysisDataCommonTest/0.CanAddModuleAfterStoredData 58: [ OK ] AnalysisDataCommonTest/0.CanAddModuleAfterStoredData (0 ms) 58: [ RUN ] AnalysisDataCommonTest/0.LimitedStorageWorks 58: [ OK ] AnalysisDataCommonTest/0.LimitedStorageWorks (0 ms) 58: [----------] 8 tests from AnalysisDataCommonTest/0 (15 ms total) 58: 58: [----------] 8 tests from AnalysisDataCommonTest/1, where TypeParam = gmx::test::(anonymous namespace)::DataSetsInputData 58: [ RUN ] AnalysisDataCommonTest/1.CallsModuleCorrectly 58: [ OK ] AnalysisDataCommonTest/1.CallsModuleCorrectly (2 ms) 58: [ RUN ] AnalysisDataCommonTest/1.CallsParallelModuleCorrectly 58: [ OK ] AnalysisDataCommonTest/1.CallsParallelModuleCorrectly (2 ms) 58: [ RUN ] AnalysisDataCommonTest/1.CallsMixedModulesCorrectly 58: [ OK ] AnalysisDataCommonTest/1.CallsMixedModulesCorrectly (2 ms) 58: [ RUN ] AnalysisDataCommonTest/1.CallsColumnModuleCorrectly 58: [ OK ] AnalysisDataCommonTest/1.CallsColumnModuleCorrectly (1 ms) 58: [ RUN ] AnalysisDataCommonTest/1.CallsModuleCorrectlyWithOutOfOrderFrames 58: [ OK ] AnalysisDataCommonTest/1.CallsModuleCorrectlyWithOutOfOrderFrames (3 ms) 58: [ RUN ] AnalysisDataCommonTest/1.FullStorageWorks 58: [ OK ] AnalysisDataCommonTest/1.FullStorageWorks (1 ms) 58: [ RUN ] AnalysisDataCommonTest/1.CanAddModuleAfterStoredData 58: [ OK ] AnalysisDataCommonTest/1.CanAddModuleAfterStoredData (1 ms) 58: [ RUN ] AnalysisDataCommonTest/1.LimitedStorageWorks 58: [ OK ] AnalysisDataCommonTest/1.LimitedStorageWorks (1 ms) 58: [----------] 8 tests from AnalysisDataCommonTest/1 (16 ms total) 58: 58: [----------] 8 tests from AnalysisDataCommonTest/2, where TypeParam = gmx::test::(anonymous namespace)::MultipointInputData 58: [ RUN ] AnalysisDataCommonTest/2.CallsModuleCorrectly 58: [ OK ] AnalysisDataCommonTest/2.CallsModuleCorrectly (2 ms) 58: [ RUN ] AnalysisDataCommonTest/2.CallsParallelModuleCorrectly 58: [ OK ] AnalysisDataCommonTest/2.CallsParallelModuleCorrectly (2 ms) 58: [ RUN ] AnalysisDataCommonTest/2.CallsMixedModulesCorrectly 58: [ OK ] AnalysisDataCommonTest/2.CallsMixedModulesCorrectly (2 ms) 58: [ RUN ] AnalysisDataCommonTest/2.CallsColumnModuleCorrectly 58: [ OK ] AnalysisDataCommonTest/2.CallsColumnModuleCorrectly (2 ms) 58: [ RUN ] AnalysisDataCommonTest/2.CallsModuleCorrectlyWithOutOfOrderFrames 58: [ OK ] AnalysisDataCommonTest/2.CallsModuleCorrectlyWithOutOfOrderFrames (3 ms) 58: [ RUN ] AnalysisDataCommonTest/2.FullStorageWorks 58: [ OK ] AnalysisDataCommonTest/2.FullStorageWorks (1 ms) 58: [ RUN ] AnalysisDataCommonTest/2.CanAddModuleAfterStoredData 58: [ OK ] AnalysisDataCommonTest/2.CanAddModuleAfterStoredData (1 ms) 58: [ RUN ] AnalysisDataCommonTest/2.LimitedStorageWorks 58: [ OK ] AnalysisDataCommonTest/2.LimitedStorageWorks (1 ms) 58: [----------] 8 tests from AnalysisDataCommonTest/2 (19 ms total) 58: 58: [----------] 8 tests from AnalysisDataCommonTest/3, where TypeParam = gmx::test::(anonymous namespace)::MultipointDataSetsInputData 58: [ RUN ] AnalysisDataCommonTest/3.CallsModuleCorrectly 58: [ OK ] AnalysisDataCommonTest/3.CallsModuleCorrectly (2 ms) 58: [ RUN ] AnalysisDataCommonTest/3.CallsParallelModuleCorrectly 58: [ OK ] AnalysisDataCommonTest/3.CallsParallelModuleCorrectly (2 ms) 58: [ RUN ] AnalysisDataCommonTest/3.CallsMixedModulesCorrectly 58: [ OK ] AnalysisDataCommonTest/3.CallsMixedModulesCorrectly (2 ms) 58: [ RUN ] AnalysisDataCommonTest/3.CallsColumnModuleCorrectly 58: [ OK ] AnalysisDataCommonTest/3.CallsColumnModuleCorrectly (2 ms) 58: [ RUN ] AnalysisDataCommonTest/3.CallsModuleCorrectlyWithOutOfOrderFrames 58: [ OK ] AnalysisDataCommonTest/3.CallsModuleCorrectlyWithOutOfOrderFrames (3 ms) 58: [ RUN ] AnalysisDataCommonTest/3.FullStorageWorks 58: [ OK ] AnalysisDataCommonTest/3.FullStorageWorks (1 ms) 58: [ RUN ] AnalysisDataCommonTest/3.CanAddModuleAfterStoredData 58: [ OK ] AnalysisDataCommonTest/3.CanAddModuleAfterStoredData (1 ms) 58: [ RUN ] AnalysisDataCommonTest/3.LimitedStorageWorks 58: [ OK ] AnalysisDataCommonTest/3.LimitedStorageWorks (1 ms) 58: [----------] 8 tests from AnalysisDataCommonTest/3 (18 ms total) 58: 58: [----------] 4 tests from AnalysisArrayDataTest 58: [ RUN ] AnalysisArrayDataTest.CallsModuleCorrectly 58: [ OK ] AnalysisArrayDataTest.CallsModuleCorrectly (2 ms) 58: [ RUN ] AnalysisArrayDataTest.StorageWorks 58: [ OK ] AnalysisArrayDataTest.StorageWorks (1 ms) 58: [ RUN ] AnalysisArrayDataTest.CanSetXAxis 58: [ OK ] AnalysisArrayDataTest.CanSetXAxis (0 ms) 58: [ RUN ] AnalysisArrayDataTest.CanSetXAxisBeforeRowCount 58: [ OK ] AnalysisArrayDataTest.CanSetXAxisBeforeRowCount (0 ms) 58: [----------] 4 tests from AnalysisArrayDataTest (3 ms total) 58: 58: [----------] 6 tests from AverageModuleTest 58: [ RUN ] AverageModuleTest.BasicTest 58: [ OK ] AverageModuleTest.BasicTest (4 ms) 58: [ RUN ] AverageModuleTest.HandlesMultipointData 58: [ OK ] AverageModuleTest.HandlesMultipointData (3 ms) 58: [ RUN ] AverageModuleTest.HandlesMultipleDataSets 58: [ OK ] AverageModuleTest.HandlesMultipleDataSets (4 ms) 58: [ RUN ] AverageModuleTest.HandlesDataSetAveraging 58: [ OK ] AverageModuleTest.HandlesDataSetAveraging (4 ms) 58: [ RUN ] AverageModuleTest.CanCustomizeXAxis 58: [ OK ] AverageModuleTest.CanCustomizeXAxis (3 ms) 58: [ RUN ] AverageModuleTest.CanCustomizeNonUniformXAxis 58: [ OK ] AverageModuleTest.CanCustomizeNonUniformXAxis (3 ms) 58: [----------] 6 tests from AverageModuleTest (25 ms total) 58: 58: [----------] 2 tests from FrameAverageModuleTest 58: [ RUN ] FrameAverageModuleTest.BasicTest 58: [ OK ] FrameAverageModuleTest.BasicTest (4 ms) 58: [ RUN ] FrameAverageModuleTest.HandlesMultipleDataSets 58: [ OK ] FrameAverageModuleTest.HandlesMultipleDataSets (4 ms) 58: [----------] 2 tests from FrameAverageModuleTest (9 ms total) 58: 58: [----------] 7 tests from AnalysisHistogramSettingsTest 58: [ RUN ] AnalysisHistogramSettingsTest.InitializesFromBins 58: [ OK ] AnalysisHistogramSettingsTest.InitializesFromBins (0 ms) 58: [ RUN ] AnalysisHistogramSettingsTest.InitializesFromBinsWithIntegerBins 58: [ OK ] AnalysisHistogramSettingsTest.InitializesFromBinsWithIntegerBins (0 ms) 58: [ RUN ] AnalysisHistogramSettingsTest.InitializesFromRangeWithBinCount 58: [ OK ] AnalysisHistogramSettingsTest.InitializesFromRangeWithBinCount (0 ms) 58: [ RUN ] AnalysisHistogramSettingsTest.InitializesFromRangeWithBinWidth 58: [ OK ] AnalysisHistogramSettingsTest.InitializesFromRangeWithBinWidth (0 ms) 58: [ RUN ] AnalysisHistogramSettingsTest.InitializesFromRangeWithBinCountAndIntegerBins 58: [ OK ] AnalysisHistogramSettingsTest.InitializesFromRangeWithBinCountAndIntegerBins (0 ms) 58: [ RUN ] AnalysisHistogramSettingsTest.InitializesFromRangeWithBinWidthAndIntegerBins 58: [ OK ] AnalysisHistogramSettingsTest.InitializesFromRangeWithBinWidthAndIntegerBins (0 ms) 58: [ RUN ] AnalysisHistogramSettingsTest.InitializesFromRangeWithRoundedRange 58: [ OK ] AnalysisHistogramSettingsTest.InitializesFromRangeWithRoundedRange (0 ms) 58: [----------] 7 tests from AnalysisHistogramSettingsTest (0 ms total) 58: 58: [----------] 2 tests from SimpleHistogramModuleTest 58: [ RUN ] SimpleHistogramModuleTest.ComputesCorrectly 58: [ OK ] SimpleHistogramModuleTest.ComputesCorrectly (5 ms) 58: [ RUN ] SimpleHistogramModuleTest.ComputesCorrectlyWithAll 58: [ OK ] SimpleHistogramModuleTest.ComputesCorrectlyWithAll (5 ms) 58: [----------] 2 tests from SimpleHistogramModuleTest (11 ms total) 58: 58: [----------] 3 tests from WeightedHistogramModuleTest 58: [ RUN ] WeightedHistogramModuleTest.ComputesCorrectly 58: [ OK ] WeightedHistogramModuleTest.ComputesCorrectly (5 ms) 58: [ RUN ] WeightedHistogramModuleTest.ComputesCorrectlyWithAll 58: [ OK ] WeightedHistogramModuleTest.ComputesCorrectlyWithAll (5 ms) 58: [ RUN ] WeightedHistogramModuleTest.HandlesMultipleDataSets 58: [ OK ] WeightedHistogramModuleTest.HandlesMultipleDataSets (6 ms) 58: [----------] 3 tests from WeightedHistogramModuleTest (18 ms total) 58: 58: [----------] 3 tests from BinAverageModuleTest 58: [ RUN ] BinAverageModuleTest.ComputesCorrectly 58: [ OK ] BinAverageModuleTest.ComputesCorrectly (4 ms) 58: [ RUN ] BinAverageModuleTest.ComputesCorrectlyWithAll 58: [ OK ] BinAverageModuleTest.ComputesCorrectlyWithAll (4 ms) 58: [ RUN ] BinAverageModuleTest.HandlesMultipleDataSets 58: [ OK ] BinAverageModuleTest.HandlesMultipleDataSets (4 ms) 58: [----------] 3 tests from BinAverageModuleTest (15 ms total) 58: 58: [----------] 4 tests from AbstractAverageHistogramTest 58: [ RUN ] AbstractAverageHistogramTest.ClonesCorrectly 58: [ OK ] AbstractAverageHistogramTest.ClonesCorrectly (5 ms) 58: [ RUN ] AbstractAverageHistogramTest.ComputesCumulativeHistogram 58: [ OK ] AbstractAverageHistogramTest.ComputesCumulativeHistogram (5 ms) 58: [ RUN ] AbstractAverageHistogramTest.ResamplesAtDoubleBinWidth 58: [ OK ] AbstractAverageHistogramTest.ResamplesAtDoubleBinWidth (4 ms) 58: [ RUN ] AbstractAverageHistogramTest.ResamplesAtDoubleBinWidthWithIntegerBins 58: [ OK ] AbstractAverageHistogramTest.ResamplesAtDoubleBinWidthWithIntegerBins (4 ms) 58: [----------] 4 tests from AbstractAverageHistogramTest (21 ms total) 58: 58: [----------] 3 tests from LifetimeModuleTest 58: [ RUN ] LifetimeModuleTest.BasicTest 58: [ OK ] LifetimeModuleTest.BasicTest (3 ms) 58: [ RUN ] LifetimeModuleTest.CumulativeTest 58: [ OK ] LifetimeModuleTest.CumulativeTest (3 ms) 58: [ RUN ] LifetimeModuleTest.HandlesMultipleDataSets 58: [ OK ] LifetimeModuleTest.HandlesMultipleDataSets (3 ms) 58: [----------] 3 tests from LifetimeModuleTest (11 ms total) 58: 58: [----------] Global test environment tear-down 58: [==========] 69 tests from 14 test suites ran. (188 ms total) 58: [ PASSED ] 69 tests. 58/92 Test #58: AnalysisDataUnitTests ..................... Passed 0.27 sec test 59 Start 59: CoordinateIOTests 59: Test command: /build/reproducible-path/gromacs-2025.1/build/basic/bin/coordinateio-test "--gtest_output=xml:/build/reproducible-path/gromacs-2025.1/build/basic/Testing/Temporary/CoordinateIOTests.xml" 59: Working Directory: /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/coordinateio/tests 59: Test timeout computed to be: 30 59: [==========] Running 67 tests from 20 test suites. 59: [----------] Global test environment set-up. 59: [----------] 1 test from OutputSelectorDeathTest 59: [ RUN ] OutputSelectorDeathTest.RejectsBadSelection 59: 59: WARNING: Masses and atomic (Van der Waals) radii will be guessed 59: based on residue and atom names, since they could not be 59: definitively assigned from the information in your input 59: files. These guessed numbers might deviate from the mass 59: and radius of the atom type. Please check the output 59: files if necessary. Note, that this functionality may 59: be removed in a future GROMACS version. Please, consider 59: using another file format for your input. 59: 59: [ OK ] OutputSelectorDeathTest.RejectsBadSelection (18 ms) 59: [----------] 1 test from OutputSelectorDeathTest (18 ms total) 59: 59: [----------] 5 tests from TrajectoryFrameWriterTest 59: [ RUN ] TrajectoryFrameWriterTest.RejectsWrongFiletype 59: 59: WARNING: Masses and atomic (Van der Waals) radii will be guessed 59: based on residue and atom names, since they could not be 59: definitively assigned from the information in your input 59: files. These guessed numbers might deviate from the mass 59: and radius of the atom type. Please check the output 59: files if necessary. Note, that this functionality may 59: be removed in a future GROMACS version. Please, consider 59: using another file format for your input. 59: 59: [ OK ] TrajectoryFrameWriterTest.RejectsWrongFiletype (10 ms) 59: [ RUN ] TrajectoryFrameWriterTest.BuilderFailsWithPdbAndNoAtoms 59: 59: WARNING: Masses and atomic (Van der Waals) radii will be guessed 59: based on residue and atom names, since they could not be 59: definitively assigned from the information in your input 59: files. These guessed numbers might deviate from the mass 59: and radius of the atom type. Please check the output 59: files if necessary. Note, that this functionality may 59: be removed in a future GROMACS version. Please, consider 59: using another file format for your input. 59: 59: [ OK ] TrajectoryFrameWriterTest.BuilderFailsWithPdbAndNoAtoms (9 ms) 59: [ RUN ] TrajectoryFrameWriterTest.BuilderFailsWithGroAndNoAtoms 59: 59: WARNING: Masses and atomic (Van der Waals) radii will be guessed 59: based on residue and atom names, since they could not be 59: definitively assigned from the information in your input 59: files. These guessed numbers might deviate from the mass 59: and radius of the atom type. Please check the output 59: files if necessary. Note, that this functionality may 59: be removed in a future GROMACS version. Please, consider 59: using another file format for your input. 59: 59: [ OK ] TrajectoryFrameWriterTest.BuilderFailsWithGroAndNoAtoms (9 ms) 59: [ RUN ] TrajectoryFrameWriterTest.BuilderImplictlyAddsAtoms 59: 59: WARNING: Masses and atomic (Van der Waals) radii will be guessed 59: based on residue and atom names, since they could not be 59: definitively assigned from the information in your input 59: files. These guessed numbers might deviate from the mass 59: and radius of the atom type. Please check the output 59: files if necessary. Note, that this functionality may 59: be removed in a future GROMACS version. Please, consider 59: using another file format for your input. 59: 59: 59: WARNING: Masses and atomic (Van der Waals) radii will be guessed 59: based on residue and atom names, since they could not be 59: definitively assigned from the information in your input 59: files. These guessed numbers might deviate from the mass 59: and radius of the atom type. Please check the output 59: files if necessary. Note, that this functionality may 59: be removed in a future GROMACS version. Please, consider 59: using another file format for your input. 59: 59: [ OK ] TrajectoryFrameWriterTest.BuilderImplictlyAddsAtoms (18 ms) 59: [ RUN ] TrajectoryFrameWriterTest.TNGOutputWorks 59: [ OK ] TrajectoryFrameWriterTest.TNGOutputWorks (0 ms) 59: [----------] 5 tests from TrajectoryFrameWriterTest (48 ms total) 59: 59: [----------] 5 tests from OutputAdapterContainer 59: [ RUN ] OutputAdapterContainer.MakeEmpty 59: [ OK ] OutputAdapterContainer.MakeEmpty (0 ms) 59: [ RUN ] OutputAdapterContainer.AddAdapter 59: [ OK ] OutputAdapterContainer.AddAdapter (0 ms) 59: [ RUN ] OutputAdapterContainer.RejectBadAdapter 59: [ OK ] OutputAdapterContainer.RejectBadAdapter (0 ms) 59: [ RUN ] OutputAdapterContainer.RejectDuplicateAdapter 59: [ OK ] OutputAdapterContainer.RejectDuplicateAdapter (0 ms) 59: [ RUN ] OutputAdapterContainer.AcceptMultipleAdapters 59: [ OK ] OutputAdapterContainer.AcceptMultipleAdapters (0 ms) 59: [----------] 5 tests from OutputAdapterContainer (0 ms total) 59: 59: [----------] 3 tests from RegisterFrameConverterTest 59: [ RUN ] RegisterFrameConverterTest.NoConverterWorks 59: [ OK ] RegisterFrameConverterTest.NoConverterWorks (0 ms) 59: [ RUN ] RegisterFrameConverterTest.RegistrationWorks 59: [ OK ] RegisterFrameConverterTest.RegistrationWorks (0 ms) 59: [ RUN ] RegisterFrameConverterTest.NewConverterCanInvalidateGuarantees 59: [ OK ] RegisterFrameConverterTest.NewConverterCanInvalidateGuarantees (0 ms) 59: [----------] 3 tests from RegisterFrameConverterTest (0 ms total) 59: 59: [----------] 5 tests from FlagTest 59: [ RUN ] FlagTest.CanSetSimpleFlag 59: [ OK ] FlagTest.CanSetSimpleFlag (0 ms) 59: [ RUN ] FlagTest.CanAddNewBox 59: [ OK ] FlagTest.CanAddNewBox (0 ms) 59: [ RUN ] FlagTest.SetsImplicitPrecisionChange 59: [ OK ] FlagTest.SetsImplicitPrecisionChange (0 ms) 59: [ RUN ] FlagTest.SetsImplicitStartTimeChange 59: [ OK ] FlagTest.SetsImplicitStartTimeChange (0 ms) 59: [ RUN ] FlagTest.SetsImplicitTimeStepChange 59: [ OK ] FlagTest.SetsImplicitTimeStepChange (0 ms) 59: [----------] 5 tests from FlagTest (1 ms total) 59: 59: [----------] 5 tests from SetAtomsTest 59: [ RUN ] SetAtomsTest.RemovesExistingAtoms 59: 59: WARNING: Masses and atomic (Van der Waals) radii will be guessed 59: based on residue and atom names, since they could not be 59: definitively assigned from the information in your input 59: files. These guessed numbers might deviate from the mass 59: and radius of the atom type. Please check the output 59: files if necessary. Note, that this functionality may 59: be removed in a future GROMACS version. Please, consider 59: using another file format for your input. 59: 59: [ OK ] SetAtomsTest.RemovesExistingAtoms (9 ms) 59: [ RUN ] SetAtomsTest.AddsNewAtoms 59: 59: WARNING: Masses and atomic (Van der Waals) radii will be guessed 59: based on residue and atom names, since they could not be 59: definitively assigned from the information in your input 59: files. These guessed numbers might deviate from the mass 59: and radius of the atom type. Please check the output 59: files if necessary. Note, that this functionality may 59: be removed in a future GROMACS version. Please, consider 59: using another file format for your input. 59: 59: [ OK ] SetAtomsTest.AddsNewAtoms (9 ms) 59: [ RUN ] SetAtomsTest.ThrowsOnRequiredAtomsNotAvailable 59: 59: WARNING: Masses and atomic (Van der Waals) radii will be guessed 59: based on residue and atom names, since they could not be 59: definitively assigned from the information in your input 59: files. These guessed numbers might deviate from the mass 59: and radius of the atom type. Please check the output 59: files if necessary. Note, that this functionality may 59: be removed in a future GROMACS version. Please, consider 59: using another file format for your input. 59: 59: [ OK ] SetAtomsTest.ThrowsOnRequiredAtomsNotAvailable (9 ms) 59: [ RUN ] SetAtomsTest.WillUseOldAtomsWhenNoNewAvailable 59: 59: WARNING: Masses and atomic (Van der Waals) radii will be guessed 59: based on residue and atom names, since they could not be 59: definitively assigned from the information in your input 59: files. These guessed numbers might deviate from the mass 59: and radius of the atom type. Please check the output 59: files if necessary. Note, that this functionality may 59: be removed in a future GROMACS version. Please, consider 59: using another file format for your input. 59: 59: [ OK ] SetAtomsTest.WillUseOldAtomsWhenNoNewAvailable (9 ms) 59: [ RUN ] SetAtomsTest.ThrowsWhenUserAtomReplacementNotPossible 59: 59: WARNING: Masses and atomic (Van der Waals) radii will be guessed 59: based on residue and atom names, since they could not be 59: definitively assigned from the information in your input 59: files. These guessed numbers might deviate from the mass 59: and radius of the atom type. Please check the output 59: files if necessary. Note, that this functionality may 59: be removed in a future GROMACS version. Please, consider 59: using another file format for your input. 59: 59: [ OK ] SetAtomsTest.ThrowsWhenUserAtomReplacementNotPossible (9 ms) 59: [----------] 5 tests from SetAtomsTest (47 ms total) 59: 59: [----------] 2 tests from SetBothTimeTest 59: [ RUN ] SetBothTimeTest.StartTimeZeroWorks 59: [ OK ] SetBothTimeTest.StartTimeZeroWorks (0 ms) 59: [ RUN ] SetBothTimeTest.SetStartTimeNonZeroWorks 59: [ OK ] SetBothTimeTest.SetStartTimeNonZeroWorks (0 ms) 59: [----------] 2 tests from SetBothTimeTest (0 ms total) 59: 59: [----------] 2 tests from SetStartTimeTest 59: [ RUN ] SetStartTimeTest.WorksWithNonZeroStart 59: [ OK ] SetStartTimeTest.WorksWithNonZeroStart (0 ms) 59: [ RUN ] SetStartTimeTest.WorksWithZeroStart 59: [ OK ] SetStartTimeTest.WorksWithZeroStart (0 ms) 59: [----------] 2 tests from SetStartTimeTest (0 ms total) 59: 59: [----------] 1 test from SetTimeStepTest 59: [ RUN ] SetTimeStepTest.SetTimeStepWorks 59: [ OK ] SetTimeStepTest.SetTimeStepWorks (0 ms) 59: [----------] 1 test from SetTimeStepTest (0 ms total) 59: 59: [----------] 6 tests from CoordinateFileFileFormats/TrajectoryFrameWriterTest 59: [ RUN ] CoordinateFileFileFormats/TrajectoryFrameWriterTest.WorksWithFormats/0 59: 59: WARNING: Masses and atomic (Van der Waals) radii will be guessed 59: based on residue and atom names, since they could not be 59: definitively assigned from the information in your input 59: files. These guessed numbers might deviate from the mass 59: and radius of the atom type. Please check the output 59: files if necessary. Note, that this functionality may 59: be removed in a future GROMACS version. Please, consider 59: using another file format for your input. 59: 59: [ OK ] CoordinateFileFileFormats/TrajectoryFrameWriterTest.WorksWithFormats/0 (9 ms) 59: [ RUN ] CoordinateFileFileFormats/TrajectoryFrameWriterTest.WorksWithFormats/1 59: 59: WARNING: Masses and atomic (Van der Waals) radii will be guessed 59: based on residue and atom names, since they could not be 59: definitively assigned from the information in your input 59: files. These guessed numbers might deviate from the mass 59: and radius of the atom type. Please check the output 59: files if necessary. Note, that this functionality may 59: be removed in a future GROMACS version. Please, consider 59: using another file format for your input. 59: 59: [ OK ] CoordinateFileFileFormats/TrajectoryFrameWriterTest.WorksWithFormats/1 (9 ms) 59: [ RUN ] CoordinateFileFileFormats/TrajectoryFrameWriterTest.WorksWithFormats/2 59: 59: WARNING: Masses and atomic (Van der Waals) radii will be guessed 59: based on residue and atom names, since they could not be 59: definitively assigned from the information in your input 59: files. These guessed numbers might deviate from the mass 59: and radius of the atom type. Please check the output 59: files if necessary. Note, that this functionality may 59: be removed in a future GROMACS version. Please, consider 59: using another file format for your input. 59: 59: [ OK ] CoordinateFileFileFormats/TrajectoryFrameWriterTest.WorksWithFormats/2 (9 ms) 59: [ RUN ] CoordinateFileFileFormats/TrajectoryFrameWriterTest.WorksWithFormats/3 59: 59: WARNING: Masses and atomic (Van der Waals) radii will be guessed 59: based on residue and atom names, since they could not be 59: definitively assigned from the information in your input 59: files. These guessed numbers might deviate from the mass 59: and radius of the atom type. Please check the output 59: files if necessary. Note, that this functionality may 59: be removed in a future GROMACS version. Please, consider 59: using another file format for your input. 59: 59: [ OK ] CoordinateFileFileFormats/TrajectoryFrameWriterTest.WorksWithFormats/3 (9 ms) 59: [ RUN ] CoordinateFileFileFormats/TrajectoryFrameWriterTest.WorksWithFormats/4 59: 59: WARNING: Masses and atomic (Van der Waals) radii will be guessed 59: based on residue and atom names, since they could not be 59: definitively assigned from the information in your input 59: files. These guessed numbers might deviate from the mass 59: and radius of the atom type. Please check the output 59: files if necessary. Note, that this functionality may 59: be removed in a future GROMACS version. Please, consider 59: using another file format for your input. 59: 59: [ OK ] CoordinateFileFileFormats/TrajectoryFrameWriterTest.WorksWithFormats/4 (9 ms) 59: [ RUN ] CoordinateFileFileFormats/TrajectoryFrameWriterTest.WorksWithFormats/5 59: 59: WARNING: Masses and atomic (Van der Waals) radii will be guessed 59: based on residue and atom names, since they could not be 59: definitively assigned from the information in your input 59: files. These guessed numbers might deviate from the mass 59: and radius of the atom type. Please check the output 59: files if necessary. Note, that this functionality may 59: be removed in a future GROMACS version. Please, consider 59: using another file format for your input. 59: 59: [ OK ] CoordinateFileFileFormats/TrajectoryFrameWriterTest.WorksWithFormats/5 (9 ms) 59: [----------] 6 tests from CoordinateFileFileFormats/TrajectoryFrameWriterTest (56 ms total) 59: 59: [----------] 3 tests from ModuleSupported/SetAtomsSupportedFiles 59: [ RUN ] ModuleSupported/SetAtomsSupportedFiles.Works/0 59: 59: WARNING: Masses and atomic (Van der Waals) radii will be guessed 59: based on residue and atom names, since they could not be 59: definitively assigned from the information in your input 59: files. These guessed numbers might deviate from the mass 59: and radius of the atom type. Please check the output 59: files if necessary. Note, that this functionality may 59: be removed in a future GROMACS version. Please, consider 59: using another file format for your input. 59: 59: [ OK ] ModuleSupported/SetAtomsSupportedFiles.Works/0 (9 ms) 59: [ RUN ] ModuleSupported/SetAtomsSupportedFiles.Works/1 59: 59: WARNING: Masses and atomic (Van der Waals) radii will be guessed 59: based on residue and atom names, since they could not be 59: definitively assigned from the information in your input 59: files. These guessed numbers might deviate from the mass 59: and radius of the atom type. Please check the output 59: files if necessary. Note, that this functionality may 59: be removed in a future GROMACS version. Please, consider 59: using another file format for your input. 59: 59: [ OK ] ModuleSupported/SetAtomsSupportedFiles.Works/1 (9 ms) 59: [ RUN ] ModuleSupported/SetAtomsSupportedFiles.Works/2 59: 59: WARNING: Masses and atomic (Van der Waals) radii will be guessed 59: based on residue and atom names, since they could not be 59: definitively assigned from the information in your input 59: files. These guessed numbers might deviate from the mass 59: and radius of the atom type. Please check the output 59: files if necessary. Note, that this functionality may 59: be removed in a future GROMACS version. Please, consider 59: using another file format for your input. 59: 59: [ OK ] ModuleSupported/SetAtomsSupportedFiles.Works/2 (10 ms) 59: [----------] 3 tests from ModuleSupported/SetAtomsSupportedFiles (29 ms total) 59: 59: [----------] 3 tests from ModuleUnSupported/SetAtomsUnSupportedFiles 59: [ RUN ] ModuleUnSupported/SetAtomsUnSupportedFiles.Works/0 59: [ OK ] ModuleUnSupported/SetAtomsUnSupportedFiles.Works/0 (0 ms) 59: [ RUN ] ModuleUnSupported/SetAtomsUnSupportedFiles.Works/1 59: [ OK ] ModuleUnSupported/SetAtomsUnSupportedFiles.Works/1 (0 ms) 59: [ RUN ] ModuleUnSupported/SetAtomsUnSupportedFiles.Works/2 59: [ OK ] ModuleUnSupported/SetAtomsUnSupportedFiles.Works/2 (0 ms) 59: [----------] 3 tests from ModuleUnSupported/SetAtomsUnSupportedFiles (1 ms total) 59: 59: [----------] 4 tests from ModuleSupported/AnyOutputSupportedFiles 59: [ RUN ] ModuleSupported/AnyOutputSupportedFiles.Works/0 59: 59: WARNING: Masses and atomic (Van der Waals) radii will be guessed 59: based on residue and atom names, since they could not be 59: definitively assigned from the information in your input 59: files. These guessed numbers might deviate from the mass 59: and radius of the atom type. Please check the output 59: files if necessary. Note, that this functionality may 59: be removed in a future GROMACS version. Please, consider 59: using another file format for your input. 59: 59: 59: WARNING: Masses and atomic (Van der Waals) radii will be guessed 59: based on residue and atom names, since they could not be 59: definitively assigned from the information in your input 59: files. These guessed numbers might deviate from the mass 59: and radius of the atom type. Please check the output 59: files if necessary. Note, that this functionality may 59: be removed in a future GROMACS version. Please, consider 59: using another file format for your input. 59: 59: [ OK ] ModuleSupported/AnyOutputSupportedFiles.Works/0 (21 ms) 59: [ RUN ] ModuleSupported/AnyOutputSupportedFiles.Works/1 59: 59: WARNING: Masses and atomic (Van der Waals) radii will be guessed 59: based on residue and atom names, since they could not be 59: definitively assigned from the information in your input 59: files. These guessed numbers might deviate from the mass 59: and radius of the atom type. Please check the output 59: files if necessary. Note, that this functionality may 59: be removed in a future GROMACS version. Please, consider 59: using another file format for your input. 59: 59: 59: WARNING: Masses and atomic (Van der Waals) radii will be guessed 59: based on residue and atom names, since they could not be 59: definitively assigned from the information in your input 59: files. These guessed numbers might deviate from the mass 59: and radius of the atom type. Please check the output 59: files if necessary. Note, that this functionality may 59: be removed in a future GROMACS version. Please, consider 59: using another file format for your input. 59: 59: [ OK ] ModuleSupported/AnyOutputSupportedFiles.Works/1 (22 ms) 59: [ RUN ] ModuleSupported/AnyOutputSupportedFiles.Works/2 59: 59: WARNING: Masses and atomic (Van der Waals) radii will be guessed 59: based on residue and atom names, since they could not be 59: definitively assigned from the information in your input 59: files. These guessed numbers might deviate from the mass 59: and radius of the atom type. Please check the output 59: files if necessary. Note, that this functionality may 59: be removed in a future GROMACS version. Please, consider 59: using another file format for your input. 59: 59: 59: WARNING: Masses and atomic (Van der Waals) radii will be guessed 59: based on residue and atom names, since they could not be 59: definitively assigned from the information in your input 59: files. These guessed numbers might deviate from the mass 59: and radius of the atom type. Please check the output 59: files if necessary. Note, that this functionality may 59: be removed in a future GROMACS version. Please, consider 59: using another file format for your input. 59: 59: [ OK ] ModuleSupported/AnyOutputSupportedFiles.Works/2 (22 ms) 59: [ RUN ] ModuleSupported/AnyOutputSupportedFiles.Works/3 59: 59: WARNING: Masses and atomic (Van der Waals) radii will be guessed 59: based on residue and atom names, since they could not be 59: definitively assigned from the information in your input 59: files. These guessed numbers might deviate from the mass 59: and radius of the atom type. Please check the output 59: files if necessary. Note, that this functionality may 59: be removed in a future GROMACS version. Please, consider 59: using another file format for your input. 59: 59: 59: WARNING: Masses and atomic (Van der Waals) radii will be guessed 59: based on residue and atom names, since they could not be 59: definitively assigned from the information in your input 59: files. These guessed numbers might deviate from the mass 59: and radius of the atom type. Please check the output 59: files if necessary. Note, that this functionality may 59: be removed in a future GROMACS version. Please, consider 59: using another file format for your input. 59: 59: [ OK ] ModuleSupported/AnyOutputSupportedFiles.Works/3 (22 ms) 59: [----------] 4 tests from ModuleSupported/AnyOutputSupportedFiles (88 ms total) 59: 59: [----------] 3 tests from ModuleSupported/SetVelocitySupportedFiles 59: [ RUN ] ModuleSupported/SetVelocitySupportedFiles.Works/0 59: 59: WARNING: Masses and atomic (Van der Waals) radii will be guessed 59: based on residue and atom names, since they could not be 59: definitively assigned from the information in your input 59: files. These guessed numbers might deviate from the mass 59: and radius of the atom type. Please check the output 59: files if necessary. Note, that this functionality may 59: be removed in a future GROMACS version. Please, consider 59: using another file format for your input. 59: 59: [ OK ] ModuleSupported/SetVelocitySupportedFiles.Works/0 (9 ms) 59: [ RUN ] ModuleSupported/SetVelocitySupportedFiles.Works/1 59: 59: WARNING: Masses and atomic (Van der Waals) radii will be guessed 59: based on residue and atom names, since they could not be 59: definitively assigned from the information in your input 59: files. These guessed numbers might deviate from the mass 59: and radius of the atom type. Please check the output 59: files if necessary. Note, that this functionality may 59: be removed in a future GROMACS version. Please, consider 59: using another file format for your input. 59: 59: [ OK ] ModuleSupported/SetVelocitySupportedFiles.Works/1 (9 ms) 59: [ RUN ] ModuleSupported/SetVelocitySupportedFiles.Works/2 59: 59: WARNING: Masses and atomic (Van der Waals) radii will be guessed 59: based on residue and atom names, since they could not be 59: definitively assigned from the information in your input 59: files. These guessed numbers might deviate from the mass 59: and radius of the atom type. Please check the output 59: files if necessary. Note, that this functionality may 59: be removed in a future GROMACS version. Please, consider 59: using another file format for your input. 59: 59: [ OK ] ModuleSupported/SetVelocitySupportedFiles.Works/2 (10 ms) 59: [----------] 3 tests from ModuleSupported/SetVelocitySupportedFiles (30 ms total) 59: 59: [----------] 3 tests from ModuleUnSupported/SetVelocityUnSupportedFiles 59: [ RUN ] ModuleUnSupported/SetVelocityUnSupportedFiles.Works/0 59: [ OK ] ModuleUnSupported/SetVelocityUnSupportedFiles.Works/0 (0 ms) 59: [ RUN ] ModuleUnSupported/SetVelocityUnSupportedFiles.Works/1 59: [ OK ] ModuleUnSupported/SetVelocityUnSupportedFiles.Works/1 (0 ms) 59: [ RUN ] ModuleUnSupported/SetVelocityUnSupportedFiles.Works/2 59: [ OK ] ModuleUnSupported/SetVelocityUnSupportedFiles.Works/2 (0 ms) 59: [----------] 3 tests from ModuleUnSupported/SetVelocityUnSupportedFiles (1 ms total) 59: 59: [----------] 2 tests from ModuleSupported/SetForceSupportedFiles 59: [ RUN ] ModuleSupported/SetForceSupportedFiles.Works/0 59: 59: WARNING: Masses and atomic (Van der Waals) radii will be guessed 59: based on residue and atom names, since they could not be 59: definitively assigned from the information in your input 59: files. These guessed numbers might deviate from the mass 59: and radius of the atom type. Please check the output 59: files if necessary. Note, that this functionality may 59: be removed in a future GROMACS version. Please, consider 59: using another file format for your input. 59: 59: [ OK ] ModuleSupported/SetForceSupportedFiles.Works/0 (9 ms) 59: [ RUN ] ModuleSupported/SetForceSupportedFiles.Works/1 59: 59: WARNING: Masses and atomic (Van der Waals) radii will be guessed 59: based on residue and atom names, since they could not be 59: definitively assigned from the information in your input 59: files. These guessed numbers might deviate from the mass 59: and radius of the atom type. Please check the output 59: files if necessary. Note, that this functionality may 59: be removed in a future GROMACS version. Please, consider 59: using another file format for your input. 59: 59: [ OK ] ModuleSupported/SetForceSupportedFiles.Works/1 (9 ms) 59: [----------] 2 tests from ModuleSupported/SetForceSupportedFiles (19 ms total) 59: 59: [----------] 4 tests from ModuleUnSupported/SetForceUnSupportedFiles 59: [ RUN ] ModuleUnSupported/SetForceUnSupportedFiles.Works/0 59: [ OK ] ModuleUnSupported/SetForceUnSupportedFiles.Works/0 (0 ms) 59: [ RUN ] ModuleUnSupported/SetForceUnSupportedFiles.Works/1 59: [ OK ] ModuleUnSupported/SetForceUnSupportedFiles.Works/1 (0 ms) 59: [ RUN ] ModuleUnSupported/SetForceUnSupportedFiles.Works/2 59: [ OK ] ModuleUnSupported/SetForceUnSupportedFiles.Works/2 (0 ms) 59: [ RUN ] ModuleUnSupported/SetForceUnSupportedFiles.Works/3 59: [ OK ] ModuleUnSupported/SetForceUnSupportedFiles.Works/3 (0 ms) 59: [----------] 4 tests from ModuleUnSupported/SetForceUnSupportedFiles (1 ms total) 59: 59: [----------] 2 tests from ModuleSupported/SetPrecisionSupportedFiles 59: [ RUN ] ModuleSupported/SetPrecisionSupportedFiles.Works/0 59: 59: WARNING: Masses and atomic (Van der Waals) radii will be guessed 59: based on residue and atom names, since they could not be 59: definitively assigned from the information in your input 59: files. These guessed numbers might deviate from the mass 59: and radius of the atom type. Please check the output 59: files if necessary. Note, that this functionality may 59: be removed in a future GROMACS version. Please, consider 59: using another file format for your input. 59: 59: [ OK ] ModuleSupported/SetPrecisionSupportedFiles.Works/0 (9 ms) 59: [ RUN ] ModuleSupported/SetPrecisionSupportedFiles.Works/1 59: 59: WARNING: Masses and atomic (Van der Waals) radii will be guessed 59: based on residue and atom names, since they could not be 59: definitively assigned from the information in your input 59: files. These guessed numbers might deviate from the mass 59: and radius of the atom type. Please check the output 59: files if necessary. Note, that this functionality may 59: be removed in a future GROMACS version. Please, consider 59: using another file format for your input. 59: 59: [ OK ] ModuleSupported/SetPrecisionSupportedFiles.Works/1 (9 ms) 59: [----------] 2 tests from ModuleSupported/SetPrecisionSupportedFiles (19 ms total) 59: 59: [----------] 4 tests from ModuleUnSupported/SetPrecisionUnSupportedFiles 59: [ RUN ] ModuleUnSupported/SetPrecisionUnSupportedFiles.Works/0 59: [ OK ] ModuleUnSupported/SetPrecisionUnSupportedFiles.Works/0 (0 ms) 59: [ RUN ] ModuleUnSupported/SetPrecisionUnSupportedFiles.Works/1 59: [ OK ] ModuleUnSupported/SetPrecisionUnSupportedFiles.Works/1 (0 ms) 59: [ RUN ] ModuleUnSupported/SetPrecisionUnSupportedFiles.Works/2 59: [ OK ] ModuleUnSupported/SetPrecisionUnSupportedFiles.Works/2 (0 ms) 59: [ RUN ] ModuleUnSupported/SetPrecisionUnSupportedFiles.Works/3 59: [ OK ] ModuleUnSupported/SetPrecisionUnSupportedFiles.Works/3 (0 ms) 59: [----------] 4 tests from ModuleUnSupported/SetPrecisionUnSupportedFiles (1 ms total) 59: 59: [----------] 4 tests from ModuleSupported/NoOptionalOutput 59: [ RUN ] ModuleSupported/NoOptionalOutput.Works/0 59: 59: WARNING: Masses and atomic (Van der Waals) radii will be guessed 59: based on residue and atom names, since they could not be 59: definitively assigned from the information in your input 59: files. These guessed numbers might deviate from the mass 59: and radius of the atom type. Please check the output 59: files if necessary. Note, that this functionality may 59: be removed in a future GROMACS version. Please, consider 59: using another file format for your input. 59: 59: [ OK ] ModuleSupported/NoOptionalOutput.Works/0 (9 ms) 59: [ RUN ] ModuleSupported/NoOptionalOutput.Works/1 59: 59: WARNING: Masses and atomic (Van der Waals) radii will be guessed 59: based on residue and atom names, since they could not be 59: definitively assigned from the information in your input 59: files. These guessed numbers might deviate from the mass 59: and radius of the atom type. Please check the output 59: files if necessary. Note, that this functionality may 59: be removed in a future GROMACS version. Please, consider 59: using another file format for your input. 59: 59: [ OK ] ModuleSupported/NoOptionalOutput.Works/1 (9 ms) 59: [ RUN ] ModuleSupported/NoOptionalOutput.Works/2 59: 59: WARNING: Masses and atomic (Van der Waals) radii will be guessed 59: based on residue and atom names, since they could not be 59: definitively assigned from the information in your input 59: files. These guessed numbers might deviate from the mass 59: and radius of the atom type. Please check the output 59: files if necessary. Note, that this functionality may 59: be removed in a future GROMACS version. Please, consider 59: using another file format for your input. 59: 59: [ OK ] ModuleSupported/NoOptionalOutput.Works/2 (9 ms) 59: [ RUN ] ModuleSupported/NoOptionalOutput.Works/3 59: 59: WARNING: Masses and atomic (Van der Waals) radii will be guessed 59: based on residue and atom names, since they could not be 59: definitively assigned from the information in your input 59: files. These guessed numbers might deviate from the mass 59: and radius of the atom type. Please check the output 59: files if necessary. Note, that this functionality may 59: be removed in a future GROMACS version. Please, consider 59: using another file format for your input. 59: 59: [ OK ] ModuleSupported/NoOptionalOutput.Works/3 (9 ms) 59: [----------] 4 tests from ModuleSupported/NoOptionalOutput (39 ms total) 59: 59: [----------] Global test environment tear-down 59: [==========] 67 tests from 20 test suites ran. (409 ms total) 59: [ PASSED ] 67 tests. 59/92 Test #59: CoordinateIOTests ......................... Passed 0.50 sec test 60 Start 60: TrajectoryAnalysisUnitTests 60: Test command: /build/reproducible-path/gromacs-2025.1/build/basic/bin/trajectoryanalysis-test "--gtest_output=xml:/build/reproducible-path/gromacs-2025.1/build/basic/Testing/Temporary/TrajectoryAnalysisUnitTests.xml" 60: Working Directory: /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/trajectoryanalysis/tests 60: Test timeout computed to be: 1920 60: [==========] Running 393 tests from 21 test suites. 60: [----------] Global test environment set-up. 60: [----------] 11 tests from AngleModuleTest 60: [ RUN ] AngleModuleTest.ComputesSimpleAngles 60: Analyzed topology coordinates 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: [ OK ] AngleModuleTest.ComputesSimpleAngles (13 ms) 60: [ RUN ] AngleModuleTest.ComputesDihedrals 60: Analyzed topology coordinates 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: [ OK ] AngleModuleTest.ComputesDihedrals (11 ms) 60: [ RUN ] AngleModuleTest.ComputesVectorPairAngles 60: Analyzed topology coordinates 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: [ OK ] AngleModuleTest.ComputesVectorPairAngles (11 ms) 60: [ RUN ] AngleModuleTest.ComputesVectorPlanePairAngles 60: Analyzed topology coordinates 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: [ OK ] AngleModuleTest.ComputesVectorPlanePairAngles (11 ms) 60: [ RUN ] AngleModuleTest.ComputesPlaneZAxisAngles 60: Analyzed topology coordinates 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: [ OK ] AngleModuleTest.ComputesPlaneZAxisAngles (11 ms) 60: [ RUN ] AngleModuleTest.ComputesVectorSphereNormalZAxisAngles 60: Analyzed topology coordinates 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: [ OK ] AngleModuleTest.ComputesVectorSphereNormalZAxisAngles (11 ms) 60: [ RUN ] AngleModuleTest.ComputesVectorTimeZeroAngles 60: Reading frames from gro file 'Test system for different angles', 33 atoms. 60: Reading frame 0 time 0.000 Reading frame 1 time 0.000 Last frame 1 time 0.000 60: Analyzed 2 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: [ OK ] AngleModuleTest.ComputesVectorTimeZeroAngles (13 ms) 60: [ RUN ] AngleModuleTest.ComputesMultipleAngles 60: Analyzed topology coordinates 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: [ OK ] AngleModuleTest.ComputesMultipleAngles (13 ms) 60: [ RUN ] AngleModuleTest.HandlesDynamicSelections 60: Analyzed topology coordinates 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: [ OK ] AngleModuleTest.HandlesDynamicSelections (12 ms) 60: [ RUN ] AngleModuleTest.HandlesOneVsMultipleVectorAngles 60: Analyzed topology coordinates 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: [ OK ] AngleModuleTest.HandlesOneVsMultipleVectorAngles (12 ms) 60: [ RUN ] AngleModuleTest.HandlesOneVsMultipleVectorGroupsAngles 60: Analyzed topology coordinates 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: [ OK ] AngleModuleTest.HandlesOneVsMultipleVectorGroupsAngles (13 ms) 60: [----------] 11 tests from AngleModuleTest (139 ms total) 60: 60: [----------] 5 tests from ClustsizeTest 60: [ RUN ] ClustsizeTest.NoMolDefaultCutoff 60: Reading frames from pdb file Reading frame 0 time 0.000 Group 0 ( SOL) has 24 elements 60: There is one group in the index 60: '', 24 atoms 60: Reading frame 1 time 0.000 Last frame 1 time 0.000 60: Total number of atoms in clusters = 24 60: cmid: 2, cmax: 4, max_size: 6 60: 16% 33% 50% 66% 83%100%cmid: 6, cmax: 18, max_size: 6 60: 16% 33% 50% 66% 83%100%[ OK ] ClustsizeTest.NoMolDefaultCutoff (11 ms) 60: [ RUN ] ClustsizeTest.NoMolShortCutoff 60: Reading frames from pdb file Reading frame 0 time 0.000 Group 0 ( SOL) has 24 elements 60: There is one group in the index 60: '', 24 atoms 60: Reading frame 1 time 0.000 Last frame 1 time 0.000 60: Total number of atoms in clusters = 24 60: cmid: 1, cmax: 6, max_size: 6 60: 16% 33% 50% 66% 83%100%cmid: 6, cmax: 18, max_size: 6 60: 16% 33% 50% 66% 83%100%[ OK ] ClustsizeTest.NoMolShortCutoff (11 ms) 60: [ RUN ] ClustsizeTest.MolDefaultCutoff 60: Reading frames from pdb file Reading frame 0 time 0.000 Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/clustsize.tpr, VERSION 2016 (single precision) 60: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/clustsize.tpr, VERSION 2016 (single precision) 60: '', 24 atoms 60: Reading frame 1 time 0.000 Last frame 1 time 0.000 60: Total number of atoms in clusters = 8 60: cmid: 2, cmax: 4, max_size: 2 60: 50%100%cmid: 2, cmax: 6, max_size: 2 60: 50%100%[ OK ] ClustsizeTest.MolDefaultCutoff (15 ms) 60: [ RUN ] ClustsizeTest.MolShortCutoff 60: Reading frames from pdb file Reading frame 0 time 0.000 Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/clustsize.tpr, VERSION 2016 (single precision) 60: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/clustsize.tpr, VERSION 2016 (single precision) 60: '', 24 atoms 60: Reading frame 1 time 0.000 Last frame 1 time 0.000 60: Total number of atoms in clusters = 8 60: cmid: 1, cmax: 6, max_size: 2 60: 50%100%cmid: 2, cmax: 6, max_size: 2 60: 50%100%[ OK ] ClustsizeTest.MolShortCutoff (15 ms) 60: [ RUN ] ClustsizeTest.MolCSize 60: Reading frames from pdb file Reading frame 0 time 0.000 Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/clustsize.tpr, VERSION 2016 (single precision) 60: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/clustsize.tpr, VERSION 2016 (single precision) 60: '', 24 atoms 60: Reading frame 1 time 0.000 Last frame 1 time 0.000 60: Total number of atoms in clusters = 8 60: cmid: 2, cmax: 4, max_size: 2 60: 50%100%cmid: 2, cmax: 6, max_size: 2 60: 50%100%[ OK ] ClustsizeTest.MolCSize (15 ms) 60: [----------] 5 tests from ClustsizeTest (69 ms total) 60: 60: [----------] 4 tests from TrajectoryAnalysisCommandLineRunnerTest 60: [ RUN ] TrajectoryAnalysisCommandLineRunnerTest.WritesHelp 60: [ OK ] TrajectoryAnalysisCommandLineRunnerTest.WritesHelp (5 ms) 60: [ RUN ] TrajectoryAnalysisCommandLineRunnerTest.RunsWithSubsetTrajectory 60: Reading frames from gro file 'Test system', 8 atoms. 60: Reading frame 0 time 0.000 Reading frame 1 time 0.000 Last frame 1 time 0.000 60: Analyzed 2 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: [ OK ] TrajectoryAnalysisCommandLineRunnerTest.RunsWithSubsetTrajectory (10 ms) 60: [ RUN ] TrajectoryAnalysisCommandLineRunnerTest.DetectsIncorrectTrajectorySubset 60: Reading frames from gro file 'Test system', 8 atoms. 60: Reading frame 0 time 0.000 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: [ OK ] TrajectoryAnalysisCommandLineRunnerTest.DetectsIncorrectTrajectorySubset (10 ms) 60: [ RUN ] TrajectoryAnalysisCommandLineRunnerTest.FailsWithTrajectorySubsetWithoutTrajectory 60: [ OK ] TrajectoryAnalysisCommandLineRunnerTest.FailsWithTrajectorySubsetWithoutTrajectory (3 ms) 60: [----------] 4 tests from TrajectoryAnalysisCommandLineRunnerTest (29 ms total) 60: 60: [----------] 4 tests from ConvertTrjModuleTest 60: [ RUN ] ConvertTrjModuleTest.WritesNormalOutput 60: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/freevolume.tpr, VERSION 4.5.5 (single precision) 60: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/freevolume.tpr, VERSION 4.5.5 (single precision) 60: Reading frame 0 time 0.000 Last frame 0 time 0.000 60: Analyzed 1 frames, last time 0.000 60: [ OK ] ConvertTrjModuleTest.WritesNormalOutput (61 ms) 60: [ RUN ] ConvertTrjModuleTest.WritesAtomSubset 60: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/freevolume.tpr, VERSION 4.5.5 (single precision) 60: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/freevolume.tpr, VERSION 4.5.5 (single precision) 60: Reading frame 0 time 0.000 Last frame 0 time 0.000 60: Analyzed 1 frames, last time 0.000 60: [ OK ] ConvertTrjModuleTest.WritesAtomSubset (63 ms) 60: [ RUN ] ConvertTrjModuleTest.WorksWithAtomAdding 60: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/clustsize.tpr, VERSION 2016 (single precision) 60: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/clustsize.tpr, VERSION 2016 (single precision) 60: Reading frames from pdb file Reading frame 0 time 0.000 '', 24 atoms 60: Reading frame 1 time 0.000 Last frame 1 time 0.000 60: Analyzed 2 frames, last time 0.000 60: [ OK ] ConvertTrjModuleTest.WorksWithAtomAdding (11 ms) 60: [ RUN ] ConvertTrjModuleTest.WorksWithAtomsAndSelection 60: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/clustsize.tpr, VERSION 2016 (single precision) 60: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/clustsize.tpr, VERSION 2016 (single precision) 60: Reading frames from pdb file Reading frame 0 time 0.000 '', 24 atoms 60: Reading frame 1 time 0.000 Last frame 1 time 0.000 60: Analyzed 2 frames, last time 0.000 60: [ OK ] ConvertTrjModuleTest.WorksWithAtomsAndSelection (12 ms) 60: [----------] 4 tests from ConvertTrjModuleTest (149 ms total) 60: 60: [----------] 6 tests from DistanceModuleTest 60: [ RUN ] DistanceModuleTest.ComputesDistances 60: Analyzed topology coordinates 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: atomname S1 S2: 60: Number of samples: 5 60: Average distance: 1.43246 nm 60: Standard deviation: 0.96700 nm 60: [ OK ] DistanceModuleTest.ComputesDistances (14 ms) 60: [ RUN ] DistanceModuleTest.ComputesMultipleDistances 60: Analyzed topology coordinates 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: atomname S1 S2: 60: Number of samples: 5 60: Average distance: 1.43246 nm 60: Standard deviation: 0.96700 nm 60: resindex 1 to 4 and atomname CB merge resindex 2 to 5 and atomname CB: 60: Number of samples: 4 60: Average distance: 1.81066 nm 60: Standard deviation: 0.79289 nm 60: [ OK ] DistanceModuleTest.ComputesMultipleDistances (16 ms) 60: [ RUN ] DistanceModuleTest.HandlesDynamicSelections 60: Analyzed topology coordinates 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: atomname S1 S2 and res_cog x < 2.8: 60: Number of samples: 3 60: Average distance: 1.72076 nm 60: Standard deviation: 1.24839 nm 60: [ OK ] DistanceModuleTest.HandlesDynamicSelections (14 ms) 60: [ RUN ] DistanceModuleTest.HandlesSelectionFromGroup 60: Analyzed topology coordinates 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: Contacts: 60: Number of samples: 2 60: Average distance: 1.00000 nm 60: Standard deviation: 0.00000 nm 60: [ OK ] DistanceModuleTest.HandlesSelectionFromGroup (40 ms) 60: [ RUN ] DistanceModuleTest.HandlesSelectionFromGroupWithSuccessiveIndices 60: Analyzed topology coordinates 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: SuccessiveContacts: 60: Number of samples: 2 60: Average distance: 1.00000 nm 60: Standard deviation: 0.00000 nm 60: [ OK ] DistanceModuleTest.HandlesSelectionFromGroupWithSuccessiveIndices (41 ms) 60: [ RUN ] DistanceModuleTest.HandlesSelectionFromLargeGroup 60: Analyzed topology coordinates 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: ManyContacts: 60: Number of samples: 10 60: Average distance: 1.82913 nm 60: Standard deviation: 0.78478 nm 60: [ OK ] DistanceModuleTest.HandlesSelectionFromLargeGroup (43 ms) 60: [----------] 6 tests from DistanceModuleTest (184 ms total) 60: 60: [----------] 2 tests from ExtractClusterModuleTest 60: [ RUN ] ExtractClusterModuleTest.WorksWithAllAtoms 60: trr version: GMX_trn_file (single precision) 60: Reading frame 0 time 0.000 Reading frame 1 time 0.002 Reading frame 2 time 0.004 Reading frame 3 time 0.006 Reading frame 4 time 0.008 Reading frame 5 time 0.010 Reading frame 6 time 0.012 Reading frame 7 time 0.014 Reading frame 8 time 0.016 Reading frame 9 time 0.018 Reading frame 10 time 0.020 Reading frame 11 time 0.022 Reading frame 12 time 0.024 Reading frame 13 time 0.026 Reading frame 14 time 0.028 Reading frame 15 time 0.030 Reading frame 16 time 0.032 Reading frame 17 time 0.034 Reading frame 18 time 0.036 Reading frame 19 time 0.038 Reading frame 20 time 0.040 60: Analyzed 26 frames, last time 0.050 60: There are 8 clusters containing 26 structures, highest framenr is 25 60: [ OK ] ExtractClusterModuleTest.WorksWithAllAtoms (17 ms) 60: [ RUN ] ExtractClusterModuleTest.WorksWithAtomSubset 60: Reading frame 0 time 0.000 Reading frame 1 time 0.002 Reading frame 2 time 0.004 Reading frame 3 time 0.006 Reading frame 4 time 0.008 Reading frame 5 time 0.010 Reading frame 6 time 0.012 Reading frame 7 time 0.014 Reading frame 8 time 0.016 Reading frame 9 time 0.018 Reading frame 10 time 0.020 Reading frame 11 time 0.022 Reading frame 12 time 0.024 Reading frame 13 time 0.026 Reading frame 14 time 0.028 Reading frame 15 time 0.030 Reading frame 16 time 0.032 Reading frame 17 time 0.034 Reading frame 18 time 0.036 Reading frame 19 time 0.038 Reading frame 20 time 0.040 60: Analyzed 26 frames, last time 0.050 60: There are 8 clusters containing 26 structures, highest framenr is 25 60: [ OK ] ExtractClusterModuleTest.WorksWithAtomSubset (15 ms) 60: [----------] 2 tests from ExtractClusterModuleTest (33 ms total) 60: 60: [----------] 2 tests from FreeVolumeModuleTest 60: [ RUN ] FreeVolumeModuleTest.ComputesFreeVolume 60: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/freevolume.tpr, VERSION 4.5.5 (single precision) 60: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/freevolume.tpr, VERSION 4.5.5 (single precision) 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: NOTE: From version 5.0 trajectoryanalysis-test uses the Van der Waals radii 60: from the source below. This means the results may be different 60: compared to previous GROMACS versions. 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: A. Bondi 60: van der Waals Volumes and Radii 60: J. Phys. Chem. (1964) 60: DOI: 10.1021/j100785a001 60: -------- -------- --- Thank You --- -------- -------- 60: 60: Could not determine VDW radius for CO2-RM. Set to zero. 60: Could not determine VDW radius for CO2-RM. Set to zero. 60: Could not determine VDW radius for CO2-RM. Set to zero. 60: Could not determine VDW radius for CO2-RM. Set to zero. 60: Could not determine VDW radius for CO2-RM. Set to zero. 60: Could not determine VDW radius for CO2-RM. Set to zero. 60: Could not determine VDW radius for CO2-RM. Set to zero. 60: Could not determine VDW radius for CO2-RM. Set to zero. 60: Could not determine VDW radius for CO2-RM. Set to zero. 60: Could not determine VDW radius for 40 particles. These were set to zero. 60: Reading frame 0 time 0.000 Last frame 0 time 0.000 60: Analyzed 1 frames, last time 0.000 60: cutoff = 0.18 nm 60: probe_radius = 0 nm 60: seed = 13 60: ninsert = 1000 probes per nm^3 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: A. Bondi 60: van der Waals Volumes and Radii 60: J. Phys. Chem. (1964) 60: DOI: 10.1021/j100785a001 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: Tuanan C. Lourenco, Mariny F. C. Coelho, Teodorico C. Ramalho, David van der 60: Spoel, Luciano T. Costa 60: Insights on the Solubility of CO2 in 1-Ethyl-3-methylimidazolium 60: Bis(trifluoromethylsulfonyl)imide from the Microscopic Point of View 60: Environ. Sci. Technol. (2013) 60: DOI: 10.1021/es4020986 60: -------- -------- --- Thank You --- -------- -------- 60: 60: Free volume 38.02 +/- 0.00 % 60: Total volume 68.92 +/- 0.00 nm^3 60: Number of molecules 340 total mass 63491.38 Dalton 60: Average molar mass: 186.74 Dalton 60: Density rho: 1529.71 +/- 0.00 nm^3 60: Molecular volume Vm assuming homogeneity: 0.2027 +/- 0.0000 nm^3 60: Molecular van der Waals volume assuming homogeneity: 0.1256 +/- 0.0000 nm^3 60: Fractional free volume 0.194 +/- 0.000 60: [ OK ] FreeVolumeModuleTest.ComputesFreeVolume (545 ms) 60: [ RUN ] FreeVolumeModuleTest.ComputesFreeVolumeSelection 60: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/freevolume.tpr, VERSION 4.5.5 (single precision) 60: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/freevolume.tpr, VERSION 4.5.5 (single precision) 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: NOTE: From version 5.0 trajectoryanalysis-test uses the Van der Waals radii 60: from the source below. This means the results may be different 60: compared to previous GROMACS versions. 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: A. Bondi 60: van der Waals Volumes and Radii 60: J. Phys. Chem. (1964) 60: DOI: 10.1021/j100785a001 60: -------- -------- --- Thank You --- -------- -------- 60: 60: Reading frame 0 time 0.000 Last frame 0 time 0.000 60: Analyzed 1 frames, last time 0.000 60: cutoff = 0.18 nm 60: probe_radius = 0 nm 60: seed = 17 60: ninsert = 1000 probes per nm^3 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: A. Bondi 60: van der Waals Volumes and Radii 60: J. Phys. Chem. (1964) 60: DOI: 10.1021/j100785a001 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: Tuanan C. Lourenco, Mariny F. C. Coelho, Teodorico C. Ramalho, David van der 60: Spoel, Luciano T. Costa 60: Insights on the Solubility of CO2 in 1-Ethyl-3-methylimidazolium 60: Bis(trifluoromethylsulfonyl)imide from the Microscopic Point of View 60: Environ. Sci. Technol. (2013) 60: DOI: 10.1021/es4020986 60: -------- -------- --- Thank You --- -------- -------- 60: 60: Free volume 38.48 +/- 0.00 % 60: Total volume 68.92 +/- 0.00 nm^3 60: Number of molecules 340 total mass 63491.38 Dalton 60: Average molar mass: 186.74 Dalton 60: Density rho: 1529.71 +/- 0.00 nm^3 60: Molecular volume Vm assuming homogeneity: 0.2027 +/- 0.0000 nm^3 60: Molecular van der Waals volume assuming homogeneity: 0.1247 +/- 0.0000 nm^3 60: Fractional free volume 0.200 +/- 0.000 60: [ OK ] FreeVolumeModuleTest.ComputesFreeVolumeSelection (567 ms) 60: [----------] 2 tests from FreeVolumeModuleTest (1112 ms total) 60: 60: [----------] 13 tests from MsdModuleTest 60: [ RUN ] MsdModuleTest.threeDimensionalDiffusion 60: Reading frame 0 time 0.000 Reading frame 1 time 1.000 Reading frame 2 time 2.000 Reading frame 3 time 3.000 Reading frame 4 time 4.000 Reading frame 5 time 5.000 Reading frame 6 time 6.000 Reading frame 7 time 7.000 Reading frame 8 time 8.000 Reading frame 9 time 9.000 Last frame 9 time 9.000 60: Analyzed 10 frames, last time 9.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: [ OK ] MsdModuleTest.threeDimensionalDiffusion (16 ms) 60: [ RUN ] MsdModuleTest.twoDimensionalDiffusion 60: Reading frame 0 time 0.000 Reading frame 1 time 1.000 Reading frame 2 time 2.000 Reading frame 3 time 3.000 Reading frame 4 time 4.000 Reading frame 5 time 5.000 Reading frame 6 time 6.000 Reading frame 7 time 7.000 Reading frame 8 time 8.000 Reading frame 9 time 9.000 Last frame 9 time 9.000 60: Analyzed 10 frames, last time 9.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: [ OK ] MsdModuleTest.twoDimensionalDiffusion (14 ms) 60: [ RUN ] MsdModuleTest.oneDimensionalDiffusion 60: Reading frame 0 time 0.000 Reading frame 1 time 1.000 Reading frame 2 time 2.000 Reading frame 3 time 3.000 Reading frame 4 time 4.000 Reading frame 5 time 5.000 Reading frame 6 time 6.000 Reading frame 7 time 7.000 Reading frame 8 time 8.000 Reading frame 9 time 9.000 Last frame 9 time 9.000 60: Analyzed 10 frames, last time 9.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: [ OK ] MsdModuleTest.oneDimensionalDiffusion (14 ms) 60: [ RUN ] MsdModuleTest.oneDimensionalDiffusionWithMaxTau 60: Reading frame 0 time 0.000 Reading frame 1 time 1.000 Reading frame 2 time 2.000 Reading frame 3 time 3.000 Reading frame 4 time 4.000 Reading frame 5 time 5.000 Reading frame 6 time 6.000 Reading frame 7 time 7.000 Reading frame 8 time 8.000 Reading frame 9 time 9.000 Last frame 9 time 9.000 60: Analyzed 10 frames, last time 9.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: [ OK ] MsdModuleTest.oneDimensionalDiffusionWithMaxTau (13 ms) 60: [ RUN ] MsdModuleTest.multipleGroupsWork 60: 60: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_multipleGroupsWork.mdp]: 60: For a correct single-point energy evaluation with nsteps = 0, use 60: continuation = yes to avoid constraining the input coordinates. 60: 60: Generating 1-4 interactions: fudge = 0.5 60: 60: NOTE 2 [file alanine_vsite_solvated.top, line 28]: 60: For energy conservation with LINCS, lincs_iter should be 2 or larger. 60: 60: 60: Number of degrees of freedom in T-Coupling group rest is 1818.00 60: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 60: 60: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_multipleGroupsWork.mdp]: 60: NVE simulation: will use the initial temperature of 288.764 K for 60: determining the Verlet buffer size 60: 60: 60: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_multipleGroupsWork.mdp]: 60: There are 9 non-linear virtual site constructions. Their contribution to 60: the energy error is approximated. In most cases this does not affect the 60: error significantly. 60: 60: 60: NOTE 5 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_multipleGroupsWork.mdp]: 60: You are using a plain Coulomb cut-off, which might produce artifacts. 60: You might want to consider using PME electrostatics. 60: 60: 60: 60: There were 5 NOTEs 60: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_multipleGroupsWork.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 60: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_multipleGroupsWork.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 60: Reading frame 0 time 0.000 Reading frame 1 time 2.000 60: WARNING: -dt and -trestart are equal. Statistics for each tau data point will not be independent. 60: Reading frame 2 time 4.000 Reading frame 3 time 6.000 Reading frame 4 time 8.000 Reading frame 5 time 10.000 Reading frame 6 time 12.000 Reading frame 7 time 14.000 Reading frame 8 time 16.000 Reading frame 9 time 18.000 Reading frame 10 time 20.000 Reading frame 11 time 22.000 Reading frame 12 time 24.000 Reading frame 13 time 26.000 Reading frame 14 time 28.000 Reading frame 15 time 30.000 Reading frame 16 time 32.000 Reading frame 17 time 34.000 Reading frame 18 time 36.000 Reading frame 19 time 38.000 Reading frame 20 time 40.000 Last frame 20 time 40.000 60: Analyzed 21 frames, last time 40.000 60: Setting the LD random seed to -1413726227 60: 60: Generated 2145 of the 2145 non-bonded parameter combinations 60: 60: Generated 2145 of the 2145 1-4 parameter combinations 60: 60: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' 60: 60: Excluding 2 bonded neighbours molecule type 'SOL' 60: 60: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/alanine_vsite_solvated.gro' 60: 60: Cleaning up constraints and constant bonded interactions with virtual sites 60: 60: Converted 15 Bonds with virtual sites to connections, 7 left 60: 60: Removed 18 Angles with virtual sites, 21 left 60: 60: Removed 10 Proper Dih.s with virtual sites, 44 left 60: 60: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 288.764 K 60: 60: Calculated rlist for 1x1 atom pair-list as 0.910 nm, buffer size 0.060 nm 60: 60: Set rlist, assuming 4x4 atom pair-list, to 0.898 nm, buffer size 0.048 nm 60: 60: Note that mdrun will redetermine rlist based on the actual pair-list setup 60: 60: This run will generate roughly 0 Mb of data 60: [ OK ] MsdModuleTest.multipleGroupsWork (182 ms) 60: [ RUN ] MsdModuleTest.subPicosecondTrajectoryWorks 60: 60: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_subPicosecondTrajectoryWorks.mdp]: 60: For a correct single-point energy evaluation with nsteps = 0, use 60: continuation = yes to avoid constraining the input coordinates. 60: 60: Generating 1-4 interactions: fudge = 0.5 60: 60: NOTE 2 [file alanine_vsite_solvated.top, line 28]: 60: For energy conservation with LINCS, lincs_iter should be 2 or larger. 60: 60: 60: Number of degrees of freedom in T-Coupling group rest is 1818.00 60: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 60: 60: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_subPicosecondTrajectoryWorks.mdp]: 60: NVE simulation: will use the initial temperature of 288.764 K for 60: determining the Verlet buffer size 60: 60: 60: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_subPicosecondTrajectoryWorks.mdp]: 60: There are 9 non-linear virtual site constructions. Their contribution to 60: the energy error is approximated. In most cases this does not affect the 60: error significantly. 60: 60: 60: NOTE 5 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_subPicosecondTrajectoryWorks.mdp]: 60: You are using a plain Coulomb cut-off, which might produce artifacts. 60: You might want to consider using PME electrostatics. 60: 60: 60: 60: There were 5 NOTEs 60: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_subPicosecondTrajectoryWorks.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 60: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_subPicosecondTrajectoryWorks.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 60: Reading frame 0 time 0.000 Reading frame 1 time 0.100 60: WARNING: -dt and -trestart are equal. Statistics for each tau data point will not be independent. 60: Reading frame 2 time 0.200 Reading frame 3 time 0.300 Reading frame 4 time 0.400 Reading frame 5 time 0.500 Reading frame 6 time 0.600 Reading frame 7 time 0.700 Reading frame 8 time 0.800 Reading frame 9 time 0.900 Reading frame 10 time 1.000 Reading frame 11 time 1.100 Reading frame 12 time 1.200 Reading frame 13 time 1.300 Reading frame 14 time 1.400 Reading frame 15 time 1.500 Reading frame 16 time 1.600 Reading frame 17 time 1.700 Reading frame 18 time 1.800 Reading frame 19 time 1.900 Reading frame 20 time 2.000 Last frame 20 time 2.000 60: Analyzed 21 frames, last time 2.000 60: Setting the LD random seed to -611327629 60: 60: Generated 2145 of the 2145 non-bonded parameter combinations 60: 60: Generated 2145 of the 2145 1-4 parameter combinations 60: 60: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' 60: 60: Excluding 2 bonded neighbours molecule type 'SOL' 60: 60: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/alanine_vsite_solvated.gro' 60: 60: Cleaning up constraints and constant bonded interactions with virtual sites 60: 60: Converted 15 Bonds with virtual sites to connections, 7 left 60: 60: Removed 18 Angles with virtual sites, 21 left 60: 60: Removed 10 Proper Dih.s with virtual sites, 44 left 60: 60: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 288.764 K 60: 60: Calculated rlist for 1x1 atom pair-list as 0.910 nm, buffer size 0.060 nm 60: 60: Set rlist, assuming 4x4 atom pair-list, to 0.898 nm, buffer size 0.048 nm 60: 60: Note that mdrun will redetermine rlist based on the actual pair-list setup 60: 60: This run will generate roughly 0 Mb of data 60: [ OK ] MsdModuleTest.subPicosecondTrajectoryWorks (179 ms) 60: [ RUN ] MsdModuleTest.trestartLessThanDt 60: 60: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_trestartLessThanDt.mdp]: 60: For a correct single-point energy evaluation with nsteps = 0, use 60: continuation = yes to avoid constraining the input coordinates. 60: 60: Generating 1-4 interactions: fudge = 0.5 60: 60: NOTE 2 [file alanine_vsite_solvated.top, line 28]: 60: For energy conservation with LINCS, lincs_iter should be 2 or larger. 60: 60: 60: Number of degrees of freedom in T-Coupling group rest is 1818.00 60: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 60: 60: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_trestartLessThanDt.mdp]: 60: NVE simulation: will use the initial temperature of 288.764 K for 60: determining the Verlet buffer size 60: 60: 60: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_trestartLessThanDt.mdp]: 60: There are 9 non-linear virtual site constructions. Their contribution to 60: the energy error is approximated. In most cases this does not affect the 60: error significantly. 60: 60: 60: NOTE 5 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_trestartLessThanDt.mdp]: 60: You are using a plain Coulomb cut-off, which might produce artifacts. 60: You might want to consider using PME electrostatics. 60: 60: 60: 60: There were 5 NOTEs 60: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_trestartLessThanDt.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 60: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_trestartLessThanDt.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 60: Reading frame 0 time 0.000 Reading frame 1 time 2.000 Setting the LD random seed to -825365716 60: 60: Generated 2145 of the 2145 non-bonded parameter combinations 60: 60: Generated 2145 of the 2145 1-4 parameter combinations 60: 60: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' 60: 60: Excluding 2 bonded neighbours molecule type 'SOL' 60: 60: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/alanine_vsite_solvated.gro' 60: 60: Cleaning up constraints and constant bonded interactions with virtual sites 60: 60: Converted 15 Bonds with virtual sites to connections, 7 left 60: 60: Removed 18 Angles with virtual sites, 21 left 60: 60: Removed 10 Proper Dih.s with virtual sites, 44 left 60: 60: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 288.764 K 60: 60: Calculated rlist for 1x1 atom pair-list as 0.910 nm, buffer size 0.060 nm 60: 60: Set rlist, assuming 4x4 atom pair-list, to 0.898 nm, buffer size 0.048 nm 60: 60: Note that mdrun will redetermine rlist based on the actual pair-list setup 60: 60: This run will generate roughly 0 Mb of data 60: [ OK ] MsdModuleTest.trestartLessThanDt (143 ms) 60: [ RUN ] MsdModuleTest.trestartGreaterThanDt 60: 60: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_trestartGreaterThanDt.mdp]: 60: For a correct single-point energy evaluation with nsteps = 0, use 60: continuation = yes to avoid constraining the input coordinates. 60: 60: Generating 1-4 interactions: fudge = 0.5 60: 60: NOTE 2 [file alanine_vsite_solvated.top, line 28]: 60: For energy conservation with LINCS, lincs_iter should be 2 or larger. 60: 60: 60: Number of degrees of freedom in T-Coupling group rest is 1818.00 60: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 60: 60: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_trestartGreaterThanDt.mdp]: 60: NVE simulation: will use the initial temperature of 288.764 K for 60: determining the Verlet buffer size 60: 60: 60: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_trestartGreaterThanDt.mdp]: 60: There are 9 non-linear virtual site constructions. Their contribution to 60: the energy error is approximated. In most cases this does not affect the 60: error significantly. 60: 60: 60: NOTE 5 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_trestartGreaterThanDt.mdp]: 60: You are using a plain Coulomb cut-off, which might produce artifacts. 60: You might want to consider using PME electrostatics. 60: 60: 60: 60: There were 5 NOTEs 60: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_trestartGreaterThanDt.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 60: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_trestartGreaterThanDt.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 60: Reading frame 0 time 0.000 Reading frame 1 time 2.000 Reading frame 2 time 4.000 Reading frame 3 time 6.000 Reading frame 4 time 8.000 Reading frame 5 time 10.000 Reading frame 6 time 12.000 Reading frame 7 time 14.000 Reading frame 8 time 16.000 Reading frame 9 time 18.000 Reading frame 10 time 20.000 Reading frame 11 time 22.000 Reading frame 12 time 24.000 Reading frame 13 time 26.000 Reading frame 14 time 28.000 Reading frame 15 time 30.000 Reading frame 16 time 32.000 Reading frame 17 time 34.000 Reading frame 18 time 36.000 Reading frame 19 time 38.000 Reading frame 20 time 40.000 Last frame 20 time 40.000 60: Analyzed 21 frames, last time 40.000 60: Setting the LD random seed to -304089211 60: 60: Generated 2145 of the 2145 non-bonded parameter combinations 60: 60: Generated 2145 of the 2145 1-4 parameter combinations 60: 60: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' 60: 60: Excluding 2 bonded neighbours molecule type 'SOL' 60: 60: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/alanine_vsite_solvated.gro' 60: 60: Cleaning up constraints and constant bonded interactions with virtual sites 60: 60: Converted 15 Bonds with virtual sites to connections, 7 left 60: 60: Removed 18 Angles with virtual sites, 21 left 60: 60: Removed 10 Proper Dih.s with virtual sites, 44 left 60: 60: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 288.764 K 60: 60: Calculated rlist for 1x1 atom pair-list as 0.910 nm, buffer size 0.060 nm 60: 60: Set rlist, assuming 4x4 atom pair-list, to 0.898 nm, buffer size 0.048 nm 60: 60: Note that mdrun will redetermine rlist based on the actual pair-list setup 60: 60: This run will generate roughly 0 Mb of data 60: [ OK ] MsdModuleTest.trestartGreaterThanDt (172 ms) 60: [ RUN ] MsdModuleTest.trestartGreaterThanDtAndNotAMultipleOfDt 60: 60: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_trestartGreaterThanDtAndNotAMultipleOfDt.mdp]: 60: For a correct single-point energy evaluation with nsteps = 0, use 60: continuation = yes to avoid constraining the input coordinates. 60: 60: Generating 1-4 interactions: fudge = 0.5 60: 60: NOTE 2 [file alanine_vsite_solvated.top, line 28]: 60: For energy conservation with LINCS, lincs_iter should be 2 or larger. 60: 60: 60: Number of degrees of freedom in T-Coupling group rest is 1818.00 60: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 60: 60: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_trestartGreaterThanDtAndNotAMultipleOfDt.mdp]: 60: NVE simulation: will use the initial temperature of 288.764 K for 60: determining the Verlet buffer size 60: 60: 60: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_trestartGreaterThanDtAndNotAMultipleOfDt.mdp]: 60: There are 9 non-linear virtual site constructions. Their contribution to 60: the energy error is approximated. In most cases this does not affect the 60: error significantly. 60: 60: 60: NOTE 5 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_trestartGreaterThanDtAndNotAMultipleOfDt.mdp]: 60: You are using a plain Coulomb cut-off, which might produce artifacts. 60: You might want to consider using PME electrostatics. 60: 60: 60: 60: There were 5 NOTEs 60: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_trestartGreaterThanDtAndNotAMultipleOfDt.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 60: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_trestartGreaterThanDtAndNotAMultipleOfDt.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 60: Reading frame 0 time 0.000 Reading frame 1 time 2.000 Setting the LD random seed to -9505285 60: 60: Generated 2145 of the 2145 non-bonded parameter combinations 60: 60: Generated 2145 of the 2145 1-4 parameter combinations 60: 60: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' 60: 60: Excluding 2 bonded neighbours molecule type 'SOL' 60: 60: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/alanine_vsite_solvated.gro' 60: 60: Cleaning up constraints and constant bonded interactions with virtual sites 60: 60: Converted 15 Bonds with virtual sites to connections, 7 left 60: 60: Removed 18 Angles with virtual sites, 21 left 60: 60: Removed 10 Proper Dih.s with virtual sites, 44 left 60: 60: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 288.764 K 60: 60: Calculated rlist for 1x1 atom pair-list as 0.910 nm, buffer size 0.060 nm 60: 60: Set rlist, assuming 4x4 atom pair-list, to 0.898 nm, buffer size 0.048 nm 60: 60: Note that mdrun will redetermine rlist based on the actual pair-list setup 60: 60: This run will generate roughly 0 Mb of data 60: [ OK ] MsdModuleTest.trestartGreaterThanDtAndNotAMultipleOfDt (136 ms) 60: [ RUN ] MsdModuleTest.molTest 60: 60: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_molTest.mdp]: 60: For a correct single-point energy evaluation with nsteps = 0, use 60: continuation = yes to avoid constraining the input coordinates. 60: 60: Generating 1-4 interactions: fudge = 0.5 60: 60: NOTE 2 [file alanine_vsite_solvated.top, line 28]: 60: For energy conservation with LINCS, lincs_iter should be 2 or larger. 60: 60: 60: Number of degrees of freedom in T-Coupling group rest is 1818.00 60: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 60: 60: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_molTest.mdp]: 60: NVE simulation: will use the initial temperature of 288.764 K for 60: determining the Verlet buffer size 60: 60: 60: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_molTest.mdp]: 60: There are 9 non-linear virtual site constructions. Their contribution to 60: the energy error is approximated. In most cases this does not affect the 60: error significantly. 60: 60: 60: NOTE 5 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_molTest.mdp]: 60: You are using a plain Coulomb cut-off, which might produce artifacts. 60: You might want to consider using PME electrostatics. 60: 60: 60: 60: There were 5 NOTEs 60: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_molTest.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 60: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_molTest.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 60: Reading frame 0 time 0.000 Reading frame 1 time 2.000 Reading frame 2 time 4.000 Reading frame 3 time 6.000 Reading frame 4 time 8.000 Reading frame 5 time 10.000 Reading frame 6 time 12.000 Reading frame 7 time 14.000 Reading frame 8 time 16.000 Reading frame 9 time 18.000 Reading frame 10 time 20.000 Reading frame 11 time 22.000 Reading frame 12 time 24.000 Reading frame 13 time 26.000 Reading frame 14 time 28.000 Reading frame 15 time 30.000 Reading frame 16 time 32.000 Reading frame 17 time 34.000 Reading frame 18 time 36.000 Reading frame 19 time 38.000 Reading frame 20 time 40.000 Last frame 20 time 40.000 60: Analyzed 21 frames, last time 40.000 60: Setting the LD random seed to -201458269 60: 60: Generated 2145 of the 2145 non-bonded parameter combinations 60: 60: Generated 2145 of the 2145 1-4 parameter combinations 60: 60: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' 60: 60: Excluding 2 bonded neighbours molecule type 'SOL' 60: 60: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/alanine_vsite_solvated.gro' 60: 60: Cleaning up constraints and constant bonded interactions with virtual sites 60: 60: Converted 15 Bonds with virtual sites to connections, 7 left 60: 60: Removed 18 Angles with virtual sites, 21 left 60: 60: Removed 10 Proper Dih.s with virtual sites, 44 left 60: 60: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 288.764 K 60: 60: Calculated rlist for 1x1 atom pair-list as 0.910 nm, buffer size 0.060 nm 60: 60: Set rlist, assuming 4x4 atom pair-list, to 0.898 nm, buffer size 0.048 nm 60: 60: Note that mdrun will redetermine rlist based on the actual pair-list setup 60: 60: This run will generate roughly 0 Mb of data 60: [ OK ] MsdModuleTest.molTest (160 ms) 60: [ RUN ] MsdModuleTest.beginFit 60: 60: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_beginFit.mdp]: 60: For a correct single-point energy evaluation with nsteps = 0, use 60: continuation = yes to avoid constraining the input coordinates. 60: 60: Generating 1-4 interactions: fudge = 0.5 60: 60: NOTE 2 [file alanine_vsite_solvated.top, line 28]: 60: For energy conservation with LINCS, lincs_iter should be 2 or larger. 60: 60: 60: Number of degrees of freedom in T-Coupling group rest is 1818.00 60: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 60: 60: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_beginFit.mdp]: 60: NVE simulation: will use the initial temperature of 288.764 K for 60: determining the Verlet buffer size 60: 60: 60: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_beginFit.mdp]: 60: There are 9 non-linear virtual site constructions. Their contribution to 60: the energy error is approximated. In most cases this does not affect the 60: error significantly. 60: 60: 60: NOTE 5 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_beginFit.mdp]: 60: You are using a plain Coulomb cut-off, which might produce artifacts. 60: You might want to consider using PME electrostatics. 60: 60: 60: 60: There were 5 NOTEs 60: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_beginFit.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 60: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_beginFit.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 60: Reading frame 0 time 0.000 Reading frame 1 time 2.000 60: WARNING: -dt and -trestart are equal. Statistics for each tau data point will not be independent. 60: Reading frame 2 time 4.000 Reading frame 3 time 6.000 Reading frame 4 time 8.000 Reading frame 5 time 10.000 Reading frame 6 time 12.000 Reading frame 7 time 14.000 Reading frame 8 time 16.000 Reading frame 9 time 18.000 Reading frame 10 time 20.000 Reading frame 11 time 22.000 Reading frame 12 time 24.000 Reading frame 13 time 26.000 Reading frame 14 time 28.000 Reading frame 15 time 30.000 Reading frame 16 time 32.000 Reading frame 17 time 34.000 Reading frame 18 time 36.000 Reading frame 19 time 38.000 Reading frame 20 time 40.000 Last frame 20 time 40.000 60: Analyzed 21 frames, last time 40.000 60: Setting the LD random seed to 2140696351 60: 60: Generated 2145 of the 2145 non-bonded parameter combinations 60: 60: Generated 2145 of the 2145 1-4 parameter combinations 60: 60: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' 60: 60: Excluding 2 bonded neighbours molecule type 'SOL' 60: 60: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/alanine_vsite_solvated.gro' 60: 60: Cleaning up constraints and constant bonded interactions with virtual sites 60: 60: Converted 15 Bonds with virtual sites to connections, 7 left 60: 60: Removed 18 Angles with virtual sites, 21 left 60: 60: Removed 10 Proper Dih.s with virtual sites, 44 left 60: 60: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 288.764 K 60: 60: Calculated rlist for 1x1 atom pair-list as 0.910 nm, buffer size 0.060 nm 60: 60: Set rlist, assuming 4x4 atom pair-list, to 0.898 nm, buffer size 0.048 nm 60: 60: Note that mdrun will redetermine rlist based on the actual pair-list setup 60: 60: This run will generate roughly 0 Mb of data 60: [ OK ] MsdModuleTest.beginFit (160 ms) 60: [ RUN ] MsdModuleTest.endFit 60: 60: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_endFit.mdp]: 60: For a correct single-point energy evaluation with nsteps = 0, use 60: continuation = yes to avoid constraining the input coordinates. 60: 60: Generating 1-4 interactions: fudge = 0.5 60: 60: NOTE 2 [file alanine_vsite_solvated.top, line 28]: 60: For energy conservation with LINCS, lincs_iter should be 2 or larger. 60: 60: 60: Number of degrees of freedom in T-Coupling group rest is 1818.00 60: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 60: 60: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_endFit.mdp]: 60: NVE simulation: will use the initial temperature of 288.764 K for 60: determining the Verlet buffer size 60: 60: 60: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_endFit.mdp]: 60: There are 9 non-linear virtual site constructions. Their contribution to 60: the energy error is approximated. In most cases this does not affect the 60: error significantly. 60: 60: 60: NOTE 5 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_endFit.mdp]: 60: You are using a plain Coulomb cut-off, which might produce artifacts. 60: You might want to consider using PME electrostatics. 60: 60: 60: 60: There were 5 NOTEs 60: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_endFit.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 60: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_endFit.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 60: Reading frame 0 time 0.000 Reading frame 1 time 2.000 60: WARNING: -dt and -trestart are equal. Statistics for each tau data point will not be independent. 60: Reading frame 2 time 4.000 Reading frame 3 time 6.000 Reading frame 4 time 8.000 Reading frame 5 time 10.000 Reading frame 6 time 12.000 Reading frame 7 time 14.000 Reading frame 8 time 16.000 Reading frame 9 time 18.000 Reading frame 10 time 20.000 Reading frame 11 time 22.000 Reading frame 12 time 24.000 Reading frame 13 time 26.000 Reading frame 14 time 28.000 Reading frame 15 time 30.000 Reading frame 16 time 32.000 Reading frame 17 time 34.000 Reading frame 18 time 36.000 Reading frame 19 time 38.000 Reading frame 20 time 40.000 Last frame 20 time 40.000 60: Analyzed 21 frames, last time 40.000 60: Setting the LD random seed to -8848798 60: 60: Generated 2145 of the 2145 non-bonded parameter combinations 60: 60: Generated 2145 of the 2145 1-4 parameter combinations 60: 60: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' 60: 60: Excluding 2 bonded neighbours molecule type 'SOL' 60: 60: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/alanine_vsite_solvated.gro' 60: 60: Cleaning up constraints and constant bonded interactions with virtual sites 60: 60: Converted 15 Bonds with virtual sites to connections, 7 left 60: 60: Removed 18 Angles with virtual sites, 21 left 60: 60: Removed 10 Proper Dih.s with virtual sites, 44 left 60: 60: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 288.764 K 60: 60: Calculated rlist for 1x1 atom pair-list as 0.910 nm, buffer size 0.060 nm 60: 60: Set rlist, assuming 4x4 atom pair-list, to 0.898 nm, buffer size 0.048 nm 60: 60: Note that mdrun will redetermine rlist based on the actual pair-list setup 60: 60: This run will generate roughly 0 Mb of data 60: [ OK ] MsdModuleTest.endFit (160 ms) 60: [ RUN ] MsdModuleTest.notEnoughPointsForFitErrorEstimate 60: 60: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_notEnoughPointsForFitErrorEstimate.mdp]: 60: For a correct single-point energy evaluation with nsteps = 0, use 60: continuation = yes to avoid constraining the input coordinates. 60: 60: Generating 1-4 interactions: fudge = 0.5 60: 60: NOTE 2 [file alanine_vsite_solvated.top, line 28]: 60: For energy conservation with LINCS, lincs_iter should be 2 or larger. 60: 60: 60: Number of degrees of freedom in T-Coupling group rest is 1818.00 60: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 60: 60: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_notEnoughPointsForFitErrorEstimate.mdp]: 60: NVE simulation: will use the initial temperature of 288.764 K for 60: determining the Verlet buffer size 60: 60: 60: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_notEnoughPointsForFitErrorEstimate.mdp]: 60: There are 9 non-linear virtual site constructions. Their contribution to 60: the energy error is approximated. In most cases this does not affect the 60: error significantly. 60: 60: 60: NOTE 5 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_notEnoughPointsForFitErrorEstimate.mdp]: 60: You are using a plain Coulomb cut-off, which might produce artifacts. 60: You might want to consider using PME electrostatics. 60: 60: 60: 60: There were 5 NOTEs 60: NOTE: You provided an index file 60: /build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/alanine_vsite_solvated.ndx 60: (with -n), but it was not used by any selection. 60: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_notEnoughPointsForFitErrorEstimate.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 60: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_notEnoughPointsForFitErrorEstimate.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 60: Reading frame 0 time 0.000 Reading frame 1 time 2.000 60: WARNING: -dt and -trestart are equal. Statistics for each tau data point will not be independent. 60: Reading frame 2 time 4.000 Reading frame 3 time 6.000 Reading frame 4 time 8.000 Reading frame 5 time 10.000 Reading frame 6 time 12.000 Reading frame 7 time 14.000 Reading frame 8 time 16.000 Reading frame 9 time 18.000 Reading frame 10 time 20.000 Reading frame 11 time 22.000 Reading frame 12 time 24.000 Reading frame 13 time 26.000 Reading frame 14 time 28.000 Reading frame 15 time 30.000 Reading frame 16 time 32.000 Reading frame 17 time 34.000 Reading frame 18 time 36.000 Reading frame 19 time 38.000 Reading frame 20 time 40.000 Last frame 20 time 40.000 60: Analyzed 21 frames, last time 40.000 60: Setting the LD random seed to -138568339 60: 60: Generated 2145 of the 2145 non-bonded parameter combinations 60: 60: Generated 2145 of the 2145 1-4 parameter combinations 60: 60: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' 60: 60: Excluding 2 bonded neighbours molecule type 'SOL' 60: 60: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/alanine_vsite_solvated.gro' 60: 60: Cleaning up constraints and constant bonded interactions with virtual sites 60: 60: Converted 15 Bonds with virtual sites to connections, 7 left 60: 60: Removed 18 Angles with virtual sites, 21 left 60: 60: Removed 10 Proper Dih.s with virtual sites, 44 left 60: 60: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 288.764 K 60: 60: Calculated rlist for 1x1 atom pair-list as 0.910 nm, buffer size 0.060 nm 60: 60: Set rlist, assuming 4x4 atom pair-list, to 0.898 nm, buffer size 0.048 nm 60: 60: Note that mdrun will redetermine rlist based on the actual pair-list setup 60: 60: This run will generate roughly 0 Mb of data 60: [ OK ] MsdModuleTest.notEnoughPointsForFitErrorEstimate (173 ms) 60: [----------] 13 tests from MsdModuleTest (1531 ms total) 60: 60: [----------] 9 tests from PairDistanceModuleTest 60: [ RUN ] PairDistanceModuleTest.ComputesAllDistances 60: Analyzed topology coordinates 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: [ OK ] PairDistanceModuleTest.ComputesAllDistances (12 ms) 60: [ RUN ] PairDistanceModuleTest.ComputesAllDistancesWithCutoff 60: Analyzed topology coordinates 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: [ OK ] PairDistanceModuleTest.ComputesAllDistancesWithCutoff (12 ms) 60: [ RUN ] PairDistanceModuleTest.ComputesMinDistanceWithCutoff 60: Analyzed topology coordinates 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: [ OK ] PairDistanceModuleTest.ComputesMinDistanceWithCutoff (12 ms) 60: [ RUN ] PairDistanceModuleTest.ComputesMaxDistance 60: Analyzed topology coordinates 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: [ OK ] PairDistanceModuleTest.ComputesMaxDistance (12 ms) 60: [ RUN ] PairDistanceModuleTest.ComputesMaxDistanceWithCutoff 60: Analyzed topology coordinates 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: [ OK ] PairDistanceModuleTest.ComputesMaxDistanceWithCutoff (13 ms) 60: [ RUN ] PairDistanceModuleTest.ComputesGroupedMinDistanceWithCutoff 60: Analyzed topology coordinates 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: [ OK ] PairDistanceModuleTest.ComputesGroupedMinDistanceWithCutoff (13 ms) 60: [ RUN ] PairDistanceModuleTest.ComputesGroupedMaxDistanceWithCutoff 60: Analyzed topology coordinates 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: [ OK ] PairDistanceModuleTest.ComputesGroupedMaxDistanceWithCutoff (12 ms) 60: [ RUN ] PairDistanceModuleTest.CoordinateSelectionIsNotOverwritten 60: Analyzed topology coordinates 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: [ OK ] PairDistanceModuleTest.CoordinateSelectionIsNotOverwritten (12 ms) 60: [ RUN ] PairDistanceModuleTest.CoordinateSelectionIsNotOverwrittenWithExplicitGroup 60: Analyzed topology coordinates 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: [ OK ] PairDistanceModuleTest.CoordinateSelectionIsNotOverwrittenWithExplicitGroup (12 ms) 60: [----------] 9 tests from PairDistanceModuleTest (115 ms total) 60: 60: [----------] 5 tests from RdfModuleTest 60: [ RUN ] RdfModuleTest.BasicTest 60: Analyzed topology coordinates 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: [ OK ] RdfModuleTest.BasicTest (167 ms) 60: [ RUN ] RdfModuleTest.SelectionsSolelyFromIndexFileWork 60: Reading frames from gro file '216H2O,WATJP01,SPC216,SPC-MODEL,300K,BOX(M)=1.86206NM,WFVG,MAR. 1984', 648 atoms. 60: Reading frame 0 time 0.000 Last frame 0 time 0.000 60: Analyzed 1 frames, last time 0.000 60: [ OK ] RdfModuleTest.SelectionsSolelyFromIndexFileWork (143 ms) 60: [ RUN ] RdfModuleTest.SelectionsFromBothTopologyFileAndIndexFileWork 60: Analyzed topology coordinates 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: [ OK ] RdfModuleTest.SelectionsFromBothTopologyFileAndIndexFileWork (167 ms) 60: [ RUN ] RdfModuleTest.CalculatesSurf 60: Analyzed topology coordinates 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: [ OK ] RdfModuleTest.CalculatesSurf (52 ms) 60: [ RUN ] RdfModuleTest.CalculatesXY 60: Analyzed topology coordinates 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: [ OK ] RdfModuleTest.CalculatesXY (209 ms) 60: [----------] 5 tests from RdfModuleTest (742 ms total) 60: 60: [----------] 5 tests from SasaModuleTest 60: [ RUN ] SasaModuleTest.BasicTest 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: Frank Eisenhaber, Philip Lijnzaad, Patrick Argos, Chris Sander, Michael Scharf 60: The Double Cube Lattice Method: Efficient Approaches to Numerical Integration 60: of Surface Area and Volume and to Dot Surface Contouring of Molecular 60: Assemblies 60: J. Comp. Chem. (1995) 60: DOI: 10.1002/jcc.540160303 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: NOTE: From version 5.0 trajectoryanalysis-test uses the Van der Waals radii 60: from the source below. This means the results may be different 60: compared to previous GROMACS versions. 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: A. Bondi 60: van der Waals Volumes and Radii 60: J. Phys. Chem. (1964) 60: DOI: 10.1021/j100785a001 60: -------- -------- --- Thank You --- -------- -------- 60: 60: Analyzed topology coordinates 60: [ OK ] SasaModuleTest.BasicTest (60 ms) 60: [ RUN ] SasaModuleTest.HandlesSelectedResidues 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: Frank Eisenhaber, Philip Lijnzaad, Patrick Argos, Chris Sander, Michael Scharf 60: The Double Cube Lattice Method: Efficient Approaches to Numerical Integration 60: of Surface Area and Volume and to Dot Surface Contouring of Molecular 60: Assemblies 60: J. Comp. Chem. (1995) 60: DOI: 10.1002/jcc.540160303 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: NOTE: From version 5.0 trajectoryanalysis-test uses the Van der Waals radii 60: from the source below. This means the results may be different 60: compared to previous GROMACS versions. 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: A. Bondi 60: van der Waals Volumes and Radii 60: J. Phys. Chem. (1964) 60: DOI: 10.1021/j100785a001 60: -------- -------- --- Thank You --- -------- -------- 60: 60: Analyzed topology coordinates 60: [ OK ] SasaModuleTest.HandlesSelectedResidues (31 ms) 60: [ RUN ] SasaModuleTest.WritesConnollySurfaceWithSolute 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: Frank Eisenhaber, Philip Lijnzaad, Patrick Argos, Chris Sander, Michael Scharf 60: The Double Cube Lattice Method: Efficient Approaches to Numerical Integration 60: of Surface Area and Volume and to Dot Surface Contouring of Molecular 60: Assemblies 60: J. Comp. Chem. (1995) 60: DOI: 10.1002/jcc.540160303 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: NOTE: From version 5.0 trajectoryanalysis-test uses the Van der Waals radii 60: from the source below. This means the results may be different 60: compared to previous GROMACS versions. 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: A. Bondi 60: van der Waals Volumes and Radii 60: J. Phys. Chem. (1964) 60: DOI: 10.1021/j100785a001 60: -------- -------- --- Thank You --- -------- -------- 60: 60: Analyzed topology coordinates 60: [ OK ] SasaModuleTest.WritesConnollySurfaceWithSolute (22 ms) 60: [ RUN ] SasaModuleTest.HandlesDynamicOutputGroup 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: Frank Eisenhaber, Philip Lijnzaad, Patrick Argos, Chris Sander, Michael Scharf 60: The Double Cube Lattice Method: Efficient Approaches to Numerical Integration 60: of Surface Area and Volume and to Dot Surface Contouring of Molecular 60: Assemblies 60: J. Comp. Chem. (1995) 60: DOI: 10.1002/jcc.540160303 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: NOTE: From version 5.0 trajectoryanalysis-test uses the Van der Waals radii 60: from the source below. This means the results may be different 60: compared to previous GROMACS versions. 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: A. Bondi 60: van der Waals Volumes and Radii 60: J. Phys. Chem. (1964) 60: DOI: 10.1021/j100785a001 60: -------- -------- --- Thank You --- -------- -------- 60: 60: Analyzed topology coordinates 60: [ OK ] SasaModuleTest.HandlesDynamicOutputGroup (39 ms) 60: [ RUN ] SasaModuleTest.HandlesDynamicCalculationGroup 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: Frank Eisenhaber, Philip Lijnzaad, Patrick Argos, Chris Sander, Michael Scharf 60: The Double Cube Lattice Method: Efficient Approaches to Numerical Integration 60: of Surface Area and Volume and to Dot Surface Contouring of Molecular 60: Assemblies 60: J. Comp. Chem. (1995) 60: DOI: 10.1002/jcc.540160303 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: NOTE: From version 5.0 trajectoryanalysis-test uses the Van der Waals radii 60: from the source below. This means the results may be different 60: compared to previous GROMACS versions. 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: A. Bondi 60: van der Waals Volumes and Radii 60: J. Phys. Chem. (1964) 60: DOI: 10.1021/j100785a001 60: -------- -------- --- Thank You --- -------- -------- 60: 60: Analyzed topology coordinates 60: [ OK ] SasaModuleTest.HandlesDynamicCalculationGroup (39 ms) 60: [----------] 5 tests from SasaModuleTest (205 ms total) 60: 60: [----------] 8 tests from SelectModuleTest 60: [ RUN ] SelectModuleTest.BasicTest 60: Reading frames from gro file 'Test system', 15 atoms. 60: Reading frame 0 time 0.000 Reading frame 1 time 0.000 Last frame 1 time 0.000 60: Analyzed 2 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: [ OK ] SelectModuleTest.BasicTest (24 ms) 60: [ RUN ] SelectModuleTest.HandlesPDBOutputWithNonPDBInput 60: Reading frames from gro file 'Test system', 15 atoms. 60: Reading frame 0 time 0.000 Reading frame 1 time 0.000 Last frame 1 time 0.000 60: Analyzed 2 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: [ OK ] SelectModuleTest.HandlesPDBOutputWithNonPDBInput (14 ms) 60: [ RUN ] SelectModuleTest.HandlesPDBOutputWithPDBInput 60: Reading frames from gro file 'Test system', 15 atoms. 60: Reading frame 0 time 0.000 Reading frame 1 time 0.000 Last frame 1 time 0.000 60: Analyzed 2 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: [ OK ] SelectModuleTest.HandlesPDBOutputWithPDBInput (15 ms) 60: [ RUN ] SelectModuleTest.HandlesMaxPDBOutput 60: Reading frames from gro file 'Test system', 15 atoms. 60: Reading frame 0 time 0.000 Reading frame 1 time 0.000 Last frame 1 time 0.000 60: Analyzed 2 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: [ OK ] SelectModuleTest.HandlesMaxPDBOutput (15 ms) 60: [ RUN ] SelectModuleTest.HandlesSelectedPDBOutput 60: Reading frames from gro file 'Test system', 15 atoms. 60: Reading frame 0 time 0.000 Reading frame 1 time 0.000 Last frame 1 time 0.000 60: Analyzed 2 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: [ OK ] SelectModuleTest.HandlesSelectedPDBOutput (15 ms) 60: [ RUN ] SelectModuleTest.NormalizesSizes 60: Analyzed topology coordinates 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: [ OK ] SelectModuleTest.NormalizesSizes (11 ms) 60: [ RUN ] SelectModuleTest.WritesResidueNumbers 60: Analyzed topology coordinates 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: [ OK ] SelectModuleTest.WritesResidueNumbers (11 ms) 60: [ RUN ] SelectModuleTest.WritesResidueIndices 60: Analyzed topology coordinates 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: [ OK ] SelectModuleTest.WritesResidueIndices (11 ms) 60: [----------] 8 tests from SelectModuleTest (122 ms total) 60: 60: [----------] 10 tests from SurfaceAreaTest 60: [ RUN ] SurfaceAreaTest.ComputesSinglePoint 60: [ OK ] SurfaceAreaTest.ComputesSinglePoint (0 ms) 60: [ RUN ] SurfaceAreaTest.ComputesTwoPoints 60: [ OK ] SurfaceAreaTest.ComputesTwoPoints (5 ms) 60: [ RUN ] SurfaceAreaTest.ComputesTwoPointsOfUnequalRadius 60: [ OK ] SurfaceAreaTest.ComputesTwoPointsOfUnequalRadius (5 ms) 60: [ RUN ] SurfaceAreaTest.SurfacePoints12 60: [ OK ] SurfaceAreaTest.SurfacePoints12 (1 ms) 60: [ RUN ] SurfaceAreaTest.SurfacePoints32 60: [ OK ] SurfaceAreaTest.SurfacePoints32 (1 ms) 60: [ RUN ] SurfaceAreaTest.SurfacePoints42 60: [ OK ] SurfaceAreaTest.SurfacePoints42 (2 ms) 60: [ RUN ] SurfaceAreaTest.SurfacePoints122 60: [ OK ] SurfaceAreaTest.SurfacePoints122 (5 ms) 60: [ RUN ] SurfaceAreaTest.Computes100Points 60: [ OK ] SurfaceAreaTest.Computes100Points (3 ms) 60: [ RUN ] SurfaceAreaTest.Computes100PointsWithRectangularPBC 60: [ OK ] SurfaceAreaTest.Computes100PointsWithRectangularPBC (14 ms) 60: [ RUN ] SurfaceAreaTest.Computes100PointsWithTriclinicPBC 60: [ OK ] SurfaceAreaTest.Computes100PointsWithTriclinicPBC (17 ms) 60: [----------] 10 tests from SurfaceAreaTest (61 ms total) 60: 60: [----------] 4 tests from TopologyInformation 60: [ RUN ] TopologyInformation.CantWorkWithoutReadingAFile 60: [ OK ] TopologyInformation.CantWorkWithoutReadingAFile (0 ms) 60: [ RUN ] TopologyInformation.WorksWithGroFile 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: [ OK ] TopologyInformation.WorksWithGroFile (9 ms) 60: [ RUN ] TopologyInformation.WorksWithPdbFile 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: [ OK ] TopologyInformation.WorksWithPdbFile (10 ms) 60: [ RUN ] TopologyInformation.WorksWithTprFromPdbFile 60: 60: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/TopologyInformation_WorksWithTprFromPdbFile_lysozyme.mdp]: 60: For a correct single-point energy evaluation with nsteps = 0, use 60: continuation = yes to avoid constraining the input coordinates. 60: 60: Generating 1-4 interactions: fudge = 0.5 60: 60: NOTE 2 [file lysozyme.top, line 1465]: 60: System has non-zero total charge: 2.000000 60: Total charge should normally be an integer. See 60: https://manual.gromacs.org/current/user-guide/floating-point.html 60: for discussion on how close it should be to an integer. 60: 60: 60: 60: Number of degrees of freedom in T-Coupling group rest is 465.00 60: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 60: 60: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/TopologyInformation_WorksWithTprFromPdbFile_lysozyme.mdp]: 60: NVE simulation with an initial temperature of zero: will use a Verlet 60: buffer of 10%. Check your energy drift! 60: 60: 60: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/TopologyInformation_WorksWithTprFromPdbFile_lysozyme.mdp]: 60: You are using a plain Coulomb cut-off, which might produce artifacts. 60: You might want to consider using PME electrostatics. 60: 60: 60: 60: There were 4 NOTEs 60: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/TopologyInformation_WorksWithTprFromPdbFile_lysozyme.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 60: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/TopologyInformation_WorksWithTprFromPdbFile_lysozyme.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 60: Setting the LD random seed to -35601 60: 60: Generated 330891 of the 330891 non-bonded parameter combinations 60: 60: Generated 330891 of the 330891 1-4 parameter combinations 60: 60: Excluding 3 bonded neighbours molecule type 'Protein_chain_B' 60: 60: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/lysozyme.pdb', all velocities are zero 60: Analysing residue names: 60: There are: 10 Protein residues 60: Analysing Protein... 60: 60: This run will generate roughly 0 Mb of data 60: [ OK ] TopologyInformation.WorksWithTprFromPdbFile (4697 ms) 60: [----------] 4 tests from TopologyInformation (4717 ms total) 60: 60: [----------] 4 tests from TrajectoryModuleTest 60: [ RUN ] TrajectoryModuleTest.BasicTest 60: Reading frames from gro file 'Test system', 15 atoms. 60: Reading frame 0 time 0.000 Reading frame 1 time 0.000 Last frame 1 time 0.000 60: Analyzed 2 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: [ OK ] TrajectoryModuleTest.BasicTest (14 ms) 60: [ RUN ] TrajectoryModuleTest.PlotsXOnly 60: Reading frames from gro file 'Test system', 15 atoms. 60: Reading frame 0 time 0.000 Reading frame 1 time 0.000 Last frame 1 time 0.000 60: Analyzed 2 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: [ OK ] TrajectoryModuleTest.PlotsXOnly (13 ms) 60: [ RUN ] TrajectoryModuleTest.HandlesNoVelocities 60: Reading frames from gro file 'Test system', 15 atoms. 60: Reading frame 0 time 0.000 Reading frame 1 time 0.000 Last frame 1 time 0.000 60: Analyzed 2 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: [ OK ] TrajectoryModuleTest.HandlesNoVelocities (11 ms) 60: [ RUN ] TrajectoryModuleTest.HandlesNoForces 60: Reading frames from gro file 'Test system', 15 atoms. 60: Reading frame 0 time 0.000 Reading frame 1 time 0.000 Last frame 1 time 0.000 60: Analyzed 2 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: [ OK ] TrajectoryModuleTest.HandlesNoForces (12 ms) 60: [----------] 4 tests from TrajectoryModuleTest (52 ms total) 60: 60: [----------] 5 tests from UnionFinderTest 60: [ RUN ] UnionFinderTest.WorksEmpty 60: [ OK ] UnionFinderTest.WorksEmpty (0 ms) 60: [ RUN ] UnionFinderTest.BasicMerges 60: [ OK ] UnionFinderTest.BasicMerges (0 ms) 60: [ RUN ] UnionFinderTest.LargerMerges 60: [ OK ] UnionFinderTest.LargerMerges (0 ms) 60: [ RUN ] UnionFinderTest.LongRightMerge 60: [ OK ] UnionFinderTest.LongRightMerge (0 ms) 60: [ RUN ] UnionFinderTest.LongLeftMerge 60: [ OK ] UnionFinderTest.LongLeftMerge (0 ms) 60: [----------] 5 tests from UnionFinderTest (0 ms total) 60: 60: [----------] 1 test from MappedUnionFinderTest 60: [ RUN ] MappedUnionFinderTest.BasicMerges 60: [ OK ] MappedUnionFinderTest.BasicMerges (0 ms) 60: [----------] 1 test from MappedUnionFinderTest (0 ms total) 60: 60: [----------] 192 tests from MoleculeTests/DsspModuleTest 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/0 60: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 60: Last frame 0 time 0.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/0 (161 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/1 60: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 60: Last frame 0 time 0.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/1 (162 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/2 60: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 60: Last frame 0 time 0.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/2 (162 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/3 60: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 60: Last frame 0 time 0.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/3 (167 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/4 60: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 60: Last frame 0 time 0.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/4 (157 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/5 60: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 60: Last frame 0 time 0.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/5 (157 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/6 60: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 60: Last frame 0 time 0.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/6 (158 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/7 60: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 60: Last frame 0 time 0.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/7 (168 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/8 60: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 60: Last frame 0 time 0.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/8 (170 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/9 60: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 60: Last frame 0 time 0.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/9 (159 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/10 60: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 60: Last frame 0 time 0.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/10 (147 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/11 60: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 60: Last frame 0 time 0.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/11 (144 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/12 60: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 60: Last frame 0 time 0.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/12 (141 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/13 60: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 60: Last frame 0 time 0.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/13 (142 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/14 60: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 60: Last frame 0 time 0.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/14 (143 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/15 60: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 60: Last frame 0 time 0.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/15 (144 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/16 60: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 60: Last frame 0 time 0.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/16 (158 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/17 60: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 60: Last frame 0 time 0.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/17 (156 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/18 60: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 60: Last frame 0 time 0.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/18 (160 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/19 60: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 60: Last frame 0 time 0.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/19 (162 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/20 60: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 60: Last frame 0 time 0.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/20 (154 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/21 60: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 60: Last frame 0 time 0.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/21 (159 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/22 60: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 60: Last frame 0 time 0.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/22 (159 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/23 60: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 60: Last frame 0 time 0.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/23 (157 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/24 60: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 60: Last frame 0 time 0.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/24 (160 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/25 60: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 60: Last frame 0 time 0.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/25 (159 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/26 60: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 60: Last frame 0 time 0.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/26 (164 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/27 60: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 60: Last frame 0 time 0.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/27 (158 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/28 60: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 60: Last frame 0 time 0.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/28 (156 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/29 60: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 60: Last frame 0 time 0.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/29 (154 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/30 60: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 60: Last frame 0 time 0.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/30 (155 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/31 60: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 60: Last frame 0 time 0.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/31 (153 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/32 60: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 60: Last frame 0 time 0.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/32 (155 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/33 60: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 60: Last frame 0 time 0.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/33 (162 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/34 60: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 60: Last frame 0 time 0.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/34 (155 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/35 60: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 60: Last frame 0 time 0.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/35 (153 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/36 60: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 60: Last frame 0 time 0.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/36 (150 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/37 60: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 60: Last frame 0 time 0.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/37 (160 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/38 60: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 60: Last frame 0 time 0.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/38 (166 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/39 60: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 60: Last frame 0 time 0.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/39 (163 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/40 60: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 60: Last frame 0 time 0.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/40 (164 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/41 60: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 60: Last frame 0 time 0.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/41 (164 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/42 60: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 60: Last frame 0 time 0.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/42 (162 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/43 60: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 60: Last frame 0 time 0.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/43 (164 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/44 60: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 60: Last frame 0 time 0.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/44 (159 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/45 60: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 60: Last frame 0 time 0.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/45 (163 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/46 60: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 60: Last frame 0 time 0.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/46 (161 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/47 60: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 60: Last frame 0 time 0.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/47 (163 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/48 60: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 60: Last frame 0 time 0.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/48 (154 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/49 60: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 60: Last frame 0 time 0.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/49 (164 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/50 60: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 60: Last frame 0 time 0.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/50 (161 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/51 60: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 60: Last frame 0 time 0.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/51 (160 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/52 60: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 60: Last frame 0 time 0.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/52 (158 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/53 60: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 60: Last frame 0 time 0.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/53 (157 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/54 60: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 60: Last frame 0 time 0.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/54 (160 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/55 60: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 60: Last frame 0 time 0.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/55 (160 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/56 60: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 60: Last frame 0 time 0.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/56 (159 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/57 60: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 60: Last frame 0 time 0.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/57 (158 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/58 60: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 60: Last frame 0 time 0.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/58 (160 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/59 60: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 60: Last frame 0 time 0.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/59 (158 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/60 60: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 60: Last frame 0 time 0.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/60 (156 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/61 60: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 60: Last frame 0 time 0.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/61 (154 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/62 60: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 60: Last frame 0 time 0.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/62 (157 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/63 60: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 60: Last frame 0 time 0.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/63 (156 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/64 60: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 60: Last frame 0 time 0.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/64 (141 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/65 60: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 60: Last frame 0 time 0.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/65 (145 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/66 60: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 60: Last frame 0 time 0.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/66 (148 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/67 60: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 60: Last frame 0 time 0.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/67 (142 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/68 60: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 60: Last frame 0 time 0.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/68 (141 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/69 60: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 60: Last frame 0 time 0.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/69 (148 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/70 60: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 60: Last frame 0 time 0.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/70 (122 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/71 60: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 60: Last frame 0 time 0.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/71 (136 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/72 60: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 60: Last frame 0 time 0.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/72 (148 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/73 60: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 60: Last frame 0 time 0.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/73 (147 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/74 60: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 60: Last frame 0 time 0.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/74 (150 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/75 60: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 60: Last frame 0 time 0.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/75 (138 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/76 60: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 60: Last frame 0 time 0.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/76 (132 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/77 60: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 60: Last frame 0 time 0.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/77 (132 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/78 60: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 60: Last frame 0 time 0.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/78 (136 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/79 60: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 60: Last frame 0 time 0.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/79 (153 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/80 60: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 60: Last frame 0 time 0.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/80 (147 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/81 60: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 60: Last frame 0 time 0.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/81 (149 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/82 60: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 60: Last frame 0 time 0.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/82 (147 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/83 60: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 60: Last frame 0 time 0.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/83 (150 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/84 60: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 60: Last frame 0 time 0.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/84 (153 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/85 60: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 60: Last frame 0 time 0.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/85 (142 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/86 60: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 60: Last frame 0 time 0.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/86 (139 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/87 60: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 60: Last frame 0 time 0.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/87 (139 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/88 60: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 60: Last frame 0 time 0.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/88 (142 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/89 60: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 60: Last frame 0 time 0.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/89 (134 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/90 60: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 60: Last frame 0 time 0.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/90 (139 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/91 60: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 60: Last frame 0 time 0.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/91 (135 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/92 60: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 60: Last frame 0 time 0.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/92 (142 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/93 60: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 60: Last frame 0 time 0.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/93 (157 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/94 60: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 60: Last frame 0 time 0.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/94 (141 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/95 60: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 60: Last frame 0 time 0.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/95 (144 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/96 60: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 60: Last frame 0 time 0.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/96 (143 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/97 60: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 60: Last frame 0 time 0.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/97 (148 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/98 60: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 60: Last frame 0 time 0.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/98 (153 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/99 60: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 60: Last frame 0 time 0.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/99 (142 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/100 60: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 60: Last frame 0 time 0.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/100 (149 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/101 60: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 60: Last frame 0 time 0.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/101 (137 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/102 60: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 60: Last frame 0 time 0.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/102 (147 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/103 60: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 60: Last frame 0 time 0.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/103 (131 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/104 60: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 60: Last frame 0 time 0.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/104 (137 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/105 60: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 60: Last frame 0 time 0.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/105 (143 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/106 60: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 60: Last frame 0 time 0.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/106 (146 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/107 60: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 60: Last frame 0 time 0.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/107 (140 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/108 60: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 60: Last frame 0 time 0.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/108 (145 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/109 60: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 60: Last frame 0 time 0.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/109 (140 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/110 60: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 60: Last frame 0 time 0.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/110 (131 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/111 60: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 60: Last frame 0 time 0.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/111 (136 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/112 60: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 60: Last frame 0 time 0.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/112 (136 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/113 60: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 60: Last frame 0 time 0.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/113 (135 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/114 60: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 60: Last frame 0 time 0.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/114 (131 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/115 60: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 60: Last frame 0 time 0.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/115 (137 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/116 60: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 60: Last frame 0 time 0.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/116 (130 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/117 60: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 60: Last frame 0 time 0.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/117 (134 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/118 60: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 60: Last frame 0 time 0.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/118 (137 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/119 60: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 60: Last frame 0 time 0.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/119 (139 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/120 60: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 60: Last frame 0 time 0.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/120 (145 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/121 60: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 60: Last frame 0 time 0.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/121 (140 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/122 60: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 60: Last frame 0 time 0.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/122 (145 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/123 60: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 60: Last frame 0 time 0.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/123 (140 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/124 60: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 60: Last frame 0 time 0.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/124 (137 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/125 60: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 60: Last frame 0 time 0.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/125 (146 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/126 60: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 60: Last frame 0 time 0.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/126 (147 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/127 60: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 60: Last frame 0 time 0.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/127 (148 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/128 60: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 60: Last frame 0 time 500.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/128 (113 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/129 60: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 60: Last frame 0 time 500.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/129 (115 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/130 60: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 60: Last frame 0 time 500.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/130 (116 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/131 60: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 60: Last frame 0 time 500.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/131 (109 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/132 60: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 60: Last frame 0 time 500.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/132 (106 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/133 60: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 60: Last frame 0 time 500.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/133 (109 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/134 60: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 60: Last frame 0 time 500.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/134 (106 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/135 60: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 60: Last frame 0 time 500.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/135 (107 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/136 60: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 60: Last frame 0 time 500.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/136 (114 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/137 60: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 60: Last frame 0 time 500.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/137 (111 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/138 60: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 60: Last frame 0 time 500.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/138 (109 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/139 60: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 60: Last frame 0 time 500.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/139 (115 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/140 60: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 60: Last frame 0 time 500.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/140 (109 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/141 60: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 60: Last frame 0 time 500.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/141 (108 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/142 60: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 60: Last frame 0 time 500.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/142 (107 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/143 60: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 60: Last frame 0 time 500.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/143 (109 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/144 60: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 60: Last frame 0 time 500.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/144 (108 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/145 60: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 60: Last frame 0 time 500.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/145 (108 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/146 60: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 60: Last frame 0 time 500.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/146 (108 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/147 60: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 60: Last frame 0 time 500.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/147 (112 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/148 60: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 60: Last frame 0 time 500.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/148 (110 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/149 60: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 60: Last frame 0 time 500.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/149 (110 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/150 60: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 60: Last frame 0 time 500.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/150 (111 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/151 60: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 60: Last frame 0 time 500.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/151 (108 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/152 60: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 60: Last frame 0 time 500.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/152 (114 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/153 60: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 60: Last frame 0 time 500.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/153 (109 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/154 60: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 60: Last frame 0 time 500.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/154 (109 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/155 60: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 60: Last frame 0 time 500.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/155 (109 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/156 60: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 60: Last frame 0 time 500.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/156 (110 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/157 60: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 60: Last frame 0 time 500.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/157 (112 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/158 60: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 60: Last frame 0 time 500.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/158 (117 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/159 60: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 60: Last frame 0 time 500.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/159 (108 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/160 60: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 60: Last frame 0 time 500.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/160 (103 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/161 60: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 60: Last frame 0 time 500.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/161 (109 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/162 60: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 60: Last frame 0 time 500.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/162 (105 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/163 60: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 60: Last frame 0 time 500.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/163 (111 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/164 60: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 60: Last frame 0 time 500.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/164 (114 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/165 60: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 60: Last frame 0 time 500.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/165 (111 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/166 60: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 60: Last frame 0 time 500.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/166 (115 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/167 60: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 60: Last frame 0 time 500.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/167 (113 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/168 60: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 60: Last frame 0 time 500.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/168 (117 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/169 60: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 60: Last frame 0 time 500.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/169 (124 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/170 60: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 60: Last frame 0 time 500.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/170 (118 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/171 60: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 60: Last frame 0 time 500.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/171 (108 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/172 60: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 60: Last frame 0 time 500.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/172 (116 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/173 60: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 60: Last frame 0 time 500.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/173 (112 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/174 60: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 60: Last frame 0 time 500.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/174 (112 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/175 60: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 60: Last frame 0 time 500.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/175 (105 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/176 60: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 60: Last frame 0 time 500.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/176 (107 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/177 60: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 60: Last frame 0 time 500.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/177 (110 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/178 60: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 60: Last frame 0 time 500.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/178 (108 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/179 60: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 60: Last frame 0 time 500.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/179 (108 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/180 60: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 60: Last frame 0 time 500.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/180 (111 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/181 60: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 60: Last frame 0 time 500.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/181 (109 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/182 60: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 60: Last frame 0 time 500.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/182 (107 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/183 60: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 60: Last frame 0 time 500.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/183 (109 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/184 60: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 60: Last frame 0 time 500.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/184 (109 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/185 60: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 60: Last frame 0 time 500.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/185 (115 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/186 60: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 60: Last frame 0 time 500.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/186 (114 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/187 60: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 60: Last frame 0 time 500.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/187 (108 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/188 60: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 60: Last frame 0 time 500.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/188 (111 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/189 60: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 60: Last frame 0 time 500.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/189 (112 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/190 60: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 60: Last frame 0 time 500.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/190 (112 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/191 60: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 60: Last frame 0 time 500.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/191 (112 ms) 60: [----------] 192 tests from MoleculeTests/DsspModuleTest (26385 ms total) 60: 60: [----------] 3 tests from GyrateTests/GyrateModuleTest 60: [ RUN ] GyrateTests/GyrateModuleTest.Works/0 60: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 60: Analyzed 2 frames, last time 10.000 60: [ OK ] GyrateTests/GyrateModuleTest.Works/0 (65 ms) 60: [ RUN ] GyrateTests/GyrateModuleTest.Works/1 60: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 60: Analyzed 2 frames, last time 10.000 60: [ OK ] GyrateTests/GyrateModuleTest.Works/1 (63 ms) 60: [ RUN ] GyrateTests/GyrateModuleTest.Works/2 60: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 60: Analyzed 2 frames, last time 10.000 60: [ OK ] GyrateTests/GyrateModuleTest.Works/2 (63 ms) 60: [----------] 3 tests from GyrateTests/GyrateModuleTest (192 ms total) 60: 60: [----------] 96 tests from HBondTests/HbondModuleTest 60: [ RUN ] HBondTests/HbondModuleTest.Works/0 60: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 60: Analyzed 2 frames, last time 10.000 60: 60: Checking for overlap in atoms between Protein (304 atoms) and Protein (304 atoms) 60: Selection 'Protein' has 56 acceptors and 27 donors. 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 60: Memory Limitation 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c02087 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] HBondTests/HbondModuleTest.Works/0 (100 ms) 60: [ RUN ] HBondTests/HbondModuleTest.Works/1 60: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 60: Analyzed 2 frames, last time 10.000 60: 60: Checking for overlap in atoms between Protein (304 atoms) and Protein (304 atoms) 60: Selection 'Protein' has 29 acceptors and 27 donors. 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 60: Memory Limitation 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c02087 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] HBondTests/HbondModuleTest.Works/1 (96 ms) 60: [ RUN ] HBondTests/HbondModuleTest.Works/2 60: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 60: Analyzed 2 frames, last time 10.000 60: 60: Checking for overlap in atoms between Protein (304 atoms) and Protein (304 atoms) 60: Selection 'Protein' has 56 acceptors and 4 donors. 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 60: Memory Limitation 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c02087 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] HBondTests/HbondModuleTest.Works/2 (89 ms) 60: [ RUN ] HBondTests/HbondModuleTest.Works/3 60: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 60: Analyzed 2 frames, last time 10.000 60: 60: Checking for overlap in atoms between Protein (304 atoms) and Protein (304 atoms) 60: Selection 'Protein' has 29 acceptors and 4 donors. 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 60: Memory Limitation 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c02087 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] HBondTests/HbondModuleTest.Works/3 (91 ms) 60: [ RUN ] HBondTests/HbondModuleTest.Works/4 60: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 60: Analyzed 2 frames, last time 10.000 60: 60: Checking for overlap in atoms between Protein (304 atoms) and Protein (304 atoms) 60: Selection 'Protein' has 56 acceptors and 27 donors. 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 60: Memory Limitation 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c02087 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] HBondTests/HbondModuleTest.Works/4 (98 ms) 60: [ RUN ] HBondTests/HbondModuleTest.Works/5 60: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 60: Analyzed 2 frames, last time 10.000 60: 60: Checking for overlap in atoms between Protein (304 atoms) and Protein (304 atoms) 60: Selection 'Protein' has 29 acceptors and 27 donors. 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 60: Memory Limitation 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c02087 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] HBondTests/HbondModuleTest.Works/5 (103 ms) 60: [ RUN ] HBondTests/HbondModuleTest.Works/6 60: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 60: Analyzed 2 frames, last time 10.000 60: 60: Checking for overlap in atoms between Protein (304 atoms) and Protein (304 atoms) 60: Selection 'Protein' has 56 acceptors and 4 donors. 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 60: Memory Limitation 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c02087 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] HBondTests/HbondModuleTest.Works/6 (99 ms) 60: [ RUN ] HBondTests/HbondModuleTest.Works/7 60: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 60: Analyzed 2 frames, last time 10.000 60: 60: Checking for overlap in atoms between Protein (304 atoms) and Protein (304 atoms) 60: Selection 'Protein' has 29 acceptors and 4 donors. 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 60: Memory Limitation 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c02087 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] HBondTests/HbondModuleTest.Works/7 (100 ms) 60: [ RUN ] HBondTests/HbondModuleTest.Works/8 60: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 60: Analyzed 2 frames, last time 10.000 60: 60: Checking for overlap in atoms between Protein (304 atoms) and Protein (304 atoms) 60: Selection 'Protein' has 56 acceptors and 27 donors. 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 60: Memory Limitation 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c02087 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] HBondTests/HbondModuleTest.Works/8 (112 ms) 60: [ RUN ] HBondTests/HbondModuleTest.Works/9 60: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 60: Analyzed 2 frames, last time 10.000 60: 60: Checking for overlap in atoms between Protein (304 atoms) and Protein (304 atoms) 60: Selection 'Protein' has 29 acceptors and 27 donors. 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 60: Memory Limitation 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c02087 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] HBondTests/HbondModuleTest.Works/9 (100 ms) 60: [ RUN ] HBondTests/HbondModuleTest.Works/10 60: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 60: Analyzed 2 frames, last time 10.000 60: 60: Checking for overlap in atoms between Protein (304 atoms) and Protein (304 atoms) 60: Selection 'Protein' has 56 acceptors and 4 donors. 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 60: Memory Limitation 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c02087 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] HBondTests/HbondModuleTest.Works/10 (99 ms) 60: [ RUN ] HBondTests/HbondModuleTest.Works/11 60: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 60: Analyzed 2 frames, last time 10.000 60: 60: Checking for overlap in atoms between Protein (304 atoms) and Protein (304 atoms) 60: Selection 'Protein' has 29 acceptors and 4 donors. 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 60: Memory Limitation 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c02087 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] HBondTests/HbondModuleTest.Works/11 (95 ms) 60: [ RUN ] HBondTests/HbondModuleTest.Works/12 60: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 60: Analyzed 2 frames, last time 10.000 60: 60: Checking for overlap in atoms between Protein (304 atoms) and Protein (304 atoms) 60: Selection 'Protein' has 56 acceptors and 27 donors. 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 60: Memory Limitation 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c02087 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] HBondTests/HbondModuleTest.Works/12 (102 ms) 60: [ RUN ] HBondTests/HbondModuleTest.Works/13 60: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 60: Analyzed 2 frames, last time 10.000 60: 60: Checking for overlap in atoms between Protein (304 atoms) and Protein (304 atoms) 60: Selection 'Protein' has 29 acceptors and 27 donors. 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 60: Memory Limitation 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c02087 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] HBondTests/HbondModuleTest.Works/13 (104 ms) 60: [ RUN ] HBondTests/HbondModuleTest.Works/14 60: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 60: Analyzed 2 frames, last time 10.000 60: 60: Checking for overlap in atoms between Protein (304 atoms) and Protein (304 atoms) 60: Selection 'Protein' has 56 acceptors and 4 donors. 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 60: Memory Limitation 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c02087 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] HBondTests/HbondModuleTest.Works/14 (95 ms) 60: [ RUN ] HBondTests/HbondModuleTest.Works/15 60: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 60: Analyzed 2 frames, last time 10.000 60: 60: Checking for overlap in atoms between Protein (304 atoms) and Protein (304 atoms) 60: Selection 'Protein' has 29 acceptors and 4 donors. 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 60: Memory Limitation 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c02087 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] HBondTests/HbondModuleTest.Works/15 (96 ms) 60: [ RUN ] HBondTests/HbondModuleTest.Works/16 60: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 60: Analyzed 2 frames, last time 10.000 60: 60: Checking for overlap in atoms between Protein (304 atoms) and Protein (304 atoms) 60: Selection 'Protein' has 56 acceptors and 27 donors. 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 60: Memory Limitation 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c02087 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] HBondTests/HbondModuleTest.Works/16 (104 ms) 60: [ RUN ] HBondTests/HbondModuleTest.Works/17 60: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 60: Analyzed 2 frames, last time 10.000 60: 60: Checking for overlap in atoms between Protein (304 atoms) and Protein (304 atoms) 60: Selection 'Protein' has 29 acceptors and 27 donors. 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 60: Memory Limitation 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c02087 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] HBondTests/HbondModuleTest.Works/17 (102 ms) 60: [ RUN ] HBondTests/HbondModuleTest.Works/18 60: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 60: Analyzed 2 frames, last time 10.000 60: 60: Checking for overlap in atoms between Protein (304 atoms) and Protein (304 atoms) 60: Selection 'Protein' has 56 acceptors and 4 donors. 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 60: Memory Limitation 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c02087 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] HBondTests/HbondModuleTest.Works/18 (94 ms) 60: [ RUN ] HBondTests/HbondModuleTest.Works/19 60: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 60: Analyzed 2 frames, last time 10.000 60: 60: Checking for overlap in atoms between Protein (304 atoms) and Protein (304 atoms) 60: Selection 'Protein' has 29 acceptors and 4 donors. 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 60: Memory Limitation 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c02087 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] HBondTests/HbondModuleTest.Works/19 (94 ms) 60: [ RUN ] HBondTests/HbondModuleTest.Works/20 60: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 60: Analyzed 2 frames, last time 10.000 60: 60: Checking for overlap in atoms between Protein (304 atoms) and Protein (304 atoms) 60: Selection 'Protein' has 56 acceptors and 27 donors. 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 60: Memory Limitation 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c02087 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] HBondTests/HbondModuleTest.Works/20 (102 ms) 60: [ RUN ] HBondTests/HbondModuleTest.Works/21 60: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 60: Analyzed 2 frames, last time 10.000 60: 60: Checking for overlap in atoms between Protein (304 atoms) and Protein (304 atoms) 60: Selection 'Protein' has 29 acceptors and 27 donors. 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 60: Memory Limitation 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c02087 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] HBondTests/HbondModuleTest.Works/21 (110 ms) 60: [ RUN ] HBondTests/HbondModuleTest.Works/22 60: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 60: Analyzed 2 frames, last time 10.000 60: 60: Checking for overlap in atoms between Protein (304 atoms) and Protein (304 atoms) 60: Selection 'Protein' has 56 acceptors and 4 donors. 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 60: Memory Limitation 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c02087 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] HBondTests/HbondModuleTest.Works/22 (94 ms) 60: [ RUN ] HBondTests/HbondModuleTest.Works/23 60: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 60: Analyzed 2 frames, last time 10.000 60: 60: Checking for overlap in atoms between Protein (304 atoms) and Protein (304 atoms) 60: Selection 'Protein' has 29 acceptors and 4 donors. 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 60: Memory Limitation 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c02087 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] HBondTests/HbondModuleTest.Works/23 (94 ms) 60: [ RUN ] HBondTests/HbondModuleTest.Works/24 60: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 60: Analyzed 2 frames, last time 10.000 60: 60: Checking for overlap in atoms between Protein (304 atoms) and Protein (304 atoms) 60: Selection 'Protein' has 56 acceptors and 27 donors. 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 60: Memory Limitation 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c02087 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] HBondTests/HbondModuleTest.Works/24 (102 ms) 60: [ RUN ] HBondTests/HbondModuleTest.Works/25 60: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 60: Analyzed 2 frames, last time 10.000 60: 60: Checking for overlap in atoms between Protein (304 atoms) and Protein (304 atoms) 60: Selection 'Protein' has 29 acceptors and 27 donors. 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 60: Memory Limitation 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c02087 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] HBondTests/HbondModuleTest.Works/25 (100 ms) 60: [ RUN ] HBondTests/HbondModuleTest.Works/26 60: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 60: Analyzed 2 frames, last time 10.000 60: 60: Checking for overlap in atoms between Protein (304 atoms) and Protein (304 atoms) 60: Selection 'Protein' has 56 acceptors and 4 donors. 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 60: Memory Limitation 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c02087 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] HBondTests/HbondModuleTest.Works/26 (97 ms) 60: [ RUN ] HBondTests/HbondModuleTest.Works/27 60: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 60: Analyzed 2 frames, last time 10.000 60: 60: Checking for overlap in atoms between Protein (304 atoms) and Protein (304 atoms) 60: Selection 'Protein' has 29 acceptors and 4 donors. 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 60: Memory Limitation 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c02087 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] HBondTests/HbondModuleTest.Works/27 (94 ms) 60: [ RUN ] HBondTests/HbondModuleTest.Works/28 60: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 60: Analyzed 2 frames, last time 10.000 60: 60: Checking for overlap in atoms between Protein (304 atoms) and Protein (304 atoms) 60: Selection 'Protein' has 56 acceptors and 27 donors. 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 60: Memory Limitation 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c02087 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] HBondTests/HbondModuleTest.Works/28 (102 ms) 60: [ RUN ] HBondTests/HbondModuleTest.Works/29 60: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 60: Analyzed 2 frames, last time 10.000 60: 60: Checking for overlap in atoms between Protein (304 atoms) and Protein (304 atoms) 60: Selection 'Protein' has 29 acceptors and 27 donors. 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 60: Memory Limitation 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c02087 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] HBondTests/HbondModuleTest.Works/29 (103 ms) 60: [ RUN ] HBondTests/HbondModuleTest.Works/30 60: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 60: Analyzed 2 frames, last time 10.000 60: 60: Checking for overlap in atoms between Protein (304 atoms) and Protein (304 atoms) 60: Selection 'Protein' has 56 acceptors and 4 donors. 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 60: Memory Limitation 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c02087 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] HBondTests/HbondModuleTest.Works/30 (100 ms) 60: [ RUN ] HBondTests/HbondModuleTest.Works/31 60: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 60: Analyzed 2 frames, last time 10.000 60: 60: Checking for overlap in atoms between Protein (304 atoms) and Protein (304 atoms) 60: Selection 'Protein' has 29 acceptors and 4 donors. 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 60: Memory Limitation 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c02087 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] HBondTests/HbondModuleTest.Works/31 (101 ms) 60: [ RUN ] HBondTests/HbondModuleTest.Works/32 60: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 60: Analyzed 2 frames, last time 10.000 60: 60: Checking for overlap in atoms between Protein (304 atoms) and Water (3480 atoms) 60: Selection 'Protein' has 56 acceptors and 27 donors. 60: Selection 'Water' has 1160 acceptors and 1160 donors. 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 60: Memory Limitation 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c02087 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] HBondTests/HbondModuleTest.Works/32 (458 ms) 60: [ RUN ] HBondTests/HbondModuleTest.Works/33 60: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 60: Analyzed 2 frames, last time 10.000 60: 60: Checking for overlap in atoms between Protein (304 atoms) and Water (3480 atoms) 60: Selection 'Protein' has 29 acceptors and 27 donors. 60: Selection 'Water' has 1160 acceptors and 1160 donors. 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 60: Memory Limitation 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c02087 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] HBondTests/HbondModuleTest.Works/33 (436 ms) 60: [ RUN ] HBondTests/HbondModuleTest.Works/34 60: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 60: Analyzed 2 frames, last time 10.000 60: 60: Checking for overlap in atoms between Protein (304 atoms) and Water (3480 atoms) 60: Selection 'Protein' has 56 acceptors and 4 donors. 60: Selection 'Water' has 1160 acceptors and 1160 donors. 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 60: Memory Limitation 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c02087 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] HBondTests/HbondModuleTest.Works/34 (438 ms) 60: [ RUN ] HBondTests/HbondModuleTest.Works/35 60: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 60: Analyzed 2 frames, last time 10.000 60: 60: Checking for overlap in atoms between Protein (304 atoms) and Water (3480 atoms) 60: Selection 'Protein' has 29 acceptors and 4 donors. 60: Selection 'Water' has 1160 acceptors and 1160 donors. 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 60: Memory Limitation 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c02087 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] HBondTests/HbondModuleTest.Works/35 (432 ms) 60: [ RUN ] HBondTests/HbondModuleTest.Works/36 60: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 60: Analyzed 2 frames, last time 10.000 60: 60: Checking for overlap in atoms between Protein (304 atoms) and Water (3480 atoms) 60: Selection 'Protein' has 56 acceptors and 27 donors. 60: Selection 'Water' has 1160 acceptors and 1160 donors. 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 60: Memory Limitation 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c02087 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] HBondTests/HbondModuleTest.Works/36 (469 ms) 60: [ RUN ] HBondTests/HbondModuleTest.Works/37 60: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 60: Analyzed 2 frames, last time 10.000 60: 60: Checking for overlap in atoms between Protein (304 atoms) and Water (3480 atoms) 60: Selection 'Protein' has 29 acceptors and 27 donors. 60: Selection 'Water' has 1160 acceptors and 1160 donors. 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 60: Memory Limitation 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c02087 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] HBondTests/HbondModuleTest.Works/37 (459 ms) 60: [ RUN ] HBondTests/HbondModuleTest.Works/38 60: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 60: Analyzed 2 frames, last time 10.000 60: 60: Checking for overlap in atoms between Protein (304 atoms) and Water (3480 atoms) 60: Selection 'Protein' has 56 acceptors and 4 donors. 60: Selection 'Water' has 1160 acceptors and 1160 donors. 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 60: Memory Limitation 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c02087 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] HBondTests/HbondModuleTest.Works/38 (454 ms) 60: [ RUN ] HBondTests/HbondModuleTest.Works/39 60: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 60: Analyzed 2 frames, last time 10.000 60: 60: Checking for overlap in atoms between Protein (304 atoms) and Water (3480 atoms) 60: Selection 'Protein' has 29 acceptors and 4 donors. 60: Selection 'Water' has 1160 acceptors and 1160 donors. 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 60: Memory Limitation 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c02087 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] HBondTests/HbondModuleTest.Works/39 (482 ms) 60: [ RUN ] HBondTests/HbondModuleTest.Works/40 60: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 60: Analyzed 2 frames, last time 10.000 60: 60: Checking for overlap in atoms between Protein (304 atoms) and Water (3480 atoms) 60: Selection 'Protein' has 56 acceptors and 27 donors. 60: Selection 'Water' has 1160 acceptors and 1160 donors. 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 60: Memory Limitation 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c02087 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] HBondTests/HbondModuleTest.Works/40 (496 ms) 60: [ RUN ] HBondTests/HbondModuleTest.Works/41 60: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 60: Analyzed 2 frames, last time 10.000 60: 60: Checking for overlap in atoms between Protein (304 atoms) and Water (3480 atoms) 60: Selection 'Protein' has 29 acceptors and 27 donors. 60: Selection 'Water' has 1160 acceptors and 1160 donors. 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 60: Memory Limitation 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c02087 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] HBondTests/HbondModuleTest.Works/41 (486 ms) 60: [ RUN ] HBondTests/HbondModuleTest.Works/42 60: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 60: Analyzed 2 frames, last time 10.000 60: 60: Checking for overlap in atoms between Protein (304 atoms) and Water (3480 atoms) 60: Selection 'Protein' has 56 acceptors and 4 donors. 60: Selection 'Water' has 1160 acceptors and 1160 donors. 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 60: Memory Limitation 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c02087 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] HBondTests/HbondModuleTest.Works/42 (485 ms) 60: [ RUN ] HBondTests/HbondModuleTest.Works/43 60: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 60: Analyzed 2 frames, last time 10.000 60: 60: Checking for overlap in atoms between Protein (304 atoms) and Water (3480 atoms) 60: Selection 'Protein' has 29 acceptors and 4 donors. 60: Selection 'Water' has 1160 acceptors and 1160 donors. 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 60: Memory Limitation 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c02087 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] HBondTests/HbondModuleTest.Works/43 (478 ms) 60: [ RUN ] HBondTests/HbondModuleTest.Works/44 60: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 60: Analyzed 2 frames, last time 10.000 60: 60: Checking for overlap in atoms between Protein (304 atoms) and Water (3480 atoms) 60: Selection 'Protein' has 56 acceptors and 27 donors. 60: Selection 'Water' has 1160 acceptors and 1160 donors. 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 60: Memory Limitation 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c02087 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] HBondTests/HbondModuleTest.Works/44 (500 ms) 60: [ RUN ] HBondTests/HbondModuleTest.Works/45 60: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 60: Analyzed 2 frames, last time 10.000 60: 60: Checking for overlap in atoms between Protein (304 atoms) and Water (3480 atoms) 60: Selection 'Protein' has 29 acceptors and 27 donors. 60: Selection 'Water' has 1160 acceptors and 1160 donors. 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 60: Memory Limitation 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c02087 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] HBondTests/HbondModuleTest.Works/45 (482 ms) 60: [ RUN ] HBondTests/HbondModuleTest.Works/46 60: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 60: Analyzed 2 frames, last time 10.000 60: 60: Checking for overlap in atoms between Protein (304 atoms) and Water (3480 atoms) 60: Selection 'Protein' has 56 acceptors and 4 donors. 60: Selection 'Water' has 1160 acceptors and 1160 donors. 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 60: Memory Limitation 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c02087 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] HBondTests/HbondModuleTest.Works/46 (485 ms) 60: [ RUN ] HBondTests/HbondModuleTest.Works/47 60: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 60: Analyzed 2 frames, last time 10.000 60: 60: Checking for overlap in atoms between Protein (304 atoms) and Water (3480 atoms) 60: Selection 'Protein' has 29 acceptors and 4 donors. 60: Selection 'Water' has 1160 acceptors and 1160 donors. 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 60: Memory Limitation 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c02087 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] HBondTests/HbondModuleTest.Works/47 (484 ms) 60: [ RUN ] HBondTests/HbondModuleTest.Works/48 60: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 60: Analyzed 2 frames, last time 10.000 60: 60: Checking for overlap in atoms between Protein (304 atoms) and Water (3480 atoms) 60: Selection 'Protein' has 56 acceptors and 27 donors. 60: Selection 'Water' has 1160 acceptors and 1160 donors. 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 60: Memory Limitation 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c02087 60: -------- -------- --- Thank You --- -------- -------- 60: 60: Merging hbonds with Acceptor and Donor swapped 60: [ OK ] HBondTests/HbondModuleTest.Works/48 (450 ms) 60: [ RUN ] HBondTests/HbondModuleTest.Works/49 60: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 60: Analyzed 2 frames, last time 10.000 60: 60: Checking for overlap in atoms between Protein (304 atoms) and Water (3480 atoms) 60: Selection 'Protein' has 29 acceptors and 27 donors. 60: Selection 'Water' has 1160 acceptors and 1160 donors. 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 60: Memory Limitation 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c02087 60: -------- -------- --- Thank You --- -------- -------- 60: 60: Merging hbonds with Acceptor and Donor swapped 60: [ OK ] HBondTests/HbondModuleTest.Works/49 (447 ms) 60: [ RUN ] HBondTests/HbondModuleTest.Works/50 60: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 60: Analyzed 2 frames, last time 10.000 60: 60: Checking for overlap in atoms between Protein (304 atoms) and Water (3480 atoms) 60: Selection 'Protein' has 56 acceptors and 4 donors. 60: Selection 'Water' has 1160 acceptors and 1160 donors. 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 60: Memory Limitation 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c02087 60: -------- -------- --- Thank You --- -------- -------- 60: 60: Merging hbonds with Acceptor and Donor swapped 60: [ OK ] HBondTests/HbondModuleTest.Works/50 (465 ms) 60: [ RUN ] HBondTests/HbondModuleTest.Works/51 60: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 60: Analyzed 2 frames, last time 10.000 60: 60: Checking for overlap in atoms between Protein (304 atoms) and Water (3480 atoms) 60: Selection 'Protein' has 29 acceptors and 4 donors. 60: Selection 'Water' has 1160 acceptors and 1160 donors. 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 60: Memory Limitation 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c02087 60: -------- -------- --- Thank You --- -------- -------- 60: 60: Merging hbonds with Acceptor and Donor swapped 60: [ OK ] HBondTests/HbondModuleTest.Works/51 (461 ms) 60: [ RUN ] HBondTests/HbondModuleTest.Works/52 60: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 60: Analyzed 2 frames, last time 10.000 60: 60: Checking for overlap in atoms between Protein (304 atoms) and Water (3480 atoms) 60: Selection 'Protein' has 56 acceptors and 27 donors. 60: Selection 'Water' has 1160 acceptors and 1160 donors. 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 60: Memory Limitation 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c02087 60: -------- -------- --- Thank You --- -------- -------- 60: 60: Merging hbonds with Acceptor and Donor swapped 60: [ OK ] HBondTests/HbondModuleTest.Works/52 (495 ms) 60: [ RUN ] HBondTests/HbondModuleTest.Works/53 60: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 60: Analyzed 2 frames, last time 10.000 60: 60: Checking for overlap in atoms between Protein (304 atoms) and Water (3480 atoms) 60: Selection 'Protein' has 29 acceptors and 27 donors. 60: Selection 'Water' has 1160 acceptors and 1160 donors. 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 60: Memory Limitation 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c02087 60: -------- -------- --- Thank You --- -------- -------- 60: 60: Merging hbonds with Acceptor and Donor swapped 60: [ OK ] HBondTests/HbondModuleTest.Works/53 (482 ms) 60: [ RUN ] HBondTests/HbondModuleTest.Works/54 60: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 60: Analyzed 2 frames, last time 10.000 60: 60: Checking for overlap in atoms between Protein (304 atoms) and Water (3480 atoms) 60: Selection 'Protein' has 56 acceptors and 4 donors. 60: Selection 'Water' has 1160 acceptors and 1160 donors. 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 60: Memory Limitation 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c02087 60: -------- -------- --- Thank You --- -------- -------- 60: 60: Merging hbonds with Acceptor and Donor swapped 60: [ OK ] HBondTests/HbondModuleTest.Works/54 (479 ms) 60: [ RUN ] HBondTests/HbondModuleTest.Works/55 60: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 60: Analyzed 2 frames, last time 10.000 60: 60: Checking for overlap in atoms between Protein (304 atoms) and Water (3480 atoms) 60: Selection 'Protein' has 29 acceptors and 4 donors. 60: Selection 'Water' has 1160 acceptors and 1160 donors. 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 60: Memory Limitation 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c02087 60: -------- -------- --- Thank You --- -------- -------- 60: 60: Merging hbonds with Acceptor and Donor swapped 60: [ OK ] HBondTests/HbondModuleTest.Works/55 (444 ms) 60: [ RUN ] HBondTests/HbondModuleTest.Works/56 60: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 60: Analyzed 2 frames, last time 10.000 60: 60: Checking for overlap in atoms between Protein (304 atoms) and Water (3480 atoms) 60: Selection 'Protein' has 56 acceptors and 27 donors. 60: Selection 'Water' has 1160 acceptors and 1160 donors. 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 60: Memory Limitation 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c02087 60: -------- -------- --- Thank You --- -------- -------- 60: 60: Merging hbonds with Acceptor and Donor swapped 60: [ OK ] HBondTests/HbondModuleTest.Works/56 (479 ms) 60: [ RUN ] HBondTests/HbondModuleTest.Works/57 60: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 60: Analyzed 2 frames, last time 10.000 60: 60: Checking for overlap in atoms between Protein (304 atoms) and Water (3480 atoms) 60: Selection 'Protein' has 29 acceptors and 27 donors. 60: Selection 'Water' has 1160 acceptors and 1160 donors. 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 60: Memory Limitation 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c02087 60: -------- -------- --- Thank You --- -------- -------- 60: 60: Merging hbonds with Acceptor and Donor swapped 60: [ OK ] HBondTests/HbondModuleTest.Works/57 (470 ms) 60: [ RUN ] HBondTests/HbondModuleTest.Works/58 60: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 60: Analyzed 2 frames, last time 10.000 60: 60: Checking for overlap in atoms between Protein (304 atoms) and Water (3480 atoms) 60: Selection 'Protein' has 56 acceptors and 4 donors. 60: Selection 'Water' has 1160 acceptors and 1160 donors. 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 60: Memory Limitation 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c02087 60: -------- -------- --- Thank You --- -------- -------- 60: 60: Merging hbonds with Acceptor and Donor swapped 60: [ OK ] HBondTests/HbondModuleTest.Works/58 (466 ms) 60: [ RUN ] HBondTests/HbondModuleTest.Works/59 60: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 60: Analyzed 2 frames, last time 10.000 60: 60: Checking for overlap in atoms between Protein (304 atoms) and Water (3480 atoms) 60: Selection 'Protein' has 29 acceptors and 4 donors. 60: Selection 'Water' has 1160 acceptors and 1160 donors. 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 60: Memory Limitation 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c02087 60: -------- -------- --- Thank You --- -------- -------- 60: 60: Merging hbonds with Acceptor and Donor swapped 60: [ OK ] HBondTests/HbondModuleTest.Works/59 (464 ms) 60: [ RUN ] HBondTests/HbondModuleTest.Works/60 60: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 60: Analyzed 2 frames, last time 10.000 60: 60: Checking for overlap in atoms between Protein (304 atoms) and Water (3480 atoms) 60: Selection 'Protein' has 56 acceptors and 27 donors. 60: Selection 'Water' has 1160 acceptors and 1160 donors. 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 60: Memory Limitation 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c02087 60: -------- -------- --- Thank You --- -------- -------- 60: 60: Merging hbonds with Acceptor and Donor swapped 60: [ OK ] HBondTests/HbondModuleTest.Works/60 (484 ms) 60: [ RUN ] HBondTests/HbondModuleTest.Works/61 60: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 60: Analyzed 2 frames, last time 10.000 60: 60: Checking for overlap in atoms between Protein (304 atoms) and Water (3480 atoms) 60: Selection 'Protein' has 29 acceptors and 27 donors. 60: Selection 'Water' has 1160 acceptors and 1160 donors. 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 60: Memory Limitation 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c02087 60: -------- -------- --- Thank You --- -------- -------- 60: 60: Merging hbonds with Acceptor and Donor swapped 60: [ OK ] HBondTests/HbondModuleTest.Works/61 (471 ms) 60: [ RUN ] HBondTests/HbondModuleTest.Works/62 60: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 60: Analyzed 2 frames, last time 10.000 60: 60: Checking for overlap in atoms between Protein (304 atoms) and Water (3480 atoms) 60: Selection 'Protein' has 56 acceptors and 4 donors. 60: Selection 'Water' has 1160 acceptors and 1160 donors. 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 60: Memory Limitation 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c02087 60: -------- -------- --- Thank You --- -------- -------- 60: 60: Merging hbonds with Acceptor and Donor swapped 60: [ OK ] HBondTests/HbondModuleTest.Works/62 (455 ms) 60: [ RUN ] HBondTests/HbondModuleTest.Works/63 60: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 60: Analyzed 2 frames, last time 10.000 60: 60: Checking for overlap in atoms between Protein (304 atoms) and Water (3480 atoms) 60: Selection 'Protein' has 29 acceptors and 4 donors. 60: Selection 'Water' has 1160 acceptors and 1160 donors. 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 60: Memory Limitation 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c02087 60: -------- -------- --- Thank You --- -------- -------- 60: 60: Merging hbonds with Acceptor and Donor swapped 60: [ OK ] HBondTests/HbondModuleTest.Works/63 (468 ms) 60: [ RUN ] HBondTests/HbondModuleTest.Works/64 60: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 60: Analyzed 2 frames, last time 10.000 60: 60: Checking for overlap in atoms between Water (3480 atoms) and Water (3480 atoms) 60: Selection 'Water' has 1160 acceptors and 1160 donors. 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 60: Memory Limitation 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c02087 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] HBondTests/HbondModuleTest.Works/64 (460 ms) 60: [ RUN ] HBondTests/HbondModuleTest.Works/65 60: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 60: Analyzed 2 frames, last time 10.000 60: 60: Checking for overlap in atoms between Water (3480 atoms) and Water (3480 atoms) 60: Selection 'Water' has 1160 acceptors and 1160 donors. 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 60: Memory Limitation 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c02087 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] HBondTests/HbondModuleTest.Works/65 (456 ms) 60: [ RUN ] HBondTests/HbondModuleTest.Works/66 60: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 60: Analyzed 2 frames, last time 10.000 60: 60: Checking for overlap in atoms between Water (3480 atoms) and Water (3480 atoms) 60: Selection 'Water' has 1160 acceptors and 1160 donors. 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 60: Memory Limitation 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c02087 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] HBondTests/HbondModuleTest.Works/66 (467 ms) 60: [ RUN ] HBondTests/HbondModuleTest.Works/67 60: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 60: Analyzed 2 frames, last time 10.000 60: 60: Checking for overlap in atoms between Water (3480 atoms) and Water (3480 atoms) 60: Selection 'Water' has 1160 acceptors and 1160 donors. 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 60: Memory Limitation 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c02087 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] HBondTests/HbondModuleTest.Works/67 (460 ms) 60: [ RUN ] HBondTests/HbondModuleTest.Works/68 60: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 60: Analyzed 2 frames, last time 10.000 60: 60: Checking for overlap in atoms between Water (3480 atoms) and Water (3480 atoms) 60: Selection 'Water' has 1160 acceptors and 1160 donors. 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 60: Memory Limitation 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c02087 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] HBondTests/HbondModuleTest.Works/68 (512 ms) 60: [ RUN ] HBondTests/HbondModuleTest.Works/69 60: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 60: Analyzed 2 frames, last time 10.000 60: 60: Checking for overlap in atoms between Water (3480 atoms) and Water (3480 atoms) 60: Selection 'Water' has 1160 acceptors and 1160 donors. 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 60: Memory Limitation 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c02087 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] HBondTests/HbondModuleTest.Works/69 (485 ms) 60: [ RUN ] HBondTests/HbondModuleTest.Works/70 60: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 60: Analyzed 2 frames, last time 10.000 60: 60: Checking for overlap in atoms between Water (3480 atoms) and Water (3480 atoms) 60: Selection 'Water' has 1160 acceptors and 1160 donors. 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 60: Memory Limitation 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c02087 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] HBondTests/HbondModuleTest.Works/70 (493 ms) 60: [ RUN ] HBondTests/HbondModuleTest.Works/71 60: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 60: Analyzed 2 frames, last time 10.000 60: 60: Checking for overlap in atoms between Water (3480 atoms) and Water (3480 atoms) 60: Selection 'Water' has 1160 acceptors and 1160 donors. 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 60: Memory Limitation 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c02087 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] HBondTests/HbondModuleTest.Works/71 (493 ms) 60: [ RUN ] HBondTests/HbondModuleTest.Works/72 60: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 60: Analyzed 2 frames, last time 10.000 60: 60: Checking for overlap in atoms between Water (3480 atoms) and Water (3480 atoms) 60: Selection 'Water' has 1160 acceptors and 1160 donors. 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 60: Memory Limitation 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c02087 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] HBondTests/HbondModuleTest.Works/72 (518 ms) 60: [ RUN ] HBondTests/HbondModuleTest.Works/73 60: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 60: Analyzed 2 frames, last time 10.000 60: 60: Checking for overlap in atoms between Water (3480 atoms) and Water (3480 atoms) 60: Selection 'Water' has 1160 acceptors and 1160 donors. 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 60: Memory Limitation 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c02087 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] HBondTests/HbondModuleTest.Works/73 (507 ms) 60: [ RUN ] HBondTests/HbondModuleTest.Works/74 60: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 60: Analyzed 2 frames, last time 10.000 60: 60: Checking for overlap in atoms between Water (3480 atoms) and Water (3480 atoms) 60: Selection 'Water' has 1160 acceptors and 1160 donors. 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 60: Memory Limitation 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c02087 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] HBondTests/HbondModuleTest.Works/74 (518 ms) 60: [ RUN ] HBondTests/HbondModuleTest.Works/75 60: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 60: Analyzed 2 frames, last time 10.000 60: 60: Checking for overlap in atoms between Water (3480 atoms) and Water (3480 atoms) 60: Selection 'Water' has 1160 acceptors and 1160 donors. 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 60: Memory Limitation 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c02087 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] HBondTests/HbondModuleTest.Works/75 (517 ms) 60: [ RUN ] HBondTests/HbondModuleTest.Works/76 60: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 60: Analyzed 2 frames, last time 10.000 60: 60: Checking for overlap in atoms between Water (3480 atoms) and Water (3480 atoms) 60: Selection 'Water' has 1160 acceptors and 1160 donors. 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 60: Memory Limitation 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c02087 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] HBondTests/HbondModuleTest.Works/76 (502 ms) 60: [ RUN ] HBondTests/HbondModuleTest.Works/77 60: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 60: Analyzed 2 frames, last time 10.000 60: 60: Checking for overlap in atoms between Water (3480 atoms) and Water (3480 atoms) 60: Selection 'Water' has 1160 acceptors and 1160 donors. 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 60: Memory Limitation 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c02087 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] HBondTests/HbondModuleTest.Works/77 (499 ms) 60: [ RUN ] HBondTests/HbondModuleTest.Works/78 60: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 60: Analyzed 2 frames, last time 10.000 60: 60: Checking for overlap in atoms between Water (3480 atoms) and Water (3480 atoms) 60: Selection 'Water' has 1160 acceptors and 1160 donors. 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 60: Memory Limitation 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c02087 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] HBondTests/HbondModuleTest.Works/78 (484 ms) 60: [ RUN ] HBondTests/HbondModuleTest.Works/79 60: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 60: Analyzed 2 frames, last time 10.000 60: 60: Checking for overlap in atoms between Water (3480 atoms) and Water (3480 atoms) 60: Selection 'Water' has 1160 acceptors and 1160 donors. 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 60: Memory Limitation 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c02087 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] HBondTests/HbondModuleTest.Works/79 (510 ms) 60: [ RUN ] HBondTests/HbondModuleTest.Works/80 60: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 60: Analyzed 2 frames, last time 10.000 60: 60: Checking for overlap in atoms between Water (3480 atoms) and Water (3480 atoms) 60: Selection 'Water' has 1160 acceptors and 1160 donors. 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 60: Memory Limitation 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c02087 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] HBondTests/HbondModuleTest.Works/80 (461 ms) 60: [ RUN ] HBondTests/HbondModuleTest.Works/81 60: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 60: Analyzed 2 frames, last time 10.000 60: 60: Checking for overlap in atoms between Water (3480 atoms) and Water (3480 atoms) 60: Selection 'Water' has 1160 acceptors and 1160 donors. 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 60: Memory Limitation 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c02087 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] HBondTests/HbondModuleTest.Works/81 (474 ms) 60: [ RUN ] HBondTests/HbondModuleTest.Works/82 60: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 60: Analyzed 2 frames, last time 10.000 60: 60: Checking for overlap in atoms between Water (3480 atoms) and Water (3480 atoms) 60: Selection 'Water' has 1160 acceptors and 1160 donors. 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 60: Memory Limitation 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c02087 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] HBondTests/HbondModuleTest.Works/82 (457 ms) 60: [ RUN ] HBondTests/HbondModuleTest.Works/83 60: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 60: Analyzed 2 frames, last time 10.000 60: 60: Checking for overlap in atoms between Water (3480 atoms) and Water (3480 atoms) 60: Selection 'Water' has 1160 acceptors and 1160 donors. 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 60: Memory Limitation 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c02087 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] HBondTests/HbondModuleTest.Works/83 (469 ms) 60: [ RUN ] HBondTests/HbondModuleTest.Works/84 60: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 60: Analyzed 2 frames, last time 10.000 60: 60: Checking for overlap in atoms between Water (3480 atoms) and Water (3480 atoms) 60: Selection 'Water' has 1160 acceptors and 1160 donors. 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 60: Memory Limitation 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c02087 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] HBondTests/HbondModuleTest.Works/84 (490 ms) 60: [ RUN ] HBondTests/HbondModuleTest.Works/85 60: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 60: Analyzed 2 frames, last time 10.000 60: 60: Checking for overlap in atoms between Water (3480 atoms) and Water (3480 atoms) 60: Selection 'Water' has 1160 acceptors and 1160 donors. 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 60: Memory Limitation 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c02087 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] HBondTests/HbondModuleTest.Works/85 (493 ms) 60: [ RUN ] HBondTests/HbondModuleTest.Works/86 60: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 60: Analyzed 2 frames, last time 10.000 60: 60: Checking for overlap in atoms between Water (3480 atoms) and Water (3480 atoms) 60: Selection 'Water' has 1160 acceptors and 1160 donors. 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 60: Memory Limitation 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c02087 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] HBondTests/HbondModuleTest.Works/86 (486 ms) 60: [ RUN ] HBondTests/HbondModuleTest.Works/87 60: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 60: Analyzed 2 frames, last time 10.000 60: 60: Checking for overlap in atoms between Water (3480 atoms) and Water (3480 atoms) 60: Selection 'Water' has 1160 acceptors and 1160 donors. 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 60: Memory Limitation 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c02087 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] HBondTests/HbondModuleTest.Works/87 (481 ms) 60: [ RUN ] HBondTests/HbondModuleTest.Works/88 60: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 60: Analyzed 2 frames, last time 10.000 60: 60: Checking for overlap in atoms between Water (3480 atoms) and Water (3480 atoms) 60: Selection 'Water' has 1160 acceptors and 1160 donors. 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 60: Memory Limitation 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c02087 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] HBondTests/HbondModuleTest.Works/88 (503 ms) 60: [ RUN ] HBondTests/HbondModuleTest.Works/89 60: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 60: Analyzed 2 frames, last time 10.000 60: 60: Checking for overlap in atoms between Water (3480 atoms) and Water (3480 atoms) 60: Selection 'Water' has 1160 acceptors and 1160 donors. 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 60: Memory Limitation 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c02087 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] HBondTests/HbondModuleTest.Works/89 (496 ms) 60: [ RUN ] HBondTests/HbondModuleTest.Works/90 60: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 60: Analyzed 2 frames, last time 10.000 60: 60: Checking for overlap in atoms between Water (3480 atoms) and Water (3480 atoms) 60: Selection 'Water' has 1160 acceptors and 1160 donors. 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 60: Memory Limitation 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c02087 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] HBondTests/HbondModuleTest.Works/90 (503 ms) 60: [ RUN ] HBondTests/HbondModuleTest.Works/91 60: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 60: Analyzed 2 frames, last time 10.000 60: 60: Checking for overlap in atoms between Water (3480 atoms) and Water (3480 atoms) 60: Selection 'Water' has 1160 acceptors and 1160 donors. 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 60: Memory Limitation 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c02087 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] HBondTests/HbondModuleTest.Works/91 (501 ms) 60: [ RUN ] HBondTests/HbondModuleTest.Works/92 60: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 60: Analyzed 2 frames, last time 10.000 60: 60: Checking for overlap in atoms between Water (3480 atoms) and Water (3480 atoms) 60: Selection 'Water' has 1160 acceptors and 1160 donors. 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 60: Memory Limitation 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c02087 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] HBondTests/HbondModuleTest.Works/92 (487 ms) 60: [ RUN ] HBondTests/HbondModuleTest.Works/93 60: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 60: Analyzed 2 frames, last time 10.000 60: 60: Checking for overlap in atoms between Water (3480 atoms) and Water (3480 atoms) 60: Selection 'Water' has 1160 acceptors and 1160 donors. 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 60: Memory Limitation 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c02087 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] HBondTests/HbondModuleTest.Works/93 (515 ms) 60: [ RUN ] HBondTests/HbondModuleTest.Works/94 60: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 60: Analyzed 2 frames, last time 10.000 60: 60: Checking for overlap in atoms between Water (3480 atoms) and Water (3480 atoms) 60: Selection 'Water' has 1160 acceptors and 1160 donors. 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 60: Memory Limitation 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c02087 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] HBondTests/HbondModuleTest.Works/94 (501 ms) 60: [ RUN ] HBondTests/HbondModuleTest.Works/95 60: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 60: Analyzed 2 frames, last time 10.000 60: 60: Checking for overlap in atoms between Water (3480 atoms) and Water (3480 atoms) 60: Selection 'Water' has 1160 acceptors and 1160 donors. 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 60: Memory Limitation 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c02087 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] HBondTests/HbondModuleTest.Works/95 (505 ms) 60: [----------] 96 tests from HBondTests/HbondModuleTest (39355 ms total) 60: 60: [----------] 4 tests from MoleculeTests/ScatteringModule 60: [ RUN ] MoleculeTests/ScatteringModule.DirectMode/0 60: Reading frames from pdb file Reading frame 0 time 0.000 '', 156 atoms 60: Last frame 0 time 0.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: A. V. Shvetsov, A. E. Schmidt, D. V. Lebedev, V. V. Isaev-Ivanov 60: Method for calculating small-angle neutron scattering spectra using all-atom 60: molecular dynamics trajectories 60: Journal of Surface Investigation. X-ray, Synchrotron and Neutron Techniques (2013) 60: DOI: 10.1134/S1027451013060372 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/ScatteringModule.DirectMode/0 (69 ms) 60: [ RUN ] MoleculeTests/ScatteringModule.DirectMode/1 60: Reading frames from pdb file Reading frame 0 time 0.000 '', 156 atoms 60: Last frame 0 time 0.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: A. V. Shvetsov, A. E. Schmidt, D. V. Lebedev, V. V. Isaev-Ivanov 60: Method for calculating small-angle neutron scattering spectra using all-atom 60: molecular dynamics trajectories 60: Journal of Surface Investigation. X-ray, Synchrotron and Neutron Techniques (2013) 60: DOI: 10.1134/S1027451013060372 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: D. T. Cromer, J. B. Mann 60: X-ray scattering factors computed from numerical Hartree-Fock wave functions 60: Acta Cryst. A (1968) 60: DOI: 10.1107/S0567739468000550 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/ScatteringModule.DirectMode/1 (1799 ms) 60: [ RUN ] MoleculeTests/ScatteringModule.MCMode/0 60: Reading frames from pdb file Reading frame 0 time 0.000 '', 156 atoms 60: Last frame 0 time 0.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: A. V. Shvetsov, A. E. Schmidt, D. V. Lebedev, V. V. Isaev-Ivanov 60: Method for calculating small-angle neutron scattering spectra using all-atom 60: molecular dynamics trajectories 60: Journal of Surface Investigation. X-ray, Synchrotron and Neutron Techniques (2013) 60: DOI: 10.1134/S1027451013060372 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/ScatteringModule.MCMode/0 (78 ms) 60: [ RUN ] MoleculeTests/ScatteringModule.MCMode/1 60: Reading frames from pdb file Reading frame 0 time 0.000 '', 156 atoms 60: Last frame 0 time 0.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: A. V. Shvetsov, A. E. Schmidt, D. V. Lebedev, V. V. Isaev-Ivanov 60: Method for calculating small-angle neutron scattering spectra using all-atom 60: molecular dynamics trajectories 60: Journal of Surface Investigation. X-ray, Synchrotron and Neutron Techniques (2013) 60: DOI: 10.1134/S1027451013060372 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: D. T. Cromer, J. B. Mann 60: X-ray scattering factors computed from numerical Hartree-Fock wave functions 60: Acta Cryst. A (1968) 60: DOI: 10.1107/S0567739468000550 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/ScatteringModule.MCMode/1 (429 ms) 60: [----------] 4 tests from MoleculeTests/ScatteringModule (2399 ms total) 60: 60: [----------] Global test environment tear-down 60: [==========] 393 tests from 21 test suites ran. (77601 ms total) 60: [ PASSED ] 393 tests. 60/92 Test #60: TrajectoryAnalysisUnitTests ............... Passed 77.77 sec test 61 Start 61: EnergyAnalysisUnitTests 61: Test command: /build/reproducible-path/gromacs-2025.1/build/basic/bin/energyanalysis-test "--gtest_output=xml:/build/reproducible-path/gromacs-2025.1/build/basic/Testing/Temporary/EnergyAnalysisUnitTests.xml" 61: Working Directory: /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/energyanalysis/tests 61: Test timeout computed to be: 30 61: [==========] Running 12 tests from 5 test suites. 61: [----------] Global test environment set-up. 61: [----------] 2 tests from EnergyTermTest 61: [ RUN ] EnergyTermTest.ConstructWorks 61: [ OK ] EnergyTermTest.ConstructWorks (0 ms) 61: [ RUN ] EnergyTermTest.AddFrameWorks 61: [ OK ] EnergyTermTest.AddFrameWorks (0 ms) 61: [----------] 2 tests from EnergyTermTest (0 ms total) 61: 61: [----------] 1 test from DhdlTest 61: [ RUN ] DhdlTest.ExtractDhdl 61: Opened /build/reproducible-path/gromacs-2025.1/src/gromacs/energyanalysis/tests/dhdl.edr as double precision energy file 61: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/energyanalysis/tests/dhdl.tpr, VERSION 2016-dev-20160810-e3ded7f (double precision) 61: Note: file tpx version 110, software tpx version 137 61: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.010 Reading energy frame 2 time 0.020 Reading energy frame 3 time 0.030 Reading energy frame 4 time 0.040 Reading energy frame 5 time 0.050 Reading energy frame 6 time 0.060 Reading energy frame 7 time 0.070 Reading energy frame 8 time 0.080 Reading energy frame 9 time 0.090 Reading energy frame 10 time 0.100 Reading energy frame 11 time 0.110 Reading energy frame 12 time 0.120 Reading energy frame 13 time 0.130 Reading energy frame 14 time 0.140 Reading energy frame 15 time 0.150 Reading energy frame 16 time 0.160 Reading energy frame 17 time 0.170 Reading energy frame 18 time 0.180 Reading energy frame 19 time 0.190 Reading energy frame 20 time 0.200 Reading energy frame 30 time 0.300 Reading energy frame 40 time 0.400 Reading energy frame 50 time 0.500 Reading energy frame 60 time 0.600 Reading energy frame 70 time 0.700 Reading energy frame 80 time 0.800 Reading energy frame 90 time 0.900 Reading energy frame 100 time 1.000 Last energy frame read 100 time 1.000 61: 61: 61: Wrote 8 lambda values with 101 samples as 808 dH data blocks to /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/energyanalysis/tests/Testing/Temporary/DhdlTest_ExtractDhdl_dhdl.xvg 61: [ OK ] DhdlTest.ExtractDhdl (55 ms) 61: [----------] 1 test from DhdlTest (58 ms total) 61: 61: [----------] 1 test from OriresTest 61: [ RUN ] OriresTest.ExtractOrires 61: Opened /build/reproducible-path/gromacs-2025.1/src/gromacs/energyanalysis/tests/orires.edr as single precision energy file 61: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/energyanalysis/tests/orires.tpr, VERSION 2017-dev-20170725-fea8651 (single precision) 61: Note: file tpx version 111, software tpx version 137 61: Found 7 orientation restraints with 1 experimentsSelect the orientation restraint labels you want (-1 is all) 61: End your selection with 0 61: Selecting all 7 orientation restraints 61: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.002 Reading energy frame 2 time 0.004 Reading energy frame 3 time 0.006 Reading energy frame 4 time 0.008 Reading energy frame 5 time 0.010 Reading energy frame 6 time 0.012 Reading energy frame 7 time 0.014 Reading energy frame 8 time 0.016 Reading energy frame 9 time 0.018 Reading energy frame 10 time 0.020 Last energy frame read 10 time 0.020 61: [ OK ] OriresTest.ExtractOrires (84 ms) 61: [----------] 1 test from OriresTest (85 ms total) 61: 61: [----------] 5 tests from EnergyTest 61: [ RUN ] EnergyTest.ExtractEnergy 61: Opened /build/reproducible-path/gromacs-2025.1/src/gromacs/energyanalysis/tests/ener.edr as single precision energy file 61: 61: Select the terms you want from the following list by 61: selecting either (part of) the name or the number or a combination. 61: End your selection with an empty line or a zero. 61: ------------------------------------------------------------------- 61: 1 LJ-(SR) 2 Disper.-corr. 3 Coulomb-(SR) 4 Coul.-recip. 61: 5 Potential 6 Kinetic-En. 7 Total-Energy 8 Temperature 61: 9 Pres.-DC 10 Pressure 11 Box-X 12 Box-Y 61: 13 Box-Z 14 Volume 15 Density 16 pV 61: 17 Enthalpy 18 Vir-XX 19 Vir-XY 20 Vir-XZ 61: 21 Vir-YX 22 Vir-YY 23 Vir-YZ 24 Vir-ZX 61: 25 Vir-ZY 26 Vir-ZZ 27 Pres-XX 28 Pres-XY 61: 29 Pres-XZ 30 Pres-YX 31 Pres-YY 32 Pres-YZ 61: 33 Pres-ZX 34 Pres-ZY 35 Pres-ZZ 36 #Surf*SurfTen 61: 37 Box-Vel-XX 38 Box-Vel-YY 39 Box-Vel-ZZ 40 T-System 61: 61: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.200 Reading energy frame 2 time 0.400 Reading energy frame 3 time 0.600 Reading energy frame 4 time 0.800 Reading energy frame 5 time 1.000 Reading energy frame 6 time 1.200 Reading energy frame 7 time 1.400 Reading energy frame 8 time 1.600 Reading energy frame 9 time 1.800 Reading energy frame 10 time 2.000 Reading energy frame 11 time 2.200 Reading energy frame 12 time 2.400 Reading energy frame 13 time 2.600 Reading energy frame 14 time 2.800 Reading energy frame 15 time 3.000 Reading energy frame 16 time 3.200 Reading energy frame 17 time 3.400 Reading energy frame 18 time 3.600 Reading energy frame 19 time 3.800 Reading energy frame 20 time 4.000 Reading energy frame 30 time 6.000 Reading energy frame 40 time 8.000 Reading energy frame 50 time 10.000 Last energy frame read 50 time 10.000 61: 61: Statistics over 5001 steps [ 0.0000 through 10.0000 ps ], 3 data sets 61: All statistics are over 5001 points 61: 61: Energy Average Err.Est. RMSD Tot-Drift 61: ------------------------------------------------------------------------------- 61: Potential -34142.2 39 228.993 -62.8906 (kJ/mol) 61: Kinetic En. 6132.38 0.42 119.428 -0.266996 (kJ/mol) 61: Total Energy -28009.8 39 258.637 -63.1577 (kJ/mol) 61: [ OK ] EnergyTest.ExtractEnergy (16 ms) 61: [ RUN ] EnergyTest.ExtractEnergyByNumber 61: Opened /build/reproducible-path/gromacs-2025.1/src/gromacs/energyanalysis/tests/ener.edr as single precision energy file 61: 61: Select the terms you want from the following list by 61: selecting either (part of) the name or the number or a combination. 61: End your selection with an empty line or a zero. 61: ------------------------------------------------------------------- 61: 1 LJ-(SR) 2 Disper.-corr. 3 Coulomb-(SR) 4 Coul.-recip. 61: 5 Potential 6 Kinetic-En. 7 Total-Energy 8 Temperature 61: 9 Pres.-DC 10 Pressure 11 Box-X 12 Box-Y 61: 13 Box-Z 14 Volume 15 Density 16 pV 61: 17 Enthalpy 18 Vir-XX 19 Vir-XY 20 Vir-XZ 61: 21 Vir-YX 22 Vir-YY 23 Vir-YZ 24 Vir-ZX 61: 25 Vir-ZY 26 Vir-ZZ 27 Pres-XX 28 Pres-XY 61: 29 Pres-XZ 30 Pres-YX 31 Pres-YY 32 Pres-YZ 61: 33 Pres-ZX 34 Pres-ZY 35 Pres-ZZ 36 #Surf*SurfTen 61: 37 Box-Vel-XX 38 Box-Vel-YY 39 Box-Vel-ZZ 40 T-System 61: 61: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.200 Reading energy frame 2 time 0.400 Reading energy frame 3 time 0.600 Reading energy frame 4 time 0.800 Reading energy frame 5 time 1.000 Reading energy frame 6 time 1.200 Reading energy frame 7 time 1.400 Reading energy frame 8 time 1.600 Reading energy frame 9 time 1.800 Reading energy frame 10 time 2.000 Reading energy frame 11 time 2.200 Reading energy frame 12 time 2.400 Reading energy frame 13 time 2.600 Reading energy frame 14 time 2.800 Reading energy frame 15 time 3.000 Reading energy frame 16 time 3.200 Reading energy frame 17 time 3.400 Reading energy frame 18 time 3.600 Reading energy frame 19 time 3.800 Reading energy frame 20 time 4.000 Reading energy frame 30 time 6.000 Reading energy frame 40 time 8.000 Reading energy frame 50 time 10.000 Last energy frame read 50 time 10.000 61: 61: Statistics over 5001 steps [ 0.0000 through 10.0000 ps ], 3 data sets 61: All statistics are over 5001 points 61: 61: Energy Average Err.Est. RMSD Tot-Drift 61: ------------------------------------------------------------------------------- 61: Coul. recip. 302.771 2.8 17.5152 12.5403 (kJ/mol) 61: Kinetic En. 6132.38 0.42 119.428 -0.266996 (kJ/mol) 61: Pres. DC -268.49 3 8.52175 13.2804 (bar) 61: [ OK ] EnergyTest.ExtractEnergyByNumber (15 ms) 61: [ RUN ] EnergyTest.ExtractEnergyMixed 61: Opened /build/reproducible-path/gromacs-2025.1/src/gromacs/energyanalysis/tests/ener.edr as single precision energy file 61: 61: Select the terms you want from the following list by 61: selecting either (part of) the name or the number or a combination. 61: End your selection with an empty line or a zero. 61: ------------------------------------------------------------------- 61: 1 LJ-(SR) 2 Disper.-corr. 3 Coulomb-(SR) 4 Coul.-recip. 61: 5 Potential 6 Kinetic-En. 7 Total-Energy 8 Temperature 61: 9 Pres.-DC 10 Pressure 11 Box-X 12 Box-Y 61: 13 Box-Z 14 Volume 15 Density 16 pV 61: 17 Enthalpy 18 Vir-XX 19 Vir-XY 20 Vir-XZ 61: 21 Vir-YX 22 Vir-YY 23 Vir-YZ 24 Vir-ZX 61: 25 Vir-ZY 26 Vir-ZZ 27 Pres-XX 28 Pres-XY 61: 29 Pres-XZ 30 Pres-YX 31 Pres-YY 32 Pres-YZ 61: 33 Pres-ZX 34 Pres-ZY 35 Pres-ZZ 36 #Surf*SurfTen 61: 37 Box-Vel-XX 38 Box-Vel-YY 39 Box-Vel-ZZ 40 T-System 61: 61: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.200 Reading energy frame 2 time 0.400 Reading energy frame 3 time 0.600 Reading energy frame 4 time 0.800 Reading energy frame 5 time 1.000 Reading energy frame 6 time 1.200 Reading energy frame 7 time 1.400 Reading energy frame 8 time 1.600 Reading energy frame 9 time 1.800 Reading energy frame 10 time 2.000 Reading energy frame 11 time 2.200 Reading energy frame 12 time 2.400 Reading energy frame 13 time 2.600 Reading energy frame 14 time 2.800 Reading energy frame 15 time 3.000 Reading energy frame 16 time 3.200 Reading energy frame 17 time 3.400 Reading energy frame 18 time 3.600 Reading energy frame 19 time 3.800 Reading energy frame 20 time 4.000 Reading energy frame 30 time 6.000 Reading energy frame 40 time 8.000 Reading energy frame 50 time 10.000 Last energy frame read 50 time 10.000 61: 61: Statistics over 5001 steps [ 0.0000 through 10.0000 ps ], 4 data sets 61: All statistics are over 5001 points 61: 61: Energy Average Err.Est. RMSD Tot-Drift 61: ------------------------------------------------------------------------------- 61: Total Energy -28009.8 39 258.637 -63.1577 (kJ/mol) 61: Pressure 5.34371 4.1 605.307 -4.88771 (bar) 61: Box-Z 2.92457 0.0054 0.0151558 0.0234974 (nm) 61: Volume 25.0162 0.14 0.386769 0.598615 (nm^3) 61: [ OK ] EnergyTest.ExtractEnergyMixed (25 ms) 61: [ RUN ] EnergyTest.ExtractEnergyWithNumberInName 61: Opened /build/reproducible-path/gromacs-2025.1/src/gromacs/energyanalysis/tests/ener_numberInName.edr as single precision energy file 61: 61: Select the terms you want from the following list by 61: selecting either (part of) the name or the number or a combination. 61: End your selection with an empty line or a zero. 61: ------------------------------------------------------------------- 61: 1 Bond 2 Angle 3 Proper-Dih. 4 Per.-Imp.-Dih. 61: 5 LJ-14 6 Coulomb-14 7 LJ-(SR) 8 Coulomb-(SR) 61: 9 Coul.-recip. 10 Potential 11 Kinetic-En. 12 Total-Energy 61: 13 Conserved-En. 14 Temperature 15 Pressure 16 Constr.-rmsd 61: 17 Vir-XX 18 Vir-XY 19 Vir-XZ 20 Vir-YX 61: 21 Vir-YY 22 Vir-YZ 23 Vir-ZX 24 Vir-ZY 61: 25 Vir-ZZ 26 Pres-XX 27 Pres-XY 28 Pres-XZ 61: 29 Pres-YX 30 Pres-YY 31 Pres-YZ 32 Pres-ZX 61: 33 Pres-ZY 34 Pres-ZZ 35 #Surf*SurfTen 36 2CosZ*Vel-X 61: 37 1/Viscosity 38 T-System 39 Lamb-System 61: 61: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.002 Reading energy frame 2 time 0.004 Last energy frame read 2 time 0.004 61: 61: Statistics over 3 steps [ 0.0000 through 0.0040 ps ], 1 data sets 61: All statistics are over 3 points (frames) 61: 61: Energy Average Err.Est. RMSD Tot-Drift 61: ------------------------------------------------------------------------------- 61: 1/Viscosity 57767.2 -- 10666.2 -25998 (m s/kg) 61: [ OK ] EnergyTest.ExtractEnergyWithNumberInName (6 ms) 61: [ RUN ] EnergyTest.ExtractEnergyWithNumberInNameAndAlsoByNumber 61: Opened /build/reproducible-path/gromacs-2025.1/src/gromacs/energyanalysis/tests/ener_numberInName.edr as single precision energy file 61: 61: Select the terms you want from the following list by 61: selecting either (part of) the name or the number or a combination. 61: End your selection with an empty line or a zero. 61: ------------------------------------------------------------------- 61: 1 Bond 2 Angle 3 Proper-Dih. 4 Per.-Imp.-Dih. 61: 5 LJ-14 6 Coulomb-14 7 LJ-(SR) 8 Coulomb-(SR) 61: 9 Coul.-recip. 10 Potential 11 Kinetic-En. 12 Total-Energy 61: 13 Conserved-En. 14 Temperature 15 Pressure 16 Constr.-rmsd 61: 17 Vir-XX 18 Vir-XY 19 Vir-XZ 20 Vir-YX 61: 21 Vir-YY 22 Vir-YZ 23 Vir-ZX 24 Vir-ZY 61: 25 Vir-ZZ 26 Pres-XX 27 Pres-XY 28 Pres-XZ 61: 29 Pres-YX 30 Pres-YY 31 Pres-YZ 32 Pres-ZX 61: 33 Pres-ZY 34 Pres-ZZ 35 #Surf*SurfTen 36 2CosZ*Vel-X 61: 37 1/Viscosity 38 T-System 39 Lamb-System 61: 61: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.002 Reading energy frame 2 time 0.004 Last energy frame read 2 time 0.004 61: 61: Statistics over 3 steps [ 0.0000 through 0.0040 ps ], 2 data sets 61: All statistics are over 3 points (frames) 61: 61: Energy Average Err.Est. RMSD Tot-Drift 61: ------------------------------------------------------------------------------- 61: LJ (SR) -14.1095 -- 0.384124 0.932214 (kJ/mol) 61: 1/Viscosity 57767.2 -- 10666.2 -25998 (m s/kg) 61: [ OK ] EnergyTest.ExtractEnergyWithNumberInNameAndAlsoByNumber (6 ms) 61: [----------] 5 tests from EnergyTest (73 ms total) 61: 61: [----------] 3 tests from ViscosityTest 61: [ RUN ] ViscosityTest.EinsteinViscosity 61: Opened /build/reproducible-path/gromacs-2025.1/src/gromacs/energyanalysis/tests/ener.edr as single precision energy file 61: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.200 Reading energy frame 2 time 0.400 Reading energy frame 3 time 0.600 Reading energy frame 4 time 0.800 Reading energy frame 5 time 1.000 Reading energy frame 6 time 1.200 Reading energy frame 7 time 1.400 Reading energy frame 8 time 1.600 Reading energy frame 9 time 1.800 Reading energy frame 10 time 2.000 Reading energy frame 11 time 2.200 Reading energy frame 12 time 2.400 Reading energy frame 13 time 2.600 Reading energy frame 14 time 2.800 Reading energy frame 15 time 3.000 Reading energy frame 16 time 3.200 Reading energy frame 17 time 3.400 Reading energy frame 18 time 3.600 Reading energy frame 19 time 3.800 Reading energy frame 20 time 4.000 Reading energy frame 30 time 6.000 Reading energy frame 40 time 8.000 Reading energy frame 50 time 10.000 Last energy frame read 50 time 10.000 61: 61: Statistics over 5001 steps [ 0.0000 through 10.0000 ps ], 12 data sets 61: All statistics are over 5001 points 61: 61: Energy Average Err.Est. RMSD Tot-Drift 61: ------------------------------------------------------------------------------- 61: Pres-XX 20.2092 65 717.193 185.978 (bar) 61: Pres-XY -47.7351 39 372.522 207.456 (bar) 61: Pres-XZ 11.477 31 379.79 6.80818 (bar) 61: Pres-YX -47.7106 39 372.525 207.5 (bar) 61: Pres-YY 38.9241 40 803.899 -27.1505 (bar) 61: Pres-YZ -41.3534 45 401.216 114.663 (bar) 61: Pres-ZX 11.5238 31 379.804 6.91707 (bar) 61: Pres-ZY -41.3119 45 401.196 114.743 (bar) 61: Pres-ZZ -43.1021 63 748.522 -173.491 (bar) 61: Temperature 300.001 0.02 5.8425 -0.0130558 (K) 61: Volume 25.0162 0.14 0.386769 0.598615 (nm^3) 61: Pressure 5.34371 4.1 605.307 -4.88771 (bar) 61: 61: Computing shear viscosity using the Einstein relation with 6 start points separated by 0.2 ps 61: [ OK ] ViscosityTest.EinsteinViscosity (43 ms) 61: [ RUN ] ViscosityTest.EinsteinViscosityIntegral 61: Opened /build/reproducible-path/gromacs-2025.1/src/gromacs/energyanalysis/tests/ener.edr as single precision energy file 61: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.200 Reading energy frame 2 time 0.400 Reading energy frame 3 time 0.600 Reading energy frame 4 time 0.800 Reading energy frame 5 time 1.000 Reading energy frame 6 time 1.200 Reading energy frame 7 time 1.400 Reading energy frame 8 time 1.600 Reading energy frame 9 time 1.800 Reading energy frame 10 time 2.000 Reading energy frame 11 time 2.200 Reading energy frame 12 time 2.400 Reading energy frame 13 time 2.600 Reading energy frame 14 time 2.800 Reading energy frame 15 time 3.000 Reading energy frame 16 time 3.200 Reading energy frame 17 time 3.400 Reading energy frame 18 time 3.600 Reading energy frame 19 time 3.800 Reading energy frame 20 time 4.000 Reading energy frame 30 time 6.000 Reading energy frame 40 time 8.000 Reading energy frame 50 time 10.000 Last energy frame read 50 time 10.000 61: 61: Statistics over 5001 steps [ 0.0000 through 10.0000 ps ], 12 data sets 61: All statistics are over 5001 points 61: 61: Energy Average Err.Est. RMSD Tot-Drift 61: ------------------------------------------------------------------------------- 61: Pres-XX 20.2092 65 717.193 185.978 (bar) 61: Pres-XY -47.7351 39 372.522 207.456 (bar) 61: Pres-XZ 11.477 31 379.79 6.80818 (bar) 61: Pres-YX -47.7106 39 372.525 207.5 (bar) 61: Pres-YY 38.9241 40 803.899 -27.1505 (bar) 61: Pres-YZ -41.3534 45 401.216 114.663 (bar) 61: Pres-ZX 11.5238 31 379.804 6.91707 (bar) 61: Pres-ZY -41.3119 45 401.196 114.743 (bar) 61: Pres-ZZ -43.1021 63 748.522 -173.491 (bar) 61: Temperature 300.001 0.02 5.8425 -0.0130558 (K) 61: Volume 25.0162 0.14 0.386769 0.598615 (nm^3) 61: Pressure 5.34371 4.1 605.307 -4.88771 (bar) 61: 61: Computing shear viscosity using the Einstein relation with 6 start points separated by 0.2 ps 61: [ OK ] ViscosityTest.EinsteinViscosityIntegral (37 ms) 61: [ RUN ] ViscosityTest.EinsteinViscosityDefaultArguments 61: Opened /build/reproducible-path/gromacs-2025.1/src/gromacs/energyanalysis/tests/ener.edr as single precision energy file 61: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.200 Reading energy frame 2 time 0.400 Reading energy frame 3 time 0.600 Reading energy frame 4 time 0.800 Reading energy frame 5 time 1.000 Reading energy frame 6 time 1.200 Reading energy frame 7 time 1.400 Reading energy frame 8 time 1.600 Reading energy frame 9 time 1.800 Reading energy frame 10 time 2.000 Reading energy frame 11 time 2.200 Reading energy frame 12 time 2.400 Reading energy frame 13 time 2.600 Reading energy frame 14 time 2.800 Reading energy frame 15 time 3.000 Reading energy frame 16 time 3.200 Reading energy frame 17 time 3.400 Reading energy frame 18 time 3.600 Reading energy frame 19 time 3.800 Reading energy frame 20 time 4.000 Reading energy frame 30 time 6.000 Reading energy frame 40 time 8.000 Reading energy frame 50 time 10.000 Last energy frame read 50 time 10.000 61: 61: Statistics over 5001 steps [ 0.0000 through 10.0000 ps ], 12 data sets 61: All statistics are over 5001 points 61: 61: Energy Average Err.Est. RMSD Tot-Drift 61: ------------------------------------------------------------------------------- 61: Pres-XX 20.2092 65 717.193 185.978 (bar) 61: Pres-XY -47.7351 39 372.522 207.456 (bar) 61: Pres-XZ 11.477 31 379.79 6.80818 (bar) 61: Pres-YX -47.7106 39 372.525 207.5 (bar) 61: Pres-YY 38.9241 40 803.899 -27.1505 (bar) 61: Pres-YZ -41.3534 45 401.216 114.663 (bar) 61: Pres-ZX 11.5238 31 379.804 6.91707 (bar) 61: Pres-ZY -41.3119 45 401.196 114.743 (bar) 61: Pres-ZZ -43.1021 63 748.522 -173.491 (bar) 61: Temperature 300.001 0.02 5.8425 -0.0130558 (K) 61: Volume 25.0162 0.14 0.386769 0.598615 (nm^3) 61: Pressure 5.34371 4.1 605.307 -4.88771 (bar) 61: 61: Computing shear viscosity using the Einstein relation with 6 start points separated by 0.2 ps 61: [ OK ] ViscosityTest.EinsteinViscosityDefaultArguments (37 ms) 61: [----------] 3 tests from ViscosityTest (119 ms total) 61: 61: [----------] Global test environment tear-down 61: [==========] 12 tests from 5 test suites ran. (337 ms total) 61: [ PASSED ] 12 tests. 61/92 Test #61: EnergyAnalysisUnitTests ................... Passed 0.41 sec test 62 Start 62: ToolUnitTests 62: Test command: /build/reproducible-path/gromacs-2025.1/build/basic/bin/tool-test "--gtest_output=xml:/build/reproducible-path/gromacs-2025.1/build/basic/Testing/Temporary/ToolUnitTests.xml" 62: Working Directory: /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/tools/tests 62: Test timeout computed to be: 1920 62: [==========] Running 63 tests from 8 test suites. 62: [----------] Global test environment set-up. 62: [----------] 2 tests from DumpTest 62: 62: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/tools/tests/Testing/Temporary/DumpTest_lysozyme.mdp]: 62: For a correct single-point energy evaluation with nsteps = 0, use 62: continuation = yes to avoid constraining the input coordinates. 62: 62: Generating 1-4 interactions: fudge = 0.5 62: 62: NOTE 2 [file lysozyme.top, line 1465]: 62: System has non-zero total charge: 2.000000 62: Total charge should normally be an integer. See 62: https://manual.gromacs.org/current/user-guide/floating-point.html 62: for discussion on how close it should be to an integer. 62: 62: 62: 62: Number of degrees of freedom in T-Coupling group rest is 465.00 62: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 62: 62: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/tools/tests/Testing/Temporary/DumpTest_lysozyme.mdp]: 62: NVE simulation with an initial temperature of zero: will use a Verlet 62: buffer of 10%. Check your energy drift! 62: 62: 62: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/tools/tests/Testing/Temporary/DumpTest_lysozyme.mdp]: 62: You are using a plain Coulomb cut-off, which might produce artifacts. 62: You might want to consider using PME electrostatics. 62: 62: 62: 62: There were 4 NOTEs 62: Setting the LD random seed to -59244577 62: 62: Generated 330891 of the 330891 non-bonded parameter combinations 62: 62: Generated 330891 of the 330891 1-4 parameter combinations 62: 62: Excluding 3 bonded neighbours molecule type 'Protein_chain_B' 62: 62: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/lysozyme.pdb', all velocities are zero 62: Analysing residue names: 62: There are: 10 Protein residues 62: Analysing Protein... 62: 62: This run will generate roughly 0 Mb of data 62: [ RUN ] DumpTest.WorksWithTpr 62: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/tools/tests/Testing/Temporary/DumpTest_lysozyme.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 62: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/tools/tests/Testing/Temporary/DumpTest_lysozyme.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 62: /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/tools/tests/Testing/Temporary/DumpTest_lysozyme.tpr: 62: inputrec: 62: integrator = md 62: tinit = 0 62: dt = 0.001 62: nsteps = 0 62: init-step = 0 62: simulation-part = 1 62: mts = false 62: mass-repartition-factor = 1 62: comm-mode = Linear 62: nstcomm = 100 62: bd-fric = 0 62: ld-seed = -59244577 62: emtol = 10 62: emstep = 0.01 62: niter = 20 62: fcstep = 0 62: nstcgsteep = 1000 62: nbfgscorr = 10 62: rtpi = 0.05 62: nstxout = 0 62: nstvout = 0 62: nstfout = 0 62: nstlog = 1000 62: nstcalcenergy = 100 62: nstenergy = 1000 62: nstxout-compressed = 0 62: compressed-x-precision = 1000 62: cutoff-scheme = Verlet 62: nstlist = 10 62: pbc = xyz 62: periodic-molecules = false 62: verlet-buffer-tolerance = -1 62: verlet-buffer-pressure-tolerance = 0.5 62: rlist = 1.1 62: coulombtype = Cut-off 62: coulomb-modifier = Potential-shift 62: rcoulomb-switch = 0 62: rcoulomb = 1 62: epsilon-r = 1 62: epsilon-rf = inf 62: vdw-type = Cut-off 62: vdw-modifier = Potential-shift 62: rvdw-switch = 0 62: rvdw = 1 62: DispCorr = No 62: table-extension = 1 62: fourierspacing = 0.12 62: fourier-nx = 0 62: fourier-ny = 0 62: fourier-nz = 0 62: pme-order = 4 62: ewald-rtol = 1e-05 62: ewald-rtol-lj = 0.001 62: lj-pme-comb-rule = Geometric 62: ewald-geometry = 3d 62: epsilon-surface = 0 62: ensemble-temperature-setting = not available 62: tcoupl = No 62: nsttcouple = -1 62: nh-chain-length = 0 62: print-nose-hoover-chain-variables = false 62: pcoupl = No 62: refcoord-scaling = No 62: posres-com: not available 62: posres-comB: not available 62: QMMM = false 62: qm-opts: 62: ngQM = 0 62: constraint-algorithm = Lincs 62: continuation = false 62: Shake-SOR = false 62: shake-tol = 0.0001 62: lincs-order = 4 62: lincs-iter = 1 62: lincs-warnangle = 30 62: nwall = 0 62: wall-type = 9-3 62: wall-r-linpot = -1 62: wall-atomtype[0] = -1 62: wall-atomtype[1] = -1 62: wall-density[0] = 0 62: wall-density[1] = 0 62: wall-ewald-zfac = 3 62: pull = false 62: awh = false 62: rotation = false 62: interactiveMD = false 62: disre = No 62: disre-weighting = Conservative 62: disre-mixed = false 62: dr-fc = 1000 62: dr-tau = 0 62: nstdisreout = 100 62: orire-fc = 0 62: orire-tau = 0 62: nstorireout = 100 62: free-energy = no 62: cos-acceleration = 0 62: deform (3x3): 62: deform[ 0]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 62: deform[ 1]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 62: deform[ 2]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 62: simulated-tempering = false 62: swapcoords = no 62: userint1 = 0 62: userint2 = 0 62: userint3 = 0 62: userint4 = 0 62: userreal1 = 0 62: userreal2 = 0 62: userreal3 = 0 62: userreal4 = 0 62: applied-forces: 62: electric-field: 62: x: 62: E0 = 0 62: omega = 0 62: t0 = 0 62: sigma = 0 62: y: 62: E0 = 0 62: omega = 0 62: t0 = 0 62: sigma = 0 62: z: 62: E0 = 0 62: omega = 0 62: t0 = 0 62: sigma = 0 62: density-guided-simulation: 62: active = false 62: group = protein 62: similarity-measure = inner-product 62: atom-spreading-weight = unity 62: force-constant = 1e+09 62: gaussian-transform-spreading-width = 0.2 62: gaussian-transform-spreading-range-in-multiples-of-width = 4 62: reference-density-filename = reference.mrc 62: nst = 1 62: normalize-densities = true 62: adaptive-force-scaling = false 62: adaptive-force-scaling-time-constant = 4 62: shift-vector = 62: transformation-matrix = 62: qmmm-cp2k: 62: active = false 62: qmgroup = System 62: qmmethod = PBE 62: qmfilenames = 62: qmcharge = 0 62: qmmultiplicity = 1 62: colvars: 62: active = false 62: configfile = 62: seed = -1 62: nnpot: 62: active = false 62: modelfile = model.pt 62: input-group = System 62: model-input1 = 62: model-input2 = 62: model-input3 = 62: model-input4 = 62: grpopts: 62: nrdf: 465 62: ref-t: 0 62: tau-t: 0 62: annealing: No 62: annealing-npoints: 0 62: acc: 0 0 0 62: nfreeze: N N N 62: energygrp-flags[ 0]: 0 62: header: 62: bIr = present 62: bBox = present 62: bTop = present 62: bX = present 62: bV = present 62: bF = not present 62: natoms = 156 62: lambda = 0.000000e+00 62: buffer size = 46382 62: topology: 62: name="First 10 residues from 1AKI" 62: #atoms = 156 62: #molblock = 1 62: molblock (0): 62: moltype = 0 "Protein_chain_B" 62: #molecules = 1 62: #posres_xA = 0 62: #posres_xB = 0 62: bIntermolecularInteractions = false 62: ffparams: 62: atnr=10 62: ntypes=212 62: functype[0]=LJ_SR, c6= 3.35274590e-03, c12= 3.95094276e-06 62: functype[1]=LJ_SR, c6= 0.00000000e+00, c12= 0.00000000e+00 62: functype[2]=LJ_SR, c6= 2.60916958e-03, c12= 3.84022405e-06 62: functype[3]=LJ_SR, c6= 6.41072227e-04, c12= 3.43856414e-07 62: functype[4]=LJ_SR, c6= 4.04775795e-03, c12= 7.32754188e-06 62: functype[5]=LJ_SR, c6= 2.81521026e-03, c12= 2.50631660e-06 62: functype[6]=LJ_SR, c6= 2.80388421e-03, c12= 4.30620821e-06 62: functype[7]=LJ_SR, c6= 5.81477652e-04, c12= 2.82897616e-07 62: functype[8]=LJ_SR, c6= 6.03335386e-04, c12= 2.35915493e-07 62: functype[9]=LJ_SR, c6= 7.20490469e-03, c12= 1.15394714e-05 62: functype[10]=LJ_SR, c6= 0.00000000e+00, c12= 0.00000000e+00 62: functype[11]=LJ_SR, c6= 0.00000000e+00, c12= 0.00000000e+00 62: functype[12]=LJ_SR, c6= 0.00000000e+00, c12= 0.00000000e+00 62: functype[13]=LJ_SR, c6= 0.00000000e+00, c12= 0.00000000e+00 62: functype[14]=LJ_SR, c6= 0.00000000e+00, c12= 0.00000000e+00 62: functype[15]=LJ_SR, c6= 0.00000000e+00, c12= 0.00000000e+00 62: functype[16]=LJ_SR, c6= 0.00000000e+00, c12= 0.00000000e+00 62: functype[17]=LJ_SR, c6= 0.00000000e+00, c12= 0.00000000e+00 62: functype[18]=LJ_SR, c6= 0.00000000e+00, c12= 0.00000000e+00 62: functype[19]=LJ_SR, c6= 0.00000000e+00, c12= 0.00000000e+00 62: functype[20]=LJ_SR, c6= 2.60916958e-03, c12= 3.84022405e-06 62: functype[21]=LJ_SR, c6= 0.00000000e+00, c12= 0.00000000e+00 62: functype[22]=LJ_SR, c6= 2.03050394e-03, c12= 3.73260514e-06 62: functype[23]=LJ_SR, c6= 4.98894195e-04, c12= 3.34220175e-07 62: functype[24]=LJ_SR, c6= 3.15004122e-03, c12= 7.12220026e-06 62: functype[25]=LJ_SR, c6= 2.19085021e-03, c12= 2.43608270e-06 62: functype[26]=LJ_SR, c6= 2.18203571e-03, c12= 4.18553600e-06 62: functype[27]=LJ_SR, c6= 4.52516542e-04, c12= 2.74969580e-07 62: functype[28]=LJ_SR, c6= 4.69526683e-04, c12= 2.29304163e-07 62: functype[29]=LJ_SR, c6= 5.60698984e-03, c12= 1.12160897e-05 62: functype[30]=LJ_SR, c6= 6.41072227e-04, c12= 3.43856414e-07 62: functype[31]=LJ_SR, c6= 0.00000000e+00, c12= 0.00000000e+00 62: functype[32]=LJ_SR, c6= 4.98894195e-04, c12= 3.34220175e-07 62: functype[33]=LJ_SR, c6= 1.22578131e-04, c12= 2.99263014e-08 62: functype[34]=LJ_SR, c6= 7.73964217e-04, c12= 6.37726998e-07 62: functype[35]=LJ_SR, c6= 5.38290828e-04, c12= 2.18128321e-07 62: functype[36]=LJ_SR, c6= 5.36125386e-04, c12= 3.74775709e-07 62: functype[37]=LJ_SR, c6= 1.11183173e-04, c12= 2.46209719e-08 62: functype[38]=LJ_SR, c6= 1.15362534e-04, c12= 2.05320472e-08 62: functype[39]=LJ_SR, c6= 1.37763575e-03, c12= 1.00429668e-06 62: functype[40]=LJ_SR, c6= 4.04775795e-03, c12= 7.32754188e-06 62: functype[41]=LJ_SR, c6= 0.00000000e+00, c12= 0.00000000e+00 62: functype[42]=LJ_SR, c6= 3.15004122e-03, c12= 7.12220026e-06 62: functype[43]=LJ_SR, c6= 7.73964217e-04, c12= 6.37726998e-07 62: functype[44]=LJ_SR, c6= 4.88684513e-03, c12= 1.35898972e-05 62: functype[45]=LJ_SR, c6= 3.39879468e-03, c12= 4.64829736e-06 62: functype[46]=LJ_SR, c6= 3.38512054e-03, c12= 7.98643487e-06 62: functype[47]=LJ_SR, c6= 7.02015939e-04, c12= 5.24670895e-07 62: functype[48]=LJ_SR, c6= 7.28404266e-04, c12= 4.37535846e-07 62: functype[49]=LJ_SR, c6= 8.69845692e-03, c12= 2.14014708e-05 62: functype[50]=LJ_SR, c6= 2.81521026e-03, c12= 2.50631660e-06 62: functype[51]=LJ_SR, c6= 0.00000000e+00, c12= 0.00000000e+00 62: functype[52]=LJ_SR, c6= 2.19085021e-03, c12= 2.43608270e-06 62: functype[53]=LJ_SR, c6= 5.38290828e-04, c12= 2.18128321e-07 62: functype[54]=LJ_SR, c6= 3.39879468e-03, c12= 4.64829736e-06 62: functype[55]=LJ_SR, c6= 2.36385735e-03, c12= 1.58990645e-06 62: functype[56]=LJ_SR, c6= 2.35434738e-03, c12= 2.73168575e-06 62: functype[57]=LJ_SR, c6= 4.88250953e-04, c12= 1.79458596e-07 62: functype[58]=LJ_SR, c6= 5.06604381e-04, c12= 1.49655136e-07 62: functype[59]=LJ_SR, c6= 6.04976481e-03, c12= 7.32016997e-06 62: functype[60]=LJ_SR, c6= 2.80388421e-03, c12= 4.30620821e-06 62: functype[61]=LJ_SR, c6= 0.00000000e+00, c12= 0.00000000e+00 62: functype[62]=LJ_SR, c6= 2.18203571e-03, c12= 4.18553600e-06 62: functype[63]=LJ_SR, c6= 5.36125386e-04, c12= 3.74775709e-07 62: functype[64]=LJ_SR, c6= 3.38512054e-03, c12= 7.98643487e-06 62: functype[65]=LJ_SR, c6= 2.35434738e-03, c12= 2.73168575e-06 62: functype[66]=LJ_SR, c6= 2.34487536e-03, c12= 4.69342376e-06 62: functype[67]=LJ_SR, c6= 4.86286852e-04, c12= 3.08335643e-07 62: functype[68]=LJ_SR, c6= 5.04566357e-04, c12= 2.57128875e-07 62: functype[69]=LJ_SR, c6= 6.02542516e-03, c12= 1.25770912e-05 62: functype[70]=LJ_SR, c6= 5.81477652e-04, c12= 2.82897616e-07 62: functype[71]=LJ_SR, c6= 0.00000000e+00, c12= 0.00000000e+00 62: functype[72]=LJ_SR, c6= 4.52516542e-04, c12= 2.74969580e-07 62: functype[73]=LJ_SR, c6= 1.11183173e-04, c12= 2.46209719e-08 62: functype[74]=LJ_SR, c6= 7.02015939e-04, c12= 5.24670895e-07 62: functype[75]=LJ_SR, c6= 4.88250953e-04, c12= 1.79458596e-07 62: functype[76]=LJ_SR, c6= 4.86286852e-04, c12= 3.08335643e-07 62: functype[77]=LJ_SR, c6= 1.00847494e-04, c12= 2.02561683e-08 62: functype[78]=LJ_SR, c6= 1.04638377e-04, c12= 1.68921392e-08 62: functype[79]=LJ_SR, c6= 1.24956947e-03, c12= 8.26254961e-07 62: functype[80]=LJ_SR, c6= 6.03335386e-04, c12= 2.35915493e-07 62: functype[81]=LJ_SR, c6= 0.00000000e+00, c12= 0.00000000e+00 62: functype[82]=LJ_SR, c6= 4.69526683e-04, c12= 2.29304163e-07 62: functype[83]=LJ_SR, c6= 1.15362534e-04, c12= 2.05320472e-08 62: functype[84]=LJ_SR, c6= 7.28404266e-04, c12= 4.37535846e-07 62: functype[85]=LJ_SR, c6= 5.06604381e-04, c12= 1.49655136e-07 62: functype[86]=LJ_SR, c6= 5.04566357e-04, c12= 2.57128875e-07 62: functype[87]=LJ_SR, c6= 1.04638377e-04, c12= 1.68921392e-08 62: functype[88]=LJ_SR, c6= 1.08571716e-04, c12= 1.40867806e-08 62: functype[89]=LJ_SR, c6= 1.29654107e-03, c12= 6.89035176e-07 62: functype[90]=LJ_SR, c6= 7.20490469e-03, c12= 1.15394714e-05 62: functype[91]=LJ_SR, c6= 0.00000000e+00, c12= 0.00000000e+00 62: functype[92]=LJ_SR, c6= 5.60698984e-03, c12= 1.12160897e-05 62: functype[93]=LJ_SR, c6= 1.37763575e-03, c12= 1.00429668e-06 62: functype[94]=LJ_SR, c6= 8.69845692e-03, c12= 2.14014708e-05 62: functype[95]=LJ_SR, c6= 6.04976481e-03, c12= 7.32016997e-06 62: functype[96]=LJ_SR, c6= 6.02542516e-03, c12= 1.25770912e-05 62: functype[97]=LJ_SR, c6= 1.24956947e-03, c12= 8.26254961e-07 62: functype[98]=LJ_SR, c6= 1.29654107e-03, c12= 6.89035176e-07 62: functype[99]=LJ_SR, c6= 1.54830217e-02, c12= 3.37031743e-05 62: functype[100]=BONDS, b0A= 1.01000e-01, cbA= 3.63171e+05, b0B= 1.01000e-01, cbB= 3.63171e+05 62: functype[101]=BONDS, b0A= 1.47100e-01, cbA= 3.07106e+05, b0B= 1.47100e-01, cbB= 3.07106e+05 62: functype[102]=BONDS, b0A= 1.09000e-01, cbA= 2.84512e+05, b0B= 1.09000e-01, cbB= 2.84512e+05 62: functype[103]=BONDS, b0A= 1.52900e-01, cbA= 2.24262e+05, b0B= 1.52900e-01, cbB= 2.24262e+05 62: functype[104]=BONDS, b0A= 1.52200e-01, cbA= 2.65266e+05, b0B= 1.52200e-01, cbB= 2.65266e+05 62: functype[105]=BONDS, b0A= 1.22900e-01, cbA= 4.76976e+05, b0B= 1.22900e-01, cbB= 4.76976e+05 62: functype[106]=BONDS, b0A= 1.33500e-01, cbA= 4.10032e+05, b0B= 1.33500e-01, cbB= 4.10032e+05 62: functype[107]=BONDS, b0A= 1.44900e-01, cbA= 2.82002e+05, b0B= 1.44900e-01, cbB= 2.82002e+05 62: functype[108]=BONDS, b0A= 1.51000e-01, cbA= 2.65266e+05, b0B= 1.51000e-01, cbB= 2.65266e+05 62: functype[109]=BONDS, b0A= 1.40000e-01, cbA= 3.92459e+05, b0B= 1.40000e-01, cbB= 3.92459e+05 62: functype[110]=BONDS, b0A= 1.08000e-01, cbA= 3.07106e+05, b0B= 1.08000e-01, cbB= 3.07106e+05 62: functype[111]=BONDS, b0A= 1.46300e-01, cbA= 2.82002e+05, b0B= 1.46300e-01, cbB= 2.82002e+05 62: functype[112]=BONDS, b0A= 1.34000e-01, cbA= 4.02501e+05, b0B= 1.34000e-01, cbB= 4.02501e+05 62: functype[113]=BONDS, b0A= 1.81000e-01, cbA= 1.85770e+05, b0B= 1.81000e-01, cbB= 1.85770e+05 62: functype[114]=BONDS, b0A= 1.33600e-01, cbA= 2.29283e+05, b0B= 1.33600e-01, cbB= 2.29283e+05 62: functype[115]=BONDS, b0A= 1.25000e-01, cbA= 5.48941e+05, b0B= 1.25000e-01, cbB= 5.48941e+05 62: functype[116]=ANGLES, thA= 1.09500e+02, ctA= 2.92880e+02, thB= 1.09500e+02, ctB= 2.92880e+02 62: functype[117]=ANGLES, thA= 1.11200e+02, ctA= 6.69440e+02, thB= 1.11200e+02, ctB= 6.69440e+02 62: functype[118]=ANGLES, thA= 1.10700e+02, ctA= 3.13800e+02, thB= 1.10700e+02, ctB= 3.13800e+02 62: functype[119]=ANGLES, thA= 1.11100e+02, ctA= 5.27184e+02, thB= 1.11100e+02, ctB= 5.27184e+02 62: functype[120]=ANGLES, thA= 1.12700e+02, ctA= 4.88273e+02, thB= 1.12700e+02, ctB= 4.88273e+02 62: functype[121]=ANGLES, thA= 1.07800e+02, ctA= 2.76144e+02, thB= 1.07800e+02, ctB= 2.76144e+02 62: functype[122]=ANGLES, thA= 1.20400e+02, ctA= 6.69440e+02, thB= 1.20400e+02, ctB= 6.69440e+02 62: functype[123]=ANGLES, thA= 1.16600e+02, ctA= 5.85760e+02, thB= 1.16600e+02, ctB= 5.85760e+02 62: functype[124]=ANGLES, thA= 1.22900e+02, ctA= 6.69440e+02, thB= 1.22900e+02, ctB= 6.69440e+02 62: functype[125]=ANGLES, thA= 1.19800e+02, ctA= 2.92880e+02, thB= 1.19800e+02, ctB= 2.92880e+02 62: functype[126]=ANGLES, thA= 1.21900e+02, ctA= 4.18400e+02, thB= 1.21900e+02, ctB= 4.18400e+02 62: functype[127]=ANGLES, thA= 1.18400e+02, ctA= 3.17984e+02, thB= 1.18400e+02, ctB= 3.17984e+02 62: functype[128]=ANGLES, thA= 1.09700e+02, ctA= 6.69440e+02, thB= 1.09700e+02, ctB= 6.69440e+02 62: functype[129]=ANGLES, thA= 1.10100e+02, ctA= 5.27184e+02, thB= 1.10100e+02, ctB= 5.27184e+02 62: functype[130]=ANGLES, thA= 1.14000e+02, ctA= 5.27184e+02, thB= 1.14000e+02, ctB= 5.27184e+02 62: functype[131]=ANGLES, thA= 1.20000e+02, ctA= 5.85760e+02, thB= 1.20000e+02, ctB= 5.85760e+02 62: functype[132]=ANGLES, thA= 1.20000e+02, ctA= 5.27184e+02, thB= 1.20000e+02, ctB= 5.27184e+02 62: functype[133]=ANGLES, thA= 1.20000e+02, ctA= 2.92880e+02, thB= 1.20000e+02, ctB= 2.92880e+02 62: functype[134]=ANGLES, thA= 1.18400e+02, ctA= 2.92880e+02, thB= 1.18400e+02, ctB= 2.92880e+02 62: functype[135]=ANGLES, thA= 1.23200e+02, ctA= 4.18400e+02, thB= 1.23200e+02, ctB= 4.18400e+02 62: functype[136]=ANGLES, thA= 1.08600e+02, ctA= 4.18400e+02, thB= 1.08600e+02, ctB= 4.18400e+02 62: functype[137]=ANGLES, thA= 9.60000e+01, ctA= 3.68192e+02, thB= 9.60000e+01, ctB= 3.68192e+02 62: functype[138]=ANGLES, thA= 1.17000e+02, ctA= 5.85760e+02, thB= 1.17000e+02, ctB= 5.85760e+02 62: functype[139]=ANGLES, thA= 1.26000e+02, ctA= 6.69440e+02, thB= 1.26000e+02, ctB= 6.69440e+02 62: functype[140]=PDIHS, phiA= 1.80000000e+02, cpA= 4.39319992e+01, phiB= 1.80000000e+02, cpB= 4.39319992e+01, mult=2 62: functype[141]=PDIHS, phiA= 1.80000000e+02, cpA= 4.18400002e+00, phiB= 1.80000000e+02, cpB= 4.18400002e+00, mult=2 62: functype[142]=PDIHS, phiA= 1.80000000e+02, cpA= 4.60239983e+00, phiB= 1.80000000e+02, cpB= 4.60239983e+00, mult=2 62: functype[143]=RBDIHS, rbcA[0]= 5.46010017e-01, rbcA[1]= 1.63803005e+00, rbcA[2]= 0.00000000e+00, rbcA[3]=-2.18405008e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 62: rbcB[0]= 5.46010017e-01, rbcB[1]= 1.63803005e+00, rbcB[2]= 0.00000000e+00, rbcB[3]=-2.18405008e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 62: functype[144]=RBDIHS, rbcA[0]= 7.25920022e-01, rbcA[1]= 2.17776990e+00, rbcA[2]= 0.00000000e+00, rbcA[3]=-2.90370011e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 62: rbcB[0]= 7.25920022e-01, rbcB[1]= 2.17776990e+00, rbcB[2]= 0.00000000e+00, rbcB[3]=-2.90370011e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 62: functype[145]=RBDIHS, rbcA[0]= 1.27611995e+00, rbcA[1]= 1.16734004e+00, rbcA[2]= 8.95380020e-01, rbcA[3]=-3.33884001e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 62: rbcB[0]= 1.27611995e+00, rbcB[1]= 1.16734004e+00, rbcB[2]= 8.95380020e-01, rbcB[3]=-3.33884001e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 62: functype[146]=RBDIHS, rbcA[0]=-6.91824007e+00, rbcA[1]= 4.67562008e+00, rbcA[2]= 2.24261999e+00, rbcA[3]= 0.00000000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 62: rbcB[0]=-6.91824007e+00, rbcB[1]= 4.67562008e+00, rbcB[2]= 2.24261999e+00, rbcB[3]= 0.00000000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 62: functype[147]=RBDIHS, rbcA[0]= 9.70690012e-01, rbcA[1]= 2.91206002e+00, rbcA[2]= 0.00000000e+00, rbcA[3]=-3.88275003e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 62: rbcB[0]= 9.70690012e-01, rbcB[1]= 2.91206002e+00, rbcB[2]= 0.00000000e+00, rbcB[3]=-3.88275003e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 62: functype[148]=RBDIHS, rbcA[0]= 6.27600014e-01, rbcA[1]= 1.88279998e+00, rbcA[2]= 0.00000000e+00, rbcA[3]=-2.51040006e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 62: rbcB[0]= 6.27600014e-01, rbcB[1]= 1.88279998e+00, rbcB[2]= 0.00000000e+00, rbcB[3]=-2.51040006e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 62: functype[149]=RBDIHS, rbcA[0]=-1.58989996e-01, rbcA[1]=-4.76980001e-01, rbcA[2]= 0.00000000e+00, rbcA[3]= 6.35959983e-01, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 62: rbcB[0]=-1.58989996e-01, rbcB[1]=-4.76980001e-01, rbcB[2]= 0.00000000e+00, rbcB[3]= 6.35959983e-01, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 62: functype[150]=RBDIHS, rbcA[0]= 1.03637600e+01, rbcA[1]=-6.60654020e+00, rbcA[2]=-1.04934702e+01, rbcA[3]= 6.73623991e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 62: rbcB[0]= 1.03637600e+01, rbcB[1]=-6.60654020e+00, rbcB[2]=-1.04934702e+01, rbcB[3]= 6.73623991e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 62: functype[151]=RBDIHS, rbcA[0]= 5.00825024e+00, rbcA[1]=-1.69869995e+00, rbcA[2]=-3.72379988e-01, rbcA[3]=-2.93716002e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 62: rbcB[0]= 5.00825024e+00, rbcB[1]=-1.69869995e+00, rbcB[2]=-3.72379988e-01, rbcB[3]=-2.93716002e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 62: functype[152]=RBDIHS, rbcA[0]= 2.92880011e+00, rbcA[1]=-1.46440005e+00, rbcA[2]= 2.09199995e-01, rbcA[3]=-1.67359996e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 62: rbcB[0]= 2.92880011e+00, rbcB[1]=-1.46440005e+00, rbcB[2]= 2.09199995e-01, rbcB[3]=-1.67359996e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 62: functype[153]=RBDIHS, rbcA[0]= 5.77183008e+00, rbcA[1]=-2.67147994e+00, rbcA[2]= 9.58140016e-01, rbcA[3]=-4.05847979e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 62: rbcB[0]= 5.77183008e+00, rbcB[1]=-2.67147994e+00, rbcB[2]= 9.58140016e-01, rbcB[3]=-4.05847979e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 62: functype[154]=RBDIHS, rbcA[0]= 8.03330004e-01, rbcA[1]= 2.40999007e+00, rbcA[2]= 0.00000000e+00, rbcA[3]=-3.21331000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 62: rbcB[0]= 8.03330004e-01, rbcB[1]= 2.40999007e+00, rbcB[2]= 0.00000000e+00, rbcB[3]=-3.21331000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 62: functype[155]=RBDIHS, rbcA[0]= 2.05016003e+01, rbcA[1]= 0.00000000e+00, rbcA[2]=-2.05016003e+01, rbcA[3]= 0.00000000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 62: rbcB[0]= 2.05016003e+01, rbcB[1]= 0.00000000e+00, rbcB[2]=-2.05016003e+01, rbcB[3]= 0.00000000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 62: functype[156]=RBDIHS, rbcA[0]= 3.02879791e+01, rbcA[1]=-4.81160021e+00, rbcA[2]=-2.54763794e+01, rbcA[3]= 0.00000000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 62: rbcB[0]= 3.02879791e+01, rbcB[1]=-4.81160021e+00, rbcB[2]=-2.54763794e+01, rbcB[3]= 0.00000000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 62: functype[157]=RBDIHS, rbcA[0]= 2.54763794e+01, rbcA[1]= 0.00000000e+00, rbcA[2]=-2.54763794e+01, rbcA[3]= 0.00000000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 62: rbcB[0]= 2.54763794e+01, rbcB[1]= 0.00000000e+00, rbcB[2]=-2.54763794e+01, rbcB[3]= 0.00000000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 62: functype[158]=RBDIHS, rbcA[0]= 1.57025499e+01, rbcA[1]= 3.17565594e+01, rbcA[2]=-3.66935992e+00, rbcA[3]=-4.37897491e+01, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 62: rbcB[0]= 1.57025499e+01, rbcB[1]= 3.17565594e+01, rbcB[2]=-3.66935992e+00, rbcB[3]=-4.37897491e+01, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 62: functype[159]=RBDIHS, rbcA[0]=-1.03574896e+01, rbcA[1]=-2.95871601e+01, rbcA[2]=-1.16734004e+00, rbcA[3]= 4.11119919e+01, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 62: rbcB[0]=-1.03574896e+01, rbcB[1]=-2.95871601e+01, rbcB[2]=-1.16734004e+00, rbcB[3]= 4.11119919e+01, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 62: functype[160]=RBDIHS, rbcA[0]= 4.50198984e+00, rbcA[1]= 7.82410026e-01, rbcA[2]=-1.60247004e+00, rbcA[3]=-3.68192005e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 62: rbcB[0]= 4.50198984e+00, rbcB[1]= 7.82410026e-01, rbcB[2]=-1.60247004e+00, rbcB[3]=-3.68192005e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 62: functype[161]=RBDIHS, rbcA[0]= 4.22589988e-01, rbcA[1]= 2.70705009e+00, rbcA[2]=-3.12964010e+00, rbcA[3]= 0.00000000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 62: rbcB[0]= 4.22589988e-01, rbcB[1]= 2.70705009e+00, rbcB[2]=-3.12964010e+00, rbcB[3]= 0.00000000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 62: functype[162]=RBDIHS, rbcA[0]=-7.65670002e-01, rbcA[1]= 2.70705009e+00, rbcA[2]= 4.02501011e+00, rbcA[3]=-5.96639013e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 62: rbcB[0]=-7.65670002e-01, rbcB[1]= 2.70705009e+00, rbcB[2]= 4.02501011e+00, rbcB[3]=-5.96639013e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 62: functype[163]=RBDIHS, rbcA[0]= 9.66499984e-01, rbcA[1]= 2.89950991e+00, rbcA[2]= 0.00000000e+00, rbcA[3]=-3.86600995e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 62: rbcB[0]= 9.66499984e-01, rbcB[1]= 2.89950991e+00, rbcB[2]= 0.00000000e+00, rbcB[3]=-3.86600995e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 62: functype[164]=RBDIHS, rbcA[0]=-4.23421001e+00, rbcA[1]= 7.22159004e+00, rbcA[2]= 1.90789998e+00, rbcA[3]=-4.89527988e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 62: rbcB[0]=-4.23421001e+00, rbcB[1]= 7.22159004e+00, rbcB[2]= 1.90789998e+00, rbcB[3]=-4.89527988e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 62: functype[165]=RBDIHS, rbcA[0]= 3.03339996e+01, rbcA[1]= 0.00000000e+00, rbcA[2]=-3.03339996e+01, rbcA[3]= 0.00000000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 62: rbcB[0]= 3.03339996e+01, rbcB[1]= 0.00000000e+00, rbcB[2]=-3.03339996e+01, rbcB[3]= 0.00000000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 62: functype[166]=RBDIHS, rbcA[0]= 1.02319698e+01, rbcA[1]= 3.52082992e+00, rbcA[2]=-3.97899008e+00, rbcA[3]=-9.77381992e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 62: rbcB[0]= 1.02319698e+01, rbcB[1]= 3.52082992e+00, rbcB[2]=-3.97899008e+00, rbcB[3]=-9.77381992e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 62: functype[167]=RBDIHS, rbcA[0]= 5.49777985e+00, rbcA[1]= 1.41838002e+00, rbcA[2]=-6.91615009e+00, rbcA[3]= 0.00000000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 62: rbcB[0]= 5.49777985e+00, rbcB[1]= 1.41838002e+00, rbcB[2]=-6.91615009e+00, rbcB[3]= 0.00000000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 62: functype[168]=RBDIHS, rbcA[0]=-1.21755004e+00, rbcA[1]=-3.65264010e+00, rbcA[2]= 0.00000000e+00, rbcA[3]= 4.87018013e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 62: rbcB[0]=-1.21755004e+00, rbcB[1]=-3.65264010e+00, rbcB[2]= 0.00000000e+00, rbcB[3]= 4.87018013e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 62: functype[169]=RBDIHS, rbcA[0]=-1.26775002e+00, rbcA[1]= 3.02084994e+00, rbcA[2]= 1.74473000e+00, rbcA[3]=-3.49781990e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 62: rbcB[0]=-1.26775002e+00, rbcB[1]= 3.02084994e+00, rbcB[2]= 1.74473000e+00, rbcB[3]=-3.49781990e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 62: functype[170]=RBDIHS, rbcA[0]= 3.80117011e+00, rbcA[1]=-6.95172024e+00, rbcA[2]=-1.01671004e+00, rbcA[3]= 4.16726017e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 62: rbcB[0]= 3.80117011e+00, rbcB[1]=-6.95172024e+00, rbcB[2]=-1.01671004e+00, rbcB[3]= 4.16726017e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 62: functype[171]=RBDIHS, rbcA[0]= 3.70279998e-01, rbcA[1]= 1.11085999e+00, rbcA[2]= 0.00000000e+00, rbcA[3]=-1.48114002e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 62: rbcB[0]= 3.70279998e-01, rbcB[1]= 1.11085999e+00, rbcB[2]= 0.00000000e+00, rbcB[3]=-1.48114002e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 62: functype[172]=RBDIHS, rbcA[0]= 3.32042198e+01, rbcA[1]= 0.00000000e+00, rbcA[2]=-3.32042198e+01, rbcA[3]= 0.00000000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 62: rbcB[0]= 3.32042198e+01, rbcB[1]= 0.00000000e+00, rbcB[2]=-3.32042198e+01, rbcB[3]= 0.00000000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 62: functype[173]=RBDIHS, rbcA[0]= 1.63176003e+01, rbcA[1]= 0.00000000e+00, rbcA[2]=-1.63176003e+01, rbcA[3]= 0.00000000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 62: rbcB[0]= 1.63176003e+01, rbcB[1]= 0.00000000e+00, rbcB[2]=-1.63176003e+01, rbcB[3]= 0.00000000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 62: functype[174]=RBDIHS, rbcA[0]= 3.40787005e+00, rbcA[1]=-2.80537009e+00, rbcA[2]=-3.59820008e-01, rbcA[3]=-2.42670000e-01, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 62: rbcB[0]= 3.40787005e+00, rbcB[1]=-2.80537009e+00, rbcB[2]=-3.59820008e-01, rbcB[3]=-2.42670000e-01, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 62: functype[175]=RBDIHS, rbcA[0]=-1.62590199e+01, rbcA[1]= 9.08765030e+00, rbcA[2]= 7.17138004e+00, rbcA[3]= 0.00000000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 62: rbcB[0]=-1.62590199e+01, rbcB[1]= 9.08765030e+00, rbcB[2]= 7.17138004e+00, rbcB[3]= 0.00000000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 62: functype[176]=RBDIHS, rbcA[0]= 9.45590019e-01, rbcA[1]= 2.83675003e+00, rbcA[2]= 0.00000000e+00, rbcA[3]=-3.78234005e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 62: rbcB[0]= 9.45590019e-01, rbcB[1]= 2.83675003e+00, rbcB[2]= 0.00000000e+00, rbcB[3]=-3.78234005e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 62: functype[177]=RBDIHS, rbcA[0]=-1.50624001e+00, rbcA[1]= 5.37225008e+00, rbcA[2]= 1.17989004e+00, rbcA[3]=-5.04589987e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 62: rbcB[0]=-1.50624001e+00, rbcB[1]= 5.37225008e+00, rbcB[2]= 1.17989004e+00, rbcB[3]=-5.04589987e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 62: functype[178]=RBDIHS, rbcA[0]= 1.00416005e+00, rbcA[1]= 3.01248002e+00, rbcA[2]= 0.00000000e+00, rbcA[3]=-4.01664019e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 62: rbcB[0]= 1.00416005e+00, rbcB[1]= 3.01248002e+00, rbcB[2]= 0.00000000e+00, rbcB[3]=-4.01664019e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 62: functype[179]=RBDIHS, rbcA[0]= 8.79267979e+00, rbcA[1]=-1.18344402e+01, rbcA[2]= 1.07528996e+00, rbcA[3]= 1.96648002e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 62: rbcB[0]= 8.79267979e+00, rbcB[1]=-1.18344402e+01, rbcB[2]= 1.07528996e+00, rbcB[3]= 1.96648002e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 62: functype[180]=RBDIHS, rbcA[0]=-5.77392006e+00, rbcA[1]= 3.38485003e+00, rbcA[2]= 2.38906002e+00, rbcA[3]= 0.00000000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 62: rbcB[0]=-5.77392006e+00, rbcB[1]= 3.38485003e+00, rbcB[2]= 2.38906002e+00, rbcB[3]= 0.00000000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 62: functype[181]=RBDIHS, rbcA[0]=-9.08345985e+00, rbcA[1]= 9.75708961e+00, rbcA[2]= 3.45180011e+00, rbcA[3]=-4.12542009e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 62: rbcB[0]=-9.08345985e+00, rbcB[1]= 9.75708961e+00, rbcB[2]= 3.45180011e+00, rbcB[3]=-4.12542009e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 62: functype[182]=RBDIHS, rbcA[0]=-4.70699996e-01, rbcA[1]=-1.41209996e+00, rbcA[2]= 0.00000000e+00, rbcA[3]= 1.88279998e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 62: rbcB[0]=-4.70699996e-01, rbcB[1]=-1.41209996e+00, rbcB[2]= 0.00000000e+00, rbcB[3]= 1.88279998e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 62: functype[183]=RBDIHS, rbcA[0]= 3.43088007e+00, rbcA[1]= 0.00000000e+00, rbcA[2]=-3.43088007e+00, rbcA[3]= 0.00000000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 62: rbcB[0]= 3.43088007e+00, rbcB[1]= 0.00000000e+00, rbcB[2]=-3.43088007e+00, rbcB[3]= 0.00000000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 62: functype[184]=RBDIHS, rbcA[0]= 2.57315993e+00, rbcA[1]= 3.49781990e+00, rbcA[2]=-1.10038996e+00, rbcA[3]=-4.97059011e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 62: rbcB[0]= 2.57315993e+00, rbcB[1]= 3.49781990e+00, rbcB[2]=-1.10038996e+00, rbcB[3]=-4.97059011e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 62: functype[185]=RBDIHS, rbcA[0]=-8.22160006e-01, rbcA[1]= 1.12758994e+00, rbcA[2]=-3.05440009e-01, rbcA[3]= 0.00000000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 62: rbcB[0]=-8.22160006e-01, rbcB[1]= 1.12758994e+00, rbcB[2]=-3.05440009e-01, rbcB[3]= 0.00000000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 62: functype[186]=LJ14, c6A= 3.20536114e-04, c12A= 1.71928207e-07, c6B= 3.20536114e-04, c12B= 1.71928207e-07 62: functype[187]=LJ14, c6A= 1.30458479e-03, c12A= 1.92011203e-06, c6B= 1.30458479e-03, c12B= 1.92011203e-06 62: functype[188]=LJ14, c6A= 1.40760513e-03, c12A= 1.25315830e-06, c6B= 1.40760513e-03, c12B= 1.25315830e-06 62: functype[189]=LJ14, c6A= 1.67637295e-03, c12A= 1.97547138e-06, c6B= 1.67637295e-03, c12B= 1.97547138e-06 62: functype[190]=LJ14, c6A= 0.00000000e+00, c12A= 0.00000000e+00, c6B= 0.00000000e+00, c12B= 0.00000000e+00 62: functype[191]=LJ14, c6A= 2.49447097e-04, c12A= 1.67110088e-07, c6B= 2.49447097e-04, c12B= 1.67110088e-07 62: functype[192]=LJ14, c6A= 1.01525197e-03, c12A= 1.86630257e-06, c6B= 1.01525197e-03, c12B= 1.86630257e-06 62: functype[193]=LJ14, c6A= 6.12890653e-05, c12A= 1.49631507e-08, c6B= 6.12890653e-05, c12B= 1.49631507e-08 62: functype[194]=LJ14, c6A= 2.69145414e-04, c12A= 1.09064160e-07, c6B= 2.69145414e-04, c12B= 1.09064160e-07 62: functype[195]=LJ14, c6A= 1.09542510e-03, c12A= 1.21804135e-06, c6B= 1.09542510e-03, c12B= 1.21804135e-06 62: functype[196]=LJ14, c6A= 3.86982108e-04, c12A= 3.18863499e-07, c6B= 3.86982108e-04, c12B= 3.18863499e-07 62: functype[197]=LJ14, c6A= 1.57502061e-03, c12A= 3.56110013e-06, c6B= 1.57502061e-03, c12B= 3.56110013e-06 62: functype[198]=LJ14, c6A= 2.44342256e-03, c12A= 6.79494860e-06, c6B= 2.44342256e-03, c12B= 6.79494860e-06 62: functype[199]=LJ14, c6A= 1.40194211e-03, c12A= 2.15310411e-06, c6B= 1.40194211e-03, c12B= 2.15310411e-06 62: functype[200]=LJ14, c6A= 1.09101785e-03, c12A= 2.09276800e-06, c6B= 1.09101785e-03, c12B= 2.09276800e-06 62: functype[201]=LJ14, c6A= 2.68062693e-04, c12A= 1.87387855e-07, c6B= 2.68062693e-04, c12B= 1.87387855e-07 62: functype[202]=LJ14, c6A= 2.26258271e-04, c12A= 1.37484790e-07, c6B= 2.26258271e-04, c12B= 1.37484790e-07 62: functype[203]=LJ14, c6A= 2.43143426e-04, c12A= 1.54167822e-07, c6B= 2.43143426e-04, c12B= 1.54167822e-07 62: functype[204]=LJ14, c6A= 1.17243768e-03, c12A= 2.34671188e-06, c6B= 1.17243768e-03, c12B= 2.34671188e-06 62: functype[205]=LJ14, c6A= 1.69256027e-03, c12A= 3.99321743e-06, c6B= 1.69256027e-03, c12B= 3.99321743e-06 62: functype[206]=LJ14, c6A= 5.04237469e-05, c12A= 1.01280841e-08, c6B= 5.04237469e-05, c12B= 1.01280841e-08 62: functype[207]=LJ14, c6A= 2.34763342e-04, c12A= 1.14652082e-07, c6B= 2.34763342e-04, c12B= 1.14652082e-07 62: functype[208]=LJ14, c6A= 5.76812672e-05, c12A= 1.02660236e-08, c6B= 5.76812672e-05, c12B= 1.02660236e-08 62: functype[209]=LJ14, c6A= 3.60245234e-03, c12A= 5.76973571e-06, c6B= 3.60245234e-03, c12B= 5.76973571e-06 62: functype[210]=LJ14, c6A= 6.88817876e-04, c12A= 5.02148339e-07, c6B= 6.88817876e-04, c12B= 5.02148339e-07 62: functype[211]=LJ14, c6A= 4.34922846e-03, c12A= 1.07007354e-05, c6B= 4.34922846e-03, c12B= 1.07007354e-05 62: reppow = 12 62: fudgeQQ = 0.5 62: cmap 62: moltype (0): 62: name="Protein_chain_B" 62: atoms: 62: atom (156): 62: atom[ 0]={type= 0, typeB= 0, ptype= Atom, m= 1.40027e+01, q=-3.00000e-01, mB= 1.40027e+01, qB=-3.00000e-01, resind= 0, atomnumber= 7} 62: atom[ 1]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 3.30000e-01, mB= 1.00800e+00, qB= 3.30000e-01, resind= 0, atomnumber= 1} 62: atom[ 2]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 3.30000e-01, mB= 1.00800e+00, qB= 3.30000e-01, resind= 0, atomnumber= 1} 62: atom[ 3]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 3.30000e-01, mB= 1.00800e+00, qB= 3.30000e-01, resind= 0, atomnumber= 1} 62: atom[ 4]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q= 2.50000e-01, mB= 1.20110e+01, qB= 2.50000e-01, resind= 0, atomnumber= 6} 62: atom[ 5]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 0, atomnumber= 1} 62: atom[ 6]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q=-1.20000e-01, mB= 1.20110e+01, qB=-1.20000e-01, resind= 0, atomnumber= 6} 62: atom[ 7]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 0, atomnumber= 1} 62: atom[ 8]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 0, atomnumber= 1} 62: atom[ 9]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q=-1.20000e-01, mB= 1.20110e+01, qB=-1.20000e-01, resind= 0, atomnumber= 6} 62: atom[ 10]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 0, atomnumber= 1} 62: atom[ 11]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 0, atomnumber= 1} 62: atom[ 12]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q=-1.20000e-01, mB= 1.20110e+01, qB=-1.20000e-01, resind= 0, atomnumber= 6} 62: atom[ 13]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 0, atomnumber= 1} 62: atom[ 14]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 0, atomnumber= 1} 62: atom[ 15]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q= 1.90000e-01, mB= 1.20110e+01, qB= 1.90000e-01, resind= 0, atomnumber= 6} 62: atom[ 16]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 0, atomnumber= 1} 62: atom[ 17]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 0, atomnumber= 1} 62: atom[ 18]={type= 0, typeB= 0, ptype= Atom, m= 1.40067e+01, q=-3.00000e-01, mB= 1.40067e+01, qB=-3.00000e-01, resind= 0, atomnumber= 7} 62: atom[ 19]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 3.30000e-01, mB= 1.00800e+00, qB= 3.30000e-01, resind= 0, atomnumber= 1} 62: atom[ 20]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 3.30000e-01, mB= 1.00800e+00, qB= 3.30000e-01, resind= 0, atomnumber= 1} 62: atom[ 21]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 3.30000e-01, mB= 1.00800e+00, qB= 3.30000e-01, resind= 0, atomnumber= 1} 62: atom[ 22]={type= 4, typeB= 4, ptype= Atom, m= 1.20110e+01, q= 5.00000e-01, mB= 1.20110e+01, qB= 5.00000e-01, resind= 0, atomnumber= 6} 62: atom[ 23]={type= 5, typeB= 5, ptype= Atom, m= 1.59994e+01, q=-5.00000e-01, mB= 1.59994e+01, qB=-5.00000e-01, resind= 0, atomnumber= 8} 62: atom[ 24]={type= 0, typeB= 0, ptype= Atom, m= 1.40067e+01, q=-5.00000e-01, mB= 1.40067e+01, qB=-5.00000e-01, resind= 1, atomnumber= 7} 62: atom[ 25]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 3.00000e-01, mB= 1.00800e+00, qB= 3.00000e-01, resind= 1, atomnumber= 1} 62: atom[ 26]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q= 1.40000e-01, mB= 1.20110e+01, qB= 1.40000e-01, resind= 1, atomnumber= 6} 62: atom[ 27]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 1, atomnumber= 1} 62: atom[ 28]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q=-6.00000e-02, mB= 1.20110e+01, qB=-6.00000e-02, resind= 1, atomnumber= 6} 62: atom[ 29]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 1, atomnumber= 1} 62: atom[ 30]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q=-1.80000e-01, mB= 1.20110e+01, qB=-1.80000e-01, resind= 1, atomnumber= 6} 62: atom[ 31]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 1, atomnumber= 1} 62: atom[ 32]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 1, atomnumber= 1} 62: atom[ 33]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 1, atomnumber= 1} 62: atom[ 34]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q=-1.80000e-01, mB= 1.20110e+01, qB=-1.80000e-01, resind= 1, atomnumber= 6} 62: atom[ 35]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 1, atomnumber= 1} 62: atom[ 36]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 1, atomnumber= 1} 62: atom[ 37]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 1, atomnumber= 1} 62: atom[ 38]={type= 4, typeB= 4, ptype= Atom, m= 1.20110e+01, q= 5.00000e-01, mB= 1.20110e+01, qB= 5.00000e-01, resind= 1, atomnumber= 6} 62: atom[ 39]={type= 5, typeB= 5, ptype= Atom, m= 1.59994e+01, q=-5.00000e-01, mB= 1.59994e+01, qB=-5.00000e-01, resind= 1, atomnumber= 8} 62: atom[ 40]={type= 0, typeB= 0, ptype= Atom, m= 1.40067e+01, q=-5.00000e-01, mB= 1.40067e+01, qB=-5.00000e-01, resind= 2, atomnumber= 7} 62: atom[ 41]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 3.00000e-01, mB= 1.00800e+00, qB= 3.00000e-01, resind= 2, atomnumber= 1} 62: atom[ 42]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q= 1.40000e-01, mB= 1.20110e+01, qB= 1.40000e-01, resind= 2, atomnumber= 6} 62: atom[ 43]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 2, atomnumber= 1} 62: atom[ 44]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q=-5.00000e-03, mB= 1.20110e+01, qB=-5.00000e-03, resind= 2, atomnumber= 6} 62: atom[ 45]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 2, atomnumber= 1} 62: atom[ 46]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 2, atomnumber= 1} 62: atom[ 47]={type= 6, typeB= 6, ptype= Atom, m= 1.20110e+01, q=-1.15000e-01, mB= 1.20110e+01, qB=-1.15000e-01, resind= 2, atomnumber= 6} 62: atom[ 48]={type= 6, typeB= 6, ptype= Atom, m= 1.20110e+01, q=-1.15000e-01, mB= 1.20110e+01, qB=-1.15000e-01, resind= 2, atomnumber= 6} 62: atom[ 49]={type= 7, typeB= 7, ptype= Atom, m= 1.00800e+00, q= 1.15000e-01, mB= 1.00800e+00, qB= 1.15000e-01, resind= 2, atomnumber= 1} 62: atom[ 50]={type= 6, typeB= 6, ptype= Atom, m= 1.20110e+01, q=-1.15000e-01, mB= 1.20110e+01, qB=-1.15000e-01, resind= 2, atomnumber= 6} 62: atom[ 51]={type= 7, typeB= 7, ptype= Atom, m= 1.00800e+00, q= 1.15000e-01, mB= 1.00800e+00, qB= 1.15000e-01, resind= 2, atomnumber= 1} 62: atom[ 52]={type= 6, typeB= 6, ptype= Atom, m= 1.20110e+01, q=-1.15000e-01, mB= 1.20110e+01, qB=-1.15000e-01, resind= 2, atomnumber= 6} 62: atom[ 53]={type= 7, typeB= 7, ptype= Atom, m= 1.00800e+00, q= 1.15000e-01, mB= 1.00800e+00, qB= 1.15000e-01, resind= 2, atomnumber= 1} 62: atom[ 54]={type= 6, typeB= 6, ptype= Atom, m= 1.20110e+01, q=-1.15000e-01, mB= 1.20110e+01, qB=-1.15000e-01, resind= 2, atomnumber= 6} 62: atom[ 55]={type= 7, typeB= 7, ptype= Atom, m= 1.00800e+00, q= 1.15000e-01, mB= 1.00800e+00, qB= 1.15000e-01, resind= 2, atomnumber= 1} 62: atom[ 56]={type= 6, typeB= 6, ptype= Atom, m= 1.20110e+01, q=-1.15000e-01, mB= 1.20110e+01, qB=-1.15000e-01, resind= 2, atomnumber= 6} 62: atom[ 57]={type= 7, typeB= 7, ptype= Atom, m= 1.00800e+00, q= 1.15000e-01, mB= 1.00800e+00, qB= 1.15000e-01, resind= 2, atomnumber= 1} 62: atom[ 58]={type= 4, typeB= 4, ptype= Atom, m= 1.20110e+01, q= 5.00000e-01, mB= 1.20110e+01, qB= 5.00000e-01, resind= 2, atomnumber= 6} 62: atom[ 59]={type= 5, typeB= 5, ptype= Atom, m= 1.59994e+01, q=-5.00000e-01, mB= 1.59994e+01, qB=-5.00000e-01, resind= 2, atomnumber= 8} 62: atom[ 60]={type= 0, typeB= 0, ptype= Atom, m= 1.40067e+01, q=-5.00000e-01, mB= 1.40067e+01, qB=-5.00000e-01, resind= 3, atomnumber= 7} 62: atom[ 61]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 3.00000e-01, mB= 1.00800e+00, qB= 3.00000e-01, resind= 3, atomnumber= 1} 62: atom[ 62]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q= 8.00000e-02, mB= 1.20110e+01, qB= 8.00000e-02, resind= 3, atomnumber= 6} 62: atom[ 63]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 3, atomnumber= 1} 62: atom[ 64]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 3, atomnumber= 1} 62: atom[ 65]={type= 4, typeB= 4, ptype= Atom, m= 1.20110e+01, q= 5.00000e-01, mB= 1.20110e+01, qB= 5.00000e-01, resind= 3, atomnumber= 6} 62: atom[ 66]={type= 5, typeB= 5, ptype= Atom, m= 1.59994e+01, q=-5.00000e-01, mB= 1.59994e+01, qB=-5.00000e-01, resind= 3, atomnumber= 8} 62: atom[ 67]={type= 0, typeB= 0, ptype= Atom, m= 1.40067e+01, q=-5.00000e-01, mB= 1.40067e+01, qB=-5.00000e-01, resind= 4, atomnumber= 7} 62: atom[ 68]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 3.00000e-01, mB= 1.00800e+00, qB= 3.00000e-01, resind= 4, atomnumber= 1} 62: atom[ 69]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q= 1.40000e-01, mB= 1.20110e+01, qB= 1.40000e-01, resind= 4, atomnumber= 6} 62: atom[ 70]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 4, atomnumber= 1} 62: atom[ 71]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q=-1.20000e-01, mB= 1.20110e+01, qB=-1.20000e-01, resind= 4, atomnumber= 6} 62: atom[ 72]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 4, atomnumber= 1} 62: atom[ 73]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 4, atomnumber= 1} 62: atom[ 74]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q=-5.00000e-02, mB= 1.20110e+01, qB=-5.00000e-02, resind= 4, atomnumber= 6} 62: atom[ 75]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 4, atomnumber= 1} 62: atom[ 76]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 4, atomnumber= 1} 62: atom[ 77]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q= 1.90000e-01, mB= 1.20110e+01, qB= 1.90000e-01, resind= 4, atomnumber= 6} 62: atom[ 78]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 4, atomnumber= 1} 62: atom[ 79]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 4, atomnumber= 1} 62: atom[ 80]={type= 0, typeB= 0, ptype= Atom, m= 1.40067e+01, q=-7.00000e-01, mB= 1.40067e+01, qB=-7.00000e-01, resind= 4, atomnumber= 7} 62: atom[ 81]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 4.40000e-01, mB= 1.00800e+00, qB= 4.40000e-01, resind= 4, atomnumber= 1} 62: atom[ 82]={type= 8, typeB= 8, ptype= Atom, m= 1.20110e+01, q= 6.40000e-01, mB= 1.20110e+01, qB= 6.40000e-01, resind= 4, atomnumber= 6} 62: atom[ 83]={type= 0, typeB= 0, ptype= Atom, m= 1.40067e+01, q=-8.00000e-01, mB= 1.40067e+01, qB=-8.00000e-01, resind= 4, atomnumber= 7} 62: atom[ 84]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 4.60000e-01, mB= 1.00800e+00, qB= 4.60000e-01, resind= 4, atomnumber= 1} 62: atom[ 85]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 4.60000e-01, mB= 1.00800e+00, qB= 4.60000e-01, resind= 4, atomnumber= 1} 62: atom[ 86]={type= 0, typeB= 0, ptype= Atom, m= 1.40067e+01, q=-8.00000e-01, mB= 1.40067e+01, qB=-8.00000e-01, resind= 4, atomnumber= 7} 62: atom[ 87]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 4.60000e-01, mB= 1.00800e+00, qB= 4.60000e-01, resind= 4, atomnumber= 1} 62: atom[ 88]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 4.60000e-01, mB= 1.00800e+00, qB= 4.60000e-01, resind= 4, atomnumber= 1} 62: atom[ 89]={type= 4, typeB= 4, ptype= Atom, m= 1.20110e+01, q= 5.00000e-01, mB= 1.20110e+01, qB= 5.00000e-01, resind= 4, atomnumber= 6} 62: atom[ 90]={type= 5, typeB= 5, ptype= Atom, m= 1.59994e+01, q=-5.00000e-01, mB= 1.59994e+01, qB=-5.00000e-01, resind= 4, atomnumber= 8} 62: atom[ 91]={type= 0, typeB= 0, ptype= Atom, m= 1.40067e+01, q=-5.00000e-01, mB= 1.40067e+01, qB=-5.00000e-01, resind= 5, atomnumber= 7} 62: atom[ 92]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 3.00000e-01, mB= 1.00800e+00, qB= 3.00000e-01, resind= 5, atomnumber= 1} 62: atom[ 93]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q= 1.40000e-01, mB= 1.20110e+01, qB= 1.40000e-01, resind= 5, atomnumber= 6} 62: atom[ 94]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 5, atomnumber= 1} 62: atom[ 95]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q= 6.00000e-02, mB= 1.20110e+01, qB= 6.00000e-02, resind= 5, atomnumber= 6} 62: atom[ 96]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 5, atomnumber= 1} 62: atom[ 97]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 5, atomnumber= 1} 62: atom[ 98]={type= 9, typeB= 9, ptype= Atom, m= 3.20600e+01, q=-3.35000e-01, mB= 3.20600e+01, qB=-3.35000e-01, resind= 5, atomnumber= 16} 62: atom[ 99]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 1.55000e-01, mB= 1.00800e+00, qB= 1.55000e-01, resind= 5, atomnumber= 1} 62: atom[ 100]={type= 4, typeB= 4, ptype= Atom, m= 1.20110e+01, q= 5.00000e-01, mB= 1.20110e+01, qB= 5.00000e-01, resind= 5, atomnumber= 6} 62: atom[ 101]={type= 5, typeB= 5, ptype= Atom, m= 1.59994e+01, q=-5.00000e-01, mB= 1.59994e+01, qB=-5.00000e-01, resind= 5, atomnumber= 8} 62: atom[ 102]={type= 0, typeB= 0, ptype= Atom, m= 1.40067e+01, q=-5.00000e-01, mB= 1.40067e+01, qB=-5.00000e-01, resind= 6, atomnumber= 7} 62: atom[ 103]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 3.00000e-01, mB= 1.00800e+00, qB= 3.00000e-01, resind= 6, atomnumber= 1} 62: atom[ 104]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q= 1.40000e-01, mB= 1.20110e+01, qB= 1.40000e-01, resind= 6, atomnumber= 6} 62: atom[ 105]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 6, atomnumber= 1} 62: atom[ 106]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q=-1.20000e-01, mB= 1.20110e+01, qB=-1.20000e-01, resind= 6, atomnumber= 6} 62: atom[ 107]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 6, atomnumber= 1} 62: atom[ 108]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 6, atomnumber= 1} 62: atom[ 109]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q=-2.20000e-01, mB= 1.20110e+01, qB=-2.20000e-01, resind= 6, atomnumber= 6} 62: atom[ 110]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 6, atomnumber= 1} 62: atom[ 111]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 6, atomnumber= 1} 62: atom[ 112]={type= 4, typeB= 4, ptype= Atom, m= 1.20110e+01, q= 7.00000e-01, mB= 1.20110e+01, qB= 7.00000e-01, resind= 6, atomnumber= 6} 62: atom[ 113]={type= 5, typeB= 5, ptype= Atom, m= 1.59994e+01, q=-8.00000e-01, mB= 1.59994e+01, qB=-8.00000e-01, resind= 6, atomnumber= 8} 62: atom[ 114]={type= 5, typeB= 5, ptype= Atom, m= 1.59994e+01, q=-8.00000e-01, mB= 1.59994e+01, qB=-8.00000e-01, resind= 6, atomnumber= 8} 62: atom[ 115]={type= 4, typeB= 4, ptype= Atom, m= 1.20110e+01, q= 5.00000e-01, mB= 1.20110e+01, qB= 5.00000e-01, resind= 6, atomnumber= 6} 62: atom[ 116]={type= 5, typeB= 5, ptype= Atom, m= 1.59994e+01, q=-5.00000e-01, mB= 1.59994e+01, qB=-5.00000e-01, resind= 6, atomnumber= 8} 62: atom[ 117]={type= 0, typeB= 0, ptype= Atom, m= 1.40067e+01, q=-5.00000e-01, mB= 1.40067e+01, qB=-5.00000e-01, resind= 7, atomnumber= 7} 62: atom[ 118]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 3.00000e-01, mB= 1.00800e+00, qB= 3.00000e-01, resind= 7, atomnumber= 1} 62: atom[ 119]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q= 1.40000e-01, mB= 1.20110e+01, qB= 1.40000e-01, resind= 7, atomnumber= 6} 62: atom[ 120]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 7, atomnumber= 1} 62: atom[ 121]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q=-1.20000e-01, mB= 1.20110e+01, qB=-1.20000e-01, resind= 7, atomnumber= 6} 62: atom[ 122]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 7, atomnumber= 1} 62: atom[ 123]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 7, atomnumber= 1} 62: atom[ 124]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q=-6.00000e-02, mB= 1.20110e+01, qB=-6.00000e-02, resind= 7, atomnumber= 6} 62: atom[ 125]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 7, atomnumber= 1} 62: atom[ 126]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q=-1.80000e-01, mB= 1.20110e+01, qB=-1.80000e-01, resind= 7, atomnumber= 6} 62: atom[ 127]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 7, atomnumber= 1} 62: atom[ 128]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 7, atomnumber= 1} 62: atom[ 129]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 7, atomnumber= 1} 62: atom[ 130]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q=-1.80000e-01, mB= 1.20110e+01, qB=-1.80000e-01, resind= 7, atomnumber= 6} 62: atom[ 131]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 7, atomnumber= 1} 62: atom[ 132]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 7, atomnumber= 1} 62: atom[ 133]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 7, atomnumber= 1} 62: atom[ 134]={type= 4, typeB= 4, ptype= Atom, m= 1.20110e+01, q= 5.00000e-01, mB= 1.20110e+01, qB= 5.00000e-01, resind= 7, atomnumber= 6} 62: atom[ 135]={type= 5, typeB= 5, ptype= Atom, m= 1.59994e+01, q=-5.00000e-01, mB= 1.59994e+01, qB=-5.00000e-01, resind= 7, atomnumber= 8} 62: atom[ 136]={type= 0, typeB= 0, ptype= Atom, m= 1.40067e+01, q=-5.00000e-01, mB= 1.40067e+01, qB=-5.00000e-01, resind= 8, atomnumber= 7} 62: atom[ 137]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 3.00000e-01, mB= 1.00800e+00, qB= 3.00000e-01, resind= 8, atomnumber= 1} 62: atom[ 138]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q= 1.40000e-01, mB= 1.20110e+01, qB= 1.40000e-01, resind= 8, atomnumber= 6} 62: atom[ 139]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 8, atomnumber= 1} 62: atom[ 140]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q=-1.80000e-01, mB= 1.20110e+01, qB=-1.80000e-01, resind= 8, atomnumber= 6} 62: atom[ 141]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 8, atomnumber= 1} 62: atom[ 142]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 8, atomnumber= 1} 62: atom[ 143]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 8, atomnumber= 1} 62: atom[ 144]={type= 4, typeB= 4, ptype= Atom, m= 1.20110e+01, q= 5.00000e-01, mB= 1.20110e+01, qB= 5.00000e-01, resind= 8, atomnumber= 6} 62: atom[ 145]={type= 5, typeB= 5, ptype= Atom, m= 1.59994e+01, q=-5.00000e-01, mB= 1.59994e+01, qB=-5.00000e-01, resind= 8, atomnumber= 8} 62: atom[ 146]={type= 0, typeB= 0, ptype= Atom, m= 1.40067e+01, q=-5.00000e-01, mB= 1.40067e+01, qB=-5.00000e-01, resind= 9, atomnumber= 7} 62: atom[ 147]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 3.00000e-01, mB= 1.00800e+00, qB= 3.00000e-01, resind= 9, atomnumber= 1} 62: atom[ 148]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q= 1.40000e-01, mB= 1.20110e+01, qB= 1.40000e-01, resind= 9, atomnumber= 6} 62: atom[ 149]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 9, atomnumber= 1} 62: atom[ 150]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q=-1.80000e-01, mB= 1.20110e+01, qB=-1.80000e-01, resind= 9, atomnumber= 6} 62: atom[ 151]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 9, atomnumber= 1} 62: atom[ 152]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 9, atomnumber= 1} 62: atom[ 153]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 9, atomnumber= 1} 62: atom[ 154]={type= 4, typeB= 4, ptype= Atom, m= 1.20110e+01, q= 5.00000e-01, mB= 1.20110e+01, qB= 5.00000e-01, resind= 9, atomnumber= 6} 62: atom[ 155]={type= 5, typeB= 5, ptype= Atom, m= 1.59994e+01, q=-5.00000e-01, mB= 1.59994e+01, qB=-5.00000e-01, resind= 9, atomnumber= 8} 62: atom (156): 62: atom[0]={name="N"} 62: atom[1]={name="H1"} 62: atom[2]={name="H2"} 62: atom[3]={name="H3"} 62: atom[4]={name="CA"} 62: atom[5]={name="HA"} 62: atom[6]={name="CB"} 62: atom[7]={name="HB1"} 62: atom[8]={name="HB2"} 62: atom[9]={name="CG"} 62: atom[10]={name="HG1"} 62: atom[11]={name="HG2"} 62: atom[12]={name="CD"} 62: atom[13]={name="HD1"} 62: atom[14]={name="HD2"} 62: atom[15]={name="CE"} 62: atom[16]={name="HE1"} 62: atom[17]={name="HE2"} 62: atom[18]={name="NZ"} 62: atom[19]={name="HZ1"} 62: atom[20]={name="HZ2"} 62: atom[21]={name="HZ3"} 62: atom[22]={name="C"} 62: atom[23]={name="O"} 62: atom[24]={name="N"} 62: atom[25]={name="H"} 62: atom[26]={name="CA"} 62: atom[27]={name="HA"} 62: atom[28]={name="CB"} 62: atom[29]={name="HB"} 62: atom[30]={name="CG1"} 62: atom[31]={name="HG11"} 62: atom[32]={name="HG12"} 62: atom[33]={name="HG13"} 62: atom[34]={name="CG2"} 62: atom[35]={name="HG21"} 62: atom[36]={name="HG22"} 62: atom[37]={name="HG23"} 62: atom[38]={name="C"} 62: atom[39]={name="O"} 62: atom[40]={name="N"} 62: atom[41]={name="H"} 62: atom[42]={name="CA"} 62: atom[43]={name="HA"} 62: atom[44]={name="CB"} 62: atom[45]={name="HB1"} 62: atom[46]={name="HB2"} 62: atom[47]={name="CG"} 62: atom[48]={name="CD1"} 62: atom[49]={name="HD1"} 62: atom[50]={name="CD2"} 62: atom[51]={name="HD2"} 62: atom[52]={name="CE1"} 62: atom[53]={name="HE1"} 62: atom[54]={name="CE2"} 62: atom[55]={name="HE2"} 62: atom[56]={name="CZ"} 62: atom[57]={name="HZ"} 62: atom[58]={name="C"} 62: atom[59]={name="O"} 62: atom[60]={name="N"} 62: atom[61]={name="H"} 62: atom[62]={name="CA"} 62: atom[63]={name="HA1"} 62: atom[64]={name="HA2"} 62: atom[65]={name="C"} 62: atom[66]={name="O"} 62: atom[67]={name="N"} 62: atom[68]={name="H"} 62: atom[69]={name="CA"} 62: atom[70]={name="HA"} 62: atom[71]={name="CB"} 62: atom[72]={name="HB1"} 62: atom[73]={name="HB2"} 62: atom[74]={name="CG"} 62: atom[75]={name="HG1"} 62: atom[76]={name="HG2"} 62: atom[77]={name="CD"} 62: atom[78]={name="HD1"} 62: atom[79]={name="HD2"} 62: atom[80]={name="NE"} 62: atom[81]={name="HE"} 62: atom[82]={name="CZ"} 62: atom[83]={name="NH1"} 62: atom[84]={name="HH11"} 62: atom[85]={name="HH12"} 62: atom[86]={name="NH2"} 62: atom[87]={name="HH21"} 62: atom[88]={name="HH22"} 62: atom[89]={name="C"} 62: atom[90]={name="O"} 62: atom[91]={name="N"} 62: atom[92]={name="H"} 62: atom[93]={name="CA"} 62: atom[94]={name="HA"} 62: atom[95]={name="CB"} 62: atom[96]={name="HB1"} 62: atom[97]={name="HB2"} 62: atom[98]={name="SG"} 62: atom[99]={name="HG"} 62: atom[100]={name="C"} 62: atom[101]={name="O"} 62: atom[102]={name="N"} 62: atom[103]={name="H"} 62: atom[104]={name="CA"} 62: atom[105]={name="HA"} 62: atom[106]={name="CB"} 62: atom[107]={name="HB1"} 62: atom[108]={name="HB2"} 62: atom[109]={name="CG"} 62: atom[110]={name="HG1"} 62: atom[111]={name="HG2"} 62: atom[112]={name="CD"} 62: atom[113]={name="OE1"} 62: atom[114]={name="OE2"} 62: atom[115]={name="C"} 62: atom[116]={name="O"} 62: atom[117]={name="N"} 62: atom[118]={name="H"} 62: atom[119]={name="CA"} 62: atom[120]={name="HA"} 62: atom[121]={name="CB"} 62: atom[122]={name="HB1"} 62: atom[123]={name="HB2"} 62: atom[124]={name="CG"} 62: atom[125]={name="HG"} 62: atom[126]={name="CD1"} 62: atom[127]={name="HD11"} 62: atom[128]={name="HD12"} 62: atom[129]={name="HD13"} 62: atom[130]={name="CD2"} 62: atom[131]={name="HD21"} 62: atom[132]={name="HD22"} 62: atom[133]={name="HD23"} 62: atom[134]={name="C"} 62: atom[135]={name="O"} 62: atom[136]={name="N"} 62: atom[137]={name="H"} 62: atom[138]={name="CA"} 62: atom[139]={name="HA"} 62: atom[140]={name="CB"} 62: atom[141]={name="HB1"} 62: atom[142]={name="HB2"} 62: atom[143]={name="HB3"} 62: atom[144]={name="C"} 62: atom[145]={name="O"} 62: atom[146]={name="N"} 62: atom[147]={name="H"} 62: atom[148]={name="CA"} 62: atom[149]={name="HA"} 62: atom[150]={name="CB"} 62: atom[151]={name="HB1"} 62: atom[152]={name="HB2"} 62: atom[153]={name="HB3"} 62: atom[154]={name="C"} 62: atom[155]={name="O"} 62: type (156): 62: type[0]={name="opls_287",nameB="opls_287"} 62: type[1]={name="opls_290",nameB="opls_290"} 62: type[2]={name="opls_290",nameB="opls_290"} 62: type[3]={name="opls_290",nameB="opls_290"} 62: type[4]={name="opls_293B",nameB="opls_293B"} 62: type[5]={name="opls_140",nameB="opls_140"} 62: type[6]={name="opls_136",nameB="opls_136"} 62: type[7]={name="opls_140",nameB="opls_140"} 62: type[8]={name="opls_140",nameB="opls_140"} 62: type[9]={name="opls_136",nameB="opls_136"} 62: type[10]={name="opls_140",nameB="opls_140"} 62: type[11]={name="opls_140",nameB="opls_140"} 62: type[12]={name="opls_136",nameB="opls_136"} 62: type[13]={name="opls_140",nameB="opls_140"} 62: type[14]={name="opls_140",nameB="opls_140"} 62: type[15]={name="opls_292",nameB="opls_292"} 62: type[16]={name="opls_140",nameB="opls_140"} 62: type[17]={name="opls_140",nameB="opls_140"} 62: type[18]={name="opls_287",nameB="opls_287"} 62: type[19]={name="opls_290",nameB="opls_290"} 62: type[20]={name="opls_290",nameB="opls_290"} 62: type[21]={name="opls_290",nameB="opls_290"} 62: type[22]={name="opls_235",nameB="opls_235"} 62: type[23]={name="opls_236",nameB="opls_236"} 62: type[24]={name="opls_238",nameB="opls_238"} 62: type[25]={name="opls_241",nameB="opls_241"} 62: type[26]={name="opls_224B",nameB="opls_224B"} 62: type[27]={name="opls_140",nameB="opls_140"} 62: type[28]={name="opls_137",nameB="opls_137"} 62: type[29]={name="opls_140",nameB="opls_140"} 62: type[30]={name="opls_135",nameB="opls_135"} 62: type[31]={name="opls_140",nameB="opls_140"} 62: type[32]={name="opls_140",nameB="opls_140"} 62: type[33]={name="opls_140",nameB="opls_140"} 62: type[34]={name="opls_135",nameB="opls_135"} 62: type[35]={name="opls_140",nameB="opls_140"} 62: type[36]={name="opls_140",nameB="opls_140"} 62: type[37]={name="opls_140",nameB="opls_140"} 62: type[38]={name="opls_235",nameB="opls_235"} 62: type[39]={name="opls_236",nameB="opls_236"} 62: type[40]={name="opls_238",nameB="opls_238"} 62: type[41]={name="opls_241",nameB="opls_241"} 62: type[42]={name="opls_224B",nameB="opls_224B"} 62: type[43]={name="opls_140",nameB="opls_140"} 62: type[44]={name="opls_149",nameB="opls_149"} 62: type[45]={name="opls_140",nameB="opls_140"} 62: type[46]={name="opls_140",nameB="opls_140"} 62: type[47]={name="opls_145",nameB="opls_145"} 62: type[48]={name="opls_145",nameB="opls_145"} 62: type[49]={name="opls_146",nameB="opls_146"} 62: type[50]={name="opls_145",nameB="opls_145"} 62: type[51]={name="opls_146",nameB="opls_146"} 62: type[52]={name="opls_145",nameB="opls_145"} 62: type[53]={name="opls_146",nameB="opls_146"} 62: type[54]={name="opls_145",nameB="opls_145"} 62: type[55]={name="opls_146",nameB="opls_146"} 62: type[56]={name="opls_145",nameB="opls_145"} 62: type[57]={name="opls_146",nameB="opls_146"} 62: type[58]={name="opls_235",nameB="opls_235"} 62: type[59]={name="opls_236",nameB="opls_236"} 62: type[60]={name="opls_238",nameB="opls_238"} 62: type[61]={name="opls_241",nameB="opls_241"} 62: type[62]={name="opls_223B",nameB="opls_223B"} 62: type[63]={name="opls_140",nameB="opls_140"} 62: type[64]={name="opls_140",nameB="opls_140"} 62: type[65]={name="opls_235",nameB="opls_235"} 62: type[66]={name="opls_236",nameB="opls_236"} 62: type[67]={name="opls_238",nameB="opls_238"} 62: type[68]={name="opls_241",nameB="opls_241"} 62: type[69]={name="opls_224B",nameB="opls_224B"} 62: type[70]={name="opls_140",nameB="opls_140"} 62: type[71]={name="opls_136",nameB="opls_136"} 62: type[72]={name="opls_140",nameB="opls_140"} 62: type[73]={name="opls_140",nameB="opls_140"} 62: type[74]={name="opls_308",nameB="opls_308"} 62: type[75]={name="opls_140",nameB="opls_140"} 62: type[76]={name="opls_140",nameB="opls_140"} 62: type[77]={name="opls_307",nameB="opls_307"} 62: type[78]={name="opls_140",nameB="opls_140"} 62: type[79]={name="opls_140",nameB="opls_140"} 62: type[80]={name="opls_303",nameB="opls_303"} 62: type[81]={name="opls_304",nameB="opls_304"} 62: type[82]={name="opls_302",nameB="opls_302"} 62: type[83]={name="opls_300",nameB="opls_300"} 62: type[84]={name="opls_301",nameB="opls_301"} 62: type[85]={name="opls_301",nameB="opls_301"} 62: type[86]={name="opls_300",nameB="opls_300"} 62: type[87]={name="opls_301",nameB="opls_301"} 62: type[88]={name="opls_301",nameB="opls_301"} 62: type[89]={name="opls_235",nameB="opls_235"} 62: type[90]={name="opls_236",nameB="opls_236"} 62: type[91]={name="opls_238",nameB="opls_238"} 62: type[92]={name="opls_241",nameB="opls_241"} 62: type[93]={name="opls_224B",nameB="opls_224B"} 62: type[94]={name="opls_140",nameB="opls_140"} 62: type[95]={name="opls_206",nameB="opls_206"} 62: type[96]={name="opls_140",nameB="opls_140"} 62: type[97]={name="opls_140",nameB="opls_140"} 62: type[98]={name="opls_200",nameB="opls_200"} 62: type[99]={name="opls_204",nameB="opls_204"} 62: type[100]={name="opls_235",nameB="opls_235"} 62: type[101]={name="opls_236",nameB="opls_236"} 62: type[102]={name="opls_238",nameB="opls_238"} 62: type[103]={name="opls_241",nameB="opls_241"} 62: type[104]={name="opls_224B",nameB="opls_224B"} 62: type[105]={name="opls_140",nameB="opls_140"} 62: type[106]={name="opls_136",nameB="opls_136"} 62: type[107]={name="opls_140",nameB="opls_140"} 62: type[108]={name="opls_140",nameB="opls_140"} 62: type[109]={name="opls_274",nameB="opls_274"} 62: type[110]={name="opls_140",nameB="opls_140"} 62: type[111]={name="opls_140",nameB="opls_140"} 62: type[112]={name="opls_271",nameB="opls_271"} 62: type[113]={name="opls_272",nameB="opls_272"} 62: type[114]={name="opls_272",nameB="opls_272"} 62: type[115]={name="opls_235",nameB="opls_235"} 62: type[116]={name="opls_236",nameB="opls_236"} 62: type[117]={name="opls_238",nameB="opls_238"} 62: type[118]={name="opls_241",nameB="opls_241"} 62: type[119]={name="opls_224B",nameB="opls_224B"} 62: type[120]={name="opls_140",nameB="opls_140"} 62: type[121]={name="opls_136",nameB="opls_136"} 62: type[122]={name="opls_140",nameB="opls_140"} 62: type[123]={name="opls_140",nameB="opls_140"} 62: type[124]={name="opls_137",nameB="opls_137"} 62: type[125]={name="opls_140",nameB="opls_140"} 62: type[126]={name="opls_135",nameB="opls_135"} 62: type[127]={name="opls_140",nameB="opls_140"} 62: type[128]={name="opls_140",nameB="opls_140"} 62: type[129]={name="opls_140",nameB="opls_140"} 62: type[130]={name="opls_135",nameB="opls_135"} 62: type[131]={name="opls_140",nameB="opls_140"} 62: type[132]={name="opls_140",nameB="opls_140"} 62: type[133]={name="opls_140",nameB="opls_140"} 62: type[134]={name="opls_235",nameB="opls_235"} 62: type[135]={name="opls_236",nameB="opls_236"} 62: type[136]={name="opls_238",nameB="opls_238"} 62: type[137]={name="opls_241",nameB="opls_241"} 62: type[138]={name="opls_224B",nameB="opls_224B"} 62: type[139]={name="opls_140",nameB="opls_140"} 62: type[140]={name="opls_135",nameB="opls_135"} 62: type[141]={name="opls_140",nameB="opls_140"} 62: type[142]={name="opls_140",nameB="opls_140"} 62: type[143]={name="opls_140",nameB="opls_140"} 62: type[144]={name="opls_235",nameB="opls_235"} 62: type[145]={name="opls_236",nameB="opls_236"} 62: type[146]={name="opls_238",nameB="opls_238"} 62: type[147]={name="opls_241",nameB="opls_241"} 62: type[148]={name="opls_224B",nameB="opls_224B"} 62: type[149]={name="opls_140",nameB="opls_140"} 62: type[150]={name="opls_135",nameB="opls_135"} 62: type[151]={name="opls_140",nameB="opls_140"} 62: type[152]={name="opls_140",nameB="opls_140"} 62: type[153]={name="opls_140",nameB="opls_140"} 62: type[154]={name="opls_235",nameB="opls_235"} 62: type[155]={name="opls_236",nameB="opls_236"} 62: residue (10): 62: residue[0]={name="LYS", nr=1, ic=' '} 62: residue[1]={name="VAL", nr=2, ic=' '} 62: residue[2]={name="PHE", nr=3, ic=' '} 62: residue[3]={name="GLY", nr=4, ic=' '} 62: residue[4]={name="ARG", nr=5, ic=' '} 62: residue[5]={name="CYS", nr=6, ic=' '} 62: residue[6]={name="GLU", nr=7, ic=' '} 62: residue[7]={name="LEU", nr=8, ic=' '} 62: residue[8]={name="ALA", nr=9, ic=' '} 62: residue[9]={name="ALA", nr=10, ic=' '} 62: excls: 62: numLists=156 62: numElements=1828 62: excls[0][num=13]={0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 22, 23, 24} 62: excls[1][num=8]={0, 1, 2, 3, 4, 5, 6, 22} 62: excls[2][num=8]={0, 1, 2, 3, 4, 5, 6, 22} 62: excls[3][num=8]={0, 1, 2, 3, 4, 5, 6, 22} 62: excls[4][num=18]={0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 22, 62: 23, 24, 25, 26} 62: excls[5][num=13]={0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 22, 23, 24} 62: excls[6][num=19]={0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 62: 14, 15, 22, 23, 24} 62: excls[7][num=11]={0, 4, 5, 6, 7, 8, 9, 10, 11, 12, 22} 62: excls[8][num=11]={0, 4, 5, 6, 7, 8, 9, 10, 11, 12, 22} 62: excls[9][num=17]={0, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 62: 16, 17, 18, 22} 62: excls[10][num=11]={4, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15} 62: excls[11][num=11]={4, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15} 62: excls[12][num=17]={4, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 62: 17, 18, 19, 20, 21} 62: excls[13][num=11]={6, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18} 62: excls[14][num=11]={6, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18} 62: excls[15][num=14]={6, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 62: 20, 21} 62: excls[16][num=11]={9, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21} 62: excls[17][num=11]={9, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21} 62: excls[18][num=11]={9, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21} 62: excls[19][num=8]={12, 15, 16, 17, 18, 19, 20, 21} 62: excls[20][num=8]={12, 15, 16, 17, 18, 19, 20, 21} 62: excls[21][num=8]={12, 15, 16, 17, 18, 19, 20, 21} 62: excls[22][num=18]={0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 22, 23, 24, 25, 62: 26, 27, 28, 38} 62: excls[23][num=9]={0, 4, 5, 6, 22, 23, 24, 25, 26} 62: excls[24][num=17]={0, 4, 5, 6, 22, 23, 24, 25, 26, 27, 28, 29, 62: 30, 34, 38, 39, 40} 62: excls[25][num=9]={4, 22, 23, 24, 25, 26, 27, 28, 38} 62: excls[26][num=22]={4, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 62: 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42} 62: excls[27][num=12]={22, 24, 25, 26, 27, 28, 29, 30, 34, 38, 39, 62: 40} 62: excls[28][num=18]={22, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 62: 34, 35, 36, 37, 38, 39, 40} 62: excls[29][num=14]={24, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 62: 36, 37, 38} 62: excls[30][num=14]={24, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 62: 36, 37, 38} 62: excls[31][num=8]={26, 28, 29, 30, 31, 32, 33, 34} 62: excls[32][num=8]={26, 28, 29, 30, 31, 32, 33, 34} 62: excls[33][num=8]={26, 28, 29, 30, 31, 32, 33, 34} 62: excls[34][num=14]={24, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 62: 36, 37, 38} 62: excls[35][num=8]={26, 28, 29, 30, 34, 35, 36, 37} 62: excls[36][num=8]={26, 28, 29, 30, 34, 35, 36, 37} 62: excls[37][num=8]={26, 28, 29, 30, 34, 35, 36, 37} 62: excls[38][num=17]={22, 24, 25, 26, 27, 28, 29, 30, 34, 38, 39, 62: 40, 41, 42, 43, 44, 58} 62: excls[39][num=9]={24, 26, 27, 28, 38, 39, 40, 41, 42} 62: excls[40][num=17]={24, 26, 27, 28, 38, 39, 40, 41, 42, 43, 44, 62: 45, 46, 47, 58, 59, 60} 62: excls[41][num=9]={26, 38, 39, 40, 41, 42, 43, 44, 58} 62: excls[42][num=18]={26, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 62: 48, 50, 58, 59, 60, 61, 62} 62: excls[43][num=12]={38, 40, 41, 42, 43, 44, 45, 46, 47, 58, 59, 62: 60} 62: excls[44][num=18]={38, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 62: 50, 51, 52, 54, 58, 59, 60} 62: excls[45][num=10]={40, 42, 43, 44, 45, 46, 47, 48, 50, 58} 62: excls[46][num=10]={40, 42, 43, 44, 45, 46, 47, 48, 50, 58} 62: excls[47][num=17]={40, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 62: 52, 53, 54, 55, 56, 58} 62: excls[48][num=14]={42, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 62: 54, 56, 57} 62: excls[49][num=8]={44, 47, 48, 49, 50, 52, 53, 56} 62: excls[50][num=14]={42, 44, 45, 46, 47, 48, 49, 50, 51, 52, 54, 62: 55, 56, 57} 62: excls[51][num=8]={44, 47, 48, 50, 51, 54, 55, 56} 62: excls[52][num=11]={44, 47, 48, 49, 50, 52, 53, 54, 55, 56, 57} 62: excls[53][num=8]={47, 48, 49, 52, 53, 54, 56, 57} 62: excls[54][num=11]={44, 47, 48, 50, 51, 52, 53, 54, 55, 56, 57} 62: excls[55][num=8]={47, 50, 51, 52, 54, 55, 56, 57} 62: excls[56][num=11]={47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57} 62: excls[57][num=8]={48, 50, 52, 53, 54, 55, 56, 57} 62: excls[58][num=17]={38, 40, 41, 42, 43, 44, 45, 46, 47, 58, 59, 62: 60, 61, 62, 63, 64, 65} 62: excls[59][num=9]={40, 42, 43, 44, 58, 59, 60, 61, 62} 62: excls[60][num=14]={40, 42, 43, 44, 58, 59, 60, 61, 62, 63, 64, 62: 65, 66, 67} 62: excls[61][num=9]={42, 58, 59, 60, 61, 62, 63, 64, 65} 62: excls[62][num=13]={42, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 62: 68, 69} 62: excls[63][num=9]={58, 60, 61, 62, 63, 64, 65, 66, 67} 62: excls[64][num=9]={58, 60, 61, 62, 63, 64, 65, 66, 67} 62: excls[65][num=14]={58, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 62: 70, 71, 89} 62: excls[66][num=9]={60, 62, 63, 64, 65, 66, 67, 68, 69} 62: excls[67][num=17]={60, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 62: 72, 73, 74, 89, 90, 91} 62: excls[68][num=9]={62, 65, 66, 67, 68, 69, 70, 71, 89} 62: excls[69][num=19]={62, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 62: 75, 76, 77, 89, 90, 91, 92, 93} 62: excls[70][num=12]={65, 67, 68, 69, 70, 71, 72, 73, 74, 89, 90, 62: 91} 62: excls[71][num=18]={65, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 62: 77, 78, 79, 80, 89, 90, 91} 62: excls[72][num=11]={67, 69, 70, 71, 72, 73, 74, 75, 76, 77, 89} 62: excls[73][num=11]={67, 69, 70, 71, 72, 73, 74, 75, 76, 77, 89} 62: excls[74][num=16]={67, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 62: 79, 80, 81, 82, 89} 62: excls[75][num=11]={69, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80} 62: excls[76][num=11]={69, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80} 62: excls[77][num=15]={69, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80, 62: 81, 82, 83, 86} 62: excls[78][num=10]={71, 74, 75, 76, 77, 78, 79, 80, 81, 82} 62: excls[79][num=10]={71, 74, 75, 76, 77, 78, 79, 80, 81, 82} 62: excls[80][num=16]={71, 74, 75, 76, 77, 78, 79, 80, 81, 82, 83, 62: 84, 85, 86, 87, 88} 62: excls[81][num=9]={74, 77, 78, 79, 80, 81, 82, 83, 86} 62: excls[82][num=13]={74, 77, 78, 79, 80, 81, 82, 83, 84, 85, 86, 62: 87, 88} 62: excls[83][num=10]={77, 80, 81, 82, 83, 84, 85, 86, 87, 88} 62: excls[84][num=6]={80, 82, 83, 84, 85, 86} 62: excls[85][num=6]={80, 82, 83, 84, 85, 86} 62: excls[86][num=10]={77, 80, 81, 82, 83, 84, 85, 86, 87, 88} 62: excls[87][num=6]={80, 82, 83, 86, 87, 88} 62: excls[88][num=6]={80, 82, 83, 86, 87, 88} 62: excls[89][num=17]={65, 67, 68, 69, 70, 71, 72, 73, 74, 89, 90, 62: 91, 92, 93, 94, 95, 100} 62: excls[90][num=9]={67, 69, 70, 71, 89, 90, 91, 92, 93} 62: excls[91][num=17]={67, 69, 70, 71, 89, 90, 91, 92, 93, 94, 95, 62: 96, 97, 98, 100, 101, 102} 62: excls[92][num=9]={69, 89, 90, 91, 92, 93, 94, 95, 100} 62: excls[93][num=17]={69, 89, 90, 91, 92, 93, 94, 95, 96, 97, 98, 62: 99, 100, 101, 102, 103, 104} 62: excls[94][num=12]={89, 91, 92, 93, 94, 95, 96, 97, 98, 100, 101, 62: 102} 62: excls[95][num=13]={89, 91, 92, 93, 94, 95, 96, 97, 98, 99, 100, 62: 101, 102} 62: excls[96][num=9]={91, 93, 94, 95, 96, 97, 98, 99, 100} 62: excls[97][num=9]={91, 93, 94, 95, 96, 97, 98, 99, 100} 62: excls[98][num=9]={91, 93, 94, 95, 96, 97, 98, 99, 100} 62: excls[99][num=6]={93, 95, 96, 97, 98, 99} 62: excls[100][num=17]={89, 91, 92, 93, 94, 95, 96, 97, 98, 100, 101, 62: 102, 103, 104, 105, 106, 115} 62: excls[101][num=9]={91, 93, 94, 95, 100, 101, 102, 103, 104} 62: excls[102][num=17]={91, 93, 94, 95, 100, 101, 102, 103, 104, 105, 62: 106, 107, 108, 109, 115, 116, 117} 62: excls[103][num=9]={93, 100, 101, 102, 103, 104, 105, 106, 115} 62: excls[104][num=19]={93, 100, 101, 102, 103, 104, 105, 106, 107, 62: 108, 109, 110, 111, 112, 115, 116, 117, 118, 119} 62: excls[105][num=12]={100, 102, 103, 104, 105, 106, 107, 108, 109, 62: 115, 116, 117} 62: excls[106][num=17]={100, 102, 103, 104, 105, 106, 107, 108, 109, 62: 110, 111, 112, 113, 114, 115, 116, 117} 62: excls[107][num=11]={102, 104, 105, 106, 107, 108, 109, 110, 111, 62: 112, 115} 62: excls[108][num=11]={102, 104, 105, 106, 107, 108, 109, 110, 111, 62: 112, 115} 62: excls[109][num=13]={102, 104, 105, 106, 107, 108, 109, 110, 111, 62: 112, 113, 114, 115} 62: excls[110][num=10]={104, 106, 107, 108, 109, 110, 111, 112, 113, 62: 114} 62: excls[111][num=10]={104, 106, 107, 108, 109, 110, 111, 112, 113, 62: 114} 62: excls[112][num=10]={104, 106, 107, 108, 109, 110, 111, 112, 113, 62: 114} 62: excls[113][num=7]={106, 109, 110, 111, 112, 113, 114} 62: excls[114][num=7]={106, 109, 110, 111, 112, 113, 114} 62: excls[115][num=17]={100, 102, 103, 104, 105, 106, 107, 108, 109, 62: 115, 116, 117, 118, 119, 120, 121, 134} 62: excls[116][num=9]={102, 104, 105, 106, 115, 116, 117, 118, 119} 62: excls[117][num=17]={102, 104, 105, 106, 115, 116, 117, 118, 119, 62: 120, 121, 122, 123, 124, 134, 135, 136} 62: excls[118][num=9]={104, 115, 116, 117, 118, 119, 120, 121, 134} 62: excls[119][num=19]={104, 115, 116, 117, 118, 119, 120, 121, 122, 62: 123, 124, 125, 126, 130, 134, 135, 136, 137, 138} 62: excls[120][num=12]={115, 117, 118, 119, 120, 121, 122, 123, 124, 62: 134, 135, 136} 62: excls[121][num=21]={115, 117, 118, 119, 120, 121, 122, 123, 124, 62: 125, 126, 127, 128, 129, 130, 131, 132, 133, 134, 135, 136} 62: excls[122][num=11]={117, 119, 120, 121, 122, 123, 124, 125, 126, 62: 130, 134} 62: excls[123][num=11]={117, 119, 120, 121, 122, 123, 124, 125, 126, 62: 130, 134} 62: excls[124][num=17]={117, 119, 120, 121, 122, 123, 124, 125, 126, 62: 127, 128, 129, 130, 131, 132, 133, 134} 62: excls[125][num=14]={119, 121, 122, 123, 124, 125, 126, 127, 128, 62: 129, 130, 131, 132, 133} 62: excls[126][num=14]={119, 121, 122, 123, 124, 125, 126, 127, 128, 62: 129, 130, 131, 132, 133} 62: excls[127][num=8]={121, 124, 125, 126, 127, 128, 129, 130} 62: excls[128][num=8]={121, 124, 125, 126, 127, 128, 129, 130} 62: excls[129][num=8]={121, 124, 125, 126, 127, 128, 129, 130} 62: excls[130][num=14]={119, 121, 122, 123, 124, 125, 126, 127, 128, 62: 129, 130, 131, 132, 133} 62: excls[131][num=8]={121, 124, 125, 126, 130, 131, 132, 133} 62: excls[132][num=8]={121, 124, 125, 126, 130, 131, 132, 133} 62: excls[133][num=8]={121, 124, 125, 126, 130, 131, 132, 133} 62: excls[134][num=17]={115, 117, 118, 119, 120, 121, 122, 123, 124, 62: 134, 135, 136, 137, 138, 139, 140, 144} 62: excls[135][num=9]={117, 119, 120, 121, 134, 135, 136, 137, 138} 62: excls[136][num=17]={117, 119, 120, 121, 134, 135, 136, 137, 138, 62: 139, 140, 141, 142, 143, 144, 145, 146} 62: excls[137][num=9]={119, 134, 135, 136, 137, 138, 139, 140, 144} 62: excls[138][num=16]={119, 134, 135, 136, 137, 138, 139, 140, 141, 62: 142, 143, 144, 145, 146, 147, 148} 62: excls[139][num=12]={134, 136, 137, 138, 139, 140, 141, 142, 143, 62: 144, 145, 146} 62: excls[140][num=12]={134, 136, 137, 138, 139, 140, 141, 142, 143, 62: 144, 145, 146} 62: excls[141][num=8]={136, 138, 139, 140, 141, 142, 143, 144} 62: excls[142][num=8]={136, 138, 139, 140, 141, 142, 143, 144} 62: excls[143][num=8]={136, 138, 139, 140, 141, 142, 143, 144} 62: excls[144][num=17]={134, 136, 137, 138, 139, 140, 141, 142, 143, 62: 144, 145, 146, 147, 148, 149, 150, 154} 62: excls[145][num=9]={136, 138, 139, 140, 144, 145, 146, 147, 148} 62: excls[146][num=16]={136, 138, 139, 140, 144, 145, 146, 147, 148, 62: 149, 150, 151, 152, 153, 154, 155} 62: excls[147][num=9]={138, 144, 145, 146, 147, 148, 149, 150, 154} 62: excls[148][num=13]={138, 144, 145, 146, 147, 148, 149, 150, 151, 62: 152, 153, 154, 155} 62: excls[149][num=11]={144, 146, 147, 148, 149, 150, 151, 152, 153, 62: 154, 155} 62: excls[150][num=11]={144, 146, 147, 148, 149, 150, 151, 152, 153, 62: 154, 155} 62: excls[151][num=8]={146, 148, 149, 150, 151, 152, 153, 154} 62: excls[152][num=8]={146, 148, 149, 150, 151, 152, 153, 154} 62: excls[153][num=8]={146, 148, 149, 150, 151, 152, 153, 154} 62: excls[154][num=11]={144, 146, 147, 148, 149, 150, 151, 152, 153, 62: 154, 155} 62: excls[155][num=6]={146, 148, 149, 150, 154, 155} 62: Bond: 62: nr: 468 62: iatoms: 62: 0 type=100 (BONDS) 0 1 62: 1 type=100 (BONDS) 0 2 62: 2 type=100 (BONDS) 0 3 62: 3 type=101 (BONDS) 0 4 62: 4 type=102 (BONDS) 4 5 62: 5 type=103 (BONDS) 4 6 62: 6 type=104 (BONDS) 4 22 62: 7 type=102 (BONDS) 6 7 62: 8 type=102 (BONDS) 6 8 62: 9 type=103 (BONDS) 6 9 62: 10 type=102 (BONDS) 9 10 62: 11 type=102 (BONDS) 9 11 62: 12 type=103 (BONDS) 9 12 62: 13 type=102 (BONDS) 12 13 62: 14 type=102 (BONDS) 12 14 62: 15 type=103 (BONDS) 12 15 62: 16 type=102 (BONDS) 15 16 62: 17 type=102 (BONDS) 15 17 62: 18 type=101 (BONDS) 15 18 62: 19 type=100 (BONDS) 18 19 62: 20 type=100 (BONDS) 18 20 62: 21 type=100 (BONDS) 18 21 62: 22 type=105 (BONDS) 22 23 62: 23 type=106 (BONDS) 22 24 62: 24 type=100 (BONDS) 24 25 62: 25 type=107 (BONDS) 24 26 62: 26 type=102 (BONDS) 26 27 62: 27 type=103 (BONDS) 26 28 62: 28 type=104 (BONDS) 26 38 62: 29 type=102 (BONDS) 28 29 62: 30 type=103 (BONDS) 28 30 62: 31 type=103 (BONDS) 28 34 62: 32 type=102 (BONDS) 30 31 62: 33 type=102 (BONDS) 30 32 62: 34 type=102 (BONDS) 30 33 62: 35 type=102 (BONDS) 34 35 62: 36 type=102 (BONDS) 34 36 62: 37 type=102 (BONDS) 34 37 62: 38 type=105 (BONDS) 38 39 62: 39 type=106 (BONDS) 38 40 62: 40 type=100 (BONDS) 40 41 62: 41 type=107 (BONDS) 40 42 62: 42 type=102 (BONDS) 42 43 62: 43 type=103 (BONDS) 42 44 62: 44 type=104 (BONDS) 42 58 62: 45 type=102 (BONDS) 44 45 62: 46 type=102 (BONDS) 44 46 62: 47 type=108 (BONDS) 44 47 62: 48 type=109 (BONDS) 47 48 62: 49 type=109 (BONDS) 47 50 62: 50 type=110 (BONDS) 48 49 62: 51 type=109 (BONDS) 48 52 62: 52 type=110 (BONDS) 50 51 62: 53 type=109 (BONDS) 50 54 62: 54 type=110 (BONDS) 52 53 62: 55 type=109 (BONDS) 52 56 62: 56 type=110 (BONDS) 54 55 62: 57 type=109 (BONDS) 54 56 62: 58 type=110 (BONDS) 56 57 62: 59 type=105 (BONDS) 58 59 62: 60 type=106 (BONDS) 58 60 62: 61 type=100 (BONDS) 60 61 62: 62 type=107 (BONDS) 60 62 62: 63 type=102 (BONDS) 62 63 62: 64 type=102 (BONDS) 62 64 62: 65 type=104 (BONDS) 62 65 62: 66 type=105 (BONDS) 65 66 62: 67 type=106 (BONDS) 65 67 62: 68 type=100 (BONDS) 67 68 62: 69 type=107 (BONDS) 67 69 62: 70 type=102 (BONDS) 69 70 62: 71 type=103 (BONDS) 69 71 62: 72 type=104 (BONDS) 69 89 62: 73 type=102 (BONDS) 71 72 62: 74 type=102 (BONDS) 71 73 62: 75 type=103 (BONDS) 71 74 62: 76 type=102 (BONDS) 74 75 62: 77 type=102 (BONDS) 74 76 62: 78 type=103 (BONDS) 74 77 62: 79 type=102 (BONDS) 77 78 62: 80 type=102 (BONDS) 77 79 62: 81 type=111 (BONDS) 77 80 62: 82 type=100 (BONDS) 80 81 62: 83 type=112 (BONDS) 80 82 62: 84 type=112 (BONDS) 82 83 62: 85 type=112 (BONDS) 82 86 62: 86 type=100 (BONDS) 83 84 62: 87 type=100 (BONDS) 83 85 62: 88 type=100 (BONDS) 86 87 62: 89 type=100 (BONDS) 86 88 62: 90 type=105 (BONDS) 89 90 62: 91 type=106 (BONDS) 89 91 62: 92 type=100 (BONDS) 91 92 62: 93 type=107 (BONDS) 91 93 62: 94 type=102 (BONDS) 93 94 62: 95 type=103 (BONDS) 93 95 62: 96 type=104 (BONDS) 93 100 62: 97 type=102 (BONDS) 95 96 62: 98 type=102 (BONDS) 95 97 62: 99 type=113 (BONDS) 95 98 62: 100 type=114 (BONDS) 98 99 62: 101 type=105 (BONDS) 100 101 62: 102 type=106 (BONDS) 100 102 62: 103 type=100 (BONDS) 102 103 62: 104 type=107 (BONDS) 102 104 62: 105 type=102 (BONDS) 104 105 62: 106 type=103 (BONDS) 104 106 62: 107 type=104 (BONDS) 104 115 62: 108 type=102 (BONDS) 106 107 62: 109 type=102 (BONDS) 106 108 62: 110 type=103 (BONDS) 106 109 62: 111 type=102 (BONDS) 109 110 62: 112 type=102 (BONDS) 109 111 62: 113 type=104 (BONDS) 109 112 62: 114 type=115 (BONDS) 112 113 62: 115 type=115 (BONDS) 112 114 62: 116 type=105 (BONDS) 115 116 62: 117 type=106 (BONDS) 115 117 62: 118 type=100 (BONDS) 117 118 62: 119 type=107 (BONDS) 117 119 62: 120 type=102 (BONDS) 119 120 62: 121 type=103 (BONDS) 119 121 62: 122 type=104 (BONDS) 119 134 62: 123 type=102 (BONDS) 121 122 62: 124 type=102 (BONDS) 121 123 62: 125 type=103 (BONDS) 121 124 62: 126 type=102 (BONDS) 124 125 62: 127 type=103 (BONDS) 124 126 62: 128 type=103 (BONDS) 124 130 62: 129 type=102 (BONDS) 126 127 62: 130 type=102 (BONDS) 126 128 62: 131 type=102 (BONDS) 126 129 62: 132 type=102 (BONDS) 130 131 62: 133 type=102 (BONDS) 130 132 62: 134 type=102 (BONDS) 130 133 62: 135 type=105 (BONDS) 134 135 62: 136 type=106 (BONDS) 134 136 62: 137 type=100 (BONDS) 136 137 62: 138 type=107 (BONDS) 136 138 62: 139 type=102 (BONDS) 138 139 62: 140 type=103 (BONDS) 138 140 62: 141 type=104 (BONDS) 138 144 62: 142 type=102 (BONDS) 140 141 62: 143 type=102 (BONDS) 140 142 62: 144 type=102 (BONDS) 140 143 62: 145 type=105 (BONDS) 144 145 62: 146 type=106 (BONDS) 144 146 62: 147 type=100 (BONDS) 146 147 62: 148 type=107 (BONDS) 146 148 62: 149 type=102 (BONDS) 148 149 62: 150 type=103 (BONDS) 148 150 62: 151 type=104 (BONDS) 148 154 62: 152 type=102 (BONDS) 150 151 62: 153 type=102 (BONDS) 150 152 62: 154 type=102 (BONDS) 150 153 62: 155 type=105 (BONDS) 154 155 62: G96Bond: 62: nr: 0 62: Morse: 62: nr: 0 62: Cubic Bonds: 62: nr: 0 62: Connect Bonds: 62: nr: 0 62: Harmonic Pot.: 62: nr: 0 62: FENE Bonds: 62: nr: 0 62: Tab. Bonds: 62: nr: 0 62: Tab. Bonds NC: 62: nr: 0 62: Restraint Pot.: 62: nr: 0 62: Angle: 62: nr: 1124 62: iatoms: 62: 0 type=116 (ANGLES) 1 0 2 62: 1 type=116 (ANGLES) 1 0 3 62: 2 type=116 (ANGLES) 1 0 4 62: 3 type=116 (ANGLES) 2 0 3 62: 4 type=116 (ANGLES) 2 0 4 62: 5 type=116 (ANGLES) 3 0 4 62: 6 type=116 (ANGLES) 0 4 5 62: 7 type=117 (ANGLES) 0 4 6 62: 8 type=117 (ANGLES) 0 4 22 62: 9 type=118 (ANGLES) 5 4 6 62: 10 type=116 (ANGLES) 5 4 22 62: 11 type=119 (ANGLES) 6 4 22 62: 12 type=118 (ANGLES) 4 6 7 62: 13 type=118 (ANGLES) 4 6 8 62: 14 type=120 (ANGLES) 4 6 9 62: 15 type=121 (ANGLES) 7 6 8 62: 16 type=118 (ANGLES) 7 6 9 62: 17 type=118 (ANGLES) 8 6 9 62: 18 type=118 (ANGLES) 6 9 10 62: 19 type=118 (ANGLES) 6 9 11 62: 20 type=120 (ANGLES) 6 9 12 62: 21 type=121 (ANGLES) 10 9 11 62: 22 type=118 (ANGLES) 10 9 12 62: 23 type=118 (ANGLES) 11 9 12 62: 24 type=118 (ANGLES) 9 12 13 62: 25 type=118 (ANGLES) 9 12 14 62: 26 type=120 (ANGLES) 9 12 15 62: 27 type=121 (ANGLES) 13 12 14 62: 28 type=118 (ANGLES) 13 12 15 62: 29 type=118 (ANGLES) 14 12 15 62: 30 type=118 (ANGLES) 12 15 16 62: 31 type=118 (ANGLES) 12 15 17 62: 32 type=117 (ANGLES) 12 15 18 62: 33 type=121 (ANGLES) 16 15 17 62: 34 type=116 (ANGLES) 16 15 18 62: 35 type=116 (ANGLES) 17 15 18 62: 36 type=116 (ANGLES) 15 18 19 62: 37 type=116 (ANGLES) 15 18 20 62: 38 type=116 (ANGLES) 15 18 21 62: 39 type=116 (ANGLES) 19 18 20 62: 40 type=116 (ANGLES) 19 18 21 62: 41 type=116 (ANGLES) 20 18 21 62: 42 type=122 (ANGLES) 4 22 23 62: 43 type=123 (ANGLES) 4 22 24 62: 44 type=124 (ANGLES) 23 22 24 62: 45 type=125 (ANGLES) 22 24 25 62: 46 type=126 (ANGLES) 22 24 26 62: 47 type=127 (ANGLES) 25 24 26 62: 48 type=116 (ANGLES) 24 26 27 62: 49 type=128 (ANGLES) 24 26 28 62: 50 type=129 (ANGLES) 24 26 38 62: 51 type=118 (ANGLES) 27 26 28 62: 52 type=116 (ANGLES) 27 26 38 62: 53 type=119 (ANGLES) 28 26 38 62: 54 type=118 (ANGLES) 26 28 29 62: 55 type=120 (ANGLES) 26 28 30 62: 56 type=120 (ANGLES) 26 28 34 62: 57 type=118 (ANGLES) 29 28 30 62: 58 type=118 (ANGLES) 29 28 34 62: 59 type=120 (ANGLES) 30 28 34 62: 60 type=118 (ANGLES) 28 30 31 62: 61 type=118 (ANGLES) 28 30 32 62: 62 type=118 (ANGLES) 28 30 33 62: 63 type=121 (ANGLES) 31 30 32 62: 64 type=121 (ANGLES) 31 30 33 62: 65 type=121 (ANGLES) 32 30 33 62: 66 type=118 (ANGLES) 28 34 35 62: 67 type=118 (ANGLES) 28 34 36 62: 68 type=118 (ANGLES) 28 34 37 62: 69 type=121 (ANGLES) 35 34 36 62: 70 type=121 (ANGLES) 35 34 37 62: 71 type=121 (ANGLES) 36 34 37 62: 72 type=122 (ANGLES) 26 38 39 62: 73 type=123 (ANGLES) 26 38 40 62: 74 type=124 (ANGLES) 39 38 40 62: 75 type=125 (ANGLES) 38 40 41 62: 76 type=126 (ANGLES) 38 40 42 62: 77 type=127 (ANGLES) 41 40 42 62: 78 type=116 (ANGLES) 40 42 43 62: 79 type=128 (ANGLES) 40 42 44 62: 80 type=129 (ANGLES) 40 42 58 62: 81 type=118 (ANGLES) 43 42 44 62: 82 type=116 (ANGLES) 43 42 58 62: 83 type=119 (ANGLES) 44 42 58 62: 84 type=118 (ANGLES) 42 44 45 62: 85 type=118 (ANGLES) 42 44 46 62: 86 type=130 (ANGLES) 42 44 47 62: 87 type=121 (ANGLES) 45 44 46 62: 88 type=116 (ANGLES) 45 44 47 62: 89 type=116 (ANGLES) 46 44 47 62: 90 type=131 (ANGLES) 44 47 48 62: 91 type=131 (ANGLES) 44 47 50 62: 92 type=132 (ANGLES) 48 47 50 62: 93 type=133 (ANGLES) 47 48 49 62: 94 type=132 (ANGLES) 47 48 52 62: 95 type=133 (ANGLES) 49 48 52 62: 96 type=133 (ANGLES) 47 50 51 62: 97 type=132 (ANGLES) 47 50 54 62: 98 type=133 (ANGLES) 51 50 54 62: 99 type=133 (ANGLES) 48 52 53 62: 100 type=132 (ANGLES) 48 52 56 62: 101 type=133 (ANGLES) 53 52 56 62: 102 type=133 (ANGLES) 50 54 55 62: 103 type=132 (ANGLES) 50 54 56 62: 104 type=133 (ANGLES) 55 54 56 62: 105 type=132 (ANGLES) 52 56 54 62: 106 type=133 (ANGLES) 52 56 57 62: 107 type=133 (ANGLES) 54 56 57 62: 108 type=122 (ANGLES) 42 58 59 62: 109 type=123 (ANGLES) 42 58 60 62: 110 type=124 (ANGLES) 59 58 60 62: 111 type=125 (ANGLES) 58 60 61 62: 112 type=126 (ANGLES) 58 60 62 62: 113 type=127 (ANGLES) 61 60 62 62: 114 type=116 (ANGLES) 60 62 63 62: 115 type=116 (ANGLES) 60 62 64 62: 116 type=129 (ANGLES) 60 62 65 62: 117 type=121 (ANGLES) 63 62 64 62: 118 type=116 (ANGLES) 63 62 65 62: 119 type=116 (ANGLES) 64 62 65 62: 120 type=122 (ANGLES) 62 65 66 62: 121 type=123 (ANGLES) 62 65 67 62: 122 type=124 (ANGLES) 66 65 67 62: 123 type=125 (ANGLES) 65 67 68 62: 124 type=126 (ANGLES) 65 67 69 62: 125 type=127 (ANGLES) 68 67 69 62: 126 type=116 (ANGLES) 67 69 70 62: 127 type=128 (ANGLES) 67 69 71 62: 128 type=129 (ANGLES) 67 69 89 62: 129 type=118 (ANGLES) 70 69 71 62: 130 type=116 (ANGLES) 70 69 89 62: 131 type=119 (ANGLES) 71 69 89 62: 132 type=118 (ANGLES) 69 71 72 62: 133 type=118 (ANGLES) 69 71 73 62: 134 type=120 (ANGLES) 69 71 74 62: 135 type=121 (ANGLES) 72 71 73 62: 136 type=118 (ANGLES) 72 71 74 62: 137 type=118 (ANGLES) 73 71 74 62: 138 type=118 (ANGLES) 71 74 75 62: 139 type=118 (ANGLES) 71 74 76 62: 140 type=120 (ANGLES) 71 74 77 62: 141 type=121 (ANGLES) 75 74 76 62: 142 type=118 (ANGLES) 75 74 77 62: 143 type=118 (ANGLES) 76 74 77 62: 144 type=118 (ANGLES) 74 77 78 62: 145 type=118 (ANGLES) 74 77 79 62: 146 type=117 (ANGLES) 74 77 80 62: 147 type=121 (ANGLES) 78 77 79 62: 148 type=116 (ANGLES) 78 77 80 62: 149 type=116 (ANGLES) 79 77 80 62: 150 type=134 (ANGLES) 77 80 81 62: 151 type=135 (ANGLES) 77 80 82 62: 152 type=133 (ANGLES) 81 80 82 62: 153 type=131 (ANGLES) 80 82 83 62: 154 type=131 (ANGLES) 80 82 86 62: 155 type=131 (ANGLES) 83 82 86 62: 156 type=133 (ANGLES) 82 83 84 62: 157 type=133 (ANGLES) 82 83 85 62: 158 type=133 (ANGLES) 84 83 85 62: 159 type=133 (ANGLES) 82 86 87 62: 160 type=133 (ANGLES) 82 86 88 62: 161 type=133 (ANGLES) 87 86 88 62: 162 type=122 (ANGLES) 69 89 90 62: 163 type=123 (ANGLES) 69 89 91 62: 164 type=124 (ANGLES) 90 89 91 62: 165 type=125 (ANGLES) 89 91 92 62: 166 type=126 (ANGLES) 89 91 93 62: 167 type=127 (ANGLES) 92 91 93 62: 168 type=116 (ANGLES) 91 93 94 62: 169 type=128 (ANGLES) 91 93 95 62: 170 type=129 (ANGLES) 91 93 100 62: 171 type=118 (ANGLES) 94 93 95 62: 172 type=116 (ANGLES) 94 93 100 62: 173 type=119 (ANGLES) 95 93 100 62: 174 type=118 (ANGLES) 93 95 96 62: 175 type=118 (ANGLES) 93 95 97 62: 176 type=136 (ANGLES) 93 95 98 62: 177 type=121 (ANGLES) 96 95 97 62: 178 type=116 (ANGLES) 96 95 98 62: 179 type=116 (ANGLES) 97 95 98 62: 180 type=137 (ANGLES) 95 98 99 62: 181 type=122 (ANGLES) 93 100 101 62: 182 type=123 (ANGLES) 93 100 102 62: 183 type=124 (ANGLES) 101 100 102 62: 184 type=125 (ANGLES) 100 102 103 62: 185 type=126 (ANGLES) 100 102 104 62: 186 type=127 (ANGLES) 103 102 104 62: 187 type=116 (ANGLES) 102 104 105 62: 188 type=128 (ANGLES) 102 104 106 62: 189 type=129 (ANGLES) 102 104 115 62: 190 type=118 (ANGLES) 105 104 106 62: 191 type=116 (ANGLES) 105 104 115 62: 192 type=119 (ANGLES) 106 104 115 62: 193 type=118 (ANGLES) 104 106 107 62: 194 type=118 (ANGLES) 104 106 108 62: 195 type=120 (ANGLES) 104 106 109 62: 196 type=121 (ANGLES) 107 106 108 62: 197 type=118 (ANGLES) 107 106 109 62: 198 type=118 (ANGLES) 108 106 109 62: 199 type=118 (ANGLES) 106 109 110 62: 200 type=118 (ANGLES) 106 109 111 62: 201 type=119 (ANGLES) 106 109 112 62: 202 type=121 (ANGLES) 110 109 111 62: 203 type=116 (ANGLES) 110 109 112 62: 204 type=116 (ANGLES) 111 109 112 62: 205 type=138 (ANGLES) 109 112 113 62: 206 type=138 (ANGLES) 109 112 114 62: 207 type=139 (ANGLES) 113 112 114 62: 208 type=122 (ANGLES) 104 115 116 62: 209 type=123 (ANGLES) 104 115 117 62: 210 type=124 (ANGLES) 116 115 117 62: 211 type=125 (ANGLES) 115 117 118 62: 212 type=126 (ANGLES) 115 117 119 62: 213 type=127 (ANGLES) 118 117 119 62: 214 type=116 (ANGLES) 117 119 120 62: 215 type=128 (ANGLES) 117 119 121 62: 216 type=129 (ANGLES) 117 119 134 62: 217 type=118 (ANGLES) 120 119 121 62: 218 type=116 (ANGLES) 120 119 134 62: 219 type=119 (ANGLES) 121 119 134 62: 220 type=118 (ANGLES) 119 121 122 62: 221 type=118 (ANGLES) 119 121 123 62: 222 type=120 (ANGLES) 119 121 124 62: 223 type=121 (ANGLES) 122 121 123 62: 224 type=118 (ANGLES) 122 121 124 62: 225 type=118 (ANGLES) 123 121 124 62: 226 type=118 (ANGLES) 121 124 125 62: 227 type=120 (ANGLES) 121 124 126 62: 228 type=120 (ANGLES) 121 124 130 62: 229 type=118 (ANGLES) 125 124 126 62: 230 type=118 (ANGLES) 125 124 130 62: 231 type=120 (ANGLES) 126 124 130 62: 232 type=118 (ANGLES) 124 126 127 62: 233 type=118 (ANGLES) 124 126 128 62: 234 type=118 (ANGLES) 124 126 129 62: 235 type=121 (ANGLES) 127 126 128 62: 236 type=121 (ANGLES) 127 126 129 62: 237 type=121 (ANGLES) 128 126 129 62: 238 type=118 (ANGLES) 124 130 131 62: 239 type=118 (ANGLES) 124 130 132 62: 240 type=118 (ANGLES) 124 130 133 62: 241 type=121 (ANGLES) 131 130 132 62: 242 type=121 (ANGLES) 131 130 133 62: 243 type=121 (ANGLES) 132 130 133 62: 244 type=122 (ANGLES) 119 134 135 62: 245 type=123 (ANGLES) 119 134 136 62: 246 type=124 (ANGLES) 135 134 136 62: 247 type=125 (ANGLES) 134 136 137 62: 248 type=126 (ANGLES) 134 136 138 62: 249 type=127 (ANGLES) 137 136 138 62: 250 type=116 (ANGLES) 136 138 139 62: 251 type=128 (ANGLES) 136 138 140 62: 252 type=129 (ANGLES) 136 138 144 62: 253 type=118 (ANGLES) 139 138 140 62: 254 type=116 (ANGLES) 139 138 144 62: 255 type=119 (ANGLES) 140 138 144 62: 256 type=118 (ANGLES) 138 140 141 62: 257 type=118 (ANGLES) 138 140 142 62: 258 type=118 (ANGLES) 138 140 143 62: 259 type=121 (ANGLES) 141 140 142 62: 260 type=121 (ANGLES) 141 140 143 62: 261 type=121 (ANGLES) 142 140 143 62: 262 type=122 (ANGLES) 138 144 145 62: 263 type=123 (ANGLES) 138 144 146 62: 264 type=124 (ANGLES) 145 144 146 62: 265 type=125 (ANGLES) 144 146 147 62: 266 type=126 (ANGLES) 144 146 148 62: 267 type=127 (ANGLES) 147 146 148 62: 268 type=116 (ANGLES) 146 148 149 62: 269 type=128 (ANGLES) 146 148 150 62: 270 type=129 (ANGLES) 146 148 154 62: 271 type=118 (ANGLES) 149 148 150 62: 272 type=116 (ANGLES) 149 148 154 62: 273 type=119 (ANGLES) 150 148 154 62: 274 type=118 (ANGLES) 148 150 151 62: 275 type=118 (ANGLES) 148 150 152 62: 276 type=118 (ANGLES) 148 150 153 62: 277 type=121 (ANGLES) 151 150 152 62: 278 type=121 (ANGLES) 151 150 153 62: 279 type=121 (ANGLES) 152 150 153 62: 280 type=122 (ANGLES) 148 154 155 62: G96Angle: 62: nr: 0 62: Restr. Angles: 62: nr: 0 62: Lin. Angle: 62: nr: 0 62: Bond-Cross: 62: nr: 0 62: BA-Cross: 62: nr: 0 62: U-B: 62: nr: 0 62: Quartic Angles: 62: nr: 0 62: Tab. Angles: 62: nr: 0 62: Proper Dih.: 62: nr: 145 62: iatoms: 62: 0 type=140 (PDIHS) 4 24 22 23 62: 1 type=141 (PDIHS) 22 26 24 25 62: 2 type=140 (PDIHS) 26 40 38 39 62: 3 type=141 (PDIHS) 38 42 40 41 62: 4 type=140 (PDIHS) 42 60 58 59 62: 5 type=142 (PDIHS) 44 47 50 48 62: 6 type=142 (PDIHS) 47 52 48 49 62: 7 type=142 (PDIHS) 47 54 50 51 62: 8 type=142 (PDIHS) 48 56 52 53 62: 9 type=142 (PDIHS) 50 56 54 55 62: 10 type=142 (PDIHS) 52 54 56 57 62: 11 type=141 (PDIHS) 58 62 60 61 62: 12 type=140 (PDIHS) 62 67 65 66 62: 13 type=141 (PDIHS) 65 69 67 68 62: 14 type=140 (PDIHS) 69 91 89 90 62: 15 type=141 (PDIHS) 77 82 80 81 62: 16 type=140 (PDIHS) 80 83 82 86 62: 17 type=141 (PDIHS) 82 84 83 85 62: 18 type=141 (PDIHS) 82 87 86 88 62: 19 type=141 (PDIHS) 89 93 91 92 62: 20 type=140 (PDIHS) 93 102 100 101 62: 21 type=141 (PDIHS) 100 104 102 103 62: 22 type=140 (PDIHS) 104 117 115 116 62: 23 type=140 (PDIHS) 109 113 112 114 62: 24 type=141 (PDIHS) 115 119 117 118 62: 25 type=140 (PDIHS) 119 136 134 135 62: 26 type=141 (PDIHS) 134 138 136 137 62: 27 type=140 (PDIHS) 138 146 144 145 62: 28 type=141 (PDIHS) 144 148 146 147 62: Ryckaert-Bell.: 62: nr: 1565 62: iatoms: 62: 0 type=143 (RBDIHS) 1 0 4 5 62: 1 type=144 (RBDIHS) 1 0 4 6 62: 2 type=144 (RBDIHS) 1 0 4 22 62: 3 type=143 (RBDIHS) 2 0 4 5 62: 4 type=144 (RBDIHS) 2 0 4 6 62: 5 type=144 (RBDIHS) 2 0 4 22 62: 6 type=143 (RBDIHS) 3 0 4 5 62: 7 type=144 (RBDIHS) 3 0 4 6 62: 8 type=144 (RBDIHS) 3 0 4 22 62: 9 type=145 (RBDIHS) 0 4 6 9 62: 10 type=146 (RBDIHS) 22 4 6 9 62: 11 type=147 (RBDIHS) 0 4 6 7 62: 12 type=147 (RBDIHS) 0 4 6 8 62: 13 type=148 (RBDIHS) 5 4 6 7 62: 14 type=148 (RBDIHS) 5 4 6 8 62: 15 type=148 (RBDIHS) 5 4 6 9 62: 16 type=149 (RBDIHS) 22 4 6 7 62: 17 type=149 (RBDIHS) 22 4 6 8 62: 18 type=150 (RBDIHS) 0 4 22 24 62: 19 type=151 (RBDIHS) 6 4 22 24 62: 20 type=148 (RBDIHS) 4 6 9 10 62: 21 type=148 (RBDIHS) 4 6 9 11 62: 22 type=152 (RBDIHS) 4 6 9 12 62: 23 type=148 (RBDIHS) 7 6 9 10 62: 24 type=148 (RBDIHS) 7 6 9 11 62: 25 type=148 (RBDIHS) 7 6 9 12 62: 26 type=148 (RBDIHS) 8 6 9 10 62: 27 type=148 (RBDIHS) 8 6 9 11 62: 28 type=148 (RBDIHS) 8 6 9 12 62: 29 type=148 (RBDIHS) 6 9 12 13 62: 30 type=148 (RBDIHS) 6 9 12 14 62: 31 type=152 (RBDIHS) 6 9 12 15 62: 32 type=148 (RBDIHS) 10 9 12 13 62: 33 type=148 (RBDIHS) 10 9 12 14 62: 34 type=148 (RBDIHS) 10 9 12 15 62: 35 type=148 (RBDIHS) 11 9 12 13 62: 36 type=148 (RBDIHS) 11 9 12 14 62: 37 type=148 (RBDIHS) 11 9 12 15 62: 38 type=148 (RBDIHS) 9 12 15 16 62: 39 type=148 (RBDIHS) 9 12 15 17 62: 40 type=153 (RBDIHS) 9 12 15 18 62: 41 type=148 (RBDIHS) 13 12 15 16 62: 42 type=148 (RBDIHS) 13 12 15 17 62: 43 type=154 (RBDIHS) 13 12 15 18 62: 44 type=148 (RBDIHS) 14 12 15 16 62: 45 type=148 (RBDIHS) 14 12 15 17 62: 46 type=154 (RBDIHS) 14 12 15 18 62: 47 type=144 (RBDIHS) 12 15 18 19 62: 48 type=144 (RBDIHS) 12 15 18 20 62: 49 type=144 (RBDIHS) 12 15 18 21 62: 50 type=143 (RBDIHS) 16 15 18 19 62: 51 type=143 (RBDIHS) 16 15 18 20 62: 52 type=143 (RBDIHS) 16 15 18 21 62: 53 type=143 (RBDIHS) 17 15 18 19 62: 54 type=143 (RBDIHS) 17 15 18 20 62: 55 type=143 (RBDIHS) 17 15 18 21 62: 56 type=155 (RBDIHS) 4 22 24 25 62: 57 type=156 (RBDIHS) 4 22 24 26 62: 58 type=155 (RBDIHS) 23 22 24 25 62: 59 type=157 (RBDIHS) 23 22 24 26 62: 60 type=158 (RBDIHS) 22 24 26 28 62: 61 type=159 (RBDIHS) 22 24 26 38 62: 62 type=160 (RBDIHS) 24 26 28 30 62: 63 type=160 (RBDIHS) 24 26 28 34 62: 64 type=161 (RBDIHS) 38 26 28 30 62: 65 type=161 (RBDIHS) 38 26 28 34 62: 66 type=147 (RBDIHS) 24 26 28 29 62: 67 type=148 (RBDIHS) 27 26 28 29 62: 68 type=148 (RBDIHS) 27 26 28 30 62: 69 type=148 (RBDIHS) 27 26 28 34 62: 70 type=149 (RBDIHS) 38 26 28 29 62: 71 type=150 (RBDIHS) 24 26 38 40 62: 72 type=151 (RBDIHS) 28 26 38 40 62: 73 type=148 (RBDIHS) 26 28 30 31 62: 74 type=148 (RBDIHS) 26 28 30 32 62: 75 type=148 (RBDIHS) 26 28 30 33 62: 76 type=148 (RBDIHS) 29 28 30 31 62: 77 type=148 (RBDIHS) 29 28 30 32 62: 78 type=148 (RBDIHS) 29 28 30 33 62: 79 type=148 (RBDIHS) 34 28 30 31 62: 80 type=148 (RBDIHS) 34 28 30 32 62: 81 type=148 (RBDIHS) 34 28 30 33 62: 82 type=148 (RBDIHS) 26 28 34 35 62: 83 type=148 (RBDIHS) 26 28 34 36 62: 84 type=148 (RBDIHS) 26 28 34 37 62: 85 type=148 (RBDIHS) 29 28 34 35 62: 86 type=148 (RBDIHS) 29 28 34 36 62: 87 type=148 (RBDIHS) 29 28 34 37 62: 88 type=148 (RBDIHS) 30 28 34 35 62: 89 type=148 (RBDIHS) 30 28 34 36 62: 90 type=148 (RBDIHS) 30 28 34 37 62: 91 type=155 (RBDIHS) 26 38 40 41 62: 92 type=156 (RBDIHS) 26 38 40 42 62: 93 type=155 (RBDIHS) 39 38 40 41 62: 94 type=157 (RBDIHS) 39 38 40 42 62: 95 type=158 (RBDIHS) 38 40 42 44 62: 96 type=159 (RBDIHS) 38 40 42 58 62: 97 type=147 (RBDIHS) 40 42 44 45 62: 98 type=147 (RBDIHS) 40 42 44 46 62: 99 type=162 (RBDIHS) 40 42 44 47 62: 100 type=148 (RBDIHS) 43 42 44 45 62: 101 type=148 (RBDIHS) 43 42 44 46 62: 102 type=163 (RBDIHS) 43 42 44 47 62: 103 type=149 (RBDIHS) 58 42 44 45 62: 104 type=149 (RBDIHS) 58 42 44 46 62: 105 type=164 (RBDIHS) 58 42 44 47 62: 106 type=150 (RBDIHS) 40 42 58 60 62: 107 type=151 (RBDIHS) 44 42 58 60 62: 108 type=165 (RBDIHS) 44 47 48 49 62: 109 type=165 (RBDIHS) 44 47 48 52 62: 110 type=165 (RBDIHS) 50 47 48 49 62: 111 type=165 (RBDIHS) 50 47 48 52 62: 112 type=165 (RBDIHS) 44 47 50 51 62: 113 type=165 (RBDIHS) 44 47 50 54 62: 114 type=165 (RBDIHS) 48 47 50 51 62: 115 type=165 (RBDIHS) 48 47 50 54 62: 116 type=165 (RBDIHS) 47 48 52 53 62: 117 type=165 (RBDIHS) 47 48 52 56 62: 118 type=165 (RBDIHS) 49 48 52 53 62: 119 type=165 (RBDIHS) 49 48 52 56 62: 120 type=165 (RBDIHS) 47 50 54 55 62: 121 type=165 (RBDIHS) 47 50 54 56 62: 122 type=165 (RBDIHS) 51 50 54 55 62: 123 type=165 (RBDIHS) 51 50 54 56 62: 124 type=165 (RBDIHS) 48 52 56 54 62: 125 type=165 (RBDIHS) 48 52 56 57 62: 126 type=165 (RBDIHS) 53 52 56 54 62: 127 type=165 (RBDIHS) 53 52 56 57 62: 128 type=165 (RBDIHS) 50 54 56 52 62: 129 type=165 (RBDIHS) 50 54 56 57 62: 130 type=165 (RBDIHS) 55 54 56 52 62: 131 type=165 (RBDIHS) 55 54 56 57 62: 132 type=155 (RBDIHS) 42 58 60 61 62: 133 type=156 (RBDIHS) 42 58 60 62 62: 134 type=155 (RBDIHS) 59 58 60 61 62: 135 type=157 (RBDIHS) 59 58 60 62 62: 136 type=159 (RBDIHS) 58 60 62 65 62: 137 type=150 (RBDIHS) 60 62 65 67 62: 138 type=155 (RBDIHS) 62 65 67 68 62: 139 type=156 (RBDIHS) 62 65 67 69 62: 140 type=155 (RBDIHS) 66 65 67 68 62: 141 type=157 (RBDIHS) 66 65 67 69 62: 142 type=158 (RBDIHS) 65 67 69 71 62: 143 type=159 (RBDIHS) 65 67 69 89 62: 144 type=166 (RBDIHS) 67 69 71 74 62: 145 type=167 (RBDIHS) 89 69 71 74 62: 146 type=147 (RBDIHS) 67 69 71 72 62: 147 type=147 (RBDIHS) 67 69 71 73 62: 148 type=148 (RBDIHS) 70 69 71 72 62: 149 type=148 (RBDIHS) 70 69 71 73 62: 150 type=148 (RBDIHS) 70 69 71 74 62: 151 type=149 (RBDIHS) 89 69 71 72 62: 152 type=149 (RBDIHS) 89 69 71 73 62: 153 type=150 (RBDIHS) 67 69 89 91 62: 154 type=151 (RBDIHS) 71 69 89 91 62: 155 type=148 (RBDIHS) 69 71 74 75 62: 156 type=148 (RBDIHS) 69 71 74 76 62: 157 type=152 (RBDIHS) 69 71 74 77 62: 158 type=148 (RBDIHS) 72 71 74 75 62: 159 type=148 (RBDIHS) 72 71 74 76 62: 160 type=148 (RBDIHS) 72 71 74 77 62: 161 type=148 (RBDIHS) 73 71 74 75 62: 162 type=148 (RBDIHS) 73 71 74 76 62: 163 type=148 (RBDIHS) 73 71 74 77 62: 164 type=148 (RBDIHS) 71 74 77 78 62: 165 type=148 (RBDIHS) 71 74 77 79 62: 166 type=153 (RBDIHS) 71 74 77 80 62: 167 type=148 (RBDIHS) 75 74 77 78 62: 168 type=148 (RBDIHS) 75 74 77 79 62: 169 type=168 (RBDIHS) 75 74 77 80 62: 170 type=148 (RBDIHS) 76 74 77 78 62: 171 type=148 (RBDIHS) 76 74 77 79 62: 172 type=168 (RBDIHS) 76 74 77 80 62: 173 type=169 (RBDIHS) 74 77 80 81 62: 174 type=170 (RBDIHS) 74 77 80 82 62: 175 type=171 (RBDIHS) 78 77 80 82 62: 176 type=171 (RBDIHS) 79 77 80 82 62: 177 type=172 (RBDIHS) 77 80 82 83 62: 178 type=172 (RBDIHS) 77 80 82 86 62: 179 type=173 (RBDIHS) 81 80 82 83 62: 180 type=173 (RBDIHS) 81 80 82 86 62: 181 type=173 (RBDIHS) 80 82 83 84 62: 182 type=173 (RBDIHS) 80 82 83 85 62: 183 type=173 (RBDIHS) 86 82 83 84 62: 184 type=173 (RBDIHS) 86 82 83 85 62: 185 type=173 (RBDIHS) 80 82 86 87 62: 186 type=173 (RBDIHS) 80 82 86 88 62: 187 type=173 (RBDIHS) 83 82 86 87 62: 188 type=173 (RBDIHS) 83 82 86 88 62: 189 type=155 (RBDIHS) 69 89 91 92 62: 190 type=156 (RBDIHS) 69 89 91 93 62: 191 type=155 (RBDIHS) 90 89 91 92 62: 192 type=157 (RBDIHS) 90 89 91 93 62: 193 type=158 (RBDIHS) 89 91 93 95 62: 194 type=159 (RBDIHS) 89 91 93 100 62: 195 type=174 (RBDIHS) 91 93 95 98 62: 196 type=175 (RBDIHS) 100 93 95 98 62: 197 type=147 (RBDIHS) 91 93 95 96 62: 198 type=147 (RBDIHS) 91 93 95 97 62: 199 type=148 (RBDIHS) 94 93 95 96 62: 200 type=148 (RBDIHS) 94 93 95 97 62: 201 type=176 (RBDIHS) 94 93 95 98 62: 202 type=149 (RBDIHS) 100 93 95 96 62: 203 type=149 (RBDIHS) 100 93 95 97 62: 204 type=150 (RBDIHS) 91 93 100 102 62: 205 type=151 (RBDIHS) 95 93 100 102 62: 206 type=177 (RBDIHS) 93 95 98 99 62: 207 type=178 (RBDIHS) 96 95 98 99 62: 208 type=178 (RBDIHS) 97 95 98 99 62: 209 type=155 (RBDIHS) 93 100 102 103 62: 210 type=156 (RBDIHS) 93 100 102 104 62: 211 type=155 (RBDIHS) 101 100 102 103 62: 212 type=157 (RBDIHS) 101 100 102 104 62: 213 type=158 (RBDIHS) 100 102 104 106 62: 214 type=159 (RBDIHS) 100 102 104 115 62: 215 type=179 (RBDIHS) 102 104 106 109 62: 216 type=180 (RBDIHS) 115 104 106 109 62: 217 type=147 (RBDIHS) 102 104 106 107 62: 218 type=147 (RBDIHS) 102 104 106 108 62: 219 type=148 (RBDIHS) 105 104 106 107 62: 220 type=148 (RBDIHS) 105 104 106 108 62: 221 type=148 (RBDIHS) 105 104 106 109 62: 222 type=149 (RBDIHS) 115 104 106 107 62: 223 type=149 (RBDIHS) 115 104 106 108 62: 224 type=150 (RBDIHS) 102 104 115 117 62: 225 type=151 (RBDIHS) 106 104 115 117 62: 226 type=148 (RBDIHS) 104 106 109 110 62: 227 type=148 (RBDIHS) 104 106 109 111 62: 228 type=181 (RBDIHS) 104 106 109 112 62: 229 type=148 (RBDIHS) 107 106 109 110 62: 230 type=148 (RBDIHS) 107 106 109 111 62: 231 type=182 (RBDIHS) 107 106 109 112 62: 232 type=148 (RBDIHS) 108 106 109 110 62: 233 type=148 (RBDIHS) 108 106 109 111 62: 234 type=182 (RBDIHS) 108 106 109 112 62: 235 type=183 (RBDIHS) 106 109 112 113 62: 236 type=183 (RBDIHS) 106 109 112 114 62: 237 type=155 (RBDIHS) 104 115 117 118 62: 238 type=156 (RBDIHS) 104 115 117 119 62: 239 type=155 (RBDIHS) 116 115 117 118 62: 240 type=157 (RBDIHS) 116 115 117 119 62: 241 type=158 (RBDIHS) 115 117 119 121 62: 242 type=159 (RBDIHS) 115 117 119 134 62: 243 type=184 (RBDIHS) 117 119 121 124 62: 244 type=185 (RBDIHS) 134 119 121 124 62: 245 type=147 (RBDIHS) 117 119 121 122 62: 246 type=147 (RBDIHS) 117 119 121 123 62: 247 type=148 (RBDIHS) 120 119 121 122 62: 248 type=148 (RBDIHS) 120 119 121 123 62: 249 type=148 (RBDIHS) 120 119 121 124 62: 250 type=149 (RBDIHS) 134 119 121 122 62: 251 type=149 (RBDIHS) 134 119 121 123 62: 252 type=150 (RBDIHS) 117 119 134 136 62: 253 type=151 (RBDIHS) 121 119 134 136 62: 254 type=148 (RBDIHS) 119 121 124 125 62: 255 type=152 (RBDIHS) 119 121 124 126 62: 256 type=152 (RBDIHS) 119 121 124 130 62: 257 type=148 (RBDIHS) 122 121 124 125 62: 258 type=148 (RBDIHS) 122 121 124 126 62: 259 type=148 (RBDIHS) 122 121 124 130 62: 260 type=148 (RBDIHS) 123 121 124 125 62: 261 type=148 (RBDIHS) 123 121 124 126 62: 262 type=148 (RBDIHS) 123 121 124 130 62: 263 type=148 (RBDIHS) 121 124 126 127 62: 264 type=148 (RBDIHS) 121 124 126 128 62: 265 type=148 (RBDIHS) 121 124 126 129 62: 266 type=148 (RBDIHS) 125 124 126 127 62: 267 type=148 (RBDIHS) 125 124 126 128 62: 268 type=148 (RBDIHS) 125 124 126 129 62: 269 type=148 (RBDIHS) 130 124 126 127 62: 270 type=148 (RBDIHS) 130 124 126 128 62: 271 type=148 (RBDIHS) 130 124 126 129 62: 272 type=148 (RBDIHS) 121 124 130 131 62: 273 type=148 (RBDIHS) 121 124 130 132 62: 274 type=148 (RBDIHS) 121 124 130 133 62: 275 type=148 (RBDIHS) 125 124 130 131 62: 276 type=148 (RBDIHS) 125 124 130 132 62: 277 type=148 (RBDIHS) 125 124 130 133 62: 278 type=148 (RBDIHS) 126 124 130 131 62: 279 type=148 (RBDIHS) 126 124 130 132 62: 280 type=148 (RBDIHS) 126 124 130 133 62: 281 type=155 (RBDIHS) 119 134 136 137 62: 282 type=156 (RBDIHS) 119 134 136 138 62: 283 type=155 (RBDIHS) 135 134 136 137 62: 284 type=157 (RBDIHS) 135 134 136 138 62: 285 type=158 (RBDIHS) 134 136 138 140 62: 286 type=159 (RBDIHS) 134 136 138 144 62: 287 type=147 (RBDIHS) 136 138 140 141 62: 288 type=147 (RBDIHS) 136 138 140 142 62: 289 type=147 (RBDIHS) 136 138 140 143 62: 290 type=148 (RBDIHS) 139 138 140 141 62: 291 type=148 (RBDIHS) 139 138 140 142 62: 292 type=148 (RBDIHS) 139 138 140 143 62: 293 type=149 (RBDIHS) 144 138 140 141 62: 294 type=149 (RBDIHS) 144 138 140 142 62: 295 type=149 (RBDIHS) 144 138 140 143 62: 296 type=150 (RBDIHS) 136 138 144 146 62: 297 type=151 (RBDIHS) 140 138 144 146 62: 298 type=155 (RBDIHS) 138 144 146 147 62: 299 type=156 (RBDIHS) 138 144 146 148 62: 300 type=155 (RBDIHS) 145 144 146 147 62: 301 type=157 (RBDIHS) 145 144 146 148 62: 302 type=158 (RBDIHS) 144 146 148 150 62: 303 type=159 (RBDIHS) 144 146 148 154 62: 304 type=147 (RBDIHS) 146 148 150 151 62: 305 type=147 (RBDIHS) 146 148 150 152 62: 306 type=147 (RBDIHS) 146 148 150 153 62: 307 type=148 (RBDIHS) 149 148 150 151 62: 308 type=148 (RBDIHS) 149 148 150 152 62: 309 type=148 (RBDIHS) 149 148 150 153 62: 310 type=149 (RBDIHS) 154 148 150 151 62: 311 type=149 (RBDIHS) 154 148 150 152 62: 312 type=149 (RBDIHS) 154 148 150 153 62: Restr. Dih.: 62: nr: 0 62: CBT Dih.: 62: nr: 0 62: Fourier Dih.: 62: nr: 0 62: Improper Dih.: 62: nr: 0 62: Per. Imp. Dih.: 62: nr: 0 62: Tab. Dih.: 62: nr: 0 62: CMAP Dih.: 62: nr: 0 62: GB 1-2 Pol.: 62: nr: 0 62: GB 1-3 Pol.: 62: nr: 0 62: GB 1-4 Pol.: 62: nr: 0 62: GB Polariz.: 62: nr: 0 62: Nonpolar Sol.: 62: nr: 0 62: LJ-14: 62: nr: 1197 62: iatoms: 62: 0 type=186 (LJ14) 0 7 62: 1 type=186 (LJ14) 0 8 62: 2 type=187 (LJ14) 0 9 62: 3 type=188 (LJ14) 0 23 62: 4 type=189 (LJ14) 0 24 62: 5 type=190 (LJ14) 1 5 62: 6 type=190 (LJ14) 1 6 62: 7 type=190 (LJ14) 1 22 62: 8 type=190 (LJ14) 2 5 62: 9 type=190 (LJ14) 2 6 62: 10 type=190 (LJ14) 2 22 62: 11 type=190 (LJ14) 3 5 62: 12 type=190 (LJ14) 3 6 62: 13 type=190 (LJ14) 3 22 62: 14 type=191 (LJ14) 4 10 62: 15 type=191 (LJ14) 4 11 62: 16 type=192 (LJ14) 4 12 62: 17 type=190 (LJ14) 4 25 62: 18 type=192 (LJ14) 4 26 62: 19 type=193 (LJ14) 5 7 62: 20 type=193 (LJ14) 5 8 62: 21 type=191 (LJ14) 5 9 62: 22 type=194 (LJ14) 5 23 62: 23 type=186 (LJ14) 5 24 62: 24 type=191 (LJ14) 6 13 62: 25 type=191 (LJ14) 6 14 62: 26 type=192 (LJ14) 6 15 62: 27 type=195 (LJ14) 6 23 62: 28 type=187 (LJ14) 6 24 62: 29 type=193 (LJ14) 7 10 62: 30 type=193 (LJ14) 7 11 62: 31 type=191 (LJ14) 7 12 62: 32 type=196 (LJ14) 7 22 62: 33 type=193 (LJ14) 8 10 62: 34 type=193 (LJ14) 8 11 62: 35 type=191 (LJ14) 8 12 62: 36 type=196 (LJ14) 8 22 62: 37 type=191 (LJ14) 9 16 62: 38 type=191 (LJ14) 9 17 62: 39 type=187 (LJ14) 9 18 62: 40 type=197 (LJ14) 9 22 62: 41 type=193 (LJ14) 10 13 62: 42 type=193 (LJ14) 10 14 62: 43 type=191 (LJ14) 10 15 62: 44 type=193 (LJ14) 11 13 62: 45 type=193 (LJ14) 11 14 62: 46 type=191 (LJ14) 11 15 62: 47 type=190 (LJ14) 12 19 62: 48 type=190 (LJ14) 12 20 62: 49 type=190 (LJ14) 12 21 62: 50 type=193 (LJ14) 13 16 62: 51 type=193 (LJ14) 13 17 62: 52 type=186 (LJ14) 13 18 62: 53 type=193 (LJ14) 14 16 62: 54 type=193 (LJ14) 14 17 62: 55 type=186 (LJ14) 14 18 62: 56 type=190 (LJ14) 16 19 62: 57 type=190 (LJ14) 16 20 62: 58 type=190 (LJ14) 16 21 62: 59 type=190 (LJ14) 17 19 62: 60 type=190 (LJ14) 17 20 62: 61 type=190 (LJ14) 17 21 62: 62 type=196 (LJ14) 22 27 62: 63 type=197 (LJ14) 22 28 62: 64 type=198 (LJ14) 22 38 62: 65 type=190 (LJ14) 23 25 62: 66 type=195 (LJ14) 23 26 62: 67 type=186 (LJ14) 24 29 62: 68 type=187 (LJ14) 24 30 62: 69 type=187 (LJ14) 24 34 62: 70 type=188 (LJ14) 24 39 62: 71 type=189 (LJ14) 24 40 62: 72 type=190 (LJ14) 25 27 62: 73 type=190 (LJ14) 25 28 62: 74 type=190 (LJ14) 25 38 62: 75 type=191 (LJ14) 26 31 62: 76 type=191 (LJ14) 26 32 62: 77 type=191 (LJ14) 26 33 62: 78 type=191 (LJ14) 26 35 62: 79 type=191 (LJ14) 26 36 62: 80 type=191 (LJ14) 26 37 62: 81 type=190 (LJ14) 26 41 62: 82 type=192 (LJ14) 26 42 62: 83 type=193 (LJ14) 27 29 62: 84 type=191 (LJ14) 27 30 62: 85 type=191 (LJ14) 27 34 62: 86 type=194 (LJ14) 27 39 62: 87 type=186 (LJ14) 27 40 62: 88 type=195 (LJ14) 28 39 62: 89 type=187 (LJ14) 28 40 62: 90 type=193 (LJ14) 29 31 62: 91 type=193 (LJ14) 29 32 62: 92 type=193 (LJ14) 29 33 62: 93 type=193 (LJ14) 29 35 62: 94 type=193 (LJ14) 29 36 62: 95 type=193 (LJ14) 29 37 62: 96 type=196 (LJ14) 29 38 62: 97 type=191 (LJ14) 30 35 62: 98 type=191 (LJ14) 30 36 62: 99 type=191 (LJ14) 30 37 62: 100 type=197 (LJ14) 30 38 62: 101 type=191 (LJ14) 31 34 62: 102 type=191 (LJ14) 32 34 62: 103 type=191 (LJ14) 33 34 62: 104 type=197 (LJ14) 34 38 62: 105 type=196 (LJ14) 38 43 62: 106 type=197 (LJ14) 38 44 62: 107 type=198 (LJ14) 38 58 62: 108 type=190 (LJ14) 39 41 62: 109 type=195 (LJ14) 39 42 62: 110 type=186 (LJ14) 40 45 62: 111 type=186 (LJ14) 40 46 62: 112 type=199 (LJ14) 40 47 62: 113 type=188 (LJ14) 40 59 62: 114 type=189 (LJ14) 40 60 62: 115 type=190 (LJ14) 41 43 62: 116 type=190 (LJ14) 41 44 62: 117 type=190 (LJ14) 41 58 62: 118 type=200 (LJ14) 42 48 62: 119 type=200 (LJ14) 42 50 62: 120 type=190 (LJ14) 42 61 62: 121 type=192 (LJ14) 42 62 62: 122 type=193 (LJ14) 43 45 62: 123 type=193 (LJ14) 43 46 62: 124 type=201 (LJ14) 43 47 62: 125 type=194 (LJ14) 43 59 62: 126 type=186 (LJ14) 43 60 62: 127 type=202 (LJ14) 44 49 62: 128 type=202 (LJ14) 44 51 62: 129 type=200 (LJ14) 44 52 62: 130 type=200 (LJ14) 44 54 62: 131 type=195 (LJ14) 44 59 62: 132 type=187 (LJ14) 44 60 62: 133 type=201 (LJ14) 45 48 62: 134 type=201 (LJ14) 45 50 62: 135 type=196 (LJ14) 45 58 62: 136 type=201 (LJ14) 46 48 62: 137 type=201 (LJ14) 46 50 62: 138 type=196 (LJ14) 46 58 62: 139 type=203 (LJ14) 47 53 62: 140 type=203 (LJ14) 47 55 62: 141 type=204 (LJ14) 47 56 62: 142 type=205 (LJ14) 47 58 62: 143 type=203 (LJ14) 48 51 62: 144 type=204 (LJ14) 48 54 62: 145 type=203 (LJ14) 48 57 62: 146 type=203 (LJ14) 49 50 62: 147 type=206 (LJ14) 49 53 62: 148 type=203 (LJ14) 49 56 62: 149 type=204 (LJ14) 50 52 62: 150 type=203 (LJ14) 50 57 62: 151 type=206 (LJ14) 51 55 62: 152 type=203 (LJ14) 51 56 62: 153 type=203 (LJ14) 52 55 62: 154 type=203 (LJ14) 53 54 62: 155 type=206 (LJ14) 53 57 62: 156 type=206 (LJ14) 55 57 62: 157 type=196 (LJ14) 58 63 62: 158 type=196 (LJ14) 58 64 62: 159 type=198 (LJ14) 58 65 62: 160 type=190 (LJ14) 59 61 62: 161 type=195 (LJ14) 59 62 62: 162 type=188 (LJ14) 60 66 62: 163 type=189 (LJ14) 60 67 62: 164 type=190 (LJ14) 61 63 62: 165 type=190 (LJ14) 61 64 62: 166 type=190 (LJ14) 61 65 62: 167 type=190 (LJ14) 62 68 62: 168 type=192 (LJ14) 62 69 62: 169 type=194 (LJ14) 63 66 62: 170 type=186 (LJ14) 63 67 62: 171 type=194 (LJ14) 64 66 62: 172 type=186 (LJ14) 64 67 62: 173 type=196 (LJ14) 65 70 62: 174 type=197 (LJ14) 65 71 62: 175 type=198 (LJ14) 65 89 62: 176 type=190 (LJ14) 66 68 62: 177 type=195 (LJ14) 66 69 62: 178 type=186 (LJ14) 67 72 62: 179 type=186 (LJ14) 67 73 62: 180 type=187 (LJ14) 67 74 62: 181 type=188 (LJ14) 67 90 62: 182 type=189 (LJ14) 67 91 62: 183 type=190 (LJ14) 68 70 62: 184 type=190 (LJ14) 68 71 62: 185 type=190 (LJ14) 68 89 62: 186 type=191 (LJ14) 69 75 62: 187 type=191 (LJ14) 69 76 62: 188 type=192 (LJ14) 69 77 62: 189 type=190 (LJ14) 69 92 62: 190 type=192 (LJ14) 69 93 62: 191 type=193 (LJ14) 70 72 62: 192 type=193 (LJ14) 70 73 62: 193 type=191 (LJ14) 70 74 62: 194 type=194 (LJ14) 70 90 62: 195 type=186 (LJ14) 70 91 62: 196 type=191 (LJ14) 71 78 62: 197 type=191 (LJ14) 71 79 62: 198 type=187 (LJ14) 71 80 62: 199 type=195 (LJ14) 71 90 62: 200 type=187 (LJ14) 71 91 62: 201 type=193 (LJ14) 72 75 62: 202 type=193 (LJ14) 72 76 62: 203 type=191 (LJ14) 72 77 62: 204 type=196 (LJ14) 72 89 62: 205 type=193 (LJ14) 73 75 62: 206 type=193 (LJ14) 73 76 62: 207 type=191 (LJ14) 73 77 62: 208 type=196 (LJ14) 73 89 62: 209 type=190 (LJ14) 74 81 62: 210 type=207 (LJ14) 74 82 62: 211 type=197 (LJ14) 74 89 62: 212 type=193 (LJ14) 75 78 62: 213 type=193 (LJ14) 75 79 62: 214 type=186 (LJ14) 75 80 62: 215 type=193 (LJ14) 76 78 62: 216 type=193 (LJ14) 76 79 62: 217 type=186 (LJ14) 76 80 62: 218 type=187 (LJ14) 77 83 62: 219 type=187 (LJ14) 77 86 62: 220 type=190 (LJ14) 78 81 62: 221 type=208 (LJ14) 78 82 62: 222 type=190 (LJ14) 79 81 62: 223 type=208 (LJ14) 79 82 62: 224 type=190 (LJ14) 80 84 62: 225 type=190 (LJ14) 80 85 62: 226 type=190 (LJ14) 80 87 62: 227 type=190 (LJ14) 80 88 62: 228 type=190 (LJ14) 81 83 62: 229 type=190 (LJ14) 81 86 62: 230 type=190 (LJ14) 83 87 62: 231 type=190 (LJ14) 83 88 62: 232 type=190 (LJ14) 84 86 62: 233 type=190 (LJ14) 85 86 62: 234 type=196 (LJ14) 89 94 62: 235 type=197 (LJ14) 89 95 62: 236 type=198 (LJ14) 89 100 62: 237 type=190 (LJ14) 90 92 62: 238 type=195 (LJ14) 90 93 62: 239 type=186 (LJ14) 91 96 62: 240 type=186 (LJ14) 91 97 62: 241 type=209 (LJ14) 91 98 62: 242 type=188 (LJ14) 91 101 62: 243 type=189 (LJ14) 91 102 62: 244 type=190 (LJ14) 92 94 62: 245 type=190 (LJ14) 92 95 62: 246 type=190 (LJ14) 92 100 62: 247 type=190 (LJ14) 93 99 62: 248 type=190 (LJ14) 93 103 62: 249 type=192 (LJ14) 93 104 62: 250 type=193 (LJ14) 94 96 62: 251 type=193 (LJ14) 94 97 62: 252 type=210 (LJ14) 94 98 62: 253 type=194 (LJ14) 94 101 62: 254 type=186 (LJ14) 94 102 62: 255 type=195 (LJ14) 95 101 62: 256 type=187 (LJ14) 95 102 62: 257 type=190 (LJ14) 96 99 62: 258 type=196 (LJ14) 96 100 62: 259 type=190 (LJ14) 97 99 62: 260 type=196 (LJ14) 97 100 62: 261 type=211 (LJ14) 98 100 62: 262 type=196 (LJ14) 100 105 62: 263 type=197 (LJ14) 100 106 62: 264 type=198 (LJ14) 100 115 62: 265 type=190 (LJ14) 101 103 62: 266 type=195 (LJ14) 101 104 62: 267 type=186 (LJ14) 102 107 62: 268 type=186 (LJ14) 102 108 62: 269 type=187 (LJ14) 102 109 62: 270 type=188 (LJ14) 102 116 62: 271 type=189 (LJ14) 102 117 62: 272 type=190 (LJ14) 103 105 62: 273 type=190 (LJ14) 103 106 62: 274 type=190 (LJ14) 103 115 62: 275 type=191 (LJ14) 104 110 62: 276 type=191 (LJ14) 104 111 62: 277 type=197 (LJ14) 104 112 62: 278 type=190 (LJ14) 104 118 62: 279 type=192 (LJ14) 104 119 62: 280 type=193 (LJ14) 105 107 62: 281 type=193 (LJ14) 105 108 62: 282 type=191 (LJ14) 105 109 62: 283 type=194 (LJ14) 105 116 62: 284 type=186 (LJ14) 105 117 62: 285 type=195 (LJ14) 106 113 62: 286 type=195 (LJ14) 106 114 62: 287 type=195 (LJ14) 106 116 62: 288 type=187 (LJ14) 106 117 62: 289 type=193 (LJ14) 107 110 62: 290 type=193 (LJ14) 107 111 62: 291 type=196 (LJ14) 107 112 62: 292 type=196 (LJ14) 107 115 62: 293 type=193 (LJ14) 108 110 62: 294 type=193 (LJ14) 108 111 62: 295 type=196 (LJ14) 108 112 62: 296 type=196 (LJ14) 108 115 62: 297 type=197 (LJ14) 109 115 62: 298 type=194 (LJ14) 110 113 62: 299 type=194 (LJ14) 110 114 62: 300 type=194 (LJ14) 111 113 62: 301 type=194 (LJ14) 111 114 62: 302 type=196 (LJ14) 115 120 62: 303 type=197 (LJ14) 115 121 62: 304 type=198 (LJ14) 115 134 62: 305 type=190 (LJ14) 116 118 62: 306 type=195 (LJ14) 116 119 62: 307 type=186 (LJ14) 117 122 62: 308 type=186 (LJ14) 117 123 62: 309 type=187 (LJ14) 117 124 62: 310 type=188 (LJ14) 117 135 62: 311 type=189 (LJ14) 117 136 62: 312 type=190 (LJ14) 118 120 62: 313 type=190 (LJ14) 118 121 62: 314 type=190 (LJ14) 118 134 62: 315 type=191 (LJ14) 119 125 62: 316 type=192 (LJ14) 119 126 62: 317 type=192 (LJ14) 119 130 62: 318 type=190 (LJ14) 119 137 62: 319 type=192 (LJ14) 119 138 62: 320 type=193 (LJ14) 120 122 62: 321 type=193 (LJ14) 120 123 62: 322 type=191 (LJ14) 120 124 62: 323 type=194 (LJ14) 120 135 62: 324 type=186 (LJ14) 120 136 62: 325 type=191 (LJ14) 121 127 62: 326 type=191 (LJ14) 121 128 62: 327 type=191 (LJ14) 121 129 62: 328 type=191 (LJ14) 121 131 62: 329 type=191 (LJ14) 121 132 62: 330 type=191 (LJ14) 121 133 62: 331 type=195 (LJ14) 121 135 62: 332 type=187 (LJ14) 121 136 62: 333 type=193 (LJ14) 122 125 62: 334 type=191 (LJ14) 122 126 62: 335 type=191 (LJ14) 122 130 62: 336 type=196 (LJ14) 122 134 62: 337 type=193 (LJ14) 123 125 62: 338 type=191 (LJ14) 123 126 62: 339 type=191 (LJ14) 123 130 62: 340 type=196 (LJ14) 123 134 62: 341 type=197 (LJ14) 124 134 62: 342 type=193 (LJ14) 125 127 62: 343 type=193 (LJ14) 125 128 62: 344 type=193 (LJ14) 125 129 62: 345 type=193 (LJ14) 125 131 62: 346 type=193 (LJ14) 125 132 62: 347 type=193 (LJ14) 125 133 62: 348 type=191 (LJ14) 126 131 62: 349 type=191 (LJ14) 126 132 62: 350 type=191 (LJ14) 126 133 62: 351 type=191 (LJ14) 127 130 62: 352 type=191 (LJ14) 128 130 62: 353 type=191 (LJ14) 129 130 62: 354 type=196 (LJ14) 134 139 62: 355 type=197 (LJ14) 134 140 62: 356 type=198 (LJ14) 134 144 62: 357 type=190 (LJ14) 135 137 62: 358 type=195 (LJ14) 135 138 62: 359 type=186 (LJ14) 136 141 62: 360 type=186 (LJ14) 136 142 62: 361 type=186 (LJ14) 136 143 62: 362 type=188 (LJ14) 136 145 62: 363 type=189 (LJ14) 136 146 62: 364 type=190 (LJ14) 137 139 62: 365 type=190 (LJ14) 137 140 62: 366 type=190 (LJ14) 137 144 62: 367 type=190 (LJ14) 138 147 62: 368 type=192 (LJ14) 138 148 62: 369 type=193 (LJ14) 139 141 62: 370 type=193 (LJ14) 139 142 62: 371 type=193 (LJ14) 139 143 62: 372 type=194 (LJ14) 139 145 62: 373 type=186 (LJ14) 139 146 62: 374 type=195 (LJ14) 140 145 62: 375 type=187 (LJ14) 140 146 62: 376 type=196 (LJ14) 141 144 62: 377 type=196 (LJ14) 142 144 62: 378 type=196 (LJ14) 143 144 62: 379 type=196 (LJ14) 144 149 62: 380 type=197 (LJ14) 144 150 62: 381 type=198 (LJ14) 144 154 62: 382 type=190 (LJ14) 145 147 62: 383 type=195 (LJ14) 145 148 62: 384 type=186 (LJ14) 146 151 62: 385 type=186 (LJ14) 146 152 62: 386 type=186 (LJ14) 146 153 62: 387 type=188 (LJ14) 146 155 62: 388 type=190 (LJ14) 147 149 62: 389 type=190 (LJ14) 147 150 62: 390 type=190 (LJ14) 147 154 62: 391 type=193 (LJ14) 149 151 62: 392 type=193 (LJ14) 149 152 62: 393 type=193 (LJ14) 149 153 62: 394 type=194 (LJ14) 149 155 62: 395 type=195 (LJ14) 150 155 62: 396 type=196 (LJ14) 151 154 62: 397 type=196 (LJ14) 152 154 62: 398 type=196 (LJ14) 153 154 62: Coulomb-14: 62: nr: 0 62: LJC-14 q: 62: nr: 0 62: LJC Pairs NB: 62: nr: 0 62: LJ (SR): 62: nr: 0 62: Buck.ham (SR): 62: nr: 0 62: LJ: 62: nr: 0 62: B.ham: 62: nr: 0 62: Disper. corr.: 62: nr: 0 62: Coulomb (SR): 62: nr: 0 62: Coul: 62: nr: 0 62: RF excl.: 62: nr: 0 62: Coul. recip.: 62: nr: 0 62: LJ recip.: 62: nr: 0 62: DPD: 62: nr: 0 62: Polarization: 62: nr: 0 62: Water Pol.: 62: nr: 0 62: Thole Pol.: 62: nr: 0 62: Anharm. Pol.: 62: nr: 0 62: Position Rest.: 62: nr: 0 62: Flat-b. P-R.: 62: nr: 0 62: Dis. Rest.: 62: nr: 0 62: D.R.Viol. (nm): 62: nr: 0 62: Orient. Rest.: 62: nr: 0 62: Ori. R. RMSD: 62: nr: 0 62: Angle Rest.: 62: nr: 0 62: Angle Rest. Z: 62: nr: 0 62: Dih. Rest.: 62: nr: 0 62: Dih. Rest. Vi.: 62: nr: 0 62: Constraint: 62: nr: 0 62: Constr. No Co.: 62: nr: 0 62: Settle: 62: nr: 0 62: Virtual site 1: 62: nr: 0 62: Virtual site 2: 62: nr: 0 62: Virt. site 2fd: 62: nr: 0 62: Virtual site 3: 62: nr: 0 62: Virt. site 3fd: 62: nr: 0 62: Vir. site 3fad: 62: nr: 0 62: Vir. site 3out: 62: nr: 0 62: Virt. site 4fd: 62: nr: 0 62: Vir. site 4fdn: 62: nr: 0 62: Virtual site N: 62: nr: 0 62: COM Pull En.: 62: nr: 0 62: Dens. fitting: 62: nr: 0 62: Quantum En.: 62: nr: 0 62: NN Potential: 62: nr: 0 62: Potential: 62: nr: 0 62: Kinetic En.: 62: nr: 0 62: Total Energy: 62: nr: 0 62: Conserved En.: 62: nr: 0 62: Temperature: 62: nr: 0 62: Vir. Temp.: 62: nr: 0 62: Pres. DC: 62: nr: 0 62: Pressure: 62: nr: 0 62: dH/dl constr.: 62: nr: 0 62: dVremain/dl: 62: nr: 0 62: dEkin/dl: 62: nr: 0 62: dVcoul/dl: 62: nr: 0 62: dVvdw/dl: 62: nr: 0 62: dVbonded/dl: 62: nr: 0 62: dVrestraint/dl: 62: nr: 0 62: dVtemp/dl: 62: nr: 0 62: grp[T-Coupling ] nr=1, name=[ rest] 62: grp[Energy Mon. ] nr=1, name=[ rest] 62: grp[Acc. not used] nr=1, name=[ rest] 62: grp[Freeze ] nr=1, name=[ rest] 62: grp[User1 ] nr=1, name=[ rest] 62: grp[User2 ] nr=1, name=[ rest] 62: grp[VCM ] nr=1, name=[ rest] 62: grp[Compressed X] nr=1, name=[ rest] 62: grp[Or. Res. Fit] nr=1, name=[ rest] 62: grp[QMMM ] nr=1, name=[ rest] 62: grpname (11): 62: grpname[0]={name="System"} 62: grpname[1]={name="Protein"} 62: grpname[2]={name="Protein-H"} 62: grpname[3]={name="C-alpha"} 62: grpname[4]={name="Backbone"} 62: grpname[5]={name="MainChain"} 62: grpname[6]={name="MainChain+Cb"} 62: grpname[7]={name="MainChain+H"} 62: grpname[8]={name="SideChain"} 62: grpname[9]={name="SideChain-H"} 62: grpname[10]={name="rest"} 62: groups T-Cou Energ Acc. Freez User1 User2 VCM Compr Or. R QMMM 62: allocated 0 0 0 0 0 0 0 0 0 0 62: groupnr[ *] = 0 0 0 0 0 0 0 0 0 0 62: box (3x3): 62: box[ 0]={ 5.90620e+00, 0.00000e+00, 0.00000e+00} 62: box[ 1]={ 0.00000e+00, 6.84510e+00, 0.00000e+00} 62: box[ 2]={ 0.00000e+00, 0.00000e+00, 3.05170e+00} 62: box_rel (3x3): 62: box_rel[ 0]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 62: box_rel[ 1]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 62: box_rel[ 2]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 62: boxv (3x3): 62: boxv[ 0]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 62: boxv[ 1]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 62: boxv[ 2]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 62: pres_prev (3x3): 62: pres_prev[ 0]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 62: pres_prev[ 1]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 62: pres_prev[ 2]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 62: svir_prev (3x3): 62: svir_prev[ 0]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 62: svir_prev[ 1]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 62: svir_prev[ 2]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 62: fvir_prev (3x3): 62: fvir_prev[ 0]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 62: fvir_prev[ 1]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 62: fvir_prev[ 2]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 62: nosehoover_xi: not available 62: x (156x3): 62: x[ 0]={ 3.53600e+00, 2.23400e+00, -1.19800e+00} 62: x[ 1]={ 3.61200e+00, 2.28800e+00, -1.23600e+00} 62: x[ 2]={ 3.47000e+00, 2.21400e+00, -1.27000e+00} 62: x[ 3]={ 3.49200e+00, 2.28600e+00, -1.12500e+00} 62: x[ 4]={ 3.58900e+00, 2.10700e+00, -1.14300e+00} 62: x[ 5]={ 3.63300e+00, 2.05500e+00, -1.21600e+00} 62: x[ 6]={ 3.68700e+00, 2.14400e+00, -1.03100e+00} 62: x[ 7]={ 3.76300e+00, 2.19500e+00, -1.07000e+00} 62: x[ 8]={ 3.63900e+00, 2.20100e+00, -9.64000e-01} 62: x[ 9]={ 3.74500e+00, 2.02500e+00, -9.56000e-01} 62: x[ 10]={ 3.67600e+00, 1.98900e+00, -8.94000e-01} 62: x[ 11]={ 3.77000e+00, 1.95400e+00, -1.02300e+00} 62: x[ 12]={ 3.86900e+00, 2.06500e+00, -8.77000e-01} 62: x[ 13]={ 3.94500e+00, 2.08300e+00, -9.40000e-01} 62: x[ 14]={ 3.84900e+00, 2.14700e+00, -8.24000e-01} 62: x[ 15]={ 3.90600e+00, 1.95100e+00, -7.84000e-01} 62: x[ 16]={ 3.84100e+00, 1.94600e+00, -7.08000e-01} 62: x[ 17]={ 3.90600e+00, 1.86400e+00, -8.33000e-01} 62: x[ 18]={ 4.04200e+00, 1.97700e+00, -7.30000e-01} 62: x[ 19]={ 4.06900e+00, 1.90300e+00, -6.68000e-01} 62: x[ 20]={ 4.10800e+00, 1.98200e+00, -8.06000e-01} 62: x[ 21]={ 4.04200e+00, 2.06400e+00, -6.80000e-01} 62: x[ 22]={ 3.47400e+00, 2.02600e+00, -1.08400e+00} 62: x[ 23]={ 3.39500e+00, 2.08100e+00, -1.00800e+00} 62: x[ 24]={ 3.47400e+00, 1.89600e+00, -1.10400e+00} 62: x[ 25]={ 3.53600e+00, 1.86000e+00, -1.17400e+00} 62: x[ 26]={ 3.39000e+00, 1.80000e+00, -1.03300e+00} 62: x[ 27]={ 3.31700e+00, 1.85200e+00, -9.90000e-01} 62: x[ 28]={ 3.31400e+00, 1.70300e+00, -1.12300e+00} 62: x[ 29]={ 3.38600e+00, 1.65200e+00, -1.17000e+00} 62: x[ 30]={ 3.22500e+00, 1.60800e+00, -1.04300e+00} 62: x[ 31]={ 3.17700e+00, 1.54700e+00, -1.10600e+00} 62: x[ 32]={ 3.28200e+00, 1.55500e+00, -9.81000e-01} 62: x[ 33]={ 3.15800e+00, 1.66100e+00, -9.91000e-01} 62: x[ 34]={ 3.22900e+00, 1.77100e+00, -1.22900e+00} 62: x[ 35]={ 3.18300e+00, 1.70200e+00, -1.28400e+00} 62: x[ 36]={ 3.16200e+00, 1.83000e+00, -1.18500e+00} 62: x[ 37]={ 3.28800e+00, 1.82700e+00, -1.28800e+00} 62: x[ 38]={ 3.48000e+00, 1.73100e+00, -9.29000e-01} 62: x[ 39]={ 3.57600e+00, 1.66100e+00, -9.66000e-01} 62: x[ 40]={ 3.44900e+00, 1.75500e+00, -8.04000e-01} 62: x[ 41]={ 3.37500e+00, 1.81900e+00, -7.84000e-01} 62: x[ 42]={ 3.51900e+00, 1.69000e+00, -6.92000e-01} 62: x[ 43]={ 3.61500e+00, 1.69700e+00, -7.17000e-01} 62: x[ 44]={ 3.49700e+00, 1.76300e+00, -5.59000e-01} 62: x[ 45]={ 3.40500e+00, 1.80200e+00, -5.58000e-01} 62: x[ 46]={ 3.50600e+00, 1.69800e+00, -4.84000e-01} 62: x[ 47]={ 3.59400e+00, 1.87400e+00, -5.38000e-01} 62: x[ 48]={ 3.56700e+00, 2.00500e+00, -5.80000e-01} 62: x[ 49]={ 3.48100e+00, 2.02500e+00, -6.27000e-01} 62: x[ 50]={ 3.70000e+00, 1.85600e+00, -4.47000e-01} 62: x[ 51]={ 3.71300e+00, 1.76600e+00, -4.05000e-01} 62: x[ 52]={ 3.65800e+00, 2.10800e+00, -5.57000e-01} 62: x[ 53]={ 3.64800e+00, 2.19500e+00, -6.04000e-01} 62: x[ 54]={ 3.78700e+00, 1.95900e+00, -4.16000e-01} 62: x[ 55]={ 3.86600e+00, 1.94200e+00, -3.57000e-01} 62: x[ 56]={ 3.76400e+00, 2.08700e+00, -4.67000e-01} 62: x[ 57]={ 3.82200e+00, 2.16400e+00, -4.39000e-01} 62: x[ 58]={ 3.47400e+00, 1.54400e+00, -6.77000e-01} 62: x[ 59]={ 3.35200e+00, 1.51600e+00, -6.86000e-01} 62: x[ 60]={ 3.57200e+00, 1.46400e+00, -6.33000e-01} 62: x[ 61]={ 3.66700e+00, 1.49500e+00, -6.32000e-01} 62: x[ 62]={ 3.53700e+00, 1.32800e+00, -5.87000e-01} 62: x[ 63]={ 3.46200e+00, 1.29200e+00, -6.43000e-01} 62: x[ 64]={ 3.61600e+00, 1.26800e+00, -5.94000e-01} 62: x[ 65]={ 3.49200e+00, 1.34200e+00, -4.42000e-01} 62: x[ 66]={ 3.53000e+00, 1.44000e+00, -3.78000e-01} 62: x[ 67]={ 3.40500e+00, 1.25400e+00, -3.97000e-01} 62: x[ 68]={ 3.37100e+00, 1.18400e+00, -4.60000e-01} 62: x[ 69]={ 3.35600e+00, 1.25400e+00, -2.59000e-01} 62: x[ 70]={ 3.29800e+00, 1.33400e+00, -2.52000e-01} 62: x[ 71]={ 3.27600e+00, 1.12600e+00, -2.33000e-01} 62: x[ 72]={ 3.20000e+00, 1.12200e+00, -2.97000e-01} 62: x[ 73]={ 3.33600e+00, 1.04700e+00, -2.47000e-01} 62: x[ 74]={ 3.22100e+00, 1.12000e+00, -9.20000e-02} 62: x[ 75]={ 3.29700e+00, 1.11700e+00, -2.70000e-02} 62: x[ 76]={ 3.16500e+00, 1.20100e+00, -7.50000e-02} 62: x[ 77]={ 3.13800e+00, 1.00000e+00, -7.20000e-02} 62: x[ 78]={ 3.10400e+00, 9.99000e-01, 2.20000e-02} 62: x[ 79]={ 3.06000e+00, 1.00500e+00, -1.35000e-01} 62: x[ 80]={ 3.20600e+00, 8.75000e-01, -9.60000e-02} 62: x[ 81]={ 3.20200e+00, 8.40000e-01, -1.89000e-01} 62: x[ 82]={ 3.27300e+00, 8.01000e-01, -1.00000e-02} 62: x[ 83]={ 3.28400e+00, 8.33000e-01, 1.19000e-01} 62: x[ 84]={ 3.23900e+00, 9.16000e-01, 1.53000e-01} 62: x[ 85]={ 3.33600e+00, 7.75000e-01, 1.81000e-01} 62: x[ 86]={ 3.32500e+00, 6.84000e-01, -5.30000e-02} 62: x[ 87]={ 3.31100e+00, 6.55000e-01, -1.47000e-01} 62: x[ 88]={ 3.37600e+00, 6.26000e-01, 1.00000e-02} 62: x[ 89]={ 3.46700e+00, 1.27300e+00, -1.56000e-01} 62: x[ 90]={ 3.46700e+00, 1.36500e+00, -7.00000e-02} 62: x[ 91]={ 3.56700e+00, 1.18500e+00, -1.61000e-01} 62: x[ 92]={ 3.56700e+00, 1.11600e+00, -2.33000e-01} 62: x[ 93]={ 3.67800e+00, 1.18700e+00, -6.50000e-02} 62: x[ 94]={ 3.63100e+00, 1.20200e+00, 2.20000e-02} 62: x[ 95]={ 3.74900e+00, 1.05300e+00, -6.20000e-02} 62: x[ 96]={ 3.77000e+00, 1.03400e+00, -1.58000e-01} 62: x[ 97]={ 3.83400e+00, 1.07200e+00, -1.30000e-02} 62: x[ 98]={ 3.65400e+00, 9.20000e-01, 1.40000e-02} 62: x[ 99]={ 3.70750e+00, 8.35500e-01, 1.20000e-02} 62: x[ 100]={ 3.77500e+00, 1.30500e+00, -7.80000e-02} 62: x[ 101]={ 3.81500e+00, 1.36100e+00, 2.60000e-02} 62: x[ 102]={ 3.78600e+00, 1.34800e+00, -2.02000e-01} 62: x[ 103]={ 3.74000e+00, 1.30000e+00, -2.76000e-01} 62: x[ 104]={ 3.86800e+00, 1.46900e+00, -2.31000e-01} 62: x[ 105]={ 3.96000e+00, 1.45500e+00, -1.93000e-01} 62: x[ 106]={ 3.87800e+00, 1.48500e+00, -3.82000e-01} 62: x[ 107]={ 3.92300e+00, 1.40200e+00, -4.17000e-01} 62: x[ 108]={ 3.78500e+00, 1.48900e+00, -4.17000e-01} 62: x[ 109]={ 3.95400e+00, 1.60500e+00, -4.38000e-01} 62: x[ 110]={ 3.91300e+00, 1.68700e+00, -3.99000e-01} 62: x[ 111]={ 4.04900e+00, 1.59800e+00, -4.07000e-01} 62: x[ 112]={ 3.95800e+00, 1.62400e+00, -5.87000e-01} 62: x[ 113]={ 3.86700e+00, 1.56400e+00, -6.49000e-01} 62: x[ 114]={ 4.04200e+00, 1.69500e+00, -6.38000e-01} 62: x[ 115]={ 3.80500e+00, 1.59300e+00, -1.66000e-01} 62: x[ 116]={ 3.87400e+00, 1.67300e+00, -1.01000e-01} 62: x[ 117]={ 3.67400e+00, 1.60500e+00, -1.82000e-01} 62: x[ 118]={ 3.62600e+00, 1.53500e+00, -2.35000e-01} 62: x[ 119]={ 3.59600e+00, 1.71600e+00, -1.25000e-01} 62: x[ 120]={ 3.64000e+00, 1.80100e+00, -1.56000e-01} 62: x[ 121]={ 3.45300e+00, 1.71700e+00, -1.81000e-01} 62: x[ 122]={ 3.45700e+00, 1.72200e+00, -2.81000e-01} 62: x[ 123]={ 3.40600e+00, 1.63300e+00, -1.53000e-01} 62: x[ 124]={ 3.37200e+00, 1.83500e+00, -1.31000e-01} 62: x[ 125]={ 3.37800e+00, 1.84200e+00, -3.10000e-02} 62: x[ 126]={ 3.43000e+00, 1.96600e+00, -1.84000e-01} 62: x[ 127]={ 3.37600e+00, 2.04300e+00, -1.50000e-01} 62: x[ 128]={ 3.52400e+00, 1.97500e+00, -1.53000e-01} 62: x[ 129]={ 3.42700e+00, 1.96500e+00, -2.84000e-01} 62: x[ 130]={ 3.22500e+00, 1.81400e+00, -1.60000e-01} 62: x[ 131]={ 3.17200e+00, 1.89300e+00, -1.26000e-01} 62: x[ 132]={ 3.21100e+00, 1.80500e+00, -2.58000e-01} 62: x[ 133]={ 3.19300e+00, 1.73100e+00, -1.14000e-01} 62: x[ 134]={ 3.60500e+00, 1.71300e+00, 2.70000e-02} 62: x[ 135]={ 3.61600e+00, 1.81700e+00, 9.20000e-02} 62: x[ 136]={ 3.57500e+00, 1.59800e+00, 8.30000e-02} 62: x[ 137]={ 3.54600e+00, 1.52200e+00, 2.40000e-02} 62: x[ 138]={ 3.58400e+00, 1.57600e+00, 2.28000e-01} 62: x[ 139]={ 3.50800e+00, 1.62600e+00, 2.69000e-01} 62: x[ 140]={ 3.56600e+00, 1.42900e+00, 2.62000e-01} 62: x[ 141]={ 3.57200e+00, 1.41600e+00, 3.61000e-01} 62: x[ 142]={ 3.47600e+00, 1.39800e+00, 2.30000e-01} 62: x[ 143]={ 3.63700e+00, 1.37500e+00, 2.18000e-01} 62: x[ 144]={ 3.71400e+00, 1.63100e+00, 2.84000e-01} 62: x[ 145]={ 3.71500e+00, 1.69800e+00, 3.90000e-01} 62: x[ 146]={ 3.82700e+00, 1.59800e+00, 2.20000e-01} 62: x[ 147]={ 3.82000e+00, 1.53900e+00, 1.40000e-01} 62: x[ 148]={ 3.96100e+00, 1.64300e+00, 2.62000e-01} 62: x[ 149]={ 3.96900e+00, 1.61900e+00, 3.58000e-01} 62: x[ 150]={ 4.07100e+00, 1.57100e+00, 1.84000e-01} 62: x[ 151]={ 4.16000e+00, 1.60300e+00, 2.15000e-01} 62: x[ 152]={ 4.06400e+00, 1.47200e+00, 2.01000e-01} 62: x[ 153]={ 4.06000e+00, 1.58900e+00, 8.60000e-02} 62: x[ 154]={ 3.97400e+00, 1.79400e+00, 2.46000e-01} 62: x[ 155]={ 4.01900e+00, 1.85000e+00, 3.47000e-01} 62: v (156x3): 62: v[ 0]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 62: v[ 1]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 62: v[ 2]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 62: v[ 3]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 62: v[ 4]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 62: v[ 5]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 62: v[ 6]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 62: v[ 7]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 62: v[ 8]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 62: v[ 9]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 62: v[ 10]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 62: v[ 11]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 62: v[ 12]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 62: v[ 13]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 62: v[ 14]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 62: v[ 15]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 62: v[ 16]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 62: v[ 17]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 62: v[ 18]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 62: v[ 19]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 62: v[ 20]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 62: v[ 21]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 62: v[ 22]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 62: v[ 23]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 62: v[ 24]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 62: v[ 25]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 62: v[ 26]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 62: v[ 27]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 62: v[ 28]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 62: v[ 29]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 62: v[ 30]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 62: v[ 31]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 62: v[ 32]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 62: v[ 33]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 62: v[ 34]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 62: v[ 35]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 62: v[ 36]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 62: v[ 37]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 62: v[ 38]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 62: v[ 39]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 62: v[ 40]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 62: v[ 41]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 62: v[ 42]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 62: v[ 43]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 62: v[ 44]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 62: v[ 45]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 62: v[ 46]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 62: v[ 47]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 62: v[ 48]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 62: v[ 49]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 62: v[ 50]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 62: v[ 51]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 62: v[ 52]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 62: v[ 53]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 62: v[ 54]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 62: v[ 55]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 62: v[ 56]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 62: v[ 57]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 62: v[ 58]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 62: v[ 59]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 62: v[ 60]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 62: v[ 61]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 62: v[ 62]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 62: v[ 63]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 62: v[ 64]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 62: v[ 65]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 62: v[ 66]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 62: v[ 67]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 62: v[ 68]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 62: v[ 69]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 62: v[ 70]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 62: v[ 71]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 62: v[ 72]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 62: v[ 73]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 62: v[ 74]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 62: v[ 75]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 62: v[ 76]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 62: v[ 77]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 62: v[ 78]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 62: v[ 79]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 62: v[ 80]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 62: v[ 81]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 62: v[ 82]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 62: v[ 83]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 62: v[ 84]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 62: v[ 85]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 62: v[ 86]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 62: v[ 87]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 62: v[ 88]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 62: v[ 89]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 62: v[ 90]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 62: v[ 91]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 62: v[ 92]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 62: v[ 93]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 62: v[ 94]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 62: v[ 95]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 62: v[ 96]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 62: v[ 97]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 62: v[ 98]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 62: v[ 99]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 62: v[ 100]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 62: v[ 101]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 62: v[ 102]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 62: v[ 103]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 62: v[ 104]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 62: v[ 105]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 62: v[ 106]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 62: v[ 107]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 62: v[ 108]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 62: v[ 109]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 62: v[ 110]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 62: v[ 111]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 62: v[ 112]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 62: v[ 113]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 62: v[ 114]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 62: v[ 115]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 62: v[ 116]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 62: v[ 117]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 62: v[ 118]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 62: v[ 119]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 62: v[ 120]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 62: v[ 121]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 62: v[ 122]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 62: v[ 123]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 62: v[ 124]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 62: v[ 125]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 62: v[ 126]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 62: v[ 127]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 62: v[ 128]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 62: v[ 129]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 62: v[ 130]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 62: v[ 131]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 62: v[ 132]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 62: v[ 133]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 62: v[ 134]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 62: v[ 135]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 62: v[ 136]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 62: v[ 137]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 62: v[ 138]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 62: v[ 139]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 62: v[ 140]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 62: v[ 141]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 62: v[ 142]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 62: v[ 143]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 62: v[ 144]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 62: v[ 145]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 62: v[ 146]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 62: v[ 147]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 62: v[ 148]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 62: v[ 149]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 62: v[ 150]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 62: v[ 151]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 62: v[ 152]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 62: v[ 153]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 62: v[ 154]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 62: v[ 155]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 62: Group statistics 62: T-Coupling : 156 (total 156 atoms) 62: Energy Mon. : 156 (total 156 atoms) 62: Acc. not used: 156 (total 156 atoms) 62: Freeze : 156 (total 156 atoms) 62: User1 : 156 (total 156 atoms) 62: User2 : 156 (total 156 atoms) 62: VCM : 156 (total 156 atoms) 62: Compressed X: 156 (total 156 atoms) 62: Or. Res. Fit: 156 (total 156 atoms) 62: QMMM : 156 (total 156 atoms) 62: [ OK ] DumpTest.WorksWithTpr (41 ms) 62: [ RUN ] DumpTest.WorksWithTprAndMdpWriting 62: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/tools/tests/Testing/Temporary/DumpTest_lysozyme.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 62: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/tools/tests/Testing/Temporary/DumpTest_lysozyme.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 62: [ OK ] DumpTest.WorksWithTprAndMdpWriting (18 ms) 62: [----------] 2 tests from DumpTest (59 ms total) 62: 62: [----------] 3 tests from HelpwritingTest 62: [ RUN ] HelpwritingTest.ConvertTprWritesHelp 62: [ OK ] HelpwritingTest.ConvertTprWritesHelp (2 ms) 62: [ RUN ] HelpwritingTest.DumpWritesHelp 62: [ OK ] HelpwritingTest.DumpWritesHelp (7 ms) 62: [ RUN ] HelpwritingTest.ReportMethodsWritesHelp 62: [ OK ] HelpwritingTest.ReportMethodsWritesHelp (1 ms) 62: [----------] 3 tests from HelpwritingTest (11 ms total) 62: 62: [----------] 7 tests from GmxMakeNdx 62: [ RUN ] GmxMakeNdx.WritesDefaultProteinIndexGroups 62: 62: Reading structure file 62: Going to read 0 old index file(s) 62: Analysing residue names: 62: There are: 16 Protein residues 62: Analysing Protein... 62: 62: 0 System : 256 atoms 62: 1 Protein : 256 atoms 62: 2 Protein-H : 139 atoms 62: 3 C-alpha : 16 atoms 62: 4 Backbone : 48 atoms 62: 5 MainChain : 63 atoms 62: 6 MainChain+Cb : 78 atoms 62: 7 MainChain+H : 81 atoms 62: 8 SideChain : 175 atoms 62: 9 SideChain-H : 76 atoms 62: 62: nr : group '!': not 'name' nr name 'splitch' nr Enter: list groups 62: 'a': atom '&': and 'del' nr 'splitres' nr 'l': list residues 62: 't': atom type '|': or 'keep' nr 'splitat' nr 'h': help 62: 'r': residue 'res' nr 'chain' char 62: "name": group 'case': case sensitive 'q': save and quit 62: 'ri': residue index 62: 62: > 62: [ OK ] GmxMakeNdx.WritesDefaultProteinIndexGroups (36 ms) 62: [ RUN ] GmxMakeNdx.HandlesNoStructureInput 62: Going to read 1 old index file(s) 62: Deducing 22 atoms in the system from indices in the index file 62: 62: 0 System : 22 atoms 62: 1 Protein : 22 atoms 62: 2 Protein-H : 10 atoms 62: 3 C-alpha : 1 atoms 62: 4 Backbone : 5 atoms 62: 5 MainChain : 7 atoms 62: 6 MainChain+Cb : 8 atoms 62: 7 MainChain+H : 9 atoms 62: 8 SideChain : 13 atoms 62: 9 SideChain-H : 3 atoms 62: 10 CA : 1 atoms 62: 11 C_&_r_1 : 1 atoms 62: 12 C_&_r_2 : 1 atoms 62: 13 N_&_r_2 : 1 atoms 62: 14 N_&_r_3 : 1 atoms 62: 62: nr : group '!': not 'name' nr name 'splitch' nr Enter: list groups 62: 'a': atom '&': and 'del' nr 'splitres' nr 'l': list residues 62: 't': atom type '|': or 'keep' nr 'splitat' nr 'h': help 62: 'r': residue 'res' nr 'chain' char 62: "name": group 'case': case sensitive 'q': save and quit 62: 'ri': residue index 62: 62: > 62: Copied index group 1 'Protein' 62: Copied index group 2 'Protein-H' 62: Merged two groups with OR: 22 10 -> 22 62: 62: > 62: [ OK ] GmxMakeNdx.HandlesNoStructureInput (10 ms) 62: [ RUN ] GmxMakeNdx.HandlesNotProtein 62: Going to read 1 old index file(s) 62: Deducing 6 atoms in the system from indices in the index file 62: 62: 0 System : 6 atoms 62: 62: nr : group '!': not 'name' nr name 'splitch' nr Enter: list groups 62: 'a': atom '&': and 'del' nr 'splitres' nr 'l': list residues 62: 't': atom type '|': or 'keep' nr 'splitat' nr 'h': help 62: 'r': residue 'res' nr 'chain' char 62: "name": group 'case': case sensitive 'q': save and quit 62: 'ri': residue index 62: 62: > 62: [ OK ] GmxMakeNdx.HandlesNotProtein (7 ms) 62: [ RUN ] GmxMakeNdx.HandlesEmptyIndexResult 62: Going to read 1 old index file(s) 62: Deducing 22 atoms in the system from indices in the index file 62: 62: 0 System : 22 atoms 62: 1 Protein : 22 atoms 62: 2 Protein-H : 10 atoms 62: 3 C-alpha : 1 atoms 62: 4 Backbone : 5 atoms 62: 5 MainChain : 7 atoms 62: 6 MainChain+Cb : 8 atoms 62: 7 MainChain+H : 9 atoms 62: 8 SideChain : 13 atoms 62: 9 SideChain-H : 3 atoms 62: 10 CA : 1 atoms 62: 11 C_&_r_1 : 1 atoms 62: 12 C_&_r_2 : 1 atoms 62: 13 N_&_r_2 : 1 atoms 62: 14 N_&_r_3 : 1 atoms 62: 62: nr : group '!': not 'name' nr name 'splitch' nr Enter: list groups 62: 'a': atom '&': and 'del' nr 'splitres' nr 'l': list residues 62: 't': atom type '|': or 'keep' nr 'splitat' nr 'h': help 62: 'r': residue 'res' nr 'chain' char 62: "name": group 'case': case sensitive 'q': save and quit 62: 'ri': residue index 62: 62: > 62: Copied index group 4 'Backbone' 62: Copied index group 8 'SideChain' 62: Merged two groups with AND: 5 13 -> 0 62: Group is empty 62: 62: > 62: [ OK ] GmxMakeNdx.HandlesEmptyIndexResult (12 ms) 62: [ RUN ] GmxMakeNdx.HandlesEmptyIndexFile 62: Going to read 1 old index file(s) 62: Deducing 6 atoms in the system from indices in the index file 62: 62: 0 System : 6 atoms 62: 62: nr : group '!': not 'name' nr name 'splitch' nr Enter: list groups 62: 'a': atom '&': and 'del' nr 'splitres' nr 'l': list residues 62: 't': atom type '|': or 'keep' nr 'splitat' nr 'h': help 62: 'r': residue 'res' nr 'chain' char 62: "name": group 'case': case sensitive 'q': save and quit 62: 'ri': residue index 62: 62: > 62: Removed group 0 'System' 62: 62: > 62: [ OK ] GmxMakeNdx.HandlesEmptyIndexFile (16 ms) 62: [ RUN ] GmxMakeNdx.Splitres 62: 62: Reading structure file 62: Going to read 0 old index file(s) 62: Analysing residue names: 62: There are: 2 Water residues 62: 62: 0 System : 6 atoms 62: 1 Water : 6 atoms 62: 2 SOL : 6 atoms 62: 62: nr : group '!': not 'name' nr name 'splitch' nr Enter: list groups 62: 'a': atom '&': and 'del' nr 'splitres' nr 'l': list residues 62: 't': atom type '|': or 'keep' nr 'splitat' nr 'h': help 62: 'r': residue 'res' nr 'chain' char 62: "name": group 'case': case sensitive 'q': save and quit 62: 'ri': residue index 62: 62: > 62: Splitting group 1 'Water' into residues 62: 62: > 62: [ OK ] GmxMakeNdx.Splitres (14 ms) 62: [ RUN ] GmxMakeNdx.Splitat 62: 62: Reading structure file 62: Going to read 0 old index file(s) 62: Analysing residue names: 62: There are: 2 Water residues 62: 62: 0 System : 6 atoms 62: 1 Water : 6 atoms 62: 2 SOL : 6 atoms 62: 62: nr : group '!': not 'name' nr name 'splitch' nr Enter: list groups 62: 'a': atom '&': and 'del' nr 'splitres' nr 'l': list residues 62: 't': atom type '|': or 'keep' nr 'splitat' nr 'h': help 62: 'r': residue 'res' nr 'chain' char 62: "name": group 'case': case sensitive 'q': save and quit 62: 'ri': residue index 62: 62: > 62: Splitting group 1 'Water' into atoms 62: 62: > 62: [ OK ] GmxMakeNdx.Splitat (10 ms) 62: [----------] 7 tests from GmxMakeNdx (111 ms total) 62: 62: [----------] 4 tests from ReportMethodsTest 62: 62: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/tools/tests/Testing/Temporary/ReportMethodsTest_lysozyme.mdp]: 62: For a correct single-point energy evaluation with nsteps = 0, use 62: continuation = yes to avoid constraining the input coordinates. 62: 62: Generating 1-4 interactions: fudge = 0.5 62: 62: NOTE 2 [file lysozyme.top, line 1465]: 62: System has non-zero total charge: 2.000000 62: Total charge should normally be an integer. See 62: https://manual.gromacs.org/current/user-guide/floating-point.html 62: for discussion on how close it should be to an integer. 62: 62: 62: 62: Number of degrees of freedom in T-Coupling group rest is 465.00 62: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 62: 62: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/tools/tests/Testing/Temporary/ReportMethodsTest_lysozyme.mdp]: 62: NVE simulation with an initial temperature of zero: will use a Verlet 62: buffer of 10%. Check your energy drift! 62: 62: 62: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/tools/tests/Testing/Temporary/ReportMethodsTest_lysozyme.mdp]: 62: You are using a plain Coulomb cut-off, which might produce artifacts. 62: You might want to consider using PME electrostatics. 62: 62: 62: 62: There were 4 NOTEs 62: Setting the LD random seed to -1643380769 62: 62: Generated 330891 of the 330891 non-bonded parameter combinations 62: 62: Generated 330891 of the 330891 1-4 parameter combinations 62: 62: Excluding 3 bonded neighbours molecule type 'Protein_chain_B' 62: 62: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/lysozyme.pdb', all velocities are zero 62: Analysing residue names: 62: There are: 10 Protein residues 62: Analysing Protein... 62: 62: This run will generate roughly 0 Mb of data 62: [ RUN ] ReportMethodsTest.WritesCorrectHeadersFormated 62: [ OK ] ReportMethodsTest.WritesCorrectHeadersFormated (0 ms) 62: [ RUN ] ReportMethodsTest.WritesCorrectHeadersUnformatted 62: [ OK ] ReportMethodsTest.WritesCorrectHeadersUnformatted (0 ms) 62: [ RUN ] ReportMethodsTest.WritesCorrectInformation 62: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/tools/tests/Testing/Temporary/ReportMethodsTest_lysozyme.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 62: [ OK ] ReportMethodsTest.WritesCorrectInformation (4 ms) 62: [ RUN ] ReportMethodsTest.ToolEndToEndTest 62: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/tools/tests/Testing/Temporary/ReportMethodsTest_lysozyme.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 62: section: Methods 62: subsection: Simulation system 62: A system of 1 molecules (156 atoms) was simulated. 62: 62: subsection: Simulation settings 62: A total of 0 ns were simulated with a time step of 1 fs. 62: Neighbor searching was performed every 10 steps. 62: The Cut-off algorithm was used for electrostatic interactions. 62: with a cut-off of 1 nm. 62: A single cut-off of 1.1 nm was used for Van der Waals interactions. 62: [ OK ] ReportMethodsTest.ToolEndToEndTest (4 ms) 62: [----------] 4 tests from ReportMethodsTest (9 ms total) 62: 62: [----------] 4 tests from ConvertTprTest 62: [ RUN ] ConvertTprTest.ExtendRuntimeExtensionTest 62: 62: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/tools/tests/Testing/Temporary/ConvertTprTest_ExtendRuntimeExtensionTest_lysozyme.mdp]: 62: For a correct single-point energy evaluation with nsteps = 0, use 62: continuation = yes to avoid constraining the input coordinates. 62: 62: Generating 1-4 interactions: fudge = 0.5 62: 62: NOTE 2 [file lysozyme.top, line 1465]: 62: System has non-zero total charge: 2.000000 62: Total charge should normally be an integer. See 62: https://manual.gromacs.org/current/user-guide/floating-point.html 62: for discussion on how close it should be to an integer. 62: 62: 62: 62: Number of degrees of freedom in T-Coupling group rest is 465.00 62: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 62: 62: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/tools/tests/Testing/Temporary/ConvertTprTest_ExtendRuntimeExtensionTest_lysozyme.mdp]: 62: NVE simulation with an initial temperature of zero: will use a Verlet 62: buffer of 10%. Check your energy drift! 62: 62: 62: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/tools/tests/Testing/Temporary/ConvertTprTest_ExtendRuntimeExtensionTest_lysozyme.mdp]: 62: You are using a plain Coulomb cut-off, which might produce artifacts. 62: You might want to consider using PME electrostatics. 62: 62: 62: 62: There were 4 NOTEs 62: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/tools/tests/Testing/Temporary/ConvertTprTest_ExtendRuntimeExtensionTest_lysozyme.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 62: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/tools/tests/Testing/Temporary/ConvertTprTest_ExtendRuntimeExtensionTest_lysozyme.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 62: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/tools/tests/Testing/Temporary/ConvertTprTest_ExtendRuntimeExtensionTest_extended.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 62: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/tools/tests/Testing/Temporary/ConvertTprTest_ExtendRuntimeExtensionTest_extended.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 62: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/tools/tests/Testing/Temporary/ConvertTprTest_ExtendRuntimeExtensionTest_extended_again.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 62: Setting the LD random seed to -1116997635 62: 62: Generated 330891 of the 330891 non-bonded parameter combinations 62: 62: Generated 330891 of the 330891 1-4 parameter combinations 62: 62: Excluding 3 bonded neighbours molecule type 'Protein_chain_B' 62: 62: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/lysozyme.pdb', all velocities are zero 62: Analysing residue names: 62: There are: 10 Protein residues 62: Analysing Protein... 62: 62: This run will generate roughly 0 Mb of data 62: Input file: 62: Run start step 0 62: Run start time 0 ps 62: Step to be made during run 0 62: Runtime for the run 0 ps 62: Run end step 0 62: Run end time 0 ps 62: 62: Extending remaining runtime by 100 ps 62: 62: Output file: 62: Run start step 0 62: Run start time 0 ps 62: Step to be made during run 100000 62: Runtime for the run 100 ps 62: Run end step 100000 62: Run end time 100 ps 62: 62: Input file: 62: Run start step 0 62: Run start time 0 ps 62: Step to be made during run 100000 62: Runtime for the run 100 ps 62: Run end step 100000 62: Run end time 100 ps 62: 62: Extending remaining runtime by 100 ps 62: 62: Output file: 62: Run start step 0 62: Run start time 0 ps 62: Step to be made during run 200000 62: Runtime for the run 200 ps 62: Run end step 200000 62: Run end time 200 ps 62: 62: [ OK ] ConvertTprTest.ExtendRuntimeExtensionTest (4582 ms) 62: [ RUN ] ConvertTprTest.UntilRuntimeExtensionTest 62: 62: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/tools/tests/Testing/Temporary/ConvertTprTest_UntilRuntimeExtensionTest_lysozyme.mdp]: 62: For a correct single-point energy evaluation with nsteps = 0, use 62: continuation = yes to avoid constraining the input coordinates. 62: 62: Generating 1-4 interactions: fudge = 0.5 62: 62: NOTE 2 [file lysozyme.top, line 1465]: 62: System has non-zero total charge: 2.000000 62: Total charge should normally be an integer. See 62: https://manual.gromacs.org/current/user-guide/floating-point.html 62: for discussion on how close it should be to an integer. 62: 62: 62: 62: Number of degrees of freedom in T-Coupling group rest is 465.00 62: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 62: 62: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/tools/tests/Testing/Temporary/ConvertTprTest_UntilRuntimeExtensionTest_lysozyme.mdp]: 62: NVE simulation with an initial temperature of zero: will use a Verlet 62: buffer of 10%. Check your energy drift! 62: 62: 62: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/tools/tests/Testing/Temporary/ConvertTprTest_UntilRuntimeExtensionTest_lysozyme.mdp]: 62: You are using a plain Coulomb cut-off, which might produce artifacts. 62: You might want to consider using PME electrostatics. 62: 62: 62: 62: There were 4 NOTEs 62: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/tools/tests/Testing/Temporary/ConvertTprTest_UntilRuntimeExtensionTest_lysozyme.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 62: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/tools/tests/Testing/Temporary/ConvertTprTest_UntilRuntimeExtensionTest_lysozyme.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 62: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/tools/tests/Testing/Temporary/ConvertTprTest_UntilRuntimeExtensionTest_extended.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 62: Setting the LD random seed to 2017308667 62: 62: Generated 330891 of the 330891 non-bonded parameter combinations 62: 62: Generated 330891 of the 330891 1-4 parameter combinations 62: 62: Excluding 3 bonded neighbours molecule type 'Protein_chain_B' 62: 62: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/lysozyme.pdb', all velocities are zero 62: Analysing residue names: 62: There are: 10 Protein residues 62: Analysing Protein... 62: 62: This run will generate roughly 0 Mb of data 62: Input file: 62: Run start step 0 62: Run start time 0 ps 62: Step to be made during run 0 62: Runtime for the run 0 ps 62: Run end step 0 62: Run end time 0 ps 62: 62: Extending remaining runtime to 100 ps 62: 62: Output file: 62: Run start step 0 62: Run start time 0 ps 62: Step to be made during run 100000 62: Runtime for the run 100 ps 62: Run end step 100000 62: Run end time 100 ps 62: 62: [ OK ] ConvertTprTest.UntilRuntimeExtensionTest (4515 ms) 62: [ RUN ] ConvertTprTest.nstepRuntimeExtensionTest 62: 62: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/tools/tests/Testing/Temporary/ConvertTprTest_nstepRuntimeExtensionTest_lysozyme.mdp]: 62: For a correct single-point energy evaluation with nsteps = 0, use 62: continuation = yes to avoid constraining the input coordinates. 62: 62: Generating 1-4 interactions: fudge = 0.5 62: 62: NOTE 2 [file lysozyme.top, line 1465]: 62: System has non-zero total charge: 2.000000 62: Total charge should normally be an integer. See 62: https://manual.gromacs.org/current/user-guide/floating-point.html 62: for discussion on how close it should be to an integer. 62: 62: 62: 62: Number of degrees of freedom in T-Coupling group rest is 465.00 62: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 62: 62: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/tools/tests/Testing/Temporary/ConvertTprTest_nstepRuntimeExtensionTest_lysozyme.mdp]: 62: NVE simulation with an initial temperature of zero: will use a Verlet 62: buffer of 10%. Check your energy drift! 62: 62: 62: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/tools/tests/Testing/Temporary/ConvertTprTest_nstepRuntimeExtensionTest_lysozyme.mdp]: 62: You are using a plain Coulomb cut-off, which might produce artifacts. 62: You might want to consider using PME electrostatics. 62: 62: 62: 62: There were 4 NOTEs 62: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/tools/tests/Testing/Temporary/ConvertTprTest_nstepRuntimeExtensionTest_lysozyme.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 62: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/tools/tests/Testing/Temporary/ConvertTprTest_nstepRuntimeExtensionTest_lysozyme.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 62: Setting nsteps to 102 62: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/tools/tests/Testing/Temporary/ConvertTprTest_nstepRuntimeExtensionTest_extended.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 62: Setting the LD random seed to -1262508033 62: 62: Generated 330891 of the 330891 non-bonded parameter combinations 62: 62: Generated 330891 of the 330891 1-4 parameter combinations 62: 62: Excluding 3 bonded neighbours molecule type 'Protein_chain_B' 62: 62: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/lysozyme.pdb', all velocities are zero 62: Analysing residue names: 62: There are: 10 Protein residues 62: Analysing Protein... 62: 62: This run will generate roughly 0 Mb of data 62: Input file: 62: Run start step 0 62: Run start time 0 ps 62: Step to be made during run 0 62: Runtime for the run 0 ps 62: Run end step 0 62: Run end time 0 ps 62: 62: 62: Output file: 62: Run start step 0 62: Run start time 0 ps 62: Step to be made during run 102 62: Runtime for the run 0.102 ps 62: Run end step 102 62: Run end time 0.102 ps 62: 62: [ OK ] ConvertTprTest.nstepRuntimeExtensionTest (4608 ms) 62: [ RUN ] ConvertTprTest.generateVelocitiesTest 62: 62: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/tools/tests/Testing/Temporary/ConvertTprTest_generateVelocitiesTest_lysozyme.mdp]: 62: For a correct single-point energy evaluation with nsteps = 0, use 62: continuation = yes to avoid constraining the input coordinates. 62: 62: Generating 1-4 interactions: fudge = 0.5 62: 62: NOTE 2 [file lysozyme.top, line 1465]: 62: System has non-zero total charge: 2.000000 62: Total charge should normally be an integer. See 62: https://manual.gromacs.org/current/user-guide/floating-point.html 62: for discussion on how close it should be to an integer. 62: 62: 62: 62: Number of degrees of freedom in T-Coupling group rest is 465.00 62: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 62: 62: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/tools/tests/Testing/Temporary/ConvertTprTest_generateVelocitiesTest_lysozyme.mdp]: 62: NVE simulation with an initial temperature of zero: will use a Verlet 62: buffer of 10%. Check your energy drift! 62: 62: 62: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/tools/tests/Testing/Temporary/ConvertTprTest_generateVelocitiesTest_lysozyme.mdp]: 62: You are using a plain Coulomb cut-off, which might produce artifacts. 62: You might want to consider using PME electrostatics. 62: 62: 62: 62: There were 4 NOTEs 62: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/tools/tests/Testing/Temporary/ConvertTprTest_generateVelocitiesTest_lysozyme.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 62: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/tools/tests/Testing/Temporary/ConvertTprTest_generateVelocitiesTest_lysozyme.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 62: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/tools/tests/Testing/Temporary/ConvertTprTest_generateVelocitiesTest_new_velocities.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 62: Setting the LD random seed to 1063103090 62: 62: Generated 330891 of the 330891 non-bonded parameter combinations 62: 62: Generated 330891 of the 330891 1-4 parameter combinations 62: 62: Excluding 3 bonded neighbours molecule type 'Protein_chain_B' 62: 62: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/lysozyme.pdb', all velocities are zero 62: Analysing residue names: 62: There are: 10 Protein residues 62: Analysing Protein... 62: 62: This run will generate roughly 0 Mb of data 62: [ OK ] ConvertTprTest.generateVelocitiesTest (4625 ms) 62: [----------] 4 tests from ConvertTprTest (18333 ms total) 62: 62: [----------] 1 test from ConvertTprNoVelocityTest 62: [ RUN ] ConvertTprNoVelocityTest.refuseToGenerateVelocitiesWhenTprDidNotHaveVelocitiesInitiallyTest 62: 62: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/tools/tests/Testing/Temporary/ConvertTprNoVelocityTest_refuseToGenerateVelocitiesWhenTprDidNotHaveVelocitiesInitiallyTest_lysozyme.mdp]: 62: For a correct single-point energy evaluation with nsteps = 0, use 62: continuation = yes to avoid constraining the input coordinates. 62: 62: Generating 1-4 interactions: fudge = 0.5 62: 62: NOTE 2 [file lysozyme.top, line 1465]: 62: System has non-zero total charge: 2.000000 62: Total charge should normally be an integer. See 62: https://manual.gromacs.org/current/user-guide/floating-point.html 62: for discussion on how close it should be to an integer. 62: 62: 62: 62: 62: NOTE 3 [file lysozyme.top, line 1465]: 62: Zero-step energy minimization will alter the coordinates before 62: calculating the energy. If you just want the energy of a single point, 62: try zero-step MD (with unconstrained_start = yes). To do multiple 62: single-point energy evaluations of different configurations of the same 62: topology, use mdrun -rerun. 62: 62: Number of degrees of freedom in T-Coupling group rest is 465.00 62: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 62: 62: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/tools/tests/Testing/Temporary/ConvertTprNoVelocityTest_refuseToGenerateVelocitiesWhenTprDidNotHaveVelocitiesInitiallyTest_lysozyme.mdp]: 62: You are using a plain Coulomb cut-off, which might produce artifacts. 62: You might want to consider using PME electrostatics. 62: 62: 62: 62: There were 4 NOTEs 62: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/tools/tests/Testing/Temporary/ConvertTprNoVelocityTest_refuseToGenerateVelocitiesWhenTprDidNotHaveVelocitiesInitiallyTest_lysozyme.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 62: Setting the LD random seed to -211288125 62: 62: Generated 330891 of the 330891 non-bonded parameter combinations 62: 62: Generated 330891 of the 330891 1-4 parameter combinations 62: 62: Excluding 3 bonded neighbours molecule type 'Protein_chain_B' 62: Analysing residue names: 62: There are: 10 Protein residues 62: Analysing Protein... 62: 62: This run will generate roughly 0 Mb of data 62: [ OK ] ConvertTprNoVelocityTest.refuseToGenerateVelocitiesWhenTprDidNotHaveVelocitiesInitiallyTest (4598 ms) 62: [----------] 1 test from ConvertTprNoVelocityTest (4598 ms total) 62: 62: [----------] 12 tests from Works/TrjconvWithDifferentInputFormats 62: [ RUN ] Works/TrjconvWithDifferentInputFormats.WithIndexGroupSubset/file_spc2_traj_trr 62: Will write trr: Trajectory in portable xdr format 62: Group 0 ( System) has 6 elements 62: Group 1 (FirstWaterMolecule) has 3 elements 62: Group 2 (SecondWaterMolecule) has 3 elements 62: Select a group: trr version: GMX_trn_file (single precision) 62: Reading frame 0 time 0.000 Reading frame 1 time 1.000 -> frame 0 time 0.000 Last frame 1 time 1.000 62: -> frame 1 time 1.000 62: Last written: frame 1 time 1.000 62: 62: 62: Note that major changes are planned in future for trjconv, to improve usability and utility. 62: Select group for output 62: Selected 2: 'SecondWaterMolecule' 62: [ OK ] Works/TrjconvWithDifferentInputFormats.WithIndexGroupSubset/file_spc2_traj_trr (5 ms) 62: [ RUN ] Works/TrjconvWithDifferentInputFormats.WithIndexGroupSubset/file_spc2_traj_tng 62: Will write trr: Trajectory in portable xdr format 62: Group 0 ( System) has 6 elements 62: Group 1 (FirstWaterMolecule) has 3 elements 62: Group 2 (SecondWaterMolecule) has 3 elements 62: Select a group: Reading frame 0 time 0.000 62: Precision of /build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/spc2-traj.tng is 0.001 (nm) 62: Reading frame 1 time 1.000 -> frame 0 time 0.000 Last frame 1 time 1.000 62: -> frame 1 time 1.000 62: Last written: frame 1 time 1.000 62: 62: 62: Note that major changes are planned in future for trjconv, to improve usability and utility. 62: Select group for output 62: Selected 2: 'SecondWaterMolecule' 62: [ OK ] Works/TrjconvWithDifferentInputFormats.WithIndexGroupSubset/file_spc2_traj_tng (5 ms) 62: [ RUN ] Works/TrjconvWithDifferentInputFormats.WithIndexGroupSubset/file_spc2_traj_xtc 62: Will write trr: Trajectory in portable xdr format 62: Group 0 ( System) has 6 elements 62: Group 1 (FirstWaterMolecule) has 3 elements 62: Group 2 (SecondWaterMolecule) has 3 elements 62: Select a group: Reading frame 0 time 0.000 Reading frame 1 time 1.000 -> frame 0 time 0.000 Last frame 1 time 1.000 62: -> frame 1 time 1.000 62: Last written: frame 1 time 1.000 62: 62: 62: Note that major changes are planned in future for trjconv, to improve usability and utility. 62: Select group for output 62: Selected 2: 'SecondWaterMolecule' 62: [ OK ] Works/TrjconvWithDifferentInputFormats.WithIndexGroupSubset/file_spc2_traj_xtc (4 ms) 62: [ RUN ] Works/TrjconvWithDifferentInputFormats.WithIndexGroupSubset/file_spc2_traj_gro 62: Will write trr: Trajectory in portable xdr format 62: Group 0 ( System) has 6 elements 62: Group 1 (FirstWaterMolecule) has 3 elements 62: Group 2 (SecondWaterMolecule) has 3 elements 62: Select a group: Reading frames from gro file 'Generated by trjconv t= 0.00000 step= 0', 6 atoms. 62: Reading frame 0 time 0.000 62: Precision of /build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/spc2-traj.gro is 0.001 (nm) 62: Reading frame 1 time 1.000 -> frame 0 time 0.000 Last frame 1 time 1.000 62: -> frame 1 time 1.000 62: Last written: frame 1 time 1.000 62: 62: 62: Note that major changes are planned in future for trjconv, to improve usability and utility. 62: Select group for output 62: Selected 2: 'SecondWaterMolecule' 62: [ OK ] Works/TrjconvWithDifferentInputFormats.WithIndexGroupSubset/file_spc2_traj_gro (4 ms) 62: [ RUN ] Works/TrjconvWithDifferentInputFormats.WithIndexGroupSubset/file_spc2_traj_pdb 62: Will write trr: Trajectory in portable xdr format 62: Group 0 ( System) has 6 elements 62: Group 1 (FirstWaterMolecule) has 3 elements 62: Group 2 (SecondWaterMolecule) has 3 elements 62: Select a group: Reading frames from pdb file Reading frame 0 time 0.000 62: Precision of /build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/spc2-traj.pdb is 0.0001 (nm) 62: 'Generated by trjconv t= 1.00000 step= 1', 6 atoms 62: Reading frame 1 time 1.000 -> frame 0 time 0.000 Last frame 1 time 1.000 62: -> frame 1 time 1.000 62: Last written: frame 1 time 1.000 62: 62: 62: Note that major changes are planned in future for trjconv, to improve usability and utility. 62: Select group for output 62: Selected 2: 'SecondWaterMolecule' 62: [ OK ] Works/TrjconvWithDifferentInputFormats.WithIndexGroupSubset/file_spc2_traj_pdb (4 ms) 62: [ RUN ] Works/TrjconvWithDifferentInputFormats.WithIndexGroupSubset/file_spc2_traj_g96 62: Will write trr: Trajectory in portable xdr format 62: Group 0 ( System) has 6 elements 62: Group 1 (FirstWaterMolecule) has 3 elements 62: Group 2 (SecondWaterMolecule) has 3 elements 62: Select a group: Reading frame 0 time 0.000 Reading frame 1 time 1.000 -> frame 0 time 0.000 Last frame 1 time 1.000 62: -> frame 1 time 1.000 62: Last written: frame 1 time 1.000 62: 62: 62: Note that major changes are planned in future for trjconv, to improve usability and utility. 62: Select group for output 62: Selected 2: 'SecondWaterMolecule' 62: [ OK ] Works/TrjconvWithDifferentInputFormats.WithIndexGroupSubset/file_spc2_traj_g96 (4 ms) 62: [ RUN ] Works/TrjconvWithDifferentInputFormats.WithoutTopologyFile/file_spc2_traj_trr 62: Will write trr: Trajectory in portable xdr format 62: Group 0 ( System) has 6 elements 62: Group 1 (FirstWaterMolecule) has 3 elements 62: Group 2 (SecondWaterMolecule) has 3 elements 62: Select a group: Reading frame 0 time 0.000 Reading frame 1 time 1.000 -> frame 0 time 0.000 Last frame 1 time 1.000 62: -> frame 1 time 1.000 62: Last written: frame 1 time 1.000 62: 62: 62: Note that major changes are planned in future for trjconv, to improve usability and utility. 62: Select group for output 62: Selected 2: 'SecondWaterMolecule' 62: [ OK ] Works/TrjconvWithDifferentInputFormats.WithoutTopologyFile/file_spc2_traj_trr (3 ms) 62: [ RUN ] Works/TrjconvWithDifferentInputFormats.WithoutTopologyFile/file_spc2_traj_tng 62: Will write trr: Trajectory in portable xdr format 62: Group 0 ( System) has 6 elements 62: Group 1 (FirstWaterMolecule) has 3 elements 62: Group 2 (SecondWaterMolecule) has 3 elements 62: Select a group: Reading frame 0 time 0.000 62: Precision of /build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/spc2-traj.tng is 0.001 (nm) 62: Reading frame 1 time 1.000 -> frame 0 time 0.000 Last frame 1 time 1.000 62: -> frame 1 time 1.000 62: Last written: frame 1 time 1.000 62: 62: 62: Note that major changes are planned in future for trjconv, to improve usability and utility. 62: Select group for output 62: Selected 2: 'SecondWaterMolecule' 62: [ OK ] Works/TrjconvWithDifferentInputFormats.WithoutTopologyFile/file_spc2_traj_tng (4 ms) 62: [ RUN ] Works/TrjconvWithDifferentInputFormats.WithoutTopologyFile/file_spc2_traj_xtc 62: Will write trr: Trajectory in portable xdr format 62: Group 0 ( System) has 6 elements 62: Group 1 (FirstWaterMolecule) has 3 elements 62: Group 2 (SecondWaterMolecule) has 3 elements 62: Select a group: Reading frame 0 time 0.000 Reading frame 1 time 1.000 -> frame 0 time 0.000 Last frame 1 time 1.000 62: -> frame 1 time 1.000 62: Last written: frame 1 time 1.000 62: 62: 62: Note that major changes are planned in future for trjconv, to improve usability and utility. 62: Select group for output 62: Selected 2: 'SecondWaterMolecule' 62: [ OK ] Works/TrjconvWithDifferentInputFormats.WithoutTopologyFile/file_spc2_traj_xtc (3 ms) 62: [ RUN ] Works/TrjconvWithDifferentInputFormats.WithoutTopologyFile/file_spc2_traj_gro 62: Will write trr: Trajectory in portable xdr format 62: Group 0 ( System) has 6 elements 62: Group 1 (FirstWaterMolecule) has 3 elements 62: Group 2 (SecondWaterMolecule) has 3 elements 62: Select a group: Reading frames from gro file 'Generated by trjconv t= 0.00000 step= 0', 6 atoms. 62: Reading frame 0 time 0.000 62: Precision of /build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/spc2-traj.gro is 0.001 (nm) 62: Reading frame 1 time 1.000 -> frame 0 time 0.000 Last frame 1 time 1.000 62: -> frame 1 time 1.000 62: Last written: frame 1 time 1.000 62: 62: 62: Note that major changes are planned in future for trjconv, to improve usability and utility. 62: Select group for output 62: Selected 2: 'SecondWaterMolecule' 62: [ OK ] Works/TrjconvWithDifferentInputFormats.WithoutTopologyFile/file_spc2_traj_gro (3 ms) 62: [ RUN ] Works/TrjconvWithDifferentInputFormats.WithoutTopologyFile/file_spc2_traj_pdb 62: Will write trr: Trajectory in portable xdr format 62: Group 0 ( System) has 6 elements 62: Group 1 (FirstWaterMolecule) has 3 elements 62: Group 2 (SecondWaterMolecule) has 3 elements 62: Select a group: Reading frames from pdb file Reading frame 0 time 0.000 62: Precision of /build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/spc2-traj.pdb is 0.0001 (nm) 62: 'Generated by trjconv t= 1.00000 step= 1', 6 atoms 62: Reading frame 1 time 1.000 -> frame 0 time 0.000 Last frame 1 time 1.000 62: -> frame 1 time 1.000 62: Last written: frame 1 time 1.000 62: 62: 62: Note that major changes are planned in future for trjconv, to improve usability and utility. 62: Select group for output 62: Selected 2: 'SecondWaterMolecule' 62: [ OK ] Works/TrjconvWithDifferentInputFormats.WithoutTopologyFile/file_spc2_traj_pdb (3 ms) 62: [ RUN ] Works/TrjconvWithDifferentInputFormats.WithoutTopologyFile/file_spc2_traj_g96 62: Will write trr: Trajectory in portable xdr format 62: Group 0 ( System) has 6 elements 62: Group 1 (FirstWaterMolecule) has 3 elements 62: Group 2 (SecondWaterMolecule) has 3 elements 62: Select a group: Reading frame 0 time 0.000 Reading frame 1 time 1.000 -> frame 0 time 0.000 Last frame 1 time 1.000 62: -> frame 1 time 1.000 62: Last written: frame 1 time 1.000 62: 62: 62: Note that major changes are planned in future for trjconv, to improve usability and utility. 62: Select group for output 62: Selected 2: 'SecondWaterMolecule' 62: [ OK ] Works/TrjconvWithDifferentInputFormats.WithoutTopologyFile/file_spc2_traj_g96 (4 ms) 62: [----------] 12 tests from Works/TrjconvWithDifferentInputFormats (56 ms total) 62: 62: [----------] 30 tests from Works/TrjconvDumpTest 62: [ RUN ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_trr_dump_time__1_00 62: Will write trr: Trajectory in portable xdr format 62: Reading frame 0 time 0.000 Reading frame 0 time 0.000 Reading frame 1 time 1.000 62: Dumping frame at t= 0 ps 62: -> frame 0 time 0.000 62: Last written: frame 0 time 0.000 62: 62: 62: Note that major changes are planned in future for trjconv, to improve usability and utility. 62: [ OK ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_trr_dump_time__1_00 (2 ms) 62: [ RUN ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_trr_dump_time_0_00 62: Will write trr: Trajectory in portable xdr format 62: Reading frame 0 time 0.000 Reading frame 0 time 0.000 Reading frame 1 time 1.000 62: Dumping frame at t= 0 ps 62: -> frame 0 time 0.000 62: Last written: frame 0 time 0.000 62: 62: 62: Note that major changes are planned in future for trjconv, to improve usability and utility. 62: [ OK ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_trr_dump_time_0_00 (2 ms) 62: [ RUN ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_trr_dump_time_0_30 62: Will write trr: Trajectory in portable xdr format 62: Reading frame 0 time 0.000 Reading frame 0 time 0.000 Reading frame 1 time 1.000 Last frame 1 time 1.000 62: 62: Dumping frame at t= 0 ps 62: -> frame 0 time 0.000 62: Last written: frame 0 time 0.000 62: 62: 62: Note that major changes are planned in future for trjconv, to improve usability and utility. 62: [ OK ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_trr_dump_time_0_30 (2 ms) 62: [ RUN ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_trr_dump_time_1_00 62: Will write trr: Trajectory in portable xdr format 62: Reading frame 0 time 0.000 Reading frame 0 time 0.000 Reading frame 1 time 1.000 Last frame 1 time 1.000 62: 62: Dumping frame at t= 1 ps 62: -> frame 0 time 1.000 62: Last written: frame 0 time 1.000 62: 62: 62: Note that major changes are planned in future for trjconv, to improve usability and utility. 62: [ OK ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_trr_dump_time_1_00 (2 ms) 62: [ RUN ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_trr_dump_time_999999_00 62: Will write trr: Trajectory in portable xdr format 62: Reading frame 0 time 0.000 Reading frame 0 time 0.000 Reading frame 1 time 1.000 Last frame 1 time 1.000 62: 62: Dumping frame at t= 1 ps 62: -> frame 0 time 1.000 62: Last written: frame 0 time 1.000 62: 62: 62: Note that major changes are planned in future for trjconv, to improve usability and utility. 62: [ OK ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_trr_dump_time_999999_00 (2 ms) 62: [ RUN ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_tng_dump_time__1_00 62: Will write trr: Trajectory in portable xdr format 62: Reading frame 0 time 0.000 Reading frame 0 time 0.000 62: Precision of /build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/spc2-traj.tng is 0.001 (nm) 62: Reading frame 1 time 1.000 62: Dumping frame at t= 0 ps 62: -> frame 0 time 0.000 62: Last written: frame 0 time 0.000 62: 62: 62: Note that major changes are planned in future for trjconv, to improve usability and utility. 62: [ OK ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_tng_dump_time__1_00 (4 ms) 62: [ RUN ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_tng_dump_time_0_00 62: Will write trr: Trajectory in portable xdr format 62: Reading frame 0 time 0.000 Reading frame 0 time 0.000 62: Precision of /build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/spc2-traj.tng is 0.001 (nm) 62: Reading frame 1 time 1.000 62: Dumping frame at t= 0 ps 62: -> frame 0 time 0.000 62: Last written: frame 0 time 0.000 62: 62: 62: Note that major changes are planned in future for trjconv, to improve usability and utility. 62: [ OK ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_tng_dump_time_0_00 (4 ms) 62: [ RUN ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_tng_dump_time_0_30 62: Will write trr: Trajectory in portable xdr format 62: Reading frame 0 time 0.000 Reading frame 0 time 0.000 62: Precision of /build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/spc2-traj.tng is 0.001 (nm) 62: Reading frame 1 time 1.000 Last frame 1 time 1.000 62: 62: Dumping frame at t= 0 ps 62: -> frame 0 time 0.000 62: Last written: frame 0 time 0.000 62: 62: 62: Note that major changes are planned in future for trjconv, to improve usability and utility. 62: [ OK ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_tng_dump_time_0_30 (4 ms) 62: [ RUN ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_tng_dump_time_1_00 62: Will write trr: Trajectory in portable xdr format 62: Reading frame 0 time 0.000 Reading frame 0 time 0.000 62: Precision of /build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/spc2-traj.tng is 0.001 (nm) 62: Reading frame 1 time 1.000 Last frame 1 time 1.000 62: 62: Dumping frame at t= 1 ps 62: -> frame 0 time 1.000 62: Last written: frame 0 time 1.000 62: 62: 62: Note that major changes are planned in future for trjconv, to improve usability and utility. 62: [ OK ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_tng_dump_time_1_00 (4 ms) 62: [ RUN ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_tng_dump_time_999999_00 62: Will write trr: Trajectory in portable xdr format 62: Reading frame 0 time 0.000 Reading frame 0 time 0.000 62: Precision of /build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/spc2-traj.tng is 0.001 (nm) 62: Reading frame 1 time 1.000 Last frame 1 time 1.000 62: 62: Dumping frame at t= 1 ps 62: -> frame 0 time 1.000 62: Last written: frame 0 time 1.000 62: 62: 62: Note that major changes are planned in future for trjconv, to improve usability and utility. 62: [ OK ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_tng_dump_time_999999_00 (4 ms) 62: [ RUN ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_xtc_dump_time__1_00 62: Will write trr: Trajectory in portable xdr format 62: Reading frame 0 time 0.000 Reading frame 0 time 0.000 Reading frame 1 time 1.000 62: Dumping frame at t= 0 ps 62: -> frame 0 time 0.000 62: Last written: frame 0 time 0.000 62: 62: 62: Note that major changes are planned in future for trjconv, to improve usability and utility. 62: [ OK ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_xtc_dump_time__1_00 (2 ms) 62: [ RUN ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_xtc_dump_time_0_00 62: Will write trr: Trajectory in portable xdr format 62: Reading frame 0 time 0.000 Reading frame 0 time 0.000 Reading frame 1 time 1.000 62: Dumping frame at t= 0 ps 62: -> frame 0 time 0.000 62: Last written: frame 0 time 0.000 62: 62: 62: Note that major changes are planned in future for trjconv, to improve usability and utility. 62: [ OK ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_xtc_dump_time_0_00 (2 ms) 62: [ RUN ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_xtc_dump_time_0_30 62: Will write trr: Trajectory in portable xdr format 62: Reading frame 0 time 0.000 Reading frame 0 time 0.000 Reading frame 1 time 1.000 Last frame 1 time 1.000 62: 62: Dumping frame at t= 0 ps 62: -> frame 0 time 0.000 62: Last written: frame 0 time 0.000 62: 62: 62: Note that major changes are planned in future for trjconv, to improve usability and utility. 62: [ OK ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_xtc_dump_time_0_30 (2 ms) 62: [ RUN ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_xtc_dump_time_1_00 62: Will write trr: Trajectory in portable xdr format 62: Reading frame 0 time 0.000 Reading frame 0 time 0.000 Reading frame 1 time 1.000 Last frame 1 time 1.000 62: 62: Dumping frame at t= 1 ps 62: -> frame 0 time 1.000 62: Last written: frame 0 time 1.000 62: 62: 62: Note that major changes are planned in future for trjconv, to improve usability and utility. 62: [ OK ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_xtc_dump_time_1_00 (2 ms) 62: [ RUN ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_xtc_dump_time_999999_00 62: Will write trr: Trajectory in portable xdr format 62: Reading frame 0 time 0.000 Reading frame 0 time 0.000 Reading frame 1 time 1.000 Last frame 1 time 1.000 62: 62: Dumping frame at t= 1 ps 62: -> frame 0 time 1.000 62: Last written: frame 0 time 1.000 62: 62: 62: Note that major changes are planned in future for trjconv, to improve usability and utility. 62: [ OK ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_xtc_dump_time_999999_00 (2 ms) 62: [ RUN ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_gro_dump_time__1_00 62: Will write trr: Trajectory in portable xdr format 62: Reading frames from gro file 'Generated by trjconv t= 0.00000 step= 0', 6 atoms. 62: Reading frame 0 time 0.000 Reading frames from gro file 'Generated by trjconv t= 0.00000 step= 0', 6 atoms. 62: Reading frame 0 time 0.000 62: Precision of /build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/spc2-traj.gro is 0.001 (nm) 62: Reading frame 1 time 1.000 62: Dumping frame at t= 0 ps 62: -> frame 0 time 0.000 62: Last written: frame 0 time 0.000 62: 62: 62: Note that major changes are planned in future for trjconv, to improve usability and utility. 62: [ OK ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_gro_dump_time__1_00 (3 ms) 62: [ RUN ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_gro_dump_time_0_00 62: Will write trr: Trajectory in portable xdr format 62: Reading frames from gro file 'Generated by trjconv t= 0.00000 step= 0', 6 atoms. 62: Reading frame 0 time 0.000 Reading frames from gro file 'Generated by trjconv t= 0.00000 step= 0', 6 atoms. 62: Reading frame 0 time 0.000 62: Precision of /build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/spc2-traj.gro is 0.001 (nm) 62: Reading frame 1 time 1.000 62: Dumping frame at t= 0 ps 62: -> frame 0 time 0.000 62: Last written: frame 0 time 0.000 62: 62: 62: Note that major changes are planned in future for trjconv, to improve usability and utility. 62: [ OK ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_gro_dump_time_0_00 (3 ms) 62: [ RUN ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_gro_dump_time_0_30 62: Will write trr: Trajectory in portable xdr format 62: Reading frames from gro file 'Generated by trjconv t= 0.00000 step= 0', 6 atoms. 62: Reading frame 0 time 0.000 Reading frames from gro file 'Generated by trjconv t= 0.00000 step= 0', 6 atoms. 62: Reading frame 0 time 0.000 62: Precision of /build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/spc2-traj.gro is 0.001 (nm) 62: Reading frame 1 time 1.000 Last frame 1 time 1.000 62: 62: Dumping frame at t= 0 ps 62: -> frame 0 time 0.000 62: Last written: frame 0 time 0.000 62: 62: 62: Note that major changes are planned in future for trjconv, to improve usability and utility. 62: [ OK ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_gro_dump_time_0_30 (3 ms) 62: [ RUN ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_gro_dump_time_1_00 62: Will write trr: Trajectory in portable xdr format 62: Reading frames from gro file 'Generated by trjconv t= 0.00000 step= 0', 6 atoms. 62: Reading frame 0 time 0.000 Reading frames from gro file 'Generated by trjconv t= 0.00000 step= 0', 6 atoms. 62: Reading frame 0 time 0.000 62: Precision of /build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/spc2-traj.gro is 0.001 (nm) 62: Reading frame 1 time 1.000 Last frame 1 time 1.000 62: 62: Dumping frame at t= 1 ps 62: -> frame 0 time 1.000 62: Last written: frame 0 time 1.000 62: 62: 62: Note that major changes are planned in future for trjconv, to improve usability and utility. 62: [ OK ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_gro_dump_time_1_00 (3 ms) 62: [ RUN ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_gro_dump_time_999999_00 62: Will write trr: Trajectory in portable xdr format 62: Reading frames from gro file 'Generated by trjconv t= 0.00000 step= 0', 6 atoms. 62: Reading frame 0 time 0.000 Reading frames from gro file 'Generated by trjconv t= 0.00000 step= 0', 6 atoms. 62: Reading frame 0 time 0.000 62: Precision of /build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/spc2-traj.gro is 0.001 (nm) 62: Reading frame 1 time 1.000 Last frame 1 time 1.000 62: 62: Dumping frame at t= 1 ps 62: -> frame 0 time 1.000 62: Last written: frame 0 time 1.000 62: 62: 62: Note that major changes are planned in future for trjconv, to improve usability and utility. 62: [ OK ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_gro_dump_time_999999_00 (3 ms) 62: [ RUN ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_pdb_dump_time__1_00 62: Will write trr: Trajectory in portable xdr format 62: Reading frames from pdb file Reading frame 0 time 0.000 Reading frames from pdb file Reading frame 0 time 0.000 62: Precision of /build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/spc2-traj.pdb is 0.0001 (nm) 62: 'Generated by trjconv t= 1.00000 step= 1', 6 atoms 62: Reading frame 1 time 1.000 62: Dumping frame at t= 0 ps 62: -> frame 0 time 0.000 62: Last written: frame 0 time 0.000 62: 62: 62: Note that major changes are planned in future for trjconv, to improve usability and utility. 62: [ OK ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_pdb_dump_time__1_00 (3 ms) 62: [ RUN ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_pdb_dump_time_0_00 62: Will write trr: Trajectory in portable xdr format 62: Reading frames from pdb file Reading frame 0 time 0.000 Reading frames from pdb file Reading frame 0 time 0.000 62: Precision of /build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/spc2-traj.pdb is 0.0001 (nm) 62: 'Generated by trjconv t= 1.00000 step= 1', 6 atoms 62: Reading frame 1 time 1.000 62: Dumping frame at t= 0 ps 62: -> frame 0 time 0.000 62: Last written: frame 0 time 0.000 62: 62: 62: Note that major changes are planned in future for trjconv, to improve usability and utility. 62: [ OK ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_pdb_dump_time_0_00 (5 ms) 62: [ RUN ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_pdb_dump_time_0_30 62: Will write trr: Trajectory in portable xdr format 62: Reading frames from pdb file Reading frame 0 time 0.000 Reading frames from pdb file Reading frame 0 time 0.000 62: Precision of /build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/spc2-traj.pdb is 0.0001 (nm) 62: 'Generated by trjconv t= 1.00000 step= 1', 6 atoms 62: Reading frame 1 time 1.000 Last frame 1 time 1.000 62: 62: Dumping frame at t= 0 ps 62: -> frame 0 time 0.000 62: Last written: frame 0 time 0.000 62: 62: 62: Note that major changes are planned in future for trjconv, to improve usability and utility. 62: [ OK ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_pdb_dump_time_0_30 (3 ms) 62: [ RUN ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_pdb_dump_time_1_00 62: Will write trr: Trajectory in portable xdr format 62: Reading frames from pdb file Reading frame 0 time 0.000 Reading frames from pdb file Reading frame 0 time 0.000 62: Precision of /build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/spc2-traj.pdb is 0.0001 (nm) 62: 'Generated by trjconv t= 1.00000 step= 1', 6 atoms 62: Reading frame 1 time 1.000 Last frame 1 time 1.000 62: 62: Dumping frame at t= 1 ps 62: -> frame 0 time 1.000 62: Last written: frame 0 time 1.000 62: 62: 62: Note that major changes are planned in future for trjconv, to improve usability and utility. 62: [ OK ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_pdb_dump_time_1_00 (4 ms) 62: [ RUN ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_pdb_dump_time_999999_00 62: Will write trr: Trajectory in portable xdr format 62: Reading frames from pdb file Reading frame 0 time 0.000 Reading frames from pdb file Reading frame 0 time 0.000 62: Precision of /build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/spc2-traj.pdb is 0.0001 (nm) 62: 'Generated by trjconv t= 1.00000 step= 1', 6 atoms 62: Reading frame 1 time 1.000 Last frame 1 time 1.000 62: 62: Dumping frame at t= 1 ps 62: -> frame 0 time 1.000 62: Last written: frame 0 time 1.000 62: 62: 62: Note that major changes are planned in future for trjconv, to improve usability and utility. 62: [ OK ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_pdb_dump_time_999999_00 (3 ms) 62: [ RUN ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_g96_dump_time__1_00 62: Will write trr: Trajectory in portable xdr format 62: Reading frame 0 time 0.000 Reading frame 0 time 0.000 Reading frame 1 time 1.000 62: Dumping frame at t= 0 ps 62: -> frame 0 time 0.000 62: Last written: frame 0 time 0.000 62: 62: 62: Note that major changes are planned in future for trjconv, to improve usability and utility. 62: [ OK ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_g96_dump_time__1_00 (3 ms) 62: [ RUN ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_g96_dump_time_0_00 62: Will write trr: Trajectory in portable xdr format 62: Reading frame 0 time 0.000 Reading frame 0 time 0.000 Reading frame 1 time 1.000 62: Dumping frame at t= 0 ps 62: -> frame 0 time 0.000 62: Last written: frame 0 time 0.000 62: 62: 62: Note that major changes are planned in future for trjconv, to improve usability and utility. 62: [ OK ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_g96_dump_time_0_00 (3 ms) 62: [ RUN ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_g96_dump_time_0_30 62: Will write trr: Trajectory in portable xdr format 62: Reading frame 0 time 0.000 Reading frame 0 time 0.000 Reading frame 1 time 1.000 Last frame 1 time 1.000 62: 62: Dumping frame at t= 0 ps 62: -> frame 0 time 0.000 62: Last written: frame 0 time 0.000 62: 62: 62: Note that major changes are planned in future for trjconv, to improve usability and utility. 62: [ OK ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_g96_dump_time_0_30 (3 ms) 62: [ RUN ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_g96_dump_time_1_00 62: Will write trr: Trajectory in portable xdr format 62: Reading frame 0 time 0.000 Reading frame 0 time 0.000 Reading frame 1 time 1.000 Last frame 1 time 1.000 62: 62: Dumping frame at t= 1 ps 62: -> frame 0 time 1.000 62: Last written: frame 0 time 1.000 62: 62: 62: Note that major changes are planned in future for trjconv, to improve usability and utility. 62: [ OK ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_g96_dump_time_1_00 (3 ms) 62: [ RUN ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_g96_dump_time_999999_00 62: Will write trr: Trajectory in portable xdr format 62: Reading frame 0 time 0.000 Reading frame 0 time 0.000 Reading frame 1 time 1.000 Last frame 1 time 1.000 62: 62: Dumping frame at t= 1 ps 62: -> frame 0 time 1.000 62: Last written: frame 0 time 1.000 62: 62: 62: Note that major changes are planned in future for trjconv, to improve usability and utility. 62: [ OK ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_g96_dump_time_999999_00 (3 ms) 62: [----------] 30 tests from Works/TrjconvDumpTest (103 ms total) 62: 62: [----------] Global test environment tear-down 62: [==========] 63 tests from 8 test suites ran. (32627 ms total) 62: [ PASSED ] 63 tests. 62/92 Test #62: ToolUnitTests ............................. Passed 32.72 sec test 63 Start 63: ToolWithLeaksUnitTests 63: Test command: /build/reproducible-path/gromacs-2025.1/build/basic/bin/tool-test-with-leaks "--gtest_output=xml:/build/reproducible-path/gromacs-2025.1/build/basic/Testing/Temporary/ToolWithLeaksUnitTests.xml" 63: Working Directory: /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/tools/tests 63: Test timeout computed to be: 1920 63: [==========] Running 2 tests from 2 test suites. 63: [----------] Global test environment set-up. 63: [----------] 1 test from ConvertTprTest 63: [ RUN ] ConvertTprTest.selectIndexTest 63: 63: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/tools/tests/Testing/Temporary/ConvertTprTest_selectIndexTest_lysozyme.mdp]: 63: For a correct single-point energy evaluation with nsteps = 0, use 63: continuation = yes to avoid constraining the input coordinates. 63: 63: Generating 1-4 interactions: fudge = 0.5 63: 63: NOTE 2 [file lysozyme.top, line 1465]: 63: System has non-zero total charge: 2.000000 63: Total charge should normally be an integer. See 63: https://manual.gromacs.org/current/user-guide/floating-point.html 63: for discussion on how close it should be to an integer. 63: 63: 63: 63: Number of degrees of freedom in T-Coupling group rest is 465.00 63: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 63: 63: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/tools/tests/Testing/Temporary/ConvertTprTest_selectIndexTest_lysozyme.mdp]: 63: NVE simulation with an initial temperature of zero: will use a Verlet 63: buffer of 10%. Check your energy drift! 63: 63: 63: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/tools/tests/Testing/Temporary/ConvertTprTest_selectIndexTest_lysozyme.mdp]: 63: You are using a plain Coulomb cut-off, which might produce artifacts. 63: You might want to consider using PME electrostatics. 63: 63: 63: 63: There were 4 NOTEs 63: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/tools/tests/Testing/Temporary/ConvertTprTest_selectIndexTest_lysozyme.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 63: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/tools/tests/Testing/Temporary/ConvertTprTest_selectIndexTest_lysozyme.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 63: Group 0 ( System) has 156 elements 63: Group 1 ( Protein) has 156 elements 63: Group 2 ( Protein-H) has 75 elements 63: Group 3 ( C-alpha) has 10 elements 63: Group 4 ( Backbone) has 30 elements 63: Group 5 ( MainChain) has 40 elements 63: Group 6 ( MainChain+Cb) has 49 elements 63: Group 7 ( MainChain+H) has 52 elements 63: Group 8 ( SideChain) has 104 elements 63: Group 9 ( SideChain-H) has 35 elements 63: Select a group: Will write subset Protein-H of original tpx containing 75 atoms 63: Reduced ilist BONDS from 156 to 75 entries 63: Reduced ilist ANGLES from 281 to 98 entries 63: Reduced ilist PDIHS from 29 to 12 entries 63: Reduced ilist RBDIHS from 313 to 89 entries 63: Reduced ilist LJ14 from 399 to 107 entries 63: Reduced block excls from 156 to 75 index-, 1828 to 635 a-entries 63: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/tools/tests/Testing/Temporary/ConvertTprTest_selectIndexTest_extended.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 63: Setting the LD random seed to -1353818721 63: 63: Generated 330891 of the 330891 non-bonded parameter combinations 63: 63: Generated 330891 of the 330891 1-4 parameter combinations 63: 63: Excluding 3 bonded neighbours molecule type 'Protein_chain_B' 63: 63: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/lysozyme.pdb', all velocities are zero 63: Analysing residue names: 63: There are: 10 Protein residues 63: Analysing Protein... 63: 63: This run will generate roughly 0 Mb of data 63: Selected 2: 'Protein-H' 63: [ OK ] ConvertTprTest.selectIndexTest (4750 ms) 63: [----------] 1 test from ConvertTprTest (4750 ms total) 63: 63: [----------] 1 test from ConvertTprNoVelocityTest 63: [ RUN ] ConvertTprNoVelocityTest.selectIndexTestWithoutVelocity 63: 63: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/tools/tests/Testing/Temporary/ConvertTprNoVelocityTest_selectIndexTestWithoutVelocity_lysozyme.mdp]: 63: For a correct single-point energy evaluation with nsteps = 0, use 63: continuation = yes to avoid constraining the input coordinates. 63: 63: Generating 1-4 interactions: fudge = 0.5 63: 63: NOTE 2 [file lysozyme.top, line 1465]: 63: System has non-zero total charge: 2.000000 63: Total charge should normally be an integer. See 63: https://manual.gromacs.org/current/user-guide/floating-point.html 63: for discussion on how close it should be to an integer. 63: 63: 63: 63: 63: NOTE 3 [file lysozyme.top, line 1465]: 63: Zero-step energy minimization will alter the coordinates before 63: calculating the energy. If you just want the energy of a single point, 63: try zero-step MD (with unconstrained_start = yes). To do multiple 63: single-point energy evaluations of different configurations of the same 63: topology, use mdrun -rerun. 63: 63: Number of degrees of freedom in T-Coupling group rest is 465.00 63: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 63: 63: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/tools/tests/Testing/Temporary/ConvertTprNoVelocityTest_selectIndexTestWithoutVelocity_lysozyme.mdp]: 63: You are using a plain Coulomb cut-off, which might produce artifacts. 63: You might want to consider using PME electrostatics. 63: 63: 63: 63: There were 4 NOTEs 63: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/tools/tests/Testing/Temporary/ConvertTprNoVelocityTest_selectIndexTestWithoutVelocity_lysozyme.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 63: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/tools/tests/Testing/Temporary/ConvertTprNoVelocityTest_selectIndexTestWithoutVelocity_lysozyme.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 63: Group 0 ( System) has 156 elements 63: Group 1 ( Protein) has 156 elements 63: Group 2 ( Protein-H) has 75 elements 63: Group 3 ( C-alpha) has 10 elements 63: Group 4 ( Backbone) has 30 elements 63: Group 5 ( MainChain) has 40 elements 63: Group 6 ( MainChain+Cb) has 49 elements 63: Group 7 ( MainChain+H) has 52 elements 63: Group 8 ( SideChain) has 104 elements 63: Group 9 ( SideChain-H) has 35 elements 63: Select a group: Will write subset Protein-H of original tpx containing 75 atoms 63: Reduced ilist BONDS from 156 to 75 entries 63: Reduced ilist ANGLES from 281 to 98 entries 63: Reduced ilist PDIHS from 29 to 12 entries 63: Reduced ilist RBDIHS from 313 to 89 entries 63: Reduced ilist LJ14 from 399 to 107 entries 63: Reduced block excls from 156 to 75 index-, 1828 to 635 a-entries 63: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/tools/tests/Testing/Temporary/ConvertTprNoVelocityTest_selectIndexTestWithoutVelocity_extended.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 63: Setting the LD random seed to 2127075646 63: 63: Generated 330891 of the 330891 non-bonded parameter combinations 63: 63: Generated 330891 of the 330891 1-4 parameter combinations 63: 63: Excluding 3 bonded neighbours molecule type 'Protein_chain_B' 63: Analysing residue names: 63: There are: 10 Protein residues 63: Analysing Protein... 63: 63: This run will generate roughly 0 Mb of data 63: Selected 2: 'Protein-H' 63: [ OK ] ConvertTprNoVelocityTest.selectIndexTestWithoutVelocity (4664 ms) 63: [----------] 1 test from ConvertTprNoVelocityTest (4664 ms total) 63: 63: [----------] Global test environment tear-down 63: [==========] 2 tests from 2 test suites ran. (9415 ms total) 63: [ PASSED ] 2 tests. 63/92 Test #63: ToolWithLeaksUnitTests .................... Passed 9.49 sec test 64 Start 64: FileIOTests 64: Test command: /build/reproducible-path/gromacs-2025.1/build/basic/bin/fileio-test "--gtest_output=xml:/build/reproducible-path/gromacs-2025.1/build/basic/Testing/Temporary/FileIOTests.xml" 64: Working Directory: /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/fileio/tests 64: Test timeout computed to be: 30 64: [==========] Running 421 tests from 17 test suites. 64: [----------] Global test environment set-up. 64: [----------] 4 tests from Checkpoint 64: [ RUN ] Checkpoint.ReadingThrowsWhenValueNotPresent 64: [ OK ] Checkpoint.ReadingThrowsWhenValueNotPresent (0 ms) 64: [ RUN ] Checkpoint.ReadingDoesNotThrowWhenValuePresent 64: [ OK ] Checkpoint.ReadingDoesNotThrowWhenValuePresent (0 ms) 64: [ RUN ] Checkpoint.KvtRoundTripInt64 64: [ OK ] Checkpoint.KvtRoundTripInt64 (0 ms) 64: [ RUN ] Checkpoint.KvtRoundTripReal 64: [ OK ] Checkpoint.KvtRoundTripReal (0 ms) 64: [----------] 4 tests from Checkpoint (0 ms total) 64: 64: [----------] 1 test from StructureIOTest 64: [ RUN ] StructureIOTest.ReadTpsConfRetainsChainids 64: [ OK ] StructureIOTest.ReadTpsConfRetainsChainids (3 ms) 64: [----------] 1 test from StructureIOTest (3 ms total) 64: 64: [----------] 2 tests from FileMD5Test 64: [ RUN ] FileMD5Test.CanComputeMD5 64: [ OK ] FileMD5Test.CanComputeMD5 (6 ms) 64: [ RUN ] FileMD5Test.ReturnsErrorIfFileModeIsWrong 64: [ OK ] FileMD5Test.ReturnsErrorIfFileModeIsWrong (0 ms) 64: [----------] 2 tests from FileMD5Test (7 ms total) 64: 64: [----------] 4 tests from FileTypeTest 64: [ RUN ] FileTypeTest.CorrectValueForEmptyString 64: [ OK ] FileTypeTest.CorrectValueForEmptyString (0 ms) 64: [ RUN ] FileTypeTest.CorrectValueForNoExtension 64: [ OK ] FileTypeTest.CorrectValueForNoExtension (0 ms) 64: [ RUN ] FileTypeTest.CorrectValueForEmptyExtension 64: [ OK ] FileTypeTest.CorrectValueForEmptyExtension (0 ms) 64: [ RUN ] FileTypeTest.CorrectValueForLongExtensionWithStrangeCharacters 64: [ OK ] FileTypeTest.CorrectValueForLongExtensionWithStrangeCharacters (0 ms) 64: [----------] 4 tests from FileTypeTest (0 ms total) 64: 64: [----------] 4 tests from ColorMapTest 64: [ RUN ] ColorMapTest.CanReadFromFile 64: [ OK ] ColorMapTest.CanReadFromFile (1 ms) 64: [ RUN ] ColorMapTest.CanWriteToFile 64: [ OK ] ColorMapTest.CanWriteToFile (1 ms) 64: [ RUN ] ColorMapTest.RoundTrip 64: [ OK ] ColorMapTest.RoundTrip (1 ms) 64: [ RUN ] ColorMapTest.SearchWorks 64: [ OK ] ColorMapTest.SearchWorks (0 ms) 64: [----------] 4 tests from ColorMapTest (4 ms total) 64: 64: [----------] 4 tests from MatioTest 64: [ RUN ] MatioTest.CanWriteToFile 64: 33% 66%100%[ OK ] MatioTest.CanWriteToFile (0 ms) 64: [ RUN ] MatioTest.CanConvertToExistingRealMatrix 64: Converted a 4x3 matrix with 4 levels to reals 64: [ OK ] MatioTest.CanConvertToExistingRealMatrix (0 ms) 64: [ RUN ] MatioTest.CanConvertToNewRealMatrix 64: Converted a 4x3 matrix with 4 levels to reals 64: [ OK ] MatioTest.CanConvertToNewRealMatrix (0 ms) 64: [ RUN ] MatioTest.CanReadSingleMatrixAfterWriting 64: 33% 66%100% 33% 66%100%[ OK ] MatioTest.CanReadSingleMatrixAfterWriting (21 ms) 64: [----------] 4 tests from MatioTest (22 ms total) 64: 64: [----------] 3 tests from MrcSerializer 64: [ RUN ] MrcSerializer.DefaultHeaderValuesAreSet 64: [ OK ] MrcSerializer.DefaultHeaderValuesAreSet (0 ms) 64: [ RUN ] MrcSerializer.DefaultHeaderHasRightSerialSize 64: [ OK ] MrcSerializer.DefaultHeaderHasRightSerialSize (0 ms) 64: [ RUN ] MrcSerializer.DefaultHeaderIdenticalAfterRoundTrip 64: [ OK ] MrcSerializer.DefaultHeaderIdenticalAfterRoundTrip (0 ms) 64: [----------] 3 tests from MrcSerializer (0 ms total) 64: 64: [----------] 4 tests from MrcDensityMap 64: [ RUN ] MrcDensityMap.RoundTripIsIdempotent 64: [ OK ] MrcDensityMap.RoundTripIsIdempotent (0 ms) 64: [ RUN ] MrcDensityMap.ThrowsFileIOErrorWhenFileNotPresent 64: [ OK ] MrcDensityMap.ThrowsFileIOErrorWhenFileNotPresent (0 ms) 64: [ RUN ] MrcDensityMap.ReadsCoordinateTransformationFromFile 64: [ OK ] MrcDensityMap.ReadsCoordinateTransformationFromFile (0 ms) 64: [ RUN ] MrcDensityMap.ReadsDensityDataFromFile 64: [ OK ] MrcDensityMap.ReadsDensityDataFromFile (6 ms) 64: [----------] 4 tests from MrcDensityMap (9 ms total) 64: 64: [----------] 8 tests from MrcDensityMapHeaderTest 64: [ RUN ] MrcDensityMapHeaderTest.DataSizeIsZeroForDefaultHeader 64: [ OK ] MrcDensityMapHeaderTest.DataSizeIsZeroForDefaultHeader (0 ms) 64: [ RUN ] MrcDensityMapHeaderTest.DataSizeIsCorrect 64: [ OK ] MrcDensityMapHeaderTest.DataSizeIsCorrect (0 ms) 64: [ RUN ] MrcDensityMapHeaderTest.DataSizeThrowsWhenInvalid 64: [ OK ] MrcDensityMapHeaderTest.DataSizeThrowsWhenInvalid (0 ms) 64: [ RUN ] MrcDensityMapHeaderTest.GetsCorrectCoordinateTransformNoOriginGiven 64: [ OK ] MrcDensityMapHeaderTest.GetsCorrectCoordinateTransformNoOriginGiven (0 ms) 64: [ RUN ] MrcDensityMapHeaderTest.GetsCorrectCoordinateTransformWithOriginDefined 64: [ OK ] MrcDensityMapHeaderTest.GetsCorrectCoordinateTransformWithOriginDefined (0 ms) 64: [ RUN ] MrcDensityMapHeaderTest.GetsCorrectCoordinateTransformWithStartValues 64: [ OK ] MrcDensityMapHeaderTest.GetsCorrectCoordinateTransformWithStartValues (0 ms) 64: [ RUN ] MrcDensityMapHeaderTest.GetsCorrectExtents 64: [ OK ] MrcDensityMapHeaderTest.GetsCorrectExtents (0 ms) 64: [ RUN ] MrcDensityMapHeaderTest.IsSane 64: [ OK ] MrcDensityMapHeaderTest.IsSane (0 ms) 64: [----------] 8 tests from MrcDensityMapHeaderTest (0 ms total) 64: 64: [----------] 10 tests from ReadTest 64: [ RUN ] ReadTest.get_eint_ReadsInteger 64: [ OK ] ReadTest.get_eint_ReadsInteger (0 ms) 64: [ RUN ] ReadTest.get_eint_WarnsAboutFloat 64: 64: ERROR 1 [file unknown]: 64: Right hand side '0.8' for parameter 'test' in parameter file is not an 64: integer value 64: 64: 64: [ OK ] ReadTest.get_eint_WarnsAboutFloat (0 ms) 64: [ RUN ] ReadTest.get_eint_WarnsAboutString 64: 64: ERROR 1 [file unknown]: 64: Right hand side 'hello' for parameter 'test' in parameter file is not an 64: integer value 64: 64: 64: [ OK ] ReadTest.get_eint_WarnsAboutString (0 ms) 64: [ RUN ] ReadTest.get_eint64_ReadsInteger 64: [ OK ] ReadTest.get_eint64_ReadsInteger (0 ms) 64: [ RUN ] ReadTest.get_eint64_WarnsAboutFloat 64: 64: ERROR 1 [file unknown]: 64: Right hand side '0.8' for parameter 'test' in parameter file is not an 64: integer value 64: 64: 64: [ OK ] ReadTest.get_eint64_WarnsAboutFloat (0 ms) 64: [ RUN ] ReadTest.get_eint64_WarnsAboutString 64: 64: ERROR 1 [file unknown]: 64: Right hand side 'hello' for parameter 'test' in parameter file is not an 64: integer value 64: 64: 64: [ OK ] ReadTest.get_eint64_WarnsAboutString (0 ms) 64: [ RUN ] ReadTest.get_ereal_ReadsInteger 64: [ OK ] ReadTest.get_ereal_ReadsInteger (0 ms) 64: [ RUN ] ReadTest.get_ereal_ReadsFloat 64: [ OK ] ReadTest.get_ereal_ReadsFloat (0 ms) 64: [ RUN ] ReadTest.get_ereal_WarnsAboutString 64: 64: ERROR 1 [file unknown]: 64: Right hand side 'hello' for parameter 'test' in parameter file is not a 64: real value 64: 64: 64: [ OK ] ReadTest.get_ereal_WarnsAboutString (0 ms) 64: [ RUN ] ReadTest.setStringEntry_ReturnsCorrectString 64: [ OK ] ReadTest.setStringEntry_ReturnsCorrectString (0 ms) 64: [----------] 10 tests from ReadTest (0 ms total) 64: 64: [----------] 3 tests from TimeControlTest 64: [ RUN ] TimeControlTest.UnSetHasNoValue 64: [ OK ] TimeControlTest.UnSetHasNoValue (0 ms) 64: [ RUN ] TimeControlTest.CanSetValue 64: [ OK ] TimeControlTest.CanSetValue (0 ms) 64: [ RUN ] TimeControlTest.CanUnsetValueAgain 64: [ OK ] TimeControlTest.CanUnsetValueAgain (0 ms) 64: [----------] 3 tests from TimeControlTest (0 ms total) 64: 64: [----------] 1 test from FileIOXdrSerializerTest 64: [ RUN ] FileIOXdrSerializerTest.SizeIsCorrect 64: [ OK ] FileIOXdrSerializerTest.SizeIsCorrect (1 ms) 64: [----------] 1 test from FileIOXdrSerializerTest (1 ms total) 64: 64: [----------] 1 test from TngTest 64: [ RUN ] TngTest.CloseBeforeOpenIsNotFatal 64: [ OK ] TngTest.CloseBeforeOpenIsNotFatal (0 ms) 64: [----------] 1 test from TngTest (0 ms total) 64: 64: [----------] 4 tests from XvgioTest 64: [ RUN ] XvgioTest.readXvgIntWorks 64: [ OK ] XvgioTest.readXvgIntWorks (0 ms) 64: [ RUN ] XvgioTest.readXvgRealWorks 64: [ OK ] XvgioTest.readXvgRealWorks (0 ms) 64: [ RUN ] XvgioTest.readXvgIgnoreCommentLineWorks 64: [ OK ] XvgioTest.readXvgIgnoreCommentLineWorks (0 ms) 64: [ RUN ] XvgioTest.readXvgDeprecatedWorks 64: [ OK ] XvgioTest.readXvgDeprecatedWorks (0 ms) 64: [----------] 4 tests from XvgioTest (3 ms total) 64: 64: [----------] 4 tests from WithDifferentFormats/StructureIORoundtripTest 64: [ RUN ] WithDifferentFormats/StructureIORoundtripTest.ReadWriteTpsConf/0 64: [ OK ] WithDifferentFormats/StructureIORoundtripTest.ReadWriteTpsConf/0 (2 ms) 64: [ RUN ] WithDifferentFormats/StructureIORoundtripTest.ReadWriteTpsConf/1 64: [ OK ] WithDifferentFormats/StructureIORoundtripTest.ReadWriteTpsConf/1 (2 ms) 64: [ RUN ] WithDifferentFormats/StructureIORoundtripTest.ReadWriteTpsConf/2 64: [ OK ] WithDifferentFormats/StructureIORoundtripTest.ReadWriteTpsConf/2 (2 ms) 64: [ RUN ] WithDifferentFormats/StructureIORoundtripTest.ReadWriteTpsConf/3 64: [ OK ] WithDifferentFormats/StructureIORoundtripTest.ReadWriteTpsConf/3 (2 ms) 64: [----------] 4 tests from WithDifferentFormats/StructureIORoundtripTest (10 ms total) 64: 64: [----------] 360 tests from FileTypeMatch/FileTypeTest 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/0 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/0 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/1 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/1 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/2 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/2 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/3 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/3 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/4 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/4 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/5 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/5 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/6 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/6 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/7 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/7 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/8 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/8 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/9 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/9 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/10 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/10 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/11 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/11 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/12 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/12 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/13 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/13 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/14 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/14 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/15 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/15 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/16 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/16 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/17 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/17 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/18 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/18 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/19 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/19 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/20 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/20 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/21 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/21 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/22 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/22 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/23 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/23 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/24 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/24 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/25 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/25 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/26 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/26 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/27 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/27 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/28 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/28 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/29 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/29 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/30 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/30 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/31 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/31 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/32 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/32 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/33 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/33 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/34 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/34 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/35 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/35 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/36 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/36 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/37 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/37 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/38 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/38 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/39 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/39 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/40 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/40 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/41 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/41 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/42 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/42 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/43 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/43 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/44 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/44 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/45 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/45 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/46 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/46 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/47 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/47 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/48 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/48 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/49 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/49 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/50 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/50 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/51 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/51 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/52 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/52 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/53 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/53 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/54 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/54 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/55 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/55 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/56 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/56 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/57 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/57 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/58 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/58 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/59 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/59 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/60 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/60 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/61 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/61 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/62 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/62 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/63 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/63 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/64 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/64 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/65 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/65 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/66 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/66 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/67 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/67 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/68 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/68 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/69 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/69 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/70 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/70 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/71 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/71 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/72 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/72 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/73 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/73 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/74 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/74 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/75 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/75 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/76 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/76 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/77 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/77 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/78 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/78 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/79 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/79 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/80 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/80 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/81 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/81 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/82 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/82 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/83 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/83 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/84 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/84 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/85 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/85 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/86 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/86 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/87 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/87 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/88 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/88 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/89 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/89 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/90 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/90 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/91 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/91 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/92 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/92 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/93 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/93 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/94 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/94 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/95 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/95 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/96 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/96 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/97 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/97 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/98 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/98 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/99 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/99 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/100 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/100 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/101 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/101 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/102 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/102 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/103 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/103 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/104 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/104 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/105 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/105 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/106 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/106 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/107 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/107 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/108 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/108 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/109 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/109 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/110 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/110 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/111 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/111 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/112 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/112 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/113 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/113 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/114 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/114 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/115 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/115 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/116 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/116 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/117 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/117 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/118 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/118 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/119 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/119 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/120 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/120 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/121 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/121 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/122 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/122 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/123 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/123 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/124 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/124 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/125 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/125 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/126 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/126 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/127 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/127 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/128 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/128 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/129 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/129 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/130 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/130 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/131 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/131 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/132 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/132 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/133 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/133 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/134 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/134 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/135 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/135 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/136 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/136 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/137 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/137 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/138 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/138 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/139 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/139 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/140 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/140 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/141 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/141 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/142 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/142 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/143 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/143 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/144 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/144 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/145 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/145 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/146 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/146 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/147 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/147 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/148 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/148 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/149 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/149 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/150 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/150 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/151 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/151 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/152 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/152 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/153 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/153 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/154 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/154 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/155 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/155 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/156 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/156 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/157 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/157 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/158 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/158 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/159 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/159 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/160 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/160 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/161 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/161 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/162 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/162 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/163 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/163 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/164 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/164 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/165 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/165 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/166 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/166 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/167 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/167 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/168 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/168 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/169 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/169 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/170 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/170 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/171 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/171 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/172 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/172 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/173 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/173 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/174 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/174 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/175 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/175 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/176 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/176 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/177 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/177 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/178 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/178 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/179 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/179 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/0 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/0 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/1 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/1 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/2 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/2 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/3 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/3 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/4 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/4 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/5 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/5 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/6 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/6 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/7 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/7 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/8 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/8 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/9 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/9 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/10 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/10 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/11 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/11 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/12 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/12 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/13 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/13 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/14 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/14 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/15 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/15 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/16 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/16 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/17 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/17 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/18 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/18 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/19 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/19 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/20 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/20 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/21 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/21 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/22 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/22 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/23 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/23 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/24 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/24 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/25 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/25 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/26 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/26 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/27 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/27 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/28 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/28 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/29 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/29 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/30 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/30 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/31 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/31 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/32 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/32 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/33 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/33 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/34 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/34 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/35 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/35 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/36 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/36 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/37 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/37 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/38 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/38 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/39 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/39 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/40 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/40 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/41 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/41 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/42 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/42 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/43 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/43 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/44 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/44 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/45 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/45 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/46 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/46 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/47 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/47 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/48 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/48 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/49 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/49 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/50 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/50 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/51 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/51 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/52 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/52 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/53 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/53 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/54 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/54 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/55 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/55 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/56 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/56 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/57 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/57 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/58 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/58 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/59 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/59 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/60 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/60 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/61 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/61 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/62 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/62 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/63 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/63 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/64 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/64 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/65 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/65 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/66 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/66 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/67 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/67 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/68 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/68 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/69 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/69 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/70 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/70 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/71 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/71 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/72 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/72 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/73 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/73 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/74 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/74 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/75 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/75 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/76 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/76 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/77 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/77 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/78 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/78 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/79 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/79 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/80 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/80 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/81 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/81 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/82 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/82 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/83 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/83 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/84 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/84 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/85 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/85 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/86 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/86 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/87 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/87 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/88 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/88 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/89 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/89 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/90 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/90 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/91 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/91 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/92 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/92 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/93 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/93 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/94 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/94 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/95 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/95 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/96 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/96 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/97 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/97 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/98 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/98 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/99 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/99 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/100 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/100 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/101 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/101 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/102 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/102 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/103 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/103 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/104 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/104 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/105 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/105 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/106 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/106 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/107 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/107 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/108 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/108 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/109 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/109 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/110 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/110 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/111 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/111 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/112 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/112 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/113 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/113 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/114 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/114 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/115 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/115 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/116 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/116 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/117 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/117 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/118 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/118 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/119 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/119 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/120 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/120 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/121 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/121 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/122 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/122 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/123 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/123 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/124 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/124 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/125 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/125 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/126 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/126 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/127 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/127 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/128 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/128 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/129 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/129 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/130 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/130 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/131 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/131 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/132 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/132 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/133 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/133 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/134 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/134 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/135 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/135 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/136 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/136 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/137 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/137 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/138 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/138 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/139 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/139 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/140 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/140 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/141 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/141 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/142 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/142 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/143 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/143 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/144 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/144 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/145 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/145 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/146 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/146 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/147 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/147 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/148 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/148 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/149 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/149 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/150 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/150 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/151 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/151 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/152 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/152 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/153 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/153 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/154 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/154 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/155 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/155 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/156 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/156 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/157 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/157 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/158 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/158 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/159 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/159 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/160 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/160 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/161 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/161 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/162 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/162 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/163 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/163 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/164 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/164 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/165 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/165 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/166 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/166 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/167 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/167 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/168 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/168 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/169 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/169 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/170 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/170 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/171 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/171 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/172 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/172 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/173 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/173 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/174 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/174 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/175 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/175 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/176 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/176 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/177 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/177 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/178 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/178 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/179 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/179 (0 ms) 64: [----------] 360 tests from FileTypeMatch/FileTypeTest (16 ms total) 64: 64: [----------] 4 tests from XvgReadTimeSeries/XvgioTest 64: [ RUN ] XvgReadTimeSeries/XvgioTest.readXvgTimeSeriesWorks/0 64: [ OK ] XvgReadTimeSeries/XvgioTest.readXvgTimeSeriesWorks/0 (1 ms) 64: [ RUN ] XvgReadTimeSeries/XvgioTest.readXvgTimeSeriesWorks/1 64: [ OK ] XvgReadTimeSeries/XvgioTest.readXvgTimeSeriesWorks/1 (1 ms) 64: [ RUN ] XvgReadTimeSeries/XvgioTest.readXvgTimeSeriesWorks/2 64: [ OK ] XvgReadTimeSeries/XvgioTest.readXvgTimeSeriesWorks/2 (1 ms) 64: [ RUN ] XvgReadTimeSeries/XvgioTest.readXvgTimeSeriesWorks/3 64: [ OK ] XvgReadTimeSeries/XvgioTest.readXvgTimeSeriesWorks/3 (1 ms) 64: [----------] 4 tests from XvgReadTimeSeries/XvgioTest (6 ms total) 64: 64: [----------] Global test environment tear-down 64: [==========] 421 tests from 17 test suites ran. (89 ms total) 64: [ PASSED ] 421 tests. 64/92 Test #64: FileIOTests ............................... Passed 0.26 sec test 65 Start 65: SelectionUnitTests 65: Test command: /build/reproducible-path/gromacs-2025.1/build/basic/bin/selection-test "--gtest_output=xml:/build/reproducible-path/gromacs-2025.1/build/basic/Testing/Temporary/SelectionUnitTests.xml" 65: Working Directory: /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/selection/tests 65: Test timeout computed to be: 30 65: [==========] Running 201 tests from 11 test suites. 65: [----------] Global test environment set-up. 65: [----------] 1 test from IndexGroupTest 65: [ RUN ] IndexGroupTest.RemovesDuplicates 65: [ OK ] IndexGroupTest.RemovesDuplicates (0 ms) 65: [----------] 1 test from IndexGroupTest (0 ms total) 65: 65: [----------] 15 tests from IndexBlockTest 65: [ RUN ] IndexBlockTest.CreatesUnknownBlock 65: [ OK ] IndexBlockTest.CreatesUnknownBlock (1 ms) 65: [ RUN ] IndexBlockTest.CreatesAtomBlock 65: [ OK ] IndexBlockTest.CreatesAtomBlock (1 ms) 65: [ RUN ] IndexBlockTest.CreatesResidueBlocksForSimpleTopology 65: [ OK ] IndexBlockTest.CreatesResidueBlocksForSimpleTopology (1 ms) 65: [ RUN ] IndexBlockTest.CreatesResidueBlocksForComplexTopology 65: [ OK ] IndexBlockTest.CreatesResidueBlocksForComplexTopology (1 ms) 65: [ RUN ] IndexBlockTest.CreatesMoleculeBlocksForSimpleTopology 65: [ OK ] IndexBlockTest.CreatesMoleculeBlocksForSimpleTopology (0 ms) 65: [ RUN ] IndexBlockTest.CreatesMoleculeBlocksForComplexTopology 65: [ OK ] IndexBlockTest.CreatesMoleculeBlocksForComplexTopology (1 ms) 65: [ RUN ] IndexBlockTest.CreatesSingleBlock 65: [ OK ] IndexBlockTest.CreatesSingleBlock (0 ms) 65: [ RUN ] IndexBlockTest.ChecksGroupForFullBlocksPositive 65: [ OK ] IndexBlockTest.ChecksGroupForFullBlocksPositive (0 ms) 65: [ RUN ] IndexBlockTest.ChecksOutOfOrderGroupForFullBlocksPositive 65: [ OK ] IndexBlockTest.ChecksOutOfOrderGroupForFullBlocksPositive (0 ms) 65: [ RUN ] IndexBlockTest.ChecksGroupForFullBlocksNegative 65: [ OK ] IndexBlockTest.ChecksGroupForFullBlocksNegative (0 ms) 65: [ RUN ] IndexBlockTest.ChecksGroupForCompleteElementsTrivial 65: [ OK ] IndexBlockTest.ChecksGroupForCompleteElementsTrivial (0 ms) 65: [ RUN ] IndexBlockTest.ChecksGroupForCompleteResiduesPositive 65: [ OK ] IndexBlockTest.ChecksGroupForCompleteResiduesPositive (0 ms) 65: [ RUN ] IndexBlockTest.ChecksGroupForCompleteResiduesNegative 65: [ OK ] IndexBlockTest.ChecksGroupForCompleteResiduesNegative (0 ms) 65: [ RUN ] IndexBlockTest.ChecksGroupForCompleteMoleculesPositive 65: [ OK ] IndexBlockTest.ChecksGroupForCompleteMoleculesPositive (0 ms) 65: [ RUN ] IndexBlockTest.ChecksGroupForCompleteMoleculesNegative 65: [ OK ] IndexBlockTest.ChecksGroupForCompleteMoleculesNegative (0 ms) 65: [----------] 15 tests from IndexBlockTest (11 ms total) 65: 65: [----------] 11 tests from IndexMapTest 65: [ RUN ] IndexMapTest.InitializesAtomBlock 65: [ OK ] IndexMapTest.InitializesAtomBlock (1 ms) 65: [ RUN ] IndexMapTest.InitializesOrgIdGroupAtom 65: [ OK ] IndexMapTest.InitializesOrgIdGroupAtom (0 ms) 65: [ RUN ] IndexMapTest.InitializesOrgIdGroupSingle 65: [ OK ] IndexMapTest.InitializesOrgIdGroupSingle (1 ms) 65: [ RUN ] IndexMapTest.InitializesOrgIdGroupResidue 65: [ OK ] IndexMapTest.InitializesOrgIdGroupResidue (0 ms) 65: [ RUN ] IndexMapTest.InitializesOrgIdGroupMolecule 65: [ OK ] IndexMapTest.InitializesOrgIdGroupMolecule (0 ms) 65: [ RUN ] IndexMapTest.InitializesOrgIdGroupAll 65: [ OK ] IndexMapTest.InitializesOrgIdGroupAll (0 ms) 65: [ RUN ] IndexMapTest.InitializesMoleculeBlock 65: [ OK ] IndexMapTest.InitializesMoleculeBlock (1 ms) 65: [ RUN ] IndexMapTest.MapsSingleBlock 65: [ OK ] IndexMapTest.MapsSingleBlock (1 ms) 65: [ RUN ] IndexMapTest.MapsResidueBlocks 65: [ OK ] IndexMapTest.MapsResidueBlocks (2 ms) 65: [ RUN ] IndexMapTest.MapsResidueBlocksWithMask 65: [ OK ] IndexMapTest.MapsResidueBlocksWithMask (2 ms) 65: [ RUN ] IndexMapTest.HandlesMultipleRequests 65: [ OK ] IndexMapTest.HandlesMultipleRequests (3 ms) 65: [----------] 11 tests from IndexMapTest (18 ms total) 65: 65: [----------] 3 tests from IndexGroupsAndNamesTest 65: [ RUN ] IndexGroupsAndNamesTest.containsNames 65: [ OK ] IndexGroupsAndNamesTest.containsNames (0 ms) 65: [ RUN ] IndexGroupsAndNamesTest.throwsWhenNameMissing 65: [ OK ] IndexGroupsAndNamesTest.throwsWhenNameMissing (0 ms) 65: [ RUN ] IndexGroupsAndNamesTest.groupIndicesCorrect 65: [ OK ] IndexGroupsAndNamesTest.groupIndicesCorrect (0 ms) 65: [----------] 3 tests from IndexGroupsAndNamesTest (0 ms total) 65: 65: [----------] 15 tests from NeighborhoodSearchTest 65: [ RUN ] NeighborhoodSearchTest.SimpleSearch 65: [ OK ] NeighborhoodSearchTest.SimpleSearch (69 ms) 65: [ RUN ] NeighborhoodSearchTest.SimpleSearchXY 65: [ OK ] NeighborhoodSearchTest.SimpleSearchXY (78 ms) 65: [ RUN ] NeighborhoodSearchTest.GridSearchBox 65: [ OK ] NeighborhoodSearchTest.GridSearchBox (11 ms) 65: [ RUN ] NeighborhoodSearchTest.GridSearchTriclinic 65: [ OK ] NeighborhoodSearchTest.GridSearchTriclinic (36 ms) 65: [ RUN ] NeighborhoodSearchTest.GridSearch2DPBC 65: [ OK ] NeighborhoodSearchTest.GridSearch2DPBC (20 ms) 65: [ RUN ] NeighborhoodSearchTest.GridSearchNoPBC 65: [ OK ] NeighborhoodSearchTest.GridSearchNoPBC (9 ms) 65: [ RUN ] NeighborhoodSearchTest.GridSearchXYBox 65: [ OK ] NeighborhoodSearchTest.GridSearchXYBox (10 ms) 65: [ RUN ] NeighborhoodSearchTest.SimpleSelfPairsSearch 65: [ OK ] NeighborhoodSearchTest.SimpleSelfPairsSearch (0 ms) 65: [ RUN ] NeighborhoodSearchTest.GridSelfPairsSearch 65: [ OK ] NeighborhoodSearchTest.GridSelfPairsSearch (178 ms) 65: [ RUN ] NeighborhoodSearchTest.HandlesConcurrentSearches 65: [ OK ] NeighborhoodSearchTest.HandlesConcurrentSearches (0 ms) 65: [ RUN ] NeighborhoodSearchTest.HandlesNoPBC 65: [ OK ] NeighborhoodSearchTest.HandlesNoPBC (0 ms) 65: [ RUN ] NeighborhoodSearchTest.HandlesNullPBC 65: [ OK ] NeighborhoodSearchTest.HandlesNullPBC (0 ms) 65: [ RUN ] NeighborhoodSearchTest.HandlesSkippingPairs 65: [ OK ] NeighborhoodSearchTest.HandlesSkippingPairs (0 ms) 65: [ RUN ] NeighborhoodSearchTest.SimpleSearchExclusions 65: [ OK ] NeighborhoodSearchTest.SimpleSearchExclusions (17 ms) 65: [ RUN ] NeighborhoodSearchTest.GridSearchExclusions 65: [ OK ] NeighborhoodSearchTest.GridSearchExclusions (3 ms) 65: [----------] 15 tests from NeighborhoodSearchTest (439 ms total) 65: 65: [----------] 13 tests from PositionCalculationTest 65: [ RUN ] PositionCalculationTest.ComputesAtomPositions 65: [ OK ] PositionCalculationTest.ComputesAtomPositions (2 ms) 65: [ RUN ] PositionCalculationTest.ComputesAtomPositionsWithRepeatedIndex 65: [ OK ] PositionCalculationTest.ComputesAtomPositionsWithRepeatedIndex (1 ms) 65: [ RUN ] PositionCalculationTest.ComputesResidueCOGPositions 65: [ OK ] PositionCalculationTest.ComputesResidueCOGPositions (1 ms) 65: [ RUN ] PositionCalculationTest.ComputesResidueCOMPositions 65: [ OK ] PositionCalculationTest.ComputesResidueCOMPositions (1 ms) 65: [ RUN ] PositionCalculationTest.ComputesGroupCOGPositions 65: [ OK ] PositionCalculationTest.ComputesGroupCOGPositions (1 ms) 65: [ RUN ] PositionCalculationTest.ComputesGroupCOMPositions 65: [ OK ] PositionCalculationTest.ComputesGroupCOMPositions (1 ms) 65: [ RUN ] PositionCalculationTest.ComputesPositionsWithCompleteWhole 65: [ OK ] PositionCalculationTest.ComputesPositionsWithCompleteWhole (1 ms) 65: [ RUN ] PositionCalculationTest.ComputesPositionsWithCompleteMax 65: [ OK ] PositionCalculationTest.ComputesPositionsWithCompleteMax (1 ms) 65: [ RUN ] PositionCalculationTest.ComputesPositionMask 65: [ OK ] PositionCalculationTest.ComputesPositionMask (1 ms) 65: [ RUN ] PositionCalculationTest.HandlesFramesWithLessAtoms 65: [ OK ] PositionCalculationTest.HandlesFramesWithLessAtoms (1 ms) 65: [ RUN ] PositionCalculationTest.HandlesFramesWithLessAtoms2 65: [ OK ] PositionCalculationTest.HandlesFramesWithLessAtoms2 (1 ms) 65: [ RUN ] PositionCalculationTest.HandlesIdenticalStaticCalculations 65: [ OK ] PositionCalculationTest.HandlesIdenticalStaticCalculations (1 ms) 65: [ RUN ] PositionCalculationTest.HandlesOverlappingStaticCalculations 65: [ OK ] PositionCalculationTest.HandlesOverlappingStaticCalculations (1 ms) 65: [----------] 13 tests from PositionCalculationTest (23 ms total) 65: 65: [----------] 33 tests from SelectionCollectionTest 65: [ RUN ] SelectionCollectionTest.HandlesNoSelections 65: [ OK ] SelectionCollectionTest.HandlesNoSelections (1 ms) 65: [ RUN ] SelectionCollectionTest.HandlesNoSelectionsWithDefaultPositionType 65: [ OK ] SelectionCollectionTest.HandlesNoSelectionsWithDefaultPositionType (3 ms) 65: [ RUN ] SelectionCollectionTest.HandlesVelocityAndForceRequests 65: [ OK ] SelectionCollectionTest.HandlesVelocityAndForceRequests (2 ms) 65: [ RUN ] SelectionCollectionTest.HandlesForceRequestForCenterOfGeometry 65: [ OK ] SelectionCollectionTest.HandlesForceRequestForCenterOfGeometry (3 ms) 65: [ RUN ] SelectionCollectionTest.ParsesSelectionsFromFile 65: [ OK ] SelectionCollectionTest.ParsesSelectionsFromFile (2 ms) 65: [ RUN ] SelectionCollectionTest.HandlesAtypicalWhitespace 65: [ OK ] SelectionCollectionTest.HandlesAtypicalWhitespace (2 ms) 65: [ RUN ] SelectionCollectionTest.HandlesInvalidRegularExpressions 65: [ OK ] SelectionCollectionTest.HandlesInvalidRegularExpressions (4 ms) 65: [ RUN ] SelectionCollectionTest.HandlesMissingMethodParamValue 65: [ OK ] SelectionCollectionTest.HandlesMissingMethodParamValue (2 ms) 65: [ RUN ] SelectionCollectionTest.HandlesMissingMethodParamValue2 65: [ OK ] SelectionCollectionTest.HandlesMissingMethodParamValue2 (2 ms) 65: [ RUN ] SelectionCollectionTest.HandlesMissingMethodParamValue3 65: [ OK ] SelectionCollectionTest.HandlesMissingMethodParamValue3 (2 ms) 65: [ RUN ] SelectionCollectionTest.HandlesUnknownGroupReferenceParser1 65: [ OK ] SelectionCollectionTest.HandlesUnknownGroupReferenceParser1 (2 ms) 65: [ RUN ] SelectionCollectionTest.HandlesUnknownGroupReferenceParser2 65: [ OK ] SelectionCollectionTest.HandlesUnknownGroupReferenceParser2 (3 ms) 65: [ RUN ] SelectionCollectionTest.HandlesUnknownGroupReferenceDelayed1 65: [ OK ] SelectionCollectionTest.HandlesUnknownGroupReferenceDelayed1 (1 ms) 65: [ RUN ] SelectionCollectionTest.HandlesUnknownGroupReferenceDelayed2 65: [ OK ] SelectionCollectionTest.HandlesUnknownGroupReferenceDelayed2 (2 ms) 65: [ RUN ] SelectionCollectionTest.HandlesUnsortedGroupReference 65: [ OK ] SelectionCollectionTest.HandlesUnsortedGroupReference (3 ms) 65: [ RUN ] SelectionCollectionTest.HandlesUnsortedGroupReferenceDelayed 65: [ OK ] SelectionCollectionTest.HandlesUnsortedGroupReferenceDelayed (2 ms) 65: [ RUN ] SelectionCollectionTest.HandlesOutOfRangeAtomIndexInGroup 65: [ OK ] SelectionCollectionTest.HandlesOutOfRangeAtomIndexInGroup (2 ms) 65: [ RUN ] SelectionCollectionTest.HandlesOutOfRangeAtomIndexInGroupDelayed 65: [ OK ] SelectionCollectionTest.HandlesOutOfRangeAtomIndexInGroupDelayed (2 ms) 65: [ RUN ] SelectionCollectionTest.HandlesOutOfRangeAtomIndexInGroupDelayed2 65: [ OK ] SelectionCollectionTest.HandlesOutOfRangeAtomIndexInGroupDelayed2 (2 ms) 65: [ RUN ] SelectionCollectionTest.RecoversFromMissingMoleculeInfo 65: [ OK ] SelectionCollectionTest.RecoversFromMissingMoleculeInfo (4 ms) 65: [ RUN ] SelectionCollectionTest.RecoversFromMissingAtomTypes 65: [ OK ] SelectionCollectionTest.RecoversFromMissingAtomTypes (3 ms) 65: [ RUN ] SelectionCollectionTest.RecoversFromMissingPDBInfo 65: [ OK ] SelectionCollectionTest.RecoversFromMissingPDBInfo (4 ms) 65: [ RUN ] SelectionCollectionTest.RecoversFromInvalidPermutation 65: [ OK ] SelectionCollectionTest.RecoversFromInvalidPermutation (2 ms) 65: [ RUN ] SelectionCollectionTest.RecoversFromInvalidPermutation2 65: [ OK ] SelectionCollectionTest.RecoversFromInvalidPermutation2 (1 ms) 65: [ RUN ] SelectionCollectionTest.RecoversFromInvalidPermutation3 65: [ OK ] SelectionCollectionTest.RecoversFromInvalidPermutation3 (3 ms) 65: [ RUN ] SelectionCollectionTest.HandlesFramesWithTooSmallAtomSubsets 65: [ OK ] SelectionCollectionTest.HandlesFramesWithTooSmallAtomSubsets (2 ms) 65: [ RUN ] SelectionCollectionTest.HandlesFramesWithTooSmallAtomSubsets2 65: [ OK ] SelectionCollectionTest.HandlesFramesWithTooSmallAtomSubsets2 (2 ms) 65: [ RUN ] SelectionCollectionTest.HandlesFramesWithTooSmallAtomSubsets3 65: [ OK ] SelectionCollectionTest.HandlesFramesWithTooSmallAtomSubsets3 (2 ms) 65: [ RUN ] SelectionCollectionTest.HandlesFramesWithTooSmallAtomSubsets4 65: [ OK ] SelectionCollectionTest.HandlesFramesWithTooSmallAtomSubsets4 (3 ms) 65: [ RUN ] SelectionCollectionTest.RetrieveValidSelection 65: [ OK ] SelectionCollectionTest.RetrieveValidSelection (1 ms) 65: [ RUN ] SelectionCollectionTest.RetrieveInvalidSelection 65: [ OK ] SelectionCollectionTest.RetrieveInvalidSelection (1 ms) 65: [ RUN ] SelectionCollectionTest.CanCopyEmptyCollection 65: [ OK ] SelectionCollectionTest.CanCopyEmptyCollection (2 ms) 65: [ RUN ] SelectionCollectionTest.CopiedSelectionListsAreHandledSeparately 65: [ OK ] SelectionCollectionTest.CopiedSelectionListsAreHandledSeparately (3 ms) 65: [----------] 33 tests from SelectionCollectionTest (92 ms total) 65: 65: [----------] 14 tests from SelectionCollectionInteractiveTest 65: [ RUN ] SelectionCollectionInteractiveTest.HandlesBasicInput 65: [ OK ] SelectionCollectionInteractiveTest.HandlesBasicInput (3 ms) 65: [ RUN ] SelectionCollectionInteractiveTest.HandlesContinuation 65: [ OK ] SelectionCollectionInteractiveTest.HandlesContinuation (3 ms) 65: [ RUN ] SelectionCollectionInteractiveTest.HandlesSingleSelectionInput 65: [ OK ] SelectionCollectionInteractiveTest.HandlesSingleSelectionInput (3 ms) 65: [ RUN ] SelectionCollectionInteractiveTest.HandlesTwoSelectionInput 65: [ OK ] SelectionCollectionInteractiveTest.HandlesTwoSelectionInput (3 ms) 65: [ RUN ] SelectionCollectionInteractiveTest.HandlesStatusWithGroups 65: [ OK ] SelectionCollectionInteractiveTest.HandlesStatusWithGroups (4 ms) 65: [ RUN ] SelectionCollectionInteractiveTest.HandlesStatusWithExistingSelections 65: [ OK ] SelectionCollectionInteractiveTest.HandlesStatusWithExistingSelections (4 ms) 65: [ RUN ] SelectionCollectionInteractiveTest.HandlesSingleSelectionInputStatus 65: [ OK ] SelectionCollectionInteractiveTest.HandlesSingleSelectionInputStatus (3 ms) 65: [ RUN ] SelectionCollectionInteractiveTest.HandlesTwoSelectionInputStatus 65: [ OK ] SelectionCollectionInteractiveTest.HandlesTwoSelectionInputStatus (3 ms) 65: [ RUN ] SelectionCollectionInteractiveTest.HandlesMultiSelectionInputStatus 65: [ OK ] SelectionCollectionInteractiveTest.HandlesMultiSelectionInputStatus (3 ms) 65: [ RUN ] SelectionCollectionInteractiveTest.HandlesNoFinalNewline 65: [ OK ] SelectionCollectionInteractiveTest.HandlesNoFinalNewline (3 ms) 65: [ RUN ] SelectionCollectionInteractiveTest.HandlesEmptySelections 65: [ OK ] SelectionCollectionInteractiveTest.HandlesEmptySelections (3 ms) 65: [ RUN ] SelectionCollectionInteractiveTest.HandlesMultipleSelectionsOnLine 65: [ OK ] SelectionCollectionInteractiveTest.HandlesMultipleSelectionsOnLine (3 ms) 65: [ RUN ] SelectionCollectionInteractiveTest.HandlesNoninteractiveInput 65: [ OK ] SelectionCollectionInteractiveTest.HandlesNoninteractiveInput (3 ms) 65: [ RUN ] SelectionCollectionInteractiveTest.HandlesSingleSelectionInputNoninteractively 65: [ OK ] SelectionCollectionInteractiveTest.HandlesSingleSelectionInputNoninteractively (2 ms) 65: [----------] 14 tests from SelectionCollectionInteractiveTest (51 ms total) 65: 65: [----------] 70 tests from SelectionCollectionDataTest 65: [ RUN ] SelectionCollectionDataTest.HandlesAllNone 65: [ OK ] SelectionCollectionDataTest.HandlesAllNone (3 ms) 65: [ RUN ] SelectionCollectionDataTest.HandlesAtomnr 65: [ OK ] SelectionCollectionDataTest.HandlesAtomnr (3 ms) 65: [ RUN ] SelectionCollectionDataTest.HandlesResnr 65: [ OK ] SelectionCollectionDataTest.HandlesResnr (4 ms) 65: [ RUN ] SelectionCollectionDataTest.HandlesResIndex 65: [ OK ] SelectionCollectionDataTest.HandlesResIndex (4 ms) 65: [ RUN ] SelectionCollectionDataTest.HandlesMolIndex 65: [ OK ] SelectionCollectionDataTest.HandlesMolIndex (3 ms) 65: [ RUN ] SelectionCollectionDataTest.HandlesAtomname 65: [ OK ] SelectionCollectionDataTest.HandlesAtomname (4 ms) 65: [ RUN ] SelectionCollectionDataTest.HandlesPdbAtomname 65: [ OK ] SelectionCollectionDataTest.HandlesPdbAtomname (4 ms) 65: [ RUN ] SelectionCollectionDataTest.HandlesAtomtype 65: [ OK ] SelectionCollectionDataTest.HandlesAtomtype (3 ms) 65: [ RUN ] SelectionCollectionDataTest.HandlesChain 65: [ OK ] SelectionCollectionDataTest.HandlesChain (4 ms) 65: [ RUN ] SelectionCollectionDataTest.HandlesMass 65: [ OK ] SelectionCollectionDataTest.HandlesMass (3 ms) 65: [ RUN ] SelectionCollectionDataTest.HandlesCharge 65: [ OK ] SelectionCollectionDataTest.HandlesCharge (3 ms) 65: [ RUN ] SelectionCollectionDataTest.HandlesAltLoc 65: [ OK ] SelectionCollectionDataTest.HandlesAltLoc (4 ms) 65: [ RUN ] SelectionCollectionDataTest.HandlesInsertCode 65: [ OK ] SelectionCollectionDataTest.HandlesInsertCode (4 ms) 65: [ RUN ] SelectionCollectionDataTest.HandlesOccupancy 65: [ OK ] SelectionCollectionDataTest.HandlesOccupancy (4 ms) 65: [ RUN ] SelectionCollectionDataTest.HandlesBeta 65: [ OK ] SelectionCollectionDataTest.HandlesBeta (4 ms) 65: [ RUN ] SelectionCollectionDataTest.HandlesResname 65: [ OK ] SelectionCollectionDataTest.HandlesResname (3 ms) 65: [ RUN ] SelectionCollectionDataTest.HandlesCoordinateKeywords 65: [ OK ] SelectionCollectionDataTest.HandlesCoordinateKeywords (6 ms) 65: [ RUN ] SelectionCollectionDataTest.HandlesSameResidue 65: [ OK ] SelectionCollectionDataTest.HandlesSameResidue (3 ms) 65: [ RUN ] SelectionCollectionDataTest.HandlesSameResidueName 65: [ OK ] SelectionCollectionDataTest.HandlesSameResidueName (3 ms) 65: [ RUN ] SelectionCollectionDataTest.HandlesPositionKeywords 65: [ OK ] SelectionCollectionDataTest.HandlesPositionKeywords (12 ms) 65: [ RUN ] SelectionCollectionDataTest.HandlesDistanceKeyword 65: [ OK ] SelectionCollectionDataTest.HandlesDistanceKeyword (5 ms) 65: [ RUN ] SelectionCollectionDataTest.HandlesMinDistanceKeyword 65: [ OK ] SelectionCollectionDataTest.HandlesMinDistanceKeyword (5 ms) 65: [ RUN ] SelectionCollectionDataTest.HandlesWithinKeyword 65: [ OK ] SelectionCollectionDataTest.HandlesWithinKeyword (5 ms) 65: [ RUN ] SelectionCollectionDataTest.HandlesInSolidAngleKeyword 65: [ OK ] SelectionCollectionDataTest.HandlesInSolidAngleKeyword (18 ms) 65: [ RUN ] SelectionCollectionDataTest.HandlesPermuteModifier 65: [ OK ] SelectionCollectionDataTest.HandlesPermuteModifier (11 ms) 65: [ RUN ] SelectionCollectionDataTest.HandlesPlusModifier 65: [ OK ] SelectionCollectionDataTest.HandlesPlusModifier (11 ms) 65: [ RUN ] SelectionCollectionDataTest.HandlesMergeModifier 65: [ OK ] SelectionCollectionDataTest.HandlesMergeModifier (12 ms) 65: [ RUN ] SelectionCollectionDataTest.ComputesMassesAndCharges 65: [ OK ] SelectionCollectionDataTest.ComputesMassesAndCharges (9 ms) 65: [ RUN ] SelectionCollectionDataTest.ComputesMassesAndChargesWithoutTopology 65: [ OK ] SelectionCollectionDataTest.ComputesMassesAndChargesWithoutTopology (5 ms) 65: [ RUN ] SelectionCollectionDataTest.HandlesFramesWithAtomSubsets 65: [ OK ] SelectionCollectionDataTest.HandlesFramesWithAtomSubsets (6 ms) 65: [ RUN ] SelectionCollectionDataTest.HandlesSelectionNames 65: [ OK ] SelectionCollectionDataTest.HandlesSelectionNames (4 ms) 65: [ RUN ] SelectionCollectionDataTest.HandlesIndexGroupsInSelections 65: [ OK ] SelectionCollectionDataTest.HandlesIndexGroupsInSelections (6 ms) 65: [ RUN ] SelectionCollectionDataTest.HandlesIndexGroupsInSelectionsDelayed 65: [ OK ] SelectionCollectionDataTest.HandlesIndexGroupsInSelectionsDelayed (5 ms) 65: [ RUN ] SelectionCollectionDataTest.HandlesUnsortedIndexGroupsInSelections 65: [ OK ] SelectionCollectionDataTest.HandlesUnsortedIndexGroupsInSelections (9 ms) 65: [ RUN ] SelectionCollectionDataTest.HandlesUnsortedIndexGroupsInSelectionsDelayed 65: [ OK ] SelectionCollectionDataTest.HandlesUnsortedIndexGroupsInSelectionsDelayed (6 ms) 65: [ RUN ] SelectionCollectionDataTest.HandlesConstantPositions 65: [ OK ] SelectionCollectionDataTest.HandlesConstantPositions (3 ms) 65: [ RUN ] SelectionCollectionDataTest.HandlesConstantPositionsWithModifiers 65: [ OK ] SelectionCollectionDataTest.HandlesConstantPositionsWithModifiers (4 ms) 65: [ RUN ] SelectionCollectionDataTest.HandlesWithinConstantPositions 65: [ OK ] SelectionCollectionDataTest.HandlesWithinConstantPositions (4 ms) 65: [ RUN ] SelectionCollectionDataTest.HandlesOverlappingIntegerRanges 65: [ OK ] SelectionCollectionDataTest.HandlesOverlappingIntegerRanges (3 ms) 65: [ RUN ] SelectionCollectionDataTest.HandlesOverlappingRealRanges 65: [ OK ] SelectionCollectionDataTest.HandlesOverlappingRealRanges (3 ms) 65: [ RUN ] SelectionCollectionDataTest.HandlesForcedStringMatchingMode 65: [ OK ] SelectionCollectionDataTest.HandlesForcedStringMatchingMode (4 ms) 65: [ RUN ] SelectionCollectionDataTest.HandlesWildcardMatching 65: [ OK ] SelectionCollectionDataTest.HandlesWildcardMatching (4 ms) 65: [ RUN ] SelectionCollectionDataTest.HandlesRegexMatching 65: [ OK ] SelectionCollectionDataTest.HandlesRegexMatching (4 ms) 65: [ RUN ] SelectionCollectionDataTest.HandlesBasicBoolean 65: [ OK ] SelectionCollectionDataTest.HandlesBasicBoolean (4 ms) 65: [ RUN ] SelectionCollectionDataTest.HandlesDynamicAtomValuedParameters 65: [ OK ] SelectionCollectionDataTest.HandlesDynamicAtomValuedParameters (6 ms) 65: [ RUN ] SelectionCollectionDataTest.HandlesEmptySelectionWithUnevaluatedExpressions 65: [ OK ] SelectionCollectionDataTest.HandlesEmptySelectionWithUnevaluatedExpressions (4 ms) 65: [ RUN ] SelectionCollectionDataTest.HandlesEmptyReferenceForSame 65: [ OK ] SelectionCollectionDataTest.HandlesEmptyReferenceForSame (4 ms) 65: [ RUN ] SelectionCollectionDataTest.HandlesPositionModifiersForKeywords 65: [ OK ] SelectionCollectionDataTest.HandlesPositionModifiersForKeywords (4 ms) 65: [ RUN ] SelectionCollectionDataTest.HandlesPositionModifiersForMethods 65: [ OK ] SelectionCollectionDataTest.HandlesPositionModifiersForMethods (5 ms) 65: [ RUN ] SelectionCollectionDataTest.HandlesKeywordOfPositions 65: [ OK ] SelectionCollectionDataTest.HandlesKeywordOfPositions (4 ms) 65: [ RUN ] SelectionCollectionDataTest.HandlesKeywordOfPositionsInArithmetic 65: [ OK ] SelectionCollectionDataTest.HandlesKeywordOfPositionsInArithmetic (4 ms) 65: [ RUN ] SelectionCollectionDataTest.HandlesNumericComparisons 65: [ OK ] SelectionCollectionDataTest.HandlesNumericComparisons (8 ms) 65: [ RUN ] SelectionCollectionDataTest.HandlesArithmeticExpressions 65: [ OK ] SelectionCollectionDataTest.HandlesArithmeticExpressions (8 ms) 65: [ RUN ] SelectionCollectionDataTest.HandlesNumericVariables 65: [ OK ] SelectionCollectionDataTest.HandlesNumericVariables (6 ms) 65: [ RUN ] SelectionCollectionDataTest.HandlesComplexNumericVariables 65: [ OK ] SelectionCollectionDataTest.HandlesComplexNumericVariables (7 ms) 65: [ RUN ] SelectionCollectionDataTest.HandlesPositionVariables 65: [ OK ] SelectionCollectionDataTest.HandlesPositionVariables (7 ms) 65: [ RUN ] SelectionCollectionDataTest.HandlesPositionVariableInModifier 65: [ OK ] SelectionCollectionDataTest.HandlesPositionVariableInModifier (6 ms) 65: [ RUN ] SelectionCollectionDataTest.HandlesConstantPositionInVariable 65: [ OK ] SelectionCollectionDataTest.HandlesConstantPositionInVariable (7 ms) 65: [ RUN ] SelectionCollectionDataTest.HandlesNumericConstantsInVariables 65: [ OK ] SelectionCollectionDataTest.HandlesNumericConstantsInVariables (7 ms) 65: [ RUN ] SelectionCollectionDataTest.HandlesBooleanStaticAnalysis 65: [ OK ] SelectionCollectionDataTest.HandlesBooleanStaticAnalysis (5 ms) 65: [ RUN ] SelectionCollectionDataTest.HandlesBooleanStaticAnalysisWithVariables 65: [ OK ] SelectionCollectionDataTest.HandlesBooleanStaticAnalysisWithVariables (4 ms) 65: [ RUN ] SelectionCollectionDataTest.HandlesBooleanStaticAnalysisWithMoreVariables 65: [ OK ] SelectionCollectionDataTest.HandlesBooleanStaticAnalysisWithMoreVariables (4 ms) 65: [ RUN ] SelectionCollectionDataTest.HandlesUnusedVariables 65: [ OK ] SelectionCollectionDataTest.HandlesUnusedVariables (3 ms) 65: [ RUN ] SelectionCollectionDataTest.HandlesVariablesWithStaticEvaluationGroups 65: [ OK ] SelectionCollectionDataTest.HandlesVariablesWithStaticEvaluationGroups (3 ms) 65: [ RUN ] SelectionCollectionDataTest.HandlesVariablesWithMixedEvaluationGroups 65: [ OK ] SelectionCollectionDataTest.HandlesVariablesWithMixedEvaluationGroups (4 ms) 65: [ RUN ] SelectionCollectionDataTest.HandlesVariablesWithMixedEvaluationGroups2 65: [ OK ] SelectionCollectionDataTest.HandlesVariablesWithMixedEvaluationGroups2 (4 ms) 65: [ RUN ] SelectionCollectionDataTest.CopiedSelectionWorksPreCompilation 65: [ OK ] SelectionCollectionDataTest.CopiedSelectionWorksPreCompilation (13 ms) 65: [ RUN ] SelectionCollectionDataTest.CopiedSelectionWorksPostCompilation 65: [ OK ] SelectionCollectionDataTest.CopiedSelectionWorksPostCompilation (14 ms) 65: [ RUN ] SelectionCollectionDataTest.CopiedSelectionsAreIndependent 65: [ OK ] SelectionCollectionDataTest.CopiedSelectionsAreIndependent (11 ms) 65: [ RUN ] SelectionCollectionDataTest.CopiedSelectionWithIndexPostCompilation 65: [ OK ] SelectionCollectionDataTest.CopiedSelectionWithIndexPostCompilation (14 ms) 65: [----------] 70 tests from SelectionCollectionDataTest (453 ms total) 65: 65: [----------] 17 tests from SelectionOptionTest 65: [ RUN ] SelectionOptionTest.ParsesSimpleSelection 65: [ OK ] SelectionOptionTest.ParsesSimpleSelection (2 ms) 65: [ RUN ] SelectionOptionTest.HandlesDynamicSelectionWhenStaticRequired 65: [ OK ] SelectionOptionTest.HandlesDynamicSelectionWhenStaticRequired (2 ms) 65: [ RUN ] SelectionOptionTest.HandlesNonAtomicSelectionWhenAtomsRequired 65: [ OK ] SelectionOptionTest.HandlesNonAtomicSelectionWhenAtomsRequired (3 ms) 65: [ RUN ] SelectionOptionTest.ChecksForSortedAtomsWhenRequired 65: [ OK ] SelectionOptionTest.ChecksForSortedAtomsWhenRequired (2 ms) 65: [ RUN ] SelectionOptionTest.ChecksEmptySelections 65: [ OK ] SelectionOptionTest.ChecksEmptySelections (2 ms) 65: [ RUN ] SelectionOptionTest.ChecksEmptyDelayedSelections 65: [ OK ] SelectionOptionTest.ChecksEmptyDelayedSelections (2 ms) 65: [ RUN ] SelectionOptionTest.HandlesTooManySelections 65: [ OK ] SelectionOptionTest.HandlesTooManySelections (1 ms) 65: [ RUN ] SelectionOptionTest.HandlesTooFewSelections 65: [ OK ] SelectionOptionTest.HandlesTooFewSelections (1 ms) 65: [ RUN ] SelectionOptionTest.HandlesDefaultSelectionText 65: [ OK ] SelectionOptionTest.HandlesDefaultSelectionText (1 ms) 65: [ RUN ] SelectionOptionTest.HandlesAdjuster 65: [ OK ] SelectionOptionTest.HandlesAdjuster (1 ms) 65: [ RUN ] SelectionOptionTest.HandlesDynamicWhenStaticRequiredWithAdjuster 65: [ OK ] SelectionOptionTest.HandlesDynamicWhenStaticRequiredWithAdjuster (1 ms) 65: [ RUN ] SelectionOptionTest.HandlesTooManySelectionsWithAdjuster 65: [ OK ] SelectionOptionTest.HandlesTooManySelectionsWithAdjuster (1 ms) 65: [ RUN ] SelectionOptionTest.HandlesTooFewSelectionsWithAdjuster 65: [ OK ] SelectionOptionTest.HandlesTooFewSelectionsWithAdjuster (1 ms) 65: [ RUN ] SelectionOptionTest.HandlesDelayedRequiredSelection 65: [ OK ] SelectionOptionTest.HandlesDelayedRequiredSelection (1 ms) 65: [ RUN ] SelectionOptionTest.HandlesTooFewDelayedRequiredSelections 65: [ OK ] SelectionOptionTest.HandlesTooFewDelayedRequiredSelections (1 ms) 65: [ RUN ] SelectionOptionTest.HandlesDelayedOptionalSelection 65: [ OK ] SelectionOptionTest.HandlesDelayedOptionalSelection (1 ms) 65: [ RUN ] SelectionOptionTest.HandlesDelayedSelectionWithAdjuster 65: [ OK ] SelectionOptionTest.HandlesDelayedSelectionWithAdjuster (1 ms) 65: [----------] 17 tests from SelectionOptionTest (36 ms total) 65: 65: [----------] 9 tests from SelectionFileOptionTest 65: [ RUN ] SelectionFileOptionTest.HandlesSingleSelectionOptionFromFile 65: [ OK ] SelectionFileOptionTest.HandlesSingleSelectionOptionFromFile (2 ms) 65: [ RUN ] SelectionFileOptionTest.HandlesTwoSeparateSelectionOptions 65: [ OK ] SelectionFileOptionTest.HandlesTwoSeparateSelectionOptions (2 ms) 65: [ RUN ] SelectionFileOptionTest.HandlesTwoSelectionOptionsFromSingleFile 65: [ OK ] SelectionFileOptionTest.HandlesTwoSelectionOptionsFromSingleFile (1 ms) 65: [ RUN ] SelectionFileOptionTest.HandlesRequiredOptionFromFile 65: [ OK ] SelectionFileOptionTest.HandlesRequiredOptionFromFile (2 ms) 65: [ RUN ] SelectionFileOptionTest.HandlesRequiredOptionFromFileWithOtherOptionSet 65: [ OK ] SelectionFileOptionTest.HandlesRequiredOptionFromFileWithOtherOptionSet (2 ms) 65: [ RUN ] SelectionFileOptionTest.HandlesTwoRequiredOptionsFromSingleFile 65: [ OK ] SelectionFileOptionTest.HandlesTwoRequiredOptionsFromSingleFile (2 ms) 65: [ RUN ] SelectionFileOptionTest.GivesErrorWithNoFile 65: [ OK ] SelectionFileOptionTest.GivesErrorWithNoFile (1 ms) 65: [ RUN ] SelectionFileOptionTest.GivesErrorWithNonExistentFile 65: [ OK ] SelectionFileOptionTest.GivesErrorWithNonExistentFile (2 ms) 65: [ RUN ] SelectionFileOptionTest.GivesErrorWithMultipleFiles 65: [ OK ] SelectionFileOptionTest.GivesErrorWithMultipleFiles (2 ms) 65: [----------] 9 tests from SelectionFileOptionTest (19 ms total) 65: 65: [----------] Global test environment tear-down 65: [==========] 201 tests from 11 test suites ran. (1146 ms total) 65: [ PASSED ] 201 tests. 65/92 Test #65: SelectionUnitTests ........................ Passed 1.26 sec test 66 Start 66: MdrunOutputTests 66: Test command: /build/reproducible-path/gromacs-2025.1/build/basic/bin/mdrun-output-test "-ntomp" "2" "--gtest_output=xml:/build/reproducible-path/gromacs-2025.1/build/basic/Testing/Temporary/MdrunOutputTests.xml" 66: Working Directory: /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests 66: Test timeout computed to be: 600 66: [==========] Running 12 tests from 5 test suites. 66: [----------] Global test environment set-up. 66: [----------] 1 test from MdrunTest 66: [ RUN ] MdrunTest.WritesHelp 66: [ OK ] MdrunTest.WritesHelp (61 ms) 66: [----------] 1 test from MdrunTest (61 ms total) 66: 66: [----------] 3 tests from WithDifferentOutputGroupSettings/MdrunCompressedXOutput 66: [ RUN ] WithDifferentOutputGroupSettings/MdrunCompressedXOutput.ExitsNormally/0 66: Generating 1-4 interactions: fudge = 0.5 66: Number of degrees of freedom in T-Coupling group rest is 9.00 66: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 66: 66: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/WithDifferentOutputGroupSettings_MdrunCompressedXOutput_ExitsNormally_0_input.mdp]: 66: NVE simulation: will use the initial temperature of 2573.591 K for 66: determining the Verlet buffer size 66: 66: 66: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/WithDifferentOutputGroupSettings_MdrunCompressedXOutput_ExitsNormally_0_input.mdp]: 66: You are using a plain Coulomb cut-off, which might produce artifacts. 66: You might want to consider using PME electrostatics. 66: 66: 66: 66: There were 2 NOTEs 66: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/WithDifferentOutputGroupSettings_MdrunCompressedXOutput_ExitsNormally_0.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 66: Can not increase nstlist because an NVE ensemble is used 66: Using 1 MPI thread 66: Using 2 OpenMP threads 66: 66: 66: NOTE: The number of threads is not equal to the number of (logical) cpus 66: and the -pin option is set to auto: will not pin threads to cpus. 66: This can lead to significant performance degradation. 66: Consider using -pin on (and -pinoffset in case you run multiple jobs). 66: starting mdrun 'spc2' 66: 1 steps, 0.0 ps. 66: Setting the LD random seed to -315661438 66: 66: Generated 3 of the 3 non-bonded parameter combinations 66: 66: Generated 3 of the 3 1-4 parameter combinations 66: 66: Excluding 2 bonded neighbours molecule type 'SOL' 66: 66: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/spc2.gro' 66: 66: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 2573.59 K 66: 66: Calculated rlist for 1x1 atom pair-list as 1.153 nm, buffer size 0.153 nm 66: 66: Set rlist, assuming 4x4 atom pair-list, to 1.127 nm, buffer size 0.127 nm 66: 66: Note that mdrun will redetermine rlist based on the actual pair-list setup 66: 66: This run will generate roughly 0 Mb of data 66: 66: Writing final coordinates. 66: 66: Core t (s) Wall t (s) (%) 66: Time: 0.087 0.044 198.5 66: (ns/day) (hour/ns) 66: Performance: 3.953 6.072 66: Reading frame 0 time 0.000 66: # Atoms 6 66: Reading frame 1 time 0.001 Last frame 1 time 0.001 66: 66: 66: Item #frames Timestep (ps) 66: Step 2 0.001 66: Time 2 0.001 66: Lambda 0 66: Coords 2 0.001 66: Velocities 0 66: Forces 0 66: Box 2 0.001 66: Checking file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/WithDifferentOutputGroupSettings_MdrunCompressedXOutput_ExitsNormally_0.xtc 66: [ OK ] WithDifferentOutputGroupSettings/MdrunCompressedXOutput.ExitsNormally/0 (94 ms) 66: [ RUN ] WithDifferentOutputGroupSettings/MdrunCompressedXOutput.ExitsNormally/1 66: Generating 1-4 interactions: fudge = 0.5 66: Number of degrees of freedom in T-Coupling group rest is 9.00 66: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 66: 66: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/WithDifferentOutputGroupSettings_MdrunCompressedXOutput_ExitsNormally_1_input.mdp]: 66: NVE simulation: will use the initial temperature of 2573.591 K for 66: determining the Verlet buffer size 66: 66: 66: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/WithDifferentOutputGroupSettings_MdrunCompressedXOutput_ExitsNormally_1_input.mdp]: 66: You are using a plain Coulomb cut-off, which might produce artifacts. 66: You might want to consider using PME electrostatics. 66: 66: 66: 66: There were 2 NOTEs 66: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/WithDifferentOutputGroupSettings_MdrunCompressedXOutput_ExitsNormally_1.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 66: Can not increase nstlist because an NVE ensemble is used 66: Using 1 MPI thread 66: Using 2 OpenMP threads 66: 66: 66: NOTE: The number of threads is not equal to the number of (logical) cpus 66: and the -pin option is set to auto: will not pin threads to cpus. 66: This can lead to significant performance degradation. 66: Consider using -pin on (and -pinoffset in case you run multiple jobs). 66: starting mdrun 'spc2' 66: 1 steps, 0.0 ps. 66: Setting the LD random seed to -46142490 66: 66: Generated 3 of the 3 non-bonded parameter combinations 66: 66: Generated 3 of the 3 1-4 parameter combinations 66: 66: Excluding 2 bonded neighbours molecule type 'SOL' 66: 66: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/spc2.gro' 66: 66: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 2573.59 K 66: 66: Calculated rlist for 1x1 atom pair-list as 1.153 nm, buffer size 0.153 nm 66: 66: Set rlist, assuming 4x4 atom pair-list, to 1.127 nm, buffer size 0.127 nm 66: 66: Note that mdrun will redetermine rlist based on the actual pair-list setup 66: 66: This run will generate roughly 0 Mb of data 66: 66: Writing final coordinates. 66: 66: NOTE: 23 % of the run time was spent in pair search, 66: you might want to increase nstlist (this has no effect on accuracy) 66: 66: Core t (s) Wall t (s) (%) 66: Time: 0.071 0.036 198.2 66: (ns/day) (hour/ns) 66: Performance: 4.818 4.981 66: Reading frame 0 time 0.000 66: # Atoms 6 66: Reading frame 1 time 0.001 Last frame 1 time 0.001 66: 66: 66: Item #frames Timestep (ps) 66: Step 2 0.001 66: Time 2 0.001 66: Lambda 0 66: Coords 2 0.001 66: Velocities 0 66: Forces 0 66: Box 2 0.001 66: Checking file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/WithDifferentOutputGroupSettings_MdrunCompressedXOutput_ExitsNormally_1.xtc 66: [ OK ] WithDifferentOutputGroupSettings/MdrunCompressedXOutput.ExitsNormally/1 (97 ms) 66: [ RUN ] WithDifferentOutputGroupSettings/MdrunCompressedXOutput.ExitsNormally/2 66: Generating 1-4 interactions: fudge = 0.5 66: Number of degrees of freedom in T-Coupling group rest is 9.00 66: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 66: 66: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/WithDifferentOutputGroupSettings_MdrunCompressedXOutput_ExitsNormally_2_input.mdp]: 66: NVE simulation: will use the initial temperature of 2573.591 K for 66: determining the Verlet buffer size 66: 66: 66: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/WithDifferentOutputGroupSettings_MdrunCompressedXOutput_ExitsNormally_2_input.mdp]: 66: You are using a plain Coulomb cut-off, which might produce artifacts. 66: You might want to consider using PME electrostatics. 66: 66: 66: 66: There were 2 NOTEs 66: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/WithDifferentOutputGroupSettings_MdrunCompressedXOutput_ExitsNormally_2.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 66: Can not increase nstlist because an NVE ensemble is used 66: Using 1 MPI thread 66: Using 2 OpenMP threads 66: 66: 66: NOTE: The number of threads is not equal to the number of (logical) cpus 66: and the -pin option is set to auto: will not pin threads to cpus. 66: This can lead to significant performance degradation. 66: Consider using -pin on (and -pinoffset in case you run multiple jobs). 66: starting mdrun 'spc2' 66: 1 steps, 0.0 ps. 66: Setting the LD random seed to -26389289 66: 66: Generated 3 of the 3 non-bonded parameter combinations 66: 66: Generated 3 of the 3 1-4 parameter combinations 66: 66: Excluding 2 bonded neighbours molecule type 'SOL' 66: 66: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/spc2.gro' 66: 66: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 2573.59 K 66: 66: Calculated rlist for 1x1 atom pair-list as 1.153 nm, buffer size 0.153 nm 66: 66: Set rlist, assuming 4x4 atom pair-list, to 1.127 nm, buffer size 0.127 nm 66: 66: Note that mdrun will redetermine rlist based on the actual pair-list setup 66: 66: This run will generate roughly 0 Mb of data 66: 66: Writing final coordinates. 66: 66: Core t (s) Wall t (s) (%) 66: Time: 0.044 0.022 197.3 66: (ns/day) (hour/ns) 66: Performance: 7.776 3.086 66: Reading frame 0 time 0.000 66: # Atoms 3 66: Reading frame 1 time 0.001 Last frame 1 time 0.001 66: 66: 66: Item #frames Timestep (ps) 66: Step 2 0.001 66: Time 2 0.001 66: Lambda 0 66: Coords 2 0.001 66: Velocities 0 66: Forces 0 66: Box 2 0.001 66: Checking file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/WithDifferentOutputGroupSettings_MdrunCompressedXOutput_ExitsNormally_2.xtc 66: [ OK ] WithDifferentOutputGroupSettings/MdrunCompressedXOutput.ExitsNormally/2 (66 ms) 66: [----------] 3 tests from WithDifferentOutputGroupSettings/MdrunCompressedXOutput (258 ms total) 66: 66: [----------] 2 tests from Argon12/OutputFiles 66: [ RUN ] Argon12/OutputFiles.FilesArePresent/0 66: 66: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/Argon12_OutputFiles_FilesArePresent_0_input.mdp]: 66: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 66: that with the Verlet scheme, nstlist has no effect on the accuracy of 66: your simulation. 66: 66: 66: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/Argon12_OutputFiles_FilesArePresent_0_input.mdp]: 66: Setting nstcalcenergy (100) equal to nstenergy (4) 66: 66: Number of degrees of freedom in T-Coupling group System is 33.00 66: 66: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/Argon12_OutputFiles_FilesArePresent_0_input.mdp]: 66: NVE simulation: will use the initial temperature of 68.810 K for 66: determining the Verlet buffer size 66: 66: 66: There were 3 NOTEs 66: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/Argon12_OutputFiles_FilesArePresent_0.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 66: Can not increase nstlist because an NVE ensemble is used 66: Using 1 MPI thread 66: Using 2 OpenMP threads 66: 66: 66: NOTE: The number of threads is not equal to the number of (logical) cpus 66: and the -pin option is set to auto: will not pin threads to cpus. 66: This can lead to significant performance degradation. 66: Consider using -pin on (and -pinoffset in case you run multiple jobs). 66: starting mdrun 'Argon' 66: 16 steps, 0.0 ps. 66: Generated 1 of the 1 non-bonded parameter combinations 66: 66: Excluding 1 bonded neighbours molecule type 'Argon' 66: 66: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 66: 66: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 66: 66: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 66: 66: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 66: 66: Note that mdrun will redetermine rlist based on the actual pair-list setup 66: 66: This run will generate roughly 0 Mb of data 66: 66: Writing final coordinates. 66: 66: Core t (s) Wall t (s) (%) 66: Time: 0.038 0.019 197.2 66: (ns/day) (hour/ns) 66: Performance: 75.813 0.317 66: [ OK ] Argon12/OutputFiles.FilesArePresent/0 (71 ms) 66: [ RUN ] Argon12/OutputFiles.FilesArePresent/1 66: 66: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/Argon12_OutputFiles_FilesArePresent_1_input.mdp]: 66: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 66: that with the Verlet scheme, nstlist has no effect on the accuracy of 66: your simulation. 66: 66: 66: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/Argon12_OutputFiles_FilesArePresent_1_input.mdp]: 66: Setting nstcalcenergy (100) equal to nstenergy (4) 66: 66: Number of degrees of freedom in T-Coupling group System is 33.00 66: 66: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/Argon12_OutputFiles_FilesArePresent_1_input.mdp]: 66: NVE simulation: will use the initial temperature of 68.810 K for 66: determining the Verlet buffer size 66: 66: 66: There were 3 NOTEs 66: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/Argon12_OutputFiles_FilesArePresent_1.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 66: Can not increase nstlist because an NVE ensemble is used 66: Using 1 MPI thread 66: Using 2 OpenMP threads 66: 66: 66: NOTE: The number of threads is not equal to the number of (logical) cpus 66: and the -pin option is set to auto: will not pin threads to cpus. 66: This can lead to significant performance degradation. 66: Consider using -pin on (and -pinoffset in case you run multiple jobs). 66: starting mdrun 'Argon' 66: 16 steps, 0.0 ps. 66: Generated 1 of the 1 non-bonded parameter combinations 66: 66: Excluding 1 bonded neighbours molecule type 'Argon' 66: 66: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 66: 66: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 66: 66: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 66: 66: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 66: 66: Note that mdrun will redetermine rlist based on the actual pair-list setup 66: 66: This run will generate roughly 0 Mb of data 66: 66: Writing final coordinates. 66: 66: Core t (s) Wall t (s) (%) 66: Time: 0.041 0.021 198.5 66: (ns/day) (hour/ns) 66: Performance: 70.399 0.341 66: [ OK ] Argon12/OutputFiles.FilesArePresent/1 (61 ms) 66: [----------] 2 tests from Argon12/OutputFiles (133 ms total) 66: 66: [----------] 3 tests from MdrunCanWrite/Trajectories 66: [ RUN ] MdrunCanWrite/Trajectories.ThatDifferInNstxout/0 66: Number of degrees of freedom in T-Coupling group System is 12.00 66: 66: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunCanWrite_Trajectories_ThatDifferInNstxout_0_input.mdp]: 66: You are using a plain Coulomb cut-off, which might produce artifacts. 66: You might want to consider using PME electrostatics. 66: 66: 66: 66: There was 1 NOTE 66: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunCanWrite_Trajectories_ThatDifferInNstxout_0.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 66: Changing nstlist from 10 to 40, rlist from 1.031 to 1.172 66: 66: Using 1 MPI thread 66: Using 2 OpenMP threads 66: 66: 66: NOTE: The number of threads is not equal to the number of (logical) cpus 66: and the -pin option is set to auto: will not pin threads to cpus. 66: This can lead to significant performance degradation. 66: Consider using -pin on (and -pinoffset in case you run multiple jobs). 66: starting mdrun 'spc-and-methanol' 66: 6 steps, 0.0 ps. 66: Setting the LD random seed to -1093962753 66: 66: Generated 8 of the 10 non-bonded parameter combinations 66: 66: Excluding 2 bonded neighbours molecule type 'Methanol' 66: 66: Excluding 2 bonded neighbours molecule type 'SOL' 66: 66: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/spc-and-methanol.gro' 66: 66: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 66: 66: Calculated rlist for 1x1 atom pair-list as 1.040 nm, buffer size 0.040 nm 66: 66: Set rlist, assuming 4x4 atom pair-list, to 1.031 nm, buffer size 0.031 nm 66: 66: Note that mdrun will redetermine rlist based on the actual pair-list setup 66: 66: This run will generate roughly 0 Mb of data 66: 66: Writing final coordinates. 66: 66: Core t (s) Wall t (s) (%) 66: Time: 0.153 0.077 199.3 66: (ns/day) (hour/ns) 66: Performance: 7.853 3.056 66: [ OK ] MdrunCanWrite/Trajectories.ThatDifferInNstxout/0 (152 ms) 66: [ RUN ] MdrunCanWrite/Trajectories.ThatDifferInNstxout/1 66: Number of degrees of freedom in T-Coupling group System is 12.00 66: 66: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunCanWrite_Trajectories_ThatDifferInNstxout_1_input.mdp]: 66: You are using a plain Coulomb cut-off, which might produce artifacts. 66: You might want to consider using PME electrostatics. 66: 66: 66: 66: There was 1 NOTE 66: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunCanWrite_Trajectories_ThatDifferInNstxout_1.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 66: Changing nstlist from 10 to 40, rlist from 1.031 to 1.172 66: 66: Using 1 MPI thread 66: Using 2 OpenMP threads 66: 66: 66: NOTE: The number of threads is not equal to the number of (logical) cpus 66: and the -pin option is set to auto: will not pin threads to cpus. 66: This can lead to significant performance degradation. 66: Consider using -pin on (and -pinoffset in case you run multiple jobs). 66: starting mdrun 'spc-and-methanol' 66: 6 steps, 0.0 ps. 66: Setting the LD random seed to -1149567541 66: 66: Generated 8 of the 10 non-bonded parameter combinations 66: 66: Excluding 2 bonded neighbours molecule type 'Methanol' 66: 66: Excluding 2 bonded neighbours molecule type 'SOL' 66: 66: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/spc-and-methanol.gro' 66: 66: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 66: 66: Calculated rlist for 1x1 atom pair-list as 1.040 nm, buffer size 0.040 nm 66: 66: Set rlist, assuming 4x4 atom pair-list, to 1.031 nm, buffer size 0.031 nm 66: 66: Note that mdrun will redetermine rlist based on the actual pair-list setup 66: 66: This run will generate roughly 0 Mb of data 66: 66: Writing final coordinates. 66: 66: Core t (s) Wall t (s) (%) 66: Time: 0.143 0.072 199.2 66: (ns/day) (hour/ns) 66: Performance: 8.398 2.858 66: [ OK ] MdrunCanWrite/Trajectories.ThatDifferInNstxout/1 (125 ms) 66: [ RUN ] MdrunCanWrite/Trajectories.ThatDifferInNstxout/2 66: Number of degrees of freedom in T-Coupling group System is 12.00 66: 66: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunCanWrite_Trajectories_ThatDifferInNstxout_2_input.mdp]: 66: You are using a plain Coulomb cut-off, which might produce artifacts. 66: You might want to consider using PME electrostatics. 66: 66: 66: 66: There was 1 NOTE 66: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunCanWrite_Trajectories_ThatDifferInNstxout_2.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 66: Changing nstlist from 10 to 40, rlist from 1.031 to 1.172 66: 66: Using 1 MPI thread 66: Using 2 OpenMP threads 66: 66: 66: NOTE: The number of threads is not equal to the number of (logical) cpus 66: and the -pin option is set to auto: will not pin threads to cpus. 66: This can lead to significant performance degradation. 66: Consider using -pin on (and -pinoffset in case you run multiple jobs). 66: starting mdrun 'spc-and-methanol' 66: 6 steps, 0.0 ps. 66: Setting the LD random seed to -612896769 66: 66: Generated 8 of the 10 non-bonded parameter combinations 66: 66: Excluding 2 bonded neighbours molecule type 'Methanol' 66: 66: Excluding 2 bonded neighbours molecule type 'SOL' 66: 66: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/spc-and-methanol.gro' 66: 66: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 66: 66: Calculated rlist for 1x1 atom pair-list as 1.040 nm, buffer size 0.040 nm 66: 66: Set rlist, assuming 4x4 atom pair-list, to 1.031 nm, buffer size 0.031 nm 66: 66: Note that mdrun will redetermine rlist based on the actual pair-list setup 66: 66: This run will generate roughly 0 Mb of data 66: 66: Writing final coordinates. 66: 66: Core t (s) Wall t (s) (%) 66: Time: 0.055 0.028 198.0 66: (ns/day) (hour/ns) 66: Performance: 21.967 1.093 66: [ OK ] MdrunCanWrite/Trajectories.ThatDifferInNstxout/2 (87 ms) 66: [----------] 3 tests from MdrunCanWrite/Trajectories (366 ms total) 66: 66: [----------] 3 tests from MdrunCanWrite/NptTrajectories 66: [ RUN ] MdrunCanWrite/NptTrajectories.WithDifferentPcoupl/0 66: Number of degrees of freedom in T-Coupling group System is 12.00 66: 66: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunCanWrite_NptTrajectories_WithDifferentPcoupl_0_input.mdp]: 66: You are using a plain Coulomb cut-off, which might produce artifacts. 66: You might want to consider using PME electrostatics. 66: 66: 66: 66: There was 1 NOTE 66: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunCanWrite_NptTrajectories_WithDifferentPcoupl_0.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 66: Changing nstlist from 10 to 40, rlist from 1.031 to 1.172 66: 66: Using 1 MPI thread 66: Using 2 OpenMP threads 66: 66: 66: NOTE: The number of threads is not equal to the number of (logical) cpus 66: and the -pin option is set to auto: will not pin threads to cpus. 66: This can lead to significant performance degradation. 66: Consider using -pin on (and -pinoffset in case you run multiple jobs). 66: starting mdrun 'spc-and-methanol' 66: 2 steps, 0.0 ps. 66: Setting the LD random seed to -17833345 66: 66: Generated 8 of the 10 non-bonded parameter combinations 66: 66: Excluding 2 bonded neighbours molecule type 'Methanol' 66: 66: Excluding 2 bonded neighbours molecule type 'SOL' 66: 66: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/spc-and-methanol.gro' 66: 66: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 66: 66: Calculated rlist for 1x1 atom pair-list as 1.040 nm, buffer size 0.040 nm 66: 66: Set rlist, assuming 4x4 atom pair-list, to 1.031 nm, buffer size 0.031 nm 66: 66: Note that mdrun will redetermine rlist based on the actual pair-list setup 66: 66: This run will generate roughly 0 Mb of data 66: 66: Writing final coordinates. 66: 66: Core t (s) Wall t (s) (%) 66: Time: 0.032 0.016 196.7 66: (ns/day) (hour/ns) 66: Performance: 15.738 1.525 66: [ OK ] MdrunCanWrite/NptTrajectories.WithDifferentPcoupl/0 (77 ms) 66: [ RUN ] MdrunCanWrite/NptTrajectories.WithDifferentPcoupl/1 66: 66: WARNING 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunCanWrite_NptTrajectories_WithDifferentPcoupl_1_input.mdp]: 66: The Berendsen barostat does not generate any strictly correct ensemble, 66: and should not be used for new production simulations (in our opinion). 66: We recommend using the C-rescale barostat instead. 66: 66: Number of degrees of freedom in T-Coupling group System is 12.00 66: 66: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunCanWrite_NptTrajectories_WithDifferentPcoupl_1_input.mdp]: 66: You are using a plain Coulomb cut-off, which might produce artifacts. 66: You might want to consider using PME electrostatics. 66: 66: 66: 66: There was 1 NOTE 66: 66: There was 1 WARNING 66: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunCanWrite_NptTrajectories_WithDifferentPcoupl_1.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 66: Changing nstlist from 10 to 40, rlist from 1.031 to 1.172 66: 66: Using 1 MPI thread 66: Using 2 OpenMP threads 66: 66: 66: NOTE: The number of threads is not equal to the number of (logical) cpus 66: and the -pin option is set to auto: will not pin threads to cpus. 66: This can lead to significant performance degradation. 66: Consider using -pin on (and -pinoffset in case you run multiple jobs). 66: starting mdrun 'spc-and-methanol' 66: 2 steps, 0.0 ps. 66: Setting the LD random seed to -408982567 66: 66: Generated 8 of the 10 non-bonded parameter combinations 66: 66: Excluding 2 bonded neighbours molecule type 'Methanol' 66: 66: Excluding 2 bonded neighbours molecule type 'SOL' 66: 66: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/spc-and-methanol.gro' 66: 66: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 66: 66: Calculated rlist for 1x1 atom pair-list as 1.040 nm, buffer size 0.040 nm 66: 66: Set rlist, assuming 4x4 atom pair-list, to 1.031 nm, buffer size 0.031 nm 66: 66: Note that mdrun will redetermine rlist based on the actual pair-list setup 66: 66: This run will generate roughly 0 Mb of data 66: 66: Writing final coordinates. 66: 66: Core t (s) Wall t (s) (%) 66: Time: 0.032 0.016 196.6 66: (ns/day) (hour/ns) 66: Performance: 16.136 1.487 66: [ OK ] MdrunCanWrite/NptTrajectories.WithDifferentPcoupl/1 (69 ms) 66: [ RUN ] MdrunCanWrite/NptTrajectories.WithDifferentPcoupl/2 66: Number of degrees of freedom in T-Coupling group System is 12.00 66: 66: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunCanWrite_NptTrajectories_WithDifferentPcoupl_2_input.mdp]: 66: You are using a plain Coulomb cut-off, which might produce artifacts. 66: You might want to consider using PME electrostatics. 66: 66: 66: 66: There was 1 NOTE 66: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunCanWrite_NptTrajectories_WithDifferentPcoupl_2.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 66: Changing nstlist from 10 to 40, rlist from 1.031 to 1.172 66: 66: Using 1 MPI thread 66: Using 2 OpenMP threads 66: 66: 66: NOTE: The number of threads is not equal to the number of (logical) cpus 66: and the -pin option is set to auto: will not pin threads to cpus. 66: This can lead to significant performance degradation. 66: Consider using -pin on (and -pinoffset in case you run multiple jobs). 66: starting mdrun 'spc-and-methanol' 66: 2 steps, 0.0 ps. 66: Setting the LD random seed to -470868617 66: 66: Generated 8 of the 10 non-bonded parameter combinations 66: 66: Excluding 2 bonded neighbours molecule type 'Methanol' 66: 66: Excluding 2 bonded neighbours molecule type 'SOL' 66: 66: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/spc-and-methanol.gro' 66: 66: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 66: 66: Calculated rlist for 1x1 atom pair-list as 1.040 nm, buffer size 0.040 nm 66: 66: Set rlist, assuming 4x4 atom pair-list, to 1.031 nm, buffer size 0.031 nm 66: 66: Note that mdrun will redetermine rlist based on the actual pair-list setup 66: 66: This run will generate roughly 0 Mb of data 66: 66: Writing final coordinates. 66: 66: Core t (s) Wall t (s) (%) 66: Time: 0.053 0.027 197.8 66: (ns/day) (hour/ns) 66: Performance: 9.598 2.501 66: [ OK ] MdrunCanWrite/NptTrajectories.WithDifferentPcoupl/2 (83 ms) 66: [----------] 3 tests from MdrunCanWrite/NptTrajectories (231 ms total) 66: 66: [----------] Global test environment tear-down 66: [==========] 12 tests from 5 test suites ran. (1241 ms total) 66: [ PASSED ] 12 tests. 66/92 Test #66: MdrunOutputTests .......................... Passed 1.35 sec test 67 Start 67: MdrunModulesTests 67: Test command: /build/reproducible-path/gromacs-2025.1/build/basic/bin/mdrun-modules-test "-ntomp" "2" "--gtest_output=xml:/build/reproducible-path/gromacs-2025.1/build/basic/Testing/Temporary/MdrunModulesTests.xml" 67: Working Directory: /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests 67: Test timeout computed to be: 600 67: [==========] Running 15 tests from 3 test suites. 67: [----------] Global test environment set-up. 67: [----------] 9 tests from DensityFittingTest 67: [ RUN ] DensityFittingTest.EnergyMinimizationEnergyCorrectInnerProduct 67: Number of degrees of freedom in T-Coupling group rest is 33.00 67: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 67: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/DensityFittingTest_EnergyMinimizationEnergyCorrectInnerProduct.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 67: Using 1 MPI thread 67: Using 2 OpenMP threads 67: 67: 67: NOTE: The number of threads is not equal to the number of (logical) cpus 67: and the -pin option is set to auto: will not pin threads to cpus. 67: This can lead to significant performance degradation. 67: Consider using -pin on (and -pinoffset in case you run multiple jobs). 67: 67: Steepest Descents: 67: Tolerance (Fmax) = 1.00000e+01 67: Number of steps = 2 67: 67: Energy minimization reached the maximum number of steps before the forces 67: reached the requested precision Fmax < 10. 67: 67: writing lowest energy coordinates. 67: 67: Steepest Descents did not converge to Fmax < 10 in 3 steps. 67: Potential Energy = -3.8565254e+03 67: Maximum force = 4.5099883e+03 on atom 3 67: Norm of force = 1.6816849e+03 67: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/DensityFittingTest_EnergyMinimizationEnergyCorrectInnerProduct.edr as single precision energy file 67: Reading energy frame 0 time 0.000 Reading energy frame 1 time 1.000 Reading energy frame 2 time 2.000 Last energy frame read 2 time 2.000 Setting the LD random seed to -1078543361 67: 67: Generated 1 of the 1 non-bonded parameter combinations 67: 67: Excluding 1 bonded neighbours molecule type 'Argon' 67: 67: This run will generate roughly 0 Mb of data 67: [ OK ] DensityFittingTest.EnergyMinimizationEnergyCorrectInnerProduct (51 ms) 67: [ RUN ] DensityFittingTest.EnergyMinimizationEnergyCorrectInnerProductTranslation 67: Number of degrees of freedom in T-Coupling group rest is 33.00 67: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 67: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/DensityFittingTest_EnergyMinimizationEnergyCorrectInnerProductTranslation.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 67: Using 1 MPI thread 67: Using 2 OpenMP threads 67: 67: 67: NOTE: The number of threads is not equal to the number of (logical) cpus 67: and the -pin option is set to auto: will not pin threads to cpus. 67: This can lead to significant performance degradation. 67: Consider using -pin on (and -pinoffset in case you run multiple jobs). 67: 67: Steepest Descents: 67: Tolerance (Fmax) = 1.00000e+01 67: Number of steps = 2 67: 67: Energy minimization reached the maximum number of steps before the forces 67: reached the requested precision Fmax < 10. 67: 67: writing lowest energy coordinates. 67: 67: Steepest Descents did not converge to Fmax < 10 in 3 steps. 67: Potential Energy = -9.8207725e+03 67: Maximum force = 7.3954834e+03 on atom 2 67: Norm of force = 2.7825089e+03 67: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/DensityFittingTest_EnergyMinimizationEnergyCorrectInnerProductTranslation.edr as single precision energy file 67: Reading energy frame 0 time 0.000 Reading energy frame 1 time 1.000 Reading energy frame 2 time 2.000 Last energy frame read 2 time 2.000 Setting the LD random seed to 1609027580 67: 67: Generated 1 of the 1 non-bonded parameter combinations 67: 67: Excluding 1 bonded neighbours molecule type 'Argon' 67: 67: This run will generate roughly 0 Mb of data 67: [ OK ] DensityFittingTest.EnergyMinimizationEnergyCorrectInnerProductTranslation (47 ms) 67: [ RUN ] DensityFittingTest.EnergyMinimizationEnergyTranslationParametersOff 67: 67: [WARNING] ./src/external/googletest/googletest/src/gtest-death-test.cc:1108:: Death tests use fork(), which is unsafe particularly in a threaded context. For this test, Google Test detected 2 threads. See https://github.com/google/googletest/blob/main/docs/advanced.md#death-tests-and-threads for more explanation and suggested solutions, especially if this is the last message you see before your test times out. 67: [ OK ] DensityFittingTest.EnergyMinimizationEnergyTranslationParametersOff (50 ms) 67: [ RUN ] DensityFittingTest.EnergyMinimizationEnergyCorrectInnerProductTranslationAndTransformationMatrix 67: Number of degrees of freedom in T-Coupling group rest is 33.00 67: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 67: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/DensityFittingTest_EnergyMinimizationEnergyCorrectInnerProductTranslationAndTransformationMatrix.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 67: Overriding nsteps with value passed on the command line: 4 steps 67: 67: Using 1 MPI thread 67: Using 2 OpenMP threads 67: 67: 67: NOTE: The number of threads is not equal to the number of (logical) cpus 67: and the -pin option is set to auto: will not pin threads to cpus. 67: This can lead to significant performance degradation. 67: Consider using -pin on (and -pinoffset in case you run multiple jobs). 67: 67: Steepest Descents: 67: Tolerance (Fmax) = 1.00000e+01 67: Number of steps = 4 67: 67: Energy minimization reached the maximum number of steps before the forces 67: reached the requested precision Fmax < 10. 67: 67: writing lowest energy coordinates. 67: 67: Steepest Descents did not converge to Fmax < 10 in 5 steps. 67: Potential Energy = -5.4739321e+03 67: Maximum force = 6.1322017e+03 on atom 2 67: Norm of force = 1.7702150e+03 67: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/DensityFittingTest_EnergyMinimizationEnergyCorrectInnerProductTranslationAndTransformationMatrix.edr as single precision energy file 67: Reading energy frame 0 time 0.000 Reading energy frame 1 time 1.000 Reading energy frame 2 time 2.000 Reading energy frame 3 time 3.000 Reading energy frame 4 time 4.000 Last energy frame read 4 time 4.000 Setting the LD random seed to -539426881 67: 67: Generated 1 of the 1 non-bonded parameter combinations 67: 67: Excluding 1 bonded neighbours molecule type 'Argon' 67: 67: This run will generate roughly 0 Mb of data 67: [ OK ] DensityFittingTest.EnergyMinimizationEnergyCorrectInnerProductTranslationAndTransformationMatrix (58 ms) 67: [ RUN ] DensityFittingTest.EnergyMinimizationEnergyMatrixTransfromationOff 67: 67: [WARNING] ./src/external/googletest/googletest/src/gtest-death-test.cc:1108:: Death tests use fork(), which is unsafe particularly in a threaded context. For this test, Google Test detected 2 threads. See https://github.com/google/googletest/blob/main/docs/advanced.md#death-tests-and-threads for more explanation and suggested solutions, especially if this is the last message you see before your test times out. 67: [ OK ] DensityFittingTest.EnergyMinimizationEnergyMatrixTransfromationOff (40 ms) 67: [ RUN ] DensityFittingTest.EnergyMinimizationEnergyCorrectInnerProductIdentityMatrix 67: Number of degrees of freedom in T-Coupling group rest is 33.00 67: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 67: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/DensityFittingTest_EnergyMinimizationEnergyCorrectInnerProductIdentityMatrix.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 67: Using 1 MPI thread 67: Using 2 OpenMP threads 67: 67: 67: NOTE: The number of threads is not equal to the number of (logical) cpus 67: and the -pin option is set to auto: will not pin threads to cpus. 67: This can lead to significant performance degradation. 67: Consider using -pin on (and -pinoffset in case you run multiple jobs). 67: 67: Steepest Descents: 67: Tolerance (Fmax) = 1.00000e+01 67: Number of steps = 2 67: 67: Energy minimization reached the maximum number of steps before the forces 67: reached the requested precision Fmax < 10. 67: 67: writing lowest energy coordinates. 67: 67: Steepest Descents did not converge to Fmax < 10 in 3 steps. 67: Potential Energy = -3.8565254e+03 67: Maximum force = 4.5099883e+03 on atom 3 67: Norm of force = 1.6816849e+03 67: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/DensityFittingTest_EnergyMinimizationEnergyCorrectInnerProductIdentityMatrix.edr as single precision energy file 67: Reading energy frame 0 time 0.000 Reading energy frame 1 time 1.000 Reading energy frame 2 time 2.000 Last energy frame read 2 time 2.000 Setting the LD random seed to -33655169 67: 67: Generated 1 of the 1 non-bonded parameter combinations 67: 67: Excluding 1 bonded neighbours molecule type 'Argon' 67: 67: This run will generate roughly 0 Mb of data 67: [ OK ] DensityFittingTest.EnergyMinimizationEnergyCorrectInnerProductIdentityMatrix (55 ms) 67: [ RUN ] DensityFittingTest.EnergyMinimizationEnergyCorrectForRelativeEntropy 67: Number of degrees of freedom in T-Coupling group rest is 33.00 67: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 67: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/DensityFittingTest_EnergyMinimizationEnergyCorrectForRelativeEntropy.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 67: Using 1 MPI thread 67: Using 2 OpenMP threads 67: 67: 67: NOTE: The number of threads is not equal to the number of (logical) cpus 67: and the -pin option is set to auto: will not pin threads to cpus. 67: This can lead to significant performance degradation. 67: Consider using -pin on (and -pinoffset in case you run multiple jobs). 67: 67: Steepest Descents: 67: Tolerance (Fmax) = 1.00000e+01 67: Number of steps = 2 67: 67: Energy minimization reached the maximum number of steps before the forces 67: reached the requested precision Fmax < 10. 67: 67: writing lowest energy coordinates. 67: 67: Steepest Descents did not converge to Fmax < 10 in 3 steps. 67: Potential Energy = -2.7138664e+04 67: Maximum force = 6.7827656e+03 on atom 2 67: Norm of force = 1.9608866e+03 67: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/DensityFittingTest_EnergyMinimizationEnergyCorrectForRelativeEntropy.edr as single precision energy file 67: Reading energy frame 0 time 0.000 Reading energy frame 1 time 1.000 Reading energy frame 2 time 2.000 Last energy frame read 2 time 2.000 Setting the LD random seed to 2104212395 67: 67: Generated 1 of the 1 non-bonded parameter combinations 67: 67: Excluding 1 bonded neighbours molecule type 'Argon' 67: 67: This run will generate roughly 0 Mb of data 67: [ OK ] DensityFittingTest.EnergyMinimizationEnergyCorrectForRelativeEntropy (50 ms) 67: [ RUN ] DensityFittingTest.GromppErrorWhenEnergyEvaluationFrequencyMismatch 67: 67: [WARNING] ./src/external/googletest/googletest/src/gtest-death-test.cc:1108:: Death tests use fork(), which is unsafe particularly in a threaded context. For this test, Google Test detected 2 threads. See https://github.com/google/googletest/blob/main/docs/advanced.md#death-tests-and-threads for more explanation and suggested solutions, especially if this is the last message you see before your test times out. 67: Setting the LD random seed to -169469089 67: 67: Generated 1 of the 1 non-bonded parameter combinations 67: 67: Excluding 1 bonded neighbours molecule type 'Argon' 67: 67: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 67: [ OK ] DensityFittingTest.GromppErrorWhenEnergyEvaluationFrequencyMismatch (50 ms) 67: [ RUN ] DensityFittingTest.CheckpointWorks 67: 67: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/DensityFittingTest_CheckpointWorks_input.mdp]: 67: Setting nstcalcenergy (100) equal to nstenergy (2) 67: 67: Number of degrees of freedom in T-Coupling group rest is 33.00 67: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 67: 67: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/DensityFittingTest_CheckpointWorks_input.mdp]: 67: NVE simulation: will use the initial temperature of 68.810 K for 67: determining the Verlet buffer size 67: 67: 67: There were 2 NOTEs 67: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/DensityFittingTest_CheckpointWorks.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 67: Can not increase nstlist because an NVE ensemble is used 67: Using 1 MPI thread 67: Using 2 OpenMP threads 67: 67: 67: NOTE: The number of threads is not equal to the number of (logical) cpus 67: and the -pin option is set to auto: will not pin threads to cpus. 67: This can lead to significant performance degradation. 67: Consider using -pin on (and -pinoffset in case you run multiple jobs). 67: starting mdrun 'Argon' 67: 2 steps, 0.0 ps. 67: Setting the LD random seed to -269484770 67: 67: Generated 1 of the 1 non-bonded parameter combinations 67: 67: Excluding 1 bonded neighbours molecule type 'Argon' 67: 67: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 67: 67: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 68.8096 K 67: 67: Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm 67: 67: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm 67: 67: Note that mdrun will redetermine rlist based on the actual pair-list setup 67: 67: This run will generate roughly 0 Mb of data 67: 67: Writing final coordinates. 67: 67: Core t (s) Wall t (s) (%) 67: Time: 0.053 0.027 197.8 67: (ns/day) (hour/ns) 67: Performance: 9.734 2.465 67: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/DensityFittingTest_CheckpointWorks.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 67: Overriding nsteps with value passed on the command line: 4 steps, 0.004 ps 67: Can not increase nstlist because an NVE ensemble is used 67: 67: Using 1 MPI thread 67: Using 2 OpenMP threads 67: 67: 67: NOTE: The number of threads is not equal to the number of (logical) cpus 67: and the -pin option is set to auto: will not pin threads to cpus. 67: This can lead to significant performance degradation. 67: Consider using -pin on (and -pinoffset in case you run multiple jobs). 67: starting mdrun 'Argon' 67: 6 steps, 0.0 ps (continuing from step 2, 0.0 ps). 67: 67: Writing final coordinates. 67: 67: Core t (s) Wall t (s) (%) 67: Time: 0.046 0.023 197.6 67: (ns/day) (hour/ns) 67: Performance: 18.497 1.298 67: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/DensityFittingTest_CheckpointWorks.edr as single precision energy file 67: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.002 Last energy frame read 1 time 0.002 [ OK ] DensityFittingTest.CheckpointWorks (134 ms) 67: [----------] 9 tests from DensityFittingTest (539 ms total) 67: 67: [----------] 4 tests from MimicTest 67: [ RUN ] MimicTest.OneQuantumMol 67: 67: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_OneQuantumMol_input.mdp]: 67: For a correct single-point energy evaluation with nsteps = 0, use 67: continuation = yes to avoid constraining the input coordinates. 67: 67: Generating 1-4 interactions: fudge = 0.5 67: Number of degrees of freedom in T-Coupling group rest is 21.00 67: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 67: 67: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_OneQuantumMol_input.mdp]: 67: NVE simulation with an initial temperature of zero: will use a Verlet 67: buffer of 10%. Check your energy drift! 67: 67: 67: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_OneQuantumMol_input.mdp]: 67: You are using a plain Coulomb cut-off, which might produce artifacts. 67: You might want to consider using PME electrostatics. 67: 67: 67: 67: There were 3 NOTEs 67: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_OneQuantumMol.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 67: Can not increase nstlist because an NVE ensemble is used 67: Using 1 MPI thread 67: Using 2 OpenMP threads 67: 67: 67: NOTE: The number of threads is not equal to the number of (logical) cpus 67: and the -pin option is set to auto: will not pin threads to cpus. 67: This can lead to significant performance degradation. 67: Consider using -pin on (and -pinoffset in case you run multiple jobs). 67: starting md rerun 'Generated by gmx solvate', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/4water.gro' 67: 67: Reading frames from gro file 'Generated by gmx solvate', 12 atoms. 67: Reading frame 0 time 0.000 Last frame 0 time 0.000 67: 67: NOTE: 46 % of the run time was spent in pair search, 67: you might want to increase nstlist (this has no effect on accuracy) 67: 67: Core t (s) Wall t (s) (%) 67: Time: 0.024 0.012 198.0 67: (ns/day) (hour/ns) 67: Performance: 7.149 3.357 67: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_OneQuantumMol.edr as single precision energy file 67: Reading energy frame 0 time 0.000 Last energy frame read 0 time 0.000 Setting the LD random seed to 2102255533 67: 67: Generated 10 of the 10 non-bonded parameter combinations 67: 67: Generated 10 of the 10 1-4 parameter combinations 67: 67: Excluding 2 bonded neighbours molecule type 'SOL' 67: 67: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/4water.gro', all velocities are zero 67: 67: This run will generate roughly 0 Mb of data 67: [ OK ] MimicTest.OneQuantumMol (69 ms) 67: [ RUN ] MimicTest.AllQuantumMol 67: 67: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_AllQuantumMol_input.mdp]: 67: For a correct single-point energy evaluation with nsteps = 0, use 67: continuation = yes to avoid constraining the input coordinates. 67: 67: Generating 1-4 interactions: fudge = 0.5 67: Number of degrees of freedom in T-Coupling group rest is 21.00 67: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 67: 67: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_AllQuantumMol_input.mdp]: 67: NVE simulation with an initial temperature of zero: will use a Verlet 67: buffer of 10%. Check your energy drift! 67: 67: 67: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_AllQuantumMol_input.mdp]: 67: You are using a plain Coulomb cut-off, which might produce artifacts. 67: You might want to consider using PME electrostatics. 67: 67: 67: 67: There were 3 NOTEs 67: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_AllQuantumMol.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 67: Can not increase nstlist because an NVE ensemble is used 67: Using 1 MPI thread 67: Using 2 OpenMP threads 67: 67: 67: NOTE: The number of threads is not equal to the number of (logical) cpus 67: and the -pin option is set to auto: will not pin threads to cpus. 67: This can lead to significant performance degradation. 67: Consider using -pin on (and -pinoffset in case you run multiple jobs). 67: starting md rerun 'Generated by gmx solvate', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/4water.gro' 67: 67: Reading frames from gro file 'Generated by gmx solvate', 12 atoms. 67: Reading frame 0 time 0.000 Last frame 0 time 0.000 67: 67: Core t (s) Wall t (s) (%) 67: Time: 0.012 0.006 196.0 67: (ns/day) (hour/ns) 67: Performance: 14.160 1.695 67: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_AllQuantumMol.edr as single precision energy file 67: Reading energy frame 0 time 0.000 Last energy frame read 0 time 0.000 Setting the LD random seed to -1174405130 67: 67: Generated 10 of the 10 non-bonded parameter combinations 67: 67: Generated 10 of the 10 1-4 parameter combinations 67: 67: Excluding 2 bonded neighbours molecule type 'SOL' 67: 67: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/4water.gro', all velocities are zero 67: 67: This run will generate roughly 0 Mb of data 67: [ OK ] MimicTest.AllQuantumMol (56 ms) 67: [ RUN ] MimicTest.TwoQuantumMol 67: 67: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_TwoQuantumMol_input.mdp]: 67: For a correct single-point energy evaluation with nsteps = 0, use 67: continuation = yes to avoid constraining the input coordinates. 67: 67: Generating 1-4 interactions: fudge = 0.5 67: Number of degrees of freedom in T-Coupling group rest is 21.00 67: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 67: 67: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_TwoQuantumMol_input.mdp]: 67: NVE simulation with an initial temperature of zero: will use a Verlet 67: buffer of 10%. Check your energy drift! 67: 67: 67: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_TwoQuantumMol_input.mdp]: 67: You are using a plain Coulomb cut-off, which might produce artifacts. 67: You might want to consider using PME electrostatics. 67: 67: 67: 67: There were 3 NOTEs 67: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_TwoQuantumMol.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 67: Can not increase nstlist because an NVE ensemble is used 67: Using 1 MPI thread 67: Using 2 OpenMP threads 67: 67: 67: NOTE: The number of threads is not equal to the number of (logical) cpus 67: and the -pin option is set to auto: will not pin threads to cpus. 67: This can lead to significant performance degradation. 67: Consider using -pin on (and -pinoffset in case you run multiple jobs). 67: starting md rerun 'Generated by gmx solvate', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/4water.gro' 67: 67: Reading frames from gro file 'Generated by gmx solvate', 12 atoms. 67: Reading frame 0 time 0.000 Last frame 0 time 0.000 67: 67: NOTE: 14 % of the run time was spent in pair search, 67: you might want to increase nstlist (this has no effect on accuracy) 67: 67: Core t (s) Wall t (s) (%) 67: Time: 0.011 0.006 195.4 67: (ns/day) (hour/ns) 67: Performance: 14.711 1.631 67: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_TwoQuantumMol.edr as single precision energy file 67: Reading energy frame 0 time 0.000 Last energy frame read 0 time 0.000 Setting the LD random seed to 1570627310 67: 67: Generated 10 of the 10 non-bonded parameter combinations 67: 67: Generated 10 of the 10 1-4 parameter combinations 67: 67: Excluding 2 bonded neighbours molecule type 'SOL' 67: 67: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/4water.gro', all velocities are zero 67: 67: This run will generate roughly 0 Mb of data 67: [ OK ] MimicTest.TwoQuantumMol (52 ms) 67: [ RUN ] MimicTest.BondCuts 67: 67: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_BondCuts_input.mdp]: 67: For a correct single-point energy evaluation with nsteps = 0, use 67: continuation = yes to avoid constraining the input coordinates. 67: 67: Generating 1-4 interactions: fudge = 0.5 67: Number of degrees of freedom in T-Coupling group rest is 66.00 67: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 67: 67: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_BondCuts_input.mdp]: 67: NVE simulation: will use the initial temperature of 300.368 K for 67: determining the Verlet buffer size 67: 67: 67: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_BondCuts_input.mdp]: 67: You are using a plain Coulomb cut-off, which might produce artifacts. 67: You might want to consider using PME electrostatics. 67: 67: 67: 67: There were 3 NOTEs 67: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_BondCuts.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 67: Can not increase nstlist because an NVE ensemble is used 67: Using 1 MPI thread 67: Using 2 OpenMP threads 67: 67: 67: NOTE: The number of threads is not equal to the number of (logical) cpus 67: and the -pin option is set to auto: will not pin threads to cpus. 67: This can lead to significant performance degradation. 67: Consider using -pin on (and -pinoffset in case you run multiple jobs). 67: starting md rerun 'UNNAMED in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/ala.gro' 67: 67: Reading frames from gro file 'Alanine dipeptide in water', 23 atoms. 67: Reading frame 0 time 0.000 Last frame 0 time 0.000 67: 67: NOTE: 14 % of the run time was spent in pair search, 67: you might want to increase nstlist (this has no effect on accuracy) 67: 67: Core t (s) Wall t (s) (%) 67: Time: 0.003 0.002 189.2 67: (ns/day) (hour/ns) 67: Performance: 51.033 0.470 67: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_BondCuts.edr as single precision energy file 67: Reading energy frame 0 time 0.000 Last energy frame read 0 time 0.000 Setting the LD random seed to -6291497 67: 67: Generated 2211 of the 2211 non-bonded parameter combinations 67: 67: Generated 2211 of the 2211 1-4 parameter combinations 67: 67: Excluding 3 bonded neighbours molecule type 'Protein_chain_A' 67: 67: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/ala.gro' 67: 67: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 300.368 K 67: 67: Calculated rlist for 1x1 atom pair-list as 1.048 nm, buffer size 0.048 nm 67: 67: Set rlist, assuming 4x4 atom pair-list, to 1.036 nm, buffer size 0.036 nm 67: 67: Note that mdrun will redetermine rlist based on the actual pair-list setup 67: 67: This run will generate roughly 0 Mb of data 67: [ OK ] MimicTest.BondCuts (126 ms) 67: [----------] 4 tests from MimicTest (305 ms total) 67: 67: [----------] 2 tests from WithIntegrator/ImdTest 67: [ RUN ] WithIntegrator/ImdTest.ImdCanRun/0 67: Generating 1-4 interactions: fudge = 1 67: 67: NOTE 1 [file glycine_vacuo.top, line 12]: 67: The bond in molecule-type Glycine between atoms 1 N and 2 H1 has an 67: estimated oscillational period of 1.0e-02 ps, which is less than 10 times 67: the time step of 2.0e-03 ps. 67: Maybe you forgot to change the constraints mdp option. 67: 67: Group 'Heavy_Atoms' with 5 atoms can be activated for interactive molecular dynamics (IMD). 67: Number of degrees of freedom in T-Coupling group System is 27.00 67: 67: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/WithIntegrator_ImdTest_ImdCanRun_0_input.mdp]: 67: You are using a plain Coulomb cut-off, which might produce artifacts. 67: You might want to consider using PME electrostatics. 67: 67: 67: 67: There were 2 NOTEs 67: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/WithIntegrator_ImdTest_ImdCanRun_0.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 67: Changing nstlist from 10 to 25, rlist from 1.071 to 1.232 67: 67: Using 1 MPI thread 67: Using 2 OpenMP threads 67: 67: 67: NOTE: The number of threads is not equal to the number of (logical) cpus 67: and the -pin option is set to auto: will not pin threads to cpus. 67: This can lead to significant performance degradation. 67: Consider using -pin on (and -pinoffset in case you run multiple jobs). 67: 67: IMD: Enabled. This simulation will accept incoming IMD connections. 67: IMD: Pulling from IMD remote is enabled (-imdpull). 67: IMD: Setting port for connection requests to 0. 67: IMD: Setting up incoming socket. 67: IMD: Listening for IMD connection on port 33449. 67: IMD: -imdwait not set, starting simulation. 67: starting mdrun 'Glycine' 67: 2 steps, 0.0 ps. 67: Setting the LD random seed to 1559211967 67: 67: Generated 20503 of the 20503 non-bonded parameter combinations 67: 67: Generated 17396 of the 20503 1-4 parameter combinations 67: 67: Excluding 3 bonded neighbours molecule type 'Glycine' 67: 67: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/glycine_vacuo.gro', all velocities are zero 67: 67: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 300 K 67: 67: Calculated rlist for 1x1 atom pair-list as 1.093 nm, buffer size 0.093 nm 67: 67: Set rlist, assuming 4x4 atom pair-list, to 1.071 nm, buffer size 0.071 nm 67: 67: Note that mdrun will redetermine rlist based on the actual pair-list setup 67: 67: This run will generate roughly 0 Mb of data 67: 67: Writing final coordinates. 67: 67: Core t (s) Wall t (s) (%) 67: Time: 0.071 0.036 198.4 67: (ns/day) (hour/ns) 67: Performance: 14.468 1.659 67: [ OK ] WithIntegrator/ImdTest.ImdCanRun/0 (881 ms) 67: [ RUN ] WithIntegrator/ImdTest.ImdCanRun/1 67: 67: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/WithIntegrator_ImdTest_ImdCanRun_1_input.mdp]: 67: Setting tcoupl from 'V-rescale' to 'no'. Temperature coupling does not 67: apply to steep. 67: 67: Generating 1-4 interactions: fudge = 1 67: Group 'Heavy_Atoms' with 5 atoms can be activated for interactive molecular dynamics (IMD). 67: Number of degrees of freedom in T-Coupling group System is 27.00 67: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 67: 67: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/WithIntegrator_ImdTest_ImdCanRun_1_input.mdp]: 67: You are using a plain Coulomb cut-off, which might produce artifacts. 67: You might want to consider using PME electrostatics. 67: 67: 67: 67: There were 2 NOTEs 67: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/WithIntegrator_ImdTest_ImdCanRun_1.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 67: Using 1 MPI thread 67: Using 2 OpenMP threads 67: 67: 67: NOTE: The number of threads is not equal to the number of (logical) cpus 67: and the -pin option is set to auto: will not pin threads to cpus. 67: This can lead to significant performance degradation. 67: Consider using -pin on (and -pinoffset in case you run multiple jobs). 67: 67: IMD: Enabled. This simulation will accept incoming IMD connections. 67: IMD: Pulling from IMD remote is enabled (-imdpull). 67: IMD: Setting port for connection requests to 0. 67: IMD: Setting up incoming socket. 67: IMD: Listening for IMD connection on port 38603. 67: IMD: -imdwait not set, starting simulation. 67: 67: Steepest Descents: 67: Tolerance (Fmax) = 1.00000e+01 67: Number of steps = 2 67: 67: Energy minimization reached the maximum number of steps before the forces 67: reached the requested precision Fmax < 10. 67: 67: writing lowest energy coordinates. 67: 67: Steepest Descents did not converge to Fmax < 10 in 3 steps. 67: Potential Energy = 1.1977061e+03 67: Maximum force = 1.7794875e+04 on atom 9 67: Norm of force = 7.8732895e+03 67: Setting the LD random seed to 1610000799 67: 67: Generated 20503 of the 20503 non-bonded parameter combinations 67: 67: Generated 17396 of the 20503 1-4 parameter combinations 67: 67: Excluding 3 bonded neighbours molecule type 'Glycine' 67: 67: This run will generate roughly 0 Mb of data 67: [ OK ] WithIntegrator/ImdTest.ImdCanRun/1 (828 ms) 67: [----------] 2 tests from WithIntegrator/ImdTest (1709 ms total) 67: 67: [----------] Global test environment tear-down 67: [==========] 15 tests from 3 test suites ran. (2708 ms total) 67: [ PASSED ] 15 tests. 67/92 Test #67: MdrunModulesTests ......................... Passed 2.80 sec test 68 Start 68: MdrunIOTests 68: Test command: /build/reproducible-path/gromacs-2025.1/build/basic/bin/mdrun-io-test "-ntomp" "2" "--gtest_output=xml:/build/reproducible-path/gromacs-2025.1/build/basic/Testing/Temporary/MdrunIOTests.xml" 68: Working Directory: /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests 68: Test timeout computed to be: 600 68: [==========] Running 76 tests from 13 test suites. 68: [----------] Global test environment set-up. 68: [----------] 9 tests from GromppTest 68: [ RUN ] GromppTest.EmptyMdpFileWorks 68: 68: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/GromppTest_EmptyMdpFileWorks_input.mdp]: 68: For a correct single-point energy evaluation with nsteps = 0, use 68: continuation = yes to avoid constraining the input coordinates. 68: 68: Number of degrees of freedom in T-Coupling group rest is 12.00 68: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 68: 68: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/GromppTest_EmptyMdpFileWorks_input.mdp]: 68: NVE simulation: will use the initial temperature of 1046.791 K for 68: determining the Verlet buffer size 68: 68: 68: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/GromppTest_EmptyMdpFileWorks_input.mdp]: 68: You are using a plain Coulomb cut-off, which might produce artifacts. 68: You might want to consider using PME electrostatics. 68: 68: 68: 68: There were 3 NOTEs 68: Setting the LD random seed to -689703441 68: 68: Generated 8 of the 10 non-bonded parameter combinations 68: 68: Excluding 2 bonded neighbours molecule type 'Methanol' 68: 68: Excluding 2 bonded neighbours molecule type 'SOL' 68: 68: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/spc-and-methanol.gro' 68: 68: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 1046.79 K 68: 68: Calculated rlist for 1x1 atom pair-list as 1.089 nm, buffer size 0.089 nm 68: 68: Set rlist, assuming 4x4 atom pair-list, to 1.072 nm, buffer size 0.072 nm 68: 68: Note that mdrun will redetermine rlist based on the actual pair-list setup 68: 68: This run will generate roughly 0 Mb of data 68: [ OK ] GromppTest.EmptyMdpFileWorks (31 ms) 68: [ RUN ] GromppTest.SimulatedAnnealingWorks 68: 68: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/GromppTest_SimulatedAnnealingWorks_input.mdp]: 68: For a correct single-point energy evaluation with nsteps = 0, use 68: continuation = yes to avoid constraining the input coordinates. 68: 68: Simulated annealing for group rest: Periodic, 4 timepoints 68: Time (ps) Temperature (K) 68: 0.0 298.0 68: 2.0 320.0 68: 4.0 320.0 68: 6.0 298.0 68: Number of degrees of freedom in T-Coupling group rest is 12.00 68: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 68: 68: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/GromppTest_SimulatedAnnealingWorks_input.mdp]: 68: NVE simulation: will use the initial temperature of 1046.791 K for 68: determining the Verlet buffer size 68: 68: 68: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/GromppTest_SimulatedAnnealingWorks_input.mdp]: 68: You are using a plain Coulomb cut-off, which might produce artifacts. 68: You might want to consider using PME electrostatics. 68: 68: 68: 68: There were 3 NOTEs 68: Setting the LD random seed to -563169281 68: 68: Generated 8 of the 10 non-bonded parameter combinations 68: 68: Excluding 2 bonded neighbours molecule type 'Methanol' 68: 68: Excluding 2 bonded neighbours molecule type 'SOL' 68: 68: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/spc-and-methanol.gro' 68: 68: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 1046.79 K 68: 68: Calculated rlist for 1x1 atom pair-list as 1.089 nm, buffer size 0.089 nm 68: 68: Set rlist, assuming 4x4 atom pair-list, to 1.072 nm, buffer size 0.072 nm 68: 68: Note that mdrun will redetermine rlist based on the actual pair-list setup 68: 68: This run will generate roughly 0 Mb of data 68: [ OK ] GromppTest.SimulatedAnnealingWorks (28 ms) 68: [ RUN ] GromppTest.SimulatedAnnealingWorksWithMultipleGroups 68: 68: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/GromppTest_SimulatedAnnealingWorksWithMultipleGroups_input.mdp]: 68: For a correct single-point energy evaluation with nsteps = 0, use 68: continuation = yes to avoid constraining the input coordinates. 68: 68: Simulated annealing for group Methanol: Single, 3 timepoints 68: Time (ps) Temperature (K) 68: 0.0 298.0 68: 3.0 280.0 68: 6.0- 270.0 68: Simulated annealing for group SOL: Periodic, 4 timepoints 68: Time (ps) Temperature (K) 68: 0.0 298.0 68: 2.0 320.0 68: 4.0 320.0 68: 6.0 298.0 68: Number of degrees of freedom in T-Coupling group Methanol is 7.20 68: Number of degrees of freedom in T-Coupling group SOL is 4.80 68: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 68: 68: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/GromppTest_SimulatedAnnealingWorksWithMultipleGroups_input.mdp]: 68: NVE simulation: will use the initial temperature of 1046.791 K for 68: determining the Verlet buffer size 68: 68: 68: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/GromppTest_SimulatedAnnealingWorksWithMultipleGroups_input.mdp]: 68: You are using a plain Coulomb cut-off, which might produce artifacts. 68: You might want to consider using PME electrostatics. 68: 68: 68: 68: There were 3 NOTEs 68: Setting the LD random seed to -71893001 68: 68: Generated 8 of the 10 non-bonded parameter combinations 68: 68: Excluding 2 bonded neighbours molecule type 'Methanol' 68: 68: Excluding 2 bonded neighbours molecule type 'SOL' 68: 68: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/spc-and-methanol.gro' 68: 68: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 1046.79 K 68: 68: Calculated rlist for 1x1 atom pair-list as 1.089 nm, buffer size 0.089 nm 68: 68: Set rlist, assuming 4x4 atom pair-list, to 1.072 nm, buffer size 0.072 nm 68: 68: Note that mdrun will redetermine rlist based on the actual pair-list setup 68: 68: This run will generate roughly 0 Mb of data 68: [ OK ] GromppTest.SimulatedAnnealingWorksWithMultipleGroups (29 ms) 68: [ RUN ] GromppTest.DeathTestHandlesNoMaxwarnError 68: Setting the LD random seed to -100663821 68: 68: Generated 8 of the 10 non-bonded parameter combinations 68: 68: Excluding 2 bonded neighbours molecule type 'Methanol' 68: 68: Excluding 2 bonded neighbours molecule type 'SOL' 68: 68: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/spc-and-methanol.gro' 68: 68: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 68: 68: Calculated rlist for 1x1 atom pair-list as 1.040 nm, buffer size 0.040 nm 68: 68: Set rlist, assuming 4x4 atom pair-list, to 1.031 nm, buffer size 0.031 nm 68: 68: Note that mdrun will redetermine rlist based on the actual pair-list setup 68: 68: This run will generate roughly 0 Mb of data 68: [ OK ] GromppTest.DeathTestHandlesNoMaxwarnError (51 ms) 68: [ RUN ] GromppTest.HandlesMaxwarn 68: 68: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/GromppTest_HandlesMaxwarn_input.mdp]: 68: For a correct single-point energy evaluation with nsteps = 0, use 68: continuation = yes to avoid constraining the input coordinates. 68: 68: 68: WARNING 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/GromppTest_HandlesMaxwarn_input.mdp]: 68: The Berendsen thermostat does not generate the correct kinetic energy 68: distribution, and should not be used for new production simulations (in 68: our opinion). We would recommend the V-rescale thermostat. 68: 68: Number of degrees of freedom in T-Coupling group System is 12.00 68: 68: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/GromppTest_HandlesMaxwarn_input.mdp]: 68: You are using a plain Coulomb cut-off, which might produce artifacts. 68: You might want to consider using PME electrostatics. 68: 68: 68: 68: There were 2 NOTEs 68: 68: There was 1 WARNING 68: Setting the LD random seed to -11151465 68: 68: Generated 8 of the 10 non-bonded parameter combinations 68: 68: Excluding 2 bonded neighbours molecule type 'Methanol' 68: 68: Excluding 2 bonded neighbours molecule type 'SOL' 68: 68: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/spc-and-methanol.gro' 68: 68: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 68: 68: Calculated rlist for 1x1 atom pair-list as 1.040 nm, buffer size 0.040 nm 68: 68: Set rlist, assuming 4x4 atom pair-list, to 1.031 nm, buffer size 0.031 nm 68: 68: Note that mdrun will redetermine rlist based on the actual pair-list setup 68: 68: This run will generate roughly 0 Mb of data 68: [ OK ] GromppTest.HandlesMaxwarn (30 ms) 68: [ RUN ] GromppTest.MaxwarnShouldBePositive 68: [ OK ] GromppTest.MaxwarnShouldBePositive (4 ms) 68: [ RUN ] GromppTest.ValidTransformationCoord 68: 68: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/GromppTest_ValidTransformationCoord_input.mdp]: 68: For a correct single-point energy evaluation with nsteps = 0, use 68: continuation = yes to avoid constraining the input coordinates. 68: 68: Pull group 1 'SOL' has 3 atoms 68: Pull group 2 'Methanol' has 3 atoms 68: Number of degrees of freedom in T-Coupling group rest is 12.00 68: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 68: 68: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/GromppTest_ValidTransformationCoord_input.mdp]: 68: NVE simulation: will use the initial temperature of 1046.791 K for 68: determining the Verlet buffer size 68: 68: 68: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/GromppTest_ValidTransformationCoord_input.mdp]: 68: You are using a plain Coulomb cut-off, which might produce artifacts. 68: You might want to consider using PME electrostatics. 68: 68: 68: Pull group natoms pbc atom distance at start reference at t=0 68: 1 3 5 68: 2 3 2 0.613 nm 0.000 nm 68: 1 3 5 68: 2 3 2 0.613 nm 0.000 nm 68: 68: There were 3 NOTEs 68: Setting the LD random seed to -1611809829 68: 68: Generated 8 of the 10 non-bonded parameter combinations 68: 68: Excluding 2 bonded neighbours molecule type 'Methanol' 68: 68: Excluding 2 bonded neighbours molecule type 'SOL' 68: 68: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/spc-and-methanol.gro' 68: 68: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 1046.79 K 68: 68: Calculated rlist for 1x1 atom pair-list as 1.089 nm, buffer size 0.089 nm 68: 68: Set rlist, assuming 4x4 atom pair-list, to 1.072 nm, buffer size 0.072 nm 68: 68: Note that mdrun will redetermine rlist based on the actual pair-list setup 68: 68: This run will generate roughly 0 Mb of data 68: [ OK ] GromppTest.ValidTransformationCoord (36 ms) 68: [ RUN ] GromppTest.InvalidTransformationCoord 68: 68: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/GromppTest_InvalidTransformationCoord_input.mdp]: 68: For a correct single-point energy evaluation with nsteps = 0, use 68: continuation = yes to avoid constraining the input coordinates. 68: 68: Pull group 1 'SOL' has 3 atoms 68: Pull group 2 'Methanol' has 3 atoms 68: Number of degrees of freedom in T-Coupling group rest is 12.00 68: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 68: 68: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/GromppTest_InvalidTransformationCoord_input.mdp]: 68: NVE simulation: will use the initial temperature of 1046.791 K for 68: determining the Verlet buffer size 68: 68: 68: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/GromppTest_InvalidTransformationCoord_input.mdp]: 68: You are using a plain Coulomb cut-off, which might produce artifacts. 68: You might want to consider using PME electrostatics. 68: 68: 68: Pull group natoms pbc atom distance at start reference at t=0 68: 1 3 5 68: 2 3 2 0.613 nm 0.000 nm 68: 1 3 5 68: 2 3 2 Setting the LD random seed to -27961033 68: 68: Generated 8 of the 10 non-bonded parameter combinations 68: 68: Excluding 2 bonded neighbours molecule type 'Methanol' 68: 68: Excluding 2 bonded neighbours molecule type 'SOL' 68: 68: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/spc-and-methanol.gro' 68: 68: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 1046.79 K 68: 68: Calculated rlist for 1x1 atom pair-list as 1.089 nm, buffer size 0.089 nm 68: 68: Set rlist, assuming 4x4 atom pair-list, to 1.072 nm, buffer size 0.072 nm 68: 68: Note that mdrun will redetermine rlist based on the actual pair-list setup 68: [ OK ] GromppTest.InvalidTransformationCoord (35 ms) 68: [ RUN ] GromppTest.RejectCRescaleAndAnisotropic 68: Setting the LD random seed to -546834577 68: 68: Generated 8 of the 10 non-bonded parameter combinations 68: 68: Excluding 2 bonded neighbours molecule type 'Methanol' 68: 68: Excluding 2 bonded neighbours molecule type 'SOL' 68: 68: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/spc-and-methanol.gro' 68: [ OK ] GromppTest.RejectCRescaleAndAnisotropic (43 ms) 68: [----------] 9 tests from GromppTest (292 ms total) 68: 68: [----------] 6 tests from MdrunTerminationTest 68: [ RUN ] MdrunTerminationTest.CheckpointRestartAppendsByDefault 68: Generating 1-4 interactions: fudge = 0.5 68: Number of degrees of freedom in T-Coupling group System is 9.00 68: 68: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartAppendsByDefault_input.mdp]: 68: You are using a plain Coulomb cut-off, which might produce artifacts. 68: You might want to consider using PME electrostatics. 68: 68: 68: 68: There was 1 NOTE 68: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartAppendsByDefault.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 68: Changing nstlist from 10 to 50, rlist from 1.032 to 1.21 68: 68: Using 1 MPI thread 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'spc2' 68: 2 steps, 0.0 ps. 68: Setting the LD random seed to 1929113561 68: 68: Generated 3 of the 3 non-bonded parameter combinations 68: 68: Generated 3 of the 3 1-4 parameter combinations 68: 68: Excluding 2 bonded neighbours molecule type 'SOL' 68: 68: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/spc2.gro' 68: 68: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 68: 68: Calculated rlist for 1x1 atom pair-list as 1.041 nm, buffer size 0.041 nm 68: 68: Set rlist, assuming 4x4 atom pair-list, to 1.032 nm, buffer size 0.032 nm 68: 68: Note that mdrun will redetermine rlist based on the actual pair-list setup 68: 68: This run will generate roughly 0 Mb of data 68: 68: Writing final coordinates. 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.056 0.028 198.3 68: (ns/day) (hour/ns) 68: Performance: 9.160 2.620 68: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartAppendsByDefault.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 68: Setting nsteps to 4 68: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartAppendsByDefault.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 68: Changing nstlist from 10 to 50, rlist from 1.032 to 1.21 68: 68: Using 1 MPI thread 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'spc2' 68: 4 steps, 0.0 ps (continuing from step 2, 0.0 ps). 68: Input file: 68: Run start step 0 68: Run start time 0 ps 68: Step to be made during run 2 68: Runtime for the run 0.002 ps 68: Run end step 2 68: Run end time 0.002 ps 68: 68: 68: Output file: 68: Run start step 0 68: Run start time 0 ps 68: Step to be made during run 4 68: Runtime for the run 0.004 ps 68: Run end step 4 68: Run end time 0.004 ps 68: 68: 68: Writing final coordinates. 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.029 0.015 196.9 68: (ns/day) (hour/ns) 68: Performance: 17.313 1.386 68: [ OK ] MdrunTerminationTest.CheckpointRestartAppendsByDefault (138 ms) 68: [ RUN ] MdrunTerminationTest.WritesCheckpointAfterMaxhTerminationAndThenRestarts 68: Generating 1-4 interactions: fudge = 0.5 68: Number of degrees of freedom in T-Coupling group System is 9.00 68: 68: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_WritesCheckpointAfterMaxhTerminationAndThenRestarts_input.mdp]: 68: You are using a plain Coulomb cut-off, which might produce artifacts. 68: You might want to consider using PME electrostatics. 68: 68: 68: 68: There was 1 NOTE 68: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_WritesCheckpointAfterMaxhTerminationAndThenRestarts.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 68: Changing nstlist from 10 to 1, rlist from 1.032 to 1 68: 68: Using 1 MPI thread 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'spc2' 68: 100 steps, 0.1 ps. 68: 68: Step 0: Run time exceeded 0.000 hours, will terminate the run within 200 steps 68: Setting the LD random seed to -203424322 68: 68: Generated 3 of the 3 non-bonded parameter combinations 68: 68: Generated 3 of the 3 1-4 parameter combinations 68: 68: Excluding 2 bonded neighbours molecule type 'SOL' 68: 68: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/spc2.gro' 68: 68: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 68: 68: Calculated rlist for 1x1 atom pair-list as 1.041 nm, buffer size 0.041 nm 68: 68: Set rlist, assuming 4x4 atom pair-list, to 1.032 nm, buffer size 0.032 nm 68: 68: Note that mdrun will redetermine rlist based on the actual pair-list setup 68: 68: This run will generate roughly 0 Mb of data 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.041 0.021 197.6 68: (ns/day) (hour/ns) 68: Performance: 8.322 2.884 68: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_WritesCheckpointAfterMaxhTerminationAndThenRestarts.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 68: Setting nsteps to 102 68: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_WritesCheckpointAfterMaxhTerminationAndThenRestarts.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 68: Changing nstlist from 10 to 50, rlist from 1.032 to 1.21 68: 68: Using 1 MPI thread 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'spc2' 68: 102 steps, 0.1 ps (continuing from step 1, 0.0 ps). 68: Input file: 68: Run start step 0 68: Run start time 0 ps 68: Step to be made during run 100 68: Runtime for the run 0.1 ps 68: Run end step 100 68: Run end time 0.1 ps 68: 68: 68: Output file: 68: Run start step 0 68: Run start time 0 ps 68: Step to be made during run 102 68: Runtime for the run 0.102 ps 68: Run end step 102 68: Run end time 0.102 ps 68: 68: 68: Writing final coordinates. 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.044 0.023 197.3 68: (ns/day) (hour/ns) 68: Performance: 391.141 0.061 68: [ OK ] MdrunTerminationTest.WritesCheckpointAfterMaxhTerminationAndThenRestarts (123 ms) 68: [ RUN ] MdrunTerminationTest.CheckpointRestartWithNoAppendWorksAndCannotLaterAppend 68: Generating 1-4 interactions: fudge = 0.5 68: Number of degrees of freedom in T-Coupling group System is 9.00 68: 68: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartWithNoAppendWorksAndCannotLaterAppend_input.mdp]: 68: You are using a plain Coulomb cut-off, which might produce artifacts. 68: You might want to consider using PME electrostatics. 68: 68: 68: 68: There was 1 NOTE 68: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartWithNoAppendWorksAndCannotLaterAppend.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 68: Changing nstlist from 10 to 50, rlist from 1.032 to 1.21 68: 68: Using 1 MPI thread 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'spc2' 68: 2 steps, 0.0 ps. 68: Setting the LD random seed to -573863 68: 68: Generated 3 of the 3 non-bonded parameter combinations 68: 68: Generated 3 of the 3 1-4 parameter combinations 68: 68: Excluding 2 bonded neighbours molecule type 'SOL' 68: 68: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/spc2.gro' 68: 68: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 68: 68: Calculated rlist for 1x1 atom pair-list as 1.041 nm, buffer size 0.041 nm 68: 68: Set rlist, assuming 4x4 atom pair-list, to 1.032 nm, buffer size 0.032 nm 68: 68: Note that mdrun will redetermine rlist based on the actual pair-list setup 68: 68: This run will generate roughly 0 Mb of data 68: 68: Writing final coordinates. 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.043 0.022 197.8 68: (ns/day) (hour/ns) 68: Performance: 11.884 2.020 68: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartWithNoAppendWorksAndCannotLaterAppend.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 68: Setting nsteps to 4 68: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartWithNoAppendWorksAndCannotLaterAppend.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 68: Changing nstlist from 10 to 50, rlist from 1.032 to 1.21 68: 68: Using 1 MPI thread 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'spc2' 68: 4 steps, 0.0 ps (continuing from step 2, 0.0 ps). 68: Input file: 68: Run start step 0 68: Run start time 0 ps 68: Step to be made during run 2 68: Runtime for the run 0.002 ps 68: Run end step 2 68: Run end time 0.002 ps 68: 68: 68: Output file: 68: Run start step 0 68: Run start time 0 ps 68: Step to be made during run 4 68: Runtime for the run 0.004 ps 68: Run end step 4 68: Run end time 0.004 ps 68: 68: 68: Writing final coordinates. 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.056 0.028 198.9 68: (ns/day) (hour/ns) 68: Performance: 9.212 2.605 68: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartWithNoAppendWorksAndCannotLaterAppend.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 68: Setting nsteps to 6 68: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartWithNoAppendWorksAndCannotLaterAppend.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 68: Changing nstlist from 10 to 50, rlist from 1.032 to 1.21 68: 68: Using 1 MPI thread 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'spc2' 68: 6 steps, 0.0 ps (continuing from step 4, 0.0 ps). 68: Input file: 68: Run start step 0 68: Run start time 0 ps 68: Step to be made during run 4 68: Runtime for the run 0.004 ps 68: Run end step 4 68: Run end time 0.004 ps 68: 68: 68: Output file: 68: Run start step 0 68: Run start time 0 ps 68: Step to be made during run 6 68: Runtime for the run 0.006 ps 68: Run end step 6 68: Run end time 0.006 ps 68: 68: 68: Writing final coordinates. 68: 68: NOTE: 20 % of the run time was spent in pair search, 68: you might want to increase nstlist (this has no effect on accuracy) 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.053 0.027 198.9 68: (ns/day) (hour/ns) 68: Performance: 9.681 2.479 68: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartWithNoAppendWorksAndCannotLaterAppend.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 68: Setting nsteps to 8 68: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartWithNoAppendWorksAndCannotLaterAppend.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 68: Changing nstlist from 10 to 50, rlist from 1.032 to 1.21 68: 68: Using 1 MPI thread 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'spc2' 68: 8 steps, 0.0 ps (continuing from step 6, 0.0 ps). 68: Input file: 68: Run start step 0 68: Run start time 0 ps 68: Step to be made during run 6 68: Runtime for the run 0.006 ps 68: Run end step 6 68: Run end time 0.006 ps 68: 68: 68: Output file: 68: Run start step 0 68: Run start time 0 ps 68: Step to be made during run 8 68: Runtime for the run 0.008 ps 68: Run end step 8 68: Run end time 0.008 ps 68: 68: 68: Writing final coordinates. 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.062 0.031 198.9 68: (ns/day) (hour/ns) 68: Performance: 8.304 2.890 68: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartWithNoAppendWorksAndCannotLaterAppend.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 68: Changing nstlist from 10 to 50, rlist from 1.032 to 1.21 68: 68: Using 1 MPI thread 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'spc2' 68: 8 steps, 0.0 ps (continuing from step 8, 0.0 ps). 68: 68: NOTE: 20 % of the run time was spent in pair search, 68: you might want to increase nstlist (this has no effect on accuracy) 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.002 0.001 169.3 68: (ns/day) (hour/ns) 68: Performance: 95.997 0.250 68: [ OK ] MdrunTerminationTest.CheckpointRestartWithNoAppendWorksAndCannotLaterAppend (265 ms) 68: [ RUN ] MdrunTerminationTest.CheckpointRestartWorksEvenWithMissingCheckpointFile 68: Generating 1-4 interactions: fudge = 0.5 68: Number of degrees of freedom in T-Coupling group System is 9.00 68: 68: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartWorksEvenWithMissingCheckpointFile_input.mdp]: 68: You are using a plain Coulomb cut-off, which might produce artifacts. 68: You might want to consider using PME electrostatics. 68: 68: 68: 68: There was 1 NOTE 68: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartWorksEvenWithMissingCheckpointFile.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 68: Changing nstlist from 10 to 50, rlist from 1.032 to 1.21 68: 68: Using 1 MPI thread 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'spc2' 68: 2 steps, 0.0 ps. 68: Setting the LD random seed to 2130571221 68: 68: Generated 3 of the 3 non-bonded parameter combinations 68: 68: Generated 3 of the 3 1-4 parameter combinations 68: 68: Excluding 2 bonded neighbours molecule type 'SOL' 68: 68: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/spc2.gro' 68: 68: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 68: 68: Calculated rlist for 1x1 atom pair-list as 1.041 nm, buffer size 0.041 nm 68: 68: Set rlist, assuming 4x4 atom pair-list, to 1.032 nm, buffer size 0.032 nm 68: 68: Note that mdrun will redetermine rlist based on the actual pair-list setup 68: 68: This run will generate roughly 0 Mb of data 68: 68: Writing final coordinates. 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.039 0.020 197.1 68: (ns/day) (hour/ns) 68: Performance: 13.068 1.836 68: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartWorksEvenWithMissingCheckpointFile.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 68: Setting nsteps to 4 68: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartWorksEvenWithMissingCheckpointFile.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 68: Changing nstlist from 10 to 50, rlist from 1.032 to 1.21 68: 68: Using 1 MPI thread 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'spc2' 68: 4 steps, 0.0 ps. 68: Input file: 68: Run start step 0 68: Run start time 0 ps 68: Step to be made during run 2 68: Runtime for the run 0.002 ps 68: Run end step 2 68: Run end time 0.002 ps 68: 68: 68: Output file: 68: Run start step 0 68: Run start time 0 ps 68: Step to be made during run 4 68: Runtime for the run 0.004 ps 68: Run end step 4 68: Run end time 0.004 ps 68: 68: 68: Writing final coordinates. 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.029 0.015 196.9 68: (ns/day) (hour/ns) 68: Performance: 28.883 0.831 68: [ OK ] MdrunTerminationTest.CheckpointRestartWorksEvenWithMissingCheckpointFile (108 ms) 68: [ RUN ] MdrunTerminationTest.CheckpointRestartWorksEvenWithAppendAndMissingCheckpointFile 68: Generating 1-4 interactions: fudge = 0.5 68: Number of degrees of freedom in T-Coupling group System is 9.00 68: 68: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartWorksEvenWithAppendAndMissingCheckpointFile_input.mdp]: 68: You are using a plain Coulomb cut-off, which might produce artifacts. 68: You might want to consider using PME electrostatics. 68: 68: 68: 68: There was 1 NOTE 68: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartWorksEvenWithAppendAndMissingCheckpointFile.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 68: Changing nstlist from 10 to 50, rlist from 1.032 to 1.21 68: 68: Using 1 MPI thread 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'spc2' 68: 2 steps, 0.0 ps. 68: Setting the LD random seed to 1472149355 68: 68: Generated 3 of the 3 non-bonded parameter combinations 68: 68: Generated 3 of the 3 1-4 parameter combinations 68: 68: Excluding 2 bonded neighbours molecule type 'SOL' 68: 68: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/spc2.gro' 68: 68: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 68: 68: Calculated rlist for 1x1 atom pair-list as 1.041 nm, buffer size 0.041 nm 68: 68: Set rlist, assuming 4x4 atom pair-list, to 1.032 nm, buffer size 0.032 nm 68: 68: Note that mdrun will redetermine rlist based on the actual pair-list setup 68: 68: This run will generate roughly 0 Mb of data 68: 68: Writing final coordinates. 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.026 0.013 196.5 68: (ns/day) (hour/ns) 68: Performance: 19.408 1.237 68: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartWorksEvenWithAppendAndMissingCheckpointFile.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 68: Setting nsteps to 4 68: Input file: 68: Run start step 0 68: Run start time 0 ps 68: Step to be made during run 2 68: Runtime for the run 0.002 ps 68: Run end step 2 68: Run end time 0.002 ps 68: 68: 68: Output file: 68: Run start step 0 68: Run start time 0 ps 68: Step to be made during run 4 68: Runtime for the run 0.004 ps 68: Run end step 4 68: Run end time 0.004 ps 68: 68: [ OK ] MdrunTerminationTest.CheckpointRestartWorksEvenWithAppendAndMissingCheckpointFile (67 ms) 68: [ RUN ] MdrunTerminationTest.RunWithNoAppendCreatesPartFiles 68: Generating 1-4 interactions: fudge = 0.5 68: Number of degrees of freedom in T-Coupling group System is 9.00 68: 68: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_RunWithNoAppendCreatesPartFiles_input.mdp]: 68: You are using a plain Coulomb cut-off, which might produce artifacts. 68: You might want to consider using PME electrostatics. 68: 68: 68: 68: There was 1 NOTE 68: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_RunWithNoAppendCreatesPartFiles.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 68: Changing nstlist from 10 to 50, rlist from 1.032 to 1.21 68: 68: Using 1 MPI thread 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'spc2' 68: 2 steps, 0.0 ps. 68: Setting the LD random seed to -281023653 68: 68: Generated 3 of the 3 non-bonded parameter combinations 68: 68: Generated 3 of the 3 1-4 parameter combinations 68: 68: Excluding 2 bonded neighbours molecule type 'SOL' 68: 68: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/spc2.gro' 68: 68: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 68: 68: Calculated rlist for 1x1 atom pair-list as 1.041 nm, buffer size 0.041 nm 68: 68: Set rlist, assuming 4x4 atom pair-list, to 1.032 nm, buffer size 0.032 nm 68: 68: Note that mdrun will redetermine rlist based on the actual pair-list setup 68: 68: This run will generate roughly 0 Mb of data 68: 68: Writing final coordinates. 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.031 0.016 196.9 68: (ns/day) (hour/ns) 68: Performance: 16.696 1.438 68: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_RunWithNoAppendCreatesPartFiles.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 68: Setting nsteps to 4 68: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_RunWithNoAppendCreatesPartFiles.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 68: Changing nstlist from 10 to 50, rlist from 1.032 to 1.21 68: 68: Using 1 MPI thread 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'spc2' 68: 4 steps, 0.0 ps (continuing from step 2, 0.0 ps). 68: Input file: 68: Run start step 0 68: Run start time 0 ps 68: Step to be made during run 2 68: Runtime for the run 0.002 ps 68: Run end step 2 68: Run end time 0.002 ps 68: 68: 68: Output file: 68: Run start step 0 68: Run start time 0 ps 68: Step to be made during run 4 68: Runtime for the run 0.004 ps 68: Run end step 4 68: Run end time 0.004 ps 68: 68: 68: Writing final coordinates. 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.059 0.030 198.8 68: (ns/day) (hour/ns) 68: Performance: 8.772 2.736 68: [ OK ] MdrunTerminationTest.RunWithNoAppendCreatesPartFiles (123 ms) 68: [----------] 6 tests from MdrunTerminationTest (826 ms total) 68: 68: [----------] 2 tests from CheckpointCoordinatesAreSane/CheckpointCoordinatesSanityChecks 68: [ RUN ] CheckpointCoordinatesAreSane/CheckpointCoordinatesSanityChecks.WithinTolerances/0 68: 68: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/CheckpointCoordinatesAreSane_CheckpointCoordinatesSanityChecks_WithinTolerances_0_input.mdp]: 68: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 68: that with the Verlet scheme, nstlist has no effect on the accuracy of 68: your simulation. 68: 68: 68: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/CheckpointCoordinatesAreSane_CheckpointCoordinatesSanityChecks_WithinTolerances_0_input.mdp]: 68: Setting nstcalcenergy (100) equal to nstenergy (4) 68: 68: Generating 1-4 interactions: fudge = 0.5 68: Number of degrees of freedom in T-Coupling group System is 9.00 68: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 68: 68: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/CheckpointCoordinatesAreSane_CheckpointCoordinatesSanityChecks_WithinTolerances_0_input.mdp]: 68: NVE simulation: will use the initial temperature of 2573.591 K for 68: determining the Verlet buffer size 68: 68: 68: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/CheckpointCoordinatesAreSane_CheckpointCoordinatesSanityChecks_WithinTolerances_0_input.mdp]: 68: You are using a plain Coulomb cut-off, which might produce artifacts. 68: You might want to consider using PME electrostatics. 68: 68: 68: 68: There were 4 NOTEs 68: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/CheckpointCoordinatesAreSane_CheckpointCoordinatesSanityChecks_WithinTolerances_0.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 68: Can not increase nstlist because an NVE ensemble is used 68: Using 1 MPI thread 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'spc2' 68: 16 steps, 0.0 ps. 68: Generated 3 of the 3 non-bonded parameter combinations 68: 68: Generated 3 of the 3 1-4 parameter combinations 68: 68: Excluding 2 bonded neighbours molecule type 'SOL' 68: 68: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/spc2.gro' 68: 68: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 2573.59 K 68: 68: Calculated rlist for 1x1 atom pair-list as 0.906 nm, buffer size 0.206 nm 68: 68: Set rlist, assuming 4x4 atom pair-list, to 0.892 nm, buffer size 0.192 nm 68: 68: Note that mdrun will redetermine rlist based on the actual pair-list setup 68: 68: This run will generate roughly 0 Mb of data 68: 68: Writing final coordinates. 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.057 0.029 197.9 68: (ns/day) (hour/ns) 68: Performance: 50.861 0.472 68: trr version: GMX_trn_file (single precision) 68: 68: 68: [ OK ] CheckpointCoordinatesAreSane/CheckpointCoordinatesSanityChecks.WithinTolerances/0 (76 ms) 68: [ RUN ] CheckpointCoordinatesAreSane/CheckpointCoordinatesSanityChecks.WithinTolerances/1 68: 68: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/CheckpointCoordinatesAreSane_CheckpointCoordinatesSanityChecks_WithinTolerances_1_input.mdp]: 68: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 68: that with the Verlet scheme, nstlist has no effect on the accuracy of 68: your simulation. 68: 68: 68: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/CheckpointCoordinatesAreSane_CheckpointCoordinatesSanityChecks_WithinTolerances_1_input.mdp]: 68: Setting nstcalcenergy (100) equal to nstenergy (4) 68: 68: Generating 1-4 interactions: fudge = 0.5 68: Number of degrees of freedom in T-Coupling group System is 9.00 68: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 68: 68: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/CheckpointCoordinatesAreSane_CheckpointCoordinatesSanityChecks_WithinTolerances_1_input.mdp]: 68: NVE simulation: will use the initial temperature of 2573.591 K for 68: determining the Verlet buffer size 68: 68: 68: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/CheckpointCoordinatesAreSane_CheckpointCoordinatesSanityChecks_WithinTolerances_1_input.mdp]: 68: You are using a plain Coulomb cut-off, which might produce artifacts. 68: You might want to consider using PME electrostatics. 68: 68: 68: 68: There were 4 NOTEs 68: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/CheckpointCoordinatesAreSane_CheckpointCoordinatesSanityChecks_WithinTolerances_1.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 68: Can not increase nstlist because an NVE ensemble is used 68: Using 1 MPI thread 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'spc2' 68: 16 steps, 0.0 ps. 68: Generated 3 of the 3 non-bonded parameter combinations 68: 68: Generated 3 of the 3 1-4 parameter combinations 68: 68: Excluding 2 bonded neighbours molecule type 'SOL' 68: 68: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/spc2.gro' 68: 68: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 2573.59 K 68: 68: Calculated rlist for 1x1 atom pair-list as 0.906 nm, buffer size 0.206 nm 68: 68: Set rlist, assuming 4x4 atom pair-list, to 0.892 nm, buffer size 0.192 nm 68: 68: Note that mdrun will redetermine rlist based on the actual pair-list setup 68: 68: This run will generate roughly 0 Mb of data 68: 68: Writing final coordinates. 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.071 0.035 199.1 68: (ns/day) (hour/ns) 68: Performance: 41.463 0.579 68: 68: 68: [ OK ] CheckpointCoordinatesAreSane/CheckpointCoordinatesSanityChecks.WithinTolerances/1 (78 ms) 68: [----------] 2 tests from CheckpointCoordinatesAreSane/CheckpointCoordinatesSanityChecks (156 ms total) 68: 68: [----------] 24 tests from NormalIntegrators/MdrunNoAppendContinuationIsExact 68: [ RUN ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/0 68: 68: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 68: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 68: that with the Verlet scheme, nstlist has no effect on the accuracy of 68: your simulation. 68: 68: 68: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 68: Setting nstcalcenergy (100) equal to nstenergy (4) 68: 68: Number of degrees of freedom in T-Coupling group System is 33.00 68: 68: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 68: NVE simulation: will use the initial temperature of 68.810 K for 68: determining the Verlet buffer size 68: 68: 68: There were 3 NOTEs 68: 68: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 68: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 68: that with the Verlet scheme, nstlist has no effect on the accuracy of 68: your simulation. 68: 68: 68: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 68: Setting nstcalcenergy (100) equal to nstenergy (4) 68: 68: Number of degrees of freedom in T-Coupling group System is 33.00 68: 68: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 68: NVE simulation: will use the initial temperature of 68.810 K for 68: determining the Verlet buffer size 68: 68: 68: There were 3 NOTEs 68: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 68: Can not increase nstlist because an NVE ensemble is used 68: Using 1 MPI thread 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'Argon' 68: 16 steps, 0.0 ps. 68: Generated 1 of the 1 non-bonded parameter combinations 68: 68: Excluding 1 bonded neighbours molecule type 'Argon' 68: 68: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 68: 68: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 68: 68: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 68: 68: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 68: 68: Note that mdrun will redetermine rlist based on the actual pair-list setup 68: 68: This run will generate roughly 0 Mb of data 68: Generated 1 of the 1 non-bonded parameter combinations 68: 68: Excluding 1 bonded neighbours molecule type 'Argon' 68: 68: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 68: 68: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 68: 68: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 68: 68: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 68: 68: Note that mdrun will redetermine rlist based on the actual pair-list setup 68: 68: This run will generate roughly 0 Mb of data 68: 68: Writing final coordinates. 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.062 0.031 198.1 68: (ns/day) (hour/ns) 68: Performance: 47.309 0.507 68: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_0_firstpart.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 68: Can not increase nstlist because an NVE ensemble is used 68: Using 1 MPI thread 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'Argon' 68: 8 steps, 0.0 ps. 68: 68: Writing final coordinates. 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.044 0.022 197.5 68: (ns/day) (hour/ns) 68: Performance: 34.768 0.690 68: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 68: Can not increase nstlist because an NVE ensemble is used 68: Using 1 MPI thread 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'Argon' 68: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 68: 68: Writing final coordinates. 68: 68: NOTE: 21 % of the run time was spent in pair search, 68: you might want to increase nstlist (this has no effect on accuracy) 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.060 0.030 198.2 68: (ns/day) (hour/ns) 68: Performance: 25.540 0.940 68: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.edr as single precision energy file 68: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_0_firstpart.edr as single precision energy file 68: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_0_secondpart.part0002.edr as single precision energy file 68: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/0 (205 ms) 68: [ RUN ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/1 68: 68: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 68: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 68: that with the Verlet scheme, nstlist has no effect on the accuracy of 68: your simulation. 68: 68: 68: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 68: Setting nstcalcenergy (100) equal to nstenergy (4) 68: 68: Number of degrees of freedom in T-Coupling group System is 33.00 68: 68: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 68: NVE simulation: will use the initial temperature of 68.810 K for 68: determining the Verlet buffer size 68: 68: 68: There were 3 NOTEs 68: 68: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 68: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 68: that with the Verlet scheme, nstlist has no effect on the accuracy of 68: your simulation. 68: 68: 68: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 68: Setting nstcalcenergy (100) equal to nstenergy (4) 68: 68: Number of degrees of freedom in T-Coupling group System is 33.00 68: 68: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 68: NVE simulation: will use the initial temperature of 68.810 K for 68: determining the Verlet buffer size 68: 68: 68: There were 3 NOTEs 68: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_1_full.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 68: Can not increase nstlist because an NVE ensemble is used 68: Using 1 MPI thread 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'Argon' 68: 16 steps, 0.0 ps. 68: Generated 1 of the 1 non-bonded parameter combinations 68: 68: Excluding 1 bonded neighbours molecule type 'Argon' 68: 68: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 68: 68: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 68.8096 K 68: 68: Calculated rlist for 1x1 atom pair-list as 0.702 nm, buffer size 0.002 nm 68: 68: Set rlist, assuming 4x4 atom pair-list, to 0.702 nm, buffer size 0.002 nm 68: 68: Note that mdrun will redetermine rlist based on the actual pair-list setup 68: 68: This run will generate roughly 0 Mb of data 68: Generated 1 of the 1 non-bonded parameter combinations 68: 68: Excluding 1 bonded neighbours molecule type 'Argon' 68: 68: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 68: 68: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 68.8096 K 68: 68: Calculated rlist for 1x1 atom pair-list as 0.702 nm, buffer size 0.002 nm 68: 68: Set rlist, assuming 4x4 atom pair-list, to 0.702 nm, buffer size 0.002 nm 68: 68: Note that mdrun will redetermine rlist based on the actual pair-list setup 68: 68: This run will generate roughly 0 Mb of data 68: 68: Writing final coordinates. 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.056 0.028 198.0 68: (ns/day) (hour/ns) 68: Performance: 51.929 0.462 68: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_1_firstpart.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 68: Can not increase nstlist because an NVE ensemble is used 68: Using 1 MPI thread 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'Argon' 68: 8 steps, 0.0 ps. 68: 68: Writing final coordinates. 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.046 0.023 197.4 68: (ns/day) (hour/ns) 68: Performance: 33.373 0.719 68: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_1_full.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 68: Can not increase nstlist because an NVE ensemble is used 68: Using 1 MPI thread 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'Argon' 68: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 68: 68: Writing final coordinates. 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.048 0.024 197.6 68: (ns/day) (hour/ns) 68: Performance: 31.919 0.752 68: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_1_full.edr as single precision energy file 68: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_1_firstpart.edr as single precision energy file 68: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_1_secondpart.part0002.edr as single precision energy file 68: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/1 (200 ms) 68: [ RUN ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/2 68: 68: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]: 68: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 68: that with the Verlet scheme, nstlist has no effect on the accuracy of 68: your simulation. 68: 68: 68: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]: 68: Setting nstcalcenergy (100) equal to nstenergy (4) 68: 68: Number of degrees of freedom in T-Coupling group System is 33.00 68: 68: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]: 68: NVE simulation: will use the initial temperature of 68.810 K for 68: determining the Verlet buffer size 68: 68: 68: There were 3 NOTEs 68: 68: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]: 68: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 68: that with the Verlet scheme, nstlist has no effect on the accuracy of 68: your simulation. 68: 68: 68: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]: 68: Setting nstcalcenergy (100) equal to nstenergy (4) 68: 68: Number of degrees of freedom in T-Coupling group System is 33.00 68: 68: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]: 68: NVE simulation: will use the initial temperature of 68.810 K for 68: determining the Verlet buffer size 68: 68: 68: There were 3 NOTEs 68: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_2_full.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 68: Can not increase nstlist because an NVE ensemble is used 68: Using 1 MPI thread 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'Argon' 68: 16 steps, 0.0 ps. 68: Generated 1 of the 1 non-bonded parameter combinations 68: 68: Excluding 1 bonded neighbours molecule type 'Argon' 68: 68: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 68: 68: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 68: 68: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 68: 68: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 68: 68: Note that mdrun will redetermine rlist based on the actual pair-list setup 68: 68: This run will generate roughly 0 Mb of data 68: Generated 1 of the 1 non-bonded parameter combinations 68: 68: Excluding 1 bonded neighbours molecule type 'Argon' 68: 68: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 68: 68: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 68: 68: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 68: 68: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 68: 68: Note that mdrun will redetermine rlist based on the actual pair-list setup 68: 68: This run will generate roughly 0 Mb of data 68: 68: Writing final coordinates. 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.051 0.026 198.0 68: (ns/day) (hour/ns) 68: Performance: 56.555 0.424 68: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_2_firstpart.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 68: Can not increase nstlist because an NVE ensemble is used 68: Using 1 MPI thread 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'Argon' 68: 8 steps, 0.0 ps. 68: 68: Writing final coordinates. 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.080 0.040 199.2 68: (ns/day) (hour/ns) 68: Performance: 19.261 1.246 68: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_2_full.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 68: Can not increase nstlist because an NVE ensemble is used 68: Using 1 MPI thread 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'Argon' 68: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 68: 68: Writing final coordinates. 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.082 0.041 198.4 68: (ns/day) (hour/ns) 68: Performance: 18.788 1.277 68: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_2_full.edr as single precision energy file 68: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_2_firstpart.edr as single precision energy file 68: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_2_secondpart.part0002.edr as single precision energy file 68: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/2 (217 ms) 68: [ RUN ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/3 68: 68: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]: 68: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 68: that with the Verlet scheme, nstlist has no effect on the accuracy of 68: your simulation. 68: 68: 68: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]: 68: Setting nstcalcenergy (100) equal to nstenergy (4) 68: 68: Number of degrees of freedom in T-Coupling group System is 33.00 68: 68: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]: 68: NVE simulation: will use the initial temperature of 68.810 K for 68: determining the Verlet buffer size 68: 68: 68: There were 3 NOTEs 68: 68: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]: 68: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 68: that with the Verlet scheme, nstlist has no effect on the accuracy of 68: your simulation. 68: 68: 68: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]: 68: Setting nstcalcenergy (100) equal to nstenergy (4) 68: 68: Number of degrees of freedom in T-Coupling group System is 33.00 68: 68: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]: 68: NVE simulation: will use the initial temperature of 68.810 K for 68: determining the Verlet buffer size 68: 68: 68: There were 3 NOTEs 68: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_3_full.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 68: Can not increase nstlist because an NVE ensemble is used 68: Using 1 MPI thread 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'Argon' 68: 16 steps, 0.0 ps. 68: Generated 1 of the 1 non-bonded parameter combinations 68: 68: Excluding 1 bonded neighbours molecule type 'Argon' 68: 68: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 68: 68: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 68.8096 K 68: 68: Calculated rlist for 1x1 atom pair-list as 0.702 nm, buffer size 0.002 nm 68: 68: Set rlist, assuming 4x4 atom pair-list, to 0.702 nm, buffer size 0.002 nm 68: 68: Note that mdrun will redetermine rlist based on the actual pair-list setup 68: 68: This run will generate roughly 0 Mb of data 68: Generated 1 of the 1 non-bonded parameter combinations 68: 68: Excluding 1 bonded neighbours molecule type 'Argon' 68: 68: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 68: 68: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 68.8096 K 68: 68: Calculated rlist for 1x1 atom pair-list as 0.702 nm, buffer size 0.002 nm 68: 68: Set rlist, assuming 4x4 atom pair-list, to 0.702 nm, buffer size 0.002 nm 68: 68: Note that mdrun will redetermine rlist based on the actual pair-list setup 68: 68: This run will generate roughly 0 Mb of data 68: 68: Writing final coordinates. 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.069 0.035 198.5 68: (ns/day) (hour/ns) 68: Performance: 42.390 0.566 68: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_3_firstpart.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 68: Can not increase nstlist because an NVE ensemble is used 68: Using 1 MPI thread 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'Argon' 68: 8 steps, 0.0 ps. 68: 68: Writing final coordinates. 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.046 0.023 198.6 68: (ns/day) (hour/ns) 68: Performance: 33.756 0.711 68: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_3_full.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 68: Can not increase nstlist because an NVE ensemble is used 68: Using 1 MPI thread 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'Argon' 68: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 68: 68: Writing final coordinates. 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.050 0.025 197.9 68: (ns/day) (hour/ns) 68: Performance: 30.985 0.775 68: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_3_full.edr as single precision energy file 68: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_3_firstpart.edr as single precision energy file 68: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_3_secondpart.part0002.edr as single precision energy file 68: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/3 (188 ms) 68: [ RUN ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/4 68: 68: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_4_input.mdp]: 68: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 68: that with the Verlet scheme, nstlist has no effect on the accuracy of 68: your simulation. 68: 68: 68: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_4_input.mdp]: 68: Setting nstcalcenergy (100) equal to nstenergy (4) 68: 68: Number of degrees of freedom in T-Coupling group System is 33.00 68: 68: There were 2 NOTEs 68: 68: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_4_input.mdp]: 68: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 68: that with the Verlet scheme, nstlist has no effect on the accuracy of 68: your simulation. 68: 68: 68: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_4_input.mdp]: 68: Setting nstcalcenergy (100) equal to nstenergy (4) 68: 68: Number of degrees of freedom in T-Coupling group System is 33.00 68: 68: There were 2 NOTEs 68: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_4_full.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 68: Using 1 MPI thread 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'Argon' 68: 16 steps, 0.0 ps. 68: Generated 1 of the 1 non-bonded parameter combinations 68: 68: Excluding 1 bonded neighbours molecule type 'Argon' 68: 68: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 68: 68: Calculated rlist for 1x1 atom pair-list as 0.713 nm, buffer size 0.013 nm 68: 68: Set rlist, assuming 4x4 atom pair-list, to 0.712 nm, buffer size 0.012 nm 68: 68: Note that mdrun will redetermine rlist based on the actual pair-list setup 68: 68: This run will generate roughly 0 Mb of data 68: Generated 1 of the 1 non-bonded parameter combinations 68: 68: Excluding 1 bonded neighbours molecule type 'Argon' 68: 68: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 68: 68: Calculated rlist for 1x1 atom pair-list as 0.713 nm, buffer size 0.013 nm 68: 68: Set rlist, assuming 4x4 atom pair-list, to 0.712 nm, buffer size 0.012 nm 68: 68: Note that mdrun will redetermine rlist based on the actual pair-list setup 68: 68: This run will generate roughly 0 Mb of data 68: 68: Writing final coordinates. 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.047 0.024 197.8 68: (ns/day) (hour/ns) 68: Performance: 61.307 0.391 68: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_4_firstpart.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 68: Using 1 MPI thread 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'Argon' 68: 8 steps, 0.0 ps. 68: 68: Writing final coordinates. 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.034 0.017 197.0 68: (ns/day) (hour/ns) 68: Performance: 45.567 0.527 68: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_4_full.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 68: Using 1 MPI thread 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'Argon' 68: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 68: 68: Writing final coordinates. 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.040 0.020 197.3 68: (ns/day) (hour/ns) 68: Performance: 38.366 0.626 68: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_4_full.edr as single precision energy file 68: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_4_firstpart.edr as single precision energy file 68: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_4_secondpart.part0002.edr as single precision energy file 68: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/4 (166 ms) 68: [ RUN ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/5 68: 68: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_5_input.mdp]: 68: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 68: that with the Verlet scheme, nstlist has no effect on the accuracy of 68: your simulation. 68: 68: 68: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_5_input.mdp]: 68: Setting nstcalcenergy (100) equal to nstenergy (4) 68: 68: Number of degrees of freedom in T-Coupling group System is 33.00 68: 68: There were 2 NOTEs 68: 68: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_5_input.mdp]: 68: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 68: that with the Verlet scheme, nstlist has no effect on the accuracy of 68: your simulation. 68: 68: 68: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_5_input.mdp]: 68: Setting nstcalcenergy (100) equal to nstenergy (4) 68: 68: Number of degrees of freedom in T-Coupling group System is 33.00 68: 68: There were 2 NOTEs 68: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_5_full.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 68: Changing nstlist from 8 to 100, rlist from 0.709 to 0.733 68: 68: Using 1 MPI thread 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'Argon' 68: 16 steps, 0.0 ps. 68: Generated 1 of the 1 non-bonded parameter combinations 68: 68: Excluding 1 bonded neighbours molecule type 'Argon' 68: 68: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 80 K 68: 68: Calculated rlist for 1x1 atom pair-list as 0.711 nm, buffer size 0.011 nm 68: 68: Set rlist, assuming 4x4 atom pair-list, to 0.709 nm, buffer size 0.009 nm 68: 68: Note that mdrun will redetermine rlist based on the actual pair-list setup 68: 68: This run will generate roughly 0 Mb of data 68: Generated 1 of the 1 non-bonded parameter combinations 68: 68: Excluding 1 bonded neighbours molecule type 'Argon' 68: 68: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 80 K 68: 68: Calculated rlist for 1x1 atom pair-list as 0.711 nm, buffer size 0.011 nm 68: 68: Set rlist, assuming 4x4 atom pair-list, to 0.709 nm, buffer size 0.009 nm 68: 68: Note that mdrun will redetermine rlist based on the actual pair-list setup 68: 68: This run will generate roughly 0 Mb of data 68: 68: Writing final coordinates. 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.057 0.029 198.1 68: (ns/day) (hour/ns) 68: Performance: 51.365 0.467 68: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_5_firstpart.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 68: Changing nstlist from 8 to 100, rlist from 0.709 to 0.733 68: 68: Using 1 MPI thread 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'Argon' 68: 8 steps, 0.0 ps. 68: 68: Writing final coordinates. 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.058 0.029 198.2 68: (ns/day) (hour/ns) 68: Performance: 26.665 0.900 68: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_5_full.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 68: Changing nstlist from 8 to 100, rlist from 0.709 to 0.733 68: 68: Using 1 MPI thread 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'Argon' 68: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 68: 68: Writing final coordinates. 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.052 0.026 198.0 68: (ns/day) (hour/ns) 68: Performance: 29.398 0.816 68: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_5_full.edr as single precision energy file 68: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_5_firstpart.edr as single precision energy file 68: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_5_secondpart.part0002.edr as single precision energy file 68: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/5 (200 ms) 68: [ RUN ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/6 68: 68: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_6_input.mdp]: 68: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 68: that with the Verlet scheme, nstlist has no effect on the accuracy of 68: your simulation. 68: 68: 68: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_6_input.mdp]: 68: Setting nstcalcenergy (100) equal to nstenergy (4) 68: 68: Number of degrees of freedom in T-Coupling group System is 33.00 68: 68: There were 2 NOTEs 68: 68: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_6_input.mdp]: 68: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 68: that with the Verlet scheme, nstlist has no effect on the accuracy of 68: your simulation. 68: 68: 68: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_6_input.mdp]: 68: Setting nstcalcenergy (100) equal to nstenergy (4) 68: 68: Number of degrees of freedom in T-Coupling group System is 33.00 68: 68: There were 2 NOTEs 68: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_6_full.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 68: Using 1 MPI thread 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'Argon' 68: 16 steps, 0.0 ps. 68: Generated 1 of the 1 non-bonded parameter combinations 68: 68: Excluding 1 bonded neighbours molecule type 'Argon' 68: 68: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 68: 68: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 68: 68: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 68: 68: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 68: 68: Note that mdrun will redetermine rlist based on the actual pair-list setup 68: 68: This run will generate roughly 0 Mb of data 68: Generated 1 of the 1 non-bonded parameter combinations 68: 68: Excluding 1 bonded neighbours molecule type 'Argon' 68: 68: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 68: 68: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 68: 68: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 68: 68: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 68: 68: Note that mdrun will redetermine rlist based on the actual pair-list setup 68: 68: This run will generate roughly 0 Mb of data 68: 68: Writing final coordinates. 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.040 0.020 197.4 68: (ns/day) (hour/ns) 68: Performance: 73.035 0.329 68: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_6_firstpart.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 68: Using 1 MPI thread 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'Argon' 68: 8 steps, 0.0 ps. 68: 68: Writing final coordinates. 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.038 0.019 197.3 68: (ns/day) (hour/ns) 68: Performance: 40.738 0.589 68: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_6_full.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 68: Using 1 MPI thread 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'Argon' 68: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 68: 68: Writing final coordinates. 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.039 0.019 197.9 68: (ns/day) (hour/ns) 68: Performance: 39.932 0.601 68: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_6_full.edr as single precision energy file 68: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_6_firstpart.edr as single precision energy file 68: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_6_secondpart.part0002.edr as single precision energy file 68: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/6 (173 ms) 68: [ RUN ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/7 68: 68: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_7_input.mdp]: 68: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 68: that with the Verlet scheme, nstlist has no effect on the accuracy of 68: your simulation. 68: 68: 68: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_7_input.mdp]: 68: Setting nstcalcenergy (100) equal to nstenergy (4) 68: 68: Number of degrees of freedom in T-Coupling group System is 33.00 68: 68: There were 2 NOTEs 68: 68: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_7_input.mdp]: 68: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 68: that with the Verlet scheme, nstlist has no effect on the accuracy of 68: your simulation. 68: 68: 68: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_7_input.mdp]: 68: Setting nstcalcenergy (100) equal to nstenergy (4) 68: 68: Number of degrees of freedom in T-Coupling group System is 33.00 68: 68: There were 2 NOTEs 68: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_7_full.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 68: Changing nstlist from 8 to 100, rlist from 0.702 to 0.738 68: 68: Using 1 MPI thread 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'Argon' 68: 16 steps, 0.0 ps. 68: Generated 1 of the 1 non-bonded parameter combinations 68: 68: Excluding 1 bonded neighbours molecule type 'Argon' 68: 68: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 68: 68: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 80 K 68: 68: Calculated rlist for 1x1 atom pair-list as 0.702 nm, buffer size 0.002 nm 68: 68: Set rlist, assuming 4x4 atom pair-list, to 0.702 nm, buffer size 0.002 nm 68: 68: Note that mdrun will redetermine rlist based on the actual pair-list setup 68: 68: This run will generate roughly 0 Mb of data 68: Generated 1 of the 1 non-bonded parameter combinations 68: 68: Excluding 1 bonded neighbours molecule type 'Argon' 68: 68: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 68: 68: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 80 K 68: 68: Calculated rlist for 1x1 atom pair-list as 0.702 nm, buffer size 0.002 nm 68: 68: Set rlist, assuming 4x4 atom pair-list, to 0.702 nm, buffer size 0.002 nm 68: 68: Note that mdrun will redetermine rlist based on the actual pair-list setup 68: 68: This run will generate roughly 0 Mb of data 68: 68: Writing final coordinates. 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.039 0.020 197.9 68: (ns/day) (hour/ns) 68: Performance: 74.687 0.321 68: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_7_firstpart.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 68: Changing nstlist from 8 to 100, rlist from 0.702 to 0.738 68: 68: Using 1 MPI thread 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'Argon' 68: 8 steps, 0.0 ps. 68: 68: Writing final coordinates. 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.090 0.045 198.9 68: (ns/day) (hour/ns) 68: Performance: 17.122 1.402 68: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_7_full.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 68: Changing nstlist from 8 to 100, rlist from 0.702 to 0.738 68: 68: Using 1 MPI thread 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'Argon' 68: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 68: 68: Writing final coordinates. 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.042 0.021 197.9 68: (ns/day) (hour/ns) 68: Performance: 36.488 0.658 68: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_7_full.edr as single precision energy file 68: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_7_firstpart.edr as single precision energy file 68: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_7_secondpart.part0002.edr as single precision energy file 68: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/7 (204 ms) 68: [ RUN ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/8 68: 68: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_8_input.mdp]: 68: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 68: that with the Verlet scheme, nstlist has no effect on the accuracy of 68: your simulation. 68: 68: 68: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_8_input.mdp]: 68: Setting nstcalcenergy (100) equal to nstenergy (4) 68: 68: Generating 1-4 interactions: fudge = 0.5 68: Number of degrees of freedom in T-Coupling group System is 9.00 68: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 68: 68: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_8_input.mdp]: 68: NVE simulation: will use the initial temperature of 2573.591 K for 68: determining the Verlet buffer size 68: 68: 68: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_8_input.mdp]: 68: You are using a plain Coulomb cut-off, which might produce artifacts. 68: You might want to consider using PME electrostatics. 68: 68: 68: 68: There were 4 NOTEs 68: 68: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_8_input.mdp]: 68: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 68: that with the Verlet scheme, nstlist has no effect on the accuracy of 68: your simulation. 68: 68: 68: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_8_input.mdp]: 68: Setting nstcalcenergy (100) equal to nstenergy (4) 68: 68: Generating 1-4 interactions: fudge = 0.5 68: Number of degrees of freedom in T-Coupling group System is 9.00 68: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 68: 68: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_8_input.mdp]: 68: NVE simulation: will use the initial temperature of 2573.591 K for 68: determining the Verlet buffer size 68: 68: 68: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_8_input.mdp]: 68: You are using a plain Coulomb cut-off, which might produce artifacts. 68: You might want to consider using PME electrostatics. 68: 68: 68: 68: There were 4 NOTEs 68: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_8_full.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 68: Can not increase nstlist because an NVE ensemble is used 68: Using 1 MPI thread 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'spc2' 68: 16 steps, 0.0 ps. 68: Generated 3 of the 3 non-bonded parameter combinations 68: 68: Generated 3 of the 3 1-4 parameter combinations 68: 68: Excluding 2 bonded neighbours molecule type 'SOL' 68: 68: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/spc2.gro' 68: 68: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 2573.59 K 68: 68: Calculated rlist for 1x1 atom pair-list as 0.906 nm, buffer size 0.206 nm 68: 68: Set rlist, assuming 4x4 atom pair-list, to 0.892 nm, buffer size 0.192 nm 68: 68: Note that mdrun will redetermine rlist based on the actual pair-list setup 68: 68: This run will generate roughly 0 Mb of data 68: Generated 3 of the 3 non-bonded parameter combinations 68: 68: Generated 3 of the 3 1-4 parameter combinations 68: 68: Excluding 2 bonded neighbours molecule type 'SOL' 68: 68: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/spc2.gro' 68: 68: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 2573.59 K 68: 68: Calculated rlist for 1x1 atom pair-list as 0.906 nm, buffer size 0.206 nm 68: 68: Set rlist, assuming 4x4 atom pair-list, to 0.892 nm, buffer size 0.192 nm 68: 68: Note that mdrun will redetermine rlist based on the actual pair-list setup 68: 68: This run will generate roughly 0 Mb of data 68: 68: Writing final coordinates. 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.041 0.021 197.1 68: (ns/day) (hour/ns) 68: Performance: 70.500 0.340 68: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_8_firstpart.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 68: Can not increase nstlist because an NVE ensemble is used 68: Using 1 MPI thread 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'spc2' 68: 8 steps, 0.0 ps. 68: 68: Writing final coordinates. 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.049 0.025 197.5 68: (ns/day) (hour/ns) 68: Performance: 31.474 0.763 68: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_8_full.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 68: Can not increase nstlist because an NVE ensemble is used 68: Using 1 MPI thread 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'spc2' 68: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 68: 68: Writing final coordinates. 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.042 0.021 197.1 68: (ns/day) (hour/ns) 68: Performance: 36.178 0.663 68: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_8_full.edr as single precision energy file 68: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_8_firstpart.edr as single precision energy file 68: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_8_secondpart.part0002.edr as single precision energy file 68: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/8 (182 ms) 68: [ RUN ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/9 68: 68: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_9_input.mdp]: 68: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 68: that with the Verlet scheme, nstlist has no effect on the accuracy of 68: your simulation. 68: 68: 68: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_9_input.mdp]: 68: Setting nstcalcenergy (100) equal to nstenergy (4) 68: 68: Generating 1-4 interactions: fudge = 0.5 68: Number of degrees of freedom in T-Coupling group System is 9.00 68: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 68: 68: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_9_input.mdp]: 68: NVE simulation: will use the initial temperature of 2573.591 K for 68: determining the Verlet buffer size 68: 68: 68: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_9_input.mdp]: 68: You are using a plain Coulomb cut-off, which might produce artifacts. 68: You might want to consider using PME electrostatics. 68: 68: 68: 68: There were 4 NOTEs 68: 68: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_9_input.mdp]: 68: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 68: that with the Verlet scheme, nstlist has no effect on the accuracy of 68: your simulation. 68: 68: 68: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_9_input.mdp]: 68: Setting nstcalcenergy (100) equal to nstenergy (4) 68: 68: Generating 1-4 interactions: fudge = 0.5 68: Number of degrees of freedom in T-Coupling group System is 9.00 68: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 68: 68: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_9_input.mdp]: 68: NVE simulation: will use the initial temperature of 2573.591 K for 68: determining the Verlet buffer size 68: 68: 68: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_9_input.mdp]: 68: You are using a plain Coulomb cut-off, which might produce artifacts. 68: You might want to consider using PME electrostatics. 68: 68: 68: 68: There were 4 NOTEs 68: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_9_full.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 68: Can not increase nstlist because an NVE ensemble is used 68: Using 1 MPI thread 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'spc2' 68: 16 steps, 0.0 ps. 68: Generated 3 of the 3 non-bonded parameter combinations 68: 68: Generated 3 of the 3 1-4 parameter combinations 68: 68: Excluding 2 bonded neighbours molecule type 'SOL' 68: 68: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/spc2.gro' 68: 68: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 2573.59 K 68: 68: Calculated rlist for 1x1 atom pair-list as 0.886 nm, buffer size 0.186 nm 68: 68: Set rlist, assuming 4x4 atom pair-list, to 0.872 nm, buffer size 0.172 nm 68: 68: Note that mdrun will redetermine rlist based on the actual pair-list setup 68: 68: This run will generate roughly 0 Mb of data 68: Generated 3 of the 3 non-bonded parameter combinations 68: 68: Generated 3 of the 3 1-4 parameter combinations 68: 68: Excluding 2 bonded neighbours molecule type 'SOL' 68: 68: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/spc2.gro' 68: 68: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 2573.59 K 68: 68: Calculated rlist for 1x1 atom pair-list as 0.886 nm, buffer size 0.186 nm 68: 68: Set rlist, assuming 4x4 atom pair-list, to 0.872 nm, buffer size 0.172 nm 68: 68: Note that mdrun will redetermine rlist based on the actual pair-list setup 68: 68: This run will generate roughly 0 Mb of data 68: 68: Writing final coordinates. 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.044 0.022 197.3 68: (ns/day) (hour/ns) 68: Performance: 65.812 0.365 68: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_9_firstpart.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 68: Can not increase nstlist because an NVE ensemble is used 68: Using 1 MPI thread 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'spc2' 68: 8 steps, 0.0 ps. 68: 68: Writing final coordinates. 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.037 0.019 196.8 68: (ns/day) (hour/ns) 68: Performance: 40.928 0.586 68: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_9_full.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 68: Can not increase nstlist because an NVE ensemble is used 68: Using 1 MPI thread 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'spc2' 68: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 68: 68: Writing final coordinates. 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.052 0.027 197.4 68: (ns/day) (hour/ns) 68: Performance: 29.270 0.820 68: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_9_full.edr as single precision energy file 68: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_9_firstpart.edr as single precision energy file 68: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_9_secondpart.part0002.edr as single precision energy file 68: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/9 (187 ms) 68: [ RUN ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/10 68: 68: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_10_input.mdp]: 68: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 68: that with the Verlet scheme, nstlist has no effect on the accuracy of 68: your simulation. 68: 68: 68: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_10_input.mdp]: 68: Setting nstcalcenergy (100) equal to nstenergy (4) 68: 68: Generating 1-4 interactions: fudge = 0.5 68: Number of degrees of freedom in T-Coupling group System is 9.00 68: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 68: 68: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_10_input.mdp]: 68: NVE simulation: will use the initial temperature of 2573.591 K for 68: determining the Verlet buffer size 68: 68: 68: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_10_input.mdp]: 68: You are using a plain Coulomb cut-off, which might produce artifacts. 68: You might want to consider using PME electrostatics. 68: 68: 68: 68: There were 4 NOTEs 68: 68: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_10_input.mdp]: 68: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 68: that with the Verlet scheme, nstlist has no effect on the accuracy of 68: your simulation. 68: 68: 68: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_10_input.mdp]: 68: Setting nstcalcenergy (100) equal to nstenergy (4) 68: 68: Generating 1-4 interactions: fudge = 0.5 68: Number of degrees of freedom in T-Coupling group System is 9.00 68: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 68: 68: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_10_input.mdp]: 68: NVE simulation: will use the initial temperature of 2573.591 K for 68: determining the Verlet buffer size 68: 68: 68: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_10_input.mdp]: 68: You are using a plain Coulomb cut-off, which might produce artifacts. 68: You might want to consider using PME electrostatics. 68: 68: 68: 68: There were 4 NOTEs 68: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_10_full.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 68: Can not increase nstlist because an NVE ensemble is used 68: Using 1 MPI thread 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'spc2' 68: 16 steps, 0.0 ps. 68: Generated 3 of the 3 non-bonded parameter combinations 68: 68: Generated 3 of the 3 1-4 parameter combinations 68: 68: Excluding 2 bonded neighbours molecule type 'SOL' 68: 68: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/spc2.gro' 68: 68: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 2573.59 K 68: 68: Calculated rlist for 1x1 atom pair-list as 0.906 nm, buffer size 0.206 nm 68: 68: Set rlist, assuming 4x4 atom pair-list, to 0.892 nm, buffer size 0.192 nm 68: 68: Note that mdrun will redetermine rlist based on the actual pair-list setup 68: 68: This run will generate roughly 0 Mb of data 68: Generated 3 of the 3 non-bonded parameter combinations 68: 68: Generated 3 of the 3 1-4 parameter combinations 68: 68: Excluding 2 bonded neighbours molecule type 'SOL' 68: 68: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/spc2.gro' 68: 68: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 2573.59 K 68: 68: Calculated rlist for 1x1 atom pair-list as 0.906 nm, buffer size 0.206 nm 68: 68: Set rlist, assuming 4x4 atom pair-list, to 0.892 nm, buffer size 0.192 nm 68: 68: Note that mdrun will redetermine rlist based on the actual pair-list setup 68: 68: This run will generate roughly 0 Mb of data 68: 68: Writing final coordinates. 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.066 0.033 199.0 68: (ns/day) (hour/ns) 68: Performance: 44.523 0.539 68: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_10_firstpart.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 68: Can not increase nstlist because an NVE ensemble is used 68: Using 1 MPI thread 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'spc2' 68: 8 steps, 0.0 ps. 68: 68: Writing final coordinates. 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.040 0.020 198.2 68: (ns/day) (hour/ns) 68: Performance: 38.296 0.627 68: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_10_full.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 68: Can not increase nstlist because an NVE ensemble is used 68: Using 1 MPI thread 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'spc2' 68: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 68: 68: Writing final coordinates. 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.051 0.026 198.0 68: (ns/day) (hour/ns) 68: Performance: 30.285 0.792 68: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_10_full.edr as single precision energy file 68: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_10_firstpart.edr as single precision energy file 68: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_10_secondpart.part0002.edr as single precision energy file 68: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/10 (183 ms) 68: [ RUN ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/11 68: 68: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_11_input.mdp]: 68: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 68: that with the Verlet scheme, nstlist has no effect on the accuracy of 68: your simulation. 68: 68: 68: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_11_input.mdp]: 68: Setting nstcalcenergy (100) equal to nstenergy (4) 68: 68: Generating 1-4 interactions: fudge = 0.5 68: Number of degrees of freedom in T-Coupling group System is 9.00 68: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 68: 68: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_11_input.mdp]: 68: NVE simulation: will use the initial temperature of 2573.591 K for 68: determining the Verlet buffer size 68: 68: 68: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_11_input.mdp]: 68: You are using a plain Coulomb cut-off, which might produce artifacts. 68: You might want to consider using PME electrostatics. 68: 68: 68: 68: There were 4 NOTEs 68: 68: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_11_input.mdp]: 68: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 68: that with the Verlet scheme, nstlist has no effect on the accuracy of 68: your simulation. 68: 68: 68: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_11_input.mdp]: 68: Setting nstcalcenergy (100) equal to nstenergy (4) 68: 68: Generating 1-4 interactions: fudge = 0.5 68: Number of degrees of freedom in T-Coupling group System is 9.00 68: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 68: 68: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_11_input.mdp]: 68: NVE simulation: will use the initial temperature of 2573.591 K for 68: determining the Verlet buffer size 68: 68: 68: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_11_input.mdp]: 68: You are using a plain Coulomb cut-off, which might produce artifacts. 68: You might want to consider using PME electrostatics. 68: 68: 68: 68: There were 4 NOTEs 68: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_11_full.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 68: Can not increase nstlist because an NVE ensemble is used 68: Using 1 MPI thread 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'spc2' 68: 16 steps, 0.0 ps. 68: Generated 3 of the 3 non-bonded parameter combinations 68: 68: Generated 3 of the 3 1-4 parameter combinations 68: 68: Excluding 2 bonded neighbours molecule type 'SOL' 68: 68: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/spc2.gro' 68: 68: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 2573.59 K 68: 68: Calculated rlist for 1x1 atom pair-list as 0.886 nm, buffer size 0.186 nm 68: 68: Set rlist, assuming 4x4 atom pair-list, to 0.872 nm, buffer size 0.172 nm 68: 68: Note that mdrun will redetermine rlist based on the actual pair-list setup 68: 68: This run will generate roughly 0 Mb of data 68: Generated 3 of the 3 non-bonded parameter combinations 68: 68: Generated 3 of the 3 1-4 parameter combinations 68: 68: Excluding 2 bonded neighbours molecule type 'SOL' 68: 68: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/spc2.gro' 68: 68: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 2573.59 K 68: 68: Calculated rlist for 1x1 atom pair-list as 0.886 nm, buffer size 0.186 nm 68: 68: Set rlist, assuming 4x4 atom pair-list, to 0.872 nm, buffer size 0.172 nm 68: 68: Note that mdrun will redetermine rlist based on the actual pair-list setup 68: 68: This run will generate roughly 0 Mb of data 68: 68: Writing final coordinates. 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.054 0.027 198.8 68: (ns/day) (hour/ns) 68: Performance: 54.026 0.444 68: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_11_firstpart.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 68: Can not increase nstlist because an NVE ensemble is used 68: Using 1 MPI thread 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'spc2' 68: 8 steps, 0.0 ps. 68: 68: Writing final coordinates. 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.042 0.021 198.3 68: (ns/day) (hour/ns) 68: Performance: 36.714 0.654 68: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_11_full.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 68: Can not increase nstlist because an NVE ensemble is used 68: Using 1 MPI thread 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'spc2' 68: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 68: 68: Writing final coordinates. 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.045 0.023 197.8 68: (ns/day) (hour/ns) 68: Performance: 33.903 0.708 68: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_11_full.edr as single precision energy file 68: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_11_firstpart.edr as single precision energy file 68: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_11_secondpart.part0002.edr as single precision energy file 68: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/11 (172 ms) 68: [ RUN ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/12 68: 68: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_12_input.mdp]: 68: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 68: that with the Verlet scheme, nstlist has no effect on the accuracy of 68: your simulation. 68: 68: 68: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_12_input.mdp]: 68: Setting nstcalcenergy (100) equal to nstenergy (4) 68: 68: Generating 1-4 interactions: fudge = 0.5 68: Number of degrees of freedom in T-Coupling group System is 9.00 68: 68: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_12_input.mdp]: 68: You are using a plain Coulomb cut-off, which might produce artifacts. 68: You might want to consider using PME electrostatics. 68: 68: 68: 68: There were 3 NOTEs 68: 68: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_12_input.mdp]: 68: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 68: that with the Verlet scheme, nstlist has no effect on the accuracy of 68: your simulation. 68: 68: 68: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_12_input.mdp]: 68: Setting nstcalcenergy (100) equal to nstenergy (4) 68: 68: Generating 1-4 interactions: fudge = 0.5 68: Number of degrees of freedom in T-Coupling group System is 9.00 68: 68: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_12_input.mdp]: 68: You are using a plain Coulomb cut-off, which might produce artifacts. 68: You might want to consider using PME electrostatics. 68: 68: 68: 68: There were 3 NOTEs 68: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_12_full.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 68: Using 1 MPI thread 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'spc2' 68: 16 steps, 0.0 ps. 68: Generated 3 of the 3 non-bonded parameter combinations 68: 68: Generated 3 of the 3 1-4 parameter combinations 68: 68: Excluding 2 bonded neighbours molecule type 'SOL' 68: 68: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 68: 68: Calculated rlist for 1x1 atom pair-list as 0.736 nm, buffer size 0.036 nm 68: 68: Set rlist, assuming 4x4 atom pair-list, to 0.734 nm, buffer size 0.034 nm 68: 68: Note that mdrun will redetermine rlist based on the actual pair-list setup 68: 68: This run will generate roughly 0 Mb of data 68: Generated 3 of the 3 non-bonded parameter combinations 68: 68: Generated 3 of the 3 1-4 parameter combinations 68: 68: Excluding 2 bonded neighbours molecule type 'SOL' 68: 68: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 68: 68: Calculated rlist for 1x1 atom pair-list as 0.736 nm, buffer size 0.036 nm 68: 68: Set rlist, assuming 4x4 atom pair-list, to 0.734 nm, buffer size 0.034 nm 68: 68: Note that mdrun will redetermine rlist based on the actual pair-list setup 68: 68: This run will generate roughly 0 Mb of data 68: 68: Writing final coordinates. 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.036 0.018 197.0 68: (ns/day) (hour/ns) 68: Performance: 79.541 0.302 68: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_12_firstpart.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 68: Using 1 MPI thread 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'spc2' 68: 8 steps, 0.0 ps. 68: 68: Writing final coordinates. 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.037 0.019 196.8 68: (ns/day) (hour/ns) 68: Performance: 41.311 0.581 68: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_12_full.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 68: Using 1 MPI thread 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'spc2' 68: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 68: 68: Writing final coordinates. 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.041 0.021 197.6 68: (ns/day) (hour/ns) 68: Performance: 37.525 0.640 68: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_12_full.edr as single precision energy file 68: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_12_firstpart.edr as single precision energy file 68: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_12_secondpart.part0002.edr as single precision energy file 68: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/12 (175 ms) 68: [ RUN ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/13 68: 68: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_13_input.mdp]: 68: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 68: that with the Verlet scheme, nstlist has no effect on the accuracy of 68: your simulation. 68: 68: 68: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_13_input.mdp]: 68: Setting nstcalcenergy (100) equal to nstenergy (4) 68: 68: Generating 1-4 interactions: fudge = 0.5 68: Number of degrees of freedom in T-Coupling group System is 9.00 68: 68: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_13_input.mdp]: 68: You are using a plain Coulomb cut-off, which might produce artifacts. 68: You might want to consider using PME electrostatics. 68: 68: 68: 68: There were 3 NOTEs 68: 68: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_13_input.mdp]: 68: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 68: that with the Verlet scheme, nstlist has no effect on the accuracy of 68: your simulation. 68: 68: 68: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_13_input.mdp]: 68: Setting nstcalcenergy (100) equal to nstenergy (4) 68: 68: Generating 1-4 interactions: fudge = 0.5 68: Number of degrees of freedom in T-Coupling group System is 9.00 68: 68: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_13_input.mdp]: 68: You are using a plain Coulomb cut-off, which might produce artifacts. 68: You might want to consider using PME electrostatics. 68: 68: 68: 68: There were 3 NOTEs 68: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_13_full.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 68: Changing nstlist from 8 to 100, rlist from 0.73 to 0.811 68: 68: Using 1 MPI thread 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'spc2' 68: 16 steps, 0.0 ps. 68: Generated 3 of the 3 non-bonded parameter combinations 68: 68: Generated 3 of the 3 1-4 parameter combinations 68: 68: Excluding 2 bonded neighbours molecule type 'SOL' 68: 68: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 298 K 68: 68: Calculated rlist for 1x1 atom pair-list as 0.732 nm, buffer size 0.032 nm 68: 68: Set rlist, assuming 4x4 atom pair-list, to 0.730 nm, buffer size 0.030 nm 68: 68: Note that mdrun will redetermine rlist based on the actual pair-list setup 68: 68: This run will generate roughly 0 Mb of data 68: Generated 3 of the 3 non-bonded parameter combinations 68: 68: Generated 3 of the 3 1-4 parameter combinations 68: 68: Excluding 2 bonded neighbours molecule type 'SOL' 68: 68: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 298 K 68: 68: Calculated rlist for 1x1 atom pair-list as 0.732 nm, buffer size 0.032 nm 68: 68: Set rlist, assuming 4x4 atom pair-list, to 0.730 nm, buffer size 0.030 nm 68: 68: Note that mdrun will redetermine rlist based on the actual pair-list setup 68: 68: This run will generate roughly 0 Mb of data 68: 68: Writing final coordinates. 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.060 0.030 198.5 68: (ns/day) (hour/ns) 68: Performance: 48.694 0.493 68: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_13_firstpart.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 68: Changing nstlist from 8 to 100, rlist from 0.73 to 0.811 68: 68: Using 1 MPI thread 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'spc2' 68: 8 steps, 0.0 ps. 68: 68: Writing final coordinates. 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.035 0.018 197.4 68: (ns/day) (hour/ns) 68: Performance: 44.091 0.544 68: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_13_full.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 68: Changing nstlist from 8 to 100, rlist from 0.73 to 0.811 68: 68: Using 1 MPI thread 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'spc2' 68: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 68: 68: Writing final coordinates. 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.053 0.027 198.2 68: (ns/day) (hour/ns) 68: Performance: 29.001 0.828 68: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_13_full.edr as single precision energy file 68: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_13_firstpart.edr as single precision energy file 68: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_13_secondpart.part0002.edr as single precision energy file 68: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/13 (211 ms) 68: [ RUN ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/14 68: 68: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_14_input.mdp]: 68: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 68: that with the Verlet scheme, nstlist has no effect on the accuracy of 68: your simulation. 68: 68: 68: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_14_input.mdp]: 68: Setting nstcalcenergy (100) equal to nstenergy (4) 68: 68: Generating 1-4 interactions: fudge = 0.5 68: Number of degrees of freedom in T-Coupling group System is 9.00 68: 68: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_14_input.mdp]: 68: You are using a plain Coulomb cut-off, which might produce artifacts. 68: You might want to consider using PME electrostatics. 68: 68: 68: 68: There were 3 NOTEs 68: 68: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_14_input.mdp]: 68: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 68: that with the Verlet scheme, nstlist has no effect on the accuracy of 68: your simulation. 68: 68: 68: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_14_input.mdp]: 68: Setting nstcalcenergy (100) equal to nstenergy (4) 68: 68: Generating 1-4 interactions: fudge = 0.5 68: Number of degrees of freedom in T-Coupling group System is 9.00 68: 68: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_14_input.mdp]: 68: You are using a plain Coulomb cut-off, which might produce artifacts. 68: You might want to consider using PME electrostatics. 68: 68: 68: 68: There were 3 NOTEs 68: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_14_full.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 68: Using 1 MPI thread 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'spc2' 68: 16 steps, 0.0 ps. 68: Generated 3 of the 3 non-bonded parameter combinations 68: 68: Generated 3 of the 3 1-4 parameter combinations 68: 68: Excluding 2 bonded neighbours molecule type 'SOL' 68: 68: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/spc2.gro' 68: 68: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 68: 68: Calculated rlist for 1x1 atom pair-list as 0.764 nm, buffer size 0.064 nm 68: 68: Set rlist, assuming 4x4 atom pair-list, to 0.760 nm, buffer size 0.060 nm 68: 68: Note that mdrun will redetermine rlist based on the actual pair-list setup 68: 68: This run will generate roughly 0 Mb of data 68: Generated 3 of the 3 non-bonded parameter combinations 68: 68: Generated 3 of the 3 1-4 parameter combinations 68: 68: Excluding 2 bonded neighbours molecule type 'SOL' 68: 68: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/spc2.gro' 68: 68: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 68: 68: Calculated rlist for 1x1 atom pair-list as 0.764 nm, buffer size 0.064 nm 68: 68: Set rlist, assuming 4x4 atom pair-list, to 0.760 nm, buffer size 0.060 nm 68: 68: Note that mdrun will redetermine rlist based on the actual pair-list setup 68: 68: This run will generate roughly 0 Mb of data 68: 68: Writing final coordinates. 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.055 0.028 198.4 68: (ns/day) (hour/ns) 68: Performance: 53.330 0.450 68: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_14_firstpart.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 68: Using 1 MPI thread 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'spc2' 68: 8 steps, 0.0 ps. 68: 68: Writing final coordinates. 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.038 0.019 197.8 68: (ns/day) (hour/ns) 68: Performance: 40.188 0.597 68: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_14_full.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 68: Using 1 MPI thread 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'spc2' 68: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 68: 68: Writing final coordinates. 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.039 0.020 197.8 68: (ns/day) (hour/ns) 68: Performance: 39.573 0.606 68: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_14_full.edr as single precision energy file 68: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_14_firstpart.edr as single precision energy file 68: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_14_secondpart.part0002.edr as single precision energy file 68: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/14 (173 ms) 68: [ RUN ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/15 68: 68: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_15_input.mdp]: 68: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 68: that with the Verlet scheme, nstlist has no effect on the accuracy of 68: your simulation. 68: 68: 68: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_15_input.mdp]: 68: Setting nstcalcenergy (100) equal to nstenergy (4) 68: 68: Generating 1-4 interactions: fudge = 0.5 68: Number of degrees of freedom in T-Coupling group System is 9.00 68: 68: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_15_input.mdp]: 68: You are using a plain Coulomb cut-off, which might produce artifacts. 68: You might want to consider using PME electrostatics. 68: 68: 68: 68: There were 3 NOTEs 68: 68: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_15_input.mdp]: 68: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 68: that with the Verlet scheme, nstlist has no effect on the accuracy of 68: your simulation. 68: 68: 68: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_15_input.mdp]: 68: Setting nstcalcenergy (100) equal to nstenergy (4) 68: 68: Generating 1-4 interactions: fudge = 0.5 68: Number of degrees of freedom in T-Coupling group System is 9.00 68: 68: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_15_input.mdp]: 68: You are using a plain Coulomb cut-off, which might produce artifacts. 68: You might want to consider using PME electrostatics. 68: 68: 68: 68: There were 3 NOTEs 68: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_15_full.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 68: Changing nstlist from 8 to 25, rlist from 0.752 to 0.89 68: 68: Using 1 MPI thread 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'spc2' 68: 16 steps, 0.0 ps. 68: Generated 3 of the 3 non-bonded parameter combinations 68: 68: Generated 3 of the 3 1-4 parameter combinations 68: 68: Excluding 2 bonded neighbours molecule type 'SOL' 68: 68: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/spc2.gro' 68: 68: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 298 K 68: 68: Calculated rlist for 1x1 atom pair-list as 0.757 nm, buffer size 0.057 nm 68: 68: Set rlist, assuming 4x4 atom pair-list, to 0.752 nm, buffer size 0.052 nm 68: 68: Note that mdrun will redetermine rlist based on the actual pair-list setup 68: 68: This run will generate roughly 0 Mb of data 68: Generated 3 of the 3 non-bonded parameter combinations 68: 68: Generated 3 of the 3 1-4 parameter combinations 68: 68: Excluding 2 bonded neighbours molecule type 'SOL' 68: 68: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/spc2.gro' 68: 68: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 298 K 68: 68: Calculated rlist for 1x1 atom pair-list as 0.757 nm, buffer size 0.057 nm 68: 68: Set rlist, assuming 4x4 atom pair-list, to 0.752 nm, buffer size 0.052 nm 68: 68: Note that mdrun will redetermine rlist based on the actual pair-list setup 68: 68: This run will generate roughly 0 Mb of data 68: 68: Writing final coordinates. 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.039 0.020 197.7 68: (ns/day) (hour/ns) 68: Performance: 74.017 0.324 68: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_15_firstpart.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 68: Changing nstlist from 8 to 25, rlist from 0.752 to 0.89 68: 68: Using 1 MPI thread 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'spc2' 68: 8 steps, 0.0 ps. 68: 68: Writing final coordinates. 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.043 0.022 197.7 68: (ns/day) (hour/ns) 68: Performance: 35.524 0.676 68: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_15_full.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 68: Changing nstlist from 8 to 25, rlist from 0.752 to 0.89 68: 68: Using 1 MPI thread 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'spc2' 68: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 68: 68: Writing final coordinates. 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.042 0.021 197.7 68: (ns/day) (hour/ns) 68: Performance: 36.868 0.651 68: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_15_full.edr as single precision energy file 68: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_15_firstpart.edr as single precision energy file 68: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_15_secondpart.part0002.edr as single precision energy file 68: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/15 (187 ms) 68: [ RUN ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/16 68: 68: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_16_input.mdp]: 68: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 68: that with the Verlet scheme, nstlist has no effect on the accuracy of 68: your simulation. 68: 68: 68: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_16_input.mdp]: 68: Setting nstcalcenergy (100) equal to nstenergy (4) 68: 68: Generating 1-4 interactions: fudge = 0.5 68: 68: NOTE 3 [file unknown]: 68: You are using constraints on all bonds, whereas the forcefield has been 68: parametrized only with constraints involving hydrogen atoms. We suggest 68: using constraints = h-bonds instead, this will also improve performance. 68: 68: Number of degrees of freedom in T-Coupling group System is 23.00 68: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 68: 68: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_16_input.mdp]: 68: NVE simulation: will use the initial temperature of 456.887 K for 68: determining the Verlet buffer size 68: 68: 68: NOTE 5 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_16_input.mdp]: 68: There are 9 non-linear virtual site constructions. Their contribution to 68: the energy error is approximated. In most cases this does not affect the 68: error significantly. 68: 68: 68: NOTE 6 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_16_input.mdp]: 68: You are using a plain Coulomb cut-off, which might produce artifacts. 68: You might want to consider using PME electrostatics. 68: 68: 68: 68: There were 6 NOTEs 68: 68: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_16_input.mdp]: 68: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 68: that with the Verlet scheme, nstlist has no effect on the accuracy of 68: your simulation. 68: 68: 68: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_16_input.mdp]: 68: Setting nstcalcenergy (100) equal to nstenergy (4) 68: 68: Generating 1-4 interactions: fudge = 0.5 68: 68: NOTE 3 [file unknown]: 68: You are using constraints on all bonds, whereas the forcefield has been 68: parametrized only with constraints involving hydrogen atoms. We suggest 68: using constraints = h-bonds instead, this will also improve performance. 68: 68: Number of degrees of freedom in T-Coupling group System is 23.00 68: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 68: 68: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_16_input.mdp]: 68: NVE simulation: will use the initial temperature of 456.887 K for 68: determining the Verlet buffer size 68: 68: 68: NOTE 5 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_16_input.mdp]: 68: There are 9 non-linear virtual site constructions. Their contribution to 68: the energy error is approximated. In most cases this does not affect the 68: error significantly. 68: 68: 68: NOTE 6 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_16_input.mdp]: 68: You are using a plain Coulomb cut-off, which might produce artifacts. 68: You might want to consider using PME electrostatics. 68: 68: 68: 68: There were 6 NOTEs 68: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_16_full.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 68: Can not increase nstlist because an NVE ensemble is used 68: Update groups can not be used for this system because an incompatible virtual site type is used 68: 68: Using 1 MPI thread 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'Alanine dipeptide in vacuo' 68: 16 steps, 0.0 ps. 68: Generated 2145 of the 2145 non-bonded parameter combinations 68: 68: Generated 2145 of the 2145 1-4 parameter combinations 68: 68: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' 68: 68: turning all bonds into constraints... 68: 68: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/alanine_vsite_vacuo.gro' 68: 68: Cleaning up constraints and constant bonded interactions with virtual sites 68: 68: Removed 18 Angles with virtual sites, 21 left 68: 68: Removed 10 Proper Dih.s with virtual sites, 44 left 68: 68: Converted 15 Constraints with virtual sites to connections, 7 left 68: 68: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 456.887 K 68: 68: Calculated rlist for 1x1 atom pair-list as 0.742 nm, buffer size 0.042 nm 68: 68: Set rlist, assuming 4x4 atom pair-list, to 0.737 nm, buffer size 0.037 nm 68: 68: Note that mdrun will redetermine rlist based on the actual pair-list setup 68: 68: This run will generate roughly 0 Mb of data 68: Generated 2145 of the 2145 non-bonded parameter combinations 68: 68: Generated 2145 of the 2145 1-4 parameter combinations 68: 68: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' 68: 68: turning all bonds into constraints... 68: 68: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/alanine_vsite_vacuo.gro' 68: 68: Cleaning up constraints and constant bonded interactions with virtual sites 68: 68: Removed 18 Angles with virtual sites, 21 left 68: 68: Removed 10 Proper Dih.s with virtual sites, 44 left 68: 68: Converted 15 Constraints with virtual sites to connections, 7 left 68: 68: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 456.887 K 68: 68: Calculated rlist for 1x1 atom pair-list as 0.742 nm, buffer size 0.042 nm 68: 68: Set rlist, assuming 4x4 atom pair-list, to 0.737 nm, buffer size 0.037 nm 68: 68: Note that mdrun will redetermine rlist based on the actual pair-list setup 68: 68: This run will generate roughly 0 Mb of data 68: 68: Writing final coordinates. 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.069 0.035 198.1 68: (ns/day) (hour/ns) 68: Performance: 41.995 0.572 68: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_16_firstpart.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 68: Can not increase nstlist because an NVE ensemble is used 68: Update groups can not be used for this system because an incompatible virtual site type is used 68: 68: Using 1 MPI thread 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'Alanine dipeptide in vacuo' 68: 8 steps, 0.0 ps. 68: 68: Writing final coordinates. 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.062 0.031 198.2 68: (ns/day) (hour/ns) 68: Performance: 24.725 0.971 68: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_16_full.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 68: Can not increase nstlist because an NVE ensemble is used 68: Update groups can not be used for this system because an incompatible virtual site type is used 68: 68: Using 1 MPI thread 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'Alanine dipeptide in vacuo' 68: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 68: 68: Writing final coordinates. 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.074 0.037 198.3 68: (ns/day) (hour/ns) 68: Performance: 20.957 1.145 68: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_16_full.edr as single precision energy file 68: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_16_firstpart.edr as single precision energy file 68: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_16_secondpart.part0002.edr as single precision energy file 68: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/16 (403 ms) 68: [ RUN ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/17 68: 68: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_17_input.mdp]: 68: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 68: that with the Verlet scheme, nstlist has no effect on the accuracy of 68: your simulation. 68: 68: 68: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_17_input.mdp]: 68: Setting nstcalcenergy (100) equal to nstenergy (4) 68: 68: Generating 1-4 interactions: fudge = 0.5 68: 68: NOTE 3 [file unknown]: 68: You are using constraints on all bonds, whereas the forcefield has been 68: parametrized only with constraints involving hydrogen atoms. We suggest 68: using constraints = h-bonds instead, this will also improve performance. 68: 68: Number of degrees of freedom in T-Coupling group System is 23.00 68: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 68: 68: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_17_input.mdp]: 68: NVE simulation: will use the initial temperature of 456.887 K for 68: determining the Verlet buffer size 68: 68: 68: NOTE 5 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_17_input.mdp]: 68: There are 9 non-linear virtual site constructions. Their contribution to 68: the energy error is approximated. In most cases this does not affect the 68: error significantly. 68: 68: 68: NOTE 6 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_17_input.mdp]: 68: You are using a plain Coulomb cut-off, which might produce artifacts. 68: You might want to consider using PME electrostatics. 68: 68: 68: 68: There were 6 NOTEs 68: 68: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_17_input.mdp]: 68: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 68: that with the Verlet scheme, nstlist has no effect on the accuracy of 68: your simulation. 68: 68: 68: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_17_input.mdp]: 68: Setting nstcalcenergy (100) equal to nstenergy (4) 68: 68: Generating 1-4 interactions: fudge = 0.5 68: 68: NOTE 3 [file unknown]: 68: You are using constraints on all bonds, whereas the forcefield has been 68: parametrized only with constraints involving hydrogen atoms. We suggest 68: using constraints = h-bonds instead, this will also improve performance. 68: 68: Number of degrees of freedom in T-Coupling group System is 23.00 68: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 68: 68: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_17_input.mdp]: 68: NVE simulation: will use the initial temperature of 456.887 K for 68: determining the Verlet buffer size 68: 68: 68: NOTE 5 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_17_input.mdp]: 68: There are 9 non-linear virtual site constructions. Their contribution to 68: the energy error is approximated. In most cases this does not affect the 68: error significantly. 68: 68: 68: NOTE 6 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_17_input.mdp]: 68: You are using a plain Coulomb cut-off, which might produce artifacts. 68: You might want to consider using PME electrostatics. 68: 68: 68: 68: There were 6 NOTEs 68: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_17_full.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 68: Can not increase nstlist because an NVE ensemble is used 68: Update groups can not be used for this system because an incompatible virtual site type is used 68: 68: Using 1 MPI thread 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'Alanine dipeptide in vacuo' 68: 16 steps, 0.0 ps. 68: Generated 2145 of the 2145 non-bonded parameter combinations 68: 68: Generated 2145 of the 2145 1-4 parameter combinations 68: 68: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' 68: 68: turning all bonds into constraints... 68: 68: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/alanine_vsite_vacuo.gro' 68: 68: Cleaning up constraints and constant bonded interactions with virtual sites 68: 68: Removed 18 Angles with virtual sites, 21 left 68: 68: Removed 10 Proper Dih.s with virtual sites, 44 left 68: 68: Converted 15 Constraints with virtual sites to connections, 7 left 68: 68: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 456.887 K 68: 68: Calculated rlist for 1x1 atom pair-list as 0.736 nm, buffer size 0.036 nm 68: 68: Set rlist, assuming 4x4 atom pair-list, to 0.731 nm, buffer size 0.031 nm 68: 68: Note that mdrun will redetermine rlist based on the actual pair-list setup 68: 68: This run will generate roughly 0 Mb of data 68: Generated 2145 of the 2145 non-bonded parameter combinations 68: 68: Generated 2145 of the 2145 1-4 parameter combinations 68: 68: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' 68: 68: turning all bonds into constraints... 68: 68: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/alanine_vsite_vacuo.gro' 68: 68: Cleaning up constraints and constant bonded interactions with virtual sites 68: 68: Removed 18 Angles with virtual sites, 21 left 68: 68: Removed 10 Proper Dih.s with virtual sites, 44 left 68: 68: Converted 15 Constraints with virtual sites to connections, 7 left 68: 68: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 456.887 K 68: 68: Calculated rlist for 1x1 atom pair-list as 0.736 nm, buffer size 0.036 nm 68: 68: Set rlist, assuming 4x4 atom pair-list, to 0.731 nm, buffer size 0.031 nm 68: 68: Note that mdrun will redetermine rlist based on the actual pair-list setup 68: 68: This run will generate roughly 0 Mb of data 68: 68: Writing final coordinates. 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.071 0.036 198.2 68: (ns/day) (hour/ns) 68: Performance: 41.209 0.582 68: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_17_firstpart.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 68: Can not increase nstlist because an NVE ensemble is used 68: Update groups can not be used for this system because an incompatible virtual site type is used 68: 68: Using 1 MPI thread 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'Alanine dipeptide in vacuo' 68: 8 steps, 0.0 ps. 68: 68: Writing final coordinates. 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.079 0.040 198.3 68: (ns/day) (hour/ns) 68: Performance: 19.519 1.230 68: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_17_full.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 68: Can not increase nstlist because an NVE ensemble is used 68: Update groups can not be used for this system because an incompatible virtual site type is used 68: 68: Using 1 MPI thread 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'Alanine dipeptide in vacuo' 68: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 68: 68: Writing final coordinates. 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.064 0.032 198.0 68: (ns/day) (hour/ns) 68: Performance: 24.062 0.997 68: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_17_full.edr as single precision energy file 68: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_17_firstpart.edr as single precision energy file 68: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_17_secondpart.part0002.edr as single precision energy file 68: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/17 (442 ms) 68: [ RUN ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/18 68: 68: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_18_input.mdp]: 68: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 68: that with the Verlet scheme, nstlist has no effect on the accuracy of 68: your simulation. 68: 68: 68: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_18_input.mdp]: 68: Setting nstcalcenergy (100) equal to nstenergy (4) 68: 68: Generating 1-4 interactions: fudge = 0.5 68: 68: NOTE 3 [file unknown]: 68: You are using constraints on all bonds, whereas the forcefield has been 68: parametrized only with constraints involving hydrogen atoms. We suggest 68: using constraints = h-bonds instead, this will also improve performance. 68: 68: Number of degrees of freedom in T-Coupling group System is 23.00 68: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 68: 68: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_18_input.mdp]: 68: NVE simulation: will use the initial temperature of 456.887 K for 68: determining the Verlet buffer size 68: 68: 68: NOTE 5 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_18_input.mdp]: 68: There are 9 non-linear virtual site constructions. Their contribution to 68: the energy error is approximated. In most cases this does not affect the 68: error significantly. 68: 68: 68: NOTE 6 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_18_input.mdp]: 68: You are using a plain Coulomb cut-off, which might produce artifacts. 68: You might want to consider using PME electrostatics. 68: 68: 68: 68: There were 6 NOTEs 68: 68: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_18_input.mdp]: 68: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 68: that with the Verlet scheme, nstlist has no effect on the accuracy of 68: your simulation. 68: 68: 68: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_18_input.mdp]: 68: Setting nstcalcenergy (100) equal to nstenergy (4) 68: 68: Generating 1-4 interactions: fudge = 0.5 68: 68: NOTE 3 [file unknown]: 68: You are using constraints on all bonds, whereas the forcefield has been 68: parametrized only with constraints involving hydrogen atoms. We suggest 68: using constraints = h-bonds instead, this will also improve performance. 68: 68: Number of degrees of freedom in T-Coupling group System is 23.00 68: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 68: 68: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_18_input.mdp]: 68: NVE simulation: will use the initial temperature of 456.887 K for 68: determining the Verlet buffer size 68: 68: 68: NOTE 5 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_18_input.mdp]: 68: There are 9 non-linear virtual site constructions. Their contribution to 68: the energy error is approximated. In most cases this does not affect the 68: error significantly. 68: 68: 68: NOTE 6 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_18_input.mdp]: 68: You are using a plain Coulomb cut-off, which might produce artifacts. 68: You might want to consider using PME electrostatics. 68: 68: 68: 68: There were 6 NOTEs 68: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_18_full.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 68: Can not increase nstlist because an NVE ensemble is used 68: Update groups can not be used for this system because an incompatible virtual site type is used 68: 68: Using 1 MPI thread 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'Alanine dipeptide in vacuo' 68: 16 steps, 0.0 ps. 68: Generated 2145 of the 2145 non-bonded parameter combinations 68: 68: Generated 2145 of the 2145 1-4 parameter combinations 68: 68: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' 68: 68: turning all bonds into constraints... 68: 68: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/alanine_vsite_vacuo.gro' 68: 68: Cleaning up constraints and constant bonded interactions with virtual sites 68: 68: Removed 18 Angles with virtual sites, 21 left 68: 68: Removed 10 Proper Dih.s with virtual sites, 44 left 68: 68: Converted 15 Constraints with virtual sites to connections, 7 left 68: 68: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 456.887 K 68: 68: Calculated rlist for 1x1 atom pair-list as 0.742 nm, buffer size 0.042 nm 68: 68: Set rlist, assuming 4x4 atom pair-list, to 0.737 nm, buffer size 0.037 nm 68: 68: Note that mdrun will redetermine rlist based on the actual pair-list setup 68: 68: This run will generate roughly 0 Mb of data 68: Generated 2145 of the 2145 non-bonded parameter combinations 68: 68: Generated 2145 of the 2145 1-4 parameter combinations 68: 68: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' 68: 68: turning all bonds into constraints... 68: 68: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/alanine_vsite_vacuo.gro' 68: 68: Cleaning up constraints and constant bonded interactions with virtual sites 68: 68: Removed 18 Angles with virtual sites, 21 left 68: 68: Removed 10 Proper Dih.s with virtual sites, 44 left 68: 68: Converted 15 Constraints with virtual sites to connections, 7 left 68: 68: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 456.887 K 68: 68: Calculated rlist for 1x1 atom pair-list as 0.742 nm, buffer size 0.042 nm 68: 68: Set rlist, assuming 4x4 atom pair-list, to 0.737 nm, buffer size 0.037 nm 68: 68: Note that mdrun will redetermine rlist based on the actual pair-list setup 68: 68: This run will generate roughly 0 Mb of data 68: 68: Writing final coordinates. 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.077 0.039 198.4 68: (ns/day) (hour/ns) 68: Performance: 37.873 0.634 68: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_18_firstpart.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 68: Can not increase nstlist because an NVE ensemble is used 68: Update groups can not be used for this system because an incompatible virtual site type is used 68: 68: Using 1 MPI thread 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'Alanine dipeptide in vacuo' 68: 8 steps, 0.0 ps. 68: 68: Writing final coordinates. 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.063 0.032 198.1 68: (ns/day) (hour/ns) 68: Performance: 24.427 0.983 68: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_18_full.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 68: Can not increase nstlist because an NVE ensemble is used 68: Update groups can not be used for this system because an incompatible virtual site type is used 68: 68: Using 1 MPI thread 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'Alanine dipeptide in vacuo' 68: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 68: 68: Writing final coordinates. 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.044 0.022 196.6 68: (ns/day) (hour/ns) 68: Performance: 34.623 0.693 68: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_18_full.edr as single precision energy file 68: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_18_firstpart.edr as single precision energy file 68: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_18_secondpart.part0002.edr as single precision energy file 68: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/18 (399 ms) 68: [ RUN ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/19 68: 68: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_19_input.mdp]: 68: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 68: that with the Verlet scheme, nstlist has no effect on the accuracy of 68: your simulation. 68: 68: 68: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_19_input.mdp]: 68: Setting nstcalcenergy (100) equal to nstenergy (4) 68: 68: Generating 1-4 interactions: fudge = 0.5 68: 68: NOTE 3 [file unknown]: 68: You are using constraints on all bonds, whereas the forcefield has been 68: parametrized only with constraints involving hydrogen atoms. We suggest 68: using constraints = h-bonds instead, this will also improve performance. 68: 68: Number of degrees of freedom in T-Coupling group System is 23.00 68: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 68: 68: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_19_input.mdp]: 68: NVE simulation: will use the initial temperature of 456.887 K for 68: determining the Verlet buffer size 68: 68: 68: NOTE 5 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_19_input.mdp]: 68: There are 9 non-linear virtual site constructions. Their contribution to 68: the energy error is approximated. In most cases this does not affect the 68: error significantly. 68: 68: 68: NOTE 6 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_19_input.mdp]: 68: You are using a plain Coulomb cut-off, which might produce artifacts. 68: You might want to consider using PME electrostatics. 68: 68: 68: 68: There were 6 NOTEs 68: 68: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_19_input.mdp]: 68: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 68: that with the Verlet scheme, nstlist has no effect on the accuracy of 68: your simulation. 68: 68: 68: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_19_input.mdp]: 68: Setting nstcalcenergy (100) equal to nstenergy (4) 68: 68: Generating 1-4 interactions: fudge = 0.5 68: 68: NOTE 3 [file unknown]: 68: You are using constraints on all bonds, whereas the forcefield has been 68: parametrized only with constraints involving hydrogen atoms. We suggest 68: using constraints = h-bonds instead, this will also improve performance. 68: 68: Number of degrees of freedom in T-Coupling group System is 23.00 68: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 68: 68: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_19_input.mdp]: 68: NVE simulation: will use the initial temperature of 456.887 K for 68: determining the Verlet buffer size 68: 68: 68: NOTE 5 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_19_input.mdp]: 68: There are 9 non-linear virtual site constructions. Their contribution to 68: the energy error is approximated. In most cases this does not affect the 68: error significantly. 68: 68: 68: NOTE 6 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_19_input.mdp]: 68: You are using a plain Coulomb cut-off, which might produce artifacts. 68: You might want to consider using PME electrostatics. 68: 68: 68: 68: There were 6 NOTEs 68: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_19_full.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 68: Can not increase nstlist because an NVE ensemble is used 68: Update groups can not be used for this system because an incompatible virtual site type is used 68: 68: Using 1 MPI thread 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'Alanine dipeptide in vacuo' 68: 16 steps, 0.0 ps. 68: Generated 2145 of the 2145 non-bonded parameter combinations 68: 68: Generated 2145 of the 2145 1-4 parameter combinations 68: 68: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' 68: 68: turning all bonds into constraints... 68: 68: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/alanine_vsite_vacuo.gro' 68: 68: Cleaning up constraints and constant bonded interactions with virtual sites 68: 68: Removed 18 Angles with virtual sites, 21 left 68: 68: Removed 10 Proper Dih.s with virtual sites, 44 left 68: 68: Converted 15 Constraints with virtual sites to connections, 7 left 68: 68: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 456.887 K 68: 68: Calculated rlist for 1x1 atom pair-list as 0.736 nm, buffer size 0.036 nm 68: 68: Set rlist, assuming 4x4 atom pair-list, to 0.731 nm, buffer size 0.031 nm 68: 68: Note that mdrun will redetermine rlist based on the actual pair-list setup 68: 68: This run will generate roughly 0 Mb of data 68: Generated 2145 of the 2145 non-bonded parameter combinations 68: 68: Generated 2145 of the 2145 1-4 parameter combinations 68: 68: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' 68: 68: turning all bonds into constraints... 68: 68: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/alanine_vsite_vacuo.gro' 68: 68: Cleaning up constraints and constant bonded interactions with virtual sites 68: 68: Removed 18 Angles with virtual sites, 21 left 68: 68: Removed 10 Proper Dih.s with virtual sites, 44 left 68: 68: Converted 15 Constraints with virtual sites to connections, 7 left 68: 68: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 456.887 K 68: 68: Calculated rlist for 1x1 atom pair-list as 0.736 nm, buffer size 0.036 nm 68: 68: Set rlist, assuming 4x4 atom pair-list, to 0.731 nm, buffer size 0.031 nm 68: 68: Note that mdrun will redetermine rlist based on the actual pair-list setup 68: 68: This run will generate roughly 0 Mb of data 68: 68: Writing final coordinates. 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.070 0.035 198.2 68: (ns/day) (hour/ns) 68: Performance: 41.857 0.573 68: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_19_firstpart.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 68: Can not increase nstlist because an NVE ensemble is used 68: Update groups can not be used for this system because an incompatible virtual site type is used 68: 68: Using 1 MPI thread 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'Alanine dipeptide in vacuo' 68: 8 steps, 0.0 ps. 68: 68: Writing final coordinates. 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.062 0.031 198.0 68: (ns/day) (hour/ns) 68: Performance: 24.750 0.970 68: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_19_full.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 68: Can not increase nstlist because an NVE ensemble is used 68: Update groups can not be used for this system because an incompatible virtual site type is used 68: 68: Using 1 MPI thread 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'Alanine dipeptide in vacuo' 68: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 68: 68: Writing final coordinates. 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.051 0.026 197.7 68: (ns/day) (hour/ns) 68: Performance: 30.029 0.799 68: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_19_full.edr as single precision energy file 68: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_19_firstpart.edr as single precision energy file 68: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_19_secondpart.part0002.edr as single precision energy file 68: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/19 (386 ms) 68: [ RUN ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/20 68: 68: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_20_input.mdp]: 68: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 68: that with the Verlet scheme, nstlist has no effect on the accuracy of 68: your simulation. 68: 68: 68: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_20_input.mdp]: 68: Setting nstcalcenergy (100) equal to nstenergy (4) 68: 68: Generating 1-4 interactions: fudge = 0.5 68: 68: NOTE 3 [file unknown]: 68: You are using constraints on all bonds, whereas the forcefield has been 68: parametrized only with constraints involving hydrogen atoms. We suggest 68: using constraints = h-bonds instead, this will also improve performance. 68: 68: Number of degrees of freedom in T-Coupling group System is 23.00 68: 68: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_20_input.mdp]: 68: There are 9 non-linear virtual site constructions. Their contribution to 68: the energy error is approximated. In most cases this does not affect the 68: error significantly. 68: 68: 68: NOTE 5 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_20_input.mdp]: 68: You are using a plain Coulomb cut-off, which might produce artifacts. 68: You might want to consider using PME electrostatics. 68: 68: 68: 68: There were 5 NOTEs 68: 68: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_20_input.mdp]: 68: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 68: that with the Verlet scheme, nstlist has no effect on the accuracy of 68: your simulation. 68: 68: 68: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_20_input.mdp]: 68: Setting nstcalcenergy (100) equal to nstenergy (4) 68: 68: Generating 1-4 interactions: fudge = 0.5 68: 68: NOTE 3 [file unknown]: 68: You are using constraints on all bonds, whereas the forcefield has been 68: parametrized only with constraints involving hydrogen atoms. We suggest 68: using constraints = h-bonds instead, this will also improve performance. 68: 68: Number of degrees of freedom in T-Coupling group System is 23.00 68: 68: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_20_input.mdp]: 68: There are 9 non-linear virtual site constructions. Their contribution to 68: the energy error is approximated. In most cases this does not affect the 68: error significantly. 68: 68: 68: NOTE 5 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_20_input.mdp]: 68: You are using a plain Coulomb cut-off, which might produce artifacts. 68: You might want to consider using PME electrostatics. 68: 68: 68: 68: There were 5 NOTEs 68: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_20_full.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 68: Update groups can not be used for this system because an incompatible virtual site type is used 68: 68: Using 1 MPI thread 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'Alanine dipeptide in vacuo' 68: 16 steps, 0.0 ps. 68: Generated 2145 of the 2145 non-bonded parameter combinations 68: 68: Generated 2145 of the 2145 1-4 parameter combinations 68: 68: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' 68: 68: turning all bonds into constraints... 68: 68: Cleaning up constraints and constant bonded interactions with virtual sites 68: 68: Removed 18 Angles with virtual sites, 21 left 68: 68: Removed 10 Proper Dih.s with virtual sites, 44 left 68: 68: Converted 15 Constraints with virtual sites to connections, 7 left 68: 68: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 68: 68: Calculated rlist for 1x1 atom pair-list as 0.754 nm, buffer size 0.054 nm 68: 68: Set rlist, assuming 4x4 atom pair-list, to 0.748 nm, buffer size 0.048 nm 68: 68: Note that mdrun will redetermine rlist based on the actual pair-list setup 68: 68: This run will generate roughly 0 Mb of data 68: Generated 2145 of the 2145 non-bonded parameter combinations 68: 68: Generated 2145 of the 2145 1-4 parameter combinations 68: 68: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' 68: 68: turning all bonds into constraints... 68: 68: Cleaning up constraints and constant bonded interactions with virtual sites 68: 68: Removed 18 Angles with virtual sites, 21 left 68: 68: Removed 10 Proper Dih.s with virtual sites, 44 left 68: 68: Converted 15 Constraints with virtual sites to connections, 7 left 68: 68: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 68: 68: Calculated rlist for 1x1 atom pair-list as 0.754 nm, buffer size 0.054 nm 68: 68: Set rlist, assuming 4x4 atom pair-list, to 0.748 nm, buffer size 0.048 nm 68: 68: Note that mdrun will redetermine rlist based on the actual pair-list setup 68: 68: This run will generate roughly 0 Mb of data 68: 68: Writing final coordinates. 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.065 0.033 198.2 68: (ns/day) (hour/ns) 68: Performance: 44.608 0.538 68: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_20_firstpart.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 68: Update groups can not be used for this system because an incompatible virtual site type is used 68: 68: Using 1 MPI thread 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'Alanine dipeptide in vacuo' 68: 8 steps, 0.0 ps. 68: 68: Writing final coordinates. 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.056 0.028 198.0 68: (ns/day) (hour/ns) 68: Performance: 27.498 0.873 68: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_20_full.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 68: Update groups can not be used for this system because an incompatible virtual site type is used 68: 68: Using 1 MPI thread 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'Alanine dipeptide in vacuo' 68: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 68: 68: Writing final coordinates. 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.051 0.026 197.7 68: (ns/day) (hour/ns) 68: Performance: 30.024 0.799 68: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_20_full.edr as single precision energy file 68: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_20_firstpart.edr as single precision energy file 68: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_20_secondpart.part0002.edr as single precision energy file 68: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/20 (602 ms) 68: [ RUN ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/21 68: 68: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_21_input.mdp]: 68: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 68: that with the Verlet scheme, nstlist has no effect on the accuracy of 68: your simulation. 68: 68: 68: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_21_input.mdp]: 68: Setting nstcalcenergy (100) equal to nstenergy (4) 68: 68: Generating 1-4 interactions: fudge = 0.5 68: 68: NOTE 3 [file unknown]: 68: You are using constraints on all bonds, whereas the forcefield has been 68: parametrized only with constraints involving hydrogen atoms. We suggest 68: using constraints = h-bonds instead, this will also improve performance. 68: 68: Number of degrees of freedom in T-Coupling group System is 23.00 68: 68: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_21_input.mdp]: 68: There are 9 non-linear virtual site constructions. Their contribution to 68: the energy error is approximated. In most cases this does not affect the 68: error significantly. 68: 68: 68: NOTE 5 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_21_input.mdp]: 68: You are using a plain Coulomb cut-off, which might produce artifacts. 68: You might want to consider using PME electrostatics. 68: 68: 68: 68: There were 5 NOTEs 68: 68: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_21_input.mdp]: 68: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 68: that with the Verlet scheme, nstlist has no effect on the accuracy of 68: your simulation. 68: 68: 68: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_21_input.mdp]: 68: Setting nstcalcenergy (100) equal to nstenergy (4) 68: 68: Generating 1-4 interactions: fudge = 0.5 68: 68: NOTE 3 [file unknown]: 68: You are using constraints on all bonds, whereas the forcefield has been 68: parametrized only with constraints involving hydrogen atoms. We suggest 68: using constraints = h-bonds instead, this will also improve performance. 68: 68: Number of degrees of freedom in T-Coupling group System is 23.00 68: 68: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_21_input.mdp]: 68: There are 9 non-linear virtual site constructions. Their contribution to 68: the energy error is approximated. In most cases this does not affect the 68: error significantly. 68: 68: 68: NOTE 5 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_21_input.mdp]: 68: You are using a plain Coulomb cut-off, which might produce artifacts. 68: You might want to consider using PME electrostatics. 68: 68: 68: 68: There were 5 NOTEs 68: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_21_full.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 68: Changing nstlist from 8 to 80, rlist from 0.741 to 0.841 68: 68: Update groups can not be used for this system because an incompatible virtual site type is used 68: 68: Using 1 MPI thread 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'Alanine dipeptide in vacuo' 68: 16 steps, 0.0 ps. 68: Generated 2145 of the 2145 non-bonded parameter combinations 68: 68: Generated 2145 of the 2145 1-4 parameter combinations 68: 68: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' 68: 68: turning all bonds into constraints... 68: 68: Cleaning up constraints and constant bonded interactions with virtual sites 68: 68: Removed 18 Angles with virtual sites, 21 left 68: 68: Removed 10 Proper Dih.s with virtual sites, 44 left 68: 68: Converted 15 Constraints with virtual sites to connections, 7 left 68: 68: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 298 K 68: 68: Calculated rlist for 1x1 atom pair-list as 0.747 nm, buffer size 0.047 nm 68: 68: Set rlist, assuming 4x4 atom pair-list, to 0.741 nm, buffer size 0.041 nm 68: 68: Note that mdrun will redetermine rlist based on the actual pair-list setup 68: 68: This run will generate roughly 0 Mb of data 68: Generated 2145 of the 2145 non-bonded parameter combinations 68: 68: Generated 2145 of the 2145 1-4 parameter combinations 68: 68: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' 68: 68: turning all bonds into constraints... 68: 68: Cleaning up constraints and constant bonded interactions with virtual sites 68: 68: Removed 18 Angles with virtual sites, 21 left 68: 68: Removed 10 Proper Dih.s with virtual sites, 44 left 68: 68: Converted 15 Constraints with virtual sites to connections, 7 left 68: 68: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 298 K 68: 68: Calculated rlist for 1x1 atom pair-list as 0.747 nm, buffer size 0.047 nm 68: 68: Set rlist, assuming 4x4 atom pair-list, to 0.741 nm, buffer size 0.041 nm 68: 68: Note that mdrun will redetermine rlist based on the actual pair-list setup 68: 68: This run will generate roughly 0 Mb of data 68: 68: Writing final coordinates. 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.130 0.065 199.0 68: (ns/day) (hour/ns) 68: Performance: 22.426 1.070 68: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_21_firstpart.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 68: Changing nstlist from 8 to 80, rlist from 0.741 to 0.841 68: 68: Update groups can not be used for this system because an incompatible virtual site type is used 68: 68: Using 1 MPI thread 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'Alanine dipeptide in vacuo' 68: 8 steps, 0.0 ps. 68: 68: Writing final coordinates. 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.049 0.025 197.5 68: (ns/day) (hour/ns) 68: Performance: 31.070 0.772 68: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_21_full.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 68: Changing nstlist from 8 to 80, rlist from 0.741 to 0.841 68: 68: Update groups can not be used for this system because an incompatible virtual site type is used 68: 68: Using 1 MPI thread 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'Alanine dipeptide in vacuo' 68: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 68: 68: Writing final coordinates. 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.046 0.023 197.6 68: (ns/day) (hour/ns) 68: Performance: 33.142 0.724 68: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_21_full.edr as single precision energy file 68: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_21_firstpart.edr as single precision energy file 68: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_21_secondpart.part0002.edr as single precision energy file 68: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/21 (1389 ms) 68: [ RUN ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/22 68: 68: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_22_input.mdp]: 68: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 68: that with the Verlet scheme, nstlist has no effect on the accuracy of 68: your simulation. 68: 68: 68: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_22_input.mdp]: 68: Setting nstcalcenergy (100) equal to nstenergy (4) 68: 68: Generating 1-4 interactions: fudge = 0.5 68: 68: NOTE 3 [file unknown]: 68: You are using constraints on all bonds, whereas the forcefield has been 68: parametrized only with constraints involving hydrogen atoms. We suggest 68: using constraints = h-bonds instead, this will also improve performance. 68: 68: Number of degrees of freedom in T-Coupling group System is 23.00 68: 68: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_22_input.mdp]: 68: There are 9 non-linear virtual site constructions. Their contribution to 68: the energy error is approximated. In most cases this does not affect the 68: error significantly. 68: 68: 68: NOTE 5 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_22_input.mdp]: 68: You are using a plain Coulomb cut-off, which might produce artifacts. 68: You might want to consider using PME electrostatics. 68: 68: 68: 68: There were 5 NOTEs 68: 68: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_22_input.mdp]: 68: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 68: that with the Verlet scheme, nstlist has no effect on the accuracy of 68: your simulation. 68: 68: 68: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_22_input.mdp]: 68: Setting nstcalcenergy (100) equal to nstenergy (4) 68: 68: Generating 1-4 interactions: fudge = 0.5 68: 68: NOTE 3 [file unknown]: 68: You are using constraints on all bonds, whereas the forcefield has been 68: parametrized only with constraints involving hydrogen atoms. We suggest 68: using constraints = h-bonds instead, this will also improve performance. 68: 68: Number of degrees of freedom in T-Coupling group System is 23.00 68: 68: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_22_input.mdp]: 68: There are 9 non-linear virtual site constructions. Their contribution to 68: the energy error is approximated. In most cases this does not affect the 68: error significantly. 68: 68: 68: NOTE 5 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_22_input.mdp]: 68: You are using a plain Coulomb cut-off, which might produce artifacts. 68: You might want to consider using PME electrostatics. 68: 68: 68: 68: There were 5 NOTEs 68: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_22_full.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 68: Update groups can not be used for this system because an incompatible virtual site type is used 68: 68: Using 1 MPI thread 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'Alanine dipeptide in vacuo' 68: 16 steps, 0.0 ps. 68: Generated 2145 of the 2145 non-bonded parameter combinations 68: 68: Generated 2145 of the 2145 1-4 parameter combinations 68: 68: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' 68: 68: turning all bonds into constraints... 68: 68: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/alanine_vsite_vacuo.gro' 68: 68: Cleaning up constraints and constant bonded interactions with virtual sites 68: 68: Removed 18 Angles with virtual sites, 21 left 68: 68: Removed 10 Proper Dih.s with virtual sites, 44 left 68: 68: Converted 15 Constraints with virtual sites to connections, 7 left 68: 68: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 68: 68: Calculated rlist for 1x1 atom pair-list as 0.733 nm, buffer size 0.033 nm 68: 68: Set rlist, assuming 4x4 atom pair-list, to 0.729 nm, buffer size 0.029 nm 68: 68: Note that mdrun will redetermine rlist based on the actual pair-list setup 68: 68: This run will generate roughly 0 Mb of data 68: Generated 2145 of the 2145 non-bonded parameter combinations 68: 68: Generated 2145 of the 2145 1-4 parameter combinations 68: 68: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' 68: 68: turning all bonds into constraints... 68: 68: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/alanine_vsite_vacuo.gro' 68: 68: Cleaning up constraints and constant bonded interactions with virtual sites 68: 68: Removed 18 Angles with virtual sites, 21 left 68: 68: Removed 10 Proper Dih.s with virtual sites, 44 left 68: 68: Converted 15 Constraints with virtual sites to connections, 7 left 68: 68: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 68: 68: Calculated rlist for 1x1 atom pair-list as 0.733 nm, buffer size 0.033 nm 68: 68: Set rlist, assuming 4x4 atom pair-list, to 0.729 nm, buffer size 0.029 nm 68: 68: Note that mdrun will redetermine rlist based on the actual pair-list setup 68: 68: This run will generate roughly 0 Mb of data 68: 68: Writing final coordinates. 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.064 0.032 198.2 68: (ns/day) (hour/ns) 68: Performance: 45.822 0.524 68: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_22_firstpart.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 68: Update groups can not be used for this system because an incompatible virtual site type is used 68: 68: Using 1 MPI thread 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'Alanine dipeptide in vacuo' 68: 8 steps, 0.0 ps. 68: 68: Writing final coordinates. 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.065 0.033 198.2 68: (ns/day) (hour/ns) 68: Performance: 23.717 1.012 68: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_22_full.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 68: Update groups can not be used for this system because an incompatible virtual site type is used 68: 68: Using 1 MPI thread 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'Alanine dipeptide in vacuo' 68: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 68: 68: Writing final coordinates. 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.071 0.036 198.3 68: (ns/day) (hour/ns) 68: Performance: 21.827 1.100 68: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_22_full.edr as single precision energy file 68: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_22_firstpart.edr as single precision energy file 68: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_22_secondpart.part0002.edr as single precision energy file 68: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/22 (568 ms) 68: [ RUN ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/23 68: 68: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_23_input.mdp]: 68: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 68: that with the Verlet scheme, nstlist has no effect on the accuracy of 68: your simulation. 68: 68: 68: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_23_input.mdp]: 68: Setting nstcalcenergy (100) equal to nstenergy (4) 68: 68: Generating 1-4 interactions: fudge = 0.5 68: 68: NOTE 3 [file unknown]: 68: You are using constraints on all bonds, whereas the forcefield has been 68: parametrized only with constraints involving hydrogen atoms. We suggest 68: using constraints = h-bonds instead, this will also improve performance. 68: 68: Number of degrees of freedom in T-Coupling group System is 23.00 68: 68: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_23_input.mdp]: 68: There are 9 non-linear virtual site constructions. Their contribution to 68: the energy error is approximated. In most cases this does not affect the 68: error significantly. 68: 68: 68: NOTE 5 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_23_input.mdp]: 68: You are using a plain Coulomb cut-off, which might produce artifacts. 68: You might want to consider using PME electrostatics. 68: 68: 68: 68: There were 5 NOTEs 68: 68: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_23_input.mdp]: 68: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 68: that with the Verlet scheme, nstlist has no effect on the accuracy of 68: your simulation. 68: 68: 68: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_23_input.mdp]: 68: Setting nstcalcenergy (100) equal to nstenergy (4) 68: 68: Generating 1-4 interactions: fudge = 0.5 68: 68: NOTE 3 [file unknown]: 68: You are using constraints on all bonds, whereas the forcefield has been 68: parametrized only with constraints involving hydrogen atoms. We suggest 68: using constraints = h-bonds instead, this will also improve performance. 68: 68: Number of degrees of freedom in T-Coupling group System is 23.00 68: 68: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_23_input.mdp]: 68: There are 9 non-linear virtual site constructions. Their contribution to 68: the energy error is approximated. In most cases this does not affect the 68: error significantly. 68: 68: 68: NOTE 5 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_23_input.mdp]: 68: You are using a plain Coulomb cut-off, which might produce artifacts. 68: You might want to consider using PME electrostatics. 68: 68: 68: 68: There were 5 NOTEs 68: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_23_full.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 68: Changing nstlist from 8 to 25, rlist from 0.724 to 0.793 68: 68: Update groups can not be used for this system because an incompatible virtual site type is used 68: 68: Using 1 MPI thread 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'Alanine dipeptide in vacuo' 68: 16 steps, 0.0 ps. 68: Generated 2145 of the 2145 non-bonded parameter combinations 68: 68: Generated 2145 of the 2145 1-4 parameter combinations 68: 68: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' 68: 68: turning all bonds into constraints... 68: 68: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/alanine_vsite_vacuo.gro' 68: 68: Cleaning up constraints and constant bonded interactions with virtual sites 68: 68: Removed 18 Angles with virtual sites, 21 left 68: 68: Removed 10 Proper Dih.s with virtual sites, 44 left 68: 68: Converted 15 Constraints with virtual sites to connections, 7 left 68: 68: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 298 K 68: 68: Calculated rlist for 1x1 atom pair-list as 0.728 nm, buffer size 0.028 nm 68: 68: Set rlist, assuming 4x4 atom pair-list, to 0.724 nm, buffer size 0.024 nm 68: 68: Note that mdrun will redetermine rlist based on the actual pair-list setup 68: 68: This run will generate roughly 0 Mb of data 68: Generated 2145 of the 2145 non-bonded parameter combinations 68: 68: Generated 2145 of the 2145 1-4 parameter combinations 68: 68: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' 68: 68: turning all bonds into constraints... 68: 68: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/alanine_vsite_vacuo.gro' 68: 68: Cleaning up constraints and constant bonded interactions with virtual sites 68: 68: Removed 18 Angles with virtual sites, 21 left 68: 68: Removed 10 Proper Dih.s with virtual sites, 44 left 68: 68: Converted 15 Constraints with virtual sites to connections, 7 left 68: 68: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 298 K 68: 68: Calculated rlist for 1x1 atom pair-list as 0.728 nm, buffer size 0.028 nm 68: 68: Set rlist, assuming 4x4 atom pair-list, to 0.724 nm, buffer size 0.024 nm 68: 68: Note that mdrun will redetermine rlist based on the actual pair-list setup 68: 68: This run will generate roughly 0 Mb of data 68: 68: Writing final coordinates. 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.066 0.033 198.3 68: (ns/day) (hour/ns) 68: Performance: 44.050 0.545 68: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_23_firstpart.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 68: Changing nstlist from 8 to 25, rlist from 0.724 to 0.793 68: 68: Update groups can not be used for this system because an incompatible virtual site type is used 68: 68: Using 1 MPI thread 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'Alanine dipeptide in vacuo' 68: 8 steps, 0.0 ps. 68: 68: Writing final coordinates. 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.050 0.025 197.7 68: (ns/day) (hour/ns) 68: Performance: 30.825 0.779 68: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_23_full.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 68: Changing nstlist from 8 to 25, rlist from 0.724 to 0.793 68: 68: Update groups can not be used for this system because an incompatible virtual site type is used 68: 68: Using 1 MPI thread 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'Alanine dipeptide in vacuo' 68: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 68: 68: Writing final coordinates. 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.061 0.031 198.2 68: (ns/day) (hour/ns) 68: Performance: 25.302 0.949 68: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_23_full.edr as single precision energy file 68: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_23_firstpart.edr as single precision energy file 68: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_23_secondpart.part0002.edr as single precision energy file 68: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/23 (760 ms) 68: [----------] 24 tests from NormalIntegrators/MdrunNoAppendContinuationIsExact (7986 ms total) 68: 68: [----------] 8 tests from NormalIntegratorsWithFEP/MdrunNoAppendContinuationIsExact 68: [ RUN ] NormalIntegratorsWithFEP/MdrunNoAppendContinuationIsExact.WithinTolerances/0 68: 68: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 68: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 68: that with the Verlet scheme, nstlist has no effect on the accuracy of 68: your simulation. 68: 68: 68: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 68: Setting nstcalcenergy (100) equal to nstenergy (4) 68: 68: Generating 1-4 interactions: fudge = 0.5 68: Number of degrees of freedom in T-Coupling group System is 79.00 68: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 68: 68: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 68: NVE simulation: will use the initial temperature of 294.908 K for 68: determining the Verlet buffer size 68: 68: 68: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 68: You are using a plain Coulomb cut-off, which might produce artifacts. 68: You might want to consider using PME electrostatics. 68: 68: 68: 68: There were 4 NOTEs 68: 68: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 68: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 68: that with the Verlet scheme, nstlist has no effect on the accuracy of 68: your simulation. 68: 68: 68: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 68: Setting nstcalcenergy (100) equal to nstenergy (4) 68: 68: Generating 1-4 interactions: fudge = 0.5 68: Number of degrees of freedom in T-Coupling group System is 79.00 68: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 68: 68: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 68: NVE simulation: will use the initial temperature of 294.908 K for 68: determining the Verlet buffer size 68: 68: 68: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 68: You are using a plain Coulomb cut-off, which might produce artifacts. 68: You might want to consider using PME electrostatics. 68: 68: 68: 68: There were 4 NOTEs 68: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 68: Can not increase nstlist because an NVE ensemble is used 68: Using 1 MPI thread 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun '30 atom system in water' 68: 16 steps, 0.0 ps. 68: Generated 2485 of the 2485 non-bonded parameter combinations 68: 68: Generated 2485 of the 2485 1-4 parameter combinations 68: 68: Excluding 3 bonded neighbours molecule type 'nonanol' 68: 68: turning H bonds into constraints... 68: 68: Excluding 2 bonded neighbours molecule type 'SOL' 68: 68: turning H bonds into constraints... 68: 68: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/nonanol_vacuo.gro' 68: 68: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 294.908 K 68: 68: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 68: 68: Set rlist, assuming 4x4 atom pair-list, to 0.757 nm, buffer size 0.057 nm 68: 68: Note that mdrun will redetermine rlist based on the actual pair-list setup 68: 68: This run will generate roughly 0 Mb of data 68: Generated 2485 of the 2485 non-bonded parameter combinations 68: 68: Generated 2485 of the 2485 1-4 parameter combinations 68: 68: Excluding 3 bonded neighbours molecule type 'nonanol' 68: 68: turning H bonds into constraints... 68: 68: Excluding 2 bonded neighbours molecule type 'SOL' 68: 68: turning H bonds into constraints... 68: 68: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/nonanol_vacuo.gro' 68: 68: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 294.908 K 68: 68: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 68: 68: Set rlist, assuming 4x4 atom pair-list, to 0.757 nm, buffer size 0.057 nm 68: 68: Note that mdrun will redetermine rlist based on the actual pair-list setup 68: 68: This run will generate roughly 0 Mb of data 68: 68: Writing final coordinates. 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.077 0.039 197.6 68: (ns/day) (hour/ns) 68: Performance: 37.531 0.639 68: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_0_firstpart.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 68: Can not increase nstlist because an NVE ensemble is used 68: Using 1 MPI thread 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun '30 atom system in water' 68: 8 steps, 0.0 ps. 68: 68: Writing final coordinates. 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.063 0.032 195.7 68: (ns/day) (hour/ns) 68: Performance: 24.078 0.997 68: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 68: Can not increase nstlist because an NVE ensemble is used 68: Using 1 MPI thread 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun '30 atom system in water' 68: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 68: 68: Writing final coordinates. 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.061 0.031 197.1 68: (ns/day) (hour/ns) 68: Performance: 25.130 0.955 68: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.edr as single precision energy file 68: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_0_firstpart.edr as single precision energy file 68: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_0_secondpart.part0002.edr as single precision energy file 68: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NormalIntegratorsWithFEP/MdrunNoAppendContinuationIsExact.WithinTolerances/0 (389 ms) 68: [ RUN ] NormalIntegratorsWithFEP/MdrunNoAppendContinuationIsExact.WithinTolerances/1 68: 68: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 68: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 68: that with the Verlet scheme, nstlist has no effect on the accuracy of 68: your simulation. 68: 68: 68: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 68: Setting nstcalcenergy (100) equal to nstenergy (4) 68: 68: Generating 1-4 interactions: fudge = 0.5 68: Number of degrees of freedom in T-Coupling group System is 79.00 68: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 68: 68: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 68: NVE simulation: will use the initial temperature of 294.908 K for 68: determining the Verlet buffer size 68: 68: 68: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 68: You are using a plain Coulomb cut-off, which might produce artifacts. 68: You might want to consider using PME electrostatics. 68: 68: 68: 68: There were 4 NOTEs 68: 68: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 68: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 68: that with the Verlet scheme, nstlist has no effect on the accuracy of 68: your simulation. 68: 68: 68: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 68: Setting nstcalcenergy (100) equal to nstenergy (4) 68: 68: Generating 1-4 interactions: fudge = 0.5 68: Number of degrees of freedom in T-Coupling group System is 79.00 68: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 68: 68: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 68: NVE simulation: will use the initial temperature of 294.908 K for 68: determining the Verlet buffer size 68: 68: 68: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 68: You are using a plain Coulomb cut-off, which might produce artifacts. 68: You might want to consider using PME electrostatics. 68: 68: 68: 68: There were 4 NOTEs 68: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_1_full.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 68: Can not increase nstlist because an NVE ensemble is used 68: Using 1 MPI thread 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun '30 atom system in water' 68: 16 steps, 0.0 ps. 68: Generated 2485 of the 2485 non-bonded parameter combinations 68: 68: Generated 2485 of the 2485 1-4 parameter combinations 68: 68: Excluding 3 bonded neighbours molecule type 'nonanol' 68: 68: turning H bonds into constraints... 68: 68: Excluding 2 bonded neighbours molecule type 'SOL' 68: 68: turning H bonds into constraints... 68: 68: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/nonanol_vacuo.gro' 68: 68: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 294.908 K 68: 68: Calculated rlist for 1x1 atom pair-list as 0.756 nm, buffer size 0.056 nm 68: 68: Set rlist, assuming 4x4 atom pair-list, to 0.749 nm, buffer size 0.049 nm 68: 68: Note that mdrun will redetermine rlist based on the actual pair-list setup 68: 68: This run will generate roughly 0 Mb of data 68: Generated 2485 of the 2485 non-bonded parameter combinations 68: 68: Generated 2485 of the 2485 1-4 parameter combinations 68: 68: Excluding 3 bonded neighbours molecule type 'nonanol' 68: 68: turning H bonds into constraints... 68: 68: Excluding 2 bonded neighbours molecule type 'SOL' 68: 68: turning H bonds into constraints... 68: 68: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/nonanol_vacuo.gro' 68: 68: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 294.908 K 68: 68: Calculated rlist for 1x1 atom pair-list as 0.756 nm, buffer size 0.056 nm 68: 68: Set rlist, assuming 4x4 atom pair-list, to 0.749 nm, buffer size 0.049 nm 68: 68: Note that mdrun will redetermine rlist based on the actual pair-list setup 68: 68: This run will generate roughly 0 Mb of data 68: 68: Writing final coordinates. 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.086 0.043 197.5 68: (ns/day) (hour/ns) 68: Performance: 33.806 0.710 68: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_1_firstpart.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 68: Can not increase nstlist because an NVE ensemble is used 68: Using 1 MPI thread 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun '30 atom system in water' 68: 8 steps, 0.0 ps. 68: 68: Writing final coordinates. 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.083 0.042 196.1 68: (ns/day) (hour/ns) 68: Performance: 18.297 1.312 68: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_1_full.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 68: Can not increase nstlist because an NVE ensemble is used 68: Using 1 MPI thread 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun '30 atom system in water' 68: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 68: 68: Writing final coordinates. 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.075 0.038 197.7 68: (ns/day) (hour/ns) 68: Performance: 20.600 1.165 68: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_1_full.edr as single precision energy file 68: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_1_firstpart.edr as single precision energy file 68: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_1_secondpart.part0002.edr as single precision energy file 68: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NormalIntegratorsWithFEP/MdrunNoAppendContinuationIsExact.WithinTolerances/1 (434 ms) 68: [ RUN ] NormalIntegratorsWithFEP/MdrunNoAppendContinuationIsExact.WithinTolerances/2 68: 68: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]: 68: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 68: that with the Verlet scheme, nstlist has no effect on the accuracy of 68: your simulation. 68: 68: 68: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]: 68: Setting nstcalcenergy (100) equal to nstenergy (4) 68: 68: Generating 1-4 interactions: fudge = 0.5 68: Number of degrees of freedom in T-Coupling group System is 79.00 68: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 68: 68: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]: 68: NVE simulation: will use the initial temperature of 294.908 K for 68: determining the Verlet buffer size 68: 68: 68: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]: 68: You are using a plain Coulomb cut-off, which might produce artifacts. 68: You might want to consider using PME electrostatics. 68: 68: 68: 68: There were 4 NOTEs 68: 68: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]: 68: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 68: that with the Verlet scheme, nstlist has no effect on the accuracy of 68: your simulation. 68: 68: 68: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]: 68: Setting nstcalcenergy (100) equal to nstenergy (4) 68: 68: Generating 1-4 interactions: fudge = 0.5 68: Number of degrees of freedom in T-Coupling group System is 79.00 68: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 68: 68: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]: 68: NVE simulation: will use the initial temperature of 294.908 K for 68: determining the Verlet buffer size 68: 68: 68: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]: 68: You are using a plain Coulomb cut-off, which might produce artifacts. 68: You might want to consider using PME electrostatics. 68: 68: 68: 68: There were 4 NOTEs 68: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_2_full.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 68: Can not increase nstlist because an NVE ensemble is used 68: Using 1 MPI thread 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun '30 atom system in water' 68: 16 steps, 0.0 ps. 68: Generated 2485 of the 2485 non-bonded parameter combinations 68: 68: Generated 2485 of the 2485 1-4 parameter combinations 68: 68: Excluding 3 bonded neighbours molecule type 'nonanol' 68: 68: turning H bonds into constraints... 68: 68: Excluding 2 bonded neighbours molecule type 'SOL' 68: 68: turning H bonds into constraints... 68: 68: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/nonanol_vacuo.gro' 68: 68: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 294.908 K 68: 68: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 68: 68: Set rlist, assuming 4x4 atom pair-list, to 0.757 nm, buffer size 0.057 nm 68: 68: Note that mdrun will redetermine rlist based on the actual pair-list setup 68: 68: This run will generate roughly 0 Mb of data 68: Generated 2485 of the 2485 non-bonded parameter combinations 68: 68: Generated 2485 of the 2485 1-4 parameter combinations 68: 68: Excluding 3 bonded neighbours molecule type 'nonanol' 68: 68: turning H bonds into constraints... 68: 68: Excluding 2 bonded neighbours molecule type 'SOL' 68: 68: turning H bonds into constraints... 68: 68: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/nonanol_vacuo.gro' 68: 68: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 294.908 K 68: 68: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 68: 68: Set rlist, assuming 4x4 atom pair-list, to 0.757 nm, buffer size 0.057 nm 68: 68: Note that mdrun will redetermine rlist based on the actual pair-list setup 68: 68: This run will generate roughly 0 Mb of data 68: 68: Writing final coordinates. 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.108 0.054 199.3 68: (ns/day) (hour/ns) 68: Performance: 27.190 0.883 68: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_2_firstpart.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 68: Can not increase nstlist because an NVE ensemble is used 68: Using 1 MPI thread 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun '30 atom system in water' 68: 8 steps, 0.0 ps. 68: 68: Writing final coordinates. 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.080 0.040 199.0 68: (ns/day) (hour/ns) 68: Performance: 19.412 1.236 68: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_2_full.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 68: Can not increase nstlist because an NVE ensemble is used 68: Using 1 MPI thread 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun '30 atom system in water' 68: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 68: 68: Writing final coordinates. 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.092 0.047 198.0 68: (ns/day) (hour/ns) 68: Performance: 16.678 1.439 68: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_2_full.edr as single precision energy file 68: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_2_firstpart.edr as single precision energy file 68: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_2_secondpart.part0002.edr as single precision energy file 68: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NormalIntegratorsWithFEP/MdrunNoAppendContinuationIsExact.WithinTolerances/2 (441 ms) 68: [ RUN ] NormalIntegratorsWithFEP/MdrunNoAppendContinuationIsExact.WithinTolerances/3 68: 68: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]: 68: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 68: that with the Verlet scheme, nstlist has no effect on the accuracy of 68: your simulation. 68: 68: 68: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]: 68: Setting nstcalcenergy (100) equal to nstenergy (4) 68: 68: Generating 1-4 interactions: fudge = 0.5 68: Number of degrees of freedom in T-Coupling group System is 79.00 68: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 68: 68: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]: 68: NVE simulation: will use the initial temperature of 294.908 K for 68: determining the Verlet buffer size 68: 68: 68: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]: 68: You are using a plain Coulomb cut-off, which might produce artifacts. 68: You might want to consider using PME electrostatics. 68: 68: 68: 68: There were 4 NOTEs 68: 68: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]: 68: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 68: that with the Verlet scheme, nstlist has no effect on the accuracy of 68: your simulation. 68: 68: 68: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]: 68: Setting nstcalcenergy (100) equal to nstenergy (4) 68: 68: Generating 1-4 interactions: fudge = 0.5 68: Number of degrees of freedom in T-Coupling group System is 79.00 68: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 68: 68: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]: 68: NVE simulation: will use the initial temperature of 294.908 K for 68: determining the Verlet buffer size 68: 68: 68: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]: 68: You are using a plain Coulomb cut-off, which might produce artifacts. 68: You might want to consider using PME electrostatics. 68: 68: 68: 68: There were 4 NOTEs 68: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_3_full.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 68: Can not increase nstlist because an NVE ensemble is used 68: Using 1 MPI thread 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun '30 atom system in water' 68: 16 steps, 0.0 ps. 68: Generated 2485 of the 2485 non-bonded parameter combinations 68: 68: Generated 2485 of the 2485 1-4 parameter combinations 68: 68: Excluding 3 bonded neighbours molecule type 'nonanol' 68: 68: turning H bonds into constraints... 68: 68: Excluding 2 bonded neighbours molecule type 'SOL' 68: 68: turning H bonds into constraints... 68: 68: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/nonanol_vacuo.gro' 68: 68: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 294.908 K 68: 68: Calculated rlist for 1x1 atom pair-list as 0.756 nm, buffer size 0.056 nm 68: 68: Set rlist, assuming 4x4 atom pair-list, to 0.749 nm, buffer size 0.049 nm 68: 68: Note that mdrun will redetermine rlist based on the actual pair-list setup 68: 68: This run will generate roughly 0 Mb of data 68: Generated 2485 of the 2485 non-bonded parameter combinations 68: 68: Generated 2485 of the 2485 1-4 parameter combinations 68: 68: Excluding 3 bonded neighbours molecule type 'nonanol' 68: 68: turning H bonds into constraints... 68: 68: Excluding 2 bonded neighbours molecule type 'SOL' 68: 68: turning H bonds into constraints... 68: 68: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/nonanol_vacuo.gro' 68: 68: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 294.908 K 68: 68: Calculated rlist for 1x1 atom pair-list as 0.756 nm, buffer size 0.056 nm 68: 68: Set rlist, assuming 4x4 atom pair-list, to 0.749 nm, buffer size 0.049 nm 68: 68: Note that mdrun will redetermine rlist based on the actual pair-list setup 68: 68: This run will generate roughly 0 Mb of data 68: 68: Writing final coordinates. 68: 68: NOTE: 22 % of the run time was spent in pair search, 68: you might want to increase nstlist (this has no effect on accuracy) 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.155 0.078 199.5 68: (ns/day) (hour/ns) 68: Performance: 18.884 1.271 68: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_3_firstpart.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 68: Can not increase nstlist because an NVE ensemble is used 68: Using 1 MPI thread 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun '30 atom system in water' 68: 8 steps, 0.0 ps. 68: 68: Writing final coordinates. 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.161 0.081 199.5 68: (ns/day) (hour/ns) 68: Performance: 9.623 2.494 68: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_3_full.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 68: Can not increase nstlist because an NVE ensemble is used 68: Using 1 MPI thread 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun '30 atom system in water' 68: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 68: 68: Writing final coordinates. 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.085 0.043 197.8 68: (ns/day) (hour/ns) 68: Performance: 18.196 1.319 68: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_3_full.edr as single precision energy file 68: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_3_firstpart.edr as single precision energy file 68: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_3_secondpart.part0002.edr as single precision energy file 68: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NormalIntegratorsWithFEP/MdrunNoAppendContinuationIsExact.WithinTolerances/3 (508 ms) 68: [ RUN ] NormalIntegratorsWithFEP/MdrunNoAppendContinuationIsExact.WithinTolerances/4 68: 68: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_4_input.mdp]: 68: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 68: that with the Verlet scheme, nstlist has no effect on the accuracy of 68: your simulation. 68: 68: 68: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_4_input.mdp]: 68: Setting nstcalcenergy (100) equal to nstenergy (4) 68: 68: Generating 1-4 interactions: fudge = 0.5 68: Number of degrees of freedom in T-Coupling group System is 79.00 68: 68: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_4_input.mdp]: 68: You are using a plain Coulomb cut-off, which might produce artifacts. 68: You might want to consider using PME electrostatics. 68: 68: 68: 68: There were 3 NOTEs 68: 68: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_4_input.mdp]: 68: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 68: that with the Verlet scheme, nstlist has no effect on the accuracy of 68: your simulation. 68: 68: 68: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_4_input.mdp]: 68: Setting nstcalcenergy (100) equal to nstenergy (4) 68: 68: Generating 1-4 interactions: fudge = 0.5 68: Number of degrees of freedom in T-Coupling group System is 79.00 68: 68: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_4_input.mdp]: 68: You are using a plain Coulomb cut-off, which might produce artifacts. 68: You might want to consider using PME electrostatics. 68: 68: 68: 68: There were 3 NOTEs 68: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_4_full.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 68: Using 1 MPI thread 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun '30 atom system in water' 68: 16 steps, 0.0 ps. 68: Generated 2485 of the 2485 non-bonded parameter combinations 68: 68: Generated 2485 of the 2485 1-4 parameter combinations 68: 68: Excluding 3 bonded neighbours molecule type 'nonanol' 68: 68: turning H bonds into constraints... 68: 68: Excluding 2 bonded neighbours molecule type 'SOL' 68: 68: turning H bonds into constraints... 68: 68: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 68: 68: Calculated rlist for 1x1 atom pair-list as 0.736 nm, buffer size 0.036 nm 68: 68: Set rlist, assuming 4x4 atom pair-list, to 0.732 nm, buffer size 0.032 nm 68: 68: Note that mdrun will redetermine rlist based on the actual pair-list setup 68: 68: This run will generate roughly 0 Mb of data 68: Generated 2485 of the 2485 non-bonded parameter combinations 68: 68: Generated 2485 of the 2485 1-4 parameter combinations 68: 68: Excluding 3 bonded neighbours molecule type 'nonanol' 68: 68: turning H bonds into constraints... 68: 68: Excluding 2 bonded neighbours molecule type 'SOL' 68: 68: turning H bonds into constraints... 68: 68: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 68: 68: Calculated rlist for 1x1 atom pair-list as 0.736 nm, buffer size 0.036 nm 68: 68: Set rlist, assuming 4x4 atom pair-list, to 0.732 nm, buffer size 0.032 nm 68: 68: Note that mdrun will redetermine rlist based on the actual pair-list setup 68: 68: This run will generate roughly 0 Mb of data 68: 68: Writing final coordinates. 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.078 0.039 198.0 68: (ns/day) (hour/ns) 68: Performance: 37.342 0.643 68: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_4_firstpart.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 68: Using 1 MPI thread 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun '30 atom system in water' 68: 8 steps, 0.0 ps. 68: 68: Writing final coordinates. 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.059 0.030 195.3 68: (ns/day) (hour/ns) 68: Performance: 25.867 0.928 68: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_4_full.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 68: Using 1 MPI thread 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun '30 atom system in water' 68: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 68: 68: Writing final coordinates. 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.088 0.044 197.9 68: (ns/day) (hour/ns) 68: Performance: 17.504 1.371 68: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_4_full.edr as single precision energy file 68: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_4_firstpart.edr as single precision energy file 68: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_4_secondpart.part0002.edr as single precision energy file 68: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NormalIntegratorsWithFEP/MdrunNoAppendContinuationIsExact.WithinTolerances/4 (577 ms) 68: [ RUN ] NormalIntegratorsWithFEP/MdrunNoAppendContinuationIsExact.WithinTolerances/5 68: 68: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_5_input.mdp]: 68: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 68: that with the Verlet scheme, nstlist has no effect on the accuracy of 68: your simulation. 68: 68: 68: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_5_input.mdp]: 68: Setting nstcalcenergy (100) equal to nstenergy (4) 68: 68: Generating 1-4 interactions: fudge = 0.5 68: Number of degrees of freedom in T-Coupling group System is 79.00 68: 68: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_5_input.mdp]: 68: You are using a plain Coulomb cut-off, which might produce artifacts. 68: You might want to consider using PME electrostatics. 68: 68: 68: 68: There were 3 NOTEs 68: 68: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_5_input.mdp]: 68: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 68: that with the Verlet scheme, nstlist has no effect on the accuracy of 68: your simulation. 68: 68: 68: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_5_input.mdp]: 68: Setting nstcalcenergy (100) equal to nstenergy (4) 68: 68: Generating 1-4 interactions: fudge = 0.5 68: Number of degrees of freedom in T-Coupling group System is 79.00 68: 68: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_5_input.mdp]: 68: You are using a plain Coulomb cut-off, which might produce artifacts. 68: You might want to consider using PME electrostatics. 68: 68: 68: 68: There were 3 NOTEs 68: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_5_full.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 68: Changing nstlist from 8 to 100, rlist from 0.728 to 0.806 68: 68: Using 1 MPI thread 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun '30 atom system in water' 68: 16 steps, 0.0 ps. 68: Generated 2485 of the 2485 non-bonded parameter combinations 68: 68: Generated 2485 of the 2485 1-4 parameter combinations 68: 68: Excluding 3 bonded neighbours molecule type 'nonanol' 68: 68: turning H bonds into constraints... 68: 68: Excluding 2 bonded neighbours molecule type 'SOL' 68: 68: turning H bonds into constraints... 68: 68: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 298 K 68: 68: Calculated rlist for 1x1 atom pair-list as 0.732 nm, buffer size 0.032 nm 68: 68: Set rlist, assuming 4x4 atom pair-list, to 0.728 nm, buffer size 0.028 nm 68: 68: Note that mdrun will redetermine rlist based on the actual pair-list setup 68: 68: This run will generate roughly 0 Mb of data 68: Generated 2485 of the 2485 non-bonded parameter combinations 68: 68: Generated 2485 of the 2485 1-4 parameter combinations 68: 68: Excluding 3 bonded neighbours molecule type 'nonanol' 68: 68: turning H bonds into constraints... 68: 68: Excluding 2 bonded neighbours molecule type 'SOL' 68: 68: turning H bonds into constraints... 68: 68: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 298 K 68: 68: Calculated rlist for 1x1 atom pair-list as 0.732 nm, buffer size 0.032 nm 68: 68: Set rlist, assuming 4x4 atom pair-list, to 0.728 nm, buffer size 0.028 nm 68: 68: Note that mdrun will redetermine rlist based on the actual pair-list setup 68: 68: This run will generate roughly 0 Mb of data 68: 68: Writing final coordinates. 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.101 0.051 197.9 68: (ns/day) (hour/ns) 68: Performance: 28.675 0.837 68: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_5_firstpart.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 68: Changing nstlist from 8 to 100, rlist from 0.728 to 0.806 68: 68: Using 1 MPI thread 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun '30 atom system in water' 68: 8 steps, 0.0 ps. 68: 68: Writing final coordinates. 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.093 0.048 193.4 68: (ns/day) (hour/ns) 68: Performance: 16.225 1.479 68: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_5_full.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 68: Changing nstlist from 8 to 100, rlist from 0.728 to 0.806 68: 68: Using 1 MPI thread 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun '30 atom system in water' 68: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 68: 68: Writing final coordinates. 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.070 0.036 197.6 68: (ns/day) (hour/ns) 68: Performance: 21.831 1.099 68: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_5_full.edr as single precision energy file 68: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_5_firstpart.edr as single precision energy file 68: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_5_secondpart.part0002.edr as single precision energy file 68: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NormalIntegratorsWithFEP/MdrunNoAppendContinuationIsExact.WithinTolerances/5 (1613 ms) 68: [ RUN ] NormalIntegratorsWithFEP/MdrunNoAppendContinuationIsExact.WithinTolerances/6 68: 68: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_6_input.mdp]: 68: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 68: that with the Verlet scheme, nstlist has no effect on the accuracy of 68: your simulation. 68: 68: 68: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_6_input.mdp]: 68: Setting nstcalcenergy (100) equal to nstenergy (4) 68: 68: Generating 1-4 interactions: fudge = 0.5 68: Number of degrees of freedom in T-Coupling group System is 79.00 68: 68: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_6_input.mdp]: 68: You are using a plain Coulomb cut-off, which might produce artifacts. 68: You might want to consider using PME electrostatics. 68: 68: 68: 68: There were 3 NOTEs 68: 68: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_6_input.mdp]: 68: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 68: that with the Verlet scheme, nstlist has no effect on the accuracy of 68: your simulation. 68: 68: 68: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_6_input.mdp]: 68: Setting nstcalcenergy (100) equal to nstenergy (4) 68: 68: Generating 1-4 interactions: fudge = 0.5 68: Number of degrees of freedom in T-Coupling group System is 79.00 68: 68: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_6_input.mdp]: 68: You are using a plain Coulomb cut-off, which might produce artifacts. 68: You might want to consider using PME electrostatics. 68: 68: 68: 68: There were 3 NOTEs 68: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_6_full.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 68: Using 1 MPI thread 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun '30 atom system in water' 68: 16 steps, 0.0 ps. 68: Generated 2485 of the 2485 non-bonded parameter combinations 68: 68: Generated 2485 of the 2485 1-4 parameter combinations 68: 68: Excluding 3 bonded neighbours molecule type 'nonanol' 68: 68: turning H bonds into constraints... 68: 68: Excluding 2 bonded neighbours molecule type 'SOL' 68: 68: turning H bonds into constraints... 68: 68: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/nonanol_vacuo.gro' 68: 68: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 68: 68: Calculated rlist for 1x1 atom pair-list as 0.764 nm, buffer size 0.064 nm 68: 68: Set rlist, assuming 4x4 atom pair-list, to 0.757 nm, buffer size 0.057 nm 68: 68: Note that mdrun will redetermine rlist based on the actual pair-list setup 68: 68: This run will generate roughly 0 Mb of data 68: Generated 2485 of the 2485 non-bonded parameter combinations 68: 68: Generated 2485 of the 2485 1-4 parameter combinations 68: 68: Excluding 3 bonded neighbours molecule type 'nonanol' 68: 68: turning H bonds into constraints... 68: 68: Excluding 2 bonded neighbours molecule type 'SOL' 68: 68: turning H bonds into constraints... 68: 68: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/nonanol_vacuo.gro' 68: 68: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 68: 68: Calculated rlist for 1x1 atom pair-list as 0.764 nm, buffer size 0.064 nm 68: 68: Set rlist, assuming 4x4 atom pair-list, to 0.757 nm, buffer size 0.057 nm 68: 68: Note that mdrun will redetermine rlist based on the actual pair-list setup 68: 68: This run will generate roughly 0 Mb of data 68: 68: Writing final coordinates. 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.167 0.084 199.0 68: (ns/day) (hour/ns) 68: Performance: 17.496 1.372 68: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_6_firstpart.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 68: Using 1 MPI thread 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun '30 atom system in water' 68: 8 steps, 0.0 ps. 68: 68: Writing final coordinates. 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.088 0.048 181.9 68: (ns/day) (hour/ns) 68: Performance: 16.142 1.487 68: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_6_full.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 68: Using 1 MPI thread 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun '30 atom system in water' 68: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 68: 68: Writing final coordinates. 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.059 0.030 197.1 68: (ns/day) (hour/ns) 68: Performance: 25.902 0.927 68: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_6_full.edr as single precision energy file 68: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_6_firstpart.edr as single precision energy file 68: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_6_secondpart.part0002.edr as single precision energy file 68: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NormalIntegratorsWithFEP/MdrunNoAppendContinuationIsExact.WithinTolerances/6 (576 ms) 68: [ RUN ] NormalIntegratorsWithFEP/MdrunNoAppendContinuationIsExact.WithinTolerances/7 68: 68: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_7_input.mdp]: 68: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 68: that with the Verlet scheme, nstlist has no effect on the accuracy of 68: your simulation. 68: 68: 68: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_7_input.mdp]: 68: Setting nstcalcenergy (100) equal to nstenergy (4) 68: 68: Generating 1-4 interactions: fudge = 0.5 68: Number of degrees of freedom in T-Coupling group System is 79.00 68: 68: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_7_input.mdp]: 68: You are using a plain Coulomb cut-off, which might produce artifacts. 68: You might want to consider using PME electrostatics. 68: 68: 68: 68: There were 3 NOTEs 68: 68: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_7_input.mdp]: 68: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 68: that with the Verlet scheme, nstlist has no effect on the accuracy of 68: your simulation. 68: 68: 68: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_7_input.mdp]: 68: Setting nstcalcenergy (100) equal to nstenergy (4) 68: 68: Generating 1-4 interactions: fudge = 0.5 68: Number of degrees of freedom in T-Coupling group System is 79.00 68: 68: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_7_input.mdp]: 68: You are using a plain Coulomb cut-off, which might produce artifacts. 68: You might want to consider using PME electrostatics. 68: 68: 68: 68: There were 3 NOTEs 68: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_7_full.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 68: Changing nstlist from 8 to 20, rlist from 0.749 to 0.842 68: 68: Using 1 MPI thread 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun '30 atom system in water' 68: 16 steps, 0.0 ps. 68: Generated 2485 of the 2485 non-bonded parameter combinations 68: 68: Generated 2485 of the 2485 1-4 parameter combinations 68: 68: Excluding 3 bonded neighbours molecule type 'nonanol' 68: 68: turning H bonds into constraints... 68: 68: Excluding 2 bonded neighbours molecule type 'SOL' 68: 68: turning H bonds into constraints... 68: 68: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/nonanol_vacuo.gro' 68: 68: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 298 K 68: 68: Calculated rlist for 1x1 atom pair-list as 0.756 nm, buffer size 0.056 nm 68: 68: Set rlist, assuming 4x4 atom pair-list, to 0.749 nm, buffer size 0.049 nm 68: 68: Note that mdrun will redetermine rlist based on the actual pair-list setup 68: 68: This run will generate roughly 0 Mb of data 68: Generated 2485 of the 2485 non-bonded parameter combinations 68: 68: Generated 2485 of the 2485 1-4 parameter combinations 68: 68: Excluding 3 bonded neighbours molecule type 'nonanol' 68: 68: turning H bonds into constraints... 68: 68: Excluding 2 bonded neighbours molecule type 'SOL' 68: 68: turning H bonds into constraints... 68: 68: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/nonanol_vacuo.gro' 68: 68: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 298 K 68: 68: Calculated rlist for 1x1 atom pair-list as 0.756 nm, buffer size 0.056 nm 68: 68: Set rlist, assuming 4x4 atom pair-list, to 0.749 nm, buffer size 0.049 nm 68: 68: Note that mdrun will redetermine rlist based on the actual pair-list setup 68: 68: This run will generate roughly 0 Mb of data 68: 68: Writing final coordinates. 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.097 0.049 198.2 68: (ns/day) (hour/ns) 68: Performance: 30.055 0.799 68: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_7_firstpart.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 68: Changing nstlist from 8 to 20, rlist from 0.749 to 0.842 68: 68: Using 1 MPI thread 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun '30 atom system in water' 68: 8 steps, 0.0 ps. 68: 68: Writing final coordinates. 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.066 0.034 195.6 68: (ns/day) (hour/ns) 68: Performance: 23.140 1.037 68: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_7_full.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 68: Changing nstlist from 8 to 20, rlist from 0.749 to 0.843 68: 68: Using 1 MPI thread 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun '30 atom system in water' 68: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 68: 68: Writing final coordinates. 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.066 0.034 197.5 68: (ns/day) (hour/ns) 68: Performance: 23.157 1.036 68: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_7_full.edr as single precision energy file 68: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_7_firstpart.edr as single precision energy file 68: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_7_secondpart.part0002.edr as single precision energy file 68: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NormalIntegratorsWithFEP/MdrunNoAppendContinuationIsExact.WithinTolerances/7 (583 ms) 68: [----------] 8 tests from NormalIntegratorsWithFEP/MdrunNoAppendContinuationIsExact (5125 ms total) 68: 68: [----------] 8 tests from NVT/MdrunNoAppendContinuationIsExact 68: [ RUN ] NVT/MdrunNoAppendContinuationIsExact.WithinTolerances/0 68: 68: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 68: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 68: that with the Verlet scheme, nstlist has no effect on the accuracy of 68: your simulation. 68: 68: 68: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 68: Setting nstcalcenergy (100) equal to nstenergy (4) 68: 68: Number of degrees of freedom in T-Coupling group System is 33.00 68: 68: There were 2 NOTEs 68: 68: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 68: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 68: that with the Verlet scheme, nstlist has no effect on the accuracy of 68: your simulation. 68: 68: 68: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 68: Setting nstcalcenergy (100) equal to nstenergy (4) 68: 68: Number of degrees of freedom in T-Coupling group System is 33.00 68: 68: There were 2 NOTEs 68: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 68: Using 1 MPI thread 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'Argon' 68: 16 steps, 0.0 ps. 68: Generated 1 of the 1 non-bonded parameter combinations 68: 68: Excluding 1 bonded neighbours molecule type 'Argon' 68: 68: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 68: 68: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 68: 68: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 68: 68: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 68: 68: Note that mdrun will redetermine rlist based on the actual pair-list setup 68: 68: This run will generate roughly 0 Mb of data 68: Generated 1 of the 1 non-bonded parameter combinations 68: 68: Excluding 1 bonded neighbours molecule type 'Argon' 68: 68: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 68: 68: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 68: 68: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 68: 68: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 68: 68: Note that mdrun will redetermine rlist based on the actual pair-list setup 68: 68: This run will generate roughly 0 Mb of data 68: 68: Writing final coordinates. 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.049 0.025 197.7 68: (ns/day) (hour/ns) 68: Performance: 59.274 0.405 68: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_firstpart.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 68: Using 1 MPI thread 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'Argon' 68: 8 steps, 0.0 ps. 68: 68: Writing final coordinates. 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.046 0.023 197.5 68: (ns/day) (hour/ns) 68: Performance: 33.504 0.716 68: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 68: Using 1 MPI thread 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'Argon' 68: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 68: 68: Writing final coordinates. 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.049 0.025 197.2 68: (ns/day) (hour/ns) 68: Performance: 31.314 0.766 68: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.edr as single precision energy file 68: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_firstpart.edr as single precision energy file 68: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_secondpart.part0002.edr as single precision energy file 68: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NVT/MdrunNoAppendContinuationIsExact.WithinTolerances/0 (207 ms) 68: [ RUN ] NVT/MdrunNoAppendContinuationIsExact.WithinTolerances/1 68: 68: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 68: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 68: that with the Verlet scheme, nstlist has no effect on the accuracy of 68: your simulation. 68: 68: 68: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 68: Setting nstcalcenergy (100) equal to nstenergy (4) 68: 68: Number of degrees of freedom in T-Coupling group System is 33.00 68: 68: There were 2 NOTEs 68: 68: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 68: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 68: that with the Verlet scheme, nstlist has no effect on the accuracy of 68: your simulation. 68: 68: 68: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 68: Setting nstcalcenergy (100) equal to nstenergy (4) 68: 68: Number of degrees of freedom in T-Coupling group System is 33.00 68: 68: There were 2 NOTEs 68: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_full.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 68: Changing nstlist from 8 to 100, rlist from 0.702 to 0.738 68: 68: Using 1 MPI thread 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'Argon' 68: 16 steps, 0.0 ps. 68: Generated 1 of the 1 non-bonded parameter combinations 68: 68: Excluding 1 bonded neighbours molecule type 'Argon' 68: 68: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 68: 68: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 80 K 68: 68: Calculated rlist for 1x1 atom pair-list as 0.702 nm, buffer size 0.002 nm 68: 68: Set rlist, assuming 4x4 atom pair-list, to 0.702 nm, buffer size 0.002 nm 68: 68: Note that mdrun will redetermine rlist based on the actual pair-list setup 68: 68: This run will generate roughly 0 Mb of data 68: Generated 1 of the 1 non-bonded parameter combinations 68: 68: Excluding 1 bonded neighbours molecule type 'Argon' 68: 68: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 68: 68: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 80 K 68: 68: Calculated rlist for 1x1 atom pair-list as 0.702 nm, buffer size 0.002 nm 68: 68: Set rlist, assuming 4x4 atom pair-list, to 0.702 nm, buffer size 0.002 nm 68: 68: Note that mdrun will redetermine rlist based on the actual pair-list setup 68: 68: This run will generate roughly 0 Mb of data 68: 68: Writing final coordinates. 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.041 0.021 197.6 68: (ns/day) (hour/ns) 68: Performance: 69.966 0.343 68: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_firstpart.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 68: Changing nstlist from 8 to 100, rlist from 0.702 to 0.738 68: 68: Using 1 MPI thread 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'Argon' 68: 8 steps, 0.0 ps. 68: 68: Writing final coordinates. 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.067 0.034 198.3 68: (ns/day) (hour/ns) 68: Performance: 23.130 1.038 68: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_full.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 68: Changing nstlist from 8 to 100, rlist from 0.702 to 0.738 68: 68: Using 1 MPI thread 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'Argon' 68: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 68: 68: Writing final coordinates. 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.040 0.020 197.4 68: (ns/day) (hour/ns) 68: Performance: 38.512 0.623 68: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_full.edr as single precision energy file 68: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_firstpart.edr as single precision energy file 68: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_secondpart.part0002.edr as single precision energy file 68: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NVT/MdrunNoAppendContinuationIsExact.WithinTolerances/1 (200 ms) 68: [ RUN ] NVT/MdrunNoAppendContinuationIsExact.WithinTolerances/2 68: 68: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]: 68: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 68: that with the Verlet scheme, nstlist has no effect on the accuracy of 68: your simulation. 68: 68: 68: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]: 68: Setting nstcalcenergy (100) equal to nstenergy (4) 68: 68: 68: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]: 68: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 68: 1 68: 68: Number of degrees of freedom in T-Coupling group System is 33.00 68: 68: There were 3 NOTEs 68: 68: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]: 68: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 68: that with the Verlet scheme, nstlist has no effect on the accuracy of 68: your simulation. 68: 68: 68: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]: 68: Setting nstcalcenergy (100) equal to nstenergy (4) 68: 68: 68: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]: 68: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 68: 1 68: 68: Number of degrees of freedom in T-Coupling group System is 33.00 68: 68: There were 3 NOTEs 68: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_full.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 68: Using 1 MPI thread 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'Argon' 68: 16 steps, 0.0 ps. 68: Generated 1 of the 1 non-bonded parameter combinations 68: 68: Excluding 1 bonded neighbours molecule type 'Argon' 68: 68: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 68: 68: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 68: 68: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 68: 68: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 68: 68: Note that mdrun will redetermine rlist based on the actual pair-list setup 68: 68: This run will generate roughly 0 Mb of data 68: Generated 1 of the 1 non-bonded parameter combinations 68: 68: Excluding 1 bonded neighbours molecule type 'Argon' 68: 68: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 68: 68: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 68: 68: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 68: 68: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 68: 68: Note that mdrun will redetermine rlist based on the actual pair-list setup 68: 68: This run will generate roughly 0 Mb of data 68: 68: Writing final coordinates. 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.044 0.022 197.3 68: (ns/day) (hour/ns) 68: Performance: 65.668 0.365 68: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_firstpart.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 68: Using 1 MPI thread 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'Argon' 68: 8 steps, 0.0 ps. 68: 68: Writing final coordinates. 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.036 0.018 196.8 68: (ns/day) (hour/ns) 68: Performance: 42.309 0.567 68: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_full.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 68: Using 1 MPI thread 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'Argon' 68: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 68: 68: Writing final coordinates. 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.046 0.023 196.5 68: (ns/day) (hour/ns) 68: Performance: 33.494 0.717 68: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_full.edr as single precision energy file 68: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_firstpart.edr as single precision energy file 68: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_secondpart.part0002.edr as single precision energy file 68: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NVT/MdrunNoAppendContinuationIsExact.WithinTolerances/2 (181 ms) 68: [ RUN ] NVT/MdrunNoAppendContinuationIsExact.WithinTolerances/3 68: 68: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]: 68: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 68: that with the Verlet scheme, nstlist has no effect on the accuracy of 68: your simulation. 68: 68: 68: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]: 68: Setting nstcalcenergy (100) equal to nstenergy (4) 68: 68: 68: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]: 68: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 68: 1 68: 68: Number of degrees of freedom in T-Coupling group System is 33.00 68: 68: There were 3 NOTEs 68: 68: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]: 68: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 68: that with the Verlet scheme, nstlist has no effect on the accuracy of 68: your simulation. 68: 68: 68: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]: 68: Setting nstcalcenergy (100) equal to nstenergy (4) 68: 68: 68: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]: 68: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 68: 1 68: 68: Number of degrees of freedom in T-Coupling group System is 33.00 68: 68: There were 3 NOTEs 68: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_full.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 68: Changing nstlist from 8 to 100, rlist from 0.702 to 0.738 68: 68: Using 1 MPI thread 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'Argon' 68: 16 steps, 0.0 ps. 68: Generated 1 of the 1 non-bonded parameter combinations 68: 68: Excluding 1 bonded neighbours molecule type 'Argon' 68: 68: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 68: 68: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 80 K 68: 68: Calculated rlist for 1x1 atom pair-list as 0.702 nm, buffer size 0.002 nm 68: 68: Set rlist, assuming 4x4 atom pair-list, to 0.702 nm, buffer size 0.002 nm 68: 68: Note that mdrun will redetermine rlist based on the actual pair-list setup 68: 68: This run will generate roughly 0 Mb of data 68: Generated 1 of the 1 non-bonded parameter combinations 68: 68: Excluding 1 bonded neighbours molecule type 'Argon' 68: 68: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 68: 68: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 80 K 68: 68: Calculated rlist for 1x1 atom pair-list as 0.702 nm, buffer size 0.002 nm 68: 68: Set rlist, assuming 4x4 atom pair-list, to 0.702 nm, buffer size 0.002 nm 68: 68: Note that mdrun will redetermine rlist based on the actual pair-list setup 68: 68: This run will generate roughly 0 Mb of data 68: 68: Writing final coordinates. 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.046 0.023 197.4 68: (ns/day) (hour/ns) 68: Performance: 63.305 0.379 68: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_firstpart.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 68: Changing nstlist from 8 to 100, rlist from 0.702 to 0.738 68: 68: Using 1 MPI thread 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'Argon' 68: 8 steps, 0.0 ps. 68: 68: Writing final coordinates. 68: 68: NOTE: 12 % of the run time was spent in pair search, 68: you might want to increase nstlist (this has no effect on accuracy) 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.196 0.098 199.0 68: (ns/day) (hour/ns) 68: Performance: 7.909 3.035 68: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_full.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 68: Changing nstlist from 8 to 100, rlist from 0.702 to 0.738 68: 68: Using 1 MPI thread 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'Argon' 68: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 68: 68: Writing final coordinates. 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.064 0.032 198.0 68: (ns/day) (hour/ns) 68: Performance: 24.013 0.999 68: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_full.edr as single precision energy file 68: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_firstpart.edr as single precision energy file 68: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_secondpart.part0002.edr as single precision energy file 68: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NVT/MdrunNoAppendContinuationIsExact.WithinTolerances/3 (292 ms) 68: [ RUN ] NVT/MdrunNoAppendContinuationIsExact.WithinTolerances/4 68: 68: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_input.mdp]: 68: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 68: that with the Verlet scheme, nstlist has no effect on the accuracy of 68: your simulation. 68: 68: 68: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_input.mdp]: 68: Setting nstcalcenergy (100) equal to nstenergy (4) 68: 68: Number of degrees of freedom in T-Coupling group System is 33.00 68: 68: There were 2 NOTEs 68: 68: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_input.mdp]: 68: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 68: that with the Verlet scheme, nstlist has no effect on the accuracy of 68: your simulation. 68: 68: 68: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_input.mdp]: 68: Setting nstcalcenergy (100) equal to nstenergy (4) 68: 68: Number of degrees of freedom in T-Coupling group System is 33.00 68: 68: There were 2 NOTEs 68: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_full.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 68: Using 1 MPI thread 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'Argon' 68: 16 steps, 0.0 ps. 68: Generated 1 of the 1 non-bonded parameter combinations 68: 68: Excluding 1 bonded neighbours molecule type 'Argon' 68: 68: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 68: 68: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 68: 68: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 68: 68: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 68: 68: Note that mdrun will redetermine rlist based on the actual pair-list setup 68: 68: This run will generate roughly 0 Mb of data 68: Generated 1 of the 1 non-bonded parameter combinations 68: 68: Excluding 1 bonded neighbours molecule type 'Argon' 68: 68: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 68: 68: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 68: 68: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 68: 68: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 68: 68: Note that mdrun will redetermine rlist based on the actual pair-list setup 68: 68: This run will generate roughly 0 Mb of data 68: 68: Writing final coordinates. 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.055 0.028 198.8 68: (ns/day) (hour/ns) 68: Performance: 53.397 0.449 68: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_firstpart.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 68: Using 1 MPI thread 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'Argon' 68: 8 steps, 0.0 ps. 68: 68: Writing final coordinates. 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.057 0.028 198.8 68: (ns/day) (hour/ns) 68: Performance: 27.316 0.879 68: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_full.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 68: Using 1 MPI thread 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'Argon' 68: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 68: 68: Writing final coordinates. 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.048 0.024 197.5 68: (ns/day) (hour/ns) 68: Performance: 31.976 0.751 68: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_full.edr as single precision energy file 68: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_firstpart.edr as single precision energy file 68: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_secondpart.part0002.edr as single precision energy file 68: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NVT/MdrunNoAppendContinuationIsExact.WithinTolerances/4 (184 ms) 68: [ RUN ] NVT/MdrunNoAppendContinuationIsExact.WithinTolerances/5 68: 68: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_5_input.mdp]: 68: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 68: that with the Verlet scheme, nstlist has no effect on the accuracy of 68: your simulation. 68: 68: 68: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_5_input.mdp]: 68: Setting nstcalcenergy (100) equal to nstenergy (4) 68: 68: Number of degrees of freedom in T-Coupling group System is 33.00 68: 68: There were 2 NOTEs 68: 68: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_5_input.mdp]: 68: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 68: that with the Verlet scheme, nstlist has no effect on the accuracy of 68: your simulation. 68: 68: 68: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_5_input.mdp]: 68: Setting nstcalcenergy (100) equal to nstenergy (4) 68: 68: Number of degrees of freedom in T-Coupling group System is 33.00 68: 68: There were 2 NOTEs 68: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_5_full.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 68: Changing nstlist from 8 to 100, rlist from 0.702 to 0.738 68: 68: Using 1 MPI thread 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'Argon' 68: 16 steps, 0.0 ps. 68: Generated 1 of the 1 non-bonded parameter combinations 68: 68: Excluding 1 bonded neighbours molecule type 'Argon' 68: 68: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 68: 68: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 80 K 68: 68: Calculated rlist for 1x1 atom pair-list as 0.702 nm, buffer size 0.002 nm 68: 68: Set rlist, assuming 4x4 atom pair-list, to 0.702 nm, buffer size 0.002 nm 68: 68: Note that mdrun will redetermine rlist based on the actual pair-list setup 68: 68: This run will generate roughly 0 Mb of data 68: Generated 1 of the 1 non-bonded parameter combinations 68: 68: Excluding 1 bonded neighbours molecule type 'Argon' 68: 68: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 68: 68: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 80 K 68: 68: Calculated rlist for 1x1 atom pair-list as 0.702 nm, buffer size 0.002 nm 68: 68: Set rlist, assuming 4x4 atom pair-list, to 0.702 nm, buffer size 0.002 nm 68: 68: Note that mdrun will redetermine rlist based on the actual pair-list setup 68: 68: This run will generate roughly 0 Mb of data 68: 68: Writing final coordinates. 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.049 0.025 198.4 68: (ns/day) (hour/ns) 68: Performance: 59.219 0.405 68: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_5_firstpart.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 68: Changing nstlist from 8 to 100, rlist from 0.702 to 0.738 68: 68: Using 1 MPI thread 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'Argon' 68: 8 steps, 0.0 ps. 68: 68: Writing final coordinates. 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.047 0.024 198.4 68: (ns/day) (hour/ns) 68: Performance: 32.564 0.737 68: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_5_full.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 68: Changing nstlist from 8 to 100, rlist from 0.702 to 0.738 68: 68: Using 1 MPI thread 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'Argon' 68: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 68: 68: Writing final coordinates. 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.053 0.027 197.3 68: (ns/day) (hour/ns) 68: Performance: 28.904 0.830 68: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_5_full.edr as single precision energy file 68: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_5_firstpart.edr as single precision energy file 68: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_5_secondpart.part0002.edr as single precision energy file 68: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NVT/MdrunNoAppendContinuationIsExact.WithinTolerances/5 (186 ms) 68: [ RUN ] NVT/MdrunNoAppendContinuationIsExact.WithinTolerances/6 68: 68: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_6_input.mdp]: 68: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 68: that with the Verlet scheme, nstlist has no effect on the accuracy of 68: your simulation. 68: 68: 68: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_6_input.mdp]: 68: Setting nstcalcenergy (100) equal to nstenergy (4) 68: 68: Number of degrees of freedom in T-Coupling group System is 33.00 68: 68: There were 2 NOTEs 68: 68: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_6_input.mdp]: 68: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 68: that with the Verlet scheme, nstlist has no effect on the accuracy of 68: your simulation. 68: 68: 68: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_6_input.mdp]: 68: Setting nstcalcenergy (100) equal to nstenergy (4) 68: 68: Number of degrees of freedom in T-Coupling group System is 33.00 68: 68: There were 2 NOTEs 68: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_6_full.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 68: Using 1 MPI thread 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'Argon' 68: 16 steps, 0.0 ps. 68: Generated 1 of the 1 non-bonded parameter combinations 68: 68: Excluding 1 bonded neighbours molecule type 'Argon' 68: 68: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 68: 68: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 68: 68: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 68: 68: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 68: 68: Note that mdrun will redetermine rlist based on the actual pair-list setup 68: 68: This run will generate roughly 0 Mb of data 68: Generated 1 of the 1 non-bonded parameter combinations 68: 68: Excluding 1 bonded neighbours molecule type 'Argon' 68: 68: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 68: 68: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 68: 68: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 68: 68: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 68: 68: Note that mdrun will redetermine rlist based on the actual pair-list setup 68: 68: This run will generate roughly 0 Mb of data 68: 68: Writing final coordinates. 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.061 0.031 198.8 68: (ns/day) (hour/ns) 68: Performance: 47.840 0.502 68: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_6_firstpart.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 68: Using 1 MPI thread 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'Argon' 68: 8 steps, 0.0 ps. 68: 68: Writing final coordinates. 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.052 0.026 198.6 68: (ns/day) (hour/ns) 68: Performance: 29.443 0.815 68: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_6_full.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 68: Using 1 MPI thread 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'Argon' 68: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 68: 68: Writing final coordinates. 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.047 0.024 197.3 68: (ns/day) (hour/ns) 68: Performance: 32.583 0.737 68: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_6_full.edr as single precision energy file 68: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_6_firstpart.edr as single precision energy file 68: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_6_secondpart.part0002.edr as single precision energy file 68: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NVT/MdrunNoAppendContinuationIsExact.WithinTolerances/6 (183 ms) 68: [ RUN ] NVT/MdrunNoAppendContinuationIsExact.WithinTolerances/7 68: 68: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_7_input.mdp]: 68: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 68: that with the Verlet scheme, nstlist has no effect on the accuracy of 68: your simulation. 68: 68: 68: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_7_input.mdp]: 68: Setting nstcalcenergy (100) equal to nstenergy (4) 68: 68: Number of degrees of freedom in T-Coupling group System is 33.00 68: 68: There were 2 NOTEs 68: 68: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_7_input.mdp]: 68: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 68: that with the Verlet scheme, nstlist has no effect on the accuracy of 68: your simulation. 68: 68: 68: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_7_input.mdp]: 68: Setting nstcalcenergy (100) equal to nstenergy (4) 68: 68: Number of degrees of freedom in T-Coupling group System is 33.00 68: 68: There were 2 NOTEs 68: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_7_full.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 68: Changing nstlist from 8 to 100, rlist from 0.702 to 0.738 68: 68: Using 1 MPI thread 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'Argon' 68: 16 steps, 0.0 ps. 68: Generated 1 of the 1 non-bonded parameter combinations 68: 68: Excluding 1 bonded neighbours molecule type 'Argon' 68: 68: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 68: 68: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 80 K 68: 68: Calculated rlist for 1x1 atom pair-list as 0.702 nm, buffer size 0.002 nm 68: 68: Set rlist, assuming 4x4 atom pair-list, to 0.702 nm, buffer size 0.002 nm 68: 68: Note that mdrun will redetermine rlist based on the actual pair-list setup 68: 68: This run will generate roughly 0 Mb of data 68: Generated 1 of the 1 non-bonded parameter combinations 68: 68: Excluding 1 bonded neighbours molecule type 'Argon' 68: 68: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 68: 68: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 80 K 68: 68: Calculated rlist for 1x1 atom pair-list as 0.702 nm, buffer size 0.002 nm 68: 68: Set rlist, assuming 4x4 atom pair-list, to 0.702 nm, buffer size 0.002 nm 68: 68: Note that mdrun will redetermine rlist based on the actual pair-list setup 68: 68: This run will generate roughly 0 Mb of data 68: 68: Writing final coordinates. 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.063 0.031 198.5 68: (ns/day) (hour/ns) 68: Performance: 46.643 0.515 68: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_7_firstpart.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 68: Changing nstlist from 8 to 100, rlist from 0.702 to 0.738 68: 68: Using 1 MPI thread 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'Argon' 68: 8 steps, 0.0 ps. 68: 68: Writing final coordinates. 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.057 0.029 198.6 68: (ns/day) (hour/ns) 68: Performance: 26.890 0.893 68: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_7_full.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 68: Changing nstlist from 8 to 100, rlist from 0.702 to 0.738 68: 68: Using 1 MPI thread 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'Argon' 68: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 68: 68: Writing final coordinates. 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.051 0.026 197.4 68: (ns/day) (hour/ns) 68: Performance: 30.343 0.791 68: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_7_full.edr as single precision energy file 68: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_7_firstpart.edr as single precision energy file 68: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_7_secondpart.part0002.edr as single precision energy file 68: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NVT/MdrunNoAppendContinuationIsExact.WithinTolerances/7 (199 ms) 68: [----------] 8 tests from NVT/MdrunNoAppendContinuationIsExact (1637 ms total) 68: 68: [----------] 2 tests from NPH/MdrunNoAppendContinuationIsExact 68: [ RUN ] NPH/MdrunNoAppendContinuationIsExact.WithinTolerances/0 68: 68: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 68: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 68: that with the Verlet scheme, nstlist has no effect on the accuracy of 68: your simulation. 68: 68: 68: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 68: Setting nstcalcenergy (100) equal to nstenergy (4) 68: 68: Number of degrees of freedom in T-Coupling group System is 33.00 68: 68: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 68: NVE simulation: will use the initial temperature of 68.810 K for 68: determining the Verlet buffer size 68: 68: 68: There were 3 NOTEs 68: 68: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 68: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 68: that with the Verlet scheme, nstlist has no effect on the accuracy of 68: your simulation. 68: 68: 68: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 68: Setting nstcalcenergy (100) equal to nstenergy (4) 68: 68: Number of degrees of freedom in T-Coupling group System is 33.00 68: 68: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 68: NVE simulation: will use the initial temperature of 68.810 K for 68: determining the Verlet buffer size 68: 68: 68: There were 3 NOTEs 68: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 68: Can not increase nstlist because an NVE ensemble is used 68: Using 1 MPI thread 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'Argon' 68: 16 steps, 0.0 ps. 68: Generated 1 of the 1 non-bonded parameter combinations 68: 68: Excluding 1 bonded neighbours molecule type 'Argon' 68: 68: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 68: 68: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 68: 68: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 68: 68: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 68: 68: Note that mdrun will redetermine rlist based on the actual pair-list setup 68: 68: This run will generate roughly 0 Mb of data 68: Generated 1 of the 1 non-bonded parameter combinations 68: 68: Excluding 1 bonded neighbours molecule type 'Argon' 68: 68: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 68: 68: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 68: 68: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 68: 68: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 68: 68: Note that mdrun will redetermine rlist based on the actual pair-list setup 68: 68: This run will generate roughly 0 Mb of data 68: 68: Writing final coordinates. 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.056 0.028 197.9 68: (ns/day) (hour/ns) 68: Performance: 52.137 0.460 68: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_0_firstpart.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 68: Can not increase nstlist because an NVE ensemble is used 68: Using 1 MPI thread 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'Argon' 68: 8 steps, 0.0 ps. 68: 68: Writing final coordinates. 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.039 0.020 197.3 68: (ns/day) (hour/ns) 68: Performance: 39.208 0.612 68: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 68: Can not increase nstlist because an NVE ensemble is used 68: Using 1 MPI thread 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'Argon' 68: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 68: 68: Writing final coordinates. 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.046 0.023 197.6 68: (ns/day) (hour/ns) 68: Performance: 33.558 0.715 68: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.edr as single precision energy file 68: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_0_firstpart.edr as single precision energy file 68: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_0_secondpart.part0002.edr as single precision energy file 68: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NPH/MdrunNoAppendContinuationIsExact.WithinTolerances/0 (190 ms) 68: [ RUN ] NPH/MdrunNoAppendContinuationIsExact.WithinTolerances/1 68: 68: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 68: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 68: that with the Verlet scheme, nstlist has no effect on the accuracy of 68: your simulation. 68: 68: 68: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 68: Setting nstcalcenergy (100) equal to nstenergy (4) 68: 68: Number of degrees of freedom in T-Coupling group System is 33.00 68: 68: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 68: NVE simulation: will use the initial temperature of 68.810 K for 68: determining the Verlet buffer size 68: 68: 68: There were 3 NOTEs 68: 68: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 68: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 68: that with the Verlet scheme, nstlist has no effect on the accuracy of 68: your simulation. 68: 68: 68: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 68: Setting nstcalcenergy (100) equal to nstenergy (4) 68: 68: Number of degrees of freedom in T-Coupling group System is 33.00 68: 68: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 68: NVE simulation: will use the initial temperature of 68.810 K for 68: determining the Verlet buffer size 68: 68: 68: There were 3 NOTEs 68: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_1_full.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 68: Can not increase nstlist because an NVE ensemble is used 68: Using 1 MPI thread 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'Argon' 68: 16 steps, 0.0 ps. 68: Generated 1 of the 1 non-bonded parameter combinations 68: 68: Excluding 1 bonded neighbours molecule type 'Argon' 68: 68: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 68: 68: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 68: 68: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 68: 68: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 68: 68: Note that mdrun will redetermine rlist based on the actual pair-list setup 68: 68: This run will generate roughly 0 Mb of data 68: Generated 1 of the 1 non-bonded parameter combinations 68: 68: Excluding 1 bonded neighbours molecule type 'Argon' 68: 68: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 68: 68: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 68: 68: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 68: 68: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 68: 68: Note that mdrun will redetermine rlist based on the actual pair-list setup 68: 68: This run will generate roughly 0 Mb of data 68: 68: Writing final coordinates. 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.070 0.035 199.0 68: (ns/day) (hour/ns) 68: Performance: 41.769 0.575 68: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_1_firstpart.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 68: Can not increase nstlist because an NVE ensemble is used 68: Using 1 MPI thread 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'Argon' 68: 8 steps, 0.0 ps. 68: 68: Writing final coordinates. 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.054 0.027 198.7 68: (ns/day) (hour/ns) 68: Performance: 28.448 0.844 68: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_1_full.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 68: Can not increase nstlist because an NVE ensemble is used 68: Using 1 MPI thread 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'Argon' 68: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 68: 68: Writing final coordinates. 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.051 0.026 197.4 68: (ns/day) (hour/ns) 68: Performance: 30.061 0.798 68: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_1_full.edr as single precision energy file 68: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_1_firstpart.edr as single precision energy file 68: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_1_secondpart.part0002.edr as single precision energy file 68: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NPH/MdrunNoAppendContinuationIsExact.WithinTolerances/1 (204 ms) 68: [----------] 2 tests from NPH/MdrunNoAppendContinuationIsExact (394 ms total) 68: 68: [----------] 8 tests from NPT/MdrunNoAppendContinuationIsExact 68: [ RUN ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/0 68: 68: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 68: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 68: that with the Verlet scheme, nstlist has no effect on the accuracy of 68: your simulation. 68: 68: 68: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 68: Setting nstcalcenergy (100) equal to nstenergy (4) 68: 68: Number of degrees of freedom in T-Coupling group System is 33.00 68: 68: There were 2 NOTEs 68: 68: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 68: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 68: that with the Verlet scheme, nstlist has no effect on the accuracy of 68: your simulation. 68: 68: 68: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 68: Setting nstcalcenergy (100) equal to nstenergy (4) 68: 68: Number of degrees of freedom in T-Coupling group System is 33.00 68: 68: There were 2 NOTEs 68: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 68: Using 1 MPI thread 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'Argon' 68: 16 steps, 0.0 ps. 68: Generated 1 of the 1 non-bonded parameter combinations 68: 68: Excluding 1 bonded neighbours molecule type 'Argon' 68: 68: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 68: 68: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 68: 68: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 68: 68: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 68: 68: Note that mdrun will redetermine rlist based on the actual pair-list setup 68: 68: This run will generate roughly 0 Mb of data 68: Generated 1 of the 1 non-bonded parameter combinations 68: 68: Excluding 1 bonded neighbours molecule type 'Argon' 68: 68: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 68: 68: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 68: 68: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 68: 68: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 68: 68: Note that mdrun will redetermine rlist based on the actual pair-list setup 68: 68: This run will generate roughly 0 Mb of data 68: 68: Writing final coordinates. 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.053 0.027 197.8 68: (ns/day) (hour/ns) 68: Performance: 54.941 0.437 68: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_firstpart.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 68: Using 1 MPI thread 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'Argon' 68: 8 steps, 0.0 ps. 68: 68: Writing final coordinates. 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.042 0.021 197.3 68: (ns/day) (hour/ns) 68: Performance: 36.700 0.654 68: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 68: Using 1 MPI thread 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'Argon' 68: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 68: 68: Writing final coordinates. 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.053 0.027 198.1 68: (ns/day) (hour/ns) 68: Performance: 29.080 0.825 68: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.edr as single precision energy file 68: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_firstpart.edr as single precision energy file 68: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_secondpart.part0002.edr as single precision energy file 68: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/0 (194 ms) 68: [ RUN ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/1 68: 68: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 68: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 68: that with the Verlet scheme, nstlist has no effect on the accuracy of 68: your simulation. 68: 68: 68: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 68: Setting nstcalcenergy (100) equal to nstenergy (4) 68: 68: Number of degrees of freedom in T-Coupling group System is 33.00 68: 68: There were 2 NOTEs 68: 68: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 68: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 68: that with the Verlet scheme, nstlist has no effect on the accuracy of 68: your simulation. 68: 68: 68: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 68: Setting nstcalcenergy (100) equal to nstenergy (4) 68: 68: Number of degrees of freedom in T-Coupling group System is 33.00 68: 68: There were 2 NOTEs 68: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_full.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 68: Using 1 MPI thread 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'Argon' 68: 16 steps, 0.0 ps. 68: Generated 1 of the 1 non-bonded parameter combinations 68: 68: Excluding 1 bonded neighbours molecule type 'Argon' 68: 68: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 68: 68: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 68: 68: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 68: 68: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 68: 68: Note that mdrun will redetermine rlist based on the actual pair-list setup 68: 68: This run will generate roughly 0 Mb of data 68: Generated 1 of the 1 non-bonded parameter combinations 68: 68: Excluding 1 bonded neighbours molecule type 'Argon' 68: 68: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 68: 68: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 68: 68: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 68: 68: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 68: 68: Note that mdrun will redetermine rlist based on the actual pair-list setup 68: 68: This run will generate roughly 0 Mb of data 68: 68: Writing final coordinates. 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.041 0.021 197.5 68: (ns/day) (hour/ns) 68: Performance: 70.885 0.339 68: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_firstpart.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 68: Using 1 MPI thread 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'Argon' 68: 8 steps, 0.0 ps. 68: 68: Writing final coordinates. 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.046 0.023 197.6 68: (ns/day) (hour/ns) 68: Performance: 33.359 0.719 68: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_full.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 68: Using 1 MPI thread 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'Argon' 68: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 68: 68: Writing final coordinates. 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.035 0.018 197.0 68: (ns/day) (hour/ns) 68: Performance: 43.480 0.552 68: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_full.edr as single precision energy file 68: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_firstpart.edr as single precision energy file 68: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_secondpart.part0002.edr as single precision energy file 68: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/1 (172 ms) 68: [ RUN ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/2 68: 68: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]: 68: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 68: that with the Verlet scheme, nstlist has no effect on the accuracy of 68: your simulation. 68: 68: 68: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]: 68: Setting nstcalcenergy (100) equal to nstenergy (4) 68: 68: 68: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]: 68: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 68: 1 68: 68: Number of degrees of freedom in T-Coupling group System is 33.00 68: 68: There were 3 NOTEs 68: 68: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]: 68: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 68: that with the Verlet scheme, nstlist has no effect on the accuracy of 68: your simulation. 68: 68: 68: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]: 68: Setting nstcalcenergy (100) equal to nstenergy (4) 68: 68: 68: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]: 68: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 68: 1 68: 68: Number of degrees of freedom in T-Coupling group System is 33.00 68: 68: There were 3 NOTEs 68: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_full.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 68: Using 1 MPI thread 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'Argon' 68: 16 steps, 0.0 ps. 68: Generated 1 of the 1 non-bonded parameter combinations 68: 68: Excluding 1 bonded neighbours molecule type 'Argon' 68: 68: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 68: 68: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 68: 68: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 68: 68: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 68: 68: Note that mdrun will redetermine rlist based on the actual pair-list setup 68: 68: This run will generate roughly 0 Mb of data 68: Generated 1 of the 1 non-bonded parameter combinations 68: 68: Excluding 1 bonded neighbours molecule type 'Argon' 68: 68: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 68: 68: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 68: 68: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 68: 68: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 68: 68: Note that mdrun will redetermine rlist based on the actual pair-list setup 68: 68: This run will generate roughly 0 Mb of data 68: 68: Writing final coordinates. 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.043 0.022 197.5 68: (ns/day) (hour/ns) 68: Performance: 67.163 0.357 68: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_firstpart.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 68: Using 1 MPI thread 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'Argon' 68: 8 steps, 0.0 ps. 68: 68: Writing final coordinates. 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.041 0.021 197.4 68: (ns/day) (hour/ns) 68: Performance: 37.476 0.640 68: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_full.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 68: Using 1 MPI thread 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'Argon' 68: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 68: 68: Writing final coordinates. 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.058 0.029 198.2 68: (ns/day) (hour/ns) 68: Performance: 26.754 0.897 68: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_full.edr as single precision energy file 68: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_firstpart.edr as single precision energy file 68: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_secondpart.part0002.edr as single precision energy file 68: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/2 (192 ms) 68: [ RUN ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/3 68: 68: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]: 68: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 68: that with the Verlet scheme, nstlist has no effect on the accuracy of 68: your simulation. 68: 68: 68: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]: 68: Setting nstcalcenergy (100) equal to nstenergy (4) 68: 68: 68: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]: 68: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 68: 1 68: 68: Number of degrees of freedom in T-Coupling group System is 33.00 68: 68: There were 3 NOTEs 68: 68: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]: 68: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 68: that with the Verlet scheme, nstlist has no effect on the accuracy of 68: your simulation. 68: 68: 68: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]: 68: Setting nstcalcenergy (100) equal to nstenergy (4) 68: 68: 68: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]: 68: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 68: 1 68: 68: Number of degrees of freedom in T-Coupling group System is 33.00 68: 68: There were 3 NOTEs 68: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_full.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 68: Using 1 MPI thread 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'Argon' 68: 16 steps, 0.0 ps. 68: Generated 1 of the 1 non-bonded parameter combinations 68: 68: Excluding 1 bonded neighbours molecule type 'Argon' 68: 68: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 68: 68: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 68: 68: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 68: 68: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 68: 68: Note that mdrun will redetermine rlist based on the actual pair-list setup 68: 68: This run will generate roughly 0 Mb of data 68: Generated 1 of the 1 non-bonded parameter combinations 68: 68: Excluding 1 bonded neighbours molecule type 'Argon' 68: 68: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 68: 68: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 68: 68: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 68: 68: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 68: 68: Note that mdrun will redetermine rlist based on the actual pair-list setup 68: 68: This run will generate roughly 0 Mb of data 68: 68: Writing final coordinates. 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.049 0.025 198.0 68: (ns/day) (hour/ns) 68: Performance: 59.106 0.406 68: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_firstpart.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 68: Using 1 MPI thread 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'Argon' 68: 8 steps, 0.0 ps. 68: 68: Writing final coordinates. 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.043 0.022 197.4 68: (ns/day) (hour/ns) 68: Performance: 36.057 0.666 68: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_full.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 68: Using 1 MPI thread 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'Argon' 68: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 68: 68: Writing final coordinates. 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.040 0.020 197.5 68: (ns/day) (hour/ns) 68: Performance: 38.466 0.624 68: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_full.edr as single precision energy file 68: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_firstpart.edr as single precision energy file 68: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_secondpart.part0002.edr as single precision energy file 68: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/3 (183 ms) 68: [ RUN ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/4 68: 68: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_input.mdp]: 68: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 68: that with the Verlet scheme, nstlist has no effect on the accuracy of 68: your simulation. 68: 68: 68: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_input.mdp]: 68: Setting nstcalcenergy (100) equal to nstenergy (4) 68: 68: Number of degrees of freedom in T-Coupling group System is 33.00 68: 68: There were 2 NOTEs 68: 68: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_input.mdp]: 68: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 68: that with the Verlet scheme, nstlist has no effect on the accuracy of 68: your simulation. 68: 68: 68: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_input.mdp]: 68: Setting nstcalcenergy (100) equal to nstenergy (4) 68: 68: Number of degrees of freedom in T-Coupling group System is 33.00 68: 68: There were 2 NOTEs 68: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_full.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 68: Using 1 MPI thread 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'Argon' 68: 16 steps, 0.0 ps. 68: Generated 1 of the 1 non-bonded parameter combinations 68: 68: Excluding 1 bonded neighbours molecule type 'Argon' 68: 68: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 68: 68: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 68: 68: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 68: 68: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 68: 68: Note that mdrun will redetermine rlist based on the actual pair-list setup 68: 68: This run will generate roughly 0 Mb of data 68: Generated 1 of the 1 non-bonded parameter combinations 68: 68: Excluding 1 bonded neighbours molecule type 'Argon' 68: 68: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 68: 68: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 68: 68: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 68: 68: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 68: 68: Note that mdrun will redetermine rlist based on the actual pair-list setup 68: 68: This run will generate roughly 0 Mb of data 68: 68: Writing final coordinates. 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.076 0.038 199.0 68: (ns/day) (hour/ns) 68: Performance: 38.639 0.621 68: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_firstpart.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 68: Using 1 MPI thread 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'Argon' 68: 8 steps, 0.0 ps. 68: 68: Writing final coordinates. 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.055 0.028 198.6 68: (ns/day) (hour/ns) 68: Performance: 28.141 0.853 68: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_full.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 68: Using 1 MPI thread 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'Argon' 68: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 68: 68: Writing final coordinates. 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.051 0.026 197.4 68: (ns/day) (hour/ns) 68: Performance: 30.086 0.798 68: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_full.edr as single precision energy file 68: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_firstpart.edr as single precision energy file 68: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_secondpart.part0002.edr as single precision energy file 68: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/4 (221 ms) 68: [ RUN ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/5 68: 68: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_5_input.mdp]: 68: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 68: that with the Verlet scheme, nstlist has no effect on the accuracy of 68: your simulation. 68: 68: 68: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_5_input.mdp]: 68: Setting nstcalcenergy (100) equal to nstenergy (4) 68: 68: Number of degrees of freedom in T-Coupling group System is 33.00 68: 68: There were 2 NOTEs 68: 68: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_5_input.mdp]: 68: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 68: that with the Verlet scheme, nstlist has no effect on the accuracy of 68: your simulation. 68: 68: 68: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_5_input.mdp]: 68: Setting nstcalcenergy (100) equal to nstenergy (4) 68: 68: Number of degrees of freedom in T-Coupling group System is 33.00 68: 68: There were 2 NOTEs 68: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_5_full.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 68: Using 1 MPI thread 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'Argon' 68: 16 steps, 0.0 ps. 68: Generated 1 of the 1 non-bonded parameter combinations 68: 68: Excluding 1 bonded neighbours molecule type 'Argon' 68: 68: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 68: 68: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 68: 68: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 68: 68: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 68: 68: Note that mdrun will redetermine rlist based on the actual pair-list setup 68: 68: This run will generate roughly 0 Mb of data 68: Generated 1 of the 1 non-bonded parameter combinations 68: 68: Excluding 1 bonded neighbours molecule type 'Argon' 68: 68: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 68: 68: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 68: 68: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 68: 68: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 68: 68: Note that mdrun will redetermine rlist based on the actual pair-list setup 68: 68: This run will generate roughly 0 Mb of data 68: 68: Writing final coordinates. 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.059 0.030 198.8 68: (ns/day) (hour/ns) 68: Performance: 49.650 0.483 68: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_5_firstpart.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 68: Using 1 MPI thread 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'Argon' 68: 8 steps, 0.0 ps. 68: 68: Writing final coordinates. 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.067 0.034 198.9 68: (ns/day) (hour/ns) 68: Performance: 23.100 1.039 68: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_5_full.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 68: Using 1 MPI thread 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'Argon' 68: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 68: 68: Writing final coordinates. 68: 68: NOTE: 11 % of the run time was spent in pair search, 68: you might want to increase nstlist (this has no effect on accuracy) 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.080 0.040 198.4 68: (ns/day) (hour/ns) 68: Performance: 19.374 1.239 68: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_5_full.edr as single precision energy file 68: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_5_firstpart.edr as single precision energy file 68: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_5_secondpart.part0002.edr as single precision energy file 68: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/5 (210 ms) 68: [ RUN ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/6 68: [ OK ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/6 (0 ms) 68: [ RUN ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/7 68: 68: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_7_input.mdp]: 68: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 68: that with the Verlet scheme, nstlist has no effect on the accuracy of 68: your simulation. 68: 68: 68: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_7_input.mdp]: 68: Setting nstcalcenergy (100) equal to nstenergy (4) 68: 68: Number of degrees of freedom in T-Coupling group System is 33.00 68: 68: There were 2 NOTEs 68: 68: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_7_input.mdp]: 68: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 68: that with the Verlet scheme, nstlist has no effect on the accuracy of 68: your simulation. 68: 68: 68: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_7_input.mdp]: 68: Setting nstcalcenergy (100) equal to nstenergy (4) 68: 68: Number of degrees of freedom in T-Coupling group System is 33.00 68: 68: There were 2 NOTEs 68: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_7_full.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 68: Using 1 MPI thread 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'Argon' 68: 16 steps, 0.0 ps. 68: Generated 1 of the 1 non-bonded parameter combinations 68: 68: Excluding 1 bonded neighbours molecule type 'Argon' 68: 68: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 68: 68: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 68: 68: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 68: 68: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 68: 68: Note that mdrun will redetermine rlist based on the actual pair-list setup 68: 68: This run will generate roughly 0 Mb of data 68: Generated 1 of the 1 non-bonded parameter combinations 68: 68: Excluding 1 bonded neighbours molecule type 'Argon' 68: 68: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 68: 68: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 68: 68: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 68: 68: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 68: 68: Note that mdrun will redetermine rlist based on the actual pair-list setup 68: 68: This run will generate roughly 0 Mb of data 68: 68: Writing final coordinates. 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.058 0.029 198.7 68: (ns/day) (hour/ns) 68: Performance: 50.739 0.473 68: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_7_firstpart.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 68: Using 1 MPI thread 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'Argon' 68: 8 steps, 0.0 ps. 68: 68: Writing final coordinates. 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.051 0.026 198.6 68: (ns/day) (hour/ns) 68: Performance: 30.016 0.800 68: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_7_full.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 68: Using 1 MPI thread 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'Argon' 68: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 68: 68: Writing final coordinates. 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.050 0.025 197.2 68: (ns/day) (hour/ns) 68: Performance: 30.602 0.784 68: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_7_full.edr as single precision energy file 68: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_7_firstpart.edr as single precision energy file 68: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_7_secondpart.part0002.edr as single precision energy file 68: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/7 (184 ms) 68: [----------] 8 tests from NPT/MdrunNoAppendContinuationIsExact (1361 ms total) 68: 68: [----------] 1 test from MTTK/MdrunNoAppendContinuationIsExact 68: [ RUN ] MTTK/MdrunNoAppendContinuationIsExact.WithinTolerances/0 68: 68: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MTTK_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 68: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 68: that with the Verlet scheme, nstlist has no effect on the accuracy of 68: your simulation. 68: 68: 68: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MTTK_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 68: Setting nstcalcenergy (100) equal to nstenergy (4) 68: 68: 68: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MTTK_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 68: MTTK coupling is deprecated and will soon be removed 68: 68: Number of degrees of freedom in T-Coupling group System is 33.00 68: 68: There were 3 NOTEs 68: 68: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MTTK_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 68: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 68: that with the Verlet scheme, nstlist has no effect on the accuracy of 68: your simulation. 68: 68: 68: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MTTK_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 68: Setting nstcalcenergy (100) equal to nstenergy (4) 68: 68: 68: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MTTK_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 68: MTTK coupling is deprecated and will soon be removed 68: 68: Number of degrees of freedom in T-Coupling group System is 33.00 68: 68: There were 3 NOTEs 68: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MTTK_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 68: Using 1 MPI thread 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'Argon' 68: 16 steps, 0.0 ps. 68: Generated 1 of the 1 non-bonded parameter combinations 68: 68: Excluding 1 bonded neighbours molecule type 'Argon' 68: 68: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 68: 68: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 68: 68: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 68: 68: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 68: 68: Note that mdrun will redetermine rlist based on the actual pair-list setup 68: 68: This run will generate roughly 0 Mb of data 68: Generated 1 of the 1 non-bonded parameter combinations 68: 68: Excluding 1 bonded neighbours molecule type 'Argon' 68: 68: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 68: 68: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 68: 68: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 68: 68: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 68: 68: Note that mdrun will redetermine rlist based on the actual pair-list setup 68: 68: This run will generate roughly 0 Mb of data 68: 68: Writing final coordinates. 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.097 0.049 199.0 68: (ns/day) (hour/ns) 68: Performance: 30.256 0.793 68: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MTTK_MdrunNoAppendContinuationIsExact_WithinTolerances_0_firstpart.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 68: Using 1 MPI thread 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'Argon' 68: 8 steps, 0.0 ps. 68: 68: Writing final coordinates. 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.056 0.028 198.4 68: (ns/day) (hour/ns) 68: Performance: 27.528 0.872 68: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MTTK_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 68: Using 1 MPI thread 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'Argon' 68: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 68: 68: Writing final coordinates. 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.050 0.025 196.7 68: (ns/day) (hour/ns) 68: Performance: 30.875 0.777 68: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MTTK_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.edr as single precision energy file 68: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MTTK_MdrunNoAppendContinuationIsExact_WithinTolerances_0_firstpart.edr as single precision energy file 68: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MTTK_MdrunNoAppendContinuationIsExact_WithinTolerances_0_secondpart.part0002.edr as single precision energy file 68: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] MTTK/MdrunNoAppendContinuationIsExact.WithinTolerances/0 (216 ms) 68: [----------] 1 test from MTTK/MdrunNoAppendContinuationIsExact (216 ms total) 68: 68: [----------] 2 tests from Pull/MdrunNoAppendContinuationIsExact 68: [ RUN ] Pull/MdrunNoAppendContinuationIsExact.WithinTolerances/0 68: 68: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/Pull_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 68: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 68: that with the Verlet scheme, nstlist has no effect on the accuracy of 68: your simulation. 68: 68: 68: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/Pull_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 68: Setting nstcalcenergy (100) equal to nstenergy (4) 68: 68: Generating 1-4 interactions: fudge = 0.5 68: Pull group 1 'FirstWaterMolecule' has 3 atoms 68: Pull group 2 'SecondWaterMolecule' has 3 atoms 68: Number of degrees of freedom in T-Coupling group System is 9.00 68: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 68: 68: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/Pull_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 68: NVE simulation: will use the initial temperature of 2573.591 K for 68: determining the Verlet buffer size 68: 68: Pull group natoms pbc atom distance at start reference at t=0 68: 1 3 2 68: 2 3 5 1.112 nm 1.000 nm 68: 68: There were 3 NOTEs 68: 68: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/Pull_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 68: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 68: that with the Verlet scheme, nstlist has no effect on the accuracy of 68: your simulation. 68: 68: 68: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/Pull_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 68: Setting nstcalcenergy (100) equal to nstenergy (4) 68: 68: Generating 1-4 interactions: fudge = 0.5 68: Pull group 1 'FirstWaterMolecule' has 3 atoms 68: Pull group 2 'SecondWaterMolecule' has 3 atoms 68: Number of degrees of freedom in T-Coupling group System is 9.00 68: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 68: 68: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/Pull_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 68: NVE simulation: will use the initial temperature of 2573.591 K for 68: determining the Verlet buffer size 68: 68: Pull group natoms pbc atom distance at start reference at t=0 68: 1 3 2 68: 2 3 5 1.112 nm 1.000 nm 68: 68: There were 3 NOTEs 68: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/Pull_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 68: Can not increase nstlist because an NVE ensemble is used 68: Using 1 MPI thread 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'spc2' 68: 16 steps, 0.0 ps. 68: Generated 3 of the 3 non-bonded parameter combinations 68: 68: Generated 3 of the 3 1-4 parameter combinations 68: 68: Excluding 2 bonded neighbours molecule type 'SOL' 68: 68: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/spc2.gro' 68: 68: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 2573.59 K 68: 68: Calculated rlist for 1x1 atom pair-list as 0.877 nm, buffer size 0.177 nm 68: 68: Set rlist, assuming 4x4 atom pair-list, to 0.862 nm, buffer size 0.162 nm 68: 68: Note that mdrun will redetermine rlist based on the actual pair-list setup 68: 68: This run will generate roughly 0 Mb of data 68: Generated 3 of the 3 non-bonded parameter combinations 68: 68: Generated 3 of the 3 1-4 parameter combinations 68: 68: Excluding 2 bonded neighbours molecule type 'SOL' 68: 68: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/spc2.gro' 68: 68: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 2573.59 K 68: 68: Calculated rlist for 1x1 atom pair-list as 0.877 nm, buffer size 0.177 nm 68: 68: Set rlist, assuming 4x4 atom pair-list, to 0.862 nm, buffer size 0.162 nm 68: 68: Note that mdrun will redetermine rlist based on the actual pair-list setup 68: 68: This run will generate roughly 0 Mb of data 68: 68: Writing final coordinates. 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.060 0.030 197.8 68: (ns/day) (hour/ns) 68: Performance: 48.216 0.498 68: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/Pull_MdrunNoAppendContinuationIsExact_WithinTolerances_0_firstpart.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 68: Can not increase nstlist because an NVE ensemble is used 68: Using 1 MPI thread 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'spc2' 68: 8 steps, 0.0 ps. 68: 68: Writing final coordinates. 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.052 0.026 197.4 68: (ns/day) (hour/ns) 68: Performance: 29.344 0.818 68: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/Pull_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 68: Can not increase nstlist because an NVE ensemble is used 68: Using 1 MPI thread 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'spc2' 68: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 68: 68: Writing final coordinates. 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.051 0.026 197.6 68: (ns/day) (hour/ns) 68: Performance: 29.877 0.803 68: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/Pull_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.edr as single precision energy file 68: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/Pull_MdrunNoAppendContinuationIsExact_WithinTolerances_0_firstpart.edr as single precision energy file 68: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/Pull_MdrunNoAppendContinuationIsExact_WithinTolerances_0_secondpart.part0002.edr as single precision energy file 68: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] Pull/MdrunNoAppendContinuationIsExact.WithinTolerances/0 (211 ms) 68: [ RUN ] Pull/MdrunNoAppendContinuationIsExact.WithinTolerances/1 68: 68: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/Pull_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 68: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 68: that with the Verlet scheme, nstlist has no effect on the accuracy of 68: your simulation. 68: 68: 68: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/Pull_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 68: Setting nstcalcenergy (100) equal to nstenergy (4) 68: 68: Generating 1-4 interactions: fudge = 0.5 68: Pull group 1 'FirstWaterMolecule' has 3 atoms 68: Pull group 2 'SecondWaterMolecule' has 3 atoms 68: Number of degrees of freedom in T-Coupling group System is 9.00 68: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 68: 68: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/Pull_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 68: NVE simulation: will use the initial temperature of 2573.591 K for 68: determining the Verlet buffer size 68: 68: Pull group natoms pbc atom distance at start reference at t=0 68: 1 3 2 68: 2 3 5 1.112 nm 1.000 nm 68: 68: There were 3 NOTEs 68: 68: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/Pull_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 68: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 68: that with the Verlet scheme, nstlist has no effect on the accuracy of 68: your simulation. 68: 68: 68: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/Pull_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 68: Setting nstcalcenergy (100) equal to nstenergy (4) 68: 68: Generating 1-4 interactions: fudge = 0.5 68: Pull group 1 'FirstWaterMolecule' has 3 atoms 68: Pull group 2 'SecondWaterMolecule' has 3 atoms 68: Number of degrees of freedom in T-Coupling group System is 9.00 68: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 68: 68: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/Pull_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 68: NVE simulation: will use the initial temperature of 2573.591 K for 68: determining the Verlet buffer size 68: 68: Pull group natoms pbc atom distance at start reference at t=0 68: 1 3 2 68: 2 3 5 1.112 nm 1.000 nm 68: 68: There were 3 NOTEs 68: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/Pull_MdrunNoAppendContinuationIsExact_WithinTolerances_1_full.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 68: Can not increase nstlist because an NVE ensemble is used 68: Using 1 MPI thread 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'spc2' 68: 16 steps, 0.0 ps. 68: Generated 3 of the 3 non-bonded parameter combinations 68: 68: Generated 3 of the 3 1-4 parameter combinations 68: 68: Excluding 2 bonded neighbours molecule type 'SOL' 68: 68: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/spc2.gro' 68: 68: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 2573.59 K 68: 68: Calculated rlist for 1x1 atom pair-list as 0.877 nm, buffer size 0.177 nm 68: 68: Set rlist, assuming 4x4 atom pair-list, to 0.862 nm, buffer size 0.162 nm 68: 68: Note that mdrun will redetermine rlist based on the actual pair-list setup 68: 68: This run will generate roughly 0 Mb of data 68: Generated 3 of the 3 non-bonded parameter combinations 68: 68: Generated 3 of the 3 1-4 parameter combinations 68: 68: Excluding 2 bonded neighbours molecule type 'SOL' 68: 68: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/spc2.gro' 68: 68: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 2573.59 K 68: 68: Calculated rlist for 1x1 atom pair-list as 0.877 nm, buffer size 0.177 nm 68: 68: Set rlist, assuming 4x4 atom pair-list, to 0.862 nm, buffer size 0.162 nm 68: 68: Note that mdrun will redetermine rlist based on the actual pair-list setup 68: 68: This run will generate roughly 0 Mb of data 68: 68: Writing final coordinates. 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.065 0.033 198.5 68: (ns/day) (hour/ns) 68: Performance: 45.083 0.532 68: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/Pull_MdrunNoAppendContinuationIsExact_WithinTolerances_1_firstpart.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 68: Can not increase nstlist because an NVE ensemble is used 68: Using 1 MPI thread 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'spc2' 68: 8 steps, 0.0 ps. 68: 68: Writing final coordinates. 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.061 0.031 198.5 68: (ns/day) (hour/ns) 68: Performance: 25.417 0.944 68: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/Pull_MdrunNoAppendContinuationIsExact_WithinTolerances_1_full.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 68: Can not increase nstlist because an NVE ensemble is used 68: Using 1 MPI thread 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'spc2' 68: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 68: 68: Writing final coordinates. 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.072 0.036 198.1 68: (ns/day) (hour/ns) 68: Performance: 21.443 1.119 68: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/Pull_MdrunNoAppendContinuationIsExact_WithinTolerances_1_full.edr as single precision energy file 68: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/Pull_MdrunNoAppendContinuationIsExact_WithinTolerances_1_firstpart.edr as single precision energy file 68: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/Pull_MdrunNoAppendContinuationIsExact_WithinTolerances_1_secondpart.part0002.edr as single precision energy file 68: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] Pull/MdrunNoAppendContinuationIsExact.WithinTolerances/1 (240 ms) 68: [----------] 2 tests from Pull/MdrunNoAppendContinuationIsExact (451 ms total) 68: 68: [----------] 2 tests from Awh/MdrunNoAppendContinuationIsExact 68: [ RUN ] Awh/MdrunNoAppendContinuationIsExact.WithinTolerances/0 68: Setting the AWH bias MC random seed to -8388611 68: 68: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/Awh_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 68: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 68: that with the Verlet scheme, nstlist has no effect on the accuracy of 68: your simulation. 68: 68: 68: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/Awh_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 68: Setting nstcalcenergy (100) equal to nstenergy (4) 68: 68: Generating 1-4 interactions: fudge = 0.5 68: Pull group 1 'C_&_r_1' has 1 atoms 68: Pull group 2 'N_&_r_2' has 1 atoms 68: Pull group 3 'CA' has 1 atoms 68: Pull group 4 'C_&_r_2' has 1 atoms 68: Pull group 5 'N_&_r_3' has 1 atoms 68: Number of degrees of freedom in T-Coupling group System is 51.00 68: 68: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/Awh_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 68: You are using a plain Coulomb cut-off, which might produce artifacts. 68: You might want to consider using PME electrostatics. 68: 68: 68: Pull group natoms pbc atom distance at start reference at t=0 68: 1 1 0 68: 2 1 0 179.098 deg 0.000 deg 68: 2 1 0 68: 3 1 0 158.667 deg 0.000 deg 68: 68: There were 3 NOTEs 68: Setting the AWH bias MC random seed to -306226433 68: 68: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/Awh_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 68: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 68: that with the Verlet scheme, nstlist has no effect on the accuracy of 68: your simulation. 68: 68: 68: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/Awh_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 68: Setting nstcalcenergy (100) equal to nstenergy (4) 68: 68: Generating 1-4 interactions: fudge = 0.5 68: Pull group 1 'C_&_r_1' has 1 atoms 68: Pull group 2 'N_&_r_2' has 1 atoms 68: Pull group 3 'CA' has 1 atoms 68: Pull group 4 'C_&_r_2' has 1 atoms 68: Pull group 5 'N_&_r_3' has 1 atoms 68: Number of degrees of freedom in T-Coupling group System is 51.00 68: 68: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/Awh_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 68: You are using a plain Coulomb cut-off, which might produce artifacts. 68: You might want to consider using PME electrostatics. 68: 68: 68: Pull group natoms pbc atom distance at start reference at t=0 68: 1 1 0 68: 2 1 0 179.098 deg 0.000 deg 68: 2 1 0 68: 3 1 0 158.667 deg 0.000 deg 68: 68: There were 3 NOTEs 68: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/Awh_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 68: Using 1 MPI thread 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'Alanine-dipeptide' 68: 16 steps, 0.0 ps. 68: Generated 2145 of the 2145 non-bonded parameter combinations 68: 68: Generated 2145 of the 2145 1-4 parameter combinations 68: 68: Excluding 3 bonded neighbours molecule type 'ALANINEDIPEPTIDE' 68: 68: turning H bonds into constraints... 68: 68: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/alanine_vacuo.gro' 68: 68: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 68: 68: Calculated rlist for 1x1 atom pair-list as 0.761 nm, buffer size 0.061 nm 68: 68: Set rlist, assuming 4x4 atom pair-list, to 0.754 nm, buffer size 0.054 nm 68: 68: Note that mdrun will redetermine rlist based on the actual pair-list setup 68: 68: This run will generate roughly 0 Mb of data 68: Generated 2145 of the 2145 non-bonded parameter combinations 68: 68: Generated 2145 of the 2145 1-4 parameter combinations 68: 68: Excluding 3 bonded neighbours molecule type 'ALANINEDIPEPTIDE' 68: 68: turning H bonds into constraints... 68: 68: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/alanine_vacuo.gro' 68: 68: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 68: 68: Calculated rlist for 1x1 atom pair-list as 0.761 nm, buffer size 0.061 nm 68: 68: Set rlist, assuming 4x4 atom pair-list, to 0.754 nm, buffer size 0.054 nm 68: 68: Note that mdrun will redetermine rlist based on the actual pair-list setup 68: 68: This run will generate roughly 0 Mb of data 68: 68: Writing final coordinates. 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.093 0.047 197.5 68: (ns/day) (hour/ns) 68: Performance: 31.303 0.767 68: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/Awh_MdrunNoAppendContinuationIsExact_WithinTolerances_0_firstpart.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 68: Using 1 MPI thread 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'Alanine-dipeptide' 68: 8 steps, 0.0 ps. 68: 68: Writing final coordinates. 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.075 0.038 197.1 68: (ns/day) (hour/ns) 68: Performance: 20.493 1.171 68: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/Awh_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 68: Using 1 MPI thread 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'Alanine-dipeptide' 68: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 68: 68: Writing final coordinates. 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.079 0.040 197.2 68: (ns/day) (hour/ns) 68: Performance: 19.294 1.244 68: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/Awh_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.edr as single precision energy file 68: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/Awh_MdrunNoAppendContinuationIsExact_WithinTolerances_0_firstpart.edr as single precision energy file 68: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/Awh_MdrunNoAppendContinuationIsExact_WithinTolerances_0_secondpart.part0002.edr as single precision energy file 68: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] Awh/MdrunNoAppendContinuationIsExact.WithinTolerances/0 (510 ms) 68: [ RUN ] Awh/MdrunNoAppendContinuationIsExact.WithinTolerances/1 68: Setting the AWH bias MC random seed to 1558019583 68: 68: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/Awh_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 68: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 68: that with the Verlet scheme, nstlist has no effect on the accuracy of 68: your simulation. 68: 68: 68: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/Awh_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 68: Setting nstcalcenergy (100) equal to nstenergy (4) 68: 68: Generating 1-4 interactions: fudge = 0.5 68: Pull group 1 'C_&_r_1' has 1 atoms 68: Pull group 2 'N_&_r_2' has 1 atoms 68: Pull group 3 'CA' has 1 atoms 68: Pull group 4 'C_&_r_2' has 1 atoms 68: Pull group 5 'N_&_r_3' has 1 atoms 68: Number of degrees of freedom in T-Coupling group System is 51.00 68: 68: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/Awh_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 68: You are using a plain Coulomb cut-off, which might produce artifacts. 68: You might want to consider using PME electrostatics. 68: 68: 68: Pull group natoms pbc atom distance at start reference at t=0 68: 1 1 0 68: 2 1 0 179.098 deg 0.000 deg 68: 2 1 0 68: 3 1 0 158.667 deg 0.000 deg 68: 68: There were 3 NOTEs 68: Setting the AWH bias MC random seed to -541336199 68: 68: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/Awh_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 68: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 68: that with the Verlet scheme, nstlist has no effect on the accuracy of 68: your simulation. 68: 68: 68: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/Awh_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 68: Setting nstcalcenergy (100) equal to nstenergy (4) 68: 68: Generating 1-4 interactions: fudge = 0.5 68: Pull group 1 'C_&_r_1' has 1 atoms 68: Pull group 2 'N_&_r_2' has 1 atoms 68: Pull group 3 'CA' has 1 atoms 68: Pull group 4 'C_&_r_2' has 1 atoms 68: Pull group 5 'N_&_r_3' has 1 atoms 68: Number of degrees of freedom in T-Coupling group System is 51.00 68: 68: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/Awh_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 68: You are using a plain Coulomb cut-off, which might produce artifacts. 68: You might want to consider using PME electrostatics. 68: 68: 68: Pull group natoms pbc atom distance at start reference at t=0 68: 1 1 0 68: 2 1 0 179.098 deg 0.000 deg 68: 2 1 0 68: 3 1 0 158.667 deg 0.000 deg 68: 68: There were 3 NOTEs 68: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/Awh_MdrunNoAppendContinuationIsExact_WithinTolerances_1_full.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 68: Using 1 MPI thread 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'Alanine-dipeptide' 68: 16 steps, 0.0 ps. 68: Generated 2145 of the 2145 non-bonded parameter combinations 68: 68: Generated 2145 of the 2145 1-4 parameter combinations 68: 68: Excluding 3 bonded neighbours molecule type 'ALANINEDIPEPTIDE' 68: 68: turning H bonds into constraints... 68: 68: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/alanine_vacuo.gro' 68: 68: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 68: 68: Calculated rlist for 1x1 atom pair-list as 0.761 nm, buffer size 0.061 nm 68: 68: Set rlist, assuming 4x4 atom pair-list, to 0.754 nm, buffer size 0.054 nm 68: 68: Note that mdrun will redetermine rlist based on the actual pair-list setup 68: 68: This run will generate roughly 0 Mb of data 68: Generated 2145 of the 2145 non-bonded parameter combinations 68: 68: Generated 2145 of the 2145 1-4 parameter combinations 68: 68: Excluding 3 bonded neighbours molecule type 'ALANINEDIPEPTIDE' 68: 68: turning H bonds into constraints... 68: 68: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/alanine_vacuo.gro' 68: 68: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 68: 68: Calculated rlist for 1x1 atom pair-list as 0.761 nm, buffer size 0.061 nm 68: 68: Set rlist, assuming 4x4 atom pair-list, to 0.754 nm, buffer size 0.054 nm 68: 68: Note that mdrun will redetermine rlist based on the actual pair-list setup 68: 68: This run will generate roughly 0 Mb of data 68: 68: Writing final coordinates. 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.097 0.049 197.6 68: (ns/day) (hour/ns) 68: Performance: 29.803 0.805 68: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/Awh_MdrunNoAppendContinuationIsExact_WithinTolerances_1_firstpart.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 68: Using 1 MPI thread 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'Alanine-dipeptide' 68: 8 steps, 0.0 ps. 68: 68: Writing final coordinates. 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.084 0.043 197.3 68: (ns/day) (hour/ns) 68: Performance: 18.271 1.314 68: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/Awh_MdrunNoAppendContinuationIsExact_WithinTolerances_1_full.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 68: Using 1 MPI thread 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'Alanine-dipeptide' 68: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 68: 68: Writing final coordinates. 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.090 0.045 197.5 68: (ns/day) (hour/ns) 68: Performance: 17.121 1.402 68: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/Awh_MdrunNoAppendContinuationIsExact_WithinTolerances_1_full.edr as single precision energy file 68: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/Awh_MdrunNoAppendContinuationIsExact_WithinTolerances_1_firstpart.edr as single precision energy file 68: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/Awh_MdrunNoAppendContinuationIsExact_WithinTolerances_1_secondpart.part0002.edr as single precision energy file 68: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] Awh/MdrunNoAppendContinuationIsExact.WithinTolerances/1 (505 ms) 68: [----------] 2 tests from Awh/MdrunNoAppendContinuationIsExact (1016 ms total) 68: 68: [----------] 1 test from ExpandedEnsemble/MdrunNoAppendContinuationIsExact 68: [ RUN ] ExpandedEnsemble/MdrunNoAppendContinuationIsExact.WithinTolerances/0 68: 68: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/ExpandedEnsemble_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 68: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 68: that with the Verlet scheme, nstlist has no effect on the accuracy of 68: your simulation. 68: 68: Generating 1-4 interactions: fudge = 0.5 68: Number of degrees of freedom in T-Coupling group System is 79.00 68: 68: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/ExpandedEnsemble_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 68: You are using a plain Coulomb cut-off, which might produce artifacts. 68: You might want to consider using PME electrostatics. 68: 68: 68: 68: There were 2 NOTEs 68: 68: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/ExpandedEnsemble_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 68: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 68: that with the Verlet scheme, nstlist has no effect on the accuracy of 68: your simulation. 68: 68: Generating 1-4 interactions: fudge = 0.5 68: Number of degrees of freedom in T-Coupling group System is 79.00 68: 68: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/ExpandedEnsemble_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 68: You are using a plain Coulomb cut-off, which might produce artifacts. 68: You might want to consider using PME electrostatics. 68: 68: 68: 68: There were 2 NOTEs 68: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/ExpandedEnsemble_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 68: Using 1 MPI thread 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun '30 atom system in water' 68: 16 steps, 0.0 ps. 68: Generated 2485 of the 2485 non-bonded parameter combinations 68: 68: Generated 2485 of the 2485 1-4 parameter combinations 68: 68: Excluding 3 bonded neighbours molecule type 'nonanol' 68: 68: turning H bonds into constraints... 68: 68: Excluding 2 bonded neighbours molecule type 'SOL' 68: 68: turning H bonds into constraints... 68: 68: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/nonanol_vacuo.gro' 68: 68: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 68: 68: Calculated rlist for 1x1 atom pair-list as 0.764 nm, buffer size 0.064 nm 68: 68: Set rlist, assuming 4x4 atom pair-list, to 0.757 nm, buffer size 0.057 nm 68: 68: Note that mdrun will redetermine rlist based on the actual pair-list setup 68: 68: This run will generate roughly 0 Mb of data 68: Generated 2485 of the 2485 non-bonded parameter combinations 68: 68: Generated 2485 of the 2485 1-4 parameter combinations 68: 68: Excluding 3 bonded neighbours molecule type 'nonanol' 68: 68: turning H bonds into constraints... 68: 68: Excluding 2 bonded neighbours molecule type 'SOL' 68: 68: turning H bonds into constraints... 68: 68: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/nonanol_vacuo.gro' 68: 68: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 68: 68: Calculated rlist for 1x1 atom pair-list as 0.764 nm, buffer size 0.064 nm 68: 68: Set rlist, assuming 4x4 atom pair-list, to 0.757 nm, buffer size 0.057 nm 68: 68: Note that mdrun will redetermine rlist based on the actual pair-list setup 68: 68: This run will generate roughly 0 Mb of data 68: 68: Writing final coordinates. 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.124 0.062 199.3 68: (ns/day) (hour/ns) 68: Performance: 23.677 1.014 68: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/ExpandedEnsemble_MdrunNoAppendContinuationIsExact_WithinTolerances_0_firstpart.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 68: Using 1 MPI thread 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun '30 atom system in water' 68: 8 steps, 0.0 ps. 68: 68: Writing final coordinates. 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.115 0.058 199.1 68: (ns/day) (hour/ns) 68: Performance: 13.502 1.777 68: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/ExpandedEnsemble_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 68: Using 1 MPI thread 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun '30 atom system in water' 68: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 68: 68: Writing final coordinates. 68: 68: NOTE: 13 % of the run time was spent in pair search, 68: you might want to increase nstlist (this has no effect on accuracy) 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.118 0.060 197.5 68: (ns/day) (hour/ns) 68: Performance: 13.001 1.846 68: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/ExpandedEnsemble_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.edr as single precision energy file 68: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/ExpandedEnsemble_MdrunNoAppendContinuationIsExact_WithinTolerances_0_firstpart.edr as single precision energy file 68: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/ExpandedEnsemble_MdrunNoAppendContinuationIsExact_WithinTolerances_0_secondpart.part0002.edr as single precision energy file 68: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] ExpandedEnsemble/MdrunNoAppendContinuationIsExact.WithinTolerances/0 (608 ms) 68: [----------] 1 test from ExpandedEnsemble/MdrunNoAppendContinuationIsExact (609 ms total) 68: 68: [----------] 3 tests from Checking/InitialConstraintsTest 68: [ RUN ] Checking/InitialConstraintsTest.Works/0 68: Number of degrees of freedom in T-Coupling group rest is 11.00 68: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 68: 68: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/Checking_InitialConstraintsTest_Works_0_input.mdp]: 68: NVE simulation: will use the initial temperature of 1141.954 K for 68: determining the Verlet buffer size 68: 68: 68: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/Checking_InitialConstraintsTest_Works_0_input.mdp]: 68: You are using a plain Coulomb cut-off, which might produce artifacts. 68: You might want to consider using PME electrostatics. 68: 68: 68: 68: There were 2 NOTEs 68: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/Checking_InitialConstraintsTest_Works_0.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 68: Can not increase nstlist because an NVE ensemble is used 68: Using 1 MPI thread 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'spc-and-methanol' 68: 1 steps, 0.0 ps. 68: Setting the LD random seed to -1191187105 68: 68: Generated 8 of the 10 non-bonded parameter combinations 68: 68: Excluding 2 bonded neighbours molecule type 'Methanol' 68: 68: turning H bonds into constraints... 68: 68: Excluding 2 bonded neighbours molecule type 'SOL' 68: 68: turning H bonds into constraints... 68: 68: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/spc-and-methanol.gro' 68: 68: Determining Verlet buffer for a tolerance of 0.0001 kJ/mol/ps at 1141.95 K 68: 68: Calculated rlist for 1x1 atom pair-list as 1.126 nm, buffer size 0.126 nm 68: 68: Set rlist, assuming 4x4 atom pair-list, to 1.110 nm, buffer size 0.110 nm 68: 68: Note that mdrun will redetermine rlist based on the actual pair-list setup 68: 68: This run will generate roughly 0 Mb of data 68: 68: Writing final coordinates. 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.037 0.019 196.2 68: (ns/day) (hour/ns) 68: Performance: 9.278 2.587 68: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/Checking_InitialConstraintsTest_Works_0_spc-and-methanol.edr as single precision energy file 68: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 [ OK ] Checking/InitialConstraintsTest.Works/0 (74 ms) 68: [ RUN ] Checking/InitialConstraintsTest.Works/1 68: Number of degrees of freedom in T-Coupling group rest is 11.00 68: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 68: 68: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/Checking_InitialConstraintsTest_Works_1_input.mdp]: 68: NVE simulation: will use the initial temperature of 1141.954 K for 68: determining the Verlet buffer size 68: 68: 68: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/Checking_InitialConstraintsTest_Works_1_input.mdp]: 68: You are using a plain Coulomb cut-off, which might produce artifacts. 68: You might want to consider using PME electrostatics. 68: 68: 68: 68: There were 2 NOTEs 68: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/Checking_InitialConstraintsTest_Works_1.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 68: Can not increase nstlist because an NVE ensemble is used 68: Using 1 MPI thread 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'spc-and-methanol' 68: 1 steps, 0.0 ps. 68: Setting the LD random seed to 1946140669 68: 68: Generated 8 of the 10 non-bonded parameter combinations 68: 68: Excluding 2 bonded neighbours molecule type 'Methanol' 68: 68: turning H bonds into constraints... 68: 68: Excluding 2 bonded neighbours molecule type 'SOL' 68: 68: turning H bonds into constraints... 68: 68: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/spc-and-methanol.gro' 68: 68: Determining Verlet buffer for a tolerance of 0.0001 kJ/mol/ps at 1141.95 K 68: 68: Calculated rlist for 1x1 atom pair-list as 1.126 nm, buffer size 0.126 nm 68: 68: Set rlist, assuming 4x4 atom pair-list, to 1.110 nm, buffer size 0.110 nm 68: 68: Note that mdrun will redetermine rlist based on the actual pair-list setup 68: 68: This run will generate roughly 0 Mb of data 68: 68: Writing final coordinates. 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.033 0.017 197.8 68: (ns/day) (hour/ns) 68: Performance: 10.404 2.307 68: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/Checking_InitialConstraintsTest_Works_1_spc-and-methanol.edr as single precision energy file 68: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 [ OK ] Checking/InitialConstraintsTest.Works/1 (73 ms) 68: [ RUN ] Checking/InitialConstraintsTest.Works/2 68: 68: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/Checking_InitialConstraintsTest_Works_2_input.mdp]: 68: Integrator method md-vv-avek is implemented primarily for validation 68: purposes; for molecular dynamics, you should probably be using md or 68: md-vv 68: 68: Number of degrees of freedom in T-Coupling group rest is 11.00 68: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 68: 68: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/Checking_InitialConstraintsTest_Works_2_input.mdp]: 68: NVE simulation: will use the initial temperature of 1141.954 K for 68: determining the Verlet buffer size 68: 68: 68: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/Checking_InitialConstraintsTest_Works_2_input.mdp]: 68: You are using a plain Coulomb cut-off, which might produce artifacts. 68: You might want to consider using PME electrostatics. 68: 68: 68: 68: There were 3 NOTEs 68: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/Checking_InitialConstraintsTest_Works_2.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 68: Can not increase nstlist because an NVE ensemble is used 68: Using 1 MPI thread 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'spc-and-methanol' 68: 1 steps, 0.0 ps. 68: Setting the LD random seed to -1073760299 68: 68: Generated 8 of the 10 non-bonded parameter combinations 68: 68: Excluding 2 bonded neighbours molecule type 'Methanol' 68: 68: turning H bonds into constraints... 68: 68: Excluding 2 bonded neighbours molecule type 'SOL' 68: 68: turning H bonds into constraints... 68: 68: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/spc-and-methanol.gro' 68: 68: Determining Verlet buffer for a tolerance of 0.0001 kJ/mol/ps at 1141.95 K 68: 68: Calculated rlist for 1x1 atom pair-list as 1.126 nm, buffer size 0.126 nm 68: 68: Set rlist, assuming 4x4 atom pair-list, to 1.110 nm, buffer size 0.110 nm 68: 68: Note that mdrun will redetermine rlist based on the actual pair-list setup 68: 68: This run will generate roughly 0 Mb of data 68: 68: Writing final coordinates. 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.042 0.021 197.3 68: (ns/day) (hour/ns) 68: Performance: 8.153 2.944 68: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/Checking_InitialConstraintsTest_Works_2_spc-and-methanol.edr as single precision energy file 68: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 [ OK ] Checking/InitialConstraintsTest.Works/2 (63 ms) 68: [----------] 3 tests from Checking/InitialConstraintsTest (211 ms total) 68: 68: [----------] Global test environment tear-down 68: [==========] 76 tests from 13 test suites ran. (20926 ms total) 68: [ PASSED ] 76 tests. 68/92 Test #68: MdrunIOTests .............................. Passed 21.03 sec test 69 Start 69: MdrunTestsOneRank 69: Test command: /build/reproducible-path/gromacs-2025.1/build/basic/bin/mdrun-test "-ntomp" "2" "-ntmpi" "1" "--gtest_output=xml:/build/reproducible-path/gromacs-2025.1/build/basic/Testing/Temporary/MdrunTestsOneRank.xml" 69: Working Directory: /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests 69: Test timeout computed to be: 600 69: [==========] Running 29 tests from 8 test suites. 69: [----------] Global test environment set-up. 69: [----------] 1 test from CompelTest 69: [ RUN ] CompelTest.SwapCanRun 69: Generating 1-4 interactions: fudge = 0.5 69: Split0 group 'Ch0' contains 83 atoms. 69: Split1 group 'Ch1' contains 83 atoms. 69: Solvent group 'SOL' contains 11931 atoms. 69: Swap group 'NA+' contains 19 atoms. 69: Swap group 'CL-' contains 19 atoms. 69: Number of degrees of freedom in T-Coupling group System is 27869.00 69: 69: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/CompelTest_SwapCanRun_input.mdp]: 69: Removing center of mass motion in the presence of position restraints 69: might cause artifacts. When you are using position restraints to 69: equilibrate a macro-molecule, the artifacts are usually negligible. 69: 69: 69: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/CompelTest_SwapCanRun_input.mdp]: 69: You are using a plain Coulomb cut-off, which might produce artifacts. 69: You might want to consider using PME electrostatics. 69: 69: 69: 69: There were 2 NOTEs 69: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/CompelTest_SwapCanRun.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 69: Update groups can not be used for this system because there are three or more consecutively coupled constraints 69: 69: Using 1 MPI thread 69: Using 2 OpenMP threads 69: 69: 69: NOTE: The number of threads is not equal to the number of (logical) cpus 69: and the -pin option is set to auto: will not pin threads to cpus. 69: This can lead to significant performance degradation. 69: Consider using -pin on (and -pinoffset in case you run multiple jobs). 69: SWAP: Determining initial numbers of ions per compartment. 69: SWAP: Setting pointers for checkpoint writing 69: SWAP: Channel 0 flux history for ion type NA+ (charge 1): 0 molecules 69: SWAP: Channel 1 flux history for ion type NA+ (charge 1): 0 molecules 69: SWAP: Channel 0 flux history for ion type CL- (charge -1): 0 molecules 69: SWAP: Channel 1 flux history for ion type CL- (charge -1): 0 molecules 69: starting mdrun 'Channel_coco in octane membrane' 69: 2 steps, 0.0 ps. 69: Setting the LD random seed to -75499661 69: 69: Generated 330891 of the 330891 non-bonded parameter combinations 69: 69: Generated 330891 of the 330891 1-4 parameter combinations 69: 69: Excluding 3 bonded neighbours molecule type 'Protein' 69: 69: turning all bonds into constraints... 69: 69: Excluding 3 bonded neighbours molecule type 'OCT' 69: 69: turning all bonds into constraints... 69: 69: Excluding 1 bonded neighbours molecule type 'NA' 69: 69: turning all bonds into constraints... 69: 69: Excluding 1 bonded neighbours molecule type 'CL' 69: 69: turning all bonds into constraints... 69: 69: Excluding 3 bonded neighbours molecule type 'Protein' 69: 69: Excluding 3 bonded neighbours molecule type 'OCT' 69: 69: Excluding 2 bonded neighbours molecule type 'SOL' 69: 69: turning all bonds into constraints... 69: 69: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/OctaneSandwich.gro' 69: 69: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 300 K 69: 69: Calculated rlist for 1x1 atom pair-list as 1.316 nm, buffer size 0.316 nm 69: 69: Set rlist, assuming 4x4 atom pair-list, to 1.262 nm, buffer size 0.262 nm 69: 69: Note that mdrun will redetermine rlist based on the actual pair-list setup 69: 69: This run will generate roughly 1 Mb of data 69: 69: Writing final coordinates. 69: 69: NOTE: 14 % of the run time was spent in pair search, 69: you might want to increase nstlist (this has no effect on accuracy) 69: 69: Core t (s) Wall t (s) (%) 69: Time: 4.119 2.060 200.0 69: (ns/day) (hour/ns) 69: Performance: 0.629 38.147 69: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/CompelTest_SwapCanRun.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 69: Overriding nsteps with value passed on the command line: 2 steps, 0.01 ps 69: 69: Update groups can not be used for this system because there are three or more consecutively coupled constraints 69: 69: Using 1 MPI thread 69: Using 2 OpenMP threads 69: 69: 69: NOTE: The number of threads is not equal to the number of (logical) cpus 69: and the -pin option is set to auto: will not pin threads to cpus. 69: This can lead to significant performance degradation. 69: Consider using -pin on (and -pinoffset in case you run multiple jobs). 69: SWAP: Setting pointers for checkpoint writing 69: SWAP: Copying channel fluxes from checkpoint file data 69: SWAP: Channel 0 flux history for ion type NA+ (charge 1): 0 molecules 69: SWAP: Channel 1 flux history for ion type NA+ (charge 1): 0 molecules 69: SWAP: Channel 0 flux history for ion type CL- (charge -1): 0 molecules 69: SWAP: Channel 1 flux history for ion type CL- (charge -1): 0 molecules 69: starting mdrun 'Channel_coco in octane membrane' 69: 4 steps, 0.0 ps (continuing from step 2, 0.0 ps). 69: 69: Writing final coordinates. 69: 69: Core t (s) Wall t (s) (%) 69: Time: 3.438 1.720 200.0 69: (ns/day) (hour/ns) 69: Performance: 0.754 31.843 69: [ OK ] CompelTest.SwapCanRun (9207 ms) 69: [----------] 1 test from CompelTest (9208 ms total) 69: 69: [----------] 6 tests from BondedInteractionsTest 69: [ RUN ] BondedInteractionsTest.NormalBondWorks 69: 69: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_NormalBondWorks_input.mdp]: 69: For a correct single-point energy evaluation with nsteps = 0, use 69: continuation = yes to avoid constraining the input coordinates. 69: 69: 69: NOTE 2 [file BondedInteractionsTest_NormalBondWorks_butane1.top, line 31]: 69: In moleculetype 'butane' 2 atoms are not bound by a potential or 69: constraint to any other atom in the same moleculetype. Although 69: technically this might not cause issues in a simulation, this often means 69: that the user forgot to add a bond/potential/constraint or put multiple 69: molecules in the same moleculetype definition by mistake. Run with -v to 69: get information for each atom. 69: 69: Number of degrees of freedom in T-Coupling group rest is 9.00 69: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 69: 69: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_NormalBondWorks_input.mdp]: 69: NVE simulation with an initial temperature of zero: will use a Verlet 69: buffer of 10%. Check your energy drift! 69: 69: 69: There were 3 NOTEs 69: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_NormalBondWorks.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 69: Can not increase nstlist because an NVE ensemble is used 69: Using 1 MPI thread 69: Using 2 OpenMP threads 69: 69: 69: NOTE: The number of threads is not equal to the number of (logical) cpus 69: and the -pin option is set to auto: will not pin threads to cpus. 69: This can lead to significant performance degradation. 69: Consider using -pin on (and -pinoffset in case you run multiple jobs). 69: starting md rerun 'A single butane', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/butane1.gro' 69: 69: Reading frames from gro file 'A single butane', 4 atoms. 69: Reading frame 0 time 0.000 Last frame 0 time 0.000 69: 69: NOTE: 14 % of the run time was spent in pair search, 69: you might want to increase nstlist (this has no effect on accuracy) 69: 69: Core t (s) Wall t (s) (%) 69: Time: 0.002 0.001 184.5 69: (ns/day) (hour/ns) 69: Performance: 70.298 0.341 69: Setting the LD random seed to -1074888721 69: 69: Generated 3 of the 3 non-bonded parameter combinations 69: 69: Excluding 3 bonded neighbours molecule type 'butane' 69: 69: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/butane1.gro', all velocities are zero 69: 69: This run will generate roughly 0 Mb of data 69: [ OK ] BondedInteractionsTest.NormalBondWorks (44 ms) 69: [ RUN ] BondedInteractionsTest.TabulatedBondWorks 69: 69: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_TabulatedBondWorks_input.mdp]: 69: For a correct single-point energy evaluation with nsteps = 0, use 69: continuation = yes to avoid constraining the input coordinates. 69: 69: 69: NOTE 2 [file BondedInteractionsTest_TabulatedBondWorks_butane1.top, line 31]: 69: In moleculetype 'butane' 2 atoms are not bound by a potential or 69: constraint to any other atom in the same moleculetype. Although 69: technically this might not cause issues in a simulation, this often means 69: that the user forgot to add a bond/potential/constraint or put multiple 69: molecules in the same moleculetype definition by mistake. Run with -v to 69: get information for each atom. 69: 69: Number of degrees of freedom in T-Coupling group rest is 9.00 69: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 69: 69: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_TabulatedBondWorks_input.mdp]: 69: NVE simulation with an initial temperature of zero: will use a Verlet 69: buffer of 10%. Check your energy drift! 69: 69: 69: There were 3 NOTEs 69: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_TabulatedBondWorks.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 69: Can not increase nstlist because an NVE ensemble is used 69: Using 1 MPI thread 69: Using 2 OpenMP threads 69: 69: 69: NOTE: The number of threads is not equal to the number of (logical) cpus 69: and the -pin option is set to auto: will not pin threads to cpus. 69: This can lead to significant performance degradation. 69: Consider using -pin on (and -pinoffset in case you run multiple jobs). 69: starting md rerun 'A single butane', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/butane1.gro' 69: 69: Reading frames from gro file 'A single butane', 4 atoms. 69: Reading frame 0 time 0.000 Last frame 0 time 0.000 69: 69: NOTE: 15 % of the run time was spent in pair search, 69: you might want to increase nstlist (this has no effect on accuracy) 69: 69: Core t (s) Wall t (s) (%) 69: Time: 0.002 0.001 185.2 69: (ns/day) (hour/ns) 69: Performance: 79.280 0.303 69: Setting the LD random seed to 2011688935 69: 69: Generated 3 of the 3 non-bonded parameter combinations 69: 69: Excluding 3 bonded neighbours molecule type 'butane' 69: 69: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/butane1.gro', all velocities are zero 69: 69: This run will generate roughly 0 Mb of data 69: [ OK ] BondedInteractionsTest.TabulatedBondWorks (44 ms) 69: [ RUN ] BondedInteractionsTest.NormalAngleWorks 69: 69: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_NormalAngleWorks_input.mdp]: 69: For a correct single-point energy evaluation with nsteps = 0, use 69: continuation = yes to avoid constraining the input coordinates. 69: 69: 69: NOTE 2 [file BondedInteractionsTest_NormalAngleWorks_butane1.top, line 31]: 69: In moleculetype 'butane' 4 atoms are not bound by a potential or 69: constraint to any other atom in the same moleculetype. Although 69: technically this might not cause issues in a simulation, this often means 69: that the user forgot to add a bond/potential/constraint or put multiple 69: molecules in the same moleculetype definition by mistake. Run with -v to 69: get information for each atom. 69: 69: Number of degrees of freedom in T-Coupling group rest is 9.00 69: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 69: 69: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_NormalAngleWorks_input.mdp]: 69: NVE simulation with an initial temperature of zero: will use a Verlet 69: buffer of 10%. Check your energy drift! 69: 69: 69: There were 3 NOTEs 69: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_NormalAngleWorks.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 69: Can not increase nstlist because an NVE ensemble is used 69: Using 1 MPI thread 69: Using 2 OpenMP threads 69: 69: 69: NOTE: The number of threads is not equal to the number of (logical) cpus 69: and the -pin option is set to auto: will not pin threads to cpus. 69: This can lead to significant performance degradation. 69: Consider using -pin on (and -pinoffset in case you run multiple jobs). 69: starting md rerun 'A single butane', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/butane1.gro' 69: 69: Reading frames from gro file 'A single butane', 4 atoms. 69: Reading frame 0 time 0.000 Last frame 0 time 0.000 69: 69: NOTE: 15 % of the run time was spent in pair search, 69: you might want to increase nstlist (this has no effect on accuracy) 69: 69: Core t (s) Wall t (s) (%) 69: Time: 0.002 0.001 184.7 69: (ns/day) (hour/ns) 69: Performance: 77.005 0.312 69: Setting the LD random seed to -151271460 69: 69: Generated 3 of the 3 non-bonded parameter combinations 69: 69: Excluding 3 bonded neighbours molecule type 'butane' 69: 69: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/butane1.gro', all velocities are zero 69: 69: This run will generate roughly 0 Mb of data 69: [ OK ] BondedInteractionsTest.NormalAngleWorks (40 ms) 69: [ RUN ] BondedInteractionsTest.TabulatedAngleWorks 69: 69: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_TabulatedAngleWorks_input.mdp]: 69: For a correct single-point energy evaluation with nsteps = 0, use 69: continuation = yes to avoid constraining the input coordinates. 69: 69: 69: NOTE 2 [file BondedInteractionsTest_TabulatedAngleWorks_butane1.top, line 31]: 69: In moleculetype 'butane' 4 atoms are not bound by a potential or 69: constraint to any other atom in the same moleculetype. Although 69: technically this might not cause issues in a simulation, this often means 69: that the user forgot to add a bond/potential/constraint or put multiple 69: molecules in the same moleculetype definition by mistake. Run with -v to 69: get information for each atom. 69: 69: Number of degrees of freedom in T-Coupling group rest is 9.00 69: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 69: 69: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_TabulatedAngleWorks_input.mdp]: 69: NVE simulation with an initial temperature of zero: will use a Verlet 69: buffer of 10%. Check your energy drift! 69: 69: 69: There were 3 NOTEs 69: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_TabulatedAngleWorks.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 69: Can not increase nstlist because an NVE ensemble is used 69: Using 1 MPI thread 69: Using 2 OpenMP threads 69: 69: 69: NOTE: The number of threads is not equal to the number of (logical) cpus 69: and the -pin option is set to auto: will not pin threads to cpus. 69: This can lead to significant performance degradation. 69: Consider using -pin on (and -pinoffset in case you run multiple jobs). 69: starting md rerun 'A single butane', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/butane1.gro' 69: 69: Reading frames from gro file 'A single butane', 4 atoms. 69: Reading frame 0 time 0.000 Last frame 0 time 0.000 69: 69: Core t (s) Wall t (s) (%) 69: Time: 0.004 0.002 190.2 69: (ns/day) (hour/ns) 69: Performance: 45.452 0.528 69: Setting the LD random seed to -337657857 69: 69: Generated 3 of the 3 non-bonded parameter combinations 69: 69: Excluding 3 bonded neighbours molecule type 'butane' 69: 69: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/butane1.gro', all velocities are zero 69: 69: This run will generate roughly 0 Mb of data 69: [ OK ] BondedInteractionsTest.TabulatedAngleWorks (56 ms) 69: [ RUN ] BondedInteractionsTest.NormalDihedralWorks 69: 69: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_NormalDihedralWorks_input.mdp]: 69: For a correct single-point energy evaluation with nsteps = 0, use 69: continuation = yes to avoid constraining the input coordinates. 69: 69: 69: NOTE 2 [file BondedInteractionsTest_NormalDihedralWorks_butane1.top, line 31]: 69: In moleculetype 'butane' 4 atoms are not bound by a potential or 69: constraint to any other atom in the same moleculetype. Although 69: technically this might not cause issues in a simulation, this often means 69: that the user forgot to add a bond/potential/constraint or put multiple 69: molecules in the same moleculetype definition by mistake. Run with -v to 69: get information for each atom. 69: 69: Number of degrees of freedom in T-Coupling group rest is 9.00 69: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 69: 69: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_NormalDihedralWorks_input.mdp]: 69: NVE simulation with an initial temperature of zero: will use a Verlet 69: buffer of 10%. Check your energy drift! 69: 69: 69: There were 3 NOTEs 69: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_NormalDihedralWorks.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 69: Can not increase nstlist because an NVE ensemble is used 69: Using 1 MPI thread 69: Using 2 OpenMP threads 69: 69: 69: NOTE: The number of threads is not equal to the number of (logical) cpus 69: and the -pin option is set to auto: will not pin threads to cpus. 69: This can lead to significant performance degradation. 69: Consider using -pin on (and -pinoffset in case you run multiple jobs). 69: starting md rerun 'A single butane', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/butane1.gro' 69: 69: Reading frames from gro file 'A single butane', 4 atoms. 69: Reading frame 0 time 0.000 Last frame 0 time 0.000 69: 69: NOTE: 14 % of the run time was spent in pair search, 69: you might want to increase nstlist (this has no effect on accuracy) 69: 69: Core t (s) Wall t (s) (%) 69: Time: 0.002 0.001 185.5 69: (ns/day) (hour/ns) 69: Performance: 74.812 0.321 69: Setting the LD random seed to -1182795825 69: 69: Generated 3 of the 3 non-bonded parameter combinations 69: 69: Excluding 3 bonded neighbours molecule type 'butane' 69: 69: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/butane1.gro', all velocities are zero 69: 69: This run will generate roughly 0 Mb of data 69: [ OK ] BondedInteractionsTest.NormalDihedralWorks (39 ms) 69: [ RUN ] BondedInteractionsTest.TabulatedDihedralWorks 69: 69: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_TabulatedDihedralWorks_input.mdp]: 69: For a correct single-point energy evaluation with nsteps = 0, use 69: continuation = yes to avoid constraining the input coordinates. 69: 69: 69: NOTE 2 [file BondedInteractionsTest_TabulatedDihedralWorks_butane1.top, line 31]: 69: In moleculetype 'butane' 4 atoms are not bound by a potential or 69: constraint to any other atom in the same moleculetype. Although 69: technically this might not cause issues in a simulation, this often means 69: that the user forgot to add a bond/potential/constraint or put multiple 69: molecules in the same moleculetype definition by mistake. Run with -v to 69: get information for each atom. 69: 69: Number of degrees of freedom in T-Coupling group rest is 9.00 69: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 69: 69: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_TabulatedDihedralWorks_input.mdp]: 69: NVE simulation with an initial temperature of zero: will use a Verlet 69: buffer of 10%. Check your energy drift! 69: 69: 69: There were 3 NOTEs 69: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_TabulatedDihedralWorks.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 69: Can not increase nstlist because an NVE ensemble is used 69: Using 1 MPI thread 69: Using 2 OpenMP threads 69: 69: 69: NOTE: The number of threads is not equal to the number of (logical) cpus 69: and the -pin option is set to auto: will not pin threads to cpus. 69: This can lead to significant performance degradation. 69: Consider using -pin on (and -pinoffset in case you run multiple jobs). 69: starting md rerun 'A single butane', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/butane1.gro' 69: 69: Reading frames from gro file 'A single butane', 4 atoms. 69: Reading frame 0 time 0.000 Last frame 0 time 0.000 69: 69: NOTE: 14 % of the run time was spent in pair search, 69: you might want to increase nstlist (this has no effect on accuracy) 69: 69: Core t (s) Wall t (s) (%) 69: Time: 0.002 0.001 184.9 69: (ns/day) (hour/ns) 69: Performance: 79.401 0.302 69: Setting the LD random seed to -1630275585 69: 69: Generated 3 of the 3 non-bonded parameter combinations 69: 69: Excluding 3 bonded neighbours molecule type 'butane' 69: 69: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/butane1.gro', all velocities are zero 69: 69: This run will generate roughly 0 Mb of data 69: [ OK ] BondedInteractionsTest.TabulatedDihedralWorks (47 ms) 69: [----------] 6 tests from BondedInteractionsTest (273 ms total) 69: 69: [----------] 2 tests from BoxDeformationTest 69: [ RUN ] BoxDeformationTest.flowDoesNotAffectEkin 69: 69: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/BoxDeformationTest_flowDoesNotAffectEkin_input.mdp]: 69: verlet-buffer-pressure-tolerance is ignored when verlet-buffer-tolerance 69: < 0 69: 69: 69: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/BoxDeformationTest_flowDoesNotAffectEkin_input.mdp]: 69: Setting nstcalcenergy (100) equal to nstenergy (10) 69: 69: 69: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/BoxDeformationTest_flowDoesNotAffectEkin_input.mdp]: 69: For a correct single-point energy evaluation with nsteps = 0, use 69: continuation = yes to avoid constraining the input coordinates. 69: 69: Number of degrees of freedom in T-Coupling group rest is 33.00 69: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 69: 69: There were 3 NOTEs 69: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/BoxDeformationTest_flowDoesNotAffectEkin.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 69: Can not increase nstlist because an NVE ensemble is used 69: Using 1 MPI thread 69: Using 2 OpenMP threads 69: 69: 69: NOTE: The number of threads is not equal to the number of (logical) cpus 69: and the -pin option is set to auto: will not pin threads to cpus. 69: This can lead to significant performance degradation. 69: Consider using -pin on (and -pinoffset in case you run multiple jobs). 69: starting mdrun 'Argon' 69: 0 steps, 0.0 ps. 69: 69: NOTE: 19 % of the run time was spent in pair search, 69: you might want to increase nstlist (this has no effect on accuracy) 69: 69: Core t (s) Wall t (s) (%) 69: Time: 0.001 0.001 154.1 69: (ns/day) (hour/ns) 69: Performance: 198.406 0.121 69: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/BoxDeformationTest_flowDoesNotAffectEkin.edr as single precision energy file 69: Reading energy frame 0 time 0.000 Last energy frame read 0 time 0.000 Setting the LD random seed to -42264875 69: 69: Generated 1 of the 1 non-bonded parameter combinations 69: 69: Excluding 1 bonded neighbours molecule type 'Argon' 69: 69: Setting gen_seed to -907085832 69: 69: Velocities were taken from a Maxwell distribution at 0 K 69: 69: This run will generate roughly 0 Mb of data 69: [ OK ] BoxDeformationTest.flowDoesNotAffectEkin (46 ms) 69: [ RUN ] BoxDeformationTest.EnergiesWithinTolerances 69: 69: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/BoxDeformationTest_EnergiesWithinTolerances_input.mdp]: 69: verlet-buffer-pressure-tolerance is ignored when verlet-buffer-tolerance 69: < 0 69: 69: 69: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/BoxDeformationTest_EnergiesWithinTolerances_input.mdp]: 69: Setting nstcalcenergy (100) equal to nstenergy (10) 69: 69: Generating 1-4 interactions: fudge = 0.5 69: Number of degrees of freedom in T-Coupling group rest is 1293.00 69: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 69: 69: There were 2 NOTEs 69: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/BoxDeformationTest_EnergiesWithinTolerances.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 69: Can not increase nstlist because an NVE ensemble is used 69: Using 1 MPI thread 69: Using 2 OpenMP threads 69: 69: 69: NOTE: The number of threads is not equal to the number of (logical) cpus 69: and the -pin option is set to auto: will not pin threads to cpus. 69: This can lead to significant performance degradation. 69: Consider using -pin on (and -pinoffset in case you run multiple jobs). 69: starting mdrun 'spc2' 69: 20 steps, 0.0 ps. 69: Setting the LD random seed to -16934529 69: 69: Generated 330891 of the 330891 non-bonded parameter combinations 69: 69: Generated 330891 of the 330891 1-4 parameter combinations 69: 69: Excluding 2 bonded neighbours molecule type 'SOL' 69: 69: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/spc216.gro' 69: 69: The largest distance between excluded atoms is 0.152 nm between atom 41 and 42 69: Calculating fourier grid dimensions for X Y Z 69: Using a fourier grid of 16x16x16, spacing 0.116 0.116 0.116 69: 69: Estimate for the relative computational load of the PME mesh part: 0.09 69: 69: This run will generate roughly 0 Mb of data 69: 69: Writing final coordinates. 69: 69: Core t (s) Wall t (s) (%) 69: Time: 1.079 0.540 199.9 69: (ns/day) (hour/ns) 69: Performance: 6.723 3.570 69: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/BoxDeformationTest_EnergiesWithinTolerances.edr as single precision energy file 69: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.020 Reading energy frame 2 time 0.040 Last energy frame read 2 time 0.040 [ OK ] BoxDeformationTest.EnergiesWithinTolerances (4957 ms) 69: [----------] 2 tests from BoxDeformationTest (5004 ms total) 69: 69: [----------] 1 test from PositionRestraintCommTest 69: [ RUN ] PositionRestraintCommTest.PositionRestraintsTwoCOMs 69: 69: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PositionRestraintCommTest_PositionRestraintsTwoCOMs_input.mdp]: 69: You have set rlist larger than the interaction cut-off, but you also have 69: verlet-buffer-tolerance > 0. Will set rlist using 69: verlet-buffer-tolerance. 69: 69: 69: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PositionRestraintCommTest_PositionRestraintsTwoCOMs_input.mdp]: 69: Setting nstcalcenergy (100) equal to nstenergy (10) 69: 69: Generating 1-4 interactions: fudge = 0.5 69: 69: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PositionRestraintCommTest_PositionRestraintsTwoCOMs_input.mdp]: 69: 13489 atoms are not part of any of the VCM groups 69: 69: 69: WARNING 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PositionRestraintCommTest_PositionRestraintsTwoCOMs_input.mdp]: 69: 13489 atoms are not part of any center of mass motion removal group. 69: This may lead to artifacts. 69: In most cases one should use one group for the whole system. 69: 69: Number of degrees of freedom in T-Coupling group System is 29527.73 69: 69: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PositionRestraintCommTest_PositionRestraintsTwoCOMs_input.mdp]: 69: Removing center of mass motion in the presence of position restraints 69: might cause artifacts. When you are using position restraints to 69: equilibrate a macro-molecule, the artifacts are usually negligible. 69: 69: 69: There were 4 NOTEs 69: 69: There was 1 WARNING 69: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PositionRestraintCommTest_PositionRestraintsTwoCOMs.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 69: Changing nstlist from 10 to 20, rlist from 0.965 to 1.066 69: 69: Using 1 MPI thread 69: Using 2 OpenMP threads 69: 69: 69: NOTE: The number of threads is not equal to the number of (logical) cpus 69: and the -pin option is set to auto: will not pin threads to cpus. 69: This can lead to significant performance degradation. 69: Consider using -pin on (and -pinoffset in case you run multiple jobs). 69: starting mdrun 'Channel_coco in octane membrane' 69: 10 steps, 0.0 ps. 69: Setting the LD random seed to -608183080 69: 69: Generated 330891 of the 330891 non-bonded parameter combinations 69: 69: Generated 330891 of the 330891 1-4 parameter combinations 69: 69: Excluding 3 bonded neighbours molecule type 'Protein' 69: 69: Excluding 3 bonded neighbours molecule type 'OCT' 69: 69: Excluding 1 bonded neighbours molecule type 'NA' 69: 69: Excluding 1 bonded neighbours molecule type 'CL' 69: 69: Excluding 3 bonded neighbours molecule type 'Protein' 69: 69: Excluding 3 bonded neighbours molecule type 'OCT' 69: 69: Excluding 2 bonded neighbours molecule type 'SOL' 69: 69: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/OctaneSandwich.gro' 69: 69: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 69: 69: Calculated rlist for 1x1 atom pair-list as 0.990 nm, buffer size 0.090 nm 69: 69: Set rlist, assuming 4x4 atom pair-list, to 0.965 nm, buffer size 0.065 nm 69: 69: Note that mdrun will redetermine rlist based on the actual pair-list setup 69: 69: Chain0: 2.207 2.168 7.330 69: Chain1: 2.228 2.186 2.401 69: Chain0: 2.207 2.168 7.330 69: Chain1: 2.228 2.186 2.401 69: 69: This run will generate roughly 1 Mb of data 69: 69: Writing final coordinates. 69: 69: Core t (s) Wall t (s) (%) 69: Time: 6.823 3.412 200.0 69: (ns/day) (hour/ns) 69: Performance: 0.557 43.080 69: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PositionRestraintCommTest_PositionRestraintsTwoCOMs.edr as single precision energy file 69: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.020 Last energy frame read 1 time 0.020 [ OK ] PositionRestraintCommTest.PositionRestraintsTwoCOMs (8584 ms) 69: [----------] 1 test from PositionRestraintCommTest (8584 ms total) 69: 69: [----------] 2 tests from MultipleTimeSteppingIsNearSingleTimeStepping/MtsComparisonTest 69: [ RUN ] MultipleTimeSteppingIsNearSingleTimeStepping/MtsComparisonTest.WithinTolerances/0 69: 69: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_0_input.mdp]: 69: verlet-buffer-pressure-tolerance is ignored when verlet-buffer-tolerance 69: < 0 69: 69: Generating 1-4 interactions: fudge = 0.5 69: 69: NOTE 2 [file ala.top, line 256]: 69: For energy conservation with LINCS, lincs_iter should be 2 or larger. 69: 69: 69: Number of degrees of freedom in T-Coupling group rest is 54.00 69: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 69: 69: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_0_input.mdp]: 69: The optimal PME mesh load for parallel simulations is below 0.5 69: and for highly parallel simulations between 0.25 and 0.33, 69: for higher performance, increase the cut-off and the PME grid spacing. 69: 69: 69: 69: There were 3 NOTEs 69: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_0_sim.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 69: Can not increase nstlist because an NVE ensemble is used 69: Using 1 MPI thread 69: Using 2 OpenMP threads 69: 69: 69: NOTE: The number of threads is not equal to the number of (logical) cpus 69: and the -pin option is set to auto: will not pin threads to cpus. 69: This can lead to significant performance degradation. 69: Consider using -pin on (and -pinoffset in case you run multiple jobs). 69: starting mdrun 'UNNAMED in water' 69: 4 steps, 0.0 ps. 69: Setting the LD random seed to -34874373 69: 69: Generated 2211 of the 2211 non-bonded parameter combinations 69: 69: Generated 2211 of the 2211 1-4 parameter combinations 69: 69: Excluding 3 bonded neighbours molecule type 'Protein_chain_A' 69: 69: turning H bonds into constraints... 69: 69: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/ala.gro' 69: 69: The largest distance between excluded atoms is 0.384 nm between atom 5 and 15 69: Calculating fourier grid dimensions for X Y Z 69: Using a fourier grid of 24x24x24, spacing 0.104 0.104 0.104 69: 69: Estimate for the relative computational load of the PME mesh part: 0.93 69: 69: This run will generate roughly 0 Mb of data 69: 69: Writing final coordinates. 69: 69: Core t (s) Wall t (s) (%) 69: Time: 0.080 0.040 198.1 69: (ns/day) (hour/ns) 69: Performance: 10.682 2.247 69: 69: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_0_input.mdp]: 69: verlet-buffer-pressure-tolerance is ignored when verlet-buffer-tolerance 69: < 0 69: 69: Generating 1-4 interactions: fudge = 0.5 69: 69: NOTE 2 [file ala.top, line 256]: 69: For energy conservation with LINCS, lincs_iter should be 2 or larger. 69: 69: 69: Number of degrees of freedom in T-Coupling group rest is 54.00 69: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 69: 69: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_0_input.mdp]: 69: The optimal PME mesh load for parallel simulations is below 0.5 69: and for highly parallel simulations between 0.25 and 0.33, 69: for higher performance, increase the cut-off and the PME grid spacing. 69: 69: 69: 69: There were 3 NOTEs 69: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_0_sim.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 69: Can not increase nstlist because an NVE ensemble is used 69: Using 1 MPI thread 69: Using 2 OpenMP threads 69: 69: 69: NOTE: The number of threads is not equal to the number of (logical) cpus 69: and the -pin option is set to auto: will not pin threads to cpus. 69: This can lead to significant performance degradation. 69: Consider using -pin on (and -pinoffset in case you run multiple jobs). 69: starting mdrun 'UNNAMED in water' 69: 4 steps, 0.0 ps. 69: Setting the LD random seed to -2111832578 69: 69: Generated 2211 of the 2211 non-bonded parameter combinations 69: 69: Generated 2211 of the 2211 1-4 parameter combinations 69: 69: Excluding 3 bonded neighbours molecule type 'Protein_chain_A' 69: 69: turning H bonds into constraints... 69: 69: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/ala.gro' 69: 69: The largest distance between excluded atoms is 0.384 nm between atom 5 and 15 69: Calculating fourier grid dimensions for X Y Z 69: Using a fourier grid of 24x24x24, spacing 0.104 0.104 0.104 69: 69: Estimate for the relative computational load of the PME mesh part: 0.93 69: 69: This run will generate roughly 0 Mb of data 69: 69: Writing final coordinates. 69: 69: Core t (s) Wall t (s) (%) 69: Time: 0.077 0.039 198.0 69: (ns/day) (hour/ns) 69: Performance: 11.044 2.173 69: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_0_sim1.edr as single precision energy file 69: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_0_sim2.edr as single precision energy file 69: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Last energy frame read 1 time 0.004 Last energy frame read 1 time 0.004 trr version: GMX_trn_file (single precision) 69: 69: 69: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_0_sim1.edr as single precision energy file 69: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_0_sim2.edr as single precision energy file 69: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Last energy frame read 1 time 0.004 Last energy frame read 1 time 0.004 [ OK ] MultipleTimeSteppingIsNearSingleTimeStepping/MtsComparisonTest.WithinTolerances/0 (382 ms) 69: [ RUN ] MultipleTimeSteppingIsNearSingleTimeStepping/MtsComparisonTest.WithinTolerances/1 69: 69: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_1_input.mdp]: 69: verlet-buffer-pressure-tolerance is ignored when verlet-buffer-tolerance 69: < 0 69: 69: Generating 1-4 interactions: fudge = 0.5 69: 69: NOTE 2 [file ala.top, line 256]: 69: For energy conservation with LINCS, lincs_iter should be 2 or larger. 69: 69: 69: Number of degrees of freedom in T-Coupling group rest is 54.00 69: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 69: 69: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_1_input.mdp]: 69: The optimal PME mesh load for parallel simulations is below 0.5 69: and for highly parallel simulations between 0.25 and 0.33, 69: for higher performance, increase the cut-off and the PME grid spacing. 69: 69: 69: 69: There were 3 NOTEs 69: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_1_sim.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 69: Can not increase nstlist because an NVE ensemble is used 69: Using 1 MPI thread 69: Using 2 OpenMP threads 69: 69: 69: NOTE: The number of threads is not equal to the number of (logical) cpus 69: and the -pin option is set to auto: will not pin threads to cpus. 69: This can lead to significant performance degradation. 69: Consider using -pin on (and -pinoffset in case you run multiple jobs). 69: starting mdrun 'UNNAMED in water' 69: 4 steps, 0.0 ps. 69: Setting the LD random seed to -42210314 69: 69: Generated 2211 of the 2211 non-bonded parameter combinations 69: 69: Generated 2211 of the 2211 1-4 parameter combinations 69: 69: Excluding 3 bonded neighbours molecule type 'Protein_chain_A' 69: 69: turning H bonds into constraints... 69: 69: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/ala.gro' 69: 69: The largest distance between excluded atoms is 0.384 nm between atom 5 and 15 69: Calculating fourier grid dimensions for X Y Z 69: Using a fourier grid of 24x24x24, spacing 0.104 0.104 0.104 69: 69: Estimate for the relative computational load of the PME mesh part: 0.93 69: 69: This run will generate roughly 0 Mb of data 69: 69: Writing final coordinates. 69: 69: Core t (s) Wall t (s) (%) 69: Time: 0.070 0.035 198.0 69: (ns/day) (hour/ns) 69: Performance: 12.265 1.957 69: 69: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_1_input.mdp]: 69: verlet-buffer-pressure-tolerance is ignored when verlet-buffer-tolerance 69: < 0 69: 69: Generating 1-4 interactions: fudge = 0.5 69: 69: NOTE 2 [file ala.top, line 256]: 69: For energy conservation with LINCS, lincs_iter should be 2 or larger. 69: 69: 69: Number of degrees of freedom in T-Coupling group rest is 54.00 69: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 69: 69: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_1_input.mdp]: 69: The optimal PME mesh load for parallel simulations is below 0.5 69: and for highly parallel simulations between 0.25 and 0.33, 69: for higher performance, increase the cut-off and the PME grid spacing. 69: 69: 69: 69: There were 3 NOTEs 69: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_1_sim.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 69: Multiple time stepping is only supported with GPUs when MTS is only applied to longrange-nonbonded forces. 69: Can not increase nstlist because an NVE ensemble is used 69: 69: Using 1 MPI thread 69: Using 2 OpenMP threads 69: 69: 69: NOTE: The number of threads is not equal to the number of (logical) cpus 69: and the -pin option is set to auto: will not pin threads to cpus. 69: This can lead to significant performance degradation. 69: Consider using -pin on (and -pinoffset in case you run multiple jobs). 69: starting mdrun 'UNNAMED in water' 69: 4 steps, 0.0 ps. 69: Setting the LD random seed to 533200766 69: 69: Generated 2211 of the 2211 non-bonded parameter combinations 69: 69: Generated 2211 of the 2211 1-4 parameter combinations 69: 69: Excluding 3 bonded neighbours molecule type 'Protein_chain_A' 69: 69: turning H bonds into constraints... 69: 69: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/ala.gro' 69: 69: The largest distance between excluded atoms is 0.384 nm between atom 5 and 15 69: Calculating fourier grid dimensions for X Y Z 69: Using a fourier grid of 24x24x24, spacing 0.104 0.104 0.104 69: 69: Estimate for the relative computational load of the PME mesh part: 0.93 69: 69: This run will generate roughly 0 Mb of data 69: 69: Writing final coordinates. 69: 69: Core t (s) Wall t (s) (%) 69: Time: 0.075 0.038 197.3 69: (ns/day) (hour/ns) 69: Performance: 11.334 2.117 69: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_1_sim1.edr as single precision energy file 69: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_1_sim2.edr as single precision energy file 69: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Last energy frame read 1 time 0.004 Last energy frame read 1 time 0.004 69: 69: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_1_sim1.edr as single precision energy file 69: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_1_sim2.edr as single precision energy file 69: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Last energy frame read 1 time 0.004 Last energy frame read 1 time 0.004 [ OK ] MultipleTimeSteppingIsNearSingleTimeStepping/MtsComparisonTest.WithinTolerances/1 (329 ms) 69: [----------] 2 tests from MultipleTimeSteppingIsNearSingleTimeStepping/MtsComparisonTest (711 ms total) 69: 69: [----------] 1 test from MultipleTimeSteppingIsNearSingleTimeSteppingPull/MtsComparisonTest 69: [ RUN ] MultipleTimeSteppingIsNearSingleTimeSteppingPull/MtsComparisonTest.WithinTolerances/0 69: 69: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeSteppingPull_MtsComparisonTest_WithinTolerances_0_input.mdp]: 69: verlet-buffer-pressure-tolerance is ignored when verlet-buffer-tolerance 69: < 0 69: 69: Generating 1-4 interactions: fudge = 0.5 69: Pull group 1 'FirstWaterMolecule' has 3 atoms 69: Pull group 2 'SecondWaterMolecule' has 3 atoms 69: Number of degrees of freedom in T-Coupling group rest is 9.00 69: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 69: Pull group natoms pbc atom distance at start reference at t=0 69: 1 3 2 69: 2 3 5 1.112 nm 1.000 nm 69: 69: There was 1 NOTE 69: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeSteppingPull_MtsComparisonTest_WithinTolerances_0_sim.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 69: Can not increase nstlist because an NVE ensemble is used 69: Using 1 MPI thread 69: Using 2 OpenMP threads 69: 69: 69: NOTE: The number of threads is not equal to the number of (logical) cpus 69: and the -pin option is set to auto: will not pin threads to cpus. 69: This can lead to significant performance degradation. 69: Consider using -pin on (and -pinoffset in case you run multiple jobs). 69: starting mdrun 'spc2' 69: 4 steps, 0.0 ps. 69: Setting the LD random seed to 905936813 69: 69: Generated 3 of the 3 non-bonded parameter combinations 69: 69: Generated 3 of the 3 1-4 parameter combinations 69: 69: Excluding 2 bonded neighbours molecule type 'SOL' 69: 69: turning H bonds into constraints... 69: 69: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/spc2.gro' 69: 69: This run will generate roughly 0 Mb of data 69: 69: Writing final coordinates. 69: 69: Core t (s) Wall t (s) (%) 69: Time: 0.049 0.025 197.3 69: (ns/day) (hour/ns) 69: Performance: 17.570 1.366 69: 69: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeSteppingPull_MtsComparisonTest_WithinTolerances_0_input.mdp]: 69: verlet-buffer-pressure-tolerance is ignored when verlet-buffer-tolerance 69: < 0 69: 69: Generating 1-4 interactions: fudge = 0.5 69: Pull group 1 'FirstWaterMolecule' has 3 atoms 69: Pull group 2 'SecondWaterMolecule' has 3 atoms 69: Number of degrees of freedom in T-Coupling group rest is 9.00 69: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 69: Pull group natoms pbc atom distance at start reference at t=0 69: 1 3 2 69: 2 3 5 1.112 nm 1.000 nm 69: 69: There was 1 NOTE 69: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeSteppingPull_MtsComparisonTest_WithinTolerances_0_sim.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 69: Multiple time stepping is only supported with GPUs when MTS is only applied to longrange-nonbonded forces. 69: Can not increase nstlist because an NVE ensemble is used 69: 69: Using 1 MPI thread 69: Using 2 OpenMP threads 69: 69: 69: NOTE: The number of threads is not equal to the number of (logical) cpus 69: and the -pin option is set to auto: will not pin threads to cpus. 69: This can lead to significant performance degradation. 69: Consider using -pin on (and -pinoffset in case you run multiple jobs). 69: starting mdrun 'spc2' 69: 4 steps, 0.0 ps. 69: Setting the LD random seed to 1877989338 69: 69: Generated 3 of the 3 non-bonded parameter combinations 69: 69: Generated 3 of the 3 1-4 parameter combinations 69: 69: Excluding 2 bonded neighbours molecule type 'SOL' 69: 69: turning H bonds into constraints... 69: 69: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/spc2.gro' 69: 69: This run will generate roughly 0 Mb of data 69: 69: Writing final coordinates. 69: 69: Core t (s) Wall t (s) (%) 69: Time: 0.056 0.028 197.7 69: (ns/day) (hour/ns) 69: Performance: 15.248 1.574 69: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeSteppingPull_MtsComparisonTest_WithinTolerances_0_sim1.edr as single precision energy file 69: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeSteppingPull_MtsComparisonTest_WithinTolerances_0_sim2.edr as single precision energy file 69: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Last energy frame read 1 time 0.004 Last energy frame read 1 time 0.004 69: 69: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeSteppingPull_MtsComparisonTest_WithinTolerances_0_sim1.edr as single precision energy file 69: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeSteppingPull_MtsComparisonTest_WithinTolerances_0_sim2.edr as single precision energy file 69: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Last energy frame read 1 time 0.004 Last energy frame read 1 time 0.004 [ OK ] MultipleTimeSteppingIsNearSingleTimeSteppingPull/MtsComparisonTest.WithinTolerances/0 (161 ms) 69: [----------] 1 test from MultipleTimeSteppingIsNearSingleTimeSteppingPull/MtsComparisonTest (161 ms total) 69: 69: [----------] 12 tests from FreezeWorks/FreezeGroupTest 69: [ RUN ] FreezeWorks/FreezeGroupTest.WithinTolerances/0 69: 69: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_0_input.mdp]: 69: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 69: that with the Verlet scheme, nstlist has no effect on the accuracy of 69: your simulation. 69: 69: 69: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_0_input.mdp]: 69: Setting nstcalcenergy (100) equal to nstenergy (4) 69: 69: Generating 1-4 interactions: fudge = 0.5 69: 69: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_0_input.mdp]: 69: There are 5 atoms that are fully frozen and part of COMM removal 69: group(s), removing these atoms from the COMM removal group(s) 69: 69: 69: WARNING 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_0_input.mdp]: 69: There are 3 atoms that are frozen along less then 3 dimensions and part 69: of COMM removal group(s), due to limitations in the code these still 69: contribute to the mass of the COM along frozen dimensions and therefore 69: the COMM correction will be too small. 69: 69: Number of degrees of freedom in T-Coupling group System is 33.00 69: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 69: 69: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_0_input.mdp]: 69: NVE simulation: will use the initial temperature of 246.451 K for 69: determining the Verlet buffer size 69: 69: 69: NOTE 5 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_0_input.mdp]: 69: You are using a plain Coulomb cut-off, which might produce artifacts. 69: You might want to consider using PME electrostatics. 69: 69: 69: 69: There were 5 NOTEs 69: 69: There was 1 WARNING 69: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_0.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 69: Can not increase nstlist because an NVE ensemble is used 69: Using 1 MPI thread 69: Using 2 OpenMP threads 69: 69: 69: NOTE: The number of threads is not equal to the number of (logical) cpus 69: and the -pin option is set to auto: will not pin threads to cpus. 69: This can lead to significant performance degradation. 69: Consider using -pin on (and -pinoffset in case you run multiple jobs). 69: starting mdrun 'Alanine-dipeptide' 69: 8 steps, 0.0 ps. 69: Generated 2145 of the 2145 non-bonded parameter combinations 69: 69: Generated 2145 of the 2145 1-4 parameter combinations 69: 69: Excluding 3 bonded neighbours molecule type 'ALANINEDIPEPTIDE' 69: 69: turning H bonds into constraints... 69: 69: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/alanine_vacuo.gro' 69: 69: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 246.451 K 69: 69: Calculated rlist for 1x1 atom pair-list as 0.755 nm, buffer size 0.055 nm 69: 69: Set rlist, assuming 4x4 atom pair-list, to 0.749 nm, buffer size 0.049 nm 69: 69: Note that mdrun will redetermine rlist based on the actual pair-list setup 69: 69: This run will generate roughly 0 Mb of data 69: 69: Writing final coordinates. 69: 69: Core t (s) Wall t (s) (%) 69: Time: 0.053 0.027 197.0 69: (ns/day) (hour/ns) 69: Performance: 29.065 0.826 69: 69: 69: [ OK ] FreezeWorks/FreezeGroupTest.WithinTolerances/0 (134 ms) 69: [ RUN ] FreezeWorks/FreezeGroupTest.WithinTolerances/1 69: 69: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_1_input.mdp]: 69: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 69: that with the Verlet scheme, nstlist has no effect on the accuracy of 69: your simulation. 69: 69: 69: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_1_input.mdp]: 69: Setting nstcalcenergy (100) equal to nstenergy (4) 69: 69: Generating 1-4 interactions: fudge = 0.5 69: 69: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_1_input.mdp]: 69: There are 5 atoms that are fully frozen and part of COMM removal 69: group(s), removing these atoms from the COMM removal group(s) 69: 69: 69: WARNING 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_1_input.mdp]: 69: There are 3 atoms that are frozen along less then 3 dimensions and part 69: of COMM removal group(s), due to limitations in the code these still 69: contribute to the mass of the COM along frozen dimensions and therefore 69: the COMM correction will be too small. 69: 69: Number of degrees of freedom in T-Coupling group System is 33.00 69: 69: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_1_input.mdp]: 69: NVE simulation: will use the initial temperature of 246.451 K for 69: determining the Verlet buffer size 69: 69: 69: NOTE 5 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_1_input.mdp]: 69: You are using a plain Coulomb cut-off, which might produce artifacts. 69: You might want to consider using PME electrostatics. 69: 69: 69: 69: There were 5 NOTEs 69: 69: There was 1 WARNING 69: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_1.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 69: Can not increase nstlist because an NVE ensemble is used 69: Using 1 MPI thread 69: Using 2 OpenMP threads 69: 69: 69: NOTE: The number of threads is not equal to the number of (logical) cpus 69: and the -pin option is set to auto: will not pin threads to cpus. 69: This can lead to significant performance degradation. 69: Consider using -pin on (and -pinoffset in case you run multiple jobs). 69: starting mdrun 'Alanine-dipeptide' 69: 8 steps, 0.0 ps. 69: Generated 2145 of the 2145 non-bonded parameter combinations 69: 69: Generated 2145 of the 2145 1-4 parameter combinations 69: 69: Excluding 3 bonded neighbours molecule type 'ALANINEDIPEPTIDE' 69: 69: turning H bonds into constraints... 69: 69: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/alanine_vacuo.gro' 69: 69: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 246.451 K 69: 69: Calculated rlist for 1x1 atom pair-list as 0.755 nm, buffer size 0.055 nm 69: 69: Set rlist, assuming 4x4 atom pair-list, to 0.749 nm, buffer size 0.049 nm 69: 69: Note that mdrun will redetermine rlist based on the actual pair-list setup 69: 69: This run will generate roughly 0 Mb of data 69: 69: Writing final coordinates. 69: 69: Core t (s) Wall t (s) (%) 69: Time: 0.042 0.021 196.9 69: (ns/day) (hour/ns) 69: Performance: 36.815 0.652 69: 69: 69: [ OK ] FreezeWorks/FreezeGroupTest.WithinTolerances/1 (132 ms) 69: [ RUN ] FreezeWorks/FreezeGroupTest.WithinTolerances/2 69: 69: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_2_input.mdp]: 69: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 69: that with the Verlet scheme, nstlist has no effect on the accuracy of 69: your simulation. 69: 69: 69: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_2_input.mdp]: 69: Setting nstcalcenergy (100) equal to nstenergy (4) 69: 69: Generating 1-4 interactions: fudge = 0.5 69: 69: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_2_input.mdp]: 69: There are 5 atoms that are fully frozen and part of COMM removal 69: group(s), removing these atoms from the COMM removal group(s) 69: 69: 69: WARNING 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_2_input.mdp]: 69: There are 3 atoms that are frozen along less then 3 dimensions and part 69: of COMM removal group(s), due to limitations in the code these still 69: contribute to the mass of the COM along frozen dimensions and therefore 69: the COMM correction will be too small. 69: 69: Number of degrees of freedom in T-Coupling group System is 33.00 69: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 69: 69: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_2_input.mdp]: 69: NVE simulation: will use the initial temperature of 246.451 K for 69: determining the Verlet buffer size 69: 69: 69: NOTE 5 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_2_input.mdp]: 69: You are using a plain Coulomb cut-off, which might produce artifacts. 69: You might want to consider using PME electrostatics. 69: 69: 69: 69: There were 5 NOTEs 69: 69: There was 1 WARNING 69: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_2.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 69: Can not increase nstlist because an NVE ensemble is used 69: Using 1 MPI thread 69: Using 2 OpenMP threads 69: 69: 69: NOTE: The number of threads is not equal to the number of (logical) cpus 69: and the -pin option is set to auto: will not pin threads to cpus. 69: This can lead to significant performance degradation. 69: Consider using -pin on (and -pinoffset in case you run multiple jobs). 69: starting mdrun 'Alanine-dipeptide' 69: 8 steps, 0.0 ps. 69: Generated 2145 of the 2145 non-bonded parameter combinations 69: 69: Generated 2145 of the 2145 1-4 parameter combinations 69: 69: Excluding 3 bonded neighbours molecule type 'ALANINEDIPEPTIDE' 69: 69: turning H bonds into constraints... 69: 69: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/alanine_vacuo.gro' 69: 69: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 246.451 K 69: 69: Calculated rlist for 1x1 atom pair-list as 0.755 nm, buffer size 0.055 nm 69: 69: Set rlist, assuming 4x4 atom pair-list, to 0.749 nm, buffer size 0.049 nm 69: 69: Note that mdrun will redetermine rlist based on the actual pair-list setup 69: 69: This run will generate roughly 0 Mb of data 69: 69: Writing final coordinates. 69: 69: Core t (s) Wall t (s) (%) 69: Time: 0.064 0.032 198.1 69: (ns/day) (hour/ns) 69: Performance: 24.175 0.993 69: 69: 69: [ OK ] FreezeWorks/FreezeGroupTest.WithinTolerances/2 (182 ms) 69: [ RUN ] FreezeWorks/FreezeGroupTest.WithinTolerances/3 69: 69: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_3_input.mdp]: 69: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 69: that with the Verlet scheme, nstlist has no effect on the accuracy of 69: your simulation. 69: 69: 69: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_3_input.mdp]: 69: Setting nstcalcenergy (100) equal to nstenergy (4) 69: 69: Generating 1-4 interactions: fudge = 0.5 69: 69: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_3_input.mdp]: 69: There are 5 atoms that are fully frozen and part of COMM removal 69: group(s), removing these atoms from the COMM removal group(s) 69: 69: 69: WARNING 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_3_input.mdp]: 69: There are 3 atoms that are frozen along less then 3 dimensions and part 69: of COMM removal group(s), due to limitations in the code these still 69: contribute to the mass of the COM along frozen dimensions and therefore 69: the COMM correction will be too small. 69: 69: Number of degrees of freedom in T-Coupling group System is 33.00 69: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 69: 69: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_3_input.mdp]: 69: NVE simulation: will use the initial temperature of 246.451 K for 69: determining the Verlet buffer size 69: 69: 69: NOTE 5 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_3_input.mdp]: 69: You are using a plain Coulomb cut-off, which might produce artifacts. 69: You might want to consider using PME electrostatics. 69: 69: 69: 69: There were 5 NOTEs 69: 69: There was 1 WARNING 69: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_3.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 69: Can not increase nstlist because an NVE ensemble is used 69: Using 1 MPI thread 69: Using 2 OpenMP threads 69: 69: 69: NOTE: The number of threads is not equal to the number of (logical) cpus 69: and the -pin option is set to auto: will not pin threads to cpus. 69: This can lead to significant performance degradation. 69: Consider using -pin on (and -pinoffset in case you run multiple jobs). 69: starting mdrun 'Alanine-dipeptide' 69: 8 steps, 0.0 ps. 69: Generated 2145 of the 2145 non-bonded parameter combinations 69: 69: Generated 2145 of the 2145 1-4 parameter combinations 69: 69: Excluding 3 bonded neighbours molecule type 'ALANINEDIPEPTIDE' 69: 69: turning H bonds into constraints... 69: 69: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/alanine_vacuo.gro' 69: 69: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 246.451 K 69: 69: Calculated rlist for 1x1 atom pair-list as 0.755 nm, buffer size 0.055 nm 69: 69: Set rlist, assuming 4x4 atom pair-list, to 0.749 nm, buffer size 0.049 nm 69: 69: Note that mdrun will redetermine rlist based on the actual pair-list setup 69: 69: This run will generate roughly 0 Mb of data 69: 69: Writing final coordinates. 69: 69: Core t (s) Wall t (s) (%) 69: Time: 0.042 0.021 197.5 69: (ns/day) (hour/ns) 69: Performance: 36.178 0.663 69: 69: 69: [ OK ] FreezeWorks/FreezeGroupTest.WithinTolerances/3 (146 ms) 69: [ RUN ] FreezeWorks/FreezeGroupTest.WithinTolerances/4 69: 69: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_4_input.mdp]: 69: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 69: that with the Verlet scheme, nstlist has no effect on the accuracy of 69: your simulation. 69: 69: 69: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_4_input.mdp]: 69: Setting nstcalcenergy (100) equal to nstenergy (4) 69: 69: Generating 1-4 interactions: fudge = 0.5 69: 69: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_4_input.mdp]: 69: There are 5 atoms that are fully frozen and part of COMM removal 69: group(s), removing these atoms from the COMM removal group(s) 69: 69: 69: WARNING 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_4_input.mdp]: 69: There are 3 atoms that are frozen along less then 3 dimensions and part 69: of COMM removal group(s), due to limitations in the code these still 69: contribute to the mass of the COM along frozen dimensions and therefore 69: the COMM correction will be too small. 69: 69: Number of degrees of freedom in T-Coupling group System is 33.00 69: 69: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_4_input.mdp]: 69: NVE simulation: will use the initial temperature of 246.451 K for 69: determining the Verlet buffer size 69: 69: 69: NOTE 5 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_4_input.mdp]: 69: You are using a plain Coulomb cut-off, which might produce artifacts. 69: You might want to consider using PME electrostatics. 69: 69: 69: 69: There were 5 NOTEs 69: 69: There was 1 WARNING 69: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_4.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 69: Can not increase nstlist because an NVE ensemble is used 69: Using 1 MPI thread 69: Using 2 OpenMP threads 69: 69: 69: NOTE: The number of threads is not equal to the number of (logical) cpus 69: and the -pin option is set to auto: will not pin threads to cpus. 69: This can lead to significant performance degradation. 69: Consider using -pin on (and -pinoffset in case you run multiple jobs). 69: starting mdrun 'Alanine-dipeptide' 69: 8 steps, 0.0 ps. 69: Generated 2145 of the 2145 non-bonded parameter combinations 69: 69: Generated 2145 of the 2145 1-4 parameter combinations 69: 69: Excluding 3 bonded neighbours molecule type 'ALANINEDIPEPTIDE' 69: 69: turning H bonds into constraints... 69: 69: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/alanine_vacuo.gro' 69: 69: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 246.451 K 69: 69: Calculated rlist for 1x1 atom pair-list as 0.755 nm, buffer size 0.055 nm 69: 69: Set rlist, assuming 4x4 atom pair-list, to 0.749 nm, buffer size 0.049 nm 69: 69: Note that mdrun will redetermine rlist based on the actual pair-list setup 69: 69: This run will generate roughly 0 Mb of data 69: 69: Writing final coordinates. 69: 69: Core t (s) Wall t (s) (%) 69: Time: 0.048 0.024 197.4 69: (ns/day) (hour/ns) 69: Performance: 31.987 0.750 69: 69: 69: [ OK ] FreezeWorks/FreezeGroupTest.WithinTolerances/4 (123 ms) 69: [ RUN ] FreezeWorks/FreezeGroupTest.WithinTolerances/5 69: ./src/programs/mdrun/tests/freezegroups.cpp:209: Skipped 69: Parrinello-Rahman is not implemented in md-vv. 69: [ SKIPPED ] FreezeWorks/FreezeGroupTest.WithinTolerances/5 (0 ms) 69: [ RUN ] FreezeWorks/FreezeGroupTest.WithinTolerances/6 69: 69: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_6_input.mdp]: 69: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 69: that with the Verlet scheme, nstlist has no effect on the accuracy of 69: your simulation. 69: 69: 69: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_6_input.mdp]: 69: Setting nstcalcenergy (100) equal to nstenergy (4) 69: 69: Generating 1-4 interactions: fudge = 0.5 69: 69: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_6_input.mdp]: 69: There are 5 atoms that are fully frozen and part of COMM removal 69: group(s), removing these atoms from the COMM removal group(s) 69: 69: 69: WARNING 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_6_input.mdp]: 69: There are 3 atoms that are frozen along less then 3 dimensions and part 69: of COMM removal group(s), due to limitations in the code these still 69: contribute to the mass of the COM along frozen dimensions and therefore 69: the COMM correction will be too small. 69: 69: Number of degrees of freedom in T-Coupling group System is 33.00 69: 69: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_6_input.mdp]: 69: You are using a plain Coulomb cut-off, which might produce artifacts. 69: You might want to consider using PME electrostatics. 69: 69: 69: 69: There were 4 NOTEs 69: 69: There was 1 WARNING 69: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_6.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 69: Changing nstlist from 8 to 20, rlist from 0.754 to 0.856 69: 69: Using 1 MPI thread 69: Using 2 OpenMP threads 69: 69: 69: NOTE: The number of threads is not equal to the number of (logical) cpus 69: and the -pin option is set to auto: will not pin threads to cpus. 69: This can lead to significant performance degradation. 69: Consider using -pin on (and -pinoffset in case you run multiple jobs). 69: starting mdrun 'Alanine-dipeptide' 69: 8 steps, 0.0 ps. 69: Generated 2145 of the 2145 non-bonded parameter combinations 69: 69: Generated 2145 of the 2145 1-4 parameter combinations 69: 69: Excluding 3 bonded neighbours molecule type 'ALANINEDIPEPTIDE' 69: 69: turning H bonds into constraints... 69: 69: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/alanine_vacuo.gro' 69: 69: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 69: 69: Calculated rlist for 1x1 atom pair-list as 0.761 nm, buffer size 0.061 nm 69: 69: Set rlist, assuming 4x4 atom pair-list, to 0.754 nm, buffer size 0.054 nm 69: 69: Note that mdrun will redetermine rlist based on the actual pair-list setup 69: 69: This run will generate roughly 0 Mb of data 69: 69: Writing final coordinates. 69: 69: Core t (s) Wall t (s) (%) 69: Time: 0.040 0.020 197.3 69: (ns/day) (hour/ns) 69: Performance: 38.468 0.624 69: 69: 69: [ OK ] FreezeWorks/FreezeGroupTest.WithinTolerances/6 (154 ms) 69: [ RUN ] FreezeWorks/FreezeGroupTest.WithinTolerances/7 69: 69: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_7_input.mdp]: 69: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 69: that with the Verlet scheme, nstlist has no effect on the accuracy of 69: your simulation. 69: 69: 69: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_7_input.mdp]: 69: Setting nstcalcenergy (100) equal to nstenergy (4) 69: 69: Generating 1-4 interactions: fudge = 0.5 69: 69: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_7_input.mdp]: 69: There are 5 atoms that are fully frozen and part of COMM removal 69: group(s), removing these atoms from the COMM removal group(s) 69: 69: 69: WARNING 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_7_input.mdp]: 69: There are 3 atoms that are frozen along less then 3 dimensions and part 69: of COMM removal group(s), due to limitations in the code these still 69: contribute to the mass of the COM along frozen dimensions and therefore 69: the COMM correction will be too small. 69: 69: Number of degrees of freedom in T-Coupling group System is 33.00 69: 69: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_7_input.mdp]: 69: You are using a plain Coulomb cut-off, which might produce artifacts. 69: You might want to consider using PME electrostatics. 69: 69: 69: 69: There were 4 NOTEs 69: 69: There was 1 WARNING 69: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_7.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 69: Changing nstlist from 8 to 20, rlist from 0.754 to 0.856 69: 69: Using 1 MPI thread 69: Using 2 OpenMP threads 69: 69: 69: NOTE: The number of threads is not equal to the number of (logical) cpus 69: and the -pin option is set to auto: will not pin threads to cpus. 69: This can lead to significant performance degradation. 69: Consider using -pin on (and -pinoffset in case you run multiple jobs). 69: starting mdrun 'Alanine-dipeptide' 69: 8 steps, 0.0 ps. 69: Generated 2145 of the 2145 non-bonded parameter combinations 69: 69: Generated 2145 of the 2145 1-4 parameter combinations 69: 69: Excluding 3 bonded neighbours molecule type 'ALANINEDIPEPTIDE' 69: 69: turning H bonds into constraints... 69: 69: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/alanine_vacuo.gro' 69: 69: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 69: 69: Calculated rlist for 1x1 atom pair-list as 0.761 nm, buffer size 0.061 nm 69: 69: Set rlist, assuming 4x4 atom pair-list, to 0.754 nm, buffer size 0.054 nm 69: 69: Note that mdrun will redetermine rlist based on the actual pair-list setup 69: 69: This run will generate roughly 0 Mb of data 69: 69: Writing final coordinates. 69: 69: Core t (s) Wall t (s) (%) 69: Time: 0.044 0.022 197.4 69: (ns/day) (hour/ns) 69: Performance: 35.259 0.681 69: 69: 69: [ OK ] FreezeWorks/FreezeGroupTest.WithinTolerances/7 (155 ms) 69: [ RUN ] FreezeWorks/FreezeGroupTest.WithinTolerances/8 69: 69: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_8_input.mdp]: 69: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 69: that with the Verlet scheme, nstlist has no effect on the accuracy of 69: your simulation. 69: 69: 69: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_8_input.mdp]: 69: Setting nstcalcenergy (100) equal to nstenergy (4) 69: 69: Generating 1-4 interactions: fudge = 0.5 69: 69: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_8_input.mdp]: 69: There are 5 atoms that are fully frozen and part of COMM removal 69: group(s), removing these atoms from the COMM removal group(s) 69: 69: 69: WARNING 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_8_input.mdp]: 69: There are 3 atoms that are frozen along less then 3 dimensions and part 69: of COMM removal group(s), due to limitations in the code these still 69: contribute to the mass of the COM along frozen dimensions and therefore 69: the COMM correction will be too small. 69: 69: Number of degrees of freedom in T-Coupling group System is 33.00 69: 69: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_8_input.mdp]: 69: You are using a plain Coulomb cut-off, which might produce artifacts. 69: You might want to consider using PME electrostatics. 69: 69: 69: 69: There were 4 NOTEs 69: 69: There was 1 WARNING 69: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_8.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 69: Changing nstlist from 8 to 20, rlist from 0.754 to 0.856 69: 69: Using 1 MPI thread 69: Using 2 OpenMP threads 69: 69: 69: NOTE: The number of threads is not equal to the number of (logical) cpus 69: and the -pin option is set to auto: will not pin threads to cpus. 69: This can lead to significant performance degradation. 69: Consider using -pin on (and -pinoffset in case you run multiple jobs). 69: starting mdrun 'Alanine-dipeptide' 69: 8 steps, 0.0 ps. 69: Generated 2145 of the 2145 non-bonded parameter combinations 69: 69: Generated 2145 of the 2145 1-4 parameter combinations 69: 69: Excluding 3 bonded neighbours molecule type 'ALANINEDIPEPTIDE' 69: 69: turning H bonds into constraints... 69: 69: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/alanine_vacuo.gro' 69: 69: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 69: 69: Calculated rlist for 1x1 atom pair-list as 0.761 nm, buffer size 0.061 nm 69: 69: Set rlist, assuming 4x4 atom pair-list, to 0.754 nm, buffer size 0.054 nm 69: 69: Note that mdrun will redetermine rlist based on the actual pair-list setup 69: 69: This run will generate roughly 0 Mb of data 69: 69: Writing final coordinates. 69: 69: Core t (s) Wall t (s) (%) 69: Time: 0.052 0.026 197.7 69: (ns/day) (hour/ns) 69: Performance: 29.391 0.817 69: 69: 69: [ OK ] FreezeWorks/FreezeGroupTest.WithinTolerances/8 (160 ms) 69: [ RUN ] FreezeWorks/FreezeGroupTest.WithinTolerances/9 69: 69: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_9_input.mdp]: 69: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 69: that with the Verlet scheme, nstlist has no effect on the accuracy of 69: your simulation. 69: 69: 69: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_9_input.mdp]: 69: Setting nstcalcenergy (100) equal to nstenergy (4) 69: 69: Generating 1-4 interactions: fudge = 0.5 69: 69: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_9_input.mdp]: 69: There are 5 atoms that are fully frozen and part of COMM removal 69: group(s), removing these atoms from the COMM removal group(s) 69: 69: 69: WARNING 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_9_input.mdp]: 69: There are 3 atoms that are frozen along less then 3 dimensions and part 69: of COMM removal group(s), due to limitations in the code these still 69: contribute to the mass of the COM along frozen dimensions and therefore 69: the COMM correction will be too small. 69: 69: Number of degrees of freedom in T-Coupling group System is 33.00 69: 69: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_9_input.mdp]: 69: You are using a plain Coulomb cut-off, which might produce artifacts. 69: You might want to consider using PME electrostatics. 69: 69: 69: 69: There were 4 NOTEs 69: 69: There was 1 WARNING 69: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_9.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 69: Changing nstlist from 8 to 100, rlist from 0.734 to 0.829 69: 69: Using 1 MPI thread 69: Using 2 OpenMP threads 69: 69: 69: NOTE: The number of threads is not equal to the number of (logical) cpus 69: and the -pin option is set to auto: will not pin threads to cpus. 69: This can lead to significant performance degradation. 69: Consider using -pin on (and -pinoffset in case you run multiple jobs). 69: starting mdrun 'Alanine-dipeptide' 69: 8 steps, 0.0 ps. 69: Generated 2145 of the 2145 non-bonded parameter combinations 69: 69: Generated 2145 of the 2145 1-4 parameter combinations 69: 69: Excluding 3 bonded neighbours molecule type 'ALANINEDIPEPTIDE' 69: 69: turning H bonds into constraints... 69: 69: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 69: 69: Calculated rlist for 1x1 atom pair-list as 0.737 nm, buffer size 0.037 nm 69: 69: Set rlist, assuming 4x4 atom pair-list, to 0.734 nm, buffer size 0.034 nm 69: 69: Note that mdrun will redetermine rlist based on the actual pair-list setup 69: 69: This run will generate roughly 0 Mb of data 69: 69: Writing final coordinates. 69: 69: Core t (s) Wall t (s) (%) 69: Time: 0.056 0.028 198.0 69: (ns/day) (hour/ns) 69: Performance: 27.502 0.873 69: 69: 69: [ OK ] FreezeWorks/FreezeGroupTest.WithinTolerances/9 (360 ms) 69: [ RUN ] FreezeWorks/FreezeGroupTest.WithinTolerances/10 69: 69: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_10_input.mdp]: 69: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 69: that with the Verlet scheme, nstlist has no effect on the accuracy of 69: your simulation. 69: 69: 69: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_10_input.mdp]: 69: Setting nstcalcenergy (100) equal to nstenergy (4) 69: 69: Generating 1-4 interactions: fudge = 0.5 69: 69: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_10_input.mdp]: 69: There are 5 atoms that are fully frozen and part of COMM removal 69: group(s), removing these atoms from the COMM removal group(s) 69: 69: 69: WARNING 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_10_input.mdp]: 69: There are 3 atoms that are frozen along less then 3 dimensions and part 69: of COMM removal group(s), due to limitations in the code these still 69: contribute to the mass of the COM along frozen dimensions and therefore 69: the COMM correction will be too small. 69: 69: Number of degrees of freedom in T-Coupling group System is 33.00 69: 69: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_10_input.mdp]: 69: You are using a plain Coulomb cut-off, which might produce artifacts. 69: You might want to consider using PME electrostatics. 69: 69: 69: 69: There were 4 NOTEs 69: 69: There was 1 WARNING 69: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_10.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 69: Changing nstlist from 8 to 100, rlist from 0.734 to 0.829 69: 69: Using 1 MPI thread 69: Using 2 OpenMP threads 69: 69: 69: NOTE: The number of threads is not equal to the number of (logical) cpus 69: and the -pin option is set to auto: will not pin threads to cpus. 69: This can lead to significant performance degradation. 69: Consider using -pin on (and -pinoffset in case you run multiple jobs). 69: starting mdrun 'Alanine-dipeptide' 69: 8 steps, 0.0 ps. 69: Generated 2145 of the 2145 non-bonded parameter combinations 69: 69: Generated 2145 of the 2145 1-4 parameter combinations 69: 69: Excluding 3 bonded neighbours molecule type 'ALANINEDIPEPTIDE' 69: 69: turning H bonds into constraints... 69: 69: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 69: 69: Calculated rlist for 1x1 atom pair-list as 0.737 nm, buffer size 0.037 nm 69: 69: Set rlist, assuming 4x4 atom pair-list, to 0.734 nm, buffer size 0.034 nm 69: 69: Note that mdrun will redetermine rlist based on the actual pair-list setup 69: 69: This run will generate roughly 0 Mb of data 69: 69: Writing final coordinates. 69: 69: Core t (s) Wall t (s) (%) 69: Time: 0.038 0.019 197.3 69: (ns/day) (hour/ns) 69: Performance: 40.336 0.595 69: 69: 69: [ OK ] FreezeWorks/FreezeGroupTest.WithinTolerances/10 (354 ms) 69: [ RUN ] FreezeWorks/FreezeGroupTest.WithinTolerances/11 69: 69: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_11_input.mdp]: 69: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 69: that with the Verlet scheme, nstlist has no effect on the accuracy of 69: your simulation. 69: 69: 69: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_11_input.mdp]: 69: Setting nstcalcenergy (100) equal to nstenergy (4) 69: 69: Generating 1-4 interactions: fudge = 0.5 69: 69: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_11_input.mdp]: 69: There are 5 atoms that are fully frozen and part of COMM removal 69: group(s), removing these atoms from the COMM removal group(s) 69: 69: 69: WARNING 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_11_input.mdp]: 69: There are 3 atoms that are frozen along less then 3 dimensions and part 69: of COMM removal group(s), due to limitations in the code these still 69: contribute to the mass of the COM along frozen dimensions and therefore 69: the COMM correction will be too small. 69: 69: Number of degrees of freedom in T-Coupling group System is 33.00 69: 69: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_11_input.mdp]: 69: You are using a plain Coulomb cut-off, which might produce artifacts. 69: You might want to consider using PME electrostatics. 69: 69: 69: 69: There were 4 NOTEs 69: 69: There was 1 WARNING 69: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_11.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 69: Changing nstlist from 8 to 100, rlist from 0.734 to 0.829 69: 69: Using 1 MPI thread 69: Using 2 OpenMP threads 69: 69: 69: NOTE: The number of threads is not equal to the number of (logical) cpus 69: and the -pin option is set to auto: will not pin threads to cpus. 69: This can lead to significant performance degradation. 69: Consider using -pin on (and -pinoffset in case you run multiple jobs). 69: starting mdrun 'Alanine-dipeptide' 69: 8 steps, 0.0 ps. 69: Generated 2145 of the 2145 non-bonded parameter combinations 69: 69: Generated 2145 of the 2145 1-4 parameter combinations 69: 69: Excluding 3 bonded neighbours molecule type 'ALANINEDIPEPTIDE' 69: 69: turning H bonds into constraints... 69: 69: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 69: 69: Calculated rlist for 1x1 atom pair-list as 0.737 nm, buffer size 0.037 nm 69: 69: Set rlist, assuming 4x4 atom pair-list, to 0.734 nm, buffer size 0.034 nm 69: 69: Note that mdrun will redetermine rlist based on the actual pair-list setup 69: 69: This run will generate roughly 0 Mb of data 69: 69: Writing final coordinates. 69: 69: Core t (s) Wall t (s) (%) 69: Time: 0.045 0.023 197.6 69: (ns/day) (hour/ns) 69: Performance: 34.479 0.696 69: 69: 69: [ OK ] FreezeWorks/FreezeGroupTest.WithinTolerances/11 (354 ms) 69: [----------] 12 tests from FreezeWorks/FreezeGroupTest (2260 ms total) 69: 69: [----------] 4 tests from AccelerationWorks/AccelerationGroupTest 69: [ RUN ] AccelerationWorks/AccelerationGroupTest.WithinTolerances/0 69: 69: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/AccelerationWorks_AccelerationGroupTest_WithinTolerances_0_input.mdp]: 69: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 69: that with the Verlet scheme, nstlist has no effect on the accuracy of 69: your simulation. 69: 69: 69: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/AccelerationWorks_AccelerationGroupTest_WithinTolerances_0_input.mdp]: 69: verlet-buffer-pressure-tolerance is ignored when verlet-buffer-tolerance 69: < 0 69: 69: 69: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/AccelerationWorks_AccelerationGroupTest_WithinTolerances_0_input.mdp]: 69: Setting nstcalcenergy (100) equal to nstenergy (4) 69: 69: Generating 1-4 interactions: fudge = 0.5 69: Number of degrees of freedom in T-Coupling group FirstWaterMolecule is 6.00 69: Number of degrees of freedom in T-Coupling group SecondWaterMolecule is 6.00 69: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 69: Net Acceleration in X direction, will not be corrected 69: Net Acceleration in Y direction, will not be corrected 69: Net Acceleration in Z direction, will not be corrected 69: 69: There were 3 NOTEs 69: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/AccelerationWorks_AccelerationGroupTest_WithinTolerances_0.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 69: Can not increase nstlist because an NVE ensemble is used 69: Using 1 MPI thread 69: Using 2 OpenMP threads 69: 69: 69: NOTE: The number of threads is not equal to the number of (logical) cpus 69: and the -pin option is set to auto: will not pin threads to cpus. 69: This can lead to significant performance degradation. 69: Consider using -pin on (and -pinoffset in case you run multiple jobs). 69: starting mdrun 'spc2' 69: 8 steps, 0.0 ps. 69: Generated 3 of the 3 non-bonded parameter combinations 69: 69: Generated 3 of the 3 1-4 parameter combinations 69: 69: Excluding 2 bonded neighbours molecule type 'SOL' 69: 69: Setting gen_seed to -270705665 69: 69: Velocities were taken from a Maxwell distribution at 0 K 69: 69: This run will generate roughly 0 Mb of data 69: 69: Writing final coordinates. 69: 69: Core t (s) Wall t (s) (%) 69: Time: 0.034 0.017 196.7 69: (ns/day) (hour/ns) 69: Performance: 90.267 0.266 69: 69: [ OK ] AccelerationWorks/AccelerationGroupTest.WithinTolerances/0 (57 ms) 69: [ RUN ] AccelerationWorks/AccelerationGroupTest.WithinTolerances/1 69: 69: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/AccelerationWorks_AccelerationGroupTest_WithinTolerances_1_input.mdp]: 69: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 69: that with the Verlet scheme, nstlist has no effect on the accuracy of 69: your simulation. 69: 69: 69: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/AccelerationWorks_AccelerationGroupTest_WithinTolerances_1_input.mdp]: 69: verlet-buffer-pressure-tolerance is ignored when verlet-buffer-tolerance 69: < 0 69: 69: 69: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/AccelerationWorks_AccelerationGroupTest_WithinTolerances_1_input.mdp]: 69: Setting nstcalcenergy (100) equal to nstenergy (4) 69: 69: Generating 1-4 interactions: fudge = 0.5 69: Number of degrees of freedom in T-Coupling group FirstWaterMolecule is 6.00 69: Number of degrees of freedom in T-Coupling group SecondWaterMolecule is 6.00 69: Net Acceleration in X direction, will not be corrected 69: Net Acceleration in Y direction, will not be corrected 69: Net Acceleration in Z direction, will not be corrected 69: 69: There were 3 NOTEs 69: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/AccelerationWorks_AccelerationGroupTest_WithinTolerances_1.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 69: Can not increase nstlist because verlet-buffer-tolerance is not set or used 69: Using 1 MPI thread 69: Using 2 OpenMP threads 69: 69: 69: NOTE: The number of threads is not equal to the number of (logical) cpus 69: and the -pin option is set to auto: will not pin threads to cpus. 69: This can lead to significant performance degradation. 69: Consider using -pin on (and -pinoffset in case you run multiple jobs). 69: starting mdrun 'spc2' 69: 8 steps, 0.0 ps. 69: Generated 3 of the 3 non-bonded parameter combinations 69: 69: Generated 3 of the 3 1-4 parameter combinations 69: 69: Excluding 2 bonded neighbours molecule type 'SOL' 69: 69: Setting gen_seed to 1772084863 69: 69: Velocities were taken from a Maxwell distribution at 0 K 69: 69: This run will generate roughly 0 Mb of data 69: 69: Writing final coordinates. 69: 69: Core t (s) Wall t (s) (%) 69: Time: 0.043 0.022 197.8 69: (ns/day) (hour/ns) 69: Performance: 71.613 0.335 69: 69: [ OK ] AccelerationWorks/AccelerationGroupTest.WithinTolerances/1 (74 ms) 69: [ RUN ] AccelerationWorks/AccelerationGroupTest.WithinTolerances/2 69: 69: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/AccelerationWorks_AccelerationGroupTest_WithinTolerances_2_input.mdp]: 69: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 69: that with the Verlet scheme, nstlist has no effect on the accuracy of 69: your simulation. 69: 69: 69: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/AccelerationWorks_AccelerationGroupTest_WithinTolerances_2_input.mdp]: 69: verlet-buffer-pressure-tolerance is ignored when verlet-buffer-tolerance 69: < 0 69: 69: 69: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/AccelerationWorks_AccelerationGroupTest_WithinTolerances_2_input.mdp]: 69: Setting nstcalcenergy (100) equal to nstenergy (4) 69: 69: Generating 1-4 interactions: fudge = 0.5 69: Number of degrees of freedom in T-Coupling group FirstWaterMolecule is 6.00 69: Number of degrees of freedom in T-Coupling group SecondWaterMolecule is 6.00 69: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 69: Net Acceleration in X direction, will not be corrected 69: Net Acceleration in Y direction, will not be corrected 69: Net Acceleration in Z direction, will not be corrected 69: 69: There were 3 NOTEs 69: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/AccelerationWorks_AccelerationGroupTest_WithinTolerances_2.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 69: Can not increase nstlist because an NVE ensemble is used 69: Using 1 MPI thread 69: Using 2 OpenMP threads 69: 69: 69: NOTE: The number of threads is not equal to the number of (logical) cpus 69: and the -pin option is set to auto: will not pin threads to cpus. 69: This can lead to significant performance degradation. 69: Consider using -pin on (and -pinoffset in case you run multiple jobs). 69: starting mdrun 'spc2' 69: 8 steps, 0.0 ps. 69: Generated 3 of the 3 non-bonded parameter combinations 69: 69: Generated 3 of the 3 1-4 parameter combinations 69: 69: Excluding 2 bonded neighbours molecule type 'SOL' 69: 69: Setting gen_seed to -311440417 69: 69: Velocities were taken from a Maxwell distribution at 0 K 69: 69: This run will generate roughly 0 Mb of data 69: 69: Writing final coordinates. 69: 69: Core t (s) Wall t (s) (%) 69: Time: 0.037 0.019 197.0 69: (ns/day) (hour/ns) 69: Performance: 82.451 0.291 69: 69: [ OK ] AccelerationWorks/AccelerationGroupTest.WithinTolerances/2 (63 ms) 69: [ RUN ] AccelerationWorks/AccelerationGroupTest.WithinTolerances/3 69: 69: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/AccelerationWorks_AccelerationGroupTest_WithinTolerances_3_input.mdp]: 69: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 69: that with the Verlet scheme, nstlist has no effect on the accuracy of 69: your simulation. 69: 69: 69: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/AccelerationWorks_AccelerationGroupTest_WithinTolerances_3_input.mdp]: 69: verlet-buffer-pressure-tolerance is ignored when verlet-buffer-tolerance 69: < 0 69: 69: 69: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/AccelerationWorks_AccelerationGroupTest_WithinTolerances_3_input.mdp]: 69: Setting nstcalcenergy (100) equal to nstenergy (4) 69: 69: Generating 1-4 interactions: fudge = 0.5 69: Number of degrees of freedom in T-Coupling group FirstWaterMolecule is 6.00 69: Number of degrees of freedom in T-Coupling group SecondWaterMolecule is 6.00 69: Net Acceleration in X direction, will not be corrected 69: Net Acceleration in Y direction, will not be corrected 69: Net Acceleration in Z direction, will not be corrected 69: 69: There were 3 NOTEs 69: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/AccelerationWorks_AccelerationGroupTest_WithinTolerances_3.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 69: Can not increase nstlist because verlet-buffer-tolerance is not set or used 69: Using 1 MPI thread 69: Using 2 OpenMP threads 69: 69: 69: NOTE: The number of threads is not equal to the number of (logical) cpus 69: and the -pin option is set to auto: will not pin threads to cpus. 69: This can lead to significant performance degradation. 69: Consider using -pin on (and -pinoffset in case you run multiple jobs). 69: starting mdrun 'spc2' 69: 8 steps, 0.0 ps. 69: Generated 3 of the 3 non-bonded parameter combinations 69: 69: Generated 3 of the 3 1-4 parameter combinations 69: 69: Excluding 2 bonded neighbours molecule type 'SOL' 69: 69: Setting gen_seed to -1275535881 69: 69: Velocities were taken from a Maxwell distribution at 0 K 69: 69: This run will generate roughly 0 Mb of data 69: 69: Writing final coordinates. 69: 69: Core t (s) Wall t (s) (%) 69: Time: 0.037 0.019 197.4 69: (ns/day) (hour/ns) 69: Performance: 82.499 0.291 69: 69: [ OK ] AccelerationWorks/AccelerationGroupTest.WithinTolerances/3 (60 ms) 69: [----------] 4 tests from AccelerationWorks/AccelerationGroupTest (256 ms total) 69: 69: [----------] Global test environment tear-down 69: [==========] 29 tests from 8 test suites ran. (26836 ms total) 69: [ PASSED ] 28 tests. 69: [ SKIPPED ] 1 test, listed below: 69: [ SKIPPED ] FreezeWorks/FreezeGroupTest.WithinTolerances/5 69/92 Test #69: MdrunTestsOneRank ......................... Passed 26.92 sec test 70 Start 70: MdrunTestsTwoRanks 70: Test command: /build/reproducible-path/gromacs-2025.1/build/basic/bin/mdrun-test "-ntomp" "2" "-ntmpi" "2" "--gtest_output=xml:/build/reproducible-path/gromacs-2025.1/build/basic/Testing/Temporary/MdrunTestsTwoRanks.xml" 70: Working Directory: /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests 70: Test timeout computed to be: 600 70: [==========] Running 29 tests from 8 test suites. 70: [----------] Global test environment set-up. 70: [----------] 1 test from CompelTest 70: [ RUN ] CompelTest.SwapCanRun 70: Generating 1-4 interactions: fudge = 0.5 70: Split0 group 'Ch0' contains 83 atoms. 70: Split1 group 'Ch1' contains 83 atoms. 70: Solvent group 'SOL' contains 11931 atoms. 70: Swap group 'NA+' contains 19 atoms. 70: Swap group 'CL-' contains 19 atoms. 70: Number of degrees of freedom in T-Coupling group System is 27869.00 70: 70: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/CompelTest_SwapCanRun_input.mdp]: 70: Removing center of mass motion in the presence of position restraints 70: might cause artifacts. When you are using position restraints to 70: equilibrate a macro-molecule, the artifacts are usually negligible. 70: 70: 70: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/CompelTest_SwapCanRun_input.mdp]: 70: You are using a plain Coulomb cut-off, which might produce artifacts. 70: You might want to consider using PME electrostatics. 70: 70: 70: 70: There were 2 NOTEs 70: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/CompelTest_SwapCanRun.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 70: Update groups can not be used for this system because there are three or more consecutively coupled constraints 70: 70: Using 2 MPI threads 70: Using 2 OpenMP threads per tMPI thread 70: 70: SWAP: Determining initial numbers of ions per compartment. 70: SWAP: Setting pointers for checkpoint writing 70: SWAP: Channel 0 flux history for ion type NA+ (charge 1): 0 molecules 70: SWAP: Channel 1 flux history for ion type NA+ (charge 1): 0 molecules 70: SWAP: Channel 0 flux history for ion type CL- (charge -1): 0 molecules 70: SWAP: Channel 1 flux history for ion type CL- (charge -1): 0 molecules 70: starting mdrun 'Channel_coco in octane membrane' 70: 2 steps, 0.0 ps. 70: Setting the LD random seed to -4916769 70: 70: Generated 330891 of the 330891 non-bonded parameter combinations 70: 70: Generated 330891 of the 330891 1-4 parameter combinations 70: 70: Excluding 3 bonded neighbours molecule type 'Protein' 70: 70: turning all bonds into constraints... 70: 70: Excluding 3 bonded neighbours molecule type 'OCT' 70: 70: turning all bonds into constraints... 70: 70: Excluding 1 bonded neighbours molecule type 'NA' 70: 70: turning all bonds into constraints... 70: 70: Excluding 1 bonded neighbours molecule type 'CL' 70: 70: turning all bonds into constraints... 70: 70: Excluding 3 bonded neighbours molecule type 'Protein' 70: 70: Excluding 3 bonded neighbours molecule type 'OCT' 70: 70: Excluding 2 bonded neighbours molecule type 'SOL' 70: 70: turning all bonds into constraints... 70: 70: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/OctaneSandwich.gro' 70: 70: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 300 K 70: 70: Calculated rlist for 1x1 atom pair-list as 1.316 nm, buffer size 0.316 nm 70: 70: Set rlist, assuming 4x4 atom pair-list, to 1.262 nm, buffer size 0.262 nm 70: 70: Note that mdrun will redetermine rlist based on the actual pair-list setup 70: 70: This run will generate roughly 1 Mb of data 70: 70: Writing final coordinates. 70: 70: 70: Dynamic load balancing report: 70: DLB was off during the run due to low measured imbalance. 70: Average load imbalance: 4.7%. 70: The balanceable part of the MD step is 50%, load imbalance is computed from this. 70: Part of the total run time spent waiting due to load imbalance: 2.3%. 70: 70: 70: NOTE: 7 % of the run time was spent in domain decomposition, 70: 12 % of the run time was spent in pair search, 70: you might want to increase nstlist (this has no effect on accuracy) 70: 70: Core t (s) Wall t (s) (%) 70: Time: 7.692 1.923 399.9 70: (ns/day) (hour/ns) 70: Performance: 0.674 35.620 70: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/CompelTest_SwapCanRun.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 70: Overriding nsteps with value passed on the command line: 2 steps, 0.01 ps 70: 70: Update groups can not be used for this system because there are three or more consecutively coupled constraints 70: 70: Using 2 MPI threads 70: 70: Non-default thread affinity set, disabling internal thread affinity 70: 70: Using 2 OpenMP threads per tMPI thread 70: 70: SWAP: Setting pointers for checkpoint writing 70: SWAP: Copying channel fluxes from checkpoint file data 70: SWAP: Channel 0 flux history for ion type NA+ (charge 1): 0 molecules 70: SWAP: Channel 1 flux history for ion type NA+ (charge 1): 0 molecules 70: SWAP: Channel 0 flux history for ion type CL- (charge -1): 0 molecules 70: SWAP: Channel 1 flux history for ion type CL- (charge -1): 0 molecules 70: starting mdrun 'Channel_coco in octane membrane' 70: 4 steps, 0.0 ps (continuing from step 2, 0.0 ps). 70: 70: Writing final coordinates. 70: 70: Core t (s) Wall t (s) (%) 70: Time: 13.365 3.357 398.1 70: (ns/day) (hour/ns) 70: Performance: 0.386 62.169 70: [ OK ] CompelTest.SwapCanRun (11861 ms) 70: [----------] 1 test from CompelTest (11861 ms total) 70: 70: [----------] 6 tests from BondedInteractionsTest 70: [ RUN ] BondedInteractionsTest.NormalBondWorks 70: 70: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_NormalBondWorks_input.mdp]: 70: For a correct single-point energy evaluation with nsteps = 0, use 70: continuation = yes to avoid constraining the input coordinates. 70: 70: 70: NOTE 2 [file BondedInteractionsTest_NormalBondWorks_butane1.top, line 31]: 70: In moleculetype 'butane' 2 atoms are not bound by a potential or 70: constraint to any other atom in the same moleculetype. Although 70: technically this might not cause issues in a simulation, this often means 70: that the user forgot to add a bond/potential/constraint or put multiple 70: molecules in the same moleculetype definition by mistake. Run with -v to 70: get information for each atom. 70: 70: Number of degrees of freedom in T-Coupling group rest is 9.00 70: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 70: 70: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_NormalBondWorks_input.mdp]: 70: NVE simulation with an initial temperature of zero: will use a Verlet 70: buffer of 10%. Check your energy drift! 70: 70: 70: There were 3 NOTEs 70: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_NormalBondWorks.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 70: Can not increase nstlist because an NVE ensemble is used 70: Using 2 MPI threads 70: 70: Non-default thread affinity set, disabling internal thread affinity 70: 70: Using 2 OpenMP threads per tMPI thread 70: 70: starting md rerun 'A single butane', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/butane1.gro' 70: 70: Reading frames from gro file 'A single butane', 4 atoms. 70: Reading frame 0 time 0.000 Last frame 0 time 0.000 70: 70: NOTE: 70 % of the run time was spent in domain decomposition, 70: 6 % of the run time was spent in pair search, 70: you might want to increase nstlist (this has no effect on accuracy) 70: 70: NOTE: 6 % of the run time was spent communicating energies, 70: you might want to increase some nst* mdp options 70: 70: Core t (s) Wall t (s) (%) 70: Time: 1.193 0.310 384.6 70: (ns/day) (hour/ns) 70: Performance: 0.279 86.165 70: Setting the LD random seed to 2147024895 70: 70: Generated 3 of the 3 non-bonded parameter combinations 70: 70: Excluding 3 bonded neighbours molecule type 'butane' 70: 70: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/butane1.gro', all velocities are zero 70: 70: This run will generate roughly 0 Mb of data 70: [ OK ] BondedInteractionsTest.NormalBondWorks (939 ms) 70: [ RUN ] BondedInteractionsTest.TabulatedBondWorks 70: 70: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_TabulatedBondWorks_input.mdp]: 70: For a correct single-point energy evaluation with nsteps = 0, use 70: continuation = yes to avoid constraining the input coordinates. 70: 70: 70: NOTE 2 [file BondedInteractionsTest_TabulatedBondWorks_butane1.top, line 31]: 70: In moleculetype 'butane' 2 atoms are not bound by a potential or 70: constraint to any other atom in the same moleculetype. Although 70: technically this might not cause issues in a simulation, this often means 70: that the user forgot to add a bond/potential/constraint or put multiple 70: molecules in the same moleculetype definition by mistake. Run with -v to 70: get information for each atom. 70: 70: Number of degrees of freedom in T-Coupling group rest is 9.00 70: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 70: 70: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_TabulatedBondWorks_input.mdp]: 70: NVE simulation with an initial temperature of zero: will use a Verlet 70: buffer of 10%. Check your energy drift! 70: 70: 70: There were 3 NOTEs 70: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_TabulatedBondWorks.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 70: Can not increase nstlist because an NVE ensemble is used 70: Using 2 MPI threads 70: 70: Non-default thread affinity set, disabling internal thread affinity 70: 70: Using 2 OpenMP threads per tMPI thread 70: 70: starting md rerun 'A single butane', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/butane1.gro' 70: 70: Reading frames from gro file 'A single butane', 4 atoms. 70: Reading frame 0 time 0.000 Last frame 0 time 0.000 70: 70: NOTE: 72 % of the run time was spent in domain decomposition, 70: 5 % of the run time was spent in pair search, 70: you might want to increase nstlist (this has no effect on accuracy) 70: 70: Core t (s) Wall t (s) (%) 70: Time: 1.143 0.298 383.9 70: (ns/day) (hour/ns) 70: Performance: 0.290 82.721 70: Setting the LD random seed to 1701539647 70: 70: Generated 3 of the 3 non-bonded parameter combinations 70: 70: Excluding 3 bonded neighbours molecule type 'butane' 70: 70: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/butane1.gro', all velocities are zero 70: 70: This run will generate roughly 0 Mb of data 70: [ OK ] BondedInteractionsTest.TabulatedBondWorks (935 ms) 70: [ RUN ] BondedInteractionsTest.NormalAngleWorks 70: 70: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_NormalAngleWorks_input.mdp]: 70: For a correct single-point energy evaluation with nsteps = 0, use 70: continuation = yes to avoid constraining the input coordinates. 70: 70: 70: NOTE 2 [file BondedInteractionsTest_NormalAngleWorks_butane1.top, line 31]: 70: In moleculetype 'butane' 4 atoms are not bound by a potential or 70: constraint to any other atom in the same moleculetype. Although 70: technically this might not cause issues in a simulation, this often means 70: that the user forgot to add a bond/potential/constraint or put multiple 70: molecules in the same moleculetype definition by mistake. Run with -v to 70: get information for each atom. 70: 70: Number of degrees of freedom in T-Coupling group rest is 9.00 70: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 70: 70: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_NormalAngleWorks_input.mdp]: 70: NVE simulation with an initial temperature of zero: will use a Verlet 70: buffer of 10%. Check your energy drift! 70: 70: 70: There were 3 NOTEs 70: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_NormalAngleWorks.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 70: Can not increase nstlist because an NVE ensemble is used 70: Using 2 MPI threads 70: 70: Non-default thread affinity set, disabling internal thread affinity 70: 70: Using 2 OpenMP threads per tMPI thread 70: 70: starting md rerun 'A single butane', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/butane1.gro' 70: 70: Reading frames from gro file 'A single butane', 4 atoms. 70: Reading frame 0 time 0.000 Last frame 0 time 0.000 70: 70: NOTE: 70 % of the run time was spent in domain decomposition, 70: 6 % of the run time was spent in pair search, 70: you might want to increase nstlist (this has no effect on accuracy) 70: 70: Core t (s) Wall t (s) (%) 70: Time: 1.175 0.306 384.4 70: (ns/day) (hour/ns) 70: Performance: 0.283 84.943 70: Setting the LD random seed to 2145804103 70: 70: Generated 3 of the 3 non-bonded parameter combinations 70: 70: Excluding 3 bonded neighbours molecule type 'butane' 70: 70: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/butane1.gro', all velocities are zero 70: 70: This run will generate roughly 0 Mb of data 70: [ OK ] BondedInteractionsTest.NormalAngleWorks (956 ms) 70: [ RUN ] BondedInteractionsTest.TabulatedAngleWorks 70: 70: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_TabulatedAngleWorks_input.mdp]: 70: For a correct single-point energy evaluation with nsteps = 0, use 70: continuation = yes to avoid constraining the input coordinates. 70: 70: 70: NOTE 2 [file BondedInteractionsTest_TabulatedAngleWorks_butane1.top, line 31]: 70: In moleculetype 'butane' 4 atoms are not bound by a potential or 70: constraint to any other atom in the same moleculetype. Although 70: technically this might not cause issues in a simulation, this often means 70: that the user forgot to add a bond/potential/constraint or put multiple 70: molecules in the same moleculetype definition by mistake. Run with -v to 70: get information for each atom. 70: 70: Number of degrees of freedom in T-Coupling group rest is 9.00 70: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 70: 70: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_TabulatedAngleWorks_input.mdp]: 70: NVE simulation with an initial temperature of zero: will use a Verlet 70: buffer of 10%. Check your energy drift! 70: 70: 70: There were 3 NOTEs 70: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_TabulatedAngleWorks.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 70: Can not increase nstlist because an NVE ensemble is used 70: Using 2 MPI threads 70: 70: Non-default thread affinity set, disabling internal thread affinity 70: 70: Using 2 OpenMP threads per tMPI thread 70: 70: starting md rerun 'A single butane', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/butane1.gro' 70: 70: Reading frames from gro file 'A single butane', 4 atoms. 70: Reading frame 0 time 0.000 Last frame 0 time 0.000 70: 70: NOTE: 73 % of the run time was spent in domain decomposition, 70: 5 % of the run time was spent in pair search, 70: you might want to increase nstlist (this has no effect on accuracy) 70: 70: Core t (s) Wall t (s) (%) 70: Time: 1.234 0.321 385.1 70: (ns/day) (hour/ns) 70: Performance: 0.270 89.042 70: Setting the LD random seed to -1414678945 70: 70: Generated 3 of the 3 non-bonded parameter combinations 70: 70: Excluding 3 bonded neighbours molecule type 'butane' 70: 70: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/butane1.gro', all velocities are zero 70: 70: This run will generate roughly 0 Mb of data 70: [ OK ] BondedInteractionsTest.TabulatedAngleWorks (964 ms) 70: [ RUN ] BondedInteractionsTest.NormalDihedralWorks 70: 70: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_NormalDihedralWorks_input.mdp]: 70: For a correct single-point energy evaluation with nsteps = 0, use 70: continuation = yes to avoid constraining the input coordinates. 70: 70: 70: NOTE 2 [file BondedInteractionsTest_NormalDihedralWorks_butane1.top, line 31]: 70: In moleculetype 'butane' 4 atoms are not bound by a potential or 70: constraint to any other atom in the same moleculetype. Although 70: technically this might not cause issues in a simulation, this often means 70: that the user forgot to add a bond/potential/constraint or put multiple 70: molecules in the same moleculetype definition by mistake. Run with -v to 70: get information for each atom. 70: 70: Number of degrees of freedom in T-Coupling group rest is 9.00 70: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 70: 70: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_NormalDihedralWorks_input.mdp]: 70: NVE simulation with an initial temperature of zero: will use a Verlet 70: buffer of 10%. Check your energy drift! 70: 70: 70: There were 3 NOTEs 70: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_NormalDihedralWorks.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 70: Can not increase nstlist because an NVE ensemble is used 70: Using 2 MPI threads 70: 70: Non-default thread affinity set, disabling internal thread affinity 70: 70: Using 2 OpenMP threads per tMPI thread 70: 70: starting md rerun 'A single butane', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/butane1.gro' 70: 70: Reading frames from gro file 'A single butane', 4 atoms. 70: Reading frame 0 time 0.000 Last frame 0 time 0.000 70: 70: NOTE: 73 % of the run time was spent in domain decomposition, 70: 7 % of the run time was spent in pair search, 70: you might want to increase nstlist (this has no effect on accuracy) 70: 70: NOTE: 6 % of the run time was spent communicating energies, 70: you might want to increase some nst* mdp options 70: 70: Core t (s) Wall t (s) (%) 70: Time: 1.122 0.292 383.8 70: (ns/day) (hour/ns) 70: Performance: 0.296 81.203 70: Setting the LD random seed to -281280777 70: 70: Generated 3 of the 3 non-bonded parameter combinations 70: 70: Excluding 3 bonded neighbours molecule type 'butane' 70: 70: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/butane1.gro', all velocities are zero 70: 70: This run will generate roughly 0 Mb of data 70: [ OK ] BondedInteractionsTest.NormalDihedralWorks (915 ms) 70: [ RUN ] BondedInteractionsTest.TabulatedDihedralWorks 70: 70: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_TabulatedDihedralWorks_input.mdp]: 70: For a correct single-point energy evaluation with nsteps = 0, use 70: continuation = yes to avoid constraining the input coordinates. 70: 70: 70: NOTE 2 [file BondedInteractionsTest_TabulatedDihedralWorks_butane1.top, line 31]: 70: In moleculetype 'butane' 4 atoms are not bound by a potential or 70: constraint to any other atom in the same moleculetype. Although 70: technically this might not cause issues in a simulation, this often means 70: that the user forgot to add a bond/potential/constraint or put multiple 70: molecules in the same moleculetype definition by mistake. Run with -v to 70: get information for each atom. 70: 70: Number of degrees of freedom in T-Coupling group rest is 9.00 70: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 70: 70: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_TabulatedDihedralWorks_input.mdp]: 70: NVE simulation with an initial temperature of zero: will use a Verlet 70: buffer of 10%. Check your energy drift! 70: 70: 70: There were 3 NOTEs 70: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_TabulatedDihedralWorks.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 70: Can not increase nstlist because an NVE ensemble is used 70: Using 2 MPI threads 70: 70: Non-default thread affinity set, disabling internal thread affinity 70: 70: Using 2 OpenMP threads per tMPI thread 70: 70: starting md rerun 'A single butane', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/butane1.gro' 70: 70: Reading frames from gro file 'A single butane', 4 atoms. 70: Reading frame 0 time 0.000 Last frame 0 time 0.000 70: 70: NOTE: 72 % of the run time was spent in domain decomposition, 70: 6 % of the run time was spent in pair search, 70: you might want to increase nstlist (this has no effect on accuracy) 70: 70: Core t (s) Wall t (s) (%) 70: Time: 1.110 0.289 383.4 70: (ns/day) (hour/ns) 70: Performance: 0.299 80.377 70: Setting the LD random seed to -85216417 70: 70: Generated 3 of the 3 non-bonded parameter combinations 70: 70: Excluding 3 bonded neighbours molecule type 'butane' 70: 70: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/butane1.gro', all velocities are zero 70: 70: This run will generate roughly 0 Mb of data 70: [ OK ] BondedInteractionsTest.TabulatedDihedralWorks (947 ms) 70: [----------] 6 tests from BondedInteractionsTest (5659 ms total) 70: 70: [----------] 2 tests from BoxDeformationTest 70: [ RUN ] BoxDeformationTest.flowDoesNotAffectEkin 70: 70: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/BoxDeformationTest_flowDoesNotAffectEkin_input.mdp]: 70: verlet-buffer-pressure-tolerance is ignored when verlet-buffer-tolerance 70: < 0 70: 70: 70: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/BoxDeformationTest_flowDoesNotAffectEkin_input.mdp]: 70: Setting nstcalcenergy (100) equal to nstenergy (10) 70: 70: 70: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/BoxDeformationTest_flowDoesNotAffectEkin_input.mdp]: 70: For a correct single-point energy evaluation with nsteps = 0, use 70: continuation = yes to avoid constraining the input coordinates. 70: 70: Number of degrees of freedom in T-Coupling group rest is 33.00 70: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 70: 70: There were 3 NOTEs 70: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/BoxDeformationTest_flowDoesNotAffectEkin.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 70: Can not increase nstlist because an NVE ensemble is used 70: Using 2 MPI threads 70: 70: Non-default thread affinity set, disabling internal thread affinity 70: 70: Using 2 OpenMP threads per tMPI thread 70: 70: starting mdrun 'Argon' 70: 0 steps, 0.0 ps. 70: 70: NOTE: 47 % of the run time was spent in domain decomposition, 70: 13 % of the run time was spent in pair search, 70: you might want to increase nstlist (this has no effect on accuracy) 70: 70: NOTE: 13 % of the run time was spent communicating energies, 70: you might want to increase some nst* mdp options 70: 70: Core t (s) Wall t (s) (%) 70: Time: 0.531 0.148 359.6 70: (ns/day) (hour/ns) 70: Performance: 1.169 20.527 70: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/BoxDeformationTest_flowDoesNotAffectEkin.edr as single precision energy file 70: Reading energy frame 0 time 0.000 Last energy frame read 0 time 0.000 Setting the LD random seed to -8826984 70: 70: Generated 1 of the 1 non-bonded parameter combinations 70: 70: Excluding 1 bonded neighbours molecule type 'Argon' 70: 70: Setting gen_seed to 533460991 70: 70: Velocities were taken from a Maxwell distribution at 0 K 70: 70: This run will generate roughly 0 Mb of data 70: [ OK ] BoxDeformationTest.flowDoesNotAffectEkin (803 ms) 70: [ RUN ] BoxDeformationTest.EnergiesWithinTolerances 70: 70: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/BoxDeformationTest_EnergiesWithinTolerances_input.mdp]: 70: verlet-buffer-pressure-tolerance is ignored when verlet-buffer-tolerance 70: < 0 70: 70: 70: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/BoxDeformationTest_EnergiesWithinTolerances_input.mdp]: 70: Setting nstcalcenergy (100) equal to nstenergy (10) 70: 70: Generating 1-4 interactions: fudge = 0.5 70: Number of degrees of freedom in T-Coupling group rest is 1293.00 70: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 70: 70: There were 2 NOTEs 70: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/BoxDeformationTest_EnergiesWithinTolerances.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 70: Can not increase nstlist because an NVE ensemble is used 70: Using 2 MPI threads 70: 70: Non-default thread affinity set, disabling internal thread affinity 70: 70: Using 2 OpenMP threads per tMPI thread 70: 70: starting mdrun 'spc2' 70: 20 steps, 0.0 ps. 70: Setting the LD random seed to -1610916033 70: 70: Generated 330891 of the 330891 non-bonded parameter combinations 70: 70: Generated 330891 of the 330891 1-4 parameter combinations 70: 70: Excluding 2 bonded neighbours molecule type 'SOL' 70: 70: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/spc216.gro' 70: 70: The largest distance between excluded atoms is 0.152 nm between atom 41 and 42 70: Calculating fourier grid dimensions for X Y Z 70: Using a fourier grid of 16x16x16, spacing 0.116 0.116 0.116 70: 70: Estimate for the relative computational load of the PME mesh part: 0.09 70: 70: This run will generate roughly 0 Mb of data 70: 70: Writing final coordinates. 70: 70: 70: Dynamic load balancing report: 70: DLB got disabled because it was unsuitable to use. 70: Average load imbalance: 12.2%. 70: The balanceable part of the MD step is 22%, load imbalance is computed from this. 70: Part of the total run time spent waiting due to load imbalance: 2.7%. 70: 70: 70: Core t (s) Wall t (s) (%) 70: Time: 19.136 4.800 398.7 70: (ns/day) (hour/ns) 70: Performance: 0.756 31.745 70: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/BoxDeformationTest_EnergiesWithinTolerances.edr as single precision energy file 70: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.020 Reading energy frame 2 time 0.040 Last energy frame read 2 time 0.040 [ OK ] BoxDeformationTest.EnergiesWithinTolerances (10118 ms) 70: [----------] 2 tests from BoxDeformationTest (10922 ms total) 70: 70: [----------] 1 test from PositionRestraintCommTest 70: [ RUN ] PositionRestraintCommTest.PositionRestraintsTwoCOMs 70: 70: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PositionRestraintCommTest_PositionRestraintsTwoCOMs_input.mdp]: 70: You have set rlist larger than the interaction cut-off, but you also have 70: verlet-buffer-tolerance > 0. Will set rlist using 70: verlet-buffer-tolerance. 70: 70: 70: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PositionRestraintCommTest_PositionRestraintsTwoCOMs_input.mdp]: 70: Setting nstcalcenergy (100) equal to nstenergy (10) 70: 70: Generating 1-4 interactions: fudge = 0.5 70: 70: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PositionRestraintCommTest_PositionRestraintsTwoCOMs_input.mdp]: 70: 13489 atoms are not part of any of the VCM groups 70: 70: 70: WARNING 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PositionRestraintCommTest_PositionRestraintsTwoCOMs_input.mdp]: 70: 13489 atoms are not part of any center of mass motion removal group. 70: This may lead to artifacts. 70: In most cases one should use one group for the whole system. 70: 70: Number of degrees of freedom in T-Coupling group System is 29527.73 70: 70: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PositionRestraintCommTest_PositionRestraintsTwoCOMs_input.mdp]: 70: Removing center of mass motion in the presence of position restraints 70: might cause artifacts. When you are using position restraints to 70: equilibrate a macro-molecule, the artifacts are usually negligible. 70: 70: 70: There were 4 NOTEs 70: 70: There was 1 WARNING 70: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PositionRestraintCommTest_PositionRestraintsTwoCOMs.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 70: Changing nstlist from 10 to 20, rlist from 0.965 to 1.066 70: 70: Using 2 MPI threads 70: 70: Non-default thread affinity set, disabling internal thread affinity 70: 70: Using 2 OpenMP threads per tMPI thread 70: 70: starting mdrun 'Channel_coco in octane membrane' 70: 10 steps, 0.0 ps. 70: Setting the LD random seed to 1199547847 70: 70: Generated 330891 of the 330891 non-bonded parameter combinations 70: 70: Generated 330891 of the 330891 1-4 parameter combinations 70: 70: Excluding 3 bonded neighbours molecule type 'Protein' 70: 70: Excluding 3 bonded neighbours molecule type 'OCT' 70: 70: Excluding 1 bonded neighbours molecule type 'NA' 70: 70: Excluding 1 bonded neighbours molecule type 'CL' 70: 70: Excluding 3 bonded neighbours molecule type 'Protein' 70: 70: Excluding 3 bonded neighbours molecule type 'OCT' 70: 70: Excluding 2 bonded neighbours molecule type 'SOL' 70: 70: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/OctaneSandwich.gro' 70: 70: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 70: 70: Calculated rlist for 1x1 atom pair-list as 0.990 nm, buffer size 0.090 nm 70: 70: Set rlist, assuming 4x4 atom pair-list, to 0.965 nm, buffer size 0.065 nm 70: 70: Note that mdrun will redetermine rlist based on the actual pair-list setup 70: 70: Chain0: 2.207 2.168 7.330 70: Chain1: 2.228 2.186 2.401 70: Chain0: 2.207 2.168 7.330 70: Chain1: 2.228 2.186 2.401 70: 70: This run will generate roughly 1 Mb of data 70: 70: Writing final coordinates. 70: 70: Core t (s) Wall t (s) (%) 70: Time: 23.825 5.972 398.9 70: (ns/day) (hour/ns) 70: Performance: 0.318 75.404 70: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PositionRestraintCommTest_PositionRestraintsTwoCOMs.edr as single precision energy file 70: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.020 Last energy frame read 1 time 0.020 [ OK ] PositionRestraintCommTest.PositionRestraintsTwoCOMs (12065 ms) 70: [----------] 1 test from PositionRestraintCommTest (12066 ms total) 70: 70: [----------] 2 tests from MultipleTimeSteppingIsNearSingleTimeStepping/MtsComparisonTest 70: [ RUN ] MultipleTimeSteppingIsNearSingleTimeStepping/MtsComparisonTest.WithinTolerances/0 70: 70: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_0_input.mdp]: 70: verlet-buffer-pressure-tolerance is ignored when verlet-buffer-tolerance 70: < 0 70: 70: Generating 1-4 interactions: fudge = 0.5 70: 70: NOTE 2 [file ala.top, line 256]: 70: For energy conservation with LINCS, lincs_iter should be 2 or larger. 70: 70: 70: Number of degrees of freedom in T-Coupling group rest is 54.00 70: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 70: 70: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_0_input.mdp]: 70: The optimal PME mesh load for parallel simulations is below 0.5 70: and for highly parallel simulations between 0.25 and 0.33, 70: for higher performance, increase the cut-off and the PME grid spacing. 70: 70: 70: 70: There were 3 NOTEs 70: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_0_sim.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 70: Can not increase nstlist because an NVE ensemble is used 70: Using 2 MPI threads 70: 70: Non-default thread affinity set, disabling internal thread affinity 70: 70: Using 2 OpenMP threads per tMPI thread 70: 70: starting mdrun 'UNNAMED in water' 70: 4 steps, 0.0 ps. 70: Setting the LD random seed to 1844694505 70: 70: Generated 2211 of the 2211 non-bonded parameter combinations 70: 70: Generated 2211 of the 2211 1-4 parameter combinations 70: 70: Excluding 3 bonded neighbours molecule type 'Protein_chain_A' 70: 70: turning H bonds into constraints... 70: 70: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/ala.gro' 70: 70: The largest distance between excluded atoms is 0.384 nm between atom 5 and 15 70: Calculating fourier grid dimensions for X Y Z 70: Using a fourier grid of 24x24x24, spacing 0.104 0.104 0.104 70: 70: Estimate for the relative computational load of the PME mesh part: 0.93 70: 70: This run will generate roughly 0 Mb of data 70: 70: Writing final coordinates. 70: 70: NOTE: 10 % of the run time was spent in domain decomposition, 70: 2 % of the run time was spent in pair search, 70: you might want to increase nstlist (this has no effect on accuracy) 70: 70: NOTE: 6 % of the run time was spent communicating energies, 70: you might want to increase some nst* mdp options 70: 70: Core t (s) Wall t (s) (%) 70: Time: 3.425 0.872 392.8 70: (ns/day) (hour/ns) 70: Performance: 0.495 48.439 70: 70: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_0_input.mdp]: 70: verlet-buffer-pressure-tolerance is ignored when verlet-buffer-tolerance 70: < 0 70: 70: Generating 1-4 interactions: fudge = 0.5 70: 70: NOTE 2 [file ala.top, line 256]: 70: For energy conservation with LINCS, lincs_iter should be 2 or larger. 70: 70: 70: Number of degrees of freedom in T-Coupling group rest is 54.00 70: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 70: 70: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_0_input.mdp]: 70: The optimal PME mesh load for parallel simulations is below 0.5 70: and for highly parallel simulations between 0.25 and 0.33, 70: for higher performance, increase the cut-off and the PME grid spacing. 70: 70: 70: 70: There were 3 NOTEs 70: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_0_sim.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 70: Can not increase nstlist because an NVE ensemble is used 70: Using 2 MPI threads 70: 70: Non-default thread affinity set, disabling internal thread affinity 70: 70: Using 2 OpenMP threads per tMPI thread 70: 70: starting mdrun 'UNNAMED in water' 70: 4 steps, 0.0 ps. 70: Setting the LD random seed to -1613253129 70: 70: Generated 2211 of the 2211 non-bonded parameter combinations 70: 70: Generated 2211 of the 2211 1-4 parameter combinations 70: 70: Excluding 3 bonded neighbours molecule type 'Protein_chain_A' 70: 70: turning H bonds into constraints... 70: 70: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/ala.gro' 70: 70: The largest distance between excluded atoms is 0.384 nm between atom 5 and 15 70: Calculating fourier grid dimensions for X Y Z 70: Using a fourier grid of 24x24x24, spacing 0.104 0.104 0.104 70: 70: Estimate for the relative computational load of the PME mesh part: 0.93 70: 70: This run will generate roughly 0 Mb of data 70: 70: Writing final coordinates. 70: 70: NOTE: 6 % of the run time was spent communicating energies, 70: you might want to increase some nst* mdp options 70: 70: Core t (s) Wall t (s) (%) 70: Time: 3.789 0.964 393.2 70: (ns/day) (hour/ns) 70: Performance: 0.448 53.545 70: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_0_sim1.edr as single precision energy file 70: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_0_sim2.edr as single precision energy file 70: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Last energy frame read 1 time 0.004 Last energy frame read 1 time 0.004 trr version: GMX_trn_file (single precision) 70: 70: 70: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_0_sim1.edr as single precision energy file 70: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_0_sim2.edr as single precision energy file 70: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Last energy frame read 1 time 0.004 Last energy frame read 1 time 0.004 [ OK ] MultipleTimeSteppingIsNearSingleTimeStepping/MtsComparisonTest.WithinTolerances/0 (3711 ms) 70: [ RUN ] MultipleTimeSteppingIsNearSingleTimeStepping/MtsComparisonTest.WithinTolerances/1 70: 70: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_1_input.mdp]: 70: verlet-buffer-pressure-tolerance is ignored when verlet-buffer-tolerance 70: < 0 70: 70: Generating 1-4 interactions: fudge = 0.5 70: 70: NOTE 2 [file ala.top, line 256]: 70: For energy conservation with LINCS, lincs_iter should be 2 or larger. 70: 70: 70: Number of degrees of freedom in T-Coupling group rest is 54.00 70: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 70: 70: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_1_input.mdp]: 70: The optimal PME mesh load for parallel simulations is below 0.5 70: and for highly parallel simulations between 0.25 and 0.33, 70: for higher performance, increase the cut-off and the PME grid spacing. 70: 70: 70: 70: There were 3 NOTEs 70: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_1_sim.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 70: Can not increase nstlist because an NVE ensemble is used 70: Using 2 MPI threads 70: 70: Non-default thread affinity set, disabling internal thread affinity 70: 70: Using 2 OpenMP threads per tMPI thread 70: 70: starting mdrun 'UNNAMED in water' 70: 4 steps, 0.0 ps. 70: Setting the LD random seed to -9773633 70: 70: Generated 2211 of the 2211 non-bonded parameter combinations 70: 70: Generated 2211 of the 2211 1-4 parameter combinations 70: 70: Excluding 3 bonded neighbours molecule type 'Protein_chain_A' 70: 70: turning H bonds into constraints... 70: 70: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/ala.gro' 70: 70: The largest distance between excluded atoms is 0.384 nm between atom 5 and 15 70: Calculating fourier grid dimensions for X Y Z 70: Using a fourier grid of 24x24x24, spacing 0.104 0.104 0.104 70: 70: Estimate for the relative computational load of the PME mesh part: 0.93 70: 70: This run will generate roughly 0 Mb of data 70: 70: Writing final coordinates. 70: 70: NOTE: 13 % of the run time was spent in domain decomposition, 70: 2 % of the run time was spent in pair search, 70: you might want to increase nstlist (this has no effect on accuracy) 70: 70: NOTE: 7 % of the run time was spent communicating energies, 70: you might want to increase some nst* mdp options 70: 70: Core t (s) Wall t (s) (%) 70: Time: 3.696 0.940 393.3 70: (ns/day) (hour/ns) 70: Performance: 0.460 52.216 70: 70: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_1_input.mdp]: 70: verlet-buffer-pressure-tolerance is ignored when verlet-buffer-tolerance 70: < 0 70: 70: Generating 1-4 interactions: fudge = 0.5 70: 70: NOTE 2 [file ala.top, line 256]: 70: For energy conservation with LINCS, lincs_iter should be 2 or larger. 70: 70: 70: Number of degrees of freedom in T-Coupling group rest is 54.00 70: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 70: 70: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_1_input.mdp]: 70: The optimal PME mesh load for parallel simulations is below 0.5 70: and for highly parallel simulations between 0.25 and 0.33, 70: for higher performance, increase the cut-off and the PME grid spacing. 70: 70: 70: 70: There were 3 NOTEs 70: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_1_sim.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 70: Multiple time stepping is only supported with GPUs when MTS is only applied to longrange-nonbonded forces. 70: Can not increase nstlist because an NVE ensemble is used 70: 70: Using 2 MPI threads 70: 70: Non-default thread affinity set, disabling internal thread affinity 70: 70: Using 2 OpenMP threads per tMPI thread 70: 70: starting mdrun 'UNNAMED in water' 70: 4 steps, 0.0 ps. 70: Setting the LD random seed to 805105246 70: 70: Generated 2211 of the 2211 non-bonded parameter combinations 70: 70: Generated 2211 of the 2211 1-4 parameter combinations 70: 70: Excluding 3 bonded neighbours molecule type 'Protein_chain_A' 70: 70: turning H bonds into constraints... 70: 70: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/ala.gro' 70: 70: The largest distance between excluded atoms is 0.384 nm between atom 5 and 15 70: Calculating fourier grid dimensions for X Y Z 70: Using a fourier grid of 24x24x24, spacing 0.104 0.104 0.104 70: 70: Estimate for the relative computational load of the PME mesh part: 0.93 70: 70: This run will generate roughly 0 Mb of data 70: 70: Writing final coordinates. 70: 70: NOTE: 14 % of the run time was spent in domain decomposition, 70: 2 % of the run time was spent in pair search, 70: you might want to increase nstlist (this has no effect on accuracy) 70: 70: NOTE: 6 % of the run time was spent communicating energies, 70: you might want to increase some nst* mdp options 70: 70: Core t (s) Wall t (s) (%) 70: Time: 3.478 0.885 392.9 70: (ns/day) (hour/ns) 70: Performance: 0.488 49.184 70: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_1_sim1.edr as single precision energy file 70: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_1_sim2.edr as single precision energy file 70: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Last energy frame read 1 time 0.004 Last energy frame read 1 time 0.004 70: 70: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_1_sim1.edr as single precision energy file 70: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_1_sim2.edr as single precision energy file 70: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Last energy frame read 1 time 0.004 Last energy frame read 1 time 0.004 [ OK ] MultipleTimeSteppingIsNearSingleTimeStepping/MtsComparisonTest.WithinTolerances/1 (3556 ms) 70: [----------] 2 tests from MultipleTimeSteppingIsNearSingleTimeStepping/MtsComparisonTest (7268 ms total) 70: 70: [----------] 1 test from MultipleTimeSteppingIsNearSingleTimeSteppingPull/MtsComparisonTest 70: [ RUN ] MultipleTimeSteppingIsNearSingleTimeSteppingPull/MtsComparisonTest.WithinTolerances/0 70: 70: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeSteppingPull_MtsComparisonTest_WithinTolerances_0_input.mdp]: 70: verlet-buffer-pressure-tolerance is ignored when verlet-buffer-tolerance 70: < 0 70: 70: Generating 1-4 interactions: fudge = 0.5 70: Pull group 1 'FirstWaterMolecule' has 3 atoms 70: Pull group 2 'SecondWaterMolecule' has 3 atoms 70: Number of degrees of freedom in T-Coupling group rest is 9.00 70: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 70: Pull group natoms pbc atom distance at start reference at t=0 70: 1 3 2 70: 2 3 5 1.112 nm 1.000 nm 70: 70: There was 1 NOTE 70: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeSteppingPull_MtsComparisonTest_WithinTolerances_0_sim.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 70: Can not increase nstlist because an NVE ensemble is used 70: Using 2 MPI threads 70: 70: Non-default thread affinity set, disabling internal thread affinity 70: 70: Using 2 OpenMP threads per tMPI thread 70: 70: starting mdrun 'spc2' 70: 4 steps, 0.0 ps. 70: Setting the LD random seed to -604402179 70: 70: Generated 3 of the 3 non-bonded parameter combinations 70: 70: Generated 3 of the 3 1-4 parameter combinations 70: 70: Excluding 2 bonded neighbours molecule type 'SOL' 70: 70: turning H bonds into constraints... 70: 70: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/spc2.gro' 70: 70: This run will generate roughly 0 Mb of data 70: 70: Writing final coordinates. 70: 70: NOTE: 11 % of the run time was spent in domain decomposition, 70: 2 % of the run time was spent in pair search, 70: you might want to increase nstlist (this has no effect on accuracy) 70: 70: NOTE: 14 % of the run time was spent communicating energies, 70: you might want to increase some nst* mdp options 70: 70: Core t (s) Wall t (s) (%) 70: Time: 2.433 0.624 389.9 70: (ns/day) (hour/ns) 70: Performance: 0.692 34.661 70: 70: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeSteppingPull_MtsComparisonTest_WithinTolerances_0_input.mdp]: 70: verlet-buffer-pressure-tolerance is ignored when verlet-buffer-tolerance 70: < 0 70: 70: Generating 1-4 interactions: fudge = 0.5 70: Pull group 1 'FirstWaterMolecule' has 3 atoms 70: Pull group 2 'SecondWaterMolecule' has 3 atoms 70: Number of degrees of freedom in T-Coupling group rest is 9.00 70: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 70: Pull group natoms pbc atom distance at start reference at t=0 70: 1 3 2 70: 2 3 5 1.112 nm 1.000 nm 70: 70: There was 1 NOTE 70: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeSteppingPull_MtsComparisonTest_WithinTolerances_0_sim.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 70: Multiple time stepping is only supported with GPUs when MTS is only applied to longrange-nonbonded forces. 70: Can not increase nstlist because an NVE ensemble is used 70: 70: Using 2 MPI threads 70: 70: Non-default thread affinity set, disabling internal thread affinity 70: 70: Using 2 OpenMP threads per tMPI thread 70: 70: starting mdrun 'spc2' 70: 4 steps, 0.0 ps. 70: Setting the LD random seed to -1125193749 70: 70: Generated 3 of the 3 non-bonded parameter combinations 70: 70: Generated 3 of the 3 1-4 parameter combinations 70: 70: Excluding 2 bonded neighbours molecule type 'SOL' 70: 70: turning H bonds into constraints... 70: 70: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/spc2.gro' 70: 70: This run will generate roughly 0 Mb of data 70: 70: Writing final coordinates. 70: 70: NOTE: 14 % of the run time was spent in domain decomposition, 70: 3 % of the run time was spent in pair search, 70: you might want to increase nstlist (this has no effect on accuracy) 70: 70: NOTE: 11 % of the run time was spent communicating energies, 70: you might want to increase some nst* mdp options 70: 70: Core t (s) Wall t (s) (%) 70: Time: 2.192 0.564 388.8 70: (ns/day) (hour/ns) 70: Performance: 0.766 31.327 70: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeSteppingPull_MtsComparisonTest_WithinTolerances_0_sim1.edr as single precision energy file 70: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeSteppingPull_MtsComparisonTest_WithinTolerances_0_sim2.edr as single precision energy file 70: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Last energy frame read 1 time 0.004 Last energy frame read 1 time 0.004 70: 70: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeSteppingPull_MtsComparisonTest_WithinTolerances_0_sim1.edr as single precision energy file 70: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeSteppingPull_MtsComparisonTest_WithinTolerances_0_sim2.edr as single precision energy file 70: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Last energy frame read 1 time 0.004 Last energy frame read 1 time 0.004 [ OK ] MultipleTimeSteppingIsNearSingleTimeSteppingPull/MtsComparisonTest.WithinTolerances/0 (2608 ms) 70: [----------] 1 test from MultipleTimeSteppingIsNearSingleTimeSteppingPull/MtsComparisonTest (2608 ms total) 70: 70: [----------] 12 tests from FreezeWorks/FreezeGroupTest 70: [ RUN ] FreezeWorks/FreezeGroupTest.WithinTolerances/0 70: 70: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_0_input.mdp]: 70: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 70: that with the Verlet scheme, nstlist has no effect on the accuracy of 70: your simulation. 70: 70: 70: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_0_input.mdp]: 70: Setting nstcalcenergy (100) equal to nstenergy (4) 70: 70: Generating 1-4 interactions: fudge = 0.5 70: 70: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_0_input.mdp]: 70: There are 5 atoms that are fully frozen and part of COMM removal 70: group(s), removing these atoms from the COMM removal group(s) 70: 70: 70: WARNING 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_0_input.mdp]: 70: There are 3 atoms that are frozen along less then 3 dimensions and part 70: of COMM removal group(s), due to limitations in the code these still 70: contribute to the mass of the COM along frozen dimensions and therefore 70: the COMM correction will be too small. 70: 70: Number of degrees of freedom in T-Coupling group System is 33.00 70: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 70: 70: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_0_input.mdp]: 70: NVE simulation: will use the initial temperature of 246.451 K for 70: determining the Verlet buffer size 70: 70: 70: NOTE 5 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_0_input.mdp]: 70: You are using a plain Coulomb cut-off, which might produce artifacts. 70: You might want to consider using PME electrostatics. 70: 70: 70: 70: There were 5 NOTEs 70: 70: There was 1 WARNING 70: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_0.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 70: Can not increase nstlist because an NVE ensemble is used 70: Using 2 MPI threads 70: 70: Non-default thread affinity set, disabling internal thread affinity 70: 70: Using 2 OpenMP threads per tMPI thread 70: 70: starting mdrun 'Alanine-dipeptide' 70: 8 steps, 0.0 ps. 70: Generated 2145 of the 2145 non-bonded parameter combinations 70: 70: Generated 2145 of the 2145 1-4 parameter combinations 70: 70: Excluding 3 bonded neighbours molecule type 'ALANINEDIPEPTIDE' 70: 70: turning H bonds into constraints... 70: 70: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/alanine_vacuo.gro' 70: 70: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 246.451 K 70: 70: Calculated rlist for 1x1 atom pair-list as 0.755 nm, buffer size 0.055 nm 70: 70: Set rlist, assuming 4x4 atom pair-list, to 0.749 nm, buffer size 0.049 nm 70: 70: Note that mdrun will redetermine rlist based on the actual pair-list setup 70: 70: This run will generate roughly 0 Mb of data 70: 70: Writing final coordinates. 70: 70: 70: Dynamic load balancing report: 70: DLB was off during the run due to low measured imbalance. 70: Average load imbalance: 42.7%. 70: The balanceable part of the MD step is 40%, load imbalance is computed from this. 70: Part of the total run time spent waiting due to load imbalance: 17.2%. 70: 70: NOTE: 17.2 % of the available CPU time was lost due to load imbalance 70: in the domain decomposition. 70: Dynamic load balancing was automatically disabled, but it might be beneficial to manually turn it on (option -dlb yes.) 70: You can also consider manually changing the decomposition (option -dd); 70: e.g. by using fewer domains along the box dimension in which there is 70: considerable inhomogeneity in the simulated system. 70: 70: NOTE: 19 % of the run time was spent in domain decomposition, 70: 4 % of the run time was spent in pair search, 70: you might want to increase nstlist (this has no effect on accuracy) 70: 70: NOTE: 10 % of the run time was spent communicating energies, 70: you might want to increase some nst* mdp options 70: 70: Core t (s) Wall t (s) (%) 70: Time: 3.305 0.844 391.6 70: (ns/day) (hour/ns) 70: Performance: 0.921 26.047 70: 70: 70: [ OK ] FreezeWorks/FreezeGroupTest.WithinTolerances/0 (1639 ms) 70: [ RUN ] FreezeWorks/FreezeGroupTest.WithinTolerances/1 70: 70: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_1_input.mdp]: 70: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 70: that with the Verlet scheme, nstlist has no effect on the accuracy of 70: your simulation. 70: 70: 70: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_1_input.mdp]: 70: Setting nstcalcenergy (100) equal to nstenergy (4) 70: 70: Generating 1-4 interactions: fudge = 0.5 70: 70: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_1_input.mdp]: 70: There are 5 atoms that are fully frozen and part of COMM removal 70: group(s), removing these atoms from the COMM removal group(s) 70: 70: 70: WARNING 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_1_input.mdp]: 70: There are 3 atoms that are frozen along less then 3 dimensions and part 70: of COMM removal group(s), due to limitations in the code these still 70: contribute to the mass of the COM along frozen dimensions and therefore 70: the COMM correction will be too small. 70: 70: Number of degrees of freedom in T-Coupling group System is 33.00 70: 70: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_1_input.mdp]: 70: NVE simulation: will use the initial temperature of 246.451 K for 70: determining the Verlet buffer size 70: 70: 70: NOTE 5 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_1_input.mdp]: 70: You are using a plain Coulomb cut-off, which might produce artifacts. 70: You might want to consider using PME electrostatics. 70: 70: 70: 70: There were 5 NOTEs 70: 70: There was 1 WARNING 70: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_1.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 70: Can not increase nstlist because an NVE ensemble is used 70: Using 2 MPI threads 70: 70: Non-default thread affinity set, disabling internal thread affinity 70: 70: Using 2 OpenMP threads per tMPI thread 70: 70: starting mdrun 'Alanine-dipeptide' 70: 8 steps, 0.0 ps. 70: Generated 2145 of the 2145 non-bonded parameter combinations 70: 70: Generated 2145 of the 2145 1-4 parameter combinations 70: 70: Excluding 3 bonded neighbours molecule type 'ALANINEDIPEPTIDE' 70: 70: turning H bonds into constraints... 70: 70: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/alanine_vacuo.gro' 70: 70: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 246.451 K 70: 70: Calculated rlist for 1x1 atom pair-list as 0.755 nm, buffer size 0.055 nm 70: 70: Set rlist, assuming 4x4 atom pair-list, to 0.749 nm, buffer size 0.049 nm 70: 70: Note that mdrun will redetermine rlist based on the actual pair-list setup 70: 70: This run will generate roughly 0 Mb of data 70: 70: Writing final coordinates. 70: 70: 70: Dynamic load balancing report: 70: DLB was off during the run due to low measured imbalance. 70: Average load imbalance: 35.5%. 70: The balanceable part of the MD step is 43%, load imbalance is computed from this. 70: Part of the total run time spent waiting due to load imbalance: 15.3%. 70: 70: NOTE: 15.3 % of the available CPU time was lost due to load imbalance 70: in the domain decomposition. 70: Dynamic load balancing was automatically disabled, but it might be beneficial to manually turn it on (option -dlb yes.) 70: You can also consider manually changing the decomposition (option -dd); 70: e.g. by using fewer domains along the box dimension in which there is 70: considerable inhomogeneity in the simulated system. 70: 70: NOTE: 18 % of the run time was spent in domain decomposition, 70: 3 % of the run time was spent in pair search, 70: you might want to increase nstlist (this has no effect on accuracy) 70: 70: NOTE: 11 % of the run time was spent communicating energies, 70: you might want to increase some nst* mdp options 70: 70: Core t (s) Wall t (s) (%) 70: Time: 3.726 0.947 393.4 70: (ns/day) (hour/ns) 70: Performance: 0.821 29.238 70: 70: 70: [ OK ] FreezeWorks/FreezeGroupTest.WithinTolerances/1 (1812 ms) 70: [ RUN ] FreezeWorks/FreezeGroupTest.WithinTolerances/2 70: 70: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_2_input.mdp]: 70: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 70: that with the Verlet scheme, nstlist has no effect on the accuracy of 70: your simulation. 70: 70: 70: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_2_input.mdp]: 70: Setting nstcalcenergy (100) equal to nstenergy (4) 70: 70: Generating 1-4 interactions: fudge = 0.5 70: 70: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_2_input.mdp]: 70: There are 5 atoms that are fully frozen and part of COMM removal 70: group(s), removing these atoms from the COMM removal group(s) 70: 70: 70: WARNING 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_2_input.mdp]: 70: There are 3 atoms that are frozen along less then 3 dimensions and part 70: of COMM removal group(s), due to limitations in the code these still 70: contribute to the mass of the COM along frozen dimensions and therefore 70: the COMM correction will be too small. 70: 70: Number of degrees of freedom in T-Coupling group System is 33.00 70: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 70: 70: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_2_input.mdp]: 70: NVE simulation: will use the initial temperature of 246.451 K for 70: determining the Verlet buffer size 70: 70: 70: NOTE 5 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_2_input.mdp]: 70: You are using a plain Coulomb cut-off, which might produce artifacts. 70: You might want to consider using PME electrostatics. 70: 70: 70: 70: There were 5 NOTEs 70: 70: There was 1 WARNING 70: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_2.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 70: Can not increase nstlist because an NVE ensemble is used 70: Using 2 MPI threads 70: 70: Non-default thread affinity set, disabling internal thread affinity 70: 70: Using 2 OpenMP threads per tMPI thread 70: 70: starting mdrun 'Alanine-dipeptide' 70: 8 steps, 0.0 ps. 70: Generated 2145 of the 2145 non-bonded parameter combinations 70: 70: Generated 2145 of the 2145 1-4 parameter combinations 70: 70: Excluding 3 bonded neighbours molecule type 'ALANINEDIPEPTIDE' 70: 70: turning H bonds into constraints... 70: 70: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/alanine_vacuo.gro' 70: 70: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 246.451 K 70: 70: Calculated rlist for 1x1 atom pair-list as 0.755 nm, buffer size 0.055 nm 70: 70: Set rlist, assuming 4x4 atom pair-list, to 0.749 nm, buffer size 0.049 nm 70: 70: Note that mdrun will redetermine rlist based on the actual pair-list setup 70: 70: This run will generate roughly 0 Mb of data 70: 70: Writing final coordinates. 70: 70: 70: Dynamic load balancing report: 70: DLB was off during the run due to low measured imbalance. 70: Average load imbalance: 33.2%. 70: The balanceable part of the MD step is 44%, load imbalance is computed from this. 70: Part of the total run time spent waiting due to load imbalance: 14.7%. 70: 70: NOTE: 14.7 % of the available CPU time was lost due to load imbalance 70: in the domain decomposition. 70: Dynamic load balancing was automatically disabled, but it might be beneficial to manually turn it on (option -dlb yes.) 70: You can also consider manually changing the decomposition (option -dd); 70: e.g. by using fewer domains along the box dimension in which there is 70: considerable inhomogeneity in the simulated system. 70: 70: NOTE: 19 % of the run time was spent in domain decomposition, 70: 4 % of the run time was spent in pair search, 70: you might want to increase nstlist (this has no effect on accuracy) 70: 70: NOTE: 8 % of the run time was spent communicating energies, 70: you might want to increase some nst* mdp options 70: 70: Core t (s) Wall t (s) (%) 70: Time: 3.327 0.842 395.2 70: (ns/day) (hour/ns) 70: Performance: 0.924 25.984 70: 70: 70: [ OK ] FreezeWorks/FreezeGroupTest.WithinTolerances/2 (1739 ms) 70: [ RUN ] FreezeWorks/FreezeGroupTest.WithinTolerances/3 70: 70: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_3_input.mdp]: 70: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 70: that with the Verlet scheme, nstlist has no effect on the accuracy of 70: your simulation. 70: 70: 70: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_3_input.mdp]: 70: Setting nstcalcenergy (100) equal to nstenergy (4) 70: 70: Generating 1-4 interactions: fudge = 0.5 70: 70: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_3_input.mdp]: 70: There are 5 atoms that are fully frozen and part of COMM removal 70: group(s), removing these atoms from the COMM removal group(s) 70: 70: 70: WARNING 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_3_input.mdp]: 70: There are 3 atoms that are frozen along less then 3 dimensions and part 70: of COMM removal group(s), due to limitations in the code these still 70: contribute to the mass of the COM along frozen dimensions and therefore 70: the COMM correction will be too small. 70: 70: Number of degrees of freedom in T-Coupling group System is 33.00 70: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 70: 70: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_3_input.mdp]: 70: NVE simulation: will use the initial temperature of 246.451 K for 70: determining the Verlet buffer size 70: 70: 70: NOTE 5 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_3_input.mdp]: 70: You are using a plain Coulomb cut-off, which might produce artifacts. 70: You might want to consider using PME electrostatics. 70: 70: 70: 70: There were 5 NOTEs 70: 70: There was 1 WARNING 70: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_3.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 70: Can not increase nstlist because an NVE ensemble is used 70: Using 2 MPI threads 70: 70: Non-default thread affinity set, disabling internal thread affinity 70: 70: Using 2 OpenMP threads per tMPI thread 70: 70: starting mdrun 'Alanine-dipeptide' 70: 8 steps, 0.0 ps. 70: Generated 2145 of the 2145 non-bonded parameter combinations 70: 70: Generated 2145 of the 2145 1-4 parameter combinations 70: 70: Excluding 3 bonded neighbours molecule type 'ALANINEDIPEPTIDE' 70: 70: turning H bonds into constraints... 70: 70: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/alanine_vacuo.gro' 70: 70: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 246.451 K 70: 70: Calculated rlist for 1x1 atom pair-list as 0.755 nm, buffer size 0.055 nm 70: 70: Set rlist, assuming 4x4 atom pair-list, to 0.749 nm, buffer size 0.049 nm 70: 70: Note that mdrun will redetermine rlist based on the actual pair-list setup 70: 70: This run will generate roughly 0 Mb of data 70: 70: Writing final coordinates. 70: 70: 70: Dynamic load balancing report: 70: DLB was off during the run due to low measured imbalance. 70: Average load imbalance: 30.9%. 70: The balanceable part of the MD step is 46%, load imbalance is computed from this. 70: Part of the total run time spent waiting due to load imbalance: 14.3%. 70: 70: NOTE: 14.3 % of the available CPU time was lost due to load imbalance 70: in the domain decomposition. 70: Dynamic load balancing was automatically disabled, but it might be beneficial to manually turn it on (option -dlb yes.) 70: You can also consider manually changing the decomposition (option -dd); 70: e.g. by using fewer domains along the box dimension in which there is 70: considerable inhomogeneity in the simulated system. 70: 70: NOTE: 18 % of the run time was spent in domain decomposition, 70: 4 % of the run time was spent in pair search, 70: you might want to increase nstlist (this has no effect on accuracy) 70: 70: NOTE: 14 % of the run time was spent communicating energies, 70: you might want to increase some nst* mdp options 70: 70: Core t (s) Wall t (s) (%) 70: Time: 3.600 0.916 393.1 70: (ns/day) (hour/ns) 70: Performance: 0.849 28.269 70: 70: 70: [ OK ] FreezeWorks/FreezeGroupTest.WithinTolerances/3 (1716 ms) 70: [ RUN ] FreezeWorks/FreezeGroupTest.WithinTolerances/4 70: 70: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_4_input.mdp]: 70: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 70: that with the Verlet scheme, nstlist has no effect on the accuracy of 70: your simulation. 70: 70: 70: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_4_input.mdp]: 70: Setting nstcalcenergy (100) equal to nstenergy (4) 70: 70: Generating 1-4 interactions: fudge = 0.5 70: 70: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_4_input.mdp]: 70: There are 5 atoms that are fully frozen and part of COMM removal 70: group(s), removing these atoms from the COMM removal group(s) 70: 70: 70: WARNING 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_4_input.mdp]: 70: There are 3 atoms that are frozen along less then 3 dimensions and part 70: of COMM removal group(s), due to limitations in the code these still 70: contribute to the mass of the COM along frozen dimensions and therefore 70: the COMM correction will be too small. 70: 70: Number of degrees of freedom in T-Coupling group System is 33.00 70: 70: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_4_input.mdp]: 70: NVE simulation: will use the initial temperature of 246.451 K for 70: determining the Verlet buffer size 70: 70: 70: NOTE 5 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_4_input.mdp]: 70: You are using a plain Coulomb cut-off, which might produce artifacts. 70: You might want to consider using PME electrostatics. 70: 70: 70: 70: There were 5 NOTEs 70: 70: There was 1 WARNING 70: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_4.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 70: Can not increase nstlist because an NVE ensemble is used 70: Using 2 MPI threads 70: 70: Non-default thread affinity set, disabling internal thread affinity 70: 70: Using 2 OpenMP threads per tMPI thread 70: 70: starting mdrun 'Alanine-dipeptide' 70: 8 steps, 0.0 ps. 70: Generated 2145 of the 2145 non-bonded parameter combinations 70: 70: Generated 2145 of the 2145 1-4 parameter combinations 70: 70: Excluding 3 bonded neighbours molecule type 'ALANINEDIPEPTIDE' 70: 70: turning H bonds into constraints... 70: 70: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/alanine_vacuo.gro' 70: 70: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 246.451 K 70: 70: Calculated rlist for 1x1 atom pair-list as 0.755 nm, buffer size 0.055 nm 70: 70: Set rlist, assuming 4x4 atom pair-list, to 0.749 nm, buffer size 0.049 nm 70: 70: Note that mdrun will redetermine rlist based on the actual pair-list setup 70: 70: This run will generate roughly 0 Mb of data 70: 70: Writing final coordinates. 70: 70: 70: Dynamic load balancing report: 70: DLB was off during the run due to low measured imbalance. 70: Average load imbalance: 15.8%. 70: The balanceable part of the MD step is 52%, load imbalance is computed from this. 70: Part of the total run time spent waiting due to load imbalance: 8.3%. 70: 70: NOTE: 8.3 % of the available CPU time was lost due to load imbalance 70: in the domain decomposition. 70: Dynamic load balancing was automatically disabled, but it might be beneficial to manually turn it on (option -dlb yes.) 70: You can also consider manually changing the decomposition (option -dd); 70: e.g. by using fewer domains along the box dimension in which there is 70: considerable inhomogeneity in the simulated system. 70: 70: NOTE: 16 % of the run time was spent in domain decomposition, 70: 3 % of the run time was spent in pair search, 70: you might want to increase nstlist (this has no effect on accuracy) 70: 70: NOTE: 21 % of the run time was spent communicating energies, 70: you might want to increase some nst* mdp options 70: 70: Core t (s) Wall t (s) (%) 70: Time: 4.484 1.136 394.7 70: (ns/day) (hour/ns) 70: Performance: 0.685 35.058 70: 70: 70: [ OK ] FreezeWorks/FreezeGroupTest.WithinTolerances/4 (1903 ms) 70: [ RUN ] FreezeWorks/FreezeGroupTest.WithinTolerances/5 70: ./src/programs/mdrun/tests/freezegroups.cpp:209: Skipped 70: Parrinello-Rahman is not implemented in md-vv. 70: [ SKIPPED ] FreezeWorks/FreezeGroupTest.WithinTolerances/5 (0 ms) 70: [ RUN ] FreezeWorks/FreezeGroupTest.WithinTolerances/6 70: 70: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_6_input.mdp]: 70: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 70: that with the Verlet scheme, nstlist has no effect on the accuracy of 70: your simulation. 70: 70: 70: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_6_input.mdp]: 70: Setting nstcalcenergy (100) equal to nstenergy (4) 70: 70: Generating 1-4 interactions: fudge = 0.5 70: 70: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_6_input.mdp]: 70: There are 5 atoms that are fully frozen and part of COMM removal 70: group(s), removing these atoms from the COMM removal group(s) 70: 70: 70: WARNING 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_6_input.mdp]: 70: There are 3 atoms that are frozen along less then 3 dimensions and part 70: of COMM removal group(s), due to limitations in the code these still 70: contribute to the mass of the COM along frozen dimensions and therefore 70: the COMM correction will be too small. 70: 70: Number of degrees of freedom in T-Coupling group System is 33.00 70: 70: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_6_input.mdp]: 70: You are using a plain Coulomb cut-off, which might produce artifacts. 70: You might want to consider using PME electrostatics. 70: 70: 70: 70: There were 4 NOTEs 70: 70: There was 1 WARNING 70: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_6.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 70: Changing nstlist from 8 to 20, rlist from 0.754 to 0.856 70: 70: Using 2 MPI threads 70: 70: Non-default thread affinity set, disabling internal thread affinity 70: 70: Using 2 OpenMP threads per tMPI thread 70: 70: starting mdrun 'Alanine-dipeptide' 70: 8 steps, 0.0 ps. 70: Generated 2145 of the 2145 non-bonded parameter combinations 70: 70: Generated 2145 of the 2145 1-4 parameter combinations 70: 70: Excluding 3 bonded neighbours molecule type 'ALANINEDIPEPTIDE' 70: 70: turning H bonds into constraints... 70: 70: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/alanine_vacuo.gro' 70: 70: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 70: 70: Calculated rlist for 1x1 atom pair-list as 0.761 nm, buffer size 0.061 nm 70: 70: Set rlist, assuming 4x4 atom pair-list, to 0.754 nm, buffer size 0.054 nm 70: 70: Note that mdrun will redetermine rlist based on the actual pair-list setup 70: 70: This run will generate roughly 0 Mb of data 70: 70: Writing final coordinates. 70: 70: NOTE: 11 % of the run time was spent in domain decomposition, 70: 2 % of the run time was spent in pair search, 70: you might want to increase nstlist (this has no effect on accuracy) 70: 70: NOTE: 10 % of the run time was spent communicating energies, 70: you might want to increase some nst* mdp options 70: 70: Core t (s) Wall t (s) (%) 70: Time: 2.967 0.757 391.7 70: (ns/day) (hour/ns) 70: Performance: 1.027 23.378 70: 70: 70: [ OK ] FreezeWorks/FreezeGroupTest.WithinTolerances/6 (1603 ms) 70: [ RUN ] FreezeWorks/FreezeGroupTest.WithinTolerances/7 70: 70: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_7_input.mdp]: 70: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 70: that with the Verlet scheme, nstlist has no effect on the accuracy of 70: your simulation. 70: 70: 70: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_7_input.mdp]: 70: Setting nstcalcenergy (100) equal to nstenergy (4) 70: 70: Generating 1-4 interactions: fudge = 0.5 70: 70: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_7_input.mdp]: 70: There are 5 atoms that are fully frozen and part of COMM removal 70: group(s), removing these atoms from the COMM removal group(s) 70: 70: 70: WARNING 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_7_input.mdp]: 70: There are 3 atoms that are frozen along less then 3 dimensions and part 70: of COMM removal group(s), due to limitations in the code these still 70: contribute to the mass of the COM along frozen dimensions and therefore 70: the COMM correction will be too small. 70: 70: Number of degrees of freedom in T-Coupling group System is 33.00 70: 70: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_7_input.mdp]: 70: You are using a plain Coulomb cut-off, which might produce artifacts. 70: You might want to consider using PME electrostatics. 70: 70: 70: 70: There were 4 NOTEs 70: 70: There was 1 WARNING 70: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_7.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 70: Changing nstlist from 8 to 20, rlist from 0.754 to 0.856 70: 70: Using 2 MPI threads 70: 70: Non-default thread affinity set, disabling internal thread affinity 70: 70: Using 2 OpenMP threads per tMPI thread 70: 70: starting mdrun 'Alanine-dipeptide' 70: 8 steps, 0.0 ps. 70: Generated 2145 of the 2145 non-bonded parameter combinations 70: 70: Generated 2145 of the 2145 1-4 parameter combinations 70: 70: Excluding 3 bonded neighbours molecule type 'ALANINEDIPEPTIDE' 70: 70: turning H bonds into constraints... 70: 70: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/alanine_vacuo.gro' 70: 70: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 70: 70: Calculated rlist for 1x1 atom pair-list as 0.761 nm, buffer size 0.061 nm 70: 70: Set rlist, assuming 4x4 atom pair-list, to 0.754 nm, buffer size 0.054 nm 70: 70: Note that mdrun will redetermine rlist based on the actual pair-list setup 70: 70: This run will generate roughly 0 Mb of data 70: 70: Writing final coordinates. 70: 70: NOTE: 11 % of the run time was spent in domain decomposition, 70: 2 % of the run time was spent in pair search, 70: you might want to increase nstlist (this has no effect on accuracy) 70: 70: NOTE: 11 % of the run time was spent communicating energies, 70: you might want to increase some nst* mdp options 70: 70: Core t (s) Wall t (s) (%) 70: Time: 3.180 0.822 386.8 70: (ns/day) (hour/ns) 70: Performance: 0.946 25.374 70: 70: 70: [ OK ] FreezeWorks/FreezeGroupTest.WithinTolerances/7 (1827 ms) 70: [ RUN ] FreezeWorks/FreezeGroupTest.WithinTolerances/8 70: 70: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_8_input.mdp]: 70: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 70: that with the Verlet scheme, nstlist has no effect on the accuracy of 70: your simulation. 70: 70: 70: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_8_input.mdp]: 70: Setting nstcalcenergy (100) equal to nstenergy (4) 70: 70: Generating 1-4 interactions: fudge = 0.5 70: 70: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_8_input.mdp]: 70: There are 5 atoms that are fully frozen and part of COMM removal 70: group(s), removing these atoms from the COMM removal group(s) 70: 70: 70: WARNING 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_8_input.mdp]: 70: There are 3 atoms that are frozen along less then 3 dimensions and part 70: of COMM removal group(s), due to limitations in the code these still 70: contribute to the mass of the COM along frozen dimensions and therefore 70: the COMM correction will be too small. 70: 70: Number of degrees of freedom in T-Coupling group System is 33.00 70: 70: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_8_input.mdp]: 70: You are using a plain Coulomb cut-off, which might produce artifacts. 70: You might want to consider using PME electrostatics. 70: 70: 70: 70: There were 4 NOTEs 70: 70: There was 1 WARNING 70: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_8.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 70: Changing nstlist from 8 to 20, rlist from 0.754 to 0.856 70: 70: Using 2 MPI threads 70: 70: Non-default thread affinity set, disabling internal thread affinity 70: 70: Using 2 OpenMP threads per tMPI thread 70: 70: starting mdrun 'Alanine-dipeptide' 70: 8 steps, 0.0 ps. 70: Generated 2145 of the 2145 non-bonded parameter combinations 70: 70: Generated 2145 of the 2145 1-4 parameter combinations 70: 70: Excluding 3 bonded neighbours molecule type 'ALANINEDIPEPTIDE' 70: 70: turning H bonds into constraints... 70: 70: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/alanine_vacuo.gro' 70: 70: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 70: 70: Calculated rlist for 1x1 atom pair-list as 0.761 nm, buffer size 0.061 nm 70: 70: Set rlist, assuming 4x4 atom pair-list, to 0.754 nm, buffer size 0.054 nm 70: 70: Note that mdrun will redetermine rlist based on the actual pair-list setup 70: 70: This run will generate roughly 0 Mb of data 70: 70: Writing final coordinates. 70: 70: NOTE: 10 % of the run time was spent in domain decomposition, 70: 2 % of the run time was spent in pair search, 70: you might want to increase nstlist (this has no effect on accuracy) 70: 70: NOTE: 12 % of the run time was spent communicating energies, 70: you might want to increase some nst* mdp options 70: 70: Core t (s) Wall t (s) (%) 70: Time: 3.035 0.773 392.5 70: (ns/day) (hour/ns) 70: Performance: 1.005 23.871 70: 70: 70: [ OK ] FreezeWorks/FreezeGroupTest.WithinTolerances/8 (1624 ms) 70: [ RUN ] FreezeWorks/FreezeGroupTest.WithinTolerances/9 70: 70: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_9_input.mdp]: 70: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 70: that with the Verlet scheme, nstlist has no effect on the accuracy of 70: your simulation. 70: 70: 70: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_9_input.mdp]: 70: Setting nstcalcenergy (100) equal to nstenergy (4) 70: 70: Generating 1-4 interactions: fudge = 0.5 70: 70: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_9_input.mdp]: 70: There are 5 atoms that are fully frozen and part of COMM removal 70: group(s), removing these atoms from the COMM removal group(s) 70: 70: 70: WARNING 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_9_input.mdp]: 70: There are 3 atoms that are frozen along less then 3 dimensions and part 70: of COMM removal group(s), due to limitations in the code these still 70: contribute to the mass of the COM along frozen dimensions and therefore 70: the COMM correction will be too small. 70: 70: Number of degrees of freedom in T-Coupling group System is 33.00 70: 70: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_9_input.mdp]: 70: You are using a plain Coulomb cut-off, which might produce artifacts. 70: You might want to consider using PME electrostatics. 70: 70: 70: 70: There were 4 NOTEs 70: 70: There was 1 WARNING 70: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_9.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 70: Changing nstlist from 8 to 100, rlist from 0.734 to 0.829 70: 70: Using 2 MPI threads 70: 70: Non-default thread affinity set, disabling internal thread affinity 70: 70: Using 2 OpenMP threads per tMPI thread 70: 70: starting mdrun 'Alanine-dipeptide' 70: 8 steps, 0.0 ps. 70: Generated 2145 of the 2145 non-bonded parameter combinations 70: 70: Generated 2145 of the 2145 1-4 parameter combinations 70: 70: Excluding 3 bonded neighbours molecule type 'ALANINEDIPEPTIDE' 70: 70: turning H bonds into constraints... 70: 70: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 70: 70: Calculated rlist for 1x1 atom pair-list as 0.737 nm, buffer size 0.037 nm 70: 70: Set rlist, assuming 4x4 atom pair-list, to 0.734 nm, buffer size 0.034 nm 70: 70: Note that mdrun will redetermine rlist based on the actual pair-list setup 70: 70: This run will generate roughly 0 Mb of data 70: 70: Writing final coordinates. 70: 70: NOTE: 12 % of the run time was spent in domain decomposition, 70: 2 % of the run time was spent in pair search, 70: you might want to increase nstlist (this has no effect on accuracy) 70: 70: NOTE: 10 % of the run time was spent communicating energies, 70: you might want to increase some nst* mdp options 70: 70: Core t (s) Wall t (s) (%) 70: Time: 2.728 0.700 389.8 70: (ns/day) (hour/ns) 70: Performance: 1.111 21.602 70: 70: 70: [ OK ] FreezeWorks/FreezeGroupTest.WithinTolerances/9 (1944 ms) 70: [ RUN ] FreezeWorks/FreezeGroupTest.WithinTolerances/10 70: 70: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_10_input.mdp]: 70: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 70: that with the Verlet scheme, nstlist has no effect on the accuracy of 70: your simulation. 70: 70: 70: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_10_input.mdp]: 70: Setting nstcalcenergy (100) equal to nstenergy (4) 70: 70: Generating 1-4 interactions: fudge = 0.5 70: 70: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_10_input.mdp]: 70: There are 5 atoms that are fully frozen and part of COMM removal 70: group(s), removing these atoms from the COMM removal group(s) 70: 70: 70: WARNING 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_10_input.mdp]: 70: There are 3 atoms that are frozen along less then 3 dimensions and part 70: of COMM removal group(s), due to limitations in the code these still 70: contribute to the mass of the COM along frozen dimensions and therefore 70: the COMM correction will be too small. 70: 70: Number of degrees of freedom in T-Coupling group System is 33.00 70: 70: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_10_input.mdp]: 70: You are using a plain Coulomb cut-off, which might produce artifacts. 70: You might want to consider using PME electrostatics. 70: 70: 70: 70: There were 4 NOTEs 70: 70: There was 1 WARNING 70: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_10.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 70: Changing nstlist from 8 to 100, rlist from 0.734 to 0.829 70: 70: Using 2 MPI threads 70: 70: Non-default thread affinity set, disabling internal thread affinity 70: 70: Using 2 OpenMP threads per tMPI thread 70: 70: starting mdrun 'Alanine-dipeptide' 70: 8 steps, 0.0 ps. 70: Generated 2145 of the 2145 non-bonded parameter combinations 70: 70: Generated 2145 of the 2145 1-4 parameter combinations 70: 70: Excluding 3 bonded neighbours molecule type 'ALANINEDIPEPTIDE' 70: 70: turning H bonds into constraints... 70: 70: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 70: 70: Calculated rlist for 1x1 atom pair-list as 0.737 nm, buffer size 0.037 nm 70: 70: Set rlist, assuming 4x4 atom pair-list, to 0.734 nm, buffer size 0.034 nm 70: 70: Note that mdrun will redetermine rlist based on the actual pair-list setup 70: 70: This run will generate roughly 0 Mb of data 70: 70: Writing final coordinates. 70: 70: NOTE: 11 % of the run time was spent in domain decomposition, 70: 2 % of the run time was spent in pair search, 70: you might want to increase nstlist (this has no effect on accuracy) 70: 70: NOTE: 11 % of the run time was spent communicating energies, 70: you might want to increase some nst* mdp options 70: 70: Core t (s) Wall t (s) (%) 70: Time: 2.712 0.692 392.0 70: (ns/day) (hour/ns) 70: Performance: 1.124 21.355 70: 70: 70: [ OK ] FreezeWorks/FreezeGroupTest.WithinTolerances/10 (1914 ms) 70: [ RUN ] FreezeWorks/FreezeGroupTest.WithinTolerances/11 70: 70: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_11_input.mdp]: 70: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 70: that with the Verlet scheme, nstlist has no effect on the accuracy of 70: your simulation. 70: 70: 70: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_11_input.mdp]: 70: Setting nstcalcenergy (100) equal to nstenergy (4) 70: 70: Generating 1-4 interactions: fudge = 0.5 70: 70: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_11_input.mdp]: 70: There are 5 atoms that are fully frozen and part of COMM removal 70: group(s), removing these atoms from the COMM removal group(s) 70: 70: 70: WARNING 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_11_input.mdp]: 70: There are 3 atoms that are frozen along less then 3 dimensions and part 70: of COMM removal group(s), due to limitations in the code these still 70: contribute to the mass of the COM along frozen dimensions and therefore 70: the COMM correction will be too small. 70: 70: Number of degrees of freedom in T-Coupling group System is 33.00 70: 70: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_11_input.mdp]: 70: You are using a plain Coulomb cut-off, which might produce artifacts. 70: You might want to consider using PME electrostatics. 70: 70: 70: 70: There were 4 NOTEs 70: 70: There was 1 WARNING 70: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_11.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 70: Changing nstlist from 8 to 100, rlist from 0.734 to 0.829 70: 70: Using 2 MPI threads 70: 70: Non-default thread affinity set, disabling internal thread affinity 70: 70: Using 2 OpenMP threads per tMPI thread 70: 70: starting mdrun 'Alanine-dipeptide' 70: 8 steps, 0.0 ps. 70: Generated 2145 of the 2145 non-bonded parameter combinations 70: 70: Generated 2145 of the 2145 1-4 parameter combinations 70: 70: Excluding 3 bonded neighbours molecule type 'ALANINEDIPEPTIDE' 70: 70: turning H bonds into constraints... 70: 70: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 70: 70: Calculated rlist for 1x1 atom pair-list as 0.737 nm, buffer size 0.037 nm 70: 70: Set rlist, assuming 4x4 atom pair-list, to 0.734 nm, buffer size 0.034 nm 70: 70: Note that mdrun will redetermine rlist based on the actual pair-list setup 70: 70: This run will generate roughly 0 Mb of data 70: 70: Writing final coordinates. 70: 70: NOTE: 10 % of the run time was spent in domain decomposition, 70: 2 % of the run time was spent in pair search, 70: you might want to increase nstlist (this has no effect on accuracy) 70: 70: NOTE: 12 % of the run time was spent communicating energies, 70: you might want to increase some nst* mdp options 70: 70: Core t (s) Wall t (s) (%) 70: Time: 2.712 0.696 389.8 70: (ns/day) (hour/ns) 70: Performance: 1.117 21.478 70: 70: 70: [ OK ] FreezeWorks/FreezeGroupTest.WithinTolerances/11 (1905 ms) 70: [----------] 12 tests from FreezeWorks/FreezeGroupTest (19632 ms total) 70: 70: [----------] 4 tests from AccelerationWorks/AccelerationGroupTest 70: [ RUN ] AccelerationWorks/AccelerationGroupTest.WithinTolerances/0 70: 70: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/AccelerationWorks_AccelerationGroupTest_WithinTolerances_0_input.mdp]: 70: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 70: that with the Verlet scheme, nstlist has no effect on the accuracy of 70: your simulation. 70: 70: 70: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/AccelerationWorks_AccelerationGroupTest_WithinTolerances_0_input.mdp]: 70: verlet-buffer-pressure-tolerance is ignored when verlet-buffer-tolerance 70: < 0 70: 70: 70: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/AccelerationWorks_AccelerationGroupTest_WithinTolerances_0_input.mdp]: 70: Setting nstcalcenergy (100) equal to nstenergy (4) 70: 70: Generating 1-4 interactions: fudge = 0.5 70: Number of degrees of freedom in T-Coupling group FirstWaterMolecule is 6.00 70: Number of degrees of freedom in T-Coupling group SecondWaterMolecule is 6.00 70: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 70: Net Acceleration in X direction, will not be corrected 70: Net Acceleration in Y direction, will not be corrected 70: Net Acceleration in Z direction, will not be corrected 70: 70: There were 3 NOTEs 70: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/AccelerationWorks_AccelerationGroupTest_WithinTolerances_0.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 70: Can not increase nstlist because an NVE ensemble is used 70: Using 2 MPI threads 70: 70: Non-default thread affinity set, disabling internal thread affinity 70: 70: Using 2 OpenMP threads per tMPI thread 70: 70: starting mdrun 'spc2' 70: 8 steps, 0.0 ps. 70: Generated 3 of the 3 non-bonded parameter combinations 70: 70: Generated 3 of the 3 1-4 parameter combinations 70: 70: Excluding 2 bonded neighbours molecule type 'SOL' 70: 70: Setting gen_seed to -1602344962 70: 70: Velocities were taken from a Maxwell distribution at 0 K 70: 70: This run will generate roughly 0 Mb of data 70: 70: Writing final coordinates. 70: 70: 70: Dynamic load balancing report: 70: DLB was off during the run due to low measured imbalance. 70: Average load imbalance: 25.0%. 70: The balanceable part of the MD step is 40%, load imbalance is computed from this. 70: Part of the total run time spent waiting due to load imbalance: 9.9%. 70: 70: NOTE: 9.9 % of the available CPU time was lost due to load imbalance 70: in the domain decomposition. 70: Dynamic load balancing was automatically disabled, but it might be beneficial to manually turn it on (option -dlb yes.) 70: You can also consider manually changing the decomposition (option -dd); 70: e.g. by using fewer domains along the box dimension in which there is 70: considerable inhomogeneity in the simulated system. 70: 70: NOTE: 19 % of the run time was spent in domain decomposition, 70: 4 % of the run time was spent in pair search, 70: you might want to increase nstlist (this has no effect on accuracy) 70: 70: NOTE: 11 % of the run time was spent communicating energies, 70: you might want to increase some nst* mdp options 70: 70: Core t (s) Wall t (s) (%) 70: Time: 2.992 0.764 391.7 70: (ns/day) (hour/ns) 70: Performance: 2.036 11.790 70: 70: [ OK ] AccelerationWorks/AccelerationGroupTest.WithinTolerances/0 (1404 ms) 70: [ RUN ] AccelerationWorks/AccelerationGroupTest.WithinTolerances/1 70: 70: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/AccelerationWorks_AccelerationGroupTest_WithinTolerances_1_input.mdp]: 70: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 70: that with the Verlet scheme, nstlist has no effect on the accuracy of 70: your simulation. 70: 70: 70: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/AccelerationWorks_AccelerationGroupTest_WithinTolerances_1_input.mdp]: 70: verlet-buffer-pressure-tolerance is ignored when verlet-buffer-tolerance 70: < 0 70: 70: 70: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/AccelerationWorks_AccelerationGroupTest_WithinTolerances_1_input.mdp]: 70: Setting nstcalcenergy (100) equal to nstenergy (4) 70: 70: Generating 1-4 interactions: fudge = 0.5 70: Number of degrees of freedom in T-Coupling group FirstWaterMolecule is 6.00 70: Number of degrees of freedom in T-Coupling group SecondWaterMolecule is 6.00 70: Net Acceleration in X direction, will not be corrected 70: Net Acceleration in Y direction, will not be corrected 70: Net Acceleration in Z direction, will not be corrected 70: 70: There were 3 NOTEs 70: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/AccelerationWorks_AccelerationGroupTest_WithinTolerances_1.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 70: Can not increase nstlist because verlet-buffer-tolerance is not set or used 70: Using 2 MPI threads 70: 70: Non-default thread affinity set, disabling internal thread affinity 70: 70: Using 2 OpenMP threads per tMPI thread 70: 70: starting mdrun 'spc2' 70: 8 steps, 0.0 ps. 70: Generated 3 of the 3 non-bonded parameter combinations 70: 70: Generated 3 of the 3 1-4 parameter combinations 70: 70: Excluding 2 bonded neighbours molecule type 'SOL' 70: 70: Setting gen_seed to -271063308 70: 70: Velocities were taken from a Maxwell distribution at 0 K 70: 70: This run will generate roughly 0 Mb of data 70: 70: Writing final coordinates. 70: 70: 70: Dynamic load balancing report: 70: DLB was off during the run due to low measured imbalance. 70: Average load imbalance: 26.3%. 70: The balanceable part of the MD step is 38%, load imbalance is computed from this. 70: Part of the total run time spent waiting due to load imbalance: 10.1%. 70: 70: NOTE: 10.1 % of the available CPU time was lost due to load imbalance 70: in the domain decomposition. 70: Dynamic load balancing was automatically disabled, but it might be beneficial to manually turn it on (option -dlb yes.) 70: You can also consider manually changing the decomposition (option -dd); 70: e.g. by using fewer domains along the box dimension in which there is 70: considerable inhomogeneity in the simulated system. 70: 70: NOTE: 20 % of the run time was spent in domain decomposition, 70: 4 % of the run time was spent in pair search, 70: you might want to increase nstlist (this has no effect on accuracy) 70: 70: NOTE: 10 % of the run time was spent communicating energies, 70: you might want to increase some nst* mdp options 70: 70: Core t (s) Wall t (s) (%) 70: Time: 2.880 0.736 391.4 70: (ns/day) (hour/ns) 70: Performance: 2.113 11.356 70: 70: [ OK ] AccelerationWorks/AccelerationGroupTest.WithinTolerances/1 (1476 ms) 70: [ RUN ] AccelerationWorks/AccelerationGroupTest.WithinTolerances/2 70: 70: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/AccelerationWorks_AccelerationGroupTest_WithinTolerances_2_input.mdp]: 70: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 70: that with the Verlet scheme, nstlist has no effect on the accuracy of 70: your simulation. 70: 70: 70: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/AccelerationWorks_AccelerationGroupTest_WithinTolerances_2_input.mdp]: 70: verlet-buffer-pressure-tolerance is ignored when verlet-buffer-tolerance 70: < 0 70: 70: 70: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/AccelerationWorks_AccelerationGroupTest_WithinTolerances_2_input.mdp]: 70: Setting nstcalcenergy (100) equal to nstenergy (4) 70: 70: Generating 1-4 interactions: fudge = 0.5 70: Number of degrees of freedom in T-Coupling group FirstWaterMolecule is 6.00 70: Number of degrees of freedom in T-Coupling group SecondWaterMolecule is 6.00 70: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 70: Net Acceleration in X direction, will not be corrected 70: Net Acceleration in Y direction, will not be corrected 70: Net Acceleration in Z direction, will not be corrected 70: 70: There were 3 NOTEs 70: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/AccelerationWorks_AccelerationGroupTest_WithinTolerances_2.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 70: Can not increase nstlist because an NVE ensemble is used 70: Using 2 MPI threads 70: 70: Non-default thread affinity set, disabling internal thread affinity 70: 70: Using 2 OpenMP threads per tMPI thread 70: 70: starting mdrun 'spc2' 70: 8 steps, 0.0 ps. 70: Generated 3 of the 3 non-bonded parameter combinations 70: 70: Generated 3 of the 3 1-4 parameter combinations 70: 70: Excluding 2 bonded neighbours molecule type 'SOL' 70: 70: Setting gen_seed to 2129644247 70: 70: Velocities were taken from a Maxwell distribution at 0 K 70: 70: This run will generate roughly 0 Mb of data 70: 70: Writing final coordinates. 70: 70: 70: Dynamic load balancing report: 70: DLB was off during the run due to low measured imbalance. 70: Average load imbalance: 21.4%. 70: The balanceable part of the MD step is 40%, load imbalance is computed from this. 70: Part of the total run time spent waiting due to load imbalance: 8.5%. 70: 70: NOTE: 8.5 % of the available CPU time was lost due to load imbalance 70: in the domain decomposition. 70: Dynamic load balancing was automatically disabled, but it might be beneficial to manually turn it on (option -dlb yes.) 70: You can also consider manually changing the decomposition (option -dd); 70: e.g. by using fewer domains along the box dimension in which there is 70: considerable inhomogeneity in the simulated system. 70: 70: NOTE: 18 % of the run time was spent in domain decomposition, 70: 4 % of the run time was spent in pair search, 70: you might want to increase nstlist (this has no effect on accuracy) 70: 70: NOTE: 14 % of the run time was spent communicating energies, 70: you might want to increase some nst* mdp options 70: 70: Core t (s) Wall t (s) (%) 70: Time: 3.398 0.865 392.7 70: (ns/day) (hour/ns) 70: Performance: 1.797 13.354 70: 70: [ OK ] AccelerationWorks/AccelerationGroupTest.WithinTolerances/2 (1527 ms) 70: [ RUN ] AccelerationWorks/AccelerationGroupTest.WithinTolerances/3 70: 70: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/AccelerationWorks_AccelerationGroupTest_WithinTolerances_3_input.mdp]: 70: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 70: that with the Verlet scheme, nstlist has no effect on the accuracy of 70: your simulation. 70: 70: 70: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/AccelerationWorks_AccelerationGroupTest_WithinTolerances_3_input.mdp]: 70: verlet-buffer-pressure-tolerance is ignored when verlet-buffer-tolerance 70: < 0 70: 70: 70: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/AccelerationWorks_AccelerationGroupTest_WithinTolerances_3_input.mdp]: 70: Setting nstcalcenergy (100) equal to nstenergy (4) 70: 70: Generating 1-4 interactions: fudge = 0.5 70: Number of degrees of freedom in T-Coupling group FirstWaterMolecule is 6.00 70: Number of degrees of freedom in T-Coupling group SecondWaterMolecule is 6.00 70: Net Acceleration in X direction, will not be corrected 70: Net Acceleration in Y direction, will not be corrected 70: Net Acceleration in Z direction, will not be corrected 70: 70: There were 3 NOTEs 70: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/AccelerationWorks_AccelerationGroupTest_WithinTolerances_3.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 70: Can not increase nstlist because verlet-buffer-tolerance is not set or used 70: Using 2 MPI threads 70: 70: Non-default thread affinity set, disabling internal thread affinity 70: 70: Using 2 OpenMP threads per tMPI thread 70: 70: starting mdrun 'spc2' 70: 8 steps, 0.0 ps. 70: Generated 3 of the 3 non-bonded parameter combinations 70: 70: Generated 3 of the 3 1-4 parameter combinations 70: 70: Excluding 2 bonded neighbours molecule type 'SOL' 70: 70: Setting gen_seed to -76547089 70: 70: Velocities were taken from a Maxwell distribution at 0 K 70: 70: This run will generate roughly 0 Mb of data 70: 70: Writing final coordinates. 70: 70: 70: Dynamic load balancing report: 70: DLB was off during the run due to low measured imbalance. 70: Average load imbalance: 16.8%. 70: The balanceable part of the MD step is 44%, load imbalance is computed from this. 70: Part of the total run time spent waiting due to load imbalance: 7.3%. 70: 70: NOTE: 7.3 % of the available CPU time was lost due to load imbalance 70: in the domain decomposition. 70: Dynamic load balancing was automatically disabled, but it might be beneficial to manually turn it on (option -dlb yes.) 70: You can also consider manually changing the decomposition (option -dd); 70: e.g. by using fewer domains along the box dimension in which there is 70: considerable inhomogeneity in the simulated system. 70: 70: NOTE: 18 % of the run time was spent in domain decomposition, 70: 4 % of the run time was spent in pair search, 70: you might want to increase nstlist (this has no effect on accuracy) 70: 70: NOTE: 16 % of the run time was spent communicating energies, 70: you might want to increase some nst* mdp options 70: 70: Core t (s) Wall t (s) (%) 70: Time: 3.184 0.812 392.2 70: (ns/day) (hour/ns) 70: Performance: 1.915 12.530 70: 70: [ OK ] AccelerationWorks/AccelerationGroupTest.WithinTolerances/3 (1503 ms) 70: [----------] 4 tests from AccelerationWorks/AccelerationGroupTest (5911 ms total) 70: 70: [----------] Global test environment tear-down 70: [==========] 29 tests from 8 test suites ran. (76368 ms total) 70: [ PASSED ] 28 tests. 70: [ SKIPPED ] 1 test, listed below: 70: [ SKIPPED ] FreezeWorks/FreezeGroupTest.WithinTolerances/5 70/92 Test #70: MdrunTestsTwoRanks ........................ Passed 76.46 sec test 71 Start 71: MdrunSingleRankAlgorithmsTests 71: Test command: /build/reproducible-path/gromacs-2025.1/build/basic/bin/mdrun-single-rank-algorithms-test "-ntomp" "2" "--gtest_output=xml:/build/reproducible-path/gromacs-2025.1/build/basic/Testing/Temporary/MdrunSingleRankAlgorithmsTests.xml" 71: Working Directory: /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests 71: Test timeout computed to be: 600 71: [==========] Running 5 tests from 3 test suites. 71: [----------] Global test environment set-up. 71: [----------] 1 test from DispersionCorrectionTest 71: [ RUN ] DispersionCorrectionTest.DispersionCorrectionCanRun 71: Generating 1-4 interactions: fudge = 0.5 71: Number of degrees of freedom in T-Coupling group System is 30.00 71: 71: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/DispersionCorrectionTest_DispersionCorrectionCanRun_input.mdp]: 71: There are 9 non-linear virtual site constructions. Their contribution to 71: the energy error is approximated. In most cases this does not affect the 71: error significantly. 71: 71: 71: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/DispersionCorrectionTest_DispersionCorrectionCanRun_input.mdp]: 71: You are using a plain Coulomb cut-off, which might produce artifacts. 71: You might want to consider using PME electrostatics. 71: 71: 71: 71: There were 2 NOTEs 71: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/DispersionCorrectionTest_DispersionCorrectionCanRun.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 71: Changing nstlist from 10 to 40, rlist from 1.023 to 1.158 71: 71: Update groups can not be used for this system because an incompatible virtual site type is used 71: 71: Using 1 MPI thread 71: Using 2 OpenMP threads 71: 71: 71: NOTE: The number of threads is not equal to the number of (logical) cpus 71: and the -pin option is set to auto: will not pin threads to cpus. 71: This can lead to significant performance degradation. 71: Consider using -pin on (and -pinoffset in case you run multiple jobs). 71: starting mdrun 'Alanine dipeptide in vacuo' 71: 200 steps, 0.4 ps. 71: Setting the LD random seed to -2167329 71: 71: Generated 2145 of the 2145 non-bonded parameter combinations 71: 71: Generated 2145 of the 2145 1-4 parameter combinations 71: 71: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' 71: 71: turning H bonds into constraints... 71: 71: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/alanine_vsite_vacuo.gro' 71: 71: Cleaning up constraints and constant bonded interactions with virtual sites 71: 71: Converted 3 Bonds with virtual sites to connections, 7 left 71: 71: Removed 18 Angles with virtual sites, 21 left 71: 71: Removed 10 Proper Dih.s with virtual sites, 44 left 71: 71: Converted 12 Constraints with virtual sites to connections, 0 left 71: 71: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 300 K 71: 71: Calculated rlist for 1x1 atom pair-list as 1.038 nm, buffer size 0.038 nm 71: 71: Set rlist, assuming 4x4 atom pair-list, to 1.023 nm, buffer size 0.023 nm 71: 71: Note that mdrun will redetermine rlist based on the actual pair-list setup 71: 71: This run will generate roughly 0 Mb of data 71: 71: Writing final coordinates. 71: 71: Core t (s) Wall t (s) (%) 71: Time: 0.397 0.199 199.7 71: (ns/day) (hour/ns) 71: Performance: 174.885 0.137 71: [ OK ] DispersionCorrectionTest.DispersionCorrectionCanRun (510 ms) 71: [----------] 1 test from DispersionCorrectionTest (510 ms total) 71: 71: [----------] 1 test from OriresTest 71: [ RUN ] OriresTest.OriresCanRun 71: Generating 1-4 interactions: fudge = 0.5 71: Number of degrees of freedom in T-Coupling group System is 518.00 71: 71: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/OriresTest_OriresCanRun_input.mdp]: 71: You are using a plain Coulomb cut-off, which might produce artifacts. 71: You might want to consider using PME electrostatics. 71: 71: 71: 71: There was 1 NOTE 71: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/OriresTest_OriresCanRun.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 71: Orientation restraints only supports a single rank. Choosing to use only a single thread-MPI rank. 71: Changing nstlist from 10 to 25, rlist from 1.07 to 1.203 71: 71: 71: Using 1 MPI thread 71: Using 2 OpenMP threads 71: 71: 71: NOTE: The number of threads is not equal to the number of (logical) cpus 71: and the -pin option is set to auto: will not pin threads to cpus. 71: This can lead to significant performance degradation. 71: Consider using -pin on (and -pinoffset in case you run multiple jobs). 71: starting mdrun 'GUANINE NUCLEOTIDE-BINDING PROTEIN G(T), ALPHA-1' 71: 10 steps, 0.0 ps. 71: Setting the LD random seed to -135274777 71: 71: Generated 2145 of the 2145 non-bonded parameter combinations 71: 71: Generated 2145 of the 2145 1-4 parameter combinations 71: 71: Excluding 3 bonded neighbours molecule type 'Protein_chain_A' 71: 71: turning H bonds into constraints... 71: 71: Excluding 2 bonded neighbours molecule type 'SOL' 71: 71: turning H bonds into constraints... 71: 71: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/orires_1lvz.gro' 71: 71: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 300 K 71: 71: Calculated rlist for 1x1 atom pair-list as 1.093 nm, buffer size 0.093 nm 71: 71: Set rlist, assuming 4x4 atom pair-list, to 1.070 nm, buffer size 0.070 nm 71: 71: Note that mdrun will redetermine rlist based on the actual pair-list setup 71: 71: This run will generate roughly 0 Mb of data 71: 71: Writing final coordinates. 71: 71: Core t (s) Wall t (s) (%) 71: Time: 0.123 0.062 198.8 71: (ns/day) (hour/ns) 71: Performance: 30.747 0.781 71: [ OK ] OriresTest.OriresCanRun (4320 ms) 71: [----------] 1 test from OriresTest (4320 ms total) 71: 71: [----------] 3 tests from EwaldSurfaceTerm/EwaldSurfaceTermTest 71: [ RUN ] EwaldSurfaceTerm/EwaldSurfaceTermTest.WithinTolerances/0 71: Number of degrees of freedom in T-Coupling group rest is 10.00 71: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 71: 71: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/EwaldSurfaceTerm_EwaldSurfaceTermTest_WithinTolerances_0_input.mdp]: 71: NVE simulation with an initial temperature of zero: will use a Verlet 71: buffer of 10%. Check your energy drift! 71: 71: 71: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/EwaldSurfaceTerm_EwaldSurfaceTermTest_WithinTolerances_0_input.mdp]: 71: The optimal PME mesh load for parallel simulations is below 0.5 71: and for highly parallel simulations between 0.25 and 0.33, 71: for higher performance, increase the cut-off and the PME grid spacing. 71: 71: 71: 71: There were 2 NOTEs 71: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/EwaldSurfaceTerm_EwaldSurfaceTermTest_WithinTolerances_0.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 71: Can not increase nstlist because an NVE ensemble is used 71: Using 1 MPI thread 71: Using 2 OpenMP threads 71: 71: 71: NOTE: The number of threads is not equal to the number of (logical) cpus 71: and the -pin option is set to auto: will not pin threads to cpus. 71: This can lead to significant performance degradation. 71: Consider using -pin on (and -pinoffset in case you run multiple jobs). 71: starting mdrun 'Dipoles' 71: 20 steps, 0.1 ps. 71: Setting the LD random seed to 928857851 71: 71: Generated 1 of the 1 non-bonded parameter combinations 71: 71: Excluding 1 bonded neighbours molecule type 'Dipole' 71: 71: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/dipoles.gro', all velocities are zero 71: 71: Searching the wall atom type(s) 71: 71: The largest distance between excluded atoms is 0.344 nm between atom 1 and 2 71: Calculating fourier grid dimensions for X Y Z 71: Using a fourier grid of 20x20x40, spacing 0.200 0.200 0.200 71: 71: Estimate for the relative computational load of the PME mesh part: 1.00 71: 71: This run will generate roughly 0 Mb of data 71: 71: Writing final coordinates. 71: 71: Core t (s) Wall t (s) (%) 71: Time: 0.304 0.152 199.5 71: (ns/day) (hour/ns) 71: Performance: 29.769 0.806 71: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/EwaldSurfaceTerm_EwaldSurfaceTermTest_WithinTolerances_0.edr as single precision energy file 71: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.010 Reading energy frame 2 time 0.020 Reading energy frame 3 time 0.030 Reading energy frame 4 time 0.040 Reading energy frame 5 time 0.050 Last energy frame read 5 time 0.050 trr version: GMX_trn_file (single precision) 71: 71: [ OK ] EwaldSurfaceTerm/EwaldSurfaceTermTest.WithinTolerances/0 (302 ms) 71: [ RUN ] EwaldSurfaceTerm/EwaldSurfaceTermTest.WithinTolerances/1 71: Test system 'epsilon-surface-constraint' cannot run with 1 ranks. 71: The supported numbers are > 1. 71: [ OK ] EwaldSurfaceTerm/EwaldSurfaceTermTest.WithinTolerances/1 (0 ms) 71: [ RUN ] EwaldSurfaceTerm/EwaldSurfaceTermTest.WithinTolerances/2 71: 71: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/EwaldSurfaceTerm_EwaldSurfaceTermTest_WithinTolerances_2_input.mdp]: 71: With epsilon_surface > 0 all molecules should be neutral. 71: 71: 71: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/EwaldSurfaceTerm_EwaldSurfaceTermTest_WithinTolerances_2_input.mdp]: 71: With epsilon_surface > 0 you can only use domain decomposition when there 71: are only small molecules with all bonds constrained (mdrun will check for 71: this). 71: 71: Number of degrees of freedom in T-Coupling group rest is 9.00 71: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 71: 71: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/EwaldSurfaceTerm_EwaldSurfaceTermTest_WithinTolerances_2_input.mdp]: 71: NVE simulation with an initial temperature of zero: will use a Verlet 71: buffer of 10%. Check your energy drift! 71: 71: 71: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/EwaldSurfaceTerm_EwaldSurfaceTermTest_WithinTolerances_2_input.mdp]: 71: The optimal PME mesh load for parallel simulations is below 0.5 71: and for highly parallel simulations between 0.25 and 0.33, 71: for higher performance, increase the cut-off and the PME grid spacing. 71: 71: 71: 71: There were 4 NOTEs 71: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/EwaldSurfaceTerm_EwaldSurfaceTermTest_WithinTolerances_2.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 71: Can not increase nstlist because an NVE ensemble is used 71: Using 1 MPI thread 71: Using 2 OpenMP threads 71: 71: 71: NOTE: The number of threads is not equal to the number of (logical) cpus 71: and the -pin option is set to auto: will not pin threads to cpus. 71: This can lead to significant performance degradation. 71: Consider using -pin on (and -pinoffset in case you run multiple jobs). 71: starting mdrun 'Dipoles' 71: 20 steps, 0.1 ps. 71: Setting the LD random seed to -1639973121 71: 71: Generated 1 of the 1 non-bonded parameter combinations 71: 71: Excluding 1 bonded neighbours molecule type 'Dipole' 71: 71: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/dipoles.gro', all velocities are zero 71: 71: The largest distance between excluded atoms is 0.344 nm between atom 1 and 2 71: Calculating fourier grid dimensions for X Y Z 71: Using a fourier grid of 20x20x20, spacing 0.200 0.200 0.200 71: 71: Estimate for the relative computational load of the PME mesh part: 1.00 71: 71: This run will generate roughly 0 Mb of data 71: 71: Writing final coordinates. 71: 71: Core t (s) Wall t (s) (%) 71: Time: 0.122 0.061 199.1 71: (ns/day) (hour/ns) 71: Performance: 74.037 0.324 71: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/EwaldSurfaceTerm_EwaldSurfaceTermTest_WithinTolerances_2.edr as single precision energy file 71: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.010 Reading energy frame 2 time 0.020 Reading energy frame 3 time 0.030 Reading energy frame 4 time 0.040 Reading energy frame 5 time 0.050 Last energy frame read 5 time 0.050 71: [ OK ] EwaldSurfaceTerm/EwaldSurfaceTermTest.WithinTolerances/2 (181 ms) 71: [----------] 3 tests from EwaldSurfaceTerm/EwaldSurfaceTermTest (485 ms total) 71: 71: [----------] Global test environment tear-down 71: [==========] 5 tests from 3 test suites ran. (5562 ms total) 71: [ PASSED ] 5 tests. 71/92 Test #71: MdrunSingleRankAlgorithmsTests ............ Passed 5.66 sec test 72 Start 72: Minimize1RankTests 72: Test command: /build/reproducible-path/gromacs-2025.1/build/basic/bin/minimize-test "-ntomp" "2" "-ntmpi" "1" "--gtest_output=xml:/build/reproducible-path/gromacs-2025.1/build/basic/Testing/Temporary/Minimize1RankTests.xml" 72: Working Directory: /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests 72: Test timeout computed to be: 600 72: [==========] Running 12 tests from 2 test suites. 72: [----------] Global test environment set-up. 72: [----------] 6 tests from MinimizersWorkWithConstraints/EnergyMinimizationTest 72: [ RUN ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/0 72: 72: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_0_input.mdp]: 72: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 72: that with the Verlet scheme, nstlist has no effect on the accuracy of 72: your simulation. 72: 72: 72: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_0_input.mdp]: 72: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 72: setting nstcomm equal to nstcalcenergy for less overhead 72: 72: Generating 1-4 interactions: fudge = 0.5 72: Number of degrees of freedom in T-Coupling group System is 27.00 72: 72: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_0_input.mdp]: 72: You are using a plain Coulomb cut-off, which might produce artifacts. 72: You might want to consider using PME electrostatics. 72: 72: 72: 72: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_0_input.mdp]: 72: COM removal frequency is set to (4). 72: Other settings require a global communication frequency of 100. 72: Note that this will require additional global communication steps, 72: which will reduce performance when using multiple ranks. 72: Consider setting nstcomm to a multiple of 100. 72: 72: 72: There were 4 NOTEs 72: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_0.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 72: Using 1 MPI thread 72: Using 2 OpenMP threads 72: 72: 72: NOTE: The number of threads is not equal to the number of (logical) cpus 72: and the -pin option is set to auto: will not pin threads to cpus. 72: This can lead to significant performance degradation. 72: Consider using -pin on (and -pinoffset in case you run multiple jobs). 72: 72: Steepest Descents: 72: Tolerance (Fmax) = 1.00000e+01 72: Number of steps = 4 72: 72: Energy minimization reached the maximum number of steps before the forces 72: reached the requested precision Fmax < 10. 72: 72: writing lowest energy coordinates. 72: 72: Steepest Descents did not converge to Fmax < 10 in 5 steps. 72: Potential Energy = -4.7990990e+01 72: Maximum force = 1.8629788e+02 on atom 13 72: Norm of force = 8.7721985e+01 72: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_0_minimize.edr as single precision energy file 72: Reading energy frame 0 time 0.000 Reading energy frame 1 time 1.000 Reading energy frame 2 time 2.000 Reading energy frame 3 time 3.000 Reading energy frame 4 time 4.000 Last energy frame read 4 time 4.000 Generated 330891 of the 330891 non-bonded parameter combinations 72: 72: Generated 330891 of the 330891 1-4 parameter combinations 72: 72: Excluding 2 bonded neighbours molecule type 'SOL' 72: 72: This run will generate roughly 0 Mb of data 72: [ OK ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/0 (5345 ms) 72: [ RUN ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/1 72: 72: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_1_input.mdp]: 72: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 72: that with the Verlet scheme, nstlist has no effect on the accuracy of 72: your simulation. 72: 72: 72: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_1_input.mdp]: 72: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 72: setting nstcomm equal to nstcalcenergy for less overhead 72: 72: Generating 1-4 interactions: fudge = 0.5 72: Number of degrees of freedom in T-Coupling group System is 27.00 72: 72: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_1_input.mdp]: 72: You are using a plain Coulomb cut-off, which might produce artifacts. 72: You might want to consider using PME electrostatics. 72: 72: 72: 72: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_1_input.mdp]: 72: COM removal frequency is set to (4). 72: Other settings require a global communication frequency of 100. 72: Note that this will require additional global communication steps, 72: which will reduce performance when using multiple ranks. 72: Consider setting nstcomm to a multiple of 100. 72: 72: 72: There were 4 NOTEs 72: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_1.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 72: Using 1 MPI thread 72: Using 2 OpenMP threads 72: 72: 72: NOTE: The number of threads is not equal to the number of (logical) cpus 72: and the -pin option is set to auto: will not pin threads to cpus. 72: This can lead to significant performance degradation. 72: Consider using -pin on (and -pinoffset in case you run multiple jobs). 72: 72: Polak-Ribiere Conjugate Gradients: 72: Tolerance (Fmax) = 1.00000e+01 72: Number of steps = 4 72: F-max = 3.02331e+02 on atom 3 72: F-Norm = 1.18024e+02 72: 72: 72: Energy minimization reached the maximum number of steps before the forces 72: reached the requested precision Fmax < 10. 72: 72: writing lowest energy coordinates. 72: 72: Polak-Ribiere Conjugate Gradients did not converge to Fmax < 10 in 5 steps. 72: Potential Energy = -5.5862488e+01 72: Maximum force = 4.2726025e+02 on atom 13 72: Norm of force = 1.8452452e+02 72: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_1_minimize.edr as single precision energy file 72: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.000 Reading energy frame 2 time 4.000 Last energy frame read 2 time 4.000 Generated 330891 of the 330891 non-bonded parameter combinations 72: 72: Generated 330891 of the 330891 1-4 parameter combinations 72: 72: Excluding 2 bonded neighbours molecule type 'SOL' 72: 72: This run will generate roughly 0 Mb of data 72: [ OK ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/1 (6569 ms) 72: [ RUN ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/2 72: 72: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_2_input.mdp]: 72: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 72: that with the Verlet scheme, nstlist has no effect on the accuracy of 72: your simulation. 72: 72: 72: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_2_input.mdp]: 72: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 72: setting nstcomm equal to nstcalcenergy for less overhead 72: 72: Generating 1-4 interactions: fudge = 1 72: Number of degrees of freedom in T-Coupling group System is 22.00 72: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 72: 72: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_2_input.mdp]: 72: You are using a plain Coulomb cut-off, which might produce artifacts. 72: You might want to consider using PME electrostatics. 72: 72: 72: 72: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_2_input.mdp]: 72: COM removal frequency is set to (4). 72: Other settings require a global communication frequency of 100. 72: Note that this will require additional global communication steps, 72: which will reduce performance when using multiple ranks. 72: Consider setting nstcomm to a multiple of 100. 72: 72: 72: There were 4 NOTEs 72: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_2.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 72: Using 1 MPI thread 72: Using 2 OpenMP threads 72: 72: 72: NOTE: The number of threads is not equal to the number of (logical) cpus 72: and the -pin option is set to auto: will not pin threads to cpus. 72: This can lead to significant performance degradation. 72: Consider using -pin on (and -pinoffset in case you run multiple jobs). 72: 72: Steepest Descents: 72: Tolerance (Fmax) = 1.00000e+01 72: Number of steps = 4 72: 72: Energy minimization reached the maximum number of steps before the forces 72: reached the requested precision Fmax < 10. 72: 72: writing lowest energy coordinates. 72: 72: Steepest Descents did not converge to Fmax < 10 in 5 steps. 72: Potential Energy = 3.1937717e+02 72: Maximum force = 9.9988662e+03 on atom 9 72: Norm of force = 4.6166996e+03 72: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_2_minimize.edr as single precision energy file 72: Reading energy frame 0 time 0.000 Reading energy frame 1 time 1.000 Reading energy frame 2 time 2.000 Reading energy frame 3 time 3.000 Reading energy frame 4 time 4.000 Last energy frame read 4 time 4.000 Generated 20503 of the 20503 non-bonded parameter combinations 72: 72: Generated 17396 of the 20503 1-4 parameter combinations 72: 72: Excluding 3 bonded neighbours molecule type 'Glycine' 72: 72: turning H bonds into constraints... 72: 72: This run will generate roughly 0 Mb of data 72: [ OK ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/2 (780 ms) 72: [ RUN ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/3 72: 72: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_3_input.mdp]: 72: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 72: that with the Verlet scheme, nstlist has no effect on the accuracy of 72: your simulation. 72: 72: 72: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_3_input.mdp]: 72: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 72: setting nstcomm equal to nstcalcenergy for less overhead 72: 72: Generating 1-4 interactions: fudge = 1 72: 72: NOTE 3 [file glycine_vacuo.top, line 12]: 72: For accurate cg with LINCS constraints, lincs-order should be 8 or more. 72: 72: Number of degrees of freedom in T-Coupling group System is 22.00 72: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 72: 72: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_3_input.mdp]: 72: You are using a plain Coulomb cut-off, which might produce artifacts. 72: You might want to consider using PME electrostatics. 72: 72: 72: 72: NOTE 5 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_3_input.mdp]: 72: COM removal frequency is set to (4). 72: Other settings require a global communication frequency of 100. 72: Note that this will require additional global communication steps, 72: which will reduce performance when using multiple ranks. 72: Consider setting nstcomm to a multiple of 100. 72: 72: 72: There were 5 NOTEs 72: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_3.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 72: Using 1 MPI thread 72: Using 2 OpenMP threads 72: 72: 72: NOTE: The number of threads is not equal to the number of (logical) cpus 72: and the -pin option is set to auto: will not pin threads to cpus. 72: This can lead to significant performance degradation. 72: Consider using -pin on (and -pinoffset in case you run multiple jobs). 72: 72: Polak-Ribiere Conjugate Gradients: 72: Tolerance (Fmax) = 1.00000e+01 72: Number of steps = 4 72: F-max = 2.41575e+04 on atom 10 72: F-Norm = 1.18451e+04 72: 72: 72: Energy minimization reached the maximum number of steps before the forces 72: reached the requested precision Fmax < 10. 72: 72: writing lowest energy coordinates. 72: 72: Polak-Ribiere Conjugate Gradients did not converge to Fmax < 10 in 5 steps. 72: Potential Energy = 1.5174423e+02 72: Maximum force = 7.4208853e+03 on atom 9 72: Norm of force = 3.5692989e+03 72: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_3_minimize.edr as single precision energy file 72: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.000 Reading energy frame 2 time 4.000 Last energy frame read 2 time 4.000 Generated 20503 of the 20503 non-bonded parameter combinations 72: 72: Generated 17396 of the 20503 1-4 parameter combinations 72: 72: Excluding 3 bonded neighbours molecule type 'Glycine' 72: 72: turning H bonds into constraints... 72: 72: This run will generate roughly 0 Mb of data 72: [ OK ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/3 (775 ms) 72: [ RUN ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/4 72: 72: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_4_input.mdp]: 72: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 72: that with the Verlet scheme, nstlist has no effect on the accuracy of 72: your simulation. 72: 72: 72: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_4_input.mdp]: 72: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 72: setting nstcomm equal to nstcalcenergy for less overhead 72: 72: Generating 1-4 interactions: fudge = 0.5 72: 72: NOTE 3 [file unknown]: 72: You are using constraints on all bonds, whereas the forcefield has been 72: parametrized only with constraints involving hydrogen atoms. We suggest 72: using constraints = h-bonds instead, this will also improve performance. 72: 72: Number of degrees of freedom in T-Coupling group System is 23.00 72: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 72: 72: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_4_input.mdp]: 72: You are using a plain Coulomb cut-off, which might produce artifacts. 72: You might want to consider using PME electrostatics. 72: 72: 72: 72: NOTE 5 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_4_input.mdp]: 72: COM removal frequency is set to (4). 72: Other settings require a global communication frequency of 100. 72: Note that this will require additional global communication steps, 72: which will reduce performance when using multiple ranks. 72: Consider setting nstcomm to a multiple of 100. 72: 72: 72: There were 5 NOTEs 72: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_4.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 72: Update groups can not be used for this system because an incompatible virtual site type is used 72: 72: Using 1 MPI thread 72: Using 2 OpenMP threads 72: 72: 72: NOTE: The number of threads is not equal to the number of (logical) cpus 72: and the -pin option is set to auto: will not pin threads to cpus. 72: This can lead to significant performance degradation. 72: Consider using -pin on (and -pinoffset in case you run multiple jobs). 72: 72: Steepest Descents: 72: Tolerance (Fmax) = 1.00000e+01 72: Number of steps = 4 72: 72: Energy minimization reached the maximum number of steps before the forces 72: reached the requested precision Fmax < 10. 72: 72: writing lowest energy coordinates. 72: 72: Steepest Descents did not converge to Fmax < 10 in 5 steps. 72: Potential Energy = -1.5698413e+02 72: Maximum force = 4.5706589e+02 on atom 17 72: Norm of force = 1.8328245e+02 72: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_4_minimize.edr as single precision energy file 72: Reading energy frame 0 time 0.000 Reading energy frame 1 time 1.000 Reading energy frame 2 time 3.000 Last energy frame read 2 time 3.000 Generated 2145 of the 2145 non-bonded parameter combinations 72: 72: Generated 2145 of the 2145 1-4 parameter combinations 72: 72: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' 72: 72: turning all bonds into constraints... 72: 72: Cleaning up constraints and constant bonded interactions with virtual sites 72: 72: Removed 18 Angles with virtual sites, 21 left 72: 72: Removed 10 Proper Dih.s with virtual sites, 44 left 72: 72: Converted 15 Constraints with virtual sites to connections, 7 left 72: 72: This run will generate roughly 0 Mb of data 72: [ OK ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/4 (121 ms) 72: [ RUN ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/5 72: 72: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_5_input.mdp]: 72: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 72: that with the Verlet scheme, nstlist has no effect on the accuracy of 72: your simulation. 72: 72: 72: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_5_input.mdp]: 72: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 72: setting nstcomm equal to nstcalcenergy for less overhead 72: 72: Generating 1-4 interactions: fudge = 0.5 72: 72: NOTE 3 [file unknown]: 72: You are using constraints on all bonds, whereas the forcefield has been 72: parametrized only with constraints involving hydrogen atoms. We suggest 72: using constraints = h-bonds instead, this will also improve performance. 72: 72: 72: NOTE 4 [file unknown]: 72: For accurate cg with LINCS constraints, lincs-order should be 8 or more. 72: 72: Number of degrees of freedom in T-Coupling group System is 23.00 72: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 72: 72: NOTE 5 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_5_input.mdp]: 72: You are using a plain Coulomb cut-off, which might produce artifacts. 72: You might want to consider using PME electrostatics. 72: 72: 72: 72: NOTE 6 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_5_input.mdp]: 72: COM removal frequency is set to (4). 72: Other settings require a global communication frequency of 100. 72: Note that this will require additional global communication steps, 72: which will reduce performance when using multiple ranks. 72: Consider setting nstcomm to a multiple of 100. 72: 72: 72: There were 6 NOTEs 72: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_5.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 72: Update groups can not be used for this system because an incompatible virtual site type is used 72: 72: Using 1 MPI thread 72: Using 2 OpenMP threads 72: 72: 72: NOTE: The number of threads is not equal to the number of (logical) cpus 72: and the -pin option is set to auto: will not pin threads to cpus. 72: This can lead to significant performance degradation. 72: Consider using -pin on (and -pinoffset in case you run multiple jobs). 72: 72: Polak-Ribiere Conjugate Gradients: 72: Tolerance (Fmax) = 1.00000e+01 72: Number of steps = 4 72: F-max = 1.06801e+03 on atom 28 72: F-Norm = 4.26917e+02 72: 72: 72: Energy minimization reached the maximum number of steps before the forces 72: reached the requested precision Fmax < 10. 72: 72: writing lowest energy coordinates. 72: 72: Polak-Ribiere Conjugate Gradients did not converge to Fmax < 10 in 5 steps. 72: Potential Energy = -1.6941089e+02 72: Maximum force = 2.1827658e+02 on atom 17 72: Norm of force = 7.9209019e+01 72: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_5_minimize.edr as single precision energy file 72: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.000 Reading energy frame 2 time 4.000 Last energy frame read 2 time 4.000 Generated 2145 of the 2145 non-bonded parameter combinations 72: 72: Generated 2145 of the 2145 1-4 parameter combinations 72: 72: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' 72: 72: turning all bonds into constraints... 72: 72: Cleaning up constraints and constant bonded interactions with virtual sites 72: 72: Removed 18 Angles with virtual sites, 21 left 72: 72: Removed 10 Proper Dih.s with virtual sites, 44 left 72: 72: Converted 15 Constraints with virtual sites to connections, 7 left 72: 72: This run will generate roughly 0 Mb of data 72: [ OK ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/5 (163 ms) 72: [----------] 6 tests from MinimizersWorkWithConstraints/EnergyMinimizationTest (13756 ms total) 72: 72: [----------] 6 tests from MinimizersWork/EnergyMinimizationTest 72: [ RUN ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/0 72: 72: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_0_input.mdp]: 72: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 72: that with the Verlet scheme, nstlist has no effect on the accuracy of 72: your simulation. 72: 72: 72: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_0_input.mdp]: 72: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 72: setting nstcomm equal to nstcalcenergy for less overhead 72: 72: Number of degrees of freedom in T-Coupling group System is 33.00 72: 72: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_0_input.mdp]: 72: COM removal frequency is set to (4). 72: Other settings require a global communication frequency of 100. 72: Note that this will require additional global communication steps, 72: which will reduce performance when using multiple ranks. 72: Consider setting nstcomm to a multiple of 100. 72: 72: 72: There were 3 NOTEs 72: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_0.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 72: Using 1 MPI thread 72: Using 2 OpenMP threads 72: 72: 72: NOTE: The number of threads is not equal to the number of (logical) cpus 72: and the -pin option is set to auto: will not pin threads to cpus. 72: This can lead to significant performance degradation. 72: Consider using -pin on (and -pinoffset in case you run multiple jobs). 72: 72: Steepest Descents: 72: Tolerance (Fmax) = 1.00000e+01 72: Number of steps = 4 72: 72: writing lowest energy coordinates. 72: 72: Steepest Descents converged to Fmax < 10 in 1 steps 72: Potential Energy = -9.7425699e-01 72: Maximum force = 4.0132303e+00 on atom 1 72: Norm of force = 1.6383944e+00 72: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_0_minimize.edr as single precision energy file 72: Reading energy frame 0 time 0.000 Last energy frame read 0 time 0.000 Generated 1 of the 1 non-bonded parameter combinations 72: 72: Excluding 1 bonded neighbours molecule type 'Argon' 72: 72: This run will generate roughly 0 Mb of data 72: [ OK ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/0 (96 ms) 72: [ RUN ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/1 72: 72: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_1_input.mdp]: 72: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 72: that with the Verlet scheme, nstlist has no effect on the accuracy of 72: your simulation. 72: 72: 72: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_1_input.mdp]: 72: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 72: setting nstcomm equal to nstcalcenergy for less overhead 72: 72: Number of degrees of freedom in T-Coupling group System is 33.00 72: 72: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_1_input.mdp]: 72: COM removal frequency is set to (4). 72: Other settings require a global communication frequency of 100. 72: Note that this will require additional global communication steps, 72: which will reduce performance when using multiple ranks. 72: Consider setting nstcomm to a multiple of 100. 72: 72: 72: There were 3 NOTEs 72: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_1.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 72: Using 1 MPI thread 72: Using 2 OpenMP threads 72: 72: 72: NOTE: The number of threads is not equal to the number of (logical) cpus 72: and the -pin option is set to auto: will not pin threads to cpus. 72: This can lead to significant performance degradation. 72: Consider using -pin on (and -pinoffset in case you run multiple jobs). 72: 72: Polak-Ribiere Conjugate Gradients: 72: Tolerance (Fmax) = 1.00000e+01 72: Number of steps = 4 72: F-max = 4.01323e+00 on atom 1 72: F-Norm = 1.63839e+00 72: 72: 72: writing lowest energy coordinates. 72: 72: Polak-Ribiere Conjugate Gradients converged to Fmax < 10 in 0 steps 72: Potential Energy = -9.9064207e-01 72: Maximum force = 2.5781615e+00 on atom 1 72: Norm of force = 1.0525300e+00 72: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_1_minimize.edr as single precision energy file 72: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.000 Last energy frame read 1 time 0.000 Generated 1 of the 1 non-bonded parameter combinations 72: 72: Excluding 1 bonded neighbours molecule type 'Argon' 72: 72: This run will generate roughly 0 Mb of data 72: [ OK ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/1 (82 ms) 72: [ RUN ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/2 72: 72: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_2_input.mdp]: 72: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 72: that with the Verlet scheme, nstlist has no effect on the accuracy of 72: your simulation. 72: 72: 72: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_2_input.mdp]: 72: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 72: setting nstcomm equal to nstcalcenergy for less overhead 72: 72: 72: WARNING 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_2_input.mdp]: 72: For efficient BFGS minimization, use switch/shift/pme instead of cut-off. 72: 72: Number of degrees of freedom in T-Coupling group System is 33.00 72: 72: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_2_input.mdp]: 72: COM removal frequency is set to (4). 72: Other settings require a global communication frequency of 100. 72: Note that this will require additional global communication steps, 72: which will reduce performance when using multiple ranks. 72: Consider setting nstcomm to a multiple of 100. 72: 72: 72: There were 3 NOTEs 72: 72: There was 1 WARNING 72: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_2.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 72: L-BFGS minimization only supports a single rank. Choosing to use only a single thread-MPI rank. 72: 72: Using 1 MPI thread 72: Using 2 OpenMP threads 72: 72: 72: NOTE: The number of threads is not equal to the number of (logical) cpus 72: and the -pin option is set to auto: will not pin threads to cpus. 72: This can lead to significant performance degradation. 72: Consider using -pin on (and -pinoffset in case you run multiple jobs). 72: 72: Low-Memory BFGS Minimizer: 72: Tolerance (Fmax) = 1.00000e+01 72: Number of steps = 4 72: Using 10 BFGS correction steps. 72: 72: F-max = 4.01323e+00 on atom 1 72: F-Norm = 1.63839e+00 72: 72: 72: writing lowest energy coordinates. 72: 72: Low-Memory BFGS Minimizer converged to Fmax < 10 in -1 steps 72: Potential Energy = -9.9064207e-01 72: Maximum force = 2.5781615e+00 on atom 1 72: Norm of force = 1.0525300e+00 72: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_2_minimize.edr as single precision energy file 72: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.000 Last energy frame read 1 time 0.000 Generated 1 of the 1 non-bonded parameter combinations 72: 72: Excluding 1 bonded neighbours molecule type 'Argon' 72: 72: This run will generate roughly 0 Mb of data 72: [ OK ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/2 (75 ms) 72: [ RUN ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/3 72: 72: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_3_input.mdp]: 72: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 72: that with the Verlet scheme, nstlist has no effect on the accuracy of 72: your simulation. 72: 72: 72: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_3_input.mdp]: 72: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 72: setting nstcomm equal to nstcalcenergy for less overhead 72: 72: Generating 1-4 interactions: fudge = 1 72: Number of degrees of freedom in T-Coupling group System is 27.00 72: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 72: 72: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_3_input.mdp]: 72: You are using a plain Coulomb cut-off, which might produce artifacts. 72: You might want to consider using PME electrostatics. 72: 72: 72: 72: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_3_input.mdp]: 72: COM removal frequency is set to (4). 72: Other settings require a global communication frequency of 100. 72: Note that this will require additional global communication steps, 72: which will reduce performance when using multiple ranks. 72: Consider setting nstcomm to a multiple of 100. 72: 72: 72: There were 4 NOTEs 72: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_3.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 72: Using 1 MPI thread 72: Using 2 OpenMP threads 72: 72: 72: NOTE: The number of threads is not equal to the number of (logical) cpus 72: and the -pin option is set to auto: will not pin threads to cpus. 72: This can lead to significant performance degradation. 72: Consider using -pin on (and -pinoffset in case you run multiple jobs). 72: 72: Steepest Descents: 72: Tolerance (Fmax) = 1.00000e+01 72: Number of steps = 4 72: 72: Energy minimization reached the maximum number of steps before the forces 72: reached the requested precision Fmax < 10. 72: 72: writing lowest energy coordinates. 72: 72: Steepest Descents did not converge to Fmax < 10 in 5 steps. 72: Potential Energy = 3.1939679e+02 72: Maximum force = 9.9704229e+03 on atom 9 72: Norm of force = 4.6227534e+03 72: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_3_minimize.edr as single precision energy file 72: Reading energy frame 0 time 0.000 Reading energy frame 1 time 1.000 Reading energy frame 2 time 2.000 Reading energy frame 3 time 3.000 Reading energy frame 4 time 4.000 Last energy frame read 4 time 4.000 Generated 20503 of the 20503 non-bonded parameter combinations 72: 72: Generated 17396 of the 20503 1-4 parameter combinations 72: 72: Excluding 3 bonded neighbours molecule type 'Glycine' 72: 72: This run will generate roughly 0 Mb of data 72: [ OK ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/3 (921 ms) 72: [ RUN ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/4 72: 72: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_4_input.mdp]: 72: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 72: that with the Verlet scheme, nstlist has no effect on the accuracy of 72: your simulation. 72: 72: 72: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_4_input.mdp]: 72: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 72: setting nstcomm equal to nstcalcenergy for less overhead 72: 72: Generating 1-4 interactions: fudge = 1 72: Number of degrees of freedom in T-Coupling group System is 27.00 72: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 72: 72: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_4_input.mdp]: 72: You are using a plain Coulomb cut-off, which might produce artifacts. 72: You might want to consider using PME electrostatics. 72: 72: 72: 72: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_4_input.mdp]: 72: COM removal frequency is set to (4). 72: Other settings require a global communication frequency of 100. 72: Note that this will require additional global communication steps, 72: which will reduce performance when using multiple ranks. 72: Consider setting nstcomm to a multiple of 100. 72: 72: 72: There were 4 NOTEs 72: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_4.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 72: Using 1 MPI thread 72: Using 2 OpenMP threads 72: 72: 72: NOTE: The number of threads is not equal to the number of (logical) cpus 72: and the -pin option is set to auto: will not pin threads to cpus. 72: This can lead to significant performance degradation. 72: Consider using -pin on (and -pinoffset in case you run multiple jobs). 72: 72: Polak-Ribiere Conjugate Gradients: 72: Tolerance (Fmax) = 1.00000e+01 72: Number of steps = 4 72: F-max = 2.41672e+04 on atom 10 72: F-Norm = 1.19357e+04 72: 72: 72: Energy minimization reached the maximum number of steps before the forces 72: reached the requested precision Fmax < 10. 72: 72: writing lowest energy coordinates. 72: 72: Polak-Ribiere Conjugate Gradients did not converge to Fmax < 10 in 5 steps. 72: Potential Energy = 1.5625757e+02 72: Maximum force = 7.5018242e+03 on atom 9 72: Norm of force = 3.6139019e+03 72: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_4_minimize.edr as single precision energy file 72: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.000 Reading energy frame 2 time 4.000 Last energy frame read 2 time 4.000 Generated 20503 of the 20503 non-bonded parameter combinations 72: 72: Generated 17396 of the 20503 1-4 parameter combinations 72: 72: Excluding 3 bonded neighbours molecule type 'Glycine' 72: 72: This run will generate roughly 0 Mb of data 72: [ OK ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/4 (887 ms) 72: [ RUN ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/5 72: 72: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_5_input.mdp]: 72: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 72: that with the Verlet scheme, nstlist has no effect on the accuracy of 72: your simulation. 72: 72: 72: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_5_input.mdp]: 72: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 72: setting nstcomm equal to nstcalcenergy for less overhead 72: 72: 72: WARNING 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_5_input.mdp]: 72: For efficient BFGS minimization, use switch/shift/pme instead of cut-off. 72: 72: Generating 1-4 interactions: fudge = 1 72: Number of degrees of freedom in T-Coupling group System is 27.00 72: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 72: 72: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_5_input.mdp]: 72: You are using a plain Coulomb cut-off, which might produce artifacts. 72: You might want to consider using PME electrostatics. 72: 72: 72: 72: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_5_input.mdp]: 72: COM removal frequency is set to (4). 72: Other settings require a global communication frequency of 100. 72: Note that this will require additional global communication steps, 72: which will reduce performance when using multiple ranks. 72: Consider setting nstcomm to a multiple of 100. 72: 72: 72: There were 4 NOTEs 72: 72: There was 1 WARNING 72: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_5.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 72: L-BFGS minimization only supports a single rank. Choosing to use only a single thread-MPI rank. 72: 72: Using 1 MPI thread 72: Using 2 OpenMP threads 72: 72: 72: NOTE: The number of threads is not equal to the number of (logical) cpus 72: and the -pin option is set to auto: will not pin threads to cpus. 72: This can lead to significant performance degradation. 72: Consider using -pin on (and -pinoffset in case you run multiple jobs). 72: 72: Low-Memory BFGS Minimizer: 72: Tolerance (Fmax) = 1.00000e+01 72: Number of steps = 4 72: Using 10 BFGS correction steps. 72: 72: F-max = 2.41672e+04 on atom 10 72: F-Norm = 1.19357e+04 72: 72: 72: Energy minimization has stopped, but the forces have not converged to the 72: requested precision Fmax < 10 (which may not be possible for your system). It 72: stopped because the algorithm tried to make a new step whose size was too 72: small, or there was no change in the energy since last step. Either way, we 72: regard the minimization as converged to within the available machine 72: precision, given your starting configuration and EM parameters. 72: 72: Double precision normally gives you higher accuracy, but this is often not 72: needed for preparing to run molecular dynamics. 72: 72: writing lowest energy coordinates. 72: 72: Low-Memory BFGS Minimizer converged to machine precision in 0 steps, 72: but did not reach the requested Fmax < 10. 72: Potential Energy = 5.6111560e+02 72: Maximum force = 1.2685396e+04 on atom 10 72: Norm of force = 6.0643518e+03 72: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_5_minimize.edr as single precision energy file 72: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.000 Reading energy frame 2 time 4.000 Last energy frame read 2 time 4.000 Generated 20503 of the 20503 non-bonded parameter combinations 72: 72: Generated 17396 of the 20503 1-4 parameter combinations 72: 72: Excluding 3 bonded neighbours molecule type 'Glycine' 72: 72: This run will generate roughly 0 Mb of data 72: [ OK ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/5 (761 ms) 72: [----------] 6 tests from MinimizersWork/EnergyMinimizationTest (2825 ms total) 72: 72: [----------] Global test environment tear-down 72: [==========] 12 tests from 2 test suites ran. (16708 ms total) 72: [ PASSED ] 12 tests. 72/92 Test #72: Minimize1RankTests ........................ Passed 16.82 sec test 73 Start 73: Minimize2RankTests 73: Test command: /build/reproducible-path/gromacs-2025.1/build/basic/bin/minimize-test "-ntomp" "2" "-ntmpi" "2" "--gtest_output=xml:/build/reproducible-path/gromacs-2025.1/build/basic/Testing/Temporary/Minimize2RankTests.xml" 73: Working Directory: /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests 73: Test timeout computed to be: 600 73: [==========] Running 12 tests from 2 test suites. 73: [----------] Global test environment set-up. 73: [----------] 6 tests from MinimizersWorkWithConstraints/EnergyMinimizationTest 73: [ RUN ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/0 73: 73: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_0_input.mdp]: 73: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 73: that with the Verlet scheme, nstlist has no effect on the accuracy of 73: your simulation. 73: 73: 73: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_0_input.mdp]: 73: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 73: setting nstcomm equal to nstcalcenergy for less overhead 73: 73: Generating 1-4 interactions: fudge = 0.5 73: Number of degrees of freedom in T-Coupling group System is 27.00 73: 73: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_0_input.mdp]: 73: You are using a plain Coulomb cut-off, which might produce artifacts. 73: You might want to consider using PME electrostatics. 73: 73: 73: 73: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_0_input.mdp]: 73: COM removal frequency is set to (4). 73: Other settings require a global communication frequency of 100. 73: Note that this will require additional global communication steps, 73: which will reduce performance when using multiple ranks. 73: Consider setting nstcomm to a multiple of 100. 73: 73: 73: There were 4 NOTEs 73: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_0.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 73: Using 2 MPI threads 73: Using 2 OpenMP threads per tMPI thread 73: 73: 73: Steepest Descents: 73: Tolerance (Fmax) = 1.00000e+01 73: Number of steps = 4 73: 73: Energy minimization reached the maximum number of steps before the forces 73: reached the requested precision Fmax < 10. 73: 73: writing lowest energy coordinates. 73: 73: Steepest Descents did not converge to Fmax < 10 in 5 steps. 73: Potential Energy = -4.7991024e+01 73: Maximum force = 1.8629745e+02 on atom 13 73: Norm of force = 8.7721978e+01 73: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_0_minimize.edr as single precision energy file 73: Reading energy frame 0 time 0.000 Reading energy frame 1 time 1.000 Reading energy frame 2 time 2.000 Reading energy frame 3 time 3.000 Reading energy frame 4 time 4.000 Last energy frame read 4 time 4.000 Generated 330891 of the 330891 non-bonded parameter combinations 73: 73: Generated 330891 of the 330891 1-4 parameter combinations 73: 73: Excluding 2 bonded neighbours molecule type 'SOL' 73: 73: This run will generate roughly 0 Mb of data 73: [ OK ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/0 (4853 ms) 73: [ RUN ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/1 73: 73: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_1_input.mdp]: 73: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 73: that with the Verlet scheme, nstlist has no effect on the accuracy of 73: your simulation. 73: 73: 73: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_1_input.mdp]: 73: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 73: setting nstcomm equal to nstcalcenergy for less overhead 73: 73: Generating 1-4 interactions: fudge = 0.5 73: Number of degrees of freedom in T-Coupling group System is 27.00 73: 73: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_1_input.mdp]: 73: You are using a plain Coulomb cut-off, which might produce artifacts. 73: You might want to consider using PME electrostatics. 73: 73: 73: 73: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_1_input.mdp]: 73: COM removal frequency is set to (4). 73: Other settings require a global communication frequency of 100. 73: Note that this will require additional global communication steps, 73: which will reduce performance when using multiple ranks. 73: Consider setting nstcomm to a multiple of 100. 73: 73: 73: There were 4 NOTEs 73: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_1.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 73: Using 2 MPI threads 73: 73: Non-default thread affinity set, disabling internal thread affinity 73: 73: Using 2 OpenMP threads per tMPI thread 73: 73: 73: Polak-Ribiere Conjugate Gradients: 73: Tolerance (Fmax) = 1.00000e+01 73: Number of steps = 4 73: F-max = 3.02331e+02 on atom 3 73: F-Norm = 1.18024e+02 73: 73: 73: Energy minimization reached the maximum number of steps before the forces 73: reached the requested precision Fmax < 10. 73: 73: writing lowest energy coordinates. 73: 73: Polak-Ribiere Conjugate Gradients did not converge to Fmax < 10 in 5 steps. 73: Potential Energy = -5.5862568e+01 73: Maximum force = 4.2725784e+02 on atom 13 73: Norm of force = 1.8452377e+02 73: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_1_minimize.edr as single precision energy file 73: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.000 Reading energy frame 2 time 4.000 Last energy frame read 2 time 4.000 Generated 330891 of the 330891 non-bonded parameter combinations 73: 73: Generated 330891 of the 330891 1-4 parameter combinations 73: 73: Excluding 2 bonded neighbours molecule type 'SOL' 73: 73: This run will generate roughly 0 Mb of data 73: [ OK ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/1 (6789 ms) 73: [ RUN ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/2 73: 73: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_2_input.mdp]: 73: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 73: that with the Verlet scheme, nstlist has no effect on the accuracy of 73: your simulation. 73: 73: 73: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_2_input.mdp]: 73: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 73: setting nstcomm equal to nstcalcenergy for less overhead 73: 73: Generating 1-4 interactions: fudge = 1 73: Number of degrees of freedom in T-Coupling group System is 22.00 73: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 73: 73: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_2_input.mdp]: 73: You are using a plain Coulomb cut-off, which might produce artifacts. 73: You might want to consider using PME electrostatics. 73: 73: 73: 73: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_2_input.mdp]: 73: COM removal frequency is set to (4). 73: Other settings require a global communication frequency of 100. 73: Note that this will require additional global communication steps, 73: which will reduce performance when using multiple ranks. 73: Consider setting nstcomm to a multiple of 100. 73: 73: 73: There were 4 NOTEs 73: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_2.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 73: Using 2 MPI threads 73: 73: Non-default thread affinity set, disabling internal thread affinity 73: 73: Using 2 OpenMP threads per tMPI thread 73: 73: 73: Steepest Descents: 73: Tolerance (Fmax) = 1.00000e+01 73: Number of steps = 4 73: 73: Energy minimization reached the maximum number of steps before the forces 73: reached the requested precision Fmax < 10. 73: 73: writing lowest energy coordinates. 73: 73: Steepest Descents did not converge to Fmax < 10 in 5 steps. 73: Potential Energy = 3.1937720e+02 73: Maximum force = 9.9988643e+03 on atom 9 73: Norm of force = 4.6166993e+03 73: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_2_minimize.edr as single precision energy file 73: Reading energy frame 0 time 0.000 Reading energy frame 1 time 1.000 Reading energy frame 2 time 2.000 Reading energy frame 3 time 3.000 Reading energy frame 4 time 4.000 Last energy frame read 4 time 4.000 Generated 20503 of the 20503 non-bonded parameter combinations 73: 73: Generated 17396 of the 20503 1-4 parameter combinations 73: 73: Excluding 3 bonded neighbours molecule type 'Glycine' 73: 73: turning H bonds into constraints... 73: 73: This run will generate roughly 0 Mb of data 73: [ OK ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/2 (2207 ms) 73: [ RUN ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/3 73: 73: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_3_input.mdp]: 73: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 73: that with the Verlet scheme, nstlist has no effect on the accuracy of 73: your simulation. 73: 73: 73: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_3_input.mdp]: 73: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 73: setting nstcomm equal to nstcalcenergy for less overhead 73: 73: Generating 1-4 interactions: fudge = 1 73: 73: NOTE 3 [file glycine_vacuo.top, line 12]: 73: For accurate cg with LINCS constraints, lincs-order should be 8 or more. 73: 73: Number of degrees of freedom in T-Coupling group System is 22.00 73: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 73: 73: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_3_input.mdp]: 73: You are using a plain Coulomb cut-off, which might produce artifacts. 73: You might want to consider using PME electrostatics. 73: 73: 73: 73: NOTE 5 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_3_input.mdp]: 73: COM removal frequency is set to (4). 73: Other settings require a global communication frequency of 100. 73: Note that this will require additional global communication steps, 73: which will reduce performance when using multiple ranks. 73: Consider setting nstcomm to a multiple of 100. 73: 73: 73: There were 5 NOTEs 73: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_3.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 73: Using 2 MPI threads 73: 73: Non-default thread affinity set, disabling internal thread affinity 73: 73: Using 2 OpenMP threads per tMPI thread 73: 73: 73: Polak-Ribiere Conjugate Gradients: 73: Tolerance (Fmax) = 1.00000e+01 73: Number of steps = 4 73: F-max = 2.41575e+04 on atom 10 73: F-Norm = 1.18451e+04 73: 73: 73: Energy minimization reached the maximum number of steps before the forces 73: reached the requested precision Fmax < 10. 73: 73: writing lowest energy coordinates. 73: 73: Polak-Ribiere Conjugate Gradients did not converge to Fmax < 10 in 5 steps. 73: Potential Energy = 1.5174437e+02 73: Maximum force = 7.4208867e+03 on atom 9 73: Norm of force = 3.5692983e+03 73: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_3_minimize.edr as single precision energy file 73: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.000 Reading energy frame 2 time 4.000 Last energy frame read 2 time 4.000 Generated 20503 of the 20503 non-bonded parameter combinations 73: 73: Generated 17396 of the 20503 1-4 parameter combinations 73: 73: Excluding 3 bonded neighbours molecule type 'Glycine' 73: 73: turning H bonds into constraints... 73: 73: This run will generate roughly 0 Mb of data 73: [ OK ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/3 (2891 ms) 73: [ RUN ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/4 73: 73: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_4_input.mdp]: 73: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 73: that with the Verlet scheme, nstlist has no effect on the accuracy of 73: your simulation. 73: 73: 73: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_4_input.mdp]: 73: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 73: setting nstcomm equal to nstcalcenergy for less overhead 73: 73: Generating 1-4 interactions: fudge = 0.5 73: 73: NOTE 3 [file unknown]: 73: You are using constraints on all bonds, whereas the forcefield has been 73: parametrized only with constraints involving hydrogen atoms. We suggest 73: using constraints = h-bonds instead, this will also improve performance. 73: 73: Number of degrees of freedom in T-Coupling group System is 23.00 73: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 73: 73: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_4_input.mdp]: 73: You are using a plain Coulomb cut-off, which might produce artifacts. 73: You might want to consider using PME electrostatics. 73: 73: 73: 73: NOTE 5 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_4_input.mdp]: 73: COM removal frequency is set to (4). 73: Other settings require a global communication frequency of 100. 73: Note that this will require additional global communication steps, 73: which will reduce performance when using multiple ranks. 73: Consider setting nstcomm to a multiple of 100. 73: 73: 73: There were 5 NOTEs 73: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_4.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 73: Update groups can not be used for this system because an incompatible virtual site type is used 73: 73: Using 2 MPI threads 73: 73: Non-default thread affinity set, disabling internal thread affinity 73: 73: Using 2 OpenMP threads per tMPI thread 73: 73: 73: Steepest Descents: 73: Tolerance (Fmax) = 1.00000e+01 73: Number of steps = 4 73: 73: Energy minimization reached the maximum number of steps before the forces 73: reached the requested precision Fmax < 10. 73: 73: writing lowest energy coordinates. 73: 73: Steepest Descents did not converge to Fmax < 10 in 5 steps. 73: Potential Energy = -1.5698407e+02 73: Maximum force = 4.5706586e+02 on atom 17 73: Norm of force = 1.8328245e+02 73: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_4_minimize.edr as single precision energy file 73: Reading energy frame 0 time 0.000 Reading energy frame 1 time 1.000 Reading energy frame 2 time 3.000 Last energy frame read 2 time 3.000 Generated 2145 of the 2145 non-bonded parameter combinations 73: 73: Generated 2145 of the 2145 1-4 parameter combinations 73: 73: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' 73: 73: turning all bonds into constraints... 73: 73: Cleaning up constraints and constant bonded interactions with virtual sites 73: 73: Removed 18 Angles with virtual sites, 21 left 73: 73: Removed 10 Proper Dih.s with virtual sites, 44 left 73: 73: Converted 15 Constraints with virtual sites to connections, 7 left 73: 73: This run will generate roughly 0 Mb of data 73: [ OK ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/4 (1747 ms) 73: [ RUN ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/5 73: 73: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_5_input.mdp]: 73: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 73: that with the Verlet scheme, nstlist has no effect on the accuracy of 73: your simulation. 73: 73: 73: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_5_input.mdp]: 73: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 73: setting nstcomm equal to nstcalcenergy for less overhead 73: 73: Generating 1-4 interactions: fudge = 0.5 73: 73: NOTE 3 [file unknown]: 73: You are using constraints on all bonds, whereas the forcefield has been 73: parametrized only with constraints involving hydrogen atoms. We suggest 73: using constraints = h-bonds instead, this will also improve performance. 73: 73: 73: NOTE 4 [file unknown]: 73: For accurate cg with LINCS constraints, lincs-order should be 8 or more. 73: 73: Number of degrees of freedom in T-Coupling group System is 23.00 73: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 73: 73: NOTE 5 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_5_input.mdp]: 73: You are using a plain Coulomb cut-off, which might produce artifacts. 73: You might want to consider using PME electrostatics. 73: 73: 73: 73: NOTE 6 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_5_input.mdp]: 73: COM removal frequency is set to (4). 73: Other settings require a global communication frequency of 100. 73: Note that this will require additional global communication steps, 73: which will reduce performance when using multiple ranks. 73: Consider setting nstcomm to a multiple of 100. 73: 73: 73: There were 6 NOTEs 73: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_5.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 73: Update groups can not be used for this system because an incompatible virtual site type is used 73: 73: Using 2 MPI threads 73: 73: Non-default thread affinity set, disabling internal thread affinity 73: 73: Using 2 OpenMP threads per tMPI thread 73: 73: 73: Polak-Ribiere Conjugate Gradients: 73: Tolerance (Fmax) = 1.00000e+01 73: Number of steps = 4 73: F-max = 1.06801e+03 on atom 28 73: F-Norm = 4.26917e+02 73: 73: 73: Energy minimization reached the maximum number of steps before the forces 73: reached the requested precision Fmax < 10. 73: 73: writing lowest energy coordinates. 73: 73: Polak-Ribiere Conjugate Gradients did not converge to Fmax < 10 in 5 steps. 73: Potential Energy = -1.6941095e+02 73: Maximum force = 2.1827661e+02 on atom 17 73: Norm of force = 7.9209030e+01 73: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_5_minimize.edr as single precision energy file 73: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.000 Reading energy frame 2 time 4.000 Last energy frame read 2 time 4.000 Generated 2145 of the 2145 non-bonded parameter combinations 73: 73: Generated 2145 of the 2145 1-4 parameter combinations 73: 73: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' 73: 73: turning all bonds into constraints... 73: 73: Cleaning up constraints and constant bonded interactions with virtual sites 73: 73: Removed 18 Angles with virtual sites, 21 left 73: 73: Removed 10 Proper Dih.s with virtual sites, 44 left 73: 73: Converted 15 Constraints with virtual sites to connections, 7 left 73: 73: This run will generate roughly 0 Mb of data 73: [ OK ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/5 (3123 ms) 73: [----------] 6 tests from MinimizersWorkWithConstraints/EnergyMinimizationTest (21615 ms total) 73: 73: [----------] 6 tests from MinimizersWork/EnergyMinimizationTest 73: [ RUN ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/0 73: 73: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_0_input.mdp]: 73: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 73: that with the Verlet scheme, nstlist has no effect on the accuracy of 73: your simulation. 73: 73: 73: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_0_input.mdp]: 73: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 73: setting nstcomm equal to nstcalcenergy for less overhead 73: 73: Number of degrees of freedom in T-Coupling group System is 33.00 73: 73: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_0_input.mdp]: 73: COM removal frequency is set to (4). 73: Other settings require a global communication frequency of 100. 73: Note that this will require additional global communication steps, 73: which will reduce performance when using multiple ranks. 73: Consider setting nstcomm to a multiple of 100. 73: 73: 73: There were 3 NOTEs 73: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_0.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 73: Using 2 MPI threads 73: 73: Non-default thread affinity set, disabling internal thread affinity 73: 73: Using 2 OpenMP threads per tMPI thread 73: 73: 73: Steepest Descents: 73: Tolerance (Fmax) = 1.00000e+01 73: Number of steps = 4 73: 73: writing lowest energy coordinates. 73: 73: Steepest Descents converged to Fmax < 10 in 1 steps 73: Potential Energy = -9.7425699e-01 73: Maximum force = 4.0132303e+00 on atom 3 73: Norm of force = 1.6383944e+00 73: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_0_minimize.edr as single precision energy file 73: Reading energy frame 0 time 0.000 Last energy frame read 0 time 0.000 Generated 1 of the 1 non-bonded parameter combinations 73: 73: Excluding 1 bonded neighbours molecule type 'Argon' 73: 73: This run will generate roughly 0 Mb of data 73: [ OK ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/0 (817 ms) 73: [ RUN ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/1 73: 73: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_1_input.mdp]: 73: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 73: that with the Verlet scheme, nstlist has no effect on the accuracy of 73: your simulation. 73: 73: 73: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_1_input.mdp]: 73: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 73: setting nstcomm equal to nstcalcenergy for less overhead 73: 73: Number of degrees of freedom in T-Coupling group System is 33.00 73: 73: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_1_input.mdp]: 73: COM removal frequency is set to (4). 73: Other settings require a global communication frequency of 100. 73: Note that this will require additional global communication steps, 73: which will reduce performance when using multiple ranks. 73: Consider setting nstcomm to a multiple of 100. 73: 73: 73: There were 3 NOTEs 73: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_1.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 73: Using 2 MPI threads 73: 73: Non-default thread affinity set, disabling internal thread affinity 73: 73: Using 2 OpenMP threads per tMPI thread 73: 73: 73: Polak-Ribiere Conjugate Gradients: 73: Tolerance (Fmax) = 1.00000e+01 73: Number of steps = 4 73: F-max = 4.01323e+00 on atom 3 73: F-Norm = 1.63839e+00 73: 73: 73: writing lowest energy coordinates. 73: 73: Polak-Ribiere Conjugate Gradients converged to Fmax < 10 in 0 steps 73: Potential Energy = -9.9064207e-01 73: Maximum force = 2.5781615e+00 on atom 3 73: Norm of force = 1.0525300e+00 73: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_1_minimize.edr as single precision energy file 73: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.000 Last energy frame read 1 time 0.000 Generated 1 of the 1 non-bonded parameter combinations 73: 73: Excluding 1 bonded neighbours molecule type 'Argon' 73: 73: This run will generate roughly 0 Mb of data 73: [ OK ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/1 (979 ms) 73: [ RUN ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/2 73: 73: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_2_input.mdp]: 73: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 73: that with the Verlet scheme, nstlist has no effect on the accuracy of 73: your simulation. 73: 73: 73: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_2_input.mdp]: 73: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 73: setting nstcomm equal to nstcalcenergy for less overhead 73: 73: 73: WARNING 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_2_input.mdp]: 73: For efficient BFGS minimization, use switch/shift/pme instead of cut-off. 73: 73: Number of degrees of freedom in T-Coupling group System is 33.00 73: 73: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_2_input.mdp]: 73: COM removal frequency is set to (4). 73: Other settings require a global communication frequency of 100. 73: Note that this will require additional global communication steps, 73: which will reduce performance when using multiple ranks. 73: Consider setting nstcomm to a multiple of 100. 73: 73: 73: There were 3 NOTEs 73: 73: There was 1 WARNING 73: Generated 1 of the 1 non-bonded parameter combinations 73: 73: Excluding 1 bonded neighbours molecule type 'Argon' 73: 73: This run will generate roughly 0 Mb of data 73: [ OK ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/2 (28 ms) 73: [ RUN ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/3 73: 73: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_3_input.mdp]: 73: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 73: that with the Verlet scheme, nstlist has no effect on the accuracy of 73: your simulation. 73: 73: 73: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_3_input.mdp]: 73: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 73: setting nstcomm equal to nstcalcenergy for less overhead 73: 73: Generating 1-4 interactions: fudge = 1 73: Number of degrees of freedom in T-Coupling group System is 27.00 73: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 73: 73: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_3_input.mdp]: 73: You are using a plain Coulomb cut-off, which might produce artifacts. 73: You might want to consider using PME electrostatics. 73: 73: 73: 73: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_3_input.mdp]: 73: COM removal frequency is set to (4). 73: Other settings require a global communication frequency of 100. 73: Note that this will require additional global communication steps, 73: which will reduce performance when using multiple ranks. 73: Consider setting nstcomm to a multiple of 100. 73: 73: 73: There were 4 NOTEs 73: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_3.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 73: Using 2 MPI threads 73: 73: Non-default thread affinity set, disabling internal thread affinity 73: 73: Using 2 OpenMP threads per tMPI thread 73: 73: 73: Steepest Descents: 73: Tolerance (Fmax) = 1.00000e+01 73: Number of steps = 4 73: 73: Energy minimization reached the maximum number of steps before the forces 73: reached the requested precision Fmax < 10. 73: 73: writing lowest energy coordinates. 73: 73: Steepest Descents did not converge to Fmax < 10 in 5 steps. 73: Potential Energy = 3.1939667e+02 73: Maximum force = 9.9704229e+03 on atom 9 73: Norm of force = 4.6227537e+03 73: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_3_minimize.edr as single precision energy file 73: Reading energy frame 0 time 0.000 Reading energy frame 1 time 1.000 Reading energy frame 2 time 2.000 Reading energy frame 3 time 3.000 Reading energy frame 4 time 4.000 Last energy frame read 4 time 4.000 Generated 20503 of the 20503 non-bonded parameter combinations 73: 73: Generated 17396 of the 20503 1-4 parameter combinations 73: 73: Excluding 3 bonded neighbours molecule type 'Glycine' 73: 73: This run will generate roughly 0 Mb of data 73: [ OK ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/3 (2220 ms) 73: [ RUN ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/4 73: 73: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_4_input.mdp]: 73: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 73: that with the Verlet scheme, nstlist has no effect on the accuracy of 73: your simulation. 73: 73: 73: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_4_input.mdp]: 73: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 73: setting nstcomm equal to nstcalcenergy for less overhead 73: 73: Generating 1-4 interactions: fudge = 1 73: Number of degrees of freedom in T-Coupling group System is 27.00 73: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 73: 73: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_4_input.mdp]: 73: You are using a plain Coulomb cut-off, which might produce artifacts. 73: You might want to consider using PME electrostatics. 73: 73: 73: 73: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_4_input.mdp]: 73: COM removal frequency is set to (4). 73: Other settings require a global communication frequency of 100. 73: Note that this will require additional global communication steps, 73: which will reduce performance when using multiple ranks. 73: Consider setting nstcomm to a multiple of 100. 73: 73: 73: There were 4 NOTEs 73: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_4.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 73: Using 2 MPI threads 73: 73: Non-default thread affinity set, disabling internal thread affinity 73: 73: Using 2 OpenMP threads per tMPI thread 73: 73: 73: Polak-Ribiere Conjugate Gradients: 73: Tolerance (Fmax) = 1.00000e+01 73: Number of steps = 4 73: F-max = 2.41672e+04 on atom 10 73: F-Norm = 1.19357e+04 73: 73: 73: Energy minimization reached the maximum number of steps before the forces 73: reached the requested precision Fmax < 10. 73: 73: writing lowest energy coordinates. 73: 73: Polak-Ribiere Conjugate Gradients did not converge to Fmax < 10 in 5 steps. 73: Potential Energy = 1.5625768e+02 73: Maximum force = 7.5018237e+03 on atom 9 73: Norm of force = 3.6139019e+03 73: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_4_minimize.edr as single precision energy file 73: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.000 Reading energy frame 2 time 4.000 Last energy frame read 2 time 4.000 Generated 20503 of the 20503 non-bonded parameter combinations 73: 73: Generated 17396 of the 20503 1-4 parameter combinations 73: 73: Excluding 3 bonded neighbours molecule type 'Glycine' 73: 73: This run will generate roughly 0 Mb of data 73: [ OK ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/4 (2663 ms) 73: [ RUN ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/5 73: 73: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_5_input.mdp]: 73: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 73: that with the Verlet scheme, nstlist has no effect on the accuracy of 73: your simulation. 73: 73: 73: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_5_input.mdp]: 73: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 73: setting nstcomm equal to nstcalcenergy for less overhead 73: 73: 73: WARNING 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_5_input.mdp]: 73: For efficient BFGS minimization, use switch/shift/pme instead of cut-off. 73: 73: Generating 1-4 interactions: fudge = 1 73: Number of degrees of freedom in T-Coupling group System is 27.00 73: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 73: 73: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_5_input.mdp]: 73: You are using a plain Coulomb cut-off, which might produce artifacts. 73: You might want to consider using PME electrostatics. 73: 73: 73: 73: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_5_input.mdp]: 73: COM removal frequency is set to (4). 73: Other settings require a global communication frequency of 100. 73: Note that this will require additional global communication steps, 73: which will reduce performance when using multiple ranks. 73: Consider setting nstcomm to a multiple of 100. 73: 73: 73: There were 4 NOTEs 73: 73: There was 1 WARNING 73: Generated 20503 of the 20503 non-bonded parameter combinations 73: 73: Generated 17396 of the 20503 1-4 parameter combinations 73: 73: Excluding 3 bonded neighbours molecule type 'Glycine' 73: 73: This run will generate roughly 0 Mb of data 73: [ OK ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/5 (734 ms) 73: [----------] 6 tests from MinimizersWork/EnergyMinimizationTest (7444 ms total) 73: 73: [----------] Global test environment tear-down 73: [==========] 12 tests from 2 test suites ran. (29164 ms total) 73: [ PASSED ] 12 tests. 73/92 Test #73: Minimize2RankTests ........................ Passed 29.26 sec test 74 Start 74: MdrunNonIntegratorTests 74: Test command: /build/reproducible-path/gromacs-2025.1/build/basic/bin/mdrun-non-integrator-test "-ntomp" "2" "--gtest_output=xml:/build/reproducible-path/gromacs-2025.1/build/basic/Testing/Temporary/MdrunNonIntegratorTests.xml" 74: Working Directory: /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests 74: Test timeout computed to be: 600 74: [==========] Running 46 tests from 3 test suites. 74: [----------] Global test environment set-up. 74: [----------] 1 test from NonbondedBenchTest 74: [ RUN ] NonbondedBenchTest.BasicEndToEndTest 74: System size: 3000 atoms 74: Cut-off radius: 1 nm 74: Number of threads: 1 74: Number of iterations: 1 74: Compute energies: no 74: Ewald excl. corr.: analytical 74: 74: Coulomb LJ comb. SIMD Mcycles Mcycles/it. pairs/cycle 74: total useful 74: Ewald all geom. no 0.191 0.1908 6.2388 3.3006 74: [ OK ] NonbondedBenchTest.BasicEndToEndTest (432 ms) 74: [----------] 1 test from NonbondedBenchTest (432 ms total) 74: 74: [----------] 12 tests from NormalMdrunIsReproduced/MdrunRerunTest 74: [ RUN ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/0 74: 74: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_0_input.mdp]: 74: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 74: that with the Verlet scheme, nstlist has no effect on the accuracy of 74: your simulation. 74: 74: 74: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_0_input.mdp]: 74: Setting nstcalcenergy (100) equal to nstenergy (4) 74: 74: Number of degrees of freedom in T-Coupling group System is 33.00 74: 74: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_0_input.mdp]: 74: NVE simulation: will use the initial temperature of 68.810 K for 74: determining the Verlet buffer size 74: 74: 74: There were 3 NOTEs 74: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_0_sim.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 74: Can not increase nstlist because an NVE ensemble is used 74: Using 1 MPI thread 74: Using 2 OpenMP threads 74: 74: 74: NOTE: The number of threads is not equal to the number of (logical) cpus 74: and the -pin option is set to auto: will not pin threads to cpus. 74: This can lead to significant performance degradation. 74: Consider using -pin on (and -pinoffset in case you run multiple jobs). 74: starting mdrun 'Argon' 74: 16 steps, 0.0 ps. 74: Generated 1 of the 1 non-bonded parameter combinations 74: 74: Excluding 1 bonded neighbours molecule type 'Argon' 74: 74: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 74: 74: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 74: 74: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 74: 74: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 74: 74: Note that mdrun will redetermine rlist based on the actual pair-list setup 74: 74: This run will generate roughly 0 Mb of data 74: 74: Writing final coordinates. 74: 74: Core t (s) Wall t (s) (%) 74: Time: 0.073 0.037 198.3 74: (ns/day) (hour/ns) 74: Performance: 39.716 0.604 74: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_0_sim.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 74: Can not increase nstlist because an NVE ensemble is used 74: Using 1 MPI thread 74: Using 2 OpenMP threads 74: 74: 74: NOTE: The number of threads is not equal to the number of (logical) cpus 74: and the -pin option is set to auto: will not pin threads to cpus. 74: This can lead to significant performance degradation. 74: Consider using -pin on (and -pinoffset in case you run multiple jobs). 74: starting md rerun 'Argon', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_0_sim1.trr' 74: 74: trr version: GMX_trn_file (single precision) 74: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 74: 74: NOTE: 15 % of the run time was spent in pair search, 74: you might want to increase nstlist (this has no effect on accuracy) 74: 74: Core t (s) Wall t (s) (%) 74: Time: 0.005 0.003 192.6 74: (ns/day) (hour/ns) 74: Performance: 539.173 0.045 74: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_0_sim1.edr as single precision energy file 74: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_0_sim2.edr as single precision energy file 74: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 74: 74: [ OK ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/0 (98 ms) 74: [ RUN ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/1 74: 74: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_1_input.mdp]: 74: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 74: that with the Verlet scheme, nstlist has no effect on the accuracy of 74: your simulation. 74: 74: 74: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_1_input.mdp]: 74: Setting nstcalcenergy (100) equal to nstenergy (4) 74: 74: Number of degrees of freedom in T-Coupling group System is 33.00 74: 74: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_1_input.mdp]: 74: NVE simulation: will use the initial temperature of 68.810 K for 74: determining the Verlet buffer size 74: 74: 74: There were 3 NOTEs 74: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_1_sim.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 74: Can not increase nstlist because an NVE ensemble is used 74: Using 1 MPI thread 74: Using 2 OpenMP threads 74: 74: 74: NOTE: The number of threads is not equal to the number of (logical) cpus 74: and the -pin option is set to auto: will not pin threads to cpus. 74: This can lead to significant performance degradation. 74: Consider using -pin on (and -pinoffset in case you run multiple jobs). 74: starting mdrun 'Argon' 74: 16 steps, 0.0 ps. 74: Generated 1 of the 1 non-bonded parameter combinations 74: 74: Excluding 1 bonded neighbours molecule type 'Argon' 74: 74: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 74: 74: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 74: 74: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 74: 74: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 74: 74: Note that mdrun will redetermine rlist based on the actual pair-list setup 74: 74: This run will generate roughly 0 Mb of data 74: 74: Writing final coordinates. 74: 74: NOTE: 20 % of the run time was spent in pair search, 74: you might want to increase nstlist (this has no effect on accuracy) 74: 74: Core t (s) Wall t (s) (%) 74: Time: 0.073 0.036 199.2 74: (ns/day) (hour/ns) 74: Performance: 40.324 0.595 74: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_1_sim.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 74: Can not increase nstlist because an NVE ensemble is used 74: Using 1 MPI thread 74: Using 2 OpenMP threads 74: 74: 74: NOTE: The number of threads is not equal to the number of (logical) cpus 74: and the -pin option is set to auto: will not pin threads to cpus. 74: This can lead to significant performance degradation. 74: Consider using -pin on (and -pinoffset in case you run multiple jobs). 74: starting md rerun 'Argon', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_1_sim1.trr' 74: 74: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 74: 74: NOTE: 17 % of the run time was spent in pair search, 74: you might want to increase nstlist (this has no effect on accuracy) 74: 74: Core t (s) Wall t (s) (%) 74: Time: 0.005 0.003 191.8 74: (ns/day) (hour/ns) 74: Performance: 540.403 0.044 74: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_1_sim1.edr as single precision energy file 74: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_1_sim2.edr as single precision energy file 74: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 74: 74: [ OK ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/1 (101 ms) 74: [ RUN ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/2 74: 74: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_2_input.mdp]: 74: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 74: that with the Verlet scheme, nstlist has no effect on the accuracy of 74: your simulation. 74: 74: 74: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_2_input.mdp]: 74: Setting nstcalcenergy (100) equal to nstenergy (4) 74: 74: Number of degrees of freedom in T-Coupling group System is 33.00 74: 74: There were 2 NOTEs 74: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_2_sim.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 74: Changing nstlist from 8 to 100, rlist from 0.712 to 0.744 74: 74: Using 1 MPI thread 74: Using 2 OpenMP threads 74: 74: 74: NOTE: The number of threads is not equal to the number of (logical) cpus 74: and the -pin option is set to auto: will not pin threads to cpus. 74: This can lead to significant performance degradation. 74: Consider using -pin on (and -pinoffset in case you run multiple jobs). 74: starting mdrun 'Argon' 74: 16 steps, 0.0 ps. 74: Generated 1 of the 1 non-bonded parameter combinations 74: 74: Excluding 1 bonded neighbours molecule type 'Argon' 74: 74: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 74: 74: Calculated rlist for 1x1 atom pair-list as 0.713 nm, buffer size 0.013 nm 74: 74: Set rlist, assuming 4x4 atom pair-list, to 0.712 nm, buffer size 0.012 nm 74: 74: Note that mdrun will redetermine rlist based on the actual pair-list setup 74: 74: This run will generate roughly 0 Mb of data 74: 74: Writing final coordinates. 74: 74: Core t (s) Wall t (s) (%) 74: Time: 0.038 0.019 197.5 74: (ns/day) (hour/ns) 74: Performance: 76.167 0.315 74: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_2_sim.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 74: Changing nstlist from 8 to 100, rlist from 0.712 to 0.744 74: 74: Using 1 MPI thread 74: Using 2 OpenMP threads 74: 74: 74: NOTE: The number of threads is not equal to the number of (logical) cpus 74: and the -pin option is set to auto: will not pin threads to cpus. 74: This can lead to significant performance degradation. 74: Consider using -pin on (and -pinoffset in case you run multiple jobs). 74: starting md rerun 'Argon', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_2_sim1.trr' 74: 74: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 74: 74: NOTE: 19 % of the run time was spent in pair search, 74: you might want to increase nstlist (this has no effect on accuracy) 74: 74: Core t (s) Wall t (s) (%) 74: Time: 0.005 0.003 192.7 74: (ns/day) (hour/ns) 74: Performance: 543.406 0.044 74: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_2_sim1.edr as single precision energy file 74: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_2_sim2.edr as single precision energy file 74: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 74: 74: [ OK ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/2 (83 ms) 74: [ RUN ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/3 74: 74: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_3_input.mdp]: 74: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 74: that with the Verlet scheme, nstlist has no effect on the accuracy of 74: your simulation. 74: 74: 74: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_3_input.mdp]: 74: Setting nstcalcenergy (100) equal to nstenergy (4) 74: 74: Number of degrees of freedom in T-Coupling group System is 33.00 74: 74: There were 2 NOTEs 74: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_3_sim.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 74: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 74: 74: Using 1 MPI thread 74: Using 2 OpenMP threads 74: 74: 74: NOTE: The number of threads is not equal to the number of (logical) cpus 74: and the -pin option is set to auto: will not pin threads to cpus. 74: This can lead to significant performance degradation. 74: Consider using -pin on (and -pinoffset in case you run multiple jobs). 74: starting mdrun 'Argon' 74: 16 steps, 0.0 ps. 74: Generated 1 of the 1 non-bonded parameter combinations 74: 74: Excluding 1 bonded neighbours molecule type 'Argon' 74: 74: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 74: 74: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 74: 74: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 74: 74: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 74: 74: Note that mdrun will redetermine rlist based on the actual pair-list setup 74: 74: This run will generate roughly 0 Mb of data 74: 74: Writing final coordinates. 74: 74: Core t (s) Wall t (s) (%) 74: Time: 0.038 0.019 198.0 74: (ns/day) (hour/ns) 74: Performance: 76.460 0.314 74: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_3_sim.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 74: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 74: 74: Using 1 MPI thread 74: Using 2 OpenMP threads 74: 74: 74: NOTE: The number of threads is not equal to the number of (logical) cpus 74: and the -pin option is set to auto: will not pin threads to cpus. 74: This can lead to significant performance degradation. 74: Consider using -pin on (and -pinoffset in case you run multiple jobs). 74: starting md rerun 'Argon', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_3_sim1.trr' 74: 74: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 74: 74: NOTE: 16 % of the run time was spent in pair search, 74: you might want to increase nstlist (this has no effect on accuracy) 74: 74: Core t (s) Wall t (s) (%) 74: Time: 0.005 0.002 192.1 74: (ns/day) (hour/ns) 74: Performance: 607.194 0.040 74: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_3_sim1.edr as single precision energy file 74: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_3_sim2.edr as single precision energy file 74: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 74: 74: [ OK ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/3 (85 ms) 74: [ RUN ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/4 74: 74: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_4_input.mdp]: 74: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 74: that with the Verlet scheme, nstlist has no effect on the accuracy of 74: your simulation. 74: 74: 74: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_4_input.mdp]: 74: Setting nstcalcenergy (100) equal to nstenergy (4) 74: 74: Generating 1-4 interactions: fudge = 0.5 74: Number of degrees of freedom in T-Coupling group System is 27.00 74: 74: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_4_input.mdp]: 74: NVE simulation: will use the initial temperature of 398.997 K for 74: determining the Verlet buffer size 74: 74: 74: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_4_input.mdp]: 74: You are using a plain Coulomb cut-off, which might produce artifacts. 74: You might want to consider using PME electrostatics. 74: 74: 74: 74: There were 4 NOTEs 74: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_4_sim.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 74: Can not increase nstlist because an NVE ensemble is used 74: Using 1 MPI thread 74: Using 2 OpenMP threads 74: 74: 74: NOTE: The number of threads is not equal to the number of (logical) cpus 74: and the -pin option is set to auto: will not pin threads to cpus. 74: This can lead to significant performance degradation. 74: Consider using -pin on (and -pinoffset in case you run multiple jobs). 74: starting mdrun 'spc2' 74: 16 steps, 0.0 ps. 74: Generated 330891 of the 330891 non-bonded parameter combinations 74: 74: Generated 330891 of the 330891 1-4 parameter combinations 74: 74: Excluding 2 bonded neighbours molecule type 'SOL' 74: 74: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/tip3p5.gro' 74: 74: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 74: 74: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 74: 74: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 74: 74: Note that mdrun will redetermine rlist based on the actual pair-list setup 74: 74: This run will generate roughly 0 Mb of data 74: 74: Writing final coordinates. 74: 74: Core t (s) Wall t (s) (%) 74: Time: 0.077 0.039 198.5 74: (ns/day) (hour/ns) 74: Performance: 38.091 0.630 74: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_4_sim.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 74: Can not increase nstlist because an NVE ensemble is used 74: Using 1 MPI thread 74: Using 2 OpenMP threads 74: 74: 74: NOTE: The number of threads is not equal to the number of (logical) cpus 74: and the -pin option is set to auto: will not pin threads to cpus. 74: This can lead to significant performance degradation. 74: Consider using -pin on (and -pinoffset in case you run multiple jobs). 74: starting md rerun 'spc2', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_4_sim1.trr' 74: 74: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 74: 74: NOTE: 13 % of the run time was spent in pair search, 74: you might want to increase nstlist (this has no effect on accuracy) 74: 74: Core t (s) Wall t (s) (%) 74: Time: 0.005 0.003 157.5 74: (ns/day) (hour/ns) 74: Performance: 450.830 0.053 74: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_4_sim1.edr as single precision energy file 74: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_4_sim2.edr as single precision energy file 74: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 74: 74: [ OK ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/4 (4644 ms) 74: [ RUN ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/5 74: 74: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_5_input.mdp]: 74: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 74: that with the Verlet scheme, nstlist has no effect on the accuracy of 74: your simulation. 74: 74: 74: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_5_input.mdp]: 74: Setting nstcalcenergy (100) equal to nstenergy (4) 74: 74: Generating 1-4 interactions: fudge = 0.5 74: Number of degrees of freedom in T-Coupling group System is 27.00 74: 74: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_5_input.mdp]: 74: NVE simulation: will use the initial temperature of 398.997 K for 74: determining the Verlet buffer size 74: 74: 74: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_5_input.mdp]: 74: You are using a plain Coulomb cut-off, which might produce artifacts. 74: You might want to consider using PME electrostatics. 74: 74: 74: 74: There were 4 NOTEs 74: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_5_sim.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 74: Can not increase nstlist because an NVE ensemble is used 74: Using 1 MPI thread 74: Using 2 OpenMP threads 74: 74: 74: NOTE: The number of threads is not equal to the number of (logical) cpus 74: and the -pin option is set to auto: will not pin threads to cpus. 74: This can lead to significant performance degradation. 74: Consider using -pin on (and -pinoffset in case you run multiple jobs). 74: starting mdrun 'spc2' 74: 16 steps, 0.0 ps. 74: Generated 330891 of the 330891 non-bonded parameter combinations 74: 74: Generated 330891 of the 330891 1-4 parameter combinations 74: 74: Excluding 2 bonded neighbours molecule type 'SOL' 74: 74: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/tip3p5.gro' 74: 74: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 74: 74: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 74: 74: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 74: 74: Note that mdrun will redetermine rlist based on the actual pair-list setup 74: 74: This run will generate roughly 0 Mb of data 74: 74: Writing final coordinates. 74: 74: NOTE: 13 % of the run time was spent in pair search, 74: you might want to increase nstlist (this has no effect on accuracy) 74: 74: Core t (s) Wall t (s) (%) 74: Time: 0.142 0.071 199.5 74: (ns/day) (hour/ns) 74: Performance: 20.680 1.161 74: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_5_sim.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 74: Can not increase nstlist because an NVE ensemble is used 74: Using 1 MPI thread 74: Using 2 OpenMP threads 74: 74: 74: NOTE: The number of threads is not equal to the number of (logical) cpus 74: and the -pin option is set to auto: will not pin threads to cpus. 74: This can lead to significant performance degradation. 74: Consider using -pin on (and -pinoffset in case you run multiple jobs). 74: starting md rerun 'spc2', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_5_sim1.trr' 74: 74: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 74: 74: NOTE: 15 % of the run time was spent in pair search, 74: you might want to increase nstlist (this has no effect on accuracy) 74: 74: Core t (s) Wall t (s) (%) 74: Time: 0.006 0.003 192.0 74: (ns/day) (hour/ns) 74: Performance: 511.805 0.047 74: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_5_sim1.edr as single precision energy file 74: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_5_sim2.edr as single precision energy file 74: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 74: 74: [ OK ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/5 (4536 ms) 74: [ RUN ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/6 74: 74: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_6_input.mdp]: 74: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 74: that with the Verlet scheme, nstlist has no effect on the accuracy of 74: your simulation. 74: 74: 74: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_6_input.mdp]: 74: Setting nstcalcenergy (100) equal to nstenergy (4) 74: 74: Generating 1-4 interactions: fudge = 0.5 74: Number of degrees of freedom in T-Coupling group System is 27.00 74: 74: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_6_input.mdp]: 74: You are using a plain Coulomb cut-off, which might produce artifacts. 74: You might want to consider using PME electrostatics. 74: 74: 74: 74: There were 3 NOTEs 74: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_6_sim.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 74: Changing nstlist from 8 to 100, rlist from 0.735 to 0.831 74: 74: Using 1 MPI thread 74: Using 2 OpenMP threads 74: 74: 74: NOTE: The number of threads is not equal to the number of (logical) cpus 74: and the -pin option is set to auto: will not pin threads to cpus. 74: This can lead to significant performance degradation. 74: Consider using -pin on (and -pinoffset in case you run multiple jobs). 74: starting mdrun 'spc2' 74: 16 steps, 0.0 ps. 74: Generated 330891 of the 330891 non-bonded parameter combinations 74: 74: Generated 330891 of the 330891 1-4 parameter combinations 74: 74: Excluding 2 bonded neighbours molecule type 'SOL' 74: 74: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 74: 74: Calculated rlist for 1x1 atom pair-list as 0.738 nm, buffer size 0.038 nm 74: 74: Set rlist, assuming 4x4 atom pair-list, to 0.735 nm, buffer size 0.035 nm 74: 74: Note that mdrun will redetermine rlist based on the actual pair-list setup 74: 74: This run will generate roughly 0 Mb of data 74: 74: Writing final coordinates. 74: 74: Core t (s) Wall t (s) (%) 74: Time: 0.046 0.023 197.9 74: (ns/day) (hour/ns) 74: Performance: 63.267 0.379 74: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_6_sim.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 74: Changing nstlist from 8 to 100, rlist from 0.735 to 0.831 74: 74: Using 1 MPI thread 74: Using 2 OpenMP threads 74: 74: 74: NOTE: The number of threads is not equal to the number of (logical) cpus 74: and the -pin option is set to auto: will not pin threads to cpus. 74: This can lead to significant performance degradation. 74: Consider using -pin on (and -pinoffset in case you run multiple jobs). 74: starting md rerun 'spc2', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_6_sim1.trr' 74: 74: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 74: 74: NOTE: 18 % of the run time was spent in pair search, 74: you might want to increase nstlist (this has no effect on accuracy) 74: 74: Core t (s) Wall t (s) (%) 74: Time: 0.005 0.003 192.7 74: (ns/day) (hour/ns) 74: Performance: 533.893 0.045 74: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_6_sim1.edr as single precision energy file 74: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_6_sim2.edr as single precision energy file 74: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 74: 74: [ OK ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/6 (4657 ms) 74: [ RUN ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/7 74: 74: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_7_input.mdp]: 74: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 74: that with the Verlet scheme, nstlist has no effect on the accuracy of 74: your simulation. 74: 74: 74: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_7_input.mdp]: 74: Setting nstcalcenergy (100) equal to nstenergy (4) 74: 74: Generating 1-4 interactions: fudge = 0.5 74: Number of degrees of freedom in T-Coupling group System is 27.00 74: 74: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_7_input.mdp]: 74: You are using a plain Coulomb cut-off, which might produce artifacts. 74: You might want to consider using PME electrostatics. 74: 74: 74: 74: There were 3 NOTEs 74: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_7_sim.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 74: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 74: 74: Using 1 MPI thread 74: Using 2 OpenMP threads 74: 74: 74: NOTE: The number of threads is not equal to the number of (logical) cpus 74: and the -pin option is set to auto: will not pin threads to cpus. 74: This can lead to significant performance degradation. 74: Consider using -pin on (and -pinoffset in case you run multiple jobs). 74: starting mdrun 'spc2' 74: 16 steps, 0.0 ps. 74: Generated 330891 of the 330891 non-bonded parameter combinations 74: 74: Generated 330891 of the 330891 1-4 parameter combinations 74: 74: Excluding 2 bonded neighbours molecule type 'SOL' 74: 74: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/tip3p5.gro' 74: 74: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 74: 74: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 74: 74: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 74: 74: Note that mdrun will redetermine rlist based on the actual pair-list setup 74: 74: This run will generate roughly 0 Mb of data 74: 74: Writing final coordinates. 74: 74: Core t (s) Wall t (s) (%) 74: Time: 0.038 0.019 197.6 74: (ns/day) (hour/ns) 74: Performance: 76.170 0.315 74: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_7_sim.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 74: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 74: 74: Using 1 MPI thread 74: Using 2 OpenMP threads 74: 74: 74: NOTE: The number of threads is not equal to the number of (logical) cpus 74: and the -pin option is set to auto: will not pin threads to cpus. 74: This can lead to significant performance degradation. 74: Consider using -pin on (and -pinoffset in case you run multiple jobs). 74: starting md rerun 'spc2', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_7_sim1.trr' 74: 74: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 74: 74: NOTE: 16 % of the run time was spent in pair search, 74: you might want to increase nstlist (this has no effect on accuracy) 74: 74: Core t (s) Wall t (s) (%) 74: Time: 0.005 0.003 192.8 74: (ns/day) (hour/ns) 74: Performance: 528.353 0.045 74: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_7_sim1.edr as single precision energy file 74: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_7_sim2.edr as single precision energy file 74: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 74: 74: [ OK ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/7 (4562 ms) 74: [ RUN ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/8 74: 74: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_8_input.mdp]: 74: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 74: that with the Verlet scheme, nstlist has no effect on the accuracy of 74: your simulation. 74: 74: 74: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_8_input.mdp]: 74: Setting nstcalcenergy (100) equal to nstenergy (4) 74: 74: Generating 1-4 interactions: fudge = 0.5 74: 74: NOTE 3 [file unknown]: 74: You are using constraints on all bonds, whereas the forcefield has been 74: parametrized only with constraints involving hydrogen atoms. We suggest 74: using constraints = h-bonds instead, this will also improve performance. 74: 74: Number of degrees of freedom in T-Coupling group System is 23.00 74: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 74: 74: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_8_input.mdp]: 74: NVE simulation: will use the initial temperature of 456.887 K for 74: determining the Verlet buffer size 74: 74: 74: NOTE 5 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_8_input.mdp]: 74: There are 9 non-linear virtual site constructions. Their contribution to 74: the energy error is approximated. In most cases this does not affect the 74: error significantly. 74: 74: 74: NOTE 6 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_8_input.mdp]: 74: You are using a plain Coulomb cut-off, which might produce artifacts. 74: You might want to consider using PME electrostatics. 74: 74: 74: 74: There were 6 NOTEs 74: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_8_sim.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 74: Can not increase nstlist because an NVE ensemble is used 74: Update groups can not be used for this system because an incompatible virtual site type is used 74: 74: Using 1 MPI thread 74: Using 2 OpenMP threads 74: 74: 74: NOTE: The number of threads is not equal to the number of (logical) cpus 74: and the -pin option is set to auto: will not pin threads to cpus. 74: This can lead to significant performance degradation. 74: Consider using -pin on (and -pinoffset in case you run multiple jobs). 74: starting mdrun 'Alanine dipeptide in vacuo' 74: 16 steps, 0.0 ps. 74: Generated 2145 of the 2145 non-bonded parameter combinations 74: 74: Generated 2145 of the 2145 1-4 parameter combinations 74: 74: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' 74: 74: turning all bonds into constraints... 74: 74: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/alanine_vsite_vacuo.gro' 74: 74: Cleaning up constraints and constant bonded interactions with virtual sites 74: 74: Removed 18 Angles with virtual sites, 21 left 74: 74: Removed 10 Proper Dih.s with virtual sites, 44 left 74: 74: Converted 15 Constraints with virtual sites to connections, 7 left 74: 74: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 456.887 K 74: 74: Calculated rlist for 1x1 atom pair-list as 0.742 nm, buffer size 0.042 nm 74: 74: Set rlist, assuming 4x4 atom pair-list, to 0.737 nm, buffer size 0.037 nm 74: 74: Note that mdrun will redetermine rlist based on the actual pair-list setup 74: 74: This run will generate roughly 0 Mb of data 74: 74: Writing final coordinates. 74: 74: Core t (s) Wall t (s) (%) 74: Time: 0.051 0.026 197.8 74: (ns/day) (hour/ns) 74: Performance: 56.772 0.423 74: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_8_sim.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 74: Can not increase nstlist because an NVE ensemble is used 74: Update groups can not be used for this system because an incompatible virtual site type is used 74: 74: Using 1 MPI thread 74: Using 2 OpenMP threads 74: 74: 74: NOTE: The number of threads is not equal to the number of (logical) cpus 74: and the -pin option is set to auto: will not pin threads to cpus. 74: This can lead to significant performance degradation. 74: Consider using -pin on (and -pinoffset in case you run multiple jobs). 74: starting md rerun 'Alanine dipeptide in vacuo', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_8_sim1.trr' 74: 74: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 74: 74: NOTE: 14 % of the run time was spent in pair search, 74: you might want to increase nstlist (this has no effect on accuracy) 74: 74: Core t (s) Wall t (s) (%) 74: Time: 0.009 0.004 194.4 74: (ns/day) (hour/ns) 74: Performance: 330.433 0.073 74: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_8_sim1.edr as single precision energy file 74: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_8_sim2.edr as single precision energy file 74: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 74: 74: [ OK ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/8 (166 ms) 74: [ RUN ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/9 74: 74: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_9_input.mdp]: 74: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 74: that with the Verlet scheme, nstlist has no effect on the accuracy of 74: your simulation. 74: 74: 74: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_9_input.mdp]: 74: Setting nstcalcenergy (100) equal to nstenergy (4) 74: 74: Generating 1-4 interactions: fudge = 0.5 74: 74: NOTE 3 [file unknown]: 74: You are using constraints on all bonds, whereas the forcefield has been 74: parametrized only with constraints involving hydrogen atoms. We suggest 74: using constraints = h-bonds instead, this will also improve performance. 74: 74: Number of degrees of freedom in T-Coupling group System is 23.00 74: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 74: 74: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_9_input.mdp]: 74: NVE simulation: will use the initial temperature of 456.887 K for 74: determining the Verlet buffer size 74: 74: 74: NOTE 5 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_9_input.mdp]: 74: There are 9 non-linear virtual site constructions. Their contribution to 74: the energy error is approximated. In most cases this does not affect the 74: error significantly. 74: 74: 74: NOTE 6 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_9_input.mdp]: 74: You are using a plain Coulomb cut-off, which might produce artifacts. 74: You might want to consider using PME electrostatics. 74: 74: 74: 74: There were 6 NOTEs 74: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_9_sim.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 74: Can not increase nstlist because an NVE ensemble is used 74: Update groups can not be used for this system because an incompatible virtual site type is used 74: 74: Using 1 MPI thread 74: Using 2 OpenMP threads 74: 74: 74: NOTE: The number of threads is not equal to the number of (logical) cpus 74: and the -pin option is set to auto: will not pin threads to cpus. 74: This can lead to significant performance degradation. 74: Consider using -pin on (and -pinoffset in case you run multiple jobs). 74: starting mdrun 'Alanine dipeptide in vacuo' 74: 16 steps, 0.0 ps. 74: Generated 2145 of the 2145 non-bonded parameter combinations 74: 74: Generated 2145 of the 2145 1-4 parameter combinations 74: 74: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' 74: 74: turning all bonds into constraints... 74: 74: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/alanine_vsite_vacuo.gro' 74: 74: Cleaning up constraints and constant bonded interactions with virtual sites 74: 74: Removed 18 Angles with virtual sites, 21 left 74: 74: Removed 10 Proper Dih.s with virtual sites, 44 left 74: 74: Converted 15 Constraints with virtual sites to connections, 7 left 74: 74: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 456.887 K 74: 74: Calculated rlist for 1x1 atom pair-list as 0.742 nm, buffer size 0.042 nm 74: 74: Set rlist, assuming 4x4 atom pair-list, to 0.737 nm, buffer size 0.037 nm 74: 74: Note that mdrun will redetermine rlist based on the actual pair-list setup 74: 74: This run will generate roughly 0 Mb of data 74: 74: Writing final coordinates. 74: 74: Core t (s) Wall t (s) (%) 74: Time: 0.049 0.025 197.6 74: (ns/day) (hour/ns) 74: Performance: 58.995 0.407 74: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_9_sim.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 74: Can not increase nstlist because an NVE ensemble is used 74: Update groups can not be used for this system because an incompatible virtual site type is used 74: 74: Using 1 MPI thread 74: Using 2 OpenMP threads 74: 74: 74: NOTE: The number of threads is not equal to the number of (logical) cpus 74: and the -pin option is set to auto: will not pin threads to cpus. 74: This can lead to significant performance degradation. 74: Consider using -pin on (and -pinoffset in case you run multiple jobs). 74: starting md rerun 'Alanine dipeptide in vacuo', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_9_sim1.trr' 74: 74: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 74: 74: NOTE: 12 % of the run time was spent in pair search, 74: you might want to increase nstlist (this has no effect on accuracy) 74: 74: Core t (s) Wall t (s) (%) 74: Time: 0.009 0.005 194.5 74: (ns/day) (hour/ns) 74: Performance: 317.164 0.076 74: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_9_sim1.edr as single precision energy file 74: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_9_sim2.edr as single precision energy file 74: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 74: 74: [ OK ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/9 (170 ms) 74: [ RUN ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/10 74: 74: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_10_input.mdp]: 74: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 74: that with the Verlet scheme, nstlist has no effect on the accuracy of 74: your simulation. 74: 74: 74: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_10_input.mdp]: 74: Setting nstcalcenergy (100) equal to nstenergy (4) 74: 74: Generating 1-4 interactions: fudge = 0.5 74: 74: NOTE 3 [file unknown]: 74: You are using constraints on all bonds, whereas the forcefield has been 74: parametrized only with constraints involving hydrogen atoms. We suggest 74: using constraints = h-bonds instead, this will also improve performance. 74: 74: Number of degrees of freedom in T-Coupling group System is 23.00 74: 74: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_10_input.mdp]: 74: There are 9 non-linear virtual site constructions. Their contribution to 74: the energy error is approximated. In most cases this does not affect the 74: error significantly. 74: 74: 74: NOTE 5 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_10_input.mdp]: 74: You are using a plain Coulomb cut-off, which might produce artifacts. 74: You might want to consider using PME electrostatics. 74: 74: 74: 74: There were 5 NOTEs 74: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_10_sim.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 74: Changing nstlist from 8 to 80, rlist from 0.748 to 0.865 74: 74: Update groups can not be used for this system because an incompatible virtual site type is used 74: 74: Using 1 MPI thread 74: Using 2 OpenMP threads 74: 74: 74: NOTE: The number of threads is not equal to the number of (logical) cpus 74: and the -pin option is set to auto: will not pin threads to cpus. 74: This can lead to significant performance degradation. 74: Consider using -pin on (and -pinoffset in case you run multiple jobs). 74: starting mdrun 'Alanine dipeptide in vacuo' 74: 16 steps, 0.0 ps. 74: Generated 2145 of the 2145 non-bonded parameter combinations 74: 74: Generated 2145 of the 2145 1-4 parameter combinations 74: 74: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' 74: 74: turning all bonds into constraints... 74: 74: Cleaning up constraints and constant bonded interactions with virtual sites 74: 74: Removed 18 Angles with virtual sites, 21 left 74: 74: Removed 10 Proper Dih.s with virtual sites, 44 left 74: 74: Converted 15 Constraints with virtual sites to connections, 7 left 74: 74: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 74: 74: Calculated rlist for 1x1 atom pair-list as 0.754 nm, buffer size 0.054 nm 74: 74: Set rlist, assuming 4x4 atom pair-list, to 0.748 nm, buffer size 0.048 nm 74: 74: Note that mdrun will redetermine rlist based on the actual pair-list setup 74: 74: This run will generate roughly 0 Mb of data 74: 74: Writing final coordinates. 74: 74: Core t (s) Wall t (s) (%) 74: Time: 0.052 0.026 197.8 74: (ns/day) (hour/ns) 74: Performance: 56.259 0.427 74: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_10_sim.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 74: Changing nstlist from 8 to 80, rlist from 0.748 to 0.865 74: 74: Update groups can not be used for this system because an incompatible virtual site type is used 74: 74: Using 1 MPI thread 74: Using 2 OpenMP threads 74: 74: 74: NOTE: The number of threads is not equal to the number of (logical) cpus 74: and the -pin option is set to auto: will not pin threads to cpus. 74: This can lead to significant performance degradation. 74: Consider using -pin on (and -pinoffset in case you run multiple jobs). 74: starting md rerun 'Alanine dipeptide in vacuo', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_10_sim1.trr' 74: 74: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 74: 74: NOTE: 20 % of the run time was spent in pair search, 74: you might want to increase nstlist (this has no effect on accuracy) 74: 74: Core t (s) Wall t (s) (%) 74: Time: 0.015 0.007 196.3 74: (ns/day) (hour/ns) 74: Performance: 198.033 0.121 74: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_10_sim1.edr as single precision energy file 74: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_10_sim2.edr as single precision energy file 74: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 74: 74: [ OK ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/10 (830 ms) 74: [ RUN ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/11 74: 74: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_11_input.mdp]: 74: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 74: that with the Verlet scheme, nstlist has no effect on the accuracy of 74: your simulation. 74: 74: 74: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_11_input.mdp]: 74: Setting nstcalcenergy (100) equal to nstenergy (4) 74: 74: Generating 1-4 interactions: fudge = 0.5 74: 74: NOTE 3 [file unknown]: 74: You are using constraints on all bonds, whereas the forcefield has been 74: parametrized only with constraints involving hydrogen atoms. We suggest 74: using constraints = h-bonds instead, this will also improve performance. 74: 74: Number of degrees of freedom in T-Coupling group System is 23.00 74: 74: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_11_input.mdp]: 74: There are 9 non-linear virtual site constructions. Their contribution to 74: the energy error is approximated. In most cases this does not affect the 74: error significantly. 74: 74: 74: NOTE 5 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_11_input.mdp]: 74: You are using a plain Coulomb cut-off, which might produce artifacts. 74: You might want to consider using PME electrostatics. 74: 74: 74: 74: There were 5 NOTEs 74: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_11_sim.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 74: Changing nstlist from 8 to 25, rlist from 0.729 to 0.81 74: 74: Update groups can not be used for this system because an incompatible virtual site type is used 74: 74: Using 1 MPI thread 74: Using 2 OpenMP threads 74: 74: 74: NOTE: The number of threads is not equal to the number of (logical) cpus 74: and the -pin option is set to auto: will not pin threads to cpus. 74: This can lead to significant performance degradation. 74: Consider using -pin on (and -pinoffset in case you run multiple jobs). 74: starting mdrun 'Alanine dipeptide in vacuo' 74: 16 steps, 0.0 ps. 74: Generated 2145 of the 2145 non-bonded parameter combinations 74: 74: Generated 2145 of the 2145 1-4 parameter combinations 74: 74: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' 74: 74: turning all bonds into constraints... 74: 74: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/alanine_vsite_vacuo.gro' 74: 74: Cleaning up constraints and constant bonded interactions with virtual sites 74: 74: Removed 18 Angles with virtual sites, 21 left 74: 74: Removed 10 Proper Dih.s with virtual sites, 44 left 74: 74: Converted 15 Constraints with virtual sites to connections, 7 left 74: 74: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 74: 74: Calculated rlist for 1x1 atom pair-list as 0.733 nm, buffer size 0.033 nm 74: 74: Set rlist, assuming 4x4 atom pair-list, to 0.729 nm, buffer size 0.029 nm 74: 74: Note that mdrun will redetermine rlist based on the actual pair-list setup 74: 74: This run will generate roughly 0 Mb of data 74: 74: Writing final coordinates. 74: 74: Core t (s) Wall t (s) (%) 74: Time: 0.069 0.035 198.4 74: (ns/day) (hour/ns) 74: Performance: 42.154 0.569 74: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_11_sim.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 74: Changing nstlist from 8 to 25, rlist from 0.729 to 0.81 74: 74: Update groups can not be used for this system because an incompatible virtual site type is used 74: 74: Using 1 MPI thread 74: Using 2 OpenMP threads 74: 74: 74: NOTE: The number of threads is not equal to the number of (logical) cpus 74: and the -pin option is set to auto: will not pin threads to cpus. 74: This can lead to significant performance degradation. 74: Consider using -pin on (and -pinoffset in case you run multiple jobs). 74: starting md rerun 'Alanine dipeptide in vacuo', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_11_sim1.trr' 74: 74: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 74: 74: Core t (s) Wall t (s) (%) 74: Time: 0.015 0.008 196.3 74: (ns/day) (hour/ns) 74: Performance: 187.514 0.128 74: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_11_sim1.edr as single precision energy file 74: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_11_sim2.edr as single precision energy file 74: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 74: 74: [ OK ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/11 (429 ms) 74: [----------] 12 tests from NormalMdrunIsReproduced/MdrunRerunTest (20366 ms total) 74: 74: [----------] 33 tests from MdrunIsReproduced/MdrunRerunFreeEnergyTest 74: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/0 74: 74: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_0_input.mdp]: 74: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 74: that with the Verlet scheme, nstlist has no effect on the accuracy of 74: your simulation. 74: 74: 74: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_0_input.mdp]: 74: Setting nstcalcenergy (100) equal to nstenergy (4) 74: 74: Generating 1-4 interactions: fudge = 0.5 74: Number of degrees of freedom in T-Coupling group System is 79.00 74: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 74: 74: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_0_input.mdp]: 74: NVE simulation: will use the initial temperature of 294.908 K for 74: determining the Verlet buffer size 74: 74: 74: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_0_input.mdp]: 74: You are using a plain Coulomb cut-off, which might produce artifacts. 74: You might want to consider using PME electrostatics. 74: 74: 74: 74: There were 4 NOTEs 74: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_0_sim.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 74: Can not increase nstlist because an NVE ensemble is used 74: Using 1 MPI thread 74: Using 2 OpenMP threads 74: 74: 74: NOTE: The number of threads is not equal to the number of (logical) cpus 74: and the -pin option is set to auto: will not pin threads to cpus. 74: This can lead to significant performance degradation. 74: Consider using -pin on (and -pinoffset in case you run multiple jobs). 74: starting mdrun '30 atom system in water' 74: 16 steps, 0.0 ps. 74: Generated 2485 of the 2485 non-bonded parameter combinations 74: 74: Generated 2485 of the 2485 1-4 parameter combinations 74: 74: Excluding 3 bonded neighbours molecule type 'nonanol' 74: 74: turning H bonds into constraints... 74: 74: Excluding 2 bonded neighbours molecule type 'SOL' 74: 74: turning H bonds into constraints... 74: 74: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/nonanol_vacuo.gro' 74: 74: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 294.908 K 74: 74: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 74: 74: Set rlist, assuming 4x4 atom pair-list, to 0.757 nm, buffer size 0.057 nm 74: 74: Note that mdrun will redetermine rlist based on the actual pair-list setup 74: 74: This run will generate roughly 0 Mb of data 74: 74: Writing final coordinates. 74: 74: Core t (s) Wall t (s) (%) 74: Time: 0.067 0.034 197.1 74: (ns/day) (hour/ns) 74: Performance: 43.110 0.557 74: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_0_sim.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 74: Can not increase nstlist because an NVE ensemble is used 74: Using 1 MPI thread 74: Using 2 OpenMP threads 74: 74: 74: NOTE: The number of threads is not equal to the number of (logical) cpus 74: and the -pin option is set to auto: will not pin threads to cpus. 74: This can lead to significant performance degradation. 74: Consider using -pin on (and -pinoffset in case you run multiple jobs). 74: starting md rerun '30 atom system in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_0_sim1.trr' 74: 74: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 74: 74: Core t (s) Wall t (s) (%) 74: Time: 0.014 0.008 184.1 74: (ns/day) (hour/ns) 74: Performance: 192.705 0.125 74: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_0_sim1.edr as single precision energy file 74: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_0_sim2.edr as single precision energy file 74: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 74: 74: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/0 (183 ms) 74: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/1 74: 74: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_1_input.mdp]: 74: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 74: that with the Verlet scheme, nstlist has no effect on the accuracy of 74: your simulation. 74: 74: 74: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_1_input.mdp]: 74: Setting nstcalcenergy (100) equal to nstenergy (4) 74: 74: Generating 1-4 interactions: fudge = 0.5 74: Number of degrees of freedom in T-Coupling group System is 79.00 74: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 74: 74: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_1_input.mdp]: 74: NVE simulation: will use the initial temperature of 294.908 K for 74: determining the Verlet buffer size 74: 74: 74: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_1_input.mdp]: 74: You are using a plain Coulomb cut-off, which might produce artifacts. 74: You might want to consider using PME electrostatics. 74: 74: 74: 74: There were 4 NOTEs 74: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_1_sim.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 74: Can not increase nstlist because an NVE ensemble is used 74: Using 1 MPI thread 74: Using 2 OpenMP threads 74: 74: 74: NOTE: The number of threads is not equal to the number of (logical) cpus 74: and the -pin option is set to auto: will not pin threads to cpus. 74: This can lead to significant performance degradation. 74: Consider using -pin on (and -pinoffset in case you run multiple jobs). 74: starting mdrun '30 atom system in water' 74: 16 steps, 0.0 ps. 74: Generated 2485 of the 2485 non-bonded parameter combinations 74: 74: Generated 2485 of the 2485 1-4 parameter combinations 74: 74: Excluding 3 bonded neighbours molecule type 'nonanol' 74: 74: turning H bonds into constraints... 74: 74: Excluding 2 bonded neighbours molecule type 'SOL' 74: 74: turning H bonds into constraints... 74: 74: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/nonanol_vacuo.gro' 74: 74: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 294.908 K 74: 74: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 74: 74: Set rlist, assuming 4x4 atom pair-list, to 0.757 nm, buffer size 0.057 nm 74: 74: Note that mdrun will redetermine rlist based on the actual pair-list setup 74: 74: This run will generate roughly 0 Mb of data 74: 74: Writing final coordinates. 74: 74: Core t (s) Wall t (s) (%) 74: Time: 0.056 0.028 197.0 74: (ns/day) (hour/ns) 74: Performance: 51.943 0.462 74: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_1_sim.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 74: Can not increase nstlist because an NVE ensemble is used 74: Using 1 MPI thread 74: Using 2 OpenMP threads 74: 74: 74: NOTE: The number of threads is not equal to the number of (logical) cpus 74: and the -pin option is set to auto: will not pin threads to cpus. 74: This can lead to significant performance degradation. 74: Consider using -pin on (and -pinoffset in case you run multiple jobs). 74: starting md rerun '30 atom system in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_1_sim1.trr' 74: 74: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 74: 74: Core t (s) Wall t (s) (%) 74: Time: 0.013 0.007 183.2 74: (ns/day) (hour/ns) 74: Performance: 200.547 0.120 74: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_1_sim1.edr as single precision energy file 74: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_1_sim2.edr as single precision energy file 74: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 74: 74: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/1 (176 ms) 74: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/2 74: 74: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_2_input.mdp]: 74: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 74: that with the Verlet scheme, nstlist has no effect on the accuracy of 74: your simulation. 74: 74: 74: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_2_input.mdp]: 74: Setting nstcalcenergy (100) equal to nstenergy (4) 74: 74: Generating 1-4 interactions: fudge = 0.5 74: Number of degrees of freedom in T-Coupling group System is 79.00 74: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 74: 74: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_2_input.mdp]: 74: NVE simulation: will use the initial temperature of 294.908 K for 74: determining the Verlet buffer size 74: 74: 74: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_2_input.mdp]: 74: You are using a plain Coulomb cut-off, which might produce artifacts. 74: You might want to consider using PME electrostatics. 74: 74: 74: 74: There were 4 NOTEs 74: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_2_sim.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 74: Can not increase nstlist because an NVE ensemble is used 74: Using 1 MPI thread 74: Using 2 OpenMP threads 74: 74: 74: NOTE: The number of threads is not equal to the number of (logical) cpus 74: and the -pin option is set to auto: will not pin threads to cpus. 74: This can lead to significant performance degradation. 74: Consider using -pin on (and -pinoffset in case you run multiple jobs). 74: starting mdrun '30 atom system in water' 74: 16 steps, 0.0 ps. 74: Generated 2485 of the 2485 non-bonded parameter combinations 74: 74: Generated 2485 of the 2485 1-4 parameter combinations 74: 74: Excluding 3 bonded neighbours molecule type 'nonanol' 74: 74: turning H bonds into constraints... 74: 74: Excluding 2 bonded neighbours molecule type 'SOL' 74: 74: turning H bonds into constraints... 74: 74: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/nonanol_vacuo.gro' 74: 74: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 294.908 K 74: 74: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 74: 74: Set rlist, assuming 4x4 atom pair-list, to 0.757 nm, buffer size 0.057 nm 74: 74: Note that mdrun will redetermine rlist based on the actual pair-list setup 74: 74: This run will generate roughly 0 Mb of data 74: 74: Writing final coordinates. 74: 74: Core t (s) Wall t (s) (%) 74: Time: 0.056 0.028 197.1 74: (ns/day) (hour/ns) 74: Performance: 51.797 0.463 74: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_2_sim.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 74: Can not increase nstlist because an NVE ensemble is used 74: Using 1 MPI thread 74: Using 2 OpenMP threads 74: 74: 74: NOTE: The number of threads is not equal to the number of (logical) cpus 74: and the -pin option is set to auto: will not pin threads to cpus. 74: This can lead to significant performance degradation. 74: Consider using -pin on (and -pinoffset in case you run multiple jobs). 74: starting md rerun '30 atom system in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_2_sim1.trr' 74: 74: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 74: 74: Core t (s) Wall t (s) (%) 74: Time: 0.013 0.007 183.6 74: (ns/day) (hour/ns) 74: Performance: 203.515 0.118 74: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_2_sim1.edr as single precision energy file 74: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_2_sim2.edr as single precision energy file 74: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 74: 74: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/2 (175 ms) 74: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/3 74: 74: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_3_input.mdp]: 74: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 74: that with the Verlet scheme, nstlist has no effect on the accuracy of 74: your simulation. 74: 74: 74: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_3_input.mdp]: 74: Setting nstcalcenergy (100) equal to nstenergy (4) 74: 74: Generating 1-4 interactions: fudge = 0.5 74: Number of degrees of freedom in T-Coupling group System is 79.00 74: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 74: 74: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_3_input.mdp]: 74: NVE simulation: will use the initial temperature of 294.908 K for 74: determining the Verlet buffer size 74: 74: 74: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_3_input.mdp]: 74: You are using a plain Coulomb cut-off, which might produce artifacts. 74: You might want to consider using PME electrostatics. 74: 74: 74: 74: There were 4 NOTEs 74: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_3_sim.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 74: Can not increase nstlist because an NVE ensemble is used 74: Using 1 MPI thread 74: Using 2 OpenMP threads 74: 74: 74: NOTE: The number of threads is not equal to the number of (logical) cpus 74: and the -pin option is set to auto: will not pin threads to cpus. 74: This can lead to significant performance degradation. 74: Consider using -pin on (and -pinoffset in case you run multiple jobs). 74: starting mdrun '30 atom system in water' 74: 16 steps, 0.0 ps. 74: Generated 2485 of the 2485 non-bonded parameter combinations 74: 74: Generated 2485 of the 2485 1-4 parameter combinations 74: 74: Excluding 3 bonded neighbours molecule type 'nonanol' 74: 74: turning H bonds into constraints... 74: 74: Excluding 2 bonded neighbours molecule type 'SOL' 74: 74: turning H bonds into constraints... 74: 74: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/nonanol_vacuo.gro' 74: 74: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 294.908 K 74: 74: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 74: 74: Set rlist, assuming 4x4 atom pair-list, to 0.757 nm, buffer size 0.057 nm 74: 74: Note that mdrun will redetermine rlist based on the actual pair-list setup 74: 74: This run will generate roughly 0 Mb of data 74: 74: Writing final coordinates. 74: 74: Core t (s) Wall t (s) (%) 74: Time: 0.056 0.028 197.0 74: (ns/day) (hour/ns) 74: Performance: 52.098 0.461 74: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_3_sim.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 74: Can not increase nstlist because an NVE ensemble is used 74: Using 1 MPI thread 74: Using 2 OpenMP threads 74: 74: 74: NOTE: The number of threads is not equal to the number of (logical) cpus 74: and the -pin option is set to auto: will not pin threads to cpus. 74: This can lead to significant performance degradation. 74: Consider using -pin on (and -pinoffset in case you run multiple jobs). 74: starting md rerun '30 atom system in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_3_sim1.trr' 74: 74: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 74: 74: Core t (s) Wall t (s) (%) 74: Time: 0.014 0.007 183.9 74: (ns/day) (hour/ns) 74: Performance: 197.658 0.121 74: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_3_sim1.edr as single precision energy file 74: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_3_sim2.edr as single precision energy file 74: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 74: 74: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/3 (175 ms) 74: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/4 74: 74: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_4_input.mdp]: 74: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 74: that with the Verlet scheme, nstlist has no effect on the accuracy of 74: your simulation. 74: 74: 74: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_4_input.mdp]: 74: Setting nstcalcenergy (100) equal to nstenergy (4) 74: 74: Generating 1-4 interactions: fudge = 0.5 74: Number of degrees of freedom in T-Coupling group System is 79.00 74: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 74: 74: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_4_input.mdp]: 74: NVE simulation: will use the initial temperature of 294.908 K for 74: determining the Verlet buffer size 74: 74: 74: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_4_input.mdp]: 74: You are using a plain Coulomb cut-off, which might produce artifacts. 74: You might want to consider using PME electrostatics. 74: 74: 74: 74: There were 4 NOTEs 74: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_4_sim.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 74: Can not increase nstlist because an NVE ensemble is used 74: Using 1 MPI thread 74: Using 2 OpenMP threads 74: 74: 74: NOTE: The number of threads is not equal to the number of (logical) cpus 74: and the -pin option is set to auto: will not pin threads to cpus. 74: This can lead to significant performance degradation. 74: Consider using -pin on (and -pinoffset in case you run multiple jobs). 74: starting mdrun '30 atom system in water' 74: 16 steps, 0.0 ps. 74: Generated 2485 of the 2485 non-bonded parameter combinations 74: 74: Generated 2485 of the 2485 1-4 parameter combinations 74: 74: Excluding 3 bonded neighbours molecule type 'nonanol' 74: 74: turning H bonds into constraints... 74: 74: Excluding 2 bonded neighbours molecule type 'SOL' 74: 74: turning H bonds into constraints... 74: 74: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/nonanol_vacuo.gro' 74: 74: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 294.908 K 74: 74: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 74: 74: Set rlist, assuming 4x4 atom pair-list, to 0.757 nm, buffer size 0.057 nm 74: 74: Note that mdrun will redetermine rlist based on the actual pair-list setup 74: 74: This run will generate roughly 0 Mb of data 74: 74: Writing final coordinates. 74: 74: Core t (s) Wall t (s) (%) 74: Time: 0.056 0.028 197.0 74: (ns/day) (hour/ns) 74: Performance: 51.846 0.463 74: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_4_sim.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 74: Can not increase nstlist because an NVE ensemble is used 74: Using 1 MPI thread 74: Using 2 OpenMP threads 74: 74: 74: NOTE: The number of threads is not equal to the number of (logical) cpus 74: and the -pin option is set to auto: will not pin threads to cpus. 74: This can lead to significant performance degradation. 74: Consider using -pin on (and -pinoffset in case you run multiple jobs). 74: starting md rerun '30 atom system in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_4_sim1.trr' 74: 74: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 74: 74: Core t (s) Wall t (s) (%) 74: Time: 0.013 0.007 183.5 74: (ns/day) (hour/ns) 74: Performance: 201.149 0.119 74: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_4_sim1.edr as single precision energy file 74: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_4_sim2.edr as single precision energy file 74: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 74: 74: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/4 (177 ms) 74: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/5 74: 74: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_5_input.mdp]: 74: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 74: that with the Verlet scheme, nstlist has no effect on the accuracy of 74: your simulation. 74: 74: 74: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_5_input.mdp]: 74: Setting nstcalcenergy (100) equal to nstenergy (4) 74: 74: Generating 1-4 interactions: fudge = 0.5 74: Number of degrees of freedom in T-Coupling group System is 79.00 74: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 74: 74: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_5_input.mdp]: 74: NVE simulation: will use the initial temperature of 294.908 K for 74: determining the Verlet buffer size 74: 74: 74: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_5_input.mdp]: 74: You are using a plain Coulomb cut-off, which might produce artifacts. 74: You might want to consider using PME electrostatics. 74: 74: 74: 74: There were 4 NOTEs 74: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_5_sim.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 74: Can not increase nstlist because an NVE ensemble is used 74: Using 1 MPI thread 74: Using 2 OpenMP threads 74: 74: 74: NOTE: The number of threads is not equal to the number of (logical) cpus 74: and the -pin option is set to auto: will not pin threads to cpus. 74: This can lead to significant performance degradation. 74: Consider using -pin on (and -pinoffset in case you run multiple jobs). 74: starting mdrun '30 atom system in water' 74: 16 steps, 0.0 ps. 74: Generated 2485 of the 2485 non-bonded parameter combinations 74: 74: Generated 2485 of the 2485 1-4 parameter combinations 74: 74: Excluding 3 bonded neighbours molecule type 'nonanol' 74: 74: turning H bonds into constraints... 74: 74: Excluding 2 bonded neighbours molecule type 'SOL' 74: 74: turning H bonds into constraints... 74: 74: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/nonanol_vacuo.gro' 74: 74: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 294.908 K 74: 74: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 74: 74: Set rlist, assuming 4x4 atom pair-list, to 0.757 nm, buffer size 0.057 nm 74: 74: Note that mdrun will redetermine rlist based on the actual pair-list setup 74: 74: This run will generate roughly 0 Mb of data 74: 74: Writing final coordinates. 74: 74: Core t (s) Wall t (s) (%) 74: Time: 0.055 0.028 197.0 74: (ns/day) (hour/ns) 74: Performance: 52.545 0.457 74: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_5_sim.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 74: Can not increase nstlist because an NVE ensemble is used 74: Using 1 MPI thread 74: Using 2 OpenMP threads 74: 74: 74: NOTE: The number of threads is not equal to the number of (logical) cpus 74: and the -pin option is set to auto: will not pin threads to cpus. 74: This can lead to significant performance degradation. 74: Consider using -pin on (and -pinoffset in case you run multiple jobs). 74: starting md rerun '30 atom system in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_5_sim1.trr' 74: 74: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 74: 74: Core t (s) Wall t (s) (%) 74: Time: 0.014 0.007 183.7 74: (ns/day) (hour/ns) 74: Performance: 198.351 0.121 74: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_5_sim1.edr as single precision energy file 74: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_5_sim2.edr as single precision energy file 74: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 74: 74: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/5 (175 ms) 74: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/6 74: 74: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_6_input.mdp]: 74: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 74: that with the Verlet scheme, nstlist has no effect on the accuracy of 74: your simulation. 74: 74: 74: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_6_input.mdp]: 74: Setting nstcalcenergy (100) equal to nstenergy (4) 74: 74: Generating 1-4 interactions: fudge = 0.5 74: Number of degrees of freedom in T-Coupling group System is 79.00 74: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 74: 74: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_6_input.mdp]: 74: NVE simulation: will use the initial temperature of 294.908 K for 74: determining the Verlet buffer size 74: 74: 74: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_6_input.mdp]: 74: You are using a plain Coulomb cut-off, which might produce artifacts. 74: You might want to consider using PME electrostatics. 74: 74: 74: 74: There were 4 NOTEs 74: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_6_sim.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 74: Can not increase nstlist because an NVE ensemble is used 74: Using 1 MPI thread 74: Using 2 OpenMP threads 74: 74: 74: NOTE: The number of threads is not equal to the number of (logical) cpus 74: and the -pin option is set to auto: will not pin threads to cpus. 74: This can lead to significant performance degradation. 74: Consider using -pin on (and -pinoffset in case you run multiple jobs). 74: starting mdrun '30 atom system in water' 74: 16 steps, 0.0 ps. 74: Generated 2485 of the 2485 non-bonded parameter combinations 74: 74: Generated 2485 of the 2485 1-4 parameter combinations 74: 74: Excluding 3 bonded neighbours molecule type 'nonanol' 74: 74: turning H bonds into constraints... 74: 74: Excluding 2 bonded neighbours molecule type 'SOL' 74: 74: turning H bonds into constraints... 74: 74: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/nonanol_vacuo.gro' 74: 74: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 294.908 K 74: 74: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 74: 74: Set rlist, assuming 4x4 atom pair-list, to 0.757 nm, buffer size 0.057 nm 74: 74: Note that mdrun will redetermine rlist based on the actual pair-list setup 74: 74: This run will generate roughly 0 Mb of data 74: 74: Writing final coordinates. 74: 74: Core t (s) Wall t (s) (%) 74: Time: 0.054 0.027 196.8 74: (ns/day) (hour/ns) 74: Performance: 53.988 0.445 74: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_6_sim.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 74: Can not increase nstlist because an NVE ensemble is used 74: Using 1 MPI thread 74: Using 2 OpenMP threads 74: 74: 74: NOTE: The number of threads is not equal to the number of (logical) cpus 74: and the -pin option is set to auto: will not pin threads to cpus. 74: This can lead to significant performance degradation. 74: Consider using -pin on (and -pinoffset in case you run multiple jobs). 74: starting md rerun '30 atom system in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_6_sim1.trr' 74: 74: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 74: 74: Core t (s) Wall t (s) (%) 74: Time: 0.012 0.007 182.6 74: (ns/day) (hour/ns) 74: Performance: 215.300 0.111 74: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_6_sim1.edr as single precision energy file 74: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_6_sim2.edr as single precision energy file 74: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 74: 74: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/6 (174 ms) 74: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/7 74: 74: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_7_input.mdp]: 74: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 74: that with the Verlet scheme, nstlist has no effect on the accuracy of 74: your simulation. 74: 74: 74: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_7_input.mdp]: 74: Setting nstcalcenergy (100) equal to nstenergy (4) 74: 74: Generating 1-4 interactions: fudge = 0.5 74: Number of degrees of freedom in T-Coupling group System is 79.00 74: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 74: 74: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_7_input.mdp]: 74: NVE simulation: will use the initial temperature of 294.908 K for 74: determining the Verlet buffer size 74: 74: 74: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_7_input.mdp]: 74: You are using a plain Coulomb cut-off, which might produce artifacts. 74: You might want to consider using PME electrostatics. 74: 74: 74: 74: There were 4 NOTEs 74: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_7_sim.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 74: Can not increase nstlist because an NVE ensemble is used 74: Using 1 MPI thread 74: Using 2 OpenMP threads 74: 74: 74: NOTE: The number of threads is not equal to the number of (logical) cpus 74: and the -pin option is set to auto: will not pin threads to cpus. 74: This can lead to significant performance degradation. 74: Consider using -pin on (and -pinoffset in case you run multiple jobs). 74: starting mdrun '30 atom system in water' 74: 16 steps, 0.0 ps. 74: Generated 2485 of the 2485 non-bonded parameter combinations 74: 74: Generated 2485 of the 2485 1-4 parameter combinations 74: 74: Excluding 3 bonded neighbours molecule type 'nonanol' 74: 74: turning H bonds into constraints... 74: 74: Excluding 2 bonded neighbours molecule type 'SOL' 74: 74: turning H bonds into constraints... 74: 74: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/nonanol_vacuo.gro' 74: 74: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 294.908 K 74: 74: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 74: 74: Set rlist, assuming 4x4 atom pair-list, to 0.757 nm, buffer size 0.057 nm 74: 74: Note that mdrun will redetermine rlist based on the actual pair-list setup 74: 74: This run will generate roughly 0 Mb of data 74: 74: Writing final coordinates. 74: 74: Core t (s) Wall t (s) (%) 74: Time: 0.053 0.027 196.8 74: (ns/day) (hour/ns) 74: Performance: 54.111 0.444 74: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_7_sim.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 74: Can not increase nstlist because an NVE ensemble is used 74: Using 1 MPI thread 74: Using 2 OpenMP threads 74: 74: 74: NOTE: The number of threads is not equal to the number of (logical) cpus 74: and the -pin option is set to auto: will not pin threads to cpus. 74: This can lead to significant performance degradation. 74: Consider using -pin on (and -pinoffset in case you run multiple jobs). 74: starting md rerun '30 atom system in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_7_sim1.trr' 74: 74: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 74: 74: Core t (s) Wall t (s) (%) 74: Time: 0.012 0.007 182.3 74: (ns/day) (hour/ns) 74: Performance: 214.550 0.112 74: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_7_sim1.edr as single precision energy file 74: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_7_sim2.edr as single precision energy file 74: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 74: 74: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/7 (174 ms) 74: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/8 74: 74: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_8_input.mdp]: 74: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 74: that with the Verlet scheme, nstlist has no effect on the accuracy of 74: your simulation. 74: 74: 74: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_8_input.mdp]: 74: Setting nstcalcenergy (100) equal to nstenergy (4) 74: 74: Generating 1-4 interactions: fudge = 0.5 74: Number of degrees of freedom in T-Coupling group System is 79.00 74: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 74: 74: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_8_input.mdp]: 74: NVE simulation: will use the initial temperature of 294.908 K for 74: determining the Verlet buffer size 74: 74: 74: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_8_input.mdp]: 74: You are using a plain Coulomb cut-off, which might produce artifacts. 74: You might want to consider using PME electrostatics. 74: 74: 74: 74: There were 4 NOTEs 74: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_8_sim.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 74: Can not increase nstlist because an NVE ensemble is used 74: Using 1 MPI thread 74: Using 2 OpenMP threads 74: 74: 74: NOTE: The number of threads is not equal to the number of (logical) cpus 74: and the -pin option is set to auto: will not pin threads to cpus. 74: This can lead to significant performance degradation. 74: Consider using -pin on (and -pinoffset in case you run multiple jobs). 74: starting mdrun '30 atom system in water' 74: 16 steps, 0.0 ps. 74: Generated 2485 of the 2485 non-bonded parameter combinations 74: 74: Generated 2485 of the 2485 1-4 parameter combinations 74: 74: Excluding 3 bonded neighbours molecule type 'nonanol' 74: 74: turning H bonds into constraints... 74: 74: Excluding 2 bonded neighbours molecule type 'SOL' 74: 74: turning H bonds into constraints... 74: 74: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/nonanol_vacuo.gro' 74: 74: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 294.908 K 74: 74: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 74: 74: Set rlist, assuming 4x4 atom pair-list, to 0.757 nm, buffer size 0.057 nm 74: 74: Note that mdrun will redetermine rlist based on the actual pair-list setup 74: 74: This run will generate roughly 0 Mb of data 74: 74: Writing final coordinates. 74: 74: Core t (s) Wall t (s) (%) 74: Time: 0.053 0.027 196.9 74: (ns/day) (hour/ns) 74: Performance: 54.218 0.443 74: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_8_sim.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 74: Can not increase nstlist because an NVE ensemble is used 74: Using 1 MPI thread 74: Using 2 OpenMP threads 74: 74: 74: NOTE: The number of threads is not equal to the number of (logical) cpus 74: and the -pin option is set to auto: will not pin threads to cpus. 74: This can lead to significant performance degradation. 74: Consider using -pin on (and -pinoffset in case you run multiple jobs). 74: starting md rerun '30 atom system in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_8_sim1.trr' 74: 74: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 74: 74: Core t (s) Wall t (s) (%) 74: Time: 0.012 0.007 182.3 74: (ns/day) (hour/ns) 74: Performance: 219.551 0.109 74: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_8_sim1.edr as single precision energy file 74: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_8_sim2.edr as single precision energy file 74: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 74: 74: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/8 (173 ms) 74: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/9 74: 74: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_9_input.mdp]: 74: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 74: that with the Verlet scheme, nstlist has no effect on the accuracy of 74: your simulation. 74: 74: 74: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_9_input.mdp]: 74: Setting nstcalcenergy (100) equal to nstenergy (4) 74: 74: Generating 1-4 interactions: fudge = 0.5 74: Number of degrees of freedom in T-Coupling group System is 79.00 74: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 74: 74: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_9_input.mdp]: 74: NVE simulation: will use the initial temperature of 294.908 K for 74: determining the Verlet buffer size 74: 74: 74: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_9_input.mdp]: 74: You are using a plain Coulomb cut-off, which might produce artifacts. 74: You might want to consider using PME electrostatics. 74: 74: 74: 74: There were 4 NOTEs 74: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_9_sim.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 74: Can not increase nstlist because an NVE ensemble is used 74: Using 1 MPI thread 74: Using 2 OpenMP threads 74: 74: 74: NOTE: The number of threads is not equal to the number of (logical) cpus 74: and the -pin option is set to auto: will not pin threads to cpus. 74: This can lead to significant performance degradation. 74: Consider using -pin on (and -pinoffset in case you run multiple jobs). 74: starting mdrun '30 atom system in water' 74: 16 steps, 0.0 ps. 74: Generated 2485 of the 2485 non-bonded parameter combinations 74: 74: Generated 2485 of the 2485 1-4 parameter combinations 74: 74: Excluding 3 bonded neighbours molecule type 'nonanol' 74: 74: turning H bonds into constraints... 74: 74: Excluding 2 bonded neighbours molecule type 'SOL' 74: 74: turning H bonds into constraints... 74: 74: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/nonanol_vacuo.gro' 74: 74: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 294.908 K 74: 74: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 74: 74: Set rlist, assuming 4x4 atom pair-list, to 0.757 nm, buffer size 0.057 nm 74: 74: Note that mdrun will redetermine rlist based on the actual pair-list setup 74: 74: This run will generate roughly 0 Mb of data 74: 74: Writing final coordinates. 74: 74: Core t (s) Wall t (s) (%) 74: Time: 0.054 0.028 196.5 74: (ns/day) (hour/ns) 74: Performance: 53.337 0.450 74: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_9_sim.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 74: Can not increase nstlist because an NVE ensemble is used 74: Using 1 MPI thread 74: Using 2 OpenMP threads 74: 74: 74: NOTE: The number of threads is not equal to the number of (logical) cpus 74: and the -pin option is set to auto: will not pin threads to cpus. 74: This can lead to significant performance degradation. 74: Consider using -pin on (and -pinoffset in case you run multiple jobs). 74: starting md rerun '30 atom system in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_9_sim1.trr' 74: 74: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 74: 74: Core t (s) Wall t (s) (%) 74: Time: 0.013 0.007 182.7 74: (ns/day) (hour/ns) 74: Performance: 208.997 0.115 74: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_9_sim1.edr as single precision energy file 74: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_9_sim2.edr as single precision energy file 74: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 74: 74: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/9 (173 ms) 74: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/10 74: 74: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_10_input.mdp]: 74: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 74: that with the Verlet scheme, nstlist has no effect on the accuracy of 74: your simulation. 74: 74: 74: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_10_input.mdp]: 74: Setting nstcalcenergy (100) equal to nstenergy (4) 74: 74: Generating 1-4 interactions: fudge = 0.5 74: Number of degrees of freedom in T-Coupling group System is 79.00 74: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 74: 74: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_10_input.mdp]: 74: NVE simulation: will use the initial temperature of 294.908 K for 74: determining the Verlet buffer size 74: 74: 74: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_10_input.mdp]: 74: You are using a plain Coulomb cut-off, which might produce artifacts. 74: You might want to consider using PME electrostatics. 74: 74: 74: 74: There were 4 NOTEs 74: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_10_sim.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 74: Can not increase nstlist because an NVE ensemble is used 74: Using 1 MPI thread 74: Using 2 OpenMP threads 74: 74: 74: NOTE: The number of threads is not equal to the number of (logical) cpus 74: and the -pin option is set to auto: will not pin threads to cpus. 74: This can lead to significant performance degradation. 74: Consider using -pin on (and -pinoffset in case you run multiple jobs). 74: starting mdrun '30 atom system in water' 74: 16 steps, 0.0 ps. 74: Generated 2485 of the 2485 non-bonded parameter combinations 74: 74: Generated 2485 of the 2485 1-4 parameter combinations 74: 74: Excluding 3 bonded neighbours molecule type 'nonanol' 74: 74: turning H bonds into constraints... 74: 74: Excluding 2 bonded neighbours molecule type 'SOL' 74: 74: turning H bonds into constraints... 74: 74: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/nonanol_vacuo.gro' 74: 74: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 294.908 K 74: 74: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 74: 74: Set rlist, assuming 4x4 atom pair-list, to 0.757 nm, buffer size 0.057 nm 74: 74: Note that mdrun will redetermine rlist based on the actual pair-list setup 74: 74: This run will generate roughly 0 Mb of data 74: 74: Writing final coordinates. 74: 74: Core t (s) Wall t (s) (%) 74: Time: 0.054 0.028 196.9 74: (ns/day) (hour/ns) 74: Performance: 53.308 0.450 74: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_10_sim.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 74: Can not increase nstlist because an NVE ensemble is used 74: Using 1 MPI thread 74: Using 2 OpenMP threads 74: 74: 74: NOTE: The number of threads is not equal to the number of (logical) cpus 74: and the -pin option is set to auto: will not pin threads to cpus. 74: This can lead to significant performance degradation. 74: Consider using -pin on (and -pinoffset in case you run multiple jobs). 74: starting md rerun '30 atom system in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_10_sim1.trr' 74: 74: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 74: 74: Core t (s) Wall t (s) (%) 74: Time: 0.013 0.007 185.4 74: (ns/day) (hour/ns) 74: Performance: 206.288 0.116 74: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_10_sim1.edr as single precision energy file 74: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_10_sim2.edr as single precision energy file 74: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 74: 74: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/10 (174 ms) 74: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/11 74: 74: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_11_input.mdp]: 74: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 74: that with the Verlet scheme, nstlist has no effect on the accuracy of 74: your simulation. 74: 74: 74: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_11_input.mdp]: 74: Setting nstcalcenergy (100) equal to nstenergy (4) 74: 74: Generating 1-4 interactions: fudge = 0.5 74: Number of degrees of freedom in T-Coupling group System is 79.00 74: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 74: 74: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_11_input.mdp]: 74: NVE simulation: will use the initial temperature of 294.908 K for 74: determining the Verlet buffer size 74: 74: 74: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_11_input.mdp]: 74: You are using a plain Coulomb cut-off, which might produce artifacts. 74: You might want to consider using PME electrostatics. 74: 74: 74: 74: There were 4 NOTEs 74: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_11_sim.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 74: Can not increase nstlist because an NVE ensemble is used 74: Using 1 MPI thread 74: Using 2 OpenMP threads 74: 74: 74: NOTE: The number of threads is not equal to the number of (logical) cpus 74: and the -pin option is set to auto: will not pin threads to cpus. 74: This can lead to significant performance degradation. 74: Consider using -pin on (and -pinoffset in case you run multiple jobs). 74: starting mdrun '30 atom system in water' 74: 16 steps, 0.0 ps. 74: Generated 2485 of the 2485 non-bonded parameter combinations 74: 74: Generated 2485 of the 2485 1-4 parameter combinations 74: 74: Excluding 3 bonded neighbours molecule type 'nonanol' 74: 74: turning H bonds into constraints... 74: 74: Excluding 2 bonded neighbours molecule type 'SOL' 74: 74: turning H bonds into constraints... 74: 74: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/nonanol_vacuo.gro' 74: 74: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 294.908 K 74: 74: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 74: 74: Set rlist, assuming 4x4 atom pair-list, to 0.757 nm, buffer size 0.057 nm 74: 74: Note that mdrun will redetermine rlist based on the actual pair-list setup 74: 74: This run will generate roughly 0 Mb of data 74: 74: Writing final coordinates. 74: 74: Core t (s) Wall t (s) (%) 74: Time: 0.065 0.033 198.8 74: (ns/day) (hour/ns) 74: Performance: 45.162 0.531 74: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_11_sim.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 74: Can not increase nstlist because an NVE ensemble is used 74: Using 1 MPI thread 74: Using 2 OpenMP threads 74: 74: 74: NOTE: The number of threads is not equal to the number of (logical) cpus 74: and the -pin option is set to auto: will not pin threads to cpus. 74: This can lead to significant performance degradation. 74: Consider using -pin on (and -pinoffset in case you run multiple jobs). 74: starting md rerun '30 atom system in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_11_sim1.trr' 74: 74: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 74: 74: NOTE: 11 % of the run time was spent in pair search, 74: you might want to increase nstlist (this has no effect on accuracy) 74: 74: Core t (s) Wall t (s) (%) 74: Time: 0.011 0.006 180.2 74: (ns/day) (hour/ns) 74: Performance: 240.432 0.100 74: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_11_sim1.edr as single precision energy file 74: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_11_sim2.edr as single precision energy file 74: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 74: 74: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/11 (175 ms) 74: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/12 74: 74: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_12_input.mdp]: 74: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 74: that with the Verlet scheme, nstlist has no effect on the accuracy of 74: your simulation. 74: 74: 74: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_12_input.mdp]: 74: Setting nstcalcenergy (100) equal to nstenergy (4) 74: 74: Generating 1-4 interactions: fudge = 0.5 74: Number of degrees of freedom in T-Coupling group System is 79.00 74: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 74: 74: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_12_input.mdp]: 74: NVE simulation: will use the initial temperature of 294.908 K for 74: determining the Verlet buffer size 74: 74: 74: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_12_input.mdp]: 74: You are using a plain Coulomb cut-off, which might produce artifacts. 74: You might want to consider using PME electrostatics. 74: 74: 74: 74: There were 4 NOTEs 74: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_12_sim.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 74: Can not increase nstlist because an NVE ensemble is used 74: Using 1 MPI thread 74: Using 2 OpenMP threads 74: 74: 74: NOTE: The number of threads is not equal to the number of (logical) cpus 74: and the -pin option is set to auto: will not pin threads to cpus. 74: This can lead to significant performance degradation. 74: Consider using -pin on (and -pinoffset in case you run multiple jobs). 74: starting mdrun '30 atom system in water' 74: 16 steps, 0.0 ps. 74: Generated 2485 of the 2485 non-bonded parameter combinations 74: 74: Generated 2485 of the 2485 1-4 parameter combinations 74: 74: Excluding 3 bonded neighbours molecule type 'nonanol' 74: 74: turning H bonds into constraints... 74: 74: Excluding 2 bonded neighbours molecule type 'SOL' 74: 74: turning H bonds into constraints... 74: 74: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/nonanol_vacuo.gro' 74: 74: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 294.908 K 74: 74: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 74: 74: Set rlist, assuming 4x4 atom pair-list, to 0.757 nm, buffer size 0.057 nm 74: 74: Note that mdrun will redetermine rlist based on the actual pair-list setup 74: 74: This run will generate roughly 0 Mb of data 74: 74: Writing final coordinates. 74: 74: Core t (s) Wall t (s) (%) 74: Time: 0.066 0.033 198.9 74: (ns/day) (hour/ns) 74: Performance: 44.562 0.539 74: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_12_sim.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 74: Can not increase nstlist because an NVE ensemble is used 74: Using 1 MPI thread 74: Using 2 OpenMP threads 74: 74: 74: NOTE: The number of threads is not equal to the number of (logical) cpus 74: and the -pin option is set to auto: will not pin threads to cpus. 74: This can lead to significant performance degradation. 74: Consider using -pin on (and -pinoffset in case you run multiple jobs). 74: starting md rerun '30 atom system in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_12_sim1.trr' 74: 74: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 74: 74: NOTE: 11 % of the run time was spent in pair search, 74: you might want to increase nstlist (this has no effect on accuracy) 74: 74: Core t (s) Wall t (s) (%) 74: Time: 0.011 0.006 180.0 74: (ns/day) (hour/ns) 74: Performance: 241.308 0.099 74: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_12_sim1.edr as single precision energy file 74: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_12_sim2.edr as single precision energy file 74: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 74: 74: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/12 (175 ms) 74: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/13 74: 74: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_13_input.mdp]: 74: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 74: that with the Verlet scheme, nstlist has no effect on the accuracy of 74: your simulation. 74: 74: 74: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_13_input.mdp]: 74: Setting nstcalcenergy (100) equal to nstenergy (4) 74: 74: Generating 1-4 interactions: fudge = 0.5 74: Number of degrees of freedom in T-Coupling group System is 79.00 74: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 74: 74: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_13_input.mdp]: 74: NVE simulation: will use the initial temperature of 294.908 K for 74: determining the Verlet buffer size 74: 74: 74: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_13_input.mdp]: 74: You are using a plain Coulomb cut-off, which might produce artifacts. 74: You might want to consider using PME electrostatics. 74: 74: 74: 74: There were 4 NOTEs 74: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_13_sim.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 74: Can not increase nstlist because an NVE ensemble is used 74: Using 1 MPI thread 74: Using 2 OpenMP threads 74: 74: 74: NOTE: The number of threads is not equal to the number of (logical) cpus 74: and the -pin option is set to auto: will not pin threads to cpus. 74: This can lead to significant performance degradation. 74: Consider using -pin on (and -pinoffset in case you run multiple jobs). 74: starting mdrun '30 atom system in water' 74: 16 steps, 0.0 ps. 74: Generated 2485 of the 2485 non-bonded parameter combinations 74: 74: Generated 2485 of the 2485 1-4 parameter combinations 74: 74: Excluding 3 bonded neighbours molecule type 'nonanol' 74: 74: turning H bonds into constraints... 74: 74: Excluding 2 bonded neighbours molecule type 'SOL' 74: 74: turning H bonds into constraints... 74: 74: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/nonanol_vacuo.gro' 74: 74: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 294.908 K 74: 74: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 74: 74: Set rlist, assuming 4x4 atom pair-list, to 0.757 nm, buffer size 0.057 nm 74: 74: Note that mdrun will redetermine rlist based on the actual pair-list setup 74: 74: This run will generate roughly 0 Mb of data 74: 74: Writing final coordinates. 74: 74: Core t (s) Wall t (s) (%) 74: Time: 0.074 0.037 199.0 74: (ns/day) (hour/ns) 74: Performance: 39.766 0.604 74: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_13_sim.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 74: Can not increase nstlist because an NVE ensemble is used 74: Using 1 MPI thread 74: Using 2 OpenMP threads 74: 74: 74: NOTE: The number of threads is not equal to the number of (logical) cpus 74: and the -pin option is set to auto: will not pin threads to cpus. 74: This can lead to significant performance degradation. 74: Consider using -pin on (and -pinoffset in case you run multiple jobs). 74: starting md rerun '30 atom system in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_13_sim1.trr' 74: 74: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 74: 74: NOTE: 11 % of the run time was spent in pair search, 74: you might want to increase nstlist (this has no effect on accuracy) 74: 74: Core t (s) Wall t (s) (%) 74: Time: 0.010 0.005 178.2 74: (ns/day) (hour/ns) 74: Performance: 267.340 0.090 74: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_13_sim1.edr as single precision energy file 74: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_13_sim2.edr as single precision energy file 74: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 74: 74: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/13 (178 ms) 74: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/14 74: 74: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_14_input.mdp]: 74: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 74: that with the Verlet scheme, nstlist has no effect on the accuracy of 74: your simulation. 74: 74: 74: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_14_input.mdp]: 74: Setting nstcalcenergy (100) equal to nstenergy (4) 74: 74: Generating 1-4 interactions: fudge = 0.5 74: Number of degrees of freedom in T-Coupling group System is 79.00 74: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 74: 74: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_14_input.mdp]: 74: NVE simulation: will use the initial temperature of 294.908 K for 74: determining the Verlet buffer size 74: 74: 74: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_14_input.mdp]: 74: You are using a plain Coulomb cut-off, which might produce artifacts. 74: You might want to consider using PME electrostatics. 74: 74: 74: 74: There were 4 NOTEs 74: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_14_sim.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 74: Can not increase nstlist because an NVE ensemble is used 74: Using 1 MPI thread 74: Using 2 OpenMP threads 74: 74: 74: NOTE: The number of threads is not equal to the number of (logical) cpus 74: and the -pin option is set to auto: will not pin threads to cpus. 74: This can lead to significant performance degradation. 74: Consider using -pin on (and -pinoffset in case you run multiple jobs). 74: starting mdrun '30 atom system in water' 74: 16 steps, 0.0 ps. 74: Generated 2485 of the 2485 non-bonded parameter combinations 74: 74: Generated 2485 of the 2485 1-4 parameter combinations 74: 74: Excluding 3 bonded neighbours molecule type 'nonanol' 74: 74: turning H bonds into constraints... 74: 74: Excluding 2 bonded neighbours molecule type 'SOL' 74: 74: turning H bonds into constraints... 74: 74: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/nonanol_vacuo.gro' 74: 74: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 294.908 K 74: 74: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 74: 74: Set rlist, assuming 4x4 atom pair-list, to 0.757 nm, buffer size 0.057 nm 74: 74: Note that mdrun will redetermine rlist based on the actual pair-list setup 74: 74: This run will generate roughly 0 Mb of data 74: 74: Writing final coordinates. 74: 74: Core t (s) Wall t (s) (%) 74: Time: 0.072 0.036 199.0 74: (ns/day) (hour/ns) 74: Performance: 40.564 0.592 74: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_14_sim.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 74: Can not increase nstlist because an NVE ensemble is used 74: Using 1 MPI thread 74: Using 2 OpenMP threads 74: 74: 74: NOTE: The number of threads is not equal to the number of (logical) cpus 74: and the -pin option is set to auto: will not pin threads to cpus. 74: This can lead to significant performance degradation. 74: Consider using -pin on (and -pinoffset in case you run multiple jobs). 74: starting md rerun '30 atom system in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_14_sim1.trr' 74: 74: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 74: 74: Core t (s) Wall t (s) (%) 74: Time: 0.014 0.007 183.8 74: (ns/day) (hour/ns) 74: Performance: 196.969 0.122 74: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_14_sim1.edr as single precision energy file 74: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_14_sim2.edr as single precision energy file 74: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 74: 74: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/14 (184 ms) 74: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/15 74: 74: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_15_input.mdp]: 74: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 74: that with the Verlet scheme, nstlist has no effect on the accuracy of 74: your simulation. 74: 74: 74: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_15_input.mdp]: 74: Setting nstcalcenergy (100) equal to nstenergy (4) 74: 74: Generating 1-4 interactions: fudge = 0.5 74: Number of degrees of freedom in T-Coupling group System is 79.00 74: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 74: 74: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_15_input.mdp]: 74: NVE simulation: will use the initial temperature of 294.908 K for 74: determining the Verlet buffer size 74: 74: 74: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_15_input.mdp]: 74: You are using a plain Coulomb cut-off, which might produce artifacts. 74: You might want to consider using PME electrostatics. 74: 74: 74: 74: There were 4 NOTEs 74: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_15_sim.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 74: Can not increase nstlist because an NVE ensemble is used 74: Using 1 MPI thread 74: Using 2 OpenMP threads 74: 74: 74: NOTE: The number of threads is not equal to the number of (logical) cpus 74: and the -pin option is set to auto: will not pin threads to cpus. 74: This can lead to significant performance degradation. 74: Consider using -pin on (and -pinoffset in case you run multiple jobs). 74: starting mdrun '30 atom system in water' 74: 16 steps, 0.0 ps. 74: Generated 2485 of the 2485 non-bonded parameter combinations 74: 74: Generated 2485 of the 2485 1-4 parameter combinations 74: 74: Excluding 3 bonded neighbours molecule type 'nonanol' 74: 74: turning H bonds into constraints... 74: 74: Excluding 2 bonded neighbours molecule type 'SOL' 74: 74: turning H bonds into constraints... 74: 74: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/nonanol_vacuo.gro' 74: 74: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 294.908 K 74: 74: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 74: 74: Set rlist, assuming 4x4 atom pair-list, to 0.757 nm, buffer size 0.057 nm 74: 74: Note that mdrun will redetermine rlist based on the actual pair-list setup 74: 74: This run will generate roughly 0 Mb of data 74: 74: Writing final coordinates. 74: 74: Core t (s) Wall t (s) (%) 74: Time: 0.066 0.033 198.9 74: (ns/day) (hour/ns) 74: Performance: 44.241 0.542 74: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_15_sim.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 74: Can not increase nstlist because an NVE ensemble is used 74: Using 1 MPI thread 74: Using 2 OpenMP threads 74: 74: 74: NOTE: The number of threads is not equal to the number of (logical) cpus 74: and the -pin option is set to auto: will not pin threads to cpus. 74: This can lead to significant performance degradation. 74: Consider using -pin on (and -pinoffset in case you run multiple jobs). 74: starting md rerun '30 atom system in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_15_sim1.trr' 74: 74: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 74: 74: Core t (s) Wall t (s) (%) 74: Time: 0.012 0.007 181.6 74: (ns/day) (hour/ns) 74: Performance: 220.937 0.109 74: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_15_sim1.edr as single precision energy file 74: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_15_sim2.edr as single precision energy file 74: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 74: 74: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/15 (173 ms) 74: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/16 74: 74: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_16_input.mdp]: 74: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 74: that with the Verlet scheme, nstlist has no effect on the accuracy of 74: your simulation. 74: 74: 74: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_16_input.mdp]: 74: Setting nstcalcenergy (100) equal to nstenergy (4) 74: 74: Generating 1-4 interactions: fudge = 0.5 74: Number of degrees of freedom in T-Coupling group System is 79.00 74: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 74: 74: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_16_input.mdp]: 74: NVE simulation: will use the initial temperature of 294.908 K for 74: determining the Verlet buffer size 74: 74: 74: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_16_input.mdp]: 74: You are using a plain Coulomb cut-off, which might produce artifacts. 74: You might want to consider using PME electrostatics. 74: 74: 74: 74: There were 4 NOTEs 74: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_16_sim.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 74: Can not increase nstlist because an NVE ensemble is used 74: Using 1 MPI thread 74: Using 2 OpenMP threads 74: 74: 74: NOTE: The number of threads is not equal to the number of (logical) cpus 74: and the -pin option is set to auto: will not pin threads to cpus. 74: This can lead to significant performance degradation. 74: Consider using -pin on (and -pinoffset in case you run multiple jobs). 74: starting mdrun '30 atom system in water' 74: 16 steps, 0.0 ps. 74: Generated 2485 of the 2485 non-bonded parameter combinations 74: 74: Generated 2485 of the 2485 1-4 parameter combinations 74: 74: Excluding 3 bonded neighbours molecule type 'nonanol' 74: 74: turning H bonds into constraints... 74: 74: Excluding 2 bonded neighbours molecule type 'SOL' 74: 74: turning H bonds into constraints... 74: 74: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/nonanol_vacuo.gro' 74: 74: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 294.908 K 74: 74: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 74: 74: Set rlist, assuming 4x4 atom pair-list, to 0.757 nm, buffer size 0.057 nm 74: 74: Note that mdrun will redetermine rlist based on the actual pair-list setup 74: 74: This run will generate roughly 0 Mb of data 74: 74: Writing final coordinates. 74: 74: Core t (s) Wall t (s) (%) 74: Time: 0.077 0.039 199.0 74: (ns/day) (hour/ns) 74: Performance: 38.000 0.632 74: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_16_sim.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 74: Can not increase nstlist because an NVE ensemble is used 74: Using 1 MPI thread 74: Using 2 OpenMP threads 74: 74: 74: NOTE: The number of threads is not equal to the number of (logical) cpus 74: and the -pin option is set to auto: will not pin threads to cpus. 74: This can lead to significant performance degradation. 74: Consider using -pin on (and -pinoffset in case you run multiple jobs). 74: starting md rerun '30 atom system in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_16_sim1.trr' 74: 74: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 74: 74: Core t (s) Wall t (s) (%) 74: Time: 0.012 0.007 181.5 74: (ns/day) (hour/ns) 74: Performance: 221.373 0.108 74: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_16_sim1.edr as single precision energy file 74: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_16_sim2.edr as single precision energy file 74: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 74: 74: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/16 (176 ms) 74: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/17 74: 74: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_17_input.mdp]: 74: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 74: that with the Verlet scheme, nstlist has no effect on the accuracy of 74: your simulation. 74: 74: 74: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_17_input.mdp]: 74: Setting nstcalcenergy (100) equal to nstenergy (4) 74: 74: Generating 1-4 interactions: fudge = 0.5 74: Number of degrees of freedom in T-Coupling group System is 79.00 74: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 74: 74: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_17_input.mdp]: 74: NVE simulation: will use the initial temperature of 294.908 K for 74: determining the Verlet buffer size 74: 74: 74: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_17_input.mdp]: 74: You are using a plain Coulomb cut-off, which might produce artifacts. 74: You might want to consider using PME electrostatics. 74: 74: 74: 74: There were 4 NOTEs 74: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_17_sim.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 74: Can not increase nstlist because an NVE ensemble is used 74: Using 1 MPI thread 74: Using 2 OpenMP threads 74: 74: 74: NOTE: The number of threads is not equal to the number of (logical) cpus 74: and the -pin option is set to auto: will not pin threads to cpus. 74: This can lead to significant performance degradation. 74: Consider using -pin on (and -pinoffset in case you run multiple jobs). 74: starting mdrun '30 atom system in water' 74: 16 steps, 0.0 ps. 74: Generated 2485 of the 2485 non-bonded parameter combinations 74: 74: Generated 2485 of the 2485 1-4 parameter combinations 74: 74: Excluding 3 bonded neighbours molecule type 'nonanol' 74: 74: turning H bonds into constraints... 74: 74: Excluding 2 bonded neighbours molecule type 'SOL' 74: 74: turning H bonds into constraints... 74: 74: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/nonanol_vacuo.gro' 74: 74: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 294.908 K 74: 74: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 74: 74: Set rlist, assuming 4x4 atom pair-list, to 0.757 nm, buffer size 0.057 nm 74: 74: Note that mdrun will redetermine rlist based on the actual pair-list setup 74: 74: This run will generate roughly 0 Mb of data 74: 74: Writing final coordinates. 74: 74: Core t (s) Wall t (s) (%) 74: Time: 0.077 0.039 199.0 74: (ns/day) (hour/ns) 74: Performance: 38.085 0.630 74: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_17_sim.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 74: Can not increase nstlist because an NVE ensemble is used 74: Using 1 MPI thread 74: Using 2 OpenMP threads 74: 74: 74: NOTE: The number of threads is not equal to the number of (logical) cpus 74: and the -pin option is set to auto: will not pin threads to cpus. 74: This can lead to significant performance degradation. 74: Consider using -pin on (and -pinoffset in case you run multiple jobs). 74: starting md rerun '30 atom system in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_17_sim1.trr' 74: 74: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 74: 74: NOTE: 10 % of the run time was spent in pair search, 74: you might want to increase nstlist (this has no effect on accuracy) 74: 74: Core t (s) Wall t (s) (%) 74: Time: 0.016 0.008 186.2 74: (ns/day) (hour/ns) 74: Performance: 175.047 0.137 74: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_17_sim1.edr as single precision energy file 74: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_17_sim2.edr as single precision energy file 74: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 74: 74: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/17 (181 ms) 74: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/18 74: 74: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_18_input.mdp]: 74: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 74: that with the Verlet scheme, nstlist has no effect on the accuracy of 74: your simulation. 74: 74: 74: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_18_input.mdp]: 74: Setting nstcalcenergy (100) equal to nstenergy (4) 74: 74: Generating 1-4 interactions: fudge = 0.5 74: Number of degrees of freedom in T-Coupling group System is 79.00 74: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 74: 74: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_18_input.mdp]: 74: NVE simulation: will use the initial temperature of 294.908 K for 74: determining the Verlet buffer size 74: 74: 74: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_18_input.mdp]: 74: You are using a plain Coulomb cut-off, which might produce artifacts. 74: You might want to consider using PME electrostatics. 74: 74: 74: 74: There were 4 NOTEs 74: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_18_sim.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 74: Can not increase nstlist because an NVE ensemble is used 74: Using 1 MPI thread 74: Using 2 OpenMP threads 74: 74: 74: NOTE: The number of threads is not equal to the number of (logical) cpus 74: and the -pin option is set to auto: will not pin threads to cpus. 74: This can lead to significant performance degradation. 74: Consider using -pin on (and -pinoffset in case you run multiple jobs). 74: starting mdrun '30 atom system in water' 74: 16 steps, 0.0 ps. 74: Generated 2485 of the 2485 non-bonded parameter combinations 74: 74: Generated 2485 of the 2485 1-4 parameter combinations 74: 74: Excluding 3 bonded neighbours molecule type 'nonanol' 74: 74: turning H bonds into constraints... 74: 74: Excluding 2 bonded neighbours molecule type 'SOL' 74: 74: turning H bonds into constraints... 74: 74: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/nonanol_vacuo.gro' 74: 74: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 294.908 K 74: 74: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 74: 74: Set rlist, assuming 4x4 atom pair-list, to 0.757 nm, buffer size 0.057 nm 74: 74: Note that mdrun will redetermine rlist based on the actual pair-list setup 74: 74: This run will generate roughly 0 Mb of data 74: 74: Writing final coordinates. 74: 74: Core t (s) Wall t (s) (%) 74: Time: 0.071 0.036 198.9 74: (ns/day) (hour/ns) 74: Performance: 40.889 0.587 74: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_18_sim.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 74: Can not increase nstlist because an NVE ensemble is used 74: Using 1 MPI thread 74: Using 2 OpenMP threads 74: 74: 74: NOTE: The number of threads is not equal to the number of (logical) cpus 74: and the -pin option is set to auto: will not pin threads to cpus. 74: This can lead to significant performance degradation. 74: Consider using -pin on (and -pinoffset in case you run multiple jobs). 74: starting md rerun '30 atom system in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_18_sim1.trr' 74: 74: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 74: 74: NOTE: 10 % of the run time was spent in pair search, 74: you might want to increase nstlist (this has no effect on accuracy) 74: 74: Core t (s) Wall t (s) (%) 74: Time: 0.012 0.006 181.1 74: (ns/day) (hour/ns) 74: Performance: 228.179 0.105 74: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_18_sim1.edr as single precision energy file 74: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_18_sim2.edr as single precision energy file 74: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 74: 74: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/18 (175 ms) 74: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/19 74: 74: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_19_input.mdp]: 74: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 74: that with the Verlet scheme, nstlist has no effect on the accuracy of 74: your simulation. 74: 74: 74: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_19_input.mdp]: 74: Setting nstcalcenergy (100) equal to nstenergy (4) 74: 74: Generating 1-4 interactions: fudge = 0.5 74: Number of degrees of freedom in T-Coupling group System is 79.00 74: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 74: 74: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_19_input.mdp]: 74: NVE simulation: will use the initial temperature of 294.908 K for 74: determining the Verlet buffer size 74: 74: 74: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_19_input.mdp]: 74: You are using a plain Coulomb cut-off, which might produce artifacts. 74: You might want to consider using PME electrostatics. 74: 74: 74: 74: There were 4 NOTEs 74: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_19_sim.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 74: Can not increase nstlist because an NVE ensemble is used 74: Using 1 MPI thread 74: Using 2 OpenMP threads 74: 74: 74: NOTE: The number of threads is not equal to the number of (logical) cpus 74: and the -pin option is set to auto: will not pin threads to cpus. 74: This can lead to significant performance degradation. 74: Consider using -pin on (and -pinoffset in case you run multiple jobs). 74: starting mdrun '30 atom system in water' 74: 16 steps, 0.0 ps. 74: Generated 2485 of the 2485 non-bonded parameter combinations 74: 74: Generated 2485 of the 2485 1-4 parameter combinations 74: 74: Excluding 3 bonded neighbours molecule type 'nonanol' 74: 74: turning H bonds into constraints... 74: 74: Excluding 2 bonded neighbours molecule type 'SOL' 74: 74: turning H bonds into constraints... 74: 74: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/nonanol_vacuo.gro' 74: 74: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 294.908 K 74: 74: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 74: 74: Set rlist, assuming 4x4 atom pair-list, to 0.757 nm, buffer size 0.057 nm 74: 74: Note that mdrun will redetermine rlist based on the actual pair-list setup 74: 74: This run will generate roughly 0 Mb of data 74: 74: Writing final coordinates. 74: 74: Core t (s) Wall t (s) (%) 74: Time: 0.068 0.034 198.9 74: (ns/day) (hour/ns) 74: Performance: 42.980 0.558 74: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_19_sim.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 74: Can not increase nstlist because an NVE ensemble is used 74: Using 1 MPI thread 74: Using 2 OpenMP threads 74: 74: 74: NOTE: The number of threads is not equal to the number of (logical) cpus 74: and the -pin option is set to auto: will not pin threads to cpus. 74: This can lead to significant performance degradation. 74: Consider using -pin on (and -pinoffset in case you run multiple jobs). 74: starting md rerun '30 atom system in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_19_sim1.trr' 74: 74: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 74: 74: Core t (s) Wall t (s) (%) 74: Time: 0.013 0.007 184.9 74: (ns/day) (hour/ns) 74: Performance: 212.838 0.113 74: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_19_sim1.edr as single precision energy file 74: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_19_sim2.edr as single precision energy file 74: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 74: 74: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/19 (173 ms) 74: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/20 74: 74: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_20_input.mdp]: 74: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 74: that with the Verlet scheme, nstlist has no effect on the accuracy of 74: your simulation. 74: 74: 74: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_20_input.mdp]: 74: Setting nstcalcenergy (100) equal to nstenergy (4) 74: 74: Generating 1-4 interactions: fudge = 0.5 74: Number of degrees of freedom in T-Coupling group System is 79.00 74: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 74: 74: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_20_input.mdp]: 74: NVE simulation: will use the initial temperature of 294.908 K for 74: determining the Verlet buffer size 74: 74: 74: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_20_input.mdp]: 74: You are using a plain Coulomb cut-off, which might produce artifacts. 74: You might want to consider using PME electrostatics. 74: 74: 74: 74: There were 4 NOTEs 74: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_20_sim.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 74: Can not increase nstlist because an NVE ensemble is used 74: Using 1 MPI thread 74: Using 2 OpenMP threads 74: 74: 74: NOTE: The number of threads is not equal to the number of (logical) cpus 74: and the -pin option is set to auto: will not pin threads to cpus. 74: This can lead to significant performance degradation. 74: Consider using -pin on (and -pinoffset in case you run multiple jobs). 74: starting mdrun '30 atom system in water' 74: 16 steps, 0.0 ps. 74: Generated 2485 of the 2485 non-bonded parameter combinations 74: 74: Generated 2485 of the 2485 1-4 parameter combinations 74: 74: Excluding 3 bonded neighbours molecule type 'nonanol' 74: 74: turning H bonds into constraints... 74: 74: Excluding 2 bonded neighbours molecule type 'SOL' 74: 74: turning H bonds into constraints... 74: 74: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/nonanol_vacuo.gro' 74: 74: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 294.908 K 74: 74: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 74: 74: Set rlist, assuming 4x4 atom pair-list, to 0.757 nm, buffer size 0.057 nm 74: 74: Note that mdrun will redetermine rlist based on the actual pair-list setup 74: 74: This run will generate roughly 0 Mb of data 74: 74: Writing final coordinates. 74: 74: Core t (s) Wall t (s) (%) 74: Time: 0.067 0.034 198.9 74: (ns/day) (hour/ns) 74: Performance: 43.686 0.549 74: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_20_sim.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 74: Can not increase nstlist because an NVE ensemble is used 74: Using 1 MPI thread 74: Using 2 OpenMP threads 74: 74: 74: NOTE: The number of threads is not equal to the number of (logical) cpus 74: and the -pin option is set to auto: will not pin threads to cpus. 74: This can lead to significant performance degradation. 74: Consider using -pin on (and -pinoffset in case you run multiple jobs). 74: starting md rerun '30 atom system in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_20_sim1.trr' 74: 74: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 74: 74: NOTE: 56 % of the run time was spent in pair search, 74: you might want to increase nstlist (this has no effect on accuracy) 74: 74: Core t (s) Wall t (s) (%) 74: Time: 0.055 0.028 195.4 74: (ns/day) (hour/ns) 74: Performance: 52.010 0.461 74: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_20_sim1.edr as single precision energy file 74: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_20_sim2.edr as single precision energy file 74: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 74: 74: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/20 (213 ms) 74: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/21 74: 74: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_21_input.mdp]: 74: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 74: that with the Verlet scheme, nstlist has no effect on the accuracy of 74: your simulation. 74: 74: 74: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_21_input.mdp]: 74: Setting nstcalcenergy (100) equal to nstenergy (4) 74: 74: Generating 1-4 interactions: fudge = 0.5 74: Number of degrees of freedom in T-Coupling group System is 79.00 74: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 74: 74: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_21_input.mdp]: 74: NVE simulation: will use the initial temperature of 294.908 K for 74: determining the Verlet buffer size 74: 74: 74: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_21_input.mdp]: 74: You are using a plain Coulomb cut-off, which might produce artifacts. 74: You might want to consider using PME electrostatics. 74: 74: 74: 74: There were 4 NOTEs 74: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_21_sim.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 74: Can not increase nstlist because an NVE ensemble is used 74: Using 1 MPI thread 74: Using 2 OpenMP threads 74: 74: 74: NOTE: The number of threads is not equal to the number of (logical) cpus 74: and the -pin option is set to auto: will not pin threads to cpus. 74: This can lead to significant performance degradation. 74: Consider using -pin on (and -pinoffset in case you run multiple jobs). 74: starting mdrun '30 atom system in water' 74: 16 steps, 0.0 ps. 74: Generated 2485 of the 2485 non-bonded parameter combinations 74: 74: Generated 2485 of the 2485 1-4 parameter combinations 74: 74: Excluding 3 bonded neighbours molecule type 'nonanol' 74: 74: turning H bonds into constraints... 74: 74: Excluding 2 bonded neighbours molecule type 'SOL' 74: 74: turning H bonds into constraints... 74: 74: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/nonanol_vacuo.gro' 74: 74: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 294.908 K 74: 74: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 74: 74: Set rlist, assuming 4x4 atom pair-list, to 0.757 nm, buffer size 0.057 nm 74: 74: Note that mdrun will redetermine rlist based on the actual pair-list setup 74: 74: This run will generate roughly 0 Mb of data 74: 74: Writing final coordinates. 74: 74: Core t (s) Wall t (s) (%) 74: Time: 0.074 0.037 199.0 74: (ns/day) (hour/ns) 74: Performance: 39.430 0.609 74: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_21_sim.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 74: Can not increase nstlist because an NVE ensemble is used 74: Using 1 MPI thread 74: Using 2 OpenMP threads 74: 74: 74: NOTE: The number of threads is not equal to the number of (logical) cpus 74: and the -pin option is set to auto: will not pin threads to cpus. 74: This can lead to significant performance degradation. 74: Consider using -pin on (and -pinoffset in case you run multiple jobs). 74: starting md rerun '30 atom system in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_21_sim1.trr' 74: 74: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 74: 74: NOTE: 11 % of the run time was spent in pair search, 74: you might want to increase nstlist (this has no effect on accuracy) 74: 74: Core t (s) Wall t (s) (%) 74: Time: 0.010 0.006 179.3 74: (ns/day) (hour/ns) 74: Performance: 251.330 0.095 74: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_21_sim1.edr as single precision energy file 74: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_21_sim2.edr as single precision energy file 74: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 74: 74: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/21 (179 ms) 74: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/22 74: 74: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_22_input.mdp]: 74: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 74: that with the Verlet scheme, nstlist has no effect on the accuracy of 74: your simulation. 74: 74: 74: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_22_input.mdp]: 74: Setting nstcalcenergy (100) equal to nstenergy (4) 74: 74: Generating 1-4 interactions: fudge = 0.5 74: Number of degrees of freedom in T-Coupling group System is 79.00 74: 74: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_22_input.mdp]: 74: You are using a plain Coulomb cut-off, which might produce artifacts. 74: You might want to consider using PME electrostatics. 74: 74: 74: 74: There were 3 NOTEs 74: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_22_sim.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 74: Changing nstlist from 8 to 20, rlist from 0.757 to 0.863 74: 74: Using 1 MPI thread 74: Using 2 OpenMP threads 74: 74: 74: NOTE: The number of threads is not equal to the number of (logical) cpus 74: and the -pin option is set to auto: will not pin threads to cpus. 74: This can lead to significant performance degradation. 74: Consider using -pin on (and -pinoffset in case you run multiple jobs). 74: starting mdrun '30 atom system in water' 74: 16 steps, 0.0 ps. 74: Generated 2485 of the 2485 non-bonded parameter combinations 74: 74: Generated 2485 of the 2485 1-4 parameter combinations 74: 74: Excluding 3 bonded neighbours molecule type 'nonanol' 74: 74: turning H bonds into constraints... 74: 74: Excluding 2 bonded neighbours molecule type 'SOL' 74: 74: turning H bonds into constraints... 74: 74: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/nonanol_vacuo.gro' 74: 74: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 74: 74: Calculated rlist for 1x1 atom pair-list as 0.764 nm, buffer size 0.064 nm 74: 74: Set rlist, assuming 4x4 atom pair-list, to 0.757 nm, buffer size 0.057 nm 74: 74: Note that mdrun will redetermine rlist based on the actual pair-list setup 74: 74: This run will generate roughly 0 Mb of data 74: 74: Writing final coordinates. 74: 74: Core t (s) Wall t (s) (%) 74: Time: 0.075 0.038 198.1 74: (ns/day) (hour/ns) 74: Performance: 38.994 0.615 74: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_22_sim.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 74: Changing nstlist from 8 to 20, rlist from 0.757 to 0.863 74: 74: Using 1 MPI thread 74: Using 2 OpenMP threads 74: 74: 74: NOTE: The number of threads is not equal to the number of (logical) cpus 74: and the -pin option is set to auto: will not pin threads to cpus. 74: This can lead to significant performance degradation. 74: Consider using -pin on (and -pinoffset in case you run multiple jobs). 74: starting md rerun '30 atom system in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_22_sim1.trr' 74: 74: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 74: 74: Core t (s) Wall t (s) (%) 74: Time: 0.016 0.008 186.7 74: (ns/day) (hour/ns) 74: Performance: 176.350 0.136 74: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_22_sim1.edr as single precision energy file 74: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_22_sim2.edr as single precision energy file 74: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 74: 74: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/22 (285 ms) 74: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/23 74: 74: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_23_input.mdp]: 74: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 74: that with the Verlet scheme, nstlist has no effect on the accuracy of 74: your simulation. 74: 74: 74: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_23_input.mdp]: 74: Setting nstcalcenergy (100) equal to nstenergy (4) 74: 74: Generating 1-4 interactions: fudge = 0.5 74: Number of degrees of freedom in T-Coupling group System is 79.00 74: 74: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_23_input.mdp]: 74: You are using a plain Coulomb cut-off, which might produce artifacts. 74: You might want to consider using PME electrostatics. 74: 74: 74: 74: There were 3 NOTEs 74: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_23_sim.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 74: Changing nstlist from 8 to 20, rlist from 0.757 to 0.863 74: 74: Using 1 MPI thread 74: Using 2 OpenMP threads 74: 74: 74: NOTE: The number of threads is not equal to the number of (logical) cpus 74: and the -pin option is set to auto: will not pin threads to cpus. 74: This can lead to significant performance degradation. 74: Consider using -pin on (and -pinoffset in case you run multiple jobs). 74: starting mdrun '30 atom system in water' 74: 16 steps, 0.0 ps. 74: Generated 2485 of the 2485 non-bonded parameter combinations 74: 74: Generated 2485 of the 2485 1-4 parameter combinations 74: 74: Excluding 3 bonded neighbours molecule type 'nonanol' 74: 74: turning H bonds into constraints... 74: 74: Excluding 2 bonded neighbours molecule type 'SOL' 74: 74: turning H bonds into constraints... 74: 74: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/nonanol_vacuo.gro' 74: 74: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 74: 74: Calculated rlist for 1x1 atom pair-list as 0.764 nm, buffer size 0.064 nm 74: 74: Set rlist, assuming 4x4 atom pair-list, to 0.757 nm, buffer size 0.057 nm 74: 74: Note that mdrun will redetermine rlist based on the actual pair-list setup 74: 74: This run will generate roughly 0 Mb of data 74: 74: Writing final coordinates. 74: 74: Core t (s) Wall t (s) (%) 74: Time: 0.072 0.036 198.0 74: (ns/day) (hour/ns) 74: Performance: 40.553 0.592 74: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_23_sim.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 74: Changing nstlist from 8 to 20, rlist from 0.757 to 0.863 74: 74: Using 1 MPI thread 74: Using 2 OpenMP threads 74: 74: 74: NOTE: The number of threads is not equal to the number of (logical) cpus 74: and the -pin option is set to auto: will not pin threads to cpus. 74: This can lead to significant performance degradation. 74: Consider using -pin on (and -pinoffset in case you run multiple jobs). 74: starting md rerun '30 atom system in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_23_sim1.trr' 74: 74: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 74: 74: Core t (s) Wall t (s) (%) 74: Time: 0.014 0.008 180.8 74: (ns/day) (hour/ns) 74: Performance: 193.468 0.124 74: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_23_sim1.edr as single precision energy file 74: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_23_sim2.edr as single precision energy file 74: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 74: 74: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/23 (282 ms) 74: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/24 74: 74: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_24_input.mdp]: 74: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 74: that with the Verlet scheme, nstlist has no effect on the accuracy of 74: your simulation. 74: 74: 74: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_24_input.mdp]: 74: Setting nstcalcenergy (100) equal to nstenergy (4) 74: 74: Generating 1-4 interactions: fudge = 0.5 74: Number of degrees of freedom in T-Coupling group System is 79.00 74: 74: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_24_input.mdp]: 74: You are using a plain Coulomb cut-off, which might produce artifacts. 74: You might want to consider using PME electrostatics. 74: 74: 74: 74: There were 3 NOTEs 74: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_24_sim.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 74: Changing nstlist from 8 to 20, rlist from 0.757 to 0.863 74: 74: Using 1 MPI thread 74: Using 2 OpenMP threads 74: 74: 74: NOTE: The number of threads is not equal to the number of (logical) cpus 74: and the -pin option is set to auto: will not pin threads to cpus. 74: This can lead to significant performance degradation. 74: Consider using -pin on (and -pinoffset in case you run multiple jobs). 74: starting mdrun '30 atom system in water' 74: 16 steps, 0.0 ps. 74: Generated 2485 of the 2485 non-bonded parameter combinations 74: 74: Generated 2485 of the 2485 1-4 parameter combinations 74: 74: Excluding 3 bonded neighbours molecule type 'nonanol' 74: 74: turning H bonds into constraints... 74: 74: Excluding 2 bonded neighbours molecule type 'SOL' 74: 74: turning H bonds into constraints... 74: 74: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/nonanol_vacuo.gro' 74: 74: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 74: 74: Calculated rlist for 1x1 atom pair-list as 0.764 nm, buffer size 0.064 nm 74: 74: Set rlist, assuming 4x4 atom pair-list, to 0.757 nm, buffer size 0.057 nm 74: 74: Note that mdrun will redetermine rlist based on the actual pair-list setup 74: 74: This run will generate roughly 0 Mb of data 74: 74: Writing final coordinates. 74: 74: Core t (s) Wall t (s) (%) 74: Time: 0.112 0.056 198.7 74: (ns/day) (hour/ns) 74: Performance: 26.031 0.922 74: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_24_sim.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 74: Changing nstlist from 8 to 20, rlist from 0.757 to 0.863 74: 74: Using 1 MPI thread 74: Using 2 OpenMP threads 74: 74: 74: NOTE: The number of threads is not equal to the number of (logical) cpus 74: and the -pin option is set to auto: will not pin threads to cpus. 74: This can lead to significant performance degradation. 74: Consider using -pin on (and -pinoffset in case you run multiple jobs). 74: starting md rerun '30 atom system in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_24_sim1.trr' 74: 74: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 74: 74: Core t (s) Wall t (s) (%) 74: Time: 0.015 0.008 183.7 74: (ns/day) (hour/ns) 74: Performance: 181.242 0.132 74: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_24_sim1.edr as single precision energy file 74: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_24_sim2.edr as single precision energy file 74: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 74: 74: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/24 (309 ms) 74: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/25 74: 74: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_25_input.mdp]: 74: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 74: that with the Verlet scheme, nstlist has no effect on the accuracy of 74: your simulation. 74: 74: 74: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_25_input.mdp]: 74: Setting nstcalcenergy (100) equal to nstenergy (4) 74: 74: Generating 1-4 interactions: fudge = 0.5 74: Number of degrees of freedom in T-Coupling group System is 79.00 74: 74: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_25_input.mdp]: 74: You are using a plain Coulomb cut-off, which might produce artifacts. 74: You might want to consider using PME electrostatics. 74: 74: 74: 74: There were 3 NOTEs 74: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_25_sim.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 74: Changing nstlist from 8 to 20, rlist from 0.757 to 0.863 74: 74: Using 1 MPI thread 74: Using 2 OpenMP threads 74: 74: 74: NOTE: The number of threads is not equal to the number of (logical) cpus 74: and the -pin option is set to auto: will not pin threads to cpus. 74: This can lead to significant performance degradation. 74: Consider using -pin on (and -pinoffset in case you run multiple jobs). 74: starting mdrun '30 atom system in water' 74: 16 steps, 0.0 ps. 74: Generated 2485 of the 2485 non-bonded parameter combinations 74: 74: Generated 2485 of the 2485 1-4 parameter combinations 74: 74: Excluding 3 bonded neighbours molecule type 'nonanol' 74: 74: turning H bonds into constraints... 74: 74: Excluding 2 bonded neighbours molecule type 'SOL' 74: 74: turning H bonds into constraints... 74: 74: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/nonanol_vacuo.gro' 74: 74: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 74: 74: Calculated rlist for 1x1 atom pair-list as 0.764 nm, buffer size 0.064 nm 74: 74: Set rlist, assuming 4x4 atom pair-list, to 0.757 nm, buffer size 0.057 nm 74: 74: Note that mdrun will redetermine rlist based on the actual pair-list setup 74: 74: This run will generate roughly 0 Mb of data 74: 74: Writing final coordinates. 74: 74: Core t (s) Wall t (s) (%) 74: Time: 0.062 0.032 197.6 74: (ns/day) (hour/ns) 74: Performance: 46.549 0.516 74: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_25_sim.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 74: Changing nstlist from 8 to 20, rlist from 0.757 to 0.863 74: 74: Using 1 MPI thread 74: Using 2 OpenMP threads 74: 74: 74: NOTE: The number of threads is not equal to the number of (logical) cpus 74: and the -pin option is set to auto: will not pin threads to cpus. 74: This can lead to significant performance degradation. 74: Consider using -pin on (and -pinoffset in case you run multiple jobs). 74: starting md rerun '30 atom system in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_25_sim1.trr' 74: 74: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 74: 74: NOTE: 10 % of the run time was spent in pair search, 74: you might want to increase nstlist (this has no effect on accuracy) 74: 74: Core t (s) Wall t (s) (%) 74: Time: 0.012 0.006 179.5 74: (ns/day) (hour/ns) 74: Performance: 228.925 0.105 74: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_25_sim1.edr as single precision energy file 74: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_25_sim2.edr as single precision energy file 74: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 74: 74: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/25 (285 ms) 74: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/26 74: 74: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_26_input.mdp]: 74: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 74: that with the Verlet scheme, nstlist has no effect on the accuracy of 74: your simulation. 74: 74: 74: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_26_input.mdp]: 74: Setting nstcalcenergy (100) equal to nstenergy (4) 74: 74: Generating 1-4 interactions: fudge = 0.5 74: Number of degrees of freedom in T-Coupling group System is 79.00 74: 74: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_26_input.mdp]: 74: You are using a plain Coulomb cut-off, which might produce artifacts. 74: You might want to consider using PME electrostatics. 74: 74: 74: 74: There were 3 NOTEs 74: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_26_sim.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 74: Changing nstlist from 8 to 20, rlist from 0.757 to 0.863 74: 74: Using 1 MPI thread 74: Using 2 OpenMP threads 74: 74: 74: NOTE: The number of threads is not equal to the number of (logical) cpus 74: and the -pin option is set to auto: will not pin threads to cpus. 74: This can lead to significant performance degradation. 74: Consider using -pin on (and -pinoffset in case you run multiple jobs). 74: starting mdrun '30 atom system in water' 74: 16 steps, 0.0 ps. 74: Generated 2485 of the 2485 non-bonded parameter combinations 74: 74: Generated 2485 of the 2485 1-4 parameter combinations 74: 74: Excluding 3 bonded neighbours molecule type 'nonanol' 74: 74: turning H bonds into constraints... 74: 74: Excluding 2 bonded neighbours molecule type 'SOL' 74: 74: turning H bonds into constraints... 74: 74: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/nonanol_vacuo.gro' 74: 74: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 74: 74: Calculated rlist for 1x1 atom pair-list as 0.764 nm, buffer size 0.064 nm 74: 74: Set rlist, assuming 4x4 atom pair-list, to 0.757 nm, buffer size 0.057 nm 74: 74: Note that mdrun will redetermine rlist based on the actual pair-list setup 74: 74: This run will generate roughly 0 Mb of data 74: 74: Writing final coordinates. 74: 74: Core t (s) Wall t (s) (%) 74: Time: 0.070 0.035 197.6 74: (ns/day) (hour/ns) 74: Performance: 41.575 0.577 74: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_26_sim.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 74: Changing nstlist from 8 to 20, rlist from 0.757 to 0.863 74: 74: Using 1 MPI thread 74: Using 2 OpenMP threads 74: 74: 74: NOTE: The number of threads is not equal to the number of (logical) cpus 74: and the -pin option is set to auto: will not pin threads to cpus. 74: This can lead to significant performance degradation. 74: Consider using -pin on (and -pinoffset in case you run multiple jobs). 74: starting md rerun '30 atom system in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_26_sim1.trr' 74: 74: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 74: 74: Core t (s) Wall t (s) (%) 74: Time: 0.020 0.011 187.2 74: (ns/day) (hour/ns) 74: Performance: 134.197 0.179 74: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_26_sim1.edr as single precision energy file 74: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_26_sim2.edr as single precision energy file 74: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 74: 74: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/26 (289 ms) 74: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/27 74: 74: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_27_input.mdp]: 74: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 74: that with the Verlet scheme, nstlist has no effect on the accuracy of 74: your simulation. 74: 74: 74: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_27_input.mdp]: 74: Setting nstcalcenergy (100) equal to nstenergy (4) 74: 74: Generating 1-4 interactions: fudge = 0.5 74: Number of degrees of freedom in T-Coupling group System is 79.00 74: 74: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_27_input.mdp]: 74: You are using a plain Coulomb cut-off, which might produce artifacts. 74: You might want to consider using PME electrostatics. 74: 74: 74: 74: There were 3 NOTEs 74: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_27_sim.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 74: Changing nstlist from 8 to 20, rlist from 0.757 to 0.863 74: 74: Using 1 MPI thread 74: Using 2 OpenMP threads 74: 74: 74: NOTE: The number of threads is not equal to the number of (logical) cpus 74: and the -pin option is set to auto: will not pin threads to cpus. 74: This can lead to significant performance degradation. 74: Consider using -pin on (and -pinoffset in case you run multiple jobs). 74: starting mdrun '30 atom system in water' 74: 16 steps, 0.0 ps. 74: Generated 2485 of the 2485 non-bonded parameter combinations 74: 74: Generated 2485 of the 2485 1-4 parameter combinations 74: 74: Excluding 3 bonded neighbours molecule type 'nonanol' 74: 74: turning H bonds into constraints... 74: 74: Excluding 2 bonded neighbours molecule type 'SOL' 74: 74: turning H bonds into constraints... 74: 74: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/nonanol_vacuo.gro' 74: 74: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 74: 74: Calculated rlist for 1x1 atom pair-list as 0.764 nm, buffer size 0.064 nm 74: 74: Set rlist, assuming 4x4 atom pair-list, to 0.757 nm, buffer size 0.057 nm 74: 74: Note that mdrun will redetermine rlist based on the actual pair-list setup 74: 74: This run will generate roughly 0 Mb of data 74: 74: Writing final coordinates. 74: 74: Core t (s) Wall t (s) (%) 74: Time: 0.068 0.034 197.8 74: (ns/day) (hour/ns) 74: Performance: 42.741 0.562 74: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_27_sim.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 74: Changing nstlist from 8 to 20, rlist from 0.757 to 0.863 74: 74: Using 1 MPI thread 74: Using 2 OpenMP threads 74: 74: 74: NOTE: The number of threads is not equal to the number of (logical) cpus 74: and the -pin option is set to auto: will not pin threads to cpus. 74: This can lead to significant performance degradation. 74: Consider using -pin on (and -pinoffset in case you run multiple jobs). 74: starting md rerun '30 atom system in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_27_sim1.trr' 74: 74: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 74: 74: Core t (s) Wall t (s) (%) 74: Time: 0.012 0.007 178.3 74: (ns/day) (hour/ns) 74: Performance: 211.008 0.114 74: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_27_sim1.edr as single precision energy file 74: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_27_sim2.edr as single precision energy file 74: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 74: 74: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/27 (298 ms) 74: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/28 74: 74: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_28_input.mdp]: 74: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 74: that with the Verlet scheme, nstlist has no effect on the accuracy of 74: your simulation. 74: 74: 74: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_28_input.mdp]: 74: Setting nstcalcenergy (100) equal to nstenergy (4) 74: 74: Generating 1-4 interactions: fudge = 0.5 74: Number of degrees of freedom in T-Coupling group System is 79.00 74: 74: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_28_input.mdp]: 74: You are using a plain Coulomb cut-off, which might produce artifacts. 74: You might want to consider using PME electrostatics. 74: 74: 74: 74: There were 3 NOTEs 74: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_28_sim.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 74: Changing nstlist from 8 to 20, rlist from 0.757 to 0.863 74: 74: Using 1 MPI thread 74: Using 2 OpenMP threads 74: 74: 74: NOTE: The number of threads is not equal to the number of (logical) cpus 74: and the -pin option is set to auto: will not pin threads to cpus. 74: This can lead to significant performance degradation. 74: Consider using -pin on (and -pinoffset in case you run multiple jobs). 74: starting mdrun '30 atom system in water' 74: 16 steps, 0.0 ps. 74: Generated 2485 of the 2485 non-bonded parameter combinations 74: 74: Generated 2485 of the 2485 1-4 parameter combinations 74: 74: Excluding 3 bonded neighbours molecule type 'nonanol' 74: 74: turning H bonds into constraints... 74: 74: Excluding 2 bonded neighbours molecule type 'SOL' 74: 74: turning H bonds into constraints... 74: 74: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/nonanol_vacuo.gro' 74: 74: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 74: 74: Calculated rlist for 1x1 atom pair-list as 0.764 nm, buffer size 0.064 nm 74: 74: Set rlist, assuming 4x4 atom pair-list, to 0.757 nm, buffer size 0.057 nm 74: 74: Note that mdrun will redetermine rlist based on the actual pair-list setup 74: 74: This run will generate roughly 0 Mb of data 74: 74: Writing final coordinates. 74: 74: Core t (s) Wall t (s) (%) 74: Time: 0.079 0.040 198.1 74: (ns/day) (hour/ns) 74: Performance: 36.997 0.649 74: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_28_sim.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 74: Changing nstlist from 8 to 20, rlist from 0.757 to 0.863 74: 74: Using 1 MPI thread 74: Using 2 OpenMP threads 74: 74: 74: NOTE: The number of threads is not equal to the number of (logical) cpus 74: and the -pin option is set to auto: will not pin threads to cpus. 74: This can lead to significant performance degradation. 74: Consider using -pin on (and -pinoffset in case you run multiple jobs). 74: starting md rerun '30 atom system in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_28_sim1.trr' 74: 74: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 74: 74: NOTE: 18 % of the run time was spent in pair search, 74: you might want to increase nstlist (this has no effect on accuracy) 74: 74: Core t (s) Wall t (s) (%) 74: Time: 0.016 0.009 184.8 74: (ns/day) (hour/ns) 74: Performance: 170.018 0.141 74: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_28_sim1.edr as single precision energy file 74: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_28_sim2.edr as single precision energy file 74: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 74: 74: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/28 (293 ms) 74: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/29 74: 74: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_29_input.mdp]: 74: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 74: that with the Verlet scheme, nstlist has no effect on the accuracy of 74: your simulation. 74: 74: 74: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_29_input.mdp]: 74: Setting nstcalcenergy (100) equal to nstenergy (4) 74: 74: Generating 1-4 interactions: fudge = 0.5 74: Number of degrees of freedom in T-Coupling group System is 79.00 74: 74: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_29_input.mdp]: 74: You are using a plain Coulomb cut-off, which might produce artifacts. 74: You might want to consider using PME electrostatics. 74: 74: 74: 74: There were 3 NOTEs 74: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_29_sim.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 74: Changing nstlist from 8 to 20, rlist from 0.757 to 0.863 74: 74: Using 1 MPI thread 74: Using 2 OpenMP threads 74: 74: 74: NOTE: The number of threads is not equal to the number of (logical) cpus 74: and the -pin option is set to auto: will not pin threads to cpus. 74: This can lead to significant performance degradation. 74: Consider using -pin on (and -pinoffset in case you run multiple jobs). 74: starting mdrun '30 atom system in water' 74: 16 steps, 0.0 ps. 74: Generated 2485 of the 2485 non-bonded parameter combinations 74: 74: Generated 2485 of the 2485 1-4 parameter combinations 74: 74: Excluding 3 bonded neighbours molecule type 'nonanol' 74: 74: turning H bonds into constraints... 74: 74: Excluding 2 bonded neighbours molecule type 'SOL' 74: 74: turning H bonds into constraints... 74: 74: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/nonanol_vacuo.gro' 74: 74: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 74: 74: Calculated rlist for 1x1 atom pair-list as 0.764 nm, buffer size 0.064 nm 74: 74: Set rlist, assuming 4x4 atom pair-list, to 0.757 nm, buffer size 0.057 nm 74: 74: Note that mdrun will redetermine rlist based on the actual pair-list setup 74: 74: This run will generate roughly 0 Mb of data 74: 74: Writing final coordinates. 74: 74: Core t (s) Wall t (s) (%) 74: Time: 0.064 0.032 197.7 74: (ns/day) (hour/ns) 74: Performance: 45.458 0.528 74: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_29_sim.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 74: Changing nstlist from 8 to 20, rlist from 0.757 to 0.863 74: 74: Using 1 MPI thread 74: Using 2 OpenMP threads 74: 74: 74: NOTE: The number of threads is not equal to the number of (logical) cpus 74: and the -pin option is set to auto: will not pin threads to cpus. 74: This can lead to significant performance degradation. 74: Consider using -pin on (and -pinoffset in case you run multiple jobs). 74: starting md rerun '30 atom system in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_29_sim1.trr' 74: 74: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 74: 74: NOTE: 23 % of the run time was spent in pair search, 74: you might want to increase nstlist (this has no effect on accuracy) 74: 74: Core t (s) Wall t (s) (%) 74: Time: 0.019 0.010 186.7 74: (ns/day) (hour/ns) 74: Performance: 141.956 0.169 74: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_29_sim1.edr as single precision energy file 74: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_29_sim2.edr as single precision energy file 74: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 74: 74: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/29 (288 ms) 74: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/30 74: 74: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_30_input.mdp]: 74: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 74: that with the Verlet scheme, nstlist has no effect on the accuracy of 74: your simulation. 74: 74: 74: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_30_input.mdp]: 74: Setting nstcalcenergy (100) equal to nstenergy (4) 74: 74: Generating 1-4 interactions: fudge = 0.5 74: Number of degrees of freedom in T-Coupling group System is 79.00 74: 74: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_30_input.mdp]: 74: You are using a plain Coulomb cut-off, which might produce artifacts. 74: You might want to consider using PME electrostatics. 74: 74: 74: 74: There were 3 NOTEs 74: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_30_sim.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 74: Changing nstlist from 8 to 20, rlist from 0.757 to 0.863 74: 74: Using 1 MPI thread 74: Using 2 OpenMP threads 74: 74: 74: NOTE: The number of threads is not equal to the number of (logical) cpus 74: and the -pin option is set to auto: will not pin threads to cpus. 74: This can lead to significant performance degradation. 74: Consider using -pin on (and -pinoffset in case you run multiple jobs). 74: starting mdrun '30 atom system in water' 74: 16 steps, 0.0 ps. 74: Generated 2485 of the 2485 non-bonded parameter combinations 74: 74: Generated 2485 of the 2485 1-4 parameter combinations 74: 74: Excluding 3 bonded neighbours molecule type 'nonanol' 74: 74: turning H bonds into constraints... 74: 74: Excluding 2 bonded neighbours molecule type 'SOL' 74: 74: turning H bonds into constraints... 74: 74: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/nonanol_vacuo.gro' 74: 74: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 74: 74: Calculated rlist for 1x1 atom pair-list as 0.764 nm, buffer size 0.064 nm 74: 74: Set rlist, assuming 4x4 atom pair-list, to 0.757 nm, buffer size 0.057 nm 74: 74: Note that mdrun will redetermine rlist based on the actual pair-list setup 74: 74: This run will generate roughly 0 Mb of data 74: 74: Writing final coordinates. 74: 74: Core t (s) Wall t (s) (%) 74: Time: 0.067 0.034 197.9 74: (ns/day) (hour/ns) 74: Performance: 43.590 0.551 74: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_30_sim.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 74: Changing nstlist from 8 to 20, rlist from 0.757 to 0.863 74: 74: Using 1 MPI thread 74: Using 2 OpenMP threads 74: 74: 74: NOTE: The number of threads is not equal to the number of (logical) cpus 74: and the -pin option is set to auto: will not pin threads to cpus. 74: This can lead to significant performance degradation. 74: Consider using -pin on (and -pinoffset in case you run multiple jobs). 74: starting md rerun '30 atom system in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_30_sim1.trr' 74: 74: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 74: 74: NOTE: 10 % of the run time was spent in pair search, 74: you might want to increase nstlist (this has no effect on accuracy) 74: 74: Core t (s) Wall t (s) (%) 74: Time: 0.012 0.007 178.2 74: (ns/day) (hour/ns) 74: Performance: 219.028 0.110 74: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_30_sim1.edr as single precision energy file 74: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_30_sim2.edr as single precision energy file 74: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 74: 74: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/30 (278 ms) 74: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/31 74: 74: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_31_input.mdp]: 74: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 74: that with the Verlet scheme, nstlist has no effect on the accuracy of 74: your simulation. 74: 74: 74: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_31_input.mdp]: 74: Setting nstcalcenergy (100) equal to nstenergy (4) 74: 74: Generating 1-4 interactions: fudge = 0.5 74: Number of degrees of freedom in T-Coupling group System is 79.00 74: 74: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_31_input.mdp]: 74: You are using a plain Coulomb cut-off, which might produce artifacts. 74: You might want to consider using PME electrostatics. 74: 74: 74: 74: There were 3 NOTEs 74: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_31_sim.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 74: Changing nstlist from 8 to 20, rlist from 0.757 to 0.863 74: 74: Using 1 MPI thread 74: Using 2 OpenMP threads 74: 74: 74: NOTE: The number of threads is not equal to the number of (logical) cpus 74: and the -pin option is set to auto: will not pin threads to cpus. 74: This can lead to significant performance degradation. 74: Consider using -pin on (and -pinoffset in case you run multiple jobs). 74: starting mdrun '30 atom system in water' 74: 16 steps, 0.0 ps. 74: Generated 2485 of the 2485 non-bonded parameter combinations 74: 74: Generated 2485 of the 2485 1-4 parameter combinations 74: 74: Excluding 3 bonded neighbours molecule type 'nonanol' 74: 74: turning H bonds into constraints... 74: 74: Excluding 2 bonded neighbours molecule type 'SOL' 74: 74: turning H bonds into constraints... 74: 74: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/nonanol_vacuo.gro' 74: 74: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 74: 74: Calculated rlist for 1x1 atom pair-list as 0.764 nm, buffer size 0.064 nm 74: 74: Set rlist, assuming 4x4 atom pair-list, to 0.757 nm, buffer size 0.057 nm 74: 74: Note that mdrun will redetermine rlist based on the actual pair-list setup 74: 74: This run will generate roughly 0 Mb of data 74: 74: Writing final coordinates. 74: 74: Core t (s) Wall t (s) (%) 74: Time: 0.070 0.035 198.0 74: (ns/day) (hour/ns) 74: Performance: 41.580 0.577 74: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_31_sim.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 74: Changing nstlist from 8 to 20, rlist from 0.757 to 0.863 74: 74: Using 1 MPI thread 74: Using 2 OpenMP threads 74: 74: 74: NOTE: The number of threads is not equal to the number of (logical) cpus 74: and the -pin option is set to auto: will not pin threads to cpus. 74: This can lead to significant performance degradation. 74: Consider using -pin on (and -pinoffset in case you run multiple jobs). 74: starting md rerun '30 atom system in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_31_sim1.trr' 74: 74: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 74: 74: NOTE: 30 % of the run time was spent in pair search, 74: you might want to increase nstlist (this has no effect on accuracy) 74: 74: Core t (s) Wall t (s) (%) 74: Time: 0.015 0.008 186.6 74: (ns/day) (hour/ns) 74: Performance: 183.920 0.130 74: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_31_sim1.edr as single precision energy file 74: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_31_sim2.edr as single precision energy file 74: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 74: 74: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/31 (277 ms) 74: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/32 74: 74: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_32_input.mdp]: 74: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 74: that with the Verlet scheme, nstlist has no effect on the accuracy of 74: your simulation. 74: 74: 74: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_32_input.mdp]: 74: Setting nstcalcenergy (100) equal to nstenergy (4) 74: 74: Generating 1-4 interactions: fudge = 0.5 74: Number of degrees of freedom in T-Coupling group System is 79.00 74: 74: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_32_input.mdp]: 74: You are using a plain Coulomb cut-off, which might produce artifacts. 74: You might want to consider using PME electrostatics. 74: 74: 74: 74: There were 3 NOTEs 74: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_32_sim.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 74: Changing nstlist from 8 to 20, rlist from 0.757 to 0.863 74: 74: Using 1 MPI thread 74: Using 2 OpenMP threads 74: 74: 74: NOTE: The number of threads is not equal to the number of (logical) cpus 74: and the -pin option is set to auto: will not pin threads to cpus. 74: This can lead to significant performance degradation. 74: Consider using -pin on (and -pinoffset in case you run multiple jobs). 74: starting mdrun '30 atom system in water' 74: 16 steps, 0.0 ps. 74: Generated 2485 of the 2485 non-bonded parameter combinations 74: 74: Generated 2485 of the 2485 1-4 parameter combinations 74: 74: Excluding 3 bonded neighbours molecule type 'nonanol' 74: 74: turning H bonds into constraints... 74: 74: Excluding 2 bonded neighbours molecule type 'SOL' 74: 74: turning H bonds into constraints... 74: 74: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/nonanol_vacuo.gro' 74: 74: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 74: 74: Calculated rlist for 1x1 atom pair-list as 0.764 nm, buffer size 0.064 nm 74: 74: Set rlist, assuming 4x4 atom pair-list, to 0.757 nm, buffer size 0.057 nm 74: 74: Note that mdrun will redetermine rlist based on the actual pair-list setup 74: 74: This run will generate roughly 0 Mb of data 74: 74: Writing final coordinates. 74: 74: Core t (s) Wall t (s) (%) 74: Time: 0.104 0.052 198.6 74: (ns/day) (hour/ns) 74: Performance: 28.178 0.852 74: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_32_sim.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 74: Changing nstlist from 8 to 20, rlist from 0.757 to 0.863 74: 74: Using 1 MPI thread 74: Using 2 OpenMP threads 74: 74: 74: NOTE: The number of threads is not equal to the number of (logical) cpus 74: and the -pin option is set to auto: will not pin threads to cpus. 74: This can lead to significant performance degradation. 74: Consider using -pin on (and -pinoffset in case you run multiple jobs). 74: starting md rerun '30 atom system in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_32_sim1.trr' 74: 74: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 74: 74: NOTE: 20 % of the run time was spent in pair search, 74: you might want to increase nstlist (this has no effect on accuracy) 74: 74: Core t (s) Wall t (s) (%) 74: Time: 0.025 0.013 189.9 74: (ns/day) (hour/ns) 74: Performance: 110.561 0.217 74: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_32_sim1.edr as single precision energy file 74: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_32_sim2.edr as single precision energy file 74: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 74: 74: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/32 (303 ms) 74: [----------] 33 tests from MdrunIsReproduced/MdrunRerunFreeEnergyTest (7122 ms total) 74: 74: [----------] Global test environment tear-down 74: [==========] 46 tests from 3 test suites ran. (28015 ms total) 74: [ PASSED ] 46 tests. 74/92 Test #74: MdrunNonIntegratorTests ................... Passed 28.11 sec test 75 Start 75: MdrunTpiTests 75: Test command: /build/reproducible-path/gromacs-2025.1/build/basic/bin/mdrun-tpi-test "--gtest_output=xml:/build/reproducible-path/gromacs-2025.1/build/basic/Testing/Temporary/MdrunTpiTests.xml" 75: Working Directory: /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests 75: Test timeout computed to be: 600 75: [==========] Running 3 tests from 1 test suite. 75: [----------] Global test environment set-up. 75: [----------] 3 tests from Simple/TpiTest 75: [ RUN ] Simple/TpiTest.ReproducesOutput/0 75: Generating 1-4 interactions: fudge = 0.5 75: Number of degrees of freedom in T-Coupling group System is 1308.00 75: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/Simple_TpiTest_ReproducesOutput_0.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 75: TPI is not implemented for GPUs. 75: 75: Using 1 MPI thread 75: Using 1 OpenMP thread 75: 75: 75: NOTE: Thread affinity was not set. 75: Reading frames from gro file '216 water molecules', 648 atoms. 75: Reading frame 0 time 0.000 mu 6.291e+01 6.291e+01 75: Last frame 0 time 0.000 75: Generated 331705 of the 331705 non-bonded parameter combinations 75: 75: Generated 331705 of the 331705 1-4 parameter combinations 75: 75: Excluding 2 bonded neighbours molecule type 'SOL' 75: 75: Excluding 3 bonded neighbours molecule type 'methane' 75: Analysing residue names: 75: There are: 216 Water residues 75: There are: 1 Other residues 75: Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups... 75: 75: This run will generate roughly 0 Mb of data 75: [ OK ] Simple/TpiTest.ReproducesOutput/0 (5014 ms) 75: [ RUN ] Simple/TpiTest.ReproducesOutput/1 75: Generating 1-4 interactions: fudge = 0.5 75: Number of degrees of freedom in T-Coupling group System is 1308.00 75: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/Simple_TpiTest_ReproducesOutput_1.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 75: TPI is not implemented for GPUs. 75: 75: Using 1 MPI thread 75: Using 1 OpenMP thread 75: 75: 75: NOTE: Thread affinity was not set. 75: Reading frames from gro file '216 water molecules', 648 atoms. 75: Reading frame 0 time 0.000 mu 4.535e+01 4.535e+01 75: Last frame 0 time 0.000 75: Generated 331705 of the 331705 non-bonded parameter combinations 75: 75: Generated 331705 of the 331705 1-4 parameter combinations 75: 75: Excluding 2 bonded neighbours molecule type 'SOL' 75: 75: Excluding 3 bonded neighbours molecule type 'methane' 75: Analysing residue names: 75: There are: 216 Water residues 75: There are: 1 Other residues 75: Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups... 75: 75: This run will generate roughly 0 Mb of data 75: [ OK ] Simple/TpiTest.ReproducesOutput/1 (4959 ms) 75: [ RUN ] Simple/TpiTest.ReproducesOutput/2 75: Generating 1-4 interactions: fudge = 0.5 75: Number of degrees of freedom in T-Coupling group System is 1308.00 75: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/Simple_TpiTest_ReproducesOutput_2.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 75: TPI is not implemented for GPUs. 75: 75: Using 1 MPI thread 75: Using 1 OpenMP thread 75: 75: 75: NOTE: Thread affinity was not set. 75: Reading frames from gro file '216 water molecules', 648 atoms. 75: Reading frame 0 time 0.000 mu 6.203e+01 6.203e+01 75: Last frame 0 time 0.000 75: Generated 331705 of the 331705 non-bonded parameter combinations 75: 75: Generated 331705 of the 331705 1-4 parameter combinations 75: 75: Excluding 2 bonded neighbours molecule type 'SOL' 75: 75: Excluding 3 bonded neighbours molecule type 'methane' 75: Analysing residue names: 75: There are: 216 Water residues 75: There are: 1 Other residues 75: Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups... 75: 75: This run will generate roughly 0 Mb of data 75: [ OK ] Simple/TpiTest.ReproducesOutput/2 (4983 ms) 75: [----------] 3 tests from Simple/TpiTest (14957 ms total) 75: 75: [----------] Global test environment tear-down 75: [==========] 3 tests from 1 test suite ran. (15016 ms total) 75: [ PASSED ] 3 tests. 75/92 Test #75: MdrunTpiTests ............................. Passed 15.11 sec test 76 Start 76: MdrunMpiTests 76: Test command: /build/reproducible-path/gromacs-2025.1/build/basic/bin/mdrun-mpi-test "-ntomp" "2" "-ntmpi" "2" "--gtest_output=xml:/build/reproducible-path/gromacs-2025.1/build/basic/Testing/Temporary/MdrunMpiTests.xml" 76: Working Directory: /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests 76: Test timeout computed to be: 600 76: [==========] Running 16 tests from 2 test suites. 76: [----------] Global test environment set-up. 76: [----------] 4 tests from MimicTest 76: [ RUN ] MimicTest.OneQuantumMol 76: 76: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_OneQuantumMol_input.mdp]: 76: For a correct single-point energy evaluation with nsteps = 0, use 76: continuation = yes to avoid constraining the input coordinates. 76: 76: Generating 1-4 interactions: fudge = 0.5 76: Number of degrees of freedom in T-Coupling group rest is 21.00 76: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 76: 76: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_OneQuantumMol_input.mdp]: 76: NVE simulation with an initial temperature of zero: will use a Verlet 76: buffer of 10%. Check your energy drift! 76: 76: 76: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_OneQuantumMol_input.mdp]: 76: You are using a plain Coulomb cut-off, which might produce artifacts. 76: You might want to consider using PME electrostatics. 76: 76: 76: 76: There were 3 NOTEs 76: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_OneQuantumMol.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 76: Can not increase nstlist because an NVE ensemble is used 76: Using 2 MPI threads 76: Using 2 OpenMP threads per tMPI thread 76: 76: starting md rerun 'Generated by gmx solvate', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/4water.gro' 76: 76: Reading frames from gro file 'Generated by gmx solvate', 12 atoms. 76: Reading frame 0 time 0.000 Last frame 0 time 0.000 76: 76: NOTE: 15 % of the run time was spent in domain decomposition, 76: 9 % of the run time was spent in pair search, 76: you might want to increase nstlist (this has no effect on accuracy) 76: 76: Core t (s) Wall t (s) (%) 76: Time: 0.006 0.002 377.9 76: (ns/day) (hour/ns) 76: Performance: 56.601 0.424 76: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_OneQuantumMol.edr as single precision energy file 76: Reading energy frame 0 time 0.000 Last energy frame read 0 time 0.000 Setting the LD random seed to -25756345 76: 76: Generated 10 of the 10 non-bonded parameter combinations 76: 76: Generated 10 of the 10 1-4 parameter combinations 76: 76: Excluding 2 bonded neighbours molecule type 'SOL' 76: 76: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/4water.gro', all velocities are zero 76: 76: This run will generate roughly 0 Mb of data 76: [ OK ] MimicTest.OneQuantumMol (91 ms) 76: [ RUN ] MimicTest.AllQuantumMol 76: 76: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_AllQuantumMol_input.mdp]: 76: For a correct single-point energy evaluation with nsteps = 0, use 76: continuation = yes to avoid constraining the input coordinates. 76: 76: Generating 1-4 interactions: fudge = 0.5 76: Number of degrees of freedom in T-Coupling group rest is 21.00 76: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 76: 76: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_AllQuantumMol_input.mdp]: 76: NVE simulation with an initial temperature of zero: will use a Verlet 76: buffer of 10%. Check your energy drift! 76: 76: 76: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_AllQuantumMol_input.mdp]: 76: You are using a plain Coulomb cut-off, which might produce artifacts. 76: You might want to consider using PME electrostatics. 76: 76: 76: 76: There were 3 NOTEs 76: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_AllQuantumMol.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 76: Can not increase nstlist because an NVE ensemble is used 76: Using 2 MPI threads 76: 76: Non-default thread affinity set, disabling internal thread affinity 76: 76: Using 2 OpenMP threads per tMPI thread 76: 76: starting md rerun 'Generated by gmx solvate', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/4water.gro' 76: 76: Reading frames from gro file 'Generated by gmx solvate', 12 atoms. 76: Reading frame 0 time 0.000 Last frame 0 time 0.000 76: 76: NOTE: 77 % of the run time was spent in domain decomposition, 76: 5 % of the run time was spent in pair search, 76: you might want to increase nstlist (this has no effect on accuracy) 76: 76: Core t (s) Wall t (s) (%) 76: Time: 1.358 0.351 386.8 76: (ns/day) (hour/ns) 76: Performance: 0.246 97.519 76: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_AllQuantumMol.edr as single precision energy file 76: Reading energy frame 0 time 0.000 Last energy frame read 0 time 0.000 Setting the LD random seed to -273682950 76: 76: Generated 10 of the 10 non-bonded parameter combinations 76: 76: Generated 10 of the 10 1-4 parameter combinations 76: 76: Excluding 2 bonded neighbours molecule type 'SOL' 76: 76: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/4water.gro', all velocities are zero 76: 76: This run will generate roughly 0 Mb of data 76: [ OK ] MimicTest.AllQuantumMol (1135 ms) 76: [ RUN ] MimicTest.TwoQuantumMol 76: 76: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_TwoQuantumMol_input.mdp]: 76: For a correct single-point energy evaluation with nsteps = 0, use 76: continuation = yes to avoid constraining the input coordinates. 76: 76: Generating 1-4 interactions: fudge = 0.5 76: Number of degrees of freedom in T-Coupling group rest is 21.00 76: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 76: 76: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_TwoQuantumMol_input.mdp]: 76: NVE simulation with an initial temperature of zero: will use a Verlet 76: buffer of 10%. Check your energy drift! 76: 76: 76: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_TwoQuantumMol_input.mdp]: 76: You are using a plain Coulomb cut-off, which might produce artifacts. 76: You might want to consider using PME electrostatics. 76: 76: 76: 76: There were 3 NOTEs 76: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_TwoQuantumMol.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 76: Can not increase nstlist because an NVE ensemble is used 76: Using 2 MPI threads 76: 76: Non-default thread affinity set, disabling internal thread affinity 76: 76: Using 2 OpenMP threads per tMPI thread 76: 76: starting md rerun 'Generated by gmx solvate', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/4water.gro' 76: 76: Reading frames from gro file 'Generated by gmx solvate', 12 atoms. 76: Reading frame 0 time 0.000 Last frame 0 time 0.000 76: 76: NOTE: 80 % of the run time was spent in domain decomposition, 76: 5 % of the run time was spent in pair search, 76: you might want to increase nstlist (this has no effect on accuracy) 76: 76: Core t (s) Wall t (s) (%) 76: Time: 1.292 0.335 385.8 76: (ns/day) (hour/ns) 76: Performance: 0.258 93.065 76: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_TwoQuantumMol.edr as single precision energy file 76: Reading energy frame 0 time 0.000 Last energy frame read 0 time 0.000 Setting the LD random seed to -135331 76: 76: Generated 10 of the 10 non-bonded parameter combinations 76: 76: Generated 10 of the 10 1-4 parameter combinations 76: 76: Excluding 2 bonded neighbours molecule type 'SOL' 76: 76: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/4water.gro', all velocities are zero 76: 76: This run will generate roughly 0 Mb of data 76: [ OK ] MimicTest.TwoQuantumMol (981 ms) 76: [ RUN ] MimicTest.BondCuts 76: 76: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_BondCuts_input.mdp]: 76: For a correct single-point energy evaluation with nsteps = 0, use 76: continuation = yes to avoid constraining the input coordinates. 76: 76: Generating 1-4 interactions: fudge = 0.5 76: Number of degrees of freedom in T-Coupling group rest is 66.00 76: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 76: 76: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_BondCuts_input.mdp]: 76: NVE simulation: will use the initial temperature of 300.368 K for 76: determining the Verlet buffer size 76: 76: 76: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_BondCuts_input.mdp]: 76: You are using a plain Coulomb cut-off, which might produce artifacts. 76: You might want to consider using PME electrostatics. 76: 76: 76: 76: There were 3 NOTEs 76: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_BondCuts.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 76: Can not increase nstlist because an NVE ensemble is used 76: Using 2 MPI threads 76: 76: Non-default thread affinity set, disabling internal thread affinity 76: 76: Using 2 OpenMP threads per tMPI thread 76: 76: starting md rerun 'UNNAMED in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/ala.gro' 76: 76: Reading frames from gro file 'Alanine dipeptide in water', 23 atoms. 76: Reading frame 0 time 0.000 Last frame 0 time 0.000 76: 76: NOTE: 66 % of the run time was spent in domain decomposition, 76: 7 % of the run time was spent in pair search, 76: you might want to increase nstlist (this has no effect on accuracy) 76: 76: NOTE: 5 % of the run time was spent communicating energies, 76: you might want to increase some nst* mdp options 76: 76: Core t (s) Wall t (s) (%) 76: Time: 1.205 0.313 384.7 76: (ns/day) (hour/ns) 76: Performance: 0.276 86.978 76: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_BondCuts.edr as single precision energy file 76: Reading energy frame 0 time 0.000 Last energy frame read 0 time 0.000 Setting the LD random seed to 2038100311 76: 76: Generated 2211 of the 2211 non-bonded parameter combinations 76: 76: Generated 2211 of the 2211 1-4 parameter combinations 76: 76: Excluding 3 bonded neighbours molecule type 'Protein_chain_A' 76: 76: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/ala.gro' 76: 76: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 300.368 K 76: 76: Calculated rlist for 1x1 atom pair-list as 1.048 nm, buffer size 0.048 nm 76: 76: Set rlist, assuming 4x4 atom pair-list, to 1.036 nm, buffer size 0.036 nm 76: 76: Note that mdrun will redetermine rlist based on the actual pair-list setup 76: 76: This run will generate roughly 0 Mb of data 76: [ OK ] MimicTest.BondCuts (1137 ms) 76: [----------] 4 tests from MimicTest (3346 ms total) 76: 76: [----------] 12 tests from DomainDecomposition/DomDecSpecialCasesTest 76: Generating 1-4 interactions: fudge = 0.5 76: Number of degrees of freedom in T-Coupling group rest is 9.00 76: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 76: 76: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/DomainDecomposition_DomDecSpecialCasesTest_input.mdp]: 76: NVE simulation with an initial temperature of zero: will use a Verlet 76: buffer of 10%. Check your energy drift! 76: 76: 76: There was 1 NOTE 76: Generating 1-4 interactions: fudge = 0.5 76: Number of degrees of freedom in T-Coupling group System is 9.00 76: Generating 1-4 interactions: fudge = 0.5 76: Number of degrees of freedom in T-Coupling group rest is 9.00 76: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 76: 76: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/DomainDecomposition_DomDecSpecialCasesTest_input.mdp]: 76: NVE simulation with an initial temperature of zero: will use a Verlet 76: buffer of 10%. Check your energy drift! 76: 76: 76: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/DomainDecomposition_DomDecSpecialCasesTest_input.mdp]: 76: The optimal PME mesh load for parallel simulations is below 0.5 76: and for highly parallel simulations between 0.25 and 0.33, 76: for higher performance, increase the cut-off and the PME grid spacing. 76: 76: 76: 76: There were 2 NOTEs 76: Generating 1-4 interactions: fudge = 0.5 76: Number of degrees of freedom in T-Coupling group System is 9.00 76: 76: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/DomainDecomposition_DomDecSpecialCasesTest_input.mdp]: 76: The optimal PME mesh load for parallel simulations is below 0.5 76: and for highly parallel simulations between 0.25 and 0.33, 76: for higher performance, increase the cut-off and the PME grid spacing. 76: 76: 76: 76: There was 1 NOTE 76: Setting the LD random seed to -1147207681 76: 76: Generated 3 of the 3 non-bonded parameter combinations 76: 76: Generated 3 of the 3 1-4 parameter combinations 76: 76: Excluding 2 bonded neighbours molecule type 'SOL' 76: 76: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/spc2_and_vacuum.gro', all velocities are zero 76: 76: This run will generate roughly 0 Mb of data 76: Setting the LD random seed to 2012954047 76: 76: Generated 3 of the 3 non-bonded parameter combinations 76: 76: Generated 3 of the 3 1-4 parameter combinations 76: 76: Excluding 2 bonded neighbours molecule type 'SOL' 76: 76: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/spc2_and_vacuum.gro', all velocities are zero 76: 76: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 76: 76: Calculated rlist for 1x1 atom pair-list as 1.017 nm, buffer size 0.017 nm 76: 76: Set rlist, assuming 4x4 atom pair-list, to 1.005 nm, buffer size 0.005 nm 76: 76: Note that mdrun will redetermine rlist based on the actual pair-list setup 76: 76: This run will generate roughly 0 Mb of data 76: Setting the LD random seed to 934254575 76: 76: Generated 3 of the 3 non-bonded parameter combinations 76: 76: Generated 3 of the 3 1-4 parameter combinations 76: 76: Excluding 2 bonded neighbours molecule type 'SOL' 76: 76: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/spc2_and_vacuum.gro', all velocities are zero 76: 76: The largest distance between excluded atoms is 0.164 nm between atom 2 and 3 76: Calculating fourier grid dimensions for X Y Z 76: Using a fourier grid of 28x28x28, spacing 0.108 0.108 0.108 76: 76: Estimate for the relative computational load of the PME mesh part: 1.00 76: 76: This run will generate roughly 0 Mb of data 76: Setting the LD random seed to -8520337 76: 76: Generated 3 of the 3 non-bonded parameter combinations 76: 76: Generated 3 of the 3 1-4 parameter combinations 76: 76: Excluding 2 bonded neighbours molecule type 'SOL' 76: 76: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/spc2_and_vacuum.gro', all velocities are zero 76: 76: The largest distance between excluded atoms is 0.164 nm between atom 2 and 3 76: 76: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 76: 76: Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm 76: 76: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm 76: 76: Note that mdrun will redetermine rlist based on the actual pair-list setup 76: Calculating fourier grid dimensions for X Y Z 76: Using a fourier grid of 28x28x28, spacing 0.108 0.108 0.108 76: 76: Estimate for the relative computational load of the PME mesh part: 1.00 76: 76: This run will generate roughly 0 Mb of data 76: [ RUN ] DomainDecomposition/DomDecSpecialCasesTest.EmptyDomain/RF_No_coupling_nbcpu_pmecpu_updatecpu_npme0 76: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/DomainDecomposition_DomDecSpecialCasesTest_RF_No.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 76: Can not increase nstlist because an NVE ensemble is used 76: Using 2 MPI threads 76: 76: Non-default thread affinity set, disabling internal thread affinity 76: 76: Using 2 OpenMP threads per tMPI thread 76: 76: starting mdrun 'spc2' 76: 20 steps, 0.0 ps. 76: 76: Writing final coordinates. 76: 76: 76: Dynamic load balancing report: 76: DLB was turned on during the run due to measured imbalance. 76: Average load imbalance: 17.6%. 76: The balanceable part of the MD step is 38%, load imbalance is computed from this. 76: Part of the total run time spent waiting due to load imbalance: 6.7%. 76: Steps where the load balancing was limited by -rdd, -rcon and/or -dds: X 0 % 76: 76: NOTE: 6.7 % of the available CPU time was lost due to load imbalance 76: in the domain decomposition. 76: You can consider manually changing the decomposition (option -dd); 76: e.g. by using fewer domains along the box dimension in which there is 76: considerable inhomogeneity in the simulated system. 76: 76: NOTE: 18 % of the run time was spent in domain decomposition, 76: 4 % of the run time was spent in pair search, 76: you might want to increase nstlist (this has no effect on accuracy) 76: 76: NOTE: 11 % of the run time was spent communicating energies, 76: you might want to increase some nst* mdp options 76: 76: Core t (s) Wall t (s) (%) 76: Time: 4.539 1.149 394.9 76: (ns/day) (hour/ns) 76: Performance: 1.579 15.204 76: [ OK ] DomainDecomposition/DomDecSpecialCasesTest.EmptyDomain/RF_No_coupling_nbcpu_pmecpu_updatecpu_npme0 (1807 ms) 76: [ RUN ] DomainDecomposition/DomDecSpecialCasesTest.EmptyDomain/RF_No_coupling_nbcpu_pmecpu_updatecpu_npme1 76: ./src/programs/mdrun/tests/domain_decomposition.cpp:385: Skipped 76: Test configuration is invalid: 76: Cannot have separate PME ranks when PME is not used 76: 76: [ SKIPPED ] DomainDecomposition/DomDecSpecialCasesTest.EmptyDomain/RF_No_coupling_nbcpu_pmecpu_updatecpu_npme1 (1 ms) 76: [ RUN ] DomainDecomposition/DomDecSpecialCasesTest.EmptyDomain/RF_No_coupling_nbcpu_pmecpu_updatecpu_npme2 76: ./src/programs/mdrun/tests/domain_decomposition.cpp:385: Skipped 76: Test configuration is invalid: 76: Cannot have separate PME ranks when PME is not used 76: Cannot use two separate PME ranks when there are less than four ranks total 76: 76: [ SKIPPED ] DomainDecomposition/DomDecSpecialCasesTest.EmptyDomain/RF_No_coupling_nbcpu_pmecpu_updatecpu_npme2 (0 ms) 76: [ RUN ] DomainDecomposition/DomDecSpecialCasesTest.EmptyDomain/RF_TemperatureAndPressure_coupling_nbcpu_pmecpu_updatecpu_npme0 76: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/DomainDecomposition_DomDecSpecialCasesTest_RF_TemperatureAndPressure.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 76: Changing nstlist from 10 to 50, rlist from 1.005 to 1.136 76: 76: Using 2 MPI threads 76: 76: Non-default thread affinity set, disabling internal thread affinity 76: 76: Using 2 OpenMP threads per tMPI thread 76: 76: starting mdrun 'spc2' 76: 20 steps, 0.0 ps. 76: 76: Writing final coordinates. 76: 76: NOTE: 13 % of the run time was spent communicating energies, 76: you might want to increase some nst* mdp options 76: 76: Core t (s) Wall t (s) (%) 76: Time: 3.959 1.000 395.9 76: (ns/day) (hour/ns) 76: Performance: 1.815 13.227 76: [ OK ] DomainDecomposition/DomDecSpecialCasesTest.EmptyDomain/RF_TemperatureAndPressure_coupling_nbcpu_pmecpu_updatecpu_npme0 (1674 ms) 76: [ RUN ] DomainDecomposition/DomDecSpecialCasesTest.EmptyDomain/RF_TemperatureAndPressure_coupling_nbcpu_pmecpu_updatecpu_npme1 76: ./src/programs/mdrun/tests/domain_decomposition.cpp:385: Skipped 76: Test configuration is invalid: 76: Cannot have separate PME ranks when PME is not used 76: 76: [ SKIPPED ] DomainDecomposition/DomDecSpecialCasesTest.EmptyDomain/RF_TemperatureAndPressure_coupling_nbcpu_pmecpu_updatecpu_npme1 (0 ms) 76: [ RUN ] DomainDecomposition/DomDecSpecialCasesTest.EmptyDomain/RF_TemperatureAndPressure_coupling_nbcpu_pmecpu_updatecpu_npme2 76: ./src/programs/mdrun/tests/domain_decomposition.cpp:385: Skipped 76: Test configuration is invalid: 76: Cannot have separate PME ranks when PME is not used 76: Cannot use two separate PME ranks when there are less than four ranks total 76: 76: [ SKIPPED ] DomainDecomposition/DomDecSpecialCasesTest.EmptyDomain/RF_TemperatureAndPressure_coupling_nbcpu_pmecpu_updatecpu_npme2 (0 ms) 76: [ RUN ] DomainDecomposition/DomDecSpecialCasesTest.EmptyDomain/PME_No_coupling_nbcpu_pmecpu_updatecpu_npme0 76: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/DomainDecomposition_DomDecSpecialCasesTest_PME_No.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 76: Can not increase nstlist because an NVE ensemble is used 76: Using 2 MPI threads 76: 76: Non-default thread affinity set, disabling internal thread affinity 76: 76: Using 2 OpenMP threads per tMPI thread 76: 76: starting mdrun 'spc2' 76: 20 steps, 0.0 ps. 76: 76: Writing final coordinates. 76: 76: 76: Dynamic load balancing report: 76: DLB was off during the run due to low measured imbalance. 76: Average load imbalance: 7.1%. 76: The balanceable part of the MD step is 15%, load imbalance is computed from this. 76: Part of the total run time spent waiting due to load imbalance: 1.1%. 76: 76: 76: Core t (s) Wall t (s) (%) 76: Time: 11.271 2.828 398.6 76: (ns/day) (hour/ns) 76: Performance: 0.642 37.406 76: [ OK ] DomainDecomposition/DomDecSpecialCasesTest.EmptyDomain/PME_No_coupling_nbcpu_pmecpu_updatecpu_npme0 (3563 ms) 76: [ RUN ] DomainDecomposition/DomDecSpecialCasesTest.EmptyDomain/PME_No_coupling_nbcpu_pmecpu_updatecpu_npme1 76: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/DomainDecomposition_DomDecSpecialCasesTest_PME_No.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 76: Can not increase nstlist because an NVE ensemble is used 76: Using 2 MPI threads 76: 76: Non-default thread affinity set, disabling internal thread affinity 76: 76: Using 2 OpenMP threads per tMPI thread 76: 76: starting mdrun 'spc2' 76: 20 steps, 0.0 ps. 76: 76: Writing final coordinates. 76: 76: Core t (s) Wall t (s) (%) 76: Time: 5.092 1.294 393.6 76: (ns/day) (hour/ns) 76: Performance: 1.402 17.115 76: [ OK ] DomainDecomposition/DomDecSpecialCasesTest.EmptyDomain/PME_No_coupling_nbcpu_pmecpu_updatecpu_npme1 (1854 ms) 76: [ RUN ] DomainDecomposition/DomDecSpecialCasesTest.EmptyDomain/PME_No_coupling_nbcpu_pmecpu_updatecpu_npme2 76: ./src/programs/mdrun/tests/domain_decomposition.cpp:385: Skipped 76: Test configuration is invalid: 76: Cannot use two separate PME ranks when there are less than four ranks total 76: 76: [ SKIPPED ] DomainDecomposition/DomDecSpecialCasesTest.EmptyDomain/PME_No_coupling_nbcpu_pmecpu_updatecpu_npme2 (1 ms) 76: [ RUN ] DomainDecomposition/DomDecSpecialCasesTest.EmptyDomain/PME_TemperatureAndPressure_coupling_nbcpu_pmecpu_updatecpu_npme0 76: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/DomainDecomposition_DomDecSpecialCasesTest_PME_TemperatureAndPressure.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 76: Changing nstlist from 10 to 100, rlist from 1 to 1 76: 76: Using 2 MPI threads 76: 76: Non-default thread affinity set, disabling internal thread affinity 76: 76: Using 2 OpenMP threads per tMPI thread 76: 76: starting mdrun 'spc2' 76: 20 steps, 0.0 ps. 76: 76: Writing final coordinates. 76: 76: Core t (s) Wall t (s) (%) 76: Time: 10.618 2.673 397.2 76: (ns/day) (hour/ns) 76: Performance: 0.679 35.362 76: [ OK ] DomainDecomposition/DomDecSpecialCasesTest.EmptyDomain/PME_TemperatureAndPressure_coupling_nbcpu_pmecpu_updatecpu_npme0 (3571 ms) 76: [ RUN ] DomainDecomposition/DomDecSpecialCasesTest.EmptyDomain/PME_TemperatureAndPressure_coupling_nbcpu_pmecpu_updatecpu_npme1 76: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/DomainDecomposition_DomDecSpecialCasesTest_PME_TemperatureAndPressure.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 76: Changing nstlist from 10 to 100, rlist from 1 to 1 76: 76: Using 2 MPI threads 76: 76: Non-default thread affinity set, disabling internal thread affinity 76: 76: Using 2 OpenMP threads per tMPI thread 76: 76: starting mdrun 'spc2' 76: 20 steps, 0.0 ps. 76: 76: Writing final coordinates. 76: 76: Core t (s) Wall t (s) (%) 76: Time: 4.489 1.144 392.5 76: (ns/day) (hour/ns) 76: Performance: 1.586 15.129 76: [ OK ] DomainDecomposition/DomDecSpecialCasesTest.EmptyDomain/PME_TemperatureAndPressure_coupling_nbcpu_pmecpu_updatecpu_npme1 (1755 ms) 76: [ RUN ] DomainDecomposition/DomDecSpecialCasesTest.EmptyDomain/PME_TemperatureAndPressure_coupling_nbcpu_pmecpu_updatecpu_npme2 76: ./src/programs/mdrun/tests/domain_decomposition.cpp:385: Skipped 76: Test configuration is invalid: 76: Cannot use two separate PME ranks when there are less than four ranks total 76: 76: [ SKIPPED ] DomainDecomposition/DomDecSpecialCasesTest.EmptyDomain/PME_TemperatureAndPressure_coupling_nbcpu_pmecpu_updatecpu_npme2 (1 ms) 76: [----------] 12 tests from DomainDecomposition/DomDecSpecialCasesTest (14233 ms total) 76: 76: [----------] Global test environment tear-down 76: [==========] 16 tests from 2 test suites ran. (17784 ms total) 76: [ PASSED ] 10 tests. 76: [ SKIPPED ] 6 tests, listed below: 76: [ SKIPPED ] DomainDecomposition/DomDecSpecialCasesTest.EmptyDomain/RF_No_coupling_nbcpu_pmecpu_updatecpu_npme1 76: [ SKIPPED ] DomainDecomposition/DomDecSpecialCasesTest.EmptyDomain/RF_No_coupling_nbcpu_pmecpu_updatecpu_npme2 76: [ SKIPPED ] DomainDecomposition/DomDecSpecialCasesTest.EmptyDomain/RF_TemperatureAndPressure_coupling_nbcpu_pmecpu_updatecpu_npme1 76: [ SKIPPED ] DomainDecomposition/DomDecSpecialCasesTest.EmptyDomain/RF_TemperatureAndPressure_coupling_nbcpu_pmecpu_updatecpu_npme2 76: [ SKIPPED ] DomainDecomposition/DomDecSpecialCasesTest.EmptyDomain/PME_No_coupling_nbcpu_pmecpu_updatecpu_npme2 76: [ SKIPPED ] DomainDecomposition/DomDecSpecialCasesTest.EmptyDomain/PME_TemperatureAndPressure_coupling_nbcpu_pmecpu_updatecpu_npme2 76/92 Test #76: MdrunMpiTests ............................. Passed 17.87 sec test 77 Start 77: MdrunMultiSimTests 77: Test command: /build/reproducible-path/gromacs-2025.1/build/basic/bin/mdrun-multisim-test "-ntmpi" "4" "--gtest_output=xml:/build/reproducible-path/gromacs-2025.1/build/basic/Testing/Temporary/MdrunMultiSimTests.xml" 77: Working Directory: /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests 77: Test timeout computed to be: 600 77: [==========] Running 2 tests from 1 test suite. 77: [----------] Global test environment set-up. 77: [----------] 2 tests from InNvt/MultiSimTerminationTest 77: [ RUN ] InNvt/MultiSimTerminationTest.WritesCheckpointAfterMaxhTerminationAndThenRestarts/0 77: [ OK ] InNvt/MultiSimTerminationTest.WritesCheckpointAfterMaxhTerminationAndThenRestarts/0 (0 ms) 77: [ RUN ] InNvt/MultiSimTerminationTest.WritesCheckpointAfterMaxhTerminationAndThenRestarts/1 77: [ OK ] InNvt/MultiSimTerminationTest.WritesCheckpointAfterMaxhTerminationAndThenRestarts/1 (0 ms) 77: [----------] 2 tests from InNvt/MultiSimTerminationTest (1 ms total) 77: 77: [----------] Global test environment tear-down 77: [==========] 2 tests from 1 test suite ran. (50 ms total) 77: [ PASSED ] 2 tests. 77: 77: YOU HAVE 4 DISABLED TESTS 77: 77/92 Test #77: MdrunMultiSimTests ........................ Passed 0.13 sec test 78 Start 78: MdrunMultiSimReplexTests 78: Test command: /build/reproducible-path/gromacs-2025.1/build/basic/bin/mdrun-multisim-replex-test "-ntmpi" "4" "--gtest_output=xml:/build/reproducible-path/gromacs-2025.1/build/basic/Testing/Temporary/MdrunMultiSimReplexTests.xml" 78: Working Directory: /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests 78: Test timeout computed to be: 600 78: [==========] Running 1 test from 1 test suite. 78: [----------] Global test environment set-up. 78: [----------] 1 test from InNvt/ReplicaExchangeTerminationTest 78: [ RUN ] InNvt/ReplicaExchangeTerminationTest.WritesCheckpointAfterMaxhTerminationAndThenRestarts/0 78: [ OK ] InNvt/ReplicaExchangeTerminationTest.WritesCheckpointAfterMaxhTerminationAndThenRestarts/0 (0 ms) 78: [----------] 1 test from InNvt/ReplicaExchangeTerminationTest (0 ms total) 78: 78: [----------] Global test environment tear-down 78: [==========] 1 test from 1 test suite ran. (51 ms total) 78: [ PASSED ] 1 test. 78: 78: YOU HAVE 4 DISABLED TESTS 78: 78/92 Test #78: MdrunMultiSimReplexTests .................. Passed 0.13 sec test 79 Start 79: MdrunMultiSimReplexEquivalenceTests 79: Test command: /build/reproducible-path/gromacs-2025.1/build/basic/bin/mdrun-multisim-replex-equivalence-test "-ntmpi" "4" "--gtest_output=xml:/build/reproducible-path/gromacs-2025.1/build/basic/Testing/Temporary/MdrunMultiSimReplexEquivalenceTests.xml" 79: Working Directory: /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests 79: Test timeout computed to be: 600 79: [==========] Running 0 tests from 0 test suites. 79: [==========] 0 tests from 0 test suites ran. (0 ms total) 79: [ PASSED ] 0 tests. 79: 79: YOU HAVE 10 DISABLED TESTS 79: 79/92 Test #79: MdrunMultiSimReplexEquivalenceTests ....... Passed 0.08 sec test 80 Start 80: MdrunMpi1RankPmeTests 80: Test command: /build/reproducible-path/gromacs-2025.1/build/basic/bin/mdrun-mpi-pme-test "-ntomp" "2" "-ntmpi" "1" "--gtest_output=xml:/build/reproducible-path/gromacs-2025.1/build/basic/Testing/Temporary/MdrunMpi1RankPmeTests.xml" 80: Working Directory: /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests 80: Test timeout computed to be: 600 80: [==========] Running 19 tests from 1 test suite. 80: [----------] Global test environment set-up. 80: [----------] 19 tests from ReproducesEnergies/PmeTest 80: Number of degrees of freedom in T-Coupling group rest is 12.00 80: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 80: 80: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_input.mdp]: 80: NVE simulation: will use the initial temperature of 1046.791 K for 80: determining the Verlet buffer size 80: 80: 80: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_input.mdp]: 80: The optimal PME mesh load for parallel simulations is below 0.5 80: and for highly parallel simulations between 0.25 and 0.33, 80: for higher performance, increase the cut-off and the PME grid spacing. 80: 80: 80: 80: There were 2 NOTEs 80: 80: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_input.mdp]: 80: For a correct single-point energy evaluation with nsteps = 0, use 80: continuation = yes to avoid constraining the input coordinates. 80: 80: Number of degrees of freedom in T-Coupling group rest is 13.00 80: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 80: 80: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_input.mdp]: 80: NVE simulation: will use the initial temperature of 966.268 K for 80: determining the Verlet buffer size 80: 80: 80: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_input.mdp]: 80: The optimal PME mesh load for parallel simulations is below 0.5 80: and for highly parallel simulations between 0.25 and 0.33, 80: for higher performance, increase the cut-off and the PME grid spacing. 80: 80: 80: 80: There were 3 NOTEs 80: Setting the LD random seed to -1476919299 80: 80: Generated 8 of the 10 non-bonded parameter combinations 80: 80: Excluding 2 bonded neighbours molecule type 'Methanol' 80: 80: Excluding 2 bonded neighbours molecule type 'SOL' 80: 80: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/spc-and-methanol.gro' 80: 80: The largest distance between excluded atoms is 0.190 nm between atom 1 and 3 80: 80: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 1046.79 K 80: 80: Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm 80: 80: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm 80: 80: Note that mdrun will redetermine rlist based on the actual pair-list setup 80: Calculating fourier grid dimensions for X Y Z 80: Using a fourier grid of 28x28x28, spacing 0.108 0.108 0.108 80: 80: Estimate for the relative computational load of the PME mesh part: 1.00 80: 80: This run will generate roughly 0 Mb of data 80: Setting the LD random seed to -1141002387 80: 80: Generated 8 of the 10 non-bonded parameter combinations 80: 80: Excluding 2 bonded neighbours molecule type 'Methanol' 80: 80: Excluding 2 bonded neighbours molecule type 'SOL' 80: 80: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/spc-and-methanol.gro' 80: 80: Searching the wall atom type(s) 80: 80: The largest distance between excluded atoms is 0.190 nm between atom 1 and 3 80: 80: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 966.268 K 80: 80: Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm 80: 80: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm 80: 80: Note that mdrun will redetermine rlist based on the actual pair-list setup 80: Calculating fourier grid dimensions for X Y Z 80: Using a fourier grid of 28x28x128, spacing 0.108 0.108 0.118 80: 80: Estimate for the relative computational load of the PME mesh part: 1.00 80: 80: This run will generate roughly 0 Mb of data 80: [ RUN ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_0__pme_cpu 80: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_basic.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 80: Can not increase nstlist because an NVE ensemble is used 80: Using 1 MPI thread 80: Using 2 OpenMP threads 80: 80: 80: NOTE: The number of threads is not equal to the number of (logical) cpus 80: and the -pin option is set to auto: will not pin threads to cpus. 80: This can lead to significant performance degradation. 80: Consider using -pin on (and -pinoffset in case you run multiple jobs). 80: starting mdrun 'spc-and-methanol' 80: 20 steps, 0.0 ps. 80: 80: Writing final coordinates. 80: 80: Core t (s) Wall t (s) (%) 80: Time: 0.277 0.139 199.6 80: (ns/day) (hour/ns) 80: Performance: 13.081 1.835 80: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_Runs_basic__notunepme__npme_0__pme_cpu.edr as single precision energy file 80: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 17 time 0.017 Reading energy frame 18 time 0.018 Reading energy frame 19 time 0.019 Reading energy frame 20 time 0.020 Last energy frame read 20 time 0.020 [ OK ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_0__pme_cpu (203 ms) 80: [ RUN ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_0__pme_auto 80: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_basic.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 80: Can not increase nstlist because an NVE ensemble is used 80: Using 1 MPI thread 80: Using 2 OpenMP threads 80: 80: 80: NOTE: The number of threads is not equal to the number of (logical) cpus 80: and the -pin option is set to auto: will not pin threads to cpus. 80: This can lead to significant performance degradation. 80: Consider using -pin on (and -pinoffset in case you run multiple jobs). 80: starting mdrun 'spc-and-methanol' 80: 20 steps, 0.0 ps. 80: 80: Writing final coordinates. 80: 80: Core t (s) Wall t (s) (%) 80: Time: 0.291 0.146 199.7 80: (ns/day) (hour/ns) 80: Performance: 12.462 1.926 80: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_Runs_basic__notunepme__npme_0__pme_auto.edr as single precision energy file 80: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 17 time 0.017 Reading energy frame 18 time 0.018 Reading energy frame 19 time 0.019 Reading energy frame 20 time 0.020 Last energy frame read 20 time 0.020 [ OK ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_0__pme_auto (195 ms) 80: [ RUN ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_0__pme_gpu__pmefft_cpu 80: ./src/programs/mdrun/tests/pmetest.cpp:309: Skipped 80: Test is being skipped because: 80: it targets GPU execution, but no compatible devices were detected 80: PME GPU does not support: 80: Non-GPU build of GROMACS. 80: 80: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_0__pme_gpu__pmefft_cpu (0 ms) 80: [ RUN ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_0__pme_gpu__pmefft_gpu 80: ./src/programs/mdrun/tests/pmetest.cpp:309: Skipped 80: Test is being skipped because: 80: it targets GPU execution, but no compatible devices were detected 80: PME GPU does not support: 80: Non-GPU build of GROMACS. 80: 80: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_0__pme_gpu__pmefft_gpu (0 ms) 80: [ RUN ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_0__pme_gpu__pmefft_auto 80: ./src/programs/mdrun/tests/pmetest.cpp:309: Skipped 80: Test is being skipped because: 80: it targets GPU execution, but no compatible devices were detected 80: PME GPU does not support: 80: Non-GPU build of GROMACS. 80: 80: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_0__pme_gpu__pmefft_auto (0 ms) 80: [ RUN ] ReproducesEnergies/PmeTest.Runs/with_walls__notunepme__npme_0__pme_cpu 80: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_with_walls.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 80: Can not increase nstlist because an NVE ensemble is used 80: Using 1 MPI thread 80: Using 2 OpenMP threads 80: 80: 80: NOTE: The number of threads is not equal to the number of (logical) cpus 80: and the -pin option is set to auto: will not pin threads to cpus. 80: This can lead to significant performance degradation. 80: Consider using -pin on (and -pinoffset in case you run multiple jobs). 80: starting mdrun 'spc-and-methanol' 80: 0 steps, 0.0 ps. 80: 80: Core t (s) Wall t (s) (%) 80: Time: 0.081 0.041 198.3 80: (ns/day) (hour/ns) 80: Performance: 2.128 11.278 80: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_Runs_with_walls__notunepme__npme_0__pme_cpu.edr as single precision energy file 80: Reading energy frame 0 time 0.000 Last energy frame read 0 time 0.000 [ OK ] ReproducesEnergies/PmeTest.Runs/with_walls__notunepme__npme_0__pme_cpu (154 ms) 80: [ RUN ] ReproducesEnergies/PmeTest.Runs/with_walls__notunepme__npme_0__pme_gpu__pmefft_cpu 80: ./src/programs/mdrun/tests/pmetest.cpp:309: Skipped 80: Test is being skipped because: 80: it targets GPU execution, but no compatible devices were detected 80: PME GPU does not support: 80: Non-GPU build of GROMACS. 80: 80: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/with_walls__notunepme__npme_0__pme_gpu__pmefft_cpu (0 ms) 80: [ RUN ] ReproducesEnergies/PmeTest.Runs/with_walls__notunepme__npme_0__pme_gpu__pmefft_gpu 80: ./src/programs/mdrun/tests/pmetest.cpp:309: Skipped 80: Test is being skipped because: 80: it targets GPU execution, but no compatible devices were detected 80: PME GPU does not support: 80: Non-GPU build of GROMACS. 80: 80: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/with_walls__notunepme__npme_0__pme_gpu__pmefft_gpu (0 ms) 80: [ RUN ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_1__pme_cpu 80: ./src/programs/mdrun/tests/pmetest.cpp:309: Skipped 80: Test is being skipped because: 80: it targets using PME rank(s) but the simulation is using only one rank 80: 80: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_1__pme_cpu (0 ms) 80: [ RUN ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_1__pme_auto 80: ./src/programs/mdrun/tests/pmetest.cpp:309: Skipped 80: Test is being skipped because: 80: it targets using PME rank(s) but the simulation is using only one rank 80: 80: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_1__pme_auto (0 ms) 80: [ RUN ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_1__pme_gpu__pmefft_cpu 80: ./src/programs/mdrun/tests/pmetest.cpp:309: Skipped 80: Test is being skipped because: 80: it targets using PME rank(s) but the simulation is using only one rank 80: it targets GPU execution, but no compatible devices were detected 80: PME GPU does not support: 80: Non-GPU build of GROMACS. 80: 80: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_1__pme_gpu__pmefft_cpu (0 ms) 80: [ RUN ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_1__pme_gpu__pmefft_gpu 80: ./src/programs/mdrun/tests/pmetest.cpp:309: Skipped 80: Test is being skipped because: 80: it targets using PME rank(s) but the simulation is using only one rank 80: it targets GPU execution, but no compatible devices were detected 80: PME GPU does not support: 80: Non-GPU build of GROMACS. 80: 80: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_1__pme_gpu__pmefft_gpu (4 ms) 80: [ RUN ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_1__pme_gpu__pmefft_auto 80: ./src/programs/mdrun/tests/pmetest.cpp:309: Skipped 80: Test is being skipped because: 80: it targets using PME rank(s) but the simulation is using only one rank 80: it targets GPU execution, but no compatible devices were detected 80: PME GPU does not support: 80: Non-GPU build of GROMACS. 80: 80: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_1__pme_gpu__pmefft_auto (0 ms) 80: [ RUN ] ReproducesEnergies/PmeTest.Runs/with_walls__notunepme__npme_1__pme_cpu 80: ./src/programs/mdrun/tests/pmetest.cpp:309: Skipped 80: Test is being skipped because: 80: it targets using PME rank(s) but the simulation is using only one rank 80: 80: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/with_walls__notunepme__npme_1__pme_cpu (0 ms) 80: [ RUN ] ReproducesEnergies/PmeTest.Runs/with_walls__notunepme__npme_1__pme_gpu__pmefft_cpu 80: ./src/programs/mdrun/tests/pmetest.cpp:309: Skipped 80: Test is being skipped because: 80: it targets using PME rank(s) but the simulation is using only one rank 80: it targets GPU execution, but no compatible devices were detected 80: PME GPU does not support: 80: Non-GPU build of GROMACS. 80: 80: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/with_walls__notunepme__npme_1__pme_gpu__pmefft_cpu (0 ms) 80: [ RUN ] ReproducesEnergies/PmeTest.Runs/with_walls__notunepme__npme_1__pme_gpu__pmefft_gpu 80: ./src/programs/mdrun/tests/pmetest.cpp:309: Skipped 80: Test is being skipped because: 80: it targets using PME rank(s) but the simulation is using only one rank 80: it targets GPU execution, but no compatible devices were detected 80: PME GPU does not support: 80: Non-GPU build of GROMACS. 80: 80: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/with_walls__notunepme__npme_1__pme_gpu__pmefft_gpu (0 ms) 80: [ RUN ] ReproducesEnergies/PmeTest.Runs/basic__tunepme__npme_0__pme_cpu 80: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_basic.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 80: Can not increase nstlist because an NVE ensemble is used 80: Using 1 MPI thread 80: Using 2 OpenMP threads 80: 80: 80: NOTE: The number of threads is not equal to the number of (logical) cpus 80: and the -pin option is set to auto: will not pin threads to cpus. 80: This can lead to significant performance degradation. 80: Consider using -pin on (and -pinoffset in case you run multiple jobs). 80: starting mdrun 'spc-and-methanol' 80: 20 steps, 0.0 ps. 80: 80: Writing final coordinates. 80: 80: Core t (s) Wall t (s) (%) 80: Time: 0.277 0.139 199.6 80: (ns/day) (hour/ns) 80: Performance: 13.058 1.838 80: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_Runs_basic__tunepme__npme_0__pme_cpu.edr as single precision energy file 80: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 17 time 0.017 Reading energy frame 18 time 0.018 Reading energy frame 19 time 0.019 Reading energy frame 20 time 0.020 Last energy frame read 20 time 0.020 [ OK ] ReproducesEnergies/PmeTest.Runs/basic__tunepme__npme_0__pme_cpu (181 ms) 80: [ RUN ] ReproducesEnergies/PmeTest.Runs/basic__tunepme__npme_0__pme_gpu__pmefft_cpu 80: ./src/programs/mdrun/tests/pmetest.cpp:309: Skipped 80: Test is being skipped because: 80: it targets GPU execution, but no compatible devices were detected 80: PME GPU does not support: 80: Non-GPU build of GROMACS. 80: 80: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic__tunepme__npme_0__pme_gpu__pmefft_cpu (0 ms) 80: [ RUN ] ReproducesEnergies/PmeTest.Runs/basic__tunepme__npme_0__pme_gpu__pmefft_gpu 80: ./src/programs/mdrun/tests/pmetest.cpp:309: Skipped 80: Test is being skipped because: 80: it targets GPU execution, but no compatible devices were detected 80: PME GPU does not support: 80: Non-GPU build of GROMACS. 80: 80: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic__tunepme__npme_0__pme_gpu__pmefft_gpu (0 ms) 80: [----------] 19 tests from ReproducesEnergies/PmeTest (751 ms total) 80: 80: [----------] Global test environment tear-down 80: [==========] 19 tests from 1 test suite ran. (866 ms total) 80: [ PASSED ] 4 tests. 80: [ SKIPPED ] 15 tests, listed below: 80: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_0__pme_gpu__pmefft_cpu 80: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_0__pme_gpu__pmefft_gpu 80: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_0__pme_gpu__pmefft_auto 80: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/with_walls__notunepme__npme_0__pme_gpu__pmefft_cpu 80: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/with_walls__notunepme__npme_0__pme_gpu__pmefft_gpu 80: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_1__pme_cpu 80: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_1__pme_auto 80: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_1__pme_gpu__pmefft_cpu 80: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_1__pme_gpu__pmefft_gpu 80: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_1__pme_gpu__pmefft_auto 80: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/with_walls__notunepme__npme_1__pme_cpu 80: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/with_walls__notunepme__npme_1__pme_gpu__pmefft_cpu 80: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/with_walls__notunepme__npme_1__pme_gpu__pmefft_gpu 80: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic__tunepme__npme_0__pme_gpu__pmefft_cpu 80: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic__tunepme__npme_0__pme_gpu__pmefft_gpu 80/92 Test #80: MdrunMpi1RankPmeTests ..................... Passed 0.95 sec test 81 Start 81: MdrunMpi2RankPmeTests 81: Test command: /build/reproducible-path/gromacs-2025.1/build/basic/bin/mdrun-mpi-pme-test "-ntomp" "2" "-ntmpi" "2" "--gtest_output=xml:/build/reproducible-path/gromacs-2025.1/build/basic/Testing/Temporary/MdrunMpi2RankPmeTests.xml" 81: Working Directory: /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests 81: Test timeout computed to be: 600 81: [==========] Running 19 tests from 1 test suite. 81: [----------] Global test environment set-up. 81: [----------] 19 tests from ReproducesEnergies/PmeTest 81: Number of degrees of freedom in T-Coupling group rest is 12.00 81: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 81: 81: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_input.mdp]: 81: NVE simulation: will use the initial temperature of 1046.791 K for 81: determining the Verlet buffer size 81: 81: 81: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_input.mdp]: 81: The optimal PME mesh load for parallel simulations is below 0.5 81: and for highly parallel simulations between 0.25 and 0.33, 81: for higher performance, increase the cut-off and the PME grid spacing. 81: 81: 81: 81: There were 2 NOTEs 81: 81: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_input.mdp]: 81: For a correct single-point energy evaluation with nsteps = 0, use 81: continuation = yes to avoid constraining the input coordinates. 81: 81: Number of degrees of freedom in T-Coupling group rest is 13.00 81: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 81: 81: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_input.mdp]: 81: NVE simulation: will use the initial temperature of 966.268 K for 81: determining the Verlet buffer size 81: 81: 81: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_input.mdp]: 81: The optimal PME mesh load for parallel simulations is below 0.5 81: and for highly parallel simulations between 0.25 and 0.33, 81: for higher performance, increase the cut-off and the PME grid spacing. 81: 81: 81: 81: There were 3 NOTEs 81: Setting the LD random seed to 2138746751 81: 81: Generated 8 of the 10 non-bonded parameter combinations 81: 81: Excluding 2 bonded neighbours molecule type 'Methanol' 81: 81: Excluding 2 bonded neighbours molecule type 'SOL' 81: 81: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/spc-and-methanol.gro' 81: 81: The largest distance between excluded atoms is 0.190 nm between atom 1 and 3 81: 81: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 1046.79 K 81: 81: Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm 81: 81: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm 81: 81: Note that mdrun will redetermine rlist based on the actual pair-list setup 81: Calculating fourier grid dimensions for X Y Z 81: Using a fourier grid of 28x28x28, spacing 0.108 0.108 0.108 81: 81: Estimate for the relative computational load of the PME mesh part: 1.00 81: 81: This run will generate roughly 0 Mb of data 81: Setting the LD random seed to -22085697 81: 81: Generated 8 of the 10 non-bonded parameter combinations 81: 81: Excluding 2 bonded neighbours molecule type 'Methanol' 81: 81: Excluding 2 bonded neighbours molecule type 'SOL' 81: 81: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/spc-and-methanol.gro' 81: 81: Searching the wall atom type(s) 81: 81: The largest distance between excluded atoms is 0.190 nm between atom 1 and 3 81: 81: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 966.268 K 81: 81: Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm 81: 81: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm 81: 81: Note that mdrun will redetermine rlist based on the actual pair-list setup 81: Calculating fourier grid dimensions for X Y Z 81: Using a fourier grid of 28x28x128, spacing 0.108 0.108 0.118 81: 81: Estimate for the relative computational load of the PME mesh part: 1.00 81: 81: This run will generate roughly 0 Mb of data 81: [ RUN ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_0__pme_cpu 81: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_basic.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 81: Can not increase nstlist because an NVE ensemble is used 81: Using 2 MPI threads 81: Using 2 OpenMP threads per tMPI thread 81: 81: starting mdrun 'spc-and-methanol' 81: 20 steps, 0.0 ps. 81: 81: Writing final coordinates. 81: 81: 81: Dynamic load balancing report: 81: DLB was off during the run due to low measured imbalance. 81: Average load imbalance: 16.7%. 81: The balanceable part of the MD step is 9%, load imbalance is computed from this. 81: Part of the total run time spent waiting due to load imbalance: 1.4%. 81: 81: 81: NOTE: 10 % of the run time was spent communicating energies, 81: you might want to increase some nst* mdp options 81: 81: Core t (s) Wall t (s) (%) 81: Time: 1.216 0.304 399.6 81: (ns/day) (hour/ns) 81: Performance: 5.962 4.025 81: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_Runs_basic__notunepme__npme_0__pme_cpu.edr as single precision energy file 81: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 17 time 0.017 Reading energy frame 18 time 0.018 Reading energy frame 19 time 0.019 Reading energy frame 20 time 0.020 Last energy frame read 20 time 0.020 [ OK ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_0__pme_cpu (404 ms) 81: [ RUN ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_0__pme_auto 81: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_basic.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 81: Can not increase nstlist because an NVE ensemble is used 81: Using 2 MPI threads 81: 81: Non-default thread affinity set, disabling internal thread affinity 81: 81: Using 2 OpenMP threads per tMPI thread 81: 81: starting mdrun 'spc-and-methanol' 81: 20 steps, 0.0 ps. 81: 81: Writing final coordinates. 81: 81: 81: Dynamic load balancing report: 81: DLB was turned on during the run due to measured imbalance. 81: Average load imbalance: 28.8%. 81: The balanceable part of the MD step is 21%, load imbalance is computed from this. 81: Part of the total run time spent waiting due to load imbalance: 6.1%. 81: Steps where the load balancing was limited by -rdd, -rcon and/or -dds: X 0 % 81: 81: NOTE: 6.1 % of the available CPU time was lost due to load imbalance 81: in the domain decomposition. 81: You can consider manually changing the decomposition (option -dd); 81: e.g. by using fewer domains along the box dimension in which there is 81: considerable inhomogeneity in the simulated system. 81: 81: NOTE: 11 % of the run time was spent communicating energies, 81: you might want to increase some nst* mdp options 81: 81: Core t (s) Wall t (s) (%) 81: Time: 13.926 3.497 398.2 81: (ns/day) (hour/ns) 81: Performance: 0.519 46.262 81: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_Runs_basic__notunepme__npme_0__pme_auto.edr as single precision energy file 81: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 17 time 0.017 Reading energy frame 18 time 0.018 Reading energy frame 19 time 0.019 Reading energy frame 20 time 0.020 Last energy frame read 20 time 0.020 [ OK ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_0__pme_auto (4242 ms) 81: [ RUN ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_0__pme_gpu__pmefft_cpu 81: ./src/programs/mdrun/tests/pmetest.cpp:309: Skipped 81: Test is being skipped because: 81: it targets GPU execution, but no compatible devices were detected 81: it targets PME decomposition, but that is not supported 81: PME GPU does not support: 81: Non-GPU build of GROMACS. 81: 81: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_0__pme_gpu__pmefft_cpu (1 ms) 81: [ RUN ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_0__pme_gpu__pmefft_gpu 81: ./src/programs/mdrun/tests/pmetest.cpp:309: Skipped 81: Test is being skipped because: 81: it targets GPU execution, but no compatible devices were detected 81: it targets PME decomposition, but that is not supported 81: PME GPU does not support: 81: Non-GPU build of GROMACS. 81: 81: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_0__pme_gpu__pmefft_gpu (0 ms) 81: [ RUN ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_0__pme_gpu__pmefft_auto 81: ./src/programs/mdrun/tests/pmetest.cpp:309: Skipped 81: Test is being skipped because: 81: it targets GPU execution, but no compatible devices were detected 81: it targets PME decomposition, but that is not supported 81: PME GPU does not support: 81: Non-GPU build of GROMACS. 81: 81: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_0__pme_gpu__pmefft_auto (0 ms) 81: [ RUN ] ReproducesEnergies/PmeTest.Runs/with_walls__notunepme__npme_0__pme_cpu 81: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_with_walls.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 81: Can not increase nstlist because an NVE ensemble is used 81: Using 2 MPI threads 81: 81: Non-default thread affinity set, disabling internal thread affinity 81: 81: Using 2 OpenMP threads per tMPI thread 81: 81: starting mdrun 'spc-and-methanol' 81: 0 steps, 0.0 ps. 81: 81: NOTE: 23 % of the run time was spent in domain decomposition, 81: 4 % of the run time was spent in pair search, 81: you might want to increase nstlist (this has no effect on accuracy) 81: 81: NOTE: 8 % of the run time was spent communicating energies, 81: you might want to increase some nst* mdp options 81: 81: Core t (s) Wall t (s) (%) 81: Time: 1.242 0.329 377.2 81: (ns/day) (hour/ns) 81: Performance: 0.262 91.494 81: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_Runs_with_walls__notunepme__npme_0__pme_cpu.edr as single precision energy file 81: Reading energy frame 0 time 0.000 Last energy frame read 0 time 0.000 [ OK ] ReproducesEnergies/PmeTest.Runs/with_walls__notunepme__npme_0__pme_cpu (1151 ms) 81: [ RUN ] ReproducesEnergies/PmeTest.Runs/with_walls__notunepme__npme_0__pme_gpu__pmefft_cpu 81: ./src/programs/mdrun/tests/pmetest.cpp:309: Skipped 81: Test is being skipped because: 81: it targets GPU execution, but no compatible devices were detected 81: it targets PME decomposition, but that is not supported 81: PME GPU does not support: 81: Non-GPU build of GROMACS. 81: 81: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/with_walls__notunepme__npme_0__pme_gpu__pmefft_cpu (0 ms) 81: [ RUN ] ReproducesEnergies/PmeTest.Runs/with_walls__notunepme__npme_0__pme_gpu__pmefft_gpu 81: ./src/programs/mdrun/tests/pmetest.cpp:309: Skipped 81: Test is being skipped because: 81: it targets GPU execution, but no compatible devices were detected 81: it targets PME decomposition, but that is not supported 81: PME GPU does not support: 81: Non-GPU build of GROMACS. 81: 81: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/with_walls__notunepme__npme_0__pme_gpu__pmefft_gpu (0 ms) 81: [ RUN ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_1__pme_cpu 81: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_basic.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 81: Can not increase nstlist because an NVE ensemble is used 81: Using 2 MPI threads 81: 81: Non-default thread affinity set, disabling internal thread affinity 81: 81: Using 2 OpenMP threads per tMPI thread 81: 81: starting mdrun 'spc-and-methanol' 81: 20 steps, 0.0 ps. 81: 81: Writing final coordinates. 81: 81: Core t (s) Wall t (s) (%) 81: Time: 4.837 1.230 393.3 81: (ns/day) (hour/ns) 81: Performance: 1.475 16.267 81: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_Runs_basic__notunepme__npme_1__pme_cpu.edr as single precision energy file 81: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 17 time 0.017 Reading energy frame 18 time 0.018 Reading energy frame 19 time 0.019 Reading energy frame 20 time 0.020 Last energy frame read 20 time 0.020 [ OK ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_1__pme_cpu (1708 ms) 81: [ RUN ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_1__pme_auto 81: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_basic.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 81: Can not increase nstlist because an NVE ensemble is used 81: Using 2 MPI threads 81: 81: Non-default thread affinity set, disabling internal thread affinity 81: 81: Using 2 OpenMP threads per tMPI thread 81: 81: starting mdrun 'spc-and-methanol' 81: 20 steps, 0.0 ps. 81: 81: Writing final coordinates. 81: 81: Core t (s) Wall t (s) (%) 81: Time: 4.961 1.262 393.2 81: (ns/day) (hour/ns) 81: Performance: 1.438 16.691 81: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_Runs_basic__notunepme__npme_1__pme_auto.edr as single precision energy file 81: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 17 time 0.017 Reading energy frame 18 time 0.018 Reading energy frame 19 time 0.019 Reading energy frame 20 time 0.020 Last energy frame read 20 time 0.020 [ OK ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_1__pme_auto (1739 ms) 81: [ RUN ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_1__pme_gpu__pmefft_cpu 81: ./src/programs/mdrun/tests/pmetest.cpp:309: Skipped 81: Test is being skipped because: 81: it targets GPU execution, but no compatible devices were detected 81: PME GPU does not support: 81: Non-GPU build of GROMACS. 81: 81: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_1__pme_gpu__pmefft_cpu (0 ms) 81: [ RUN ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_1__pme_gpu__pmefft_gpu 81: ./src/programs/mdrun/tests/pmetest.cpp:309: Skipped 81: Test is being skipped because: 81: it targets GPU execution, but no compatible devices were detected 81: PME GPU does not support: 81: Non-GPU build of GROMACS. 81: 81: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_1__pme_gpu__pmefft_gpu (0 ms) 81: [ RUN ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_1__pme_gpu__pmefft_auto 81: ./src/programs/mdrun/tests/pmetest.cpp:309: Skipped 81: Test is being skipped because: 81: it targets GPU execution, but no compatible devices were detected 81: PME GPU does not support: 81: Non-GPU build of GROMACS. 81: 81: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_1__pme_gpu__pmefft_auto (0 ms) 81: [ RUN ] ReproducesEnergies/PmeTest.Runs/with_walls__notunepme__npme_1__pme_cpu 81: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_with_walls.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 81: Can not increase nstlist because an NVE ensemble is used 81: Using 2 MPI threads 81: 81: Non-default thread affinity set, disabling internal thread affinity 81: 81: Using 2 OpenMP threads per tMPI thread 81: 81: starting mdrun 'spc-and-methanol' 81: 0 steps, 0.0 ps. 81: 81: NOTE: 13 % of the run time was spent in domain decomposition, 81: 0 % of the run time was spent in pair search, 81: you might want to increase nstlist (this has no effect on accuracy) 81: 81: Core t (s) Wall t (s) (%) 81: Time: 0.526 0.146 360.5 81: (ns/day) (hour/ns) 81: Performance: 0.592 40.525 81: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_Runs_with_walls__notunepme__npme_1__pme_cpu.edr as single precision energy file 81: Reading energy frame 0 time 0.000 Last energy frame read 0 time 0.000 [ OK ] ReproducesEnergies/PmeTest.Runs/with_walls__notunepme__npme_1__pme_cpu (804 ms) 81: [ RUN ] ReproducesEnergies/PmeTest.Runs/with_walls__notunepme__npme_1__pme_gpu__pmefft_cpu 81: ./src/programs/mdrun/tests/pmetest.cpp:309: Skipped 81: Test is being skipped because: 81: it targets GPU execution, but no compatible devices were detected 81: PME GPU does not support: 81: Non-GPU build of GROMACS. 81: 81: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/with_walls__notunepme__npme_1__pme_gpu__pmefft_cpu (0 ms) 81: [ RUN ] ReproducesEnergies/PmeTest.Runs/with_walls__notunepme__npme_1__pme_gpu__pmefft_gpu 81: ./src/programs/mdrun/tests/pmetest.cpp:309: Skipped 81: Test is being skipped because: 81: it targets GPU execution, but no compatible devices were detected 81: PME GPU does not support: 81: Non-GPU build of GROMACS. 81: 81: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/with_walls__notunepme__npme_1__pme_gpu__pmefft_gpu (0 ms) 81: [ RUN ] ReproducesEnergies/PmeTest.Runs/basic__tunepme__npme_0__pme_cpu 81: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_basic.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 81: Can not increase nstlist because an NVE ensemble is used 81: Using 2 MPI threads 81: 81: Non-default thread affinity set, disabling internal thread affinity 81: 81: Using 2 OpenMP threads per tMPI thread 81: 81: starting mdrun 'spc-and-methanol' 81: 20 steps, 0.0 ps. 81: 81: Writing final coordinates. 81: 81: 81: Dynamic load balancing report: 81: DLB was turned on during the run due to measured imbalance. 81: Average load imbalance: 27.8%. 81: The balanceable part of the MD step is 22%, load imbalance is computed from this. 81: Part of the total run time spent waiting due to load imbalance: 6.0%. 81: Steps where the load balancing was limited by -rdd, -rcon and/or -dds: X 0 % 81: 81: NOTE: 6.0 % of the available CPU time was lost due to load imbalance 81: in the domain decomposition. 81: You can consider manually changing the decomposition (option -dd); 81: e.g. by using fewer domains along the box dimension in which there is 81: considerable inhomogeneity in the simulated system. 81: 81: NOTE: 11 % of the run time was spent communicating energies, 81: you might want to increase some nst* mdp options 81: 81: Core t (s) Wall t (s) (%) 81: Time: 14.583 3.661 398.3 81: (ns/day) (hour/ns) 81: Performance: 0.496 48.431 81: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_Runs_basic__tunepme__npme_0__pme_cpu.edr as single precision energy file 81: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 17 time 0.017 Reading energy frame 18 time 0.018 Reading energy frame 19 time 0.019 Reading energy frame 20 time 0.020 Last energy frame read 20 time 0.020 [ OK ] ReproducesEnergies/PmeTest.Runs/basic__tunepme__npme_0__pme_cpu (4409 ms) 81: [ RUN ] ReproducesEnergies/PmeTest.Runs/basic__tunepme__npme_0__pme_gpu__pmefft_cpu 81: ./src/programs/mdrun/tests/pmetest.cpp:309: Skipped 81: Test is being skipped because: 81: it targets GPU execution, but no compatible devices were detected 81: it targets PME decomposition, but that is not supported 81: PME GPU does not support: 81: Non-GPU build of GROMACS. 81: 81: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic__tunepme__npme_0__pme_gpu__pmefft_cpu (2 ms) 81: [ RUN ] ReproducesEnergies/PmeTest.Runs/basic__tunepme__npme_0__pme_gpu__pmefft_gpu 81: ./src/programs/mdrun/tests/pmetest.cpp:309: Skipped 81: Test is being skipped because: 81: it targets GPU execution, but no compatible devices were detected 81: it targets PME decomposition, but that is not supported 81: PME GPU does not support: 81: Non-GPU build of GROMACS. 81: 81: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic__tunepme__npme_0__pme_gpu__pmefft_gpu (0 ms) 81: [----------] 19 tests from ReproducesEnergies/PmeTest (14470 ms total) 81: 81: [----------] Global test environment tear-down 81: [==========] 19 tests from 1 test suite ran. (14579 ms total) 81: [ PASSED ] 7 tests. 81: [ SKIPPED ] 12 tests, listed below: 81: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_0__pme_gpu__pmefft_cpu 81: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_0__pme_gpu__pmefft_gpu 81: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_0__pme_gpu__pmefft_auto 81: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/with_walls__notunepme__npme_0__pme_gpu__pmefft_cpu 81: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/with_walls__notunepme__npme_0__pme_gpu__pmefft_gpu 81: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_1__pme_gpu__pmefft_cpu 81: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_1__pme_gpu__pmefft_gpu 81: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_1__pme_gpu__pmefft_auto 81: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/with_walls__notunepme__npme_1__pme_gpu__pmefft_cpu 81: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/with_walls__notunepme__npme_1__pme_gpu__pmefft_gpu 81: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic__tunepme__npme_0__pme_gpu__pmefft_cpu 81: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic__tunepme__npme_0__pme_gpu__pmefft_gpu 81/92 Test #81: MdrunMpi2RankPmeTests ..................... Passed 14.68 sec test 82 Start 82: MdrunCoordinationBasicTests1Rank 82: Test command: /build/reproducible-path/gromacs-2025.1/build/basic/bin/mdrun-coordination-basic-test "-ntmpi" "1" "--gtest_output=xml:/build/reproducible-path/gromacs-2025.1/build/basic/Testing/Temporary/MdrunCoordinationBasicTests1Rank.xml" 82: Working Directory: /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests 82: Test timeout computed to be: 1920 82: [==========] Running 1 test from 1 test suite. 82: [----------] Global test environment set-up. 82: [----------] 1 test from BasicPropagators/PeriodicActionsTest 82: [ RUN ] BasicPropagators/PeriodicActionsTest.PeriodicActionsAgreeWithReference/0 82: 82: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 82: Setting nstcalcenergy (100) equal to nstenergy (1) 82: 82: Number of degrees of freedom in T-Coupling group System is 33.00 82: 82: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 82: NVE simulation: will use the initial temperature of 68.810 K for 82: determining the Verlet buffer size 82: 82: 82: There were 3 NOTEs 82: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 82: Can not increase nstlist because an NVE ensemble is used 82: Using 1 MPI thread 82: Using 1 OpenMP thread 82: 82: 82: NOTE: Thread affinity was not set. 82: starting mdrun 'Argon' 82: 16 steps, 0.0 ps. 82: Generated 1 of the 1 non-bonded parameter combinations 82: 82: Excluding 1 bonded neighbours molecule type 'Argon' 82: 82: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: Writing final coordinates. 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.030 0.030 99.2 82: (ns/day) (hour/ns) 82: Performance: 49.055 0.489 82: 82: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 82: Setting nstcalcenergy (100) equal to nstenergy (1) 82: 82: Number of degrees of freedom in T-Coupling group System is 33.00 82: 82: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 82: NVE simulation: will use the initial temperature of 68.810 K for 82: determining the Verlet buffer size 82: 82: 82: There were 3 NOTEs 82: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 82: Can not increase nstlist because an NVE ensemble is used 82: Using 1 MPI thread 82: Using 1 OpenMP thread 82: 82: 82: NOTE: Thread affinity was not set. 82: starting mdrun 'Argon' 82: 16 steps, 0.0 ps. 82: Generated 1 of the 1 non-bonded parameter combinations 82: 82: Excluding 1 bonded neighbours molecule type 'Argon' 82: 82: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: Writing final coordinates. 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.019 0.019 98.6 82: (ns/day) (hour/ns) 82: Performance: 76.588 0.313 82: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as single precision energy file 82: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as single precision energy file 82: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 82: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 82: Setting nstcalcenergy (100) equal to nstenergy (4) 82: 82: 82: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 82: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 82: setting nstcomm equal to nstcalcenergy for less overhead 82: 82: Number of degrees of freedom in T-Coupling group System is 33.00 82: 82: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 82: NVE simulation: will use the initial temperature of 68.810 K for 82: determining the Verlet buffer size 82: 82: 82: NOTE 5 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 82: COM removal frequency is set to (1). 82: Other settings require a global communication frequency of 4. 82: Note that this will require additional global communication steps, 82: which will reduce performance when using multiple ranks. 82: Consider setting nstcomm to a multiple of 4. 82: 82: 82: There were 5 NOTEs 82: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 82: Can not increase nstlist because an NVE ensemble is used 82: Using 1 MPI thread 82: Using 1 OpenMP thread 82: 82: 82: NOTE: Thread affinity was not set. 82: starting mdrun 'Argon' 82: 16 steps, 0.0 ps. 82: Generated 1 of the 1 non-bonded parameter combinations 82: 82: Excluding 1 bonded neighbours molecule type 'Argon' 82: 82: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: Writing final coordinates. 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.020 0.020 98.7 82: (ns/day) (hour/ns) 82: Performance: 72.216 0.332 82: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as single precision energy file 82: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as single precision energy file 82: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 82: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 82: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 82: setting nstcomm equal to nstcalcenergy for less overhead 82: 82: Number of degrees of freedom in T-Coupling group System is 33.00 82: 82: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 82: NVE simulation: will use the initial temperature of 68.810 K for 82: determining the Verlet buffer size 82: 82: 82: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 82: COM removal frequency is set to (1). 82: Other settings require a global communication frequency of 100. 82: Note that this will require additional global communication steps, 82: which will reduce performance when using multiple ranks. 82: Consider setting nstcomm to a multiple of 100. 82: 82: 82: There were 4 NOTEs 82: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 82: Can not increase nstlist because an NVE ensemble is used 82: Using 1 MPI thread 82: Using 1 OpenMP thread 82: 82: 82: NOTE: Thread affinity was not set. 82: starting mdrun 'Argon' 82: 16 steps, 0.0 ps. 82: Generated 1 of the 1 non-bonded parameter combinations 82: 82: Excluding 1 bonded neighbours molecule type 'Argon' 82: 82: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: Writing final coordinates. 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.020 0.020 98.7 82: (ns/day) (hour/ns) 82: Performance: 72.092 0.333 82: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as single precision energy file 82: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as single precision energy file 82: 82: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 82: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 82: setting nstcomm equal to nstcalcenergy for less overhead 82: 82: Number of degrees of freedom in T-Coupling group System is 33.00 82: 82: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 82: NVE simulation: will use the initial temperature of 68.810 K for 82: determining the Verlet buffer size 82: 82: 82: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 82: COM removal frequency is set to (1). 82: Other settings require a global communication frequency of 100. 82: Note that this will require additional global communication steps, 82: which will reduce performance when using multiple ranks. 82: Consider setting nstcomm to a multiple of 100. 82: 82: 82: There were 4 NOTEs 82: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 82: Can not increase nstlist because an NVE ensemble is used 82: Using 1 MPI thread 82: Using 1 OpenMP thread 82: 82: 82: NOTE: Thread affinity was not set. 82: starting mdrun 'Argon' 82: 16 steps, 0.0 ps. 82: Generated 1 of the 1 non-bonded parameter combinations 82: 82: Excluding 1 bonded neighbours molecule type 'Argon' 82: 82: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: Writing final coordinates. 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.023 0.023 98.9 82: (ns/day) (hour/ns) 82: Performance: 62.627 0.383 82: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as single precision energy file 82: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as single precision energy file 82: 82: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 82: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 82: setting nstcomm equal to nstcalcenergy for less overhead 82: 82: Number of degrees of freedom in T-Coupling group System is 33.00 82: 82: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 82: NVE simulation: will use the initial temperature of 68.810 K for 82: determining the Verlet buffer size 82: 82: 82: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 82: COM removal frequency is set to (1). 82: Other settings require a global communication frequency of 100. 82: Note that this will require additional global communication steps, 82: which will reduce performance when using multiple ranks. 82: Consider setting nstcomm to a multiple of 100. 82: 82: 82: There were 4 NOTEs 82: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 82: Can not increase nstlist because an NVE ensemble is used 82: Using 1 MPI thread 82: Using 1 OpenMP thread 82: 82: 82: NOTE: Thread affinity was not set. 82: starting mdrun 'Argon' 82: 16 steps, 0.0 ps. 82: Generated 1 of the 1 non-bonded parameter combinations 82: 82: Excluding 1 bonded neighbours molecule type 'Argon' 82: 82: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: Writing final coordinates. 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.023 0.023 98.8 82: (ns/day) (hour/ns) 82: Performance: 64.039 0.375 82: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as single precision energy file 82: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as single precision energy file 82: [ OK ] BasicPropagators/PeriodicActionsTest.PeriodicActionsAgreeWithReference/0 (425 ms) 82: [----------] 1 test from BasicPropagators/PeriodicActionsTest (425 ms total) 82: 82: [----------] Global test environment tear-down 82: [==========] 1 test from 1 test suite ran. (474 ms total) 82: [ PASSED ] 1 test. 82/92 Test #82: MdrunCoordinationBasicTests1Rank .......... Passed 0.55 sec test 83 Start 83: MdrunCoordinationBasicTests2Ranks 83: Test command: /build/reproducible-path/gromacs-2025.1/build/basic/bin/mdrun-coordination-basic-test "-ntmpi" "2" "--gtest_output=xml:/build/reproducible-path/gromacs-2025.1/build/basic/Testing/Temporary/MdrunCoordinationBasicTests2Ranks.xml" 83: Working Directory: /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests 83: Test timeout computed to be: 1920 83: [==========] Running 1 test from 1 test suite. 83: [----------] Global test environment set-up. 83: [----------] 1 test from BasicPropagators/PeriodicActionsTest 83: [ RUN ] BasicPropagators/PeriodicActionsTest.PeriodicActionsAgreeWithReference/0 83: 83: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 83: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 83: that with the Verlet scheme, nstlist has no effect on the accuracy of 83: your simulation. 83: 83: 83: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 83: Setting nstcalcenergy (100) equal to nstenergy (1) 83: 83: Number of degrees of freedom in T-Coupling group System is 33.00 83: 83: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 83: NVE simulation: will use the initial temperature of 68.810 K for 83: determining the Verlet buffer size 83: 83: 83: There were 3 NOTEs 83: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 83: Can not increase nstlist because an NVE ensemble is used 83: Using 2 MPI threads 83: Using 1 OpenMP thread per tMPI thread 83: 83: 83: NOTE: The number of threads is not equal to the number of (logical) cpus 83: and the -pin option is set to auto: will not pin threads to cpus. 83: This can lead to significant performance degradation. 83: Consider using -pin on (and -pinoffset in case you run multiple jobs). 83: starting mdrun 'Argon' 83: 16 steps, 0.0 ps. 83: Generated 1 of the 1 non-bonded parameter combinations 83: 83: Excluding 1 bonded neighbours molecule type 'Argon' 83: 83: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 83: 83: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 83: 83: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 83: 83: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 83: 83: Note that mdrun will redetermine rlist based on the actual pair-list setup 83: 83: This run will generate roughly 0 Mb of data 83: 83: Writing final coordinates. 83: 83: 83: Dynamic load balancing report: 83: DLB was off during the run due to low measured imbalance. 83: Average load imbalance: 1.9%. 83: The balanceable part of the MD step is 57%, load imbalance is computed from this. 83: Part of the total run time spent waiting due to load imbalance: 1.1%. 83: 83: 83: NOTE: 43 % of the run time was spent communicating energies, 83: you might want to increase some nst* mdp options 83: 83: Core t (s) Wall t (s) (%) 83: Time: 0.071 0.036 198.1 83: (ns/day) (hour/ns) 83: Performance: 40.800 0.588 83: 83: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 83: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 83: that with the Verlet scheme, nstlist has no effect on the accuracy of 83: your simulation. 83: 83: 83: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 83: Setting nstcalcenergy (100) equal to nstenergy (1) 83: 83: Number of degrees of freedom in T-Coupling group System is 33.00 83: 83: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 83: NVE simulation: will use the initial temperature of 68.810 K for 83: determining the Verlet buffer size 83: 83: 83: There were 3 NOTEs 83: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 83: Can not increase nstlist because an NVE ensemble is used 83: Using 2 MPI threads 83: Using 1 OpenMP thread per tMPI thread 83: 83: 83: NOTE: The number of threads is not equal to the number of (logical) cpus 83: and the -pin option is set to auto: will not pin threads to cpus. 83: This can lead to significant performance degradation. 83: Consider using -pin on (and -pinoffset in case you run multiple jobs). 83: starting mdrun 'Argon' 83: 16 steps, 0.0 ps. 83: Generated 1 of the 1 non-bonded parameter combinations 83: 83: Excluding 1 bonded neighbours molecule type 'Argon' 83: 83: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 83: 83: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 83: 83: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 83: 83: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 83: 83: Note that mdrun will redetermine rlist based on the actual pair-list setup 83: 83: This run will generate roughly 0 Mb of data 83: 83: Writing final coordinates. 83: 83: 83: Dynamic load balancing report: 83: DLB was off during the run due to low measured imbalance. 83: Average load imbalance: 1.1%. 83: The balanceable part of the MD step is 38%, load imbalance is computed from this. 83: Part of the total run time spent waiting due to load imbalance: 0.4%. 83: 83: 83: NOTE: 38 % of the run time was spent communicating energies, 83: you might want to increase some nst* mdp options 83: 83: Core t (s) Wall t (s) (%) 83: Time: 0.047 0.024 197.5 83: (ns/day) (hour/ns) 83: Performance: 62.202 0.386 83: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as single precision energy file 83: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as single precision energy file 83: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 83: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 83: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 83: that with the Verlet scheme, nstlist has no effect on the accuracy of 83: your simulation. 83: 83: 83: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 83: Setting nstcalcenergy (100) equal to nstenergy (4) 83: 83: 83: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 83: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 83: setting nstcomm equal to nstcalcenergy for less overhead 83: 83: Number of degrees of freedom in T-Coupling group System is 33.00 83: 83: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 83: NVE simulation: will use the initial temperature of 68.810 K for 83: determining the Verlet buffer size 83: 83: 83: NOTE 5 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 83: COM removal frequency is set to (1). 83: Other settings require a global communication frequency of 4. 83: Note that this will require additional global communication steps, 83: which will reduce performance when using multiple ranks. 83: Consider setting nstcomm to a multiple of 4. 83: 83: 83: There were 5 NOTEs 83: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 83: Can not increase nstlist because an NVE ensemble is used 83: Using 2 MPI threads 83: Using 1 OpenMP thread per tMPI thread 83: 83: 83: NOTE: The number of threads is not equal to the number of (logical) cpus 83: and the -pin option is set to auto: will not pin threads to cpus. 83: This can lead to significant performance degradation. 83: Consider using -pin on (and -pinoffset in case you run multiple jobs). 83: starting mdrun 'Argon' 83: 16 steps, 0.0 ps. 83: Generated 1 of the 1 non-bonded parameter combinations 83: 83: Excluding 1 bonded neighbours molecule type 'Argon' 83: 83: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 83: 83: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 83: 83: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 83: 83: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 83: 83: Note that mdrun will redetermine rlist based on the actual pair-list setup 83: 83: This run will generate roughly 0 Mb of data 83: 83: Writing final coordinates. 83: 83: 83: Dynamic load balancing report: 83: DLB was off during the run due to low measured imbalance. 83: Average load imbalance: 1.1%. 83: The balanceable part of the MD step is 51%, load imbalance is computed from this. 83: Part of the total run time spent waiting due to load imbalance: 0.5%. 83: 83: 83: NOTE: 44 % of the run time was spent communicating energies, 83: you might want to increase some nst* mdp options 83: 83: Core t (s) Wall t (s) (%) 83: Time: 0.050 0.025 197.5 83: (ns/day) (hour/ns) 83: Performance: 58.470 0.410 83: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as single precision energy file 83: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as single precision energy file 83: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 83: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 83: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 83: that with the Verlet scheme, nstlist has no effect on the accuracy of 83: your simulation. 83: 83: 83: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 83: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 83: setting nstcomm equal to nstcalcenergy for less overhead 83: 83: Number of degrees of freedom in T-Coupling group System is 33.00 83: 83: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 83: NVE simulation: will use the initial temperature of 68.810 K for 83: determining the Verlet buffer size 83: 83: 83: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 83: COM removal frequency is set to (1). 83: Other settings require a global communication frequency of 100. 83: Note that this will require additional global communication steps, 83: which will reduce performance when using multiple ranks. 83: Consider setting nstcomm to a multiple of 100. 83: 83: 83: There were 4 NOTEs 83: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 83: Can not increase nstlist because an NVE ensemble is used 83: Using 2 MPI threads 83: Using 1 OpenMP thread per tMPI thread 83: 83: 83: NOTE: The number of threads is not equal to the number of (logical) cpus 83: and the -pin option is set to auto: will not pin threads to cpus. 83: This can lead to significant performance degradation. 83: Consider using -pin on (and -pinoffset in case you run multiple jobs). 83: starting mdrun 'Argon' 83: 16 steps, 0.0 ps. 83: Generated 1 of the 1 non-bonded parameter combinations 83: 83: Excluding 1 bonded neighbours molecule type 'Argon' 83: 83: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 83: 83: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 83: 83: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 83: 83: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 83: 83: Note that mdrun will redetermine rlist based on the actual pair-list setup 83: 83: This run will generate roughly 0 Mb of data 83: 83: Writing final coordinates. 83: 83: 83: Dynamic load balancing report: 83: DLB was off during the run due to low measured imbalance. 83: Average load imbalance: 0.7%. 83: The balanceable part of the MD step is 48%, load imbalance is computed from this. 83: Part of the total run time spent waiting due to load imbalance: 0.3%. 83: 83: 83: NOTE: 45 % of the run time was spent communicating energies, 83: you might want to increase some nst* mdp options 83: 83: Core t (s) Wall t (s) (%) 83: Time: 0.059 0.030 197.9 83: (ns/day) (hour/ns) 83: Performance: 48.931 0.490 83: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as single precision energy file 83: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as single precision energy file 83: 83: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 83: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 83: that with the Verlet scheme, nstlist has no effect on the accuracy of 83: your simulation. 83: 83: 83: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 83: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 83: setting nstcomm equal to nstcalcenergy for less overhead 83: 83: Number of degrees of freedom in T-Coupling group System is 33.00 83: 83: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 83: NVE simulation: will use the initial temperature of 68.810 K for 83: determining the Verlet buffer size 83: 83: 83: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 83: COM removal frequency is set to (1). 83: Other settings require a global communication frequency of 100. 83: Note that this will require additional global communication steps, 83: which will reduce performance when using multiple ranks. 83: Consider setting nstcomm to a multiple of 100. 83: 83: 83: There were 4 NOTEs 83: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 83: Can not increase nstlist because an NVE ensemble is used 83: Using 2 MPI threads 83: Using 1 OpenMP thread per tMPI thread 83: 83: 83: NOTE: The number of threads is not equal to the number of (logical) cpus 83: and the -pin option is set to auto: will not pin threads to cpus. 83: This can lead to significant performance degradation. 83: Consider using -pin on (and -pinoffset in case you run multiple jobs). 83: starting mdrun 'Argon' 83: 16 steps, 0.0 ps. 83: Generated 1 of the 1 non-bonded parameter combinations 83: 83: Excluding 1 bonded neighbours molecule type 'Argon' 83: 83: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 83: 83: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 83: 83: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 83: 83: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 83: 83: Note that mdrun will redetermine rlist based on the actual pair-list setup 83: 83: This run will generate roughly 0 Mb of data 83: 83: Writing final coordinates. 83: 83: 83: Dynamic load balancing report: 83: DLB was off during the run due to low measured imbalance. 83: Average load imbalance: 3.5%. 83: The balanceable part of the MD step is 38%, load imbalance is computed from this. 83: Part of the total run time spent waiting due to load imbalance: 1.3%. 83: 83: 83: NOTE: 45 % of the run time was spent communicating energies, 83: you might want to increase some nst* mdp options 83: 83: Core t (s) Wall t (s) (%) 83: Time: 0.067 0.034 198.2 83: (ns/day) (hour/ns) 83: Performance: 43.488 0.552 83: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as single precision energy file 83: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as single precision energy file 83: 83: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 83: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 83: that with the Verlet scheme, nstlist has no effect on the accuracy of 83: your simulation. 83: 83: 83: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 83: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 83: setting nstcomm equal to nstcalcenergy for less overhead 83: 83: Number of degrees of freedom in T-Coupling group System is 33.00 83: 83: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 83: NVE simulation: will use the initial temperature of 68.810 K for 83: determining the Verlet buffer size 83: 83: 83: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 83: COM removal frequency is set to (1). 83: Other settings require a global communication frequency of 100. 83: Note that this will require additional global communication steps, 83: which will reduce performance when using multiple ranks. 83: Consider setting nstcomm to a multiple of 100. 83: 83: 83: There were 4 NOTEs 83: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 83: Can not increase nstlist because an NVE ensemble is used 83: Using 2 MPI threads 83: Using 1 OpenMP thread per tMPI thread 83: 83: 83: NOTE: The number of threads is not equal to the number of (logical) cpus 83: and the -pin option is set to auto: will not pin threads to cpus. 83: This can lead to significant performance degradation. 83: Consider using -pin on (and -pinoffset in case you run multiple jobs). 83: starting mdrun 'Argon' 83: 16 steps, 0.0 ps. 83: Generated 1 of the 1 non-bonded parameter combinations 83: 83: Excluding 1 bonded neighbours molecule type 'Argon' 83: 83: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 83: 83: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 83: 83: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 83: 83: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 83: 83: Note that mdrun will redetermine rlist based on the actual pair-list setup 83: 83: This run will generate roughly 0 Mb of data 83: 83: Writing final coordinates. 83: 83: 83: Dynamic load balancing report: 83: DLB was turned on during the run due to measured imbalance. 83: Average load imbalance: 9.1%. 83: The balanceable part of the MD step is 41%, load imbalance is computed from this. 83: Part of the total run time spent waiting due to load imbalance: 3.8%. 83: Steps where the load balancing was limited by -rdd, -rcon and/or -dds: X 0 % 83: 83: 83: NOTE: 44 % of the run time was spent communicating energies, 83: you might want to increase some nst* mdp options 83: 83: Core t (s) Wall t (s) (%) 83: Time: 0.068 0.034 198.1 83: (ns/day) (hour/ns) 83: Performance: 43.027 0.558 83: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as single precision energy file 83: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as single precision energy file 83: [ OK ] BasicPropagators/PeriodicActionsTest.PeriodicActionsAgreeWithReference/0 (493 ms) 83: [----------] 1 test from BasicPropagators/PeriodicActionsTest (493 ms total) 83: 83: [----------] Global test environment tear-down 83: [==========] 1 test from 1 test suite ran. (546 ms total) 83: [ PASSED ] 1 test. 83/92 Test #83: MdrunCoordinationBasicTests2Ranks ......... Passed 0.62 sec test 84 Start 84: MdrunCoordinationCouplingTests1Rank 84: Test command: /build/reproducible-path/gromacs-2025.1/build/basic/bin/mdrun-coordination-coupling-test "-ntmpi" "1" "--gtest_output=xml:/build/reproducible-path/gromacs-2025.1/build/basic/Testing/Temporary/MdrunCoordinationCouplingTests1Rank.xml" 84: Working Directory: /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests 84: Test timeout computed to be: 1920 84: [==========] Running 25 tests from 1 test suite. 84: [----------] Global test environment set-up. 84: [----------] 25 tests from PropagatorsWithCoupling/PeriodicActionsTest 84: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/0 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 84: Setting nstcalcenergy (100) equal to nstenergy (1) 84: 84: Number of degrees of freedom in T-Coupling group System is 33.00 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 84: NVE simulation: will use the initial temperature of 68.810 K for 84: determining the Verlet buffer size 84: 84: 84: There were 3 NOTEs 84: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 84: Can not increase nstlist because an NVE ensemble is used 84: Using 1 MPI thread 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'Argon' 84: 16 steps, 0.0 ps. 84: Generated 1 of the 1 non-bonded parameter combinations 84: 84: Excluding 1 bonded neighbours molecule type 'Argon' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.028 0.028 99.1 84: (ns/day) (hour/ns) 84: Performance: 52.440 0.458 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 84: Setting nstcalcenergy (100) equal to nstenergy (1) 84: 84: Number of degrees of freedom in T-Coupling group System is 33.00 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 84: NVE simulation: will use the initial temperature of 68.810 K for 84: determining the Verlet buffer size 84: 84: 84: There were 3 NOTEs 84: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 84: Can not increase nstlist because an NVE ensemble is used 84: Using 1 MPI thread 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'Argon' 84: 16 steps, 0.0 ps. 84: Generated 1 of the 1 non-bonded parameter combinations 84: 84: Excluding 1 bonded neighbours molecule type 'Argon' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.017 0.018 98.6 84: (ns/day) (hour/ns) 84: Performance: 83.232 0.288 84: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as single precision energy file 84: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as single precision energy file 84: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 84: Setting nstcalcenergy (100) equal to nstenergy (4) 84: 84: Number of degrees of freedom in T-Coupling group System is 33.00 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 84: NVE simulation: will use the initial temperature of 68.810 K for 84: determining the Verlet buffer size 84: 84: 84: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 84: COM removal frequency is set to (5). 84: Other settings require a global communication frequency of 4. 84: Note that this will require additional global communication steps, 84: which will reduce performance when using multiple ranks. 84: Consider setting nstcomm to a multiple of 4. 84: 84: 84: There were 4 NOTEs 84: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 84: Can not increase nstlist because an NVE ensemble is used 84: Using 1 MPI thread 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'Argon' 84: 16 steps, 0.0 ps. 84: Generated 1 of the 1 non-bonded parameter combinations 84: 84: Excluding 1 bonded neighbours molecule type 'Argon' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.016 0.017 98.5 84: (ns/day) (hour/ns) 84: Performance: 88.792 0.270 84: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as single precision energy file 84: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as single precision energy file 84: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 84: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 84: setting nstcomm equal to nstcalcenergy for less overhead 84: 84: Number of degrees of freedom in T-Coupling group System is 33.00 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 84: NVE simulation: will use the initial temperature of 68.810 K for 84: determining the Verlet buffer size 84: 84: 84: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 84: COM removal frequency is set to (5). 84: Other settings require a global communication frequency of 100. 84: Note that this will require additional global communication steps, 84: which will reduce performance when using multiple ranks. 84: Consider setting nstcomm to a multiple of 100. 84: 84: 84: There were 4 NOTEs 84: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 84: Can not increase nstlist because an NVE ensemble is used 84: Using 1 MPI thread 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'Argon' 84: 16 steps, 0.0 ps. 84: Generated 1 of the 1 non-bonded parameter combinations 84: 84: Excluding 1 bonded neighbours molecule type 'Argon' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.029 0.030 99.1 84: (ns/day) (hour/ns) 84: Performance: 49.680 0.483 84: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as single precision energy file 84: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as single precision energy file 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 84: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 84: setting nstcomm equal to nstcalcenergy for less overhead 84: 84: Number of degrees of freedom in T-Coupling group System is 33.00 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 84: NVE simulation: will use the initial temperature of 68.810 K for 84: determining the Verlet buffer size 84: 84: 84: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 84: COM removal frequency is set to (5). 84: Other settings require a global communication frequency of 100. 84: Note that this will require additional global communication steps, 84: which will reduce performance when using multiple ranks. 84: Consider setting nstcomm to a multiple of 100. 84: 84: 84: There were 4 NOTEs 84: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 84: Can not increase nstlist because an NVE ensemble is used 84: Using 1 MPI thread 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'Argon' 84: 16 steps, 0.0 ps. 84: Generated 1 of the 1 non-bonded parameter combinations 84: 84: Excluding 1 bonded neighbours molecule type 'Argon' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.019 0.020 98.6 84: (ns/day) (hour/ns) 84: Performance: 74.943 0.320 84: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as single precision energy file 84: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as single precision energy file 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 84: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 84: setting nstcomm equal to nstcalcenergy for less overhead 84: 84: Number of degrees of freedom in T-Coupling group System is 33.00 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 84: NVE simulation: will use the initial temperature of 68.810 K for 84: determining the Verlet buffer size 84: 84: 84: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 84: COM removal frequency is set to (5). 84: Other settings require a global communication frequency of 100. 84: Note that this will require additional global communication steps, 84: which will reduce performance when using multiple ranks. 84: Consider setting nstcomm to a multiple of 100. 84: 84: 84: There were 4 NOTEs 84: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 84: Can not increase nstlist because an NVE ensemble is used 84: Using 1 MPI thread 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'Argon' 84: 16 steps, 0.0 ps. 84: Generated 1 of the 1 non-bonded parameter combinations 84: 84: Excluding 1 bonded neighbours molecule type 'Argon' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.031 0.032 98.9 84: (ns/day) (hour/ns) 84: Performance: 46.269 0.519 84: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as single precision energy file 84: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as single precision energy file 84: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/0 (405 ms) 84: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/1 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 84: Setting nstcalcenergy (100) equal to nstenergy (1) 84: 84: 84: WARNING 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 84: The Berendsen barostat does not generate any strictly correct ensemble, 84: and should not be used for new production simulations (in our opinion). 84: We recommend using the C-rescale barostat instead. 84: 84: Number of degrees of freedom in T-Coupling group System is 33.00 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 84: NVE simulation: will use the initial temperature of 68.810 K for 84: determining the Verlet buffer size 84: 84: 84: There were 3 NOTEs 84: 84: There was 1 WARNING 84: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 84: Can not increase nstlist because an NVE ensemble is used 84: Using 1 MPI thread 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'Argon' 84: 16 steps, 0.0 ps. 84: Generated 1 of the 1 non-bonded parameter combinations 84: 84: Excluding 1 bonded neighbours molecule type 'Argon' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.028 0.028 99.1 84: (ns/day) (hour/ns) 84: Performance: 52.553 0.457 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 84: Setting nstcalcenergy (100) equal to nstenergy (1) 84: 84: 84: WARNING 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 84: The Berendsen barostat does not generate any strictly correct ensemble, 84: and should not be used for new production simulations (in our opinion). 84: We recommend using the C-rescale barostat instead. 84: 84: Number of degrees of freedom in T-Coupling group System is 33.00 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 84: NVE simulation: will use the initial temperature of 68.810 K for 84: determining the Verlet buffer size 84: 84: 84: There were 3 NOTEs 84: 84: There was 1 WARNING 84: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 84: Can not increase nstlist because an NVE ensemble is used 84: Using 1 MPI thread 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'Argon' 84: 16 steps, 0.0 ps. 84: Generated 1 of the 1 non-bonded parameter combinations 84: 84: Excluding 1 bonded neighbours molecule type 'Argon' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.026 0.026 99.0 84: (ns/day) (hour/ns) 84: Performance: 56.545 0.424 84: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as single precision energy file 84: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as single precision energy file 84: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 84: Setting nstcalcenergy (100) equal to nstenergy (4) 84: 84: 84: WARNING 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 84: The Berendsen barostat does not generate any strictly correct ensemble, 84: and should not be used for new production simulations (in our opinion). 84: We recommend using the C-rescale barostat instead. 84: 84: Number of degrees of freedom in T-Coupling group System is 33.00 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 84: NVE simulation: will use the initial temperature of 68.810 K for 84: determining the Verlet buffer size 84: 84: 84: There were 3 NOTEs 84: 84: There was 1 WARNING 84: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 84: Can not increase nstlist because an NVE ensemble is used 84: Using 1 MPI thread 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'Argon' 84: 16 steps, 0.0 ps. 84: Generated 1 of the 1 non-bonded parameter combinations 84: 84: Excluding 1 bonded neighbours molecule type 'Argon' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.016 0.016 98.3 84: (ns/day) (hour/ns) 84: Performance: 91.469 0.262 84: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as single precision energy file 84: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as single precision energy file 84: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 84: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 84: setting nstcomm equal to nstcalcenergy for less overhead 84: 84: 84: WARNING 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 84: The Berendsen barostat does not generate any strictly correct ensemble, 84: and should not be used for new production simulations (in our opinion). 84: We recommend using the C-rescale barostat instead. 84: 84: Number of degrees of freedom in T-Coupling group System is 33.00 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 84: NVE simulation: will use the initial temperature of 68.810 K for 84: determining the Verlet buffer size 84: 84: 84: There were 3 NOTEs 84: 84: There was 1 WARNING 84: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 84: Can not increase nstlist because an NVE ensemble is used 84: Using 1 MPI thread 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'Argon' 84: 16 steps, 0.0 ps. 84: Generated 1 of the 1 non-bonded parameter combinations 84: 84: Excluding 1 bonded neighbours molecule type 'Argon' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.022 0.023 98.7 84: (ns/day) (hour/ns) 84: Performance: 64.433 0.372 84: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as single precision energy file 84: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as single precision energy file 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 84: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 84: setting nstcomm equal to nstcalcenergy for less overhead 84: 84: 84: WARNING 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 84: The Berendsen barostat does not generate any strictly correct ensemble, 84: and should not be used for new production simulations (in our opinion). 84: We recommend using the C-rescale barostat instead. 84: 84: Number of degrees of freedom in T-Coupling group System is 33.00 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 84: NVE simulation: will use the initial temperature of 68.810 K for 84: determining the Verlet buffer size 84: 84: 84: There were 3 NOTEs 84: 84: There was 1 WARNING 84: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 84: Can not increase nstlist because an NVE ensemble is used 84: Using 1 MPI thread 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'Argon' 84: 16 steps, 0.0 ps. 84: Generated 1 of the 1 non-bonded parameter combinations 84: 84: Excluding 1 bonded neighbours molecule type 'Argon' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.022 0.022 98.7 84: (ns/day) (hour/ns) 84: Performance: 66.504 0.361 84: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as single precision energy file 84: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as single precision energy file 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 84: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 84: setting nstcomm equal to nstcalcenergy for less overhead 84: 84: 84: WARNING 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 84: The Berendsen barostat does not generate any strictly correct ensemble, 84: and should not be used for new production simulations (in our opinion). 84: We recommend using the C-rescale barostat instead. 84: 84: Number of degrees of freedom in T-Coupling group System is 33.00 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 84: NVE simulation: will use the initial temperature of 68.810 K for 84: determining the Verlet buffer size 84: 84: 84: There were 3 NOTEs 84: 84: There was 1 WARNING 84: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 84: Can not increase nstlist because an NVE ensemble is used 84: Using 1 MPI thread 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'Argon' 84: 16 steps, 0.0 ps. 84: Generated 1 of the 1 non-bonded parameter combinations 84: 84: Excluding 1 bonded neighbours molecule type 'Argon' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.021 0.021 98.5 84: (ns/day) (hour/ns) 84: Performance: 68.990 0.348 84: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as single precision energy file 84: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as single precision energy file 84: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/1 (424 ms) 84: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/2 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 84: Setting nstcalcenergy (100) equal to nstenergy (1) 84: 84: Number of degrees of freedom in T-Coupling group System is 33.00 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 84: NVE simulation: will use the initial temperature of 68.810 K for 84: determining the Verlet buffer size 84: 84: 84: There were 3 NOTEs 84: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 84: Can not increase nstlist because an NVE ensemble is used 84: Using 1 MPI thread 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'Argon' 84: 16 steps, 0.0 ps. 84: Generated 1 of the 1 non-bonded parameter combinations 84: 84: Excluding 1 bonded neighbours molecule type 'Argon' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.022 0.022 98.9 84: (ns/day) (hour/ns) 84: Performance: 66.384 0.362 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 84: Setting nstcalcenergy (100) equal to nstenergy (1) 84: 84: Number of degrees of freedom in T-Coupling group System is 33.00 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 84: NVE simulation: will use the initial temperature of 68.810 K for 84: determining the Verlet buffer size 84: 84: 84: There were 3 NOTEs 84: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 84: Can not increase nstlist because an NVE ensemble is used 84: Using 1 MPI thread 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'Argon' 84: 16 steps, 0.0 ps. 84: Generated 1 of the 1 non-bonded parameter combinations 84: 84: Excluding 1 bonded neighbours molecule type 'Argon' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.016 0.016 98.2 84: (ns/day) (hour/ns) 84: Performance: 90.740 0.264 84: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as single precision energy file 84: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as single precision energy file 84: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 84: Setting nstcalcenergy (100) equal to nstenergy (4) 84: 84: Number of degrees of freedom in T-Coupling group System is 33.00 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 84: NVE simulation: will use the initial temperature of 68.810 K for 84: determining the Verlet buffer size 84: 84: 84: There were 3 NOTEs 84: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 84: Can not increase nstlist because an NVE ensemble is used 84: Using 1 MPI thread 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'Argon' 84: 16 steps, 0.0 ps. 84: Generated 1 of the 1 non-bonded parameter combinations 84: 84: Excluding 1 bonded neighbours molecule type 'Argon' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.023 0.023 98.8 84: (ns/day) (hour/ns) 84: Performance: 63.601 0.377 84: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as single precision energy file 84: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as single precision energy file 84: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 84: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 84: setting nstcomm equal to nstcalcenergy for less overhead 84: 84: Number of degrees of freedom in T-Coupling group System is 33.00 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 84: NVE simulation: will use the initial temperature of 68.810 K for 84: determining the Verlet buffer size 84: 84: 84: There were 3 NOTEs 84: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 84: Can not increase nstlist because an NVE ensemble is used 84: Using 1 MPI thread 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'Argon' 84: 16 steps, 0.0 ps. 84: Generated 1 of the 1 non-bonded parameter combinations 84: 84: Excluding 1 bonded neighbours molecule type 'Argon' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.022 0.023 98.7 84: (ns/day) (hour/ns) 84: Performance: 64.956 0.369 84: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as single precision energy file 84: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as single precision energy file 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 84: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 84: setting nstcomm equal to nstcalcenergy for less overhead 84: 84: Number of degrees of freedom in T-Coupling group System is 33.00 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 84: NVE simulation: will use the initial temperature of 68.810 K for 84: determining the Verlet buffer size 84: 84: 84: There were 3 NOTEs 84: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 84: Can not increase nstlist because an NVE ensemble is used 84: Using 1 MPI thread 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'Argon' 84: 16 steps, 0.0 ps. 84: Generated 1 of the 1 non-bonded parameter combinations 84: 84: Excluding 1 bonded neighbours molecule type 'Argon' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.020 0.020 98.6 84: (ns/day) (hour/ns) 84: Performance: 73.735 0.325 84: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as single precision energy file 84: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as single precision energy file 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 84: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 84: setting nstcomm equal to nstcalcenergy for less overhead 84: 84: Number of degrees of freedom in T-Coupling group System is 33.00 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 84: NVE simulation: will use the initial temperature of 68.810 K for 84: determining the Verlet buffer size 84: 84: 84: There were 3 NOTEs 84: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 84: Can not increase nstlist because an NVE ensemble is used 84: Using 1 MPI thread 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'Argon' 84: 16 steps, 0.0 ps. 84: Generated 1 of the 1 non-bonded parameter combinations 84: 84: Excluding 1 bonded neighbours molecule type 'Argon' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.040 0.042 96.4 84: (ns/day) (hour/ns) 84: Performance: 35.089 0.684 84: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as single precision energy file 84: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as single precision energy file 84: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/2 (420 ms) 84: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/3 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 84: Setting nstcalcenergy (100) equal to nstenergy (1) 84: 84: Number of degrees of freedom in T-Coupling group System is 33.00 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 84: NVE simulation: will use the initial temperature of 68.810 K for 84: determining the Verlet buffer size 84: 84: 84: There were 3 NOTEs 84: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 84: Can not increase nstlist because an NVE ensemble is used 84: Using 1 MPI thread 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'Argon' 84: 16 steps, 0.0 ps. 84: Generated 1 of the 1 non-bonded parameter combinations 84: 84: Excluding 1 bonded neighbours molecule type 'Argon' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.024 0.024 99.0 84: (ns/day) (hour/ns) 84: Performance: 60.984 0.394 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 84: Setting nstcalcenergy (100) equal to nstenergy (1) 84: 84: Number of degrees of freedom in T-Coupling group System is 33.00 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 84: NVE simulation: will use the initial temperature of 68.810 K for 84: determining the Verlet buffer size 84: 84: 84: There were 3 NOTEs 84: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 84: Can not increase nstlist because an NVE ensemble is used 84: Using 1 MPI thread 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'Argon' 84: 16 steps, 0.0 ps. 84: Generated 1 of the 1 non-bonded parameter combinations 84: 84: Excluding 1 bonded neighbours molecule type 'Argon' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.032 0.032 99.3 84: (ns/day) (hour/ns) 84: Performance: 46.015 0.522 84: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as single precision energy file 84: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as single precision energy file 84: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 84: Setting nstcalcenergy (100) equal to nstenergy (4) 84: 84: Number of degrees of freedom in T-Coupling group System is 33.00 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 84: NVE simulation: will use the initial temperature of 68.810 K for 84: determining the Verlet buffer size 84: 84: 84: There were 3 NOTEs 84: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 84: Can not increase nstlist because an NVE ensemble is used 84: Using 1 MPI thread 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'Argon' 84: 16 steps, 0.0 ps. 84: Generated 1 of the 1 non-bonded parameter combinations 84: 84: Excluding 1 bonded neighbours molecule type 'Argon' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.026 0.027 99.2 84: (ns/day) (hour/ns) 84: Performance: 55.125 0.435 84: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as single precision energy file 84: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as single precision energy file 84: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 84: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 84: setting nstcomm equal to nstcalcenergy for less overhead 84: 84: Number of degrees of freedom in T-Coupling group System is 33.00 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 84: NVE simulation: will use the initial temperature of 68.810 K for 84: determining the Verlet buffer size 84: 84: 84: There were 3 NOTEs 84: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 84: Can not increase nstlist because an NVE ensemble is used 84: Using 1 MPI thread 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'Argon' 84: 16 steps, 0.0 ps. 84: Generated 1 of the 1 non-bonded parameter combinations 84: 84: Excluding 1 bonded neighbours molecule type 'Argon' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.033 0.034 99.3 84: (ns/day) (hour/ns) 84: Performance: 43.714 0.549 84: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as single precision energy file 84: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as single precision energy file 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 84: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 84: setting nstcomm equal to nstcalcenergy for less overhead 84: 84: Number of degrees of freedom in T-Coupling group System is 33.00 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 84: NVE simulation: will use the initial temperature of 68.810 K for 84: determining the Verlet buffer size 84: 84: 84: There were 3 NOTEs 84: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 84: Can not increase nstlist because an NVE ensemble is used 84: Using 1 MPI thread 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'Argon' 84: 16 steps, 0.0 ps. 84: Generated 1 of the 1 non-bonded parameter combinations 84: 84: Excluding 1 bonded neighbours molecule type 'Argon' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.021 0.021 98.8 84: (ns/day) (hour/ns) 84: Performance: 69.270 0.346 84: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as single precision energy file 84: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as single precision energy file 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 84: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 84: setting nstcomm equal to nstcalcenergy for less overhead 84: 84: Number of degrees of freedom in T-Coupling group System is 33.00 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 84: NVE simulation: will use the initial temperature of 68.810 K for 84: determining the Verlet buffer size 84: 84: 84: There were 3 NOTEs 84: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 84: Can not increase nstlist because an NVE ensemble is used 84: Using 1 MPI thread 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'Argon' 84: 16 steps, 0.0 ps. 84: Generated 1 of the 1 non-bonded parameter combinations 84: 84: Excluding 1 bonded neighbours molecule type 'Argon' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.019 0.020 98.5 84: (ns/day) (hour/ns) 84: Performance: 75.289 0.319 84: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as single precision energy file 84: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as single precision energy file 84: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/3 (446 ms) 84: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/4 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 84: Setting nstcalcenergy (100) equal to nstenergy (1) 84: 84: Number of degrees of freedom in T-Coupling group System is 33.00 84: 84: There were 2 NOTEs 84: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 84: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 84: 84: Using 1 MPI thread 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'Argon' 84: 16 steps, 0.0 ps. 84: Generated 1 of the 1 non-bonded parameter combinations 84: 84: Excluding 1 bonded neighbours molecule type 'Argon' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.019 0.020 98.3 84: (ns/day) (hour/ns) 84: Performance: 74.661 0.321 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 84: Setting nstcalcenergy (100) equal to nstenergy (1) 84: 84: Number of degrees of freedom in T-Coupling group System is 33.00 84: 84: There were 2 NOTEs 84: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 84: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 84: 84: Using 1 MPI thread 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'Argon' 84: 16 steps, 0.0 ps. 84: Generated 1 of the 1 non-bonded parameter combinations 84: 84: Excluding 1 bonded neighbours molecule type 'Argon' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.015 0.016 98.2 84: (ns/day) (hour/ns) 84: Performance: 93.256 0.257 84: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as single precision energy file 84: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as single precision energy file 84: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 84: Setting nstcalcenergy (100) equal to nstenergy (4) 84: 84: Number of degrees of freedom in T-Coupling group System is 33.00 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 84: COM removal frequency is set to (5). 84: Other settings require a global communication frequency of 2. 84: Note that this will require additional global communication steps, 84: which will reduce performance when using multiple ranks. 84: Consider setting nstcomm to a multiple of 2. 84: 84: 84: There were 3 NOTEs 84: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 84: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 84: 84: Using 1 MPI thread 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'Argon' 84: 16 steps, 0.0 ps. 84: Generated 1 of the 1 non-bonded parameter combinations 84: 84: Excluding 1 bonded neighbours molecule type 'Argon' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.016 0.016 98.3 84: (ns/day) (hour/ns) 84: Performance: 90.722 0.265 84: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as single precision energy file 84: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as single precision energy file 84: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 84: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 84: setting nstcomm equal to nstcalcenergy for less overhead 84: 84: Number of degrees of freedom in T-Coupling group System is 33.00 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 84: COM removal frequency is set to (5). 84: Other settings require a global communication frequency of 2. 84: Note that this will require additional global communication steps, 84: which will reduce performance when using multiple ranks. 84: Consider setting nstcomm to a multiple of 2. 84: 84: 84: There were 3 NOTEs 84: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 84: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 84: 84: Using 1 MPI thread 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'Argon' 84: 16 steps, 0.0 ps. 84: Generated 1 of the 1 non-bonded parameter combinations 84: 84: Excluding 1 bonded neighbours molecule type 'Argon' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.025 0.026 98.9 84: (ns/day) (hour/ns) 84: Performance: 57.139 0.420 84: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as single precision energy file 84: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as single precision energy file 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 84: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 84: setting nstcomm equal to nstcalcenergy for less overhead 84: 84: Number of degrees of freedom in T-Coupling group System is 33.00 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 84: COM removal frequency is set to (5). 84: Other settings require a global communication frequency of 2. 84: Note that this will require additional global communication steps, 84: which will reduce performance when using multiple ranks. 84: Consider setting nstcomm to a multiple of 2. 84: 84: 84: There were 3 NOTEs 84: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 84: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 84: 84: Using 1 MPI thread 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'Argon' 84: 16 steps, 0.0 ps. 84: Generated 1 of the 1 non-bonded parameter combinations 84: 84: Excluding 1 bonded neighbours molecule type 'Argon' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.026 0.027 98.9 84: (ns/day) (hour/ns) 84: Performance: 54.839 0.438 84: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as single precision energy file 84: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as single precision energy file 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 84: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 84: setting nstcomm equal to nstcalcenergy for less overhead 84: 84: Number of degrees of freedom in T-Coupling group System is 33.00 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 84: COM removal frequency is set to (5). 84: Other settings require a global communication frequency of 2. 84: Note that this will require additional global communication steps, 84: which will reduce performance when using multiple ranks. 84: Consider setting nstcomm to a multiple of 2. 84: 84: 84: There were 3 NOTEs 84: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 84: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 84: 84: Using 1 MPI thread 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'Argon' 84: 16 steps, 0.0 ps. 84: Generated 1 of the 1 non-bonded parameter combinations 84: 84: Excluding 1 bonded neighbours molecule type 'Argon' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.028 0.029 99.0 84: (ns/day) (hour/ns) 84: Performance: 51.369 0.467 84: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as single precision energy file 84: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as single precision energy file 84: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/4 (396 ms) 84: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/5 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 84: Setting nstcalcenergy (100) equal to nstenergy (1) 84: 84: 84: WARNING 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 84: The Berendsen barostat does not generate any strictly correct ensemble, 84: and should not be used for new production simulations (in our opinion). 84: We recommend using the C-rescale barostat instead. 84: 84: Number of degrees of freedom in T-Coupling group System is 33.00 84: 84: There were 2 NOTEs 84: 84: There was 1 WARNING 84: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 84: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 84: 84: Using 1 MPI thread 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'Argon' 84: 16 steps, 0.0 ps. 84: Generated 1 of the 1 non-bonded parameter combinations 84: 84: Excluding 1 bonded neighbours molecule type 'Argon' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.031 0.034 90.6 84: (ns/day) (hour/ns) 84: Performance: 42.912 0.559 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 84: Setting nstcalcenergy (100) equal to nstenergy (1) 84: 84: 84: WARNING 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 84: The Berendsen barostat does not generate any strictly correct ensemble, 84: and should not be used for new production simulations (in our opinion). 84: We recommend using the C-rescale barostat instead. 84: 84: Number of degrees of freedom in T-Coupling group System is 33.00 84: 84: There were 2 NOTEs 84: 84: There was 1 WARNING 84: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 84: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 84: 84: Using 1 MPI thread 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'Argon' 84: 16 steps, 0.0 ps. 84: Generated 1 of the 1 non-bonded parameter combinations 84: 84: Excluding 1 bonded neighbours molecule type 'Argon' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.027 0.028 99.1 84: (ns/day) (hour/ns) 84: Performance: 53.376 0.450 84: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as single precision energy file 84: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as single precision energy file 84: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 84: Setting nstcalcenergy (100) equal to nstenergy (4) 84: 84: 84: WARNING 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 84: The Berendsen barostat does not generate any strictly correct ensemble, 84: and should not be used for new production simulations (in our opinion). 84: We recommend using the C-rescale barostat instead. 84: 84: Number of degrees of freedom in T-Coupling group System is 33.00 84: 84: There were 2 NOTEs 84: 84: There was 1 WARNING 84: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 84: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 84: 84: Using 1 MPI thread 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'Argon' 84: 16 steps, 0.0 ps. 84: Generated 1 of the 1 non-bonded parameter combinations 84: 84: Excluding 1 bonded neighbours molecule type 'Argon' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.018 0.018 97.2 84: (ns/day) (hour/ns) 84: Performance: 80.403 0.298 84: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as single precision energy file 84: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as single precision energy file 84: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 84: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 84: setting nstcomm equal to nstcalcenergy for less overhead 84: 84: 84: WARNING 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 84: The Berendsen barostat does not generate any strictly correct ensemble, 84: and should not be used for new production simulations (in our opinion). 84: We recommend using the C-rescale barostat instead. 84: 84: Number of degrees of freedom in T-Coupling group System is 33.00 84: 84: There were 2 NOTEs 84: 84: There was 1 WARNING 84: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 84: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 84: 84: Using 1 MPI thread 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'Argon' 84: 16 steps, 0.0 ps. 84: Generated 1 of the 1 non-bonded parameter combinations 84: 84: Excluding 1 bonded neighbours molecule type 'Argon' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.030 0.031 99.2 84: (ns/day) (hour/ns) 84: Performance: 48.109 0.499 84: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as single precision energy file 84: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as single precision energy file 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 84: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 84: setting nstcomm equal to nstcalcenergy for less overhead 84: 84: 84: WARNING 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 84: The Berendsen barostat does not generate any strictly correct ensemble, 84: and should not be used for new production simulations (in our opinion). 84: We recommend using the C-rescale barostat instead. 84: 84: Number of degrees of freedom in T-Coupling group System is 33.00 84: 84: There were 2 NOTEs 84: 84: There was 1 WARNING 84: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 84: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 84: 84: Using 1 MPI thread 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'Argon' 84: 16 steps, 0.0 ps. 84: Generated 1 of the 1 non-bonded parameter combinations 84: 84: Excluding 1 bonded neighbours molecule type 'Argon' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.024 0.024 98.8 84: (ns/day) (hour/ns) 84: Performance: 60.687 0.395 84: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as single precision energy file 84: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as single precision energy file 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 84: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 84: setting nstcomm equal to nstcalcenergy for less overhead 84: 84: 84: WARNING 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 84: The Berendsen barostat does not generate any strictly correct ensemble, 84: and should not be used for new production simulations (in our opinion). 84: We recommend using the C-rescale barostat instead. 84: 84: Number of degrees of freedom in T-Coupling group System is 33.00 84: 84: There were 2 NOTEs 84: 84: There was 1 WARNING 84: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 84: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 84: 84: Using 1 MPI thread 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'Argon' 84: 16 steps, 0.0 ps. 84: Generated 1 of the 1 non-bonded parameter combinations 84: 84: Excluding 1 bonded neighbours molecule type 'Argon' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.021 0.021 98.6 84: (ns/day) (hour/ns) 84: Performance: 68.646 0.350 84: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as single precision energy file 84: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as single precision energy file 84: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/5 (459 ms) 84: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/6 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 84: Setting nstcalcenergy (100) equal to nstenergy (1) 84: 84: Number of degrees of freedom in T-Coupling group System is 33.00 84: 84: There were 2 NOTEs 84: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 84: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 84: 84: Using 1 MPI thread 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'Argon' 84: 16 steps, 0.0 ps. 84: Generated 1 of the 1 non-bonded parameter combinations 84: 84: Excluding 1 bonded neighbours molecule type 'Argon' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.057 0.058 99.6 84: (ns/day) (hour/ns) 84: Performance: 25.453 0.943 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 84: Setting nstcalcenergy (100) equal to nstenergy (1) 84: 84: Number of degrees of freedom in T-Coupling group System is 33.00 84: 84: There were 2 NOTEs 84: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 84: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 84: 84: Using 1 MPI thread 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'Argon' 84: 16 steps, 0.0 ps. 84: Generated 1 of the 1 non-bonded parameter combinations 84: 84: Excluding 1 bonded neighbours molecule type 'Argon' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.037 0.037 99.4 84: (ns/day) (hour/ns) 84: Performance: 39.882 0.602 84: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as single precision energy file 84: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as single precision energy file 84: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 84: Setting nstcalcenergy (100) equal to nstenergy (4) 84: 84: Number of degrees of freedom in T-Coupling group System is 33.00 84: 84: There were 2 NOTEs 84: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 84: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 84: 84: Using 1 MPI thread 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'Argon' 84: 16 steps, 0.0 ps. 84: Generated 1 of the 1 non-bonded parameter combinations 84: 84: Excluding 1 bonded neighbours molecule type 'Argon' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.025 0.025 99.1 84: (ns/day) (hour/ns) 84: Performance: 58.085 0.413 84: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as single precision energy file 84: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as single precision energy file 84: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 84: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 84: setting nstcomm equal to nstcalcenergy for less overhead 84: 84: Number of degrees of freedom in T-Coupling group System is 33.00 84: 84: There were 2 NOTEs 84: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 84: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 84: 84: Using 1 MPI thread 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'Argon' 84: 16 steps, 0.0 ps. 84: Generated 1 of the 1 non-bonded parameter combinations 84: 84: Excluding 1 bonded neighbours molecule type 'Argon' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.027 0.028 99.1 84: (ns/day) (hour/ns) 84: Performance: 53.409 0.449 84: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as single precision energy file 84: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as single precision energy file 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 84: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 84: setting nstcomm equal to nstcalcenergy for less overhead 84: 84: Number of degrees of freedom in T-Coupling group System is 33.00 84: 84: There were 2 NOTEs 84: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 84: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 84: 84: Using 1 MPI thread 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'Argon' 84: 16 steps, 0.0 ps. 84: Generated 1 of the 1 non-bonded parameter combinations 84: 84: Excluding 1 bonded neighbours molecule type 'Argon' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.046 0.046 99.2 84: (ns/day) (hour/ns) 84: Performance: 31.713 0.757 84: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as single precision energy file 84: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as single precision energy file 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 84: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 84: setting nstcomm equal to nstcalcenergy for less overhead 84: 84: Number of degrees of freedom in T-Coupling group System is 33.00 84: 84: There were 2 NOTEs 84: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 84: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 84: 84: Using 1 MPI thread 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'Argon' 84: 16 steps, 0.0 ps. 84: Generated 1 of the 1 non-bonded parameter combinations 84: 84: Excluding 1 bonded neighbours molecule type 'Argon' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.236 0.237 99.9 84: (ns/day) (hour/ns) 84: Performance: 6.206 3.867 84: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as single precision energy file 84: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as single precision energy file 84: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/6 (862 ms) 84: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/7 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 84: Setting nstcalcenergy (100) equal to nstenergy (1) 84: 84: Number of degrees of freedom in T-Coupling group System is 33.00 84: 84: There were 2 NOTEs 84: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 84: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 84: 84: Using 1 MPI thread 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'Argon' 84: 16 steps, 0.0 ps. 84: Generated 1 of the 1 non-bonded parameter combinations 84: 84: Excluding 1 bonded neighbours molecule type 'Argon' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.032 0.032 99.2 84: (ns/day) (hour/ns) 84: Performance: 45.562 0.527 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 84: Setting nstcalcenergy (100) equal to nstenergy (1) 84: 84: Number of degrees of freedom in T-Coupling group System is 33.00 84: 84: There were 2 NOTEs 84: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 84: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 84: 84: Using 1 MPI thread 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'Argon' 84: 16 steps, 0.0 ps. 84: Generated 1 of the 1 non-bonded parameter combinations 84: 84: Excluding 1 bonded neighbours molecule type 'Argon' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.059 0.059 99.5 84: (ns/day) (hour/ns) 84: Performance: 24.771 0.969 84: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as single precision energy file 84: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as single precision energy file 84: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 84: Setting nstcalcenergy (100) equal to nstenergy (4) 84: 84: Number of degrees of freedom in T-Coupling group System is 33.00 84: 84: There were 2 NOTEs 84: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 84: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 84: 84: Using 1 MPI thread 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'Argon' 84: 16 steps, 0.0 ps. 84: Generated 1 of the 1 non-bonded parameter combinations 84: 84: Excluding 1 bonded neighbours molecule type 'Argon' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.052 0.052 99.5 84: (ns/day) (hour/ns) 84: Performance: 28.310 0.848 84: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as single precision energy file 84: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as single precision energy file 84: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 84: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 84: setting nstcomm equal to nstcalcenergy for less overhead 84: 84: Number of degrees of freedom in T-Coupling group System is 33.00 84: 84: There were 2 NOTEs 84: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 84: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 84: 84: Using 1 MPI thread 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'Argon' 84: 16 steps, 0.0 ps. 84: Generated 1 of the 1 non-bonded parameter combinations 84: 84: Excluding 1 bonded neighbours molecule type 'Argon' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.063 0.063 99.5 84: (ns/day) (hour/ns) 84: Performance: 23.301 1.030 84: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as single precision energy file 84: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as single precision energy file 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 84: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 84: setting nstcomm equal to nstcalcenergy for less overhead 84: 84: Number of degrees of freedom in T-Coupling group System is 33.00 84: 84: There were 2 NOTEs 84: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 84: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 84: 84: Using 1 MPI thread 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'Argon' 84: 16 steps, 0.0 ps. 84: Generated 1 of the 1 non-bonded parameter combinations 84: 84: Excluding 1 bonded neighbours molecule type 'Argon' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.068 0.069 99.6 84: (ns/day) (hour/ns) 84: Performance: 21.431 1.120 84: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as single precision energy file 84: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as single precision energy file 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 84: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 84: setting nstcomm equal to nstcalcenergy for less overhead 84: 84: Number of degrees of freedom in T-Coupling group System is 33.00 84: 84: There were 2 NOTEs 84: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 84: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 84: 84: Using 1 MPI thread 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'Argon' 84: 16 steps, 0.0 ps. 84: Generated 1 of the 1 non-bonded parameter combinations 84: 84: Excluding 1 bonded neighbours molecule type 'Argon' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.050 0.051 99.5 84: (ns/day) (hour/ns) 84: Performance: 29.014 0.827 84: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as single precision energy file 84: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as single precision energy file 84: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/7 (758 ms) 84: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/8 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 84: Setting nstcalcenergy (100) equal to nstenergy (1) 84: 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 84: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 84: 1 84: 84: Number of degrees of freedom in T-Coupling group System is 33.00 84: 84: There were 3 NOTEs 84: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 84: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 84: 84: Using 1 MPI thread 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'Argon' 84: 16 steps, 0.0 ps. 84: Generated 1 of the 1 non-bonded parameter combinations 84: 84: Excluding 1 bonded neighbours molecule type 'Argon' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.101 0.101 99.7 84: (ns/day) (hour/ns) 84: Performance: 14.529 1.652 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 84: Setting nstcalcenergy (100) equal to nstenergy (1) 84: 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 84: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 84: 1 84: 84: Number of degrees of freedom in T-Coupling group System is 33.00 84: 84: There were 3 NOTEs 84: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 84: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 84: 84: Using 1 MPI thread 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'Argon' 84: 16 steps, 0.0 ps. 84: Generated 1 of the 1 non-bonded parameter combinations 84: 84: Excluding 1 bonded neighbours molecule type 'Argon' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.054 0.054 99.5 84: (ns/day) (hour/ns) 84: Performance: 27.144 0.884 84: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_reference.edr as single precision energy file 84: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.edr as single precision energy file 84: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 84: Setting nstcalcenergy (100) equal to nstenergy (4) 84: 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 84: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 84: 1 84: 84: Number of degrees of freedom in T-Coupling group System is 33.00 84: 84: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 84: COM removal frequency is set to (5). 84: Other settings require a global communication frequency of 2. 84: Note that this will require additional global communication steps, 84: which will reduce performance when using multiple ranks. 84: Consider setting nstcomm to a multiple of 2. 84: 84: 84: There were 4 NOTEs 84: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 84: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 84: 84: Using 1 MPI thread 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'Argon' 84: 16 steps, 0.0 ps. 84: Generated 1 of the 1 non-bonded parameter combinations 84: 84: Excluding 1 bonded neighbours molecule type 'Argon' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.018 0.019 98.6 84: (ns/day) (hour/ns) 84: Performance: 78.697 0.305 84: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_reference.edr as single precision energy file 84: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.edr as single precision energy file 84: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 84: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 84: setting nstcomm equal to nstcalcenergy for less overhead 84: 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 84: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 84: 1 84: 84: Number of degrees of freedom in T-Coupling group System is 33.00 84: 84: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 84: COM removal frequency is set to (5). 84: Other settings require a global communication frequency of 2. 84: Note that this will require additional global communication steps, 84: which will reduce performance when using multiple ranks. 84: Consider setting nstcomm to a multiple of 2. 84: 84: 84: There were 4 NOTEs 84: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 84: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 84: 84: Using 1 MPI thread 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'Argon' 84: 16 steps, 0.0 ps. 84: Generated 1 of the 1 non-bonded parameter combinations 84: 84: Excluding 1 bonded neighbours molecule type 'Argon' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.029 0.029 99.1 84: (ns/day) (hour/ns) 84: Performance: 50.717 0.473 84: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_reference.edr as single precision energy file 84: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.edr as single precision energy file 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 84: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 84: setting nstcomm equal to nstcalcenergy for less overhead 84: 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 84: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 84: 1 84: 84: Number of degrees of freedom in T-Coupling group System is 33.00 84: 84: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 84: COM removal frequency is set to (5). 84: Other settings require a global communication frequency of 2. 84: Note that this will require additional global communication steps, 84: which will reduce performance when using multiple ranks. 84: Consider setting nstcomm to a multiple of 2. 84: 84: 84: There were 4 NOTEs 84: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 84: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 84: 84: Using 1 MPI thread 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'Argon' 84: 16 steps, 0.0 ps. 84: Generated 1 of the 1 non-bonded parameter combinations 84: 84: Excluding 1 bonded neighbours molecule type 'Argon' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.022 0.022 98.8 84: (ns/day) (hour/ns) 84: Performance: 66.046 0.363 84: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_reference.edr as single precision energy file 84: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.edr as single precision energy file 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 84: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 84: setting nstcomm equal to nstcalcenergy for less overhead 84: 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 84: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 84: 1 84: 84: Number of degrees of freedom in T-Coupling group System is 33.00 84: 84: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 84: COM removal frequency is set to (5). 84: Other settings require a global communication frequency of 2. 84: Note that this will require additional global communication steps, 84: which will reduce performance when using multiple ranks. 84: Consider setting nstcomm to a multiple of 2. 84: 84: 84: There were 4 NOTEs 84: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 84: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 84: 84: Using 1 MPI thread 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'Argon' 84: 16 steps, 0.0 ps. 84: Generated 1 of the 1 non-bonded parameter combinations 84: 84: Excluding 1 bonded neighbours molecule type 'Argon' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.021 0.022 98.7 84: (ns/day) (hour/ns) 84: Performance: 68.085 0.353 84: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_reference.edr as single precision energy file 84: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.edr as single precision energy file 84: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/8 (629 ms) 84: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/9 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 84: Setting nstcalcenergy (100) equal to nstenergy (1) 84: 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 84: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 84: 1 84: 84: 84: WARNING 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 84: The Berendsen barostat does not generate any strictly correct ensemble, 84: and should not be used for new production simulations (in our opinion). 84: We recommend using the C-rescale barostat instead. 84: 84: Number of degrees of freedom in T-Coupling group System is 33.00 84: 84: There were 3 NOTEs 84: 84: There was 1 WARNING 84: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 84: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 84: 84: Using 1 MPI thread 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'Argon' 84: 16 steps, 0.0 ps. 84: Generated 1 of the 1 non-bonded parameter combinations 84: 84: Excluding 1 bonded neighbours molecule type 'Argon' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.023 0.023 98.9 84: (ns/day) (hour/ns) 84: Performance: 64.230 0.374 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 84: Setting nstcalcenergy (100) equal to nstenergy (1) 84: 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 84: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 84: 1 84: 84: 84: WARNING 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 84: The Berendsen barostat does not generate any strictly correct ensemble, 84: and should not be used for new production simulations (in our opinion). 84: We recommend using the C-rescale barostat instead. 84: 84: Number of degrees of freedom in T-Coupling group System is 33.00 84: 84: There were 3 NOTEs 84: 84: There was 1 WARNING 84: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 84: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 84: 84: Using 1 MPI thread 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'Argon' 84: 16 steps, 0.0 ps. 84: Generated 1 of the 1 non-bonded parameter combinations 84: 84: Excluding 1 bonded neighbours molecule type 'Argon' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.034 0.034 99.3 84: (ns/day) (hour/ns) 84: Performance: 43.073 0.557 84: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_reference.edr as single precision energy file 84: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.edr as single precision energy file 84: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 84: Setting nstcalcenergy (100) equal to nstenergy (4) 84: 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 84: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 84: 1 84: 84: 84: WARNING 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 84: The Berendsen barostat does not generate any strictly correct ensemble, 84: and should not be used for new production simulations (in our opinion). 84: We recommend using the C-rescale barostat instead. 84: 84: Number of degrees of freedom in T-Coupling group System is 33.00 84: 84: There were 3 NOTEs 84: 84: There was 1 WARNING 84: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 84: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 84: 84: Using 1 MPI thread 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'Argon' 84: 16 steps, 0.0 ps. 84: Generated 1 of the 1 non-bonded parameter combinations 84: 84: Excluding 1 bonded neighbours molecule type 'Argon' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.037 0.037 99.4 84: (ns/day) (hour/ns) 84: Performance: 39.266 0.611 84: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_reference.edr as single precision energy file 84: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.edr as single precision energy file 84: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 84: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 84: setting nstcomm equal to nstcalcenergy for less overhead 84: 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 84: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 84: 1 84: 84: 84: WARNING 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 84: The Berendsen barostat does not generate any strictly correct ensemble, 84: and should not be used for new production simulations (in our opinion). 84: We recommend using the C-rescale barostat instead. 84: 84: Number of degrees of freedom in T-Coupling group System is 33.00 84: 84: There were 3 NOTEs 84: 84: There was 1 WARNING 84: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 84: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 84: 84: Using 1 MPI thread 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'Argon' 84: 16 steps, 0.0 ps. 84: Generated 1 of the 1 non-bonded parameter combinations 84: 84: Excluding 1 bonded neighbours molecule type 'Argon' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.022 0.022 98.9 84: (ns/day) (hour/ns) 84: Performance: 67.243 0.357 84: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_reference.edr as single precision energy file 84: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.edr as single precision energy file 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 84: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 84: setting nstcomm equal to nstcalcenergy for less overhead 84: 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 84: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 84: 1 84: 84: 84: WARNING 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 84: The Berendsen barostat does not generate any strictly correct ensemble, 84: and should not be used for new production simulations (in our opinion). 84: We recommend using the C-rescale barostat instead. 84: 84: Number of degrees of freedom in T-Coupling group System is 33.00 84: 84: There were 3 NOTEs 84: 84: There was 1 WARNING 84: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 84: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 84: 84: Using 1 MPI thread 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'Argon' 84: 16 steps, 0.0 ps. 84: Generated 1 of the 1 non-bonded parameter combinations 84: 84: Excluding 1 bonded neighbours molecule type 'Argon' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.020 0.021 98.8 84: (ns/day) (hour/ns) 84: Performance: 71.582 0.335 84: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_reference.edr as single precision energy file 84: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.edr as single precision energy file 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 84: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 84: setting nstcomm equal to nstcalcenergy for less overhead 84: 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 84: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 84: 1 84: 84: 84: WARNING 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 84: The Berendsen barostat does not generate any strictly correct ensemble, 84: and should not be used for new production simulations (in our opinion). 84: We recommend using the C-rescale barostat instead. 84: 84: Number of degrees of freedom in T-Coupling group System is 33.00 84: 84: There were 3 NOTEs 84: 84: There was 1 WARNING 84: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 84: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 84: 84: Using 1 MPI thread 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'Argon' 84: 16 steps, 0.0 ps. 84: Generated 1 of the 1 non-bonded parameter combinations 84: 84: Excluding 1 bonded neighbours molecule type 'Argon' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.039 0.039 99.3 84: (ns/day) (hour/ns) 84: Performance: 37.458 0.641 84: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_reference.edr as single precision energy file 84: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.edr as single precision energy file 84: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/9 (472 ms) 84: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/10 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 84: Setting nstcalcenergy (100) equal to nstenergy (1) 84: 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 84: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 84: 1 84: 84: Number of degrees of freedom in T-Coupling group System is 33.00 84: 84: There were 3 NOTEs 84: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 84: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 84: 84: Using 1 MPI thread 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'Argon' 84: 16 steps, 0.0 ps. 84: Generated 1 of the 1 non-bonded parameter combinations 84: 84: Excluding 1 bonded neighbours molecule type 'Argon' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.033 0.034 99.2 84: (ns/day) (hour/ns) 84: Performance: 43.645 0.550 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 84: Setting nstcalcenergy (100) equal to nstenergy (1) 84: 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 84: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 84: 1 84: 84: Number of degrees of freedom in T-Coupling group System is 33.00 84: 84: There were 3 NOTEs 84: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 84: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 84: 84: Using 1 MPI thread 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'Argon' 84: 16 steps, 0.0 ps. 84: Generated 1 of the 1 non-bonded parameter combinations 84: 84: Excluding 1 bonded neighbours molecule type 'Argon' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.038 0.039 99.4 84: (ns/day) (hour/ns) 84: Performance: 38.092 0.630 84: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_reference.edr as single precision energy file 84: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.edr as single precision energy file 84: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 84: Setting nstcalcenergy (100) equal to nstenergy (4) 84: 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 84: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 84: 1 84: 84: Number of degrees of freedom in T-Coupling group System is 33.00 84: 84: There were 3 NOTEs 84: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 84: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 84: 84: Using 1 MPI thread 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'Argon' 84: 16 steps, 0.0 ps. 84: Generated 1 of the 1 non-bonded parameter combinations 84: 84: Excluding 1 bonded neighbours molecule type 'Argon' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.029 0.029 99.2 84: (ns/day) (hour/ns) 84: Performance: 50.452 0.476 84: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_reference.edr as single precision energy file 84: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.edr as single precision energy file 84: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 84: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 84: setting nstcomm equal to nstcalcenergy for less overhead 84: 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 84: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 84: 1 84: 84: Number of degrees of freedom in T-Coupling group System is 33.00 84: 84: There were 3 NOTEs 84: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 84: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 84: 84: Using 1 MPI thread 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'Argon' 84: 16 steps, 0.0 ps. 84: Generated 1 of the 1 non-bonded parameter combinations 84: 84: Excluding 1 bonded neighbours molecule type 'Argon' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.041 0.041 99.4 84: (ns/day) (hour/ns) 84: Performance: 36.012 0.666 84: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_reference.edr as single precision energy file 84: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.edr as single precision energy file 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 84: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 84: setting nstcomm equal to nstcalcenergy for less overhead 84: 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 84: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 84: 1 84: 84: Number of degrees of freedom in T-Coupling group System is 33.00 84: 84: There were 3 NOTEs 84: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 84: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 84: 84: Using 1 MPI thread 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'Argon' 84: 16 steps, 0.0 ps. 84: Generated 1 of the 1 non-bonded parameter combinations 84: 84: Excluding 1 bonded neighbours molecule type 'Argon' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.025 0.025 99.0 84: (ns/day) (hour/ns) 84: Performance: 58.818 0.408 84: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_reference.edr as single precision energy file 84: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.edr as single precision energy file 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 84: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 84: setting nstcomm equal to nstcalcenergy for less overhead 84: 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 84: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 84: 1 84: 84: Number of degrees of freedom in T-Coupling group System is 33.00 84: 84: There were 3 NOTEs 84: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 84: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 84: 84: Using 1 MPI thread 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'Argon' 84: 16 steps, 0.0 ps. 84: Generated 1 of the 1 non-bonded parameter combinations 84: 84: Excluding 1 bonded neighbours molecule type 'Argon' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.033 0.033 99.3 84: (ns/day) (hour/ns) 84: Performance: 44.684 0.537 84: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_reference.edr as single precision energy file 84: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.edr as single precision energy file 84: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/10 (502 ms) 84: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/11 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 84: Setting nstcalcenergy (100) equal to nstenergy (1) 84: 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 84: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 84: 1 84: 84: Number of degrees of freedom in T-Coupling group System is 33.00 84: 84: There were 3 NOTEs 84: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 84: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 84: 84: Using 1 MPI thread 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'Argon' 84: 16 steps, 0.0 ps. 84: Generated 1 of the 1 non-bonded parameter combinations 84: 84: Excluding 1 bonded neighbours molecule type 'Argon' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.025 0.025 99.0 84: (ns/day) (hour/ns) 84: Performance: 58.219 0.412 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 84: Setting nstcalcenergy (100) equal to nstenergy (1) 84: 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 84: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 84: 1 84: 84: Number of degrees of freedom in T-Coupling group System is 33.00 84: 84: There were 3 NOTEs 84: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 84: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 84: 84: Using 1 MPI thread 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'Argon' 84: 16 steps, 0.0 ps. 84: Generated 1 of the 1 non-bonded parameter combinations 84: 84: Excluding 1 bonded neighbours molecule type 'Argon' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.026 0.026 99.0 84: (ns/day) (hour/ns) 84: Performance: 56.571 0.424 84: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_reference.edr as single precision energy file 84: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.edr as single precision energy file 84: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 84: Setting nstcalcenergy (100) equal to nstenergy (4) 84: 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 84: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 84: 1 84: 84: Number of degrees of freedom in T-Coupling group System is 33.00 84: 84: There were 3 NOTEs 84: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 84: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 84: 84: Using 1 MPI thread 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'Argon' 84: 16 steps, 0.0 ps. 84: Generated 1 of the 1 non-bonded parameter combinations 84: 84: Excluding 1 bonded neighbours molecule type 'Argon' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.029 0.029 99.2 84: (ns/day) (hour/ns) 84: Performance: 50.895 0.472 84: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_reference.edr as single precision energy file 84: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.edr as single precision energy file 84: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 84: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 84: setting nstcomm equal to nstcalcenergy for less overhead 84: 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 84: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 84: 1 84: 84: Number of degrees of freedom in T-Coupling group System is 33.00 84: 84: There were 3 NOTEs 84: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 84: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 84: 84: Using 1 MPI thread 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'Argon' 84: 16 steps, 0.0 ps. 84: Generated 1 of the 1 non-bonded parameter combinations 84: 84: Excluding 1 bonded neighbours molecule type 'Argon' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.025 0.025 99.0 84: (ns/day) (hour/ns) 84: Performance: 58.929 0.407 84: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_reference.edr as single precision energy file 84: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.edr as single precision energy file 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 84: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 84: setting nstcomm equal to nstcalcenergy for less overhead 84: 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 84: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 84: 1 84: 84: Number of degrees of freedom in T-Coupling group System is 33.00 84: 84: There were 3 NOTEs 84: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 84: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 84: 84: Using 1 MPI thread 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'Argon' 84: 16 steps, 0.0 ps. 84: Generated 1 of the 1 non-bonded parameter combinations 84: 84: Excluding 1 bonded neighbours molecule type 'Argon' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.026 0.026 99.1 84: (ns/day) (hour/ns) 84: Performance: 56.571 0.424 84: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_reference.edr as single precision energy file 84: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.edr as single precision energy file 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 84: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 84: setting nstcomm equal to nstcalcenergy for less overhead 84: 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 84: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 84: 1 84: 84: Number of degrees of freedom in T-Coupling group System is 33.00 84: 84: There were 3 NOTEs 84: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 84: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 84: 84: Using 1 MPI thread 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'Argon' 84: 16 steps, 0.0 ps. 84: Generated 1 of the 1 non-bonded parameter combinations 84: 84: Excluding 1 bonded neighbours molecule type 'Argon' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.031 0.031 99.2 84: (ns/day) (hour/ns) 84: Performance: 47.247 0.508 84: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_reference.edr as single precision energy file 84: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.edr as single precision energy file 84: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/11 (463 ms) 84: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/12 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 84: Setting nstcalcenergy (100) equal to nstenergy (1) 84: 84: Number of degrees of freedom in T-Coupling group System is 33.00 84: 84: There were 2 NOTEs 84: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 84: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 84: 84: Using 1 MPI thread 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'Argon' 84: 16 steps, 0.0 ps. 84: Generated 1 of the 1 non-bonded parameter combinations 84: 84: Excluding 1 bonded neighbours molecule type 'Argon' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.029 0.029 99.2 84: (ns/day) (hour/ns) 84: Performance: 50.945 0.471 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 84: Setting nstcalcenergy (100) equal to nstenergy (1) 84: 84: Number of degrees of freedom in T-Coupling group System is 33.00 84: 84: There were 2 NOTEs 84: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 84: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 84: 84: Using 1 MPI thread 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'Argon' 84: 16 steps, 0.0 ps. 84: Generated 1 of the 1 non-bonded parameter combinations 84: 84: Excluding 1 bonded neighbours molecule type 'Argon' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.022 0.022 98.9 84: (ns/day) (hour/ns) 84: Performance: 65.975 0.364 84: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_reference.edr as single precision energy file 84: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.edr as single precision energy file 84: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 84: Setting nstcalcenergy (100) equal to nstenergy (4) 84: 84: Number of degrees of freedom in T-Coupling group System is 33.00 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 84: COM removal frequency is set to (5). 84: Other settings require a global communication frequency of 4. 84: Note that this will require additional global communication steps, 84: which will reduce performance when using multiple ranks. 84: Consider setting nstcomm to a multiple of 4. 84: 84: 84: There were 3 NOTEs 84: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 84: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 84: 84: Using 1 MPI thread 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'Argon' 84: 16 steps, 0.0 ps. 84: Generated 1 of the 1 non-bonded parameter combinations 84: 84: Excluding 1 bonded neighbours molecule type 'Argon' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.020 0.020 98.9 84: (ns/day) (hour/ns) 84: Performance: 72.380 0.332 84: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_reference.edr as single precision energy file 84: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.edr as single precision energy file 84: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 84: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 84: setting nstcomm equal to nstcalcenergy for less overhead 84: 84: Number of degrees of freedom in T-Coupling group System is 33.00 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 84: COM removal frequency is set to (5). 84: Other settings require a global communication frequency of 100. 84: Note that this will require additional global communication steps, 84: which will reduce performance when using multiple ranks. 84: Consider setting nstcomm to a multiple of 100. 84: 84: 84: There were 3 NOTEs 84: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 84: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 84: 84: Using 1 MPI thread 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'Argon' 84: 16 steps, 0.0 ps. 84: Generated 1 of the 1 non-bonded parameter combinations 84: 84: Excluding 1 bonded neighbours molecule type 'Argon' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.030 0.030 99.2 84: (ns/day) (hour/ns) 84: Performance: 48.170 0.498 84: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_reference.edr as single precision energy file 84: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.edr as single precision energy file 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 84: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 84: setting nstcomm equal to nstcalcenergy for less overhead 84: 84: Number of degrees of freedom in T-Coupling group System is 33.00 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 84: COM removal frequency is set to (5). 84: Other settings require a global communication frequency of 100. 84: Note that this will require additional global communication steps, 84: which will reduce performance when using multiple ranks. 84: Consider setting nstcomm to a multiple of 100. 84: 84: 84: There were 3 NOTEs 84: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 84: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 84: 84: Using 1 MPI thread 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'Argon' 84: 16 steps, 0.0 ps. 84: Generated 1 of the 1 non-bonded parameter combinations 84: 84: Excluding 1 bonded neighbours molecule type 'Argon' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.035 0.035 99.3 84: (ns/day) (hour/ns) 84: Performance: 41.476 0.579 84: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_reference.edr as single precision energy file 84: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.edr as single precision energy file 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 84: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 84: setting nstcomm equal to nstcalcenergy for less overhead 84: 84: Number of degrees of freedom in T-Coupling group System is 33.00 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 84: COM removal frequency is set to (5). 84: Other settings require a global communication frequency of 100. 84: Note that this will require additional global communication steps, 84: which will reduce performance when using multiple ranks. 84: Consider setting nstcomm to a multiple of 100. 84: 84: 84: There were 3 NOTEs 84: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 84: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 84: 84: Using 1 MPI thread 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'Argon' 84: 16 steps, 0.0 ps. 84: Generated 1 of the 1 non-bonded parameter combinations 84: 84: Excluding 1 bonded neighbours molecule type 'Argon' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.020 0.020 98.7 84: (ns/day) (hour/ns) 84: Performance: 71.686 0.335 84: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_reference.edr as single precision energy file 84: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.edr as single precision energy file 84: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/12 (441 ms) 84: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/13 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: 84: Setting nstcalcenergy (100) equal to nstenergy (1) 84: 84: 84: WARNING 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: 84: The Berendsen barostat does not generate any strictly correct ensemble, 84: and should not be used for new production simulations (in our opinion). 84: We recommend using the C-rescale barostat instead. 84: 84: Number of degrees of freedom in T-Coupling group System is 33.00 84: 84: There were 2 NOTEs 84: 84: There was 1 WARNING 84: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 84: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 84: 84: Using 1 MPI thread 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'Argon' 84: 16 steps, 0.0 ps. 84: Generated 1 of the 1 non-bonded parameter combinations 84: 84: Excluding 1 bonded neighbours molecule type 'Argon' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.023 0.024 99.0 84: (ns/day) (hour/ns) 84: Performance: 61.930 0.388 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: 84: Setting nstcalcenergy (100) equal to nstenergy (1) 84: 84: 84: WARNING 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: 84: The Berendsen barostat does not generate any strictly correct ensemble, 84: and should not be used for new production simulations (in our opinion). 84: We recommend using the C-rescale barostat instead. 84: 84: Number of degrees of freedom in T-Coupling group System is 33.00 84: 84: There were 2 NOTEs 84: 84: There was 1 WARNING 84: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 84: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 84: 84: Using 1 MPI thread 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'Argon' 84: 16 steps, 0.0 ps. 84: Generated 1 of the 1 non-bonded parameter combinations 84: 84: Excluding 1 bonded neighbours molecule type 'Argon' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.025 0.025 99.1 84: (ns/day) (hour/ns) 84: Performance: 58.242 0.412 84: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_reference.edr as single precision energy file 84: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.edr as single precision energy file 84: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: 84: Setting nstcalcenergy (100) equal to nstenergy (4) 84: 84: 84: WARNING 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: 84: The Berendsen barostat does not generate any strictly correct ensemble, 84: and should not be used for new production simulations (in our opinion). 84: We recommend using the C-rescale barostat instead. 84: 84: Number of degrees of freedom in T-Coupling group System is 33.00 84: 84: There were 2 NOTEs 84: 84: There was 1 WARNING 84: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 84: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 84: 84: Using 1 MPI thread 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'Argon' 84: 16 steps, 0.0 ps. 84: Generated 1 of the 1 non-bonded parameter combinations 84: 84: Excluding 1 bonded neighbours molecule type 'Argon' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.021 0.021 99.0 84: (ns/day) (hour/ns) 84: Performance: 70.291 0.341 84: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_reference.edr as single precision energy file 84: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.edr as single precision energy file 84: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: 84: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 84: setting nstcomm equal to nstcalcenergy for less overhead 84: 84: 84: WARNING 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: 84: The Berendsen barostat does not generate any strictly correct ensemble, 84: and should not be used for new production simulations (in our opinion). 84: We recommend using the C-rescale barostat instead. 84: 84: Number of degrees of freedom in T-Coupling group System is 33.00 84: 84: There were 2 NOTEs 84: 84: There was 1 WARNING 84: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 84: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 84: 84: Using 1 MPI thread 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'Argon' 84: 16 steps, 0.0 ps. 84: Generated 1 of the 1 non-bonded parameter combinations 84: 84: Excluding 1 bonded neighbours molecule type 'Argon' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.024 0.024 99.0 84: (ns/day) (hour/ns) 84: Performance: 61.175 0.392 84: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_reference.edr as single precision energy file 84: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.edr as single precision energy file 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: 84: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 84: setting nstcomm equal to nstcalcenergy for less overhead 84: 84: 84: WARNING 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: 84: The Berendsen barostat does not generate any strictly correct ensemble, 84: and should not be used for new production simulations (in our opinion). 84: We recommend using the C-rescale barostat instead. 84: 84: Number of degrees of freedom in T-Coupling group System is 33.00 84: 84: There were 2 NOTEs 84: 84: There was 1 WARNING 84: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 84: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 84: 84: Using 1 MPI thread 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'Argon' 84: 16 steps, 0.0 ps. 84: Generated 1 of the 1 non-bonded parameter combinations 84: 84: Excluding 1 bonded neighbours molecule type 'Argon' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.027 0.027 99.2 84: (ns/day) (hour/ns) 84: Performance: 53.881 0.445 84: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_reference.edr as single precision energy file 84: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.edr as single precision energy file 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: 84: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 84: setting nstcomm equal to nstcalcenergy for less overhead 84: 84: 84: WARNING 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: 84: The Berendsen barostat does not generate any strictly correct ensemble, 84: and should not be used for new production simulations (in our opinion). 84: We recommend using the C-rescale barostat instead. 84: 84: Number of degrees of freedom in T-Coupling group System is 33.00 84: 84: There were 2 NOTEs 84: 84: There was 1 WARNING 84: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 84: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 84: 84: Using 1 MPI thread 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'Argon' 84: 16 steps, 0.0 ps. 84: Generated 1 of the 1 non-bonded parameter combinations 84: 84: Excluding 1 bonded neighbours molecule type 'Argon' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.030 0.030 99.2 84: (ns/day) (hour/ns) 84: Performance: 49.333 0.486 84: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_reference.edr as single precision energy file 84: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.edr as single precision energy file 84: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/13 (471 ms) 84: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/14 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]: 84: Setting nstcalcenergy (100) equal to nstenergy (1) 84: 84: Number of degrees of freedom in T-Coupling group System is 33.00 84: 84: There were 2 NOTEs 84: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 84: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 84: 84: Using 1 MPI thread 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'Argon' 84: 16 steps, 0.0 ps. 84: Generated 1 of the 1 non-bonded parameter combinations 84: 84: Excluding 1 bonded neighbours molecule type 'Argon' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.022 0.022 99.0 84: (ns/day) (hour/ns) 84: Performance: 66.570 0.361 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]: 84: Setting nstcalcenergy (100) equal to nstenergy (1) 84: 84: Number of degrees of freedom in T-Coupling group System is 33.00 84: 84: There were 2 NOTEs 84: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 84: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 84: 84: Using 1 MPI thread 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'Argon' 84: 16 steps, 0.0 ps. 84: Generated 1 of the 1 non-bonded parameter combinations 84: 84: Excluding 1 bonded neighbours molecule type 'Argon' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.026 0.026 99.2 84: (ns/day) (hour/ns) 84: Performance: 56.248 0.427 84: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_reference.edr as single precision energy file 84: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.edr as single precision energy file 84: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]: 84: Setting nstcalcenergy (100) equal to nstenergy (4) 84: 84: Number of degrees of freedom in T-Coupling group System is 33.00 84: 84: There were 2 NOTEs 84: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 84: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 84: 84: Using 1 MPI thread 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'Argon' 84: 16 steps, 0.0 ps. 84: Generated 1 of the 1 non-bonded parameter combinations 84: 84: Excluding 1 bonded neighbours molecule type 'Argon' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.037 0.037 99.5 84: (ns/day) (hour/ns) 84: Performance: 39.213 0.612 84: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_reference.edr as single precision energy file 84: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.edr as single precision energy file 84: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]: 84: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 84: setting nstcomm equal to nstcalcenergy for less overhead 84: 84: Number of degrees of freedom in T-Coupling group System is 33.00 84: 84: There were 2 NOTEs 84: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 84: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 84: 84: Using 1 MPI thread 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'Argon' 84: 16 steps, 0.0 ps. 84: Generated 1 of the 1 non-bonded parameter combinations 84: 84: Excluding 1 bonded neighbours molecule type 'Argon' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.026 0.026 99.1 84: (ns/day) (hour/ns) 84: Performance: 57.010 0.421 84: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_reference.edr as single precision energy file 84: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.edr as single precision energy file 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]: 84: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 84: setting nstcomm equal to nstcalcenergy for less overhead 84: 84: Number of degrees of freedom in T-Coupling group System is 33.00 84: 84: There were 2 NOTEs 84: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 84: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 84: 84: Using 1 MPI thread 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'Argon' 84: 16 steps, 0.0 ps. 84: Generated 1 of the 1 non-bonded parameter combinations 84: 84: Excluding 1 bonded neighbours molecule type 'Argon' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.025 0.025 99.1 84: (ns/day) (hour/ns) 84: Performance: 58.700 0.409 84: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_reference.edr as single precision energy file 84: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.edr as single precision energy file 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]: 84: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 84: setting nstcomm equal to nstcalcenergy for less overhead 84: 84: Number of degrees of freedom in T-Coupling group System is 33.00 84: 84: There were 2 NOTEs 84: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 84: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 84: 84: Using 1 MPI thread 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'Argon' 84: 16 steps, 0.0 ps. 84: Generated 1 of the 1 non-bonded parameter combinations 84: 84: Excluding 1 bonded neighbours molecule type 'Argon' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.028 0.028 99.1 84: (ns/day) (hour/ns) 84: Performance: 51.664 0.465 84: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_reference.edr as single precision energy file 84: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.edr as single precision energy file 84: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/14 (447 ms) 84: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/15 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]: 84: Setting nstcalcenergy (100) equal to nstenergy (1) 84: 84: Number of degrees of freedom in T-Coupling group System is 33.00 84: 84: There were 2 NOTEs 84: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 84: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 84: 84: Using 1 MPI thread 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'Argon' 84: 16 steps, 0.0 ps. 84: Generated 1 of the 1 non-bonded parameter combinations 84: 84: Excluding 1 bonded neighbours molecule type 'Argon' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.027 0.028 99.2 84: (ns/day) (hour/ns) 84: Performance: 53.380 0.450 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]: 84: Setting nstcalcenergy (100) equal to nstenergy (1) 84: 84: Number of degrees of freedom in T-Coupling group System is 33.00 84: 84: There were 2 NOTEs 84: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 84: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 84: 84: Using 1 MPI thread 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'Argon' 84: 16 steps, 0.0 ps. 84: Generated 1 of the 1 non-bonded parameter combinations 84: 84: Excluding 1 bonded neighbours molecule type 'Argon' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.030 0.030 99.3 84: (ns/day) (hour/ns) 84: Performance: 48.687 0.493 84: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_reference.edr as single precision energy file 84: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.edr as single precision energy file 84: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]: 84: Setting nstcalcenergy (100) equal to nstenergy (4) 84: 84: Number of degrees of freedom in T-Coupling group System is 33.00 84: 84: There were 2 NOTEs 84: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 84: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 84: 84: Using 1 MPI thread 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'Argon' 84: 16 steps, 0.0 ps. 84: Generated 1 of the 1 non-bonded parameter combinations 84: 84: Excluding 1 bonded neighbours molecule type 'Argon' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.028 0.028 99.2 84: (ns/day) (hour/ns) 84: Performance: 52.853 0.454 84: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_reference.edr as single precision energy file 84: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.edr as single precision energy file 84: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]: 84: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 84: setting nstcomm equal to nstcalcenergy for less overhead 84: 84: Number of degrees of freedom in T-Coupling group System is 33.00 84: 84: There were 2 NOTEs 84: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 84: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 84: 84: Using 1 MPI thread 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'Argon' 84: 16 steps, 0.0 ps. 84: Generated 1 of the 1 non-bonded parameter combinations 84: 84: Excluding 1 bonded neighbours molecule type 'Argon' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.043 0.044 99.1 84: (ns/day) (hour/ns) 84: Performance: 33.477 0.717 84: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_reference.edr as single precision energy file 84: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.edr as single precision energy file 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]: 84: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 84: setting nstcomm equal to nstcalcenergy for less overhead 84: 84: Number of degrees of freedom in T-Coupling group System is 33.00 84: 84: There were 2 NOTEs 84: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 84: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 84: 84: Using 1 MPI thread 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'Argon' 84: 16 steps, 0.0 ps. 84: Generated 1 of the 1 non-bonded parameter combinations 84: 84: Excluding 1 bonded neighbours molecule type 'Argon' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.025 0.025 98.7 84: (ns/day) (hour/ns) 84: Performance: 58.126 0.413 84: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_reference.edr as single precision energy file 84: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.edr as single precision energy file 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]: 84: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 84: setting nstcomm equal to nstcalcenergy for less overhead 84: 84: Number of degrees of freedom in T-Coupling group System is 33.00 84: 84: There were 2 NOTEs 84: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 84: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 84: 84: Using 1 MPI thread 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'Argon' 84: 16 steps, 0.0 ps. 84: Generated 1 of the 1 non-bonded parameter combinations 84: 84: Excluding 1 bonded neighbours molecule type 'Argon' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.035 0.035 99.4 84: (ns/day) (hour/ns) 84: Performance: 41.441 0.579 84: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_reference.edr as single precision energy file 84: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.edr as single precision energy file 84: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/15 (467 ms) 84: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/16 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 84: Setting nstcalcenergy (100) equal to nstenergy (1) 84: 84: Number of degrees of freedom in T-Coupling group System is 33.00 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 84: NVE simulation: will use the initial temperature of 68.810 K for 84: determining the Verlet buffer size 84: 84: 84: There were 3 NOTEs 84: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 84: Can not increase nstlist because an NVE ensemble is used 84: Using 1 MPI thread 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'Argon' 84: 16 steps, 0.0 ps. 84: Generated 1 of the 1 non-bonded parameter combinations 84: 84: Excluding 1 bonded neighbours molecule type 'Argon' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.025 0.025 99.3 84: (ns/day) (hour/ns) 84: Performance: 58.014 0.414 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 84: Setting nstcalcenergy (100) equal to nstenergy (1) 84: 84: Number of degrees of freedom in T-Coupling group System is 33.00 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 84: NVE simulation: will use the initial temperature of 68.810 K for 84: determining the Verlet buffer size 84: 84: 84: There were 3 NOTEs 84: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 84: Can not increase nstlist because an NVE ensemble is used 84: Using 1 MPI thread 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'Argon' 84: 16 steps, 0.0 ps. 84: Generated 1 of the 1 non-bonded parameter combinations 84: 84: Excluding 1 bonded neighbours molecule type 'Argon' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.022 0.022 98.4 84: (ns/day) (hour/ns) 84: Performance: 67.112 0.358 84: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_reference.edr as single precision energy file 84: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.edr as single precision energy file 84: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 84: Setting nstcalcenergy (100) equal to nstenergy (4) 84: 84: Number of degrees of freedom in T-Coupling group System is 33.00 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 84: NVE simulation: will use the initial temperature of 68.810 K for 84: determining the Verlet buffer size 84: 84: 84: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 84: COM removal frequency is set to (5). 84: Other settings require a global communication frequency of 4. 84: Note that this will require additional global communication steps, 84: which will reduce performance when using multiple ranks. 84: Consider setting nstcomm to a multiple of 4. 84: 84: 84: There were 4 NOTEs 84: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 84: Can not increase nstlist because an NVE ensemble is used 84: Using 1 MPI thread 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'Argon' 84: 16 steps, 0.0 ps. 84: Generated 1 of the 1 non-bonded parameter combinations 84: 84: Excluding 1 bonded neighbours molecule type 'Argon' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.035 0.035 99.6 84: (ns/day) (hour/ns) 84: Performance: 41.582 0.577 84: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_reference.edr as single precision energy file 84: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.edr as single precision energy file 84: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 84: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 84: setting nstcomm equal to nstcalcenergy for less overhead 84: 84: Number of degrees of freedom in T-Coupling group System is 33.00 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 84: NVE simulation: will use the initial temperature of 68.810 K for 84: determining the Verlet buffer size 84: 84: 84: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 84: COM removal frequency is set to (5). 84: Other settings require a global communication frequency of 100. 84: Note that this will require additional global communication steps, 84: which will reduce performance when using multiple ranks. 84: Consider setting nstcomm to a multiple of 100. 84: 84: 84: There were 4 NOTEs 84: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 84: Can not increase nstlist because an NVE ensemble is used 84: Using 1 MPI thread 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'Argon' 84: 16 steps, 0.0 ps. 84: Generated 1 of the 1 non-bonded parameter combinations 84: 84: Excluding 1 bonded neighbours molecule type 'Argon' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.038 0.039 99.6 84: (ns/day) (hour/ns) 84: Performance: 38.073 0.630 84: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_reference.edr as single precision energy file 84: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.edr as single precision energy file 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 84: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 84: setting nstcomm equal to nstcalcenergy for less overhead 84: 84: Number of degrees of freedom in T-Coupling group System is 33.00 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 84: NVE simulation: will use the initial temperature of 68.810 K for 84: determining the Verlet buffer size 84: 84: 84: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 84: COM removal frequency is set to (5). 84: Other settings require a global communication frequency of 100. 84: Note that this will require additional global communication steps, 84: which will reduce performance when using multiple ranks. 84: Consider setting nstcomm to a multiple of 100. 84: 84: 84: There were 4 NOTEs 84: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 84: Can not increase nstlist because an NVE ensemble is used 84: Using 1 MPI thread 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'Argon' 84: 16 steps, 0.0 ps. 84: Generated 1 of the 1 non-bonded parameter combinations 84: 84: Excluding 1 bonded neighbours molecule type 'Argon' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.024 0.025 99.4 84: (ns/day) (hour/ns) 84: Performance: 59.746 0.402 84: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_reference.edr as single precision energy file 84: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.edr as single precision energy file 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 84: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 84: setting nstcomm equal to nstcalcenergy for less overhead 84: 84: Number of degrees of freedom in T-Coupling group System is 33.00 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 84: NVE simulation: will use the initial temperature of 68.810 K for 84: determining the Verlet buffer size 84: 84: 84: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 84: COM removal frequency is set to (5). 84: Other settings require a global communication frequency of 100. 84: Note that this will require additional global communication steps, 84: which will reduce performance when using multiple ranks. 84: Consider setting nstcomm to a multiple of 100. 84: 84: 84: There were 4 NOTEs 84: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 84: Can not increase nstlist because an NVE ensemble is used 84: Using 1 MPI thread 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'Argon' 84: 16 steps, 0.0 ps. 84: Generated 1 of the 1 non-bonded parameter combinations 84: 84: Excluding 1 bonded neighbours molecule type 'Argon' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.032 0.032 99.5 84: (ns/day) (hour/ns) 84: Performance: 45.598 0.526 84: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_reference.edr as single precision energy file 84: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.edr as single precision energy file 84: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/16 (472 ms) 84: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/17 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 84: Setting nstcalcenergy (100) equal to nstenergy (1) 84: 84: 84: WARNING 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 84: The Berendsen barostat does not generate any strictly correct ensemble, 84: and should not be used for new production simulations (in our opinion). 84: We recommend using the C-rescale barostat instead. 84: 84: Number of degrees of freedom in T-Coupling group System is 33.00 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 84: NVE simulation: will use the initial temperature of 68.810 K for 84: determining the Verlet buffer size 84: 84: 84: There were 3 NOTEs 84: 84: There was 1 WARNING 84: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 84: Can not increase nstlist because an NVE ensemble is used 84: Using 1 MPI thread 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'Argon' 84: 16 steps, 0.0 ps. 84: Generated 1 of the 1 non-bonded parameter combinations 84: 84: Excluding 1 bonded neighbours molecule type 'Argon' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.028 0.028 99.4 84: (ns/day) (hour/ns) 84: Performance: 51.571 0.465 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 84: Setting nstcalcenergy (100) equal to nstenergy (1) 84: 84: 84: WARNING 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 84: The Berendsen barostat does not generate any strictly correct ensemble, 84: and should not be used for new production simulations (in our opinion). 84: We recommend using the C-rescale barostat instead. 84: 84: Number of degrees of freedom in T-Coupling group System is 33.00 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 84: NVE simulation: will use the initial temperature of 68.810 K for 84: determining the Verlet buffer size 84: 84: 84: There were 3 NOTEs 84: 84: There was 1 WARNING 84: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 84: Can not increase nstlist because an NVE ensemble is used 84: Using 1 MPI thread 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'Argon' 84: 16 steps, 0.0 ps. 84: Generated 1 of the 1 non-bonded parameter combinations 84: 84: Excluding 1 bonded neighbours molecule type 'Argon' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.023 0.023 99.3 84: (ns/day) (hour/ns) 84: Performance: 62.718 0.383 84: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_reference.edr as single precision energy file 84: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.edr as single precision energy file 84: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 84: Setting nstcalcenergy (100) equal to nstenergy (4) 84: 84: 84: WARNING 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 84: The Berendsen barostat does not generate any strictly correct ensemble, 84: and should not be used for new production simulations (in our opinion). 84: We recommend using the C-rescale barostat instead. 84: 84: Number of degrees of freedom in T-Coupling group System is 33.00 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 84: NVE simulation: will use the initial temperature of 68.810 K for 84: determining the Verlet buffer size 84: 84: 84: There were 3 NOTEs 84: 84: There was 1 WARNING 84: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 84: Can not increase nstlist because an NVE ensemble is used 84: Using 1 MPI thread 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'Argon' 84: 16 steps, 0.0 ps. 84: Generated 1 of the 1 non-bonded parameter combinations 84: 84: Excluding 1 bonded neighbours molecule type 'Argon' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.030 0.030 99.4 84: (ns/day) (hour/ns) 84: Performance: 48.496 0.495 84: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_reference.edr as single precision energy file 84: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.edr as single precision energy file 84: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 84: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 84: setting nstcomm equal to nstcalcenergy for less overhead 84: 84: 84: WARNING 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 84: The Berendsen barostat does not generate any strictly correct ensemble, 84: and should not be used for new production simulations (in our opinion). 84: We recommend using the C-rescale barostat instead. 84: 84: Number of degrees of freedom in T-Coupling group System is 33.00 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 84: NVE simulation: will use the initial temperature of 68.810 K for 84: determining the Verlet buffer size 84: 84: 84: There were 3 NOTEs 84: 84: There was 1 WARNING 84: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 84: Can not increase nstlist because an NVE ensemble is used 84: Using 1 MPI thread 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'Argon' 84: 16 steps, 0.0 ps. 84: Generated 1 of the 1 non-bonded parameter combinations 84: 84: Excluding 1 bonded neighbours molecule type 'Argon' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.040 0.040 99.6 84: (ns/day) (hour/ns) 84: Performance: 36.816 0.652 84: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_reference.edr as single precision energy file 84: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.edr as single precision energy file 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 84: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 84: setting nstcomm equal to nstcalcenergy for less overhead 84: 84: 84: WARNING 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 84: The Berendsen barostat does not generate any strictly correct ensemble, 84: and should not be used for new production simulations (in our opinion). 84: We recommend using the C-rescale barostat instead. 84: 84: Number of degrees of freedom in T-Coupling group System is 33.00 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 84: NVE simulation: will use the initial temperature of 68.810 K for 84: determining the Verlet buffer size 84: 84: 84: There were 3 NOTEs 84: 84: There was 1 WARNING 84: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 84: Can not increase nstlist because an NVE ensemble is used 84: Using 1 MPI thread 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'Argon' 84: 16 steps, 0.0 ps. 84: Generated 1 of the 1 non-bonded parameter combinations 84: 84: Excluding 1 bonded neighbours molecule type 'Argon' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.031 0.032 99.5 84: (ns/day) (hour/ns) 84: Performance: 46.602 0.515 84: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_reference.edr as single precision energy file 84: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.edr as single precision energy file 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 84: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 84: setting nstcomm equal to nstcalcenergy for less overhead 84: 84: 84: WARNING 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 84: The Berendsen barostat does not generate any strictly correct ensemble, 84: and should not be used for new production simulations (in our opinion). 84: We recommend using the C-rescale barostat instead. 84: 84: Number of degrees of freedom in T-Coupling group System is 33.00 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 84: NVE simulation: will use the initial temperature of 68.810 K for 84: determining the Verlet buffer size 84: 84: 84: There were 3 NOTEs 84: 84: There was 1 WARNING 84: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 84: Can not increase nstlist because an NVE ensemble is used 84: Using 1 MPI thread 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'Argon' 84: 16 steps, 0.0 ps. 84: Generated 1 of the 1 non-bonded parameter combinations 84: 84: Excluding 1 bonded neighbours molecule type 'Argon' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.032 0.032 99.5 84: (ns/day) (hour/ns) 84: Performance: 45.933 0.522 84: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_reference.edr as single precision energy file 84: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.edr as single precision energy file 84: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/17 (478 ms) 84: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/18 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]: 84: Setting nstcalcenergy (100) equal to nstenergy (1) 84: 84: Number of degrees of freedom in T-Coupling group System is 33.00 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]: 84: NVE simulation: will use the initial temperature of 68.810 K for 84: determining the Verlet buffer size 84: 84: 84: There were 3 NOTEs 84: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 84: Can not increase nstlist because an NVE ensemble is used 84: Using 1 MPI thread 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'Argon' 84: 16 steps, 0.0 ps. 84: Generated 1 of the 1 non-bonded parameter combinations 84: 84: Excluding 1 bonded neighbours molecule type 'Argon' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.034 0.034 99.5 84: (ns/day) (hour/ns) 84: Performance: 43.283 0.554 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]: 84: Setting nstcalcenergy (100) equal to nstenergy (1) 84: 84: Number of degrees of freedom in T-Coupling group System is 33.00 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]: 84: NVE simulation: will use the initial temperature of 68.810 K for 84: determining the Verlet buffer size 84: 84: 84: There were 3 NOTEs 84: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 84: Can not increase nstlist because an NVE ensemble is used 84: Using 1 MPI thread 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'Argon' 84: 16 steps, 0.0 ps. 84: Generated 1 of the 1 non-bonded parameter combinations 84: 84: Excluding 1 bonded neighbours molecule type 'Argon' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.031 0.031 99.5 84: (ns/day) (hour/ns) 84: Performance: 47.534 0.505 84: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_reference.edr as single precision energy file 84: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18.edr as single precision energy file 84: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]: 84: Setting nstcalcenergy (100) equal to nstenergy (4) 84: 84: Number of degrees of freedom in T-Coupling group System is 33.00 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]: 84: NVE simulation: will use the initial temperature of 68.810 K for 84: determining the Verlet buffer size 84: 84: 84: There were 3 NOTEs 84: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 84: Can not increase nstlist because an NVE ensemble is used 84: Using 1 MPI thread 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'Argon' 84: 16 steps, 0.0 ps. 84: Generated 1 of the 1 non-bonded parameter combinations 84: 84: Excluding 1 bonded neighbours molecule type 'Argon' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.025 0.025 99.3 84: (ns/day) (hour/ns) 84: Performance: 58.420 0.411 84: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_reference.edr as single precision energy file 84: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18.edr as single precision energy file 84: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]: 84: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 84: setting nstcomm equal to nstcalcenergy for less overhead 84: 84: Number of degrees of freedom in T-Coupling group System is 33.00 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]: 84: NVE simulation: will use the initial temperature of 68.810 K for 84: determining the Verlet buffer size 84: 84: 84: There were 3 NOTEs 84: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 84: Can not increase nstlist because an NVE ensemble is used 84: Using 1 MPI thread 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'Argon' 84: 16 steps, 0.0 ps. 84: Generated 1 of the 1 non-bonded parameter combinations 84: 84: Excluding 1 bonded neighbours molecule type 'Argon' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.034 0.035 99.5 84: (ns/day) (hour/ns) 84: Performance: 42.554 0.564 84: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_reference.edr as single precision energy file 84: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18.edr as single precision energy file 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]: 84: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 84: setting nstcomm equal to nstcalcenergy for less overhead 84: 84: Number of degrees of freedom in T-Coupling group System is 33.00 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]: 84: NVE simulation: will use the initial temperature of 68.810 K for 84: determining the Verlet buffer size 84: 84: 84: There were 3 NOTEs 84: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 84: Can not increase nstlist because an NVE ensemble is used 84: Using 1 MPI thread 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'Argon' 84: 16 steps, 0.0 ps. 84: Generated 1 of the 1 non-bonded parameter combinations 84: 84: Excluding 1 bonded neighbours molecule type 'Argon' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.040 0.040 99.5 84: (ns/day) (hour/ns) 84: Performance: 36.946 0.650 84: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_reference.edr as single precision energy file 84: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18.edr as single precision energy file 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]: 84: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 84: setting nstcomm equal to nstcalcenergy for less overhead 84: 84: Number of degrees of freedom in T-Coupling group System is 33.00 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]: 84: NVE simulation: will use the initial temperature of 68.810 K for 84: determining the Verlet buffer size 84: 84: 84: There were 3 NOTEs 84: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 84: Can not increase nstlist because an NVE ensemble is used 84: Using 1 MPI thread 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'Argon' 84: 16 steps, 0.0 ps. 84: Generated 1 of the 1 non-bonded parameter combinations 84: 84: Excluding 1 bonded neighbours molecule type 'Argon' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.033 0.033 99.5 84: (ns/day) (hour/ns) 84: Performance: 44.639 0.538 84: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_reference.edr as single precision energy file 84: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18.edr as single precision energy file 84: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/18 (478 ms) 84: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/19 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_input.mdp]: 84: Setting nstcalcenergy (100) equal to nstenergy (1) 84: 84: Number of degrees of freedom in T-Coupling group System is 33.00 84: 84: There were 2 NOTEs 84: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 84: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 84: 84: Using 1 MPI thread 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'Argon' 84: 16 steps, 0.0 ps. 84: Generated 1 of the 1 non-bonded parameter combinations 84: 84: Excluding 1 bonded neighbours molecule type 'Argon' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.029 0.029 99.1 84: (ns/day) (hour/ns) 84: Performance: 50.312 0.477 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_input.mdp]: 84: Setting nstcalcenergy (100) equal to nstenergy (1) 84: 84: Number of degrees of freedom in T-Coupling group System is 33.00 84: 84: There were 2 NOTEs 84: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 84: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 84: 84: Using 1 MPI thread 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'Argon' 84: 16 steps, 0.0 ps. 84: Generated 1 of the 1 non-bonded parameter combinations 84: 84: Excluding 1 bonded neighbours molecule type 'Argon' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.024 0.025 98.9 84: (ns/day) (hour/ns) 84: Performance: 59.829 0.401 84: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_reference.edr as single precision energy file 84: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19.edr as single precision energy file 84: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_input.mdp]: 84: Setting nstcalcenergy (100) equal to nstenergy (4) 84: 84: Number of degrees of freedom in T-Coupling group System is 33.00 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_input.mdp]: 84: COM removal frequency is set to (5). 84: Other settings require a global communication frequency of 2. 84: Note that this will require additional global communication steps, 84: which will reduce performance when using multiple ranks. 84: Consider setting nstcomm to a multiple of 2. 84: 84: 84: There were 3 NOTEs 84: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 84: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 84: 84: Using 1 MPI thread 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'Argon' 84: 16 steps, 0.0 ps. 84: Generated 1 of the 1 non-bonded parameter combinations 84: 84: Excluding 1 bonded neighbours molecule type 'Argon' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.028 0.028 99.1 84: (ns/day) (hour/ns) 84: Performance: 52.613 0.456 84: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_reference.edr as single precision energy file 84: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19.edr as single precision energy file 84: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_input.mdp]: 84: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 84: setting nstcomm equal to nstcalcenergy for less overhead 84: 84: Number of degrees of freedom in T-Coupling group System is 33.00 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_input.mdp]: 84: COM removal frequency is set to (5). 84: Other settings require a global communication frequency of 2. 84: Note that this will require additional global communication steps, 84: which will reduce performance when using multiple ranks. 84: Consider setting nstcomm to a multiple of 2. 84: 84: 84: There were 3 NOTEs 84: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 84: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 84: 84: Using 1 MPI thread 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'Argon' 84: 16 steps, 0.0 ps. 84: Generated 1 of the 1 non-bonded parameter combinations 84: 84: Excluding 1 bonded neighbours molecule type 'Argon' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.035 0.036 99.4 84: (ns/day) (hour/ns) 84: Performance: 41.195 0.583 84: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_reference.edr as single precision energy file 84: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19.edr as single precision energy file 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_input.mdp]: 84: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 84: setting nstcomm equal to nstcalcenergy for less overhead 84: 84: Number of degrees of freedom in T-Coupling group System is 33.00 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_input.mdp]: 84: COM removal frequency is set to (5). 84: Other settings require a global communication frequency of 2. 84: Note that this will require additional global communication steps, 84: which will reduce performance when using multiple ranks. 84: Consider setting nstcomm to a multiple of 2. 84: 84: 84: There were 3 NOTEs 84: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 84: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 84: 84: Using 1 MPI thread 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'Argon' 84: 16 steps, 0.0 ps. 84: Generated 1 of the 1 non-bonded parameter combinations 84: 84: Excluding 1 bonded neighbours molecule type 'Argon' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.034 0.034 99.3 84: (ns/day) (hour/ns) 84: Performance: 43.340 0.554 84: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_reference.edr as single precision energy file 84: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19.edr as single precision energy file 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_input.mdp]: 84: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 84: setting nstcomm equal to nstcalcenergy for less overhead 84: 84: Number of degrees of freedom in T-Coupling group System is 33.00 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_input.mdp]: 84: COM removal frequency is set to (5). 84: Other settings require a global communication frequency of 2. 84: Note that this will require additional global communication steps, 84: which will reduce performance when using multiple ranks. 84: Consider setting nstcomm to a multiple of 2. 84: 84: 84: There were 3 NOTEs 84: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 84: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 84: 84: Using 1 MPI thread 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'Argon' 84: 16 steps, 0.0 ps. 84: Generated 1 of the 1 non-bonded parameter combinations 84: 84: Excluding 1 bonded neighbours molecule type 'Argon' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.030 0.030 99.1 84: (ns/day) (hour/ns) 84: Performance: 49.287 0.487 84: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_reference.edr as single precision energy file 84: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19.edr as single precision energy file 84: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/19 (508 ms) 84: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/20 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]: 84: Setting nstcalcenergy (100) equal to nstenergy (1) 84: 84: 84: WARNING 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]: 84: The Berendsen barostat does not generate any strictly correct ensemble, 84: and should not be used for new production simulations (in our opinion). 84: We recommend using the C-rescale barostat instead. 84: 84: Number of degrees of freedom in T-Coupling group System is 33.00 84: 84: There were 2 NOTEs 84: 84: There was 1 WARNING 84: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 84: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 84: 84: Using 1 MPI thread 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'Argon' 84: 16 steps, 0.0 ps. 84: Generated 1 of the 1 non-bonded parameter combinations 84: 84: Excluding 1 bonded neighbours molecule type 'Argon' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.047 0.047 99.5 84: (ns/day) (hour/ns) 84: Performance: 31.301 0.767 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]: 84: Setting nstcalcenergy (100) equal to nstenergy (1) 84: 84: 84: WARNING 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]: 84: The Berendsen barostat does not generate any strictly correct ensemble, 84: and should not be used for new production simulations (in our opinion). 84: We recommend using the C-rescale barostat instead. 84: 84: Number of degrees of freedom in T-Coupling group System is 33.00 84: 84: There were 2 NOTEs 84: 84: There was 1 WARNING 84: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 84: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 84: 84: Using 1 MPI thread 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'Argon' 84: 16 steps, 0.0 ps. 84: Generated 1 of the 1 non-bonded parameter combinations 84: 84: Excluding 1 bonded neighbours molecule type 'Argon' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.036 0.037 99.3 84: (ns/day) (hour/ns) 84: Performance: 40.138 0.598 84: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_reference.edr as single precision energy file 84: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20.edr as single precision energy file 84: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]: 84: Setting nstcalcenergy (100) equal to nstenergy (4) 84: 84: 84: WARNING 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]: 84: The Berendsen barostat does not generate any strictly correct ensemble, 84: and should not be used for new production simulations (in our opinion). 84: We recommend using the C-rescale barostat instead. 84: 84: Number of degrees of freedom in T-Coupling group System is 33.00 84: 84: There were 2 NOTEs 84: 84: There was 1 WARNING 84: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 84: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 84: 84: Using 1 MPI thread 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'Argon' 84: 16 steps, 0.0 ps. 84: Generated 1 of the 1 non-bonded parameter combinations 84: 84: Excluding 1 bonded neighbours molecule type 'Argon' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.028 0.029 99.1 84: (ns/day) (hour/ns) 84: Performance: 51.122 0.469 84: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_reference.edr as single precision energy file 84: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20.edr as single precision energy file 84: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]: 84: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 84: setting nstcomm equal to nstcalcenergy for less overhead 84: 84: 84: WARNING 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]: 84: The Berendsen barostat does not generate any strictly correct ensemble, 84: and should not be used for new production simulations (in our opinion). 84: We recommend using the C-rescale barostat instead. 84: 84: Number of degrees of freedom in T-Coupling group System is 33.00 84: 84: There were 2 NOTEs 84: 84: There was 1 WARNING 84: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 84: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 84: 84: Using 1 MPI thread 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'Argon' 84: 16 steps, 0.0 ps. 84: Generated 1 of the 1 non-bonded parameter combinations 84: 84: Excluding 1 bonded neighbours molecule type 'Argon' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.030 0.030 99.2 84: (ns/day) (hour/ns) 84: Performance: 48.465 0.495 84: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_reference.edr as single precision energy file 84: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20.edr as single precision energy file 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]: 84: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 84: setting nstcomm equal to nstcalcenergy for less overhead 84: 84: 84: WARNING 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]: 84: The Berendsen barostat does not generate any strictly correct ensemble, 84: and should not be used for new production simulations (in our opinion). 84: We recommend using the C-rescale barostat instead. 84: 84: Number of degrees of freedom in T-Coupling group System is 33.00 84: 84: There were 2 NOTEs 84: 84: There was 1 WARNING 84: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 84: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 84: 84: Using 1 MPI thread 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'Argon' 84: 16 steps, 0.0 ps. 84: Generated 1 of the 1 non-bonded parameter combinations 84: 84: Excluding 1 bonded neighbours molecule type 'Argon' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.039 0.039 99.4 84: (ns/day) (hour/ns) 84: Performance: 37.254 0.644 84: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_reference.edr as single precision energy file 84: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20.edr as single precision energy file 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]: 84: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 84: setting nstcomm equal to nstcalcenergy for less overhead 84: 84: 84: WARNING 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]: 84: The Berendsen barostat does not generate any strictly correct ensemble, 84: and should not be used for new production simulations (in our opinion). 84: We recommend using the C-rescale barostat instead. 84: 84: Number of degrees of freedom in T-Coupling group System is 33.00 84: 84: There were 2 NOTEs 84: 84: There was 1 WARNING 84: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 84: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 84: 84: Using 1 MPI thread 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'Argon' 84: 16 steps, 0.0 ps. 84: Generated 1 of the 1 non-bonded parameter combinations 84: 84: Excluding 1 bonded neighbours molecule type 'Argon' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.033 0.033 99.1 84: (ns/day) (hour/ns) 84: Performance: 44.515 0.539 84: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_reference.edr as single precision energy file 84: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20.edr as single precision energy file 84: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/20 (526 ms) 84: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/21 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_input.mdp]: 84: Setting nstcalcenergy (100) equal to nstenergy (1) 84: 84: Number of degrees of freedom in T-Coupling group System is 33.00 84: 84: There were 2 NOTEs 84: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 84: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 84: 84: Using 1 MPI thread 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'Argon' 84: 16 steps, 0.0 ps. 84: Generated 1 of the 1 non-bonded parameter combinations 84: 84: Excluding 1 bonded neighbours molecule type 'Argon' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.042 0.043 99.3 84: (ns/day) (hour/ns) 84: Performance: 34.372 0.698 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_input.mdp]: 84: Setting nstcalcenergy (100) equal to nstenergy (1) 84: 84: Number of degrees of freedom in T-Coupling group System is 33.00 84: 84: There were 2 NOTEs 84: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 84: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 84: 84: Using 1 MPI thread 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'Argon' 84: 16 steps, 0.0 ps. 84: Generated 1 of the 1 non-bonded parameter combinations 84: 84: Excluding 1 bonded neighbours molecule type 'Argon' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.022 0.023 98.8 84: (ns/day) (hour/ns) 84: Performance: 64.765 0.371 84: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_reference.edr as single precision energy file 84: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21.edr as single precision energy file 84: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_input.mdp]: 84: Setting nstcalcenergy (100) equal to nstenergy (4) 84: 84: Number of degrees of freedom in T-Coupling group System is 33.00 84: 84: There were 2 NOTEs 84: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 84: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 84: 84: Using 1 MPI thread 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'Argon' 84: 16 steps, 0.0 ps. 84: Generated 1 of the 1 non-bonded parameter combinations 84: 84: Excluding 1 bonded neighbours molecule type 'Argon' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.032 0.032 98.9 84: (ns/day) (hour/ns) 84: Performance: 45.426 0.528 84: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_reference.edr as single precision energy file 84: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21.edr as single precision energy file 84: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_input.mdp]: 84: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 84: setting nstcomm equal to nstcalcenergy for less overhead 84: 84: Number of degrees of freedom in T-Coupling group System is 33.00 84: 84: There were 2 NOTEs 84: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 84: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 84: 84: Using 1 MPI thread 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'Argon' 84: 16 steps, 0.0 ps. 84: Generated 1 of the 1 non-bonded parameter combinations 84: 84: Excluding 1 bonded neighbours molecule type 'Argon' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.031 0.031 99.1 84: (ns/day) (hour/ns) 84: Performance: 46.658 0.514 84: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_reference.edr as single precision energy file 84: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21.edr as single precision energy file 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_input.mdp]: 84: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 84: setting nstcomm equal to nstcalcenergy for less overhead 84: 84: Number of degrees of freedom in T-Coupling group System is 33.00 84: 84: There were 2 NOTEs 84: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 84: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 84: 84: Using 1 MPI thread 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'Argon' 84: 16 steps, 0.0 ps. 84: Generated 1 of the 1 non-bonded parameter combinations 84: 84: Excluding 1 bonded neighbours molecule type 'Argon' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.029 0.029 99.0 84: (ns/day) (hour/ns) 84: Performance: 50.792 0.473 84: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_reference.edr as single precision energy file 84: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21.edr as single precision energy file 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_input.mdp]: 84: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 84: setting nstcomm equal to nstcalcenergy for less overhead 84: 84: Number of degrees of freedom in T-Coupling group System is 33.00 84: 84: There were 2 NOTEs 84: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 84: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 84: 84: Using 1 MPI thread 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'Argon' 84: 16 steps, 0.0 ps. 84: Generated 1 of the 1 non-bonded parameter combinations 84: 84: Excluding 1 bonded neighbours molecule type 'Argon' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.037 0.038 99.2 84: (ns/day) (hour/ns) 84: Performance: 38.952 0.616 84: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_reference.edr as single precision energy file 84: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21.edr as single precision energy file 84: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/21 (500 ms) 84: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/22 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_input.mdp]: 84: Setting nstcalcenergy (100) equal to nstenergy (1) 84: 84: Number of degrees of freedom in T-Coupling group System is 33.00 84: 84: There were 2 NOTEs 84: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 84: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 84: 84: Using 1 MPI thread 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'Argon' 84: 16 steps, 0.0 ps. 84: Generated 1 of the 1 non-bonded parameter combinations 84: 84: Excluding 1 bonded neighbours molecule type 'Argon' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.039 0.039 99.2 84: (ns/day) (hour/ns) 84: Performance: 37.540 0.639 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_input.mdp]: 84: Setting nstcalcenergy (100) equal to nstenergy (1) 84: 84: Number of degrees of freedom in T-Coupling group System is 33.00 84: 84: There were 2 NOTEs 84: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 84: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 84: 84: Using 1 MPI thread 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'Argon' 84: 16 steps, 0.0 ps. 84: Generated 1 of the 1 non-bonded parameter combinations 84: 84: Excluding 1 bonded neighbours molecule type 'Argon' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.030 0.030 99.2 84: (ns/day) (hour/ns) 84: Performance: 49.211 0.488 84: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_reference.edr as single precision energy file 84: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22.edr as single precision energy file 84: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_input.mdp]: 84: Setting nstcalcenergy (100) equal to nstenergy (4) 84: 84: Number of degrees of freedom in T-Coupling group System is 33.00 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_input.mdp]: 84: COM removal frequency is set to (5). 84: Other settings require a global communication frequency of 2. 84: Note that this will require additional global communication steps, 84: which will reduce performance when using multiple ranks. 84: Consider setting nstcomm to a multiple of 2. 84: 84: 84: There were 3 NOTEs 84: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 84: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 84: 84: Using 1 MPI thread 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'Argon' 84: 16 steps, 0.0 ps. 84: Generated 1 of the 1 non-bonded parameter combinations 84: 84: Excluding 1 bonded neighbours molecule type 'Argon' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.028 0.029 98.8 84: (ns/day) (hour/ns) 84: Performance: 51.199 0.469 84: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_reference.edr as single precision energy file 84: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22.edr as single precision energy file 84: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_input.mdp]: 84: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 84: setting nstcomm equal to nstcalcenergy for less overhead 84: 84: Number of degrees of freedom in T-Coupling group System is 33.00 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_input.mdp]: 84: COM removal frequency is set to (5). 84: Other settings require a global communication frequency of 2. 84: Note that this will require additional global communication steps, 84: which will reduce performance when using multiple ranks. 84: Consider setting nstcomm to a multiple of 2. 84: 84: 84: There were 3 NOTEs 84: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 84: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 84: 84: Using 1 MPI thread 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'Argon' 84: 16 steps, 0.0 ps. 84: Generated 1 of the 1 non-bonded parameter combinations 84: 84: Excluding 1 bonded neighbours molecule type 'Argon' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.051 0.052 99.4 84: (ns/day) (hour/ns) 84: Performance: 28.511 0.842 84: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_reference.edr as single precision energy file 84: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22.edr as single precision energy file 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_input.mdp]: 84: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 84: setting nstcomm equal to nstcalcenergy for less overhead 84: 84: Number of degrees of freedom in T-Coupling group System is 33.00 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_input.mdp]: 84: COM removal frequency is set to (5). 84: Other settings require a global communication frequency of 2. 84: Note that this will require additional global communication steps, 84: which will reduce performance when using multiple ranks. 84: Consider setting nstcomm to a multiple of 2. 84: 84: 84: There were 3 NOTEs 84: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 84: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 84: 84: Using 1 MPI thread 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'Argon' 84: 16 steps, 0.0 ps. 84: Generated 1 of the 1 non-bonded parameter combinations 84: 84: Excluding 1 bonded neighbours molecule type 'Argon' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.043 0.044 99.4 84: (ns/day) (hour/ns) 84: Performance: 33.732 0.711 84: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_reference.edr as single precision energy file 84: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22.edr as single precision energy file 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_input.mdp]: 84: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 84: setting nstcomm equal to nstcalcenergy for less overhead 84: 84: Number of degrees of freedom in T-Coupling group System is 33.00 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_input.mdp]: 84: COM removal frequency is set to (5). 84: Other settings require a global communication frequency of 2. 84: Note that this will require additional global communication steps, 84: which will reduce performance when using multiple ranks. 84: Consider setting nstcomm to a multiple of 2. 84: 84: 84: There were 3 NOTEs 84: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 84: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 84: 84: Using 1 MPI thread 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'Argon' 84: 16 steps, 0.0 ps. 84: Generated 1 of the 1 non-bonded parameter combinations 84: 84: Excluding 1 bonded neighbours molecule type 'Argon' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.027 0.027 98.9 84: (ns/day) (hour/ns) 84: Performance: 54.343 0.442 84: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_reference.edr as single precision energy file 84: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22.edr as single precision energy file 84: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/22 (522 ms) 84: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/23 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 84: Setting nstcalcenergy (100) equal to nstenergy (1) 84: 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 84: MTTK coupling is deprecated and will soon be removed 84: 84: 84: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 84: for current Trotter decomposition methods with vv, nsttcouple and 84: nstpcouple must be equal. Both have been reset to 84: min(nsttcouple,nstpcouple) = 2 84: 84: Number of degrees of freedom in T-Coupling group System is 33.00 84: 84: There were 4 NOTEs 84: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 84: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 84: 84: Using 1 MPI thread 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'Argon' 84: 16 steps, 0.0 ps. 84: Generated 1 of the 1 non-bonded parameter combinations 84: 84: Excluding 1 bonded neighbours molecule type 'Argon' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.046 0.046 99.2 84: (ns/day) (hour/ns) 84: Performance: 31.615 0.759 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 84: Setting nstcalcenergy (100) equal to nstenergy (1) 84: 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 84: MTTK coupling is deprecated and will soon be removed 84: 84: 84: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 84: for current Trotter decomposition methods with vv, nsttcouple and 84: nstpcouple must be equal. Both have been reset to 84: min(nsttcouple,nstpcouple) = 2 84: 84: Number of degrees of freedom in T-Coupling group System is 33.00 84: 84: There were 4 NOTEs 84: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 84: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 84: 84: Using 1 MPI thread 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'Argon' 84: 16 steps, 0.0 ps. 84: Generated 1 of the 1 non-bonded parameter combinations 84: 84: Excluding 1 bonded neighbours molecule type 'Argon' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.060 0.060 99.4 84: (ns/day) (hour/ns) 84: Performance: 24.467 0.981 84: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_reference.edr as single precision energy file 84: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23.edr as single precision energy file 84: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 84: Setting nstcalcenergy (100) equal to nstenergy (4) 84: 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 84: MTTK coupling is deprecated and will soon be removed 84: 84: 84: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 84: for current Trotter decomposition methods with vv, nsttcouple and 84: nstpcouple must be equal. Both have been reset to 84: min(nsttcouple,nstpcouple) = 2 84: 84: Number of degrees of freedom in T-Coupling group System is 33.00 84: 84: NOTE 5 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 84: COM removal frequency is set to (5). 84: Other settings require a global communication frequency of 2. 84: Note that this will require additional global communication steps, 84: which will reduce performance when using multiple ranks. 84: Consider setting nstcomm to a multiple of 2. 84: 84: 84: There were 5 NOTEs 84: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 84: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 84: 84: Using 1 MPI thread 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'Argon' 84: 16 steps, 0.0 ps. 84: Generated 1 of the 1 non-bonded parameter combinations 84: 84: Excluding 1 bonded neighbours molecule type 'Argon' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.027 0.027 98.8 84: (ns/day) (hour/ns) 84: Performance: 53.471 0.449 84: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_reference.edr as single precision energy file 84: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23.edr as single precision energy file 84: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 84: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 84: setting nstcomm equal to nstcalcenergy for less overhead 84: 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 84: MTTK coupling is deprecated and will soon be removed 84: 84: 84: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 84: for current Trotter decomposition methods with vv, nsttcouple and 84: nstpcouple must be equal. Both have been reset to 84: min(nsttcouple,nstpcouple) = 2 84: 84: Number of degrees of freedom in T-Coupling group System is 33.00 84: 84: NOTE 5 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 84: COM removal frequency is set to (5). 84: Other settings require a global communication frequency of 2. 84: Note that this will require additional global communication steps, 84: which will reduce performance when using multiple ranks. 84: Consider setting nstcomm to a multiple of 2. 84: 84: 84: There were 5 NOTEs 84: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 84: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 84: 84: Using 1 MPI thread 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'Argon' 84: 16 steps, 0.0 ps. 84: Generated 1 of the 1 non-bonded parameter combinations 84: 84: Excluding 1 bonded neighbours molecule type 'Argon' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.029 0.029 98.8 84: (ns/day) (hour/ns) 84: Performance: 50.534 0.475 84: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_reference.edr as single precision energy file 84: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23.edr as single precision energy file 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 84: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 84: setting nstcomm equal to nstcalcenergy for less overhead 84: 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 84: MTTK coupling is deprecated and will soon be removed 84: 84: 84: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 84: for current Trotter decomposition methods with vv, nsttcouple and 84: nstpcouple must be equal. Both have been reset to 84: min(nsttcouple,nstpcouple) = 2 84: 84: Number of degrees of freedom in T-Coupling group System is 33.00 84: 84: NOTE 5 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 84: COM removal frequency is set to (5). 84: Other settings require a global communication frequency of 2. 84: Note that this will require additional global communication steps, 84: which will reduce performance when using multiple ranks. 84: Consider setting nstcomm to a multiple of 2. 84: 84: 84: There were 5 NOTEs 84: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 84: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 84: 84: Using 1 MPI thread 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'Argon' 84: 16 steps, 0.0 ps. 84: Generated 1 of the 1 non-bonded parameter combinations 84: 84: Excluding 1 bonded neighbours molecule type 'Argon' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.027 0.027 98.7 84: (ns/day) (hour/ns) 84: Performance: 53.647 0.447 84: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_reference.edr as single precision energy file 84: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23.edr as single precision energy file 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 84: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 84: setting nstcomm equal to nstcalcenergy for less overhead 84: 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 84: MTTK coupling is deprecated and will soon be removed 84: 84: 84: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 84: for current Trotter decomposition methods with vv, nsttcouple and 84: nstpcouple must be equal. Both have been reset to 84: min(nsttcouple,nstpcouple) = 2 84: 84: Number of degrees of freedom in T-Coupling group System is 33.00 84: 84: NOTE 5 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 84: COM removal frequency is set to (5). 84: Other settings require a global communication frequency of 2. 84: Note that this will require additional global communication steps, 84: which will reduce performance when using multiple ranks. 84: Consider setting nstcomm to a multiple of 2. 84: 84: 84: There were 5 NOTEs 84: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 84: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 84: 84: Using 1 MPI thread 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'Argon' 84: 16 steps, 0.0 ps. 84: Generated 1 of the 1 non-bonded parameter combinations 84: 84: Excluding 1 bonded neighbours molecule type 'Argon' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.036 0.036 99.0 84: (ns/day) (hour/ns) 84: Performance: 40.910 0.587 84: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_reference.edr as single precision energy file 84: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23.edr as single precision energy file 84: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/23 (512 ms) 84: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/24 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24_input.mdp]: 84: Setting nstcalcenergy (100) equal to nstenergy (1) 84: 84: Number of degrees of freedom in T-Coupling group System is 33.00 84: 84: There were 2 NOTEs 84: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 84: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 84: 84: Using 1 MPI thread 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'Argon' 84: 16 steps, 0.0 ps. 84: Generated 1 of the 1 non-bonded parameter combinations 84: 84: Excluding 1 bonded neighbours molecule type 'Argon' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.040 0.040 99.3 84: (ns/day) (hour/ns) 84: Performance: 36.538 0.657 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24_input.mdp]: 84: Setting nstcalcenergy (100) equal to nstenergy (1) 84: 84: Number of degrees of freedom in T-Coupling group System is 33.00 84: 84: There were 2 NOTEs 84: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 84: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 84: 84: Using 1 MPI thread 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'Argon' 84: 16 steps, 0.0 ps. 84: Generated 1 of the 1 non-bonded parameter combinations 84: 84: Excluding 1 bonded neighbours molecule type 'Argon' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.024 0.025 98.9 84: (ns/day) (hour/ns) 84: Performance: 59.375 0.404 84: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24_reference.edr as single precision energy file 84: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24.edr as single precision energy file 84: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24_input.mdp]: 84: Setting nstcalcenergy (100) equal to nstenergy (4) 84: 84: Number of degrees of freedom in T-Coupling group System is 33.00 84: 84: There were 2 NOTEs 84: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 84: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 84: 84: Using 1 MPI thread 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'Argon' 84: 16 steps, 0.0 ps. 84: Generated 1 of the 1 non-bonded parameter combinations 84: 84: Excluding 1 bonded neighbours molecule type 'Argon' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.023 0.023 98.7 84: (ns/day) (hour/ns) 84: Performance: 64.030 0.375 84: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24_reference.edr as single precision energy file 84: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24.edr as single precision energy file 84: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24_input.mdp]: 84: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 84: setting nstcomm equal to nstcalcenergy for less overhead 84: 84: Number of degrees of freedom in T-Coupling group System is 33.00 84: 84: There were 2 NOTEs 84: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 84: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 84: 84: Using 1 MPI thread 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'Argon' 84: 16 steps, 0.0 ps. 84: Generated 1 of the 1 non-bonded parameter combinations 84: 84: Excluding 1 bonded neighbours molecule type 'Argon' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.032 0.033 99.0 84: (ns/day) (hour/ns) 84: Performance: 45.040 0.533 84: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24_reference.edr as single precision energy file 84: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24.edr as single precision energy file 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24_input.mdp]: 84: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 84: setting nstcomm equal to nstcalcenergy for less overhead 84: 84: Number of degrees of freedom in T-Coupling group System is 33.00 84: 84: There were 2 NOTEs 84: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 84: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 84: 84: Using 1 MPI thread 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'Argon' 84: 16 steps, 0.0 ps. 84: Generated 1 of the 1 non-bonded parameter combinations 84: 84: Excluding 1 bonded neighbours molecule type 'Argon' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.026 0.026 99.1 84: (ns/day) (hour/ns) 84: Performance: 56.410 0.425 84: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24_reference.edr as single precision energy file 84: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24.edr as single precision energy file 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24_input.mdp]: 84: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 84: setting nstcomm equal to nstcalcenergy for less overhead 84: 84: Number of degrees of freedom in T-Coupling group System is 33.00 84: 84: There were 2 NOTEs 84: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 84: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 84: 84: Using 1 MPI thread 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'Argon' 84: 16 steps, 0.0 ps. 84: Generated 1 of the 1 non-bonded parameter combinations 84: 84: Excluding 1 bonded neighbours molecule type 'Argon' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.025 0.025 98.9 84: (ns/day) (hour/ns) 84: Performance: 58.376 0.411 84: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24_reference.edr as single precision energy file 84: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24.edr as single precision energy file 84: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/24 (428 ms) 84: [----------] 25 tests from PropagatorsWithCoupling/PeriodicActionsTest (12499 ms total) 84: 84: [----------] Global test environment tear-down 84: [==========] 25 tests from 1 test suite ran. (12551 ms total) 84: [ PASSED ] 25 tests. 84/92 Test #84: MdrunCoordinationCouplingTests1Rank ....... Passed 12.64 sec test 85 Start 85: MdrunCoordinationCouplingTests2Ranks 85: Test command: /build/reproducible-path/gromacs-2025.1/build/basic/bin/mdrun-coordination-coupling-test "-ntmpi" "2" "--gtest_output=xml:/build/reproducible-path/gromacs-2025.1/build/basic/Testing/Temporary/MdrunCoordinationCouplingTests2Ranks.xml" 85: Working Directory: /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests 85: Test timeout computed to be: 1920 85: [==========] Running 25 tests from 1 test suite. 85: [----------] Global test environment set-up. 85: [----------] 25 tests from PropagatorsWithCoupling/PeriodicActionsTest 85: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/0 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 85: Setting nstcalcenergy (100) equal to nstenergy (1) 85: 85: Number of degrees of freedom in T-Coupling group System is 33.00 85: 85: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 85: NVE simulation: will use the initial temperature of 68.810 K for 85: determining the Verlet buffer size 85: 85: 85: There were 3 NOTEs 85: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 85: Can not increase nstlist because an NVE ensemble is used 85: Using 2 MPI threads 85: Using 1 OpenMP thread per tMPI thread 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'Argon' 85: 16 steps, 0.0 ps. 85: Generated 1 of the 1 non-bonded parameter combinations 85: 85: Excluding 1 bonded neighbours molecule type 'Argon' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: 85: Dynamic load balancing report: 85: DLB was off during the run due to low measured imbalance. 85: Average load imbalance: 0.8%. 85: The balanceable part of the MD step is 43%, load imbalance is computed from this. 85: Part of the total run time spent waiting due to load imbalance: 0.3%. 85: 85: 85: NOTE: 43 % of the run time was spent communicating energies, 85: you might want to increase some nst* mdp options 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.092 0.046 198.6 85: (ns/day) (hour/ns) 85: Performance: 31.737 0.756 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 85: Setting nstcalcenergy (100) equal to nstenergy (1) 85: 85: Number of degrees of freedom in T-Coupling group System is 33.00 85: 85: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 85: NVE simulation: will use the initial temperature of 68.810 K for 85: determining the Verlet buffer size 85: 85: 85: There were 3 NOTEs 85: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 85: Can not increase nstlist because an NVE ensemble is used 85: Using 2 MPI threads 85: Using 1 OpenMP thread per tMPI thread 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'Argon' 85: 16 steps, 0.0 ps. 85: Generated 1 of the 1 non-bonded parameter combinations 85: 85: Excluding 1 bonded neighbours molecule type 'Argon' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: 85: Dynamic load balancing report: 85: DLB was off during the run due to low measured imbalance. 85: Average load imbalance: 1.1%. 85: The balanceable part of the MD step is 57%, load imbalance is computed from this. 85: Part of the total run time spent waiting due to load imbalance: 0.6%. 85: 85: 85: NOTE: 42 % of the run time was spent communicating energies, 85: you might want to increase some nst* mdp options 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.047 0.024 197.4 85: (ns/day) (hour/ns) 85: Performance: 61.577 0.390 85: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as single precision energy file 85: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 85: Setting nstcalcenergy (100) equal to nstenergy (4) 85: 85: Number of degrees of freedom in T-Coupling group System is 33.00 85: 85: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 85: NVE simulation: will use the initial temperature of 68.810 K for 85: determining the Verlet buffer size 85: 85: 85: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 85: COM removal frequency is set to (5). 85: Other settings require a global communication frequency of 4. 85: Note that this will require additional global communication steps, 85: which will reduce performance when using multiple ranks. 85: Consider setting nstcomm to a multiple of 4. 85: 85: 85: There were 4 NOTEs 85: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 85: Can not increase nstlist because an NVE ensemble is used 85: Using 2 MPI threads 85: Using 1 OpenMP thread per tMPI thread 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'Argon' 85: 16 steps, 0.0 ps. 85: Generated 1 of the 1 non-bonded parameter combinations 85: 85: Excluding 1 bonded neighbours molecule type 'Argon' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: 85: Dynamic load balancing report: 85: DLB was off during the run due to low measured imbalance. 85: Average load imbalance: 1.0%. 85: The balanceable part of the MD step is 19%, load imbalance is computed from this. 85: Part of the total run time spent waiting due to load imbalance: 0.2%. 85: 85: 85: NOTE: 48 % of the run time was spent communicating energies, 85: you might want to increase some nst* mdp options 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.377 0.193 195.5 85: (ns/day) (hour/ns) 85: Performance: 7.620 3.150 85: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as single precision energy file 85: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 85: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 85: setting nstcomm equal to nstcalcenergy for less overhead 85: 85: Number of degrees of freedom in T-Coupling group System is 33.00 85: 85: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 85: NVE simulation: will use the initial temperature of 68.810 K for 85: determining the Verlet buffer size 85: 85: 85: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 85: COM removal frequency is set to (5). 85: Other settings require a global communication frequency of 100. 85: Note that this will require additional global communication steps, 85: which will reduce performance when using multiple ranks. 85: Consider setting nstcomm to a multiple of 100. 85: 85: 85: There were 4 NOTEs 85: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 85: Can not increase nstlist because an NVE ensemble is used 85: Using 2 MPI threads 85: Using 1 OpenMP thread per tMPI thread 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'Argon' 85: 16 steps, 0.0 ps. 85: Generated 1 of the 1 non-bonded parameter combinations 85: 85: Excluding 1 bonded neighbours molecule type 'Argon' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: 85: Dynamic load balancing report: 85: DLB was turned on during the run due to measured imbalance. 85: Average load imbalance: 9.1%. 85: The balanceable part of the MD step is 37%, load imbalance is computed from this. 85: Part of the total run time spent waiting due to load imbalance: 3.3%. 85: Steps where the load balancing was limited by -rdd, -rcon and/or -dds: X 0 % 85: 85: 85: NOTE: 44 % of the run time was spent communicating energies, 85: you might want to increase some nst* mdp options 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.084 0.044 189.0 85: (ns/day) (hour/ns) 85: Performance: 33.240 0.722 85: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as single precision energy file 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 85: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 85: setting nstcomm equal to nstcalcenergy for less overhead 85: 85: Number of degrees of freedom in T-Coupling group System is 33.00 85: 85: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 85: NVE simulation: will use the initial temperature of 68.810 K for 85: determining the Verlet buffer size 85: 85: 85: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 85: COM removal frequency is set to (5). 85: Other settings require a global communication frequency of 100. 85: Note that this will require additional global communication steps, 85: which will reduce performance when using multiple ranks. 85: Consider setting nstcomm to a multiple of 100. 85: 85: 85: There were 4 NOTEs 85: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 85: Can not increase nstlist because an NVE ensemble is used 85: Using 2 MPI threads 85: Using 1 OpenMP thread per tMPI thread 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'Argon' 85: 16 steps, 0.0 ps. 85: Generated 1 of the 1 non-bonded parameter combinations 85: 85: Excluding 1 bonded neighbours molecule type 'Argon' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: 85: Dynamic load balancing report: 85: DLB was off during the run due to low measured imbalance. 85: Average load imbalance: 2.0%. 85: The balanceable part of the MD step is 40%, load imbalance is computed from this. 85: Part of the total run time spent waiting due to load imbalance: 0.8%. 85: 85: 85: NOTE: 44 % of the run time was spent communicating energies, 85: you might want to increase some nst* mdp options 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.048 0.024 197.3 85: (ns/day) (hour/ns) 85: Performance: 60.815 0.395 85: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as single precision energy file 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 85: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 85: setting nstcomm equal to nstcalcenergy for less overhead 85: 85: Number of degrees of freedom in T-Coupling group System is 33.00 85: 85: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 85: NVE simulation: will use the initial temperature of 68.810 K for 85: determining the Verlet buffer size 85: 85: 85: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 85: COM removal frequency is set to (5). 85: Other settings require a global communication frequency of 100. 85: Note that this will require additional global communication steps, 85: which will reduce performance when using multiple ranks. 85: Consider setting nstcomm to a multiple of 100. 85: 85: 85: There were 4 NOTEs 85: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 85: Can not increase nstlist because an NVE ensemble is used 85: Using 2 MPI threads 85: Using 1 OpenMP thread per tMPI thread 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'Argon' 85: 16 steps, 0.0 ps. 85: Generated 1 of the 1 non-bonded parameter combinations 85: 85: Excluding 1 bonded neighbours molecule type 'Argon' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: 85: Dynamic load balancing report: 85: DLB was off during the run due to low measured imbalance. 85: Average load imbalance: 2.2%. 85: The balanceable part of the MD step is 43%, load imbalance is computed from this. 85: Part of the total run time spent waiting due to load imbalance: 0.9%. 85: 85: 85: NOTE: 44 % of the run time was spent communicating energies, 85: you might want to increase some nst* mdp options 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.050 0.025 197.6 85: (ns/day) (hour/ns) 85: Performance: 57.974 0.414 85: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as single precision energy file 85: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/0 (730 ms) 85: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/1 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 85: Setting nstcalcenergy (100) equal to nstenergy (1) 85: 85: 85: WARNING 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 85: The Berendsen barostat does not generate any strictly correct ensemble, 85: and should not be used for new production simulations (in our opinion). 85: We recommend using the C-rescale barostat instead. 85: 85: Number of degrees of freedom in T-Coupling group System is 33.00 85: 85: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 85: NVE simulation: will use the initial temperature of 68.810 K for 85: determining the Verlet buffer size 85: 85: 85: There were 3 NOTEs 85: 85: There was 1 WARNING 85: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 85: Can not increase nstlist because an NVE ensemble is used 85: Using 2 MPI threads 85: Using 1 OpenMP thread per tMPI thread 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'Argon' 85: 16 steps, 0.0 ps. 85: Generated 1 of the 1 non-bonded parameter combinations 85: 85: Excluding 1 bonded neighbours molecule type 'Argon' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: 85: Dynamic load balancing report: 85: DLB was turned on during the run due to measured imbalance. 85: Average load imbalance: 26.9%. 85: The balanceable part of the MD step is 42%, load imbalance is computed from this. 85: Part of the total run time spent waiting due to load imbalance: 11.3%. 85: Steps where the load balancing was limited by -rdd, -rcon and/or -dds: X 0 % 85: 85: NOTE: 11.3 % of the available CPU time was lost due to load imbalance 85: in the domain decomposition. 85: You can consider manually changing the decomposition (option -dd); 85: e.g. by using fewer domains along the box dimension in which there is 85: considerable inhomogeneity in the simulated system. 85: 85: NOTE: 35 % of the run time was spent communicating energies, 85: you might want to increase some nst* mdp options 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.052 0.026 197.4 85: (ns/day) (hour/ns) 85: Performance: 55.457 0.433 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 85: Setting nstcalcenergy (100) equal to nstenergy (1) 85: 85: 85: WARNING 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 85: The Berendsen barostat does not generate any strictly correct ensemble, 85: and should not be used for new production simulations (in our opinion). 85: We recommend using the C-rescale barostat instead. 85: 85: Number of degrees of freedom in T-Coupling group System is 33.00 85: 85: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 85: NVE simulation: will use the initial temperature of 68.810 K for 85: determining the Verlet buffer size 85: 85: 85: There were 3 NOTEs 85: 85: There was 1 WARNING 85: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 85: Can not increase nstlist because an NVE ensemble is used 85: Using 2 MPI threads 85: Using 1 OpenMP thread per tMPI thread 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'Argon' 85: 16 steps, 0.0 ps. 85: Generated 1 of the 1 non-bonded parameter combinations 85: 85: Excluding 1 bonded neighbours molecule type 'Argon' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: 85: Dynamic load balancing report: 85: DLB was off during the run due to low measured imbalance. 85: Average load imbalance: 1.0%. 85: The balanceable part of the MD step is 43%, load imbalance is computed from this. 85: Part of the total run time spent waiting due to load imbalance: 0.4%. 85: 85: 85: NOTE: 54 % of the run time was spent communicating energies, 85: you might want to increase some nst* mdp options 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.069 0.035 197.7 85: (ns/day) (hour/ns) 85: Performance: 42.375 0.566 85: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as single precision energy file 85: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 85: Setting nstcalcenergy (100) equal to nstenergy (4) 85: 85: 85: WARNING 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 85: The Berendsen barostat does not generate any strictly correct ensemble, 85: and should not be used for new production simulations (in our opinion). 85: We recommend using the C-rescale barostat instead. 85: 85: Number of degrees of freedom in T-Coupling group System is 33.00 85: 85: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 85: NVE simulation: will use the initial temperature of 68.810 K for 85: determining the Verlet buffer size 85: 85: 85: There were 3 NOTEs 85: 85: There was 1 WARNING 85: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 85: Can not increase nstlist because an NVE ensemble is used 85: Using 2 MPI threads 85: Using 1 OpenMP thread per tMPI thread 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'Argon' 85: 16 steps, 0.0 ps. 85: Generated 1 of the 1 non-bonded parameter combinations 85: 85: Excluding 1 bonded neighbours molecule type 'Argon' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: 85: Dynamic load balancing report: 85: DLB was off during the run due to low measured imbalance. 85: Average load imbalance: 1.3%. 85: The balanceable part of the MD step is 13%, load imbalance is computed from this. 85: Part of the total run time spent waiting due to load imbalance: 0.2%. 85: 85: 85: NOTE: 11 % of the run time was spent in domain decomposition, 85: 1 % of the run time was spent in pair search, 85: you might want to increase nstlist (this has no effect on accuracy) 85: 85: NOTE: 38 % of the run time was spent communicating energies, 85: you might want to increase some nst* mdp options 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.092 0.046 198.6 85: (ns/day) (hour/ns) 85: Performance: 31.679 0.758 85: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as single precision energy file 85: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 85: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 85: setting nstcomm equal to nstcalcenergy for less overhead 85: 85: 85: WARNING 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 85: The Berendsen barostat does not generate any strictly correct ensemble, 85: and should not be used for new production simulations (in our opinion). 85: We recommend using the C-rescale barostat instead. 85: 85: Number of degrees of freedom in T-Coupling group System is 33.00 85: 85: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 85: NVE simulation: will use the initial temperature of 68.810 K for 85: determining the Verlet buffer size 85: 85: 85: There were 3 NOTEs 85: 85: There was 1 WARNING 85: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 85: Can not increase nstlist because an NVE ensemble is used 85: Using 2 MPI threads 85: Using 1 OpenMP thread per tMPI thread 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'Argon' 85: 16 steps, 0.0 ps. 85: Generated 1 of the 1 non-bonded parameter combinations 85: 85: Excluding 1 bonded neighbours molecule type 'Argon' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: 85: Dynamic load balancing report: 85: DLB was off during the run due to low measured imbalance. 85: Average load imbalance: 1.7%. 85: The balanceable part of the MD step is 21%, load imbalance is computed from this. 85: Part of the total run time spent waiting due to load imbalance: 0.4%. 85: 85: 85: NOTE: 13 % of the run time was spent in domain decomposition, 85: 1 % of the run time was spent in pair search, 85: you might want to increase nstlist (this has no effect on accuracy) 85: 85: NOTE: 39 % of the run time was spent communicating energies, 85: you might want to increase some nst* mdp options 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.059 0.030 197.8 85: (ns/day) (hour/ns) 85: Performance: 49.326 0.487 85: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as single precision energy file 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 85: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 85: setting nstcomm equal to nstcalcenergy for less overhead 85: 85: 85: WARNING 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 85: The Berendsen barostat does not generate any strictly correct ensemble, 85: and should not be used for new production simulations (in our opinion). 85: We recommend using the C-rescale barostat instead. 85: 85: Number of degrees of freedom in T-Coupling group System is 33.00 85: 85: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 85: NVE simulation: will use the initial temperature of 68.810 K for 85: determining the Verlet buffer size 85: 85: 85: There were 3 NOTEs 85: 85: There was 1 WARNING 85: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 85: Can not increase nstlist because an NVE ensemble is used 85: Using 2 MPI threads 85: Using 1 OpenMP thread per tMPI thread 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'Argon' 85: 16 steps, 0.0 ps. 85: Generated 1 of the 1 non-bonded parameter combinations 85: 85: Excluding 1 bonded neighbours molecule type 'Argon' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: 85: Dynamic load balancing report: 85: DLB was off during the run due to low measured imbalance. 85: Average load imbalance: 1.4%. 85: The balanceable part of the MD step is 25%, load imbalance is computed from this. 85: Part of the total run time spent waiting due to load imbalance: 0.4%. 85: 85: 85: NOTE: 41 % of the run time was spent communicating energies, 85: you might want to increase some nst* mdp options 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.065 0.033 197.8 85: (ns/day) (hour/ns) 85: Performance: 44.895 0.535 85: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as single precision energy file 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 85: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 85: setting nstcomm equal to nstcalcenergy for less overhead 85: 85: 85: WARNING 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 85: The Berendsen barostat does not generate any strictly correct ensemble, 85: and should not be used for new production simulations (in our opinion). 85: We recommend using the C-rescale barostat instead. 85: 85: Number of degrees of freedom in T-Coupling group System is 33.00 85: 85: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 85: NVE simulation: will use the initial temperature of 68.810 K for 85: determining the Verlet buffer size 85: 85: 85: There were 3 NOTEs 85: 85: There was 1 WARNING 85: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 85: Can not increase nstlist because an NVE ensemble is used 85: Using 2 MPI threads 85: Using 1 OpenMP thread per tMPI thread 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'Argon' 85: 16 steps, 0.0 ps. 85: Generated 1 of the 1 non-bonded parameter combinations 85: 85: Excluding 1 bonded neighbours molecule type 'Argon' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: 85: Dynamic load balancing report: 85: DLB was off during the run due to low measured imbalance. 85: Average load imbalance: 1.4%. 85: The balanceable part of the MD step is 24%, load imbalance is computed from this. 85: Part of the total run time spent waiting due to load imbalance: 0.3%. 85: 85: 85: NOTE: 50 % of the run time was spent communicating energies, 85: you might want to increase some nst* mdp options 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.100 0.050 198.7 85: (ns/day) (hour/ns) 85: Performance: 29.152 0.823 85: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as single precision energy file 85: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/1 (526 ms) 85: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/2 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 85: Setting nstcalcenergy (100) equal to nstenergy (1) 85: 85: Number of degrees of freedom in T-Coupling group System is 33.00 85: 85: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 85: NVE simulation: will use the initial temperature of 68.810 K for 85: determining the Verlet buffer size 85: 85: 85: There were 3 NOTEs 85: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 85: Can not increase nstlist because an NVE ensemble is used 85: Using 2 MPI threads 85: Using 1 OpenMP thread per tMPI thread 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'Argon' 85: 16 steps, 0.0 ps. 85: Generated 1 of the 1 non-bonded parameter combinations 85: 85: Excluding 1 bonded neighbours molecule type 'Argon' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: 85: Dynamic load balancing report: 85: DLB was off during the run due to low measured imbalance. 85: Average load imbalance: 1.2%. 85: The balanceable part of the MD step is 46%, load imbalance is computed from this. 85: Part of the total run time spent waiting due to load imbalance: 0.6%. 85: 85: 85: NOTE: 41 % of the run time was spent communicating energies, 85: you might want to increase some nst* mdp options 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.068 0.034 197.9 85: (ns/day) (hour/ns) 85: Performance: 42.592 0.563 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 85: Setting nstcalcenergy (100) equal to nstenergy (1) 85: 85: Number of degrees of freedom in T-Coupling group System is 33.00 85: 85: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 85: NVE simulation: will use the initial temperature of 68.810 K for 85: determining the Verlet buffer size 85: 85: 85: There were 3 NOTEs 85: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 85: Can not increase nstlist because an NVE ensemble is used 85: Using 2 MPI threads 85: Using 1 OpenMP thread per tMPI thread 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'Argon' 85: 16 steps, 0.0 ps. 85: Generated 1 of the 1 non-bonded parameter combinations 85: 85: Excluding 1 bonded neighbours molecule type 'Argon' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: 85: Dynamic load balancing report: 85: DLB was off during the run due to low measured imbalance. 85: Average load imbalance: 1.1%. 85: The balanceable part of the MD step is 54%, load imbalance is computed from this. 85: Part of the total run time spent waiting due to load imbalance: 0.6%. 85: 85: 85: NOTE: 42 % of the run time was spent communicating energies, 85: you might want to increase some nst* mdp options 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.053 0.027 197.6 85: (ns/day) (hour/ns) 85: Performance: 54.380 0.441 85: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as single precision energy file 85: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 85: Setting nstcalcenergy (100) equal to nstenergy (4) 85: 85: Number of degrees of freedom in T-Coupling group System is 33.00 85: 85: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 85: NVE simulation: will use the initial temperature of 68.810 K for 85: determining the Verlet buffer size 85: 85: 85: There were 3 NOTEs 85: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 85: Can not increase nstlist because an NVE ensemble is used 85: Using 2 MPI threads 85: Using 1 OpenMP thread per tMPI thread 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'Argon' 85: 16 steps, 0.0 ps. 85: Generated 1 of the 1 non-bonded parameter combinations 85: 85: Excluding 1 bonded neighbours molecule type 'Argon' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: 85: Dynamic load balancing report: 85: DLB was off during the run due to low measured imbalance. 85: Average load imbalance: 1.1%. 85: The balanceable part of the MD step is 53%, load imbalance is computed from this. 85: Part of the total run time spent waiting due to load imbalance: 0.6%. 85: 85: 85: NOTE: 57 % of the run time was spent communicating energies, 85: you might want to increase some nst* mdp options 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.050 0.025 196.7 85: (ns/day) (hour/ns) 85: Performance: 57.841 0.415 85: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as single precision energy file 85: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 85: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 85: setting nstcomm equal to nstcalcenergy for less overhead 85: 85: Number of degrees of freedom in T-Coupling group System is 33.00 85: 85: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 85: NVE simulation: will use the initial temperature of 68.810 K for 85: determining the Verlet buffer size 85: 85: 85: There were 3 NOTEs 85: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 85: Can not increase nstlist because an NVE ensemble is used 85: Using 2 MPI threads 85: Using 1 OpenMP thread per tMPI thread 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'Argon' 85: 16 steps, 0.0 ps. 85: Generated 1 of the 1 non-bonded parameter combinations 85: 85: Excluding 1 bonded neighbours molecule type 'Argon' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: 85: Dynamic load balancing report: 85: DLB was off during the run due to low measured imbalance. 85: Average load imbalance: 1.0%. 85: The balanceable part of the MD step is 41%, load imbalance is computed from this. 85: Part of the total run time spent waiting due to load imbalance: 0.4%. 85: 85: 85: NOTE: 44 % of the run time was spent communicating energies, 85: you might want to increase some nst* mdp options 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.042 0.021 196.8 85: (ns/day) (hour/ns) 85: Performance: 68.396 0.351 85: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as single precision energy file 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 85: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 85: setting nstcomm equal to nstcalcenergy for less overhead 85: 85: Number of degrees of freedom in T-Coupling group System is 33.00 85: 85: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 85: NVE simulation: will use the initial temperature of 68.810 K for 85: determining the Verlet buffer size 85: 85: 85: There were 3 NOTEs 85: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 85: Can not increase nstlist because an NVE ensemble is used 85: Using 2 MPI threads 85: Using 1 OpenMP thread per tMPI thread 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'Argon' 85: 16 steps, 0.0 ps. 85: Generated 1 of the 1 non-bonded parameter combinations 85: 85: Excluding 1 bonded neighbours molecule type 'Argon' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: 85: Dynamic load balancing report: 85: DLB was off during the run due to low measured imbalance. 85: Average load imbalance: 0.7%. 85: The balanceable part of the MD step is 35%, load imbalance is computed from this. 85: Part of the total run time spent waiting due to load imbalance: 0.3%. 85: 85: 85: NOTE: 47 % of the run time was spent communicating energies, 85: you might want to increase some nst* mdp options 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.049 0.025 197.4 85: (ns/day) (hour/ns) 85: Performance: 59.173 0.406 85: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as single precision energy file 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 85: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 85: setting nstcomm equal to nstcalcenergy for less overhead 85: 85: Number of degrees of freedom in T-Coupling group System is 33.00 85: 85: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 85: NVE simulation: will use the initial temperature of 68.810 K for 85: determining the Verlet buffer size 85: 85: 85: There were 3 NOTEs 85: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 85: Can not increase nstlist because an NVE ensemble is used 85: Using 2 MPI threads 85: Using 1 OpenMP thread per tMPI thread 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'Argon' 85: 16 steps, 0.0 ps. 85: Generated 1 of the 1 non-bonded parameter combinations 85: 85: Excluding 1 bonded neighbours molecule type 'Argon' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: 85: Dynamic load balancing report: 85: DLB was off during the run due to low measured imbalance. 85: Average load imbalance: 1.3%. 85: The balanceable part of the MD step is 54%, load imbalance is computed from this. 85: Part of the total run time spent waiting due to load imbalance: 0.7%. 85: 85: 85: NOTE: 43 % of the run time was spent communicating energies, 85: you might want to increase some nst* mdp options 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.040 0.020 196.6 85: (ns/day) (hour/ns) 85: Performance: 72.924 0.329 85: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as single precision energy file 85: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/2 (458 ms) 85: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/3 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 85: Setting nstcalcenergy (100) equal to nstenergy (1) 85: 85: Number of degrees of freedom in T-Coupling group System is 33.00 85: 85: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 85: NVE simulation: will use the initial temperature of 68.810 K for 85: determining the Verlet buffer size 85: 85: 85: There were 3 NOTEs 85: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 85: Can not increase nstlist because an NVE ensemble is used 85: Using 2 MPI threads 85: Using 1 OpenMP thread per tMPI thread 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'Argon' 85: 16 steps, 0.0 ps. 85: Generated 1 of the 1 non-bonded parameter combinations 85: 85: Excluding 1 bonded neighbours molecule type 'Argon' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: 85: Dynamic load balancing report: 85: DLB was off during the run due to low measured imbalance. 85: Average load imbalance: 0.9%. 85: The balanceable part of the MD step is 57%, load imbalance is computed from this. 85: Part of the total run time spent waiting due to load imbalance: 0.5%. 85: 85: 85: NOTE: 38 % of the run time was spent communicating energies, 85: you might want to increase some nst* mdp options 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.044 0.022 196.8 85: (ns/day) (hour/ns) 85: Performance: 66.058 0.363 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 85: Setting nstcalcenergy (100) equal to nstenergy (1) 85: 85: Number of degrees of freedom in T-Coupling group System is 33.00 85: 85: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 85: NVE simulation: will use the initial temperature of 68.810 K for 85: determining the Verlet buffer size 85: 85: 85: There were 3 NOTEs 85: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 85: Can not increase nstlist because an NVE ensemble is used 85: Using 2 MPI threads 85: Using 1 OpenMP thread per tMPI thread 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'Argon' 85: 16 steps, 0.0 ps. 85: Generated 1 of the 1 non-bonded parameter combinations 85: 85: Excluding 1 bonded neighbours molecule type 'Argon' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: 85: Dynamic load balancing report: 85: DLB was off during the run due to low measured imbalance. 85: Average load imbalance: 0.9%. 85: The balanceable part of the MD step is 24%, load imbalance is computed from this. 85: Part of the total run time spent waiting due to load imbalance: 0.2%. 85: 85: 85: NOTE: 28 % of the run time was spent communicating energies, 85: you might want to increase some nst* mdp options 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.046 0.029 157.7 85: (ns/day) (hour/ns) 85: Performance: 50.598 0.474 85: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as single precision energy file 85: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 85: Setting nstcalcenergy (100) equal to nstenergy (4) 85: 85: Number of degrees of freedom in T-Coupling group System is 33.00 85: 85: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 85: NVE simulation: will use the initial temperature of 68.810 K for 85: determining the Verlet buffer size 85: 85: 85: There were 3 NOTEs 85: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 85: Can not increase nstlist because an NVE ensemble is used 85: Using 2 MPI threads 85: Using 1 OpenMP thread per tMPI thread 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'Argon' 85: 16 steps, 0.0 ps. 85: Generated 1 of the 1 non-bonded parameter combinations 85: 85: Excluding 1 bonded neighbours molecule type 'Argon' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: 85: Dynamic load balancing report: 85: DLB was off during the run due to low measured imbalance. 85: Average load imbalance: 1.0%. 85: The balanceable part of the MD step is 49%, load imbalance is computed from this. 85: Part of the total run time spent waiting due to load imbalance: 0.5%. 85: 85: 85: NOTE: 45 % of the run time was spent communicating energies, 85: you might want to increase some nst* mdp options 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.062 0.031 197.5 85: (ns/day) (hour/ns) 85: Performance: 46.999 0.511 85: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as single precision energy file 85: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 85: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 85: setting nstcomm equal to nstcalcenergy for less overhead 85: 85: Number of degrees of freedom in T-Coupling group System is 33.00 85: 85: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 85: NVE simulation: will use the initial temperature of 68.810 K for 85: determining the Verlet buffer size 85: 85: 85: There were 3 NOTEs 85: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 85: Can not increase nstlist because an NVE ensemble is used 85: Using 2 MPI threads 85: Using 1 OpenMP thread per tMPI thread 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'Argon' 85: 16 steps, 0.0 ps. 85: Generated 1 of the 1 non-bonded parameter combinations 85: 85: Excluding 1 bonded neighbours molecule type 'Argon' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: 85: Dynamic load balancing report: 85: DLB was off during the run due to low measured imbalance. 85: Average load imbalance: 1.2%. 85: The balanceable part of the MD step is 46%, load imbalance is computed from this. 85: Part of the total run time spent waiting due to load imbalance: 0.5%. 85: 85: 85: NOTE: 45 % of the run time was spent communicating energies, 85: you might want to increase some nst* mdp options 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.056 0.028 197.5 85: (ns/day) (hour/ns) 85: Performance: 51.575 0.465 85: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as single precision energy file 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 85: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 85: setting nstcomm equal to nstcalcenergy for less overhead 85: 85: Number of degrees of freedom in T-Coupling group System is 33.00 85: 85: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 85: NVE simulation: will use the initial temperature of 68.810 K for 85: determining the Verlet buffer size 85: 85: 85: There were 3 NOTEs 85: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 85: Can not increase nstlist because an NVE ensemble is used 85: Using 2 MPI threads 85: Using 1 OpenMP thread per tMPI thread 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'Argon' 85: 16 steps, 0.0 ps. 85: Generated 1 of the 1 non-bonded parameter combinations 85: 85: Excluding 1 bonded neighbours molecule type 'Argon' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: 85: Dynamic load balancing report: 85: DLB was off during the run due to low measured imbalance. 85: Average load imbalance: 1.1%. 85: The balanceable part of the MD step is 44%, load imbalance is computed from this. 85: Part of the total run time spent waiting due to load imbalance: 0.5%. 85: 85: 85: NOTE: 43 % of the run time was spent communicating energies, 85: you might want to increase some nst* mdp options 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.046 0.023 197.2 85: (ns/day) (hour/ns) 85: Performance: 63.211 0.380 85: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as single precision energy file 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 85: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 85: setting nstcomm equal to nstcalcenergy for less overhead 85: 85: Number of degrees of freedom in T-Coupling group System is 33.00 85: 85: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 85: NVE simulation: will use the initial temperature of 68.810 K for 85: determining the Verlet buffer size 85: 85: 85: There were 3 NOTEs 85: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 85: Can not increase nstlist because an NVE ensemble is used 85: Using 2 MPI threads 85: Using 1 OpenMP thread per tMPI thread 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'Argon' 85: 16 steps, 0.0 ps. 85: Generated 1 of the 1 non-bonded parameter combinations 85: 85: Excluding 1 bonded neighbours molecule type 'Argon' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: 85: Dynamic load balancing report: 85: DLB was off during the run due to low measured imbalance. 85: Average load imbalance: 0.7%. 85: The balanceable part of the MD step is 39%, load imbalance is computed from this. 85: Part of the total run time spent waiting due to load imbalance: 0.3%. 85: 85: 85: NOTE: 44 % of the run time was spent communicating energies, 85: you might want to increase some nst* mdp options 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.064 0.032 197.9 85: (ns/day) (hour/ns) 85: Performance: 45.510 0.527 85: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as single precision energy file 85: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/3 (475 ms) 85: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/4 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 85: Setting nstcalcenergy (100) equal to nstenergy (1) 85: 85: Number of degrees of freedom in T-Coupling group System is 33.00 85: 85: There were 2 NOTEs 85: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 85: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 85: 85: Using 2 MPI threads 85: Using 1 OpenMP thread per tMPI thread 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'Argon' 85: 16 steps, 0.0 ps. 85: Generated 1 of the 1 non-bonded parameter combinations 85: 85: Excluding 1 bonded neighbours molecule type 'Argon' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: NOTE: 38 % of the run time was spent communicating energies, 85: you might want to increase some nst* mdp options 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.053 0.027 197.5 85: (ns/day) (hour/ns) 85: Performance: 54.336 0.442 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 85: Setting nstcalcenergy (100) equal to nstenergy (1) 85: 85: Number of degrees of freedom in T-Coupling group System is 33.00 85: 85: There were 2 NOTEs 85: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 85: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 85: 85: Using 2 MPI threads 85: Using 1 OpenMP thread per tMPI thread 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'Argon' 85: 16 steps, 0.0 ps. 85: Generated 1 of the 1 non-bonded parameter combinations 85: 85: Excluding 1 bonded neighbours molecule type 'Argon' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: NOTE: 41 % of the run time was spent communicating energies, 85: you might want to increase some nst* mdp options 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.039 0.020 197.0 85: (ns/day) (hour/ns) 85: Performance: 74.449 0.322 85: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as single precision energy file 85: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 85: Setting nstcalcenergy (100) equal to nstenergy (4) 85: 85: Number of degrees of freedom in T-Coupling group System is 33.00 85: 85: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 85: COM removal frequency is set to (5). 85: Other settings require a global communication frequency of 2. 85: Note that this will require additional global communication steps, 85: which will reduce performance when using multiple ranks. 85: Consider setting nstcomm to a multiple of 2. 85: 85: 85: There were 3 NOTEs 85: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 85: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 85: 85: Using 2 MPI threads 85: Using 1 OpenMP thread per tMPI thread 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'Argon' 85: 16 steps, 0.0 ps. 85: Generated 1 of the 1 non-bonded parameter combinations 85: 85: Excluding 1 bonded neighbours molecule type 'Argon' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: NOTE: 48 % of the run time was spent communicating energies, 85: you might want to increase some nst* mdp options 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.073 0.037 198.2 85: (ns/day) (hour/ns) 85: Performance: 39.721 0.604 85: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as single precision energy file 85: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 85: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 85: setting nstcomm equal to nstcalcenergy for less overhead 85: 85: Number of degrees of freedom in T-Coupling group System is 33.00 85: 85: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 85: COM removal frequency is set to (5). 85: Other settings require a global communication frequency of 2. 85: Note that this will require additional global communication steps, 85: which will reduce performance when using multiple ranks. 85: Consider setting nstcomm to a multiple of 2. 85: 85: 85: There were 3 NOTEs 85: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 85: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 85: 85: Using 2 MPI threads 85: Using 1 OpenMP thread per tMPI thread 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'Argon' 85: 16 steps, 0.0 ps. 85: Generated 1 of the 1 non-bonded parameter combinations 85: 85: Excluding 1 bonded neighbours molecule type 'Argon' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: NOTE: 45 % of the run time was spent communicating energies, 85: you might want to increase some nst* mdp options 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.056 0.028 197.6 85: (ns/day) (hour/ns) 85: Performance: 51.582 0.465 85: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as single precision energy file 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 85: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 85: setting nstcomm equal to nstcalcenergy for less overhead 85: 85: Number of degrees of freedom in T-Coupling group System is 33.00 85: 85: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 85: COM removal frequency is set to (5). 85: Other settings require a global communication frequency of 2. 85: Note that this will require additional global communication steps, 85: which will reduce performance when using multiple ranks. 85: Consider setting nstcomm to a multiple of 2. 85: 85: 85: There were 3 NOTEs 85: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 85: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 85: 85: Using 2 MPI threads 85: Using 1 OpenMP thread per tMPI thread 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'Argon' 85: 16 steps, 0.0 ps. 85: Generated 1 of the 1 non-bonded parameter combinations 85: 85: Excluding 1 bonded neighbours molecule type 'Argon' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: NOTE: 47 % of the run time was spent communicating energies, 85: you might want to increase some nst* mdp options 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.073 0.037 198.2 85: (ns/day) (hour/ns) 85: Performance: 39.829 0.603 85: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as single precision energy file 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 85: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 85: setting nstcomm equal to nstcalcenergy for less overhead 85: 85: Number of degrees of freedom in T-Coupling group System is 33.00 85: 85: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 85: COM removal frequency is set to (5). 85: Other settings require a global communication frequency of 2. 85: Note that this will require additional global communication steps, 85: which will reduce performance when using multiple ranks. 85: Consider setting nstcomm to a multiple of 2. 85: 85: 85: There were 3 NOTEs 85: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 85: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 85: 85: Using 2 MPI threads 85: Using 1 OpenMP thread per tMPI thread 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'Argon' 85: 16 steps, 0.0 ps. 85: Generated 1 of the 1 non-bonded parameter combinations 85: 85: Excluding 1 bonded neighbours molecule type 'Argon' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: NOTE: 38 % of the run time was spent communicating energies, 85: you might want to increase some nst* mdp options 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.053 0.027 197.6 85: (ns/day) (hour/ns) 85: Performance: 55.053 0.436 85: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as single precision energy file 85: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/4 (482 ms) 85: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/5 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 85: Setting nstcalcenergy (100) equal to nstenergy (1) 85: 85: 85: WARNING 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 85: The Berendsen barostat does not generate any strictly correct ensemble, 85: and should not be used for new production simulations (in our opinion). 85: We recommend using the C-rescale barostat instead. 85: 85: Number of degrees of freedom in T-Coupling group System is 33.00 85: 85: There were 2 NOTEs 85: 85: There was 1 WARNING 85: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 85: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 85: 85: Using 2 MPI threads 85: Using 1 OpenMP thread per tMPI thread 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'Argon' 85: 16 steps, 0.0 ps. 85: Generated 1 of the 1 non-bonded parameter combinations 85: 85: Excluding 1 bonded neighbours molecule type 'Argon' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: NOTE: 44 % of the run time was spent communicating energies, 85: you might want to increase some nst* mdp options 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.074 0.037 197.5 85: (ns/day) (hour/ns) 85: Performance: 39.430 0.609 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 85: Setting nstcalcenergy (100) equal to nstenergy (1) 85: 85: 85: WARNING 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 85: The Berendsen barostat does not generate any strictly correct ensemble, 85: and should not be used for new production simulations (in our opinion). 85: We recommend using the C-rescale barostat instead. 85: 85: Number of degrees of freedom in T-Coupling group System is 33.00 85: 85: There were 2 NOTEs 85: 85: There was 1 WARNING 85: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 85: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 85: 85: Using 2 MPI threads 85: Using 1 OpenMP thread per tMPI thread 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'Argon' 85: 16 steps, 0.0 ps. 85: Generated 1 of the 1 non-bonded parameter combinations 85: 85: Excluding 1 bonded neighbours molecule type 'Argon' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: NOTE: 38 % of the run time was spent communicating energies, 85: you might want to increase some nst* mdp options 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.067 0.034 198.0 85: (ns/day) (hour/ns) 85: Performance: 43.406 0.553 85: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as single precision energy file 85: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 85: Setting nstcalcenergy (100) equal to nstenergy (4) 85: 85: 85: WARNING 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 85: The Berendsen barostat does not generate any strictly correct ensemble, 85: and should not be used for new production simulations (in our opinion). 85: We recommend using the C-rescale barostat instead. 85: 85: Number of degrees of freedom in T-Coupling group System is 33.00 85: 85: There were 2 NOTEs 85: 85: There was 1 WARNING 85: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 85: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 85: 85: Using 2 MPI threads 85: Using 1 OpenMP thread per tMPI thread 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'Argon' 85: 16 steps, 0.0 ps. 85: Generated 1 of the 1 non-bonded parameter combinations 85: 85: Excluding 1 bonded neighbours molecule type 'Argon' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: NOTE: 34 % of the run time was spent communicating energies, 85: you might want to increase some nst* mdp options 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.041 0.021 197.0 85: (ns/day) (hour/ns) 85: Performance: 71.273 0.337 85: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as single precision energy file 85: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 85: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 85: setting nstcomm equal to nstcalcenergy for less overhead 85: 85: 85: WARNING 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 85: The Berendsen barostat does not generate any strictly correct ensemble, 85: and should not be used for new production simulations (in our opinion). 85: We recommend using the C-rescale barostat instead. 85: 85: Number of degrees of freedom in T-Coupling group System is 33.00 85: 85: There were 2 NOTEs 85: 85: There was 1 WARNING 85: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 85: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 85: 85: Using 2 MPI threads 85: Using 1 OpenMP thread per tMPI thread 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'Argon' 85: 16 steps, 0.0 ps. 85: Generated 1 of the 1 non-bonded parameter combinations 85: 85: Excluding 1 bonded neighbours molecule type 'Argon' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: NOTE: 45 % of the run time was spent communicating energies, 85: you might want to increase some nst* mdp options 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.062 0.031 197.9 85: (ns/day) (hour/ns) 85: Performance: 46.640 0.515 85: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as single precision energy file 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 85: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 85: setting nstcomm equal to nstcalcenergy for less overhead 85: 85: 85: WARNING 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 85: The Berendsen barostat does not generate any strictly correct ensemble, 85: and should not be used for new production simulations (in our opinion). 85: We recommend using the C-rescale barostat instead. 85: 85: Number of degrees of freedom in T-Coupling group System is 33.00 85: 85: There were 2 NOTEs 85: 85: There was 1 WARNING 85: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 85: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 85: 85: Using 2 MPI threads 85: Using 1 OpenMP thread per tMPI thread 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'Argon' 85: 16 steps, 0.0 ps. 85: Generated 1 of the 1 non-bonded parameter combinations 85: 85: Excluding 1 bonded neighbours molecule type 'Argon' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: NOTE: 46 % of the run time was spent communicating energies, 85: you might want to increase some nst* mdp options 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.056 0.028 197.4 85: (ns/day) (hour/ns) 85: Performance: 51.617 0.465 85: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as single precision energy file 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 85: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 85: setting nstcomm equal to nstcalcenergy for less overhead 85: 85: 85: WARNING 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 85: The Berendsen barostat does not generate any strictly correct ensemble, 85: and should not be used for new production simulations (in our opinion). 85: We recommend using the C-rescale barostat instead. 85: 85: Number of degrees of freedom in T-Coupling group System is 33.00 85: 85: There were 2 NOTEs 85: 85: There was 1 WARNING 85: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 85: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 85: 85: Using 2 MPI threads 85: Using 1 OpenMP thread per tMPI thread 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'Argon' 85: 16 steps, 0.0 ps. 85: Generated 1 of the 1 non-bonded parameter combinations 85: 85: Excluding 1 bonded neighbours molecule type 'Argon' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: NOTE: 47 % of the run time was spent communicating energies, 85: you might want to increase some nst* mdp options 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.056 0.028 197.7 85: (ns/day) (hour/ns) 85: Performance: 51.977 0.462 85: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as single precision energy file 85: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/5 (497 ms) 85: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/6 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 85: Setting nstcalcenergy (100) equal to nstenergy (1) 85: 85: Number of degrees of freedom in T-Coupling group System is 33.00 85: 85: There were 2 NOTEs 85: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 85: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 85: 85: Using 2 MPI threads 85: Using 1 OpenMP thread per tMPI thread 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'Argon' 85: 16 steps, 0.0 ps. 85: Generated 1 of the 1 non-bonded parameter combinations 85: 85: Excluding 1 bonded neighbours molecule type 'Argon' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: NOTE: 38 % of the run time was spent communicating energies, 85: you might want to increase some nst* mdp options 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.047 0.024 196.9 85: (ns/day) (hour/ns) 85: Performance: 61.572 0.390 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 85: Setting nstcalcenergy (100) equal to nstenergy (1) 85: 85: Number of degrees of freedom in T-Coupling group System is 33.00 85: 85: There were 2 NOTEs 85: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 85: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 85: 85: Using 2 MPI threads 85: Using 1 OpenMP thread per tMPI thread 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'Argon' 85: 16 steps, 0.0 ps. 85: Generated 1 of the 1 non-bonded parameter combinations 85: 85: Excluding 1 bonded neighbours molecule type 'Argon' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: NOTE: 39 % of the run time was spent communicating energies, 85: you might want to increase some nst* mdp options 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.059 0.030 197.7 85: (ns/day) (hour/ns) 85: Performance: 49.338 0.486 85: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as single precision energy file 85: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 85: Setting nstcalcenergy (100) equal to nstenergy (4) 85: 85: Number of degrees of freedom in T-Coupling group System is 33.00 85: 85: There were 2 NOTEs 85: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 85: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 85: 85: Using 2 MPI threads 85: Using 1 OpenMP thread per tMPI thread 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'Argon' 85: 16 steps, 0.0 ps. 85: Generated 1 of the 1 non-bonded parameter combinations 85: 85: Excluding 1 bonded neighbours molecule type 'Argon' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: NOTE: 46 % of the run time was spent communicating energies, 85: you might want to increase some nst* mdp options 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.079 0.040 198.3 85: (ns/day) (hour/ns) 85: Performance: 36.993 0.649 85: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as single precision energy file 85: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 85: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 85: setting nstcomm equal to nstcalcenergy for less overhead 85: 85: Number of degrees of freedom in T-Coupling group System is 33.00 85: 85: There were 2 NOTEs 85: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 85: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 85: 85: Using 2 MPI threads 85: Using 1 OpenMP thread per tMPI thread 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'Argon' 85: 16 steps, 0.0 ps. 85: Generated 1 of the 1 non-bonded parameter combinations 85: 85: Excluding 1 bonded neighbours molecule type 'Argon' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: NOTE: 43 % of the run time was spent communicating energies, 85: you might want to increase some nst* mdp options 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.050 0.026 197.4 85: (ns/day) (hour/ns) 85: Performance: 57.558 0.417 85: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as single precision energy file 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 85: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 85: setting nstcomm equal to nstcalcenergy for less overhead 85: 85: Number of degrees of freedom in T-Coupling group System is 33.00 85: 85: There were 2 NOTEs 85: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 85: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 85: 85: Using 2 MPI threads 85: Using 1 OpenMP thread per tMPI thread 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'Argon' 85: 16 steps, 0.0 ps. 85: Generated 1 of the 1 non-bonded parameter combinations 85: 85: Excluding 1 bonded neighbours molecule type 'Argon' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: NOTE: 45 % of the run time was spent communicating energies, 85: you might want to increase some nst* mdp options 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.049 0.025 197.1 85: (ns/day) (hour/ns) 85: Performance: 59.022 0.407 85: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as single precision energy file 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 85: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 85: setting nstcomm equal to nstcalcenergy for less overhead 85: 85: Number of degrees of freedom in T-Coupling group System is 33.00 85: 85: There were 2 NOTEs 85: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 85: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 85: 85: Using 2 MPI threads 85: Using 1 OpenMP thread per tMPI thread 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'Argon' 85: 16 steps, 0.0 ps. 85: Generated 1 of the 1 non-bonded parameter combinations 85: 85: Excluding 1 bonded neighbours molecule type 'Argon' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: NOTE: 47 % of the run time was spent communicating energies, 85: you might want to increase some nst* mdp options 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.044 0.022 196.9 85: (ns/day) (hour/ns) 85: Performance: 66.219 0.362 85: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as single precision energy file 85: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/6 (497 ms) 85: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/7 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 85: Setting nstcalcenergy (100) equal to nstenergy (1) 85: 85: Number of degrees of freedom in T-Coupling group System is 33.00 85: 85: There were 2 NOTEs 85: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 85: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 85: 85: Using 2 MPI threads 85: Using 1 OpenMP thread per tMPI thread 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'Argon' 85: 16 steps, 0.0 ps. 85: Generated 1 of the 1 non-bonded parameter combinations 85: 85: Excluding 1 bonded neighbours molecule type 'Argon' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: NOTE: 37 % of the run time was spent communicating energies, 85: you might want to increase some nst* mdp options 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.053 0.027 197.3 85: (ns/day) (hour/ns) 85: Performance: 54.365 0.441 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 85: Setting nstcalcenergy (100) equal to nstenergy (1) 85: 85: Number of degrees of freedom in T-Coupling group System is 33.00 85: 85: There were 2 NOTEs 85: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 85: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 85: 85: Using 2 MPI threads 85: Using 1 OpenMP thread per tMPI thread 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'Argon' 85: 16 steps, 0.0 ps. 85: Generated 1 of the 1 non-bonded parameter combinations 85: 85: Excluding 1 bonded neighbours molecule type 'Argon' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: NOTE: 37 % of the run time was spent communicating energies, 85: you might want to increase some nst* mdp options 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.037 0.019 196.6 85: (ns/day) (hour/ns) 85: Performance: 78.190 0.307 85: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as single precision energy file 85: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 85: Setting nstcalcenergy (100) equal to nstenergy (4) 85: 85: Number of degrees of freedom in T-Coupling group System is 33.00 85: 85: There were 2 NOTEs 85: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 85: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 85: 85: Using 2 MPI threads 85: Using 1 OpenMP thread per tMPI thread 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'Argon' 85: 16 steps, 0.0 ps. 85: Generated 1 of the 1 non-bonded parameter combinations 85: 85: Excluding 1 bonded neighbours molecule type 'Argon' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: NOTE: 44 % of the run time was spent communicating energies, 85: you might want to increase some nst* mdp options 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.036 0.019 196.4 85: (ns/day) (hour/ns) 85: Performance: 79.093 0.303 85: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as single precision energy file 85: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 85: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 85: setting nstcomm equal to nstcalcenergy for less overhead 85: 85: Number of degrees of freedom in T-Coupling group System is 33.00 85: 85: There were 2 NOTEs 85: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 85: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 85: 85: Using 2 MPI threads 85: Using 1 OpenMP thread per tMPI thread 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'Argon' 85: 16 steps, 0.0 ps. 85: Generated 1 of the 1 non-bonded parameter combinations 85: 85: Excluding 1 bonded neighbours molecule type 'Argon' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: NOTE: 45 % of the run time was spent communicating energies, 85: you might want to increase some nst* mdp options 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.047 0.024 197.3 85: (ns/day) (hour/ns) 85: Performance: 61.563 0.390 85: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as single precision energy file 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 85: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 85: setting nstcomm equal to nstcalcenergy for less overhead 85: 85: Number of degrees of freedom in T-Coupling group System is 33.00 85: 85: There were 2 NOTEs 85: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 85: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 85: 85: Using 2 MPI threads 85: Using 1 OpenMP thread per tMPI thread 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'Argon' 85: 16 steps, 0.0 ps. 85: Generated 1 of the 1 non-bonded parameter combinations 85: 85: Excluding 1 bonded neighbours molecule type 'Argon' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: NOTE: 45 % of the run time was spent communicating energies, 85: you might want to increase some nst* mdp options 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.054 0.028 194.8 85: (ns/day) (hour/ns) 85: Performance: 53.188 0.451 85: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as single precision energy file 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 85: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 85: setting nstcomm equal to nstcalcenergy for less overhead 85: 85: Number of degrees of freedom in T-Coupling group System is 33.00 85: 85: There were 2 NOTEs 85: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 85: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 85: 85: Using 2 MPI threads 85: Using 1 OpenMP thread per tMPI thread 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'Argon' 85: 16 steps, 0.0 ps. 85: Generated 1 of the 1 non-bonded parameter combinations 85: 85: Excluding 1 bonded neighbours molecule type 'Argon' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: NOTE: 45 % of the run time was spent communicating energies, 85: you might want to increase some nst* mdp options 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.052 0.026 197.5 85: (ns/day) (hour/ns) 85: Performance: 55.920 0.429 85: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as single precision energy file 85: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/7 (440 ms) 85: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/8 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 85: Setting nstcalcenergy (100) equal to nstenergy (1) 85: 85: 85: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 85: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 85: 1 85: 85: Number of degrees of freedom in T-Coupling group System is 33.00 85: 85: There were 3 NOTEs 85: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 85: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 85: 85: Using 2 MPI threads 85: Using 1 OpenMP thread per tMPI thread 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'Argon' 85: 16 steps, 0.0 ps. 85: Generated 1 of the 1 non-bonded parameter combinations 85: 85: Excluding 1 bonded neighbours molecule type 'Argon' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: NOTE: 47 % of the run time was spent communicating energies, 85: you might want to increase some nst* mdp options 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.073 0.037 198.1 85: (ns/day) (hour/ns) 85: Performance: 39.996 0.600 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 85: Setting nstcalcenergy (100) equal to nstenergy (1) 85: 85: 85: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 85: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 85: 1 85: 85: Number of degrees of freedom in T-Coupling group System is 33.00 85: 85: There were 3 NOTEs 85: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 85: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 85: 85: Using 2 MPI threads 85: Using 1 OpenMP thread per tMPI thread 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'Argon' 85: 16 steps, 0.0 ps. 85: Generated 1 of the 1 non-bonded parameter combinations 85: 85: Excluding 1 bonded neighbours molecule type 'Argon' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: NOTE: 33 % of the run time was spent communicating energies, 85: you might want to increase some nst* mdp options 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.039 0.020 197.2 85: (ns/day) (hour/ns) 85: Performance: 73.403 0.327 85: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_reference.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.edr as single precision energy file 85: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 85: Setting nstcalcenergy (100) equal to nstenergy (4) 85: 85: 85: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 85: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 85: 1 85: 85: Number of degrees of freedom in T-Coupling group System is 33.00 85: 85: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 85: COM removal frequency is set to (5). 85: Other settings require a global communication frequency of 2. 85: Note that this will require additional global communication steps, 85: which will reduce performance when using multiple ranks. 85: Consider setting nstcomm to a multiple of 2. 85: 85: 85: There were 4 NOTEs 85: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 85: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 85: 85: Using 2 MPI threads 85: Using 1 OpenMP thread per tMPI thread 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'Argon' 85: 16 steps, 0.0 ps. 85: Generated 1 of the 1 non-bonded parameter combinations 85: 85: Excluding 1 bonded neighbours molecule type 'Argon' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: NOTE: 43 % of the run time was spent communicating energies, 85: you might want to increase some nst* mdp options 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.048 0.024 197.4 85: (ns/day) (hour/ns) 85: Performance: 60.975 0.394 85: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_reference.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.edr as single precision energy file 85: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 85: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 85: setting nstcomm equal to nstcalcenergy for less overhead 85: 85: 85: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 85: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 85: 1 85: 85: Number of degrees of freedom in T-Coupling group System is 33.00 85: 85: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 85: COM removal frequency is set to (5). 85: Other settings require a global communication frequency of 2. 85: Note that this will require additional global communication steps, 85: which will reduce performance when using multiple ranks. 85: Consider setting nstcomm to a multiple of 2. 85: 85: 85: There were 4 NOTEs 85: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 85: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 85: 85: Using 2 MPI threads 85: Using 1 OpenMP thread per tMPI thread 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'Argon' 85: 16 steps, 0.0 ps. 85: Generated 1 of the 1 non-bonded parameter combinations 85: 85: Excluding 1 bonded neighbours molecule type 'Argon' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: NOTE: 46 % of the run time was spent communicating energies, 85: you might want to increase some nst* mdp options 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.062 0.031 197.9 85: (ns/day) (hour/ns) 85: Performance: 46.633 0.515 85: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_reference.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.edr as single precision energy file 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 85: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 85: setting nstcomm equal to nstcalcenergy for less overhead 85: 85: 85: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 85: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 85: 1 85: 85: Number of degrees of freedom in T-Coupling group System is 33.00 85: 85: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 85: COM removal frequency is set to (5). 85: Other settings require a global communication frequency of 2. 85: Note that this will require additional global communication steps, 85: which will reduce performance when using multiple ranks. 85: Consider setting nstcomm to a multiple of 2. 85: 85: 85: There were 4 NOTEs 85: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 85: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 85: 85: Using 2 MPI threads 85: Using 1 OpenMP thread per tMPI thread 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'Argon' 85: 16 steps, 0.0 ps. 85: Generated 1 of the 1 non-bonded parameter combinations 85: 85: Excluding 1 bonded neighbours molecule type 'Argon' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: NOTE: 58 % of the run time was spent communicating energies, 85: you might want to increase some nst* mdp options 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.110 0.058 188.8 85: (ns/day) (hour/ns) 85: Performance: 25.120 0.955 85: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_reference.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.edr as single precision energy file 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 85: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 85: setting nstcomm equal to nstcalcenergy for less overhead 85: 85: 85: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 85: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 85: 1 85: 85: Number of degrees of freedom in T-Coupling group System is 33.00 85: 85: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 85: COM removal frequency is set to (5). 85: Other settings require a global communication frequency of 2. 85: Note that this will require additional global communication steps, 85: which will reduce performance when using multiple ranks. 85: Consider setting nstcomm to a multiple of 2. 85: 85: 85: There were 4 NOTEs 85: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 85: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 85: 85: Using 2 MPI threads 85: Using 1 OpenMP thread per tMPI thread 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'Argon' 85: 16 steps, 0.0 ps. 85: Generated 1 of the 1 non-bonded parameter combinations 85: 85: Excluding 1 bonded neighbours molecule type 'Argon' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: NOTE: 43 % of the run time was spent communicating energies, 85: you might want to increase some nst* mdp options 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.059 0.030 197.8 85: (ns/day) (hour/ns) 85: Performance: 49.074 0.489 85: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_reference.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.edr as single precision energy file 85: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/8 (591 ms) 85: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/9 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 85: Setting nstcalcenergy (100) equal to nstenergy (1) 85: 85: 85: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 85: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 85: 1 85: 85: 85: WARNING 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 85: The Berendsen barostat does not generate any strictly correct ensemble, 85: and should not be used for new production simulations (in our opinion). 85: We recommend using the C-rescale barostat instead. 85: 85: Number of degrees of freedom in T-Coupling group System is 33.00 85: 85: There were 3 NOTEs 85: 85: There was 1 WARNING 85: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 85: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 85: 85: Using 2 MPI threads 85: Using 1 OpenMP thread per tMPI thread 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'Argon' 85: 16 steps, 0.0 ps. 85: Generated 1 of the 1 non-bonded parameter combinations 85: 85: Excluding 1 bonded neighbours molecule type 'Argon' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: NOTE: 39 % of the run time was spent communicating energies, 85: you might want to increase some nst* mdp options 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.077 0.039 198.1 85: (ns/day) (hour/ns) 85: Performance: 38.007 0.631 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 85: Setting nstcalcenergy (100) equal to nstenergy (1) 85: 85: 85: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 85: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 85: 1 85: 85: 85: WARNING 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 85: The Berendsen barostat does not generate any strictly correct ensemble, 85: and should not be used for new production simulations (in our opinion). 85: We recommend using the C-rescale barostat instead. 85: 85: Number of degrees of freedom in T-Coupling group System is 33.00 85: 85: There were 3 NOTEs 85: 85: There was 1 WARNING 85: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 85: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 85: 85: Using 2 MPI threads 85: Using 1 OpenMP thread per tMPI thread 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'Argon' 85: 16 steps, 0.0 ps. 85: Generated 1 of the 1 non-bonded parameter combinations 85: 85: Excluding 1 bonded neighbours molecule type 'Argon' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: NOTE: 40 % of the run time was spent communicating energies, 85: you might want to increase some nst* mdp options 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.043 0.022 197.1 85: (ns/day) (hour/ns) 85: Performance: 68.076 0.353 85: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_reference.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.edr as single precision energy file 85: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 85: Setting nstcalcenergy (100) equal to nstenergy (4) 85: 85: 85: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 85: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 85: 1 85: 85: 85: WARNING 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 85: The Berendsen barostat does not generate any strictly correct ensemble, 85: and should not be used for new production simulations (in our opinion). 85: We recommend using the C-rescale barostat instead. 85: 85: Number of degrees of freedom in T-Coupling group System is 33.00 85: 85: There were 3 NOTEs 85: 85: There was 1 WARNING 85: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 85: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 85: 85: Using 2 MPI threads 85: Using 1 OpenMP thread per tMPI thread 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'Argon' 85: 16 steps, 0.0 ps. 85: Generated 1 of the 1 non-bonded parameter combinations 85: 85: Excluding 1 bonded neighbours molecule type 'Argon' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: NOTE: 42 % of the run time was spent communicating energies, 85: you might want to increase some nst* mdp options 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.044 0.022 197.1 85: (ns/day) (hour/ns) 85: Performance: 65.972 0.364 85: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_reference.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.edr as single precision energy file 85: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 85: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 85: setting nstcomm equal to nstcalcenergy for less overhead 85: 85: 85: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 85: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 85: 1 85: 85: 85: WARNING 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 85: The Berendsen barostat does not generate any strictly correct ensemble, 85: and should not be used for new production simulations (in our opinion). 85: We recommend using the C-rescale barostat instead. 85: 85: Number of degrees of freedom in T-Coupling group System is 33.00 85: 85: There were 3 NOTEs 85: 85: There was 1 WARNING 85: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 85: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 85: 85: Using 2 MPI threads 85: Using 1 OpenMP thread per tMPI thread 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'Argon' 85: 16 steps, 0.0 ps. 85: Generated 1 of the 1 non-bonded parameter combinations 85: 85: Excluding 1 bonded neighbours molecule type 'Argon' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: NOTE: 46 % of the run time was spent communicating energies, 85: you might want to increase some nst* mdp options 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.057 0.029 197.7 85: (ns/day) (hour/ns) 85: Performance: 51.324 0.468 85: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_reference.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.edr as single precision energy file 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 85: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 85: setting nstcomm equal to nstcalcenergy for less overhead 85: 85: 85: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 85: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 85: 1 85: 85: 85: WARNING 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 85: The Berendsen barostat does not generate any strictly correct ensemble, 85: and should not be used for new production simulations (in our opinion). 85: We recommend using the C-rescale barostat instead. 85: 85: Number of degrees of freedom in T-Coupling group System is 33.00 85: 85: There were 3 NOTEs 85: 85: There was 1 WARNING 85: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 85: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 85: 85: Using 2 MPI threads 85: Using 1 OpenMP thread per tMPI thread 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'Argon' 85: 16 steps, 0.0 ps. 85: Generated 1 of the 1 non-bonded parameter combinations 85: 85: Excluding 1 bonded neighbours molecule type 'Argon' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: NOTE: 40 % of the run time was spent communicating energies, 85: you might want to increase some nst* mdp options 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.041 0.025 165.6 85: (ns/day) (hour/ns) 85: Performance: 59.505 0.403 85: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_reference.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.edr as single precision energy file 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 85: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 85: setting nstcomm equal to nstcalcenergy for less overhead 85: 85: 85: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 85: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 85: 1 85: 85: 85: WARNING 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 85: The Berendsen barostat does not generate any strictly correct ensemble, 85: and should not be used for new production simulations (in our opinion). 85: We recommend using the C-rescale barostat instead. 85: 85: Number of degrees of freedom in T-Coupling group System is 33.00 85: 85: There were 3 NOTEs 85: 85: There was 1 WARNING 85: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 85: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 85: 85: Using 2 MPI threads 85: Using 1 OpenMP thread per tMPI thread 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'Argon' 85: 16 steps, 0.0 ps. 85: Generated 1 of the 1 non-bonded parameter combinations 85: 85: Excluding 1 bonded neighbours molecule type 'Argon' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: NOTE: 37 % of the run time was spent communicating energies, 85: you might want to increase some nst* mdp options 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.049 0.025 197.5 85: (ns/day) (hour/ns) 85: Performance: 59.496 0.403 85: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_reference.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.edr as single precision energy file 85: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/9 (530 ms) 85: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/10 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 85: Setting nstcalcenergy (100) equal to nstenergy (1) 85: 85: 85: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 85: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 85: 1 85: 85: Number of degrees of freedom in T-Coupling group System is 33.00 85: 85: There were 3 NOTEs 85: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 85: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 85: 85: Using 2 MPI threads 85: Using 1 OpenMP thread per tMPI thread 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'Argon' 85: 16 steps, 0.0 ps. 85: Generated 1 of the 1 non-bonded parameter combinations 85: 85: Excluding 1 bonded neighbours molecule type 'Argon' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: NOTE: 37 % of the run time was spent communicating energies, 85: you might want to increase some nst* mdp options 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.046 0.024 197.0 85: (ns/day) (hour/ns) 85: Performance: 62.391 0.385 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 85: Setting nstcalcenergy (100) equal to nstenergy (1) 85: 85: 85: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 85: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 85: 1 85: 85: Number of degrees of freedom in T-Coupling group System is 33.00 85: 85: There were 3 NOTEs 85: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 85: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 85: 85: Using 2 MPI threads 85: Using 1 OpenMP thread per tMPI thread 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'Argon' 85: 16 steps, 0.0 ps. 85: Generated 1 of the 1 non-bonded parameter combinations 85: 85: Excluding 1 bonded neighbours molecule type 'Argon' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: NOTE: 35 % of the run time was spent communicating energies, 85: you might want to increase some nst* mdp options 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.066 0.034 194.3 85: (ns/day) (hour/ns) 85: Performance: 43.103 0.557 85: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_reference.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.edr as single precision energy file 85: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 85: Setting nstcalcenergy (100) equal to nstenergy (4) 85: 85: 85: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 85: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 85: 1 85: 85: Number of degrees of freedom in T-Coupling group System is 33.00 85: 85: There were 3 NOTEs 85: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 85: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 85: 85: Using 2 MPI threads 85: Using 1 OpenMP thread per tMPI thread 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'Argon' 85: 16 steps, 0.0 ps. 85: Generated 1 of the 1 non-bonded parameter combinations 85: 85: Excluding 1 bonded neighbours molecule type 'Argon' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: NOTE: 43 % of the run time was spent communicating energies, 85: you might want to increase some nst* mdp options 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.045 0.023 197.0 85: (ns/day) (hour/ns) 85: Performance: 64.646 0.371 85: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_reference.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.edr as single precision energy file 85: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 85: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 85: setting nstcomm equal to nstcalcenergy for less overhead 85: 85: 85: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 85: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 85: 1 85: 85: Number of degrees of freedom in T-Coupling group System is 33.00 85: 85: There were 3 NOTEs 85: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 85: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 85: 85: Using 2 MPI threads 85: Using 1 OpenMP thread per tMPI thread 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'Argon' 85: 16 steps, 0.0 ps. 85: Generated 1 of the 1 non-bonded parameter combinations 85: 85: Excluding 1 bonded neighbours molecule type 'Argon' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: NOTE: 43 % of the run time was spent communicating energies, 85: you might want to increase some nst* mdp options 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.064 0.033 192.5 85: (ns/day) (hour/ns) 85: Performance: 44.192 0.543 85: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_reference.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.edr as single precision energy file 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 85: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 85: setting nstcomm equal to nstcalcenergy for less overhead 85: 85: 85: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 85: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 85: 1 85: 85: Number of degrees of freedom in T-Coupling group System is 33.00 85: 85: There were 3 NOTEs 85: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 85: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 85: 85: Using 2 MPI threads 85: Using 1 OpenMP thread per tMPI thread 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'Argon' 85: 16 steps, 0.0 ps. 85: Generated 1 of the 1 non-bonded parameter combinations 85: 85: Excluding 1 bonded neighbours molecule type 'Argon' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: NOTE: 49 % of the run time was spent communicating energies, 85: you might want to increase some nst* mdp options 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.492 0.247 199.6 85: (ns/day) (hour/ns) 85: Performance: 5.953 4.032 85: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_reference.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.edr as single precision energy file 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 85: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 85: setting nstcomm equal to nstcalcenergy for less overhead 85: 85: 85: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 85: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 85: 1 85: 85: Number of degrees of freedom in T-Coupling group System is 33.00 85: 85: There were 3 NOTEs 85: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 85: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 85: 85: Using 2 MPI threads 85: Using 1 OpenMP thread per tMPI thread 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'Argon' 85: 16 steps, 0.0 ps. 85: Generated 1 of the 1 non-bonded parameter combinations 85: 85: Excluding 1 bonded neighbours molecule type 'Argon' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: NOTE: 48 % of the run time was spent communicating energies, 85: you might want to increase some nst* mdp options 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.099 0.050 198.5 85: (ns/day) (hour/ns) 85: Performance: 29.454 0.815 85: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_reference.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.edr as single precision energy file 85: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/10 (731 ms) 85: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/11 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 85: Setting nstcalcenergy (100) equal to nstenergy (1) 85: 85: 85: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 85: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 85: 1 85: 85: Number of degrees of freedom in T-Coupling group System is 33.00 85: 85: There were 3 NOTEs 85: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 85: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 85: 85: Using 2 MPI threads 85: Using 1 OpenMP thread per tMPI thread 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'Argon' 85: 16 steps, 0.0 ps. 85: Generated 1 of the 1 non-bonded parameter combinations 85: 85: Excluding 1 bonded neighbours molecule type 'Argon' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: NOTE: 49 % of the run time was spent communicating energies, 85: you might want to increase some nst* mdp options 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.482 0.242 199.4 85: (ns/day) (hour/ns) 85: Performance: 6.079 3.948 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 85: Setting nstcalcenergy (100) equal to nstenergy (1) 85: 85: 85: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 85: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 85: 1 85: 85: Number of degrees of freedom in T-Coupling group System is 33.00 85: 85: There were 3 NOTEs 85: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 85: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 85: 85: Using 2 MPI threads 85: Using 1 OpenMP thread per tMPI thread 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'Argon' 85: 16 steps, 0.0 ps. 85: Generated 1 of the 1 non-bonded parameter combinations 85: 85: Excluding 1 bonded neighbours molecule type 'Argon' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: NOTE: 49 % of the run time was spent communicating energies, 85: you might want to increase some nst* mdp options 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.405 0.203 199.7 85: (ns/day) (hour/ns) 85: Performance: 7.247 3.312 85: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_reference.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.edr as single precision energy file 85: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 85: Setting nstcalcenergy (100) equal to nstenergy (4) 85: 85: 85: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 85: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 85: 1 85: 85: Number of degrees of freedom in T-Coupling group System is 33.00 85: 85: There were 3 NOTEs 85: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 85: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 85: 85: Using 2 MPI threads 85: Using 1 OpenMP thread per tMPI thread 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'Argon' 85: 16 steps, 0.0 ps. 85: Generated 1 of the 1 non-bonded parameter combinations 85: 85: Excluding 1 bonded neighbours molecule type 'Argon' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: NOTE: 28 % of the run time was spent communicating energies, 85: you might want to increase some nst* mdp options 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.054 0.027 197.7 85: (ns/day) (hour/ns) 85: Performance: 53.720 0.447 85: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_reference.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.edr as single precision energy file 85: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 85: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 85: setting nstcomm equal to nstcalcenergy for less overhead 85: 85: 85: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 85: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 85: 1 85: 85: Number of degrees of freedom in T-Coupling group System is 33.00 85: 85: There were 3 NOTEs 85: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 85: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 85: 85: Using 2 MPI threads 85: Using 1 OpenMP thread per tMPI thread 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'Argon' 85: 16 steps, 0.0 ps. 85: Generated 1 of the 1 non-bonded parameter combinations 85: 85: Excluding 1 bonded neighbours molecule type 'Argon' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: NOTE: 46 % of the run time was spent communicating energies, 85: you might want to increase some nst* mdp options 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.059 0.030 197.3 85: (ns/day) (hour/ns) 85: Performance: 49.409 0.486 85: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_reference.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.edr as single precision energy file 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 85: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 85: setting nstcomm equal to nstcalcenergy for less overhead 85: 85: 85: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 85: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 85: 1 85: 85: Number of degrees of freedom in T-Coupling group System is 33.00 85: 85: There were 3 NOTEs 85: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 85: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 85: 85: Using 2 MPI threads 85: Using 1 OpenMP thread per tMPI thread 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'Argon' 85: 16 steps, 0.0 ps. 85: Generated 1 of the 1 non-bonded parameter combinations 85: 85: Excluding 1 bonded neighbours molecule type 'Argon' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: NOTE: 52 % of the run time was spent communicating energies, 85: you might want to increase some nst* mdp options 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.081 0.041 198.2 85: (ns/day) (hour/ns) 85: Performance: 35.850 0.669 85: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_reference.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.edr as single precision energy file 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 85: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 85: setting nstcomm equal to nstcalcenergy for less overhead 85: 85: 85: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 85: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 85: 1 85: 85: Number of degrees of freedom in T-Coupling group System is 33.00 85: 85: There were 3 NOTEs 85: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 85: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 85: 85: Using 2 MPI threads 85: Using 1 OpenMP thread per tMPI thread 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'Argon' 85: 16 steps, 0.0 ps. 85: Generated 1 of the 1 non-bonded parameter combinations 85: 85: Excluding 1 bonded neighbours molecule type 'Argon' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: NOTE: 45 % of the run time was spent communicating energies, 85: you might want to increase some nst* mdp options 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.050 0.025 195.8 85: (ns/day) (hour/ns) 85: Performance: 57.604 0.417 85: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_reference.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.edr as single precision energy file 85: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/11 (911 ms) 85: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/12 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 85: Setting nstcalcenergy (100) equal to nstenergy (1) 85: 85: Number of degrees of freedom in T-Coupling group System is 33.00 85: 85: There were 2 NOTEs 85: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 85: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 85: 85: Using 2 MPI threads 85: Using 1 OpenMP thread per tMPI thread 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'Argon' 85: 16 steps, 0.0 ps. 85: Generated 1 of the 1 non-bonded parameter combinations 85: 85: Excluding 1 bonded neighbours molecule type 'Argon' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: NOTE: 44 % of the run time was spent communicating energies, 85: you might want to increase some nst* mdp options 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.066 0.034 198.1 85: (ns/day) (hour/ns) 85: Performance: 43.763 0.548 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 85: Setting nstcalcenergy (100) equal to nstenergy (1) 85: 85: Number of degrees of freedom in T-Coupling group System is 33.00 85: 85: There were 2 NOTEs 85: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 85: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 85: 85: Using 2 MPI threads 85: Using 1 OpenMP thread per tMPI thread 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'Argon' 85: 16 steps, 0.0 ps. 85: Generated 1 of the 1 non-bonded parameter combinations 85: 85: Excluding 1 bonded neighbours molecule type 'Argon' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: NOTE: 45 % of the run time was spent communicating energies, 85: you might want to increase some nst* mdp options 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.070 0.035 198.5 85: (ns/day) (hour/ns) 85: Performance: 41.735 0.575 85: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_reference.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.edr as single precision energy file 85: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 85: Setting nstcalcenergy (100) equal to nstenergy (4) 85: 85: Number of degrees of freedom in T-Coupling group System is 33.00 85: 85: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 85: COM removal frequency is set to (5). 85: Other settings require a global communication frequency of 4. 85: Note that this will require additional global communication steps, 85: which will reduce performance when using multiple ranks. 85: Consider setting nstcomm to a multiple of 4. 85: 85: 85: There were 3 NOTEs 85: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 85: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 85: 85: Using 2 MPI threads 85: Using 1 OpenMP thread per tMPI thread 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'Argon' 85: 16 steps, 0.0 ps. 85: Generated 1 of the 1 non-bonded parameter combinations 85: 85: Excluding 1 bonded neighbours molecule type 'Argon' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: NOTE: 42 % of the run time was spent communicating energies, 85: you might want to increase some nst* mdp options 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.037 0.019 197.1 85: (ns/day) (hour/ns) 85: Performance: 78.409 0.306 85: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_reference.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.edr as single precision energy file 85: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 85: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 85: setting nstcomm equal to nstcalcenergy for less overhead 85: 85: Number of degrees of freedom in T-Coupling group System is 33.00 85: 85: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 85: COM removal frequency is set to (5). 85: Other settings require a global communication frequency of 100. 85: Note that this will require additional global communication steps, 85: which will reduce performance when using multiple ranks. 85: Consider setting nstcomm to a multiple of 100. 85: 85: 85: There were 3 NOTEs 85: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 85: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 85: 85: Using 2 MPI threads 85: Using 1 OpenMP thread per tMPI thread 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'Argon' 85: 16 steps, 0.0 ps. 85: Generated 1 of the 1 non-bonded parameter combinations 85: 85: Excluding 1 bonded neighbours molecule type 'Argon' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: NOTE: 49 % of the run time was spent communicating energies, 85: you might want to increase some nst* mdp options 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.084 0.043 198.3 85: (ns/day) (hour/ns) 85: Performance: 34.506 0.696 85: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_reference.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.edr as single precision energy file 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 85: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 85: setting nstcomm equal to nstcalcenergy for less overhead 85: 85: Number of degrees of freedom in T-Coupling group System is 33.00 85: 85: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 85: COM removal frequency is set to (5). 85: Other settings require a global communication frequency of 100. 85: Note that this will require additional global communication steps, 85: which will reduce performance when using multiple ranks. 85: Consider setting nstcomm to a multiple of 100. 85: 85: 85: There were 3 NOTEs 85: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 85: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 85: 85: Using 2 MPI threads 85: Using 1 OpenMP thread per tMPI thread 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'Argon' 85: 16 steps, 0.0 ps. 85: Generated 1 of the 1 non-bonded parameter combinations 85: 85: Excluding 1 bonded neighbours molecule type 'Argon' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: NOTE: 46 % of the run time was spent communicating energies, 85: you might want to increase some nst* mdp options 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.060 0.030 198.2 85: (ns/day) (hour/ns) 85: Performance: 48.809 0.492 85: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_reference.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.edr as single precision energy file 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 85: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 85: setting nstcomm equal to nstcalcenergy for less overhead 85: 85: Number of degrees of freedom in T-Coupling group System is 33.00 85: 85: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 85: COM removal frequency is set to (5). 85: Other settings require a global communication frequency of 100. 85: Note that this will require additional global communication steps, 85: which will reduce performance when using multiple ranks. 85: Consider setting nstcomm to a multiple of 100. 85: 85: 85: There were 3 NOTEs 85: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 85: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 85: 85: Using 2 MPI threads 85: Using 1 OpenMP thread per tMPI thread 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'Argon' 85: 16 steps, 0.0 ps. 85: Generated 1 of the 1 non-bonded parameter combinations 85: 85: Excluding 1 bonded neighbours molecule type 'Argon' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: NOTE: 51 % of the run time was spent communicating energies, 85: you might want to increase some nst* mdp options 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.652 0.326 199.8 85: (ns/day) (hour/ns) 85: Performance: 4.503 5.330 85: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_reference.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.edr as single precision energy file 85: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/12 (803 ms) 85: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/13 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: 85: Setting nstcalcenergy (100) equal to nstenergy (1) 85: 85: 85: WARNING 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: 85: The Berendsen barostat does not generate any strictly correct ensemble, 85: and should not be used for new production simulations (in our opinion). 85: We recommend using the C-rescale barostat instead. 85: 85: Number of degrees of freedom in T-Coupling group System is 33.00 85: 85: There were 2 NOTEs 85: 85: There was 1 WARNING 85: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 85: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 85: 85: Using 2 MPI threads 85: Using 1 OpenMP thread per tMPI thread 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'Argon' 85: 16 steps, 0.0 ps. 85: Generated 1 of the 1 non-bonded parameter combinations 85: 85: Excluding 1 bonded neighbours molecule type 'Argon' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: NOTE: 44 % of the run time was spent communicating energies, 85: you might want to increase some nst* mdp options 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.074 0.037 198.2 85: (ns/day) (hour/ns) 85: Performance: 39.260 0.611 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: 85: Setting nstcalcenergy (100) equal to nstenergy (1) 85: 85: 85: WARNING 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: 85: The Berendsen barostat does not generate any strictly correct ensemble, 85: and should not be used for new production simulations (in our opinion). 85: We recommend using the C-rescale barostat instead. 85: 85: Number of degrees of freedom in T-Coupling group System is 33.00 85: 85: There were 2 NOTEs 85: 85: There was 1 WARNING 85: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 85: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 85: 85: Using 2 MPI threads 85: Using 1 OpenMP thread per tMPI thread 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'Argon' 85: 16 steps, 0.0 ps. 85: Generated 1 of the 1 non-bonded parameter combinations 85: 85: Excluding 1 bonded neighbours molecule type 'Argon' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: NOTE: 42 % of the run time was spent communicating energies, 85: you might want to increase some nst* mdp options 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.062 0.031 198.0 85: (ns/day) (hour/ns) 85: Performance: 46.759 0.513 85: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_reference.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.edr as single precision energy file 85: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: 85: Setting nstcalcenergy (100) equal to nstenergy (4) 85: 85: 85: WARNING 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: 85: The Berendsen barostat does not generate any strictly correct ensemble, 85: and should not be used for new production simulations (in our opinion). 85: We recommend using the C-rescale barostat instead. 85: 85: Number of degrees of freedom in T-Coupling group System is 33.00 85: 85: There were 2 NOTEs 85: 85: There was 1 WARNING 85: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 85: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 85: 85: Using 2 MPI threads 85: Using 1 OpenMP thread per tMPI thread 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'Argon' 85: 16 steps, 0.0 ps. 85: Generated 1 of the 1 non-bonded parameter combinations 85: 85: Excluding 1 bonded neighbours molecule type 'Argon' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: NOTE: 44 % of the run time was spent communicating energies, 85: you might want to increase some nst* mdp options 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.045 0.023 197.3 85: (ns/day) (hour/ns) 85: Performance: 64.698 0.371 85: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_reference.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.edr as single precision energy file 85: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: 85: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 85: setting nstcomm equal to nstcalcenergy for less overhead 85: 85: 85: WARNING 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: 85: The Berendsen barostat does not generate any strictly correct ensemble, 85: and should not be used for new production simulations (in our opinion). 85: We recommend using the C-rescale barostat instead. 85: 85: Number of degrees of freedom in T-Coupling group System is 33.00 85: 85: There were 2 NOTEs 85: 85: There was 1 WARNING 85: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 85: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 85: 85: Using 2 MPI threads 85: Using 1 OpenMP thread per tMPI thread 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'Argon' 85: 16 steps, 0.0 ps. 85: Generated 1 of the 1 non-bonded parameter combinations 85: 85: Excluding 1 bonded neighbours molecule type 'Argon' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: NOTE: 46 % of the run time was spent communicating energies, 85: you might want to increase some nst* mdp options 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.062 0.032 198.0 85: (ns/day) (hour/ns) 85: Performance: 46.545 0.516 85: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_reference.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.edr as single precision energy file 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: 85: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 85: setting nstcomm equal to nstcalcenergy for less overhead 85: 85: 85: WARNING 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: 85: The Berendsen barostat does not generate any strictly correct ensemble, 85: and should not be used for new production simulations (in our opinion). 85: We recommend using the C-rescale barostat instead. 85: 85: Number of degrees of freedom in T-Coupling group System is 33.00 85: 85: There were 2 NOTEs 85: 85: There was 1 WARNING 85: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 85: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 85: 85: Using 2 MPI threads 85: Using 1 OpenMP thread per tMPI thread 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'Argon' 85: 16 steps, 0.0 ps. 85: Generated 1 of the 1 non-bonded parameter combinations 85: 85: Excluding 1 bonded neighbours molecule type 'Argon' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: NOTE: 45 % of the run time was spent communicating energies, 85: you might want to increase some nst* mdp options 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.045 0.023 197.2 85: (ns/day) (hour/ns) 85: Performance: 64.810 0.370 85: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_reference.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.edr as single precision energy file 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: 85: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 85: setting nstcomm equal to nstcalcenergy for less overhead 85: 85: 85: WARNING 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: 85: The Berendsen barostat does not generate any strictly correct ensemble, 85: and should not be used for new production simulations (in our opinion). 85: We recommend using the C-rescale barostat instead. 85: 85: Number of degrees of freedom in T-Coupling group System is 33.00 85: 85: There were 2 NOTEs 85: 85: There was 1 WARNING 85: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 85: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 85: 85: Using 2 MPI threads 85: Using 1 OpenMP thread per tMPI thread 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'Argon' 85: 16 steps, 0.0 ps. 85: Generated 1 of the 1 non-bonded parameter combinations 85: 85: Excluding 1 bonded neighbours molecule type 'Argon' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: NOTE: 44 % of the run time was spent communicating energies, 85: you might want to increase some nst* mdp options 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.041 0.021 197.4 85: (ns/day) (hour/ns) 85: Performance: 70.133 0.342 85: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_reference.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.edr as single precision energy file 85: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/13 (495 ms) 85: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/14 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]: 85: Setting nstcalcenergy (100) equal to nstenergy (1) 85: 85: Number of degrees of freedom in T-Coupling group System is 33.00 85: 85: There were 2 NOTEs 85: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 85: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 85: 85: Using 2 MPI threads 85: Using 1 OpenMP thread per tMPI thread 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'Argon' 85: 16 steps, 0.0 ps. 85: Generated 1 of the 1 non-bonded parameter combinations 85: 85: Excluding 1 bonded neighbours molecule type 'Argon' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: NOTE: 41 % of the run time was spent communicating energies, 85: you might want to increase some nst* mdp options 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.055 0.028 197.2 85: (ns/day) (hour/ns) 85: Performance: 53.093 0.452 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]: 85: Setting nstcalcenergy (100) equal to nstenergy (1) 85: 85: Number of degrees of freedom in T-Coupling group System is 33.00 85: 85: There were 2 NOTEs 85: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 85: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 85: 85: Using 2 MPI threads 85: Using 1 OpenMP thread per tMPI thread 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'Argon' 85: 16 steps, 0.0 ps. 85: Generated 1 of the 1 non-bonded parameter combinations 85: 85: Excluding 1 bonded neighbours molecule type 'Argon' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: NOTE: 45 % of the run time was spent communicating energies, 85: you might want to increase some nst* mdp options 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.046 0.023 197.4 85: (ns/day) (hour/ns) 85: Performance: 63.516 0.378 85: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_reference.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.edr as single precision energy file 85: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]: 85: Setting nstcalcenergy (100) equal to nstenergy (4) 85: 85: Number of degrees of freedom in T-Coupling group System is 33.00 85: 85: There were 2 NOTEs 85: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 85: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 85: 85: Using 2 MPI threads 85: Using 1 OpenMP thread per tMPI thread 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'Argon' 85: 16 steps, 0.0 ps. 85: Generated 1 of the 1 non-bonded parameter combinations 85: 85: Excluding 1 bonded neighbours molecule type 'Argon' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: NOTE: 43 % of the run time was spent communicating energies, 85: you might want to increase some nst* mdp options 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.036 0.018 196.8 85: (ns/day) (hour/ns) 85: Performance: 81.033 0.296 85: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_reference.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.edr as single precision energy file 85: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]: 85: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 85: setting nstcomm equal to nstcalcenergy for less overhead 85: 85: Number of degrees of freedom in T-Coupling group System is 33.00 85: 85: There were 2 NOTEs 85: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 85: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 85: 85: Using 2 MPI threads 85: Using 1 OpenMP thread per tMPI thread 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'Argon' 85: 16 steps, 0.0 ps. 85: Generated 1 of the 1 non-bonded parameter combinations 85: 85: Excluding 1 bonded neighbours molecule type 'Argon' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: NOTE: 46 % of the run time was spent communicating energies, 85: you might want to increase some nst* mdp options 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.072 0.036 198.3 85: (ns/day) (hour/ns) 85: Performance: 40.264 0.596 85: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_reference.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.edr as single precision energy file 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]: 85: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 85: setting nstcomm equal to nstcalcenergy for less overhead 85: 85: Number of degrees of freedom in T-Coupling group System is 33.00 85: 85: There were 2 NOTEs 85: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 85: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 85: 85: Using 2 MPI threads 85: Using 1 OpenMP thread per tMPI thread 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'Argon' 85: 16 steps, 0.0 ps. 85: Generated 1 of the 1 non-bonded parameter combinations 85: 85: Excluding 1 bonded neighbours molecule type 'Argon' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: NOTE: 43 % of the run time was spent communicating energies, 85: you might want to increase some nst* mdp options 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.056 0.028 197.8 85: (ns/day) (hour/ns) 85: Performance: 51.852 0.463 85: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_reference.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.edr as single precision energy file 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]: 85: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 85: setting nstcomm equal to nstcalcenergy for less overhead 85: 85: Number of degrees of freedom in T-Coupling group System is 33.00 85: 85: There were 2 NOTEs 85: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 85: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 85: 85: Using 2 MPI threads 85: Using 1 OpenMP thread per tMPI thread 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'Argon' 85: 16 steps, 0.0 ps. 85: Generated 1 of the 1 non-bonded parameter combinations 85: 85: Excluding 1 bonded neighbours molecule type 'Argon' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: NOTE: 45 % of the run time was spent communicating energies, 85: you might want to increase some nst* mdp options 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.050 0.027 187.2 85: (ns/day) (hour/ns) 85: Performance: 55.248 0.434 85: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_reference.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.edr as single precision energy file 85: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/14 (482 ms) 85: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/15 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]: 85: Setting nstcalcenergy (100) equal to nstenergy (1) 85: 85: Number of degrees of freedom in T-Coupling group System is 33.00 85: 85: There were 2 NOTEs 85: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 85: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 85: 85: Using 2 MPI threads 85: Using 1 OpenMP thread per tMPI thread 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'Argon' 85: 16 steps, 0.0 ps. 85: Generated 1 of the 1 non-bonded parameter combinations 85: 85: Excluding 1 bonded neighbours molecule type 'Argon' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: NOTE: 56 % of the run time was spent communicating energies, 85: you might want to increase some nst* mdp options 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.075 0.040 189.4 85: (ns/day) (hour/ns) 85: Performance: 36.870 0.651 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]: 85: Setting nstcalcenergy (100) equal to nstenergy (1) 85: 85: Number of degrees of freedom in T-Coupling group System is 33.00 85: 85: There were 2 NOTEs 85: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 85: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 85: 85: Using 2 MPI threads 85: Using 1 OpenMP thread per tMPI thread 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'Argon' 85: 16 steps, 0.0 ps. 85: Generated 1 of the 1 non-bonded parameter combinations 85: 85: Excluding 1 bonded neighbours molecule type 'Argon' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: NOTE: 42 % of the run time was spent communicating energies, 85: you might want to increase some nst* mdp options 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.050 0.026 194.9 85: (ns/day) (hour/ns) 85: Performance: 57.468 0.418 85: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_reference.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.edr as single precision energy file 85: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]: 85: Setting nstcalcenergy (100) equal to nstenergy (4) 85: 85: Number of degrees of freedom in T-Coupling group System is 33.00 85: 85: There were 2 NOTEs 85: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 85: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 85: 85: Using 2 MPI threads 85: Using 1 OpenMP thread per tMPI thread 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'Argon' 85: 16 steps, 0.0 ps. 85: Generated 1 of the 1 non-bonded parameter combinations 85: 85: Excluding 1 bonded neighbours molecule type 'Argon' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: NOTE: 41 % of the run time was spent communicating energies, 85: you might want to increase some nst* mdp options 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.035 0.018 197.1 85: (ns/day) (hour/ns) 85: Performance: 83.376 0.288 85: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_reference.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.edr as single precision energy file 85: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]: 85: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 85: setting nstcomm equal to nstcalcenergy for less overhead 85: 85: Number of degrees of freedom in T-Coupling group System is 33.00 85: 85: There were 2 NOTEs 85: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 85: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 85: 85: Using 2 MPI threads 85: Using 1 OpenMP thread per tMPI thread 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'Argon' 85: 16 steps, 0.0 ps. 85: Generated 1 of the 1 non-bonded parameter combinations 85: 85: Excluding 1 bonded neighbours molecule type 'Argon' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: NOTE: 46 % of the run time was spent communicating energies, 85: you might want to increase some nst* mdp options 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.068 0.034 198.2 85: (ns/day) (hour/ns) 85: Performance: 42.834 0.560 85: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_reference.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.edr as single precision energy file 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]: 85: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 85: setting nstcomm equal to nstcalcenergy for less overhead 85: 85: Number of degrees of freedom in T-Coupling group System is 33.00 85: 85: There were 2 NOTEs 85: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 85: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 85: 85: Using 2 MPI threads 85: Using 1 OpenMP thread per tMPI thread 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'Argon' 85: 16 steps, 0.0 ps. 85: Generated 1 of the 1 non-bonded parameter combinations 85: 85: Excluding 1 bonded neighbours molecule type 'Argon' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: NOTE: 46 % of the run time was spent communicating energies, 85: you might want to increase some nst* mdp options 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.060 0.030 197.8 85: (ns/day) (hour/ns) 85: Performance: 48.638 0.493 85: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_reference.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.edr as single precision energy file 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]: 85: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 85: setting nstcomm equal to nstcalcenergy for less overhead 85: 85: Number of degrees of freedom in T-Coupling group System is 33.00 85: 85: There were 2 NOTEs 85: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 85: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 85: 85: Using 2 MPI threads 85: Using 1 OpenMP thread per tMPI thread 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'Argon' 85: 16 steps, 0.0 ps. 85: Generated 1 of the 1 non-bonded parameter combinations 85: 85: Excluding 1 bonded neighbours molecule type 'Argon' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: NOTE: 49 % of the run time was spent communicating energies, 85: you might want to increase some nst* mdp options 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.069 0.035 198.2 85: (ns/day) (hour/ns) 85: Performance: 42.455 0.565 85: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_reference.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.edr as single precision energy file 85: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/15 (530 ms) 85: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/16 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 85: Setting nstcalcenergy (100) equal to nstenergy (1) 85: 85: Number of degrees of freedom in T-Coupling group System is 33.00 85: 85: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 85: NVE simulation: will use the initial temperature of 68.810 K for 85: determining the Verlet buffer size 85: 85: 85: There were 3 NOTEs 85: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 85: Can not increase nstlist because an NVE ensemble is used 85: Using 2 MPI threads 85: Using 1 OpenMP thread per tMPI thread 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'Argon' 85: 16 steps, 0.0 ps. 85: Generated 1 of the 1 non-bonded parameter combinations 85: 85: Excluding 1 bonded neighbours molecule type 'Argon' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: 85: Dynamic load balancing report: 85: DLB was off during the run due to low measured imbalance. 85: Average load imbalance: 0.8%. 85: The balanceable part of the MD step is 41%, load imbalance is computed from this. 85: Part of the total run time spent waiting due to load imbalance: 0.3%. 85: 85: 85: NOTE: 6 % of the run time was spent communicating energies, 85: you might want to increase some nst* mdp options 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.069 0.037 188.5 85: (ns/day) (hour/ns) 85: Performance: 40.099 0.599 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 85: Setting nstcalcenergy (100) equal to nstenergy (1) 85: 85: Number of degrees of freedom in T-Coupling group System is 33.00 85: 85: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 85: NVE simulation: will use the initial temperature of 68.810 K for 85: determining the Verlet buffer size 85: 85: 85: There were 3 NOTEs 85: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 85: Can not increase nstlist because an NVE ensemble is used 85: Using 2 MPI threads 85: Using 1 OpenMP thread per tMPI thread 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'Argon' 85: 16 steps, 0.0 ps. 85: Generated 1 of the 1 non-bonded parameter combinations 85: 85: Excluding 1 bonded neighbours molecule type 'Argon' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: 85: Dynamic load balancing report: 85: DLB was off during the run due to low measured imbalance. 85: Average load imbalance: 1.5%. 85: The balanceable part of the MD step is 51%, load imbalance is computed from this. 85: Part of the total run time spent waiting due to load imbalance: 0.8%. 85: 85: 85: NOTE: 6 % of the run time was spent communicating energies, 85: you might want to increase some nst* mdp options 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.061 0.031 195.7 85: (ns/day) (hour/ns) 85: Performance: 46.953 0.511 85: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_reference.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.edr as single precision energy file 85: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 85: Setting nstcalcenergy (100) equal to nstenergy (4) 85: 85: Number of degrees of freedom in T-Coupling group System is 33.00 85: 85: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 85: NVE simulation: will use the initial temperature of 68.810 K for 85: determining the Verlet buffer size 85: 85: 85: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 85: COM removal frequency is set to (5). 85: Other settings require a global communication frequency of 4. 85: Note that this will require additional global communication steps, 85: which will reduce performance when using multiple ranks. 85: Consider setting nstcomm to a multiple of 4. 85: 85: 85: There were 4 NOTEs 85: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 85: Can not increase nstlist because an NVE ensemble is used 85: Using 2 MPI threads 85: Using 1 OpenMP thread per tMPI thread 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'Argon' 85: 16 steps, 0.0 ps. 85: Generated 1 of the 1 non-bonded parameter combinations 85: 85: Excluding 1 bonded neighbours molecule type 'Argon' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: 85: Dynamic load balancing report: 85: DLB was off during the run due to low measured imbalance. 85: Average load imbalance: 0.6%. 85: The balanceable part of the MD step is 12%, load imbalance is computed from this. 85: Part of the total run time spent waiting due to load imbalance: 0.1%. 85: 85: 85: NOTE: 22 % of the run time was spent communicating energies, 85: you might want to increase some nst* mdp options 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.072 0.037 196.1 85: (ns/day) (hour/ns) 85: Performance: 40.152 0.598 85: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_reference.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.edr as single precision energy file 85: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 85: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 85: setting nstcomm equal to nstcalcenergy for less overhead 85: 85: Number of degrees of freedom in T-Coupling group System is 33.00 85: 85: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 85: NVE simulation: will use the initial temperature of 68.810 K for 85: determining the Verlet buffer size 85: 85: 85: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 85: COM removal frequency is set to (5). 85: Other settings require a global communication frequency of 100. 85: Note that this will require additional global communication steps, 85: which will reduce performance when using multiple ranks. 85: Consider setting nstcomm to a multiple of 100. 85: 85: 85: There were 4 NOTEs 85: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 85: Can not increase nstlist because an NVE ensemble is used 85: Using 2 MPI threads 85: Using 1 OpenMP thread per tMPI thread 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'Argon' 85: 16 steps, 0.0 ps. 85: Generated 1 of the 1 non-bonded parameter combinations 85: 85: Excluding 1 bonded neighbours molecule type 'Argon' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: 85: Dynamic load balancing report: 85: DLB was off during the run due to low measured imbalance. 85: Average load imbalance: 1.8%. 85: The balanceable part of the MD step is 38%, load imbalance is computed from this. 85: Part of the total run time spent waiting due to load imbalance: 0.7%. 85: 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.071 0.037 194.7 85: (ns/day) (hour/ns) 85: Performance: 40.120 0.598 85: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_reference.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.edr as single precision energy file 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 85: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 85: setting nstcomm equal to nstcalcenergy for less overhead 85: 85: Number of degrees of freedom in T-Coupling group System is 33.00 85: 85: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 85: NVE simulation: will use the initial temperature of 68.810 K for 85: determining the Verlet buffer size 85: 85: 85: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 85: COM removal frequency is set to (5). 85: Other settings require a global communication frequency of 100. 85: Note that this will require additional global communication steps, 85: which will reduce performance when using multiple ranks. 85: Consider setting nstcomm to a multiple of 100. 85: 85: 85: There were 4 NOTEs 85: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 85: Can not increase nstlist because an NVE ensemble is used 85: Using 2 MPI threads 85: Using 1 OpenMP thread per tMPI thread 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'Argon' 85: 16 steps, 0.0 ps. 85: Generated 1 of the 1 non-bonded parameter combinations 85: 85: Excluding 1 bonded neighbours molecule type 'Argon' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: 85: Dynamic load balancing report: 85: DLB was off during the run due to low measured imbalance. 85: Average load imbalance: 1.1%. 85: The balanceable part of the MD step is 47%, load imbalance is computed from this. 85: Part of the total run time spent waiting due to load imbalance: 0.5%. 85: 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.065 0.035 183.2 85: (ns/day) (hour/ns) 85: Performance: 41.667 0.576 85: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_reference.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.edr as single precision energy file 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 85: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 85: setting nstcomm equal to nstcalcenergy for less overhead 85: 85: Number of degrees of freedom in T-Coupling group System is 33.00 85: 85: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 85: NVE simulation: will use the initial temperature of 68.810 K for 85: determining the Verlet buffer size 85: 85: 85: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 85: COM removal frequency is set to (5). 85: Other settings require a global communication frequency of 100. 85: Note that this will require additional global communication steps, 85: which will reduce performance when using multiple ranks. 85: Consider setting nstcomm to a multiple of 100. 85: 85: 85: There were 4 NOTEs 85: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 85: Can not increase nstlist because an NVE ensemble is used 85: Using 2 MPI threads 85: Using 1 OpenMP thread per tMPI thread 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'Argon' 85: 16 steps, 0.0 ps. 85: Generated 1 of the 1 non-bonded parameter combinations 85: 85: Excluding 1 bonded neighbours molecule type 'Argon' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: 85: Dynamic load balancing report: 85: DLB was off during the run due to low measured imbalance. 85: Average load imbalance: 1.2%. 85: The balanceable part of the MD step is 39%, load imbalance is computed from this. 85: Part of the total run time spent waiting due to load imbalance: 0.5%. 85: 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.065 0.033 196.1 85: (ns/day) (hour/ns) 85: Performance: 44.569 0.538 85: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_reference.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.edr as single precision energy file 85: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/16 (506 ms) 85: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/17 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 85: Setting nstcalcenergy (100) equal to nstenergy (1) 85: 85: 85: WARNING 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 85: The Berendsen barostat does not generate any strictly correct ensemble, 85: and should not be used for new production simulations (in our opinion). 85: We recommend using the C-rescale barostat instead. 85: 85: Number of degrees of freedom in T-Coupling group System is 33.00 85: 85: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 85: NVE simulation: will use the initial temperature of 68.810 K for 85: determining the Verlet buffer size 85: 85: 85: There were 3 NOTEs 85: 85: There was 1 WARNING 85: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 85: Can not increase nstlist because an NVE ensemble is used 85: Using 2 MPI threads 85: Using 1 OpenMP thread per tMPI thread 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'Argon' 85: 16 steps, 0.0 ps. 85: Generated 1 of the 1 non-bonded parameter combinations 85: 85: Excluding 1 bonded neighbours molecule type 'Argon' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: 85: Dynamic load balancing report: 85: DLB was off during the run due to low measured imbalance. 85: Average load imbalance: 0.9%. 85: The balanceable part of the MD step is 63%, load imbalance is computed from this. 85: Part of the total run time spent waiting due to load imbalance: 0.6%. 85: 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.059 0.030 196.1 85: (ns/day) (hour/ns) 85: Performance: 49.219 0.488 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 85: Setting nstcalcenergy (100) equal to nstenergy (1) 85: 85: 85: WARNING 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 85: The Berendsen barostat does not generate any strictly correct ensemble, 85: and should not be used for new production simulations (in our opinion). 85: We recommend using the C-rescale barostat instead. 85: 85: Number of degrees of freedom in T-Coupling group System is 33.00 85: 85: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 85: NVE simulation: will use the initial temperature of 68.810 K for 85: determining the Verlet buffer size 85: 85: 85: There were 3 NOTEs 85: 85: There was 1 WARNING 85: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 85: Can not increase nstlist because an NVE ensemble is used 85: Using 2 MPI threads 85: Using 1 OpenMP thread per tMPI thread 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'Argon' 85: 16 steps, 0.0 ps. 85: Generated 1 of the 1 non-bonded parameter combinations 85: 85: Excluding 1 bonded neighbours molecule type 'Argon' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: 85: Dynamic load balancing report: 85: DLB was off during the run due to low measured imbalance. 85: Average load imbalance: 0.7%. 85: The balanceable part of the MD step is 54%, load imbalance is computed from this. 85: Part of the total run time spent waiting due to load imbalance: 0.4%. 85: 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.056 0.029 193.8 85: (ns/day) (hour/ns) 85: Performance: 50.510 0.475 85: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_reference.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.edr as single precision energy file 85: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 85: Setting nstcalcenergy (100) equal to nstenergy (4) 85: 85: 85: WARNING 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 85: The Berendsen barostat does not generate any strictly correct ensemble, 85: and should not be used for new production simulations (in our opinion). 85: We recommend using the C-rescale barostat instead. 85: 85: Number of degrees of freedom in T-Coupling group System is 33.00 85: 85: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 85: NVE simulation: will use the initial temperature of 68.810 K for 85: determining the Verlet buffer size 85: 85: 85: There were 3 NOTEs 85: 85: There was 1 WARNING 85: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 85: Can not increase nstlist because an NVE ensemble is used 85: Using 2 MPI threads 85: Using 1 OpenMP thread per tMPI thread 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'Argon' 85: 16 steps, 0.0 ps. 85: Generated 1 of the 1 non-bonded parameter combinations 85: 85: Excluding 1 bonded neighbours molecule type 'Argon' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: 85: Dynamic load balancing report: 85: DLB was off during the run due to low measured imbalance. 85: Average load imbalance: 0.3%. 85: The balanceable part of the MD step is 51%, load imbalance is computed from this. 85: Part of the total run time spent waiting due to load imbalance: 0.2%. 85: 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.076 0.039 194.2 85: (ns/day) (hour/ns) 85: Performance: 37.419 0.641 85: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_reference.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.edr as single precision energy file 85: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 85: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 85: setting nstcomm equal to nstcalcenergy for less overhead 85: 85: 85: WARNING 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 85: The Berendsen barostat does not generate any strictly correct ensemble, 85: and should not be used for new production simulations (in our opinion). 85: We recommend using the C-rescale barostat instead. 85: 85: Number of degrees of freedom in T-Coupling group System is 33.00 85: 85: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 85: NVE simulation: will use the initial temperature of 68.810 K for 85: determining the Verlet buffer size 85: 85: 85: There were 3 NOTEs 85: 85: There was 1 WARNING 85: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 85: Can not increase nstlist because an NVE ensemble is used 85: Using 2 MPI threads 85: Using 1 OpenMP thread per tMPI thread 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'Argon' 85: 16 steps, 0.0 ps. 85: Generated 1 of the 1 non-bonded parameter combinations 85: 85: Excluding 1 bonded neighbours molecule type 'Argon' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: 85: Dynamic load balancing report: 85: DLB was off during the run due to low measured imbalance. 85: Average load imbalance: 0.6%. 85: The balanceable part of the MD step is 45%, load imbalance is computed from this. 85: Part of the total run time spent waiting due to load imbalance: 0.3%. 85: 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.067 0.035 191.0 85: (ns/day) (hour/ns) 85: Performance: 41.643 0.576 85: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_reference.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.edr as single precision energy file 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 85: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 85: setting nstcomm equal to nstcalcenergy for less overhead 85: 85: 85: WARNING 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 85: The Berendsen barostat does not generate any strictly correct ensemble, 85: and should not be used for new production simulations (in our opinion). 85: We recommend using the C-rescale barostat instead. 85: 85: Number of degrees of freedom in T-Coupling group System is 33.00 85: 85: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 85: NVE simulation: will use the initial temperature of 68.810 K for 85: determining the Verlet buffer size 85: 85: 85: There were 3 NOTEs 85: 85: There was 1 WARNING 85: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 85: Can not increase nstlist because an NVE ensemble is used 85: Using 2 MPI threads 85: Using 1 OpenMP thread per tMPI thread 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'Argon' 85: 16 steps, 0.0 ps. 85: Generated 1 of the 1 non-bonded parameter combinations 85: 85: Excluding 1 bonded neighbours molecule type 'Argon' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: 85: Dynamic load balancing report: 85: DLB was off during the run due to low measured imbalance. 85: Average load imbalance: 0.7%. 85: The balanceable part of the MD step is 56%, load imbalance is computed from this. 85: Part of the total run time spent waiting due to load imbalance: 0.4%. 85: 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.083 0.042 197.0 85: (ns/day) (hour/ns) 85: Performance: 34.678 0.692 85: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_reference.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.edr as single precision energy file 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 85: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 85: setting nstcomm equal to nstcalcenergy for less overhead 85: 85: 85: WARNING 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 85: The Berendsen barostat does not generate any strictly correct ensemble, 85: and should not be used for new production simulations (in our opinion). 85: We recommend using the C-rescale barostat instead. 85: 85: Number of degrees of freedom in T-Coupling group System is 33.00 85: 85: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 85: NVE simulation: will use the initial temperature of 68.810 K for 85: determining the Verlet buffer size 85: 85: 85: There were 3 NOTEs 85: 85: There was 1 WARNING 85: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 85: Can not increase nstlist because an NVE ensemble is used 85: Using 2 MPI threads 85: Using 1 OpenMP thread per tMPI thread 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'Argon' 85: 16 steps, 0.0 ps. 85: Generated 1 of the 1 non-bonded parameter combinations 85: 85: Excluding 1 bonded neighbours molecule type 'Argon' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: 85: Dynamic load balancing report: 85: DLB was off during the run due to low measured imbalance. 85: Average load imbalance: 0.6%. 85: The balanceable part of the MD step is 33%, load imbalance is computed from this. 85: Part of the total run time spent waiting due to load imbalance: 0.2%. 85: 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.073 0.037 196.5 85: (ns/day) (hour/ns) 85: Performance: 39.522 0.607 85: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_reference.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.edr as single precision energy file 85: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/17 (542 ms) 85: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/18 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]: 85: Setting nstcalcenergy (100) equal to nstenergy (1) 85: 85: Number of degrees of freedom in T-Coupling group System is 33.00 85: 85: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]: 85: NVE simulation: will use the initial temperature of 68.810 K for 85: determining the Verlet buffer size 85: 85: 85: There were 3 NOTEs 85: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 85: Can not increase nstlist because an NVE ensemble is used 85: Using 2 MPI threads 85: Using 1 OpenMP thread per tMPI thread 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'Argon' 85: 16 steps, 0.0 ps. 85: Generated 1 of the 1 non-bonded parameter combinations 85: 85: Excluding 1 bonded neighbours molecule type 'Argon' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: 85: Dynamic load balancing report: 85: DLB was off during the run due to low measured imbalance. 85: Average load imbalance: 2.5%. 85: The balanceable part of the MD step is 48%, load imbalance is computed from this. 85: Part of the total run time spent waiting due to load imbalance: 1.2%. 85: 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.058 0.029 196.2 85: (ns/day) (hour/ns) 85: Performance: 49.864 0.481 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]: 85: Setting nstcalcenergy (100) equal to nstenergy (1) 85: 85: Number of degrees of freedom in T-Coupling group System is 33.00 85: 85: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]: 85: NVE simulation: will use the initial temperature of 68.810 K for 85: determining the Verlet buffer size 85: 85: 85: There were 3 NOTEs 85: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 85: Can not increase nstlist because an NVE ensemble is used 85: Using 2 MPI threads 85: Using 1 OpenMP thread per tMPI thread 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'Argon' 85: 16 steps, 0.0 ps. 85: Generated 1 of the 1 non-bonded parameter combinations 85: 85: Excluding 1 bonded neighbours molecule type 'Argon' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: 85: Dynamic load balancing report: 85: DLB was off during the run due to low measured imbalance. 85: Average load imbalance: 0.9%. 85: The balanceable part of the MD step is 64%, load imbalance is computed from this. 85: Part of the total run time spent waiting due to load imbalance: 0.6%. 85: 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.052 0.027 195.1 85: (ns/day) (hour/ns) 85: Performance: 54.729 0.439 85: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_reference.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18.edr as single precision energy file 85: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]: 85: Setting nstcalcenergy (100) equal to nstenergy (4) 85: 85: Number of degrees of freedom in T-Coupling group System is 33.00 85: 85: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]: 85: NVE simulation: will use the initial temperature of 68.810 K for 85: determining the Verlet buffer size 85: 85: 85: There were 3 NOTEs 85: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 85: Can not increase nstlist because an NVE ensemble is used 85: Using 2 MPI threads 85: Using 1 OpenMP thread per tMPI thread 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'Argon' 85: 16 steps, 0.0 ps. 85: Generated 1 of the 1 non-bonded parameter combinations 85: 85: Excluding 1 bonded neighbours molecule type 'Argon' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: 85: Dynamic load balancing report: 85: DLB was off during the run due to low measured imbalance. 85: Average load imbalance: 1.4%. 85: The balanceable part of the MD step is 37%, load imbalance is computed from this. 85: Part of the total run time spent waiting due to load imbalance: 0.5%. 85: 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.051 0.028 186.4 85: (ns/day) (hour/ns) 85: Performance: 53.350 0.450 85: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_reference.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18.edr as single precision energy file 85: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]: 85: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 85: setting nstcomm equal to nstcalcenergy for less overhead 85: 85: Number of degrees of freedom in T-Coupling group System is 33.00 85: 85: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]: 85: NVE simulation: will use the initial temperature of 68.810 K for 85: determining the Verlet buffer size 85: 85: 85: There were 3 NOTEs 85: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 85: Can not increase nstlist because an NVE ensemble is used 85: Using 2 MPI threads 85: Using 1 OpenMP thread per tMPI thread 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'Argon' 85: 16 steps, 0.0 ps. 85: Generated 1 of the 1 non-bonded parameter combinations 85: 85: Excluding 1 bonded neighbours molecule type 'Argon' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: 85: Dynamic load balancing report: 85: DLB was off during the run due to low measured imbalance. 85: Average load imbalance: 1.2%. 85: The balanceable part of the MD step is 39%, load imbalance is computed from this. 85: Part of the total run time spent waiting due to load imbalance: 0.5%. 85: 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.059 0.031 193.3 85: (ns/day) (hour/ns) 85: Performance: 48.040 0.500 85: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_reference.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18.edr as single precision energy file 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]: 85: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 85: setting nstcomm equal to nstcalcenergy for less overhead 85: 85: Number of degrees of freedom in T-Coupling group System is 33.00 85: 85: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]: 85: NVE simulation: will use the initial temperature of 68.810 K for 85: determining the Verlet buffer size 85: 85: 85: There were 3 NOTEs 85: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 85: Can not increase nstlist because an NVE ensemble is used 85: Using 2 MPI threads 85: Using 1 OpenMP thread per tMPI thread 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'Argon' 85: 16 steps, 0.0 ps. 85: Generated 1 of the 1 non-bonded parameter combinations 85: 85: Excluding 1 bonded neighbours molecule type 'Argon' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: 85: Dynamic load balancing report: 85: DLB was off during the run due to low measured imbalance. 85: Average load imbalance: 2.1%. 85: The balanceable part of the MD step is 25%, load imbalance is computed from this. 85: Part of the total run time spent waiting due to load imbalance: 0.5%. 85: 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.066 0.035 187.2 85: (ns/day) (hour/ns) 85: Performance: 41.409 0.580 85: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_reference.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18.edr as single precision energy file 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]: 85: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 85: setting nstcomm equal to nstcalcenergy for less overhead 85: 85: Number of degrees of freedom in T-Coupling group System is 33.00 85: 85: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]: 85: NVE simulation: will use the initial temperature of 68.810 K for 85: determining the Verlet buffer size 85: 85: 85: There were 3 NOTEs 85: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 85: Can not increase nstlist because an NVE ensemble is used 85: Using 2 MPI threads 85: Using 1 OpenMP thread per tMPI thread 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'Argon' 85: 16 steps, 0.0 ps. 85: Generated 1 of the 1 non-bonded parameter combinations 85: 85: Excluding 1 bonded neighbours molecule type 'Argon' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: 85: Dynamic load balancing report: 85: DLB was off during the run due to low measured imbalance. 85: Average load imbalance: 0.6%. 85: The balanceable part of the MD step is 51%, load imbalance is computed from this. 85: Part of the total run time spent waiting due to load imbalance: 0.3%. 85: 85: 85: NOTE: 10 % of the run time was spent communicating energies, 85: you might want to increase some nst* mdp options 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.113 0.057 197.4 85: (ns/day) (hour/ns) 85: Performance: 25.698 0.934 85: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_reference.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18.edr as single precision energy file 85: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/18 (516 ms) 85: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/19 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_input.mdp]: 85: Setting nstcalcenergy (100) equal to nstenergy (1) 85: 85: Number of degrees of freedom in T-Coupling group System is 33.00 85: 85: There were 2 NOTEs 85: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 85: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 85: 85: Using 2 MPI threads 85: Using 1 OpenMP thread per tMPI thread 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'Argon' 85: 16 steps, 0.0 ps. 85: Generated 1 of the 1 non-bonded parameter combinations 85: 85: Excluding 1 bonded neighbours molecule type 'Argon' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.065 0.033 196.2 85: (ns/day) (hour/ns) 85: Performance: 44.528 0.539 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_input.mdp]: 85: Setting nstcalcenergy (100) equal to nstenergy (1) 85: 85: Number of degrees of freedom in T-Coupling group System is 33.00 85: 85: There were 2 NOTEs 85: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 85: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 85: 85: Using 2 MPI threads 85: Using 1 OpenMP thread per tMPI thread 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'Argon' 85: 16 steps, 0.0 ps. 85: Generated 1 of the 1 non-bonded parameter combinations 85: 85: Excluding 1 bonded neighbours molecule type 'Argon' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.048 0.025 193.5 85: (ns/day) (hour/ns) 85: Performance: 58.632 0.409 85: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_reference.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19.edr as single precision energy file 85: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_input.mdp]: 85: Setting nstcalcenergy (100) equal to nstenergy (4) 85: 85: Number of degrees of freedom in T-Coupling group System is 33.00 85: 85: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_input.mdp]: 85: COM removal frequency is set to (5). 85: Other settings require a global communication frequency of 2. 85: Note that this will require additional global communication steps, 85: which will reduce performance when using multiple ranks. 85: Consider setting nstcomm to a multiple of 2. 85: 85: 85: There were 3 NOTEs 85: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 85: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 85: 85: Using 2 MPI threads 85: Using 1 OpenMP thread per tMPI thread 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'Argon' 85: 16 steps, 0.0 ps. 85: Generated 1 of the 1 non-bonded parameter combinations 85: 85: Excluding 1 bonded neighbours molecule type 'Argon' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.056 0.029 194.1 85: (ns/day) (hour/ns) 85: Performance: 51.208 0.469 85: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_reference.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19.edr as single precision energy file 85: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_input.mdp]: 85: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 85: setting nstcomm equal to nstcalcenergy for less overhead 85: 85: Number of degrees of freedom in T-Coupling group System is 33.00 85: 85: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_input.mdp]: 85: COM removal frequency is set to (5). 85: Other settings require a global communication frequency of 2. 85: Note that this will require additional global communication steps, 85: which will reduce performance when using multiple ranks. 85: Consider setting nstcomm to a multiple of 2. 85: 85: 85: There were 3 NOTEs 85: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 85: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 85: 85: Using 2 MPI threads 85: Using 1 OpenMP thread per tMPI thread 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'Argon' 85: 16 steps, 0.0 ps. 85: Generated 1 of the 1 non-bonded parameter combinations 85: 85: Excluding 1 bonded neighbours molecule type 'Argon' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.084 0.043 196.2 85: (ns/day) (hour/ns) 85: Performance: 34.451 0.697 85: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_reference.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19.edr as single precision energy file 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_input.mdp]: 85: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 85: setting nstcomm equal to nstcalcenergy for less overhead 85: 85: Number of degrees of freedom in T-Coupling group System is 33.00 85: 85: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_input.mdp]: 85: COM removal frequency is set to (5). 85: Other settings require a global communication frequency of 2. 85: Note that this will require additional global communication steps, 85: which will reduce performance when using multiple ranks. 85: Consider setting nstcomm to a multiple of 2. 85: 85: 85: There were 3 NOTEs 85: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 85: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 85: 85: Using 2 MPI threads 85: Using 1 OpenMP thread per tMPI thread 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'Argon' 85: 16 steps, 0.0 ps. 85: Generated 1 of the 1 non-bonded parameter combinations 85: 85: Excluding 1 bonded neighbours molecule type 'Argon' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.078 0.040 195.9 85: (ns/day) (hour/ns) 85: Performance: 36.724 0.654 85: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_reference.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19.edr as single precision energy file 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_input.mdp]: 85: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 85: setting nstcomm equal to nstcalcenergy for less overhead 85: 85: Number of degrees of freedom in T-Coupling group System is 33.00 85: 85: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_input.mdp]: 85: COM removal frequency is set to (5). 85: Other settings require a global communication frequency of 2. 85: Note that this will require additional global communication steps, 85: which will reduce performance when using multiple ranks. 85: Consider setting nstcomm to a multiple of 2. 85: 85: 85: There were 3 NOTEs 85: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 85: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 85: 85: Using 2 MPI threads 85: Using 1 OpenMP thread per tMPI thread 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'Argon' 85: 16 steps, 0.0 ps. 85: Generated 1 of the 1 non-bonded parameter combinations 85: 85: Excluding 1 bonded neighbours molecule type 'Argon' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.053 0.028 193.6 85: (ns/day) (hour/ns) 85: Performance: 53.230 0.451 85: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_reference.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19.edr as single precision energy file 85: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/19 (501 ms) 85: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/20 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]: 85: Setting nstcalcenergy (100) equal to nstenergy (1) 85: 85: 85: WARNING 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]: 85: The Berendsen barostat does not generate any strictly correct ensemble, 85: and should not be used for new production simulations (in our opinion). 85: We recommend using the C-rescale barostat instead. 85: 85: Number of degrees of freedom in T-Coupling group System is 33.00 85: 85: There were 2 NOTEs 85: 85: There was 1 WARNING 85: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 85: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 85: 85: Using 2 MPI threads 85: Using 1 OpenMP thread per tMPI thread 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'Argon' 85: 16 steps, 0.0 ps. 85: Generated 1 of the 1 non-bonded parameter combinations 85: 85: Excluding 1 bonded neighbours molecule type 'Argon' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: NOTE: 5 % of the run time was spent communicating energies, 85: you might want to increase some nst* mdp options 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.074 0.038 196.4 85: (ns/day) (hour/ns) 85: Performance: 38.999 0.615 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]: 85: Setting nstcalcenergy (100) equal to nstenergy (1) 85: 85: 85: WARNING 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]: 85: The Berendsen barostat does not generate any strictly correct ensemble, 85: and should not be used for new production simulations (in our opinion). 85: We recommend using the C-rescale barostat instead. 85: 85: Number of degrees of freedom in T-Coupling group System is 33.00 85: 85: There were 2 NOTEs 85: 85: There was 1 WARNING 85: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 85: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 85: 85: Using 2 MPI threads 85: Using 1 OpenMP thread per tMPI thread 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'Argon' 85: 16 steps, 0.0 ps. 85: Generated 1 of the 1 non-bonded parameter combinations 85: 85: Excluding 1 bonded neighbours molecule type 'Argon' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.087 0.049 177.4 85: (ns/day) (hour/ns) 85: Performance: 29.804 0.805 85: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_reference.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20.edr as single precision energy file 85: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]: 85: Setting nstcalcenergy (100) equal to nstenergy (4) 85: 85: 85: WARNING 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]: 85: The Berendsen barostat does not generate any strictly correct ensemble, 85: and should not be used for new production simulations (in our opinion). 85: We recommend using the C-rescale barostat instead. 85: 85: Number of degrees of freedom in T-Coupling group System is 33.00 85: 85: There were 2 NOTEs 85: 85: There was 1 WARNING 85: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 85: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 85: 85: Using 2 MPI threads 85: Using 1 OpenMP thread per tMPI thread 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'Argon' 85: 16 steps, 0.0 ps. 85: Generated 1 of the 1 non-bonded parameter combinations 85: 85: Excluding 1 bonded neighbours molecule type 'Argon' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.074 0.038 193.1 85: (ns/day) (hour/ns) 85: Performance: 38.226 0.628 85: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_reference.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20.edr as single precision energy file 85: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]: 85: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 85: setting nstcomm equal to nstcalcenergy for less overhead 85: 85: 85: WARNING 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]: 85: The Berendsen barostat does not generate any strictly correct ensemble, 85: and should not be used for new production simulations (in our opinion). 85: We recommend using the C-rescale barostat instead. 85: 85: Number of degrees of freedom in T-Coupling group System is 33.00 85: 85: There were 2 NOTEs 85: 85: There was 1 WARNING 85: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 85: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 85: 85: Using 2 MPI threads 85: Using 1 OpenMP thread per tMPI thread 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'Argon' 85: 16 steps, 0.0 ps. 85: Generated 1 of the 1 non-bonded parameter combinations 85: 85: Excluding 1 bonded neighbours molecule type 'Argon' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.101 0.051 196.4 85: (ns/day) (hour/ns) 85: Performance: 28.689 0.837 85: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_reference.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20.edr as single precision energy file 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]: 85: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 85: setting nstcomm equal to nstcalcenergy for less overhead 85: 85: 85: WARNING 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]: 85: The Berendsen barostat does not generate any strictly correct ensemble, 85: and should not be used for new production simulations (in our opinion). 85: We recommend using the C-rescale barostat instead. 85: 85: Number of degrees of freedom in T-Coupling group System is 33.00 85: 85: There were 2 NOTEs 85: 85: There was 1 WARNING 85: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 85: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 85: 85: Using 2 MPI threads 85: Using 1 OpenMP thread per tMPI thread 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'Argon' 85: 16 steps, 0.0 ps. 85: Generated 1 of the 1 non-bonded parameter combinations 85: 85: Excluding 1 bonded neighbours molecule type 'Argon' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.126 0.064 197.6 85: (ns/day) (hour/ns) 85: Performance: 23.056 1.041 85: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_reference.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20.edr as single precision energy file 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]: 85: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 85: setting nstcomm equal to nstcalcenergy for less overhead 85: 85: 85: WARNING 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]: 85: The Berendsen barostat does not generate any strictly correct ensemble, 85: and should not be used for new production simulations (in our opinion). 85: We recommend using the C-rescale barostat instead. 85: 85: Number of degrees of freedom in T-Coupling group System is 33.00 85: 85: There were 2 NOTEs 85: 85: There was 1 WARNING 85: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 85: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 85: 85: Using 2 MPI threads 85: Using 1 OpenMP thread per tMPI thread 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'Argon' 85: 16 steps, 0.0 ps. 85: Generated 1 of the 1 non-bonded parameter combinations 85: 85: Excluding 1 bonded neighbours molecule type 'Argon' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.092 0.048 193.1 85: (ns/day) (hour/ns) 85: Performance: 30.881 0.777 85: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_reference.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20.edr as single precision energy file 85: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/20 (877 ms) 85: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/21 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_input.mdp]: 85: Setting nstcalcenergy (100) equal to nstenergy (1) 85: 85: Number of degrees of freedom in T-Coupling group System is 33.00 85: 85: There were 2 NOTEs 85: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 85: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 85: 85: Using 2 MPI threads 85: Using 1 OpenMP thread per tMPI thread 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'Argon' 85: 16 steps, 0.0 ps. 85: Generated 1 of the 1 non-bonded parameter combinations 85: 85: Excluding 1 bonded neighbours molecule type 'Argon' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.080 0.041 196.6 85: (ns/day) (hour/ns) 85: Performance: 36.088 0.665 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_input.mdp]: 85: Setting nstcalcenergy (100) equal to nstenergy (1) 85: 85: Number of degrees of freedom in T-Coupling group System is 33.00 85: 85: There were 2 NOTEs 85: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 85: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 85: 85: Using 2 MPI threads 85: Using 1 OpenMP thread per tMPI thread 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'Argon' 85: 16 steps, 0.0 ps. 85: Generated 1 of the 1 non-bonded parameter combinations 85: 85: Excluding 1 bonded neighbours molecule type 'Argon' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.057 0.029 194.8 85: (ns/day) (hour/ns) 85: Performance: 49.895 0.481 85: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_reference.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21.edr as single precision energy file 85: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_input.mdp]: 85: Setting nstcalcenergy (100) equal to nstenergy (4) 85: 85: Number of degrees of freedom in T-Coupling group System is 33.00 85: 85: There were 2 NOTEs 85: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 85: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 85: 85: Using 2 MPI threads 85: Using 1 OpenMP thread per tMPI thread 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'Argon' 85: 16 steps, 0.0 ps. 85: Generated 1 of the 1 non-bonded parameter combinations 85: 85: Excluding 1 bonded neighbours molecule type 'Argon' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: NOTE: 25 % of the run time was spent communicating energies, 85: you might want to increase some nst* mdp options 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.118 0.062 190.7 85: (ns/day) (hour/ns) 85: Performance: 23.734 1.011 85: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_reference.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21.edr as single precision energy file 85: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_input.mdp]: 85: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 85: setting nstcomm equal to nstcalcenergy for less overhead 85: 85: Number of degrees of freedom in T-Coupling group System is 33.00 85: 85: There were 2 NOTEs 85: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 85: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 85: 85: Using 2 MPI threads 85: Using 1 OpenMP thread per tMPI thread 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'Argon' 85: 16 steps, 0.0 ps. 85: Generated 1 of the 1 non-bonded parameter combinations 85: 85: Excluding 1 bonded neighbours molecule type 'Argon' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.055 0.028 193.6 85: (ns/day) (hour/ns) 85: Performance: 51.952 0.462 85: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_reference.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21.edr as single precision energy file 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_input.mdp]: 85: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 85: setting nstcomm equal to nstcalcenergy for less overhead 85: 85: Number of degrees of freedom in T-Coupling group System is 33.00 85: 85: There were 2 NOTEs 85: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 85: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 85: 85: Using 2 MPI threads 85: Using 1 OpenMP thread per tMPI thread 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'Argon' 85: 16 steps, 0.0 ps. 85: Generated 1 of the 1 non-bonded parameter combinations 85: 85: Excluding 1 bonded neighbours molecule type 'Argon' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.065 0.033 194.6 85: (ns/day) (hour/ns) 85: Performance: 44.286 0.542 85: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_reference.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21.edr as single precision energy file 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_input.mdp]: 85: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 85: setting nstcomm equal to nstcalcenergy for less overhead 85: 85: Number of degrees of freedom in T-Coupling group System is 33.00 85: 85: There were 2 NOTEs 85: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 85: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 85: 85: Using 2 MPI threads 85: Using 1 OpenMP thread per tMPI thread 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'Argon' 85: 16 steps, 0.0 ps. 85: Generated 1 of the 1 non-bonded parameter combinations 85: 85: Excluding 1 bonded neighbours molecule type 'Argon' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.067 0.037 184.4 85: (ns/day) (hour/ns) 85: Performance: 40.183 0.597 85: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_reference.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21.edr as single precision energy file 85: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/21 (561 ms) 85: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/22 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_input.mdp]: 85: Setting nstcalcenergy (100) equal to nstenergy (1) 85: 85: Number of degrees of freedom in T-Coupling group System is 33.00 85: 85: There were 2 NOTEs 85: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 85: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 85: 85: Using 2 MPI threads 85: Using 1 OpenMP thread per tMPI thread 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'Argon' 85: 16 steps, 0.0 ps. 85: Generated 1 of the 1 non-bonded parameter combinations 85: 85: Excluding 1 bonded neighbours molecule type 'Argon' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: Core t (s) Wall t (s) (%) 85: Time: 1.596 0.799 199.8 85: (ns/day) (hour/ns) 85: Performance: 1.839 13.052 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_input.mdp]: 85: Setting nstcalcenergy (100) equal to nstenergy (1) 85: 85: Number of degrees of freedom in T-Coupling group System is 33.00 85: 85: There were 2 NOTEs 85: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 85: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 85: 85: Using 2 MPI threads 85: Using 1 OpenMP thread per tMPI thread 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'Argon' 85: 16 steps, 0.0 ps. 85: Generated 1 of the 1 non-bonded parameter combinations 85: 85: Excluding 1 bonded neighbours molecule type 'Argon' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.094 0.048 195.2 85: (ns/day) (hour/ns) 85: Performance: 30.598 0.784 85: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_reference.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22.edr as single precision energy file 85: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_input.mdp]: 85: Setting nstcalcenergy (100) equal to nstenergy (4) 85: 85: Number of degrees of freedom in T-Coupling group System is 33.00 85: 85: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_input.mdp]: 85: COM removal frequency is set to (5). 85: Other settings require a global communication frequency of 2. 85: Note that this will require additional global communication steps, 85: which will reduce performance when using multiple ranks. 85: Consider setting nstcomm to a multiple of 2. 85: 85: 85: There were 3 NOTEs 85: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 85: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 85: 85: Using 2 MPI threads 85: Using 1 OpenMP thread per tMPI thread 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'Argon' 85: 16 steps, 0.0 ps. 85: Generated 1 of the 1 non-bonded parameter combinations 85: 85: Excluding 1 bonded neighbours molecule type 'Argon' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.374 0.188 198.3 85: (ns/day) (hour/ns) 85: Performance: 7.792 3.080 85: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_reference.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22.edr as single precision energy file 85: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_input.mdp]: 85: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 85: setting nstcomm equal to nstcalcenergy for less overhead 85: 85: Number of degrees of freedom in T-Coupling group System is 33.00 85: 85: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_input.mdp]: 85: COM removal frequency is set to (5). 85: Other settings require a global communication frequency of 2. 85: Note that this will require additional global communication steps, 85: which will reduce performance when using multiple ranks. 85: Consider setting nstcomm to a multiple of 2. 85: 85: 85: There were 3 NOTEs 85: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 85: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 85: 85: Using 2 MPI threads 85: Using 1 OpenMP thread per tMPI thread 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'Argon' 85: 16 steps, 0.0 ps. 85: Generated 1 of the 1 non-bonded parameter combinations 85: 85: Excluding 1 bonded neighbours molecule type 'Argon' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.178 0.090 197.9 85: (ns/day) (hour/ns) 85: Performance: 16.370 1.466 85: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_reference.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22.edr as single precision energy file 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_input.mdp]: 85: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 85: setting nstcomm equal to nstcalcenergy for less overhead 85: 85: Number of degrees of freedom in T-Coupling group System is 33.00 85: 85: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_input.mdp]: 85: COM removal frequency is set to (5). 85: Other settings require a global communication frequency of 2. 85: Note that this will require additional global communication steps, 85: which will reduce performance when using multiple ranks. 85: Consider setting nstcomm to a multiple of 2. 85: 85: 85: There were 3 NOTEs 85: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 85: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 85: 85: Using 2 MPI threads 85: Using 1 OpenMP thread per tMPI thread 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'Argon' 85: 16 steps, 0.0 ps. 85: Generated 1 of the 1 non-bonded parameter combinations 85: 85: Excluding 1 bonded neighbours molecule type 'Argon' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.436 0.223 195.4 85: (ns/day) (hour/ns) 85: Performance: 6.588 3.643 85: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_reference.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22.edr as single precision energy file 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_input.mdp]: 85: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 85: setting nstcomm equal to nstcalcenergy for less overhead 85: 85: Number of degrees of freedom in T-Coupling group System is 33.00 85: 85: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_input.mdp]: 85: COM removal frequency is set to (5). 85: Other settings require a global communication frequency of 2. 85: Note that this will require additional global communication steps, 85: which will reduce performance when using multiple ranks. 85: Consider setting nstcomm to a multiple of 2. 85: 85: 85: There were 3 NOTEs 85: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 85: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 85: 85: Using 2 MPI threads 85: Using 1 OpenMP thread per tMPI thread 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'Argon' 85: 16 steps, 0.0 ps. 85: Generated 1 of the 1 non-bonded parameter combinations 85: 85: Excluding 1 bonded neighbours molecule type 'Argon' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.103 0.059 176.0 85: (ns/day) (hour/ns) 85: Performance: 25.032 0.959 85: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_reference.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22.edr as single precision energy file 85: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/22 (1816 ms) 85: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/23 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 85: Setting nstcalcenergy (100) equal to nstenergy (1) 85: 85: 85: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 85: MTTK coupling is deprecated and will soon be removed 85: 85: 85: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 85: for current Trotter decomposition methods with vv, nsttcouple and 85: nstpcouple must be equal. Both have been reset to 85: min(nsttcouple,nstpcouple) = 2 85: 85: Number of degrees of freedom in T-Coupling group System is 33.00 85: 85: There were 4 NOTEs 85: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 85: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 85: 85: Using 2 MPI threads 85: Using 1 OpenMP thread per tMPI thread 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'Argon' 85: 16 steps, 0.0 ps. 85: Generated 1 of the 1 non-bonded parameter combinations 85: 85: Excluding 1 bonded neighbours molecule type 'Argon' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: NOTE: 20 % of the run time was spent communicating energies, 85: you might want to increase some nst* mdp options 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.351 0.186 189.2 85: (ns/day) (hour/ns) 85: Performance: 7.910 3.034 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 85: Setting nstcalcenergy (100) equal to nstenergy (1) 85: 85: 85: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 85: MTTK coupling is deprecated and will soon be removed 85: 85: 85: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 85: for current Trotter decomposition methods with vv, nsttcouple and 85: nstpcouple must be equal. Both have been reset to 85: min(nsttcouple,nstpcouple) = 2 85: 85: Number of degrees of freedom in T-Coupling group System is 33.00 85: 85: There were 4 NOTEs 85: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 85: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 85: 85: Using 2 MPI threads 85: Using 1 OpenMP thread per tMPI thread 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'Argon' 85: 16 steps, 0.0 ps. 85: Generated 1 of the 1 non-bonded parameter combinations 85: 85: Excluding 1 bonded neighbours molecule type 'Argon' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: NOTE: 8 % of the run time was spent communicating energies, 85: you might want to increase some nst* mdp options 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.206 0.104 198.0 85: (ns/day) (hour/ns) 85: Performance: 14.086 1.704 85: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_reference.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23.edr as single precision energy file 85: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 85: Setting nstcalcenergy (100) equal to nstenergy (4) 85: 85: 85: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 85: MTTK coupling is deprecated and will soon be removed 85: 85: 85: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 85: for current Trotter decomposition methods with vv, nsttcouple and 85: nstpcouple must be equal. Both have been reset to 85: min(nsttcouple,nstpcouple) = 2 85: 85: Number of degrees of freedom in T-Coupling group System is 33.00 85: 85: NOTE 5 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 85: COM removal frequency is set to (5). 85: Other settings require a global communication frequency of 2. 85: Note that this will require additional global communication steps, 85: which will reduce performance when using multiple ranks. 85: Consider setting nstcomm to a multiple of 2. 85: 85: 85: There were 5 NOTEs 85: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 85: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 85: 85: Using 2 MPI threads 85: Using 1 OpenMP thread per tMPI thread 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'Argon' 85: 16 steps, 0.0 ps. 85: Generated 1 of the 1 non-bonded parameter combinations 85: 85: Excluding 1 bonded neighbours molecule type 'Argon' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: NOTE: 10 % of the run time was spent communicating energies, 85: you might want to increase some nst* mdp options 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.140 0.071 197.5 85: (ns/day) (hour/ns) 85: Performance: 20.709 1.159 85: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_reference.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23.edr as single precision energy file 85: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 85: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 85: setting nstcomm equal to nstcalcenergy for less overhead 85: 85: 85: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 85: MTTK coupling is deprecated and will soon be removed 85: 85: 85: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 85: for current Trotter decomposition methods with vv, nsttcouple and 85: nstpcouple must be equal. Both have been reset to 85: min(nsttcouple,nstpcouple) = 2 85: 85: Number of degrees of freedom in T-Coupling group System is 33.00 85: 85: NOTE 5 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 85: COM removal frequency is set to (5). 85: Other settings require a global communication frequency of 2. 85: Note that this will require additional global communication steps, 85: which will reduce performance when using multiple ranks. 85: Consider setting nstcomm to a multiple of 2. 85: 85: 85: There were 5 NOTEs 85: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 85: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 85: 85: Using 2 MPI threads 85: Using 1 OpenMP thread per tMPI thread 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'Argon' 85: 16 steps, 0.0 ps. 85: Generated 1 of the 1 non-bonded parameter combinations 85: 85: Excluding 1 bonded neighbours molecule type 'Argon' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.088 0.046 193.1 85: (ns/day) (hour/ns) 85: Performance: 32.253 0.744 85: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_reference.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23.edr as single precision energy file 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 85: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 85: setting nstcomm equal to nstcalcenergy for less overhead 85: 85: 85: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 85: MTTK coupling is deprecated and will soon be removed 85: 85: 85: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 85: for current Trotter decomposition methods with vv, nsttcouple and 85: nstpcouple must be equal. Both have been reset to 85: min(nsttcouple,nstpcouple) = 2 85: 85: Number of degrees of freedom in T-Coupling group System is 33.00 85: 85: NOTE 5 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 85: COM removal frequency is set to (5). 85: Other settings require a global communication frequency of 2. 85: Note that this will require additional global communication steps, 85: which will reduce performance when using multiple ranks. 85: Consider setting nstcomm to a multiple of 2. 85: 85: 85: There were 5 NOTEs 85: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 85: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 85: 85: Using 2 MPI threads 85: Using 1 OpenMP thread per tMPI thread 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'Argon' 85: 16 steps, 0.0 ps. 85: Generated 1 of the 1 non-bonded parameter combinations 85: 85: Excluding 1 bonded neighbours molecule type 'Argon' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: NOTE: 8 % of the run time was spent communicating energies, 85: you might want to increase some nst* mdp options 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.094 0.058 160.6 85: (ns/day) (hour/ns) 85: Performance: 25.139 0.955 85: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_reference.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23.edr as single precision energy file 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 85: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 85: setting nstcomm equal to nstcalcenergy for less overhead 85: 85: 85: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 85: MTTK coupling is deprecated and will soon be removed 85: 85: 85: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 85: for current Trotter decomposition methods with vv, nsttcouple and 85: nstpcouple must be equal. Both have been reset to 85: min(nsttcouple,nstpcouple) = 2 85: 85: Number of degrees of freedom in T-Coupling group System is 33.00 85: 85: NOTE 5 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 85: COM removal frequency is set to (5). 85: Other settings require a global communication frequency of 2. 85: Note that this will require additional global communication steps, 85: which will reduce performance when using multiple ranks. 85: Consider setting nstcomm to a multiple of 2. 85: 85: 85: There were 5 NOTEs 85: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 85: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 85: 85: Using 2 MPI threads 85: Using 1 OpenMP thread per tMPI thread 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'Argon' 85: 16 steps, 0.0 ps. 85: Generated 1 of the 1 non-bonded parameter combinations 85: 85: Excluding 1 bonded neighbours molecule type 'Argon' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.139 0.070 197.7 85: (ns/day) (hour/ns) 85: Performance: 20.898 1.148 85: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_reference.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23.edr as single precision energy file 85: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/23 (1002 ms) 85: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/24 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24_input.mdp]: 85: Setting nstcalcenergy (100) equal to nstenergy (1) 85: 85: Number of degrees of freedom in T-Coupling group System is 33.00 85: 85: There were 2 NOTEs 85: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 85: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 85: 85: Using 2 MPI threads 85: Using 1 OpenMP thread per tMPI thread 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'Argon' 85: 16 steps, 0.0 ps. 85: Generated 1 of the 1 non-bonded parameter combinations 85: 85: Excluding 1 bonded neighbours molecule type 'Argon' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.116 0.059 197.6 85: (ns/day) (hour/ns) 85: Performance: 24.972 0.961 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24_input.mdp]: 85: Setting nstcalcenergy (100) equal to nstenergy (1) 85: 85: Number of degrees of freedom in T-Coupling group System is 33.00 85: 85: There were 2 NOTEs 85: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 85: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 85: 85: Using 2 MPI threads 85: Using 1 OpenMP thread per tMPI thread 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'Argon' 85: 16 steps, 0.0 ps. 85: Generated 1 of the 1 non-bonded parameter combinations 85: 85: Excluding 1 bonded neighbours molecule type 'Argon' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.090 0.046 197.0 85: (ns/day) (hour/ns) 85: Performance: 32.207 0.745 85: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24_reference.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24.edr as single precision energy file 85: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24_input.mdp]: 85: Setting nstcalcenergy (100) equal to nstenergy (4) 85: 85: Number of degrees of freedom in T-Coupling group System is 33.00 85: 85: There were 2 NOTEs 85: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 85: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 85: 85: Using 2 MPI threads 85: Using 1 OpenMP thread per tMPI thread 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'Argon' 85: 16 steps, 0.0 ps. 85: Generated 1 of the 1 non-bonded parameter combinations 85: 85: Excluding 1 bonded neighbours molecule type 'Argon' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.085 0.043 195.6 85: (ns/day) (hour/ns) 85: Performance: 33.896 0.708 85: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24_reference.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24.edr as single precision energy file 85: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24_input.mdp]: 85: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 85: setting nstcomm equal to nstcalcenergy for less overhead 85: 85: Number of degrees of freedom in T-Coupling group System is 33.00 85: 85: There were 2 NOTEs 85: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 85: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 85: 85: Using 2 MPI threads 85: Using 1 OpenMP thread per tMPI thread 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'Argon' 85: 16 steps, 0.0 ps. 85: Generated 1 of the 1 non-bonded parameter combinations 85: 85: Excluding 1 bonded neighbours molecule type 'Argon' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.126 0.064 195.7 85: (ns/day) (hour/ns) 85: Performance: 22.822 1.052 85: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24_reference.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24.edr as single precision energy file 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24_input.mdp]: 85: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 85: setting nstcomm equal to nstcalcenergy for less overhead 85: 85: Number of degrees of freedom in T-Coupling group System is 33.00 85: 85: There were 2 NOTEs 85: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 85: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 85: 85: Using 2 MPI threads 85: Using 1 OpenMP thread per tMPI thread 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'Argon' 85: 16 steps, 0.0 ps. 85: Generated 1 of the 1 non-bonded parameter combinations 85: 85: Excluding 1 bonded neighbours molecule type 'Argon' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: NOTE: 5 % of the run time was spent communicating energies, 85: you might want to increase some nst* mdp options 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.109 0.055 197.5 85: (ns/day) (hour/ns) 85: Performance: 26.657 0.900 85: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24_reference.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24.edr as single precision energy file 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24_input.mdp]: 85: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 85: setting nstcomm equal to nstcalcenergy for less overhead 85: 85: Number of degrees of freedom in T-Coupling group System is 33.00 85: 85: There were 2 NOTEs 85: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 85: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 85: 85: Using 2 MPI threads 85: Using 1 OpenMP thread per tMPI thread 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'Argon' 85: 16 steps, 0.0 ps. 85: Generated 1 of the 1 non-bonded parameter combinations 85: 85: Excluding 1 bonded neighbours molecule type 'Argon' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.075 0.039 194.2 85: (ns/day) (hour/ns) 85: Performance: 37.860 0.634 85: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24_reference.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24.edr as single precision energy file 85: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/24 (694 ms) 85: [----------] 25 tests from PropagatorsWithCoupling/PeriodicActionsTest (16208 ms total) 85: 85: [----------] Global test environment tear-down 85: [==========] 25 tests from 1 test suite ran. (16259 ms total) 85: [ PASSED ] 25 tests. 85/92 Test #85: MdrunCoordinationCouplingTests2Ranks ...... Passed 16.34 sec test 86 Start 86: MdrunCoordinationConstraintsTests1Rank 86: Test command: /build/reproducible-path/gromacs-2025.1/build/basic/bin/mdrun-coordination-constraints-test "-ntmpi" "1" "--gtest_output=xml:/build/reproducible-path/gromacs-2025.1/build/basic/Testing/Temporary/MdrunCoordinationConstraintsTests1Rank.xml" 86: Working Directory: /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests 86: Test timeout computed to be: 1920 86: [==========] Running 13 tests from 1 test suite. 86: [----------] Global test environment set-up. 86: [----------] 13 tests from PropagatorsWithConstraints/PeriodicActionsTest 86: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/0 86: 86: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 86: that with the Verlet scheme, nstlist has no effect on the accuracy of 86: your simulation. 86: 86: 86: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 86: Setting nstcalcenergy (100) equal to nstenergy (1) 86: 86: Generating 1-4 interactions: fudge = 0.5 86: Number of degrees of freedom in T-Coupling group System is 27.00 86: 86: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 86: NVE simulation: will use the initial temperature of 398.997 K for 86: determining the Verlet buffer size 86: 86: 86: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 86: You are using a plain Coulomb cut-off, which might produce artifacts. 86: You might want to consider using PME electrostatics. 86: 86: 86: 86: There were 4 NOTEs 86: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 86: Can not increase nstlist because an NVE ensemble is used 86: Using 1 MPI thread 86: Using 1 OpenMP thread 86: 86: 86: NOTE: Thread affinity was not set. 86: starting mdrun 'spc2' 86: 16 steps, 0.0 ps. 86: Generated 330891 of the 330891 non-bonded parameter combinations 86: 86: Generated 330891 of the 330891 1-4 parameter combinations 86: 86: Excluding 2 bonded neighbours molecule type 'SOL' 86: 86: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/tip3p5.gro' 86: 86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 86: 86: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 86: 86: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 86: 86: Note that mdrun will redetermine rlist based on the actual pair-list setup 86: 86: This run will generate roughly 0 Mb of data 86: 86: Writing final coordinates. 86: 86: Core t (s) Wall t (s) (%) 86: Time: 0.022 0.022 98.8 86: (ns/day) (hour/ns) 86: Performance: 65.522 0.366 86: 86: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 86: that with the Verlet scheme, nstlist has no effect on the accuracy of 86: your simulation. 86: 86: 86: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 86: Setting nstcalcenergy (100) equal to nstenergy (1) 86: 86: Generating 1-4 interactions: fudge = 0.5 86: Number of degrees of freedom in T-Coupling group System is 27.00 86: 86: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 86: NVE simulation: will use the initial temperature of 398.997 K for 86: determining the Verlet buffer size 86: 86: 86: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 86: You are using a plain Coulomb cut-off, which might produce artifacts. 86: You might want to consider using PME electrostatics. 86: 86: 86: 86: There were 4 NOTEs 86: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 86: Can not increase nstlist because an NVE ensemble is used 86: Using 1 MPI thread 86: Using 1 OpenMP thread 86: 86: 86: NOTE: Thread affinity was not set. 86: starting mdrun 'spc2' 86: 16 steps, 0.0 ps. 86: Generated 330891 of the 330891 non-bonded parameter combinations 86: 86: Generated 330891 of the 330891 1-4 parameter combinations 86: 86: Excluding 2 bonded neighbours molecule type 'SOL' 86: 86: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/tip3p5.gro' 86: 86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 86: 86: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 86: 86: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 86: 86: Note that mdrun will redetermine rlist based on the actual pair-list setup 86: 86: This run will generate roughly 0 Mb of data 86: 86: Writing final coordinates. 86: 86: Core t (s) Wall t (s) (%) 86: Time: 0.019 0.019 98.5 86: (ns/day) (hour/ns) 86: Performance: 77.232 0.311 86: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as single precision energy file 86: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as single precision energy file 86: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 86: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 86: that with the Verlet scheme, nstlist has no effect on the accuracy of 86: your simulation. 86: 86: 86: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 86: Setting nstcalcenergy (100) equal to nstenergy (4) 86: 86: Generating 1-4 interactions: fudge = 0.5 86: Number of degrees of freedom in T-Coupling group System is 27.00 86: 86: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 86: NVE simulation: will use the initial temperature of 398.997 K for 86: determining the Verlet buffer size 86: 86: 86: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 86: You are using a plain Coulomb cut-off, which might produce artifacts. 86: You might want to consider using PME electrostatics. 86: 86: 86: 86: NOTE 5 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 86: COM removal frequency is set to (5). 86: Other settings require a global communication frequency of 4. 86: Note that this will require additional global communication steps, 86: which will reduce performance when using multiple ranks. 86: Consider setting nstcomm to a multiple of 4. 86: 86: 86: There were 5 NOTEs 86: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 86: Can not increase nstlist because an NVE ensemble is used 86: Using 1 MPI thread 86: Using 1 OpenMP thread 86: 86: 86: NOTE: Thread affinity was not set. 86: starting mdrun 'spc2' 86: 16 steps, 0.0 ps. 86: Generated 330891 of the 330891 non-bonded parameter combinations 86: 86: Generated 330891 of the 330891 1-4 parameter combinations 86: 86: Excluding 2 bonded neighbours molecule type 'SOL' 86: 86: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/tip3p5.gro' 86: 86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 86: 86: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 86: 86: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 86: 86: Note that mdrun will redetermine rlist based on the actual pair-list setup 86: 86: This run will generate roughly 0 Mb of data 86: 86: Writing final coordinates. 86: 86: Core t (s) Wall t (s) (%) 86: Time: 0.022 0.022 98.7 86: (ns/day) (hour/ns) 86: Performance: 66.129 0.363 86: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as single precision energy file 86: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as single precision energy file 86: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 86: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 86: that with the Verlet scheme, nstlist has no effect on the accuracy of 86: your simulation. 86: 86: 86: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 86: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 86: setting nstcomm equal to nstcalcenergy for less overhead 86: 86: Generating 1-4 interactions: fudge = 0.5 86: Number of degrees of freedom in T-Coupling group System is 27.00 86: 86: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 86: NVE simulation: will use the initial temperature of 398.997 K for 86: determining the Verlet buffer size 86: 86: 86: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 86: You are using a plain Coulomb cut-off, which might produce artifacts. 86: You might want to consider using PME electrostatics. 86: 86: 86: 86: NOTE 5 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 86: COM removal frequency is set to (5). 86: Other settings require a global communication frequency of 100. 86: Note that this will require additional global communication steps, 86: which will reduce performance when using multiple ranks. 86: Consider setting nstcomm to a multiple of 100. 86: 86: 86: There were 5 NOTEs 86: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 86: Can not increase nstlist because an NVE ensemble is used 86: Using 1 MPI thread 86: Using 1 OpenMP thread 86: 86: 86: NOTE: Thread affinity was not set. 86: starting mdrun 'spc2' 86: 16 steps, 0.0 ps. 86: Generated 330891 of the 330891 non-bonded parameter combinations 86: 86: Generated 330891 of the 330891 1-4 parameter combinations 86: 86: Excluding 2 bonded neighbours molecule type 'SOL' 86: 86: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/tip3p5.gro' 86: 86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 86: 86: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 86: 86: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 86: 86: Note that mdrun will redetermine rlist based on the actual pair-list setup 86: 86: This run will generate roughly 0 Mb of data 86: 86: Writing final coordinates. 86: 86: Core t (s) Wall t (s) (%) 86: Time: 0.025 0.025 98.8 86: (ns/day) (hour/ns) 86: Performance: 58.689 0.409 86: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as single precision energy file 86: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as single precision energy file 86: 86: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 86: that with the Verlet scheme, nstlist has no effect on the accuracy of 86: your simulation. 86: 86: 86: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 86: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 86: setting nstcomm equal to nstcalcenergy for less overhead 86: 86: Generating 1-4 interactions: fudge = 0.5 86: Number of degrees of freedom in T-Coupling group System is 27.00 86: 86: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 86: NVE simulation: will use the initial temperature of 398.997 K for 86: determining the Verlet buffer size 86: 86: 86: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 86: You are using a plain Coulomb cut-off, which might produce artifacts. 86: You might want to consider using PME electrostatics. 86: 86: 86: 86: NOTE 5 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 86: COM removal frequency is set to (5). 86: Other settings require a global communication frequency of 100. 86: Note that this will require additional global communication steps, 86: which will reduce performance when using multiple ranks. 86: Consider setting nstcomm to a multiple of 100. 86: 86: 86: There were 5 NOTEs 86: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 86: Can not increase nstlist because an NVE ensemble is used 86: Using 1 MPI thread 86: Using 1 OpenMP thread 86: 86: 86: NOTE: Thread affinity was not set. 86: starting mdrun 'spc2' 86: 16 steps, 0.0 ps. 86: Generated 330891 of the 330891 non-bonded parameter combinations 86: 86: Generated 330891 of the 330891 1-4 parameter combinations 86: 86: Excluding 2 bonded neighbours molecule type 'SOL' 86: 86: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/tip3p5.gro' 86: 86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 86: 86: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 86: 86: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 86: 86: Note that mdrun will redetermine rlist based on the actual pair-list setup 86: 86: This run will generate roughly 0 Mb of data 86: 86: Writing final coordinates. 86: 86: Core t (s) Wall t (s) (%) 86: Time: 0.024 0.025 98.8 86: (ns/day) (hour/ns) 86: Performance: 59.729 0.402 86: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as single precision energy file 86: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as single precision energy file 86: 86: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 86: that with the Verlet scheme, nstlist has no effect on the accuracy of 86: your simulation. 86: 86: 86: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 86: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 86: setting nstcomm equal to nstcalcenergy for less overhead 86: 86: Generating 1-4 interactions: fudge = 0.5 86: Number of degrees of freedom in T-Coupling group System is 27.00 86: 86: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 86: NVE simulation: will use the initial temperature of 398.997 K for 86: determining the Verlet buffer size 86: 86: 86: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 86: You are using a plain Coulomb cut-off, which might produce artifacts. 86: You might want to consider using PME electrostatics. 86: 86: 86: 86: NOTE 5 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 86: COM removal frequency is set to (5). 86: Other settings require a global communication frequency of 100. 86: Note that this will require additional global communication steps, 86: which will reduce performance when using multiple ranks. 86: Consider setting nstcomm to a multiple of 100. 86: 86: 86: There were 5 NOTEs 86: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 86: Can not increase nstlist because an NVE ensemble is used 86: Using 1 MPI thread 86: Using 1 OpenMP thread 86: 86: 86: NOTE: Thread affinity was not set. 86: starting mdrun 'spc2' 86: 16 steps, 0.0 ps. 86: Generated 330891 of the 330891 non-bonded parameter combinations 86: 86: Generated 330891 of the 330891 1-4 parameter combinations 86: 86: Excluding 2 bonded neighbours molecule type 'SOL' 86: 86: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/tip3p5.gro' 86: 86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 86: 86: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 86: 86: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 86: 86: Note that mdrun will redetermine rlist based on the actual pair-list setup 86: 86: This run will generate roughly 0 Mb of data 86: 86: Writing final coordinates. 86: 86: Core t (s) Wall t (s) (%) 86: Time: 0.037 0.037 99.2 86: (ns/day) (hour/ns) 86: Performance: 39.500 0.608 86: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as single precision energy file 86: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as single precision energy file 86: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/0 (27343 ms) 86: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/1 86: 86: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 86: that with the Verlet scheme, nstlist has no effect on the accuracy of 86: your simulation. 86: 86: 86: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 86: Setting nstcalcenergy (100) equal to nstenergy (1) 86: 86: Generating 1-4 interactions: fudge = 0.5 86: Number of degrees of freedom in T-Coupling group System is 27.00 86: 86: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 86: NVE simulation: will use the initial temperature of 398.997 K for 86: determining the Verlet buffer size 86: 86: 86: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 86: You are using a plain Coulomb cut-off, which might produce artifacts. 86: You might want to consider using PME electrostatics. 86: 86: 86: 86: There were 4 NOTEs 86: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 86: Can not increase nstlist because an NVE ensemble is used 86: Using 1 MPI thread 86: Using 1 OpenMP thread 86: 86: 86: NOTE: Thread affinity was not set. 86: starting mdrun 'spc2' 86: 16 steps, 0.0 ps. 86: Generated 330891 of the 330891 non-bonded parameter combinations 86: 86: Generated 330891 of the 330891 1-4 parameter combinations 86: 86: Excluding 2 bonded neighbours molecule type 'SOL' 86: 86: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/tip3p5.gro' 86: 86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 86: 86: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 86: 86: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 86: 86: Note that mdrun will redetermine rlist based on the actual pair-list setup 86: 86: This run will generate roughly 0 Mb of data 86: 86: Writing final coordinates. 86: 86: Core t (s) Wall t (s) (%) 86: Time: 0.024 0.024 98.9 86: (ns/day) (hour/ns) 86: Performance: 59.978 0.400 86: 86: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 86: that with the Verlet scheme, nstlist has no effect on the accuracy of 86: your simulation. 86: 86: 86: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 86: Setting nstcalcenergy (100) equal to nstenergy (1) 86: 86: Generating 1-4 interactions: fudge = 0.5 86: Number of degrees of freedom in T-Coupling group System is 27.00 86: 86: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 86: NVE simulation: will use the initial temperature of 398.997 K for 86: determining the Verlet buffer size 86: 86: 86: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 86: You are using a plain Coulomb cut-off, which might produce artifacts. 86: You might want to consider using PME electrostatics. 86: 86: 86: 86: There were 4 NOTEs 86: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 86: Can not increase nstlist because an NVE ensemble is used 86: Using 1 MPI thread 86: Using 1 OpenMP thread 86: 86: 86: NOTE: Thread affinity was not set. 86: starting mdrun 'spc2' 86: 16 steps, 0.0 ps. 86: Generated 330891 of the 330891 non-bonded parameter combinations 86: 86: Generated 330891 of the 330891 1-4 parameter combinations 86: 86: Excluding 2 bonded neighbours molecule type 'SOL' 86: 86: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/tip3p5.gro' 86: 86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 86: 86: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 86: 86: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 86: 86: Note that mdrun will redetermine rlist based on the actual pair-list setup 86: 86: This run will generate roughly 0 Mb of data 86: 86: Writing final coordinates. 86: 86: Core t (s) Wall t (s) (%) 86: Time: 0.023 0.024 98.9 86: (ns/day) (hour/ns) 86: Performance: 62.202 0.386 86: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as single precision energy file 86: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as single precision energy file 86: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 86: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 86: that with the Verlet scheme, nstlist has no effect on the accuracy of 86: your simulation. 86: 86: 86: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 86: Setting nstcalcenergy (100) equal to nstenergy (4) 86: 86: Generating 1-4 interactions: fudge = 0.5 86: Number of degrees of freedom in T-Coupling group System is 27.00 86: 86: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 86: NVE simulation: will use the initial temperature of 398.997 K for 86: determining the Verlet buffer size 86: 86: 86: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 86: You are using a plain Coulomb cut-off, which might produce artifacts. 86: You might want to consider using PME electrostatics. 86: 86: 86: 86: There were 4 NOTEs 86: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 86: Can not increase nstlist because an NVE ensemble is used 86: Using 1 MPI thread 86: Using 1 OpenMP thread 86: 86: 86: NOTE: Thread affinity was not set. 86: starting mdrun 'spc2' 86: 16 steps, 0.0 ps. 86: Generated 330891 of the 330891 non-bonded parameter combinations 86: 86: Generated 330891 of the 330891 1-4 parameter combinations 86: 86: Excluding 2 bonded neighbours molecule type 'SOL' 86: 86: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/tip3p5.gro' 86: 86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 86: 86: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 86: 86: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 86: 86: Note that mdrun will redetermine rlist based on the actual pair-list setup 86: 86: This run will generate roughly 0 Mb of data 86: 86: Writing final coordinates. 86: 86: Core t (s) Wall t (s) (%) 86: Time: 0.026 0.026 98.0 86: (ns/day) (hour/ns) 86: Performance: 56.330 0.426 86: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as single precision energy file 86: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as single precision energy file 86: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 86: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 86: that with the Verlet scheme, nstlist has no effect on the accuracy of 86: your simulation. 86: 86: 86: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 86: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 86: setting nstcomm equal to nstcalcenergy for less overhead 86: 86: Generating 1-4 interactions: fudge = 0.5 86: Number of degrees of freedom in T-Coupling group System is 27.00 86: 86: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 86: NVE simulation: will use the initial temperature of 398.997 K for 86: determining the Verlet buffer size 86: 86: 86: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 86: You are using a plain Coulomb cut-off, which might produce artifacts. 86: You might want to consider using PME electrostatics. 86: 86: 86: 86: There were 4 NOTEs 86: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 86: Can not increase nstlist because an NVE ensemble is used 86: Using 1 MPI thread 86: Using 1 OpenMP thread 86: 86: 86: NOTE: Thread affinity was not set. 86: starting mdrun 'spc2' 86: 16 steps, 0.0 ps. 86: Generated 330891 of the 330891 non-bonded parameter combinations 86: 86: Generated 330891 of the 330891 1-4 parameter combinations 86: 86: Excluding 2 bonded neighbours molecule type 'SOL' 86: 86: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/tip3p5.gro' 86: 86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 86: 86: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 86: 86: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 86: 86: Note that mdrun will redetermine rlist based on the actual pair-list setup 86: 86: This run will generate roughly 0 Mb of data 86: 86: Writing final coordinates. 86: 86: Core t (s) Wall t (s) (%) 86: Time: 0.024 0.024 98.9 86: (ns/day) (hour/ns) 86: Performance: 61.088 0.393 86: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as single precision energy file 86: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as single precision energy file 86: 86: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 86: that with the Verlet scheme, nstlist has no effect on the accuracy of 86: your simulation. 86: 86: 86: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 86: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 86: setting nstcomm equal to nstcalcenergy for less overhead 86: 86: Generating 1-4 interactions: fudge = 0.5 86: Number of degrees of freedom in T-Coupling group System is 27.00 86: 86: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 86: NVE simulation: will use the initial temperature of 398.997 K for 86: determining the Verlet buffer size 86: 86: 86: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 86: You are using a plain Coulomb cut-off, which might produce artifacts. 86: You might want to consider using PME electrostatics. 86: 86: 86: 86: There were 4 NOTEs 86: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 86: Can not increase nstlist because an NVE ensemble is used 86: Using 1 MPI thread 86: Using 1 OpenMP thread 86: 86: 86: NOTE: Thread affinity was not set. 86: starting mdrun 'spc2' 86: 16 steps, 0.0 ps. 86: Generated 330891 of the 330891 non-bonded parameter combinations 86: 86: Generated 330891 of the 330891 1-4 parameter combinations 86: 86: Excluding 2 bonded neighbours molecule type 'SOL' 86: 86: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/tip3p5.gro' 86: 86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 86: 86: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 86: 86: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 86: 86: Note that mdrun will redetermine rlist based on the actual pair-list setup 86: 86: This run will generate roughly 0 Mb of data 86: 86: Writing final coordinates. 86: 86: Core t (s) Wall t (s) (%) 86: Time: 0.020 0.020 98.6 86: (ns/day) (hour/ns) 86: Performance: 72.813 0.330 86: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as single precision energy file 86: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as single precision energy file 86: 86: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 86: that with the Verlet scheme, nstlist has no effect on the accuracy of 86: your simulation. 86: 86: 86: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 86: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 86: setting nstcomm equal to nstcalcenergy for less overhead 86: 86: Generating 1-4 interactions: fudge = 0.5 86: Number of degrees of freedom in T-Coupling group System is 27.00 86: 86: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 86: NVE simulation: will use the initial temperature of 398.997 K for 86: determining the Verlet buffer size 86: 86: 86: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 86: You are using a plain Coulomb cut-off, which might produce artifacts. 86: You might want to consider using PME electrostatics. 86: 86: 86: 86: There were 4 NOTEs 86: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 86: Can not increase nstlist because an NVE ensemble is used 86: Using 1 MPI thread 86: Using 1 OpenMP thread 86: 86: 86: NOTE: Thread affinity was not set. 86: starting mdrun 'spc2' 86: 16 steps, 0.0 ps. 86: Generated 330891 of the 330891 non-bonded parameter combinations 86: 86: Generated 330891 of the 330891 1-4 parameter combinations 86: 86: Excluding 2 bonded neighbours molecule type 'SOL' 86: 86: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/tip3p5.gro' 86: 86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 86: 86: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 86: 86: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 86: 86: Note that mdrun will redetermine rlist based on the actual pair-list setup 86: 86: This run will generate roughly 0 Mb of data 86: 86: Writing final coordinates. 86: 86: Core t (s) Wall t (s) (%) 86: Time: 0.024 0.024 98.9 86: (ns/day) (hour/ns) 86: Performance: 60.382 0.397 86: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as single precision energy file 86: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as single precision energy file 86: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/1 (27620 ms) 86: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/2 86: 86: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 86: that with the Verlet scheme, nstlist has no effect on the accuracy of 86: your simulation. 86: 86: 86: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 86: Setting nstcalcenergy (100) equal to nstenergy (1) 86: 86: Generating 1-4 interactions: fudge = 0.5 86: Number of degrees of freedom in T-Coupling group System is 27.00 86: 86: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 86: NVE simulation: will use the initial temperature of 398.997 K for 86: determining the Verlet buffer size 86: 86: 86: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 86: You are using a plain Coulomb cut-off, which might produce artifacts. 86: You might want to consider using PME electrostatics. 86: 86: 86: 86: There were 4 NOTEs 86: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 86: Can not increase nstlist because an NVE ensemble is used 86: Using 1 MPI thread 86: Using 1 OpenMP thread 86: 86: 86: NOTE: Thread affinity was not set. 86: starting mdrun 'spc2' 86: 16 steps, 0.0 ps. 86: Generated 330891 of the 330891 non-bonded parameter combinations 86: 86: Generated 330891 of the 330891 1-4 parameter combinations 86: 86: Excluding 2 bonded neighbours molecule type 'SOL' 86: 86: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/tip3p5.gro' 86: 86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 86: 86: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 86: 86: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 86: 86: Note that mdrun will redetermine rlist based on the actual pair-list setup 86: 86: This run will generate roughly 0 Mb of data 86: 86: Writing final coordinates. 86: 86: Core t (s) Wall t (s) (%) 86: Time: 0.023 0.023 98.9 86: (ns/day) (hour/ns) 86: Performance: 63.565 0.378 86: 86: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 86: that with the Verlet scheme, nstlist has no effect on the accuracy of 86: your simulation. 86: 86: 86: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 86: Setting nstcalcenergy (100) equal to nstenergy (1) 86: 86: Generating 1-4 interactions: fudge = 0.5 86: Number of degrees of freedom in T-Coupling group System is 27.00 86: 86: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 86: NVE simulation: will use the initial temperature of 398.997 K for 86: determining the Verlet buffer size 86: 86: 86: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 86: You are using a plain Coulomb cut-off, which might produce artifacts. 86: You might want to consider using PME electrostatics. 86: 86: 86: 86: There were 4 NOTEs 86: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 86: Can not increase nstlist because an NVE ensemble is used 86: Using 1 MPI thread 86: Using 1 OpenMP thread 86: 86: 86: NOTE: Thread affinity was not set. 86: starting mdrun 'spc2' 86: 16 steps, 0.0 ps. 86: Generated 330891 of the 330891 non-bonded parameter combinations 86: 86: Generated 330891 of the 330891 1-4 parameter combinations 86: 86: Excluding 2 bonded neighbours molecule type 'SOL' 86: 86: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/tip3p5.gro' 86: 86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 86: 86: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 86: 86: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 86: 86: Note that mdrun will redetermine rlist based on the actual pair-list setup 86: 86: This run will generate roughly 0 Mb of data 86: 86: Writing final coordinates. 86: 86: Core t (s) Wall t (s) (%) 86: Time: 0.020 0.020 98.7 86: (ns/day) (hour/ns) 86: Performance: 73.217 0.328 86: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as single precision energy file 86: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as single precision energy file 86: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 86: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 86: that with the Verlet scheme, nstlist has no effect on the accuracy of 86: your simulation. 86: 86: 86: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 86: Setting nstcalcenergy (100) equal to nstenergy (4) 86: 86: Generating 1-4 interactions: fudge = 0.5 86: Number of degrees of freedom in T-Coupling group System is 27.00 86: 86: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 86: NVE simulation: will use the initial temperature of 398.997 K for 86: determining the Verlet buffer size 86: 86: 86: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 86: You are using a plain Coulomb cut-off, which might produce artifacts. 86: You might want to consider using PME electrostatics. 86: 86: 86: 86: There were 4 NOTEs 86: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 86: Can not increase nstlist because an NVE ensemble is used 86: Using 1 MPI thread 86: Using 1 OpenMP thread 86: 86: 86: NOTE: Thread affinity was not set. 86: starting mdrun 'spc2' 86: 16 steps, 0.0 ps. 86: Generated 330891 of the 330891 non-bonded parameter combinations 86: 86: Generated 330891 of the 330891 1-4 parameter combinations 86: 86: Excluding 2 bonded neighbours molecule type 'SOL' 86: 86: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/tip3p5.gro' 86: 86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 86: 86: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 86: 86: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 86: 86: Note that mdrun will redetermine rlist based on the actual pair-list setup 86: 86: This run will generate roughly 0 Mb of data 86: 86: Writing final coordinates. 86: 86: Core t (s) Wall t (s) (%) 86: Time: 0.023 0.023 98.6 86: (ns/day) (hour/ns) 86: Performance: 64.131 0.374 86: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as single precision energy file 86: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as single precision energy file 86: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 86: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 86: that with the Verlet scheme, nstlist has no effect on the accuracy of 86: your simulation. 86: 86: 86: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 86: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 86: setting nstcomm equal to nstcalcenergy for less overhead 86: 86: Generating 1-4 interactions: fudge = 0.5 86: Number of degrees of freedom in T-Coupling group System is 27.00 86: 86: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 86: NVE simulation: will use the initial temperature of 398.997 K for 86: determining the Verlet buffer size 86: 86: 86: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 86: You are using a plain Coulomb cut-off, which might produce artifacts. 86: You might want to consider using PME electrostatics. 86: 86: 86: 86: There were 4 NOTEs 86: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 86: Can not increase nstlist because an NVE ensemble is used 86: Using 1 MPI thread 86: Using 1 OpenMP thread 86: 86: 86: NOTE: Thread affinity was not set. 86: starting mdrun 'spc2' 86: 16 steps, 0.0 ps. 86: Generated 330891 of the 330891 non-bonded parameter combinations 86: 86: Generated 330891 of the 330891 1-4 parameter combinations 86: 86: Excluding 2 bonded neighbours molecule type 'SOL' 86: 86: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/tip3p5.gro' 86: 86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 86: 86: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 86: 86: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 86: 86: Note that mdrun will redetermine rlist based on the actual pair-list setup 86: 86: This run will generate roughly 0 Mb of data 86: 86: Writing final coordinates. 86: 86: Core t (s) Wall t (s) (%) 86: Time: 0.029 0.029 99.1 86: (ns/day) (hour/ns) 86: Performance: 50.975 0.471 86: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as single precision energy file 86: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as single precision energy file 86: 86: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 86: that with the Verlet scheme, nstlist has no effect on the accuracy of 86: your simulation. 86: 86: 86: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 86: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 86: setting nstcomm equal to nstcalcenergy for less overhead 86: 86: Generating 1-4 interactions: fudge = 0.5 86: Number of degrees of freedom in T-Coupling group System is 27.00 86: 86: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 86: NVE simulation: will use the initial temperature of 398.997 K for 86: determining the Verlet buffer size 86: 86: 86: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 86: You are using a plain Coulomb cut-off, which might produce artifacts. 86: You might want to consider using PME electrostatics. 86: 86: 86: 86: There were 4 NOTEs 86: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 86: Can not increase nstlist because an NVE ensemble is used 86: Using 1 MPI thread 86: Using 1 OpenMP thread 86: 86: 86: NOTE: Thread affinity was not set. 86: starting mdrun 'spc2' 86: 16 steps, 0.0 ps. 86: Generated 330891 of the 330891 non-bonded parameter combinations 86: 86: Generated 330891 of the 330891 1-4 parameter combinations 86: 86: Excluding 2 bonded neighbours molecule type 'SOL' 86: 86: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/tip3p5.gro' 86: 86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 86: 86: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 86: 86: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 86: 86: Note that mdrun will redetermine rlist based on the actual pair-list setup 86: 86: This run will generate roughly 0 Mb of data 86: 86: Writing final coordinates. 86: 86: Core t (s) Wall t (s) (%) 86: Time: 0.024 0.025 99.0 86: (ns/day) (hour/ns) 86: Performance: 59.379 0.404 86: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as single precision energy file 86: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as single precision energy file 86: 86: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 86: that with the Verlet scheme, nstlist has no effect on the accuracy of 86: your simulation. 86: 86: 86: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 86: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 86: setting nstcomm equal to nstcalcenergy for less overhead 86: 86: Generating 1-4 interactions: fudge = 0.5 86: Number of degrees of freedom in T-Coupling group System is 27.00 86: 86: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 86: NVE simulation: will use the initial temperature of 398.997 K for 86: determining the Verlet buffer size 86: 86: 86: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 86: You are using a plain Coulomb cut-off, which might produce artifacts. 86: You might want to consider using PME electrostatics. 86: 86: 86: 86: There were 4 NOTEs 86: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 86: Can not increase nstlist because an NVE ensemble is used 86: Using 1 MPI thread 86: Using 1 OpenMP thread 86: 86: 86: NOTE: Thread affinity was not set. 86: starting mdrun 'spc2' 86: 16 steps, 0.0 ps. 86: Generated 330891 of the 330891 non-bonded parameter combinations 86: 86: Generated 330891 of the 330891 1-4 parameter combinations 86: 86: Excluding 2 bonded neighbours molecule type 'SOL' 86: 86: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/tip3p5.gro' 86: 86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 86: 86: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 86: 86: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 86: 86: Note that mdrun will redetermine rlist based on the actual pair-list setup 86: 86: This run will generate roughly 0 Mb of data 86: 86: Writing final coordinates. 86: 86: Core t (s) Wall t (s) (%) 86: Time: 0.026 0.026 98.9 86: (ns/day) (hour/ns) 86: Performance: 56.244 0.427 86: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as single precision energy file 86: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as single precision energy file 86: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/2 (28044 ms) 86: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/3 86: 86: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 86: that with the Verlet scheme, nstlist has no effect on the accuracy of 86: your simulation. 86: 86: 86: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 86: Setting nstcalcenergy (100) equal to nstenergy (1) 86: 86: Generating 1-4 interactions: fudge = 0.5 86: Number of degrees of freedom in T-Coupling group System is 27.00 86: 86: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 86: You are using a plain Coulomb cut-off, which might produce artifacts. 86: You might want to consider using PME electrostatics. 86: 86: 86: 86: There were 3 NOTEs 86: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 86: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 86: 86: Using 1 MPI thread 86: Using 1 OpenMP thread 86: 86: 86: NOTE: Thread affinity was not set. 86: starting mdrun 'spc2' 86: 16 steps, 0.0 ps. 86: Generated 330891 of the 330891 non-bonded parameter combinations 86: 86: Generated 330891 of the 330891 1-4 parameter combinations 86: 86: Excluding 2 bonded neighbours molecule type 'SOL' 86: 86: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/tip3p5.gro' 86: 86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 86: 86: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 86: 86: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 86: 86: Note that mdrun will redetermine rlist based on the actual pair-list setup 86: 86: This run will generate roughly 0 Mb of data 86: 86: Writing final coordinates. 86: 86: Core t (s) Wall t (s) (%) 86: Time: 0.031 0.031 99.2 86: (ns/day) (hour/ns) 86: Performance: 46.870 0.512 86: 86: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 86: that with the Verlet scheme, nstlist has no effect on the accuracy of 86: your simulation. 86: 86: 86: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 86: Setting nstcalcenergy (100) equal to nstenergy (1) 86: 86: Generating 1-4 interactions: fudge = 0.5 86: Number of degrees of freedom in T-Coupling group System is 27.00 86: 86: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 86: You are using a plain Coulomb cut-off, which might produce artifacts. 86: You might want to consider using PME electrostatics. 86: 86: 86: 86: There were 3 NOTEs 86: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 86: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 86: 86: Using 1 MPI thread 86: Using 1 OpenMP thread 86: 86: 86: NOTE: Thread affinity was not set. 86: starting mdrun 'spc2' 86: 16 steps, 0.0 ps. 86: Generated 330891 of the 330891 non-bonded parameter combinations 86: 86: Generated 330891 of the 330891 1-4 parameter combinations 86: 86: Excluding 2 bonded neighbours molecule type 'SOL' 86: 86: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/tip3p5.gro' 86: 86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 86: 86: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 86: 86: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 86: 86: Note that mdrun will redetermine rlist based on the actual pair-list setup 86: 86: This run will generate roughly 0 Mb of data 86: 86: Writing final coordinates. 86: 86: Core t (s) Wall t (s) (%) 86: Time: 0.018 0.019 98.7 86: (ns/day) (hour/ns) 86: Performance: 78.592 0.305 86: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as single precision energy file 86: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as single precision energy file 86: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 86: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 86: that with the Verlet scheme, nstlist has no effect on the accuracy of 86: your simulation. 86: 86: 86: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 86: Setting nstcalcenergy (100) equal to nstenergy (4) 86: 86: Generating 1-4 interactions: fudge = 0.5 86: Number of degrees of freedom in T-Coupling group System is 27.00 86: 86: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 86: You are using a plain Coulomb cut-off, which might produce artifacts. 86: You might want to consider using PME electrostatics. 86: 86: 86: 86: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 86: COM removal frequency is set to (5). 86: Other settings require a global communication frequency of 2. 86: Note that this will require additional global communication steps, 86: which will reduce performance when using multiple ranks. 86: Consider setting nstcomm to a multiple of 2. 86: 86: 86: There were 4 NOTEs 86: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 86: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 86: 86: Using 1 MPI thread 86: Using 1 OpenMP thread 86: 86: 86: NOTE: Thread affinity was not set. 86: starting mdrun 'spc2' 86: 16 steps, 0.0 ps. 86: Generated 330891 of the 330891 non-bonded parameter combinations 86: 86: Generated 330891 of the 330891 1-4 parameter combinations 86: 86: Excluding 2 bonded neighbours molecule type 'SOL' 86: 86: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/tip3p5.gro' 86: 86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 86: 86: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 86: 86: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 86: 86: Note that mdrun will redetermine rlist based on the actual pair-list setup 86: 86: This run will generate roughly 0 Mb of data 86: 86: Writing final coordinates. 86: 86: Core t (s) Wall t (s) (%) 86: Time: 0.024 0.024 99.0 86: (ns/day) (hour/ns) 86: Performance: 60.936 0.394 86: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as single precision energy file 86: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as single precision energy file 86: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 86: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 86: that with the Verlet scheme, nstlist has no effect on the accuracy of 86: your simulation. 86: 86: 86: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 86: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 86: setting nstcomm equal to nstcalcenergy for less overhead 86: 86: Generating 1-4 interactions: fudge = 0.5 86: Number of degrees of freedom in T-Coupling group System is 27.00 86: 86: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 86: You are using a plain Coulomb cut-off, which might produce artifacts. 86: You might want to consider using PME electrostatics. 86: 86: 86: 86: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 86: COM removal frequency is set to (5). 86: Other settings require a global communication frequency of 2. 86: Note that this will require additional global communication steps, 86: which will reduce performance when using multiple ranks. 86: Consider setting nstcomm to a multiple of 2. 86: 86: 86: There were 4 NOTEs 86: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 86: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 86: 86: Using 1 MPI thread 86: Using 1 OpenMP thread 86: 86: 86: NOTE: Thread affinity was not set. 86: starting mdrun 'spc2' 86: 16 steps, 0.0 ps. 86: Generated 330891 of the 330891 non-bonded parameter combinations 86: 86: Generated 330891 of the 330891 1-4 parameter combinations 86: 86: Excluding 2 bonded neighbours molecule type 'SOL' 86: 86: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/tip3p5.gro' 86: 86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 86: 86: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 86: 86: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 86: 86: Note that mdrun will redetermine rlist based on the actual pair-list setup 86: 86: This run will generate roughly 0 Mb of data 86: 86: Writing final coordinates. 86: 86: Core t (s) Wall t (s) (%) 86: Time: 0.032 0.033 99.3 86: (ns/day) (hour/ns) 86: Performance: 45.122 0.532 86: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as single precision energy file 86: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as single precision energy file 86: 86: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 86: that with the Verlet scheme, nstlist has no effect on the accuracy of 86: your simulation. 86: 86: 86: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 86: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 86: setting nstcomm equal to nstcalcenergy for less overhead 86: 86: Generating 1-4 interactions: fudge = 0.5 86: Number of degrees of freedom in T-Coupling group System is 27.00 86: 86: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 86: You are using a plain Coulomb cut-off, which might produce artifacts. 86: You might want to consider using PME electrostatics. 86: 86: 86: 86: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 86: COM removal frequency is set to (5). 86: Other settings require a global communication frequency of 2. 86: Note that this will require additional global communication steps, 86: which will reduce performance when using multiple ranks. 86: Consider setting nstcomm to a multiple of 2. 86: 86: 86: There were 4 NOTEs 86: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 86: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 86: 86: Using 1 MPI thread 86: Using 1 OpenMP thread 86: 86: 86: NOTE: Thread affinity was not set. 86: starting mdrun 'spc2' 86: 16 steps, 0.0 ps. 86: Generated 330891 of the 330891 non-bonded parameter combinations 86: 86: Generated 330891 of the 330891 1-4 parameter combinations 86: 86: Excluding 2 bonded neighbours molecule type 'SOL' 86: 86: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/tip3p5.gro' 86: 86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 86: 86: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 86: 86: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 86: 86: Note that mdrun will redetermine rlist based on the actual pair-list setup 86: 86: This run will generate roughly 0 Mb of data 86: 86: Writing final coordinates. 86: 86: Core t (s) Wall t (s) (%) 86: Time: 0.030 0.031 98.2 86: (ns/day) (hour/ns) 86: Performance: 47.856 0.502 86: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as single precision energy file 86: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as single precision energy file 86: 86: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 86: that with the Verlet scheme, nstlist has no effect on the accuracy of 86: your simulation. 86: 86: 86: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 86: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 86: setting nstcomm equal to nstcalcenergy for less overhead 86: 86: Generating 1-4 interactions: fudge = 0.5 86: Number of degrees of freedom in T-Coupling group System is 27.00 86: 86: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 86: You are using a plain Coulomb cut-off, which might produce artifacts. 86: You might want to consider using PME electrostatics. 86: 86: 86: 86: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 86: COM removal frequency is set to (5). 86: Other settings require a global communication frequency of 2. 86: Note that this will require additional global communication steps, 86: which will reduce performance when using multiple ranks. 86: Consider setting nstcomm to a multiple of 2. 86: 86: 86: There were 4 NOTEs 86: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 86: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 86: 86: Using 1 MPI thread 86: Using 1 OpenMP thread 86: 86: 86: NOTE: Thread affinity was not set. 86: starting mdrun 'spc2' 86: 16 steps, 0.0 ps. 86: Generated 330891 of the 330891 non-bonded parameter combinations 86: 86: Generated 330891 of the 330891 1-4 parameter combinations 86: 86: Excluding 2 bonded neighbours molecule type 'SOL' 86: 86: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/tip3p5.gro' 86: 86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 86: 86: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 86: 86: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 86: 86: Note that mdrun will redetermine rlist based on the actual pair-list setup 86: 86: This run will generate roughly 0 Mb of data 86: 86: Writing final coordinates. 86: 86: Core t (s) Wall t (s) (%) 86: Time: 0.022 0.023 98.9 86: (ns/day) (hour/ns) 86: Performance: 64.685 0.371 86: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as single precision energy file 86: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as single precision energy file 86: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/3 (28542 ms) 86: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/4 86: 86: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 86: that with the Verlet scheme, nstlist has no effect on the accuracy of 86: your simulation. 86: 86: 86: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 86: Setting nstcalcenergy (100) equal to nstenergy (1) 86: 86: Generating 1-4 interactions: fudge = 0.5 86: Number of degrees of freedom in T-Coupling group System is 27.00 86: 86: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 86: You are using a plain Coulomb cut-off, which might produce artifacts. 86: You might want to consider using PME electrostatics. 86: 86: 86: 86: There were 3 NOTEs 86: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 86: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 86: 86: Using 1 MPI thread 86: Using 1 OpenMP thread 86: 86: 86: NOTE: Thread affinity was not set. 86: starting mdrun 'spc2' 86: 16 steps, 0.0 ps. 86: Generated 330891 of the 330891 non-bonded parameter combinations 86: 86: Generated 330891 of the 330891 1-4 parameter combinations 86: 86: Excluding 2 bonded neighbours molecule type 'SOL' 86: 86: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/tip3p5.gro' 86: 86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 86: 86: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 86: 86: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 86: 86: Note that mdrun will redetermine rlist based on the actual pair-list setup 86: 86: This run will generate roughly 0 Mb of data 86: 86: Writing final coordinates. 86: 86: Core t (s) Wall t (s) (%) 86: Time: 0.028 0.029 99.0 86: (ns/day) (hour/ns) 86: Performance: 51.133 0.469 86: 86: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 86: that with the Verlet scheme, nstlist has no effect on the accuracy of 86: your simulation. 86: 86: 86: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 86: Setting nstcalcenergy (100) equal to nstenergy (1) 86: 86: Generating 1-4 interactions: fudge = 0.5 86: Number of degrees of freedom in T-Coupling group System is 27.00 86: 86: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 86: You are using a plain Coulomb cut-off, which might produce artifacts. 86: You might want to consider using PME electrostatics. 86: 86: 86: 86: There were 3 NOTEs 86: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 86: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 86: 86: Using 1 MPI thread 86: Using 1 OpenMP thread 86: 86: 86: NOTE: Thread affinity was not set. 86: starting mdrun 'spc2' 86: 16 steps, 0.0 ps. 86: Generated 330891 of the 330891 non-bonded parameter combinations 86: 86: Generated 330891 of the 330891 1-4 parameter combinations 86: 86: Excluding 2 bonded neighbours molecule type 'SOL' 86: 86: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/tip3p5.gro' 86: 86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 86: 86: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 86: 86: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 86: 86: Note that mdrun will redetermine rlist based on the actual pair-list setup 86: 86: This run will generate roughly 0 Mb of data 86: 86: Writing final coordinates. 86: 86: Core t (s) Wall t (s) (%) 86: Time: 0.042 0.042 99.3 86: (ns/day) (hour/ns) 86: Performance: 35.013 0.685 86: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as single precision energy file 86: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as single precision energy file 86: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 86: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 86: that with the Verlet scheme, nstlist has no effect on the accuracy of 86: your simulation. 86: 86: 86: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 86: Setting nstcalcenergy (100) equal to nstenergy (4) 86: 86: Generating 1-4 interactions: fudge = 0.5 86: Number of degrees of freedom in T-Coupling group System is 27.00 86: 86: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 86: You are using a plain Coulomb cut-off, which might produce artifacts. 86: You might want to consider using PME electrostatics. 86: 86: 86: 86: There were 3 NOTEs 86: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 86: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 86: 86: Using 1 MPI thread 86: Using 1 OpenMP thread 86: 86: 86: NOTE: Thread affinity was not set. 86: starting mdrun 'spc2' 86: 16 steps, 0.0 ps. 86: Generated 330891 of the 330891 non-bonded parameter combinations 86: 86: Generated 330891 of the 330891 1-4 parameter combinations 86: 86: Excluding 2 bonded neighbours molecule type 'SOL' 86: 86: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/tip3p5.gro' 86: 86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 86: 86: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 86: 86: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 86: 86: Note that mdrun will redetermine rlist based on the actual pair-list setup 86: 86: This run will generate roughly 0 Mb of data 86: 86: Writing final coordinates. 86: 86: Core t (s) Wall t (s) (%) 86: Time: 0.019 0.019 98.6 86: (ns/day) (hour/ns) 86: Performance: 77.497 0.310 86: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as single precision energy file 86: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as single precision energy file 86: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 86: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 86: that with the Verlet scheme, nstlist has no effect on the accuracy of 86: your simulation. 86: 86: 86: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 86: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 86: setting nstcomm equal to nstcalcenergy for less overhead 86: 86: Generating 1-4 interactions: fudge = 0.5 86: Number of degrees of freedom in T-Coupling group System is 27.00 86: 86: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 86: You are using a plain Coulomb cut-off, which might produce artifacts. 86: You might want to consider using PME electrostatics. 86: 86: 86: 86: There were 3 NOTEs 86: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 86: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 86: 86: Using 1 MPI thread 86: Using 1 OpenMP thread 86: 86: 86: NOTE: Thread affinity was not set. 86: starting mdrun 'spc2' 86: 16 steps, 0.0 ps. 86: Generated 330891 of the 330891 non-bonded parameter combinations 86: 86: Generated 330891 of the 330891 1-4 parameter combinations 86: 86: Excluding 2 bonded neighbours molecule type 'SOL' 86: 86: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/tip3p5.gro' 86: 86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 86: 86: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 86: 86: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 86: 86: Note that mdrun will redetermine rlist based on the actual pair-list setup 86: 86: This run will generate roughly 0 Mb of data 86: 86: Writing final coordinates. 86: 86: Core t (s) Wall t (s) (%) 86: Time: 0.021 0.021 98.8 86: (ns/day) (hour/ns) 86: Performance: 69.276 0.346 86: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as single precision energy file 86: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as single precision energy file 86: 86: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 86: that with the Verlet scheme, nstlist has no effect on the accuracy of 86: your simulation. 86: 86: 86: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 86: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 86: setting nstcomm equal to nstcalcenergy for less overhead 86: 86: Generating 1-4 interactions: fudge = 0.5 86: Number of degrees of freedom in T-Coupling group System is 27.00 86: 86: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 86: You are using a plain Coulomb cut-off, which might produce artifacts. 86: You might want to consider using PME electrostatics. 86: 86: 86: 86: There were 3 NOTEs 86: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 86: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 86: 86: Using 1 MPI thread 86: Using 1 OpenMP thread 86: 86: 86: NOTE: Thread affinity was not set. 86: starting mdrun 'spc2' 86: 16 steps, 0.0 ps. 86: Generated 330891 of the 330891 non-bonded parameter combinations 86: 86: Generated 330891 of the 330891 1-4 parameter combinations 86: 86: Excluding 2 bonded neighbours molecule type 'SOL' 86: 86: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/tip3p5.gro' 86: 86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 86: 86: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 86: 86: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 86: 86: Note that mdrun will redetermine rlist based on the actual pair-list setup 86: 86: This run will generate roughly 0 Mb of data 86: 86: Writing final coordinates. 86: 86: Core t (s) Wall t (s) (%) 86: Time: 0.027 0.028 99.0 86: (ns/day) (hour/ns) 86: Performance: 53.240 0.451 86: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as single precision energy file 86: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as single precision energy file 86: 86: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 86: that with the Verlet scheme, nstlist has no effect on the accuracy of 86: your simulation. 86: 86: 86: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 86: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 86: setting nstcomm equal to nstcalcenergy for less overhead 86: 86: Generating 1-4 interactions: fudge = 0.5 86: Number of degrees of freedom in T-Coupling group System is 27.00 86: 86: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 86: You are using a plain Coulomb cut-off, which might produce artifacts. 86: You might want to consider using PME electrostatics. 86: 86: 86: 86: There were 3 NOTEs 86: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 86: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 86: 86: Using 1 MPI thread 86: Using 1 OpenMP thread 86: 86: 86: NOTE: Thread affinity was not set. 86: starting mdrun 'spc2' 86: 16 steps, 0.0 ps. 86: Generated 330891 of the 330891 non-bonded parameter combinations 86: 86: Generated 330891 of the 330891 1-4 parameter combinations 86: 86: Excluding 2 bonded neighbours molecule type 'SOL' 86: 86: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/tip3p5.gro' 86: 86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 86: 86: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 86: 86: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 86: 86: Note that mdrun will redetermine rlist based on the actual pair-list setup 86: 86: This run will generate roughly 0 Mb of data 86: 86: Writing final coordinates. 86: 86: Core t (s) Wall t (s) (%) 86: Time: 0.021 0.021 98.7 86: (ns/day) (hour/ns) 86: Performance: 70.207 0.342 86: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as single precision energy file 86: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as single precision energy file 86: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/4 (29227 ms) 86: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/5 86: 86: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 86: that with the Verlet scheme, nstlist has no effect on the accuracy of 86: your simulation. 86: 86: 86: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 86: Setting nstcalcenergy (100) equal to nstenergy (1) 86: 86: Generating 1-4 interactions: fudge = 0.5 86: Number of degrees of freedom in T-Coupling group System is 27.00 86: 86: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 86: You are using a plain Coulomb cut-off, which might produce artifacts. 86: You might want to consider using PME electrostatics. 86: 86: 86: 86: There were 3 NOTEs 86: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 86: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 86: 86: Using 1 MPI thread 86: Using 1 OpenMP thread 86: 86: 86: NOTE: Thread affinity was not set. 86: starting mdrun 'spc2' 86: 16 steps, 0.0 ps. 86: Generated 330891 of the 330891 non-bonded parameter combinations 86: 86: Generated 330891 of the 330891 1-4 parameter combinations 86: 86: Excluding 2 bonded neighbours molecule type 'SOL' 86: 86: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/tip3p5.gro' 86: 86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 86: 86: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 86: 86: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 86: 86: Note that mdrun will redetermine rlist based on the actual pair-list setup 86: 86: This run will generate roughly 0 Mb of data 86: 86: Writing final coordinates. 86: 86: Core t (s) Wall t (s) (%) 86: Time: 0.024 0.024 98.8 86: (ns/day) (hour/ns) 86: Performance: 61.663 0.389 86: 86: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 86: that with the Verlet scheme, nstlist has no effect on the accuracy of 86: your simulation. 86: 86: 86: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 86: Setting nstcalcenergy (100) equal to nstenergy (1) 86: 86: Generating 1-4 interactions: fudge = 0.5 86: Number of degrees of freedom in T-Coupling group System is 27.00 86: 86: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 86: You are using a plain Coulomb cut-off, which might produce artifacts. 86: You might want to consider using PME electrostatics. 86: 86: 86: 86: There were 3 NOTEs 86: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 86: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 86: 86: Using 1 MPI thread 86: Using 1 OpenMP thread 86: 86: 86: NOTE: Thread affinity was not set. 86: starting mdrun 'spc2' 86: 16 steps, 0.0 ps. 86: Generated 330891 of the 330891 non-bonded parameter combinations 86: 86: Generated 330891 of the 330891 1-4 parameter combinations 86: 86: Excluding 2 bonded neighbours molecule type 'SOL' 86: 86: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/tip3p5.gro' 86: 86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 86: 86: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 86: 86: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 86: 86: Note that mdrun will redetermine rlist based on the actual pair-list setup 86: 86: This run will generate roughly 0 Mb of data 86: 86: Writing final coordinates. 86: 86: Core t (s) Wall t (s) (%) 86: Time: 0.023 0.023 98.9 86: (ns/day) (hour/ns) 86: Performance: 63.475 0.378 86: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as single precision energy file 86: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as single precision energy file 86: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 86: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 86: that with the Verlet scheme, nstlist has no effect on the accuracy of 86: your simulation. 86: 86: 86: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 86: Setting nstcalcenergy (100) equal to nstenergy (4) 86: 86: Generating 1-4 interactions: fudge = 0.5 86: Number of degrees of freedom in T-Coupling group System is 27.00 86: 86: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 86: You are using a plain Coulomb cut-off, which might produce artifacts. 86: You might want to consider using PME electrostatics. 86: 86: 86: 86: There were 3 NOTEs 86: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 86: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 86: 86: Using 1 MPI thread 86: Using 1 OpenMP thread 86: 86: 86: NOTE: Thread affinity was not set. 86: starting mdrun 'spc2' 86: 16 steps, 0.0 ps. 86: Generated 330891 of the 330891 non-bonded parameter combinations 86: 86: Generated 330891 of the 330891 1-4 parameter combinations 86: 86: Excluding 2 bonded neighbours molecule type 'SOL' 86: 86: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/tip3p5.gro' 86: 86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 86: 86: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 86: 86: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 86: 86: Note that mdrun will redetermine rlist based on the actual pair-list setup 86: 86: This run will generate roughly 0 Mb of data 86: 86: Writing final coordinates. 86: 86: Core t (s) Wall t (s) (%) 86: Time: 0.021 0.021 98.9 86: (ns/day) (hour/ns) 86: Performance: 68.754 0.349 86: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as single precision energy file 86: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as single precision energy file 86: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 86: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 86: that with the Verlet scheme, nstlist has no effect on the accuracy of 86: your simulation. 86: 86: 86: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 86: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 86: setting nstcomm equal to nstcalcenergy for less overhead 86: 86: Generating 1-4 interactions: fudge = 0.5 86: Number of degrees of freedom in T-Coupling group System is 27.00 86: 86: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 86: You are using a plain Coulomb cut-off, which might produce artifacts. 86: You might want to consider using PME electrostatics. 86: 86: 86: 86: There were 3 NOTEs 86: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 86: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 86: 86: Using 1 MPI thread 86: Using 1 OpenMP thread 86: 86: 86: NOTE: Thread affinity was not set. 86: starting mdrun 'spc2' 86: 16 steps, 0.0 ps. 86: Generated 330891 of the 330891 non-bonded parameter combinations 86: 86: Generated 330891 of the 330891 1-4 parameter combinations 86: 86: Excluding 2 bonded neighbours molecule type 'SOL' 86: 86: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/tip3p5.gro' 86: 86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 86: 86: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 86: 86: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 86: 86: Note that mdrun will redetermine rlist based on the actual pair-list setup 86: 86: This run will generate roughly 0 Mb of data 86: 86: Writing final coordinates. 86: 86: Core t (s) Wall t (s) (%) 86: Time: 0.019 0.020 98.7 86: (ns/day) (hour/ns) 86: Performance: 74.434 0.322 86: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as single precision energy file 86: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as single precision energy file 86: 86: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 86: that with the Verlet scheme, nstlist has no effect on the accuracy of 86: your simulation. 86: 86: 86: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 86: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 86: setting nstcomm equal to nstcalcenergy for less overhead 86: 86: Generating 1-4 interactions: fudge = 0.5 86: Number of degrees of freedom in T-Coupling group System is 27.00 86: 86: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 86: You are using a plain Coulomb cut-off, which might produce artifacts. 86: You might want to consider using PME electrostatics. 86: 86: 86: 86: There were 3 NOTEs 86: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 86: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 86: 86: Using 1 MPI thread 86: Using 1 OpenMP thread 86: 86: 86: NOTE: Thread affinity was not set. 86: starting mdrun 'spc2' 86: 16 steps, 0.0 ps. 86: Generated 330891 of the 330891 non-bonded parameter combinations 86: 86: Generated 330891 of the 330891 1-4 parameter combinations 86: 86: Excluding 2 bonded neighbours molecule type 'SOL' 86: 86: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/tip3p5.gro' 86: 86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 86: 86: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 86: 86: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 86: 86: Note that mdrun will redetermine rlist based on the actual pair-list setup 86: 86: This run will generate roughly 0 Mb of data 86: 86: Writing final coordinates. 86: 86: Core t (s) Wall t (s) (%) 86: Time: 0.023 0.023 98.8 86: (ns/day) (hour/ns) 86: Performance: 63.505 0.378 86: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as single precision energy file 86: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as single precision energy file 86: 86: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 86: that with the Verlet scheme, nstlist has no effect on the accuracy of 86: your simulation. 86: 86: 86: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 86: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 86: setting nstcomm equal to nstcalcenergy for less overhead 86: 86: Generating 1-4 interactions: fudge = 0.5 86: Number of degrees of freedom in T-Coupling group System is 27.00 86: 86: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 86: You are using a plain Coulomb cut-off, which might produce artifacts. 86: You might want to consider using PME electrostatics. 86: 86: 86: 86: There were 3 NOTEs 86: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 86: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 86: 86: Using 1 MPI thread 86: Using 1 OpenMP thread 86: 86: 86: NOTE: Thread affinity was not set. 86: starting mdrun 'spc2' 86: 16 steps, 0.0 ps. 86: Generated 330891 of the 330891 non-bonded parameter combinations 86: 86: Generated 330891 of the 330891 1-4 parameter combinations 86: 86: Excluding 2 bonded neighbours molecule type 'SOL' 86: 86: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/tip3p5.gro' 86: 86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 86: 86: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 86: 86: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 86: 86: Note that mdrun will redetermine rlist based on the actual pair-list setup 86: 86: This run will generate roughly 0 Mb of data 86: 86: Writing final coordinates. 86: 86: Core t (s) Wall t (s) (%) 86: Time: 0.028 0.029 99.1 86: (ns/day) (hour/ns) 86: Performance: 51.274 0.468 86: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as single precision energy file 86: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as single precision energy file 86: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/5 (27705 ms) 86: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/6 86: 86: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 86: that with the Verlet scheme, nstlist has no effect on the accuracy of 86: your simulation. 86: 86: 86: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 86: Setting nstcalcenergy (100) equal to nstenergy (1) 86: 86: Generating 1-4 interactions: fudge = 0.5 86: Number of degrees of freedom in T-Coupling group System is 27.00 86: 86: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 86: You are using a plain Coulomb cut-off, which might produce artifacts. 86: You might want to consider using PME electrostatics. 86: 86: 86: 86: There were 3 NOTEs 86: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 86: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 86: 86: Using 1 MPI thread 86: Using 1 OpenMP thread 86: 86: 86: NOTE: Thread affinity was not set. 86: starting mdrun 'spc2' 86: 16 steps, 0.0 ps. 86: Generated 330891 of the 330891 non-bonded parameter combinations 86: 86: Generated 330891 of the 330891 1-4 parameter combinations 86: 86: Excluding 2 bonded neighbours molecule type 'SOL' 86: 86: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/tip3p5.gro' 86: 86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 86: 86: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 86: 86: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 86: 86: Note that mdrun will redetermine rlist based on the actual pair-list setup 86: 86: This run will generate roughly 0 Mb of data 86: 86: Writing final coordinates. 86: 86: Core t (s) Wall t (s) (%) 86: Time: 0.026 0.026 98.7 86: (ns/day) (hour/ns) 86: Performance: 56.735 0.423 86: 86: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 86: that with the Verlet scheme, nstlist has no effect on the accuracy of 86: your simulation. 86: 86: 86: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 86: Setting nstcalcenergy (100) equal to nstenergy (1) 86: 86: Generating 1-4 interactions: fudge = 0.5 86: Number of degrees of freedom in T-Coupling group System is 27.00 86: 86: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 86: You are using a plain Coulomb cut-off, which might produce artifacts. 86: You might want to consider using PME electrostatics. 86: 86: 86: 86: There were 3 NOTEs 86: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 86: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 86: 86: Using 1 MPI thread 86: Using 1 OpenMP thread 86: 86: 86: NOTE: Thread affinity was not set. 86: starting mdrun 'spc2' 86: 16 steps, 0.0 ps. 86: Generated 330891 of the 330891 non-bonded parameter combinations 86: 86: Generated 330891 of the 330891 1-4 parameter combinations 86: 86: Excluding 2 bonded neighbours molecule type 'SOL' 86: 86: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/tip3p5.gro' 86: 86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 86: 86: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 86: 86: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 86: 86: Note that mdrun will redetermine rlist based on the actual pair-list setup 86: 86: This run will generate roughly 0 Mb of data 86: 86: Writing final coordinates. 86: 86: Core t (s) Wall t (s) (%) 86: Time: 0.017 0.017 98.7 86: (ns/day) (hour/ns) 86: Performance: 86.670 0.277 86: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as single precision energy file 86: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as single precision energy file 86: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 86: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 86: that with the Verlet scheme, nstlist has no effect on the accuracy of 86: your simulation. 86: 86: 86: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 86: Setting nstcalcenergy (100) equal to nstenergy (4) 86: 86: Generating 1-4 interactions: fudge = 0.5 86: Number of degrees of freedom in T-Coupling group System is 27.00 86: 86: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 86: You are using a plain Coulomb cut-off, which might produce artifacts. 86: You might want to consider using PME electrostatics. 86: 86: 86: 86: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 86: COM removal frequency is set to (5). 86: Other settings require a global communication frequency of 4. 86: Note that this will require additional global communication steps, 86: which will reduce performance when using multiple ranks. 86: Consider setting nstcomm to a multiple of 4. 86: 86: 86: There were 4 NOTEs 86: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 86: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 86: 86: Using 1 MPI thread 86: Using 1 OpenMP thread 86: 86: 86: NOTE: Thread affinity was not set. 86: starting mdrun 'spc2' 86: 16 steps, 0.0 ps. 86: Generated 330891 of the 330891 non-bonded parameter combinations 86: 86: Generated 330891 of the 330891 1-4 parameter combinations 86: 86: Excluding 2 bonded neighbours molecule type 'SOL' 86: 86: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/tip3p5.gro' 86: 86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 86: 86: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 86: 86: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 86: 86: Note that mdrun will redetermine rlist based on the actual pair-list setup 86: 86: This run will generate roughly 0 Mb of data 86: 86: Writing final coordinates. 86: 86: Core t (s) Wall t (s) (%) 86: Time: 0.041 0.041 99.5 86: (ns/day) (hour/ns) 86: Performance: 35.415 0.678 86: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as single precision energy file 86: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as single precision energy file 86: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 86: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 86: that with the Verlet scheme, nstlist has no effect on the accuracy of 86: your simulation. 86: 86: 86: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 86: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 86: setting nstcomm equal to nstcalcenergy for less overhead 86: 86: Generating 1-4 interactions: fudge = 0.5 86: Number of degrees of freedom in T-Coupling group System is 27.00 86: 86: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 86: You are using a plain Coulomb cut-off, which might produce artifacts. 86: You might want to consider using PME electrostatics. 86: 86: 86: 86: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 86: COM removal frequency is set to (5). 86: Other settings require a global communication frequency of 100. 86: Note that this will require additional global communication steps, 86: which will reduce performance when using multiple ranks. 86: Consider setting nstcomm to a multiple of 100. 86: 86: 86: There were 4 NOTEs 86: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 86: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 86: 86: Using 1 MPI thread 86: Using 1 OpenMP thread 86: 86: 86: NOTE: Thread affinity was not set. 86: starting mdrun 'spc2' 86: 16 steps, 0.0 ps. 86: Generated 330891 of the 330891 non-bonded parameter combinations 86: 86: Generated 330891 of the 330891 1-4 parameter combinations 86: 86: Excluding 2 bonded neighbours molecule type 'SOL' 86: 86: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/tip3p5.gro' 86: 86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 86: 86: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 86: 86: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 86: 86: Note that mdrun will redetermine rlist based on the actual pair-list setup 86: 86: This run will generate roughly 0 Mb of data 86: 86: Writing final coordinates. 86: 86: Core t (s) Wall t (s) (%) 86: Time: 0.023 0.023 99.1 86: (ns/day) (hour/ns) 86: Performance: 62.576 0.384 86: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as single precision energy file 86: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as single precision energy file 86: 86: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 86: that with the Verlet scheme, nstlist has no effect on the accuracy of 86: your simulation. 86: 86: 86: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 86: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 86: setting nstcomm equal to nstcalcenergy for less overhead 86: 86: Generating 1-4 interactions: fudge = 0.5 86: Number of degrees of freedom in T-Coupling group System is 27.00 86: 86: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 86: You are using a plain Coulomb cut-off, which might produce artifacts. 86: You might want to consider using PME electrostatics. 86: 86: 86: 86: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 86: COM removal frequency is set to (5). 86: Other settings require a global communication frequency of 100. 86: Note that this will require additional global communication steps, 86: which will reduce performance when using multiple ranks. 86: Consider setting nstcomm to a multiple of 100. 86: 86: 86: There were 4 NOTEs 86: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 86: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 86: 86: Using 1 MPI thread 86: Using 1 OpenMP thread 86: 86: 86: NOTE: Thread affinity was not set. 86: starting mdrun 'spc2' 86: 16 steps, 0.0 ps. 86: Generated 330891 of the 330891 non-bonded parameter combinations 86: 86: Generated 330891 of the 330891 1-4 parameter combinations 86: 86: Excluding 2 bonded neighbours molecule type 'SOL' 86: 86: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/tip3p5.gro' 86: 86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 86: 86: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 86: 86: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 86: 86: Note that mdrun will redetermine rlist based on the actual pair-list setup 86: 86: This run will generate roughly 0 Mb of data 86: 86: Writing final coordinates. 86: 86: Core t (s) Wall t (s) (%) 86: Time: 0.020 0.021 99.0 86: (ns/day) (hour/ns) 86: Performance: 71.145 0.337 86: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as single precision energy file 86: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as single precision energy file 86: 86: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 86: that with the Verlet scheme, nstlist has no effect on the accuracy of 86: your simulation. 86: 86: 86: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 86: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 86: setting nstcomm equal to nstcalcenergy for less overhead 86: 86: Generating 1-4 interactions: fudge = 0.5 86: Number of degrees of freedom in T-Coupling group System is 27.00 86: 86: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 86: You are using a plain Coulomb cut-off, which might produce artifacts. 86: You might want to consider using PME electrostatics. 86: 86: 86: 86: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 86: COM removal frequency is set to (5). 86: Other settings require a global communication frequency of 100. 86: Note that this will require additional global communication steps, 86: which will reduce performance when using multiple ranks. 86: Consider setting nstcomm to a multiple of 100. 86: 86: 86: There were 4 NOTEs 86: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 86: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 86: 86: Using 1 MPI thread 86: Using 1 OpenMP thread 86: 86: 86: NOTE: Thread affinity was not set. 86: starting mdrun 'spc2' 86: 16 steps, 0.0 ps. 86: Generated 330891 of the 330891 non-bonded parameter combinations 86: 86: Generated 330891 of the 330891 1-4 parameter combinations 86: 86: Excluding 2 bonded neighbours molecule type 'SOL' 86: 86: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/tip3p5.gro' 86: 86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 86: 86: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 86: 86: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 86: 86: Note that mdrun will redetermine rlist based on the actual pair-list setup 86: 86: This run will generate roughly 0 Mb of data 86: 86: Writing final coordinates. 86: 86: Core t (s) Wall t (s) (%) 86: Time: 0.021 0.022 98.9 86: (ns/day) (hour/ns) 86: Performance: 68.218 0.352 86: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as single precision energy file 86: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as single precision energy file 86: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/6 (30632 ms) 86: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/7 86: 86: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 86: that with the Verlet scheme, nstlist has no effect on the accuracy of 86: your simulation. 86: 86: 86: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 86: Setting nstcalcenergy (100) equal to nstenergy (1) 86: 86: Generating 1-4 interactions: fudge = 0.5 86: Number of degrees of freedom in T-Coupling group System is 27.00 86: 86: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 86: You are using a plain Coulomb cut-off, which might produce artifacts. 86: You might want to consider using PME electrostatics. 86: 86: 86: 86: There were 3 NOTEs 86: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 86: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 86: 86: Using 1 MPI thread 86: Using 1 OpenMP thread 86: 86: 86: NOTE: Thread affinity was not set. 86: starting mdrun 'spc2' 86: 16 steps, 0.0 ps. 86: Generated 330891 of the 330891 non-bonded parameter combinations 86: 86: Generated 330891 of the 330891 1-4 parameter combinations 86: 86: Excluding 2 bonded neighbours molecule type 'SOL' 86: 86: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/tip3p5.gro' 86: 86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 86: 86: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 86: 86: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 86: 86: Note that mdrun will redetermine rlist based on the actual pair-list setup 86: 86: This run will generate roughly 0 Mb of data 86: 86: Writing final coordinates. 86: 86: Core t (s) Wall t (s) (%) 86: Time: 0.023 0.023 98.9 86: (ns/day) (hour/ns) 86: Performance: 64.227 0.374 86: 86: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 86: that with the Verlet scheme, nstlist has no effect on the accuracy of 86: your simulation. 86: 86: 86: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 86: Setting nstcalcenergy (100) equal to nstenergy (1) 86: 86: Generating 1-4 interactions: fudge = 0.5 86: Number of degrees of freedom in T-Coupling group System is 27.00 86: 86: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 86: You are using a plain Coulomb cut-off, which might produce artifacts. 86: You might want to consider using PME electrostatics. 86: 86: 86: 86: There were 3 NOTEs 86: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 86: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 86: 86: Using 1 MPI thread 86: Using 1 OpenMP thread 86: 86: 86: NOTE: Thread affinity was not set. 86: starting mdrun 'spc2' 86: 16 steps, 0.0 ps. 86: Generated 330891 of the 330891 non-bonded parameter combinations 86: 86: Generated 330891 of the 330891 1-4 parameter combinations 86: 86: Excluding 2 bonded neighbours molecule type 'SOL' 86: 86: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/tip3p5.gro' 86: 86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 86: 86: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 86: 86: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 86: 86: Note that mdrun will redetermine rlist based on the actual pair-list setup 86: 86: This run will generate roughly 0 Mb of data 86: 86: Writing final coordinates. 86: 86: Core t (s) Wall t (s) (%) 86: Time: 0.023 0.023 99.0 86: (ns/day) (hour/ns) 86: Performance: 63.606 0.377 86: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as single precision energy file 86: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as single precision energy file 86: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 86: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 86: that with the Verlet scheme, nstlist has no effect on the accuracy of 86: your simulation. 86: 86: 86: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 86: Setting nstcalcenergy (100) equal to nstenergy (4) 86: 86: Generating 1-4 interactions: fudge = 0.5 86: Number of degrees of freedom in T-Coupling group System is 27.00 86: 86: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 86: You are using a plain Coulomb cut-off, which might produce artifacts. 86: You might want to consider using PME electrostatics. 86: 86: 86: 86: There were 3 NOTEs 86: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 86: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 86: 86: Using 1 MPI thread 86: Using 1 OpenMP thread 86: 86: 86: NOTE: Thread affinity was not set. 86: starting mdrun 'spc2' 86: 16 steps, 0.0 ps. 86: Generated 330891 of the 330891 non-bonded parameter combinations 86: 86: Generated 330891 of the 330891 1-4 parameter combinations 86: 86: Excluding 2 bonded neighbours molecule type 'SOL' 86: 86: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/tip3p5.gro' 86: 86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 86: 86: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 86: 86: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 86: 86: Note that mdrun will redetermine rlist based on the actual pair-list setup 86: 86: This run will generate roughly 0 Mb of data 86: 86: Writing final coordinates. 86: 86: Core t (s) Wall t (s) (%) 86: Time: 0.018 0.018 98.8 86: (ns/day) (hour/ns) 86: Performance: 80.641 0.298 86: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as single precision energy file 86: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as single precision energy file 86: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 86: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 86: that with the Verlet scheme, nstlist has no effect on the accuracy of 86: your simulation. 86: 86: 86: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 86: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 86: setting nstcomm equal to nstcalcenergy for less overhead 86: 86: Generating 1-4 interactions: fudge = 0.5 86: Number of degrees of freedom in T-Coupling group System is 27.00 86: 86: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 86: You are using a plain Coulomb cut-off, which might produce artifacts. 86: You might want to consider using PME electrostatics. 86: 86: 86: 86: There were 3 NOTEs 86: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 86: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 86: 86: Using 1 MPI thread 86: Using 1 OpenMP thread 86: 86: 86: NOTE: Thread affinity was not set. 86: starting mdrun 'spc2' 86: 16 steps, 0.0 ps. 86: Generated 330891 of the 330891 non-bonded parameter combinations 86: 86: Generated 330891 of the 330891 1-4 parameter combinations 86: 86: Excluding 2 bonded neighbours molecule type 'SOL' 86: 86: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/tip3p5.gro' 86: 86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 86: 86: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 86: 86: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 86: 86: Note that mdrun will redetermine rlist based on the actual pair-list setup 86: 86: This run will generate roughly 0 Mb of data 86: 86: Writing final coordinates. 86: 86: Core t (s) Wall t (s) (%) 86: Time: 0.025 0.025 99.1 86: (ns/day) (hour/ns) 86: Performance: 57.625 0.416 86: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as single precision energy file 86: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as single precision energy file 86: 86: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 86: that with the Verlet scheme, nstlist has no effect on the accuracy of 86: your simulation. 86: 86: 86: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 86: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 86: setting nstcomm equal to nstcalcenergy for less overhead 86: 86: Generating 1-4 interactions: fudge = 0.5 86: Number of degrees of freedom in T-Coupling group System is 27.00 86: 86: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 86: You are using a plain Coulomb cut-off, which might produce artifacts. 86: You might want to consider using PME electrostatics. 86: 86: 86: 86: There were 3 NOTEs 86: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 86: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 86: 86: Using 1 MPI thread 86: Using 1 OpenMP thread 86: 86: 86: NOTE: Thread affinity was not set. 86: starting mdrun 'spc2' 86: 16 steps, 0.0 ps. 86: Generated 330891 of the 330891 non-bonded parameter combinations 86: 86: Generated 330891 of the 330891 1-4 parameter combinations 86: 86: Excluding 2 bonded neighbours molecule type 'SOL' 86: 86: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/tip3p5.gro' 86: 86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 86: 86: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 86: 86: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 86: 86: Note that mdrun will redetermine rlist based on the actual pair-list setup 86: 86: This run will generate roughly 0 Mb of data 86: 86: Writing final coordinates. 86: 86: Core t (s) Wall t (s) (%) 86: Time: 0.025 0.025 99.0 86: (ns/day) (hour/ns) 86: Performance: 58.695 0.409 86: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as single precision energy file 86: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as single precision energy file 86: 86: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 86: that with the Verlet scheme, nstlist has no effect on the accuracy of 86: your simulation. 86: 86: 86: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 86: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 86: setting nstcomm equal to nstcalcenergy for less overhead 86: 86: Generating 1-4 interactions: fudge = 0.5 86: Number of degrees of freedom in T-Coupling group System is 27.00 86: 86: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 86: You are using a plain Coulomb cut-off, which might produce artifacts. 86: You might want to consider using PME electrostatics. 86: 86: 86: 86: There were 3 NOTEs 86: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 86: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 86: 86: Using 1 MPI thread 86: Using 1 OpenMP thread 86: 86: 86: NOTE: Thread affinity was not set. 86: starting mdrun 'spc2' 86: 16 steps, 0.0 ps. 86: Generated 330891 of the 330891 non-bonded parameter combinations 86: 86: Generated 330891 of the 330891 1-4 parameter combinations 86: 86: Excluding 2 bonded neighbours molecule type 'SOL' 86: 86: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/tip3p5.gro' 86: 86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 86: 86: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 86: 86: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 86: 86: Note that mdrun will redetermine rlist based on the actual pair-list setup 86: 86: This run will generate roughly 0 Mb of data 86: 86: Writing final coordinates. 86: 86: Core t (s) Wall t (s) (%) 86: Time: 0.023 0.023 99.0 86: (ns/day) (hour/ns) 86: Performance: 62.700 0.383 86: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as single precision energy file 86: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as single precision energy file 86: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/7 (27322 ms) 86: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/8 86: 86: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 86: that with the Verlet scheme, nstlist has no effect on the accuracy of 86: your simulation. 86: 86: 86: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 86: Setting nstcalcenergy (100) equal to nstenergy (1) 86: 86: Generating 1-4 interactions: fudge = 0.5 86: Number of degrees of freedom in T-Coupling group System is 27.00 86: 86: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 86: You are using a plain Coulomb cut-off, which might produce artifacts. 86: You might want to consider using PME electrostatics. 86: 86: 86: 86: There were 3 NOTEs 86: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 86: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 86: 86: Using 1 MPI thread 86: Using 1 OpenMP thread 86: 86: 86: NOTE: Thread affinity was not set. 86: starting mdrun 'spc2' 86: 16 steps, 0.0 ps. 86: Generated 330891 of the 330891 non-bonded parameter combinations 86: 86: Generated 330891 of the 330891 1-4 parameter combinations 86: 86: Excluding 2 bonded neighbours molecule type 'SOL' 86: 86: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/tip3p5.gro' 86: 86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 86: 86: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 86: 86: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 86: 86: Note that mdrun will redetermine rlist based on the actual pair-list setup 86: 86: This run will generate roughly 0 Mb of data 86: 86: Writing final coordinates. 86: 86: Core t (s) Wall t (s) (%) 86: Time: 0.022 0.022 98.9 86: (ns/day) (hour/ns) 86: Performance: 65.498 0.366 86: 86: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 86: that with the Verlet scheme, nstlist has no effect on the accuracy of 86: your simulation. 86: 86: 86: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 86: Setting nstcalcenergy (100) equal to nstenergy (1) 86: 86: Generating 1-4 interactions: fudge = 0.5 86: Number of degrees of freedom in T-Coupling group System is 27.00 86: 86: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 86: You are using a plain Coulomb cut-off, which might produce artifacts. 86: You might want to consider using PME electrostatics. 86: 86: 86: 86: There were 3 NOTEs 86: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 86: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 86: 86: Using 1 MPI thread 86: Using 1 OpenMP thread 86: 86: 86: NOTE: Thread affinity was not set. 86: starting mdrun 'spc2' 86: 16 steps, 0.0 ps. 86: Generated 330891 of the 330891 non-bonded parameter combinations 86: 86: Generated 330891 of the 330891 1-4 parameter combinations 86: 86: Excluding 2 bonded neighbours molecule type 'SOL' 86: 86: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/tip3p5.gro' 86: 86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 86: 86: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 86: 86: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 86: 86: Note that mdrun will redetermine rlist based on the actual pair-list setup 86: 86: This run will generate roughly 0 Mb of data 86: 86: Writing final coordinates. 86: 86: Core t (s) Wall t (s) (%) 86: Time: 0.018 0.019 98.8 86: (ns/day) (hour/ns) 86: Performance: 78.671 0.305 86: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_reference.edr as single precision energy file 86: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.edr as single precision energy file 86: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 86: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 86: that with the Verlet scheme, nstlist has no effect on the accuracy of 86: your simulation. 86: 86: 86: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 86: Setting nstcalcenergy (100) equal to nstenergy (4) 86: 86: Generating 1-4 interactions: fudge = 0.5 86: Number of degrees of freedom in T-Coupling group System is 27.00 86: 86: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 86: You are using a plain Coulomb cut-off, which might produce artifacts. 86: You might want to consider using PME electrostatics. 86: 86: 86: 86: There were 3 NOTEs 86: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 86: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 86: 86: Using 1 MPI thread 86: Using 1 OpenMP thread 86: 86: 86: NOTE: Thread affinity was not set. 86: starting mdrun 'spc2' 86: 16 steps, 0.0 ps. 86: Generated 330891 of the 330891 non-bonded parameter combinations 86: 86: Generated 330891 of the 330891 1-4 parameter combinations 86: 86: Excluding 2 bonded neighbours molecule type 'SOL' 86: 86: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/tip3p5.gro' 86: 86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 86: 86: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 86: 86: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 86: 86: Note that mdrun will redetermine rlist based on the actual pair-list setup 86: 86: This run will generate roughly 0 Mb of data 86: 86: Writing final coordinates. 86: 86: Core t (s) Wall t (s) (%) 86: Time: 0.023 0.023 99.1 86: (ns/day) (hour/ns) 86: Performance: 62.665 0.383 86: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_reference.edr as single precision energy file 86: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.edr as single precision energy file 86: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 86: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 86: that with the Verlet scheme, nstlist has no effect on the accuracy of 86: your simulation. 86: 86: 86: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 86: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 86: setting nstcomm equal to nstcalcenergy for less overhead 86: 86: Generating 1-4 interactions: fudge = 0.5 86: Number of degrees of freedom in T-Coupling group System is 27.00 86: 86: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 86: You are using a plain Coulomb cut-off, which might produce artifacts. 86: You might want to consider using PME electrostatics. 86: 86: 86: 86: There were 3 NOTEs 86: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 86: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 86: 86: Using 1 MPI thread 86: Using 1 OpenMP thread 86: 86: 86: NOTE: Thread affinity was not set. 86: starting mdrun 'spc2' 86: 16 steps, 0.0 ps. 86: Generated 330891 of the 330891 non-bonded parameter combinations 86: 86: Generated 330891 of the 330891 1-4 parameter combinations 86: 86: Excluding 2 bonded neighbours molecule type 'SOL' 86: 86: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/tip3p5.gro' 86: 86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 86: 86: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 86: 86: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 86: 86: Note that mdrun will redetermine rlist based on the actual pair-list setup 86: 86: This run will generate roughly 0 Mb of data 86: 86: Writing final coordinates. 86: 86: Core t (s) Wall t (s) (%) 86: Time: 0.028 0.028 99.1 86: (ns/day) (hour/ns) 86: Performance: 52.416 0.458 86: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_reference.edr as single precision energy file 86: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.edr as single precision energy file 86: 86: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 86: that with the Verlet scheme, nstlist has no effect on the accuracy of 86: your simulation. 86: 86: 86: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 86: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 86: setting nstcomm equal to nstcalcenergy for less overhead 86: 86: Generating 1-4 interactions: fudge = 0.5 86: Number of degrees of freedom in T-Coupling group System is 27.00 86: 86: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 86: You are using a plain Coulomb cut-off, which might produce artifacts. 86: You might want to consider using PME electrostatics. 86: 86: 86: 86: There were 3 NOTEs 86: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 86: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 86: 86: Using 1 MPI thread 86: Using 1 OpenMP thread 86: 86: 86: NOTE: Thread affinity was not set. 86: starting mdrun 'spc2' 86: 16 steps, 0.0 ps. 86: Generated 330891 of the 330891 non-bonded parameter combinations 86: 86: Generated 330891 of the 330891 1-4 parameter combinations 86: 86: Excluding 2 bonded neighbours molecule type 'SOL' 86: 86: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/tip3p5.gro' 86: 86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 86: 86: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 86: 86: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 86: 86: Note that mdrun will redetermine rlist based on the actual pair-list setup 86: 86: This run will generate roughly 0 Mb of data 86: 86: Writing final coordinates. 86: 86: Core t (s) Wall t (s) (%) 86: Time: 0.026 0.026 99.1 86: (ns/day) (hour/ns) 86: Performance: 56.447 0.425 86: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_reference.edr as single precision energy file 86: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.edr as single precision energy file 86: 86: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 86: that with the Verlet scheme, nstlist has no effect on the accuracy of 86: your simulation. 86: 86: 86: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 86: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 86: setting nstcomm equal to nstcalcenergy for less overhead 86: 86: Generating 1-4 interactions: fudge = 0.5 86: Number of degrees of freedom in T-Coupling group System is 27.00 86: 86: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 86: You are using a plain Coulomb cut-off, which might produce artifacts. 86: You might want to consider using PME electrostatics. 86: 86: 86: 86: There were 3 NOTEs 86: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 86: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 86: 86: Using 1 MPI thread 86: Using 1 OpenMP thread 86: 86: 86: NOTE: Thread affinity was not set. 86: starting mdrun 'spc2' 86: 16 steps, 0.0 ps. 86: Generated 330891 of the 330891 non-bonded parameter combinations 86: 86: Generated 330891 of the 330891 1-4 parameter combinations 86: 86: Excluding 2 bonded neighbours molecule type 'SOL' 86: 86: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/tip3p5.gro' 86: 86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 86: 86: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 86: 86: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 86: 86: Note that mdrun will redetermine rlist based on the actual pair-list setup 86: 86: This run will generate roughly 0 Mb of data 86: 86: Writing final coordinates. 86: 86: Core t (s) Wall t (s) (%) 86: Time: 0.020 0.021 98.9 86: (ns/day) (hour/ns) 86: Performance: 71.398 0.336 86: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_reference.edr as single precision energy file 86: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.edr as single precision energy file 86: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/8 (26802 ms) 86: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/9 86: 86: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 86: that with the Verlet scheme, nstlist has no effect on the accuracy of 86: your simulation. 86: 86: 86: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 86: Setting nstcalcenergy (100) equal to nstenergy (1) 86: 86: Generating 1-4 interactions: fudge = 0.5 86: Number of degrees of freedom in T-Coupling group System is 27.00 86: 86: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 86: NVE simulation: will use the initial temperature of 398.997 K for 86: determining the Verlet buffer size 86: 86: 86: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 86: You are using a plain Coulomb cut-off, which might produce artifacts. 86: You might want to consider using PME electrostatics. 86: 86: 86: 86: There were 4 NOTEs 86: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 86: Can not increase nstlist because an NVE ensemble is used 86: Using 1 MPI thread 86: Using 1 OpenMP thread 86: 86: 86: NOTE: Thread affinity was not set. 86: starting mdrun 'spc2' 86: 16 steps, 0.0 ps. 86: Generated 330891 of the 330891 non-bonded parameter combinations 86: 86: Generated 330891 of the 330891 1-4 parameter combinations 86: 86: Excluding 2 bonded neighbours molecule type 'SOL' 86: 86: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/tip3p5.gro' 86: 86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 86: 86: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 86: 86: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 86: 86: Note that mdrun will redetermine rlist based on the actual pair-list setup 86: 86: This run will generate roughly 0 Mb of data 86: 86: Writing final coordinates. 86: 86: Core t (s) Wall t (s) (%) 86: Time: 0.024 0.024 99.4 86: (ns/day) (hour/ns) 86: Performance: 61.946 0.387 86: 86: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 86: that with the Verlet scheme, nstlist has no effect on the accuracy of 86: your simulation. 86: 86: 86: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 86: Setting nstcalcenergy (100) equal to nstenergy (1) 86: 86: Generating 1-4 interactions: fudge = 0.5 86: Number of degrees of freedom in T-Coupling group System is 27.00 86: 86: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 86: NVE simulation: will use the initial temperature of 398.997 K for 86: determining the Verlet buffer size 86: 86: 86: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 86: You are using a plain Coulomb cut-off, which might produce artifacts. 86: You might want to consider using PME electrostatics. 86: 86: 86: 86: There were 4 NOTEs 86: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 86: Can not increase nstlist because an NVE ensemble is used 86: Using 1 MPI thread 86: Using 1 OpenMP thread 86: 86: 86: NOTE: Thread affinity was not set. 86: starting mdrun 'spc2' 86: 16 steps, 0.0 ps. 86: Generated 330891 of the 330891 non-bonded parameter combinations 86: 86: Generated 330891 of the 330891 1-4 parameter combinations 86: 86: Excluding 2 bonded neighbours molecule type 'SOL' 86: 86: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/tip3p5.gro' 86: 86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 86: 86: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 86: 86: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 86: 86: Note that mdrun will redetermine rlist based on the actual pair-list setup 86: 86: This run will generate roughly 0 Mb of data 86: 86: Writing final coordinates. 86: 86: Core t (s) Wall t (s) (%) 86: Time: 0.026 0.026 99.4 86: (ns/day) (hour/ns) 86: Performance: 55.761 0.430 86: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_reference.edr as single precision energy file 86: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.edr as single precision energy file 86: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 86: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 86: that with the Verlet scheme, nstlist has no effect on the accuracy of 86: your simulation. 86: 86: 86: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 86: Setting nstcalcenergy (100) equal to nstenergy (4) 86: 86: Generating 1-4 interactions: fudge = 0.5 86: Number of degrees of freedom in T-Coupling group System is 27.00 86: 86: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 86: NVE simulation: will use the initial temperature of 398.997 K for 86: determining the Verlet buffer size 86: 86: 86: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 86: You are using a plain Coulomb cut-off, which might produce artifacts. 86: You might want to consider using PME electrostatics. 86: 86: 86: 86: NOTE 5 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 86: COM removal frequency is set to (5). 86: Other settings require a global communication frequency of 4. 86: Note that this will require additional global communication steps, 86: which will reduce performance when using multiple ranks. 86: Consider setting nstcomm to a multiple of 4. 86: 86: 86: There were 5 NOTEs 86: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 86: Can not increase nstlist because an NVE ensemble is used 86: Using 1 MPI thread 86: Using 1 OpenMP thread 86: 86: 86: NOTE: Thread affinity was not set. 86: starting mdrun 'spc2' 86: 16 steps, 0.0 ps. 86: Generated 330891 of the 330891 non-bonded parameter combinations 86: 86: Generated 330891 of the 330891 1-4 parameter combinations 86: 86: Excluding 2 bonded neighbours molecule type 'SOL' 86: 86: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/tip3p5.gro' 86: 86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 86: 86: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 86: 86: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 86: 86: Note that mdrun will redetermine rlist based on the actual pair-list setup 86: 86: This run will generate roughly 0 Mb of data 86: 86: Writing final coordinates. 86: 86: Core t (s) Wall t (s) (%) 86: Time: 0.026 0.026 99.4 86: (ns/day) (hour/ns) 86: Performance: 56.805 0.422 86: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_reference.edr as single precision energy file 86: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.edr as single precision energy file 86: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 86: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 86: that with the Verlet scheme, nstlist has no effect on the accuracy of 86: your simulation. 86: 86: 86: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 86: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 86: setting nstcomm equal to nstcalcenergy for less overhead 86: 86: Generating 1-4 interactions: fudge = 0.5 86: Number of degrees of freedom in T-Coupling group System is 27.00 86: 86: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 86: NVE simulation: will use the initial temperature of 398.997 K for 86: determining the Verlet buffer size 86: 86: 86: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 86: You are using a plain Coulomb cut-off, which might produce artifacts. 86: You might want to consider using PME electrostatics. 86: 86: 86: 86: NOTE 5 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 86: COM removal frequency is set to (5). 86: Other settings require a global communication frequency of 100. 86: Note that this will require additional global communication steps, 86: which will reduce performance when using multiple ranks. 86: Consider setting nstcomm to a multiple of 100. 86: 86: 86: There were 5 NOTEs 86: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 86: Can not increase nstlist because an NVE ensemble is used 86: Using 1 MPI thread 86: Using 1 OpenMP thread 86: 86: 86: NOTE: Thread affinity was not set. 86: starting mdrun 'spc2' 86: 16 steps, 0.0 ps. 86: Generated 330891 of the 330891 non-bonded parameter combinations 86: 86: Generated 330891 of the 330891 1-4 parameter combinations 86: 86: Excluding 2 bonded neighbours molecule type 'SOL' 86: 86: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/tip3p5.gro' 86: 86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 86: 86: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 86: 86: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 86: 86: Note that mdrun will redetermine rlist based on the actual pair-list setup 86: 86: This run will generate roughly 0 Mb of data 86: 86: Writing final coordinates. 86: 86: Core t (s) Wall t (s) (%) 86: Time: 0.024 0.024 99.3 86: (ns/day) (hour/ns) 86: Performance: 61.045 0.393 86: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_reference.edr as single precision energy file 86: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.edr as single precision energy file 86: 86: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 86: that with the Verlet scheme, nstlist has no effect on the accuracy of 86: your simulation. 86: 86: 86: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 86: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 86: setting nstcomm equal to nstcalcenergy for less overhead 86: 86: Generating 1-4 interactions: fudge = 0.5 86: Number of degrees of freedom in T-Coupling group System is 27.00 86: 86: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 86: NVE simulation: will use the initial temperature of 398.997 K for 86: determining the Verlet buffer size 86: 86: 86: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 86: You are using a plain Coulomb cut-off, which might produce artifacts. 86: You might want to consider using PME electrostatics. 86: 86: 86: 86: NOTE 5 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 86: COM removal frequency is set to (5). 86: Other settings require a global communication frequency of 100. 86: Note that this will require additional global communication steps, 86: which will reduce performance when using multiple ranks. 86: Consider setting nstcomm to a multiple of 100. 86: 86: 86: There were 5 NOTEs 86: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 86: Can not increase nstlist because an NVE ensemble is used 86: Using 1 MPI thread 86: Using 1 OpenMP thread 86: 86: 86: NOTE: Thread affinity was not set. 86: starting mdrun 'spc2' 86: 16 steps, 0.0 ps. 86: Generated 330891 of the 330891 non-bonded parameter combinations 86: 86: Generated 330891 of the 330891 1-4 parameter combinations 86: 86: Excluding 2 bonded neighbours molecule type 'SOL' 86: 86: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/tip3p5.gro' 86: 86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 86: 86: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 86: 86: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 86: 86: Note that mdrun will redetermine rlist based on the actual pair-list setup 86: 86: This run will generate roughly 0 Mb of data 86: 86: Writing final coordinates. 86: 86: Core t (s) Wall t (s) (%) 86: Time: 0.026 0.026 99.4 86: (ns/day) (hour/ns) 86: Performance: 55.708 0.431 86: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_reference.edr as single precision energy file 86: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.edr as single precision energy file 86: 86: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 86: that with the Verlet scheme, nstlist has no effect on the accuracy of 86: your simulation. 86: 86: 86: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 86: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 86: setting nstcomm equal to nstcalcenergy for less overhead 86: 86: Generating 1-4 interactions: fudge = 0.5 86: Number of degrees of freedom in T-Coupling group System is 27.00 86: 86: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 86: NVE simulation: will use the initial temperature of 398.997 K for 86: determining the Verlet buffer size 86: 86: 86: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 86: You are using a plain Coulomb cut-off, which might produce artifacts. 86: You might want to consider using PME electrostatics. 86: 86: 86: 86: NOTE 5 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 86: COM removal frequency is set to (5). 86: Other settings require a global communication frequency of 100. 86: Note that this will require additional global communication steps, 86: which will reduce performance when using multiple ranks. 86: Consider setting nstcomm to a multiple of 100. 86: 86: 86: There were 5 NOTEs 86: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 86: Can not increase nstlist because an NVE ensemble is used 86: Using 1 MPI thread 86: Using 1 OpenMP thread 86: 86: 86: NOTE: Thread affinity was not set. 86: starting mdrun 'spc2' 86: 16 steps, 0.0 ps. 86: Generated 330891 of the 330891 non-bonded parameter combinations 86: 86: Generated 330891 of the 330891 1-4 parameter combinations 86: 86: Excluding 2 bonded neighbours molecule type 'SOL' 86: 86: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/tip3p5.gro' 86: 86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 86: 86: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 86: 86: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 86: 86: Note that mdrun will redetermine rlist based on the actual pair-list setup 86: 86: This run will generate roughly 0 Mb of data 86: 86: Writing final coordinates. 86: 86: Core t (s) Wall t (s) (%) 86: Time: 0.033 0.033 99.5 86: (ns/day) (hour/ns) 86: Performance: 44.491 0.539 86: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_reference.edr as single precision energy file 86: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.edr as single precision energy file 86: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/9 (26787 ms) 86: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/10 86: 86: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 86: that with the Verlet scheme, nstlist has no effect on the accuracy of 86: your simulation. 86: 86: 86: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 86: Setting nstcalcenergy (100) equal to nstenergy (1) 86: 86: Generating 1-4 interactions: fudge = 0.5 86: Number of degrees of freedom in T-Coupling group System is 27.00 86: 86: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 86: NVE simulation: will use the initial temperature of 398.997 K for 86: determining the Verlet buffer size 86: 86: 86: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 86: You are using a plain Coulomb cut-off, which might produce artifacts. 86: You might want to consider using PME electrostatics. 86: 86: 86: 86: There were 4 NOTEs 86: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 86: Can not increase nstlist because an NVE ensemble is used 86: Using 1 MPI thread 86: Using 1 OpenMP thread 86: 86: 86: NOTE: Thread affinity was not set. 86: starting mdrun 'spc2' 86: 16 steps, 0.0 ps. 86: Generated 330891 of the 330891 non-bonded parameter combinations 86: 86: Generated 330891 of the 330891 1-4 parameter combinations 86: 86: Excluding 2 bonded neighbours molecule type 'SOL' 86: 86: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/tip3p5.gro' 86: 86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 86: 86: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 86: 86: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 86: 86: Note that mdrun will redetermine rlist based on the actual pair-list setup 86: 86: This run will generate roughly 0 Mb of data 86: 86: Writing final coordinates. 86: 86: Core t (s) Wall t (s) (%) 86: Time: 0.029 0.029 99.4 86: (ns/day) (hour/ns) 86: Performance: 51.041 0.470 86: 86: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 86: that with the Verlet scheme, nstlist has no effect on the accuracy of 86: your simulation. 86: 86: 86: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 86: Setting nstcalcenergy (100) equal to nstenergy (1) 86: 86: Generating 1-4 interactions: fudge = 0.5 86: Number of degrees of freedom in T-Coupling group System is 27.00 86: 86: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 86: NVE simulation: will use the initial temperature of 398.997 K for 86: determining the Verlet buffer size 86: 86: 86: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 86: You are using a plain Coulomb cut-off, which might produce artifacts. 86: You might want to consider using PME electrostatics. 86: 86: 86: 86: There were 4 NOTEs 86: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 86: Can not increase nstlist because an NVE ensemble is used 86: Using 1 MPI thread 86: Using 1 OpenMP thread 86: 86: 86: NOTE: Thread affinity was not set. 86: starting mdrun 'spc2' 86: 16 steps, 0.0 ps. 86: Generated 330891 of the 330891 non-bonded parameter combinations 86: 86: Generated 330891 of the 330891 1-4 parameter combinations 86: 86: Excluding 2 bonded neighbours molecule type 'SOL' 86: 86: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/tip3p5.gro' 86: 86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 86: 86: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 86: 86: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 86: 86: Note that mdrun will redetermine rlist based on the actual pair-list setup 86: 86: This run will generate roughly 0 Mb of data 86: 86: Writing final coordinates. 86: 86: Core t (s) Wall t (s) (%) 86: Time: 0.022 0.022 99.2 86: (ns/day) (hour/ns) 86: Performance: 67.299 0.357 86: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_reference.edr as single precision energy file 86: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.edr as single precision energy file 86: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 86: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 86: that with the Verlet scheme, nstlist has no effect on the accuracy of 86: your simulation. 86: 86: 86: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 86: Setting nstcalcenergy (100) equal to nstenergy (4) 86: 86: Generating 1-4 interactions: fudge = 0.5 86: Number of degrees of freedom in T-Coupling group System is 27.00 86: 86: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 86: NVE simulation: will use the initial temperature of 398.997 K for 86: determining the Verlet buffer size 86: 86: 86: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 86: You are using a plain Coulomb cut-off, which might produce artifacts. 86: You might want to consider using PME electrostatics. 86: 86: 86: 86: There were 4 NOTEs 86: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 86: Can not increase nstlist because an NVE ensemble is used 86: Using 1 MPI thread 86: Using 1 OpenMP thread 86: 86: 86: NOTE: Thread affinity was not set. 86: starting mdrun 'spc2' 86: 16 steps, 0.0 ps. 86: Generated 330891 of the 330891 non-bonded parameter combinations 86: 86: Generated 330891 of the 330891 1-4 parameter combinations 86: 86: Excluding 2 bonded neighbours molecule type 'SOL' 86: 86: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/tip3p5.gro' 86: 86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 86: 86: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 86: 86: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 86: 86: Note that mdrun will redetermine rlist based on the actual pair-list setup 86: 86: This run will generate roughly 0 Mb of data 86: 86: Writing final coordinates. 86: 86: Core t (s) Wall t (s) (%) 86: Time: 0.023 0.023 99.2 86: (ns/day) (hour/ns) 86: Performance: 63.076 0.380 86: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_reference.edr as single precision energy file 86: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.edr as single precision energy file 86: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 86: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 86: that with the Verlet scheme, nstlist has no effect on the accuracy of 86: your simulation. 86: 86: 86: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 86: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 86: setting nstcomm equal to nstcalcenergy for less overhead 86: 86: Generating 1-4 interactions: fudge = 0.5 86: Number of degrees of freedom in T-Coupling group System is 27.00 86: 86: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 86: NVE simulation: will use the initial temperature of 398.997 K for 86: determining the Verlet buffer size 86: 86: 86: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 86: You are using a plain Coulomb cut-off, which might produce artifacts. 86: You might want to consider using PME electrostatics. 86: 86: 86: 86: There were 4 NOTEs 86: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 86: Can not increase nstlist because an NVE ensemble is used 86: Using 1 MPI thread 86: Using 1 OpenMP thread 86: 86: 86: NOTE: Thread affinity was not set. 86: starting mdrun 'spc2' 86: 16 steps, 0.0 ps. 86: Generated 330891 of the 330891 non-bonded parameter combinations 86: 86: Generated 330891 of the 330891 1-4 parameter combinations 86: 86: Excluding 2 bonded neighbours molecule type 'SOL' 86: 86: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/tip3p5.gro' 86: 86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 86: 86: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 86: 86: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 86: 86: Note that mdrun will redetermine rlist based on the actual pair-list setup 86: 86: This run will generate roughly 0 Mb of data 86: 86: Writing final coordinates. 86: 86: Core t (s) Wall t (s) (%) 86: Time: 0.045 0.046 99.6 86: (ns/day) (hour/ns) 86: Performance: 32.243 0.744 86: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_reference.edr as single precision energy file 86: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.edr as single precision energy file 86: 86: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 86: that with the Verlet scheme, nstlist has no effect on the accuracy of 86: your simulation. 86: 86: 86: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 86: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 86: setting nstcomm equal to nstcalcenergy for less overhead 86: 86: Generating 1-4 interactions: fudge = 0.5 86: Number of degrees of freedom in T-Coupling group System is 27.00 86: 86: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 86: NVE simulation: will use the initial temperature of 398.997 K for 86: determining the Verlet buffer size 86: 86: 86: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 86: You are using a plain Coulomb cut-off, which might produce artifacts. 86: You might want to consider using PME electrostatics. 86: 86: 86: 86: There were 4 NOTEs 86: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 86: Can not increase nstlist because an NVE ensemble is used 86: Using 1 MPI thread 86: Using 1 OpenMP thread 86: 86: 86: NOTE: Thread affinity was not set. 86: starting mdrun 'spc2' 86: 16 steps, 0.0 ps. 86: Generated 330891 of the 330891 non-bonded parameter combinations 86: 86: Generated 330891 of the 330891 1-4 parameter combinations 86: 86: Excluding 2 bonded neighbours molecule type 'SOL' 86: 86: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/tip3p5.gro' 86: 86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 86: 86: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 86: 86: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 86: 86: Note that mdrun will redetermine rlist based on the actual pair-list setup 86: 86: This run will generate roughly 0 Mb of data 86: 86: Writing final coordinates. 86: 86: Core t (s) Wall t (s) (%) 86: Time: 0.045 0.045 99.6 86: (ns/day) (hour/ns) 86: Performance: 32.764 0.733 86: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_reference.edr as single precision energy file 86: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.edr as single precision energy file 86: 86: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 86: that with the Verlet scheme, nstlist has no effect on the accuracy of 86: your simulation. 86: 86: 86: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 86: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 86: setting nstcomm equal to nstcalcenergy for less overhead 86: 86: Generating 1-4 interactions: fudge = 0.5 86: Number of degrees of freedom in T-Coupling group System is 27.00 86: 86: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 86: NVE simulation: will use the initial temperature of 398.997 K for 86: determining the Verlet buffer size 86: 86: 86: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 86: You are using a plain Coulomb cut-off, which might produce artifacts. 86: You might want to consider using PME electrostatics. 86: 86: 86: 86: There were 4 NOTEs 86: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 86: Can not increase nstlist because an NVE ensemble is used 86: Using 1 MPI thread 86: Using 1 OpenMP thread 86: 86: 86: NOTE: Thread affinity was not set. 86: starting mdrun 'spc2' 86: 16 steps, 0.0 ps. 86: Generated 330891 of the 330891 non-bonded parameter combinations 86: 86: Generated 330891 of the 330891 1-4 parameter combinations 86: 86: Excluding 2 bonded neighbours molecule type 'SOL' 86: 86: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/tip3p5.gro' 86: 86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 86: 86: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 86: 86: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 86: 86: Note that mdrun will redetermine rlist based on the actual pair-list setup 86: 86: This run will generate roughly 0 Mb of data 86: 86: Writing final coordinates. 86: 86: Core t (s) Wall t (s) (%) 86: Time: 0.033 0.033 99.3 86: (ns/day) (hour/ns) 86: Performance: 43.923 0.546 86: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_reference.edr as single precision energy file 86: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.edr as single precision energy file 86: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/10 (27087 ms) 86: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/11 86: 86: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 86: that with the Verlet scheme, nstlist has no effect on the accuracy of 86: your simulation. 86: 86: 86: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 86: Setting nstcalcenergy (100) equal to nstenergy (1) 86: 86: Generating 1-4 interactions: fudge = 0.5 86: Number of degrees of freedom in T-Coupling group System is 27.00 86: 86: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 86: You are using a plain Coulomb cut-off, which might produce artifacts. 86: You might want to consider using PME electrostatics. 86: 86: 86: 86: There were 3 NOTEs 86: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 86: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 86: 86: Using 1 MPI thread 86: Using 1 OpenMP thread 86: 86: 86: NOTE: Thread affinity was not set. 86: starting mdrun 'spc2' 86: 16 steps, 0.0 ps. 86: Generated 330891 of the 330891 non-bonded parameter combinations 86: 86: Generated 330891 of the 330891 1-4 parameter combinations 86: 86: Excluding 2 bonded neighbours molecule type 'SOL' 86: 86: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/tip3p5.gro' 86: 86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 86: 86: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 86: 86: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 86: 86: Note that mdrun will redetermine rlist based on the actual pair-list setup 86: 86: This run will generate roughly 0 Mb of data 86: 86: Writing final coordinates. 86: 86: Core t (s) Wall t (s) (%) 86: Time: 0.029 0.029 98.7 86: (ns/day) (hour/ns) 86: Performance: 50.173 0.478 86: 86: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 86: that with the Verlet scheme, nstlist has no effect on the accuracy of 86: your simulation. 86: 86: 86: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 86: Setting nstcalcenergy (100) equal to nstenergy (1) 86: 86: Generating 1-4 interactions: fudge = 0.5 86: Number of degrees of freedom in T-Coupling group System is 27.00 86: 86: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 86: You are using a plain Coulomb cut-off, which might produce artifacts. 86: You might want to consider using PME electrostatics. 86: 86: 86: 86: There were 3 NOTEs 86: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 86: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 86: 86: Using 1 MPI thread 86: Using 1 OpenMP thread 86: 86: 86: NOTE: Thread affinity was not set. 86: starting mdrun 'spc2' 86: 16 steps, 0.0 ps. 86: Generated 330891 of the 330891 non-bonded parameter combinations 86: 86: Generated 330891 of the 330891 1-4 parameter combinations 86: 86: Excluding 2 bonded neighbours molecule type 'SOL' 86: 86: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/tip3p5.gro' 86: 86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 86: 86: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 86: 86: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 86: 86: Note that mdrun will redetermine rlist based on the actual pair-list setup 86: 86: This run will generate roughly 0 Mb of data 86: 86: Writing final coordinates. 86: 86: Core t (s) Wall t (s) (%) 86: Time: 0.025 0.025 98.9 86: (ns/day) (hour/ns) 86: Performance: 57.647 0.416 86: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_reference.edr as single precision energy file 86: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.edr as single precision energy file 86: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 86: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 86: that with the Verlet scheme, nstlist has no effect on the accuracy of 86: your simulation. 86: 86: 86: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 86: Setting nstcalcenergy (100) equal to nstenergy (4) 86: 86: Generating 1-4 interactions: fudge = 0.5 86: Number of degrees of freedom in T-Coupling group System is 27.00 86: 86: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 86: You are using a plain Coulomb cut-off, which might produce artifacts. 86: You might want to consider using PME electrostatics. 86: 86: 86: 86: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 86: COM removal frequency is set to (5). 86: Other settings require a global communication frequency of 2. 86: Note that this will require additional global communication steps, 86: which will reduce performance when using multiple ranks. 86: Consider setting nstcomm to a multiple of 2. 86: 86: 86: There were 4 NOTEs 86: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 86: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 86: 86: Using 1 MPI thread 86: Using 1 OpenMP thread 86: 86: 86: NOTE: Thread affinity was not set. 86: starting mdrun 'spc2' 86: 16 steps, 0.0 ps. 86: Generated 330891 of the 330891 non-bonded parameter combinations 86: 86: Generated 330891 of the 330891 1-4 parameter combinations 86: 86: Excluding 2 bonded neighbours molecule type 'SOL' 86: 86: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/tip3p5.gro' 86: 86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 86: 86: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 86: 86: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 86: 86: Note that mdrun will redetermine rlist based on the actual pair-list setup 86: 86: This run will generate roughly 0 Mb of data 86: 86: Writing final coordinates. 86: 86: Core t (s) Wall t (s) (%) 86: Time: 0.022 0.022 99.0 86: (ns/day) (hour/ns) 86: Performance: 65.548 0.366 86: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_reference.edr as single precision energy file 86: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.edr as single precision energy file 86: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 86: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 86: that with the Verlet scheme, nstlist has no effect on the accuracy of 86: your simulation. 86: 86: 86: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 86: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 86: setting nstcomm equal to nstcalcenergy for less overhead 86: 86: Generating 1-4 interactions: fudge = 0.5 86: Number of degrees of freedom in T-Coupling group System is 27.00 86: 86: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 86: You are using a plain Coulomb cut-off, which might produce artifacts. 86: You might want to consider using PME electrostatics. 86: 86: 86: 86: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 86: COM removal frequency is set to (5). 86: Other settings require a global communication frequency of 2. 86: Note that this will require additional global communication steps, 86: which will reduce performance when using multiple ranks. 86: Consider setting nstcomm to a multiple of 2. 86: 86: 86: There were 4 NOTEs 86: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 86: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 86: 86: Using 1 MPI thread 86: Using 1 OpenMP thread 86: 86: 86: NOTE: Thread affinity was not set. 86: starting mdrun 'spc2' 86: 16 steps, 0.0 ps. 86: Generated 330891 of the 330891 non-bonded parameter combinations 86: 86: Generated 330891 of the 330891 1-4 parameter combinations 86: 86: Excluding 2 bonded neighbours molecule type 'SOL' 86: 86: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/tip3p5.gro' 86: 86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 86: 86: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 86: 86: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 86: 86: Note that mdrun will redetermine rlist based on the actual pair-list setup 86: 86: This run will generate roughly 0 Mb of data 86: 86: Writing final coordinates. 86: 86: Core t (s) Wall t (s) (%) 86: Time: 0.030 0.030 99.2 86: (ns/day) (hour/ns) 86: Performance: 48.426 0.496 86: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_reference.edr as single precision energy file 86: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.edr as single precision energy file 86: 86: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 86: that with the Verlet scheme, nstlist has no effect on the accuracy of 86: your simulation. 86: 86: 86: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 86: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 86: setting nstcomm equal to nstcalcenergy for less overhead 86: 86: Generating 1-4 interactions: fudge = 0.5 86: Number of degrees of freedom in T-Coupling group System is 27.00 86: 86: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 86: You are using a plain Coulomb cut-off, which might produce artifacts. 86: You might want to consider using PME electrostatics. 86: 86: 86: 86: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 86: COM removal frequency is set to (5). 86: Other settings require a global communication frequency of 2. 86: Note that this will require additional global communication steps, 86: which will reduce performance when using multiple ranks. 86: Consider setting nstcomm to a multiple of 2. 86: 86: 86: There were 4 NOTEs 86: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 86: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 86: 86: Using 1 MPI thread 86: Using 1 OpenMP thread 86: 86: 86: NOTE: Thread affinity was not set. 86: starting mdrun 'spc2' 86: 16 steps, 0.0 ps. 86: Generated 330891 of the 330891 non-bonded parameter combinations 86: 86: Generated 330891 of the 330891 1-4 parameter combinations 86: 86: Excluding 2 bonded neighbours molecule type 'SOL' 86: 86: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/tip3p5.gro' 86: 86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 86: 86: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 86: 86: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 86: 86: Note that mdrun will redetermine rlist based on the actual pair-list setup 86: 86: This run will generate roughly 0 Mb of data 86: 86: Writing final coordinates. 86: 86: Core t (s) Wall t (s) (%) 86: Time: 0.034 0.035 99.3 86: (ns/day) (hour/ns) 86: Performance: 42.316 0.567 86: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_reference.edr as single precision energy file 86: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.edr as single precision energy file 86: 86: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 86: that with the Verlet scheme, nstlist has no effect on the accuracy of 86: your simulation. 86: 86: 86: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 86: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 86: setting nstcomm equal to nstcalcenergy for less overhead 86: 86: Generating 1-4 interactions: fudge = 0.5 86: Number of degrees of freedom in T-Coupling group System is 27.00 86: 86: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 86: You are using a plain Coulomb cut-off, which might produce artifacts. 86: You might want to consider using PME electrostatics. 86: 86: 86: 86: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 86: COM removal frequency is set to (5). 86: Other settings require a global communication frequency of 2. 86: Note that this will require additional global communication steps, 86: which will reduce performance when using multiple ranks. 86: Consider setting nstcomm to a multiple of 2. 86: 86: 86: There were 4 NOTEs 86: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 86: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 86: 86: Using 1 MPI thread 86: Using 1 OpenMP thread 86: 86: 86: NOTE: Thread affinity was not set. 86: starting mdrun 'spc2' 86: 16 steps, 0.0 ps. 86: Generated 330891 of the 330891 non-bonded parameter combinations 86: 86: Generated 330891 of the 330891 1-4 parameter combinations 86: 86: Excluding 2 bonded neighbours molecule type 'SOL' 86: 86: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/tip3p5.gro' 86: 86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 86: 86: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 86: 86: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 86: 86: Note that mdrun will redetermine rlist based on the actual pair-list setup 86: 86: This run will generate roughly 0 Mb of data 86: 86: Writing final coordinates. 86: 86: Core t (s) Wall t (s) (%) 86: Time: 0.042 0.042 99.4 86: (ns/day) (hour/ns) 86: Performance: 34.642 0.693 86: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_reference.edr as single precision energy file 86: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.edr as single precision energy file 86: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/11 (27487 ms) 86: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/12 86: 86: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 86: that with the Verlet scheme, nstlist has no effect on the accuracy of 86: your simulation. 86: 86: 86: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 86: Setting nstcalcenergy (100) equal to nstenergy (1) 86: 86: Generating 1-4 interactions: fudge = 0.5 86: Number of degrees of freedom in T-Coupling group System is 27.00 86: 86: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 86: You are using a plain Coulomb cut-off, which might produce artifacts. 86: You might want to consider using PME electrostatics. 86: 86: 86: 86: There were 3 NOTEs 86: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 86: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 86: 86: Using 1 MPI thread 86: Using 1 OpenMP thread 86: 86: 86: NOTE: Thread affinity was not set. 86: starting mdrun 'spc2' 86: 16 steps, 0.0 ps. 86: Generated 330891 of the 330891 non-bonded parameter combinations 86: 86: Generated 330891 of the 330891 1-4 parameter combinations 86: 86: Excluding 2 bonded neighbours molecule type 'SOL' 86: 86: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/tip3p5.gro' 86: 86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 86: 86: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 86: 86: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 86: 86: Note that mdrun will redetermine rlist based on the actual pair-list setup 86: 86: This run will generate roughly 0 Mb of data 86: 86: Writing final coordinates. 86: 86: Core t (s) Wall t (s) (%) 86: Time: 0.056 0.056 99.5 86: (ns/day) (hour/ns) 86: Performance: 26.204 0.916 86: 86: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 86: that with the Verlet scheme, nstlist has no effect on the accuracy of 86: your simulation. 86: 86: 86: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 86: Setting nstcalcenergy (100) equal to nstenergy (1) 86: 86: Generating 1-4 interactions: fudge = 0.5 86: Number of degrees of freedom in T-Coupling group System is 27.00 86: 86: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 86: You are using a plain Coulomb cut-off, which might produce artifacts. 86: You might want to consider using PME electrostatics. 86: 86: 86: 86: There were 3 NOTEs 86: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 86: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 86: 86: Using 1 MPI thread 86: Using 1 OpenMP thread 86: 86: 86: NOTE: Thread affinity was not set. 86: starting mdrun 'spc2' 86: 16 steps, 0.0 ps. 86: Generated 330891 of the 330891 non-bonded parameter combinations 86: 86: Generated 330891 of the 330891 1-4 parameter combinations 86: 86: Excluding 2 bonded neighbours molecule type 'SOL' 86: 86: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/tip3p5.gro' 86: 86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 86: 86: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 86: 86: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 86: 86: Note that mdrun will redetermine rlist based on the actual pair-list setup 86: 86: This run will generate roughly 0 Mb of data 86: 86: Writing final coordinates. 86: 86: Core t (s) Wall t (s) (%) 86: Time: 0.038 0.039 99.3 86: (ns/day) (hour/ns) 86: Performance: 38.007 0.631 86: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_reference.edr as single precision energy file 86: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.edr as single precision energy file 86: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 86: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 86: that with the Verlet scheme, nstlist has no effect on the accuracy of 86: your simulation. 86: 86: 86: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 86: Setting nstcalcenergy (100) equal to nstenergy (4) 86: 86: Generating 1-4 interactions: fudge = 0.5 86: Number of degrees of freedom in T-Coupling group System is 27.00 86: 86: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 86: You are using a plain Coulomb cut-off, which might produce artifacts. 86: You might want to consider using PME electrostatics. 86: 86: 86: 86: There were 3 NOTEs 86: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 86: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 86: 86: Using 1 MPI thread 86: Using 1 OpenMP thread 86: 86: 86: NOTE: Thread affinity was not set. 86: starting mdrun 'spc2' 86: 16 steps, 0.0 ps. 86: Generated 330891 of the 330891 non-bonded parameter combinations 86: 86: Generated 330891 of the 330891 1-4 parameter combinations 86: 86: Excluding 2 bonded neighbours molecule type 'SOL' 86: 86: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/tip3p5.gro' 86: 86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 86: 86: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 86: 86: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 86: 86: Note that mdrun will redetermine rlist based on the actual pair-list setup 86: 86: This run will generate roughly 0 Mb of data 86: 86: Writing final coordinates. 86: 86: Core t (s) Wall t (s) (%) 86: Time: 0.079 0.079 99.7 86: (ns/day) (hour/ns) 86: Performance: 18.577 1.292 86: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_reference.edr as single precision energy file 86: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.edr as single precision energy file 86: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 86: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 86: that with the Verlet scheme, nstlist has no effect on the accuracy of 86: your simulation. 86: 86: 86: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 86: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 86: setting nstcomm equal to nstcalcenergy for less overhead 86: 86: Generating 1-4 interactions: fudge = 0.5 86: Number of degrees of freedom in T-Coupling group System is 27.00 86: 86: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 86: You are using a plain Coulomb cut-off, which might produce artifacts. 86: You might want to consider using PME electrostatics. 86: 86: 86: 86: There were 3 NOTEs 86: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 86: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 86: 86: Using 1 MPI thread 86: Using 1 OpenMP thread 86: 86: 86: NOTE: Thread affinity was not set. 86: starting mdrun 'spc2' 86: 16 steps, 0.0 ps. 86: Generated 330891 of the 330891 non-bonded parameter combinations 86: 86: Generated 330891 of the 330891 1-4 parameter combinations 86: 86: Excluding 2 bonded neighbours molecule type 'SOL' 86: 86: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/tip3p5.gro' 86: 86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 86: 86: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 86: 86: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 86: 86: Note that mdrun will redetermine rlist based on the actual pair-list setup 86: 86: This run will generate roughly 0 Mb of data 86: 86: Writing final coordinates. 86: 86: Core t (s) Wall t (s) (%) 86: Time: 0.102 0.102 99.8 86: (ns/day) (hour/ns) 86: Performance: 14.354 1.672 86: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_reference.edr as single precision energy file 86: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.edr as single precision energy file 86: 86: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 86: that with the Verlet scheme, nstlist has no effect on the accuracy of 86: your simulation. 86: 86: 86: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 86: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 86: setting nstcomm equal to nstcalcenergy for less overhead 86: 86: Generating 1-4 interactions: fudge = 0.5 86: Number of degrees of freedom in T-Coupling group System is 27.00 86: 86: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 86: You are using a plain Coulomb cut-off, which might produce artifacts. 86: You might want to consider using PME electrostatics. 86: 86: 86: 86: There were 3 NOTEs 86: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 86: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 86: 86: Using 1 MPI thread 86: Using 1 OpenMP thread 86: 86: 86: NOTE: Thread affinity was not set. 86: starting mdrun 'spc2' 86: 16 steps, 0.0 ps. 86: Generated 330891 of the 330891 non-bonded parameter combinations 86: 86: Generated 330891 of the 330891 1-4 parameter combinations 86: 86: Excluding 2 bonded neighbours molecule type 'SOL' 86: 86: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/tip3p5.gro' 86: 86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 86: 86: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 86: 86: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 86: 86: Note that mdrun will redetermine rlist based on the actual pair-list setup 86: 86: This run will generate roughly 0 Mb of data 86: 86: Writing final coordinates. 86: 86: Core t (s) Wall t (s) (%) 86: Time: 0.104 0.105 99.7 86: (ns/day) (hour/ns) 86: Performance: 14.040 1.709 86: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_reference.edr as single precision energy file 86: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.edr as single precision energy file 86: 86: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 86: that with the Verlet scheme, nstlist has no effect on the accuracy of 86: your simulation. 86: 86: 86: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 86: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 86: setting nstcomm equal to nstcalcenergy for less overhead 86: 86: Generating 1-4 interactions: fudge = 0.5 86: Number of degrees of freedom in T-Coupling group System is 27.00 86: 86: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 86: You are using a plain Coulomb cut-off, which might produce artifacts. 86: You might want to consider using PME electrostatics. 86: 86: 86: 86: There were 3 NOTEs 86: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 86: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 86: 86: Using 1 MPI thread 86: Using 1 OpenMP thread 86: 86: 86: NOTE: Thread affinity was not set. 86: starting mdrun 'spc2' 86: 16 steps, 0.0 ps. 86: Generated 330891 of the 330891 non-bonded parameter combinations 86: 86: Generated 330891 of the 330891 1-4 parameter combinations 86: 86: Excluding 2 bonded neighbours molecule type 'SOL' 86: 86: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/tip3p5.gro' 86: 86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 86: 86: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 86: 86: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 86: 86: Note that mdrun will redetermine rlist based on the actual pair-list setup 86: 86: This run will generate roughly 0 Mb of data 86: 86: Writing final coordinates. 86: 86: Core t (s) Wall t (s) (%) 86: Time: 0.048 0.048 99.5 86: (ns/day) (hour/ns) 86: Performance: 30.431 0.789 86: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_reference.edr as single precision energy file 86: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.edr as single precision energy file 86: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/12 (27492 ms) 86: [----------] 13 tests from PropagatorsWithConstraints/PeriodicActionsTest (362097 ms total) 86: 86: [----------] Global test environment tear-down 86: [==========] 13 tests from 1 test suite ran. (362147 ms total) 86: [ PASSED ] 13 tests. 86/92 Test #86: MdrunCoordinationConstraintsTests1Rank .... Passed 362.23 sec test 87 Start 87: MdrunCoordinationConstraintsTests2Ranks 87: Test command: /build/reproducible-path/gromacs-2025.1/build/basic/bin/mdrun-coordination-constraints-test "-ntmpi" "2" "--gtest_output=xml:/build/reproducible-path/gromacs-2025.1/build/basic/Testing/Temporary/MdrunCoordinationConstraintsTests2Ranks.xml" 87: Working Directory: /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests 87: Test timeout computed to be: 1920 87: [==========] Running 13 tests from 1 test suite. 87: [----------] Global test environment set-up. 87: [----------] 13 tests from PropagatorsWithConstraints/PeriodicActionsTest 87: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/0 87: 87: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 87: that with the Verlet scheme, nstlist has no effect on the accuracy of 87: your simulation. 87: 87: 87: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 87: Setting nstcalcenergy (100) equal to nstenergy (1) 87: 87: Generating 1-4 interactions: fudge = 0.5 87: Number of degrees of freedom in T-Coupling group System is 27.00 87: 87: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 87: NVE simulation: will use the initial temperature of 398.997 K for 87: determining the Verlet buffer size 87: 87: 87: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 87: You are using a plain Coulomb cut-off, which might produce artifacts. 87: You might want to consider using PME electrostatics. 87: 87: 87: 87: There were 4 NOTEs 87: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 87: Can not increase nstlist because an NVE ensemble is used 87: Using 2 MPI threads 87: Using 1 OpenMP thread per tMPI thread 87: 87: 87: NOTE: The number of threads is not equal to the number of (logical) cpus 87: and the -pin option is set to auto: will not pin threads to cpus. 87: This can lead to significant performance degradation. 87: Consider using -pin on (and -pinoffset in case you run multiple jobs). 87: starting mdrun 'spc2' 87: 16 steps, 0.0 ps. 87: Generated 330891 of the 330891 non-bonded parameter combinations 87: 87: Generated 330891 of the 330891 1-4 parameter combinations 87: 87: Excluding 2 bonded neighbours molecule type 'SOL' 87: 87: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/tip3p5.gro' 87: 87: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 87: 87: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 87: 87: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 87: 87: Note that mdrun will redetermine rlist based on the actual pair-list setup 87: 87: This run will generate roughly 0 Mb of data 87: 87: Writing final coordinates. 87: 87: 87: Dynamic load balancing report: 87: DLB was off during the run due to low measured imbalance. 87: Average load imbalance: 2.8%. 87: The balanceable part of the MD step is 56%, load imbalance is computed from this. 87: Part of the total run time spent waiting due to load imbalance: 1.6%. 87: 87: 87: NOTE: 45 % of the run time was spent communicating energies, 87: you might want to increase some nst* mdp options 87: 87: Core t (s) Wall t (s) (%) 87: Time: 0.112 0.056 198.7 87: (ns/day) (hour/ns) 87: Performance: 26.155 0.918 87: 87: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 87: that with the Verlet scheme, nstlist has no effect on the accuracy of 87: your simulation. 87: 87: 87: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 87: Setting nstcalcenergy (100) equal to nstenergy (1) 87: 87: Generating 1-4 interactions: fudge = 0.5 87: Number of degrees of freedom in T-Coupling group System is 27.00 87: 87: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 87: NVE simulation: will use the initial temperature of 398.997 K for 87: determining the Verlet buffer size 87: 87: 87: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 87: You are using a plain Coulomb cut-off, which might produce artifacts. 87: You might want to consider using PME electrostatics. 87: 87: 87: 87: There were 4 NOTEs 87: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 87: Can not increase nstlist because an NVE ensemble is used 87: Using 2 MPI threads 87: Using 1 OpenMP thread per tMPI thread 87: 87: 87: NOTE: The number of threads is not equal to the number of (logical) cpus 87: and the -pin option is set to auto: will not pin threads to cpus. 87: This can lead to significant performance degradation. 87: Consider using -pin on (and -pinoffset in case you run multiple jobs). 87: starting mdrun 'spc2' 87: 16 steps, 0.0 ps. 87: Generated 330891 of the 330891 non-bonded parameter combinations 87: 87: Generated 330891 of the 330891 1-4 parameter combinations 87: 87: Excluding 2 bonded neighbours molecule type 'SOL' 87: 87: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/tip3p5.gro' 87: 87: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 87: 87: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 87: 87: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 87: 87: Note that mdrun will redetermine rlist based on the actual pair-list setup 87: 87: This run will generate roughly 0 Mb of data 87: 87: Writing final coordinates. 87: 87: 87: Dynamic load balancing report: 87: DLB got disabled because it was unsuitable to use. 87: Average load imbalance: 5.4%. 87: The balanceable part of the MD step is 51%, load imbalance is computed from this. 87: Part of the total run time spent waiting due to load imbalance: 2.8%. 87: 87: 87: NOTE: 45 % of the run time was spent communicating energies, 87: you might want to increase some nst* mdp options 87: 87: Core t (s) Wall t (s) (%) 87: Time: 0.101 0.055 184.2 87: (ns/day) (hour/ns) 87: Performance: 26.839 0.894 87: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as single precision energy file 87: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as single precision energy file 87: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 87: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 87: that with the Verlet scheme, nstlist has no effect on the accuracy of 87: your simulation. 87: 87: 87: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 87: Setting nstcalcenergy (100) equal to nstenergy (4) 87: 87: Generating 1-4 interactions: fudge = 0.5 87: Number of degrees of freedom in T-Coupling group System is 27.00 87: 87: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 87: NVE simulation: will use the initial temperature of 398.997 K for 87: determining the Verlet buffer size 87: 87: 87: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 87: You are using a plain Coulomb cut-off, which might produce artifacts. 87: You might want to consider using PME electrostatics. 87: 87: 87: 87: NOTE 5 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 87: COM removal frequency is set to (5). 87: Other settings require a global communication frequency of 4. 87: Note that this will require additional global communication steps, 87: which will reduce performance when using multiple ranks. 87: Consider setting nstcomm to a multiple of 4. 87: 87: 87: There were 5 NOTEs 87: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 87: Can not increase nstlist because an NVE ensemble is used 87: Using 2 MPI threads 87: Using 1 OpenMP thread per tMPI thread 87: 87: 87: NOTE: The number of threads is not equal to the number of (logical) cpus 87: and the -pin option is set to auto: will not pin threads to cpus. 87: This can lead to significant performance degradation. 87: Consider using -pin on (and -pinoffset in case you run multiple jobs). 87: starting mdrun 'spc2' 87: 16 steps, 0.0 ps. 87: Generated 330891 of the 330891 non-bonded parameter combinations 87: 87: Generated 330891 of the 330891 1-4 parameter combinations 87: 87: Excluding 2 bonded neighbours molecule type 'SOL' 87: 87: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/tip3p5.gro' 87: 87: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 87: 87: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 87: 87: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 87: 87: Note that mdrun will redetermine rlist based on the actual pair-list setup 87: 87: This run will generate roughly 0 Mb of data 87: 87: Writing final coordinates. 87: 87: 87: Dynamic load balancing report: 87: DLB was off during the run due to low measured imbalance. 87: Average load imbalance: 5.8%. 87: The balanceable part of the MD step is 31%, load imbalance is computed from this. 87: Part of the total run time spent waiting due to load imbalance: 1.8%. 87: 87: 87: NOTE: 58 % of the run time was spent communicating energies, 87: you might want to increase some nst* mdp options 87: 87: Core t (s) Wall t (s) (%) 87: Time: 0.092 0.047 197.7 87: (ns/day) (hour/ns) 87: Performance: 31.464 0.763 87: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as single precision energy file 87: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as single precision energy file 87: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 87: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 87: that with the Verlet scheme, nstlist has no effect on the accuracy of 87: your simulation. 87: 87: 87: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 87: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 87: setting nstcomm equal to nstcalcenergy for less overhead 87: 87: Generating 1-4 interactions: fudge = 0.5 87: Number of degrees of freedom in T-Coupling group System is 27.00 87: 87: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 87: NVE simulation: will use the initial temperature of 398.997 K for 87: determining the Verlet buffer size 87: 87: 87: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 87: You are using a plain Coulomb cut-off, which might produce artifacts. 87: You might want to consider using PME electrostatics. 87: 87: 87: 87: NOTE 5 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 87: COM removal frequency is set to (5). 87: Other settings require a global communication frequency of 100. 87: Note that this will require additional global communication steps, 87: which will reduce performance when using multiple ranks. 87: Consider setting nstcomm to a multiple of 100. 87: 87: 87: There were 5 NOTEs 87: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 87: Can not increase nstlist because an NVE ensemble is used 87: Using 2 MPI threads 87: Using 1 OpenMP thread per tMPI thread 87: 87: 87: NOTE: The number of threads is not equal to the number of (logical) cpus 87: and the -pin option is set to auto: will not pin threads to cpus. 87: This can lead to significant performance degradation. 87: Consider using -pin on (and -pinoffset in case you run multiple jobs). 87: starting mdrun 'spc2' 87: 16 steps, 0.0 ps. 87: Generated 330891 of the 330891 non-bonded parameter combinations 87: 87: Generated 330891 of the 330891 1-4 parameter combinations 87: 87: Excluding 2 bonded neighbours molecule type 'SOL' 87: 87: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/tip3p5.gro' 87: 87: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 87: 87: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 87: 87: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 87: 87: Note that mdrun will redetermine rlist based on the actual pair-list setup 87: 87: This run will generate roughly 0 Mb of data 87: 87: Writing final coordinates. 87: 87: 87: Dynamic load balancing report: 87: DLB got disabled because it was unsuitable to use. 87: Average load imbalance: 6.9%. 87: The balanceable part of the MD step is 45%, load imbalance is computed from this. 87: Part of the total run time spent waiting due to load imbalance: 3.1%. 87: 87: 87: NOTE: 43 % of the run time was spent communicating energies, 87: you might want to increase some nst* mdp options 87: 87: Core t (s) Wall t (s) (%) 87: Time: 0.057 0.029 197.8 87: (ns/day) (hour/ns) 87: Performance: 50.906 0.471 87: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as single precision energy file 87: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as single precision energy file 87: 87: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 87: that with the Verlet scheme, nstlist has no effect on the accuracy of 87: your simulation. 87: 87: 87: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 87: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 87: setting nstcomm equal to nstcalcenergy for less overhead 87: 87: Generating 1-4 interactions: fudge = 0.5 87: Number of degrees of freedom in T-Coupling group System is 27.00 87: 87: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 87: NVE simulation: will use the initial temperature of 398.997 K for 87: determining the Verlet buffer size 87: 87: 87: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 87: You are using a plain Coulomb cut-off, which might produce artifacts. 87: You might want to consider using PME electrostatics. 87: 87: 87: 87: NOTE 5 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 87: COM removal frequency is set to (5). 87: Other settings require a global communication frequency of 100. 87: Note that this will require additional global communication steps, 87: which will reduce performance when using multiple ranks. 87: Consider setting nstcomm to a multiple of 100. 87: 87: 87: There were 5 NOTEs 87: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 87: Can not increase nstlist because an NVE ensemble is used 87: Using 2 MPI threads 87: Using 1 OpenMP thread per tMPI thread 87: 87: 87: NOTE: The number of threads is not equal to the number of (logical) cpus 87: and the -pin option is set to auto: will not pin threads to cpus. 87: This can lead to significant performance degradation. 87: Consider using -pin on (and -pinoffset in case you run multiple jobs). 87: starting mdrun 'spc2' 87: 16 steps, 0.0 ps. 87: Generated 330891 of the 330891 non-bonded parameter combinations 87: 87: Generated 330891 of the 330891 1-4 parameter combinations 87: 87: Excluding 2 bonded neighbours molecule type 'SOL' 87: 87: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/tip3p5.gro' 87: 87: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 87: 87: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 87: 87: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 87: 87: Note that mdrun will redetermine rlist based on the actual pair-list setup 87: 87: This run will generate roughly 0 Mb of data 87: 87: Writing final coordinates. 87: 87: 87: Dynamic load balancing report: 87: DLB was off during the run due to low measured imbalance. 87: Average load imbalance: 4.7%. 87: The balanceable part of the MD step is 18%, load imbalance is computed from this. 87: Part of the total run time spent waiting due to load imbalance: 0.8%. 87: 87: 87: NOTE: 41 % of the run time was spent communicating energies, 87: you might want to increase some nst* mdp options 87: 87: Core t (s) Wall t (s) (%) 87: Time: 0.109 0.055 198.9 87: (ns/day) (hour/ns) 87: Performance: 26.826 0.895 87: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as single precision energy file 87: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as single precision energy file 87: 87: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 87: that with the Verlet scheme, nstlist has no effect on the accuracy of 87: your simulation. 87: 87: 87: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 87: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 87: setting nstcomm equal to nstcalcenergy for less overhead 87: 87: Generating 1-4 interactions: fudge = 0.5 87: Number of degrees of freedom in T-Coupling group System is 27.00 87: 87: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 87: NVE simulation: will use the initial temperature of 398.997 K for 87: determining the Verlet buffer size 87: 87: 87: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 87: You are using a plain Coulomb cut-off, which might produce artifacts. 87: You might want to consider using PME electrostatics. 87: 87: 87: 87: NOTE 5 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 87: COM removal frequency is set to (5). 87: Other settings require a global communication frequency of 100. 87: Note that this will require additional global communication steps, 87: which will reduce performance when using multiple ranks. 87: Consider setting nstcomm to a multiple of 100. 87: 87: 87: There were 5 NOTEs 87: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 87: Can not increase nstlist because an NVE ensemble is used 87: Using 2 MPI threads 87: Using 1 OpenMP thread per tMPI thread 87: 87: 87: NOTE: The number of threads is not equal to the number of (logical) cpus 87: and the -pin option is set to auto: will not pin threads to cpus. 87: This can lead to significant performance degradation. 87: Consider using -pin on (and -pinoffset in case you run multiple jobs). 87: starting mdrun 'spc2' 87: 16 steps, 0.0 ps. 87: Generated 330891 of the 330891 non-bonded parameter combinations 87: 87: Generated 330891 of the 330891 1-4 parameter combinations 87: 87: Excluding 2 bonded neighbours molecule type 'SOL' 87: 87: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/tip3p5.gro' 87: 87: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 87: 87: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 87: 87: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 87: 87: Note that mdrun will redetermine rlist based on the actual pair-list setup 87: 87: This run will generate roughly 0 Mb of data 87: 87: Writing final coordinates. 87: 87: 87: Dynamic load balancing report: 87: DLB was off during the run due to low measured imbalance. 87: Average load imbalance: 6.6%. 87: The balanceable part of the MD step is 19%, load imbalance is computed from this. 87: Part of the total run time spent waiting due to load imbalance: 1.2%. 87: 87: 87: NOTE: 49 % of the run time was spent communicating energies, 87: you might want to increase some nst* mdp options 87: 87: Core t (s) Wall t (s) (%) 87: Time: 0.221 0.111 199.3 87: (ns/day) (hour/ns) 87: Performance: 13.264 1.809 87: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as single precision energy file 87: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as single precision energy file 87: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/0 (28180 ms) 87: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/1 87: 87: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 87: that with the Verlet scheme, nstlist has no effect on the accuracy of 87: your simulation. 87: 87: 87: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 87: Setting nstcalcenergy (100) equal to nstenergy (1) 87: 87: Generating 1-4 interactions: fudge = 0.5 87: Number of degrees of freedom in T-Coupling group System is 27.00 87: 87: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 87: NVE simulation: will use the initial temperature of 398.997 K for 87: determining the Verlet buffer size 87: 87: 87: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 87: You are using a plain Coulomb cut-off, which might produce artifacts. 87: You might want to consider using PME electrostatics. 87: 87: 87: 87: There were 4 NOTEs 87: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 87: Can not increase nstlist because an NVE ensemble is used 87: Using 2 MPI threads 87: Using 1 OpenMP thread per tMPI thread 87: 87: 87: NOTE: The number of threads is not equal to the number of (logical) cpus 87: and the -pin option is set to auto: will not pin threads to cpus. 87: This can lead to significant performance degradation. 87: Consider using -pin on (and -pinoffset in case you run multiple jobs). 87: starting mdrun 'spc2' 87: 16 steps, 0.0 ps. 87: Generated 330891 of the 330891 non-bonded parameter combinations 87: 87: Generated 330891 of the 330891 1-4 parameter combinations 87: 87: Excluding 2 bonded neighbours molecule type 'SOL' 87: 87: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/tip3p5.gro' 87: 87: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 87: 87: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 87: 87: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 87: 87: Note that mdrun will redetermine rlist based on the actual pair-list setup 87: 87: This run will generate roughly 0 Mb of data 87: 87: Writing final coordinates. 87: 87: 87: Dynamic load balancing report: 87: DLB was off during the run due to low measured imbalance. 87: Average load imbalance: 4.0%. 87: The balanceable part of the MD step is 37%, load imbalance is computed from this. 87: Part of the total run time spent waiting due to load imbalance: 1.5%. 87: 87: 87: NOTE: 40 % of the run time was spent communicating energies, 87: you might want to increase some nst* mdp options 87: 87: Core t (s) Wall t (s) (%) 87: Time: 0.095 0.048 198.4 87: (ns/day) (hour/ns) 87: Performance: 30.829 0.778 87: 87: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 87: that with the Verlet scheme, nstlist has no effect on the accuracy of 87: your simulation. 87: 87: 87: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 87: Setting nstcalcenergy (100) equal to nstenergy (1) 87: 87: Generating 1-4 interactions: fudge = 0.5 87: Number of degrees of freedom in T-Coupling group System is 27.00 87: 87: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 87: NVE simulation: will use the initial temperature of 398.997 K for 87: determining the Verlet buffer size 87: 87: 87: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 87: You are using a plain Coulomb cut-off, which might produce artifacts. 87: You might want to consider using PME electrostatics. 87: 87: 87: 87: There were 4 NOTEs 87: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 87: Can not increase nstlist because an NVE ensemble is used 87: Using 2 MPI threads 87: Using 1 OpenMP thread per tMPI thread 87: 87: 87: NOTE: The number of threads is not equal to the number of (logical) cpus 87: and the -pin option is set to auto: will not pin threads to cpus. 87: This can lead to significant performance degradation. 87: Consider using -pin on (and -pinoffset in case you run multiple jobs). 87: starting mdrun 'spc2' 87: 16 steps, 0.0 ps. 87: Generated 330891 of the 330891 non-bonded parameter combinations 87: 87: Generated 330891 of the 330891 1-4 parameter combinations 87: 87: Excluding 2 bonded neighbours molecule type 'SOL' 87: 87: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/tip3p5.gro' 87: 87: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 87: 87: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 87: 87: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 87: 87: Note that mdrun will redetermine rlist based on the actual pair-list setup 87: 87: This run will generate roughly 0 Mb of data 87: 87: Writing final coordinates. 87: 87: 87: Dynamic load balancing report: 87: DLB got disabled because it was unsuitable to use. 87: Average load imbalance: 4.0%. 87: The balanceable part of the MD step is 53%, load imbalance is computed from this. 87: Part of the total run time spent waiting due to load imbalance: 2.1%. 87: 87: 87: NOTE: 48 % of the run time was spent communicating energies, 87: you might want to increase some nst* mdp options 87: 87: Core t (s) Wall t (s) (%) 87: Time: 0.218 0.109 199.3 87: (ns/day) (hour/ns) 87: Performance: 13.427 1.787 87: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as single precision energy file 87: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as single precision energy file 87: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 87: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 87: that with the Verlet scheme, nstlist has no effect on the accuracy of 87: your simulation. 87: 87: 87: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 87: Setting nstcalcenergy (100) equal to nstenergy (4) 87: 87: Generating 1-4 interactions: fudge = 0.5 87: Number of degrees of freedom in T-Coupling group System is 27.00 87: 87: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 87: NVE simulation: will use the initial temperature of 398.997 K for 87: determining the Verlet buffer size 87: 87: 87: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 87: You are using a plain Coulomb cut-off, which might produce artifacts. 87: You might want to consider using PME electrostatics. 87: 87: 87: 87: There were 4 NOTEs 87: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 87: Can not increase nstlist because an NVE ensemble is used 87: Using 2 MPI threads 87: Using 1 OpenMP thread per tMPI thread 87: 87: 87: NOTE: The number of threads is not equal to the number of (logical) cpus 87: and the -pin option is set to auto: will not pin threads to cpus. 87: This can lead to significant performance degradation. 87: Consider using -pin on (and -pinoffset in case you run multiple jobs). 87: starting mdrun 'spc2' 87: 16 steps, 0.0 ps. 87: Generated 330891 of the 330891 non-bonded parameter combinations 87: 87: Generated 330891 of the 330891 1-4 parameter combinations 87: 87: Excluding 2 bonded neighbours molecule type 'SOL' 87: 87: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/tip3p5.gro' 87: 87: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 87: 87: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 87: 87: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 87: 87: Note that mdrun will redetermine rlist based on the actual pair-list setup 87: 87: This run will generate roughly 0 Mb of data 87: 87: Writing final coordinates. 87: 87: 87: Dynamic load balancing report: 87: DLB was off during the run due to low measured imbalance. 87: Average load imbalance: 3.9%. 87: The balanceable part of the MD step is 51%, load imbalance is computed from this. 87: Part of the total run time spent waiting due to load imbalance: 2.0%. 87: 87: 87: NOTE: 41 % of the run time was spent communicating energies, 87: you might want to increase some nst* mdp options 87: 87: Core t (s) Wall t (s) (%) 87: Time: 0.039 0.020 196.7 87: (ns/day) (hour/ns) 87: Performance: 74.570 0.322 87: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as single precision energy file 87: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as single precision energy file 87: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 87: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 87: that with the Verlet scheme, nstlist has no effect on the accuracy of 87: your simulation. 87: 87: 87: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 87: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 87: setting nstcomm equal to nstcalcenergy for less overhead 87: 87: Generating 1-4 interactions: fudge = 0.5 87: Number of degrees of freedom in T-Coupling group System is 27.00 87: 87: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 87: NVE simulation: will use the initial temperature of 398.997 K for 87: determining the Verlet buffer size 87: 87: 87: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 87: You are using a plain Coulomb cut-off, which might produce artifacts. 87: You might want to consider using PME electrostatics. 87: 87: 87: 87: There were 4 NOTEs 87: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 87: Can not increase nstlist because an NVE ensemble is used 87: Using 2 MPI threads 87: Using 1 OpenMP thread per tMPI thread 87: 87: 87: NOTE: The number of threads is not equal to the number of (logical) cpus 87: and the -pin option is set to auto: will not pin threads to cpus. 87: This can lead to significant performance degradation. 87: Consider using -pin on (and -pinoffset in case you run multiple jobs). 87: starting mdrun 'spc2' 87: 16 steps, 0.0 ps. 87: Generated 330891 of the 330891 non-bonded parameter combinations 87: 87: Generated 330891 of the 330891 1-4 parameter combinations 87: 87: Excluding 2 bonded neighbours molecule type 'SOL' 87: 87: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/tip3p5.gro' 87: 87: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 87: 87: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 87: 87: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 87: 87: Note that mdrun will redetermine rlist based on the actual pair-list setup 87: 87: This run will generate roughly 0 Mb of data 87: 87: Writing final coordinates. 87: 87: 87: Dynamic load balancing report: 87: DLB got disabled because it was unsuitable to use. 87: Average load imbalance: 16.9%. 87: The balanceable part of the MD step is 48%, load imbalance is computed from this. 87: Part of the total run time spent waiting due to load imbalance: 8.1%. 87: 87: NOTE: 8.1 % of the available CPU time was lost due to load imbalance 87: in the domain decomposition. 87: You can consider manually changing the decomposition (option -dd); 87: e.g. by using fewer domains along the box dimension in which there is 87: considerable inhomogeneity in the simulated system. 87: 87: NOTE: 44 % of the run time was spent communicating energies, 87: you might want to increase some nst* mdp options 87: 87: Core t (s) Wall t (s) (%) 87: Time: 0.061 0.031 197.8 87: (ns/day) (hour/ns) 87: Performance: 47.311 0.507 87: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as single precision energy file 87: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as single precision energy file 87: 87: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 87: that with the Verlet scheme, nstlist has no effect on the accuracy of 87: your simulation. 87: 87: 87: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 87: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 87: setting nstcomm equal to nstcalcenergy for less overhead 87: 87: Generating 1-4 interactions: fudge = 0.5 87: Number of degrees of freedom in T-Coupling group System is 27.00 87: 87: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 87: NVE simulation: will use the initial temperature of 398.997 K for 87: determining the Verlet buffer size 87: 87: 87: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 87: You are using a plain Coulomb cut-off, which might produce artifacts. 87: You might want to consider using PME electrostatics. 87: 87: 87: 87: There were 4 NOTEs 87: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 87: Can not increase nstlist because an NVE ensemble is used 87: Using 2 MPI threads 87: Using 1 OpenMP thread per tMPI thread 87: 87: 87: NOTE: The number of threads is not equal to the number of (logical) cpus 87: and the -pin option is set to auto: will not pin threads to cpus. 87: This can lead to significant performance degradation. 87: Consider using -pin on (and -pinoffset in case you run multiple jobs). 87: starting mdrun 'spc2' 87: 16 steps, 0.0 ps. 87: Generated 330891 of the 330891 non-bonded parameter combinations 87: 87: Generated 330891 of the 330891 1-4 parameter combinations 87: 87: Excluding 2 bonded neighbours molecule type 'SOL' 87: 87: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/tip3p5.gro' 87: 87: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 87: 87: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 87: 87: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 87: 87: Note that mdrun will redetermine rlist based on the actual pair-list setup 87: 87: This run will generate roughly 0 Mb of data 87: 87: Writing final coordinates. 87: 87: 87: Dynamic load balancing report: 87: DLB got disabled because it was unsuitable to use. 87: Average load imbalance: 5.7%. 87: The balanceable part of the MD step is 51%, load imbalance is computed from this. 87: Part of the total run time spent waiting due to load imbalance: 2.9%. 87: 87: 87: NOTE: 43 % of the run time was spent communicating energies, 87: you might want to increase some nst* mdp options 87: 87: Core t (s) Wall t (s) (%) 87: Time: 0.052 0.027 197.4 87: (ns/day) (hour/ns) 87: Performance: 55.405 0.433 87: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as single precision energy file 87: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as single precision energy file 87: 87: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 87: that with the Verlet scheme, nstlist has no effect on the accuracy of 87: your simulation. 87: 87: 87: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 87: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 87: setting nstcomm equal to nstcalcenergy for less overhead 87: 87: Generating 1-4 interactions: fudge = 0.5 87: Number of degrees of freedom in T-Coupling group System is 27.00 87: 87: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 87: NVE simulation: will use the initial temperature of 398.997 K for 87: determining the Verlet buffer size 87: 87: 87: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 87: You are using a plain Coulomb cut-off, which might produce artifacts. 87: You might want to consider using PME electrostatics. 87: 87: 87: 87: There were 4 NOTEs 87: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 87: Can not increase nstlist because an NVE ensemble is used 87: Using 2 MPI threads 87: Using 1 OpenMP thread per tMPI thread 87: 87: 87: NOTE: The number of threads is not equal to the number of (logical) cpus 87: and the -pin option is set to auto: will not pin threads to cpus. 87: This can lead to significant performance degradation. 87: Consider using -pin on (and -pinoffset in case you run multiple jobs). 87: starting mdrun 'spc2' 87: 16 steps, 0.0 ps. 87: Generated 330891 of the 330891 non-bonded parameter combinations 87: 87: Generated 330891 of the 330891 1-4 parameter combinations 87: 87: Excluding 2 bonded neighbours molecule type 'SOL' 87: 87: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/tip3p5.gro' 87: 87: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 87: 87: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 87: 87: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 87: 87: Note that mdrun will redetermine rlist based on the actual pair-list setup 87: 87: This run will generate roughly 0 Mb of data 87: 87: Writing final coordinates. 87: 87: 87: Dynamic load balancing report: 87: DLB got disabled because it was unsuitable to use. 87: Average load imbalance: 5.8%. 87: The balanceable part of the MD step is 39%, load imbalance is computed from this. 87: Part of the total run time spent waiting due to load imbalance: 2.2%. 87: 87: 87: NOTE: 42 % of the run time was spent communicating energies, 87: you might want to increase some nst* mdp options 87: 87: Core t (s) Wall t (s) (%) 87: Time: 0.044 0.023 197.0 87: (ns/day) (hour/ns) 87: Performance: 65.030 0.369 87: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as single precision energy file 87: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as single precision energy file 87: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/1 (28490 ms) 87: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/2 87: 87: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 87: that with the Verlet scheme, nstlist has no effect on the accuracy of 87: your simulation. 87: 87: 87: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 87: Setting nstcalcenergy (100) equal to nstenergy (1) 87: 87: Generating 1-4 interactions: fudge = 0.5 87: Number of degrees of freedom in T-Coupling group System is 27.00 87: 87: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 87: NVE simulation: will use the initial temperature of 398.997 K for 87: determining the Verlet buffer size 87: 87: 87: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 87: You are using a plain Coulomb cut-off, which might produce artifacts. 87: You might want to consider using PME electrostatics. 87: 87: 87: 87: There were 4 NOTEs 87: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 87: Can not increase nstlist because an NVE ensemble is used 87: Using 2 MPI threads 87: Using 1 OpenMP thread per tMPI thread 87: 87: 87: NOTE: The number of threads is not equal to the number of (logical) cpus 87: and the -pin option is set to auto: will not pin threads to cpus. 87: This can lead to significant performance degradation. 87: Consider using -pin on (and -pinoffset in case you run multiple jobs). 87: starting mdrun 'spc2' 87: 16 steps, 0.0 ps. 87: Generated 330891 of the 330891 non-bonded parameter combinations 87: 87: Generated 330891 of the 330891 1-4 parameter combinations 87: 87: Excluding 2 bonded neighbours molecule type 'SOL' 87: 87: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/tip3p5.gro' 87: 87: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 87: 87: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 87: 87: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 87: 87: Note that mdrun will redetermine rlist based on the actual pair-list setup 87: 87: This run will generate roughly 0 Mb of data 87: 87: Writing final coordinates. 87: 87: 87: Dynamic load balancing report: 87: DLB got disabled because it was unsuitable to use. 87: Average load imbalance: 3.9%. 87: The balanceable part of the MD step is 57%, load imbalance is computed from this. 87: Part of the total run time spent waiting due to load imbalance: 2.2%. 87: 87: 87: NOTE: 43 % of the run time was spent communicating energies, 87: you might want to increase some nst* mdp options 87: 87: Core t (s) Wall t (s) (%) 87: Time: 0.080 0.040 198.3 87: (ns/day) (hour/ns) 87: Performance: 36.278 0.662 87: 87: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 87: that with the Verlet scheme, nstlist has no effect on the accuracy of 87: your simulation. 87: 87: 87: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 87: Setting nstcalcenergy (100) equal to nstenergy (1) 87: 87: Generating 1-4 interactions: fudge = 0.5 87: Number of degrees of freedom in T-Coupling group System is 27.00 87: 87: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 87: NVE simulation: will use the initial temperature of 398.997 K for 87: determining the Verlet buffer size 87: 87: 87: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 87: You are using a plain Coulomb cut-off, which might produce artifacts. 87: You might want to consider using PME electrostatics. 87: 87: 87: 87: There were 4 NOTEs 87: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 87: Can not increase nstlist because an NVE ensemble is used 87: Using 2 MPI threads 87: Using 1 OpenMP thread per tMPI thread 87: 87: 87: NOTE: The number of threads is not equal to the number of (logical) cpus 87: and the -pin option is set to auto: will not pin threads to cpus. 87: This can lead to significant performance degradation. 87: Consider using -pin on (and -pinoffset in case you run multiple jobs). 87: starting mdrun 'spc2' 87: 16 steps, 0.0 ps. 87: Generated 330891 of the 330891 non-bonded parameter combinations 87: 87: Generated 330891 of the 330891 1-4 parameter combinations 87: 87: Excluding 2 bonded neighbours molecule type 'SOL' 87: 87: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/tip3p5.gro' 87: 87: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 87: 87: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 87: 87: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 87: 87: Note that mdrun will redetermine rlist based on the actual pair-list setup 87: 87: This run will generate roughly 0 Mb of data 87: 87: Writing final coordinates. 87: 87: 87: Dynamic load balancing report: 87: DLB got disabled because it was unsuitable to use. 87: Average load imbalance: 11.4%. 87: The balanceable part of the MD step is 45%, load imbalance is computed from this. 87: Part of the total run time spent waiting due to load imbalance: 5.1%. 87: 87: NOTE: 5.1 % of the available CPU time was lost due to load imbalance 87: in the domain decomposition. 87: You can consider manually changing the decomposition (option -dd); 87: e.g. by using fewer domains along the box dimension in which there is 87: considerable inhomogeneity in the simulated system. 87: 87: NOTE: 44 % of the run time was spent communicating energies, 87: you might want to increase some nst* mdp options 87: 87: Core t (s) Wall t (s) (%) 87: Time: 0.092 0.046 198.6 87: (ns/day) (hour/ns) 87: Performance: 31.722 0.757 87: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as single precision energy file 87: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as single precision energy file 87: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 87: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 87: that with the Verlet scheme, nstlist has no effect on the accuracy of 87: your simulation. 87: 87: 87: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 87: Setting nstcalcenergy (100) equal to nstenergy (4) 87: 87: Generating 1-4 interactions: fudge = 0.5 87: Number of degrees of freedom in T-Coupling group System is 27.00 87: 87: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 87: NVE simulation: will use the initial temperature of 398.997 K for 87: determining the Verlet buffer size 87: 87: 87: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 87: You are using a plain Coulomb cut-off, which might produce artifacts. 87: You might want to consider using PME electrostatics. 87: 87: 87: 87: There were 4 NOTEs 87: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 87: Can not increase nstlist because an NVE ensemble is used 87: Using 2 MPI threads 87: Using 1 OpenMP thread per tMPI thread 87: 87: 87: NOTE: The number of threads is not equal to the number of (logical) cpus 87: and the -pin option is set to auto: will not pin threads to cpus. 87: This can lead to significant performance degradation. 87: Consider using -pin on (and -pinoffset in case you run multiple jobs). 87: starting mdrun 'spc2' 87: 16 steps, 0.0 ps. 87: Generated 330891 of the 330891 non-bonded parameter combinations 87: 87: Generated 330891 of the 330891 1-4 parameter combinations 87: 87: Excluding 2 bonded neighbours molecule type 'SOL' 87: 87: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/tip3p5.gro' 87: 87: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 87: 87: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 87: 87: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 87: 87: Note that mdrun will redetermine rlist based on the actual pair-list setup 87: 87: This run will generate roughly 0 Mb of data 87: 87: Writing final coordinates. 87: 87: 87: Dynamic load balancing report: 87: DLB was off during the run due to low measured imbalance. 87: Average load imbalance: 3.9%. 87: The balanceable part of the MD step is 28%, load imbalance is computed from this. 87: Part of the total run time spent waiting due to load imbalance: 1.1%. 87: 87: 87: NOTE: 49 % of the run time was spent communicating energies, 87: you might want to increase some nst* mdp options 87: 87: Core t (s) Wall t (s) (%) 87: Time: 0.144 0.073 199.0 87: (ns/day) (hour/ns) 87: Performance: 20.252 1.185 87: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as single precision energy file 87: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as single precision energy file 87: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 87: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 87: that with the Verlet scheme, nstlist has no effect on the accuracy of 87: your simulation. 87: 87: 87: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 87: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 87: setting nstcomm equal to nstcalcenergy for less overhead 87: 87: Generating 1-4 interactions: fudge = 0.5 87: Number of degrees of freedom in T-Coupling group System is 27.00 87: 87: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 87: NVE simulation: will use the initial temperature of 398.997 K for 87: determining the Verlet buffer size 87: 87: 87: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 87: You are using a plain Coulomb cut-off, which might produce artifacts. 87: You might want to consider using PME electrostatics. 87: 87: 87: 87: There were 4 NOTEs 87: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 87: Can not increase nstlist because an NVE ensemble is used 87: Using 2 MPI threads 87: Using 1 OpenMP thread per tMPI thread 87: 87: 87: NOTE: The number of threads is not equal to the number of (logical) cpus 87: and the -pin option is set to auto: will not pin threads to cpus. 87: This can lead to significant performance degradation. 87: Consider using -pin on (and -pinoffset in case you run multiple jobs). 87: starting mdrun 'spc2' 87: 16 steps, 0.0 ps. 87: Generated 330891 of the 330891 non-bonded parameter combinations 87: 87: Generated 330891 of the 330891 1-4 parameter combinations 87: 87: Excluding 2 bonded neighbours molecule type 'SOL' 87: 87: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/tip3p5.gro' 87: 87: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 87: 87: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 87: 87: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 87: 87: Note that mdrun will redetermine rlist based on the actual pair-list setup 87: 87: This run will generate roughly 0 Mb of data 87: 87: Writing final coordinates. 87: 87: 87: Dynamic load balancing report: 87: DLB got disabled because it was unsuitable to use. 87: Average load imbalance: 5.8%. 87: The balanceable part of the MD step is 51%, load imbalance is computed from this. 87: Part of the total run time spent waiting due to load imbalance: 3.0%. 87: 87: 87: NOTE: 43 % of the run time was spent communicating energies, 87: you might want to increase some nst* mdp options 87: 87: Core t (s) Wall t (s) (%) 87: Time: 0.047 0.024 197.3 87: (ns/day) (hour/ns) 87: Performance: 61.717 0.389 87: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as single precision energy file 87: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as single precision energy file 87: 87: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 87: that with the Verlet scheme, nstlist has no effect on the accuracy of 87: your simulation. 87: 87: 87: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 87: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 87: setting nstcomm equal to nstcalcenergy for less overhead 87: 87: Generating 1-4 interactions: fudge = 0.5 87: Number of degrees of freedom in T-Coupling group System is 27.00 87: 87: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 87: NVE simulation: will use the initial temperature of 398.997 K for 87: determining the Verlet buffer size 87: 87: 87: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 87: You are using a plain Coulomb cut-off, which might produce artifacts. 87: You might want to consider using PME electrostatics. 87: 87: 87: 87: There were 4 NOTEs 87: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 87: Can not increase nstlist because an NVE ensemble is used 87: Using 2 MPI threads 87: Using 1 OpenMP thread per tMPI thread 87: 87: 87: NOTE: The number of threads is not equal to the number of (logical) cpus 87: and the -pin option is set to auto: will not pin threads to cpus. 87: This can lead to significant performance degradation. 87: Consider using -pin on (and -pinoffset in case you run multiple jobs). 87: starting mdrun 'spc2' 87: 16 steps, 0.0 ps. 87: Generated 330891 of the 330891 non-bonded parameter combinations 87: 87: Generated 330891 of the 330891 1-4 parameter combinations 87: 87: Excluding 2 bonded neighbours molecule type 'SOL' 87: 87: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/tip3p5.gro' 87: 87: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 87: 87: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 87: 87: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 87: 87: Note that mdrun will redetermine rlist based on the actual pair-list setup 87: 87: This run will generate roughly 0 Mb of data 87: 87: Writing final coordinates. 87: 87: 87: Dynamic load balancing report: 87: DLB got disabled because it was unsuitable to use. 87: Average load imbalance: 7.1%. 87: The balanceable part of the MD step is 47%, load imbalance is computed from this. 87: Part of the total run time spent waiting due to load imbalance: 3.3%. 87: 87: 87: NOTE: 42 % of the run time was spent communicating energies, 87: you might want to increase some nst* mdp options 87: 87: Core t (s) Wall t (s) (%) 87: Time: 0.044 0.022 197.0 87: (ns/day) (hour/ns) 87: Performance: 65.719 0.365 87: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as single precision energy file 87: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as single precision energy file 87: 87: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 87: that with the Verlet scheme, nstlist has no effect on the accuracy of 87: your simulation. 87: 87: 87: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 87: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 87: setting nstcomm equal to nstcalcenergy for less overhead 87: 87: Generating 1-4 interactions: fudge = 0.5 87: Number of degrees of freedom in T-Coupling group System is 27.00 87: 87: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 87: NVE simulation: will use the initial temperature of 398.997 K for 87: determining the Verlet buffer size 87: 87: 87: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 87: You are using a plain Coulomb cut-off, which might produce artifacts. 87: You might want to consider using PME electrostatics. 87: 87: 87: 87: There were 4 NOTEs 87: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 87: Can not increase nstlist because an NVE ensemble is used 87: Using 2 MPI threads 87: Using 1 OpenMP thread per tMPI thread 87: 87: 87: NOTE: The number of threads is not equal to the number of (logical) cpus 87: and the -pin option is set to auto: will not pin threads to cpus. 87: This can lead to significant performance degradation. 87: Consider using -pin on (and -pinoffset in case you run multiple jobs). 87: starting mdrun 'spc2' 87: 16 steps, 0.0 ps. 87: Generated 330891 of the 330891 non-bonded parameter combinations 87: 87: Generated 330891 of the 330891 1-4 parameter combinations 87: 87: Excluding 2 bonded neighbours molecule type 'SOL' 87: 87: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/tip3p5.gro' 87: 87: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 87: 87: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 87: 87: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 87: 87: Note that mdrun will redetermine rlist based on the actual pair-list setup 87: 87: This run will generate roughly 0 Mb of data 87: 87: Writing final coordinates. 87: 87: 87: Dynamic load balancing report: 87: DLB got disabled because it was unsuitable to use. 87: Average load imbalance: 6.1%. 87: The balanceable part of the MD step is 47%, load imbalance is computed from this. 87: Part of the total run time spent waiting due to load imbalance: 2.9%. 87: 87: 87: NOTE: 41 % of the run time was spent communicating energies, 87: you might want to increase some nst* mdp options 87: 87: Core t (s) Wall t (s) (%) 87: Time: 0.046 0.023 197.1 87: (ns/day) (hour/ns) 87: Performance: 63.341 0.379 87: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as single precision energy file 87: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as single precision energy file 87: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/2 (27277 ms) 87: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/3 87: 87: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 87: that with the Verlet scheme, nstlist has no effect on the accuracy of 87: your simulation. 87: 87: 87: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 87: Setting nstcalcenergy (100) equal to nstenergy (1) 87: 87: Generating 1-4 interactions: fudge = 0.5 87: Number of degrees of freedom in T-Coupling group System is 27.00 87: 87: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 87: You are using a plain Coulomb cut-off, which might produce artifacts. 87: You might want to consider using PME electrostatics. 87: 87: 87: 87: There were 3 NOTEs 87: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 87: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 87: 87: Using 2 MPI threads 87: Using 1 OpenMP thread per tMPI thread 87: 87: 87: NOTE: The number of threads is not equal to the number of (logical) cpus 87: and the -pin option is set to auto: will not pin threads to cpus. 87: This can lead to significant performance degradation. 87: Consider using -pin on (and -pinoffset in case you run multiple jobs). 87: starting mdrun 'spc2' 87: 16 steps, 0.0 ps. 87: Generated 330891 of the 330891 non-bonded parameter combinations 87: 87: Generated 330891 of the 330891 1-4 parameter combinations 87: 87: Excluding 2 bonded neighbours molecule type 'SOL' 87: 87: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/tip3p5.gro' 87: 87: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 87: 87: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 87: 87: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 87: 87: Note that mdrun will redetermine rlist based on the actual pair-list setup 87: 87: This run will generate roughly 0 Mb of data 87: 87: Writing final coordinates. 87: 87: Core t (s) Wall t (s) (%) 87: Time: 0.058 0.029 197.5 87: (ns/day) (hour/ns) 87: Performance: 50.370 0.476 87: 87: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 87: that with the Verlet scheme, nstlist has no effect on the accuracy of 87: your simulation. 87: 87: 87: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 87: Setting nstcalcenergy (100) equal to nstenergy (1) 87: 87: Generating 1-4 interactions: fudge = 0.5 87: Number of degrees of freedom in T-Coupling group System is 27.00 87: 87: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 87: You are using a plain Coulomb cut-off, which might produce artifacts. 87: You might want to consider using PME electrostatics. 87: 87: 87: 87: There were 3 NOTEs 87: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 87: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 87: 87: Using 2 MPI threads 87: Using 1 OpenMP thread per tMPI thread 87: 87: 87: NOTE: The number of threads is not equal to the number of (logical) cpus 87: and the -pin option is set to auto: will not pin threads to cpus. 87: This can lead to significant performance degradation. 87: Consider using -pin on (and -pinoffset in case you run multiple jobs). 87: starting mdrun 'spc2' 87: 16 steps, 0.0 ps. 87: Generated 330891 of the 330891 non-bonded parameter combinations 87: 87: Generated 330891 of the 330891 1-4 parameter combinations 87: 87: Excluding 2 bonded neighbours molecule type 'SOL' 87: 87: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/tip3p5.gro' 87: 87: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 87: 87: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 87: 87: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 87: 87: Note that mdrun will redetermine rlist based on the actual pair-list setup 87: 87: This run will generate roughly 0 Mb of data 87: 87: Writing final coordinates. 87: 87: Core t (s) Wall t (s) (%) 87: Time: 0.044 0.022 196.6 87: (ns/day) (hour/ns) 87: Performance: 66.290 0.362 87: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as single precision energy file 87: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as single precision energy file 87: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 87: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 87: that with the Verlet scheme, nstlist has no effect on the accuracy of 87: your simulation. 87: 87: 87: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 87: Setting nstcalcenergy (100) equal to nstenergy (4) 87: 87: Generating 1-4 interactions: fudge = 0.5 87: Number of degrees of freedom in T-Coupling group System is 27.00 87: 87: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 87: You are using a plain Coulomb cut-off, which might produce artifacts. 87: You might want to consider using PME electrostatics. 87: 87: 87: 87: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 87: COM removal frequency is set to (5). 87: Other settings require a global communication frequency of 2. 87: Note that this will require additional global communication steps, 87: which will reduce performance when using multiple ranks. 87: Consider setting nstcomm to a multiple of 2. 87: 87: 87: There were 4 NOTEs 87: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 87: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 87: 87: Using 2 MPI threads 87: Using 1 OpenMP thread per tMPI thread 87: 87: 87: NOTE: The number of threads is not equal to the number of (logical) cpus 87: and the -pin option is set to auto: will not pin threads to cpus. 87: This can lead to significant performance degradation. 87: Consider using -pin on (and -pinoffset in case you run multiple jobs). 87: starting mdrun 'spc2' 87: 16 steps, 0.0 ps. 87: Generated 330891 of the 330891 non-bonded parameter combinations 87: 87: Generated 330891 of the 330891 1-4 parameter combinations 87: 87: Excluding 2 bonded neighbours molecule type 'SOL' 87: 87: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/tip3p5.gro' 87: 87: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 87: 87: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 87: 87: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 87: 87: Note that mdrun will redetermine rlist based on the actual pair-list setup 87: 87: This run will generate roughly 0 Mb of data 87: 87: Writing final coordinates. 87: 87: Core t (s) Wall t (s) (%) 87: Time: 0.041 0.021 197.0 87: (ns/day) (hour/ns) 87: Performance: 71.422 0.336 87: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as single precision energy file 87: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as single precision energy file 87: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 87: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 87: that with the Verlet scheme, nstlist has no effect on the accuracy of 87: your simulation. 87: 87: 87: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 87: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 87: setting nstcomm equal to nstcalcenergy for less overhead 87: 87: Generating 1-4 interactions: fudge = 0.5 87: Number of degrees of freedom in T-Coupling group System is 27.00 87: 87: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 87: You are using a plain Coulomb cut-off, which might produce artifacts. 87: You might want to consider using PME electrostatics. 87: 87: 87: 87: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 87: COM removal frequency is set to (5). 87: Other settings require a global communication frequency of 2. 87: Note that this will require additional global communication steps, 87: which will reduce performance when using multiple ranks. 87: Consider setting nstcomm to a multiple of 2. 87: 87: 87: There were 4 NOTEs 87: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 87: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 87: 87: Using 2 MPI threads 87: Using 1 OpenMP thread per tMPI thread 87: 87: 87: NOTE: The number of threads is not equal to the number of (logical) cpus 87: and the -pin option is set to auto: will not pin threads to cpus. 87: This can lead to significant performance degradation. 87: Consider using -pin on (and -pinoffset in case you run multiple jobs). 87: starting mdrun 'spc2' 87: 16 steps, 0.0 ps. 87: Generated 330891 of the 330891 non-bonded parameter combinations 87: 87: Generated 330891 of the 330891 1-4 parameter combinations 87: 87: Excluding 2 bonded neighbours molecule type 'SOL' 87: 87: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/tip3p5.gro' 87: 87: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 87: 87: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 87: 87: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 87: 87: Note that mdrun will redetermine rlist based on the actual pair-list setup 87: 87: This run will generate roughly 0 Mb of data 87: 87: Writing final coordinates. 87: 87: Core t (s) Wall t (s) (%) 87: Time: 0.049 0.025 196.8 87: (ns/day) (hour/ns) 87: Performance: 59.416 0.404 87: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as single precision energy file 87: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as single precision energy file 87: 87: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 87: that with the Verlet scheme, nstlist has no effect on the accuracy of 87: your simulation. 87: 87: 87: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 87: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 87: setting nstcomm equal to nstcalcenergy for less overhead 87: 87: Generating 1-4 interactions: fudge = 0.5 87: Number of degrees of freedom in T-Coupling group System is 27.00 87: 87: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 87: You are using a plain Coulomb cut-off, which might produce artifacts. 87: You might want to consider using PME electrostatics. 87: 87: 87: 87: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 87: COM removal frequency is set to (5). 87: Other settings require a global communication frequency of 2. 87: Note that this will require additional global communication steps, 87: which will reduce performance when using multiple ranks. 87: Consider setting nstcomm to a multiple of 2. 87: 87: 87: There were 4 NOTEs 87: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 87: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 87: 87: Using 2 MPI threads 87: Using 1 OpenMP thread per tMPI thread 87: 87: 87: NOTE: The number of threads is not equal to the number of (logical) cpus 87: and the -pin option is set to auto: will not pin threads to cpus. 87: This can lead to significant performance degradation. 87: Consider using -pin on (and -pinoffset in case you run multiple jobs). 87: starting mdrun 'spc2' 87: 16 steps, 0.0 ps. 87: Generated 330891 of the 330891 non-bonded parameter combinations 87: 87: Generated 330891 of the 330891 1-4 parameter combinations 87: 87: Excluding 2 bonded neighbours molecule type 'SOL' 87: 87: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/tip3p5.gro' 87: 87: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 87: 87: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 87: 87: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 87: 87: Note that mdrun will redetermine rlist based on the actual pair-list setup 87: 87: This run will generate roughly 0 Mb of data 87: 87: Writing final coordinates. 87: 87: Core t (s) Wall t (s) (%) 87: Time: 0.048 0.024 197.2 87: (ns/day) (hour/ns) 87: Performance: 60.507 0.397 87: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as single precision energy file 87: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as single precision energy file 87: 87: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 87: that with the Verlet scheme, nstlist has no effect on the accuracy of 87: your simulation. 87: 87: 87: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 87: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 87: setting nstcomm equal to nstcalcenergy for less overhead 87: 87: Generating 1-4 interactions: fudge = 0.5 87: Number of degrees of freedom in T-Coupling group System is 27.00 87: 87: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 87: You are using a plain Coulomb cut-off, which might produce artifacts. 87: You might want to consider using PME electrostatics. 87: 87: 87: 87: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 87: COM removal frequency is set to (5). 87: Other settings require a global communication frequency of 2. 87: Note that this will require additional global communication steps, 87: which will reduce performance when using multiple ranks. 87: Consider setting nstcomm to a multiple of 2. 87: 87: 87: There were 4 NOTEs 87: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 87: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 87: 87: Using 2 MPI threads 87: Using 1 OpenMP thread per tMPI thread 87: 87: 87: NOTE: The number of threads is not equal to the number of (logical) cpus 87: and the -pin option is set to auto: will not pin threads to cpus. 87: This can lead to significant performance degradation. 87: Consider using -pin on (and -pinoffset in case you run multiple jobs). 87: starting mdrun 'spc2' 87: 16 steps, 0.0 ps. 87: Generated 330891 of the 330891 non-bonded parameter combinations 87: 87: Generated 330891 of the 330891 1-4 parameter combinations 87: 87: Excluding 2 bonded neighbours molecule type 'SOL' 87: 87: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/tip3p5.gro' 87: 87: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 87: 87: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 87: 87: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 87: 87: Note that mdrun will redetermine rlist based on the actual pair-list setup 87: 87: This run will generate roughly 0 Mb of data 87: 87: Writing final coordinates. 87: 87: Core t (s) Wall t (s) (%) 87: Time: 0.044 0.022 197.1 87: (ns/day) (hour/ns) 87: Performance: 66.424 0.361 87: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as single precision energy file 87: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as single precision energy file 87: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/3 (27240 ms) 87: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/4 87: 87: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 87: that with the Verlet scheme, nstlist has no effect on the accuracy of 87: your simulation. 87: 87: 87: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 87: Setting nstcalcenergy (100) equal to nstenergy (1) 87: 87: Generating 1-4 interactions: fudge = 0.5 87: Number of degrees of freedom in T-Coupling group System is 27.00 87: 87: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 87: You are using a plain Coulomb cut-off, which might produce artifacts. 87: You might want to consider using PME electrostatics. 87: 87: 87: 87: There were 3 NOTEs 87: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 87: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 87: 87: Using 2 MPI threads 87: Using 1 OpenMP thread per tMPI thread 87: 87: 87: NOTE: The number of threads is not equal to the number of (logical) cpus 87: and the -pin option is set to auto: will not pin threads to cpus. 87: This can lead to significant performance degradation. 87: Consider using -pin on (and -pinoffset in case you run multiple jobs). 87: starting mdrun 'spc2' 87: 16 steps, 0.0 ps. 87: Generated 330891 of the 330891 non-bonded parameter combinations 87: 87: Generated 330891 of the 330891 1-4 parameter combinations 87: 87: Excluding 2 bonded neighbours molecule type 'SOL' 87: 87: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/tip3p5.gro' 87: 87: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 87: 87: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 87: 87: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 87: 87: Note that mdrun will redetermine rlist based on the actual pair-list setup 87: 87: This run will generate roughly 0 Mb of data 87: 87: Writing final coordinates. 87: 87: Core t (s) Wall t (s) (%) 87: Time: 0.089 0.045 198.3 87: (ns/day) (hour/ns) 87: Performance: 32.574 0.737 87: 87: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 87: that with the Verlet scheme, nstlist has no effect on the accuracy of 87: your simulation. 87: 87: 87: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 87: Setting nstcalcenergy (100) equal to nstenergy (1) 87: 87: Generating 1-4 interactions: fudge = 0.5 87: Number of degrees of freedom in T-Coupling group System is 27.00 87: 87: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 87: You are using a plain Coulomb cut-off, which might produce artifacts. 87: You might want to consider using PME electrostatics. 87: 87: 87: 87: There were 3 NOTEs 87: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 87: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 87: 87: Using 2 MPI threads 87: Using 1 OpenMP thread per tMPI thread 87: 87: 87: NOTE: The number of threads is not equal to the number of (logical) cpus 87: and the -pin option is set to auto: will not pin threads to cpus. 87: This can lead to significant performance degradation. 87: Consider using -pin on (and -pinoffset in case you run multiple jobs). 87: starting mdrun 'spc2' 87: 16 steps, 0.0 ps. 87: Generated 330891 of the 330891 non-bonded parameter combinations 87: 87: Generated 330891 of the 330891 1-4 parameter combinations 87: 87: Excluding 2 bonded neighbours molecule type 'SOL' 87: 87: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/tip3p5.gro' 87: 87: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 87: 87: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 87: 87: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 87: 87: Note that mdrun will redetermine rlist based on the actual pair-list setup 87: 87: This run will generate roughly 0 Mb of data 87: 87: Writing final coordinates. 87: 87: Core t (s) Wall t (s) (%) 87: Time: 0.043 0.022 197.1 87: (ns/day) (hour/ns) 87: Performance: 67.721 0.354 87: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as single precision energy file 87: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as single precision energy file 87: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 87: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 87: that with the Verlet scheme, nstlist has no effect on the accuracy of 87: your simulation. 87: 87: 87: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 87: Setting nstcalcenergy (100) equal to nstenergy (4) 87: 87: Generating 1-4 interactions: fudge = 0.5 87: Number of degrees of freedom in T-Coupling group System is 27.00 87: 87: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 87: You are using a plain Coulomb cut-off, which might produce artifacts. 87: You might want to consider using PME electrostatics. 87: 87: 87: 87: There were 3 NOTEs 87: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 87: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 87: 87: Using 2 MPI threads 87: Using 1 OpenMP thread per tMPI thread 87: 87: 87: NOTE: The number of threads is not equal to the number of (logical) cpus 87: and the -pin option is set to auto: will not pin threads to cpus. 87: This can lead to significant performance degradation. 87: Consider using -pin on (and -pinoffset in case you run multiple jobs). 87: starting mdrun 'spc2' 87: 16 steps, 0.0 ps. 87: Generated 330891 of the 330891 non-bonded parameter combinations 87: 87: Generated 330891 of the 330891 1-4 parameter combinations 87: 87: Excluding 2 bonded neighbours molecule type 'SOL' 87: 87: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/tip3p5.gro' 87: 87: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 87: 87: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 87: 87: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 87: 87: Note that mdrun will redetermine rlist based on the actual pair-list setup 87: 87: This run will generate roughly 0 Mb of data 87: 87: Writing final coordinates. 87: 87: Core t (s) Wall t (s) (%) 87: Time: 0.043 0.022 196.4 87: (ns/day) (hour/ns) 87: Performance: 67.548 0.355 87: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as single precision energy file 87: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as single precision energy file 87: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 87: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 87: that with the Verlet scheme, nstlist has no effect on the accuracy of 87: your simulation. 87: 87: 87: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 87: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 87: setting nstcomm equal to nstcalcenergy for less overhead 87: 87: Generating 1-4 interactions: fudge = 0.5 87: Number of degrees of freedom in T-Coupling group System is 27.00 87: 87: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 87: You are using a plain Coulomb cut-off, which might produce artifacts. 87: You might want to consider using PME electrostatics. 87: 87: 87: 87: There were 3 NOTEs 87: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 87: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 87: 87: Using 2 MPI threads 87: Using 1 OpenMP thread per tMPI thread 87: 87: 87: NOTE: The number of threads is not equal to the number of (logical) cpus 87: and the -pin option is set to auto: will not pin threads to cpus. 87: This can lead to significant performance degradation. 87: Consider using -pin on (and -pinoffset in case you run multiple jobs). 87: starting mdrun 'spc2' 87: 16 steps, 0.0 ps. 87: Generated 330891 of the 330891 non-bonded parameter combinations 87: 87: Generated 330891 of the 330891 1-4 parameter combinations 87: 87: Excluding 2 bonded neighbours molecule type 'SOL' 87: 87: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/tip3p5.gro' 87: 87: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 87: 87: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 87: 87: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 87: 87: Note that mdrun will redetermine rlist based on the actual pair-list setup 87: 87: This run will generate roughly 0 Mb of data 87: 87: Writing final coordinates. 87: 87: Core t (s) Wall t (s) (%) 87: Time: 0.049 0.025 197.1 87: (ns/day) (hour/ns) 87: Performance: 59.481 0.403 87: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as single precision energy file 87: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as single precision energy file 87: 87: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 87: that with the Verlet scheme, nstlist has no effect on the accuracy of 87: your simulation. 87: 87: 87: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 87: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 87: setting nstcomm equal to nstcalcenergy for less overhead 87: 87: Generating 1-4 interactions: fudge = 0.5 87: Number of degrees of freedom in T-Coupling group System is 27.00 87: 87: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 87: You are using a plain Coulomb cut-off, which might produce artifacts. 87: You might want to consider using PME electrostatics. 87: 87: 87: 87: There were 3 NOTEs 87: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 87: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 87: 87: Using 2 MPI threads 87: Using 1 OpenMP thread per tMPI thread 87: 87: 87: NOTE: The number of threads is not equal to the number of (logical) cpus 87: and the -pin option is set to auto: will not pin threads to cpus. 87: This can lead to significant performance degradation. 87: Consider using -pin on (and -pinoffset in case you run multiple jobs). 87: starting mdrun 'spc2' 87: 16 steps, 0.0 ps. 87: Generated 330891 of the 330891 non-bonded parameter combinations 87: 87: Generated 330891 of the 330891 1-4 parameter combinations 87: 87: Excluding 2 bonded neighbours molecule type 'SOL' 87: 87: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/tip3p5.gro' 87: 87: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 87: 87: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 87: 87: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 87: 87: Note that mdrun will redetermine rlist based on the actual pair-list setup 87: 87: This run will generate roughly 0 Mb of data 87: 87: Writing final coordinates. 87: 87: Core t (s) Wall t (s) (%) 87: Time: 0.046 0.024 197.1 87: (ns/day) (hour/ns) 87: Performance: 62.412 0.385 87: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as single precision energy file 87: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as single precision energy file 87: 87: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 87: that with the Verlet scheme, nstlist has no effect on the accuracy of 87: your simulation. 87: 87: 87: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 87: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 87: setting nstcomm equal to nstcalcenergy for less overhead 87: 87: Generating 1-4 interactions: fudge = 0.5 87: Number of degrees of freedom in T-Coupling group System is 27.00 87: 87: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 87: You are using a plain Coulomb cut-off, which might produce artifacts. 87: You might want to consider using PME electrostatics. 87: 87: 87: 87: There were 3 NOTEs 87: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 87: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 87: 87: Using 2 MPI threads 87: Using 1 OpenMP thread per tMPI thread 87: 87: 87: NOTE: The number of threads is not equal to the number of (logical) cpus 87: and the -pin option is set to auto: will not pin threads to cpus. 87: This can lead to significant performance degradation. 87: Consider using -pin on (and -pinoffset in case you run multiple jobs). 87: starting mdrun 'spc2' 87: 16 steps, 0.0 ps. 87: Generated 330891 of the 330891 non-bonded parameter combinations 87: 87: Generated 330891 of the 330891 1-4 parameter combinations 87: 87: Excluding 2 bonded neighbours molecule type 'SOL' 87: 87: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/tip3p5.gro' 87: 87: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 87: 87: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 87: 87: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 87: 87: Note that mdrun will redetermine rlist based on the actual pair-list setup 87: 87: This run will generate roughly 0 Mb of data 87: 87: Writing final coordinates. 87: 87: Core t (s) Wall t (s) (%) 87: Time: 0.044 0.022 196.9 87: (ns/day) (hour/ns) 87: Performance: 66.456 0.361 87: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as single precision energy file 87: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as single precision energy file 87: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/4 (26936 ms) 87: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/5 87: 87: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 87: that with the Verlet scheme, nstlist has no effect on the accuracy of 87: your simulation. 87: 87: 87: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 87: Setting nstcalcenergy (100) equal to nstenergy (1) 87: 87: Generating 1-4 interactions: fudge = 0.5 87: Number of degrees of freedom in T-Coupling group System is 27.00 87: 87: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 87: You are using a plain Coulomb cut-off, which might produce artifacts. 87: You might want to consider using PME electrostatics. 87: 87: 87: 87: There were 3 NOTEs 87: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 87: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 87: 87: Using 2 MPI threads 87: Using 1 OpenMP thread per tMPI thread 87: 87: 87: NOTE: The number of threads is not equal to the number of (logical) cpus 87: and the -pin option is set to auto: will not pin threads to cpus. 87: This can lead to significant performance degradation. 87: Consider using -pin on (and -pinoffset in case you run multiple jobs). 87: starting mdrun 'spc2' 87: 16 steps, 0.0 ps. 87: Generated 330891 of the 330891 non-bonded parameter combinations 87: 87: Generated 330891 of the 330891 1-4 parameter combinations 87: 87: Excluding 2 bonded neighbours molecule type 'SOL' 87: 87: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/tip3p5.gro' 87: 87: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 87: 87: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 87: 87: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 87: 87: Note that mdrun will redetermine rlist based on the actual pair-list setup 87: 87: This run will generate roughly 0 Mb of data 87: 87: Writing final coordinates. 87: 87: Core t (s) Wall t (s) (%) 87: Time: 0.046 0.023 197.0 87: (ns/day) (hour/ns) 87: Performance: 62.639 0.383 87: 87: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 87: that with the Verlet scheme, nstlist has no effect on the accuracy of 87: your simulation. 87: 87: 87: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 87: Setting nstcalcenergy (100) equal to nstenergy (1) 87: 87: Generating 1-4 interactions: fudge = 0.5 87: Number of degrees of freedom in T-Coupling group System is 27.00 87: 87: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 87: You are using a plain Coulomb cut-off, which might produce artifacts. 87: You might want to consider using PME electrostatics. 87: 87: 87: 87: There were 3 NOTEs 87: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 87: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 87: 87: Using 2 MPI threads 87: Using 1 OpenMP thread per tMPI thread 87: 87: 87: NOTE: The number of threads is not equal to the number of (logical) cpus 87: and the -pin option is set to auto: will not pin threads to cpus. 87: This can lead to significant performance degradation. 87: Consider using -pin on (and -pinoffset in case you run multiple jobs). 87: starting mdrun 'spc2' 87: 16 steps, 0.0 ps. 87: Generated 330891 of the 330891 non-bonded parameter combinations 87: 87: Generated 330891 of the 330891 1-4 parameter combinations 87: 87: Excluding 2 bonded neighbours molecule type 'SOL' 87: 87: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/tip3p5.gro' 87: 87: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 87: 87: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 87: 87: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 87: 87: Note that mdrun will redetermine rlist based on the actual pair-list setup 87: 87: This run will generate roughly 0 Mb of data 87: 87: Writing final coordinates. 87: 87: Core t (s) Wall t (s) (%) 87: Time: 0.056 0.028 197.4 87: (ns/day) (hour/ns) 87: Performance: 51.898 0.462 87: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as single precision energy file 87: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as single precision energy file 87: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 87: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 87: that with the Verlet scheme, nstlist has no effect on the accuracy of 87: your simulation. 87: 87: 87: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 87: Setting nstcalcenergy (100) equal to nstenergy (4) 87: 87: Generating 1-4 interactions: fudge = 0.5 87: Number of degrees of freedom in T-Coupling group System is 27.00 87: 87: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 87: You are using a plain Coulomb cut-off, which might produce artifacts. 87: You might want to consider using PME electrostatics. 87: 87: 87: 87: There were 3 NOTEs 87: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 87: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 87: 87: Using 2 MPI threads 87: Using 1 OpenMP thread per tMPI thread 87: 87: 87: NOTE: The number of threads is not equal to the number of (logical) cpus 87: and the -pin option is set to auto: will not pin threads to cpus. 87: This can lead to significant performance degradation. 87: Consider using -pin on (and -pinoffset in case you run multiple jobs). 87: starting mdrun 'spc2' 87: 16 steps, 0.0 ps. 87: Generated 330891 of the 330891 non-bonded parameter combinations 87: 87: Generated 330891 of the 330891 1-4 parameter combinations 87: 87: Excluding 2 bonded neighbours molecule type 'SOL' 87: 87: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/tip3p5.gro' 87: 87: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 87: 87: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 87: 87: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 87: 87: Note that mdrun will redetermine rlist based on the actual pair-list setup 87: 87: This run will generate roughly 0 Mb of data 87: 87: Writing final coordinates. 87: 87: Core t (s) Wall t (s) (%) 87: Time: 0.042 0.021 196.4 87: (ns/day) (hour/ns) 87: Performance: 68.636 0.350 87: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as single precision energy file 87: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as single precision energy file 87: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 87: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 87: that with the Verlet scheme, nstlist has no effect on the accuracy of 87: your simulation. 87: 87: 87: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 87: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 87: setting nstcomm equal to nstcalcenergy for less overhead 87: 87: Generating 1-4 interactions: fudge = 0.5 87: Number of degrees of freedom in T-Coupling group System is 27.00 87: 87: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 87: You are using a plain Coulomb cut-off, which might produce artifacts. 87: You might want to consider using PME electrostatics. 87: 87: 87: 87: There were 3 NOTEs 87: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 87: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 87: 87: Using 2 MPI threads 87: Using 1 OpenMP thread per tMPI thread 87: 87: 87: NOTE: The number of threads is not equal to the number of (logical) cpus 87: and the -pin option is set to auto: will not pin threads to cpus. 87: This can lead to significant performance degradation. 87: Consider using -pin on (and -pinoffset in case you run multiple jobs). 87: starting mdrun 'spc2' 87: 16 steps, 0.0 ps. 87: Generated 330891 of the 330891 non-bonded parameter combinations 87: 87: Generated 330891 of the 330891 1-4 parameter combinations 87: 87: Excluding 2 bonded neighbours molecule type 'SOL' 87: 87: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/tip3p5.gro' 87: 87: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 87: 87: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 87: 87: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 87: 87: Note that mdrun will redetermine rlist based on the actual pair-list setup 87: 87: This run will generate roughly 0 Mb of data 87: 87: Writing final coordinates. 87: 87: Core t (s) Wall t (s) (%) 87: Time: 0.071 0.036 197.8 87: (ns/day) (hour/ns) 87: Performance: 40.943 0.586 87: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as single precision energy file 87: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as single precision energy file 87: 87: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 87: that with the Verlet scheme, nstlist has no effect on the accuracy of 87: your simulation. 87: 87: 87: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 87: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 87: setting nstcomm equal to nstcalcenergy for less overhead 87: 87: Generating 1-4 interactions: fudge = 0.5 87: Number of degrees of freedom in T-Coupling group System is 27.00 87: 87: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 87: You are using a plain Coulomb cut-off, which might produce artifacts. 87: You might want to consider using PME electrostatics. 87: 87: 87: 87: There were 3 NOTEs 87: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 87: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 87: 87: Using 2 MPI threads 87: Using 1 OpenMP thread per tMPI thread 87: 87: 87: NOTE: The number of threads is not equal to the number of (logical) cpus 87: and the -pin option is set to auto: will not pin threads to cpus. 87: This can lead to significant performance degradation. 87: Consider using -pin on (and -pinoffset in case you run multiple jobs). 87: starting mdrun 'spc2' 87: 16 steps, 0.0 ps. 87: Generated 330891 of the 330891 non-bonded parameter combinations 87: 87: Generated 330891 of the 330891 1-4 parameter combinations 87: 87: Excluding 2 bonded neighbours molecule type 'SOL' 87: 87: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/tip3p5.gro' 87: 87: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 87: 87: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 87: 87: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 87: 87: Note that mdrun will redetermine rlist based on the actual pair-list setup 87: 87: This run will generate roughly 0 Mb of data 87: 87: Writing final coordinates. 87: 87: Core t (s) Wall t (s) (%) 87: Time: 0.075 0.038 197.9 87: (ns/day) (hour/ns) 87: Performance: 38.632 0.621 87: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as single precision energy file 87: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as single precision energy file 87: 87: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 87: that with the Verlet scheme, nstlist has no effect on the accuracy of 87: your simulation. 87: 87: 87: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 87: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 87: setting nstcomm equal to nstcalcenergy for less overhead 87: 87: Generating 1-4 interactions: fudge = 0.5 87: Number of degrees of freedom in T-Coupling group System is 27.00 87: 87: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 87: You are using a plain Coulomb cut-off, which might produce artifacts. 87: You might want to consider using PME electrostatics. 87: 87: 87: 87: There were 3 NOTEs 87: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 87: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 87: 87: Using 2 MPI threads 87: Using 1 OpenMP thread per tMPI thread 87: 87: 87: NOTE: The number of threads is not equal to the number of (logical) cpus 87: and the -pin option is set to auto: will not pin threads to cpus. 87: This can lead to significant performance degradation. 87: Consider using -pin on (and -pinoffset in case you run multiple jobs). 87: starting mdrun 'spc2' 87: 16 steps, 0.0 ps. 87: Generated 330891 of the 330891 non-bonded parameter combinations 87: 87: Generated 330891 of the 330891 1-4 parameter combinations 87: 87: Excluding 2 bonded neighbours molecule type 'SOL' 87: 87: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/tip3p5.gro' 87: 87: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 87: 87: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 87: 87: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 87: 87: Note that mdrun will redetermine rlist based on the actual pair-list setup 87: 87: This run will generate roughly 0 Mb of data 87: 87: Writing final coordinates. 87: 87: Core t (s) Wall t (s) (%) 87: Time: 0.062 0.032 197.7 87: (ns/day) (hour/ns) 87: Performance: 46.507 0.516 87: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as single precision energy file 87: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as single precision energy file 87: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/5 (27124 ms) 87: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/6 87: 87: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 87: that with the Verlet scheme, nstlist has no effect on the accuracy of 87: your simulation. 87: 87: 87: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 87: Setting nstcalcenergy (100) equal to nstenergy (1) 87: 87: Generating 1-4 interactions: fudge = 0.5 87: Number of degrees of freedom in T-Coupling group System is 27.00 87: 87: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 87: You are using a plain Coulomb cut-off, which might produce artifacts. 87: You might want to consider using PME electrostatics. 87: 87: 87: 87: There were 3 NOTEs 87: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 87: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 87: 87: Using 2 MPI threads 87: Using 1 OpenMP thread per tMPI thread 87: 87: 87: NOTE: The number of threads is not equal to the number of (logical) cpus 87: and the -pin option is set to auto: will not pin threads to cpus. 87: This can lead to significant performance degradation. 87: Consider using -pin on (and -pinoffset in case you run multiple jobs). 87: starting mdrun 'spc2' 87: 16 steps, 0.0 ps. 87: Generated 330891 of the 330891 non-bonded parameter combinations 87: 87: Generated 330891 of the 330891 1-4 parameter combinations 87: 87: Excluding 2 bonded neighbours molecule type 'SOL' 87: 87: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/tip3p5.gro' 87: 87: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 87: 87: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 87: 87: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 87: 87: Note that mdrun will redetermine rlist based on the actual pair-list setup 87: 87: This run will generate roughly 0 Mb of data 87: 87: Writing final coordinates. 87: 87: Core t (s) Wall t (s) (%) 87: Time: 0.060 0.030 198.0 87: (ns/day) (hour/ns) 87: Performance: 48.538 0.494 87: 87: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 87: that with the Verlet scheme, nstlist has no effect on the accuracy of 87: your simulation. 87: 87: 87: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 87: Setting nstcalcenergy (100) equal to nstenergy (1) 87: 87: Generating 1-4 interactions: fudge = 0.5 87: Number of degrees of freedom in T-Coupling group System is 27.00 87: 87: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 87: You are using a plain Coulomb cut-off, which might produce artifacts. 87: You might want to consider using PME electrostatics. 87: 87: 87: 87: There were 3 NOTEs 87: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 87: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 87: 87: Using 2 MPI threads 87: Using 1 OpenMP thread per tMPI thread 87: 87: 87: NOTE: The number of threads is not equal to the number of (logical) cpus 87: and the -pin option is set to auto: will not pin threads to cpus. 87: This can lead to significant performance degradation. 87: Consider using -pin on (and -pinoffset in case you run multiple jobs). 87: starting mdrun 'spc2' 87: 16 steps, 0.0 ps. 87: Generated 330891 of the 330891 non-bonded parameter combinations 87: 87: Generated 330891 of the 330891 1-4 parameter combinations 87: 87: Excluding 2 bonded neighbours molecule type 'SOL' 87: 87: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/tip3p5.gro' 87: 87: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 87: 87: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 87: 87: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 87: 87: Note that mdrun will redetermine rlist based on the actual pair-list setup 87: 87: This run will generate roughly 0 Mb of data 87: 87: Writing final coordinates. 87: 87: Core t (s) Wall t (s) (%) 87: Time: 0.057 0.029 197.8 87: (ns/day) (hour/ns) 87: Performance: 50.754 0.473 87: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as single precision energy file 87: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as single precision energy file 87: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 87: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 87: that with the Verlet scheme, nstlist has no effect on the accuracy of 87: your simulation. 87: 87: 87: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 87: Setting nstcalcenergy (100) equal to nstenergy (4) 87: 87: Generating 1-4 interactions: fudge = 0.5 87: Number of degrees of freedom in T-Coupling group System is 27.00 87: 87: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 87: You are using a plain Coulomb cut-off, which might produce artifacts. 87: You might want to consider using PME electrostatics. 87: 87: 87: 87: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 87: COM removal frequency is set to (5). 87: Other settings require a global communication frequency of 4. 87: Note that this will require additional global communication steps, 87: which will reduce performance when using multiple ranks. 87: Consider setting nstcomm to a multiple of 4. 87: 87: 87: There were 4 NOTEs 87: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 87: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 87: 87: Using 2 MPI threads 87: Using 1 OpenMP thread per tMPI thread 87: 87: 87: NOTE: The number of threads is not equal to the number of (logical) cpus 87: and the -pin option is set to auto: will not pin threads to cpus. 87: This can lead to significant performance degradation. 87: Consider using -pin on (and -pinoffset in case you run multiple jobs). 87: starting mdrun 'spc2' 87: 16 steps, 0.0 ps. 87: Generated 330891 of the 330891 non-bonded parameter combinations 87: 87: Generated 330891 of the 330891 1-4 parameter combinations 87: 87: Excluding 2 bonded neighbours molecule type 'SOL' 87: 87: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/tip3p5.gro' 87: 87: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 87: 87: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 87: 87: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 87: 87: Note that mdrun will redetermine rlist based on the actual pair-list setup 87: 87: This run will generate roughly 0 Mb of data 87: 87: Writing final coordinates. 87: 87: Core t (s) Wall t (s) (%) 87: Time: 0.167 0.084 199.2 87: (ns/day) (hour/ns) 87: Performance: 17.559 1.367 87: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as single precision energy file 87: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as single precision energy file 87: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 87: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 87: that with the Verlet scheme, nstlist has no effect on the accuracy of 87: your simulation. 87: 87: 87: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 87: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 87: setting nstcomm equal to nstcalcenergy for less overhead 87: 87: Generating 1-4 interactions: fudge = 0.5 87: Number of degrees of freedom in T-Coupling group System is 27.00 87: 87: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 87: You are using a plain Coulomb cut-off, which might produce artifacts. 87: You might want to consider using PME electrostatics. 87: 87: 87: 87: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 87: COM removal frequency is set to (5). 87: Other settings require a global communication frequency of 100. 87: Note that this will require additional global communication steps, 87: which will reduce performance when using multiple ranks. 87: Consider setting nstcomm to a multiple of 100. 87: 87: 87: There were 4 NOTEs 87: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 87: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 87: 87: Using 2 MPI threads 87: Using 1 OpenMP thread per tMPI thread 87: 87: 87: NOTE: The number of threads is not equal to the number of (logical) cpus 87: and the -pin option is set to auto: will not pin threads to cpus. 87: This can lead to significant performance degradation. 87: Consider using -pin on (and -pinoffset in case you run multiple jobs). 87: starting mdrun 'spc2' 87: 16 steps, 0.0 ps. 87: Generated 330891 of the 330891 non-bonded parameter combinations 87: 87: Generated 330891 of the 330891 1-4 parameter combinations 87: 87: Excluding 2 bonded neighbours molecule type 'SOL' 87: 87: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/tip3p5.gro' 87: 87: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 87: 87: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 87: 87: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 87: 87: Note that mdrun will redetermine rlist based on the actual pair-list setup 87: 87: This run will generate roughly 0 Mb of data 87: 87: Writing final coordinates. 87: 87: NOTE: 11 % of the run time was spent communicating energies, 87: you might want to increase some nst* mdp options 87: 87: Core t (s) Wall t (s) (%) 87: Time: 0.110 0.056 198.8 87: (ns/day) (hour/ns) 87: Performance: 26.432 0.908 87: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as single precision energy file 87: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as single precision energy file 87: 87: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 87: that with the Verlet scheme, nstlist has no effect on the accuracy of 87: your simulation. 87: 87: 87: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 87: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 87: setting nstcomm equal to nstcalcenergy for less overhead 87: 87: Generating 1-4 interactions: fudge = 0.5 87: Number of degrees of freedom in T-Coupling group System is 27.00 87: 87: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 87: You are using a plain Coulomb cut-off, which might produce artifacts. 87: You might want to consider using PME electrostatics. 87: 87: 87: 87: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 87: COM removal frequency is set to (5). 87: Other settings require a global communication frequency of 100. 87: Note that this will require additional global communication steps, 87: which will reduce performance when using multiple ranks. 87: Consider setting nstcomm to a multiple of 100. 87: 87: 87: There were 4 NOTEs 87: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 87: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 87: 87: Using 2 MPI threads 87: Using 1 OpenMP thread per tMPI thread 87: 87: 87: NOTE: The number of threads is not equal to the number of (logical) cpus 87: and the -pin option is set to auto: will not pin threads to cpus. 87: This can lead to significant performance degradation. 87: Consider using -pin on (and -pinoffset in case you run multiple jobs). 87: starting mdrun 'spc2' 87: 16 steps, 0.0 ps. 87: Generated 330891 of the 330891 non-bonded parameter combinations 87: 87: Generated 330891 of the 330891 1-4 parameter combinations 87: 87: Excluding 2 bonded neighbours molecule type 'SOL' 87: 87: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/tip3p5.gro' 87: 87: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 87: 87: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 87: 87: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 87: 87: Note that mdrun will redetermine rlist based on the actual pair-list setup 87: 87: This run will generate roughly 0 Mb of data 87: 87: Writing final coordinates. 87: 87: Core t (s) Wall t (s) (%) 87: Time: 0.143 0.072 198.9 87: (ns/day) (hour/ns) 87: Performance: 20.496 1.171 87: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as single precision energy file 87: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as single precision energy file 87: 87: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 87: that with the Verlet scheme, nstlist has no effect on the accuracy of 87: your simulation. 87: 87: 87: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 87: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 87: setting nstcomm equal to nstcalcenergy for less overhead 87: 87: Generating 1-4 interactions: fudge = 0.5 87: Number of degrees of freedom in T-Coupling group System is 27.00 87: 87: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 87: You are using a plain Coulomb cut-off, which might produce artifacts. 87: You might want to consider using PME electrostatics. 87: 87: 87: 87: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 87: COM removal frequency is set to (5). 87: Other settings require a global communication frequency of 100. 87: Note that this will require additional global communication steps, 87: which will reduce performance when using multiple ranks. 87: Consider setting nstcomm to a multiple of 100. 87: 87: 87: There were 4 NOTEs 87: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 87: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 87: 87: Using 2 MPI threads 87: Using 1 OpenMP thread per tMPI thread 87: 87: 87: NOTE: The number of threads is not equal to the number of (logical) cpus 87: and the -pin option is set to auto: will not pin threads to cpus. 87: This can lead to significant performance degradation. 87: Consider using -pin on (and -pinoffset in case you run multiple jobs). 87: starting mdrun 'spc2' 87: 16 steps, 0.0 ps. 87: Generated 330891 of the 330891 non-bonded parameter combinations 87: 87: Generated 330891 of the 330891 1-4 parameter combinations 87: 87: Excluding 2 bonded neighbours molecule type 'SOL' 87: 87: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/tip3p5.gro' 87: 87: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 87: 87: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 87: 87: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 87: 87: Note that mdrun will redetermine rlist based on the actual pair-list setup 87: 87: This run will generate roughly 0 Mb of data 87: 87: Writing final coordinates. 87: 87: Core t (s) Wall t (s) (%) 87: Time: 0.124 0.063 199.0 87: (ns/day) (hour/ns) 87: Performance: 23.486 1.022 87: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as single precision energy file 87: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as single precision energy file 87: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/6 (35658 ms) 87: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/7 87: 87: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 87: that with the Verlet scheme, nstlist has no effect on the accuracy of 87: your simulation. 87: 87: 87: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 87: Setting nstcalcenergy (100) equal to nstenergy (1) 87: 87: Generating 1-4 interactions: fudge = 0.5 87: Number of degrees of freedom in T-Coupling group System is 27.00 87: 87: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 87: You are using a plain Coulomb cut-off, which might produce artifacts. 87: You might want to consider using PME electrostatics. 87: 87: 87: 87: There were 3 NOTEs 87: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 87: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 87: 87: Using 2 MPI threads 87: Using 1 OpenMP thread per tMPI thread 87: 87: 87: NOTE: The number of threads is not equal to the number of (logical) cpus 87: and the -pin option is set to auto: will not pin threads to cpus. 87: This can lead to significant performance degradation. 87: Consider using -pin on (and -pinoffset in case you run multiple jobs). 87: starting mdrun 'spc2' 87: 16 steps, 0.0 ps. 87: Generated 330891 of the 330891 non-bonded parameter combinations 87: 87: Generated 330891 of the 330891 1-4 parameter combinations 87: 87: Excluding 2 bonded neighbours molecule type 'SOL' 87: 87: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/tip3p5.gro' 87: 87: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 87: 87: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 87: 87: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 87: 87: Note that mdrun will redetermine rlist based on the actual pair-list setup 87: 87: This run will generate roughly 0 Mb of data 87: 87: Writing final coordinates. 87: 87: NOTE: 14 % of the run time was spent communicating energies, 87: you might want to increase some nst* mdp options 87: 87: Core t (s) Wall t (s) (%) 87: Time: 0.348 0.197 176.6 87: (ns/day) (hour/ns) 87: Performance: 7.457 3.219 87: 87: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 87: that with the Verlet scheme, nstlist has no effect on the accuracy of 87: your simulation. 87: 87: 87: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 87: Setting nstcalcenergy (100) equal to nstenergy (1) 87: 87: Generating 1-4 interactions: fudge = 0.5 87: Number of degrees of freedom in T-Coupling group System is 27.00 87: 87: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 87: You are using a plain Coulomb cut-off, which might produce artifacts. 87: You might want to consider using PME electrostatics. 87: 87: 87: 87: There were 3 NOTEs 87: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 87: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 87: 87: Using 2 MPI threads 87: Using 1 OpenMP thread per tMPI thread 87: 87: 87: NOTE: The number of threads is not equal to the number of (logical) cpus 87: and the -pin option is set to auto: will not pin threads to cpus. 87: This can lead to significant performance degradation. 87: Consider using -pin on (and -pinoffset in case you run multiple jobs). 87: starting mdrun 'spc2' 87: 16 steps, 0.0 ps. 87: Generated 330891 of the 330891 non-bonded parameter combinations 87: 87: Generated 330891 of the 330891 1-4 parameter combinations 87: 87: Excluding 2 bonded neighbours molecule type 'SOL' 87: 87: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/tip3p5.gro' 87: 87: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 87: 87: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 87: 87: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 87: 87: Note that mdrun will redetermine rlist based on the actual pair-list setup 87: 87: This run will generate roughly 0 Mb of data 87: 87: Writing final coordinates. 87: 87: Core t (s) Wall t (s) (%) 87: Time: 0.130 0.065 198.7 87: (ns/day) (hour/ns) 87: Performance: 22.513 1.066 87: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as single precision energy file 87: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as single precision energy file 87: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 87: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 87: that with the Verlet scheme, nstlist has no effect on the accuracy of 87: your simulation. 87: 87: 87: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 87: Setting nstcalcenergy (100) equal to nstenergy (4) 87: 87: Generating 1-4 interactions: fudge = 0.5 87: Number of degrees of freedom in T-Coupling group System is 27.00 87: 87: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 87: You are using a plain Coulomb cut-off, which might produce artifacts. 87: You might want to consider using PME electrostatics. 87: 87: 87: 87: There were 3 NOTEs 87: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 87: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 87: 87: Using 2 MPI threads 87: Using 1 OpenMP thread per tMPI thread 87: 87: 87: NOTE: The number of threads is not equal to the number of (logical) cpus 87: and the -pin option is set to auto: will not pin threads to cpus. 87: This can lead to significant performance degradation. 87: Consider using -pin on (and -pinoffset in case you run multiple jobs). 87: starting mdrun 'spc2' 87: 16 steps, 0.0 ps. 87: Generated 330891 of the 330891 non-bonded parameter combinations 87: 87: Generated 330891 of the 330891 1-4 parameter combinations 87: 87: Excluding 2 bonded neighbours molecule type 'SOL' 87: 87: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/tip3p5.gro' 87: 87: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 87: 87: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 87: 87: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 87: 87: Note that mdrun will redetermine rlist based on the actual pair-list setup 87: 87: This run will generate roughly 0 Mb of data 87: 87: Writing final coordinates. 87: 87: Core t (s) Wall t (s) (%) 87: Time: 0.137 0.069 198.9 87: (ns/day) (hour/ns) 87: Performance: 21.282 1.128 87: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as single precision energy file 87: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as single precision energy file 87: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 87: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 87: that with the Verlet scheme, nstlist has no effect on the accuracy of 87: your simulation. 87: 87: 87: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 87: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 87: setting nstcomm equal to nstcalcenergy for less overhead 87: 87: Generating 1-4 interactions: fudge = 0.5 87: Number of degrees of freedom in T-Coupling group System is 27.00 87: 87: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 87: You are using a plain Coulomb cut-off, which might produce artifacts. 87: You might want to consider using PME electrostatics. 87: 87: 87: 87: There were 3 NOTEs 87: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 87: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 87: 87: Using 2 MPI threads 87: Using 1 OpenMP thread per tMPI thread 87: 87: 87: NOTE: The number of threads is not equal to the number of (logical) cpus 87: and the -pin option is set to auto: will not pin threads to cpus. 87: This can lead to significant performance degradation. 87: Consider using -pin on (and -pinoffset in case you run multiple jobs). 87: starting mdrun 'spc2' 87: 16 steps, 0.0 ps. 87: Generated 330891 of the 330891 non-bonded parameter combinations 87: 87: Generated 330891 of the 330891 1-4 parameter combinations 87: 87: Excluding 2 bonded neighbours molecule type 'SOL' 87: 87: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/tip3p5.gro' 87: 87: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 87: 87: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 87: 87: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 87: 87: Note that mdrun will redetermine rlist based on the actual pair-list setup 87: 87: This run will generate roughly 0 Mb of data 87: 87: Writing final coordinates. 87: 87: Core t (s) Wall t (s) (%) 87: Time: 0.131 0.068 192.6 87: (ns/day) (hour/ns) 87: Performance: 21.527 1.115 87: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as single precision energy file 87: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as single precision energy file 87: 87: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 87: that with the Verlet scheme, nstlist has no effect on the accuracy of 87: your simulation. 87: 87: 87: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 87: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 87: setting nstcomm equal to nstcalcenergy for less overhead 87: 87: Generating 1-4 interactions: fudge = 0.5 87: Number of degrees of freedom in T-Coupling group System is 27.00 87: 87: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 87: You are using a plain Coulomb cut-off, which might produce artifacts. 87: You might want to consider using PME electrostatics. 87: 87: 87: 87: There were 3 NOTEs 87: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 87: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 87: 87: Using 2 MPI threads 87: Using 1 OpenMP thread per tMPI thread 87: 87: 87: NOTE: The number of threads is not equal to the number of (logical) cpus 87: and the -pin option is set to auto: will not pin threads to cpus. 87: This can lead to significant performance degradation. 87: Consider using -pin on (and -pinoffset in case you run multiple jobs). 87: starting mdrun 'spc2' 87: 16 steps, 0.0 ps. 87: Generated 330891 of the 330891 non-bonded parameter combinations 87: 87: Generated 330891 of the 330891 1-4 parameter combinations 87: 87: Excluding 2 bonded neighbours molecule type 'SOL' 87: 87: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/tip3p5.gro' 87: 87: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 87: 87: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 87: 87: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 87: 87: Note that mdrun will redetermine rlist based on the actual pair-list setup 87: 87: This run will generate roughly 0 Mb of data 87: 87: Writing final coordinates. 87: 87: Core t (s) Wall t (s) (%) 87: Time: 0.105 0.053 198.6 87: (ns/day) (hour/ns) 87: Performance: 27.835 0.862 87: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as single precision energy file 87: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as single precision energy file 87: 87: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 87: that with the Verlet scheme, nstlist has no effect on the accuracy of 87: your simulation. 87: 87: 87: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 87: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 87: setting nstcomm equal to nstcalcenergy for less overhead 87: 87: Generating 1-4 interactions: fudge = 0.5 87: Number of degrees of freedom in T-Coupling group System is 27.00 87: 87: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 87: You are using a plain Coulomb cut-off, which might produce artifacts. 87: You might want to consider using PME electrostatics. 87: 87: 87: 87: There were 3 NOTEs 87: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 87: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 87: 87: Using 2 MPI threads 87: Using 1 OpenMP thread per tMPI thread 87: 87: 87: NOTE: The number of threads is not equal to the number of (logical) cpus 87: and the -pin option is set to auto: will not pin threads to cpus. 87: This can lead to significant performance degradation. 87: Consider using -pin on (and -pinoffset in case you run multiple jobs). 87: starting mdrun 'spc2' 87: 16 steps, 0.0 ps. 87: Generated 330891 of the 330891 non-bonded parameter combinations 87: 87: Generated 330891 of the 330891 1-4 parameter combinations 87: 87: Excluding 2 bonded neighbours molecule type 'SOL' 87: 87: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/tip3p5.gro' 87: 87: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 87: 87: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 87: 87: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 87: 87: Note that mdrun will redetermine rlist based on the actual pair-list setup 87: 87: This run will generate roughly 0 Mb of data 87: 87: Writing final coordinates. 87: 87: NOTE: 26 % of the run time was spent communicating energies, 87: you might want to increase some nst* mdp options 87: 87: Core t (s) Wall t (s) (%) 87: Time: 0.968 0.492 196.6 87: (ns/day) (hour/ns) 87: Performance: 2.983 8.045 87: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as single precision energy file 87: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as single precision energy file 87: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/7 (42271 ms) 87: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/8 87: 87: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 87: that with the Verlet scheme, nstlist has no effect on the accuracy of 87: your simulation. 87: 87: 87: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 87: Setting nstcalcenergy (100) equal to nstenergy (1) 87: 87: Generating 1-4 interactions: fudge = 0.5 87: Number of degrees of freedom in T-Coupling group System is 27.00 87: 87: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 87: You are using a plain Coulomb cut-off, which might produce artifacts. 87: You might want to consider using PME electrostatics. 87: 87: 87: 87: There were 3 NOTEs 87: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 87: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 87: 87: Using 2 MPI threads 87: Using 1 OpenMP thread per tMPI thread 87: 87: 87: NOTE: The number of threads is not equal to the number of (logical) cpus 87: and the -pin option is set to auto: will not pin threads to cpus. 87: This can lead to significant performance degradation. 87: Consider using -pin on (and -pinoffset in case you run multiple jobs). 87: starting mdrun 'spc2' 87: 16 steps, 0.0 ps. 87: Generated 330891 of the 330891 non-bonded parameter combinations 87: 87: Generated 330891 of the 330891 1-4 parameter combinations 87: 87: Excluding 2 bonded neighbours molecule type 'SOL' 87: 87: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/tip3p5.gro' 87: 87: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 87: 87: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 87: 87: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 87: 87: Note that mdrun will redetermine rlist based on the actual pair-list setup 87: 87: This run will generate roughly 0 Mb of data 87: 87: Writing final coordinates. 87: 87: Core t (s) Wall t (s) (%) 87: Time: 0.134 0.067 198.8 87: (ns/day) (hour/ns) 87: Performance: 21.851 1.098 87: 87: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 87: that with the Verlet scheme, nstlist has no effect on the accuracy of 87: your simulation. 87: 87: 87: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 87: Setting nstcalcenergy (100) equal to nstenergy (1) 87: 87: Generating 1-4 interactions: fudge = 0.5 87: Number of degrees of freedom in T-Coupling group System is 27.00 87: 87: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 87: You are using a plain Coulomb cut-off, which might produce artifacts. 87: You might want to consider using PME electrostatics. 87: 87: 87: 87: There were 3 NOTEs 87: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 87: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 87: 87: Using 2 MPI threads 87: Using 1 OpenMP thread per tMPI thread 87: 87: 87: NOTE: The number of threads is not equal to the number of (logical) cpus 87: and the -pin option is set to auto: will not pin threads to cpus. 87: This can lead to significant performance degradation. 87: Consider using -pin on (and -pinoffset in case you run multiple jobs). 87: starting mdrun 'spc2' 87: 16 steps, 0.0 ps. 87: Generated 330891 of the 330891 non-bonded parameter combinations 87: 87: Generated 330891 of the 330891 1-4 parameter combinations 87: 87: Excluding 2 bonded neighbours molecule type 'SOL' 87: 87: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/tip3p5.gro' 87: 87: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 87: 87: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 87: 87: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 87: 87: Note that mdrun will redetermine rlist based on the actual pair-list setup 87: 87: This run will generate roughly 0 Mb of data 87: 87: Writing final coordinates. 87: 87: NOTE: 10 % of the run time was spent communicating energies, 87: you might want to increase some nst* mdp options 87: 87: Core t (s) Wall t (s) (%) 87: Time: 0.234 0.117 199.3 87: (ns/day) (hour/ns) 87: Performance: 12.504 1.919 87: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_reference.edr as single precision energy file 87: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.edr as single precision energy file 87: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 87: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 87: that with the Verlet scheme, nstlist has no effect on the accuracy of 87: your simulation. 87: 87: 87: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 87: Setting nstcalcenergy (100) equal to nstenergy (4) 87: 87: Generating 1-4 interactions: fudge = 0.5 87: Number of degrees of freedom in T-Coupling group System is 27.00 87: 87: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 87: You are using a plain Coulomb cut-off, which might produce artifacts. 87: You might want to consider using PME electrostatics. 87: 87: 87: 87: There were 3 NOTEs 87: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 87: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 87: 87: Using 2 MPI threads 87: Using 1 OpenMP thread per tMPI thread 87: 87: 87: NOTE: The number of threads is not equal to the number of (logical) cpus 87: and the -pin option is set to auto: will not pin threads to cpus. 87: This can lead to significant performance degradation. 87: Consider using -pin on (and -pinoffset in case you run multiple jobs). 87: starting mdrun 'spc2' 87: 16 steps, 0.0 ps. 87: Generated 330891 of the 330891 non-bonded parameter combinations 87: 87: Generated 330891 of the 330891 1-4 parameter combinations 87: 87: Excluding 2 bonded neighbours molecule type 'SOL' 87: 87: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/tip3p5.gro' 87: 87: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 87: 87: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 87: 87: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 87: 87: Note that mdrun will redetermine rlist based on the actual pair-list setup 87: 87: This run will generate roughly 0 Mb of data 87: 87: Writing final coordinates. 87: 87: NOTE: 7 % of the run time was spent communicating energies, 87: you might want to increase some nst* mdp options 87: 87: Core t (s) Wall t (s) (%) 87: Time: 0.122 0.061 198.8 87: (ns/day) (hour/ns) 87: Performance: 23.888 1.005 87: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_reference.edr as single precision energy file 87: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.edr as single precision energy file 87: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 87: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 87: that with the Verlet scheme, nstlist has no effect on the accuracy of 87: your simulation. 87: 87: 87: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 87: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 87: setting nstcomm equal to nstcalcenergy for less overhead 87: 87: Generating 1-4 interactions: fudge = 0.5 87: Number of degrees of freedom in T-Coupling group System is 27.00 87: 87: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 87: You are using a plain Coulomb cut-off, which might produce artifacts. 87: You might want to consider using PME electrostatics. 87: 87: 87: 87: There were 3 NOTEs 87: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 87: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 87: 87: Using 2 MPI threads 87: Using 1 OpenMP thread per tMPI thread 87: 87: 87: NOTE: The number of threads is not equal to the number of (logical) cpus 87: and the -pin option is set to auto: will not pin threads to cpus. 87: This can lead to significant performance degradation. 87: Consider using -pin on (and -pinoffset in case you run multiple jobs). 87: starting mdrun 'spc2' 87: 16 steps, 0.0 ps. 87: Generated 330891 of the 330891 non-bonded parameter combinations 87: 87: Generated 330891 of the 330891 1-4 parameter combinations 87: 87: Excluding 2 bonded neighbours molecule type 'SOL' 87: 87: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/tip3p5.gro' 87: 87: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 87: 87: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 87: 87: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 87: 87: Note that mdrun will redetermine rlist based on the actual pair-list setup 87: 87: This run will generate roughly 0 Mb of data 87: 87: Writing final coordinates. 87: 87: Core t (s) Wall t (s) (%) 87: Time: 0.193 0.097 199.1 87: (ns/day) (hour/ns) 87: Performance: 15.174 1.582 87: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_reference.edr as single precision energy file 87: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.edr as single precision energy file 87: 87: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 87: that with the Verlet scheme, nstlist has no effect on the accuracy of 87: your simulation. 87: 87: 87: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 87: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 87: setting nstcomm equal to nstcalcenergy for less overhead 87: 87: Generating 1-4 interactions: fudge = 0.5 87: Number of degrees of freedom in T-Coupling group System is 27.00 87: 87: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 87: You are using a plain Coulomb cut-off, which might produce artifacts. 87: You might want to consider using PME electrostatics. 87: 87: 87: 87: There were 3 NOTEs 87: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 87: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 87: 87: Using 2 MPI threads 87: Using 1 OpenMP thread per tMPI thread 87: 87: 87: NOTE: The number of threads is not equal to the number of (logical) cpus 87: and the -pin option is set to auto: will not pin threads to cpus. 87: This can lead to significant performance degradation. 87: Consider using -pin on (and -pinoffset in case you run multiple jobs). 87: starting mdrun 'spc2' 87: 16 steps, 0.0 ps. 87: Generated 330891 of the 330891 non-bonded parameter combinations 87: 87: Generated 330891 of the 330891 1-4 parameter combinations 87: 87: Excluding 2 bonded neighbours molecule type 'SOL' 87: 87: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/tip3p5.gro' 87: 87: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 87: 87: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 87: 87: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 87: 87: Note that mdrun will redetermine rlist based on the actual pair-list setup 87: 87: This run will generate roughly 0 Mb of data 87: 87: Writing final coordinates. 87: 87: Core t (s) Wall t (s) (%) 87: Time: 0.087 0.044 198.5 87: (ns/day) (hour/ns) 87: Performance: 33.638 0.713 87: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_reference.edr as single precision energy file 87: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.edr as single precision energy file 87: 87: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 87: that with the Verlet scheme, nstlist has no effect on the accuracy of 87: your simulation. 87: 87: 87: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 87: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 87: setting nstcomm equal to nstcalcenergy for less overhead 87: 87: Generating 1-4 interactions: fudge = 0.5 87: Number of degrees of freedom in T-Coupling group System is 27.00 87: 87: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 87: You are using a plain Coulomb cut-off, which might produce artifacts. 87: You might want to consider using PME electrostatics. 87: 87: 87: 87: There were 3 NOTEs 87: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 87: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 87: 87: Using 2 MPI threads 87: Using 1 OpenMP thread per tMPI thread 87: 87: 87: NOTE: The number of threads is not equal to the number of (logical) cpus 87: and the -pin option is set to auto: will not pin threads to cpus. 87: This can lead to significant performance degradation. 87: Consider using -pin on (and -pinoffset in case you run multiple jobs). 87: starting mdrun 'spc2' 87: 16 steps, 0.0 ps. 87: Generated 330891 of the 330891 non-bonded parameter combinations 87: 87: Generated 330891 of the 330891 1-4 parameter combinations 87: 87: Excluding 2 bonded neighbours molecule type 'SOL' 87: 87: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/tip3p5.gro' 87: 87: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 87: 87: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 87: 87: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 87: 87: Note that mdrun will redetermine rlist based on the actual pair-list setup 87: 87: This run will generate roughly 0 Mb of data 87: 87: Writing final coordinates. 87: 87: NOTE: 19 % of the run time was spent in domain decomposition, 87: 0 % of the run time was spent in pair search, 87: you might want to increase nstlist (this has no effect on accuracy) 87: 87: Core t (s) Wall t (s) (%) 87: Time: 0.128 0.076 167.6 87: (ns/day) (hour/ns) 87: Performance: 19.270 1.245 87: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_reference.edr as single precision energy file 87: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.edr as single precision energy file 87: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/8 (36480 ms) 87: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/9 87: 87: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 87: that with the Verlet scheme, nstlist has no effect on the accuracy of 87: your simulation. 87: 87: 87: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 87: Setting nstcalcenergy (100) equal to nstenergy (1) 87: 87: Generating 1-4 interactions: fudge = 0.5 87: Number of degrees of freedom in T-Coupling group System is 27.00 87: 87: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 87: NVE simulation: will use the initial temperature of 398.997 K for 87: determining the Verlet buffer size 87: 87: 87: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 87: You are using a plain Coulomb cut-off, which might produce artifacts. 87: You might want to consider using PME electrostatics. 87: 87: 87: 87: There were 4 NOTEs 87: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 87: Can not increase nstlist because an NVE ensemble is used 87: Using 2 MPI threads 87: Using 1 OpenMP thread per tMPI thread 87: 87: 87: NOTE: The number of threads is not equal to the number of (logical) cpus 87: and the -pin option is set to auto: will not pin threads to cpus. 87: This can lead to significant performance degradation. 87: Consider using -pin on (and -pinoffset in case you run multiple jobs). 87: starting mdrun 'spc2' 87: 16 steps, 0.0 ps. 87: Generated 330891 of the 330891 non-bonded parameter combinations 87: 87: Generated 330891 of the 330891 1-4 parameter combinations 87: 87: Excluding 2 bonded neighbours molecule type 'SOL' 87: 87: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/tip3p5.gro' 87: 87: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 87: 87: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 87: 87: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 87: 87: Note that mdrun will redetermine rlist based on the actual pair-list setup 87: 87: This run will generate roughly 0 Mb of data 87: 87: Writing final coordinates. 87: 87: 87: Dynamic load balancing report: 87: DLB was off during the run due to low measured imbalance. 87: Average load imbalance: 2.9%. 87: The balanceable part of the MD step is 12%, load imbalance is computed from this. 87: Part of the total run time spent waiting due to load imbalance: 0.3%. 87: 87: 87: NOTE: 20 % of the run time was spent communicating energies, 87: you might want to increase some nst* mdp options 87: 87: Core t (s) Wall t (s) (%) 87: Time: 0.206 0.104 198.7 87: (ns/day) (hour/ns) 87: Performance: 14.149 1.696 87: 87: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 87: that with the Verlet scheme, nstlist has no effect on the accuracy of 87: your simulation. 87: 87: 87: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 87: Setting nstcalcenergy (100) equal to nstenergy (1) 87: 87: Generating 1-4 interactions: fudge = 0.5 87: Number of degrees of freedom in T-Coupling group System is 27.00 87: 87: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 87: NVE simulation: will use the initial temperature of 398.997 K for 87: determining the Verlet buffer size 87: 87: 87: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 87: You are using a plain Coulomb cut-off, which might produce artifacts. 87: You might want to consider using PME electrostatics. 87: 87: 87: 87: There were 4 NOTEs 87: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 87: Can not increase nstlist because an NVE ensemble is used 87: Using 2 MPI threads 87: Using 1 OpenMP thread per tMPI thread 87: 87: 87: NOTE: The number of threads is not equal to the number of (logical) cpus 87: and the -pin option is set to auto: will not pin threads to cpus. 87: This can lead to significant performance degradation. 87: Consider using -pin on (and -pinoffset in case you run multiple jobs). 87: starting mdrun 'spc2' 87: 16 steps, 0.0 ps. 87: Generated 330891 of the 330891 non-bonded parameter combinations 87: 87: Generated 330891 of the 330891 1-4 parameter combinations 87: 87: Excluding 2 bonded neighbours molecule type 'SOL' 87: 87: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/tip3p5.gro' 87: 87: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 87: 87: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 87: 87: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 87: 87: Note that mdrun will redetermine rlist based on the actual pair-list setup 87: 87: This run will generate roughly 0 Mb of data 87: 87: Writing final coordinates. 87: 87: 87: Dynamic load balancing report: 87: DLB got disabled because it was unsuitable to use. 87: Average load imbalance: 5.1%. 87: The balanceable part of the MD step is 48%, load imbalance is computed from this. 87: Part of the total run time spent waiting due to load imbalance: 2.5%. 87: 87: 87: Core t (s) Wall t (s) (%) 87: Time: 0.074 0.042 176.7 87: (ns/day) (hour/ns) 87: Performance: 35.159 0.683 87: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_reference.edr as single precision energy file 87: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.edr as single precision energy file 87: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 87: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 87: that with the Verlet scheme, nstlist has no effect on the accuracy of 87: your simulation. 87: 87: 87: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 87: Setting nstcalcenergy (100) equal to nstenergy (4) 87: 87: Generating 1-4 interactions: fudge = 0.5 87: Number of degrees of freedom in T-Coupling group System is 27.00 87: 87: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 87: NVE simulation: will use the initial temperature of 398.997 K for 87: determining the Verlet buffer size 87: 87: 87: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 87: You are using a plain Coulomb cut-off, which might produce artifacts. 87: You might want to consider using PME electrostatics. 87: 87: 87: 87: NOTE 5 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 87: COM removal frequency is set to (5). 87: Other settings require a global communication frequency of 4. 87: Note that this will require additional global communication steps, 87: which will reduce performance when using multiple ranks. 87: Consider setting nstcomm to a multiple of 4. 87: 87: 87: There were 5 NOTEs 87: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 87: Can not increase nstlist because an NVE ensemble is used 87: Using 2 MPI threads 87: Using 1 OpenMP thread per tMPI thread 87: 87: 87: NOTE: The number of threads is not equal to the number of (logical) cpus 87: and the -pin option is set to auto: will not pin threads to cpus. 87: This can lead to significant performance degradation. 87: Consider using -pin on (and -pinoffset in case you run multiple jobs). 87: starting mdrun 'spc2' 87: 16 steps, 0.0 ps. 87: Generated 330891 of the 330891 non-bonded parameter combinations 87: 87: Generated 330891 of the 330891 1-4 parameter combinations 87: 87: Excluding 2 bonded neighbours molecule type 'SOL' 87: 87: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/tip3p5.gro' 87: 87: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 87: 87: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 87: 87: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 87: 87: Note that mdrun will redetermine rlist based on the actual pair-list setup 87: 87: This run will generate roughly 0 Mb of data 87: 87: Writing final coordinates. 87: 87: 87: Dynamic load balancing report: 87: DLB got disabled because it was unsuitable to use. 87: Average load imbalance: 6.9%. 87: The balanceable part of the MD step is 53%, load imbalance is computed from this. 87: Part of the total run time spent waiting due to load imbalance: 3.6%. 87: 87: 87: Core t (s) Wall t (s) (%) 87: Time: 0.049 0.025 193.1 87: (ns/day) (hour/ns) 87: Performance: 58.454 0.411 87: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_reference.edr as single precision energy file 87: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.edr as single precision energy file 87: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 87: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 87: that with the Verlet scheme, nstlist has no effect on the accuracy of 87: your simulation. 87: 87: 87: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 87: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 87: setting nstcomm equal to nstcalcenergy for less overhead 87: 87: Generating 1-4 interactions: fudge = 0.5 87: Number of degrees of freedom in T-Coupling group System is 27.00 87: 87: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 87: NVE simulation: will use the initial temperature of 398.997 K for 87: determining the Verlet buffer size 87: 87: 87: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 87: You are using a plain Coulomb cut-off, which might produce artifacts. 87: You might want to consider using PME electrostatics. 87: 87: 87: 87: NOTE 5 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 87: COM removal frequency is set to (5). 87: Other settings require a global communication frequency of 100. 87: Note that this will require additional global communication steps, 87: which will reduce performance when using multiple ranks. 87: Consider setting nstcomm to a multiple of 100. 87: 87: 87: There were 5 NOTEs 87: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 87: Can not increase nstlist because an NVE ensemble is used 87: Using 2 MPI threads 87: Using 1 OpenMP thread per tMPI thread 87: 87: 87: NOTE: The number of threads is not equal to the number of (logical) cpus 87: and the -pin option is set to auto: will not pin threads to cpus. 87: This can lead to significant performance degradation. 87: Consider using -pin on (and -pinoffset in case you run multiple jobs). 87: starting mdrun 'spc2' 87: 16 steps, 0.0 ps. 87: Generated 330891 of the 330891 non-bonded parameter combinations 87: 87: Generated 330891 of the 330891 1-4 parameter combinations 87: 87: Excluding 2 bonded neighbours molecule type 'SOL' 87: 87: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/tip3p5.gro' 87: 87: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 87: 87: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 87: 87: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 87: 87: Note that mdrun will redetermine rlist based on the actual pair-list setup 87: 87: This run will generate roughly 0 Mb of data 87: 87: Writing final coordinates. 87: 87: 87: Dynamic load balancing report: 87: DLB was off during the run due to low measured imbalance. 87: Average load imbalance: 6.5%. 87: The balanceable part of the MD step is 25%, load imbalance is computed from this. 87: Part of the total run time spent waiting due to load imbalance: 1.6%. 87: 87: 87: Core t (s) Wall t (s) (%) 87: Time: 0.080 0.042 192.3 87: (ns/day) (hour/ns) 87: Performance: 35.276 0.680 87: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_reference.edr as single precision energy file 87: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.edr as single precision energy file 87: 87: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 87: that with the Verlet scheme, nstlist has no effect on the accuracy of 87: your simulation. 87: 87: 87: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 87: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 87: setting nstcomm equal to nstcalcenergy for less overhead 87: 87: Generating 1-4 interactions: fudge = 0.5 87: Number of degrees of freedom in T-Coupling group System is 27.00 87: 87: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 87: NVE simulation: will use the initial temperature of 398.997 K for 87: determining the Verlet buffer size 87: 87: 87: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 87: You are using a plain Coulomb cut-off, which might produce artifacts. 87: You might want to consider using PME electrostatics. 87: 87: 87: 87: NOTE 5 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 87: COM removal frequency is set to (5). 87: Other settings require a global communication frequency of 100. 87: Note that this will require additional global communication steps, 87: which will reduce performance when using multiple ranks. 87: Consider setting nstcomm to a multiple of 100. 87: 87: 87: There were 5 NOTEs 87: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 87: Can not increase nstlist because an NVE ensemble is used 87: Using 2 MPI threads 87: Using 1 OpenMP thread per tMPI thread 87: 87: 87: NOTE: The number of threads is not equal to the number of (logical) cpus 87: and the -pin option is set to auto: will not pin threads to cpus. 87: This can lead to significant performance degradation. 87: Consider using -pin on (and -pinoffset in case you run multiple jobs). 87: starting mdrun 'spc2' 87: 16 steps, 0.0 ps. 87: Generated 330891 of the 330891 non-bonded parameter combinations 87: 87: Generated 330891 of the 330891 1-4 parameter combinations 87: 87: Excluding 2 bonded neighbours molecule type 'SOL' 87: 87: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/tip3p5.gro' 87: 87: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 87: 87: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 87: 87: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 87: 87: Note that mdrun will redetermine rlist based on the actual pair-list setup 87: 87: This run will generate roughly 0 Mb of data 87: 87: Writing final coordinates. 87: 87: 87: Dynamic load balancing report: 87: DLB got disabled because it was unsuitable to use. 87: Average load imbalance: 7.4%. 87: The balanceable part of the MD step is 49%, load imbalance is computed from this. 87: Part of the total run time spent waiting due to load imbalance: 3.7%. 87: 87: 87: Core t (s) Wall t (s) (%) 87: Time: 0.067 0.034 194.5 87: (ns/day) (hour/ns) 87: Performance: 42.659 0.563 87: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_reference.edr as single precision energy file 87: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.edr as single precision energy file 87: 87: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 87: that with the Verlet scheme, nstlist has no effect on the accuracy of 87: your simulation. 87: 87: 87: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 87: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 87: setting nstcomm equal to nstcalcenergy for less overhead 87: 87: Generating 1-4 interactions: fudge = 0.5 87: Number of degrees of freedom in T-Coupling group System is 27.00 87: 87: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 87: NVE simulation: will use the initial temperature of 398.997 K for 87: determining the Verlet buffer size 87: 87: 87: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 87: You are using a plain Coulomb cut-off, which might produce artifacts. 87: You might want to consider using PME electrostatics. 87: 87: 87: 87: NOTE 5 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 87: COM removal frequency is set to (5). 87: Other settings require a global communication frequency of 100. 87: Note that this will require additional global communication steps, 87: which will reduce performance when using multiple ranks. 87: Consider setting nstcomm to a multiple of 100. 87: 87: 87: There were 5 NOTEs 87: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 87: Can not increase nstlist because an NVE ensemble is used 87: Using 2 MPI threads 87: Using 1 OpenMP thread per tMPI thread 87: 87: 87: NOTE: The number of threads is not equal to the number of (logical) cpus 87: and the -pin option is set to auto: will not pin threads to cpus. 87: This can lead to significant performance degradation. 87: Consider using -pin on (and -pinoffset in case you run multiple jobs). 87: starting mdrun 'spc2' 87: 16 steps, 0.0 ps. 87: Generated 330891 of the 330891 non-bonded parameter combinations 87: 87: Generated 330891 of the 330891 1-4 parameter combinations 87: 87: Excluding 2 bonded neighbours molecule type 'SOL' 87: 87: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/tip3p5.gro' 87: 87: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 87: 87: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 87: 87: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 87: 87: Note that mdrun will redetermine rlist based on the actual pair-list setup 87: 87: This run will generate roughly 0 Mb of data 87: 87: Writing final coordinates. 87: 87: 87: Dynamic load balancing report: 87: DLB got disabled because it was unsuitable to use. 87: Average load imbalance: 6.3%. 87: The balanceable part of the MD step is 50%, load imbalance is computed from this. 87: Part of the total run time spent waiting due to load imbalance: 3.2%. 87: 87: 87: Core t (s) Wall t (s) (%) 87: Time: 0.074 0.038 194.7 87: (ns/day) (hour/ns) 87: Performance: 38.857 0.618 87: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_reference.edr as single precision energy file 87: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.edr as single precision energy file 87: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/9 (29301 ms) 87: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/10 87: 87: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 87: that with the Verlet scheme, nstlist has no effect on the accuracy of 87: your simulation. 87: 87: 87: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 87: Setting nstcalcenergy (100) equal to nstenergy (1) 87: 87: Generating 1-4 interactions: fudge = 0.5 87: Number of degrees of freedom in T-Coupling group System is 27.00 87: 87: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 87: NVE simulation: will use the initial temperature of 398.997 K for 87: determining the Verlet buffer size 87: 87: 87: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 87: You are using a plain Coulomb cut-off, which might produce artifacts. 87: You might want to consider using PME electrostatics. 87: 87: 87: 87: There were 4 NOTEs 87: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 87: Can not increase nstlist because an NVE ensemble is used 87: Using 2 MPI threads 87: Using 1 OpenMP thread per tMPI thread 87: 87: 87: NOTE: The number of threads is not equal to the number of (logical) cpus 87: and the -pin option is set to auto: will not pin threads to cpus. 87: This can lead to significant performance degradation. 87: Consider using -pin on (and -pinoffset in case you run multiple jobs). 87: starting mdrun 'spc2' 87: 16 steps, 0.0 ps. 87: Generated 330891 of the 330891 non-bonded parameter combinations 87: 87: Generated 330891 of the 330891 1-4 parameter combinations 87: 87: Excluding 2 bonded neighbours molecule type 'SOL' 87: 87: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/tip3p5.gro' 87: 87: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 87: 87: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 87: 87: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 87: 87: Note that mdrun will redetermine rlist based on the actual pair-list setup 87: 87: This run will generate roughly 0 Mb of data 87: 87: Writing final coordinates. 87: 87: 87: Dynamic load balancing report: 87: DLB was off during the run due to low measured imbalance. 87: Average load imbalance: 2.8%. 87: The balanceable part of the MD step is 38%, load imbalance is computed from this. 87: Part of the total run time spent waiting due to load imbalance: 1.0%. 87: 87: 87: Core t (s) Wall t (s) (%) 87: Time: 0.087 0.044 197.2 87: (ns/day) (hour/ns) 87: Performance: 33.338 0.720 87: 87: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 87: that with the Verlet scheme, nstlist has no effect on the accuracy of 87: your simulation. 87: 87: 87: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 87: Setting nstcalcenergy (100) equal to nstenergy (1) 87: 87: Generating 1-4 interactions: fudge = 0.5 87: Number of degrees of freedom in T-Coupling group System is 27.00 87: 87: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 87: NVE simulation: will use the initial temperature of 398.997 K for 87: determining the Verlet buffer size 87: 87: 87: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 87: You are using a plain Coulomb cut-off, which might produce artifacts. 87: You might want to consider using PME electrostatics. 87: 87: 87: 87: There were 4 NOTEs 87: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 87: Can not increase nstlist because an NVE ensemble is used 87: Using 2 MPI threads 87: Using 1 OpenMP thread per tMPI thread 87: 87: 87: NOTE: The number of threads is not equal to the number of (logical) cpus 87: and the -pin option is set to auto: will not pin threads to cpus. 87: This can lead to significant performance degradation. 87: Consider using -pin on (and -pinoffset in case you run multiple jobs). 87: starting mdrun 'spc2' 87: 16 steps, 0.0 ps. 87: Generated 330891 of the 330891 non-bonded parameter combinations 87: 87: Generated 330891 of the 330891 1-4 parameter combinations 87: 87: Excluding 2 bonded neighbours molecule type 'SOL' 87: 87: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/tip3p5.gro' 87: 87: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 87: 87: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 87: 87: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 87: 87: Note that mdrun will redetermine rlist based on the actual pair-list setup 87: 87: This run will generate roughly 0 Mb of data 87: 87: Writing final coordinates. 87: 87: 87: Dynamic load balancing report: 87: DLB got disabled because it was unsuitable to use. 87: Average load imbalance: 3.7%. 87: The balanceable part of the MD step is 60%, load imbalance is computed from this. 87: Part of the total run time spent waiting due to load imbalance: 2.2%. 87: 87: 87: Core t (s) Wall t (s) (%) 87: Time: 0.079 0.040 195.8 87: (ns/day) (hour/ns) 87: Performance: 36.338 0.660 87: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_reference.edr as single precision energy file 87: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.edr as single precision energy file 87: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 87: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 87: that with the Verlet scheme, nstlist has no effect on the accuracy of 87: your simulation. 87: 87: 87: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 87: Setting nstcalcenergy (100) equal to nstenergy (4) 87: 87: Generating 1-4 interactions: fudge = 0.5 87: Number of degrees of freedom in T-Coupling group System is 27.00 87: 87: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 87: NVE simulation: will use the initial temperature of 398.997 K for 87: determining the Verlet buffer size 87: 87: 87: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 87: You are using a plain Coulomb cut-off, which might produce artifacts. 87: You might want to consider using PME electrostatics. 87: 87: 87: 87: There were 4 NOTEs 87: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 87: Can not increase nstlist because an NVE ensemble is used 87: Using 2 MPI threads 87: Using 1 OpenMP thread per tMPI thread 87: 87: 87: NOTE: The number of threads is not equal to the number of (logical) cpus 87: and the -pin option is set to auto: will not pin threads to cpus. 87: This can lead to significant performance degradation. 87: Consider using -pin on (and -pinoffset in case you run multiple jobs). 87: starting mdrun 'spc2' 87: 16 steps, 0.0 ps. 87: Generated 330891 of the 330891 non-bonded parameter combinations 87: 87: Generated 330891 of the 330891 1-4 parameter combinations 87: 87: Excluding 2 bonded neighbours molecule type 'SOL' 87: 87: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/tip3p5.gro' 87: 87: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 87: 87: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 87: 87: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 87: 87: Note that mdrun will redetermine rlist based on the actual pair-list setup 87: 87: This run will generate roughly 0 Mb of data 87: 87: Writing final coordinates. 87: 87: 87: Dynamic load balancing report: 87: DLB got disabled because it was unsuitable to use. 87: Average load imbalance: 5.4%. 87: The balanceable part of the MD step is 48%, load imbalance is computed from this. 87: Part of the total run time spent waiting due to load imbalance: 2.6%. 87: 87: 87: Core t (s) Wall t (s) (%) 87: Time: 0.077 0.042 186.2 87: (ns/day) (hour/ns) 87: Performance: 35.351 0.679 87: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_reference.edr as single precision energy file 87: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.edr as single precision energy file 87: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 87: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 87: that with the Verlet scheme, nstlist has no effect on the accuracy of 87: your simulation. 87: 87: 87: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 87: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 87: setting nstcomm equal to nstcalcenergy for less overhead 87: 87: Generating 1-4 interactions: fudge = 0.5 87: Number of degrees of freedom in T-Coupling group System is 27.00 87: 87: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 87: NVE simulation: will use the initial temperature of 398.997 K for 87: determining the Verlet buffer size 87: 87: 87: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 87: You are using a plain Coulomb cut-off, which might produce artifacts. 87: You might want to consider using PME electrostatics. 87: 87: 87: 87: There were 4 NOTEs 87: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 87: Can not increase nstlist because an NVE ensemble is used 87: Using 2 MPI threads 87: Using 1 OpenMP thread per tMPI thread 87: 87: 87: NOTE: The number of threads is not equal to the number of (logical) cpus 87: and the -pin option is set to auto: will not pin threads to cpus. 87: This can lead to significant performance degradation. 87: Consider using -pin on (and -pinoffset in case you run multiple jobs). 87: starting mdrun 'spc2' 87: 16 steps, 0.0 ps. 87: Generated 330891 of the 330891 non-bonded parameter combinations 87: 87: Generated 330891 of the 330891 1-4 parameter combinations 87: 87: Excluding 2 bonded neighbours molecule type 'SOL' 87: 87: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/tip3p5.gro' 87: 87: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 87: 87: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 87: 87: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 87: 87: Note that mdrun will redetermine rlist based on the actual pair-list setup 87: 87: This run will generate roughly 0 Mb of data 87: 87: Writing final coordinates. 87: 87: 87: Dynamic load balancing report: 87: DLB got disabled because it was unsuitable to use. 87: Average load imbalance: 5.2%. 87: The balanceable part of the MD step is 48%, load imbalance is computed from this. 87: Part of the total run time spent waiting due to load imbalance: 2.5%. 87: 87: 87: Core t (s) Wall t (s) (%) 87: Time: 0.052 0.027 195.2 87: (ns/day) (hour/ns) 87: Performance: 55.173 0.435 87: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_reference.edr as single precision energy file 87: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.edr as single precision energy file 87: 87: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 87: that with the Verlet scheme, nstlist has no effect on the accuracy of 87: your simulation. 87: 87: 87: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 87: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 87: setting nstcomm equal to nstcalcenergy for less overhead 87: 87: Generating 1-4 interactions: fudge = 0.5 87: Number of degrees of freedom in T-Coupling group System is 27.00 87: 87: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 87: NVE simulation: will use the initial temperature of 398.997 K for 87: determining the Verlet buffer size 87: 87: 87: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 87: You are using a plain Coulomb cut-off, which might produce artifacts. 87: You might want to consider using PME electrostatics. 87: 87: 87: 87: There were 4 NOTEs 87: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 87: Can not increase nstlist because an NVE ensemble is used 87: Using 2 MPI threads 87: Using 1 OpenMP thread per tMPI thread 87: 87: 87: NOTE: The number of threads is not equal to the number of (logical) cpus 87: and the -pin option is set to auto: will not pin threads to cpus. 87: This can lead to significant performance degradation. 87: Consider using -pin on (and -pinoffset in case you run multiple jobs). 87: starting mdrun 'spc2' 87: 16 steps, 0.0 ps. 87: Generated 330891 of the 330891 non-bonded parameter combinations 87: 87: Generated 330891 of the 330891 1-4 parameter combinations 87: 87: Excluding 2 bonded neighbours molecule type 'SOL' 87: 87: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/tip3p5.gro' 87: 87: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 87: 87: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 87: 87: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 87: 87: Note that mdrun will redetermine rlist based on the actual pair-list setup 87: 87: This run will generate roughly 0 Mb of data 87: 87: Writing final coordinates. 87: 87: 87: Dynamic load balancing report: 87: DLB was off during the run due to low measured imbalance. 87: Average load imbalance: 6.2%. 87: The balanceable part of the MD step is 12%, load imbalance is computed from this. 87: Part of the total run time spent waiting due to load imbalance: 0.7%. 87: 87: 87: Core t (s) Wall t (s) (%) 87: Time: 0.095 0.049 195.1 87: (ns/day) (hour/ns) 87: Performance: 30.230 0.794 87: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_reference.edr as single precision energy file 87: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.edr as single precision energy file 87: 87: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 87: that with the Verlet scheme, nstlist has no effect on the accuracy of 87: your simulation. 87: 87: 87: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 87: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 87: setting nstcomm equal to nstcalcenergy for less overhead 87: 87: Generating 1-4 interactions: fudge = 0.5 87: Number of degrees of freedom in T-Coupling group System is 27.00 87: 87: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 87: NVE simulation: will use the initial temperature of 398.997 K for 87: determining the Verlet buffer size 87: 87: 87: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 87: You are using a plain Coulomb cut-off, which might produce artifacts. 87: You might want to consider using PME electrostatics. 87: 87: 87: 87: There were 4 NOTEs 87: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 87: Can not increase nstlist because an NVE ensemble is used 87: Using 2 MPI threads 87: Using 1 OpenMP thread per tMPI thread 87: 87: 87: NOTE: The number of threads is not equal to the number of (logical) cpus 87: and the -pin option is set to auto: will not pin threads to cpus. 87: This can lead to significant performance degradation. 87: Consider using -pin on (and -pinoffset in case you run multiple jobs). 87: starting mdrun 'spc2' 87: 16 steps, 0.0 ps. 87: Generated 330891 of the 330891 non-bonded parameter combinations 87: 87: Generated 330891 of the 330891 1-4 parameter combinations 87: 87: Excluding 2 bonded neighbours molecule type 'SOL' 87: 87: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/tip3p5.gro' 87: 87: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 87: 87: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 87: 87: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 87: 87: Note that mdrun will redetermine rlist based on the actual pair-list setup 87: 87: This run will generate roughly 0 Mb of data 87: 87: Writing final coordinates. 87: 87: 87: Dynamic load balancing report: 87: DLB got disabled because it was unsuitable to use. 87: Average load imbalance: 4.6%. 87: The balanceable part of the MD step is 58%, load imbalance is computed from this. 87: Part of the total run time spent waiting due to load imbalance: 2.7%. 87: 87: 87: Core t (s) Wall t (s) (%) 87: Time: 0.059 0.030 194.7 87: (ns/day) (hour/ns) 87: Performance: 48.711 0.493 87: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_reference.edr as single precision energy file 87: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.edr as single precision energy file 87: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/10 (27401 ms) 87: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/11 87: 87: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 87: that with the Verlet scheme, nstlist has no effect on the accuracy of 87: your simulation. 87: 87: 87: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 87: Setting nstcalcenergy (100) equal to nstenergy (1) 87: 87: Generating 1-4 interactions: fudge = 0.5 87: Number of degrees of freedom in T-Coupling group System is 27.00 87: 87: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 87: You are using a plain Coulomb cut-off, which might produce artifacts. 87: You might want to consider using PME electrostatics. 87: 87: 87: 87: There were 3 NOTEs 87: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 87: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 87: 87: Using 2 MPI threads 87: Using 1 OpenMP thread per tMPI thread 87: 87: 87: NOTE: The number of threads is not equal to the number of (logical) cpus 87: and the -pin option is set to auto: will not pin threads to cpus. 87: This can lead to significant performance degradation. 87: Consider using -pin on (and -pinoffset in case you run multiple jobs). 87: starting mdrun 'spc2' 87: 16 steps, 0.0 ps. 87: Generated 330891 of the 330891 non-bonded parameter combinations 87: 87: Generated 330891 of the 330891 1-4 parameter combinations 87: 87: Excluding 2 bonded neighbours molecule type 'SOL' 87: 87: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/tip3p5.gro' 87: 87: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 87: 87: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 87: 87: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 87: 87: Note that mdrun will redetermine rlist based on the actual pair-list setup 87: 87: This run will generate roughly 0 Mb of data 87: 87: Writing final coordinates. 87: 87: NOTE: 7 % of the run time was spent communicating energies, 87: you might want to increase some nst* mdp options 87: 87: Core t (s) Wall t (s) (%) 87: Time: 0.188 0.095 198.5 87: (ns/day) (hour/ns) 87: Performance: 15.542 1.544 87: 87: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 87: that with the Verlet scheme, nstlist has no effect on the accuracy of 87: your simulation. 87: 87: 87: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 87: Setting nstcalcenergy (100) equal to nstenergy (1) 87: 87: Generating 1-4 interactions: fudge = 0.5 87: Number of degrees of freedom in T-Coupling group System is 27.00 87: 87: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 87: You are using a plain Coulomb cut-off, which might produce artifacts. 87: You might want to consider using PME electrostatics. 87: 87: 87: 87: There were 3 NOTEs 87: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 87: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 87: 87: Using 2 MPI threads 87: Using 1 OpenMP thread per tMPI thread 87: 87: 87: NOTE: The number of threads is not equal to the number of (logical) cpus 87: and the -pin option is set to auto: will not pin threads to cpus. 87: This can lead to significant performance degradation. 87: Consider using -pin on (and -pinoffset in case you run multiple jobs). 87: starting mdrun 'spc2' 87: 16 steps, 0.0 ps. 87: Generated 330891 of the 330891 non-bonded parameter combinations 87: 87: Generated 330891 of the 330891 1-4 parameter combinations 87: 87: Excluding 2 bonded neighbours molecule type 'SOL' 87: 87: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/tip3p5.gro' 87: 87: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 87: 87: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 87: 87: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 87: 87: Note that mdrun will redetermine rlist based on the actual pair-list setup 87: 87: This run will generate roughly 0 Mb of data 87: 87: Writing final coordinates. 87: 87: NOTE: 11 % of the run time was spent communicating energies, 87: you might want to increase some nst* mdp options 87: 87: Core t (s) Wall t (s) (%) 87: Time: 0.085 0.049 175.1 87: (ns/day) (hour/ns) 87: Performance: 30.149 0.796 87: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_reference.edr as single precision energy file 87: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.edr as single precision energy file 87: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 87: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 87: that with the Verlet scheme, nstlist has no effect on the accuracy of 87: your simulation. 87: 87: 87: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 87: Setting nstcalcenergy (100) equal to nstenergy (4) 87: 87: Generating 1-4 interactions: fudge = 0.5 87: Number of degrees of freedom in T-Coupling group System is 27.00 87: 87: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 87: You are using a plain Coulomb cut-off, which might produce artifacts. 87: You might want to consider using PME electrostatics. 87: 87: 87: 87: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 87: COM removal frequency is set to (5). 87: Other settings require a global communication frequency of 2. 87: Note that this will require additional global communication steps, 87: which will reduce performance when using multiple ranks. 87: Consider setting nstcomm to a multiple of 2. 87: 87: 87: There were 4 NOTEs 87: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 87: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 87: 87: Using 2 MPI threads 87: Using 1 OpenMP thread per tMPI thread 87: 87: 87: NOTE: The number of threads is not equal to the number of (logical) cpus 87: and the -pin option is set to auto: will not pin threads to cpus. 87: This can lead to significant performance degradation. 87: Consider using -pin on (and -pinoffset in case you run multiple jobs). 87: starting mdrun 'spc2' 87: 16 steps, 0.0 ps. 87: Generated 330891 of the 330891 non-bonded parameter combinations 87: 87: Generated 330891 of the 330891 1-4 parameter combinations 87: 87: Excluding 2 bonded neighbours molecule type 'SOL' 87: 87: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/tip3p5.gro' 87: 87: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 87: 87: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 87: 87: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 87: 87: Note that mdrun will redetermine rlist based on the actual pair-list setup 87: 87: This run will generate roughly 0 Mb of data 87: 87: Writing final coordinates. 87: 87: Core t (s) Wall t (s) (%) 87: Time: 0.051 0.026 193.0 87: (ns/day) (hour/ns) 87: Performance: 55.901 0.429 87: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_reference.edr as single precision energy file 87: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.edr as single precision energy file 87: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 87: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 87: that with the Verlet scheme, nstlist has no effect on the accuracy of 87: your simulation. 87: 87: 87: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 87: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 87: setting nstcomm equal to nstcalcenergy for less overhead 87: 87: Generating 1-4 interactions: fudge = 0.5 87: Number of degrees of freedom in T-Coupling group System is 27.00 87: 87: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 87: You are using a plain Coulomb cut-off, which might produce artifacts. 87: You might want to consider using PME electrostatics. 87: 87: 87: 87: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 87: COM removal frequency is set to (5). 87: Other settings require a global communication frequency of 2. 87: Note that this will require additional global communication steps, 87: which will reduce performance when using multiple ranks. 87: Consider setting nstcomm to a multiple of 2. 87: 87: 87: There were 4 NOTEs 87: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 87: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 87: 87: Using 2 MPI threads 87: Using 1 OpenMP thread per tMPI thread 87: 87: 87: NOTE: The number of threads is not equal to the number of (logical) cpus 87: and the -pin option is set to auto: will not pin threads to cpus. 87: This can lead to significant performance degradation. 87: Consider using -pin on (and -pinoffset in case you run multiple jobs). 87: starting mdrun 'spc2' 87: 16 steps, 0.0 ps. 87: Generated 330891 of the 330891 non-bonded parameter combinations 87: 87: Generated 330891 of the 330891 1-4 parameter combinations 87: 87: Excluding 2 bonded neighbours molecule type 'SOL' 87: 87: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/tip3p5.gro' 87: 87: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 87: 87: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 87: 87: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 87: 87: Note that mdrun will redetermine rlist based on the actual pair-list setup 87: 87: This run will generate roughly 0 Mb of data 87: 87: Writing final coordinates. 87: 87: Core t (s) Wall t (s) (%) 87: Time: 0.085 0.045 187.7 87: (ns/day) (hour/ns) 87: Performance: 32.317 0.743 87: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_reference.edr as single precision energy file 87: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.edr as single precision energy file 87: 87: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 87: that with the Verlet scheme, nstlist has no effect on the accuracy of 87: your simulation. 87: 87: 87: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 87: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 87: setting nstcomm equal to nstcalcenergy for less overhead 87: 87: Generating 1-4 interactions: fudge = 0.5 87: Number of degrees of freedom in T-Coupling group System is 27.00 87: 87: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 87: You are using a plain Coulomb cut-off, which might produce artifacts. 87: You might want to consider using PME electrostatics. 87: 87: 87: 87: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 87: COM removal frequency is set to (5). 87: Other settings require a global communication frequency of 2. 87: Note that this will require additional global communication steps, 87: which will reduce performance when using multiple ranks. 87: Consider setting nstcomm to a multiple of 2. 87: 87: 87: There were 4 NOTEs 87: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 87: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 87: 87: Using 2 MPI threads 87: Using 1 OpenMP thread per tMPI thread 87: 87: 87: NOTE: The number of threads is not equal to the number of (logical) cpus 87: and the -pin option is set to auto: will not pin threads to cpus. 87: This can lead to significant performance degradation. 87: Consider using -pin on (and -pinoffset in case you run multiple jobs). 87: starting mdrun 'spc2' 87: 16 steps, 0.0 ps. 87: Generated 330891 of the 330891 non-bonded parameter combinations 87: 87: Generated 330891 of the 330891 1-4 parameter combinations 87: 87: Excluding 2 bonded neighbours molecule type 'SOL' 87: 87: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/tip3p5.gro' 87: 87: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 87: 87: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 87: 87: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 87: 87: Note that mdrun will redetermine rlist based on the actual pair-list setup 87: 87: This run will generate roughly 0 Mb of data 87: 87: Writing final coordinates. 87: 87: Core t (s) Wall t (s) (%) 87: Time: 0.102 0.052 195.3 87: (ns/day) (hour/ns) 87: Performance: 28.178 0.852 87: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_reference.edr as single precision energy file 87: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.edr as single precision energy file 87: 87: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 87: that with the Verlet scheme, nstlist has no effect on the accuracy of 87: your simulation. 87: 87: 87: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 87: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 87: setting nstcomm equal to nstcalcenergy for less overhead 87: 87: Generating 1-4 interactions: fudge = 0.5 87: Number of degrees of freedom in T-Coupling group System is 27.00 87: 87: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 87: You are using a plain Coulomb cut-off, which might produce artifacts. 87: You might want to consider using PME electrostatics. 87: 87: 87: 87: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 87: COM removal frequency is set to (5). 87: Other settings require a global communication frequency of 2. 87: Note that this will require additional global communication steps, 87: which will reduce performance when using multiple ranks. 87: Consider setting nstcomm to a multiple of 2. 87: 87: 87: There were 4 NOTEs 87: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 87: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 87: 87: Using 2 MPI threads 87: Using 1 OpenMP thread per tMPI thread 87: 87: 87: NOTE: The number of threads is not equal to the number of (logical) cpus 87: and the -pin option is set to auto: will not pin threads to cpus. 87: This can lead to significant performance degradation. 87: Consider using -pin on (and -pinoffset in case you run multiple jobs). 87: starting mdrun 'spc2' 87: 16 steps, 0.0 ps. 87: Generated 330891 of the 330891 non-bonded parameter combinations 87: 87: Generated 330891 of the 330891 1-4 parameter combinations 87: 87: Excluding 2 bonded neighbours molecule type 'SOL' 87: 87: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/tip3p5.gro' 87: 87: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 87: 87: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 87: 87: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 87: 87: Note that mdrun will redetermine rlist based on the actual pair-list setup 87: 87: This run will generate roughly 0 Mb of data 87: 87: Writing final coordinates. 87: 87: Core t (s) Wall t (s) (%) 87: Time: 0.054 0.028 193.4 87: (ns/day) (hour/ns) 87: Performance: 52.878 0.454 87: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_reference.edr as single precision energy file 87: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.edr as single precision energy file 87: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/11 (27778 ms) 87: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/12 87: 87: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 87: that with the Verlet scheme, nstlist has no effect on the accuracy of 87: your simulation. 87: 87: 87: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 87: Setting nstcalcenergy (100) equal to nstenergy (1) 87: 87: Generating 1-4 interactions: fudge = 0.5 87: Number of degrees of freedom in T-Coupling group System is 27.00 87: 87: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 87: You are using a plain Coulomb cut-off, which might produce artifacts. 87: You might want to consider using PME electrostatics. 87: 87: 87: 87: There were 3 NOTEs 87: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 87: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 87: 87: Using 2 MPI threads 87: Using 1 OpenMP thread per tMPI thread 87: 87: 87: NOTE: The number of threads is not equal to the number of (logical) cpus 87: and the -pin option is set to auto: will not pin threads to cpus. 87: This can lead to significant performance degradation. 87: Consider using -pin on (and -pinoffset in case you run multiple jobs). 87: starting mdrun 'spc2' 87: 16 steps, 0.0 ps. 87: Generated 330891 of the 330891 non-bonded parameter combinations 87: 87: Generated 330891 of the 330891 1-4 parameter combinations 87: 87: Excluding 2 bonded neighbours molecule type 'SOL' 87: 87: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/tip3p5.gro' 87: 87: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 87: 87: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 87: 87: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 87: 87: Note that mdrun will redetermine rlist based on the actual pair-list setup 87: 87: This run will generate roughly 0 Mb of data 87: 87: Writing final coordinates. 87: 87: NOTE: 9 % of the run time was spent communicating energies, 87: you might want to increase some nst* mdp options 87: 87: Core t (s) Wall t (s) (%) 87: Time: 0.074 0.038 195.9 87: (ns/day) (hour/ns) 87: Performance: 38.665 0.621 87: 87: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 87: that with the Verlet scheme, nstlist has no effect on the accuracy of 87: your simulation. 87: 87: 87: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 87: Setting nstcalcenergy (100) equal to nstenergy (1) 87: 87: Generating 1-4 interactions: fudge = 0.5 87: Number of degrees of freedom in T-Coupling group System is 27.00 87: 87: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 87: You are using a plain Coulomb cut-off, which might produce artifacts. 87: You might want to consider using PME electrostatics. 87: 87: 87: 87: There were 3 NOTEs 87: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 87: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 87: 87: Using 2 MPI threads 87: Using 1 OpenMP thread per tMPI thread 87: 87: 87: NOTE: The number of threads is not equal to the number of (logical) cpus 87: and the -pin option is set to auto: will not pin threads to cpus. 87: This can lead to significant performance degradation. 87: Consider using -pin on (and -pinoffset in case you run multiple jobs). 87: starting mdrun 'spc2' 87: 16 steps, 0.0 ps. 87: Generated 330891 of the 330891 non-bonded parameter combinations 87: 87: Generated 330891 of the 330891 1-4 parameter combinations 87: 87: Excluding 2 bonded neighbours molecule type 'SOL' 87: 87: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/tip3p5.gro' 87: 87: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 87: 87: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 87: 87: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 87: 87: Note that mdrun will redetermine rlist based on the actual pair-list setup 87: 87: This run will generate roughly 0 Mb of data 87: 87: Writing final coordinates. 87: 87: Core t (s) Wall t (s) (%) 87: Time: 0.103 0.053 195.6 87: (ns/day) (hour/ns) 87: Performance: 27.868 0.861 87: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_reference.edr as single precision energy file 87: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.edr as single precision energy file 87: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 87: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 87: that with the Verlet scheme, nstlist has no effect on the accuracy of 87: your simulation. 87: 87: 87: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 87: Setting nstcalcenergy (100) equal to nstenergy (4) 87: 87: Generating 1-4 interactions: fudge = 0.5 87: Number of degrees of freedom in T-Coupling group System is 27.00 87: 87: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 87: You are using a plain Coulomb cut-off, which might produce artifacts. 87: You might want to consider using PME electrostatics. 87: 87: 87: 87: There were 3 NOTEs 87: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 87: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 87: 87: Using 2 MPI threads 87: Using 1 OpenMP thread per tMPI thread 87: 87: 87: NOTE: The number of threads is not equal to the number of (logical) cpus 87: and the -pin option is set to auto: will not pin threads to cpus. 87: This can lead to significant performance degradation. 87: Consider using -pin on (and -pinoffset in case you run multiple jobs). 87: starting mdrun 'spc2' 87: 16 steps, 0.0 ps. 87: Generated 330891 of the 330891 non-bonded parameter combinations 87: 87: Generated 330891 of the 330891 1-4 parameter combinations 87: 87: Excluding 2 bonded neighbours molecule type 'SOL' 87: 87: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/tip3p5.gro' 87: 87: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 87: 87: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 87: 87: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 87: 87: Note that mdrun will redetermine rlist based on the actual pair-list setup 87: 87: This run will generate roughly 0 Mb of data 87: 87: Writing final coordinates. 87: 87: Core t (s) Wall t (s) (%) 87: Time: 0.056 0.029 193.9 87: (ns/day) (hour/ns) 87: Performance: 50.671 0.474 87: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_reference.edr as single precision energy file 87: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.edr as single precision energy file 87: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 87: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 87: that with the Verlet scheme, nstlist has no effect on the accuracy of 87: your simulation. 87: 87: 87: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 87: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 87: setting nstcomm equal to nstcalcenergy for less overhead 87: 87: Generating 1-4 interactions: fudge = 0.5 87: Number of degrees of freedom in T-Coupling group System is 27.00 87: 87: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 87: You are using a plain Coulomb cut-off, which might produce artifacts. 87: You might want to consider using PME electrostatics. 87: 87: 87: 87: There were 3 NOTEs 87: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 87: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 87: 87: Using 2 MPI threads 87: Using 1 OpenMP thread per tMPI thread 87: 87: 87: NOTE: The number of threads is not equal to the number of (logical) cpus 87: and the -pin option is set to auto: will not pin threads to cpus. 87: This can lead to significant performance degradation. 87: Consider using -pin on (and -pinoffset in case you run multiple jobs). 87: starting mdrun 'spc2' 87: 16 steps, 0.0 ps. 87: Generated 330891 of the 330891 non-bonded parameter combinations 87: 87: Generated 330891 of the 330891 1-4 parameter combinations 87: 87: Excluding 2 bonded neighbours molecule type 'SOL' 87: 87: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/tip3p5.gro' 87: 87: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 87: 87: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 87: 87: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 87: 87: Note that mdrun will redetermine rlist based on the actual pair-list setup 87: 87: This run will generate roughly 0 Mb of data 87: 87: Writing final coordinates. 87: 87: Core t (s) Wall t (s) (%) 87: Time: 0.192 0.097 198.1 87: (ns/day) (hour/ns) 87: Performance: 15.165 1.583 87: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_reference.edr as single precision energy file 87: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.edr as single precision energy file 87: 87: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 87: that with the Verlet scheme, nstlist has no effect on the accuracy of 87: your simulation. 87: 87: 87: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 87: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 87: setting nstcomm equal to nstcalcenergy for less overhead 87: 87: Generating 1-4 interactions: fudge = 0.5 87: Number of degrees of freedom in T-Coupling group System is 27.00 87: 87: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 87: You are using a plain Coulomb cut-off, which might produce artifacts. 87: You might want to consider using PME electrostatics. 87: 87: 87: 87: There were 3 NOTEs 87: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 87: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 87: 87: Using 2 MPI threads 87: Using 1 OpenMP thread per tMPI thread 87: 87: 87: NOTE: The number of threads is not equal to the number of (logical) cpus 87: and the -pin option is set to auto: will not pin threads to cpus. 87: This can lead to significant performance degradation. 87: Consider using -pin on (and -pinoffset in case you run multiple jobs). 87: starting mdrun 'spc2' 87: 16 steps, 0.0 ps. 87: Generated 330891 of the 330891 non-bonded parameter combinations 87: 87: Generated 330891 of the 330891 1-4 parameter combinations 87: 87: Excluding 2 bonded neighbours molecule type 'SOL' 87: 87: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/tip3p5.gro' 87: 87: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 87: 87: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 87: 87: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 87: 87: Note that mdrun will redetermine rlist based on the actual pair-list setup 87: 87: This run will generate roughly 0 Mb of data 87: 87: Writing final coordinates. 87: 87: Core t (s) Wall t (s) (%) 87: Time: 0.204 0.103 198.1 87: (ns/day) (hour/ns) 87: Performance: 14.268 1.682 87: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_reference.edr as single precision energy file 87: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.edr as single precision energy file 87: 87: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 87: that with the Verlet scheme, nstlist has no effect on the accuracy of 87: your simulation. 87: 87: 87: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 87: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 87: setting nstcomm equal to nstcalcenergy for less overhead 87: 87: Generating 1-4 interactions: fudge = 0.5 87: Number of degrees of freedom in T-Coupling group System is 27.00 87: 87: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 87: You are using a plain Coulomb cut-off, which might produce artifacts. 87: You might want to consider using PME electrostatics. 87: 87: 87: 87: There were 3 NOTEs 87: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 87: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 87: 87: Using 2 MPI threads 87: Using 1 OpenMP thread per tMPI thread 87: 87: 87: NOTE: The number of threads is not equal to the number of (logical) cpus 87: and the -pin option is set to auto: will not pin threads to cpus. 87: This can lead to significant performance degradation. 87: Consider using -pin on (and -pinoffset in case you run multiple jobs). 87: starting mdrun 'spc2' 87: 16 steps, 0.0 ps. 87: Generated 330891 of the 330891 non-bonded parameter combinations 87: 87: Generated 330891 of the 330891 1-4 parameter combinations 87: 87: Excluding 2 bonded neighbours molecule type 'SOL' 87: 87: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/tip3p5.gro' 87: 87: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 87: 87: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 87: 87: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 87: 87: Note that mdrun will redetermine rlist based on the actual pair-list setup 87: 87: This run will generate roughly 0 Mb of data 87: 87: Writing final coordinates. 87: 87: Core t (s) Wall t (s) (%) 87: Time: 0.062 0.032 195.3 87: (ns/day) (hour/ns) 87: Performance: 45.931 0.523 87: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_reference.edr as single precision energy file 87: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.edr as single precision energy file 87: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/12 (27417 ms) 87: [----------] 13 tests from PropagatorsWithConstraints/PeriodicActionsTest (391560 ms total) 87: 87: [----------] Global test environment tear-down 87: [==========] 13 tests from 1 test suite ran. (391612 ms total) 87: [ PASSED ] 13 tests. 87/92 Test #87: MdrunCoordinationConstraintsTests2Ranks ... Passed 391.70 sec test 88 Start 88: MdrunFEPTests 88: Test command: /build/reproducible-path/gromacs-2025.1/build/basic/bin/mdrun-fep-test "-ntomp" "2" "--gtest_output=xml:/build/reproducible-path/gromacs-2025.1/build/basic/Testing/Temporary/MdrunFEPTests.xml" 88: Working Directory: /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests 88: Test timeout computed to be: 600 88: [==========] Running 14 tests from 2 test suites. 88: [----------] Global test environment set-up. 88: [----------] 2 tests from ExpandedEnsembleTest 88: [ RUN ] ExpandedEnsembleTest.ContinuationPreservesExpandedEnsembleState 88: 88: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/ExpandedEnsembleTest_ContinuationPreservesExpandedEnsembleState_input.mdp]: 88: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 88: that with the Verlet scheme, nstlist has no effect on the accuracy of 88: your simulation. 88: 88: Generating 1-4 interactions: fudge = 0.5 88: Number of degrees of freedom in T-Coupling group System is 79.00 88: 88: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/ExpandedEnsembleTest_ContinuationPreservesExpandedEnsembleState_input.mdp]: 88: You are using a plain Coulomb cut-off, which might produce artifacts. 88: You might want to consider using PME electrostatics. 88: 88: 88: 88: There were 2 NOTEs 88: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/ExpandedEnsembleTest_ContinuationPreservesExpandedEnsembleState.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 88: Changing nstlist from 8 to 20, rlist from 0.757 to 0.863 88: 88: Using 1 MPI thread 88: Using 2 OpenMP threads 88: 88: 88: NOTE: The number of threads is not equal to the number of (logical) cpus 88: and the -pin option is set to auto: will not pin threads to cpus. 88: This can lead to significant performance degradation. 88: Consider using -pin on (and -pinoffset in case you run multiple jobs). 88: starting mdrun '30 atom system in water' 88: 16 steps, 0.0 ps. 88: Generated 2485 of the 2485 non-bonded parameter combinations 88: 88: Generated 2485 of the 2485 1-4 parameter combinations 88: 88: Excluding 3 bonded neighbours molecule type 'nonanol' 88: 88: turning H bonds into constraints... 88: 88: Excluding 2 bonded neighbours molecule type 'SOL' 88: 88: turning H bonds into constraints... 88: 88: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/nonanol_vacuo.gro' 88: 88: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 88: 88: Calculated rlist for 1x1 atom pair-list as 0.764 nm, buffer size 0.064 nm 88: 88: Set rlist, assuming 4x4 atom pair-list, to 0.757 nm, buffer size 0.057 nm 88: 88: Note that mdrun will redetermine rlist based on the actual pair-list setup 88: 88: This run will generate roughly 0 Mb of data 88: 88: Writing final coordinates. 88: 88: Core t (s) Wall t (s) (%) 88: Time: 0.086 0.043 198.7 88: (ns/day) (hour/ns) 88: Performance: 33.914 0.708 88: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/ExpandedEnsembleTest_ContinuationPreservesExpandedEnsembleState.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 88: Overriding nsteps with value passed on the command line: 8 steps, 0.008 ps 88: Changing nstlist from 8 to 20, rlist from 0.757 to 0.863 88: 88: 88: Using 1 MPI thread 88: Using 2 OpenMP threads 88: 88: 88: NOTE: The number of threads is not equal to the number of (logical) cpus 88: and the -pin option is set to auto: will not pin threads to cpus. 88: This can lead to significant performance degradation. 88: Consider using -pin on (and -pinoffset in case you run multiple jobs). 88: starting mdrun '30 atom system in water' 88: 24 steps, 0.0 ps (continuing from step 16, 0.0 ps). 88: 88: Writing final coordinates. 88: 88: Core t (s) Wall t (s) (%) 88: Time: 0.064 0.033 196.2 88: (ns/day) (hour/ns) 88: Performance: 23.866 1.006 88: [ OK ] ExpandedEnsembleTest.ContinuationPreservesExpandedEnsembleState (338 ms) 88: [ RUN ] ExpandedEnsembleTest.WeightEquilibrationReported 88: 88: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/ExpandedEnsembleTest_WeightEquilibrationReported_input.mdp]: 88: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 88: that with the Verlet scheme, nstlist has no effect on the accuracy of 88: your simulation. 88: 88: Generating 1-4 interactions: fudge = 0.5 88: Number of degrees of freedom in T-Coupling group System is 79.00 88: 88: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/ExpandedEnsembleTest_WeightEquilibrationReported_input.mdp]: 88: You are using a plain Coulomb cut-off, which might produce artifacts. 88: You might want to consider using PME electrostatics. 88: 88: 88: 88: There were 2 NOTEs 88: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/ExpandedEnsembleTest_WeightEquilibrationReported.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 88: Changing nstlist from 8 to 20, rlist from 0.757 to 0.863 88: 88: Using 1 MPI thread 88: Using 2 OpenMP threads 88: 88: 88: NOTE: The number of threads is not equal to the number of (logical) cpus 88: and the -pin option is set to auto: will not pin threads to cpus. 88: This can lead to significant performance degradation. 88: Consider using -pin on (and -pinoffset in case you run multiple jobs). 88: starting mdrun '30 atom system in water' 88: 1 steps, 0.0 ps. 88: Generated 2485 of the 2485 non-bonded parameter combinations 88: 88: Generated 2485 of the 2485 1-4 parameter combinations 88: 88: Excluding 3 bonded neighbours molecule type 'nonanol' 88: 88: turning H bonds into constraints... 88: 88: Excluding 2 bonded neighbours molecule type 'SOL' 88: 88: turning H bonds into constraints... 88: 88: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/nonanol_vacuo.gro' 88: 88: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 88: 88: Calculated rlist for 1x1 atom pair-list as 0.764 nm, buffer size 0.064 nm 88: 88: Set rlist, assuming 4x4 atom pair-list, to 0.757 nm, buffer size 0.057 nm 88: 88: Note that mdrun will redetermine rlist based on the actual pair-list setup 88: 88: This run will generate roughly 0 Mb of data 88: 88: Writing final coordinates. 88: 88: Core t (s) Wall t (s) (%) 88: Time: 0.051 0.026 198.5 88: (ns/day) (hour/ns) 88: Performance: 6.758 3.552 88: [ OK ] ExpandedEnsembleTest.WeightEquilibrationReported (189 ms) 88: [----------] 2 tests from ExpandedEnsembleTest (528 ms total) 88: 88: [----------] 12 tests from EquivalentToReference/FreeEnergyReferenceTest 88: [ RUN ] EquivalentToReference/FreeEnergyReferenceTest.WithinTolerances/coulandvdwsequential_coul_s 88: 88: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/freeenergy/coulandvdwsequential_coul/grompp.mdp, line 149]: 88: For proper sampling of the (nearly) decoupled state, stochastic dynamics 88: should be used 88: 88: 88: WARNING 1 [file /build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/freeenergy/coulandvdwsequential_coul/grompp.mdp]: 88: The Berendsen thermostat does not generate the correct kinetic energy 88: distribution, and should not be used for new production simulations (in 88: our opinion). We would recommend the V-rescale thermostat. 88: 88: Generating 1-4 interactions: fudge = 0.5 88: Number of degrees of freedom in T-Coupling group System is 355.00 88: 88: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/freeenergy/coulandvdwsequential_coul/grompp.mdp]: 88: The optimal PME mesh load for parallel simulations is below 0.5 88: and for highly parallel simulations between 0.25 and 0.33, 88: for higher performance, increase the cut-off and the PME grid spacing. 88: 88: 88: 88: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/freeenergy/coulandvdwsequential_coul/grompp.mdp]: 88: For free energy simulations, the optimal load limit increases from 0.5 to 88: 0.667 88: 88: 88: 88: There were 3 NOTEs 88: 88: There was 1 WARNING 88: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/EquivalentToReference_FreeEnergyReferenceTest_WithinTolerances_coulandvdwsequential_coul_s_sim.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 88: Changing nstlist from 10 to 100, rlist from 1 to 1 88: 88: Using 1 MPI thread 88: Using 2 OpenMP threads 88: 88: 88: NOTE: The number of threads is not equal to the number of (logical) cpus 88: and the -pin option is set to auto: will not pin threads to cpus. 88: This can lead to significant performance degradation. 88: Consider using -pin on (and -pinoffset in case you run multiple jobs). 88: starting mdrun 'AA' 88: 20 steps, 0.0 ps. 88: Setting the LD random seed to -570589443 88: 88: Generated 153 of the 153 non-bonded parameter combinations 88: 88: Generated 153 of the 153 1-4 parameter combinations 88: 88: Excluding 3 bonded neighbours molecule type 'ASN' 88: 88: turning H bonds into constraints... 88: 88: Excluding 2 bonded neighbours molecule type 'SOL' 88: 88: turning H bonds into constraints... 88: 88: Coupling 1 copies of molecule type 'ASN' 88: 88: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/freeenergy/coulandvdwsequential_coul/conf.gro' 88: Analysing residue names: 88: There are: 1 Protein residues 88: There are: 56 Water residues 88: Analysing Protein... 88: 88: The largest distance between non-perturbed excluded atoms is 0.164 nm between atom 41 and 42 88: 88: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 88: 88: Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm 88: 88: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm 88: 88: Note that mdrun will redetermine rlist based on the actual pair-list setup 88: Calculating fourier grid dimensions for X Y Z 88: Using a fourier grid of 28x28x28, spacing 0.108 0.108 0.108 88: 88: Estimate for the relative computational load of the PME mesh part: 0.89 88: 88: This run will generate roughly 0 Mb of data 88: 88: Writing final coordinates. 88: 88: Core t (s) Wall t (s) (%) 88: Time: 0.760 0.380 199.8 88: (ns/day) (hour/ns) 88: Performance: 4.772 5.030 88: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/EquivalentToReference_FreeEnergyReferenceTest_WithinTolerances_coulandvdwsequential_coul_s_energy.edr as single precision energy file 88: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 17 time 0.017 Reading energy frame 18 time 0.018 Reading energy frame 19 time 0.019 Reading energy frame 20 time 0.020 Last energy frame read 20 time 0.020 trr version: GMX_trn_file (single precision) 88: [ OK ] EquivalentToReference/FreeEnergyReferenceTest.WithinTolerances/coulandvdwsequential_coul_s (1367 ms) 88: [ RUN ] EquivalentToReference/FreeEnergyReferenceTest.WithinTolerances/coulandvdwsequential_vdw_s 88: 88: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/freeenergy/coulandvdwsequential_vdw/grompp.mdp, line 148]: 88: For proper sampling of the (nearly) decoupled state, stochastic dynamics 88: should be used 88: 88: 88: WARNING 1 [file /build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/freeenergy/coulandvdwsequential_vdw/grompp.mdp]: 88: The Berendsen thermostat does not generate the correct kinetic energy 88: distribution, and should not be used for new production simulations (in 88: our opinion). We would recommend the V-rescale thermostat. 88: 88: Generating 1-4 interactions: fudge = 0.5 88: Number of degrees of freedom in T-Coupling group System is 355.00 88: 88: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/freeenergy/coulandvdwsequential_vdw/grompp.mdp]: 88: The optimal PME mesh load for parallel simulations is below 0.5 88: and for highly parallel simulations between 0.25 and 0.33, 88: for higher performance, increase the cut-off and the PME grid spacing. 88: 88: 88: 88: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/freeenergy/coulandvdwsequential_vdw/grompp.mdp]: 88: For free energy simulations, the optimal load limit increases from 0.5 to 88: 0.667 88: 88: 88: 88: There were 3 NOTEs 88: 88: There was 1 WARNING 88: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/EquivalentToReference_FreeEnergyReferenceTest_WithinTolerances_coulandvdwsequential_vdw_s_sim.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 88: Changing nstlist from 10 to 100, rlist from 1 to 1 88: 88: Using 1 MPI thread 88: Using 2 OpenMP threads 88: 88: 88: NOTE: The number of threads is not equal to the number of (logical) cpus 88: and the -pin option is set to auto: will not pin threads to cpus. 88: This can lead to significant performance degradation. 88: Consider using -pin on (and -pinoffset in case you run multiple jobs). 88: starting mdrun 'AA' 88: 20 steps, 0.0 ps. 88: Setting the LD random seed to -537005447 88: 88: Generated 153 of the 153 non-bonded parameter combinations 88: 88: Generated 153 of the 153 1-4 parameter combinations 88: 88: Excluding 3 bonded neighbours molecule type 'ASN' 88: 88: turning H bonds into constraints... 88: 88: Excluding 2 bonded neighbours molecule type 'SOL' 88: 88: turning H bonds into constraints... 88: 88: Coupling 1 copies of molecule type 'ASN' 88: 88: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/freeenergy/coulandvdwsequential_vdw/conf.gro' 88: Analysing residue names: 88: There are: 1 Protein residues 88: There are: 56 Water residues 88: Analysing Protein... 88: 88: The largest distance between non-perturbed excluded atoms is 0.164 nm between atom 41 and 42 88: 88: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 88: 88: Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm 88: 88: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm 88: 88: Note that mdrun will redetermine rlist based on the actual pair-list setup 88: Calculating fourier grid dimensions for X Y Z 88: Using a fourier grid of 28x28x28, spacing 0.108 0.108 0.108 88: 88: Estimate for the relative computational load of the PME mesh part: 0.89 88: 88: This run will generate roughly 0 Mb of data 88: 88: Writing final coordinates. 88: 88: Core t (s) Wall t (s) (%) 88: Time: 0.808 0.404 199.8 88: (ns/day) (hour/ns) 88: Performance: 4.489 5.347 88: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/EquivalentToReference_FreeEnergyReferenceTest_WithinTolerances_coulandvdwsequential_vdw_s_energy.edr as single precision energy file 88: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 17 time 0.017 Reading energy frame 18 time 0.018 Reading energy frame 19 time 0.019 Reading energy frame 20 time 0.020 Last energy frame read 20 time 0.020 [ OK ] EquivalentToReference/FreeEnergyReferenceTest.WithinTolerances/coulandvdwsequential_vdw_s (1369 ms) 88: [ RUN ] EquivalentToReference/FreeEnergyReferenceTest.WithinTolerances/coulandvdwtogether_s 88: 88: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/freeenergy/coulandvdwtogether/grompp.mdp, line 147]: 88: For proper sampling of the (nearly) decoupled state, stochastic dynamics 88: should be used 88: 88: 88: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/freeenergy/coulandvdwtogether/grompp.mdp]: 88: With PME there is a minor soft core effect present at the cut-off, 88: proportional to (LJsigma/rcoulomb)^6. This could have a minor effect on 88: energy conservation, but usually other effects dominate. With a common 88: sigma value of 0.34 nm the fraction of the particle-particle potential at 88: the cut-off at lambda=0.5 is around 6.4e-05, while ewald-rtol is 1.0e-06. 88: 88: 88: WARNING 1 [file /build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/freeenergy/coulandvdwtogether/grompp.mdp]: 88: The Berendsen thermostat does not generate the correct kinetic energy 88: distribution, and should not be used for new production simulations (in 88: our opinion). We would recommend the V-rescale thermostat. 88: 88: Generating 1-4 interactions: fudge = 0.5 88: Number of degrees of freedom in T-Coupling group System is 355.00 88: 88: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/freeenergy/coulandvdwtogether/grompp.mdp]: 88: The optimal PME mesh load for parallel simulations is below 0.5 88: and for highly parallel simulations between 0.25 and 0.33, 88: for higher performance, increase the cut-off and the PME grid spacing. 88: 88: 88: 88: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/freeenergy/coulandvdwtogether/grompp.mdp]: 88: For free energy simulations, the optimal load limit increases from 0.5 to 88: 0.667 88: 88: 88: 88: There were 4 NOTEs 88: 88: There was 1 WARNING 88: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/EquivalentToReference_FreeEnergyReferenceTest_WithinTolerances_coulandvdwtogether_s_sim.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 88: Changing nstlist from 10 to 100, rlist from 1 to 1 88: 88: Using 1 MPI thread 88: Using 2 OpenMP threads 88: 88: 88: NOTE: The number of threads is not equal to the number of (logical) cpus 88: and the -pin option is set to auto: will not pin threads to cpus. 88: This can lead to significant performance degradation. 88: Consider using -pin on (and -pinoffset in case you run multiple jobs). 88: starting mdrun 'AA' 88: 20 steps, 0.0 ps. 88: Setting the LD random seed to -277520387 88: 88: Generated 153 of the 153 non-bonded parameter combinations 88: 88: Generated 153 of the 153 1-4 parameter combinations 88: 88: Excluding 3 bonded neighbours molecule type 'ASN' 88: 88: turning H bonds into constraints... 88: 88: Excluding 2 bonded neighbours molecule type 'SOL' 88: 88: turning H bonds into constraints... 88: 88: Coupling 1 copies of molecule type 'ASN' 88: 88: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/freeenergy/coulandvdwtogether/conf.gro' 88: Analysing residue names: 88: There are: 1 Protein residues 88: There are: 56 Water residues 88: Analysing Protein... 88: 88: The largest distance between non-perturbed excluded atoms is 0.164 nm between atom 41 and 42 88: 88: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 88: 88: Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm 88: 88: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm 88: 88: Note that mdrun will redetermine rlist based on the actual pair-list setup 88: Calculating fourier grid dimensions for X Y Z 88: Using a fourier grid of 28x28x28, spacing 0.108 0.108 0.108 88: 88: Estimate for the relative computational load of the PME mesh part: 0.89 88: 88: This run will generate roughly 0 Mb of data 88: 88: Writing final coordinates. 88: 88: Core t (s) Wall t (s) (%) 88: Time: 0.588 0.295 199.8 88: (ns/day) (hour/ns) 88: Performance: 6.161 3.896 88: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/EquivalentToReference_FreeEnergyReferenceTest_WithinTolerances_coulandvdwtogether_s_energy.edr as single precision energy file 88: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 17 time 0.017 Reading energy frame 18 time 0.018 Reading energy frame 19 time 0.019 Reading energy frame 20 time 0.020 Last energy frame read 20 time 0.020 [ OK ] EquivalentToReference/FreeEnergyReferenceTest.WithinTolerances/coulandvdwtogether_s (1263 ms) 88: [ RUN ] EquivalentToReference/FreeEnergyReferenceTest.WithinTolerances/coulandvdwtogether_net_charge_s 88: 88: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/freeenergy/coulandvdwtogether-net-charge/grompp.mdp, line 147]: 88: For proper sampling of the (nearly) decoupled state, stochastic dynamics 88: should be used 88: 88: 88: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/freeenergy/coulandvdwtogether-net-charge/grompp.mdp]: 88: With PME there is a minor soft core effect present at the cut-off, 88: proportional to (LJsigma/rcoulomb)^6. This could have a minor effect on 88: energy conservation, but usually other effects dominate. With a common 88: sigma value of 0.34 nm the fraction of the particle-particle potential at 88: the cut-off at lambda=0.5 is around 6.4e-05, while ewald-rtol is 1.0e-06. 88: 88: 88: WARNING 1 [file /build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/freeenergy/coulandvdwtogether-net-charge/grompp.mdp]: 88: The Berendsen thermostat does not generate the correct kinetic energy 88: distribution, and should not be used for new production simulations (in 88: our opinion). We would recommend the V-rescale thermostat. 88: 88: Generating 1-4 interactions: fudge = 0.5 88: 88: NOTE 3 [file topol.top, line 155]: 88: System has non-zero total charge: 1.000000 88: Total charge should normally be an integer. See 88: https://manual.gromacs.org/current/user-guide/floating-point.html 88: for discussion on how close it should be to an integer. 88: 88: 88: 88: 88: WARNING 2 [file topol.top, line 155]: 88: You are using Ewald electrostatics in a system with net charge. This can 88: lead to severe artifacts, such as ions moving into regions with low 88: dielectric, due to the uniform background charge. We suggest to 88: neutralize your system with counter ions, possibly in combination with a 88: physiological salt concentration. 88: 88: Setting the LD random seed to -285278344 88: 88: Generated 171 of the 171 non-bonded parameter combinations 88: 88: Generated 171 of the 171 1-4 parameter combinations 88: 88: Excluding 3 bonded neighbours molecule type 'ASN' 88: 88: turning H bonds into constraints... 88: 88: Excluding 2 bonded neighbours molecule type 'SOL' 88: 88: turning H bonds into constraints... 88: 88: Excluding 1 bonded neighbours molecule type 'NA' 88: 88: turning H bonds into constraints... 88: 88: Coupling 1 copies of molecule type 'ASN' 88: 88: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 88: J. S. Hub, B. L. de Groot, H. Grubmueller, G. Groenhof 88: Quantifying Artifacts in Ewald Simulations of Inhomogeneous Systems with a Net 88: Charge 88: J. Chem. Theory Comput. (2014) 88: DOI: 10.1021/ct400626b 88: -------- -------- --- Thank You --- -------- -------- 88: 88: Number of degrees of freedom in T-Coupling group System is 358.00 88: 88: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/freeenergy/coulandvdwtogether-net-charge/grompp.mdp]: 88: The optimal PME mesh load for parallel simulations is below 0.5 88: and for highly parallel simulations between 0.25 and 0.33, 88: for higher performance, increase the cut-off and the PME grid spacing. 88: 88: 88: 88: NOTE 5 [file /build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/freeenergy/coulandvdwtogether-net-charge/grompp.mdp]: 88: For free energy simulations, the optimal load limit increases from 0.5 to 88: 0.667 88: 88: 88: 88: There were 5 NOTEs 88: 88: There were 2 WARNINGs 88: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/EquivalentToReference_FreeEnergyReferenceTest_WithinTolerances_coulandvdwtogether_net_charge_s_sim.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 88: Changing nstlist from 10 to 50, rlist from 1.004 to 1.101 88: 88: Using 1 MPI thread 88: Using 2 OpenMP threads 88: 88: 88: NOTE: The number of threads is not equal to the number of (logical) cpus 88: and the -pin option is set to auto: will not pin threads to cpus. 88: This can lead to significant performance degradation. 88: Consider using -pin on (and -pinoffset in case you run multiple jobs). 88: starting mdrun 'AA' 88: 20 steps, 0.0 ps. 88: 88: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/freeenergy/coulandvdwtogether-net-charge/conf.gro' 88: Analysing residue names: 88: There are: 1 Protein residues 88: There are: 56 Water residues 88: There are: 1 Ion residues 88: Analysing Protein... 88: 88: The largest distance between non-perturbed excluded atoms is 0.164 nm between atom 41 and 42 88: 88: Determining Verlet buffer for a tolerance of 5e-05 kJ/mol/ps at 298 K 88: 88: Calculated rlist for 1x1 atom pair-list as 1.020 nm, buffer size 0.020 nm 88: 88: Set rlist, assuming 4x4 atom pair-list, to 1.004 nm, buffer size 0.004 nm 88: 88: Note that mdrun will redetermine rlist based on the actual pair-list setup 88: Calculating fourier grid dimensions for X Y Z 88: Using a fourier grid of 32x32x32, spacing 0.095 0.095 0.095 88: 88: Estimate for the relative computational load of the PME mesh part: 0.92 88: 88: This run will generate roughly 0 Mb of data 88: 88: Writing final coordinates. 88: 88: Core t (s) Wall t (s) (%) 88: Time: 0.847 0.424 199.8 88: (ns/day) (hour/ns) 88: Performance: 4.279 5.609 88: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/EquivalentToReference_FreeEnergyReferenceTest_WithinTolerances_coulandvdwtogether_net_charge_s_energy.edr as single precision energy file 88: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 17 time 0.017 Reading energy frame 18 time 0.018 Reading energy frame 19 time 0.019 Reading energy frame 20 time 0.020 Last energy frame read 20 time 0.020 [ OK ] EquivalentToReference/FreeEnergyReferenceTest.WithinTolerances/coulandvdwtogether_net_charge_s (611 ms) 88: [ RUN ] EquivalentToReference/FreeEnergyReferenceTest.WithinTolerances/coulandvdwtogether_decouple_counter_charge_s 88: 88: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/freeenergy/coulandvdwtogether-decouple-counter-charge/grompp.mdp, line 147]: 88: For proper sampling of the (nearly) decoupled state, stochastic dynamics 88: should be used 88: 88: 88: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/freeenergy/coulandvdwtogether-decouple-counter-charge/grompp.mdp]: 88: With PME there is a minor soft core effect present at the cut-off, 88: proportional to (LJsigma/rcoulomb)^6. This could have a minor effect on 88: energy conservation, but usually other effects dominate. With a common 88: sigma value of 0.34 nm the fraction of the particle-particle potential at 88: the cut-off at lambda=0.5 is around 6.4e-05, while ewald-rtol is 1.0e-06. 88: 88: 88: WARNING 1 [file /build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/freeenergy/coulandvdwtogether-decouple-counter-charge/grompp.mdp]: 88: The Berendsen thermostat does not generate the correct kinetic energy 88: distribution, and should not be used for new production simulations (in 88: our opinion). We would recommend the V-rescale thermostat. 88: 88: Generating 1-4 interactions: fudge = 0.5 88: 88: NOTE 3 [file topol.top, line 165]: 88: System has non-zero total charge: 1.000000 88: Total charge should normally be an integer. See 88: https://manual.gromacs.org/current/user-guide/floating-point.html 88: for discussion on how close it should be to an integer. 88: 88: 88: 88: 88: WARNING 2 [file topol.top, line 165]: 88: You are using Ewald electrostatics in a system with net charge. This can 88: lead to severe artifacts, such as ions moving into regions with low 88: dielectric, due to the uniform background charge. We suggest to 88: neutralize your system with counter ions, possibly in combination with a 88: physiological salt concentration. 88: 88: Setting the LD random seed to -673778417 88: 88: Generated 190 of the 190 non-bonded parameter combinations 88: 88: Generated 190 of the 190 1-4 parameter combinations 88: 88: Excluding 3 bonded neighbours molecule type 'ASN' 88: 88: turning H bonds into constraints... 88: 88: Excluding 2 bonded neighbours molecule type 'SOL' 88: 88: turning H bonds into constraints... 88: 88: Excluding 1 bonded neighbours molecule type 'NA' 88: 88: turning H bonds into constraints... 88: 88: Excluding 1 bonded neighbours molecule type 'CL' 88: 88: turning H bonds into constraints... 88: 88: Coupling 1 copies of molecule type 'CL' 88: 88: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 88: J. S. Hub, B. L. de Groot, H. Grubmueller, G. Groenhof 88: Quantifying Artifacts in Ewald Simulations of Inhomogeneous Systems with a Net 88: Charge 88: J. Chem. Theory Comput. (2014) 88: DOI: 10.1021/ct400626b 88: -------- -------- --- Thank You --- -------- -------- 88: 88: Number of degrees of freedom in T-Coupling group System is 361.00 88: 88: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/freeenergy/coulandvdwtogether-decouple-counter-charge/grompp.mdp]: 88: The optimal PME mesh load for parallel simulations is below 0.5 88: and for highly parallel simulations between 0.25 and 0.33, 88: for higher performance, increase the cut-off and the PME grid spacing. 88: 88: 88: 88: NOTE 5 [file /build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/freeenergy/coulandvdwtogether-decouple-counter-charge/grompp.mdp]: 88: For free energy simulations, the optimal load limit increases from 0.5 to 88: 0.667 88: 88: 88: 88: There were 5 NOTEs 88: 88: There were 2 WARNINGs 88: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/EquivalentToReference_FreeEnergyReferenceTest_WithinTolerances_coulandvdwtogether_decouple_counter_charge_s_sim.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 88: Changing nstlist from 10 to 50, rlist from 1.004 to 1.102 88: 88: Using 1 MPI thread 88: Using 2 OpenMP threads 88: 88: 88: NOTE: The number of threads is not equal to the number of (logical) cpus 88: and the -pin option is set to auto: will not pin threads to cpus. 88: This can lead to significant performance degradation. 88: Consider using -pin on (and -pinoffset in case you run multiple jobs). 88: starting mdrun 'AA' 88: 20 steps, 0.0 ps. 88: 88: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/freeenergy/coulandvdwtogether-decouple-counter-charge/conf.gro' 88: Analysing residue names: 88: There are: 1 Protein residues 88: There are: 56 Water residues 88: There are: 2 Ion residues 88: Analysing Protein... 88: 88: The largest distance between non-perturbed excluded atoms is 0.331 nm between atom 1 and 9 88: 88: Determining Verlet buffer for a tolerance of 5e-05 kJ/mol/ps at 298 K 88: 88: Calculated rlist for 1x1 atom pair-list as 1.020 nm, buffer size 0.020 nm 88: 88: Set rlist, assuming 4x4 atom pair-list, to 1.004 nm, buffer size 0.004 nm 88: 88: Note that mdrun will redetermine rlist based on the actual pair-list setup 88: Calculating fourier grid dimensions for X Y Z 88: Using a fourier grid of 32x32x32, spacing 0.095 0.095 0.095 88: 88: Estimate for the relative computational load of the PME mesh part: 0.92 88: 88: This run will generate roughly 0 Mb of data 88: 88: Writing final coordinates. 88: 88: Core t (s) Wall t (s) (%) 88: Time: 0.752 0.376 199.8 88: (ns/day) (hour/ns) 88: Performance: 4.822 4.977 88: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/EquivalentToReference_FreeEnergyReferenceTest_WithinTolerances_coulandvdwtogether_decouple_counter_charge_s_energy.edr as single precision energy file 88: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 17 time 0.017 Reading energy frame 18 time 0.018 Reading energy frame 19 time 0.019 Reading energy frame 20 time 0.020 Last energy frame read 20 time 0.020 [ OK ] EquivalentToReference/FreeEnergyReferenceTest.WithinTolerances/coulandvdwtogether_decouple_counter_charge_s (554 ms) 88: [ RUN ] EquivalentToReference/FreeEnergyReferenceTest.WithinTolerances/expanded_s 88: 88: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/freeenergy/expanded/grompp.mdp, line 171]: 88: For proper sampling of the (nearly) decoupled state, stochastic dynamics 88: should be used 88: 88: 88: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/freeenergy/expanded/grompp.mdp]: 88: Replacing vdwtype=Shift by the equivalent combination of vdwtype=Cut-off 88: and vdw_modifier=Force-switch 88: 88: 88: WARNING 1 [file /build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/freeenergy/expanded/grompp.mdp]: 88: The Berendsen thermostat does not generate the correct kinetic energy 88: distribution, and should not be used for new production simulations (in 88: our opinion). We would recommend the V-rescale thermostat. 88: 88: Generating 1-4 interactions: fudge = 0.5 88: Number of degrees of freedom in T-Coupling group System is 355.00 88: 88: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/freeenergy/expanded/grompp.mdp]: 88: The optimal PME mesh load for parallel simulations is below 0.5 88: and for highly parallel simulations between 0.25 and 0.33, 88: for higher performance, increase the cut-off and the PME grid spacing. 88: 88: 88: 88: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/freeenergy/expanded/grompp.mdp]: 88: For free energy simulations, the optimal load limit increases from 0.5 to 88: 0.667 88: 88: 88: 88: There were 4 NOTEs 88: 88: There was 1 WARNING 88: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/EquivalentToReference_FreeEnergyReferenceTest_WithinTolerances_expanded_s_sim.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 88: Changing nstlist from 10 to 100, rlist from 1 to 1 88: 88: Using 1 MPI thread 88: Using 2 OpenMP threads 88: 88: 88: NOTE: The number of threads is not equal to the number of (logical) cpus 88: and the -pin option is set to auto: will not pin threads to cpus. 88: This can lead to significant performance degradation. 88: Consider using -pin on (and -pinoffset in case you run multiple jobs). 88: starting mdrun 'AA' 88: 100 steps, 0.1 ps. 88: Setting the LD random seed to -11029012 88: 88: Generated 153 of the 153 non-bonded parameter combinations 88: 88: Generated 153 of the 153 1-4 parameter combinations 88: 88: Excluding 3 bonded neighbours molecule type 'ASN' 88: 88: turning H bonds into constraints... 88: 88: Excluding 2 bonded neighbours molecule type 'SOL' 88: 88: turning H bonds into constraints... 88: 88: Coupling 1 copies of molecule type 'ASN' 88: 88: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/freeenergy/expanded/conf.gro' 88: Analysing residue names: 88: There are: 1 Protein residues 88: There are: 56 Water residues 88: Analysing Protein... 88: 88: The largest distance between non-perturbed excluded atoms is 0.164 nm between atom 41 and 42 88: 88: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 88: 88: Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm 88: 88: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm 88: 88: Note that mdrun will redetermine rlist based on the actual pair-list setup 88: Calculating fourier grid dimensions for X Y Z 88: Using a fourier grid of 28x28x28, spacing 0.108 0.108 0.108 88: 88: Estimate for the relative computational load of the PME mesh part: 0.89 88: 88: This run will generate roughly 0 Mb of data 88: 88: Writing final coordinates. 88: 88: Core t (s) Wall t (s) (%) 88: Time: 5.908 2.954 200.0 88: (ns/day) (hour/ns) 88: Performance: 2.954 8.125 88: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/EquivalentToReference_FreeEnergyReferenceTest_WithinTolerances_expanded_s_energy.edr as single precision energy file 88: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 17 time 0.017 Reading energy frame 18 time 0.018 Reading energy frame 19 time 0.019 Reading energy frame 20 time 0.020 Reading energy frame 30 time 0.030 Reading energy frame 40 time 0.040 Reading energy frame 50 time 0.050 Reading energy frame 60 time 0.060 Reading energy frame 70 time 0.070 Reading energy frame 80 time 0.080 Reading energy frame 90 time 0.090 Reading energy frame 100 time 0.100 Last energy frame read 100 time 0.100 [ OK ] EquivalentToReference/FreeEnergyReferenceTest.WithinTolerances/expanded_s (4051 ms) 88: [ RUN ] EquivalentToReference/FreeEnergyReferenceTest.WithinTolerances/relative_s 88: 88: WARNING 1 [file /build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/freeenergy/relative/grompp.mdp]: 88: The Berendsen thermostat does not generate the correct kinetic energy 88: distribution, and should not be used for new production simulations (in 88: our opinion). We would recommend the V-rescale thermostat. 88: 88: Generating 1-4 interactions: fudge = 0.5 88: 88: WARNING 2 [file topol.top, line 72]: 88: No default Bond types for perturbed atoms in interaction, using normal 88: values. The interaction was 88: '7 8 1'. 88: 88: 88: WARNING 3 [file topol.top, line 73]: 88: No default Bond types for perturbed atoms in interaction, using normal 88: values. The interaction was 88: '7 9 1'. 88: 88: 88: WARNING 4 [file topol.top, line 98]: 88: No default Angle types for perturbed atoms in interaction, using normal 88: values. The interaction was 88: '6 5 7 1'. 88: 88: 88: WARNING 5 [file topol.top, line 99]: 88: No default Angle types for perturbed atoms in interaction, using normal 88: values. The interaction was 88: '5 7 8 1'. 88: 88: 88: WARNING 6 [file topol.top, line 100]: 88: No default Angle types for perturbed atoms in interaction, using normal 88: values. The interaction was 88: '5 7 9 1'. 88: 88: 88: WARNING 7 [file topol.top, line 101]: 88: No default Angle types for perturbed atoms in interaction, using normal 88: values. The interaction was 88: '8 7 9 1'. 88: 88: 88: WARNING 8 [file topol.top, line 111]: 88: No default Ryckaert-Bell. types for perturbed atoms in interaction, using 88: normal values. The interaction was 88: '1 5 7 8 3'. 88: 88: 88: WARNING 9 [file topol.top, line 112]: 88: No default Ryckaert-Bell. types for perturbed atoms in interaction, using 88: normal values. The interaction was 88: '1 5 7 9 3'. 88: 88: 88: WARNING 10 [file topol.top, line 113]: 88: No default Ryckaert-Bell. types for perturbed atoms in interaction, using 88: normal values. The interaction was 88: '6 5 7 8 3'. 88: 88: 88: WARNING 11 [file topol.top, line 114]: 88: No default Ryckaert-Bell. types for perturbed atoms in interaction, using 88: normal values. The interaction was 88: '6 5 7 9 3'. 88: 88: Number of degrees of freedom in T-Coupling group System is 355.00 88: 88: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/freeenergy/relative/grompp.mdp]: 88: The optimal PME mesh load for parallel simulations is below 0.5 88: and for highly parallel simulations between 0.25 and 0.33, 88: for higher performance, increase the cut-off and the PME grid spacing. 88: 88: 88: 88: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/freeenergy/relative/grompp.mdp]: 88: For free energy simulations, the optimal load limit increases from 0.5 to 88: 0.667 88: 88: 88: 88: There were 2 NOTEs 88: 88: There were 11 WARNINGs 88: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/EquivalentToReference_FreeEnergyReferenceTest_WithinTolerances_relative_s_sim.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 88: Changing nstlist from 10 to 100, rlist from 1 to 1 88: 88: Using 1 MPI thread 88: Using 2 OpenMP threads 88: 88: 88: NOTE: The number of threads is not equal to the number of (logical) cpus 88: and the -pin option is set to auto: will not pin threads to cpus. 88: This can lead to significant performance degradation. 88: Consider using -pin on (and -pinoffset in case you run multiple jobs). 88: starting mdrun 'AA' 88: 20 steps, 0.0 ps. 88: Setting the LD random seed to -1497923682 88: 88: Generated 136 of the 136 non-bonded parameter combinations 88: 88: Generated 136 of the 136 1-4 parameter combinations 88: 88: Excluding 3 bonded neighbours molecule type 'ASN' 88: 88: turning H bonds into constraints... 88: 88: Excluding 2 bonded neighbours molecule type 'SOL' 88: 88: turning H bonds into constraints... 88: 88: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/freeenergy/relative/conf.gro' 88: Analysing residue names: 88: There are: 1 Protein residues 88: There are: 56 Water residues 88: Analysing Protein... 88: 88: The largest distance between non-perturbed excluded atoms is 0.164 nm between atom 41 and 42 88: 88: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 88: 88: Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm 88: 88: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm 88: 88: Note that mdrun will redetermine rlist based on the actual pair-list setup 88: Calculating fourier grid dimensions for X Y Z 88: Using a fourier grid of 28x28x28, spacing 0.108 0.108 0.108 88: 88: Estimate for the relative computational load of the PME mesh part: 0.89 88: 88: This run will generate roughly 0 Mb of data 88: 88: Writing final coordinates. 88: 88: Core t (s) Wall t (s) (%) 88: Time: 1.316 0.658 199.9 88: (ns/day) (hour/ns) 88: Performance: 2.757 8.707 88: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/EquivalentToReference_FreeEnergyReferenceTest_WithinTolerances_relative_s_energy.edr as single precision energy file 88: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 17 time 0.017 Reading energy frame 18 time 0.018 Reading energy frame 19 time 0.019 Reading energy frame 20 time 0.020 Last energy frame read 20 time 0.020 [ OK ] EquivalentToReference/FreeEnergyReferenceTest.WithinTolerances/relative_s (1617 ms) 88: [ RUN ] EquivalentToReference/FreeEnergyReferenceTest.WithinTolerances/relative_position_restraints_s 88: 88: WARNING 1 [file /build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/freeenergy/relative-position-restraints/grompp.mdp]: 88: The Berendsen thermostat does not generate the correct kinetic energy 88: distribution, and should not be used for new production simulations (in 88: our opinion). We would recommend the V-rescale thermostat. 88: 88: Generating 1-4 interactions: fudge = 0.5 88: 88: WARNING 2 [file topol.top, line 72]: 88: No default Bond types for perturbed atoms in interaction, using normal 88: values. The interaction was 88: '7 8 1'. 88: 88: 88: WARNING 3 [file topol.top, line 73]: 88: No default Bond types for perturbed atoms in interaction, using normal 88: values. The interaction was 88: '7 9 1'. 88: 88: 88: WARNING 4 [file topol.top, line 98]: 88: No default Angle types for perturbed atoms in interaction, using normal 88: values. The interaction was 88: '6 5 7 1'. 88: 88: 88: WARNING 5 [file topol.top, line 99]: 88: No default Angle types for perturbed atoms in interaction, using normal 88: values. The interaction was 88: '5 7 8 1'. 88: 88: 88: WARNING 6 [file topol.top, line 100]: 88: No default Angle types for perturbed atoms in interaction, using normal 88: values. The interaction was 88: '5 7 9 1'. 88: 88: 88: WARNING 7 [file topol.top, line 101]: 88: No default Angle types for perturbed atoms in interaction, using normal 88: values. The interaction was 88: '8 7 9 1'. 88: 88: 88: WARNING 8 [file topol.top, line 111]: 88: No default Ryckaert-Bell. types for perturbed atoms in interaction, using 88: normal values. The interaction was 88: '1 5 7 8 3'. 88: 88: 88: WARNING 9 [file topol.top, line 112]: 88: No default Ryckaert-Bell. types for perturbed atoms in interaction, using 88: normal values. The interaction was 88: '1 5 7 9 3'. 88: 88: 88: WARNING 10 [file topol.top, line 113]: 88: No default Ryckaert-Bell. types for perturbed atoms in interaction, using 88: normal values. The interaction was 88: '6 5 7 8 3'. 88: 88: 88: WARNING 11 [file topol.top, line 114]: 88: No default Ryckaert-Bell. types for perturbed atoms in interaction, using 88: normal values. The interaction was 88: '6 5 7 9 3'. 88: 88: Number of degrees of freedom in T-Coupling group System is 355.00 88: 88: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/freeenergy/relative-position-restraints/grompp.mdp]: 88: Removing center of mass motion in the presence of position restraints 88: might cause artifacts. When you are using position restraints to 88: equilibrate a macro-molecule, the artifacts are usually negligible. 88: 88: 88: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/freeenergy/relative-position-restraints/grompp.mdp]: 88: The optimal PME mesh load for parallel simulations is below 0.5 88: and for highly parallel simulations between 0.25 and 0.33, 88: for higher performance, increase the cut-off and the PME grid spacing. 88: 88: 88: 88: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/freeenergy/relative-position-restraints/grompp.mdp]: 88: For free energy simulations, the optimal load limit increases from 0.5 to 88: 0.667 88: 88: 88: 88: There were 3 NOTEs 88: 88: There were 11 WARNINGs 88: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/EquivalentToReference_FreeEnergyReferenceTest_WithinTolerances_relative_position_restraints_s_sim.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 88: Changing nstlist from 10 to 100, rlist from 1 to 1 88: 88: Using 1 MPI thread 88: Using 2 OpenMP threads 88: 88: 88: NOTE: The number of threads is not equal to the number of (logical) cpus 88: and the -pin option is set to auto: will not pin threads to cpus. 88: This can lead to significant performance degradation. 88: Consider using -pin on (and -pinoffset in case you run multiple jobs). 88: starting mdrun 'AA' 88: 20 steps, 0.0 ps. 88: Setting the LD random seed to 863334257 88: 88: Generated 136 of the 136 non-bonded parameter combinations 88: 88: Generated 136 of the 136 1-4 parameter combinations 88: 88: Excluding 3 bonded neighbours molecule type 'ASN' 88: 88: turning H bonds into constraints... 88: 88: Excluding 2 bonded neighbours molecule type 'SOL' 88: 88: turning H bonds into constraints... 88: 88: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/freeenergy/relative-position-restraints/conf.gro' 88: Analysing residue names: 88: There are: 1 Protein residues 88: There are: 56 Water residues 88: Analysing Protein... 88: 88: The largest distance between non-perturbed excluded atoms is 0.164 nm between atom 41 and 42 88: 88: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 88: 88: Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm 88: 88: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm 88: 88: Note that mdrun will redetermine rlist based on the actual pair-list setup 88: Calculating fourier grid dimensions for X Y Z 88: Using a fourier grid of 28x28x28, spacing 0.108 0.108 0.108 88: 88: Estimate for the relative computational load of the PME mesh part: 0.89 88: 88: This run will generate roughly 0 Mb of data 88: 88: Writing final coordinates. 88: 88: Core t (s) Wall t (s) (%) 88: Time: 1.275 0.638 199.9 88: (ns/day) (hour/ns) 88: Performance: 2.845 8.437 88: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/EquivalentToReference_FreeEnergyReferenceTest_WithinTolerances_relative_position_restraints_s_energy.edr as single precision energy file 88: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 17 time 0.017 Reading energy frame 18 time 0.018 Reading energy frame 19 time 0.019 Reading energy frame 20 time 0.020 Last energy frame read 20 time 0.020 [ OK ] EquivalentToReference/FreeEnergyReferenceTest.WithinTolerances/relative_position_restraints_s (1597 ms) 88: [ RUN ] EquivalentToReference/FreeEnergyReferenceTest.WithinTolerances/restraints_s 88: 88: WARNING 1 [file /build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/freeenergy/restraints/grompp.mdp]: 88: The Berendsen thermostat does not generate the correct kinetic energy 88: distribution, and should not be used for new production simulations (in 88: our opinion). We would recommend the V-rescale thermostat. 88: 88: Generating 1-4 interactions: fudge = 0.5 88: Number of degrees of freedom in T-Coupling group System is 355.00 88: 88: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/freeenergy/restraints/grompp.mdp]: 88: The optimal PME mesh load for parallel simulations is below 0.5 88: and for highly parallel simulations between 0.25 and 0.33, 88: for higher performance, increase the cut-off and the PME grid spacing. 88: 88: 88: 88: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/freeenergy/restraints/grompp.mdp]: 88: For free energy simulations, the optimal load limit increases from 0.5 to 88: 0.667 88: 88: 88: 88: There were 2 NOTEs 88: 88: There was 1 WARNING 88: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/EquivalentToReference_FreeEnergyReferenceTest_WithinTolerances_restraints_s_sim.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 88: Changing nstlist from 10 to 100, rlist from 1 to 1 88: 88: Using 1 MPI thread 88: Using 2 OpenMP threads 88: 88: 88: NOTE: The number of threads is not equal to the number of (logical) cpus 88: and the -pin option is set to auto: will not pin threads to cpus. 88: This can lead to significant performance degradation. 88: Consider using -pin on (and -pinoffset in case you run multiple jobs). 88: starting mdrun 'AA' 88: 20 steps, 0.0 ps. 88: Setting the LD random seed to -1191249954 88: 88: Generated 136 of the 136 non-bonded parameter combinations 88: 88: Generated 136 of the 136 1-4 parameter combinations 88: 88: Excluding 3 bonded neighbours molecule type 'ASN' 88: 88: turning H bonds into constraints... 88: 88: Excluding 2 bonded neighbours molecule type 'SOL' 88: 88: turning H bonds into constraints... 88: 88: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/freeenergy/restraints/conf.gro' 88: Analysing residue names: 88: There are: 1 Protein residues 88: There are: 56 Water residues 88: Analysing Protein... 88: 88: The largest distance between non-perturbed excluded atoms is 0.331 nm between atom 1 and 9 88: 88: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 88: 88: Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm 88: 88: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm 88: 88: Note that mdrun will redetermine rlist based on the actual pair-list setup 88: Calculating fourier grid dimensions for X Y Z 88: Using a fourier grid of 28x28x28, spacing 0.108 0.108 0.108 88: 88: Estimate for the relative computational load of the PME mesh part: 0.81 88: 88: This run will generate roughly 0 Mb of data 88: 88: Writing final coordinates. 88: 88: Core t (s) Wall t (s) (%) 88: Time: 0.487 0.244 199.7 88: (ns/day) (hour/ns) 88: Performance: 7.444 3.224 88: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/EquivalentToReference_FreeEnergyReferenceTest_WithinTolerances_restraints_s_energy.edr as single precision energy file 88: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 17 time 0.017 Reading energy frame 18 time 0.018 Reading energy frame 19 time 0.019 Reading energy frame 20 time 0.020 Last energy frame read 20 time 0.020 [ OK ] EquivalentToReference/FreeEnergyReferenceTest.WithinTolerances/restraints_s (1254 ms) 88: [ RUN ] EquivalentToReference/FreeEnergyReferenceTest.WithinTolerances/simtemp_s 88: 88: WARNING 1 [file /build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/freeenergy/simtemp/grompp.mdp]: 88: The Berendsen thermostat does not generate the correct kinetic energy 88: distribution, and should not be used for new production simulations (in 88: our opinion). We would recommend the V-rescale thermostat. 88: 88: Generating 1-4 interactions: fudge = 0.5 88: Number of degrees of freedom in T-Coupling group System is 355.00 88: 88: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/freeenergy/simtemp/grompp.mdp]: 88: The optimal PME mesh load for parallel simulations is below 0.5 88: and for highly parallel simulations between 0.25 and 0.33, 88: for higher performance, increase the cut-off and the PME grid spacing. 88: 88: 88: 88: There was 1 NOTE 88: 88: There was 1 WARNING 88: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/EquivalentToReference_FreeEnergyReferenceTest_WithinTolerances_simtemp_s_sim.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 88: Changing nstlist from 10 to 100, rlist from 1 to 1 88: 88: Using 1 MPI thread 88: Using 2 OpenMP threads 88: 88: 88: NOTE: The number of threads is not equal to the number of (logical) cpus 88: and the -pin option is set to auto: will not pin threads to cpus. 88: This can lead to significant performance degradation. 88: Consider using -pin on (and -pinoffset in case you run multiple jobs). 88: starting mdrun 'AA' 88: 20 steps, 0.0 ps. 88: 88: Writing final coordinates. 88: 88: Core t (s) Wall t (s) (%) 88: Time: 0.376 0.189 199.5 88: (ns/day) (hour/ns) 88: Performance: 9.618 2.495 88: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/EquivalentToReference_FreeEnergyReferenceTest_WithinTolerances_simtemp_s_energy.edr as single precision energy file 88: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 17 time 0.017 Reading energy frame 18 time 0.018 Reading energy frame 19 time 0.019 Reading energy frame 20 time 0.020 Last energy frame read 20 time 0.020 Setting the LD random seed to -68587531 88: 88: Generated 136 of the 136 non-bonded parameter combinations 88: 88: Generated 136 of the 136 1-4 parameter combinations 88: 88: Excluding 3 bonded neighbours molecule type 'ASN' 88: 88: turning H bonds into constraints... 88: 88: Excluding 2 bonded neighbours molecule type 'SOL' 88: 88: turning H bonds into constraints... 88: 88: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/freeenergy/simtemp/conf.gro' 88: Analysing residue names: 88: There are: 1 Protein residues 88: There are: 56 Water residues 88: Analysing Protein... 88: 88: The largest distance between excluded atoms is 0.331 nm between atom 1 and 9 88: 88: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 88: 88: Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm 88: 88: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm 88: 88: Note that mdrun will redetermine rlist based on the actual pair-list setup 88: Calculating fourier grid dimensions for X Y Z 88: Using a fourier grid of 28x28x28, spacing 0.108 0.108 0.108 88: 88: Estimate for the relative computational load of the PME mesh part: 0.81 88: 88: This run will generate roughly 0 Mb of data 88: [ OK ] EquivalentToReference/FreeEnergyReferenceTest.WithinTolerances/simtemp_s (1182 ms) 88: [ RUN ] EquivalentToReference/FreeEnergyReferenceTest.WithinTolerances/transformAtoB_s 88: 88: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/freeenergy/transformAtoB/grompp.mdp]: 88: With PME there is a minor soft core effect present at the cut-off, 88: proportional to (LJsigma/rcoulomb)^6. This could have a minor effect on 88: energy conservation, but usually other effects dominate. With a common 88: sigma value of 0.34 nm the fraction of the particle-particle potential at 88: the cut-off at lambda=0.5 is around 6.4e-05, while ewald-rtol is 1.0e-06. 88: 88: 88: WARNING 1 [file /build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/freeenergy/transformAtoB/grompp.mdp]: 88: The Berendsen thermostat does not generate the correct kinetic energy 88: distribution, and should not be used for new production simulations (in 88: our opinion). We would recommend the V-rescale thermostat. 88: 88: Generating 1-4 interactions: fudge = 0.5 88: Number of degrees of freedom in T-Coupling group System is 355.00 88: 88: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/freeenergy/transformAtoB/grompp.mdp]: 88: The optimal PME mesh load for parallel simulations is below 0.5 88: and for highly parallel simulations between 0.25 and 0.33, 88: for higher performance, increase the cut-off and the PME grid spacing. 88: 88: 88: 88: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/freeenergy/transformAtoB/grompp.mdp]: 88: For free energy simulations, the optimal load limit increases from 0.5 to 88: 0.667 88: 88: 88: 88: There were 3 NOTEs 88: 88: There was 1 WARNING 88: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/EquivalentToReference_FreeEnergyReferenceTest_WithinTolerances_transformAtoB_s_sim.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 88: Changing nstlist from 10 to 100, rlist from 1 to 1 88: 88: Using 1 MPI thread 88: Using 2 OpenMP threads 88: 88: 88: NOTE: The number of threads is not equal to the number of (logical) cpus 88: and the -pin option is set to auto: will not pin threads to cpus. 88: This can lead to significant performance degradation. 88: Consider using -pin on (and -pinoffset in case you run multiple jobs). 88: starting mdrun 'AA' 88: 20 steps, 0.0 ps. 88: Setting the LD random seed to -672235590 88: 88: Generated 136 of the 136 non-bonded parameter combinations 88: 88: Generated 136 of the 136 1-4 parameter combinations 88: 88: Excluding 3 bonded neighbours molecule type 'ASN' 88: 88: turning H bonds into constraints... 88: 88: Excluding 2 bonded neighbours molecule type 'SOL' 88: 88: turning H bonds into constraints... 88: 88: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/freeenergy/transformAtoB/conf.gro' 88: Analysing residue names: 88: There are: 1 Protein residues 88: There are: 56 Water residues 88: Analysing Protein... 88: 88: The largest distance between non-perturbed excluded atoms is 0.164 nm between atom 41 and 42 88: 88: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 88: 88: Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm 88: 88: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm 88: 88: Note that mdrun will redetermine rlist based on the actual pair-list setup 88: Calculating fourier grid dimensions for X Y Z 88: Using a fourier grid of 28x28x28, spacing 0.108 0.108 0.108 88: 88: Estimate for the relative computational load of the PME mesh part: 0.89 88: 88: This run will generate roughly 0 Mb of data 88: 88: Writing final coordinates. 88: 88: Core t (s) Wall t (s) (%) 88: Time: 0.838 0.419 199.8 88: (ns/day) (hour/ns) 88: Performance: 4.329 5.544 88: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/EquivalentToReference_FreeEnergyReferenceTest_WithinTolerances_transformAtoB_s_energy.edr as single precision energy file 88: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 17 time 0.017 Reading energy frame 18 time 0.018 Reading energy frame 19 time 0.019 Reading energy frame 20 time 0.020 Last energy frame read 20 time 0.020 [ OK ] EquivalentToReference/FreeEnergyReferenceTest.WithinTolerances/transformAtoB_s (1404 ms) 88: [ RUN ] EquivalentToReference/FreeEnergyReferenceTest.WithinTolerances/vdwalone_s 88: 88: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/freeenergy/vdwalone/grompp.mdp]: 88: With PME there is a minor soft core effect present at the cut-off, 88: proportional to (LJsigma/rcoulomb)^6. This could have a minor effect on 88: energy conservation, but usually other effects dominate. With a common 88: sigma value of 0.34 nm the fraction of the particle-particle potential at 88: the cut-off at lambda=0.5 is around 6.4e-05, while ewald-rtol is 1.0e-06. 88: 88: 88: WARNING 1 [file /build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/freeenergy/vdwalone/grompp.mdp]: 88: The Berendsen thermostat does not generate the correct kinetic energy 88: distribution, and should not be used for new production simulations (in 88: our opinion). We would recommend the V-rescale thermostat. 88: 88: Generating 1-4 interactions: fudge = 0.5 88: Number of degrees of freedom in T-Coupling group System is 355.00 88: 88: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/freeenergy/vdwalone/grompp.mdp]: 88: The optimal PME mesh load for parallel simulations is below 0.5 88: and for highly parallel simulations between 0.25 and 0.33, 88: for higher performance, increase the cut-off and the PME grid spacing. 88: 88: 88: 88: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/freeenergy/vdwalone/grompp.mdp]: 88: For free energy simulations, the optimal load limit increases from 0.5 to 88: 0.667 88: 88: 88: 88: There were 3 NOTEs 88: 88: There was 1 WARNING 88: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/EquivalentToReference_FreeEnergyReferenceTest_WithinTolerances_vdwalone_s_sim.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 88: Changing nstlist from 10 to 100, rlist from 1 to 1 88: 88: Using 1 MPI thread 88: Using 2 OpenMP threads 88: 88: 88: NOTE: The number of threads is not equal to the number of (logical) cpus 88: and the -pin option is set to auto: will not pin threads to cpus. 88: This can lead to significant performance degradation. 88: Consider using -pin on (and -pinoffset in case you run multiple jobs). 88: starting mdrun 'AA' 88: 20 steps, 0.0 ps. 88: Setting the LD random seed to -1208774858 88: 88: Generated 136 of the 136 non-bonded parameter combinations 88: 88: Generated 136 of the 136 1-4 parameter combinations 88: 88: Excluding 3 bonded neighbours molecule type 'ASN' 88: 88: turning H bonds into constraints... 88: 88: Excluding 2 bonded neighbours molecule type 'SOL' 88: 88: turning H bonds into constraints... 88: 88: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/freeenergy/vdwalone/conf.gro' 88: Analysing residue names: 88: There are: 1 Protein residues 88: There are: 56 Water residues 88: Analysing Protein... 88: 88: The largest distance between non-perturbed excluded atoms is 0.172 nm between atom 8 and 9 88: 88: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 88: 88: Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm 88: 88: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm 88: 88: Note that mdrun will redetermine rlist based on the actual pair-list setup 88: Calculating fourier grid dimensions for X Y Z 88: Using a fourier grid of 28x28x28, spacing 0.108 0.108 0.108 88: 88: Estimate for the relative computational load of the PME mesh part: 0.81 88: 88: This run will generate roughly 0 Mb of data 88: 88: Writing final coordinates. 88: 88: Core t (s) Wall t (s) (%) 88: Time: 0.390 0.195 199.7 88: (ns/day) (hour/ns) 88: Performance: 9.288 2.584 88: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/EquivalentToReference_FreeEnergyReferenceTest_WithinTolerances_vdwalone_s_energy.edr as single precision energy file 88: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 17 time 0.017 Reading energy frame 18 time 0.018 Reading energy frame 19 time 0.019 Reading energy frame 20 time 0.020 Last energy frame read 20 time 0.020 [ OK ] EquivalentToReference/FreeEnergyReferenceTest.WithinTolerances/vdwalone_s (1159 ms) 88: [----------] 12 tests from EquivalentToReference/FreeEnergyReferenceTest (17436 ms total) 88: 88: [----------] Global test environment tear-down 88: [==========] 14 tests from 2 test suites ran. (18050 ms total) 88: [ PASSED ] 14 tests. 88/92 Test #88: MdrunFEPTests ............................. Passed 18.12 sec test 89 Start 89: MdrunPullTests 89: Test command: /build/reproducible-path/gromacs-2025.1/build/basic/bin/mdrun-pull-test "-ntomp" "2" "--gtest_output=xml:/build/reproducible-path/gromacs-2025.1/build/basic/Testing/Temporary/MdrunPullTests.xml" 89: Working Directory: /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests 89: Test timeout computed to be: 600 89: [==========] Running 4 tests from 1 test suite. 89: [----------] Global test environment set-up. 89: [----------] 4 tests from PullTest/PullIntegrationTest 89: [ RUN ] PullTest/PullIntegrationTest.WithinTolerances/0 89: Generating 1-4 interactions: fudge = 0.5 89: Pull group 1 'r_1' has 3 atoms 89: Pull group 2 'r_2' has 3 atoms 89: Number of degrees of freedom in T-Coupling group System is 1293.00 89: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 89: 89: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PullTest_PullIntegrationTest_WithinTolerances_0_input.mdp]: 89: NVE simulation: will use the initial temperature of 303.122 K for 89: determining the Verlet buffer size 89: 89: Pull group natoms pbc atom distance at start reference at t=0 89: 1 3 2 89: 2 3 5 0.575 nm 0.600 nm 89: 89: There was 1 NOTE 89: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PullTest_PullIntegrationTest_WithinTolerances_0.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 89: Can not increase nstlist because an NVE ensemble is used 89: Using 1 MPI thread 89: Using 2 OpenMP threads 89: 89: 89: NOTE: The number of threads is not equal to the number of (logical) cpus 89: and the -pin option is set to auto: will not pin threads to cpus. 89: This can lead to significant performance degradation. 89: Consider using -pin on (and -pinoffset in case you run multiple jobs). 89: starting mdrun 'spc2' 89: 20 steps, 0.0 ps. 89: Generated 330891 of the 330891 non-bonded parameter combinations 89: 89: Generated 330891 of the 330891 1-4 parameter combinations 89: 89: Excluding 2 bonded neighbours molecule type 'SOL' 89: 89: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/spc216.gro' 89: 89: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 303.122 K 89: 89: Calculated rlist for 1x1 atom pair-list as 0.781 nm, buffer size 0.081 nm 89: 89: Set rlist, assuming 4x4 atom pair-list, to 0.772 nm, buffer size 0.072 nm 89: 89: Note that mdrun will redetermine rlist based on the actual pair-list setup 89: 89: This run will generate roughly 0 Mb of data 89: 89: Writing final coordinates. 89: 89: Core t (s) Wall t (s) (%) 89: Time: 0.516 0.258 199.8 89: (ns/day) (hour/ns) 89: Performance: 7.027 3.415 89: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PullTest_PullIntegrationTest_WithinTolerances_0.edr as single precision energy file 89: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.005 Reading energy frame 2 time 0.010 Reading energy frame 3 time 0.015 Reading energy frame 4 time 0.020 Last energy frame read 4 time 0.020 [ OK ] PullTest/PullIntegrationTest.WithinTolerances/0 (4760 ms) 89: [ RUN ] PullTest/PullIntegrationTest.WithinTolerances/1 89: Generating 1-4 interactions: fudge = 0.5 89: Pull group 1 'r_1' has 3 atoms 89: Pull group 2 'r_2' has 3 atoms 89: Number of degrees of freedom in T-Coupling group System is 1293.00 89: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 89: 89: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PullTest_PullIntegrationTest_WithinTolerances_1_input.mdp]: 89: NVE simulation: will use the initial temperature of 303.122 K for 89: determining the Verlet buffer size 89: 89: Pull group natoms pbc atom distance at start reference at t=0 89: 1 3 2 89: 2 3 5 0.301 nm 0.400 nm 89: 89: There was 1 NOTE 89: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PullTest_PullIntegrationTest_WithinTolerances_1.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 89: Can not increase nstlist because an NVE ensemble is used 89: Using 1 MPI thread 89: Using 2 OpenMP threads 89: 89: 89: NOTE: The number of threads is not equal to the number of (logical) cpus 89: and the -pin option is set to auto: will not pin threads to cpus. 89: This can lead to significant performance degradation. 89: Consider using -pin on (and -pinoffset in case you run multiple jobs). 89: starting mdrun 'spc2' 89: 20 steps, 0.0 ps. 89: Generated 330891 of the 330891 non-bonded parameter combinations 89: 89: Generated 330891 of the 330891 1-4 parameter combinations 89: 89: Excluding 2 bonded neighbours molecule type 'SOL' 89: 89: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/spc216.gro' 89: 89: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 303.122 K 89: 89: Calculated rlist for 1x1 atom pair-list as 0.781 nm, buffer size 0.081 nm 89: 89: Set rlist, assuming 4x4 atom pair-list, to 0.772 nm, buffer size 0.072 nm 89: 89: Note that mdrun will redetermine rlist based on the actual pair-list setup 89: 89: This run will generate roughly 0 Mb of data 89: 89: Writing final coordinates. 89: 89: Core t (s) Wall t (s) (%) 89: Time: 1.150 0.575 199.9 89: (ns/day) (hour/ns) 89: Performance: 3.154 7.610 89: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PullTest_PullIntegrationTest_WithinTolerances_1.edr as single precision energy file 89: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.005 Reading energy frame 2 time 0.010 Reading energy frame 3 time 0.015 Reading energy frame 4 time 0.020 Last energy frame read 4 time 0.020 [ OK ] PullTest/PullIntegrationTest.WithinTolerances/1 (5030 ms) 89: [ RUN ] PullTest/PullIntegrationTest.WithinTolerances/2 89: Generating 1-4 interactions: fudge = 0.5 89: Pull group 1 'r_1' has 3 atoms 89: Pull group 2 'r_2' has 3 atoms 89: Pull group 3 'r_3' has 3 atoms 89: Number of degrees of freedom in T-Coupling group System is 1292.00 89: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 89: 89: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PullTest_PullIntegrationTest_WithinTolerances_2_input.mdp]: 89: NVE simulation: will use the initial temperature of 303.357 K for 89: determining the Verlet buffer size 89: 89: Pull group natoms pbc atom distance at start reference at t=0 89: 1 3 2 89: 2 3 5 0.575 nm 0.500 nm 89: 1 3 2 89: 3 3 8 0.331 nm 0.400 nm 89: 89: There was 1 NOTE 89: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PullTest_PullIntegrationTest_WithinTolerances_2.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 89: Can not increase nstlist because an NVE ensemble is used 89: Using 1 MPI thread 89: Using 2 OpenMP threads 89: 89: 89: NOTE: The number of threads is not equal to the number of (logical) cpus 89: and the -pin option is set to auto: will not pin threads to cpus. 89: This can lead to significant performance degradation. 89: Consider using -pin on (and -pinoffset in case you run multiple jobs). 89: starting mdrun 'spc2' 89: 20 steps, 0.0 ps. 89: Generated 330891 of the 330891 non-bonded parameter combinations 89: 89: Generated 330891 of the 330891 1-4 parameter combinations 89: 89: Excluding 2 bonded neighbours molecule type 'SOL' 89: 89: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/spc216.gro' 89: 89: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 303.357 K 89: 89: Calculated rlist for 1x1 atom pair-list as 0.781 nm, buffer size 0.081 nm 89: 89: Set rlist, assuming 4x4 atom pair-list, to 0.772 nm, buffer size 0.072 nm 89: 89: Note that mdrun will redetermine rlist based on the actual pair-list setup 89: 89: This run will generate roughly 0 Mb of data 89: 89: Writing final coordinates. 89: 89: Core t (s) Wall t (s) (%) 89: Time: 0.500 0.250 199.8 89: (ns/day) (hour/ns) 89: Performance: 7.255 3.308 89: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PullTest_PullIntegrationTest_WithinTolerances_2.edr as single precision energy file 89: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.005 Reading energy frame 2 time 0.010 Reading energy frame 3 time 0.015 Reading energy frame 4 time 0.020 Last energy frame read 4 time 0.020 [ OK ] PullTest/PullIntegrationTest.WithinTolerances/2 (4869 ms) 89: [ RUN ] PullTest/PullIntegrationTest.WithinTolerances/3 89: Generating 1-4 interactions: fudge = 0.5 89: Pull group 1 'r_1' has 3 atoms 89: Pull group 2 'r_2' has 3 atoms 89: Number of degrees of freedom in T-Coupling group System is 1293.00 89: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 89: 89: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PullTest_PullIntegrationTest_WithinTolerances_3_input.mdp]: 89: NVE simulation: will use the initial temperature of 303.122 K for 89: determining the Verlet buffer size 89: 89: Pull group natoms pbc atom distance at start reference at t=0 89: 1 3 2 89: 2 3 5 0.575 nm 0.000 nm 89: 1 3 2 89: 2 3 5 0.050 nm 0.000 nm 89: 89: There was 1 NOTE 89: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PullTest_PullIntegrationTest_WithinTolerances_3.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 89: Can not increase nstlist because an NVE ensemble is used 89: Using 1 MPI thread 89: Using 2 OpenMP threads 89: 89: 89: NOTE: The number of threads is not equal to the number of (logical) cpus 89: and the -pin option is set to auto: will not pin threads to cpus. 89: This can lead to significant performance degradation. 89: Consider using -pin on (and -pinoffset in case you run multiple jobs). 89: starting mdrun 'spc2' 89: 20 steps, 0.0 ps. 89: Generated 330891 of the 330891 non-bonded parameter combinations 89: 89: Generated 330891 of the 330891 1-4 parameter combinations 89: 89: Excluding 2 bonded neighbours molecule type 'SOL' 89: 89: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/spc216.gro' 89: 89: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 303.122 K 89: 89: Calculated rlist for 1x1 atom pair-list as 0.781 nm, buffer size 0.081 nm 89: 89: Set rlist, assuming 4x4 atom pair-list, to 0.772 nm, buffer size 0.072 nm 89: 89: Note that mdrun will redetermine rlist based on the actual pair-list setup 89: 89: This run will generate roughly 0 Mb of data 89: 89: Writing final coordinates. 89: 89: Core t (s) Wall t (s) (%) 89: Time: 0.523 0.262 199.8 89: (ns/day) (hour/ns) 89: Performance: 6.926 3.465 89: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PullTest_PullIntegrationTest_WithinTolerances_3.edr as single precision energy file 89: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.005 Reading energy frame 2 time 0.010 Reading energy frame 3 time 0.015 Reading energy frame 4 time 0.020 Last energy frame read 4 time 0.020 [ OK ] PullTest/PullIntegrationTest.WithinTolerances/3 (4751 ms) 89: [----------] 4 tests from PullTest/PullIntegrationTest (19412 ms total) 89: 89: [----------] Global test environment tear-down 89: [==========] 4 tests from 1 test suite ran. (19459 ms total) 89: [ PASSED ] 4 tests. 89/92 Test #89: MdrunPullTests ............................ Passed 19.55 sec test 90 Start 90: MdrunRotationTests 90: Test command: /build/reproducible-path/gromacs-2025.1/build/basic/bin/mdrun-rotation-test "-ntomp" "2" "--gtest_output=xml:/build/reproducible-path/gromacs-2025.1/build/basic/Testing/Temporary/MdrunRotationTests.xml" 90: Working Directory: /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests 90: Test timeout computed to be: 600 90: [==========] Running 12 tests from 1 test suite. 90: [----------] Global test environment set-up. 90: [----------] 12 tests from RotationWorks/RotationTest 90: [ RUN ] RotationWorks/RotationTest.CheckEnergiesForcesAndTraj/0 90: Enforced rotation: Group 0 (iso) normalized rot. vector: 0.267261 0.534522 0.801784 90: 90: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_0_input.mdp]: 90: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 90: that with the Verlet scheme, nstlist has no effect on the accuracy of 90: your simulation. 90: 90: Rotation group 0 'system' has 4 atoms 90: Number of degrees of freedom in T-Coupling group rest is 9.00 90: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 90: 90: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_0_input.mdp]: 90: NVE simulation with an initial temperature of zero: will use a Verlet 90: buffer of 10%. Check your energy drift! 90: 90: Enforced rotation: group 0 has 4 reference positions. 90: Reading them from /build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/rotref.0.trr. 90: trr version: GMX_trn_file (single precision) 90: 90: There were 2 NOTEs 90: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_0.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 90: Can not increase nstlist because an NVE ensemble is used 90: Using 1 MPI thread 90: Using 2 OpenMP threads 90: 90: 90: NOTE: The number of threads is not equal to the number of (logical) cpus 90: and the -pin option is set to auto: will not pin threads to cpus. 90: This can lead to significant performance degradation. 90: Consider using -pin on (and -pinoffset in case you run multiple jobs). 90: starting mdrun 'Good gRace! Old Maple Actually Chews Slate' 90: 25 steps, 0.1 ps. 90: Setting the LD random seed to 1577016697 90: 90: Generated 1 of the 1 non-bonded parameter combinations 90: 90: Excluding 1 bonded neighbours molecule type 'ArgonA' 90: 90: Excluding 1 bonded neighbours molecule type 'ArgonB' 90: 90: Excluding 1 bonded neighbours molecule type 'ArgonC' 90: 90: Excluding 1 bonded neighbours molecule type 'ArgonD' 90: 90: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon4.gro', all velocities are zero 90: 90: This run will generate roughly 0 Mb of data 90: 90: Writing final coordinates. 90: 90: Core t (s) Wall t (s) (%) 90: Time: 0.072 0.036 198.4 90: (ns/day) (hour/ns) 90: Performance: 123.960 0.194 90: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_0.edr as single precision energy file 90: Reading energy frame 0 time 0.002 Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_0.edr as single precision energy file 90: Reading energy frame 0 time 0.002 Reading energy frame 1 time 0.012 Reading energy frame 2 time 0.022 Reading energy frame 3 time 0.032 Reading energy frame 4 time 0.042 Reading energy frame 5 time 0.052 Last energy frame read 5 time 0.052 90: [ OK ] RotationWorks/RotationTest.CheckEnergiesForcesAndTraj/0 (100 ms) 90: [ RUN ] RotationWorks/RotationTest.CheckEnergiesForcesAndTraj/1 90: Enforced rotation: Group 0 (iso-pf) normalized rot. vector: 0.267261 0.534522 0.801784 90: 90: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_1_input.mdp]: 90: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 90: that with the Verlet scheme, nstlist has no effect on the accuracy of 90: your simulation. 90: 90: Rotation group 0 'system' has 4 atoms 90: Number of degrees of freedom in T-Coupling group rest is 9.00 90: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 90: 90: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_1_input.mdp]: 90: NVE simulation with an initial temperature of zero: will use a Verlet 90: buffer of 10%. Check your energy drift! 90: 90: Enforced rotation: group 0 has 4 reference positions. 90: Reading them from /build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/rotref.0.trr. 90: 90: There were 2 NOTEs 90: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_1.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 90: Can not increase nstlist because an NVE ensemble is used 90: Using 1 MPI thread 90: Using 2 OpenMP threads 90: 90: 90: NOTE: The number of threads is not equal to the number of (logical) cpus 90: and the -pin option is set to auto: will not pin threads to cpus. 90: This can lead to significant performance degradation. 90: Consider using -pin on (and -pinoffset in case you run multiple jobs). 90: starting mdrun 'Good gRace! Old Maple Actually Chews Slate' 90: 25 steps, 0.1 ps. 90: Setting the LD random seed to -553994625 90: 90: Generated 1 of the 1 non-bonded parameter combinations 90: 90: Excluding 1 bonded neighbours molecule type 'ArgonA' 90: 90: Excluding 1 bonded neighbours molecule type 'ArgonB' 90: 90: Excluding 1 bonded neighbours molecule type 'ArgonC' 90: 90: Excluding 1 bonded neighbours molecule type 'ArgonD' 90: 90: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon4.gro', all velocities are zero 90: 90: This run will generate roughly 0 Mb of data 90: 90: Writing final coordinates. 90: 90: Core t (s) Wall t (s) (%) 90: Time: 0.054 0.027 197.8 90: (ns/day) (hour/ns) 90: Performance: 165.657 0.145 90: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_1.edr as single precision energy file 90: Reading energy frame 0 time 0.002 Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_1.edr as single precision energy file 90: Reading energy frame 0 time 0.002 Reading energy frame 1 time 0.012 Reading energy frame 2 time 0.022 Reading energy frame 3 time 0.032 Reading energy frame 4 time 0.042 Reading energy frame 5 time 0.052 Last energy frame read 5 time 0.052 90: [ OK ] RotationWorks/RotationTest.CheckEnergiesForcesAndTraj/1 (86 ms) 90: [ RUN ] RotationWorks/RotationTest.CheckEnergiesForcesAndTraj/2 90: Enforced rotation: Group 0 (pm) normalized rot. vector: 0.267261 0.534522 0.801784 90: 90: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_2_input.mdp]: 90: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 90: that with the Verlet scheme, nstlist has no effect on the accuracy of 90: your simulation. 90: 90: Rotation group 0 'system' has 4 atoms 90: Number of degrees of freedom in T-Coupling group rest is 9.00 90: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 90: 90: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_2_input.mdp]: 90: NVE simulation with an initial temperature of zero: will use a Verlet 90: buffer of 10%. Check your energy drift! 90: 90: Enforced rotation: group 0 has 4 reference positions. 90: Reading them from /build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/rotref.0.trr. 90: 90: There were 2 NOTEs 90: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_2.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 90: Can not increase nstlist because an NVE ensemble is used 90: Using 1 MPI thread 90: Using 2 OpenMP threads 90: 90: 90: NOTE: The number of threads is not equal to the number of (logical) cpus 90: and the -pin option is set to auto: will not pin threads to cpus. 90: This can lead to significant performance degradation. 90: Consider using -pin on (and -pinoffset in case you run multiple jobs). 90: starting mdrun 'Good gRace! Old Maple Actually Chews Slate' 90: 25 steps, 0.1 ps. 90: Setting the LD random seed to 1990777853 90: 90: Generated 1 of the 1 non-bonded parameter combinations 90: 90: Excluding 1 bonded neighbours molecule type 'ArgonA' 90: 90: Excluding 1 bonded neighbours molecule type 'ArgonB' 90: 90: Excluding 1 bonded neighbours molecule type 'ArgonC' 90: 90: Excluding 1 bonded neighbours molecule type 'ArgonD' 90: 90: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon4.gro', all velocities are zero 90: 90: This run will generate roughly 0 Mb of data 90: 90: Writing final coordinates. 90: 90: Core t (s) Wall t (s) (%) 90: Time: 0.047 0.024 197.1 90: (ns/day) (hour/ns) 90: Performance: 188.717 0.127 90: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_2.edr as single precision energy file 90: Reading energy frame 0 time 0.002 Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_2.edr as single precision energy file 90: Reading energy frame 0 time 0.002 Reading energy frame 1 time 0.012 Reading energy frame 2 time 0.022 Reading energy frame 3 time 0.032 Reading energy frame 4 time 0.042 Reading energy frame 5 time 0.052 Last energy frame read 5 time 0.052 90: [ OK ] RotationWorks/RotationTest.CheckEnergiesForcesAndTraj/2 (82 ms) 90: [ RUN ] RotationWorks/RotationTest.CheckEnergiesForcesAndTraj/3 90: Enforced rotation: Group 0 (pm-pf) normalized rot. vector: 0.267261 0.534522 0.801784 90: 90: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_3_input.mdp]: 90: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 90: that with the Verlet scheme, nstlist has no effect on the accuracy of 90: your simulation. 90: 90: Rotation group 0 'system' has 4 atoms 90: Number of degrees of freedom in T-Coupling group rest is 9.00 90: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 90: 90: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_3_input.mdp]: 90: NVE simulation with an initial temperature of zero: will use a Verlet 90: buffer of 10%. Check your energy drift! 90: 90: Enforced rotation: group 0 has 4 reference positions. 90: Reading them from /build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/rotref.0.trr. 90: 90: There were 2 NOTEs 90: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_3.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 90: Can not increase nstlist because an NVE ensemble is used 90: Using 1 MPI thread 90: Using 2 OpenMP threads 90: 90: 90: NOTE: The number of threads is not equal to the number of (logical) cpus 90: and the -pin option is set to auto: will not pin threads to cpus. 90: This can lead to significant performance degradation. 90: Consider using -pin on (and -pinoffset in case you run multiple jobs). 90: starting mdrun 'Good gRace! Old Maple Actually Chews Slate' 90: 25 steps, 0.1 ps. 90: Setting the LD random seed to 2113923039 90: 90: Generated 1 of the 1 non-bonded parameter combinations 90: 90: Excluding 1 bonded neighbours molecule type 'ArgonA' 90: 90: Excluding 1 bonded neighbours molecule type 'ArgonB' 90: 90: Excluding 1 bonded neighbours molecule type 'ArgonC' 90: 90: Excluding 1 bonded neighbours molecule type 'ArgonD' 90: 90: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon4.gro', all velocities are zero 90: 90: This run will generate roughly 0 Mb of data 90: 90: Writing final coordinates. 90: 90: Core t (s) Wall t (s) (%) 90: Time: 0.048 0.024 197.8 90: (ns/day) (hour/ns) 90: Performance: 185.186 0.130 90: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_3.edr as single precision energy file 90: Reading energy frame 0 time 0.002 Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_3.edr as single precision energy file 90: Reading energy frame 0 time 0.002 Reading energy frame 1 time 0.012 Reading energy frame 2 time 0.022 Reading energy frame 3 time 0.032 Reading energy frame 4 time 0.042 Reading energy frame 5 time 0.052 Last energy frame read 5 time 0.052 90: [ OK ] RotationWorks/RotationTest.CheckEnergiesForcesAndTraj/3 (82 ms) 90: [ RUN ] RotationWorks/RotationTest.CheckEnergiesForcesAndTraj/4 90: Enforced rotation: Group 0 (rm) normalized rot. vector: 0.267261 0.534522 0.801784 90: 90: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_4_input.mdp]: 90: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 90: that with the Verlet scheme, nstlist has no effect on the accuracy of 90: your simulation. 90: 90: Rotation group 0 'system' has 4 atoms 90: Number of degrees of freedom in T-Coupling group rest is 9.00 90: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 90: 90: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_4_input.mdp]: 90: NVE simulation with an initial temperature of zero: will use a Verlet 90: buffer of 10%. Check your energy drift! 90: 90: Enforced rotation: group 0 has 4 reference positions. 90: Reading them from /build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/rotref.0.trr. 90: 90: There were 2 NOTEs 90: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_4.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 90: Can not increase nstlist because an NVE ensemble is used 90: Using 1 MPI thread 90: Using 2 OpenMP threads 90: 90: 90: NOTE: The number of threads is not equal to the number of (logical) cpus 90: and the -pin option is set to auto: will not pin threads to cpus. 90: This can lead to significant performance degradation. 90: Consider using -pin on (and -pinoffset in case you run multiple jobs). 90: starting mdrun 'Good gRace! Old Maple Actually Chews Slate' 90: 25 steps, 0.1 ps. 90: Setting the LD random seed to -537137425 90: 90: Generated 1 of the 1 non-bonded parameter combinations 90: 90: Excluding 1 bonded neighbours molecule type 'ArgonA' 90: 90: Excluding 1 bonded neighbours molecule type 'ArgonB' 90: 90: Excluding 1 bonded neighbours molecule type 'ArgonC' 90: 90: Excluding 1 bonded neighbours molecule type 'ArgonD' 90: 90: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon4.gro', all velocities are zero 90: 90: This run will generate roughly 0 Mb of data 90: 90: Writing final coordinates. 90: 90: Core t (s) Wall t (s) (%) 90: Time: 0.046 0.023 197.6 90: (ns/day) (hour/ns) 90: Performance: 192.172 0.125 90: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_4.edr as single precision energy file 90: Reading energy frame 0 time 0.002 Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_4.edr as single precision energy file 90: Reading energy frame 0 time 0.002 Reading energy frame 1 time 0.012 Reading energy frame 2 time 0.022 Reading energy frame 3 time 0.032 Reading energy frame 4 time 0.042 Reading energy frame 5 time 0.052 Last energy frame read 5 time 0.052 90: [ OK ] RotationWorks/RotationTest.CheckEnergiesForcesAndTraj/4 (82 ms) 90: [ RUN ] RotationWorks/RotationTest.CheckEnergiesForcesAndTraj/5 90: Enforced rotation: Group 0 (rm-pf) normalized rot. vector: 0.267261 0.534522 0.801784 90: 90: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_5_input.mdp]: 90: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 90: that with the Verlet scheme, nstlist has no effect on the accuracy of 90: your simulation. 90: 90: Rotation group 0 'system' has 4 atoms 90: Number of degrees of freedom in T-Coupling group rest is 9.00 90: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 90: 90: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_5_input.mdp]: 90: NVE simulation with an initial temperature of zero: will use a Verlet 90: buffer of 10%. Check your energy drift! 90: 90: Enforced rotation: group 0 has 4 reference positions. 90: Reading them from /build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/rotref.0.trr. 90: 90: There were 2 NOTEs 90: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_5.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 90: Can not increase nstlist because an NVE ensemble is used 90: Using 1 MPI thread 90: Using 2 OpenMP threads 90: 90: 90: NOTE: The number of threads is not equal to the number of (logical) cpus 90: and the -pin option is set to auto: will not pin threads to cpus. 90: This can lead to significant performance degradation. 90: Consider using -pin on (and -pinoffset in case you run multiple jobs). 90: starting mdrun 'Good gRace! Old Maple Actually Chews Slate' 90: 25 steps, 0.1 ps. 90: Setting the LD random seed to -2244786 90: 90: Generated 1 of the 1 non-bonded parameter combinations 90: 90: Excluding 1 bonded neighbours molecule type 'ArgonA' 90: 90: Excluding 1 bonded neighbours molecule type 'ArgonB' 90: 90: Excluding 1 bonded neighbours molecule type 'ArgonC' 90: 90: Excluding 1 bonded neighbours molecule type 'ArgonD' 90: 90: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon4.gro', all velocities are zero 90: 90: This run will generate roughly 0 Mb of data 90: 90: Writing final coordinates. 90: 90: Core t (s) Wall t (s) (%) 90: Time: 0.049 0.025 197.8 90: (ns/day) (hour/ns) 90: Performance: 180.318 0.133 90: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_5.edr as single precision energy file 90: Reading energy frame 0 time 0.002 Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_5.edr as single precision energy file 90: Reading energy frame 0 time 0.002 Reading energy frame 1 time 0.012 Reading energy frame 2 time 0.022 Reading energy frame 3 time 0.032 Reading energy frame 4 time 0.042 Reading energy frame 5 time 0.052 Last energy frame read 5 time 0.052 90: [ OK ] RotationWorks/RotationTest.CheckEnergiesForcesAndTraj/5 (81 ms) 90: [ RUN ] RotationWorks/RotationTest.CheckEnergiesForcesAndTraj/6 90: Enforced rotation: Group 0 (rm2) normalized rot. vector: 0.267261 0.534522 0.801784 90: 90: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_6_input.mdp]: 90: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 90: that with the Verlet scheme, nstlist has no effect on the accuracy of 90: your simulation. 90: 90: Rotation group 0 'system' has 4 atoms 90: Number of degrees of freedom in T-Coupling group rest is 9.00 90: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 90: 90: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_6_input.mdp]: 90: NVE simulation with an initial temperature of zero: will use a Verlet 90: buffer of 10%. Check your energy drift! 90: 90: Enforced rotation: group 0 has 4 reference positions. 90: Reading them from /build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/rotref.0.trr. 90: 90: There were 2 NOTEs 90: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_6.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 90: Can not increase nstlist because an NVE ensemble is used 90: Using 1 MPI thread 90: Using 2 OpenMP threads 90: 90: 90: NOTE: The number of threads is not equal to the number of (logical) cpus 90: and the -pin option is set to auto: will not pin threads to cpus. 90: This can lead to significant performance degradation. 90: Consider using -pin on (and -pinoffset in case you run multiple jobs). 90: starting mdrun 'Good gRace! Old Maple Actually Chews Slate' 90: 25 steps, 0.1 ps. 90: Setting the LD random seed to -1359013985 90: 90: Generated 1 of the 1 non-bonded parameter combinations 90: 90: Excluding 1 bonded neighbours molecule type 'ArgonA' 90: 90: Excluding 1 bonded neighbours molecule type 'ArgonB' 90: 90: Excluding 1 bonded neighbours molecule type 'ArgonC' 90: 90: Excluding 1 bonded neighbours molecule type 'ArgonD' 90: 90: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon4.gro', all velocities are zero 90: 90: This run will generate roughly 0 Mb of data 90: 90: Writing final coordinates. 90: 90: Core t (s) Wall t (s) (%) 90: Time: 0.047 0.024 197.3 90: (ns/day) (hour/ns) 90: Performance: 189.971 0.126 90: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_6.edr as single precision energy file 90: Reading energy frame 0 time 0.002 Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_6.edr as single precision energy file 90: Reading energy frame 0 time 0.002 Reading energy frame 1 time 0.012 Reading energy frame 2 time 0.022 Reading energy frame 3 time 0.032 Reading energy frame 4 time 0.042 Reading energy frame 5 time 0.052 Last energy frame read 5 time 0.052 90: [ OK ] RotationWorks/RotationTest.CheckEnergiesForcesAndTraj/6 (81 ms) 90: [ RUN ] RotationWorks/RotationTest.CheckEnergiesForcesAndTraj/7 90: Enforced rotation: Group 0 (rm2-pf) normalized rot. vector: 0.267261 0.534522 0.801784 90: 90: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_7_input.mdp]: 90: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 90: that with the Verlet scheme, nstlist has no effect on the accuracy of 90: your simulation. 90: 90: Rotation group 0 'system' has 4 atoms 90: Number of degrees of freedom in T-Coupling group rest is 9.00 90: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 90: 90: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_7_input.mdp]: 90: NVE simulation with an initial temperature of zero: will use a Verlet 90: buffer of 10%. Check your energy drift! 90: 90: Enforced rotation: group 0 has 4 reference positions. 90: Reading them from /build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/rotref.0.trr. 90: 90: There were 2 NOTEs 90: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_7.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 90: Can not increase nstlist because an NVE ensemble is used 90: Using 1 MPI thread 90: Using 2 OpenMP threads 90: 90: 90: NOTE: The number of threads is not equal to the number of (logical) cpus 90: and the -pin option is set to auto: will not pin threads to cpus. 90: This can lead to significant performance degradation. 90: Consider using -pin on (and -pinoffset in case you run multiple jobs). 90: starting mdrun 'Good gRace! Old Maple Actually Chews Slate' 90: 25 steps, 0.1 ps. 90: Setting the LD random seed to -1225675306 90: 90: Generated 1 of the 1 non-bonded parameter combinations 90: 90: Excluding 1 bonded neighbours molecule type 'ArgonA' 90: 90: Excluding 1 bonded neighbours molecule type 'ArgonB' 90: 90: Excluding 1 bonded neighbours molecule type 'ArgonC' 90: 90: Excluding 1 bonded neighbours molecule type 'ArgonD' 90: 90: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon4.gro', all velocities are zero 90: 90: This run will generate roughly 0 Mb of data 90: 90: Writing final coordinates. 90: 90: Core t (s) Wall t (s) (%) 90: Time: 0.047 0.024 197.8 90: (ns/day) (hour/ns) 90: Performance: 190.713 0.126 90: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_7.edr as single precision energy file 90: Reading energy frame 0 time 0.002 Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_7.edr as single precision energy file 90: Reading energy frame 0 time 0.002 Reading energy frame 1 time 0.012 Reading energy frame 2 time 0.022 Reading energy frame 3 time 0.032 Reading energy frame 4 time 0.042 Reading energy frame 5 time 0.052 Last energy frame read 5 time 0.052 90: [ OK ] RotationWorks/RotationTest.CheckEnergiesForcesAndTraj/7 (81 ms) 90: [ RUN ] RotationWorks/RotationTest.CheckEnergiesForcesAndTraj/8 90: Enforced rotation: Group 0 (flex) normalized rot. vector: 0.267261 0.534522 0.801784 90: 90: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_8_input.mdp]: 90: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 90: that with the Verlet scheme, nstlist has no effect on the accuracy of 90: your simulation. 90: 90: Rotation group 0 'system' has 4 atoms 90: Number of degrees of freedom in T-Coupling group rest is 9.00 90: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 90: 90: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_8_input.mdp]: 90: NVE simulation with an initial temperature of zero: will use a Verlet 90: buffer of 10%. Check your energy drift! 90: 90: Enforced rotation: group 0 has 4 reference positions. 90: Reading them from /build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/rotref.0.trr. 90: 90: There were 2 NOTEs 90: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_8.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 90: Can not increase nstlist because an NVE ensemble is used 90: Using 1 MPI thread 90: Using 2 OpenMP threads 90: 90: 90: NOTE: The number of threads is not equal to the number of (logical) cpus 90: and the -pin option is set to auto: will not pin threads to cpus. 90: This can lead to significant performance degradation. 90: Consider using -pin on (and -pinoffset in case you run multiple jobs). 90: starting mdrun 'Good gRace! Old Maple Actually Chews Slate' 90: 25 steps, 0.1 ps. 90: Setting the LD random seed to -2097225 90: 90: Generated 1 of the 1 non-bonded parameter combinations 90: 90: Excluding 1 bonded neighbours molecule type 'ArgonA' 90: 90: Excluding 1 bonded neighbours molecule type 'ArgonB' 90: 90: Excluding 1 bonded neighbours molecule type 'ArgonC' 90: 90: Excluding 1 bonded neighbours molecule type 'ArgonD' 90: 90: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon4.gro', all velocities are zero 90: 90: This run will generate roughly 0 Mb of data 90: 90: Writing final coordinates. 90: 90: Core t (s) Wall t (s) (%) 90: Time: 0.065 0.033 198.4 90: (ns/day) (hour/ns) 90: Performance: 137.197 0.175 90: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_8.edr as single precision energy file 90: Reading energy frame 0 time 0.002 Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_8.edr as single precision energy file 90: Reading energy frame 0 time 0.002 Reading energy frame 1 time 0.012 Reading energy frame 2 time 0.022 Reading energy frame 3 time 0.032 Reading energy frame 4 time 0.042 Reading energy frame 5 time 0.052 Last energy frame read 5 time 0.052 90: [ OK ] RotationWorks/RotationTest.CheckEnergiesForcesAndTraj/8 (90 ms) 90: [ RUN ] RotationWorks/RotationTest.CheckEnergiesForcesAndTraj/9 90: Enforced rotation: Group 0 (flex-t) normalized rot. vector: 0.267261 0.534522 0.801784 90: 90: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_9_input.mdp]: 90: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 90: that with the Verlet scheme, nstlist has no effect on the accuracy of 90: your simulation. 90: 90: Rotation group 0 'system' has 4 atoms 90: Number of degrees of freedom in T-Coupling group rest is 9.00 90: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 90: 90: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_9_input.mdp]: 90: NVE simulation with an initial temperature of zero: will use a Verlet 90: buffer of 10%. Check your energy drift! 90: 90: Enforced rotation: group 0 has 4 reference positions. 90: Reading them from /build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/rotref.0.trr. 90: 90: There were 2 NOTEs 90: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_9.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 90: Can not increase nstlist because an NVE ensemble is used 90: Using 1 MPI thread 90: Using 2 OpenMP threads 90: 90: 90: NOTE: The number of threads is not equal to the number of (logical) cpus 90: and the -pin option is set to auto: will not pin threads to cpus. 90: This can lead to significant performance degradation. 90: Consider using -pin on (and -pinoffset in case you run multiple jobs). 90: starting mdrun 'Good gRace! Old Maple Actually Chews Slate' 90: 25 steps, 0.1 ps. 90: Setting the LD random seed to -738568456 90: 90: Generated 1 of the 1 non-bonded parameter combinations 90: 90: Excluding 1 bonded neighbours molecule type 'ArgonA' 90: 90: Excluding 1 bonded neighbours molecule type 'ArgonB' 90: 90: Excluding 1 bonded neighbours molecule type 'ArgonC' 90: 90: Excluding 1 bonded neighbours molecule type 'ArgonD' 90: 90: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon4.gro', all velocities are zero 90: 90: This run will generate roughly 0 Mb of data 90: 90: Writing final coordinates. 90: 90: Core t (s) Wall t (s) (%) 90: Time: 0.065 0.033 198.4 90: (ns/day) (hour/ns) 90: Performance: 136.838 0.175 90: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_9.edr as single precision energy file 90: Reading energy frame 0 time 0.002 Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_9.edr as single precision energy file 90: Reading energy frame 0 time 0.002 Reading energy frame 1 time 0.012 Reading energy frame 2 time 0.022 Reading energy frame 3 time 0.032 Reading energy frame 4 time 0.042 Reading energy frame 5 time 0.052 Last energy frame read 5 time 0.052 90: [ OK ] RotationWorks/RotationTest.CheckEnergiesForcesAndTraj/9 (91 ms) 90: [ RUN ] RotationWorks/RotationTest.CheckEnergiesForcesAndTraj/10 90: Enforced rotation: Group 0 (flex2) normalized rot. vector: 0.267261 0.534522 0.801784 90: 90: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_10_input.mdp]: 90: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 90: that with the Verlet scheme, nstlist has no effect on the accuracy of 90: your simulation. 90: 90: Rotation group 0 'system' has 4 atoms 90: Number of degrees of freedom in T-Coupling group rest is 9.00 90: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 90: 90: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_10_input.mdp]: 90: NVE simulation with an initial temperature of zero: will use a Verlet 90: buffer of 10%. Check your energy drift! 90: 90: Enforced rotation: group 0 has 4 reference positions. 90: Reading them from /build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/rotref.0.trr. 90: 90: There were 2 NOTEs 90: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_10.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 90: Can not increase nstlist because an NVE ensemble is used 90: Using 1 MPI thread 90: Using 2 OpenMP threads 90: 90: 90: NOTE: The number of threads is not equal to the number of (logical) cpus 90: and the -pin option is set to auto: will not pin threads to cpus. 90: This can lead to significant performance degradation. 90: Consider using -pin on (and -pinoffset in case you run multiple jobs). 90: starting mdrun 'Good gRace! Old Maple Actually Chews Slate' 90: 25 steps, 0.1 ps. 90: Setting the LD random seed to -1745422594 90: 90: Generated 1 of the 1 non-bonded parameter combinations 90: 90: Excluding 1 bonded neighbours molecule type 'ArgonA' 90: 90: Excluding 1 bonded neighbours molecule type 'ArgonB' 90: 90: Excluding 1 bonded neighbours molecule type 'ArgonC' 90: 90: Excluding 1 bonded neighbours molecule type 'ArgonD' 90: 90: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon4.gro', all velocities are zero 90: 90: This run will generate roughly 0 Mb of data 90: 90: Writing final coordinates. 90: 90: Core t (s) Wall t (s) (%) 90: Time: 0.065 0.033 198.3 90: (ns/day) (hour/ns) 90: Performance: 136.178 0.176 90: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_10.edr as single precision energy file 90: Reading energy frame 0 time 0.002 Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_10.edr as single precision energy file 90: Reading energy frame 0 time 0.002 Reading energy frame 1 time 0.012 Reading energy frame 2 time 0.022 Reading energy frame 3 time 0.032 Reading energy frame 4 time 0.042 Reading energy frame 5 time 0.052 Last energy frame read 5 time 0.052 90: [ OK ] RotationWorks/RotationTest.CheckEnergiesForcesAndTraj/10 (92 ms) 90: [ RUN ] RotationWorks/RotationTest.CheckEnergiesForcesAndTraj/11 90: Enforced rotation: Group 0 (flex2-t) normalized rot. vector: 0.267261 0.534522 0.801784 90: 90: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_11_input.mdp]: 90: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 90: that with the Verlet scheme, nstlist has no effect on the accuracy of 90: your simulation. 90: 90: Rotation group 0 'system' has 4 atoms 90: Number of degrees of freedom in T-Coupling group rest is 9.00 90: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 90: 90: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_11_input.mdp]: 90: NVE simulation with an initial temperature of zero: will use a Verlet 90: buffer of 10%. Check your energy drift! 90: 90: Enforced rotation: group 0 has 4 reference positions. 90: Reading them from /build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/rotref.0.trr. 90: 90: There were 2 NOTEs 90: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_11.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 90: Can not increase nstlist because an NVE ensemble is used 90: Using 1 MPI thread 90: Using 2 OpenMP threads 90: 90: 90: NOTE: The number of threads is not equal to the number of (logical) cpus 90: and the -pin option is set to auto: will not pin threads to cpus. 90: This can lead to significant performance degradation. 90: Consider using -pin on (and -pinoffset in case you run multiple jobs). 90: starting mdrun 'Good gRace! Old Maple Actually Chews Slate' 90: 25 steps, 0.1 ps. 90: Setting the LD random seed to -84751489 90: 90: Generated 1 of the 1 non-bonded parameter combinations 90: 90: Excluding 1 bonded neighbours molecule type 'ArgonA' 90: 90: Excluding 1 bonded neighbours molecule type 'ArgonB' 90: 90: Excluding 1 bonded neighbours molecule type 'ArgonC' 90: 90: Excluding 1 bonded neighbours molecule type 'ArgonD' 90: 90: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon4.gro', all velocities are zero 90: 90: This run will generate roughly 0 Mb of data 90: 90: Writing final coordinates. 90: 90: Core t (s) Wall t (s) (%) 90: Time: 0.068 0.035 197.9 90: (ns/day) (hour/ns) 90: Performance: 129.906 0.185 90: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_11.edr as single precision energy file 90: Reading energy frame 0 time 0.002 Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_11.edr as single precision energy file 90: Reading energy frame 0 time 0.002 Reading energy frame 1 time 0.012 Reading energy frame 2 time 0.022 Reading energy frame 3 time 0.032 Reading energy frame 4 time 0.042 Reading energy frame 5 time 0.052 Last energy frame read 5 time 0.052 90: [ OK ] RotationWorks/RotationTest.CheckEnergiesForcesAndTraj/11 (96 ms) 90: [----------] 12 tests from RotationWorks/RotationTest (1061 ms total) 90: 90: [----------] Global test environment tear-down 90: [==========] 12 tests from 1 test suite ran. (1111 ms total) 90: [ PASSED ] 12 tests. 90/92 Test #90: MdrunRotationTests ........................ Passed 1.20 sec test 91 Start 91: MdrunSimulatorComparison 91: Test command: /build/reproducible-path/gromacs-2025.1/build/basic/bin/mdrun-simulator-comparison-test "-ntomp" "2" "--gtest_output=xml:/build/reproducible-path/gromacs-2025.1/build/basic/Testing/Temporary/MdrunSimulatorComparison.xml" 91: Working Directory: /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests 91: Test timeout computed to be: 600 91: [==========] Running 0 tests from 0 test suites. 91: [==========] 0 tests from 0 test suites ran. (0 ms total) 91: [ PASSED ] 0 tests. 91: 91: YOU HAVE 82 DISABLED TESTS 91: 91/92 Test #91: MdrunSimulatorComparison .................. Passed 0.10 sec test 92 Start 92: MdrunVirtualSiteTests 92: Test command: /build/reproducible-path/gromacs-2025.1/build/basic/bin/mdrun-vsites-test "-ntmpi" "2" "--gtest_output=xml:/build/reproducible-path/gromacs-2025.1/build/basic/Testing/Temporary/MdrunVirtualSiteTests.xml" 92: Working Directory: /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests 92: Test timeout computed to be: 600 92: [==========] Running 37 tests from 2 test suites. 92: [----------] Global test environment set-up. 92: [----------] 1 test from VirtualSiteVelocityTest 92: [ RUN ] VirtualSiteVelocityTest.ReferenceIsCorrect 92: [ OK ] VirtualSiteVelocityTest.ReferenceIsCorrect (0 ms) 92: [----------] 1 test from VirtualSiteVelocityTest (0 ms total) 92: 92: [----------] 36 tests from VelocitiesConformToExpectations/VirtualSiteTest 92: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/0 92: 92: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_0_input.mdp]: 92: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 92: that with the Verlet scheme, nstlist has no effect on the accuracy of 92: your simulation. 92: 92: 92: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_0_input.mdp]: 92: Setting nstcalcenergy (100) equal to nstenergy (4) 92: 92: Number of degrees of freedom in T-Coupling group System is 45.00 92: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 92: 92: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_0_input.mdp]: 92: NVE simulation with an initial temperature of zero: will use a Verlet 92: buffer of 10%. Check your energy drift! 92: 92: 92: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_0_input.mdp]: 92: You are using a plain Coulomb cut-off, which might produce artifacts. 92: You might want to consider using PME electrostatics. 92: 92: 92: 92: There were 4 NOTEs 92: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_0.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 92: Can not increase nstlist because an NVE ensemble is used 92: Update groups can not be used for this system because an incompatible virtual site type is used 92: 92: Using 2 MPI threads 92: Using 1 OpenMP thread per tMPI thread 92: 92: 92: NOTE: The number of threads is not equal to the number of (logical) cpus 92: and the -pin option is set to auto: will not pin threads to cpus. 92: This can lead to significant performance degradation. 92: Consider using -pin on (and -pinoffset in case you run multiple jobs). 92: starting mdrun 'Virtual sites test system in vacuo' 92: 8 steps, 0.0 ps. 92: Generated 3 of the 6 non-bonded parameter combinations 92: 92: Excluding 3 bonded neighbours molecule type 'VSTEST' 92: 92: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/vsite_test.gro', all velocities are zero 92: 92: Cleaning up constraints and constant bonded interactions with virtual sites 92: 92: This run will generate roughly 0 Mb of data 92: 92: Writing final coordinates. 92: 92: 92: Dynamic load balancing report: 92: DLB was off during the run due to low measured imbalance. 92: Average load imbalance: 7.4%. 92: The balanceable part of the MD step is 44%, load imbalance is computed from this. 92: Part of the total run time spent waiting due to load imbalance: 3.3%. 92: 92: 92: NOTE: 42 % of the run time was spent communicating energies, 92: you might want to increase some nst* mdp options 92: 92: Core t (s) Wall t (s) (%) 92: Time: 0.046 0.023 197.2 92: (ns/day) (hour/ns) 92: Performance: 33.679 0.713 92: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_0.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 92: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_0.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 92: trr version: GMX_trn_file (single precision) 92: 92: Reading virtual site types... 92: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/0 (76 ms) 92: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/1 92: 92: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_1_input.mdp]: 92: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 92: that with the Verlet scheme, nstlist has no effect on the accuracy of 92: your simulation. 92: 92: 92: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_1_input.mdp]: 92: Setting nstcalcenergy (100) equal to nstenergy (4) 92: 92: Number of degrees of freedom in T-Coupling group System is 45.00 92: 92: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_1_input.mdp]: 92: NVE simulation with an initial temperature of zero: will use a Verlet 92: buffer of 10%. Check your energy drift! 92: 92: 92: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_1_input.mdp]: 92: You are using a plain Coulomb cut-off, which might produce artifacts. 92: You might want to consider using PME electrostatics. 92: 92: 92: 92: There were 4 NOTEs 92: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_1.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 92: Can not increase nstlist because an NVE ensemble is used 92: Update groups can not be used for this system because an incompatible virtual site type is used 92: 92: Using 2 MPI threads 92: Using 1 OpenMP thread per tMPI thread 92: 92: 92: NOTE: The number of threads is not equal to the number of (logical) cpus 92: and the -pin option is set to auto: will not pin threads to cpus. 92: This can lead to significant performance degradation. 92: Consider using -pin on (and -pinoffset in case you run multiple jobs). 92: starting mdrun 'Virtual sites test system in vacuo' 92: 8 steps, 0.0 ps. 92: Generated 3 of the 6 non-bonded parameter combinations 92: 92: Excluding 3 bonded neighbours molecule type 'VSTEST' 92: 92: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/vsite_test.gro', all velocities are zero 92: 92: Cleaning up constraints and constant bonded interactions with virtual sites 92: 92: This run will generate roughly 0 Mb of data 92: 92: Writing final coordinates. 92: 92: 92: Dynamic load balancing report: 92: DLB was off during the run due to low measured imbalance. 92: Average load imbalance: 8.1%. 92: The balanceable part of the MD step is 45%, load imbalance is computed from this. 92: Part of the total run time spent waiting due to load imbalance: 3.7%. 92: 92: 92: NOTE: 40 % of the run time was spent communicating energies, 92: you might want to increase some nst* mdp options 92: 92: Core t (s) Wall t (s) (%) 92: Time: 0.037 0.019 196.3 92: (ns/day) (hour/ns) 92: Performance: 40.889 0.587 92: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_1.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 92: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_1.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 92: 92: Reading virtual site types... 92: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/1 (67 ms) 92: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/2 92: 92: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_2_input.mdp]: 92: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 92: that with the Verlet scheme, nstlist has no effect on the accuracy of 92: your simulation. 92: 92: 92: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_2_input.mdp]: 92: Setting nstcalcenergy (100) equal to nstenergy (4) 92: 92: Number of degrees of freedom in T-Coupling group System is 45.00 92: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 92: 92: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_2_input.mdp]: 92: NVE simulation with an initial temperature of zero: will use a Verlet 92: buffer of 10%. Check your energy drift! 92: 92: 92: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_2_input.mdp]: 92: You are using a plain Coulomb cut-off, which might produce artifacts. 92: You might want to consider using PME electrostatics. 92: 92: 92: 92: There were 4 NOTEs 92: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_2.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 92: Can not increase nstlist because an NVE ensemble is used 92: Update groups can not be used for this system because an incompatible virtual site type is used 92: 92: Using 2 MPI threads 92: Using 1 OpenMP thread per tMPI thread 92: 92: 92: NOTE: The number of threads is not equal to the number of (logical) cpus 92: and the -pin option is set to auto: will not pin threads to cpus. 92: This can lead to significant performance degradation. 92: Consider using -pin on (and -pinoffset in case you run multiple jobs). 92: starting mdrun 'Virtual sites test system in vacuo' 92: 8 steps, 0.0 ps. 92: Generated 3 of the 6 non-bonded parameter combinations 92: 92: Excluding 3 bonded neighbours molecule type 'VSTEST' 92: 92: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/vsite_test.gro', all velocities are zero 92: 92: Cleaning up constraints and constant bonded interactions with virtual sites 92: 92: This run will generate roughly 0 Mb of data 92: 92: Writing final coordinates. 92: 92: 92: Dynamic load balancing report: 92: DLB was off during the run due to low measured imbalance. 92: Average load imbalance: 1.3%. 92: The balanceable part of the MD step is 47%, load imbalance is computed from this. 92: Part of the total run time spent waiting due to load imbalance: 0.6%. 92: 92: 92: NOTE: 40 % of the run time was spent communicating energies, 92: you might want to increase some nst* mdp options 92: 92: Core t (s) Wall t (s) (%) 92: Time: 0.036 0.019 196.1 92: (ns/day) (hour/ns) 92: Performance: 42.004 0.571 92: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_2.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 92: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_2.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 92: 92: Reading virtual site types... 92: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/2 (68 ms) 92: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/3 92: 92: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_3_input.mdp]: 92: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 92: that with the Verlet scheme, nstlist has no effect on the accuracy of 92: your simulation. 92: 92: 92: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_3_input.mdp]: 92: Setting nstcalcenergy (100) equal to nstenergy (4) 92: 92: Number of degrees of freedom in T-Coupling group System is 45.00 92: 92: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_3_input.mdp]: 92: There are 6 non-linear virtual site constructions. Their contribution to 92: the energy error is approximated. In most cases this does not affect the 92: error significantly. 92: 92: 92: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_3_input.mdp]: 92: You are using a plain Coulomb cut-off, which might produce artifacts. 92: You might want to consider using PME electrostatics. 92: 92: 92: 92: There were 4 NOTEs 92: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_3.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 92: Changing nstlist from 8 to 50, rlist from 0.712 to 0.801 92: 92: Update groups can not be used for this system because an incompatible virtual site type is used 92: 92: Using 2 MPI threads 92: Using 1 OpenMP thread per tMPI thread 92: 92: 92: NOTE: The number of threads is not equal to the number of (logical) cpus 92: and the -pin option is set to auto: will not pin threads to cpus. 92: This can lead to significant performance degradation. 92: Consider using -pin on (and -pinoffset in case you run multiple jobs). 92: starting mdrun 'Virtual sites test system in vacuo' 92: 8 steps, 0.0 ps. 92: Generated 3 of the 6 non-bonded parameter combinations 92: 92: Excluding 3 bonded neighbours molecule type 'VSTEST' 92: 92: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/vsite_test.gro', all velocities are zero 92: 92: Cleaning up constraints and constant bonded interactions with virtual sites 92: 92: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 92: 92: Calculated rlist for 1x1 atom pair-list as 0.715 nm, buffer size 0.015 nm 92: 92: Set rlist, assuming 4x4 atom pair-list, to 0.712 nm, buffer size 0.012 nm 92: 92: Note that mdrun will redetermine rlist based on the actual pair-list setup 92: 92: This run will generate roughly 0 Mb of data 92: 92: Writing final coordinates. 92: 92: NOTE: 42 % of the run time was spent communicating energies, 92: you might want to increase some nst* mdp options 92: 92: Core t (s) Wall t (s) (%) 92: Time: 0.037 0.019 196.5 92: (ns/day) (hour/ns) 92: Performance: 41.671 0.576 92: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_3.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 92: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_3.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 92: 92: Reading virtual site types... 92: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/3 (111 ms) 92: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/4 92: 92: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_4_input.mdp]: 92: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 92: that with the Verlet scheme, nstlist has no effect on the accuracy of 92: your simulation. 92: 92: 92: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_4_input.mdp]: 92: Setting nstcalcenergy (100) equal to nstenergy (4) 92: 92: Number of degrees of freedom in T-Coupling group System is 45.00 92: 92: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_4_input.mdp]: 92: There are 6 non-linear virtual site constructions. Their contribution to 92: the energy error is approximated. In most cases this does not affect the 92: error significantly. 92: 92: 92: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_4_input.mdp]: 92: You are using a plain Coulomb cut-off, which might produce artifacts. 92: You might want to consider using PME electrostatics. 92: 92: 92: 92: There were 4 NOTEs 92: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_4.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 92: Changing nstlist from 8 to 50, rlist from 0.712 to 0.801 92: 92: Update groups can not be used for this system because an incompatible virtual site type is used 92: 92: Using 2 MPI threads 92: Using 1 OpenMP thread per tMPI thread 92: 92: 92: NOTE: The number of threads is not equal to the number of (logical) cpus 92: and the -pin option is set to auto: will not pin threads to cpus. 92: This can lead to significant performance degradation. 92: Consider using -pin on (and -pinoffset in case you run multiple jobs). 92: starting mdrun 'Virtual sites test system in vacuo' 92: 8 steps, 0.0 ps. 92: Generated 3 of the 6 non-bonded parameter combinations 92: 92: Excluding 3 bonded neighbours molecule type 'VSTEST' 92: 92: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/vsite_test.gro', all velocities are zero 92: 92: Cleaning up constraints and constant bonded interactions with virtual sites 92: 92: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 92: 92: Calculated rlist for 1x1 atom pair-list as 0.715 nm, buffer size 0.015 nm 92: 92: Set rlist, assuming 4x4 atom pair-list, to 0.712 nm, buffer size 0.012 nm 92: 92: Note that mdrun will redetermine rlist based on the actual pair-list setup 92: 92: This run will generate roughly 0 Mb of data 92: 92: Writing final coordinates. 92: 92: NOTE: 42 % of the run time was spent communicating energies, 92: you might want to increase some nst* mdp options 92: 92: Core t (s) Wall t (s) (%) 92: Time: 0.036 0.018 195.7 92: (ns/day) (hour/ns) 92: Performance: 42.053 0.571 92: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_4.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 92: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_4.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 92: 92: Reading virtual site types... 92: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/4 (111 ms) 92: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/5 92: 92: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_5_input.mdp]: 92: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 92: that with the Verlet scheme, nstlist has no effect on the accuracy of 92: your simulation. 92: 92: 92: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_5_input.mdp]: 92: Setting nstcalcenergy (100) equal to nstenergy (4) 92: 92: Number of degrees of freedom in T-Coupling group System is 45.00 92: 92: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_5_input.mdp]: 92: There are 6 non-linear virtual site constructions. Their contribution to 92: the energy error is approximated. In most cases this does not affect the 92: error significantly. 92: 92: 92: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_5_input.mdp]: 92: You are using a plain Coulomb cut-off, which might produce artifacts. 92: You might want to consider using PME electrostatics. 92: 92: 92: 92: There were 4 NOTEs 92: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_5.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 92: Changing nstlist from 8 to 50, rlist from 0.712 to 0.801 92: 92: Update groups can not be used for this system because an incompatible virtual site type is used 92: 92: Using 2 MPI threads 92: Using 1 OpenMP thread per tMPI thread 92: 92: 92: NOTE: The number of threads is not equal to the number of (logical) cpus 92: and the -pin option is set to auto: will not pin threads to cpus. 92: This can lead to significant performance degradation. 92: Consider using -pin on (and -pinoffset in case you run multiple jobs). 92: starting mdrun 'Virtual sites test system in vacuo' 92: 8 steps, 0.0 ps. 92: Generated 3 of the 6 non-bonded parameter combinations 92: 92: Excluding 3 bonded neighbours molecule type 'VSTEST' 92: 92: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/vsite_test.gro', all velocities are zero 92: 92: Cleaning up constraints and constant bonded interactions with virtual sites 92: 92: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 92: 92: Calculated rlist for 1x1 atom pair-list as 0.715 nm, buffer size 0.015 nm 92: 92: Set rlist, assuming 4x4 atom pair-list, to 0.712 nm, buffer size 0.012 nm 92: 92: Note that mdrun will redetermine rlist based on the actual pair-list setup 92: 92: This run will generate roughly 0 Mb of data 92: 92: Writing final coordinates. 92: 92: NOTE: 41 % of the run time was spent communicating energies, 92: you might want to increase some nst* mdp options 92: 92: Core t (s) Wall t (s) (%) 92: Time: 0.037 0.019 195.9 92: (ns/day) (hour/ns) 92: Performance: 41.019 0.585 92: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_5.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 92: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_5.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 92: 92: Reading virtual site types... 92: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/5 (110 ms) 92: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/6 92: 92: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_6_input.mdp]: 92: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 92: that with the Verlet scheme, nstlist has no effect on the accuracy of 92: your simulation. 92: 92: 92: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_6_input.mdp]: 92: Setting nstcalcenergy (100) equal to nstenergy (4) 92: 92: 92: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_6_input.mdp]: 92: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 92: 1 92: 92: Number of degrees of freedom in T-Coupling group System is 45.00 92: 92: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_6_input.mdp]: 92: There are 6 non-linear virtual site constructions. Their contribution to 92: the energy error is approximated. In most cases this does not affect the 92: error significantly. 92: 92: 92: NOTE 5 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_6_input.mdp]: 92: You are using a plain Coulomb cut-off, which might produce artifacts. 92: You might want to consider using PME electrostatics. 92: 92: 92: 92: There were 5 NOTEs 92: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_6.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 92: Changing nstlist from 8 to 50, rlist from 0.712 to 0.801 92: 92: Update groups can not be used for this system because an incompatible virtual site type is used 92: 92: Using 2 MPI threads 92: Using 1 OpenMP thread per tMPI thread 92: 92: 92: NOTE: The number of threads is not equal to the number of (logical) cpus 92: and the -pin option is set to auto: will not pin threads to cpus. 92: This can lead to significant performance degradation. 92: Consider using -pin on (and -pinoffset in case you run multiple jobs). 92: starting mdrun 'Virtual sites test system in vacuo' 92: 8 steps, 0.0 ps. 92: Generated 3 of the 6 non-bonded parameter combinations 92: 92: Excluding 3 bonded neighbours molecule type 'VSTEST' 92: 92: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/vsite_test.gro', all velocities are zero 92: 92: Cleaning up constraints and constant bonded interactions with virtual sites 92: 92: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 92: 92: Calculated rlist for 1x1 atom pair-list as 0.715 nm, buffer size 0.015 nm 92: 92: Set rlist, assuming 4x4 atom pair-list, to 0.712 nm, buffer size 0.012 nm 92: 92: Note that mdrun will redetermine rlist based on the actual pair-list setup 92: 92: This run will generate roughly 0 Mb of data 92: 92: Writing final coordinates. 92: 92: NOTE: 41 % of the run time was spent communicating energies, 92: you might want to increase some nst* mdp options 92: 92: Core t (s) Wall t (s) (%) 92: Time: 0.036 0.019 196.1 92: (ns/day) (hour/ns) 92: Performance: 41.846 0.574 92: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_6.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 92: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_6.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 92: 92: Reading virtual site types... 92: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/6 (110 ms) 92: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/7 92: 92: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_7_input.mdp]: 92: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 92: that with the Verlet scheme, nstlist has no effect on the accuracy of 92: your simulation. 92: 92: 92: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_7_input.mdp]: 92: Setting nstcalcenergy (100) equal to nstenergy (4) 92: 92: 92: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_7_input.mdp]: 92: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 92: 1 92: 92: Number of degrees of freedom in T-Coupling group System is 45.00 92: 92: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_7_input.mdp]: 92: There are 6 non-linear virtual site constructions. Their contribution to 92: the energy error is approximated. In most cases this does not affect the 92: error significantly. 92: 92: 92: NOTE 5 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_7_input.mdp]: 92: You are using a plain Coulomb cut-off, which might produce artifacts. 92: You might want to consider using PME electrostatics. 92: 92: 92: 92: There were 5 NOTEs 92: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_7.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 92: Changing nstlist from 8 to 50, rlist from 0.712 to 0.801 92: 92: Update groups can not be used for this system because an incompatible virtual site type is used 92: 92: Using 2 MPI threads 92: Using 1 OpenMP thread per tMPI thread 92: 92: 92: NOTE: The number of threads is not equal to the number of (logical) cpus 92: and the -pin option is set to auto: will not pin threads to cpus. 92: This can lead to significant performance degradation. 92: Consider using -pin on (and -pinoffset in case you run multiple jobs). 92: starting mdrun 'Virtual sites test system in vacuo' 92: 8 steps, 0.0 ps. 92: Generated 3 of the 6 non-bonded parameter combinations 92: 92: Excluding 3 bonded neighbours molecule type 'VSTEST' 92: 92: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/vsite_test.gro', all velocities are zero 92: 92: Cleaning up constraints and constant bonded interactions with virtual sites 92: 92: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 92: 92: Calculated rlist for 1x1 atom pair-list as 0.715 nm, buffer size 0.015 nm 92: 92: Set rlist, assuming 4x4 atom pair-list, to 0.712 nm, buffer size 0.012 nm 92: 92: Note that mdrun will redetermine rlist based on the actual pair-list setup 92: 92: This run will generate roughly 0 Mb of data 92: 92: Writing final coordinates. 92: 92: NOTE: 40 % of the run time was spent communicating energies, 92: you might want to increase some nst* mdp options 92: 92: Core t (s) Wall t (s) (%) 92: Time: 0.037 0.019 195.2 92: (ns/day) (hour/ns) 92: Performance: 41.046 0.585 92: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_7.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 92: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_7.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 92: 92: Reading virtual site types... 92: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/7 (110 ms) 92: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/8 92: 92: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_8_input.mdp]: 92: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 92: that with the Verlet scheme, nstlist has no effect on the accuracy of 92: your simulation. 92: 92: 92: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_8_input.mdp]: 92: Setting nstcalcenergy (100) equal to nstenergy (4) 92: 92: 92: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_8_input.mdp]: 92: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 92: 1 92: 92: Number of degrees of freedom in T-Coupling group System is 45.00 92: 92: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_8_input.mdp]: 92: There are 6 non-linear virtual site constructions. Their contribution to 92: the energy error is approximated. In most cases this does not affect the 92: error significantly. 92: 92: 92: NOTE 5 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_8_input.mdp]: 92: You are using a plain Coulomb cut-off, which might produce artifacts. 92: You might want to consider using PME electrostatics. 92: 92: 92: 92: There were 5 NOTEs 92: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_8.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 92: Changing nstlist from 8 to 50, rlist from 0.712 to 0.801 92: 92: Update groups can not be used for this system because an incompatible virtual site type is used 92: 92: Using 2 MPI threads 92: Using 1 OpenMP thread per tMPI thread 92: 92: 92: NOTE: The number of threads is not equal to the number of (logical) cpus 92: and the -pin option is set to auto: will not pin threads to cpus. 92: This can lead to significant performance degradation. 92: Consider using -pin on (and -pinoffset in case you run multiple jobs). 92: starting mdrun 'Virtual sites test system in vacuo' 92: 8 steps, 0.0 ps. 92: Generated 3 of the 6 non-bonded parameter combinations 92: 92: Excluding 3 bonded neighbours molecule type 'VSTEST' 92: 92: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/vsite_test.gro', all velocities are zero 92: 92: Cleaning up constraints and constant bonded interactions with virtual sites 92: 92: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 92: 92: Calculated rlist for 1x1 atom pair-list as 0.715 nm, buffer size 0.015 nm 92: 92: Set rlist, assuming 4x4 atom pair-list, to 0.712 nm, buffer size 0.012 nm 92: 92: Note that mdrun will redetermine rlist based on the actual pair-list setup 92: 92: This run will generate roughly 0 Mb of data 92: 92: Writing final coordinates. 92: 92: NOTE: 42 % of the run time was spent communicating energies, 92: you might want to increase some nst* mdp options 92: 92: Core t (s) Wall t (s) (%) 92: Time: 0.036 0.018 195.6 92: (ns/day) (hour/ns) 92: Performance: 42.515 0.565 92: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_8.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 92: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_8.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 92: 92: Reading virtual site types... 92: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/8 (111 ms) 92: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/9 92: 92: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_9_input.mdp]: 92: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 92: that with the Verlet scheme, nstlist has no effect on the accuracy of 92: your simulation. 92: 92: 92: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_9_input.mdp]: 92: Setting nstcalcenergy (100) equal to nstenergy (4) 92: 92: Number of degrees of freedom in T-Coupling group System is 45.00 92: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 92: 92: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_9_input.mdp]: 92: NVE simulation with an initial temperature of zero: will use a Verlet 92: buffer of 10%. Check your energy drift! 92: 92: 92: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_9_input.mdp]: 92: You are using a plain Coulomb cut-off, which might produce artifacts. 92: You might want to consider using PME electrostatics. 92: 92: 92: 92: There were 4 NOTEs 92: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_9.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 92: Can not increase nstlist because an NVE ensemble is used 92: Update groups can not be used for this system because an incompatible virtual site type is used 92: 92: Using 2 MPI threads 92: Using 1 OpenMP thread per tMPI thread 92: 92: 92: NOTE: The number of threads is not equal to the number of (logical) cpus 92: and the -pin option is set to auto: will not pin threads to cpus. 92: This can lead to significant performance degradation. 92: Consider using -pin on (and -pinoffset in case you run multiple jobs). 92: starting mdrun 'Virtual sites test system in vacuo' 92: 8 steps, 0.0 ps. 92: Generated 3 of the 6 non-bonded parameter combinations 92: 92: Excluding 3 bonded neighbours molecule type 'VSTEST' 92: 92: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/vsite_test.gro', all velocities are zero 92: 92: Cleaning up constraints and constant bonded interactions with virtual sites 92: 92: This run will generate roughly 0 Mb of data 92: 92: Writing final coordinates. 92: 92: 92: Dynamic load balancing report: 92: DLB was off during the run due to low measured imbalance. 92: Average load imbalance: 5.4%. 92: The balanceable part of the MD step is 55%, load imbalance is computed from this. 92: Part of the total run time spent waiting due to load imbalance: 3.0%. 92: 92: 92: NOTE: 39 % of the run time was spent communicating energies, 92: you might want to increase some nst* mdp options 92: 92: Core t (s) Wall t (s) (%) 92: Time: 0.037 0.019 194.7 92: (ns/day) (hour/ns) 92: Performance: 40.491 0.593 92: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_9.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 92: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_9.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 92: 92: Reading virtual site types... 92: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/9 (67 ms) 92: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/10 92: 92: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_10_input.mdp]: 92: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 92: that with the Verlet scheme, nstlist has no effect on the accuracy of 92: your simulation. 92: 92: 92: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_10_input.mdp]: 92: Setting nstcalcenergy (100) equal to nstenergy (4) 92: 92: Number of degrees of freedom in T-Coupling group System is 45.00 92: 92: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_10_input.mdp]: 92: NVE simulation with an initial temperature of zero: will use a Verlet 92: buffer of 10%. Check your energy drift! 92: 92: 92: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_10_input.mdp]: 92: You are using a plain Coulomb cut-off, which might produce artifacts. 92: You might want to consider using PME electrostatics. 92: 92: 92: 92: There were 4 NOTEs 92: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_10.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 92: Can not increase nstlist because an NVE ensemble is used 92: Update groups can not be used for this system because an incompatible virtual site type is used 92: 92: Using 2 MPI threads 92: Using 1 OpenMP thread per tMPI thread 92: 92: 92: NOTE: The number of threads is not equal to the number of (logical) cpus 92: and the -pin option is set to auto: will not pin threads to cpus. 92: This can lead to significant performance degradation. 92: Consider using -pin on (and -pinoffset in case you run multiple jobs). 92: starting mdrun 'Virtual sites test system in vacuo' 92: 8 steps, 0.0 ps. 92: Generated 3 of the 6 non-bonded parameter combinations 92: 92: Excluding 3 bonded neighbours molecule type 'VSTEST' 92: 92: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/vsite_test.gro', all velocities are zero 92: 92: Cleaning up constraints and constant bonded interactions with virtual sites 92: 92: This run will generate roughly 0 Mb of data 92: 92: Writing final coordinates. 92: 92: 92: Dynamic load balancing report: 92: DLB was off during the run due to low measured imbalance. 92: Average load imbalance: 5.9%. 92: The balanceable part of the MD step is 48%, load imbalance is computed from this. 92: Part of the total run time spent waiting due to load imbalance: 2.8%. 92: 92: 92: NOTE: 40 % of the run time was spent communicating energies, 92: you might want to increase some nst* mdp options 92: 92: Core t (s) Wall t (s) (%) 92: Time: 0.037 0.019 196.1 92: (ns/day) (hour/ns) 92: Performance: 40.908 0.587 92: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_10.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 92: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_10.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 92: 92: Reading virtual site types... 92: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/10 (68 ms) 92: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/11 92: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/11 (0 ms) 92: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/12 92: 92: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_12_input.mdp]: 92: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 92: that with the Verlet scheme, nstlist has no effect on the accuracy of 92: your simulation. 92: 92: 92: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_12_input.mdp]: 92: Setting nstcalcenergy (100) equal to nstenergy (4) 92: 92: Number of degrees of freedom in T-Coupling group System is 45.00 92: 92: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_12_input.mdp]: 92: There are 6 non-linear virtual site constructions. Their contribution to 92: the energy error is approximated. In most cases this does not affect the 92: error significantly. 92: 92: 92: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_12_input.mdp]: 92: You are using a plain Coulomb cut-off, which might produce artifacts. 92: You might want to consider using PME electrostatics. 92: 92: 92: 92: There were 4 NOTEs 92: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_12.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 92: Changing nstlist from 8 to 50, rlist from 0.712 to 0.801 92: 92: Update groups can not be used for this system because an incompatible virtual site type is used 92: 92: Using 2 MPI threads 92: Using 1 OpenMP thread per tMPI thread 92: 92: 92: NOTE: The number of threads is not equal to the number of (logical) cpus 92: and the -pin option is set to auto: will not pin threads to cpus. 92: This can lead to significant performance degradation. 92: Consider using -pin on (and -pinoffset in case you run multiple jobs). 92: starting mdrun 'Virtual sites test system in vacuo' 92: 8 steps, 0.0 ps. 92: Generated 3 of the 6 non-bonded parameter combinations 92: 92: Excluding 3 bonded neighbours molecule type 'VSTEST' 92: 92: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/vsite_test.gro', all velocities are zero 92: 92: Cleaning up constraints and constant bonded interactions with virtual sites 92: 92: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 92: 92: Calculated rlist for 1x1 atom pair-list as 0.715 nm, buffer size 0.015 nm 92: 92: Set rlist, assuming 4x4 atom pair-list, to 0.712 nm, buffer size 0.012 nm 92: 92: Note that mdrun will redetermine rlist based on the actual pair-list setup 92: 92: This run will generate roughly 0 Mb of data 92: 92: Writing final coordinates. 92: 92: NOTE: 40 % of the run time was spent communicating energies, 92: you might want to increase some nst* mdp options 92: 92: Core t (s) Wall t (s) (%) 92: Time: 0.037 0.019 196.2 92: (ns/day) (hour/ns) 92: Performance: 40.737 0.589 92: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_12.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 92: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_12.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 92: 92: Reading virtual site types... 92: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/12 (112 ms) 92: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/13 92: 92: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_13_input.mdp]: 92: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 92: that with the Verlet scheme, nstlist has no effect on the accuracy of 92: your simulation. 92: 92: 92: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_13_input.mdp]: 92: Setting nstcalcenergy (100) equal to nstenergy (4) 92: 92: Number of degrees of freedom in T-Coupling group System is 45.00 92: 92: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_13_input.mdp]: 92: There are 6 non-linear virtual site constructions. Their contribution to 92: the energy error is approximated. In most cases this does not affect the 92: error significantly. 92: 92: 92: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_13_input.mdp]: 92: You are using a plain Coulomb cut-off, which might produce artifacts. 92: You might want to consider using PME electrostatics. 92: 92: 92: 92: There were 4 NOTEs 92: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_13.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 92: Changing nstlist from 8 to 50, rlist from 0.712 to 0.801 92: 92: Update groups can not be used for this system because an incompatible virtual site type is used 92: 92: Using 2 MPI threads 92: Using 1 OpenMP thread per tMPI thread 92: 92: 92: NOTE: The number of threads is not equal to the number of (logical) cpus 92: and the -pin option is set to auto: will not pin threads to cpus. 92: This can lead to significant performance degradation. 92: Consider using -pin on (and -pinoffset in case you run multiple jobs). 92: starting mdrun 'Virtual sites test system in vacuo' 92: 8 steps, 0.0 ps. 92: Generated 3 of the 6 non-bonded parameter combinations 92: 92: Excluding 3 bonded neighbours molecule type 'VSTEST' 92: 92: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/vsite_test.gro', all velocities are zero 92: 92: Cleaning up constraints and constant bonded interactions with virtual sites 92: 92: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 92: 92: Calculated rlist for 1x1 atom pair-list as 0.715 nm, buffer size 0.015 nm 92: 92: Set rlist, assuming 4x4 atom pair-list, to 0.712 nm, buffer size 0.012 nm 92: 92: Note that mdrun will redetermine rlist based on the actual pair-list setup 92: 92: This run will generate roughly 0 Mb of data 92: 92: Writing final coordinates. 92: 92: NOTE: 39 % of the run time was spent communicating energies, 92: you might want to increase some nst* mdp options 92: 92: Core t (s) Wall t (s) (%) 92: Time: 0.039 0.020 195.8 92: (ns/day) (hour/ns) 92: Performance: 39.122 0.613 92: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_13.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 92: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_13.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 92: 92: Reading virtual site types... 92: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/13 (112 ms) 92: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/14 92: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/14 (0 ms) 92: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/15 92: 92: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_15_input.mdp]: 92: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 92: that with the Verlet scheme, nstlist has no effect on the accuracy of 92: your simulation. 92: 92: 92: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_15_input.mdp]: 92: Setting nstcalcenergy (100) equal to nstenergy (4) 92: 92: Number of degrees of freedom in T-Coupling group System is 45.00 92: 92: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_15_input.mdp]: 92: There are 6 non-linear virtual site constructions. Their contribution to 92: the energy error is approximated. In most cases this does not affect the 92: error significantly. 92: 92: 92: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_15_input.mdp]: 92: You are using a plain Coulomb cut-off, which might produce artifacts. 92: You might want to consider using PME electrostatics. 92: 92: 92: 92: There were 4 NOTEs 92: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_15.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 92: Changing nstlist from 8 to 50, rlist from 0.712 to 0.801 92: 92: Update groups can not be used for this system because an incompatible virtual site type is used 92: 92: Using 2 MPI threads 92: Using 1 OpenMP thread per tMPI thread 92: 92: 92: NOTE: The number of threads is not equal to the number of (logical) cpus 92: and the -pin option is set to auto: will not pin threads to cpus. 92: This can lead to significant performance degradation. 92: Consider using -pin on (and -pinoffset in case you run multiple jobs). 92: starting mdrun 'Virtual sites test system in vacuo' 92: 8 steps, 0.0 ps. 92: Generated 3 of the 6 non-bonded parameter combinations 92: 92: Excluding 3 bonded neighbours molecule type 'VSTEST' 92: 92: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/vsite_test.gro', all velocities are zero 92: 92: Cleaning up constraints and constant bonded interactions with virtual sites 92: 92: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 92: 92: Calculated rlist for 1x1 atom pair-list as 0.715 nm, buffer size 0.015 nm 92: 92: Set rlist, assuming 4x4 atom pair-list, to 0.712 nm, buffer size 0.012 nm 92: 92: Note that mdrun will redetermine rlist based on the actual pair-list setup 92: 92: This run will generate roughly 0 Mb of data 92: 92: Writing final coordinates. 92: 92: NOTE: 41 % of the run time was spent communicating energies, 92: you might want to increase some nst* mdp options 92: 92: Core t (s) Wall t (s) (%) 92: Time: 0.041 0.021 196.7 92: (ns/day) (hour/ns) 92: Performance: 37.535 0.639 92: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_15.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 92: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_15.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 92: 92: Reading virtual site types... 92: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/15 (112 ms) 92: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/16 92: 92: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_16_input.mdp]: 92: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 92: that with the Verlet scheme, nstlist has no effect on the accuracy of 92: your simulation. 92: 92: 92: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_16_input.mdp]: 92: Setting nstcalcenergy (100) equal to nstenergy (4) 92: 92: Number of degrees of freedom in T-Coupling group System is 45.00 92: 92: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_16_input.mdp]: 92: There are 6 non-linear virtual site constructions. Their contribution to 92: the energy error is approximated. In most cases this does not affect the 92: error significantly. 92: 92: 92: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_16_input.mdp]: 92: You are using a plain Coulomb cut-off, which might produce artifacts. 92: You might want to consider using PME electrostatics. 92: 92: 92: 92: There were 4 NOTEs 92: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_16.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 92: Changing nstlist from 8 to 50, rlist from 0.712 to 0.801 92: 92: Update groups can not be used for this system because an incompatible virtual site type is used 92: 92: Using 2 MPI threads 92: Using 1 OpenMP thread per tMPI thread 92: 92: 92: NOTE: The number of threads is not equal to the number of (logical) cpus 92: and the -pin option is set to auto: will not pin threads to cpus. 92: This can lead to significant performance degradation. 92: Consider using -pin on (and -pinoffset in case you run multiple jobs). 92: starting mdrun 'Virtual sites test system in vacuo' 92: 8 steps, 0.0 ps. 92: Generated 3 of the 6 non-bonded parameter combinations 92: 92: Excluding 3 bonded neighbours molecule type 'VSTEST' 92: 92: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/vsite_test.gro', all velocities are zero 92: 92: Cleaning up constraints and constant bonded interactions with virtual sites 92: 92: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 92: 92: Calculated rlist for 1x1 atom pair-list as 0.715 nm, buffer size 0.015 nm 92: 92: Set rlist, assuming 4x4 atom pair-list, to 0.712 nm, buffer size 0.012 nm 92: 92: Note that mdrun will redetermine rlist based on the actual pair-list setup 92: 92: This run will generate roughly 0 Mb of data 92: 92: Writing final coordinates. 92: 92: NOTE: 41 % of the run time was spent communicating energies, 92: you might want to increase some nst* mdp options 92: 92: Core t (s) Wall t (s) (%) 92: Time: 0.040 0.021 195.8 92: (ns/day) (hour/ns) 92: Performance: 37.758 0.636 92: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_16.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 92: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_16.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 92: 92: Reading virtual site types... 92: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/16 (119 ms) 92: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/17 92: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/17 (0 ms) 92: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/18 92: 92: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_18_input.mdp]: 92: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 92: that with the Verlet scheme, nstlist has no effect on the accuracy of 92: your simulation. 92: 92: 92: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_18_input.mdp]: 92: Setting nstcalcenergy (100) equal to nstenergy (4) 92: 92: Number of degrees of freedom in T-Coupling group System is 45.00 92: 92: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_18_input.mdp]: 92: There are 6 non-linear virtual site constructions. Their contribution to 92: the energy error is approximated. In most cases this does not affect the 92: error significantly. 92: 92: 92: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_18_input.mdp]: 92: You are using a plain Coulomb cut-off, which might produce artifacts. 92: You might want to consider using PME electrostatics. 92: 92: 92: 92: There were 4 NOTEs 92: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_18.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 92: Changing nstlist from 8 to 50, rlist from 0.712 to 0.801 92: 92: Update groups can not be used for this system because an incompatible virtual site type is used 92: 92: Using 2 MPI threads 92: Using 1 OpenMP thread per tMPI thread 92: 92: 92: NOTE: The number of threads is not equal to the number of (logical) cpus 92: and the -pin option is set to auto: will not pin threads to cpus. 92: This can lead to significant performance degradation. 92: Consider using -pin on (and -pinoffset in case you run multiple jobs). 92: starting mdrun 'Virtual sites test system in vacuo' 92: 8 steps, 0.0 ps. 92: Generated 3 of the 6 non-bonded parameter combinations 92: 92: Excluding 3 bonded neighbours molecule type 'VSTEST' 92: 92: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/vsite_test.gro', all velocities are zero 92: 92: Cleaning up constraints and constant bonded interactions with virtual sites 92: 92: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 92: 92: Calculated rlist for 1x1 atom pair-list as 0.715 nm, buffer size 0.015 nm 92: 92: Set rlist, assuming 4x4 atom pair-list, to 0.712 nm, buffer size 0.012 nm 92: 92: Note that mdrun will redetermine rlist based on the actual pair-list setup 92: 92: This run will generate roughly 0 Mb of data 92: 92: Writing final coordinates. 92: 92: NOTE: 39 % of the run time was spent communicating energies, 92: you might want to increase some nst* mdp options 92: 92: Core t (s) Wall t (s) (%) 92: Time: 0.039 0.020 196.9 92: (ns/day) (hour/ns) 92: Performance: 39.661 0.605 92: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_18.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 92: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_18.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 92: 92: Reading virtual site types... 92: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/18 (113 ms) 92: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/19 92: 92: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_19_input.mdp]: 92: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 92: that with the Verlet scheme, nstlist has no effect on the accuracy of 92: your simulation. 92: 92: 92: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_19_input.mdp]: 92: Setting nstcalcenergy (100) equal to nstenergy (4) 92: 92: Number of degrees of freedom in T-Coupling group System is 45.00 92: 92: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_19_input.mdp]: 92: There are 6 non-linear virtual site constructions. Their contribution to 92: the energy error is approximated. In most cases this does not affect the 92: error significantly. 92: 92: 92: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_19_input.mdp]: 92: You are using a plain Coulomb cut-off, which might produce artifacts. 92: You might want to consider using PME electrostatics. 92: 92: 92: 92: There were 4 NOTEs 92: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_19.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 92: Changing nstlist from 8 to 50, rlist from 0.712 to 0.801 92: 92: Update groups can not be used for this system because an incompatible virtual site type is used 92: 92: Using 2 MPI threads 92: Using 1 OpenMP thread per tMPI thread 92: 92: 92: NOTE: The number of threads is not equal to the number of (logical) cpus 92: and the -pin option is set to auto: will not pin threads to cpus. 92: This can lead to significant performance degradation. 92: Consider using -pin on (and -pinoffset in case you run multiple jobs). 92: starting mdrun 'Virtual sites test system in vacuo' 92: 8 steps, 0.0 ps. 92: Generated 3 of the 6 non-bonded parameter combinations 92: 92: Excluding 3 bonded neighbours molecule type 'VSTEST' 92: 92: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/vsite_test.gro', all velocities are zero 92: 92: Cleaning up constraints and constant bonded interactions with virtual sites 92: 92: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 92: 92: Calculated rlist for 1x1 atom pair-list as 0.715 nm, buffer size 0.015 nm 92: 92: Set rlist, assuming 4x4 atom pair-list, to 0.712 nm, buffer size 0.012 nm 92: 92: Note that mdrun will redetermine rlist based on the actual pair-list setup 92: 92: This run will generate roughly 0 Mb of data 92: 92: Writing final coordinates. 92: 92: NOTE: 43 % of the run time was spent communicating energies, 92: you might want to increase some nst* mdp options 92: 92: Core t (s) Wall t (s) (%) 92: Time: 0.041 0.021 195.7 92: (ns/day) (hour/ns) 92: Performance: 37.148 0.646 92: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_19.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 92: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_19.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 92: 92: Reading virtual site types... 92: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/19 (118 ms) 92: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/20 92: 92: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_20_input.mdp]: 92: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 92: that with the Verlet scheme, nstlist has no effect on the accuracy of 92: your simulation. 92: 92: 92: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_20_input.mdp]: 92: Setting nstcalcenergy (100) equal to nstenergy (4) 92: 92: Number of degrees of freedom in T-Coupling group System is 45.00 92: 92: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_20_input.mdp]: 92: There are 6 non-linear virtual site constructions. Their contribution to 92: the energy error is approximated. In most cases this does not affect the 92: error significantly. 92: 92: 92: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_20_input.mdp]: 92: You are using a plain Coulomb cut-off, which might produce artifacts. 92: You might want to consider using PME electrostatics. 92: 92: 92: 92: There were 4 NOTEs 92: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_20.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 92: Changing nstlist from 8 to 50, rlist from 0.712 to 0.801 92: 92: Update groups can not be used for this system because an incompatible virtual site type is used 92: 92: Using 2 MPI threads 92: Using 1 OpenMP thread per tMPI thread 92: 92: 92: NOTE: The number of threads is not equal to the number of (logical) cpus 92: and the -pin option is set to auto: will not pin threads to cpus. 92: This can lead to significant performance degradation. 92: Consider using -pin on (and -pinoffset in case you run multiple jobs). 92: starting mdrun 'Virtual sites test system in vacuo' 92: 8 steps, 0.0 ps. 92: Generated 3 of the 6 non-bonded parameter combinations 92: 92: Excluding 3 bonded neighbours molecule type 'VSTEST' 92: 92: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/vsite_test.gro', all velocities are zero 92: 92: Cleaning up constraints and constant bonded interactions with virtual sites 92: 92: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 92: 92: Calculated rlist for 1x1 atom pair-list as 0.715 nm, buffer size 0.015 nm 92: 92: Set rlist, assuming 4x4 atom pair-list, to 0.712 nm, buffer size 0.012 nm 92: 92: Note that mdrun will redetermine rlist based on the actual pair-list setup 92: 92: This run will generate roughly 0 Mb of data 92: 92: Writing final coordinates. 92: 92: NOTE: 41 % of the run time was spent communicating energies, 92: you might want to increase some nst* mdp options 92: 92: Core t (s) Wall t (s) (%) 92: Time: 0.040 0.020 196.0 92: (ns/day) (hour/ns) 92: Performance: 38.320 0.626 92: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_20.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 92: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_20.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 92: 92: Reading virtual site types... 92: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/20 (115 ms) 92: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/21 92: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/21 (0 ms) 92: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/22 92: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/22 (0 ms) 92: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/23 92: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/23 (0 ms) 92: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/24 92: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/24 (0 ms) 92: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/25 92: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/25 (0 ms) 92: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/26 92: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/26 (0 ms) 92: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/27 92: 92: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_27_input.mdp]: 92: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 92: that with the Verlet scheme, nstlist has no effect on the accuracy of 92: your simulation. 92: 92: 92: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_27_input.mdp]: 92: Setting nstcalcenergy (100) equal to nstenergy (4) 92: 92: Number of degrees of freedom in T-Coupling group System is 45.00 92: 92: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_27_input.mdp]: 92: There are 6 non-linear virtual site constructions. Their contribution to 92: the energy error is approximated. In most cases this does not affect the 92: error significantly. 92: 92: 92: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_27_input.mdp]: 92: You are using a plain Coulomb cut-off, which might produce artifacts. 92: You might want to consider using PME electrostatics. 92: 92: 92: 92: There were 4 NOTEs 92: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_27.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 92: Changing nstlist from 8 to 100, rlist from 0.728 to 0.805 92: 92: Update groups can not be used for this system because an incompatible virtual site type is used 92: 92: Using 2 MPI threads 92: Using 1 OpenMP thread per tMPI thread 92: 92: 92: NOTE: The number of threads is not equal to the number of (logical) cpus 92: and the -pin option is set to auto: will not pin threads to cpus. 92: This can lead to significant performance degradation. 92: Consider using -pin on (and -pinoffset in case you run multiple jobs). 92: starting mdrun 'Virtual sites test system in vacuo' 92: 8 steps, 0.0 ps. 92: Generated 3 of the 6 non-bonded parameter combinations 92: 92: Excluding 3 bonded neighbours molecule type 'VSTEST' 92: 92: Cleaning up constraints and constant bonded interactions with virtual sites 92: 92: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 92: 92: Calculated rlist for 1x1 atom pair-list as 0.732 nm, buffer size 0.032 nm 92: 92: Set rlist, assuming 4x4 atom pair-list, to 0.728 nm, buffer size 0.028 nm 92: 92: Note that mdrun will redetermine rlist based on the actual pair-list setup 92: 92: This run will generate roughly 0 Mb of data 92: 92: Writing final coordinates. 92: 92: NOTE: 41 % of the run time was spent communicating energies, 92: you might want to increase some nst* mdp options 92: 92: Core t (s) Wall t (s) (%) 92: Time: 0.036 0.018 195.7 92: (ns/day) (hour/ns) 92: Performance: 42.296 0.567 92: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_27.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 92: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_27.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 92: 92: Reading virtual site types... 92: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/27 (148 ms) 92: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/28 92: 92: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_28_input.mdp]: 92: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 92: that with the Verlet scheme, nstlist has no effect on the accuracy of 92: your simulation. 92: 92: 92: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_28_input.mdp]: 92: Setting nstcalcenergy (100) equal to nstenergy (4) 92: 92: Number of degrees of freedom in T-Coupling group System is 45.00 92: 92: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_28_input.mdp]: 92: There are 6 non-linear virtual site constructions. Their contribution to 92: the energy error is approximated. In most cases this does not affect the 92: error significantly. 92: 92: 92: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_28_input.mdp]: 92: You are using a plain Coulomb cut-off, which might produce artifacts. 92: You might want to consider using PME electrostatics. 92: 92: 92: 92: There were 4 NOTEs 92: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_28.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 92: Changing nstlist from 8 to 100, rlist from 0.728 to 0.805 92: 92: Update groups can not be used for this system because an incompatible virtual site type is used 92: 92: Using 2 MPI threads 92: Using 1 OpenMP thread per tMPI thread 92: 92: 92: NOTE: The number of threads is not equal to the number of (logical) cpus 92: and the -pin option is set to auto: will not pin threads to cpus. 92: This can lead to significant performance degradation. 92: Consider using -pin on (and -pinoffset in case you run multiple jobs). 92: starting mdrun 'Virtual sites test system in vacuo' 92: 8 steps, 0.0 ps. 92: Generated 3 of the 6 non-bonded parameter combinations 92: 92: Excluding 3 bonded neighbours molecule type 'VSTEST' 92: 92: Cleaning up constraints and constant bonded interactions with virtual sites 92: 92: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 92: 92: Calculated rlist for 1x1 atom pair-list as 0.732 nm, buffer size 0.032 nm 92: 92: Set rlist, assuming 4x4 atom pair-list, to 0.728 nm, buffer size 0.028 nm 92: 92: Note that mdrun will redetermine rlist based on the actual pair-list setup 92: 92: This run will generate roughly 0 Mb of data 92: 92: Writing final coordinates. 92: 92: NOTE: 41 % of the run time was spent communicating energies, 92: you might want to increase some nst* mdp options 92: 92: Core t (s) Wall t (s) (%) 92: Time: 0.042 0.021 196.6 92: (ns/day) (hour/ns) 92: Performance: 36.500 0.658 92: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_28.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 92: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_28.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 92: 92: Reading virtual site types... 92: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/28 (150 ms) 92: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/29 92: 92: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_29_input.mdp]: 92: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 92: that with the Verlet scheme, nstlist has no effect on the accuracy of 92: your simulation. 92: 92: 92: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_29_input.mdp]: 92: Setting nstcalcenergy (100) equal to nstenergy (4) 92: 92: Number of degrees of freedom in T-Coupling group System is 45.00 92: 92: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_29_input.mdp]: 92: There are 6 non-linear virtual site constructions. Their contribution to 92: the energy error is approximated. In most cases this does not affect the 92: error significantly. 92: 92: 92: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_29_input.mdp]: 92: You are using a plain Coulomb cut-off, which might produce artifacts. 92: You might want to consider using PME electrostatics. 92: 92: 92: 92: There were 4 NOTEs 92: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_29.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 92: Changing nstlist from 8 to 100, rlist from 0.728 to 0.805 92: 92: Update groups can not be used for this system because an incompatible virtual site type is used 92: 92: Using 2 MPI threads 92: Using 1 OpenMP thread per tMPI thread 92: 92: 92: NOTE: The number of threads is not equal to the number of (logical) cpus 92: and the -pin option is set to auto: will not pin threads to cpus. 92: This can lead to significant performance degradation. 92: Consider using -pin on (and -pinoffset in case you run multiple jobs). 92: starting mdrun 'Virtual sites test system in vacuo' 92: 8 steps, 0.0 ps. 92: Generated 3 of the 6 non-bonded parameter combinations 92: 92: Excluding 3 bonded neighbours molecule type 'VSTEST' 92: 92: Cleaning up constraints and constant bonded interactions with virtual sites 92: 92: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 92: 92: Calculated rlist for 1x1 atom pair-list as 0.732 nm, buffer size 0.032 nm 92: 92: Set rlist, assuming 4x4 atom pair-list, to 0.728 nm, buffer size 0.028 nm 92: 92: Note that mdrun will redetermine rlist based on the actual pair-list setup 92: 92: This run will generate roughly 0 Mb of data 92: 92: Writing final coordinates. 92: 92: NOTE: 41 % of the run time was spent communicating energies, 92: you might want to increase some nst* mdp options 92: 92: Core t (s) Wall t (s) (%) 92: Time: 0.036 0.018 196.4 92: (ns/day) (hour/ns) 92: Performance: 42.587 0.564 92: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_29.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 92: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_29.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 92: 92: Reading virtual site types... 92: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/29 (144 ms) 92: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/30 92: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/30 (0 ms) 92: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/31 92: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/31 (0 ms) 92: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/32 92: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/32 (0 ms) 92: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/33 92: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/33 (0 ms) 92: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/34 92: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/34 (0 ms) 92: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/35 92: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/35 (0 ms) 92: [----------] 36 tests from VelocitiesConformToExpectations/VirtualSiteTest (2274 ms total) 92: 92: [----------] Global test environment tear-down 92: [==========] 37 tests from 2 test suites ran. (2325 ms total) 92: [ PASSED ] 37 tests. 92/92 Test #92: MdrunVirtualSiteTests ..................... Passed 2.40 sec 100% tests passed, 0 tests failed out of 92 Label Time Summary: GTest = 2337.67 sec*proc (90 tests) IntegrationTest = 943.31 sec*proc (29 tests) MpiTest = 1846.87 sec*proc (21 tests) QuickGpuTest = 373.99 sec*proc (23 tests) SlowGpuTest = 1757.62 sec*proc (14 tests) SlowTest = 1367.45 sec*proc (14 tests) UnitTest = 26.92 sec*proc (47 tests) Total Test time (real) = 1327.90 sec /usr/bin/make -j4 -C build/basic-dp tests make[1]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/basic-dp' /usr/bin/cmake -S/build/reproducible-path/gromacs-2025.1 -B/build/reproducible-path/gromacs-2025.1/build/basic-dp --check-build-system CMakeFiles/Makefile.cmake 0 /usr/bin/make -f CMakeFiles/Makefile2 tests make[2]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/basic-dp' /usr/bin/cmake -S/build/reproducible-path/gromacs-2025.1 -B/build/reproducible-path/gromacs-2025.1/build/basic-dp --check-build-system CMakeFiles/Makefile.cmake 0 /usr/bin/cmake -E 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src/gromacs/pulling/CMakeFiles/pulling.dir/build.make src/gromacs/pulling/CMakeFiles/pulling.dir/depend make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/basic-dp' /usr/bin/make -f src/gromacs/energyanalysis/CMakeFiles/energyanalysis.dir/build.make src/gromacs/energyanalysis/CMakeFiles/energyanalysis.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/basic-dp' cd /build/reproducible-path/gromacs-2025.1/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.1 /build/reproducible-path/gromacs-2025.1/src/gromacs/pulling /build/reproducible-path/gromacs-2025.1/build/basic-dp /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/pulling /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/pulling/CMakeFiles/pulling.dir/DependInfo.cmake "--color=" make[4]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/basic-dp' make[4]: Nothing to be done 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src/gromacs/taskassignment/CMakeFiles/taskassignment.dir/build.make src/gromacs/taskassignment/CMakeFiles/taskassignment.dir/depend /usr/bin/make -f src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/build.make src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/basic-dp' cd /build/reproducible-path/gromacs-2025.1/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.1 /build/reproducible-path/gromacs-2025.1/src/gromacs/taskassignment /build/reproducible-path/gromacs-2025.1/build/basic-dp /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/taskassignment /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/taskassignment/CMakeFiles/taskassignment.dir/DependInfo.cmake "--color=" make[4]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/basic-dp' cd 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cd /build/reproducible-path/gromacs-2025.1/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.1 /build/reproducible-path/gromacs-2025.1/api/gmxapi /build/reproducible-path/gromacs-2025.1/build/basic-dp /build/reproducible-path/gromacs-2025.1/build/basic-dp/api/gmxapi /build/reproducible-path/gromacs-2025.1/build/basic-dp/api/gmxapi/CMakeFiles/gmxapi.dir/DependInfo.cmake "--color=" make[4]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/basic-dp' cd /build/reproducible-path/gromacs-2025.1/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.1 /build/reproducible-path/gromacs-2025.1/api/nblib /build/reproducible-path/gromacs-2025.1/build/basic-dp /build/reproducible-path/gromacs-2025.1/build/basic-dp/api/nblib /build/reproducible-path/gromacs-2025.1/build/basic-dp/api/nblib/CMakeFiles/nblib.dir/DependInfo.cmake "--color=" make[4]: Leaving directory 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api/nblib/samples/CMakeFiles/argon-forces-integration.dir/depend /usr/bin/make -f api/nblib/samples/CMakeFiles/methane-water-integration.dir/build.make api/nblib/samples/CMakeFiles/methane-water-integration.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/basic-dp' cd /build/reproducible-path/gromacs-2025.1/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.1 /build/reproducible-path/gromacs-2025.1/api/nblib/samples /build/reproducible-path/gromacs-2025.1/build/basic-dp /build/reproducible-path/gromacs-2025.1/build/basic-dp/api/nblib/samples /build/reproducible-path/gromacs-2025.1/build/basic-dp/api/nblib/samples/CMakeFiles/argon-forces-integration.dir/DependInfo.cmake "--color=" make[4]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/basic-dp' cd /build/reproducible-path/gromacs-2025.1/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" 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../../../../lib/libgtest.so.1.13.0 "CMakeFiles/gtest.dir/src/gtest-all.cc.o" cd /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/external/googletest/googletest && /usr/bin/cmake -E cmake_symlink_library ../../../../lib/libgtest.so.1.13.0 ../../../../lib/libgtest.so.1.13.0 ../../../../lib/libgtest.so make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/basic-dp' [ 60%] Built target gtest /usr/bin/make -f src/external/googletest/googlemock/CMakeFiles/gmock.dir/build.make src/external/googletest/googlemock/CMakeFiles/gmock.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/basic-dp' cd /build/reproducible-path/gromacs-2025.1/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.1 /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock /build/reproducible-path/gromacs-2025.1/build/basic-dp /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/external/googletest/googlemock /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/external/googletest/googlemock/CMakeFiles/gmock.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/basic-dp' /usr/bin/make -f src/external/googletest/googlemock/CMakeFiles/gmock.dir/build.make src/external/googletest/googlemock/CMakeFiles/gmock.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/basic-dp' cd /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/external/googletest/googlemock && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_CAN_STREAM_RESULTS=0 -DGTEST_CREATE_SHARED_LIBRARY=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -D_GNU_SOURCE=1 -Dgmock_EXPORTS -I/build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock -I/build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -Wall -Wshadow -Wno-error=dangling-else -DGTEST_HAS_PTHREAD=1 -fexceptions -Wextra -Wno-unused-parameter -Wno-missing-field-initializers -Wno-deprecated-copy -MD -MT src/external/googletest/googlemock/CMakeFiles/gmock.dir/src/gmock-all.cc.o -MF CMakeFiles/gmock.dir/src/gmock-all.cc.o.d -o CMakeFiles/gmock.dir/src/gmock-all.cc.o -c /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock/src/gmock-all.cc cd /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/external/googletest/googlemock && /usr/bin/cmake -E cmake_link_script CMakeFiles/gmock.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,--dependency-file=CMakeFiles/gmock.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libgmock.so.1.13.0 -o ../../../../lib/libgmock.so.1.13.0 "CMakeFiles/gmock.dir/src/gmock-all.cc.o" ../../../../lib/libgtest.so.1.13.0 cd /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/external/googletest/googlemock && /usr/bin/cmake -E cmake_symlink_library ../../../../lib/libgmock.so.1.13.0 ../../../../lib/libgmock.so.1.13.0 ../../../../lib/libgmock.so make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/basic-dp' [ 61%] Built target gmock /usr/bin/make -f src/testutils/CMakeFiles/testutils.dir/build.make src/testutils/CMakeFiles/testutils.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/basic-dp' cd /build/reproducible-path/gromacs-2025.1/build/basic-dp && 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mdrun_test_infrastructure /usr/bin/make -f src/gromacs/utility/tests/CMakeFiles/utility-mpi-test.dir/build.make src/gromacs/utility/tests/CMakeFiles/utility-mpi-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/basic-dp' cd /build/reproducible-path/gromacs-2025.1/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.1 /build/reproducible-path/gromacs-2025.1/src/gromacs/utility/tests /build/reproducible-path/gromacs-2025.1/build/basic-dp /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/utility/tests /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/utility/tests/CMakeFiles/utility-mpi-test.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/basic-dp' /usr/bin/make -f src/gromacs/utility/tests/CMakeFiles/utility-mpi-test.dir/build.make src/gromacs/utility/tests/CMakeFiles/utility-mpi-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/basic-dp' cd /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/utility/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/utility/tests/Testing/Temporary\" -DTEST_USES_MPI=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/src/testutils/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -isystem 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src/gromacs/utility/tests/CMakeFiles/utility-mpi-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/utility-mpi-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/utility-mpi-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/testutils/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/testutils/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/testutils/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/src/testutils/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include 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-ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/testutils/tests/CMakeFiles/testutils-test.dir/__/unittest_main.cpp.o -MF CMakeFiles/testutils-test.dir/__/unittest_main.cpp.o.d -o CMakeFiles/testutils-test.dir/__/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/utility/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/utility/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/src/testutils/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/utility/tests/CMakeFiles/utility-test.dir/booltype.cpp.o -MF CMakeFiles/utility-test.dir/booltype.cpp.o.d -o CMakeFiles/utility-test.dir/booltype.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/utility/tests/booltype.cpp /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/utility-mpi-test.dir/link.d "CMakeFiles/utility-mpi-test.dir/physicalnodecommunicator_mpi.cpp.o" "CMakeFiles/utility-mpi-test.dir/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../bin/utility-mpi-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.10.0.0 ../../../../lib/libgmock.so.1.13.0 /usr/lib/riscv64-linux-gnu/libm.so /usr/lib/gcc/riscv64-linux-gnu/14/libgomp.so /lib/riscv64-linux-gnu/libpthread.a ../../../../lib/libgtest.so.1.13.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/basic-dp' [ 64%] Built target utility-mpi-test /usr/bin/make -f src/gromacs/gmxlib/nonbonded/tests/CMakeFiles/nonbonded-fep-test.dir/build.make src/gromacs/gmxlib/nonbonded/tests/CMakeFiles/nonbonded-fep-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/basic-dp' cd /build/reproducible-path/gromacs-2025.1/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.1 /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxlib/nonbonded/tests /build/reproducible-path/gromacs-2025.1/build/basic-dp /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/gmxlib/nonbonded/tests /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/gmxlib/nonbonded/tests/CMakeFiles/nonbonded-fep-test.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/basic-dp' /usr/bin/make -f src/gromacs/gmxlib/nonbonded/tests/CMakeFiles/nonbonded-fep-test.dir/build.make src/gromacs/gmxlib/nonbonded/tests/CMakeFiles/nonbonded-fep-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/basic-dp' cd /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/gmxlib/nonbonded/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gmxlib/nonbonded/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/gmxlib/nonbonded/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/src/testutils/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/timing/include -isystem 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../../../lib/libgromacs_d.so.10.0.0 /usr/lib/riscv64-linux-gnu/libm.so /usr/lib/gcc/riscv64-linux-gnu/14/libgomp.so /lib/riscv64-linux-gnu/libpthread.a ../../../lib/libgmock.so.1.13.0 ../../../lib/libgtest.so.1.13.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/basic-dp' [ 65%] Built target testutils-test /usr/bin/make -f src/gromacs/mdlib/tests/CMakeFiles/mdlib-test.dir/build.make src/gromacs/mdlib/tests/CMakeFiles/mdlib-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/basic-dp' cd /build/reproducible-path/gromacs-2025.1/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.1 /build/reproducible-path/gromacs-2025.1/src/gromacs/mdlib/tests /build/reproducible-path/gromacs-2025.1/build/basic-dp /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/mdlib/tests 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&& /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/utility/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/src/testutils/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/utility/tests/CMakeFiles/utility-test.dir/cstringutil.cpp.o -MF CMakeFiles/utility-test.dir/cstringutil.cpp.o.d -o CMakeFiles/utility-test.dir/cstringutil.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/utility/tests/cstringutil.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/utility/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/utility/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/src/testutils/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/utility/tests/CMakeFiles/utility-test.dir/defaultinitializationallocator.cpp.o -MF CMakeFiles/utility-test.dir/defaultinitializationallocator.cpp.o.d -o CMakeFiles/utility-test.dir/defaultinitializationallocator.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/utility/tests/defaultinitializationallocator.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/gmxlib/nonbonded/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/nonbonded-fep-test.dir/link.txt --verbose=1 /usr/bin/make -f src/gromacs/applied_forces/awh/tests/CMakeFiles/awh-test.dir/build.make src/gromacs/applied_forces/awh/tests/CMakeFiles/awh-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/basic-dp' cd /build/reproducible-path/gromacs-2025.1/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.1 /build/reproducible-path/gromacs-2025.1/src/gromacs/applied_forces/awh/tests /build/reproducible-path/gromacs-2025.1/build/basic-dp /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/applied_forces/awh/tests /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/applied_forces/awh/tests/CMakeFiles/awh-test.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/basic-dp' /usr/bin/make -f src/gromacs/applied_forces/awh/tests/CMakeFiles/awh-test.dir/build.make src/gromacs/applied_forces/awh/tests/CMakeFiles/awh-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/basic-dp' cd /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/applied_forces/awh/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/applied_forces/awh/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/applied_forces/awh/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/src/testutils/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/applied_forces/awh/tests/CMakeFiles/awh-test.dir/awh_setup.cpp.o -MF CMakeFiles/awh-test.dir/awh_setup.cpp.o.d -o CMakeFiles/awh-test.dir/awh_setup.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/applied_forces/awh/tests/awh_setup.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/utility/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/utility/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/src/testutils/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/utility/tests/CMakeFiles/utility-test.dir/enumerationhelpers.cpp.o -MF CMakeFiles/utility-test.dir/enumerationhelpers.cpp.o.d -o CMakeFiles/utility-test.dir/enumerationhelpers.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/utility/tests/enumerationhelpers.cpp /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/nonbonded-fep-test.dir/link.d "CMakeFiles/nonbonded-fep-test.dir/nb_free_energy.cpp.o" "CMakeFiles/nonbonded-fep-test.dir/__/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../../bin/nonbonded-fep-test ../../../../../lib/libtestutils.a ../../../../../lib/libtestutils.a ../../../../../lib/libgromacs_d.so.10.0.0 /usr/lib/riscv64-linux-gnu/libm.so ../../../../../lib/libgmock.so.1.13.0 ../../../../../lib/libgtest.so.1.13.0 /usr/lib/gcc/riscv64-linux-gnu/14/libgomp.so /lib/riscv64-linux-gnu/libpthread.a /usr/lib/riscv64-linux-gnu/libmuparser.so.2.3.4 make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/basic-dp' [ 65%] Built target nonbonded-fep-test cd /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/mdlib/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/mdlib/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/src/testutils/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/timing/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/external/muparser 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/usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/mdlib/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/src/testutils/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pulling/include 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/build/reproducible-path/gromacs-2025.1/src/gromacs/applied_forces/awh/tests/biasgrid.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/mdlib/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/mdlib/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/src/testutils/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include 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-D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/mdlib/tests/CMakeFiles/mdlib-test.dir/freeenergyparameters.cpp.o -MF CMakeFiles/mdlib-test.dir/freeenergyparameters.cpp.o.d -o CMakeFiles/mdlib-test.dir/freeenergyparameters.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/mdlib/tests/freeenergyparameters.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/applied_forces/awh/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/applied_forces/awh/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/applied_forces/awh/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/src/testutils/include -I/build/reproducible-path/gromacs-2025.1/src/include 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-ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/applied_forces/awh/tests/CMakeFiles/awh-test.dir/biassharing.cpp.o -MF CMakeFiles/awh-test.dir/biassharing.cpp.o.d -o CMakeFiles/awh-test.dir/biassharing.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/applied_forces/awh/tests/biassharing.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/mdlib/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/mdlib/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/src/testutils/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/timing/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/mdlib/tests/CMakeFiles/mdlib-test.dir/langevin.cpp.o -MF CMakeFiles/mdlib-test.dir/langevin.cpp.o.d -o CMakeFiles/mdlib-test.dir/langevin.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/mdlib/tests/langevin.cpp /usr/bin/make -f src/gromacs/applied_forces/densityfitting/tests/CMakeFiles/density_fitting_applied_forces-test.dir/build.make src/gromacs/applied_forces/densityfitting/tests/CMakeFiles/density_fitting_applied_forces-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/basic-dp' cd /build/reproducible-path/gromacs-2025.1/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.1 /build/reproducible-path/gromacs-2025.1/src/gromacs/applied_forces/densityfitting/tests /build/reproducible-path/gromacs-2025.1/build/basic-dp /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/applied_forces/densityfitting/tests /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/applied_forces/densityfitting/tests/CMakeFiles/density_fitting_applied_forces-test.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/basic-dp' /usr/bin/make -f src/gromacs/applied_forces/densityfitting/tests/CMakeFiles/density_fitting_applied_forces-test.dir/build.make src/gromacs/applied_forces/densityfitting/tests/CMakeFiles/density_fitting_applied_forces-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/basic-dp' cd /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/applied_forces/densityfitting/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/applied_forces/densityfitting/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/applied_forces/densityfitting/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/src/testutils/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/applied_forces/densityfitting/tests/CMakeFiles/density_fitting_applied_forces-test.dir/densityfitting.cpp.o -MF CMakeFiles/density_fitting_applied_forces-test.dir/densityfitting.cpp.o.d -o CMakeFiles/density_fitting_applied_forces-test.dir/densityfitting.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/applied_forces/densityfitting/tests/densityfitting.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/applied_forces/awh/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/applied_forces/awh/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/applied_forces/awh/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/src/testutils/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/include 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-Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/applied_forces/awh/tests/CMakeFiles/awh-test.dir/biasstate.cpp.o -MF CMakeFiles/awh-test.dir/biasstate.cpp.o.d -o CMakeFiles/awh-test.dir/biasstate.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/applied_forces/awh/tests/biasstate.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/utility/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/utility/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/src/testutils/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/include 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-Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/utility/tests/CMakeFiles/utility-test.dir/listoflists.cpp.o -MF CMakeFiles/utility-test.dir/listoflists.cpp.o.d -o CMakeFiles/utility-test.dir/listoflists.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/utility/tests/listoflists.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/mdlib/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/mdlib/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/src/testutils/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/timing/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock/include -isystem 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-Wl,--dependency-file=CMakeFiles/density_fitting_applied_forces-test.dir/link.d "CMakeFiles/density_fitting_applied_forces-test.dir/densityfitting.cpp.o" "CMakeFiles/density_fitting_applied_forces-test.dir/densityfittingamplitudelookup.cpp.o" "CMakeFiles/density_fitting_applied_forces-test.dir/densityfittingforceprovider.cpp.o" "CMakeFiles/density_fitting_applied_forces-test.dir/densityfittingoptions.cpp.o" "CMakeFiles/density_fitting_applied_forces-test.dir/__/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../../bin/density_fitting_applied_forces-test ../../../../../lib/libtestutils.a ../../../../../lib/libgromacs_d.so.10.0.0 ../../../../../lib/libgmock.so.1.13.0 /usr/lib/riscv64-linux-gnu/libm.so /usr/lib/gcc/riscv64-linux-gnu/14/libgomp.so /lib/riscv64-linux-gnu/libpthread.a ../../../../../lib/libgtest.so.1.13.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/basic-dp' [ 66%] Built target density_fitting_applied_forces-test /usr/bin/make -f src/gromacs/applied_forces/qmmm/tests/CMakeFiles/qmmm_applied_forces-test.dir/build.make src/gromacs/applied_forces/qmmm/tests/CMakeFiles/qmmm_applied_forces-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/basic-dp' cd /build/reproducible-path/gromacs-2025.1/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.1 /build/reproducible-path/gromacs-2025.1/src/gromacs/applied_forces/qmmm/tests /build/reproducible-path/gromacs-2025.1/build/basic-dp /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/applied_forces/qmmm/tests /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/applied_forces/qmmm/tests/CMakeFiles/qmmm_applied_forces-test.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/basic-dp' /usr/bin/make -f src/gromacs/applied_forces/qmmm/tests/CMakeFiles/qmmm_applied_forces-test.dir/build.make 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/build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/utility/tests/CMakeFiles/utility-test.dir/strconvert.cpp.o -MF CMakeFiles/utility-test.dir/strconvert.cpp.o.d -o CMakeFiles/utility-test.dir/strconvert.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/utility/tests/strconvert.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/applied_forces/qmmm/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/applied_forces/qmmm/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/src/testutils/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock -isystem 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67%] Built target awh-test /usr/bin/make -f src/gromacs/applied_forces/colvars/tests/CMakeFiles/colvars_applied_forces-test.dir/build.make src/gromacs/applied_forces/colvars/tests/CMakeFiles/colvars_applied_forces-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/basic-dp' cd /build/reproducible-path/gromacs-2025.1/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.1 /build/reproducible-path/gromacs-2025.1/src/gromacs/applied_forces/colvars/tests /build/reproducible-path/gromacs-2025.1/build/basic-dp /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/applied_forces/colvars/tests /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/applied_forces/colvars/tests/CMakeFiles/colvars_applied_forces-test.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/basic-dp' /usr/bin/make -f src/gromacs/applied_forces/colvars/tests/CMakeFiles/colvars_applied_forces-test.dir/build.make src/gromacs/applied_forces/colvars/tests/CMakeFiles/colvars_applied_forces-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/basic-dp' cd /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/applied_forces/colvars/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/applied_forces/colvars/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/applied_forces/colvars/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/src/testutils/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include 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/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/tests/textreader.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/applied_forces/colvars/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/applied_forces/colvars/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/applied_forces/colvars/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/src/testutils/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/timing/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/applied_forces/colvars/tests/CMakeFiles/colvars_applied_forces-test.dir/__/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/colvars_applied_forces-test.dir/__/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/colvars_applied_forces-test.dir/__/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/testutils/unittest_main.cpp /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/qmmm_applied_forces-test.dir/link.d "CMakeFiles/qmmm_applied_forces-test.dir/qmmminputgenerator.cpp.o" "CMakeFiles/qmmm_applied_forces-test.dir/qmmmtopologypreprocessor.cpp.o" "CMakeFiles/qmmm_applied_forces-test.dir/qmmmoptions.cpp.o" "CMakeFiles/qmmm_applied_forces-test.dir/qmmmforceprovider.cpp.o" "CMakeFiles/qmmm_applied_forces-test.dir/qmmm.cpp.o" "CMakeFiles/qmmm_applied_forces-test.dir/__/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../../bin/qmmm_applied_forces-test ../../../../../lib/libtestutils.a ../../../../../lib/libgromacs_d.so.10.0.0 ../../../../../lib/libgmock.so.1.13.0 /usr/lib/riscv64-linux-gnu/libm.so /usr/lib/gcc/riscv64-linux-gnu/14/libgomp.so /lib/riscv64-linux-gnu/libpthread.a ../../../../../lib/libgtest.so.1.13.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/basic-dp' [ 68%] Built target qmmm_applied_forces-test /usr/bin/make -f src/gromacs/applied_forces/plumed/tests/CMakeFiles/plumed_applied_forces-test.dir/build.make src/gromacs/applied_forces/plumed/tests/CMakeFiles/plumed_applied_forces-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/basic-dp' cd /build/reproducible-path/gromacs-2025.1/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.1 /build/reproducible-path/gromacs-2025.1/src/gromacs/applied_forces/plumed/tests /build/reproducible-path/gromacs-2025.1/build/basic-dp /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/applied_forces/plumed/tests /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/applied_forces/plumed/tests/CMakeFiles/plumed_applied_forces-test.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/basic-dp' /usr/bin/make -f src/gromacs/applied_forces/plumed/tests/CMakeFiles/plumed_applied_forces-test.dir/build.make src/gromacs/applied_forces/plumed/tests/CMakeFiles/plumed_applied_forces-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/basic-dp' cd /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/applied_forces/plumed/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/applied_forces/plumed/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/applied_forces/plumed/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/src/testutils/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/timing/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/applied_forces/plumed/tests/CMakeFiles/plumed_applied_forces-test.dir/plumedOptions.cpp.o -MF CMakeFiles/plumed_applied_forces-test.dir/plumedOptions.cpp.o.d -o CMakeFiles/plumed_applied_forces-test.dir/plumedOptions.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/applied_forces/plumed/tests/plumedOptions.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/mdlib/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/mdlib/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/src/testutils/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/timing/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/mdlib/tests/CMakeFiles/mdlib-test.dir/updategroups.cpp.o -MF CMakeFiles/mdlib-test.dir/updategroups.cpp.o.d -o CMakeFiles/mdlib-test.dir/updategroups.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/mdlib/tests/updategroups.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/applied_forces/colvars/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/colvars_applied_forces-test.dir/link.txt --verbose=1 cd /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/applied_forces/plumed/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/applied_forces/plumed/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/applied_forces/plumed/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/src/testutils/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/timing/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/applied_forces/plumed/tests/CMakeFiles/plumed_applied_forces-test.dir/__/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/plumed_applied_forces-test.dir/__/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/plumed_applied_forces-test.dir/__/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/applied_forces/plumed/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/plumed_applied_forces-test.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/colvars_applied_forces-test.dir/link.d "CMakeFiles/colvars_applied_forces-test.dir/colvars.cpp.o" "CMakeFiles/colvars_applied_forces-test.dir/colvarsoptions.cpp.o" "CMakeFiles/colvars_applied_forces-test.dir/colvarspreprocessor.cpp.o" "CMakeFiles/colvars_applied_forces-test.dir/colvarsforceprovider.cpp.o" "CMakeFiles/colvars_applied_forces-test.dir/__/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../../bin/colvars_applied_forces-test ../../../../../lib/libtestutils.a ../../../../../lib/libgromacs_d.so.10.0.0 ../../../../../lib/libgmock.so.1.13.0 /usr/lib/riscv64-linux-gnu/libm.so ../../../../../lib/libgtest.so.1.13.0 /usr/lib/gcc/riscv64-linux-gnu/14/libgomp.so /lib/riscv64-linux-gnu/libpthread.a /usr/lib/riscv64-linux-gnu/libmuparser.so.2.3.4 make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/basic-dp' [ 69%] Built target colvars_applied_forces-test /usr/bin/make -f src/gromacs/applied_forces/plumed/tests/CMakeFiles/plumed_md-test.dir/build.make src/gromacs/applied_forces/plumed/tests/CMakeFiles/plumed_md-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/basic-dp' cd /build/reproducible-path/gromacs-2025.1/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.1 /build/reproducible-path/gromacs-2025.1/src/gromacs/applied_forces/plumed/tests /build/reproducible-path/gromacs-2025.1/build/basic-dp /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/applied_forces/plumed/tests /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/applied_forces/plumed/tests/CMakeFiles/plumed_md-test.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/basic-dp' /usr/bin/make -f src/gromacs/applied_forces/plumed/tests/CMakeFiles/plumed_md-test.dir/build.make src/gromacs/applied_forces/plumed/tests/CMakeFiles/plumed_md-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/basic-dp' cd /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/applied_forces/plumed/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/applied_forces/plumed/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/applied_forces/plumed/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/src/testutils/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/applied_forces/plumed/tests/CMakeFiles/plumed_md-test.dir/plumed_md_test.cpp.o -MF CMakeFiles/plumed_md-test.dir/plumed_md_test.cpp.o.d -o CMakeFiles/plumed_md-test.dir/plumed_md_test.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/applied_forces/plumed/tests/plumed_md_test.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/mdlib/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/mdlib/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/src/testutils/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/timing/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops 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/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/mdlib/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/mdlib/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/src/testutils/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/timing/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops 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/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/applied_forces/nnpot/tests/CMakeFiles/nnpot_applied_forces-test.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/basic-dp' /usr/bin/make -f src/gromacs/applied_forces/nnpot/tests/CMakeFiles/nnpot_applied_forces-test.dir/build.make src/gromacs/applied_forces/nnpot/tests/CMakeFiles/nnpot_applied_forces-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/basic-dp' cd /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/applied_forces/nnpot/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/applied_forces/nnpot/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/applied_forces/nnpot/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/src/testutils/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock -isystem 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/usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/mdlib/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/src/testutils/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pulling/include 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-fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/applied_forces/nnpot/tests/CMakeFiles/nnpot_applied_forces-test.dir/nnpotoptions.cpp.o -MF CMakeFiles/nnpot_applied_forces-test.dir/nnpotoptions.cpp.o.d -o CMakeFiles/nnpot_applied_forces-test.dir/nnpotoptions.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/applied_forces/nnpot/tests/nnpotoptions.cpp /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/plumed_md-test.dir/link.d "CMakeFiles/plumed_md-test.dir/plumed_md_test.cpp.o" "CMakeFiles/plumed_md-test.dir/plumedTestUtils.cpp.o" "CMakeFiles/plumed_md-test.dir/__/__/__/__/testutils/unittest_main.cpp.o" ../../../../programs/CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o ../../../../programs/CMakeFiles/mdrun_objlib.dir/mdrun/nonbonded_bench.cpp.o -o ../../../../../bin/plumed_md-test ../../../../../lib/libtestutils.a ../../../../../lib/libmdrun_test_infrastructure.a -ldl ../../../../../lib/libtestutils.a ../../../../../lib/libgromacs_d.so.10.0.0 /usr/lib/riscv64-linux-gnu/libm.so /usr/lib/gcc/riscv64-linux-gnu/14/libgomp.so /lib/riscv64-linux-gnu/libpthread.a ../../../../../lib/libgmock.so.1.13.0 ../../../../../lib/libgtest.so.1.13.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/basic-dp' [ 70%] Built target plumed_md-test /usr/bin/make -f src/gromacs/applied_forces/tests/CMakeFiles/applied_forces-test.dir/build.make src/gromacs/applied_forces/tests/CMakeFiles/applied_forces-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/basic-dp' cd /build/reproducible-path/gromacs-2025.1/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.1 /build/reproducible-path/gromacs-2025.1/src/gromacs/applied_forces/tests /build/reproducible-path/gromacs-2025.1/build/basic-dp /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/applied_forces/tests /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/applied_forces/tests/CMakeFiles/applied_forces-test.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/basic-dp' /usr/bin/make -f src/gromacs/applied_forces/tests/CMakeFiles/applied_forces-test.dir/build.make src/gromacs/applied_forces/tests/CMakeFiles/applied_forces-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/basic-dp' cd /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/applied_forces/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H 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-fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/mdlib/tests/CMakeFiles/mdlib-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/mdlib-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/mdlib-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/mdlib/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/mdlib-test.dir/link.txt --verbose=1 cd /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/applied_forces/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/applied_forces/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/applied_forces/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/src/testutils/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/timing/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/applied_forces/tests/CMakeFiles/applied_forces-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/applied_forces-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/applied_forces-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/applied_forces/nnpot/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/applied_forces/nnpot/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/applied_forces/nnpot/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/src/testutils/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/applied_forces/nnpot/tests/CMakeFiles/nnpot_applied_forces-test.dir/nnpottopologypreprocessor.cpp.o -MF CMakeFiles/nnpot_applied_forces-test.dir/nnpottopologypreprocessor.cpp.o.d -o CMakeFiles/nnpot_applied_forces-test.dir/nnpottopologypreprocessor.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/applied_forces/nnpot/tests/nnpottopologypreprocessor.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/applied_forces/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/applied_forces-test.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/applied_forces-test.dir/link.d "CMakeFiles/applied_forces-test.dir/electricfield.cpp.o" "CMakeFiles/applied_forces-test.dir/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../bin/applied_forces-test ../../../../lib/libtestutils.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.10.0.0 /usr/lib/riscv64-linux-gnu/libm.so ../../../../lib/libgmock.so.1.13.0 ../../../../lib/libgtest.so.1.13.0 /usr/lib/gcc/riscv64-linux-gnu/14/libgomp.so /lib/riscv64-linux-gnu/libpthread.a /usr/lib/riscv64-linux-gnu/libmuparser.so.2.3.4 make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/basic-dp' [ 70%] Built target applied_forces-test /usr/bin/make -f src/gromacs/listed_forces/tests/CMakeFiles/listed_forces-test.dir/build.make src/gromacs/listed_forces/tests/CMakeFiles/listed_forces-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/basic-dp' cd /build/reproducible-path/gromacs-2025.1/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.1 /build/reproducible-path/gromacs-2025.1/src/gromacs/listed_forces/tests /build/reproducible-path/gromacs-2025.1/build/basic-dp /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/listed_forces/tests /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/listed_forces/tests/CMakeFiles/listed_forces-test.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/basic-dp' /usr/bin/make -f src/gromacs/listed_forces/tests/CMakeFiles/listed_forces-test.dir/build.make src/gromacs/listed_forces/tests/CMakeFiles/listed_forces-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/basic-dp' cd /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/listed_forces/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/listed_forces/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/listed_forces/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/src/testutils/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pbcutil/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/listed_forces/tests/CMakeFiles/listed_forces-test.dir/bonded.cpp.o -MF CMakeFiles/listed_forces-test.dir/bonded.cpp.o.d -o CMakeFiles/listed_forces-test.dir/bonded.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/listed_forces/tests/bonded.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/applied_forces/nnpot/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/applied_forces/nnpot/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/applied_forces/nnpot/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/src/testutils/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/applied_forces/nnpot/tests/CMakeFiles/nnpot_applied_forces-test.dir/nnpotforceprovider.cpp.o -MF CMakeFiles/nnpot_applied_forces-test.dir/nnpotforceprovider.cpp.o.d -o CMakeFiles/nnpot_applied_forces-test.dir/nnpotforceprovider.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/applied_forces/nnpot/tests/nnpotforceprovider.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/applied_forces/nnpot/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/applied_forces/nnpot/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/applied_forces/nnpot/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/src/testutils/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/applied_forces/nnpot/tests/CMakeFiles/nnpot_applied_forces-test.dir/__/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/nnpot_applied_forces-test.dir/__/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/nnpot_applied_forces-test.dir/__/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/testutils/unittest_main.cpp /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/mdlib-test.dir/link.d "CMakeFiles/mdlib-test.dir/calc_verletbuf.cpp.o" "CMakeFiles/mdlib-test.dir/calcvir.cpp.o" "CMakeFiles/mdlib-test.dir/constr.cpp.o" "CMakeFiles/mdlib-test.dir/constrtestdata.cpp.o" "CMakeFiles/mdlib-test.dir/constrtestrunners.cpp.o" "CMakeFiles/mdlib-test.dir/ebin.cpp.o" "CMakeFiles/mdlib-test.dir/energydrifttracker.cpp.o" "CMakeFiles/mdlib-test.dir/energyoutput.cpp.o" "CMakeFiles/mdlib-test.dir/expanded.cpp.o" "CMakeFiles/mdlib-test.dir/freeenergyparameters.cpp.o" "CMakeFiles/mdlib-test.dir/langevin.cpp.o" "CMakeFiles/mdlib-test.dir/langevintestdata.cpp.o" "CMakeFiles/mdlib-test.dir/langevintestrunners.cpp.o" "CMakeFiles/mdlib-test.dir/leapfrog.cpp.o" "CMakeFiles/mdlib-test.dir/leapfrogtestdata.cpp.o" "CMakeFiles/mdlib-test.dir/leapfrogtestrunners.cpp.o" "CMakeFiles/mdlib-test.dir/parrinellorahman.cpp.o" "CMakeFiles/mdlib-test.dir/settle.cpp.o" "CMakeFiles/mdlib-test.dir/settletestdata.cpp.o" "CMakeFiles/mdlib-test.dir/settletestrunners.cpp.o" "CMakeFiles/mdlib-test.dir/shake.cpp.o" "CMakeFiles/mdlib-test.dir/simulationsignal.cpp.o" "CMakeFiles/mdlib-test.dir/updategroups.cpp.o" "CMakeFiles/mdlib-test.dir/updategroupscog.cpp.o" "CMakeFiles/mdlib-test.dir/constrtestrunners_gpu.cpp.o" "CMakeFiles/mdlib-test.dir/leapfrogtestrunners_gpu.cpp.o" "CMakeFiles/mdlib-test.dir/mdgpugraph.cpp.o" "CMakeFiles/mdlib-test.dir/settletestrunners_gpu.cpp.o" "CMakeFiles/mdlib-test.dir/wholemoleculetransform.cpp.o" "CMakeFiles/mdlib-test.dir/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../bin/mdlib-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.10.0.0 ../../../../lib/libgmock.so.1.13.0 /usr/lib/riscv64-linux-gnu/libm.so ../../../../lib/libgtest.so.1.13.0 /usr/lib/gcc/riscv64-linux-gnu/14/libgomp.so /lib/riscv64-linux-gnu/libpthread.a /usr/lib/riscv64-linux-gnu/libmuparser.so.2.3.4 make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/basic-dp' [ 72%] Built target mdlib-test /usr/bin/make -f src/gromacs/nbnxm/tests/CMakeFiles/nbnxm-test.dir/build.make src/gromacs/nbnxm/tests/CMakeFiles/nbnxm-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/basic-dp' cd /build/reproducible-path/gromacs-2025.1/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.1 /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/tests /build/reproducible-path/gromacs-2025.1/build/basic-dp /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/nbnxm/tests /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/nbnxm/tests/CMakeFiles/nbnxm-test.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/basic-dp' /usr/bin/make -f src/gromacs/nbnxm/tests/CMakeFiles/nbnxm-test.dir/build.make src/gromacs/nbnxm/tests/CMakeFiles/nbnxm-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/basic-dp' cd /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/nbnxm/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/nbnxm/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/nbnxm/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/src/testutils/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/timing/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/nbnxm/tests/CMakeFiles/nbnxm-test.dir/exclusions.cpp.o -MF CMakeFiles/nbnxm-test.dir/exclusions.cpp.o.d -o CMakeFiles/nbnxm-test.dir/exclusions.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/tests/exclusions.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/applied_forces/nnpot/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/nnpot_applied_forces-test.dir/link.txt --verbose=1 cd /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/nbnxm/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/nbnxm/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/nbnxm/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/src/testutils/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/timing/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/nbnxm/tests/CMakeFiles/nbnxm-test.dir/kernel_test.cpp.o -MF CMakeFiles/nbnxm-test.dir/kernel_test.cpp.o.d -o CMakeFiles/nbnxm-test.dir/kernel_test.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/tests/kernel_test.cpp /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/nnpot_applied_forces-test.dir/link.d "CMakeFiles/nnpot_applied_forces-test.dir/nnpot.cpp.o" "CMakeFiles/nnpot_applied_forces-test.dir/nnpotoptions.cpp.o" "CMakeFiles/nnpot_applied_forces-test.dir/nnpottopologypreprocessor.cpp.o" "CMakeFiles/nnpot_applied_forces-test.dir/nnpotforceprovider.cpp.o" "CMakeFiles/nnpot_applied_forces-test.dir/__/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../../bin/nnpot_applied_forces-test ../../../../../lib/libtestutils.a ../../../../../lib/libtestutils.a ../../../../../lib/libgromacs_d.so.10.0.0 /usr/lib/riscv64-linux-gnu/libm.so /usr/lib/gcc/riscv64-linux-gnu/14/libgomp.so /lib/riscv64-linux-gnu/libpthread.a ../../../../../lib/libgmock.so.1.13.0 ../../../../../lib/libgtest.so.1.13.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/basic-dp' [ 73%] Built target nnpot_applied_forces-test /usr/bin/make -f src/gromacs/nbnxm/tests/CMakeFiles/nbnxm-gpu-test.dir/build.make src/gromacs/nbnxm/tests/CMakeFiles/nbnxm-gpu-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/basic-dp' cd /build/reproducible-path/gromacs-2025.1/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.1 /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/tests /build/reproducible-path/gromacs-2025.1/build/basic-dp /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/nbnxm/tests /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/nbnxm/tests/CMakeFiles/nbnxm-gpu-test.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/basic-dp' /usr/bin/make -f src/gromacs/nbnxm/tests/CMakeFiles/nbnxm-gpu-test.dir/build.make src/gromacs/nbnxm/tests/CMakeFiles/nbnxm-gpu-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/basic-dp' cd /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/nbnxm/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/nbnxm/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/nbnxm/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/src/testutils/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/timing/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/nbnxm/tests/CMakeFiles/nbnxm-gpu-test.dir/pairlist.cpp.o -MF CMakeFiles/nbnxm-gpu-test.dir/pairlist.cpp.o.d -o CMakeFiles/nbnxm-gpu-test.dir/pairlist.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/tests/pairlist.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/listed_forces/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/listed_forces/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/listed_forces/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/src/testutils/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pbcutil/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/listed_forces/tests/CMakeFiles/listed_forces-test.dir/pairs.cpp.o -MF CMakeFiles/listed_forces-test.dir/pairs.cpp.o.d -o CMakeFiles/listed_forces-test.dir/pairs.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/listed_forces/tests/pairs.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/nbnxm/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/nbnxm/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/nbnxm/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/src/testutils/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/timing/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/nbnxm/tests/CMakeFiles/nbnxm-gpu-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/nbnxm-gpu-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/nbnxm-gpu-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/nbnxm/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/nbnxm-gpu-test.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/nbnxm-gpu-test.dir/link.d "CMakeFiles/nbnxm-gpu-test.dir/pairlist.cpp.o" "CMakeFiles/nbnxm-gpu-test.dir/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../bin/nbnxm-gpu-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.10.0.0 ../../../../lib/libgmock.so.1.13.0 /usr/lib/riscv64-linux-gnu/libm.so /usr/lib/gcc/riscv64-linux-gnu/14/libgomp.so /lib/riscv64-linux-gnu/libpthread.a ../../../../lib/libgtest.so.1.13.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/basic-dp' [ 73%] Built target nbnxm-gpu-test cd /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/listed_forces/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/listed_forces/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/listed_forces/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/src/testutils/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pbcutil/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/listed_forces/tests/CMakeFiles/listed_forces-test.dir/position_restraints.cpp.o -MF CMakeFiles/listed_forces-test.dir/position_restraints.cpp.o.d -o CMakeFiles/listed_forces-test.dir/position_restraints.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/listed_forces/tests/position_restraints.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/nbnxm/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/nbnxm/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/nbnxm/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/src/testutils/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/timing/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/nbnxm/tests/CMakeFiles/nbnxm-test.dir/kernelsetup.cpp.o -MF CMakeFiles/nbnxm-test.dir/kernelsetup.cpp.o.d -o CMakeFiles/nbnxm-test.dir/kernelsetup.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/tests/kernelsetup.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/listed_forces/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/listed_forces/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/listed_forces/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/src/testutils/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pbcutil/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/listed_forces/tests/CMakeFiles/listed_forces-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/listed_forces-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/listed_forces-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/nbnxm/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/nbnxm/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/nbnxm/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/src/testutils/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/timing/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external 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/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/nbnxm/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/nbnxm/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/nbnxm/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/src/testutils/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/timing/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/nbnxm/tests/CMakeFiles/nbnxm-test.dir/testsystem.cpp.o -MF CMakeFiles/nbnxm-test.dir/testsystem.cpp.o.d -o CMakeFiles/nbnxm-test.dir/testsystem.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/tests/testsystem.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/listed_forces/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/listed_forces-test.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/utility-test.dir/link.d "CMakeFiles/utility-test.dir/alignedallocator.cpp.o" "CMakeFiles/utility-test.dir/arrayref.cpp.o" "CMakeFiles/utility-test.dir/booltype.cpp.o" "CMakeFiles/utility-test.dir/bitmask32.cpp.o" "CMakeFiles/utility-test.dir/bitmask64.cpp.o" "CMakeFiles/utility-test.dir/bitmask128.cpp.o" "CMakeFiles/utility-test.dir/cstringutil.cpp.o" "CMakeFiles/utility-test.dir/defaultinitializationallocator.cpp.o" "CMakeFiles/utility-test.dir/enumerationhelpers.cpp.o" "CMakeFiles/utility-test.dir/fixedcapacityvector.cpp.o" "CMakeFiles/utility-test.dir/inmemoryserializer.cpp.o" "CMakeFiles/utility-test.dir/keyvaluetreeserializer.cpp.o" "CMakeFiles/utility-test.dir/keyvaluetreetransform.cpp.o" "CMakeFiles/utility-test.dir/listoflists.cpp.o" "CMakeFiles/utility-test.dir/logger.cpp.o" "CMakeFiles/utility-test.dir/message_string_collector.cpp.o" "CMakeFiles/utility-test.dir/path.cpp.o" "CMakeFiles/utility-test.dir/physicalnodecommunicator.cpp.o" "CMakeFiles/utility-test.dir/range.cpp.o" "CMakeFiles/utility-test.dir/scope_guard.cpp.o" "CMakeFiles/utility-test.dir/strconvert.cpp.o" "CMakeFiles/utility-test.dir/stringtoenumvalueconverter.cpp.o" "CMakeFiles/utility-test.dir/stringutil.cpp.o" "CMakeFiles/utility-test.dir/template_mp.cpp.o" "CMakeFiles/utility-test.dir/textreader.cpp.o" "CMakeFiles/utility-test.dir/textwriter.cpp.o" "CMakeFiles/utility-test.dir/typetraits.cpp.o" "CMakeFiles/utility-test.dir/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../bin/utility-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.10.0.0 ../../../../lib/libgmock.so.1.13.0 /usr/lib/riscv64-linux-gnu/libm.so /usr/lib/gcc/riscv64-linux-gnu/14/libgomp.so /lib/riscv64-linux-gnu/libpthread.a ../../../../lib/libgtest.so.1.13.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/basic-dp' [ 74%] Built target utility-test /usr/bin/make -f src/gromacs/onlinehelp/tests/CMakeFiles/onlinehelp-test-shared.dir/build.make src/gromacs/onlinehelp/tests/CMakeFiles/onlinehelp-test-shared.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/basic-dp' cd /build/reproducible-path/gromacs-2025.1/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.1 /build/reproducible-path/gromacs-2025.1/src/gromacs/onlinehelp/tests /build/reproducible-path/gromacs-2025.1/build/basic-dp /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/onlinehelp/tests /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/onlinehelp/tests/CMakeFiles/onlinehelp-test-shared.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/basic-dp' /usr/bin/make -f src/gromacs/onlinehelp/tests/CMakeFiles/onlinehelp-test-shared.dir/build.make src/gromacs/onlinehelp/tests/CMakeFiles/onlinehelp-test-shared.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/basic-dp' cd /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/onlinehelp/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/src/testutils/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -MD -MT src/gromacs/onlinehelp/tests/CMakeFiles/onlinehelp-test-shared.dir/mock_helptopic.cpp.o -MF CMakeFiles/onlinehelp-test-shared.dir/mock_helptopic.cpp.o.d -o CMakeFiles/onlinehelp-test-shared.dir/mock_helptopic.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/onlinehelp/tests/mock_helptopic.cpp /usr/bin/make -f src/gromacs/domdec/tests/CMakeFiles/domdec-test.dir/build.make src/gromacs/domdec/tests/CMakeFiles/domdec-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/basic-dp' cd /build/reproducible-path/gromacs-2025.1/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.1 /build/reproducible-path/gromacs-2025.1/src/gromacs/domdec/tests /build/reproducible-path/gromacs-2025.1/build/basic-dp /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/domdec/tests /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/domdec/tests/CMakeFiles/domdec-test.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/basic-dp' /usr/bin/make -f src/gromacs/domdec/tests/CMakeFiles/domdec-test.dir/build.make src/gromacs/domdec/tests/CMakeFiles/domdec-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/basic-dp' cd /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/domdec/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/domdec/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/domdec/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/src/testutils/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/timing/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/domdec/tests/CMakeFiles/domdec-test.dir/hashedmap.cpp.o -MF CMakeFiles/domdec-test.dir/hashedmap.cpp.o.d -o CMakeFiles/domdec-test.dir/hashedmap.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/domdec/tests/hashedmap.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/nbnxm/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/nbnxm/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/nbnxm/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/src/testutils/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/timing/include -isystem 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CMakeFiles/nbnxm-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/nbnxm/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/nbnxm-test.dir/link.txt --verbose=1 cd /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/domdec/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/domdec/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/domdec/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/src/testutils/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include 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/build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/domdec/tests/CMakeFiles/domdec-test.dir/localatomsetmanager.cpp.o -MF CMakeFiles/domdec-test.dir/localatomsetmanager.cpp.o.d -o CMakeFiles/domdec-test.dir/localatomsetmanager.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/domdec/tests/localatomsetmanager.cpp /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/listed_forces-test.dir/link.d "CMakeFiles/listed_forces-test.dir/bonded.cpp.o" "CMakeFiles/listed_forces-test.dir/pairs.cpp.o" "CMakeFiles/listed_forces-test.dir/position_restraints.cpp.o" "CMakeFiles/listed_forces-test.dir/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../bin/listed_forces-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.10.0.0 ../../../../lib/libgmock.so.1.13.0 /usr/lib/riscv64-linux-gnu/libm.so /usr/lib/gcc/riscv64-linux-gnu/14/libgomp.so /lib/riscv64-linux-gnu/libpthread.a ../../../../lib/libgtest.so.1.13.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/basic-dp' [ 75%] Built target listed_forces-test /usr/bin/make -f src/gromacs/domdec/tests/CMakeFiles/domdec-mpi-test.dir/build.make src/gromacs/domdec/tests/CMakeFiles/domdec-mpi-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/basic-dp' cd /build/reproducible-path/gromacs-2025.1/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.1 /build/reproducible-path/gromacs-2025.1/src/gromacs/domdec/tests /build/reproducible-path/gromacs-2025.1/build/basic-dp /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/domdec/tests /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/domdec/tests/CMakeFiles/domdec-mpi-test.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/basic-dp' /usr/bin/make -f src/gromacs/domdec/tests/CMakeFiles/domdec-mpi-test.dir/build.make src/gromacs/domdec/tests/CMakeFiles/domdec-mpi-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/basic-dp' cd /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/domdec/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/domdec/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/domdec/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -DTEST_USES_MPI=true 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/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/onlinehelp/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/src/testutils/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock -isystem 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-Wl,--dependency-file=CMakeFiles/nbnxm-test.dir/link.d "CMakeFiles/nbnxm-test.dir/exclusions.cpp.o" "CMakeFiles/nbnxm-test.dir/kernel_test.cpp.o" "CMakeFiles/nbnxm-test.dir/kernelsetup.cpp.o" "CMakeFiles/nbnxm-test.dir/simd_energy_accumulator.cpp.o" "CMakeFiles/nbnxm-test.dir/testsystem.cpp.o" "CMakeFiles/nbnxm-test.dir/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../bin/nbnxm-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.10.0.0 ../../../../lib/libgmock.so.1.13.0 /usr/lib/riscv64-linux-gnu/libm.so /usr/lib/gcc/riscv64-linux-gnu/14/libgomp.so /lib/riscv64-linux-gnu/libpthread.a ../../../../lib/libgtest.so.1.13.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/basic-dp' [ 75%] Built target nbnxm-test /usr/bin/make -f src/gromacs/ewald/tests/CMakeFiles/ewald-test.dir/build.make src/gromacs/ewald/tests/CMakeFiles/ewald-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/basic-dp' cd /build/reproducible-path/gromacs-2025.1/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.1 /build/reproducible-path/gromacs-2025.1/src/gromacs/ewald/tests /build/reproducible-path/gromacs-2025.1/build/basic-dp /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/ewald/tests /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/ewald/tests/CMakeFiles/ewald-test.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/basic-dp' /usr/bin/make -f src/gromacs/ewald/tests/CMakeFiles/ewald-test.dir/build.make src/gromacs/ewald/tests/CMakeFiles/ewald-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/basic-dp' cd /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/ewald/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/ewald/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/ewald/tests/Testing/Temporary\" -DTEST_USES_DYNAMIC_REGISTRATION=true -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/src/testutils/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/timing/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/ewald/tests/CMakeFiles/ewald-test.dir/pmebsplinetest.cpp.o -MF 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/usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/fft/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/fft/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/src/testutils/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/timing/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem 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-Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/domdec/tests/CMakeFiles/domdec-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/domdec-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/domdec-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/domdec/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/domdec-test.dir/link.txt --verbose=1 cd /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/domdec/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/domdec/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/domdec/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -DTEST_USES_MPI=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/src/testutils/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/timing/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/domdec/tests/CMakeFiles/domdec-mpi-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/domdec-mpi-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/domdec-mpi-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/testutils/unittest_main.cpp /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/domdec-test.dir/link.d "CMakeFiles/domdec-test.dir/hashedmap.cpp.o" "CMakeFiles/domdec-test.dir/localatomsetmanager.cpp.o" "CMakeFiles/domdec-test.dir/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../bin/domdec-test ../../../../lib/libtestutils.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.10.0.0 /usr/lib/riscv64-linux-gnu/libm.so ../../../../lib/libgmock.so.1.13.0 ../../../../lib/libgtest.so.1.13.0 /usr/lib/gcc/riscv64-linux-gnu/14/libgomp.so /lib/riscv64-linux-gnu/libpthread.a /usr/lib/riscv64-linux-gnu/libmuparser.so.2.3.4 make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/basic-dp' [ 75%] Built target domdec-test /usr/bin/make -f src/gromacs/gpu_utils/tests/CMakeFiles/gpu_utils-test.dir/build.make src/gromacs/gpu_utils/tests/CMakeFiles/gpu_utils-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/basic-dp' cd /build/reproducible-path/gromacs-2025.1/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.1 /build/reproducible-path/gromacs-2025.1/src/gromacs/gpu_utils/tests /build/reproducible-path/gromacs-2025.1/build/basic-dp /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/gpu_utils/tests /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/gpu_utils/tests/CMakeFiles/gpu_utils-test.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/basic-dp' /usr/bin/make -f src/gromacs/gpu_utils/tests/CMakeFiles/gpu_utils-test.dir/build.make src/gromacs/gpu_utils/tests/CMakeFiles/gpu_utils-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/basic-dp' cd 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/build/reproducible-path/gromacs-2025.1/src/gromacs/gpu_utils/tests/clfftinitializer.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/domdec/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/domdec-mpi-test.dir/link.txt --verbose=1 cd /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/gpu_utils/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gpu_utils/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/gpu_utils/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/src/testutils/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include 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-DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/gpu_utils/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/src/testutils/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock/include 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-D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/domdec-mpi-test.dir/link.d "CMakeFiles/domdec-mpi-test.dir/haloexchange_mpi.cpp.o" "CMakeFiles/domdec-mpi-test.dir/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../bin/domdec-mpi-test ../../../../lib/libtestutils.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.10.0.0 /usr/lib/riscv64-linux-gnu/libm.so ../../../../lib/libgmock.so.1.13.0 ../../../../lib/libgtest.so.1.13.0 /usr/lib/gcc/riscv64-linux-gnu/14/libgomp.so /lib/riscv64-linux-gnu/libpthread.a /usr/lib/riscv64-linux-gnu/libmuparser.so.2.3.4 make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/basic-dp' [ 75%] Built target domdec-mpi-test cd /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/gpu_utils/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gpu_utils/tests\" 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-isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/gpu_utils/tests/CMakeFiles/gpu_utils-test.dir/devicetransfers.cpp.o -MF CMakeFiles/gpu_utils-test.dir/devicetransfers.cpp.o.d -o CMakeFiles/gpu_utils-test.dir/devicetransfers.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/gpu_utils/tests/devicetransfers.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/fft/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/fft/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/fft/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/src/testutils/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/timing/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/fft/tests/CMakeFiles/fft-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/fft-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/fft-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/gpu_utils/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gpu_utils/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/gpu_utils/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/src/testutils/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include 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src/gromacs/gpu_utils/tests/CMakeFiles/gpu_utils-test.dir/hostallocator.cpp.o -MF CMakeFiles/gpu_utils-test.dir/hostallocator.cpp.o.d -o CMakeFiles/gpu_utils-test.dir/hostallocator.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/gpu_utils/tests/hostallocator.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/fft/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/fft-test.dir/link.txt --verbose=1 cd /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/ewald/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/ewald/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/ewald/tests/Testing/Temporary\" -DTEST_USES_DYNAMIC_REGISTRATION=true -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/src/testutils/include -I/build/reproducible-path/gromacs-2025.1/src/include 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/build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/ewald/tests/CMakeFiles/ewald-test.dir/pmesolvetest.cpp.o -MF CMakeFiles/ewald-test.dir/pmesolvetest.cpp.o.d -o CMakeFiles/ewald-test.dir/pmesolvetest.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/ewald/tests/pmesolvetest.cpp /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/fft-test.dir/link.d "CMakeFiles/fft-test.dir/fft.cpp.o" "CMakeFiles/fft-test.dir/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../bin/fft-test ../../../../lib/libtestutils.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.10.0.0 /usr/lib/riscv64-linux-gnu/libm.so /usr/lib/gcc/riscv64-linux-gnu/14/libgomp.so /lib/riscv64-linux-gnu/libpthread.a ../../../../lib/libgmock.so.1.13.0 ../../../../lib/libgtest.so.1.13.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/basic-dp' [ 76%] Built target fft-test /usr/bin/make -f src/gromacs/hardware/tests/CMakeFiles/hardware-test.dir/build.make src/gromacs/hardware/tests/CMakeFiles/hardware-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/basic-dp' cd /build/reproducible-path/gromacs-2025.1/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.1 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/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/ewald/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/ewald/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/ewald/tests/Testing/Temporary\" -DTEST_USES_DYNAMIC_REGISTRATION=true -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/src/testutils/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include 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-I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -Wformat 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-I/build/reproducible-path/gromacs-2025.1/src/testutils/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest/include -isystem 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-DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/src/testutils/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/gpu_utils/tests/CMakeFiles/gpu_utils-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/gpu_utils-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/gpu_utils-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/hardware/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/hardware-test.dir/link.txt --verbose=1 /usr/bin/make -f src/gromacs/math/tests/CMakeFiles/math-test.dir/build.make src/gromacs/math/tests/CMakeFiles/math-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/basic-dp' cd /build/reproducible-path/gromacs-2025.1/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.1 /build/reproducible-path/gromacs-2025.1/src/gromacs/math/tests /build/reproducible-path/gromacs-2025.1/build/basic-dp /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/math/tests /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/math/tests/CMakeFiles/math-test.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/basic-dp' /usr/bin/make -f src/gromacs/math/tests/CMakeFiles/math-test.dir/build.make src/gromacs/math/tests/CMakeFiles/math-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/basic-dp' cd 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/build/reproducible-path/gromacs-2025.1/src/gromacs/math/tests/arrayrefwithpadding.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/ewald/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/ewald/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/ewald/tests/Testing/Temporary\" -DTEST_USES_DYNAMIC_REGISTRATION=true -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/src/testutils/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/api/legacy/include 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-fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/ewald/tests/CMakeFiles/ewald-test.dir/pme.cpp.o -MF CMakeFiles/ewald-test.dir/pme.cpp.o.d -o CMakeFiles/ewald-test.dir/pme.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/ewald/tests/pme.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/gpu_utils/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/gpu_utils-test.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/hardware-test.dir/link.d "CMakeFiles/hardware-test.dir/cpuinfo.cpp.o" "CMakeFiles/hardware-test.dir/hardwaretopology.cpp.o" "CMakeFiles/hardware-test.dir/mockhardwaretopology.cpp.o" "CMakeFiles/hardware-test.dir/device_management.cpp.o" "CMakeFiles/hardware-test.dir/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../bin/hardware-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.10.0.0 ../../../../lib/libgmock.so.1.13.0 /usr/lib/riscv64-linux-gnu/libm.so /usr/lib/gcc/riscv64-linux-gnu/14/libgomp.so /lib/riscv64-linux-gnu/libpthread.a ../../../../lib/libgtest.so.1.13.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/basic-dp' [ 76%] Built target hardware-test /usr/bin/make -f src/gromacs/mdrunutility/tests/CMakeFiles/mdrunutility-test-shared.dir/build.make src/gromacs/mdrunutility/tests/CMakeFiles/mdrunutility-test-shared.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/basic-dp' cd /build/reproducible-path/gromacs-2025.1/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" 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-isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/ewald/tests/CMakeFiles/ewald-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/ewald-test.dir/__/__/__/testutils/unittest_main.cpp.o.d 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/build/reproducible-path/gromacs-2025.1/src/gromacs/mdspan/tests/accessor_policy.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/ewald/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/ewald-test.dir/link.txt --verbose=1 cd /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/math/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/math/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/math/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/src/testutils/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include 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src/gromacs/math/tests/CMakeFiles/math-test.dir/coordinatetransformation.cpp.o -MF CMakeFiles/math-test.dir/coordinatetransformation.cpp.o.d -o CMakeFiles/math-test.dir/coordinatetransformation.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/math/tests/coordinatetransformation.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/mdspan/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdspan/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/mdspan/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/src/testutils/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include 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-Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/mdspan/tests/CMakeFiles/mdspan-test.dir/extensions.cpp.o -MF CMakeFiles/mdspan-test.dir/extensions.cpp.o.d -o CMakeFiles/mdspan-test.dir/extensions.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/mdspan/tests/extensions.cpp /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/gpu_utils-test.dir/link.d "CMakeFiles/gpu_utils-test.dir/clfftinitializer.cpp.o" "CMakeFiles/gpu_utils-test.dir/device_availability.cpp.o" "CMakeFiles/gpu_utils-test.dir/device_stream_manager.cpp.o" "CMakeFiles/gpu_utils-test.dir/pinnedmemorychecker.cpp.o" "CMakeFiles/gpu_utils-test.dir/devicetransfers.cpp.o" "CMakeFiles/gpu_utils-test.dir/device_buffer.cpp.o" "CMakeFiles/gpu_utils-test.dir/gpueventsynchronizer.cpp.o" "CMakeFiles/gpu_utils-test.dir/hostallocator.cpp.o" "CMakeFiles/gpu_utils-test.dir/typecasts.cpp.o" "CMakeFiles/gpu_utils-test.dir/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../bin/gpu_utils-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.10.0.0 ../../../../lib/libgmock.so.1.13.0 /usr/lib/riscv64-linux-gnu/libm.so /usr/lib/gcc/riscv64-linux-gnu/14/libgomp.so /lib/riscv64-linux-gnu/libpthread.a ../../../../lib/libgtest.so.1.13.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/basic-dp' [ 76%] Built target gpu_utils-test /usr/bin/make -f src/gromacs/mdtypes/tests/CMakeFiles/mdtypes-test.dir/build.make src/gromacs/mdtypes/tests/CMakeFiles/mdtypes-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/basic-dp' cd /build/reproducible-path/gromacs-2025.1/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.1 /build/reproducible-path/gromacs-2025.1/src/gromacs/mdtypes/tests /build/reproducible-path/gromacs-2025.1/build/basic-dp /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/mdtypes/tests /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/mdtypes/tests/CMakeFiles/mdtypes-test.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/basic-dp' /usr/bin/make -f src/gromacs/mdtypes/tests/CMakeFiles/mdtypes-test.dir/build.make src/gromacs/mdtypes/tests/CMakeFiles/mdtypes-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/basic-dp' cd /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/mdtypes/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdtypes/tests\" 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-Wl,--dependency-file=CMakeFiles/ewald-test.dir/link.d "CMakeFiles/ewald-test.dir/pmebsplinetest.cpp.o" "CMakeFiles/ewald-test.dir/pmegathertest.cpp.o" "CMakeFiles/ewald-test.dir/pmesolvetest.cpp.o" "CMakeFiles/ewald-test.dir/pmesplinespreadtest.cpp.o" "CMakeFiles/ewald-test.dir/pme.cpp.o" "CMakeFiles/ewald-test.dir/pmetestcommon.cpp.o" "CMakeFiles/ewald-test.dir/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../bin/ewald-test ../../../../lib/libtestutils.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.10.0.0 /usr/lib/riscv64-linux-gnu/libm.so ../../../../lib/libgmock.so.1.13.0 ../../../../lib/libgtest.so.1.13.0 /usr/lib/gcc/riscv64-linux-gnu/14/libgomp.so /lib/riscv64-linux-gnu/libpthread.a /usr/lib/riscv64-linux-gnu/libmuparser.so.2.3.4 make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/basic-dp' [ 76%] Built target ewald-test /usr/bin/make -f src/gromacs/onlinehelp/tests/CMakeFiles/onlinehelp-test.dir/build.make 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'/build/reproducible-path/gromacs-2025.1/build/basic-dp' cd /build/reproducible-path/gromacs-2025.1/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.1 /build/reproducible-path/gromacs-2025.1/src/gromacs/options/tests /build/reproducible-path/gromacs-2025.1/build/basic-dp /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/options/tests /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/options/tests/CMakeFiles/options-test.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/basic-dp' /usr/bin/make -f src/gromacs/options/tests/CMakeFiles/options-test.dir/build.make src/gromacs/options/tests/CMakeFiles/options-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/basic-dp' cd /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/options/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 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../../../../lib/libgtest.so.1.13.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/basic-dp' [ 77%] Built target mdspan-test /usr/bin/make -f src/gromacs/pbcutil/tests/CMakeFiles/pbcutil-test.dir/build.make src/gromacs/pbcutil/tests/CMakeFiles/pbcutil-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/basic-dp' cd /build/reproducible-path/gromacs-2025.1/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.1 /build/reproducible-path/gromacs-2025.1/src/gromacs/pbcutil/tests /build/reproducible-path/gromacs-2025.1/build/basic-dp /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/pbcutil/tests /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/pbcutil/tests/CMakeFiles/pbcutil-test.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/basic-dp' /usr/bin/make -f 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/build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/mdtypes/tests/CMakeFiles/mdtypes-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/mdtypes-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/mdtypes-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/options/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/options/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/options/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/src/testutils/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/options/tests/CMakeFiles/options-test.dir/option.cpp.o -MF CMakeFiles/options-test.dir/option.cpp.o.d -o CMakeFiles/options-test.dir/option.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/options/tests/option.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/mdtypes/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/mdtypes-test.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 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src/gromacs/random/tests/CMakeFiles/random-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/basic-dp' cd /build/reproducible-path/gromacs-2025.1/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.1 /build/reproducible-path/gromacs-2025.1/src/gromacs/random/tests /build/reproducible-path/gromacs-2025.1/build/basic-dp /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/random/tests /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/random/tests/CMakeFiles/random-test.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/basic-dp' /usr/bin/make -f src/gromacs/random/tests/CMakeFiles/random-test.dir/build.make src/gromacs/random/tests/CMakeFiles/random-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/basic-dp' cd 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/build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/options/tests/CMakeFiles/options-test.dir/optionsassigner.cpp.o -MF CMakeFiles/options-test.dir/optionsassigner.cpp.o.d -o 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-I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/random/tests/CMakeFiles/random-test.dir/gammadistribution.cpp.o -MF 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/usr/lib/gcc/riscv64-linux-gnu/14/libgomp.so /lib/riscv64-linux-gnu/libpthread.a ../../../../lib/libgtest.so.1.13.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/basic-dp' [ 78%] Built target mdtypes-test /usr/bin/make -f src/gromacs/restraint/tests/CMakeFiles/restraintpotential-test.dir/build.make src/gromacs/restraint/tests/CMakeFiles/restraintpotential-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/basic-dp' cd /build/reproducible-path/gromacs-2025.1/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.1 /build/reproducible-path/gromacs-2025.1/src/gromacs/restraint/tests /build/reproducible-path/gromacs-2025.1/build/basic-dp /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/restraint/tests /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/restraint/tests/CMakeFiles/restraintpotential-test.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/basic-dp' /usr/bin/make -f src/gromacs/restraint/tests/CMakeFiles/restraintpotential-test.dir/build.make src/gromacs/restraint/tests/CMakeFiles/restraintpotential-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/basic-dp' cd /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/restraint/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/restraint/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/restraint/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/src/testutils/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 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-Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/restraint/tests/CMakeFiles/restraintpotential-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/restraintpotential-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/restraintpotential-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/restraint/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/restraintpotential-test.dir/link.txt --verbose=1 cd /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/math/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/math/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/math/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/src/testutils/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/math/tests/CMakeFiles/math-test.dir/neldermead.cpp.o -MF CMakeFiles/math-test.dir/neldermead.cpp.o.d -o CMakeFiles/math-test.dir/neldermead.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/math/tests/neldermead.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/random/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/random/tests\" 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/build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/random/tests/CMakeFiles/random-test.dir/seed.cpp.o -MF CMakeFiles/random-test.dir/seed.cpp.o.d -o CMakeFiles/random-test.dir/seed.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/random/tests/seed.cpp /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/restraintpotential-test.dir/link.d "CMakeFiles/restraintpotential-test.dir/manager.cpp.o" "CMakeFiles/restraintpotential-test.dir/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../bin/restraintpotential-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.10.0.0 ../../../../lib/libgmock.so.1.13.0 /usr/lib/riscv64-linux-gnu/libm.so /usr/lib/gcc/riscv64-linux-gnu/14/libgomp.so /lib/riscv64-linux-gnu/libpthread.a ../../../../lib/libgtest.so.1.13.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/basic-dp' [ 80%] Built target restraintpotential-test /usr/bin/make -f src/gromacs/tables/tests/CMakeFiles/table-test.dir/build.make src/gromacs/tables/tests/CMakeFiles/table-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/basic-dp' cd /build/reproducible-path/gromacs-2025.1/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.1 /build/reproducible-path/gromacs-2025.1/src/gromacs/tables/tests /build/reproducible-path/gromacs-2025.1/build/basic-dp /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/tables/tests /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/tables/tests/CMakeFiles/table-test.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/basic-dp' /usr/bin/make -f src/gromacs/tables/tests/CMakeFiles/table-test.dir/build.make src/gromacs/tables/tests/CMakeFiles/table-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/basic-dp' cd /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/tables/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/tables/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/tables/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/src/testutils/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/simd/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/external/muparser -isystem 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/build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/options/tests/CMakeFiles/options-test.dir/treesupport.cpp.o -MF CMakeFiles/options-test.dir/treesupport.cpp.o.d -o CMakeFiles/options-test.dir/treesupport.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/options/tests/treesupport.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/random/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/random/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/random/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/src/testutils/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/random/tests/CMakeFiles/random-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/random-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/random-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/testutils/unittest_main.cpp /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/table-test.dir/link.d "CMakeFiles/table-test.dir/splinetable.cpp.o" 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/build/reproducible-path/gromacs-2025.1/build/basic-dp /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/taskassignment/tests /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/taskassignment/tests/CMakeFiles/taskassignment-test.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/basic-dp' /usr/bin/make -f src/gromacs/taskassignment/tests/CMakeFiles/taskassignment-test.dir/build.make src/gromacs/taskassignment/tests/CMakeFiles/taskassignment-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/basic-dp' cd /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/taskassignment/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/taskassignment/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/taskassignment/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/src/testutils/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/external/muparser -isystem 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/usr/bin/cmake -E cmake_link_script CMakeFiles/random-test.dir/link.txt --verbose=1 cd /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/options/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/options/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/options/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/src/testutils/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/options/tests/CMakeFiles/options-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/options-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/options-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/testutils/unittest_main.cpp /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/random-test.dir/link.d "CMakeFiles/random-test.dir/exponentialdistribution.cpp.o" "CMakeFiles/random-test.dir/gammadistribution.cpp.o" "CMakeFiles/random-test.dir/normaldistribution.cpp.o" "CMakeFiles/random-test.dir/seed.cpp.o" "CMakeFiles/random-test.dir/tabulatednormaldistribution.cpp.o" "CMakeFiles/random-test.dir/threefry.cpp.o" "CMakeFiles/random-test.dir/uniformintdistribution.cpp.o" "CMakeFiles/random-test.dir/uniformrealdistribution.cpp.o" "CMakeFiles/random-test.dir/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../bin/random-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.10.0.0 ../../../../lib/libgmock.so.1.13.0 /usr/lib/riscv64-linux-gnu/libm.so /usr/lib/gcc/riscv64-linux-gnu/14/libgomp.so /lib/riscv64-linux-gnu/libpthread.a ../../../../lib/libgtest.so.1.13.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/basic-dp' [ 80%] Built target random-test /usr/bin/make -f src/gromacs/timing/tests/CMakeFiles/timing-test.dir/build.make src/gromacs/timing/tests/CMakeFiles/timing-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/basic-dp' cd /build/reproducible-path/gromacs-2025.1/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.1 /build/reproducible-path/gromacs-2025.1/src/gromacs/timing/tests /build/reproducible-path/gromacs-2025.1/build/basic-dp /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/timing/tests /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/timing/tests/CMakeFiles/timing-test.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/basic-dp' /usr/bin/make -f src/gromacs/timing/tests/CMakeFiles/timing-test.dir/build.make src/gromacs/timing/tests/CMakeFiles/timing-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/basic-dp' cd /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/timing/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/timing/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/timing/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/src/testutils/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/timing/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/timing/tests/CMakeFiles/timing-test.dir/timing.cpp.o -MF CMakeFiles/timing-test.dir/timing.cpp.o.d -o CMakeFiles/timing-test.dir/timing.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/timing/tests/timing.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/options/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/options-test.dir/link.txt --verbose=1 cd /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/taskassignment/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/taskassignment/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/taskassignment/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/src/testutils/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/taskassignment/tests/CMakeFiles/taskassignment-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/taskassignment-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/taskassignment-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/timing/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/timing/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/timing/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/src/testutils/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/timing/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/timing/tests/CMakeFiles/timing-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/timing-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/timing-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/taskassignment/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/taskassignment-test.dir/link.txt --verbose=1 cd /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/timing/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/timing-test.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/taskassignment-test.dir/link.d "CMakeFiles/taskassignment-test.dir/usergpuids.cpp.o" "CMakeFiles/taskassignment-test.dir/__/__/__/testutils/unittest_main.cpp.o" ../CMakeFiles/taskassignment.dir/decidegpuusage.cpp.o ../CMakeFiles/taskassignment.dir/decidesimulationworkload.cpp.o ../CMakeFiles/taskassignment.dir/findallgputasks.cpp.o ../CMakeFiles/taskassignment.dir/reportgpuusage.cpp.o ../CMakeFiles/taskassignment.dir/resourcedivision.cpp.o ../CMakeFiles/taskassignment.dir/taskassignment.cpp.o ../CMakeFiles/taskassignment.dir/usergpuids.cpp.o -o ../../../../bin/taskassignment-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.10.0.0 ../../../../lib/libgmock.so.1.13.0 /usr/lib/riscv64-linux-gnu/libm.so ../../../../lib/libgtest.so.1.13.0 /usr/lib/gcc/riscv64-linux-gnu/14/libgomp.so /lib/riscv64-linux-gnu/libpthread.a /usr/lib/riscv64-linux-gnu/libmuparser.so.2.3.4 make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/basic-dp' [ 80%] Built target taskassignment-test /usr/bin/make -f src/gromacs/topology/tests/CMakeFiles/topology-test.dir/build.make src/gromacs/topology/tests/CMakeFiles/topology-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/basic-dp' cd /build/reproducible-path/gromacs-2025.1/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.1 /build/reproducible-path/gromacs-2025.1/src/gromacs/topology/tests /build/reproducible-path/gromacs-2025.1/build/basic-dp /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/topology/tests /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/topology/tests/CMakeFiles/topology-test.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/basic-dp' /usr/bin/make -f src/gromacs/topology/tests/CMakeFiles/topology-test.dir/build.make src/gromacs/topology/tests/CMakeFiles/topology-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/basic-dp' cd /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/topology/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 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/build/reproducible-path/gromacs-2025.1/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.1 /build/reproducible-path/gromacs-2025.1/src/gromacs/pulling/tests /build/reproducible-path/gromacs-2025.1/build/basic-dp /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/pulling/tests /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/pulling/tests/CMakeFiles/pull-test.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/basic-dp' /usr/bin/make -f src/gromacs/pulling/tests/CMakeFiles/pull-test.dir/build.make src/gromacs/pulling/tests/CMakeFiles/pull-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/basic-dp' cd /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/pulling/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H 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-DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/math/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/math/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/src/testutils/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/external/muparser -isystem 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/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/pulling/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/pull-test.dir/link.txt --verbose=1 cd /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/topology/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/topology/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/topology/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/src/testutils/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/api/legacy/include 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src/gromacs/topology/tests/CMakeFiles/topology-test.dir/exclusionblocks.cpp.o -MF CMakeFiles/topology-test.dir/exclusionblocks.cpp.o.d -o CMakeFiles/topology-test.dir/exclusionblocks.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/topology/tests/exclusionblocks.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/math/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/math/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/math/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/src/testutils/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include 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-Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/math/tests/CMakeFiles/math-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/math-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/math-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/math/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/math-test.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/pull-test.dir/link.d "CMakeFiles/pull-test.dir/pull.cpp.o" "CMakeFiles/pull-test.dir/__/__/__/testutils/unittest_main.cpp.o" ../CMakeFiles/pulling.dir/output.cpp.o ../CMakeFiles/pulling.dir/pull.cpp.o ../CMakeFiles/pulling.dir/pull_rotation.cpp.o ../CMakeFiles/pulling.dir/pullcoordexpressionparser.cpp.o ../CMakeFiles/pulling.dir/pullutil.cpp.o ../CMakeFiles/pulling.dir/transformationcoordinate.cpp.o -o ../../../../bin/pull-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.10.0.0 ../../../../lib/libgmock.so.1.13.0 /usr/lib/riscv64-linux-gnu/libm.so ../../../../lib/libgtest.so.1.13.0 /usr/lib/gcc/riscv64-linux-gnu/14/libgomp.so /lib/riscv64-linux-gnu/libpthread.a /usr/lib/riscv64-linux-gnu/libmuparser.so.2.3.4 make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/basic-dp' [ 81%] Built target pull-test /usr/bin/make -f src/gromacs/simd/tests/CMakeFiles/simd-test.dir/build.make src/gromacs/simd/tests/CMakeFiles/simd-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/basic-dp' cd /build/reproducible-path/gromacs-2025.1/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.1 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-I/build/reproducible-path/gromacs-2025.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/simd/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/simd/tests/CMakeFiles/simd-test.dir/scalar_util.cpp.o -MF CMakeFiles/simd-test.dir/scalar_util.cpp.o.d -o CMakeFiles/simd-test.dir/scalar_util.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/simd/tests/scalar_util.cpp /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/options-test.dir/link.d "CMakeFiles/options-test.dir/abstractoptionstorage.cpp.o" "CMakeFiles/options-test.dir/filenameoption.cpp.o" "CMakeFiles/options-test.dir/filenameoptionmanager.cpp.o" "CMakeFiles/options-test.dir/option.cpp.o" "CMakeFiles/options-test.dir/optionsassigner.cpp.o" "CMakeFiles/options-test.dir/repeatingsection.cpp.o" "CMakeFiles/options-test.dir/timeunitmanager.cpp.o" "CMakeFiles/options-test.dir/treesupport.cpp.o" "CMakeFiles/options-test.dir/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../bin/options-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.10.0.0 ../../../../lib/libgmock.so.1.13.0 /usr/lib/riscv64-linux-gnu/libm.so /usr/lib/gcc/riscv64-linux-gnu/14/libgomp.so /lib/riscv64-linux-gnu/libpthread.a ../../../../lib/libgtest.so.1.13.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/basic-dp' [ 81%] Built target options-test /usr/bin/make -f src/gromacs/compat/tests/CMakeFiles/compat-test.dir/build.make src/gromacs/compat/tests/CMakeFiles/compat-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/basic-dp' cd /build/reproducible-path/gromacs-2025.1/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.1 /build/reproducible-path/gromacs-2025.1/src/gromacs/compat/tests /build/reproducible-path/gromacs-2025.1/build/basic-dp 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/build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/gmxana/tests/CMakeFiles/gmxana-test.dir/gmx_traj.cpp.o -MF CMakeFiles/gmxana-test.dir/gmx_traj.cpp.o.d -o CMakeFiles/gmxana-test.dir/gmx_traj.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxana/tests/gmx_traj.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/simd/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/simd/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/simd/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/src/testutils/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/simd/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/simd/tests/CMakeFiles/simd-test.dir/simd_vector_operations.cpp.o -MF CMakeFiles/simd-test.dir/simd_vector_operations.cpp.o.d -o CMakeFiles/simd-test.dir/simd_vector_operations.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/simd/tests/simd_vector_operations.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/simd/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/simd/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/simd/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/src/testutils/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include 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-Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/simd/tests/CMakeFiles/simd-test.dir/simd4.cpp.o -MF CMakeFiles/simd-test.dir/simd4.cpp.o.d -o CMakeFiles/simd-test.dir/simd4.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/simd/tests/simd4.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/gmxana/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gmxana/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/gmxana/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/src/testutils/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include 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-I/build/reproducible-path/gromacs-2025.1/src/testutils/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/simd/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock -isystem 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/usr/lib/gcc/riscv64-linux-gnu/14/libgomp.so /lib/riscv64-linux-gnu/libpthread.a ../../../../lib/libgtest.so.1.13.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/basic-dp' [ 82%] Built target math-test /usr/bin/make -f src/gromacs/gmxpreprocess/tests/CMakeFiles/gmxpreprocess-test.dir/build.make src/gromacs/gmxpreprocess/tests/CMakeFiles/gmxpreprocess-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/basic-dp' cd /build/reproducible-path/gromacs-2025.1/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.1 /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests /build/reproducible-path/gromacs-2025.1/build/basic-dp /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/gmxpreprocess/tests /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/gmxpreprocess/tests/CMakeFiles/gmxpreprocess-test.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/basic-dp' /usr/bin/make -f src/gromacs/gmxpreprocess/tests/CMakeFiles/gmxpreprocess-test.dir/build.make src/gromacs/gmxpreprocess/tests/CMakeFiles/gmxpreprocess-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/basic-dp' cd /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/gmxpreprocess/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gmxpreprocess/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/src/testutils/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/gmxpreprocess/tests/CMakeFiles/gmxpreprocess-test.dir/convparm.cpp.o -MF CMakeFiles/gmxpreprocess-test.dir/convparm.cpp.o.d -o CMakeFiles/gmxpreprocess-test.dir/convparm.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/convparm.cpp /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/topology-test.dir/link.d "CMakeFiles/topology-test.dir/atoms.cpp.o" "CMakeFiles/topology-test.dir/exclusionblocks.cpp.o" "CMakeFiles/topology-test.dir/idef.cpp.o" "CMakeFiles/topology-test.dir/index.cpp.o" "CMakeFiles/topology-test.dir/mtop.cpp.o" "CMakeFiles/topology-test.dir/symtab.cpp.o" "CMakeFiles/topology-test.dir/topsort.cpp.o" "CMakeFiles/topology-test.dir/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../bin/topology-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.10.0.0 ../../../../lib/libgmock.so.1.13.0 /usr/lib/riscv64-linux-gnu/libm.so /usr/lib/gcc/riscv64-linux-gnu/14/libgomp.so /lib/riscv64-linux-gnu/libpthread.a ../../../../lib/libgtest.so.1.13.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/basic-dp' [ 83%] Built target topology-test /usr/bin/make -f src/gromacs/gmxpreprocess/tests/CMakeFiles/pdb2gmx1-test.dir/build.make src/gromacs/gmxpreprocess/tests/CMakeFiles/pdb2gmx1-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/basic-dp' cd /build/reproducible-path/gromacs-2025.1/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.1 /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests /build/reproducible-path/gromacs-2025.1/build/basic-dp /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/gmxpreprocess/tests /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/gmxpreprocess/tests/CMakeFiles/pdb2gmx1-test.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/basic-dp' /usr/bin/make -f src/gromacs/gmxpreprocess/tests/CMakeFiles/pdb2gmx1-test.dir/build.make src/gromacs/gmxpreprocess/tests/CMakeFiles/pdb2gmx1-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/basic-dp' cd /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/gmxpreprocess/tests && /usr/bin/c++ -DAMBER=0 -DCHARMM=0 -DGMX_DOUBLE=1 -DGROMOS=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DOPLSAA=1 -DTEST_DATA_PATH=\"src/gromacs/gmxpreprocess/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/src/testutils/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/gmxpreprocess/tests/CMakeFiles/pdb2gmx1-test.dir/pdb2gmx.cpp.o -MF CMakeFiles/pdb2gmx1-test.dir/pdb2gmx.cpp.o.d -o CMakeFiles/pdb2gmx1-test.dir/pdb2gmx.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/pdb2gmx.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/simd/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/simd/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/simd/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/src/testutils/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/simd/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/simd/tests/CMakeFiles/simd-test.dir/simd4_vector_operations.cpp.o -MF CMakeFiles/simd-test.dir/simd4_vector_operations.cpp.o.d -o CMakeFiles/simd-test.dir/simd4_vector_operations.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/simd/tests/simd4_vector_operations.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/simd/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/simd/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/simd/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/src/testutils/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/simd/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/simd/tests/CMakeFiles/simd-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/simd-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/simd-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/testutils/unittest_main.cpp /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/gmxana-test.dir/link.d "CMakeFiles/gmxana-test.dir/entropy.cpp.o" "CMakeFiles/gmxana-test.dir/gmx_chi.cpp.o" "CMakeFiles/gmxana-test.dir/gmx_mindist.cpp.o" "CMakeFiles/gmxana-test.dir/gmx_traj.cpp.o" "CMakeFiles/gmxana-test.dir/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../bin/gmxana-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.10.0.0 ../../../../lib/libgmock.so.1.13.0 /usr/lib/riscv64-linux-gnu/libm.so /usr/lib/gcc/riscv64-linux-gnu/14/libgomp.so /lib/riscv64-linux-gnu/libpthread.a ../../../../lib/libgtest.so.1.13.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/basic-dp' [ 83%] Built target gmxana-test /usr/bin/make -f src/gromacs/gmxpreprocess/tests/CMakeFiles/pdb2gmx2-test.dir/build.make src/gromacs/gmxpreprocess/tests/CMakeFiles/pdb2gmx2-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/basic-dp' cd /build/reproducible-path/gromacs-2025.1/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.1 /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests /build/reproducible-path/gromacs-2025.1/build/basic-dp /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/gmxpreprocess/tests /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/gmxpreprocess/tests/CMakeFiles/pdb2gmx2-test.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/basic-dp' /usr/bin/make -f src/gromacs/gmxpreprocess/tests/CMakeFiles/pdb2gmx2-test.dir/build.make src/gromacs/gmxpreprocess/tests/CMakeFiles/pdb2gmx2-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/basic-dp' cd /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/gmxpreprocess/tests && /usr/bin/c++ -DAMBER=0 -DCHARMM=0 -DGMX_DOUBLE=1 -DGROMOS=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DOPLSAA=0 -DTEST_DATA_PATH=\"src/gromacs/gmxpreprocess/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/src/testutils/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/gmxpreprocess/tests/CMakeFiles/pdb2gmx2-test.dir/pdb2gmx.cpp.o -MF CMakeFiles/pdb2gmx2-test.dir/pdb2gmx.cpp.o.d -o CMakeFiles/pdb2gmx2-test.dir/pdb2gmx.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/pdb2gmx.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/simd/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/simd-test.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/simd-test.dir/link.d "CMakeFiles/simd-test.dir/base.cpp.o" "CMakeFiles/simd-test.dir/bootstrap_loadstore.cpp.o" "CMakeFiles/simd-test.dir/scalar.cpp.o" "CMakeFiles/simd-test.dir/scalar_util.cpp.o" "CMakeFiles/simd-test.dir/scalar_math.cpp.o" "CMakeFiles/simd-test.dir/simd.cpp.o" "CMakeFiles/simd-test.dir/simd_floatingpoint.cpp.o" "CMakeFiles/simd-test.dir/simd_floatingpoint_util.cpp.o" "CMakeFiles/simd-test.dir/simd_integer.cpp.o" "CMakeFiles/simd-test.dir/simd_math.cpp.o" "CMakeFiles/simd-test.dir/simd_memory.cpp.o" "CMakeFiles/simd-test.dir/simd_vector_operations.cpp.o" "CMakeFiles/simd-test.dir/simd4.cpp.o" "CMakeFiles/simd-test.dir/simd4_floatingpoint.cpp.o" "CMakeFiles/simd-test.dir/simd4_math.cpp.o" "CMakeFiles/simd-test.dir/simd4_vector_operations.cpp.o" "CMakeFiles/simd-test.dir/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../bin/simd-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.10.0.0 ../../../../lib/libgmock.so.1.13.0 /usr/lib/riscv64-linux-gnu/libm.so /usr/lib/gcc/riscv64-linux-gnu/14/libgomp.so /lib/riscv64-linux-gnu/libpthread.a ../../../../lib/libgtest.so.1.13.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/basic-dp' [ 84%] Built target simd-test cd /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/gmxpreprocess/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gmxpreprocess/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/src/testutils/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/gmxpreprocess/tests/CMakeFiles/gmxpreprocess-test.dir/editconf.cpp.o -MF CMakeFiles/gmxpreprocess-test.dir/editconf.cpp.o.d -o CMakeFiles/gmxpreprocess-test.dir/editconf.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/editconf.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/gmxpreprocess/tests && /usr/bin/c++ -DAMBER=0 -DCHARMM=0 -DGMX_DOUBLE=1 -DGROMOS=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DOPLSAA=1 -DTEST_DATA_PATH=\"src/gromacs/gmxpreprocess/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/src/testutils/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/gmxpreprocess/tests/CMakeFiles/pdb2gmx1-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/pdb2gmx1-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/pdb2gmx1-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/gmxpreprocess/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gmxpreprocess/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/src/testutils/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/gmxpreprocess/tests/CMakeFiles/gmxpreprocess-test.dir/genconf.cpp.o -MF CMakeFiles/gmxpreprocess-test.dir/genconf.cpp.o.d -o CMakeFiles/gmxpreprocess-test.dir/genconf.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/genconf.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/gmxpreprocess/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/pdb2gmx1-test.dir/link.txt --verbose=1 cd /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/gmxpreprocess/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gmxpreprocess/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/src/testutils/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/gmxpreprocess/tests/CMakeFiles/gmxpreprocess-test.dir/genion.cpp.o -MF CMakeFiles/gmxpreprocess-test.dir/genion.cpp.o.d -o CMakeFiles/gmxpreprocess-test.dir/genion.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/genion.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/gmxpreprocess/tests && /usr/bin/c++ -DAMBER=0 -DCHARMM=0 -DGMX_DOUBLE=1 -DGROMOS=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DOPLSAA=0 -DTEST_DATA_PATH=\"src/gromacs/gmxpreprocess/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/src/testutils/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/gmxpreprocess/tests/CMakeFiles/pdb2gmx2-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/pdb2gmx2-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/pdb2gmx2-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/gmxpreprocess/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gmxpreprocess/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/src/testutils/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/gmxpreprocess/tests/CMakeFiles/gmxpreprocess-test.dir/genrestr.cpp.o -MF CMakeFiles/gmxpreprocess-test.dir/genrestr.cpp.o.d -o CMakeFiles/gmxpreprocess-test.dir/genrestr.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/genrestr.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/gmxpreprocess/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/pdb2gmx2-test.dir/link.txt --verbose=1 cd /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/gmxpreprocess/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gmxpreprocess/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/src/testutils/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/gmxpreprocess/tests/CMakeFiles/gmxpreprocess-test.dir/gen_maxwell_velocities.cpp.o -MF CMakeFiles/gmxpreprocess-test.dir/gen_maxwell_velocities.cpp.o.d -o CMakeFiles/gmxpreprocess-test.dir/gen_maxwell_velocities.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/gen_maxwell_velocities.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/gmxpreprocess/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gmxpreprocess/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/src/testutils/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/gmxpreprocess/tests/CMakeFiles/gmxpreprocess-test.dir/gpp_atomtype.cpp.o -MF CMakeFiles/gmxpreprocess-test.dir/gpp_atomtype.cpp.o.d -o CMakeFiles/gmxpreprocess-test.dir/gpp_atomtype.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/gpp_atomtype.cpp /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/pdb2gmx1-test.dir/link.d "CMakeFiles/pdb2gmx1-test.dir/pdb2gmx.cpp.o" "CMakeFiles/pdb2gmx1-test.dir/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../bin/pdb2gmx1-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.10.0.0 ../../../../lib/libgmock.so.1.13.0 /usr/lib/riscv64-linux-gnu/libm.so /usr/lib/gcc/riscv64-linux-gnu/14/libgomp.so /lib/riscv64-linux-gnu/libpthread.a ../../../../lib/libgtest.so.1.13.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/basic-dp' [ 84%] Built target pdb2gmx1-test /usr/bin/make -f src/gromacs/gmxpreprocess/tests/CMakeFiles/pdb2gmx3-test.dir/build.make src/gromacs/gmxpreprocess/tests/CMakeFiles/pdb2gmx3-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/basic-dp' cd /build/reproducible-path/gromacs-2025.1/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.1 /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests /build/reproducible-path/gromacs-2025.1/build/basic-dp /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/gmxpreprocess/tests /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/gmxpreprocess/tests/CMakeFiles/pdb2gmx3-test.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/basic-dp' /usr/bin/make -f src/gromacs/gmxpreprocess/tests/CMakeFiles/pdb2gmx3-test.dir/build.make src/gromacs/gmxpreprocess/tests/CMakeFiles/pdb2gmx3-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/basic-dp' cd /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/gmxpreprocess/tests && /usr/bin/c++ -DAMBER=1 -DCHARMM=1 -DGMX_DOUBLE=1 -DGROMOS=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DOPLSAA=0 -DTEST_DATA_PATH=\"src/gromacs/gmxpreprocess/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/src/testutils/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/gmxpreprocess/tests/CMakeFiles/pdb2gmx3-test.dir/pdb2gmx.cpp.o -MF CMakeFiles/pdb2gmx3-test.dir/pdb2gmx.cpp.o.d -o CMakeFiles/pdb2gmx3-test.dir/pdb2gmx.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/pdb2gmx.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/gmxpreprocess/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gmxpreprocess/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/src/testutils/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/gmxpreprocess/tests/CMakeFiles/gmxpreprocess-test.dir/gpp_bond_atomtype.cpp.o -MF CMakeFiles/gmxpreprocess-test.dir/gpp_bond_atomtype.cpp.o.d -o CMakeFiles/gmxpreprocess-test.dir/gpp_bond_atomtype.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/gpp_bond_atomtype.cpp /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/pdb2gmx2-test.dir/link.d "CMakeFiles/pdb2gmx2-test.dir/pdb2gmx.cpp.o" "CMakeFiles/pdb2gmx2-test.dir/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../bin/pdb2gmx2-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.10.0.0 ../../../../lib/libgmock.so.1.13.0 /usr/lib/riscv64-linux-gnu/libm.so /usr/lib/gcc/riscv64-linux-gnu/14/libgomp.so /lib/riscv64-linux-gnu/libpthread.a ../../../../lib/libgtest.so.1.13.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/basic-dp' [ 84%] Built target pdb2gmx2-test /usr/bin/make -f src/gromacs/correlationfunctions/tests/CMakeFiles/correlations-test.dir/build.make src/gromacs/correlationfunctions/tests/CMakeFiles/correlations-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/basic-dp' cd /build/reproducible-path/gromacs-2025.1/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.1 /build/reproducible-path/gromacs-2025.1/src/gromacs/correlationfunctions/tests /build/reproducible-path/gromacs-2025.1/build/basic-dp /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/correlationfunctions/tests /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/correlationfunctions/tests/CMakeFiles/correlations-test.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/basic-dp' /usr/bin/make -f src/gromacs/correlationfunctions/tests/CMakeFiles/correlations-test.dir/build.make src/gromacs/correlationfunctions/tests/CMakeFiles/correlations-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/basic-dp' cd /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/correlationfunctions/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/correlationfunctions/tests\" 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/build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/correlationfunctions/tests/CMakeFiles/correlations-test.dir/autocorr.cpp.o -MF CMakeFiles/correlations-test.dir/autocorr.cpp.o.d -o CMakeFiles/correlations-test.dir/autocorr.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/correlationfunctions/tests/autocorr.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/gmxpreprocess/tests && 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/build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/grompp_directives.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/correlationfunctions/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/correlationfunctions/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/correlationfunctions/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/src/testutils/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/api/legacy/include 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src/gromacs/correlationfunctions/tests/CMakeFiles/correlations-test.dir/correlationdataset.cpp.o -MF CMakeFiles/correlations-test.dir/correlationdataset.cpp.o.d -o CMakeFiles/correlations-test.dir/correlationdataset.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/correlationfunctions/tests/correlationdataset.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/gmxpreprocess/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gmxpreprocess/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/src/testutils/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.1/src 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-fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/gmxpreprocess/tests/CMakeFiles/gmxpreprocess-test.dir/insert_molecules.cpp.o -MF CMakeFiles/gmxpreprocess-test.dir/insert_molecules.cpp.o.d -o CMakeFiles/gmxpreprocess-test.dir/insert_molecules.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/insert_molecules.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/correlationfunctions/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/correlationfunctions/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/correlationfunctions/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/src/testutils/include 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-ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/correlationfunctions/tests/CMakeFiles/correlations-test.dir/manyautocorrelation.cpp.o -MF CMakeFiles/correlations-test.dir/manyautocorrelation.cpp.o.d -o CMakeFiles/correlations-test.dir/manyautocorrelation.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/correlationfunctions/tests/manyautocorrelation.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/gmxpreprocess/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gmxpreprocess/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY 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/build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/correlationfunctions/tests/CMakeFiles/correlations-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/correlations-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/correlations-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/correlationfunctions/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/correlations-test.dir/link.txt --verbose=1 cd /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/gmxpreprocess/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gmxpreprocess/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/src/testutils/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/gmxpreprocess/tests/CMakeFiles/gmxpreprocess-test.dir/topdirs.cpp.o -MF CMakeFiles/gmxpreprocess-test.dir/topdirs.cpp.o.d -o CMakeFiles/gmxpreprocess-test.dir/topdirs.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/topdirs.cpp /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/pdb2gmx3-test.dir/link.d "CMakeFiles/pdb2gmx3-test.dir/pdb2gmx.cpp.o" "CMakeFiles/pdb2gmx3-test.dir/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../bin/pdb2gmx3-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.10.0.0 ../../../../lib/libgmock.so.1.13.0 /usr/lib/riscv64-linux-gnu/libm.so /usr/lib/gcc/riscv64-linux-gnu/14/libgomp.so /lib/riscv64-linux-gnu/libpthread.a ../../../../lib/libgtest.so.1.13.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/basic-dp' [ 84%] Built target pdb2gmx3-test /usr/bin/make -f src/gromacs/analysisdata/tests/CMakeFiles/analysisdata-test-shared.dir/build.make src/gromacs/analysisdata/tests/CMakeFiles/analysisdata-test-shared.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/basic-dp' cd /build/reproducible-path/gromacs-2025.1/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.1 /build/reproducible-path/gromacs-2025.1/src/gromacs/analysisdata/tests /build/reproducible-path/gromacs-2025.1/build/basic-dp /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/analysisdata/tests /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/analysisdata/tests/CMakeFiles/analysisdata-test-shared.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/basic-dp' /usr/bin/make -f src/gromacs/analysisdata/tests/CMakeFiles/analysisdata-test-shared.dir/build.make src/gromacs/analysisdata/tests/CMakeFiles/analysisdata-test-shared.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/basic-dp' cd /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/analysisdata/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/src/testutils/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -MD -MT src/gromacs/analysisdata/tests/CMakeFiles/analysisdata-test-shared.dir/datatest.cpp.o -MF CMakeFiles/analysisdata-test-shared.dir/datatest.cpp.o.d -o CMakeFiles/analysisdata-test-shared.dir/datatest.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/analysisdata/tests/datatest.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/gmxpreprocess/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gmxpreprocess/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/src/testutils/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include 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"CMakeFiles/correlations-test.dir/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../bin/correlations-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.10.0.0 ../../../../lib/libgmock.so.1.13.0 /usr/lib/riscv64-linux-gnu/libm.so /usr/lib/gcc/riscv64-linux-gnu/14/libgomp.so /lib/riscv64-linux-gnu/libpthread.a ../../../../lib/libgtest.so.1.13.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/basic-dp' [ 84%] Built target correlations-test /usr/bin/make -f src/gromacs/coordinateio/tests/CMakeFiles/coordinateio-test.dir/build.make src/gromacs/coordinateio/tests/CMakeFiles/coordinateio-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/basic-dp' cd /build/reproducible-path/gromacs-2025.1/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.1 /build/reproducible-path/gromacs-2025.1/src/gromacs/coordinateio/tests 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-isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/energyanalysis/tests/CMakeFiles/energyanalysis-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF 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-I/build/reproducible-path/gromacs-2025.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/coordinateio/tests/CMakeFiles/coordinateio-test.dir/outputadapters.cpp.o -MF CMakeFiles/coordinateio-test.dir/outputadapters.cpp.o.d -o CMakeFiles/coordinateio-test.dir/outputadapters.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/coordinateio/tests/outputadapters.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/energyanalysis/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/energyanalysis-test.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/gmxpreprocess-test.dir/link.d "CMakeFiles/gmxpreprocess-test.dir/convparm.cpp.o" "CMakeFiles/gmxpreprocess-test.dir/editconf.cpp.o" "CMakeFiles/gmxpreprocess-test.dir/genconf.cpp.o" "CMakeFiles/gmxpreprocess-test.dir/genion.cpp.o" "CMakeFiles/gmxpreprocess-test.dir/genrestr.cpp.o" "CMakeFiles/gmxpreprocess-test.dir/gen_maxwell_velocities.cpp.o" "CMakeFiles/gmxpreprocess-test.dir/gpp_atomtype.cpp.o" "CMakeFiles/gmxpreprocess-test.dir/gpp_bond_atomtype.cpp.o" "CMakeFiles/gmxpreprocess-test.dir/grompp_directives.cpp.o" "CMakeFiles/gmxpreprocess-test.dir/insert_molecules.cpp.o" "CMakeFiles/gmxpreprocess-test.dir/massrepartitioning.cpp.o" "CMakeFiles/gmxpreprocess-test.dir/readir.cpp.o" "CMakeFiles/gmxpreprocess-test.dir/solvate.cpp.o" "CMakeFiles/gmxpreprocess-test.dir/topdirs.cpp.o" "CMakeFiles/gmxpreprocess-test.dir/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../bin/gmxpreprocess-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.10.0.0 ../../../../lib/libgmock.so.1.13.0 /usr/lib/riscv64-linux-gnu/libm.so /usr/lib/gcc/riscv64-linux-gnu/14/libgomp.so /lib/riscv64-linux-gnu/libpthread.a ../../../../lib/libgtest.so.1.13.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/basic-dp' [ 85%] Built target gmxpreprocess-test cd /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/analysisdata/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/src/testutils/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock/include -isystem 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-Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/energyanalysis-test.dir/link.d "CMakeFiles/energyanalysis-test.dir/energyterm.cpp.o" "CMakeFiles/energyanalysis-test.dir/legacyenergy.cpp.o" "CMakeFiles/energyanalysis-test.dir/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../bin/energyanalysis-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.10.0.0 ../../../../lib/libgmock.so.1.13.0 /usr/lib/riscv64-linux-gnu/libm.so /usr/lib/gcc/riscv64-linux-gnu/14/libgomp.so /lib/riscv64-linux-gnu/libpthread.a ../../../../lib/libgtest.so.1.13.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/basic-dp' [ 85%] Built target energyanalysis-test /usr/bin/make -f src/gromacs/tools/tests/CMakeFiles/tool-test.dir/build.make src/gromacs/tools/tests/CMakeFiles/tool-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/basic-dp' cd /build/reproducible-path/gromacs-2025.1/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.1 /build/reproducible-path/gromacs-2025.1/src/gromacs/tools/tests /build/reproducible-path/gromacs-2025.1/build/basic-dp /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/tools/tests /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/tools/tests/CMakeFiles/tool-test.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/basic-dp' /usr/bin/make -f src/gromacs/tools/tests/CMakeFiles/tool-test.dir/build.make src/gromacs/tools/tests/CMakeFiles/tool-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/basic-dp' cd /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/tools/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H 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-isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/tools/tests/CMakeFiles/tool-test.dir/make_ndx.cpp.o -MF CMakeFiles/tool-test.dir/make_ndx.cpp.o.d -o CMakeFiles/tool-test.dir/make_ndx.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/tools/tests/make_ndx.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/analysisdata/tests && /usr/bin/cmake -P CMakeFiles/analysisdata-test-shared.dir/cmake_clean_target.cmake cd 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-I/build/reproducible-path/gromacs-2025.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT 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'/build/reproducible-path/gromacs-2025.1/build/basic-dp' [ 85%] Built target tool-test /usr/bin/make -f src/gromacs/selection/tests/CMakeFiles/selection-test.dir/build.make src/gromacs/selection/tests/CMakeFiles/selection-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/basic-dp' cd /build/reproducible-path/gromacs-2025.1/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.1 /build/reproducible-path/gromacs-2025.1/src/gromacs/selection/tests /build/reproducible-path/gromacs-2025.1/build/basic-dp /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/selection/tests /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/selection/tests/CMakeFiles/selection-test.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/basic-dp' /usr/bin/make -f src/gromacs/selection/tests/CMakeFiles/selection-test.dir/build.make 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src/gromacs/selection/tests/CMakeFiles/selection-test.dir/indexutil.cpp.o -MF CMakeFiles/selection-test.dir/indexutil.cpp.o.d -o CMakeFiles/selection-test.dir/indexutil.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/selection/tests/indexutil.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/fileio/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/fileio/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/fileio/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/src/testutils/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include 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"CMakeFiles/coordinateio-test.dir/setstarttime.cpp.o" "CMakeFiles/coordinateio-test.dir/settimestep.cpp.o" "CMakeFiles/coordinateio-test.dir/testmodule.cpp.o" "CMakeFiles/coordinateio-test.dir/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../bin/coordinateio-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.10.0.0 ../../../../lib/libgmock.so.1.13.0 /usr/lib/riscv64-linux-gnu/libm.so /usr/lib/gcc/riscv64-linux-gnu/14/libgomp.so /lib/riscv64-linux-gnu/libpthread.a ../../../../lib/libgtest.so.1.13.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/basic-dp' [ 86%] Built target coordinateio-test /usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-output-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-output-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/basic-dp' cd /build/reproducible-path/gromacs-2025.1/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" 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-DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/src/testutils/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock/include -isystem 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CMakeFiles/selection-test.dir/nbsearch.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/selection/tests/nbsearch.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/fileio/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/fileio/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/fileio/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/src/testutils/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/api/legacy/include 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-I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -Wformat 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-I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/selection/tests/CMakeFiles/selection-test.dir/poscalc.cpp.o -MF CMakeFiles/selection-test.dir/poscalc.cpp.o.d -o CMakeFiles/selection-test.dir/poscalc.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/selection/tests/poscalc.cpp /usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-modules-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-modules-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/basic-dp' cd /build/reproducible-path/gromacs-2025.1/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.1 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/build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-modules-test.dir/densityfittingmodule.cpp.o -MF CMakeFiles/mdrun-modules-test.dir/densityfittingmodule.cpp.o.d -o CMakeFiles/mdrun-modules-test.dir/densityfittingmodule.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/programs/mdrun/tests/densityfittingmodule.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 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&& /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/selection/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/selection/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/src/testutils/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem 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/build/reproducible-path/gromacs-2025.1/src/gromacs/selection/tests/selectioncollection.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/src/testutils/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -isystem 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CMakeFiles/mdrun-modules-test.dir/interactiveMD.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/programs/mdrun/tests/interactiveMD.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/src/testutils/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/api/legacy/include 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-DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/src/testutils/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock/include -isystem 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-Wl,--dependency-file=CMakeFiles/fileio-test.dir/link.d "CMakeFiles/fileio-test.dir/checkpoint.cpp.o" "CMakeFiles/fileio-test.dir/confio.cpp.o" "CMakeFiles/fileio-test.dir/filemd5.cpp.o" "CMakeFiles/fileio-test.dir/filetypes.cpp.o" "CMakeFiles/fileio-test.dir/matio.cpp.o" "CMakeFiles/fileio-test.dir/mrcserializer.cpp.o" "CMakeFiles/fileio-test.dir/mrcdensitymap.cpp.o" "CMakeFiles/fileio-test.dir/mrcdensitymapheader.cpp.o" "CMakeFiles/fileio-test.dir/readinp.cpp.o" "CMakeFiles/fileio-test.dir/timecontrol.cpp.o" "CMakeFiles/fileio-test.dir/fileioxdrserializer.cpp.o" "CMakeFiles/fileio-test.dir/tngio.cpp.o" "CMakeFiles/fileio-test.dir/xvgio.cpp.o" "CMakeFiles/fileio-test.dir/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../bin/fileio-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.10.0.0 ../../../../lib/libgmock.so.1.13.0 /usr/lib/riscv64-linux-gnu/libm.so /usr/lib/gcc/riscv64-linux-gnu/14/libgomp.so /lib/riscv64-linux-gnu/libpthread.a ../../../../lib/libgtest.so.1.13.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/basic-dp' [ 86%] Built target fileio-test /usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-io-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-io-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/basic-dp' cd /build/reproducible-path/gromacs-2025.1/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.1 /build/reproducible-path/gromacs-2025.1/src/programs/mdrun/tests /build/reproducible-path/gromacs-2025.1/build/basic-dp /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/CMakeFiles/mdrun-io-test.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/basic-dp' /usr/bin/make -f 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directory '/build/reproducible-path/gromacs-2025.1/build/basic-dp' [ 86%] Built target mdrun-modules-test /usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-single-rank-algorithms-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-single-rank-algorithms-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/basic-dp' cd /build/reproducible-path/gromacs-2025.1/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.1 /build/reproducible-path/gromacs-2025.1/src/programs/mdrun/tests /build/reproducible-path/gromacs-2025.1/build/basic-dp /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/CMakeFiles/mdrun-single-rank-algorithms-test.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/basic-dp' /usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-single-rank-algorithms-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-single-rank-algorithms-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/basic-dp' cd /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/src/testutils/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include 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src/programs/mdrun/tests/CMakeFiles/mdrun-single-rank-algorithms-test.dir/dispersion_correction.cpp.o -MF CMakeFiles/mdrun-single-rank-algorithms-test.dir/dispersion_correction.cpp.o.d -o CMakeFiles/mdrun-single-rank-algorithms-test.dir/dispersion_correction.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/programs/mdrun/tests/dispersion_correction.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/selection/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/selection/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/selection/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/src/testutils/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.1/src 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-ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-io-test.dir/exactcontinuation.cpp.o -MF CMakeFiles/mdrun-io-test.dir/exactcontinuation.cpp.o.d -o CMakeFiles/mdrun-io-test.dir/exactcontinuation.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/programs/mdrun/tests/exactcontinuation.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/src/testutils/include 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/build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-single-rank-algorithms-test.dir/ewaldsurfaceterm.cpp.o -MF CMakeFiles/mdrun-single-rank-algorithms-test.dir/ewaldsurfaceterm.cpp.o.d -o CMakeFiles/mdrun-single-rank-algorithms-test.dir/ewaldsurfaceterm.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/programs/mdrun/tests/ewaldsurfaceterm.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary\" -DTEST_USES_MPI=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/src/testutils/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-test.dir/tabulated_bonded_interactions.cpp.o -MF CMakeFiles/mdrun-test.dir/tabulated_bonded_interactions.cpp.o.d -o CMakeFiles/mdrun-test.dir/tabulated_bonded_interactions.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/programs/mdrun/tests/tabulated_bonded_interactions.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 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/build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-test.dir/freezegroups.cpp.o -MF CMakeFiles/mdrun-test.dir/freezegroups.cpp.o.d -o CMakeFiles/mdrun-test.dir/freezegroups.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/programs/mdrun/tests/freezegroups.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=1 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/usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/src/testutils/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem 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/build/reproducible-path/gromacs-2025.1/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/src/testutils/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -isystem 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/build/reproducible-path/gromacs-2025.1/src/programs/mdrun/tests/grompp.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/mdrun-single-rank-algorithms-test.dir/link.txt --verbose=1 cd /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/src/testutils/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-io-test.dir/initialconstraints.cpp.o -MF CMakeFiles/mdrun-io-test.dir/initialconstraints.cpp.o.d -o CMakeFiles/mdrun-io-test.dir/initialconstraints.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/programs/mdrun/tests/initialconstraints.cpp /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/mdrun-single-rank-algorithms-test.dir/link.d "CMakeFiles/mdrun-single-rank-algorithms-test.dir/dispersion_correction.cpp.o" "CMakeFiles/mdrun-single-rank-algorithms-test.dir/ewaldsurfaceterm.cpp.o" "CMakeFiles/mdrun-single-rank-algorithms-test.dir/orires.cpp.o" "CMakeFiles/mdrun-single-rank-algorithms-test.dir/__/__/__/testutils/unittest_main.cpp.o" ../../CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o ../../CMakeFiles/mdrun_objlib.dir/mdrun/nonbonded_bench.cpp.o -o ../../../../bin/mdrun-single-rank-algorithms-test ../../../../lib/libtestutils.a ../../../../lib/libmdrun_test_infrastructure.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.10.0.0 /usr/lib/riscv64-linux-gnu/libm.so /usr/lib/gcc/riscv64-linux-gnu/14/libgomp.so /lib/riscv64-linux-gnu/libpthread.a ../../../../lib/libgmock.so.1.13.0 ../../../../lib/libgtest.so.1.13.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/basic-dp' [ 86%] Built target mdrun-single-rank-algorithms-test /usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/minimize-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/minimize-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/basic-dp' cd /build/reproducible-path/gromacs-2025.1/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.1 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/build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-non-integrator-test.dir/normalmodes.cpp.o -MF CMakeFiles/mdrun-non-integrator-test.dir/normalmodes.cpp.o.d -o CMakeFiles/mdrun-non-integrator-test.dir/normalmodes.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/programs/mdrun/tests/normalmodes.cpp /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/mdrun-io-test.dir/link.d "CMakeFiles/mdrun-io-test.dir/checkpoint.cpp.o" "CMakeFiles/mdrun-io-test.dir/exactcontinuation.cpp.o" "CMakeFiles/mdrun-io-test.dir/grompp.cpp.o" "CMakeFiles/mdrun-io-test.dir/initialconstraints.cpp.o" "CMakeFiles/mdrun-io-test.dir/termination.cpp.o" "CMakeFiles/mdrun-io-test.dir/__/__/__/testutils/unittest_main.cpp.o" ../../CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o ../../CMakeFiles/mdrun_objlib.dir/mdrun/nonbonded_bench.cpp.o -o ../../../../bin/mdrun-io-test ../../../../lib/libtestutils.a ../../../../lib/libmdrun_test_infrastructure.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.10.0.0 /usr/lib/riscv64-linux-gnu/libm.so /usr/lib/gcc/riscv64-linux-gnu/14/libgomp.so /lib/riscv64-linux-gnu/libpthread.a ../../../../lib/libgmock.so.1.13.0 ../../../../lib/libgtest.so.1.13.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/basic-dp' [ 86%] Built target mdrun-io-test /usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-tpi-test.dir/build.make 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/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/mdrun-test.dir/link.d "CMakeFiles/mdrun-test.dir/multiple_time_stepping.cpp.o" "CMakeFiles/mdrun-test.dir/swapcoords.cpp.o" "CMakeFiles/mdrun-test.dir/tabulated_bonded_interactions.cpp.o" "CMakeFiles/mdrun-test.dir/freezegroups.cpp.o" "CMakeFiles/mdrun-test.dir/constantacceleration.cpp.o" "CMakeFiles/mdrun-test.dir/boxdeformation.cpp.o" "CMakeFiles/mdrun-test.dir/__/__/__/testutils/unittest_main.cpp.o" ../../CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o ../../CMakeFiles/mdrun_objlib.dir/mdrun/nonbonded_bench.cpp.o -o ../../../../bin/mdrun-test ../../../../lib/libtestutils.a ../../../../lib/libmdrun_test_infrastructure.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.10.0.0 /usr/lib/riscv64-linux-gnu/libm.so /usr/lib/gcc/riscv64-linux-gnu/14/libgomp.so /lib/riscv64-linux-gnu/libpthread.a ../../../../lib/libgmock.so.1.13.0 ../../../../lib/libgtest.so.1.13.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/basic-dp' [ 87%] Built target mdrun-test /usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-mpi-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-mpi-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/basic-dp' cd /build/reproducible-path/gromacs-2025.1/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.1 /build/reproducible-path/gromacs-2025.1/src/programs/mdrun/tests /build/reproducible-path/gromacs-2025.1/build/basic-dp /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/CMakeFiles/mdrun-mpi-test.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/basic-dp' /usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-mpi-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-mpi-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/basic-dp' cd /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary\" -DTEST_USES_MPI=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/src/testutils/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include 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-I/build/reproducible-path/gromacs-2025.1/src/testutils/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-mpi-test.dir/mimic.cpp.o -MF CMakeFiles/mdrun-mpi-test.dir/mimic.cpp.o.d -o CMakeFiles/mdrun-mpi-test.dir/mimic.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/programs/mdrun/tests/mimic.cpp /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/mdrun-tpi-test.dir/link.d "CMakeFiles/mdrun-tpi-test.dir/tpitest.cpp.o" "CMakeFiles/mdrun-tpi-test.dir/__/__/__/testutils/unittest_main.cpp.o" ../../CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o ../../CMakeFiles/mdrun_objlib.dir/mdrun/nonbonded_bench.cpp.o -o ../../../../bin/mdrun-tpi-test ../../../../lib/libtestutils.a ../../../../lib/libmdrun_test_infrastructure.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.10.0.0 /usr/lib/riscv64-linux-gnu/libm.so /usr/lib/gcc/riscv64-linux-gnu/14/libgomp.so /lib/riscv64-linux-gnu/libpthread.a ../../../../lib/libgmock.so.1.13.0 ../../../../lib/libgtest.so.1.13.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/basic-dp' [ 87%] Built target mdrun-tpi-test cd /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary\" -DTEST_USES_MPI=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/src/testutils/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-mpi-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/mdrun-mpi-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/mdrun-mpi-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/testutils/unittest_main.cpp /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/selection-test.dir/link.d "CMakeFiles/selection-test.dir/indexutil.cpp.o" "CMakeFiles/selection-test.dir/nbsearch.cpp.o" "CMakeFiles/selection-test.dir/poscalc.cpp.o" "CMakeFiles/selection-test.dir/selectioncollection.cpp.o" "CMakeFiles/selection-test.dir/selectionoption.cpp.o" "CMakeFiles/selection-test.dir/toputils.cpp.o" "CMakeFiles/selection-test.dir/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../bin/selection-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.10.0.0 ../../../../lib/libgmock.so.1.13.0 /usr/lib/riscv64-linux-gnu/libm.so /usr/lib/gcc/riscv64-linux-gnu/14/libgomp.so /lib/riscv64-linux-gnu/libpthread.a ../../../../lib/libgtest.so.1.13.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/basic-dp' [ 88%] Built target selection-test /usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-multisim-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-multisim-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/basic-dp' cd 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/usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/src/testutils/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem 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/build/reproducible-path/gromacs-2025.1/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/mdrun-mpi-test.dir/link.txt --verbose=1 /usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-multisim-replex-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-multisim-replex-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/basic-dp' cd /build/reproducible-path/gromacs-2025.1/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.1 /build/reproducible-path/gromacs-2025.1/src/programs/mdrun/tests /build/reproducible-path/gromacs-2025.1/build/basic-dp /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/CMakeFiles/mdrun-multisim-replex-test.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/basic-dp' /usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-multisim-replex-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-multisim-replex-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/basic-dp' cd /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary\" -DTEST_USES_MPI=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/src/testutils/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.1/src 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-I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-multisim-replex-test.dir/replicaexchange.cpp.o -MF CMakeFiles/mdrun-multisim-replex-test.dir/replicaexchange.cpp.o.d -o CMakeFiles/mdrun-multisim-replex-test.dir/replicaexchange.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/programs/mdrun/tests/replicaexchange.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary\" -DTEST_USES_MPI=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/src/testutils/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-multisim-test.dir/multisimtest.cpp.o -MF CMakeFiles/mdrun-multisim-test.dir/multisimtest.cpp.o.d -o CMakeFiles/mdrun-multisim-test.dir/multisimtest.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/programs/mdrun/tests/multisimtest.cpp /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/mdrun-mpi-test.dir/link.d "CMakeFiles/mdrun-mpi-test.dir/domain_decomposition.cpp.o" "CMakeFiles/mdrun-mpi-test.dir/mimic.cpp.o" "CMakeFiles/mdrun-mpi-test.dir/__/__/__/testutils/unittest_main.cpp.o" ../../CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o ../../CMakeFiles/mdrun_objlib.dir/mdrun/nonbonded_bench.cpp.o -o ../../../../bin/mdrun-mpi-test ../../../../lib/libtestutils.a ../../../../lib/libmdrun_test_infrastructure.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.10.0.0 /usr/lib/riscv64-linux-gnu/libm.so /usr/lib/gcc/riscv64-linux-gnu/14/libgomp.so /lib/riscv64-linux-gnu/libpthread.a ../../../../lib/libgmock.so.1.13.0 ../../../../lib/libgtest.so.1.13.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/basic-dp' [ 88%] Built target mdrun-mpi-test /usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-multisim-replex-equivalence-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-multisim-replex-equivalence-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/basic-dp' cd /build/reproducible-path/gromacs-2025.1/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.1 /build/reproducible-path/gromacs-2025.1/src/programs/mdrun/tests /build/reproducible-path/gromacs-2025.1/build/basic-dp /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/CMakeFiles/mdrun-multisim-replex-equivalence-test.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/basic-dp' /usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-multisim-replex-equivalence-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-multisim-replex-equivalence-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/basic-dp' cd /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary\" -DTEST_USES_MPI=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/src/testutils/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock/include -isystem 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-I/build/reproducible-path/gromacs-2025.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-multisim-replex-equivalence-test.dir/replicaexchange_equivalence.cpp.o -MF CMakeFiles/mdrun-multisim-replex-equivalence-test.dir/replicaexchange_equivalence.cpp.o.d -o CMakeFiles/mdrun-multisim-replex-equivalence-test.dir/replicaexchange_equivalence.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/programs/mdrun/tests/replicaexchange_equivalence.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/mdrun-multisim-test.dir/link.txt --verbose=1 cd /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary\" -DTEST_USES_MPI=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/src/testutils/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-multisim-replex-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/mdrun-multisim-replex-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/mdrun-multisim-replex-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/mdrun-multisim-replex-test.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/mdrun-multisim-test.dir/link.d "CMakeFiles/mdrun-multisim-test.dir/multisim.cpp.o" "CMakeFiles/mdrun-multisim-test.dir/multisimtest.cpp.o" "CMakeFiles/mdrun-multisim-test.dir/__/__/__/testutils/unittest_main.cpp.o" ../../CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o ../../CMakeFiles/mdrun_objlib.dir/mdrun/nonbonded_bench.cpp.o -o ../../../../bin/mdrun-multisim-test ../../../../lib/libtestutils.a ../../../../lib/libmdrun_test_infrastructure.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.10.0.0 /usr/lib/riscv64-linux-gnu/libm.so /usr/lib/gcc/riscv64-linux-gnu/14/libgomp.so /lib/riscv64-linux-gnu/libpthread.a ../../../../lib/libgmock.so.1.13.0 ../../../../lib/libgtest.so.1.13.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/basic-dp' [ 89%] Built target mdrun-multisim-test /usr/bin/make -f 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'/build/reproducible-path/gromacs-2025.1/build/basic-dp' cd /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary\" -DTEST_USES_MPI=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/src/testutils/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -isystem 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CMakeFiles/mdrun-mpi-pme-test.dir/pmetest.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/programs/mdrun/tests/pmetest.cpp /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/mdrun-non-integrator-test.dir/link.d "CMakeFiles/mdrun-non-integrator-test.dir/nonbonded_bench.cpp.o" "CMakeFiles/mdrun-non-integrator-test.dir/normalmodes.cpp.o" "CMakeFiles/mdrun-non-integrator-test.dir/rerun.cpp.o" "CMakeFiles/mdrun-non-integrator-test.dir/simple_mdrun.cpp.o" "CMakeFiles/mdrun-non-integrator-test.dir/__/__/__/testutils/unittest_main.cpp.o" ../../CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o ../../CMakeFiles/mdrun_objlib.dir/mdrun/nonbonded_bench.cpp.o -o ../../../../bin/mdrun-non-integrator-test ../../../../lib/libtestutils.a ../../../../lib/libmdrun_test_infrastructure.a ../../../../lib/libtestutils.a 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/build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-coordination-basic-test.dir/periodicactions.cpp.o -MF CMakeFiles/mdrun-coordination-basic-test.dir/periodicactions.cpp.o.d -o CMakeFiles/mdrun-coordination-basic-test.dir/periodicactions.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/programs/mdrun/tests/periodicactions.cpp /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/mdrun-multisim-replex-test.dir/link.d "CMakeFiles/mdrun-multisim-replex-test.dir/multisimtest.cpp.o" "CMakeFiles/mdrun-multisim-replex-test.dir/replicaexchange.cpp.o" "CMakeFiles/mdrun-multisim-replex-test.dir/__/__/__/testutils/unittest_main.cpp.o" ../../CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o ../../CMakeFiles/mdrun_objlib.dir/mdrun/nonbonded_bench.cpp.o -o ../../../../bin/mdrun-multisim-replex-test ../../../../lib/libtestutils.a ../../../../lib/libmdrun_test_infrastructure.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.10.0.0 /usr/lib/riscv64-linux-gnu/libm.so /usr/lib/gcc/riscv64-linux-gnu/14/libgomp.so /lib/riscv64-linux-gnu/libpthread.a ../../../../lib/libgmock.so.1.13.0 ../../../../lib/libgtest.so.1.13.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/basic-dp' [ 89%] Built target mdrun-multisim-replex-test /usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-coordination-coupling-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-coordination-coupling-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/basic-dp' cd /build/reproducible-path/gromacs-2025.1/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.1 /build/reproducible-path/gromacs-2025.1/src/programs/mdrun/tests /build/reproducible-path/gromacs-2025.1/build/basic-dp /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/CMakeFiles/mdrun-coordination-coupling-test.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/basic-dp' /usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-coordination-coupling-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-coordination-coupling-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/basic-dp' cd /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary\" -DTEST_USES_MPI=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/src/testutils/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -isystem 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-o CMakeFiles/mdrun-coordination-coupling-test.dir/periodicactions.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/programs/mdrun/tests/periodicactions.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary\" -DTEST_USES_MPI=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/src/testutils/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/api/legacy/include 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src/programs/mdrun/tests/CMakeFiles/mdrun-mpi-pme-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/mdrun-mpi-pme-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/mdrun-mpi-pme-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary\" -DTEST_USES_MPI=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/src/testutils/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-coordination-basic-test.dir/periodicactions_basic.cpp.o -MF CMakeFiles/mdrun-coordination-basic-test.dir/periodicactions_basic.cpp.o.d -o CMakeFiles/mdrun-coordination-basic-test.dir/periodicactions_basic.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/programs/mdrun/tests/periodicactions_basic.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/mdrun-mpi-pme-test.dir/link.txt --verbose=1 cd /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary\" -DTEST_USES_MPI=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/src/testutils/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-multisim-replex-equivalence-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/mdrun-multisim-replex-equivalence-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/mdrun-multisim-replex-equivalence-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/mdrun-multisim-replex-equivalence-test.dir/link.txt --verbose=1 cd /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary\" -DTEST_USES_MPI=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/src/testutils/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -isystem 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/usr/lib/gcc/riscv64-linux-gnu/14/libgomp.so /lib/riscv64-linux-gnu/libpthread.a ../../../../lib/libgmock.so.1.13.0 ../../../../lib/libgtest.so.1.13.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/basic-dp' [ 90%] Built target mdrun-mpi-pme-test /usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-coordination-constraints-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-coordination-constraints-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/basic-dp' cd /build/reproducible-path/gromacs-2025.1/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.1 /build/reproducible-path/gromacs-2025.1/src/programs/mdrun/tests /build/reproducible-path/gromacs-2025.1/build/basic-dp /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests 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cmake_link_script CMakeFiles/mdrun-coordination-basic-test.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/mdrun-multisim-replex-equivalence-test.dir/link.d "CMakeFiles/mdrun-multisim-replex-equivalence-test.dir/multisimtest.cpp.o" "CMakeFiles/mdrun-multisim-replex-equivalence-test.dir/replicaexchange_equivalence.cpp.o" "CMakeFiles/mdrun-multisim-replex-equivalence-test.dir/__/__/__/testutils/unittest_main.cpp.o" ../../CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o ../../CMakeFiles/mdrun_objlib.dir/mdrun/nonbonded_bench.cpp.o -o ../../../../bin/mdrun-multisim-replex-equivalence-test ../../../../lib/libtestutils.a ../../../../lib/libmdrun_test_infrastructure.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.10.0.0 /usr/lib/riscv64-linux-gnu/libm.so /usr/lib/gcc/riscv64-linux-gnu/14/libgomp.so /lib/riscv64-linux-gnu/libpthread.a ../../../../lib/libgmock.so.1.13.0 ../../../../lib/libgtest.so.1.13.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/basic-dp' [ 90%] Built target mdrun-multisim-replex-equivalence-test /usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-fep-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-fep-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/basic-dp' cd /build/reproducible-path/gromacs-2025.1/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.1 /build/reproducible-path/gromacs-2025.1/src/programs/mdrun/tests /build/reproducible-path/gromacs-2025.1/build/basic-dp /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/CMakeFiles/mdrun-fep-test.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/basic-dp' /usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-fep-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-fep-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/basic-dp' cd /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/src/testutils/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include 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-fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/mdrun-coordination-basic-test.dir/link.d "CMakeFiles/mdrun-coordination-basic-test.dir/periodicactions.cpp.o" "CMakeFiles/mdrun-coordination-basic-test.dir/periodicactions_basic.cpp.o" "CMakeFiles/mdrun-coordination-basic-test.dir/__/__/__/testutils/unittest_main.cpp.o" ../../CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o ../../CMakeFiles/mdrun_objlib.dir/mdrun/nonbonded_bench.cpp.o -o ../../../../bin/mdrun-coordination-basic-test ../../../../lib/libtestutils.a ../../../../lib/libmdrun_test_infrastructure.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.10.0.0 /usr/lib/riscv64-linux-gnu/libm.so /usr/lib/gcc/riscv64-linux-gnu/14/libgomp.so /lib/riscv64-linux-gnu/libpthread.a ../../../../lib/libgmock.so.1.13.0 ../../../../lib/libgtest.so.1.13.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/basic-dp' [ 90%] Built target mdrun-coordination-basic-test /usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-pull-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-pull-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/basic-dp' cd /build/reproducible-path/gromacs-2025.1/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.1 /build/reproducible-path/gromacs-2025.1/src/programs/mdrun/tests /build/reproducible-path/gromacs-2025.1/build/basic-dp /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/CMakeFiles/mdrun-pull-test.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/basic-dp' /usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-pull-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-pull-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/basic-dp' cd /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/src/testutils/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-pull-test.dir/pull.cpp.o -MF CMakeFiles/mdrun-pull-test.dir/pull.cpp.o.d -o CMakeFiles/mdrun-pull-test.dir/pull.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/programs/mdrun/tests/pull.cpp /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/mdrun-coordination-coupling-test.dir/link.d "CMakeFiles/mdrun-coordination-coupling-test.dir/periodicactions.cpp.o" "CMakeFiles/mdrun-coordination-coupling-test.dir/periodicactions_coupling.cpp.o" "CMakeFiles/mdrun-coordination-coupling-test.dir/__/__/__/testutils/unittest_main.cpp.o" ../../CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o ../../CMakeFiles/mdrun_objlib.dir/mdrun/nonbonded_bench.cpp.o -o ../../../../bin/mdrun-coordination-coupling-test ../../../../lib/libtestutils.a ../../../../lib/libmdrun_test_infrastructure.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.10.0.0 /usr/lib/riscv64-linux-gnu/libm.so /usr/lib/gcc/riscv64-linux-gnu/14/libgomp.so /lib/riscv64-linux-gnu/libpthread.a ../../../../lib/libgmock.so.1.13.0 ../../../../lib/libgtest.so.1.13.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/basic-dp' [ 91%] Built target mdrun-coordination-coupling-test cd /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/src/testutils/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.1/src 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-I/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-coordination-constraints-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/mdrun-coordination-constraints-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/mdrun-coordination-constraints-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/testutils/unittest_main.cpp /usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-rotation-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-rotation-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/basic-dp' cd /build/reproducible-path/gromacs-2025.1/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.1 /build/reproducible-path/gromacs-2025.1/src/programs/mdrun/tests /build/reproducible-path/gromacs-2025.1/build/basic-dp /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/CMakeFiles/mdrun-rotation-test.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/basic-dp' /usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-rotation-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-rotation-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/basic-dp' cd /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/src/testutils/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/api/legacy/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-rotation-test.dir/pull_rotation.cpp.o -MF CMakeFiles/mdrun-rotation-test.dir/pull_rotation.cpp.o.d -o CMakeFiles/mdrun-rotation-test.dir/pull_rotation.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/programs/mdrun/tests/pull_rotation.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/mdrun-coordination-constraints-test.dir/link.txt --verbose=1 cd /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/src/testutils/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-fep-test.dir/freeenergy.cpp.o -MF CMakeFiles/mdrun-fep-test.dir/freeenergy.cpp.o.d -o CMakeFiles/mdrun-fep-test.dir/freeenergy.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/programs/mdrun/tests/freeenergy.cpp /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/mdrun-coordination-constraints-test.dir/link.d "CMakeFiles/mdrun-coordination-constraints-test.dir/periodicactions.cpp.o" "CMakeFiles/mdrun-coordination-constraints-test.dir/periodicactions_constraints.cpp.o" "CMakeFiles/mdrun-coordination-constraints-test.dir/__/__/__/testutils/unittest_main.cpp.o" ../../CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o ../../CMakeFiles/mdrun_objlib.dir/mdrun/nonbonded_bench.cpp.o -o ../../../../bin/mdrun-coordination-constraints-test ../../../../lib/libtestutils.a ../../../../lib/libmdrun_test_infrastructure.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.10.0.0 /usr/lib/riscv64-linux-gnu/libm.so /usr/lib/gcc/riscv64-linux-gnu/14/libgomp.so /lib/riscv64-linux-gnu/libpthread.a ../../../../lib/libgmock.so.1.13.0 ../../../../lib/libgtest.so.1.13.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/basic-dp' [ 91%] Built target mdrun-coordination-constraints-test /usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-simulator-comparison-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-simulator-comparison-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/basic-dp' cd /build/reproducible-path/gromacs-2025.1/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.1 /build/reproducible-path/gromacs-2025.1/src/programs/mdrun/tests /build/reproducible-path/gromacs-2025.1/build/basic-dp /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/CMakeFiles/mdrun-simulator-comparison-test.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/basic-dp' /usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-simulator-comparison-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-simulator-comparison-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/basic-dp' cd /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/src/testutils/include -I/build/reproducible-path/gromacs-2025.1/src/include 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/build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-rotation-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/mdrun-rotation-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/mdrun-rotation-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/mdrun-pull-test.dir/link.txt --verbose=1 cd /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests && /usr/bin/cmake -E cmake_link_script 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"CMakeFiles/mdrun-rotation-test.dir/__/__/__/testutils/unittest_main.cpp.o" ../../CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o ../../CMakeFiles/mdrun_objlib.dir/mdrun/nonbonded_bench.cpp.o -o ../../../../bin/mdrun-rotation-test ../../../../lib/libtestutils.a ../../../../lib/libmdrun_test_infrastructure.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.10.0.0 /usr/lib/riscv64-linux-gnu/libm.so /usr/lib/gcc/riscv64-linux-gnu/14/libgomp.so /lib/riscv64-linux-gnu/libpthread.a ../../../../lib/libgmock.so.1.13.0 ../../../../lib/libgtest.so.1.13.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/basic-dp' [ 92%] Built target mdrun-rotation-test /usr/bin/make -f api/gmxapi/cpp/tests/CMakeFiles/gmxapi-test.dir/build.make api/gmxapi/cpp/tests/CMakeFiles/gmxapi-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/basic-dp' cd /build/reproducible-path/gromacs-2025.1/build/basic-dp && /usr/bin/cmake -E cmake_depends 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/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/mdrun-simulator-comparison-test.dir/link.txt --verbose=1 cd /build/reproducible-path/gromacs-2025.1/build/basic-dp/api/gmxapi/cpp/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"api/gmxapi/cpp/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.1/build/basic-dp/api/gmxapi/cpp/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/src/testutils/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/api/legacy/include 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-DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT api/gmxapi/cpp/tests/CMakeFiles/gmxapi-test.dir/runner.cpp.o -MF CMakeFiles/gmxapi-test.dir/runner.cpp.o.d -o CMakeFiles/gmxapi-test.dir/runner.cpp.o -c /build/reproducible-path/gromacs-2025.1/api/gmxapi/cpp/tests/runner.cpp /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/mdrun-fep-test.dir/link.d "CMakeFiles/mdrun-fep-test.dir/expandedensemble.cpp.o" "CMakeFiles/mdrun-fep-test.dir/freeenergy.cpp.o" "CMakeFiles/mdrun-fep-test.dir/__/__/__/testutils/unittest_main.cpp.o" ../../CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o ../../CMakeFiles/mdrun_objlib.dir/mdrun/nonbonded_bench.cpp.o -o ../../../../bin/mdrun-fep-test ../../../../lib/libtestutils.a ../../../../lib/libmdrun_test_infrastructure.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.10.0.0 /usr/lib/riscv64-linux-gnu/libm.so /usr/lib/gcc/riscv64-linux-gnu/14/libgomp.so /lib/riscv64-linux-gnu/libpthread.a ../../../../lib/libgmock.so.1.13.0 ../../../../lib/libgtest.so.1.13.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/basic-dp' [ 92%] Built target mdrun-fep-test /usr/bin/make -f api/gmxapi/cpp/workflow/tests/CMakeFiles/workflow-details-test.dir/build.make api/gmxapi/cpp/workflow/tests/CMakeFiles/workflow-details-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/basic-dp' cd /build/reproducible-path/gromacs-2025.1/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.1 /build/reproducible-path/gromacs-2025.1/api/gmxapi/cpp/workflow/tests /build/reproducible-path/gromacs-2025.1/build/basic-dp /build/reproducible-path/gromacs-2025.1/build/basic-dp/api/gmxapi/cpp/workflow/tests /build/reproducible-path/gromacs-2025.1/build/basic-dp/api/gmxapi/cpp/workflow/tests/CMakeFiles/workflow-details-test.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/basic-dp' /usr/bin/make -f api/gmxapi/cpp/workflow/tests/CMakeFiles/workflow-details-test.dir/build.make api/gmxapi/cpp/workflow/tests/CMakeFiles/workflow-details-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/basic-dp' cd /build/reproducible-path/gromacs-2025.1/build/basic-dp/api/gmxapi/cpp/workflow/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"api/gmxapi/cpp/workflow/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.1/build/basic-dp/api/gmxapi/cpp/workflow/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/src/testutils/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/api/gmxapi/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/api/gmxapi/include -I/build/reproducible-path/gromacs-2025.1/api/gmxapi/cpp -I/build/reproducible-path/gromacs-2025.1/api/gmxapi/cpp/tests -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT api/gmxapi/cpp/workflow/tests/CMakeFiles/workflow-details-test.dir/workflow.cpp.o -MF CMakeFiles/workflow-details-test.dir/workflow.cpp.o.d -o CMakeFiles/workflow-details-test.dir/workflow.cpp.o -c /build/reproducible-path/gromacs-2025.1/api/gmxapi/cpp/workflow/tests/workflow.cpp /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/mdrun-simulator-comparison-test.dir/link.d "CMakeFiles/mdrun-simulator-comparison-test.dir/simulator.cpp.o" "CMakeFiles/mdrun-simulator-comparison-test.dir/__/__/__/testutils/unittest_main.cpp.o" ../../CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o ../../CMakeFiles/mdrun_objlib.dir/mdrun/nonbonded_bench.cpp.o -o ../../../../bin/mdrun-simulator-comparison-test ../../../../lib/libtestutils.a ../../../../lib/libmdrun_test_infrastructure.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.10.0.0 /usr/lib/riscv64-linux-gnu/libm.so /usr/lib/gcc/riscv64-linux-gnu/14/libgomp.so /lib/riscv64-linux-gnu/libpthread.a ../../../../lib/libgmock.so.1.13.0 ../../../../lib/libgtest.so.1.13.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/basic-dp' [ 92%] Built target mdrun-simulator-comparison-test cd /build/reproducible-path/gromacs-2025.1/build/basic-dp/api/gmxapi/cpp/workflow/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"api/gmxapi/cpp/workflow/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.1/build/basic-dp/api/gmxapi/cpp/workflow/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/src/testutils/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/api/gmxapi/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/api/gmxapi/include -I/build/reproducible-path/gromacs-2025.1/api/gmxapi/cpp -I/build/reproducible-path/gromacs-2025.1/api/gmxapi/cpp/tests -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops 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-I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-vsites-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/mdrun-vsites-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/mdrun-vsites-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic-dp/api/gmxapi/cpp/workflow/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/workflow-details-test.dir/link.txt --verbose=1 /usr/bin/make -f api/nblib/tests/CMakeFiles/nblib-integrator-test.dir/build.make api/nblib/tests/CMakeFiles/nblib-integrator-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/basic-dp' cd /build/reproducible-path/gromacs-2025.1/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.1 /build/reproducible-path/gromacs-2025.1/api/nblib/tests /build/reproducible-path/gromacs-2025.1/build/basic-dp /build/reproducible-path/gromacs-2025.1/build/basic-dp/api/nblib/tests /build/reproducible-path/gromacs-2025.1/build/basic-dp/api/nblib/tests/CMakeFiles/nblib-integrator-test.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/basic-dp' /usr/bin/make -f api/nblib/tests/CMakeFiles/nblib-integrator-test.dir/build.make api/nblib/tests/CMakeFiles/nblib-integrator-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/basic-dp' cd /build/reproducible-path/gromacs-2025.1/build/basic-dp/api/nblib/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"api/nblib/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.1/build/basic-dp/api/nblib/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/src/testutils/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/api/nblib/tests -I/build/reproducible-path/gromacs-2025.1/api/nblib/include -I/build/reproducible-path/gromacs-2025.1/api/nblib -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT api/nblib/tests/CMakeFiles/nblib-integrator-test.dir/integrator.cpp.o -MF 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-I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/api/gmxapi/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/api/gmxapi/include -I/build/reproducible-path/gromacs-2025.1/api/gmxapi/cpp/tests -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT api/gmxapi/cpp/tests/CMakeFiles/gmxapi-test.dir/status.cpp.o -MF CMakeFiles/gmxapi-test.dir/status.cpp.o.d -o CMakeFiles/gmxapi-test.dir/status.cpp.o -c /build/reproducible-path/gromacs-2025.1/api/gmxapi/cpp/tests/status.cpp /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/workflow-details-test.dir/link.d "CMakeFiles/workflow-details-test.dir/workflow.cpp.o" "CMakeFiles/workflow-details-test.dir/__/__/__/__/__/src/testutils/unittest_main.cpp.o" ../../../../../src/programs/CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o ../../../../../src/programs/CMakeFiles/mdrun_objlib.dir/mdrun/nonbonded_bench.cpp.o -o ../../../../../bin/workflow-details-test ../../../../../lib/libtestutils.a ../../../../../lib/libgmxapi_d.so.0.4.0 ../../../../../lib/libmdrun_test_infrastructure.a ../../../../../lib/libtestutils.a ../../../../../lib/libgromacs_d.so.10.0.0 /usr/lib/riscv64-linux-gnu/libm.so /usr/lib/gcc/riscv64-linux-gnu/14/libgomp.so /lib/riscv64-linux-gnu/libpthread.a ../../../../../lib/libgmock.so.1.13.0 ../../../../../lib/libgtest.so.1.13.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/basic-dp' [ 93%] Built target workflow-details-test /usr/bin/make -f api/nblib/tests/CMakeFiles/nblib-setup-test.dir/build.make api/nblib/tests/CMakeFiles/nblib-setup-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/basic-dp' cd /build/reproducible-path/gromacs-2025.1/build/basic-dp && 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api/nblib/tests/CMakeFiles/nblib-setup-test.dir/box.cpp.o -MF CMakeFiles/nblib-setup-test.dir/box.cpp.o.d -o CMakeFiles/nblib-setup-test.dir/box.cpp.o -c /build/reproducible-path/gromacs-2025.1/api/nblib/tests/box.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic-dp/api/gmxapi/cpp/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"api/gmxapi/cpp/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.1/build/basic-dp/api/gmxapi/cpp/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/src/testutils/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include 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-Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT api/gmxapi/cpp/tests/CMakeFiles/gmxapi-test.dir/stopsignaler.cpp.o -MF CMakeFiles/gmxapi-test.dir/stopsignaler.cpp.o.d -o CMakeFiles/gmxapi-test.dir/stopsignaler.cpp.o -c /build/reproducible-path/gromacs-2025.1/api/gmxapi/cpp/tests/stopsignaler.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic-dp/api/nblib/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"api/nblib/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.1/build/basic-dp/api/nblib/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/api -I/build/reproducible-path/gromacs-2025.1/src/testutils/include -I/build/reproducible-path/gromacs-2025.1/src/include 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-Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/mdrun-vsites-test.dir/link.d "CMakeFiles/mdrun-vsites-test.dir/virtualsites.cpp.o" "CMakeFiles/mdrun-vsites-test.dir/__/__/__/testutils/unittest_main.cpp.o" ../../CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o ../../CMakeFiles/mdrun_objlib.dir/mdrun/nonbonded_bench.cpp.o -o ../../../../bin/mdrun-vsites-test ../../../../lib/libtestutils.a ../../../../lib/libmdrun_test_infrastructure.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.10.0.0 /usr/lib/riscv64-linux-gnu/libm.so /usr/lib/gcc/riscv64-linux-gnu/14/libgomp.so /lib/riscv64-linux-gnu/libpthread.a ../../../../lib/libgmock.so.1.13.0 ../../../../lib/libgtest.so.1.13.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/basic-dp' [ 93%] Built target mdrun-vsites-test /usr/bin/make -f api/nblib/tests/CMakeFiles/nblib-tpr-test.dir/build.make api/nblib/tests/CMakeFiles/nblib-tpr-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/basic-dp' cd /build/reproducible-path/gromacs-2025.1/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.1 /build/reproducible-path/gromacs-2025.1/api/nblib/tests /build/reproducible-path/gromacs-2025.1/build/basic-dp /build/reproducible-path/gromacs-2025.1/build/basic-dp/api/nblib/tests /build/reproducible-path/gromacs-2025.1/build/basic-dp/api/nblib/tests/CMakeFiles/nblib-tpr-test.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/basic-dp' /usr/bin/make -f api/nblib/tests/CMakeFiles/nblib-tpr-test.dir/build.make api/nblib/tests/CMakeFiles/nblib-tpr-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/basic-dp' cd /build/reproducible-path/gromacs-2025.1/build/basic-dp/api/nblib/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"api/nblib/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.1/build/basic-dp/api/nblib/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/src/testutils/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/api/nblib/tests -I/build/reproducible-path/gromacs-2025.1/api/nblib/include -I/build/reproducible-path/gromacs-2025.1/api/nblib -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pbcutil/include 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/build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT api/nblib/tests/CMakeFiles/nblib-integrator-test.dir/__/__/__/src/testutils/unittest_main.cpp.o -MF CMakeFiles/nblib-integrator-test.dir/__/__/__/src/testutils/unittest_main.cpp.o.d -o CMakeFiles/nblib-integrator-test.dir/__/__/__/src/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic-dp/api/gmxapi/cpp/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"api/gmxapi/cpp/tests\" 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/usr/bin/cmake -E cmake_link_script CMakeFiles/nblib-integrator-test.dir/link.txt --verbose=1 cd /build/reproducible-path/gromacs-2025.1/build/basic-dp/api/nblib/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"api/nblib/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.1/build/basic-dp/api/nblib/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/api -I/build/reproducible-path/gromacs-2025.1/src/testutils/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/api/legacy/include 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/build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT api/nblib/tests/CMakeFiles/nblib-setup-test.dir/particletype.cpp.o -MF CMakeFiles/nblib-setup-test.dir/particletype.cpp.o.d -o CMakeFiles/nblib-setup-test.dir/particletype.cpp.o -c /build/reproducible-path/gromacs-2025.1/api/nblib/tests/particletype.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic-dp/api/nblib/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"api/nblib/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.1/build/basic-dp/api/nblib/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/src/testutils/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/api/nblib/tests -I/build/reproducible-path/gromacs-2025.1/api/nblib/include -I/build/reproducible-path/gromacs-2025.1/api/nblib -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem 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/build/reproducible-path/gromacs-2025.1/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic-dp/api/gmxapi/cpp/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"api/gmxapi/cpp/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.1/build/basic-dp/api/gmxapi/cpp/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/src/testutils/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/api/gmxapi/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/api/gmxapi/include -I/build/reproducible-path/gromacs-2025.1/api/gmxapi/cpp/tests -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT 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/lib/riscv64-linux-gnu/libpthread.a make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/basic-dp' [ 93%] Built target nblib-integrator-test cd /build/reproducible-path/gromacs-2025.1/build/basic-dp/api/nblib/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"api/nblib/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.1/build/basic-dp/api/nblib/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/api -I/build/reproducible-path/gromacs-2025.1/src/testutils/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include 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-I/build/reproducible-path/gromacs-2025.1/api -I/build/reproducible-path/gromacs-2025.1/src/testutils/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/api/nblib/tests -I/build/reproducible-path/gromacs-2025.1/api/nblib/include -I/build/reproducible-path/gromacs-2025.1/api/nblib -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -isystem 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CMakeFiles/nblib-setup-test.dir/nbnxmsetup.cpp.o -c /build/reproducible-path/gromacs-2025.1/api/nblib/tests/nbnxmsetup.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic-dp/api/gmxapi/cpp/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/gmxapi-test.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/nblib-tpr-test.dir/link.d "CMakeFiles/nblib-tpr-test.dir/tpr.cpp.o" "CMakeFiles/nblib-tpr-test.dir/__/__/__/src/testutils/unittest_main.cpp.o" -o ../../../bin/nblib-tpr-test ../../../lib/libtestutils.a ../../../lib/libmdrun_test_infrastructure.a ../../../lib/libnblib_test_infrastructure.a ../../../lib/libnblib_gmx.so.0.1.0 ../../../lib/libtestutils.a ../../../lib/libgmock.so.1.13.0 ../../../lib/libgtest.so.1.13.0 ../../../lib/libgromacs_d.so.10.0.0 /usr/lib/riscv64-linux-gnu/libm.so /usr/lib/gcc/riscv64-linux-gnu/14/libgomp.so /lib/riscv64-linux-gnu/libpthread.a make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/basic-dp' [ 93%] Built target nblib-tpr-test /usr/bin/make -f api/nblib/tests/CMakeFiles/nblib-integration-test.dir/build.make api/nblib/tests/CMakeFiles/nblib-integration-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/basic-dp' cd /build/reproducible-path/gromacs-2025.1/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.1 /build/reproducible-path/gromacs-2025.1/api/nblib/tests /build/reproducible-path/gromacs-2025.1/build/basic-dp /build/reproducible-path/gromacs-2025.1/build/basic-dp/api/nblib/tests /build/reproducible-path/gromacs-2025.1/build/basic-dp/api/nblib/tests/CMakeFiles/nblib-integration-test.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/basic-dp' /usr/bin/make -f api/nblib/tests/CMakeFiles/nblib-integration-test.dir/build.make api/nblib/tests/CMakeFiles/nblib-integration-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/basic-dp' cd /build/reproducible-path/gromacs-2025.1/build/basic-dp/api/nblib/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"api/nblib/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.1/build/basic-dp/api/nblib/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/src/testutils/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include 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-DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"api/nblib/listed_forces/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.1/build/basic-dp/api/nblib/listed_forces/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/src/testutils/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/api/nblib/tests -I/build/reproducible-path/gromacs-2025.1/api/nblib/include -I/build/reproducible-path/gromacs-2025.1/api/nblib -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pbcutil/include 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-Wno-missing-field-initializers -fopenmp -MD -MT api/nblib/listed_forces/tests/CMakeFiles/nblib-listed-forces-test.dir/bondtypes.cpp.o -MF CMakeFiles/nblib-listed-forces-test.dir/bondtypes.cpp.o.d -o CMakeFiles/nblib-listed-forces-test.dir/bondtypes.cpp.o -c /build/reproducible-path/gromacs-2025.1/api/nblib/listed_forces/tests/bondtypes.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic-dp/api/nblib/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"api/nblib/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.1/build/basic-dp/api/nblib/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/api -I/build/reproducible-path/gromacs-2025.1/src/testutils/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/include 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-Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/gmxapi-test.dir/link.d "CMakeFiles/gmxapi-test.dir/restraint.cpp.o" "CMakeFiles/gmxapi-test.dir/runner.cpp.o" "CMakeFiles/gmxapi-test.dir/status.cpp.o" "CMakeFiles/gmxapi-test.dir/stopsignaler.cpp.o" "CMakeFiles/gmxapi-test.dir/system.cpp.o" "CMakeFiles/gmxapi-test.dir/version.cpp.o" "CMakeFiles/gmxapi-test.dir/__/__/__/__/src/testutils/unittest_main.cpp.o" ../../../../src/programs/CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o ../../../../src/programs/CMakeFiles/mdrun_objlib.dir/mdrun/nonbonded_bench.cpp.o -o ../../../../bin/gmxapi-test ../../../../lib/libtestutils.a ../../../../lib/libgmxapi_d.so.0.4.0 ../../../../lib/libmdrun_test_infrastructure.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.10.0.0 /usr/lib/riscv64-linux-gnu/libm.so /usr/lib/gcc/riscv64-linux-gnu/14/libgomp.so /lib/riscv64-linux-gnu/libpthread.a ../../../../lib/libgmock.so.1.13.0 ../../../../lib/libgtest.so.1.13.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/basic-dp' [ 94%] Built target gmxapi-test /usr/bin/make -f api/nblib/util/tests/CMakeFiles/nblib-util-test.dir/build.make api/nblib/util/tests/CMakeFiles/nblib-util-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/basic-dp' cd /build/reproducible-path/gromacs-2025.1/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.1 /build/reproducible-path/gromacs-2025.1/api/nblib/util/tests /build/reproducible-path/gromacs-2025.1/build/basic-dp /build/reproducible-path/gromacs-2025.1/build/basic-dp/api/nblib/util/tests /build/reproducible-path/gromacs-2025.1/build/basic-dp/api/nblib/util/tests/CMakeFiles/nblib-util-test.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/basic-dp' /usr/bin/make -f api/nblib/util/tests/CMakeFiles/nblib-util-test.dir/build.make api/nblib/util/tests/CMakeFiles/nblib-util-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/basic-dp' cd /build/reproducible-path/gromacs-2025.1/build/basic-dp/api/nblib/util/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"api/nblib/util/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.1/build/basic-dp/api/nblib/util/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/src/testutils/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include 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api/nblib/listed_forces/tests/CMakeFiles/nblib-listed-forces-test.dir/gmxcalculator.cpp.o -MF CMakeFiles/nblib-listed-forces-test.dir/gmxcalculator.cpp.o.d -o CMakeFiles/nblib-listed-forces-test.dir/gmxcalculator.cpp.o -c /build/reproducible-path/gromacs-2025.1/api/nblib/listed_forces/tests/gmxcalculator.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic-dp/api/nblib/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"api/nblib/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.1/build/basic-dp/api/nblib/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/src/testutils/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/api/nblib/tests -I/build/reproducible-path/gromacs-2025.1/api/nblib/include -I/build/reproducible-path/gromacs-2025.1/api/nblib -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT api/nblib/tests/CMakeFiles/nblib-integration-test.dir/nbkernelsystem.cpp.o -MF CMakeFiles/nblib-integration-test.dir/nbkernelsystem.cpp.o.d -o CMakeFiles/nblib-integration-test.dir/nbkernelsystem.cpp.o -c /build/reproducible-path/gromacs-2025.1/api/nblib/tests/nbkernelsystem.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic-dp/api/nblib/util/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"api/nblib/util/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.1/build/basic-dp/api/nblib/util/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/src/testutils/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/api/nblib/tests -I/build/reproducible-path/gromacs-2025.1/api/nblib/include -I/build/reproducible-path/gromacs-2025.1/api/nblib -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT api/nblib/util/tests/CMakeFiles/nblib-util-test.dir/traits.cpp.o -MF CMakeFiles/nblib-util-test.dir/traits.cpp.o.d -o CMakeFiles/nblib-util-test.dir/traits.cpp.o -c /build/reproducible-path/gromacs-2025.1/api/nblib/util/tests/traits.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic-dp/api/nblib/listed_forces/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"api/nblib/listed_forces/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.1/build/basic-dp/api/nblib/listed_forces/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/src/testutils/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/api/legacy/include 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-isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT api/nblib/listed_forces/tests/CMakeFiles/nblib-listed-forces-test.dir/helpers.cpp.o -MF CMakeFiles/nblib-listed-forces-test.dir/helpers.cpp.o.d -o CMakeFiles/nblib-listed-forces-test.dir/helpers.cpp.o -c /build/reproducible-path/gromacs-2025.1/api/nblib/listed_forces/tests/helpers.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic-dp/api/nblib/util/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"api/nblib/util/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.1/build/basic-dp/api/nblib/util/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/src/testutils/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/api/nblib/tests -I/build/reproducible-path/gromacs-2025.1/api/nblib/include -I/build/reproducible-path/gromacs-2025.1/api/nblib -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT api/nblib/util/tests/CMakeFiles/nblib-util-test.dir/__/__/__/__/src/testutils/unittest_main.cpp.o -MF CMakeFiles/nblib-util-test.dir/__/__/__/__/src/testutils/unittest_main.cpp.o.d -o CMakeFiles/nblib-util-test.dir/__/__/__/__/src/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic-dp/api/nblib/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"api/nblib/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.1/build/basic-dp/api/nblib/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/src/testutils/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/api/nblib/tests -I/build/reproducible-path/gromacs-2025.1/api/nblib/include -I/build/reproducible-path/gromacs-2025.1/api/nblib -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT api/nblib/tests/CMakeFiles/nblib-integration-test.dir/simstate.cpp.o -MF CMakeFiles/nblib-integration-test.dir/simstate.cpp.o.d -o CMakeFiles/nblib-integration-test.dir/simstate.cpp.o -c /build/reproducible-path/gromacs-2025.1/api/nblib/tests/simstate.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic-dp/api/nblib/util/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/nblib-util-test.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/nblib-util-test.dir/link.d "CMakeFiles/nblib-util-test.dir/setup.cpp.o" "CMakeFiles/nblib-util-test.dir/traits.cpp.o" "CMakeFiles/nblib-util-test.dir/__/__/__/__/src/testutils/unittest_main.cpp.o" -o ../../../../bin/nblib-util-test ../../../../lib/libtestutils.a ../../../../lib/libnblib_test_infrastructure.a ../../../../lib/libnblib_gmx.so.0.1.0 ../../../../lib/libtestutils.a ../../../../lib/libgmock.so.1.13.0 ../../../../lib/libgtest.so.1.13.0 ../../../../lib/libgromacs_d.so.10.0.0 /usr/lib/riscv64-linux-gnu/libm.so /usr/lib/gcc/riscv64-linux-gnu/14/libgomp.so /lib/riscv64-linux-gnu/libpthread.a make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/basic-dp' [ 95%] Built target nblib-util-test /usr/bin/make -f src/gromacs/commandline/tests/CMakeFiles/commandline-test.dir/build.make src/gromacs/commandline/tests/CMakeFiles/commandline-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/basic-dp' cd /build/reproducible-path/gromacs-2025.1/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.1 /build/reproducible-path/gromacs-2025.1/src/gromacs/commandline/tests /build/reproducible-path/gromacs-2025.1/build/basic-dp /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/commandline/tests /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/commandline/tests/CMakeFiles/commandline-test.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/basic-dp' /usr/bin/make -f src/gromacs/commandline/tests/CMakeFiles/commandline-test.dir/build.make src/gromacs/commandline/tests/CMakeFiles/commandline-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/basic-dp' cd /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/commandline/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/commandline/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/commandline/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/src/testutils/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/commandline/tests/CMakeFiles/commandline-test.dir/cmdlinehelpmodule.cpp.o -MF CMakeFiles/commandline-test.dir/cmdlinehelpmodule.cpp.o.d -o CMakeFiles/commandline-test.dir/cmdlinehelpmodule.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/commandline/tests/cmdlinehelpmodule.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic-dp/api/nblib/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"api/nblib/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.1/build/basic-dp/api/nblib/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/src/testutils/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/api/nblib/tests -I/build/reproducible-path/gromacs-2025.1/api/nblib/include -I/build/reproducible-path/gromacs-2025.1/api/nblib 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-I/build/reproducible-path/gromacs-2025.1/src/testutils/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/api/nblib/tests -I/build/reproducible-path/gromacs-2025.1/api/nblib/include -I/build/reproducible-path/gromacs-2025.1/api/nblib -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/timing/include -isystem 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/build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/commandline/tests/CMakeFiles/commandline-test.dir/cmdlinemodulemanager.cpp.o -MF CMakeFiles/commandline-test.dir/cmdlinemodulemanager.cpp.o.d -o CMakeFiles/commandline-test.dir/cmdlinemodulemanager.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/commandline/tests/cmdlinemodulemanager.cpp /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/nblib-integration-test.dir/link.d "CMakeFiles/nblib-integration-test.dir/gmxcalculator.cpp.o" "CMakeFiles/nblib-integration-test.dir/nbkernelsystem.cpp.o" "CMakeFiles/nblib-integration-test.dir/simstate.cpp.o" "CMakeFiles/nblib-integration-test.dir/__/__/__/src/testutils/unittest_main.cpp.o" -o ../../../bin/nblib-integration-test ../../../lib/libtestutils.a ../../../lib/libnblib_test_infrastructure.a ../../../lib/libnblib_gmx.so.0.1.0 ../../../lib/libtestutils.a ../../../lib/libgmock.so.1.13.0 ../../../lib/libgtest.so.1.13.0 ../../../lib/libgromacs_d.so.10.0.0 /usr/lib/riscv64-linux-gnu/libm.so /usr/lib/gcc/riscv64-linux-gnu/14/libgomp.so /lib/riscv64-linux-gnu/libpthread.a make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/basic-dp' [ 96%] Built target nblib-integration-test cd /build/reproducible-path/gromacs-2025.1/build/basic-dp/api/nblib/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"api/nblib/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.1/build/basic-dp/api/nblib/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/api -I/build/reproducible-path/gromacs-2025.1/src/testutils/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/api/nblib/tests -I/build/reproducible-path/gromacs-2025.1/api/nblib/include -I/build/reproducible-path/gromacs-2025.1/api/nblib -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG 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-I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/api/nblib/tests -I/build/reproducible-path/gromacs-2025.1/api/nblib/include -I/build/reproducible-path/gromacs-2025.1/api/nblib -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/timing/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/external/muparser -isystem 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/usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"api/nblib/listed_forces/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.1/build/basic-dp/api/nblib/listed_forces/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/src/testutils/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/api/nblib/tests -I/build/reproducible-path/gromacs-2025.1/api/nblib/include -I/build/reproducible-path/gromacs-2025.1/api/nblib 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-O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT api/nblib/listed_forces/tests/CMakeFiles/nblib-listed-forces-test.dir/typetests.cpp.o -MF CMakeFiles/nblib-listed-forces-test.dir/typetests.cpp.o.d -o CMakeFiles/nblib-listed-forces-test.dir/typetests.cpp.o -c /build/reproducible-path/gromacs-2025.1/api/nblib/listed_forces/tests/typetests.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic-dp/api/nblib/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/nblib-setup-test.dir/link.txt --verbose=1 /usr/bin/make -f src/gromacs/mdrunutility/tests/CMakeFiles/mdrunutility-test.dir/build.make src/gromacs/mdrunutility/tests/CMakeFiles/mdrunutility-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/basic-dp' cd /build/reproducible-path/gromacs-2025.1/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.1 /build/reproducible-path/gromacs-2025.1/src/gromacs/mdrunutility/tests /build/reproducible-path/gromacs-2025.1/build/basic-dp /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/mdrunutility/tests /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/mdrunutility/tests/CMakeFiles/mdrunutility-test.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/basic-dp' /usr/bin/make -f src/gromacs/mdrunutility/tests/CMakeFiles/mdrunutility-test.dir/build.make src/gromacs/mdrunutility/tests/CMakeFiles/mdrunutility-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/basic-dp' cd /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/mdrunutility/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdrunutility/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/mdrunutility/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/src/testutils/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/mdrunutility/tests/CMakeFiles/mdrunutility-test.dir/mdmodulesnotifier.cpp.o -MF CMakeFiles/mdrunutility-test.dir/mdmodulesnotifier.cpp.o.d -o CMakeFiles/mdrunutility-test.dir/mdmodulesnotifier.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/mdrunutility/tests/mdmodulesnotifier.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/mdrunutility/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdrunutility/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/mdrunutility/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/src/testutils/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/mdrunutility/tests/CMakeFiles/mdrunutility-test.dir/threadaffinity.cpp.o -MF CMakeFiles/mdrunutility-test.dir/threadaffinity.cpp.o.d -o CMakeFiles/mdrunutility-test.dir/threadaffinity.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/mdrunutility/tests/threadaffinity.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/commandline/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/commandline/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/commandline/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/src/testutils/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/commandline/tests/CMakeFiles/commandline-test.dir/cmdlinemodulemanagertest.cpp.o -MF CMakeFiles/commandline-test.dir/cmdlinemodulemanagertest.cpp.o.d -o CMakeFiles/commandline-test.dir/cmdlinemodulemanagertest.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/commandline/tests/cmdlinemodulemanagertest.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic-dp/api/nblib/listed_forces/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"api/nblib/listed_forces/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.1/build/basic-dp/api/nblib/listed_forces/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/src/testutils/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/api/nblib/tests -I/build/reproducible-path/gromacs-2025.1/api/nblib/include -I/build/reproducible-path/gromacs-2025.1/api/nblib -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/timing/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT api/nblib/listed_forces/tests/CMakeFiles/nblib-listed-forces-test.dir/calculator.cpp.o -MF CMakeFiles/nblib-listed-forces-test.dir/calculator.cpp.o.d -o CMakeFiles/nblib-listed-forces-test.dir/calculator.cpp.o -c /build/reproducible-path/gromacs-2025.1/api/nblib/listed_forces/tests/calculator.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/mdrunutility/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdrunutility/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/mdrunutility/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/src/testutils/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/mdrunutility/tests/CMakeFiles/mdrunutility-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/mdrunutility-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/mdrunutility-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/testutils/unittest_main.cpp /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/nblib-setup-test.dir/link.d "CMakeFiles/nblib-setup-test.dir/box.cpp.o" "CMakeFiles/nblib-setup-test.dir/interactions.cpp.o" "CMakeFiles/nblib-setup-test.dir/particletype.cpp.o" "CMakeFiles/nblib-setup-test.dir/pbcholder.cpp.o" "CMakeFiles/nblib-setup-test.dir/molecules.cpp.o" "CMakeFiles/nblib-setup-test.dir/nbnxmsetup.cpp.o" "CMakeFiles/nblib-setup-test.dir/topology.cpp.o" "CMakeFiles/nblib-setup-test.dir/virials.cpp.o" "CMakeFiles/nblib-setup-test.dir/__/__/__/src/testutils/unittest_main.cpp.o" -o ../../../bin/nblib-setup-test ../../../lib/libtestutils.a ../../../lib/libmdrun_test_infrastructure.a ../../../lib/libnblib_test_infrastructure.a ../../../lib/libnblib_gmx.so.0.1.0 ../../../lib/libtestutils.a ../../../lib/libgmock.so.1.13.0 ../../../lib/libgtest.so.1.13.0 ../../../lib/libgromacs_d.so.10.0.0 /usr/lib/riscv64-linux-gnu/libm.so /usr/lib/gcc/riscv64-linux-gnu/14/libgomp.so /lib/riscv64-linux-gnu/libpthread.a make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/basic-dp' [ 96%] Built target nblib-setup-test /usr/bin/make -f src/gromacs/mdrunutility/tests/CMakeFiles/mdrunutility-mpi-test.dir/build.make src/gromacs/mdrunutility/tests/CMakeFiles/mdrunutility-mpi-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/basic-dp' cd /build/reproducible-path/gromacs-2025.1/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.1 /build/reproducible-path/gromacs-2025.1/src/gromacs/mdrunutility/tests /build/reproducible-path/gromacs-2025.1/build/basic-dp /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/mdrunutility/tests /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/mdrunutility/tests/CMakeFiles/mdrunutility-mpi-test.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/basic-dp' /usr/bin/make -f src/gromacs/mdrunutility/tests/CMakeFiles/mdrunutility-mpi-test.dir/build.make src/gromacs/mdrunutility/tests/CMakeFiles/mdrunutility-mpi-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/basic-dp' cd /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/mdrunutility/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdrunutility/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/mdrunutility/tests/Testing/Temporary\" -DTEST_USES_MPI=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/src/testutils/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/mdrunutility/tests/CMakeFiles/mdrunutility-mpi-test.dir/threadaffinity_mpi.cpp.o -MF CMakeFiles/mdrunutility-mpi-test.dir/threadaffinity_mpi.cpp.o.d -o CMakeFiles/mdrunutility-mpi-test.dir/threadaffinity_mpi.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/mdrunutility/tests/threadaffinity_mpi.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/mdrunutility/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/mdrunutility-test.dir/link.txt --verbose=1 cd /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/commandline/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/commandline/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/commandline/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/src/testutils/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/commandline/tests/CMakeFiles/commandline-test.dir/cmdlineparser.cpp.o -MF CMakeFiles/commandline-test.dir/cmdlineparser.cpp.o.d -o CMakeFiles/commandline-test.dir/cmdlineparser.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/commandline/tests/cmdlineparser.cpp /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/mdrunutility-test.dir/link.d "CMakeFiles/mdrunutility-test.dir/mdmodulesnotifier.cpp.o" "CMakeFiles/mdrunutility-test.dir/threadaffinity.cpp.o" "CMakeFiles/mdrunutility-test.dir/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../bin/mdrunutility-test ../../../../lib/libtestutils.a ../../../../lib/libmdrunutility-test-shared.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.10.0.0 /usr/lib/riscv64-linux-gnu/libm.so /usr/lib/gcc/riscv64-linux-gnu/14/libgomp.so /lib/riscv64-linux-gnu/libpthread.a ../../../../lib/libgmock.so.1.13.0 ../../../../lib/libgtest.so.1.13.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/basic-dp' [ 96%] Built target mdrunutility-test /usr/bin/make -f src/gromacs/analysisdata/tests/CMakeFiles/analysisdata-test.dir/build.make src/gromacs/analysisdata/tests/CMakeFiles/analysisdata-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/basic-dp' cd /build/reproducible-path/gromacs-2025.1/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.1 /build/reproducible-path/gromacs-2025.1/src/gromacs/analysisdata/tests /build/reproducible-path/gromacs-2025.1/build/basic-dp /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/analysisdata/tests /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/analysisdata/tests/CMakeFiles/analysisdata-test.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/basic-dp' /usr/bin/make -f src/gromacs/analysisdata/tests/CMakeFiles/analysisdata-test.dir/build.make src/gromacs/analysisdata/tests/CMakeFiles/analysisdata-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/basic-dp' cd /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/analysisdata/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H 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/build/reproducible-path/gromacs-2025.1/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/mdrunutility/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/mdrunutility-mpi-test.dir/link.txt --verbose=1 cd /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/commandline/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/commandline/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/commandline/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/src/testutils/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include 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-Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/commandline/tests/CMakeFiles/commandline-test.dir/cmdlineprogramcontext.cpp.o -MF CMakeFiles/commandline-test.dir/cmdlineprogramcontext.cpp.o.d -o CMakeFiles/commandline-test.dir/cmdlineprogramcontext.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/commandline/tests/cmdlineprogramcontext.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic-dp/api/nblib/listed_forces/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"api/nblib/listed_forces/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.1/build/basic-dp/api/nblib/listed_forces/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/src/testutils/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.1/src 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/build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT api/nblib/listed_forces/tests/CMakeFiles/nblib-listed-forces-test.dir/conversions.cpp.o -MF CMakeFiles/nblib-listed-forces-test.dir/conversions.cpp.o.d -o CMakeFiles/nblib-listed-forces-test.dir/conversions.cpp.o -c /build/reproducible-path/gromacs-2025.1/api/nblib/listed_forces/tests/conversions.cpp /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/mdrunutility-mpi-test.dir/link.d "CMakeFiles/mdrunutility-mpi-test.dir/threadaffinity_mpi.cpp.o" "CMakeFiles/mdrunutility-mpi-test.dir/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../bin/mdrunutility-mpi-test ../../../../lib/libtestutils.a ../../../../lib/libmdrunutility-test-shared.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.10.0.0 /usr/lib/riscv64-linux-gnu/libm.so /usr/lib/gcc/riscv64-linux-gnu/14/libgomp.so /lib/riscv64-linux-gnu/libpthread.a ../../../../lib/libgmock.so.1.13.0 ../../../../lib/libgtest.so.1.13.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/basic-dp' [ 96%] Built target mdrunutility-mpi-test /usr/bin/make -f src/gromacs/trajectoryanalysis/tests/CMakeFiles/trajectoryanalysis-test.dir/build.make src/gromacs/trajectoryanalysis/tests/CMakeFiles/trajectoryanalysis-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/basic-dp' cd /build/reproducible-path/gromacs-2025.1/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.1 /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests /build/reproducible-path/gromacs-2025.1/build/basic-dp /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/trajectoryanalysis/tests /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/trajectoryanalysis/tests/CMakeFiles/trajectoryanalysis-test.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/basic-dp' /usr/bin/make -f src/gromacs/trajectoryanalysis/tests/CMakeFiles/trajectoryanalysis-test.dir/build.make src/gromacs/trajectoryanalysis/tests/CMakeFiles/trajectoryanalysis-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/basic-dp' cd /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/trajectoryanalysis/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/trajectoryanalysis/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/trajectoryanalysis/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/src/testutils/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -isystem 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/usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/trajectoryanalysis/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/trajectoryanalysis/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/src/testutils/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/trajectoryanalysis/tests/CMakeFiles/trajectoryanalysis-test.dir/convert_trj.cpp.o -MF CMakeFiles/trajectoryanalysis-test.dir/convert_trj.cpp.o.d -o CMakeFiles/trajectoryanalysis-test.dir/convert_trj.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/convert_trj.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic-dp/api/nblib/listed_forces/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"api/nblib/listed_forces/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.1/build/basic-dp/api/nblib/listed_forces/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/src/testutils/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/api/nblib/tests -I/build/reproducible-path/gromacs-2025.1/api/nblib/include -I/build/reproducible-path/gromacs-2025.1/api/nblib -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/timing/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT api/nblib/listed_forces/tests/CMakeFiles/nblib-listed-forces-test.dir/shiftforces.cpp.o -MF CMakeFiles/nblib-listed-forces-test.dir/shiftforces.cpp.o.d -o CMakeFiles/nblib-listed-forces-test.dir/shiftforces.cpp.o -c /build/reproducible-path/gromacs-2025.1/api/nblib/listed_forces/tests/shiftforces.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/trajectoryanalysis/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/trajectoryanalysis/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/trajectoryanalysis/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/src/testutils/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/trajectoryanalysis/tests/CMakeFiles/trajectoryanalysis-test.dir/distance.cpp.o -MF CMakeFiles/trajectoryanalysis-test.dir/distance.cpp.o.d -o CMakeFiles/trajectoryanalysis-test.dir/distance.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/distance.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic-dp/api/nblib/listed_forces/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"api/nblib/listed_forces/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.1/build/basic-dp/api/nblib/listed_forces/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/src/testutils/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/api/nblib/tests -I/build/reproducible-path/gromacs-2025.1/api/nblib/include -I/build/reproducible-path/gromacs-2025.1/api/nblib -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/timing/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT api/nblib/listed_forces/tests/CMakeFiles/nblib-listed-forces-test.dir/transformations.cpp.o -MF CMakeFiles/nblib-listed-forces-test.dir/transformations.cpp.o.d -o CMakeFiles/nblib-listed-forces-test.dir/transformations.cpp.o -c /build/reproducible-path/gromacs-2025.1/api/nblib/listed_forces/tests/transformations.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/trajectoryanalysis/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/trajectoryanalysis/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/trajectoryanalysis/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/src/testutils/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/trajectoryanalysis/tests/CMakeFiles/trajectoryanalysis-test.dir/dssp.cpp.o -MF CMakeFiles/trajectoryanalysis-test.dir/dssp.cpp.o.d -o CMakeFiles/trajectoryanalysis-test.dir/dssp.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/dssp.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/analysisdata/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/analysisdata/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/analysisdata/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/src/testutils/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/analysisdata/tests/CMakeFiles/analysisdata-test.dir/lifetime.cpp.o -MF CMakeFiles/analysisdata-test.dir/lifetime.cpp.o.d -o CMakeFiles/analysisdata-test.dir/lifetime.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/analysisdata/tests/lifetime.cpp /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/commandline-test.dir/link.d "CMakeFiles/commandline-test.dir/cmdlinehelpmodule.cpp.o" "CMakeFiles/commandline-test.dir/cmdlinehelpwriter.cpp.o" "CMakeFiles/commandline-test.dir/cmdlinemodulemanager.cpp.o" "CMakeFiles/commandline-test.dir/cmdlinemodulemanagertest.cpp.o" "CMakeFiles/commandline-test.dir/cmdlineparser.cpp.o" "CMakeFiles/commandline-test.dir/cmdlineprogramcontext.cpp.o" "CMakeFiles/commandline-test.dir/filenm.cpp.o" "CMakeFiles/commandline-test.dir/pargs.cpp.o" "CMakeFiles/commandline-test.dir/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../bin/commandline-test ../../../../lib/libtestutils.a ../../../../lib/libonlinehelp-test-shared.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.10.0.0 /usr/lib/riscv64-linux-gnu/libm.so /usr/lib/gcc/riscv64-linux-gnu/14/libgomp.so /lib/riscv64-linux-gnu/libpthread.a ../../../../lib/libgmock.so.1.13.0 ../../../../lib/libgtest.so.1.13.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/basic-dp' [ 97%] Built target commandline-test /usr/bin/make -f api/nblib/CMakeFiles/nblib-tests.dir/build.make api/nblib/CMakeFiles/nblib-tests.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/basic-dp' cd /build/reproducible-path/gromacs-2025.1/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.1 /build/reproducible-path/gromacs-2025.1/api/nblib /build/reproducible-path/gromacs-2025.1/build/basic-dp /build/reproducible-path/gromacs-2025.1/build/basic-dp/api/nblib /build/reproducible-path/gromacs-2025.1/build/basic-dp/api/nblib/CMakeFiles/nblib-tests.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/basic-dp' /usr/bin/make -f api/nblib/CMakeFiles/nblib-tests.dir/build.make api/nblib/CMakeFiles/nblib-tests.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/basic-dp' make[4]: Nothing to be done for 'api/nblib/CMakeFiles/nblib-tests.dir/build'. make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/basic-dp' [ 97%] Built target nblib-tests cd /build/reproducible-path/gromacs-2025.1/build/basic-dp/api/nblib/listed_forces/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"api/nblib/listed_forces/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.1/build/basic-dp/api/nblib/listed_forces/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/src/testutils/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/api/nblib/tests -I/build/reproducible-path/gromacs-2025.1/api/nblib/include -I/build/reproducible-path/gromacs-2025.1/api/nblib -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/timing/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 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/build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/unionfind.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/trajectoryanalysis/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/trajectoryanalysis/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/trajectoryanalysis/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/src/testutils/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/api/legacy/include 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src/gromacs/trajectoryanalysis/tests/CMakeFiles/trajectoryanalysis-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/trajectoryanalysis-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/trajectoryanalysis-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/trajectoryanalysis/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/trajectoryanalysis-test.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/trajectoryanalysis-test.dir/link.d "CMakeFiles/trajectoryanalysis-test.dir/moduletest.cpp.o" "CMakeFiles/trajectoryanalysis-test.dir/angle.cpp.o" "CMakeFiles/trajectoryanalysis-test.dir/clustsize.cpp.o" "CMakeFiles/trajectoryanalysis-test.dir/cmdlinerunner.cpp.o" "CMakeFiles/trajectoryanalysis-test.dir/convert_trj.cpp.o" "CMakeFiles/trajectoryanalysis-test.dir/distance.cpp.o" "CMakeFiles/trajectoryanalysis-test.dir/dssp.cpp.o" "CMakeFiles/trajectoryanalysis-test.dir/extract_cluster.cpp.o" "CMakeFiles/trajectoryanalysis-test.dir/freevolume.cpp.o" "CMakeFiles/trajectoryanalysis-test.dir/gyrate.cpp.o" "CMakeFiles/trajectoryanalysis-test.dir/hbond.cpp.o" "CMakeFiles/trajectoryanalysis-test.dir/msd.cpp.o" "CMakeFiles/trajectoryanalysis-test.dir/pairdist.cpp.o" "CMakeFiles/trajectoryanalysis-test.dir/rdf.cpp.o" "CMakeFiles/trajectoryanalysis-test.dir/sasa.cpp.o" "CMakeFiles/trajectoryanalysis-test.dir/select.cpp.o" "CMakeFiles/trajectoryanalysis-test.dir/scattering.cpp.o" "CMakeFiles/trajectoryanalysis-test.dir/surfacearea.cpp.o" "CMakeFiles/trajectoryanalysis-test.dir/topologyinformation.cpp.o" "CMakeFiles/trajectoryanalysis-test.dir/trajectory.cpp.o" "CMakeFiles/trajectoryanalysis-test.dir/unionfind.cpp.o" "CMakeFiles/trajectoryanalysis-test.dir/__/__/__/testutils/unittest_main.cpp.o" ../../../programs/CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o ../../../programs/CMakeFiles/mdrun_objlib.dir/mdrun/nonbonded_bench.cpp.o -o ../../../../bin/trajectoryanalysis-test ../../../../lib/libtestutils.a ../../../../lib/libanalysisdata-test-shared.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.10.0.0 /usr/lib/riscv64-linux-gnu/libm.so /usr/lib/gcc/riscv64-linux-gnu/14/libgomp.so /lib/riscv64-linux-gnu/libpthread.a ../../../../lib/libgmock.so.1.13.0 ../../../../lib/libgtest.so.1.13.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/basic-dp' [100%] Built target trajectoryanalysis-test /usr/bin/make -f CMakeFiles/tests.dir/build.make CMakeFiles/tests.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/basic-dp' cd /build/reproducible-path/gromacs-2025.1/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.1 /build/reproducible-path/gromacs-2025.1 /build/reproducible-path/gromacs-2025.1/build/basic-dp /build/reproducible-path/gromacs-2025.1/build/basic-dp /build/reproducible-path/gromacs-2025.1/build/basic-dp/CMakeFiles/tests.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/basic-dp' /usr/bin/make -f CMakeFiles/tests.dir/build.make CMakeFiles/tests.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/basic-dp' make[4]: Nothing to be done for 'CMakeFiles/tests.dir/build'. make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/basic-dp' [100%] Built target tests make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/basic-dp' /usr/bin/cmake -E cmake_progress_start /build/reproducible-path/gromacs-2025.1/build/basic-dp/CMakeFiles 0 make[2]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/basic-dp' make[1]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/basic-dp' (cd build/basic-dp; LD_LIBRARY_PATH=/build/reproducible-path/gromacs-2025.1/build/basic-dp/lib ctest -V) UpdateCTestConfiguration from :/build/reproducible-path/gromacs-2025.1/build/basic-dp/DartConfiguration.tcl Parse Config file:/build/reproducible-path/gromacs-2025.1/build/basic-dp/DartConfiguration.tcl UpdateCTestConfiguration from :/build/reproducible-path/gromacs-2025.1/build/basic-dp/DartConfiguration.tcl Parse Config file:/build/reproducible-path/gromacs-2025.1/build/basic-dp/DartConfiguration.tcl Test project /build/reproducible-path/gromacs-2025.1/build/basic-dp Constructing a list of tests Done constructing a list of tests Updating test list for fixtures Added 0 tests to meet fixture requirements Checking test dependency graph... Checking test dependency graph end test 1 Start 1: GmxapiExternalInterfaceTests 1: Test command: /build/reproducible-path/gromacs-2025.1/build/basic-dp/bin/gmxapi-test "-ntomp" "2" "--gtest_output=xml:/build/reproducible-path/gromacs-2025.1/build/basic-dp/Testing/Temporary/GmxapiExternalInterfaceTests.xml" 1: Working Directory: /build/reproducible-path/gromacs-2025.1/build/basic-dp/api/gmxapi/cpp/tests 1: Test timeout computed to be: 600 1: [==========] Running 9 tests from 1 test suite. 1: [----------] Global test environment set-up. 1: [----------] 9 tests from GmxApiTest 1: [ RUN ] GmxApiTest.ApiRunnerRestrainedMD 1: Generating 1-4 interactions: fudge = 0.5 1: 1: NOTE 1 [file spc_and_methane.top, line 33]: 1: The bond in molecule-type methane between atoms 1 C and 2 H1 has an 1: estimated oscillational period of 1.1e-02 ps, which is less than 10 times 1: the time step of 2.0e-03 ps. 1: Maybe you forgot to change the constraints mdp option. 1: 1: Number of degrees of freedom in T-Coupling group System is 18.00 1: 1: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/api/gmxapi/cpp/tests/Testing/Temporary/GmxApiTest_ApiRunnerRestrainedMD_input.mdp]: 1: You are using a plain Coulomb cut-off, which might produce artifacts. 1: You might want to consider using PME electrostatics. 1: 1: 1: 1: There were 2 NOTEs 1: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/api/gmxapi/cpp/tests/Testing/Temporary/GmxApiTest_ApiRunnerRestrainedMD.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 1: Changing nstlist from 10 to 25, rlist from 1.057 to 1.183 1: 1: Using 1 MPI thread 1: Using 2 OpenMP threads 1: 1: 1: NOTE: The number of threads is not equal to the number of (logical) cpus 1: and the -pin option is set to auto: will not pin threads to cpus. 1: This can lead to significant performance degradation. 1: Consider using -pin on (and -pinoffset in case you run multiple jobs). 1: starting mdrun 'Water and methane' 1: 2 steps, 0.0 ps. 1: Setting the LD random seed to 1058932590 1: 1: Generated 331705 of the 331705 non-bonded parameter combinations 1: 1: Generated 331705 of the 331705 1-4 parameter combinations 1: 1: Excluding 2 bonded neighbours molecule type 'SOL' 1: 1: Excluding 3 bonded neighbours molecule type 'methane' 1: 1: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/spc_and_methane.gro' 1: 1: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 1: 1: Calculated rlist for 1x1 atom pair-list as 1.077 nm, buffer size 0.077 nm 1: 1: Set rlist, assuming 4x4 atom pair-list, to 1.057 nm, buffer size 0.057 nm 1: 1: Note that mdrun will redetermine rlist based on the actual pair-list setup 1: 1: This run will generate roughly 0 Mb of data 1: 1: Writing final coordinates. 1: 1: Core t (s) Wall t (s) (%) 1: Time: 0.065 0.033 198.1 1: (ns/day) (hour/ns) 1: Performance: 15.483 1.550 1: [ OK ] GmxApiTest.ApiRunnerRestrainedMD (6084 ms) 1: [ RUN ] GmxApiTest.RunnerBasicMD 1: Generating 1-4 interactions: fudge = 0.5 1: 1: NOTE 1 [file spc_and_methane.top, line 33]: 1: The bond in molecule-type methane between atoms 1 C and 2 H1 has an 1: estimated oscillational period of 1.1e-02 ps, which is less than 10 times 1: the time step of 2.0e-03 ps. 1: Maybe you forgot to change the constraints mdp option. 1: 1: Number of degrees of freedom in T-Coupling group System is 18.00 1: 1: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/api/gmxapi/cpp/tests/Testing/Temporary/GmxApiTest_RunnerBasicMD_input.mdp]: 1: You are using a plain Coulomb cut-off, which might produce artifacts. 1: You might want to consider using PME electrostatics. 1: 1: 1: 1: There were 2 NOTEs 1: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/api/gmxapi/cpp/tests/Testing/Temporary/GmxApiTest_RunnerBasicMD.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 1: Changing nstlist from 10 to 25, rlist from 1.057 to 1.183 1: 1: Using 1 MPI thread 1: Using 2 OpenMP threads 1: 1: 1: NOTE: The number of threads is not equal to the number of (logical) cpus 1: and the -pin option is set to auto: will not pin threads to cpus. 1: This can lead to significant performance degradation. 1: Consider using -pin on (and -pinoffset in case you run multiple jobs). 1: starting mdrun 'Water and methane' 1: 2 steps, 0.0 ps. 1: Setting the LD random seed to -1831938362 1: 1: Generated 331705 of the 331705 non-bonded parameter combinations 1: 1: Generated 331705 of the 331705 1-4 parameter combinations 1: 1: Excluding 2 bonded neighbours molecule type 'SOL' 1: 1: Excluding 3 bonded neighbours molecule type 'methane' 1: 1: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/spc_and_methane.gro' 1: 1: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 1: 1: Calculated rlist for 1x1 atom pair-list as 1.077 nm, buffer size 0.077 nm 1: 1: Set rlist, assuming 4x4 atom pair-list, to 1.057 nm, buffer size 0.057 nm 1: 1: Note that mdrun will redetermine rlist based on the actual pair-list setup 1: 1: This run will generate roughly 0 Mb of data 1: 1: Writing final coordinates. 1: 1: Core t (s) Wall t (s) (%) 1: Time: 0.057 0.029 197.6 1: (ns/day) (hour/ns) 1: Performance: 17.542 1.368 1: [ OK ] GmxApiTest.RunnerBasicMD (5941 ms) 1: [ RUN ] GmxApiTest.RunnerReinitialize 1: Generating 1-4 interactions: fudge = 0.5 1: 1: NOTE 1 [file spc_and_methane.top, line 33]: 1: The bond in molecule-type methane between atoms 1 C and 2 H1 has an 1: estimated oscillational period of 1.1e-02 ps, which is less than 10 times 1: the time step of 2.0e-03 ps. 1: Maybe you forgot to change the constraints mdp option. 1: 1: Number of degrees of freedom in T-Coupling group System is 18.00 1: 1: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/api/gmxapi/cpp/tests/Testing/Temporary/GmxApiTest_RunnerReinitialize_input.mdp]: 1: You are using a plain Coulomb cut-off, which might produce artifacts. 1: You might want to consider using PME electrostatics. 1: 1: 1: 1: There were 2 NOTEs 1: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/api/gmxapi/cpp/tests/Testing/Temporary/GmxApiTest_RunnerReinitialize.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 1: Changing nstlist from 10 to 25, rlist from 1.057 to 1.183 1: 1: Using 1 MPI thread 1: Using 2 OpenMP threads 1: 1: 1: NOTE: The number of threads is not equal to the number of (logical) cpus 1: and the -pin option is set to auto: will not pin threads to cpus. 1: This can lead to significant performance degradation. 1: Consider using -pin on (and -pinoffset in case you run multiple jobs). 1: starting mdrun 'Water and methane' 1: 20 steps, 0.0 ps. 1: 1: 1: Received the remote INT/TERM signal, stopping within 200 steps 1: 1: Setting the LD random seed to -1074810900 1: 1: Generated 331705 of the 331705 non-bonded parameter combinations 1: 1: Generated 331705 of the 331705 1-4 parameter combinations 1: 1: Excluding 2 bonded neighbours molecule type 'SOL' 1: 1: Excluding 3 bonded neighbours molecule type 'methane' 1: 1: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/spc_and_methane.gro' 1: 1: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 1: 1: Calculated rlist for 1x1 atom pair-list as 1.077 nm, buffer size 0.077 nm 1: 1: Set rlist, assuming 4x4 atom pair-list, to 1.057 nm, buffer size 0.057 nm 1: 1: Note that mdrun will redetermine rlist based on the actual pair-list setup 1: 1: This run will generate roughly 0 Mb of data 1: 1: Writing final coordinates. 1: 1: Core t (s) Wall t (s) (%) 1: Time: 0.061 0.032 194.4 1: (ns/day) (hour/ns) 1: Performance: 112.059 0.214 1: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/api/gmxapi/cpp/tests/Testing/Temporary/GmxApiTest_RunnerReinitialize.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 1: Changing nstlist from 10 to 25, rlist from 1.057 to 1.183 1: 1: Using 1 MPI thread 1: Using 2 OpenMP threads 1: 1: 1: NOTE: The number of threads is not equal to the number of (logical) cpus 1: and the -pin option is set to auto: will not pin threads to cpus. 1: This can lead to significant performance degradation. 1: Consider using -pin on (and -pinoffset in case you run multiple jobs). 1: starting mdrun 'Water and methane' 1: 20 steps, 0.0 ps. 1: 1: Writing final coordinates. 1: 1: Core t (s) Wall t (s) (%) 1: Time: 0.049 0.025 197.6 1: (ns/day) (hour/ns) 1: Performance: 143.984 0.167 1: [ OK ] GmxApiTest.RunnerReinitialize (5959 ms) 1: [ RUN ] GmxApiTest.RunnerChainedMD 1: Generating 1-4 interactions: fudge = 0.5 1: 1: NOTE 1 [file spc_and_methane.top, line 33]: 1: The bond in molecule-type methane between atoms 1 C and 2 H1 has an 1: estimated oscillational period of 1.1e-02 ps, which is less than 10 times 1: the time step of 2.0e-03 ps. 1: Maybe you forgot to change the constraints mdp option. 1: 1: Number of degrees of freedom in T-Coupling group System is 18.00 1: 1: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/api/gmxapi/cpp/tests/Testing/Temporary/GmxApiTest_RunnerChainedMD_input.mdp]: 1: You are using a plain Coulomb cut-off, which might produce artifacts. 1: You might want to consider using PME electrostatics. 1: 1: 1: 1: There were 2 NOTEs 1: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/api/gmxapi/cpp/tests/Testing/Temporary/GmxApiTest_RunnerChainedMD.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 1: Changing nstlist from 10 to 25, rlist from 1.057 to 1.183 1: 1: Using 1 MPI thread 1: Using 2 OpenMP threads 1: 1: 1: NOTE: The number of threads is not equal to the number of (logical) cpus 1: and the -pin option is set to auto: will not pin threads to cpus. 1: This can lead to significant performance degradation. 1: Consider using -pin on (and -pinoffset in case you run multiple jobs). 1: starting mdrun 'Water and methane' 1: 2 steps, 0.0 ps. 1: Setting the LD random seed to -1654702083 1: 1: Generated 331705 of the 331705 non-bonded parameter combinations 1: 1: Generated 331705 of the 331705 1-4 parameter combinations 1: 1: Excluding 2 bonded neighbours molecule type 'SOL' 1: 1: Excluding 3 bonded neighbours molecule type 'methane' 1: 1: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/spc_and_methane.gro' 1: 1: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 1: 1: Calculated rlist for 1x1 atom pair-list as 1.077 nm, buffer size 0.077 nm 1: 1: Set rlist, assuming 4x4 atom pair-list, to 1.057 nm, buffer size 0.057 nm 1: 1: Note that mdrun will redetermine rlist based on the actual pair-list setup 1: 1: This run will generate roughly 0 Mb of data 1: 1: Writing final coordinates. 1: 1: Core t (s) Wall t (s) (%) 1: Time: 0.051 0.026 197.6 1: (ns/day) (hour/ns) 1: Performance: 19.775 1.214 1: trr version: GMX_trn_file (double precision) 1: 1: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/api/gmxapi/cpp/tests/Testing/Temporary/GmxApiTest_RunnerChainedMD.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 1: Setting nsteps to 4 1: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/api/gmxapi/cpp/tests/Testing/Temporary/GmxApiTest_RunnerChainedMD.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 1: Changing nstlist from 10 to 25, rlist from 1.057 to 1.183 1: 1: Using 1 MPI thread 1: Using 2 OpenMP threads 1: 1: 1: NOTE: The number of threads is not equal to the number of (logical) cpus 1: and the -pin option is set to auto: will not pin threads to cpus. 1: This can lead to significant performance degradation. 1: Consider using -pin on (and -pinoffset in case you run multiple jobs). 1: starting mdrun 'Water and methane' 1: 4 steps, 0.0 ps (continuing from step 2, 0.0 ps). 1: Input file: 1: Run start step 0 1: Run start time 0 ps 1: Step to be made during run 2 1: Runtime for the run 0.00390625 ps 1: Run end step 2 1: Run end time 0.00390625 ps 1: 1: 1: Output file: 1: Run start step 0 1: Run start time 0 ps 1: Step to be made during run 4 1: Runtime for the run 0.0078125 ps 1: Run end step 4 1: Run end time 0.0078125 ps 1: 1: 1: Writing final coordinates. 1: 1: Core t (s) Wall t (s) (%) 1: Time: 0.073 0.037 198.9 1: (ns/day) (hour/ns) 1: Performance: 13.855 1.732 1: 1: [ OK ] GmxApiTest.RunnerChainedMD (6016 ms) 1: [ RUN ] GmxApiTest.Status 1: [ OK ] GmxApiTest.Status (0 ms) 1: [ RUN ] GmxApiTest.ApiRunnerStopSignalClient 1: Generating 1-4 interactions: fudge = 0.5 1: 1: NOTE 1 [file spc_and_methane.top, line 33]: 1: The bond in molecule-type methane between atoms 1 C and 2 H1 has an 1: estimated oscillational period of 1.1e-02 ps, which is less than 10 times 1: the time step of 2.0e-03 ps. 1: Maybe you forgot to change the constraints mdp option. 1: 1: Number of degrees of freedom in T-Coupling group System is 18.00 1: 1: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/api/gmxapi/cpp/tests/Testing/Temporary/GmxApiTest_ApiRunnerStopSignalClient_input.mdp]: 1: You are using a plain Coulomb cut-off, which might produce artifacts. 1: You might want to consider using PME electrostatics. 1: 1: 1: 1: There were 2 NOTEs 1: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/api/gmxapi/cpp/tests/Testing/Temporary/GmxApiTest_ApiRunnerStopSignalClient.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 1: Changing nstlist from 10 to 1, rlist from 1.057 to 1 1: 1: Using 1 MPI thread 1: Using 2 OpenMP threads 1: 1: 1: NOTE: The number of threads is not equal to the number of (logical) cpus 1: and the -pin option is set to auto: will not pin threads to cpus. 1: This can lead to significant performance degradation. 1: Consider using -pin on (and -pinoffset in case you run multiple jobs). 1: starting mdrun 'Water and methane' 1: 4 steps, 0.0 ps. 1: Setting the LD random seed to -538464321 1: 1: Generated 331705 of the 331705 non-bonded parameter combinations 1: 1: Generated 331705 of the 331705 1-4 parameter combinations 1: 1: Excluding 2 bonded neighbours molecule type 'SOL' 1: 1: Excluding 3 bonded neighbours molecule type 'methane' 1: 1: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/spc_and_methane.gro' 1: 1: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 1: 1: Calculated rlist for 1x1 atom pair-list as 1.077 nm, buffer size 0.077 nm 1: 1: Set rlist, assuming 4x4 atom pair-list, to 1.057 nm, buffer size 0.057 nm 1: 1: Note that mdrun will redetermine rlist based on the actual pair-list setup 1: 1: This run will generate roughly 0 Mb of data 1: 1: Writing final coordinates. 1: 1: Core t (s) Wall t (s) (%) 1: Time: 0.051 0.026 197.3 1: (ns/day) (hour/ns) 1: Performance: 32.831 0.731 1: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/api/gmxapi/cpp/tests/Testing/Temporary/GmxApiTest_ApiRunnerStopSignalClient.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 1: Overriding nsteps with value passed on the command line: 4 steps, 0.00781 ps 1: Changing nstlist from 10 to 1, rlist from 1.057 to 1 1: 1: 1: Using 1 MPI thread 1: Using 2 OpenMP threads 1: 1: 1: NOTE: The number of threads is not equal to the number of (logical) cpus 1: and the -pin option is set to auto: will not pin threads to cpus. 1: This can lead to significant performance degradation. 1: Consider using -pin on (and -pinoffset in case you run multiple jobs). 1: starting mdrun 'Water and methane' 1: 4 steps, 0.0 ps. 1: 1: Core t (s) Wall t (s) (%) 1: Time: 0.042 0.021 197.3 1: (ns/day) (hour/ns) 1: Performance: 15.772 1.522 1: [ OK ] GmxApiTest.ApiRunnerStopSignalClient (6023 ms) 1: [ RUN ] GmxApiTest.SystemConstruction 1: Generating 1-4 interactions: fudge = 0.5 1: 1: NOTE 1 [file spc_and_methane.top, line 33]: 1: The bond in molecule-type methane between atoms 1 C and 2 H1 has an 1: estimated oscillational period of 1.1e-02 ps, which is less than 10 times 1: the time step of 2.0e-03 ps. 1: Maybe you forgot to change the constraints mdp option. 1: 1: Number of degrees of freedom in T-Coupling group System is 18.00 1: 1: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/api/gmxapi/cpp/tests/Testing/Temporary/GmxApiTest_SystemConstruction_input.mdp]: 1: You are using a plain Coulomb cut-off, which might produce artifacts. 1: You might want to consider using PME electrostatics. 1: 1: 1: 1: There were 2 NOTEs 1: Setting the LD random seed to 2141675353 1: 1: Generated 331705 of the 331705 non-bonded parameter combinations 1: 1: Generated 331705 of the 331705 1-4 parameter combinations 1: 1: Excluding 2 bonded neighbours molecule type 'SOL' 1: 1: Excluding 3 bonded neighbours molecule type 'methane' 1: 1: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/spc_and_methane.gro' 1: 1: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 1: 1: Calculated rlist for 1x1 atom pair-list as 1.077 nm, buffer size 0.077 nm 1: 1: Set rlist, assuming 4x4 atom pair-list, to 1.057 nm, buffer size 0.057 nm 1: 1: Note that mdrun will redetermine rlist based on the actual pair-list setup 1: 1: This run will generate roughly 0 Mb of data 1: [ OK ] GmxApiTest.SystemConstruction (5838 ms) 1: [ RUN ] GmxApiTest.SaneVersionComparisons 1: [ OK ] GmxApiTest.SaneVersionComparisons (0 ms) 1: [ RUN ] GmxApiTest.VersionNamed0_1_Features 1: [ OK ] GmxApiTest.VersionNamed0_1_Features (0 ms) 1: [----------] 9 tests from GmxApiTest (35866 ms total) 1: 1: [----------] Global test environment tear-down 1: [==========] 9 tests from 1 test suite ran. (35919 ms total) 1: [ PASSED ] 9 tests. 1/92 Test #1: GmxapiExternalInterfaceTests .............. Passed 36.07 sec test 2 Start 2: GmxapiInternalInterfaceTests 2: Test command: /build/reproducible-path/gromacs-2025.1/build/basic-dp/bin/workflow-details-test "-ntomp" "2" "--gtest_output=xml:/build/reproducible-path/gromacs-2025.1/build/basic-dp/Testing/Temporary/GmxapiInternalInterfaceTests.xml" 2: Working Directory: /build/reproducible-path/gromacs-2025.1/build/basic-dp/api/gmxapi/cpp/workflow/tests 2: Test timeout computed to be: 600 2: [==========] Running 2 tests from 1 test suite. 2: [----------] Global test environment set-up. 2: [----------] 2 tests from GmxApiTest 2: [ RUN ] GmxApiTest.BuildApiWorkflowImpl 2: Generating 1-4 interactions: fudge = 0.5 2: 2: NOTE 1 [file spc_and_methane.top, line 33]: 2: The bond in molecule-type methane between atoms 1 C and 2 H1 has an 2: estimated oscillational period of 1.1e-02 ps, which is less than 10 times 2: the time step of 2.0e-03 ps. 2: Maybe you forgot to change the constraints mdp option. 2: 2: Number of degrees of freedom in T-Coupling group System is 18.00 2: 2: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/api/gmxapi/cpp/workflow/tests/Testing/Temporary/GmxApiTest_BuildApiWorkflowImpl_input.mdp]: 2: You are using a plain Coulomb cut-off, which might produce artifacts. 2: You might want to consider using PME electrostatics. 2: 2: 2: 2: There were 2 NOTEs 2: Setting the LD random seed to -20982279 2: 2: Generated 331705 of the 331705 non-bonded parameter combinations 2: 2: Generated 331705 of the 331705 1-4 parameter combinations 2: 2: Excluding 2 bonded neighbours molecule type 'SOL' 2: 2: Excluding 3 bonded neighbours molecule type 'methane' 2: 2: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/spc_and_methane.gro' 2: 2: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 2: 2: Calculated rlist for 1x1 atom pair-list as 1.077 nm, buffer size 0.077 nm 2: 2: Set rlist, assuming 4x4 atom pair-list, to 1.057 nm, buffer size 0.057 nm 2: 2: Note that mdrun will redetermine rlist based on the actual pair-list setup 2: 2: This run will generate roughly 0 Mb of data 2: [ OK ] GmxApiTest.BuildApiWorkflowImpl (5837 ms) 2: [ RUN ] GmxApiTest.CreateApiWorkflow 2: Generating 1-4 interactions: fudge = 0.5 2: 2: NOTE 1 [file spc_and_methane.top, line 33]: 2: The bond in molecule-type methane between atoms 1 C and 2 H1 has an 2: estimated oscillational period of 1.1e-02 ps, which is less than 10 times 2: the time step of 2.0e-03 ps. 2: Maybe you forgot to change the constraints mdp option. 2: 2: Number of degrees of freedom in T-Coupling group System is 18.00 2: 2: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/api/gmxapi/cpp/workflow/tests/Testing/Temporary/GmxApiTest_CreateApiWorkflow_input.mdp]: 2: You are using a plain Coulomb cut-off, which might produce artifacts. 2: You might want to consider using PME electrostatics. 2: 2: 2: 2: There were 2 NOTEs 2: Setting the LD random seed to -275923206 2: 2: Generated 331705 of the 331705 non-bonded parameter combinations 2: 2: Generated 331705 of the 331705 1-4 parameter combinations 2: 2: Excluding 2 bonded neighbours molecule type 'SOL' 2: 2: Excluding 3 bonded neighbours molecule type 'methane' 2: 2: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/spc_and_methane.gro' 2: 2: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 2: 2: Calculated rlist for 1x1 atom pair-list as 1.077 nm, buffer size 0.077 nm 2: 2: Set rlist, assuming 4x4 atom pair-list, to 1.057 nm, buffer size 0.057 nm 2: 2: Note that mdrun will redetermine rlist based on the actual pair-list setup 2: 2: This run will generate roughly 0 Mb of data 2: [ OK ] GmxApiTest.CreateApiWorkflow (6004 ms) 2: [----------] 2 tests from GmxApiTest (11842 ms total) 2: 2: [----------] Global test environment tear-down 2: [==========] 2 tests from 1 test suite ran. (11890 ms total) 2: [ PASSED ] 2 tests. 2/92 Test #2: GmxapiInternalInterfaceTests .............. Passed 11.99 sec test 3 Start 3: NbLibListedForcesTests 3: Test command: /build/reproducible-path/gromacs-2025.1/build/basic-dp/bin/nblib-listed-forces-test "--gtest_output=xml:/build/reproducible-path/gromacs-2025.1/build/basic-dp/Testing/Temporary/NbLibListedForcesTests.xml" 3: Working Directory: /build/reproducible-path/gromacs-2025.1/build/basic-dp/api/nblib/listed_forces/tests 3: Test timeout computed to be: 600 3: [==========] Running 44 tests from 22 test suites. 3: [----------] Global test environment set-up. 3: [----------] 8 tests from NBlibTest 3: [ RUN ] NBlibTest.BondTypesOperatorEqualWorks 3: [ OK ] NBlibTest.BondTypesOperatorEqualWorks (0 ms) 3: [ RUN ] NBlibTest.BondTypesLessThanWorks 3: [ OK ] NBlibTest.BondTypesLessThanWorks (0 ms) 3: [ RUN ] NBlibTest.CanSplitListedWork 3: [ OK ] NBlibTest.CanSplitListedWork (0 ms) 3: [ RUN ] NBlibTest.ListedForceBuffer 3: [ OK ] NBlibTest.ListedForceBuffer (0 ms) 3: [ RUN ] NBlibTest.ListedForceCalculatorCanConstruct 3: [ OK ] NBlibTest.ListedForceCalculatorCanConstruct (1 ms) 3: [ RUN ] NBlibTest.GmxToNblibConversionAllTypes 3: [ OK ] NBlibTest.GmxToNblibConversionAllTypes (1 ms) 3: [ RUN ] NBlibTest.EndToEndListedComparison 3: [ OK ] NBlibTest.EndToEndListedComparison (1 ms) 3: [ RUN ] NBlibTest.shiftForcesAreCorrect 3: [ OK ] NBlibTest.shiftForcesAreCorrect (147 ms) 3: [----------] 8 tests from NBlibTest (152 ms total) 3: 3: [----------] 1 test from Kernels 3: [ RUN ] Kernels.HarmonicScalarKernelCanCompute 3: [ OK ] Kernels.HarmonicScalarKernelCanCompute (0 ms) 3: [----------] 1 test from Kernels (0 ms total) 3: 3: [----------] 1 test from FourCenter 3: [ RUN ] FourCenter.ListedForcesProperDihedralTest 3: [ OK ] FourCenter.ListedForcesProperDihedralTest (0 ms) 3: [----------] 1 test from FourCenter (0 ms total) 3: 3: [----------] 7 tests from ThreeCenter 3: [ RUN ] ThreeCenter.ListedForcesG96AngleTest 3: [ OK ] ThreeCenter.ListedForcesG96AngleTest (0 ms) 3: [ RUN ] ThreeCenter.ListedForcesHarmonicAngleTest 3: [ OK ] ThreeCenter.ListedForcesHarmonicAngleTest (0 ms) 3: [ RUN ] ThreeCenter.ListedForcesLinearAngleTest 3: [ OK ] ThreeCenter.ListedForcesLinearAngleTest (0 ms) 3: [ RUN ] ThreeCenter.ListedForcesCrossBondBondTest 3: [ OK ] ThreeCenter.ListedForcesCrossBondBondTest (0 ms) 3: [ RUN ] ThreeCenter.ListedForcesCrossBondAngleTest 3: [ OK ] ThreeCenter.ListedForcesCrossBondAngleTest (0 ms) 3: [ RUN ] ThreeCenter.ListedForcesQuarticAngleTest 3: [ OK ] ThreeCenter.ListedForcesQuarticAngleTest (0 ms) 3: [ RUN ] ThreeCenter.ListedForcesRestrictedAngleTest 3: [ OK ] ThreeCenter.ListedForcesRestrictedAngleTest (0 ms) 3: [----------] 7 tests from ThreeCenter (3 ms total) 3: 3: [----------] 5 tests from TwoCenter 3: [ RUN ] TwoCenter.ListedForcesHarmonicBondTest 3: [ OK ] TwoCenter.ListedForcesHarmonicBondTest (0 ms) 3: [ RUN ] TwoCenter.ListedForcesG96BondTest 3: [ OK ] TwoCenter.ListedForcesG96BondTest (0 ms) 3: [ RUN ] TwoCenter.ListedForcesCubicBondTest 3: [ OK ] TwoCenter.ListedForcesCubicBondTest (0 ms) 3: [ RUN ] TwoCenter.ListedForcesMorseBondTest 3: [ OK ] TwoCenter.ListedForcesMorseBondTest (0 ms) 3: [ RUN ] TwoCenter.ListedForcesFeneBondTest 3: [ OK ] TwoCenter.ListedForcesFeneBondTest (0 ms) 3: [----------] 5 tests from TwoCenter (2 ms total) 3: 3: [----------] 5 tests from ListedExampleData 3: [ RUN ] ListedExampleData.ComputeHarmonicBondForces 3: [ OK ] ListedExampleData.ComputeHarmonicBondForces (0 ms) 3: [ RUN ] ListedExampleData.ComputeHarmonicBondEnergies 3: [ OK ] ListedExampleData.ComputeHarmonicBondEnergies (0 ms) 3: [ RUN ] ListedExampleData.ComputeHarmonicAngleForces 3: [ OK ] ListedExampleData.ComputeHarmonicAngleForces (0 ms) 3: [ RUN ] ListedExampleData.CanReduceForces 3: [ OK ] ListedExampleData.CanReduceForces (0 ms) 3: [ RUN ] ListedExampleData.CanReduceEnergies 3: [ OK ] ListedExampleData.CanReduceEnergies (0 ms) 3: [----------] 5 tests from ListedExampleData (2 ms total) 3: 3: [----------] 1 test from LinearChainDataFixture 3: [ RUN ] LinearChainDataFixture.Multithreading 3: [ OK ] LinearChainDataFixture.Multithreading (23 ms) 3: [----------] 1 test from LinearChainDataFixture (23 ms total) 3: 3: [----------] 2 tests from ListedShims 3: [ RUN ] ListedShims.ParameterConversion 3: [ OK ] ListedShims.ParameterConversion (0 ms) 3: [ RUN ] ListedShims.GmxToNblibConversion 3: [ OK ] ListedShims.GmxToNblibConversion (0 ms) 3: [----------] 2 tests from ListedShims (0 ms total) 3: 3: [----------] 1 test from CompareEachTypeInNblibAndGmx/NblibGmxListed/0, where TypeParam = nblib::TwoParameterInteraction 3: [ RUN ] CompareEachTypeInNblibAndGmx/NblibGmxListed/0.SameForcesOnBoth 3: [ OK ] CompareEachTypeInNblibAndGmx/NblibGmxListed/0.SameForcesOnBoth (0 ms) 3: [----------] 1 test from CompareEachTypeInNblibAndGmx/NblibGmxListed/0 (0 ms total) 3: 3: [----------] 1 test from CompareEachTypeInNblibAndGmx/NblibGmxListed/1, where TypeParam = nblib::G96BondType 3: [ RUN ] CompareEachTypeInNblibAndGmx/NblibGmxListed/1.SameForcesOnBoth 3: [ OK ] CompareEachTypeInNblibAndGmx/NblibGmxListed/1.SameForcesOnBoth (0 ms) 3: [----------] 1 test from CompareEachTypeInNblibAndGmx/NblibGmxListed/1 (0 ms total) 3: 3: [----------] 1 test from CompareEachTypeInNblibAndGmx/NblibGmxListed/2, where TypeParam = nblib::CubicBondType 3: [ RUN ] CompareEachTypeInNblibAndGmx/NblibGmxListed/2.SameForcesOnBoth 3: [ OK ] CompareEachTypeInNblibAndGmx/NblibGmxListed/2.SameForcesOnBoth (0 ms) 3: [----------] 1 test from CompareEachTypeInNblibAndGmx/NblibGmxListed/2 (0 ms total) 3: 3: [----------] 1 test from CompareEachTypeInNblibAndGmx/NblibGmxListed/3, where TypeParam = nblib::MorseBondType 3: [ RUN ] CompareEachTypeInNblibAndGmx/NblibGmxListed/3.SameForcesOnBoth 3: [ OK ] CompareEachTypeInNblibAndGmx/NblibGmxListed/3.SameForcesOnBoth (0 ms) 3: [----------] 1 test from CompareEachTypeInNblibAndGmx/NblibGmxListed/3 (0 ms total) 3: 3: [----------] 1 test from CompareEachTypeInNblibAndGmx/NblibGmxListed/4, where TypeParam = nblib::TwoParameterInteraction 3: [ RUN ] CompareEachTypeInNblibAndGmx/NblibGmxListed/4.SameForcesOnBoth 3: [ OK ] CompareEachTypeInNblibAndGmx/NblibGmxListed/4.SameForcesOnBoth (0 ms) 3: [----------] 1 test from CompareEachTypeInNblibAndGmx/NblibGmxListed/4 (0 ms total) 3: 3: [----------] 1 test from CompareEachTypeInNblibAndGmx/NblibGmxListed/5, where TypeParam = nblib::AngleInteractionType 3: [ RUN ] CompareEachTypeInNblibAndGmx/NblibGmxListed/5.SameForcesOnBoth 3: [ OK ] CompareEachTypeInNblibAndGmx/NblibGmxListed/5.SameForcesOnBoth (0 ms) 3: [----------] 1 test from CompareEachTypeInNblibAndGmx/NblibGmxListed/5 (0 ms total) 3: 3: [----------] 1 test from CompareEachTypeInNblibAndGmx/NblibGmxListed/6, where TypeParam = nblib::CosineParamAngle 3: [ RUN ] CompareEachTypeInNblibAndGmx/NblibGmxListed/6.SameForcesOnBoth 3: [ OK ] CompareEachTypeInNblibAndGmx/NblibGmxListed/6.SameForcesOnBoth (0 ms) 3: [----------] 1 test from CompareEachTypeInNblibAndGmx/NblibGmxListed/6 (0 ms total) 3: 3: [----------] 1 test from CompareEachTypeInNblibAndGmx/NblibGmxListed/7, where TypeParam = nblib::CosineParamAngle 3: [ RUN ] CompareEachTypeInNblibAndGmx/NblibGmxListed/7.SameForcesOnBoth 3: [ OK ] CompareEachTypeInNblibAndGmx/NblibGmxListed/7.SameForcesOnBoth (0 ms) 3: [----------] 1 test from CompareEachTypeInNblibAndGmx/NblibGmxListed/7 (0 ms total) 3: 3: [----------] 1 test from CompareEachTypeInNblibAndGmx/NblibGmxListed/8, where TypeParam = nblib::TwoParameterInteraction 3: [ RUN ] CompareEachTypeInNblibAndGmx/NblibGmxListed/8.SameForcesOnBoth 3: [ OK ] CompareEachTypeInNblibAndGmx/NblibGmxListed/8.SameForcesOnBoth (0 ms) 3: [----------] 1 test from CompareEachTypeInNblibAndGmx/NblibGmxListed/8 (0 ms total) 3: 3: [----------] 1 test from CompareEachTypeInNblibAndGmx/NblibGmxListed/9, where TypeParam = nblib::QuarticAngle 3: [ RUN ] CompareEachTypeInNblibAndGmx/NblibGmxListed/9.SameForcesOnBoth 3: [ OK ] CompareEachTypeInNblibAndGmx/NblibGmxListed/9.SameForcesOnBoth (0 ms) 3: [----------] 1 test from CompareEachTypeInNblibAndGmx/NblibGmxListed/9 (0 ms total) 3: 3: [----------] 1 test from CompareEachTypeInNblibAndGmx/NblibGmxListed/10, where TypeParam = nblib::CrossBondBond 3: [ RUN ] CompareEachTypeInNblibAndGmx/NblibGmxListed/10.SameForcesOnBoth 3: [ OK ] CompareEachTypeInNblibAndGmx/NblibGmxListed/10.SameForcesOnBoth (0 ms) 3: [----------] 1 test from CompareEachTypeInNblibAndGmx/NblibGmxListed/10 (0 ms total) 3: 3: [----------] 1 test from CompareEachTypeInNblibAndGmx/NblibGmxListed/11, where TypeParam = nblib::CrossBondAngle 3: [ RUN ] CompareEachTypeInNblibAndGmx/NblibGmxListed/11.SameForcesOnBoth 3: [ OK ] CompareEachTypeInNblibAndGmx/NblibGmxListed/11.SameForcesOnBoth (0 ms) 3: [----------] 1 test from CompareEachTypeInNblibAndGmx/NblibGmxListed/11 (0 ms total) 3: 3: [----------] 1 test from CompareEachTypeInNblibAndGmx/NblibGmxListed/12, where TypeParam = nblib::ProperDihedral 3: [ RUN ] CompareEachTypeInNblibAndGmx/NblibGmxListed/12.SameForcesOnBoth 3: [ OK ] CompareEachTypeInNblibAndGmx/NblibGmxListed/12.SameForcesOnBoth (0 ms) 3: [----------] 1 test from CompareEachTypeInNblibAndGmx/NblibGmxListed/12 (0 ms total) 3: 3: [----------] 1 test from ListedTransformations 3: [ RUN ] ListedTransformations.SortInteractionIndices 3: [ OK ] ListedTransformations.SortInteractionIndices (0 ms) 3: [----------] 1 test from ListedTransformations (0 ms total) 3: 3: [----------] Global test environment tear-down 3: [==========] 44 tests from 22 test suites ran. (189 ms total) 3: [ PASSED ] 44 tests. 3/92 Test #3: NbLibListedForcesTests .................... Passed 0.29 sec test 4 Start 4: NbLibSamplesTestArgon 4: Test command: /build/reproducible-path/gromacs-2025.1/build/basic-dp/bin/argon-forces-integration 4: Working Directory: /build/reproducible-path/gromacs-2025.1/build/basic-dp/api/nblib/samples 4: Test timeout computed to be: 1500 4: initial forces on particle 0: x 0.000000 y 0.000000 z 0.000000 4: final forces on particle 0: x -0.412988 y -1.098243 z -0.113189 4: initial position of particle 0: x 0.794000 y 1.439000 z 0.610000 4: final position of particle 0: x 0.789162 y 1.271508 z 0.819867 4/92 Test #4: NbLibSamplesTestArgon ..................... Passed 0.08 sec test 5 Start 5: NbLibSamplesTestMethaneWater 5: Test command: /build/reproducible-path/gromacs-2025.1/build/basic-dp/bin/methane-water-integration 5: Working Directory: /build/reproducible-path/gromacs-2025.1/build/basic-dp/api/nblib/samples 5: Test timeout computed to be: 1500 5: initial position of particle 0: x 0.005000 y 0.600000 z 0.244000 5: final position of particle 9: x 77.358372 y 5.325207 z -80.600064 5/92 Test #5: NbLibSamplesTestMethaneWater .............. Passed 0.10 sec test 6 Start 6: NbLibUtilTests 6: Test command: /build/reproducible-path/gromacs-2025.1/build/basic-dp/bin/nblib-util-test "--gtest_output=xml:/build/reproducible-path/gromacs-2025.1/build/basic-dp/Testing/Temporary/NbLibUtilTests.xml" 6: Working Directory: /build/reproducible-path/gromacs-2025.1/build/basic-dp/api/nblib/util/tests 6: Test timeout computed to be: 30 6: [==========] Running 16 tests from 2 test suites. 6: [----------] Global test environment set-up. 6: [----------] 6 tests from NBlibTest 6: [ RUN ] NBlibTest.isRealValued 6: [ OK ] NBlibTest.isRealValued (0 ms) 6: [ RUN ] NBlibTest.checkNumericValuesHasNan 6: [ OK ] NBlibTest.checkNumericValuesHasNan (0 ms) 6: [ RUN ] NBlibTest.checkNumericValuesHasInf 6: [ OK ] NBlibTest.checkNumericValuesHasInf (0 ms) 6: [ RUN ] NBlibTest.GeneratedVelocitiesAreCorrect 6: Velocities were taken from a Maxwell distribution at 300 K 6: [ OK ] NBlibTest.GeneratedVelocitiesAreCorrect (1 ms) 6: [ RUN ] NBlibTest.generateVelocitySize 6: Velocities were taken from a Maxwell distribution at 300 K 6: [ OK ] NBlibTest.generateVelocitySize (0 ms) 6: [ RUN ] NBlibTest.generateVelocityCheckNumbers 6: Velocities were taken from a Maxwell distribution at 300 K 6: [ OK ] NBlibTest.generateVelocityCheckNumbers (0 ms) 6: [----------] 6 tests from NBlibTest (1 ms total) 6: 6: [----------] 10 tests from NblibTraitsUtils 6: [ RUN ] NblibTraitsUtils.FuseTwo 6: [ OK ] NblibTraitsUtils.FuseTwo (0 ms) 6: [ RUN ] NblibTraitsUtils.Fuse 6: [ OK ] NblibTraitsUtils.Fuse (0 ms) 6: [ RUN ] NblibTraitsUtils.Repeat 6: [ OK ] NblibTraitsUtils.Repeat (0 ms) 6: [ RUN ] NblibTraitsUtils.FindIndexTuple1 6: [ OK ] NblibTraitsUtils.FindIndexTuple1 (0 ms) 6: [ RUN ] NblibTraitsUtils.FindIndexTuple2 6: [ OK ] NblibTraitsUtils.FindIndexTuple2 (0 ms) 6: [ RUN ] NblibTraitsUtils.FindIndexTypeList1 6: [ OK ] NblibTraitsUtils.FindIndexTypeList1 (0 ms) 6: [ RUN ] NblibTraitsUtils.FindIndexTypeList2 6: [ OK ] NblibTraitsUtils.FindIndexTypeList2 (0 ms) 6: [ RUN ] NblibTraitsUtils.Contains 6: [ OK ] NblibTraitsUtils.Contains (0 ms) 6: [ RUN ] NblibTraitsUtils.FindIndexTupleRepeated 6: [ OK ] NblibTraitsUtils.FindIndexTupleRepeated (0 ms) 6: [ RUN ] NblibTraitsUtils.FindIndexTypeListRepeated 6: [ OK ] NblibTraitsUtils.FindIndexTypeListRepeated (0 ms) 6: [----------] 10 tests from NblibTraitsUtils (0 ms total) 6: 6: [----------] Global test environment tear-down 6: [==========] 16 tests from 2 test suites ran. (2 ms total) 6: [ PASSED ] 16 tests. 6/92 Test #6: NbLibUtilTests ............................ Passed 0.09 sec test 7 Start 7: NbLibSetupTests 7: Test command: /build/reproducible-path/gromacs-2025.1/build/basic-dp/bin/nblib-setup-test "--gtest_output=xml:/build/reproducible-path/gromacs-2025.1/build/basic-dp/Testing/Temporary/NbLibSetupTests.xml" 7: Working Directory: /build/reproducible-path/gromacs-2025.1/build/basic-dp/api/nblib/tests 7: Test timeout computed to be: 600 7: [==========] Running 57 tests from 3 test suites. 7: [----------] Global test environment set-up. 7: [----------] 41 tests from NBlibTest 7: [ RUN ] NBlibTest.CubicBoxCannotHaveNaN 7: [ OK ] NBlibTest.CubicBoxCannotHaveNaN (0 ms) 7: [ RUN ] NBlibTest.CubicBoxCannotHaveInf 7: [ OK ] NBlibTest.CubicBoxCannotHaveInf (0 ms) 7: [ RUN ] NBlibTest.RectangularBoxCannotHaveNaN 7: [ OK ] NBlibTest.RectangularBoxCannotHaveNaN (0 ms) 7: [ RUN ] NBlibTest.RectangularBoxCannotHaveInf 7: [ OK ] NBlibTest.RectangularBoxCannotHaveInf (0 ms) 7: [ RUN ] NBlibTest.CubicBoxWorks 7: [ OK ] NBlibTest.CubicBoxWorks (0 ms) 7: [ RUN ] NBlibTest.BoxEqual 7: [ OK ] NBlibTest.BoxEqual (0 ms) 7: [ RUN ] NBlibTest.NonBondedForceParamsCorrect 7: [ OK ] NBlibTest.NonBondedForceParamsCorrect (0 ms) 7: [ RUN ] NBlibTest.CanMergeInteractions 7: [ OK ] NBlibTest.CanMergeInteractions (0 ms) 7: [ RUN ] NBlibTest.ParticleTypeNameCanBeConstructed 7: [ OK ] NBlibTest.ParticleTypeNameCanBeConstructed (0 ms) 7: [ RUN ] NBlibTest.ParticleTypeMassCanBeConstructed 7: [ OK ] NBlibTest.ParticleTypeMassCanBeConstructed (0 ms) 7: [ RUN ] NBlibTest.PbcHolderWorks 7: [ OK ] NBlibTest.PbcHolderWorks (0 ms) 7: [ RUN ] NBlibTest.CanConstructMoleculeWithoutChargeOrResidueName 7: [ OK ] NBlibTest.CanConstructMoleculeWithoutChargeOrResidueName (0 ms) 7: [ RUN ] NBlibTest.CanConstructMoleculeWithChargeWithoutResidueName 7: [ OK ] NBlibTest.CanConstructMoleculeWithChargeWithoutResidueName (0 ms) 7: [ RUN ] NBlibTest.CanConstructMoleculeWithoutChargeWithResidueName 7: [ OK ] NBlibTest.CanConstructMoleculeWithoutChargeWithResidueName (0 ms) 7: [ RUN ] NBlibTest.CanConstructMoleculeWithChargeWithResidueName 7: [ OK ] NBlibTest.CanConstructMoleculeWithChargeWithResidueName (0 ms) 7: [ RUN ] NBlibTest.CanGetNumParticlesInMolecule 7: [ OK ] NBlibTest.CanGetNumParticlesInMolecule (0 ms) 7: [ RUN ] NBlibTest.CanConstructExclusionListFromNames 7: [ OK ] NBlibTest.CanConstructExclusionListFromNames (0 ms) 7: [ RUN ] NBlibTest.CanConstructExclusionListFromNamesAndIndicesMixed 7: [ OK ] NBlibTest.CanConstructExclusionListFromNamesAndIndicesMixed (0 ms) 7: [ RUN ] NBlibTest.AtWorks 7: [ OK ] NBlibTest.AtWorks (0 ms) 7: [ RUN ] NBlibTest.AtThrows 7: [ OK ] NBlibTest.AtThrows (0 ms) 7: [ RUN ] NBlibTest.MoleculeThrowsSameParticleTypeNameDifferentMass 7: [ OK ] NBlibTest.MoleculeThrowsSameParticleTypeNameDifferentMass (0 ms) 7: [ RUN ] NBlibTest.MoleculeDontThrowsSameParticleTypeNameDifferentMass 7: [ OK ] NBlibTest.MoleculeDontThrowsSameParticleTypeNameDifferentMass (0 ms) 7: [ RUN ] NBlibTest.MoleculeNoThrowsSameParticleTypeName 7: [ OK ] NBlibTest.MoleculeNoThrowsSameParticleTypeName (0 ms) 7: [ RUN ] NBlibTest.CanAddInteractions 7: [ OK ] NBlibTest.CanAddInteractions (0 ms) 7: [ RUN ] NBlibTest.CanAddUreyBradley 7: [ OK ] NBlibTest.CanAddUreyBradley (0 ms) 7: [ RUN ] NBlibTest.TopologyHasNumParticles 7: [ OK ] NBlibTest.TopologyHasNumParticles (0 ms) 7: [ RUN ] NBlibTest.TopologyHasCharges 7: [ OK ] NBlibTest.TopologyHasCharges (0 ms) 7: [ RUN ] NBlibTest.TopologyHasMasses 7: [ OK ] NBlibTest.TopologyHasMasses (0 ms) 7: [ RUN ] NBlibTest.TopologyHasParticleTypes 7: [ OK ] NBlibTest.TopologyHasParticleTypes (0 ms) 7: [ RUN ] NBlibTest.TopologyHasParticleTypeIds 7: [ OK ] NBlibTest.TopologyHasParticleTypeIds (0 ms) 7: [ RUN ] NBlibTest.TopologyThrowsIdenticalParticleType 7: [ OK ] NBlibTest.TopologyThrowsIdenticalParticleType (0 ms) 7: [ RUN ] NBlibTest.TopologyHasExclusions 7: [ OK ] NBlibTest.TopologyHasExclusions (0 ms) 7: [ RUN ] NBlibTest.TopologyHasSequencing 7: [ OK ] NBlibTest.TopologyHasSequencing (0 ms) 7: [ RUN ] NBlibTest.TopologyCanAggregateBonds 7: [ OK ] NBlibTest.TopologyCanAggregateBonds (0 ms) 7: [ RUN ] NBlibTest.TopologyCanSequencePairIDs 7: [ OK ] NBlibTest.TopologyCanSequencePairIDs (0 ms) 7: [ RUN ] NBlibTest.TopologySequenceIdThrows 7: No particle O-Atom in residue SOL in molecule SOL found 7: [ OK ] NBlibTest.TopologySequenceIdThrows (0 ms) 7: [ RUN ] NBlibTest.TopologyCanEliminateDuplicateBonds 7: [ OK ] NBlibTest.TopologyCanEliminateDuplicateBonds (0 ms) 7: [ RUN ] NBlibTest.TopologyListedInteractions 7: [ OK ] NBlibTest.TopologyListedInteractions (0 ms) 7: [ RUN ] NBlibTest.TopologyListedInteractionsMultipleTypes 7: [ OK ] NBlibTest.TopologyListedInteractionsMultipleTypes (0 ms) 7: [ RUN ] NBlibTest.TopologyInvalidParticleInInteractionThrows 7: No particle Iron in residue SOL in molecule SOL found 7: [ OK ] NBlibTest.TopologyInvalidParticleInInteractionThrows (0 ms) 7: [ RUN ] NBlibTest.toGmxExclusionBlockWorks 7: [ OK ] NBlibTest.toGmxExclusionBlockWorks (0 ms) 7: [----------] 41 tests from NBlibTest (9 ms total) 7: 7: [----------] 15 tests from NbnxmSetupTest 7: [ RUN ] NbnxmSetupTest.findNumEnergyGroups 7: [ OK ] NbnxmSetupTest.findNumEnergyGroups (0 ms) 7: [ RUN ] NbnxmSetupTest.canTranslateBenchmarkEnumAuto 7: [ OK ] NbnxmSetupTest.canTranslateBenchmarkEnumAuto (0 ms) 7: [ RUN ] NbnxmSetupTest.canTranslateBenchmarkEnumNo 7: [ OK ] NbnxmSetupTest.canTranslateBenchmarkEnumNo (0 ms) 7: [ RUN ] NbnxmSetupTest.canTranslateBenchmarkEnum2XM 7: [ OK ] NbnxmSetupTest.canTranslateBenchmarkEnum2XM (0 ms) 7: [ RUN ] NbnxmSetupTest.canTranslateBenchmarkEnum4XM 7: [ OK ] NbnxmSetupTest.canTranslateBenchmarkEnum4XM (0 ms) 7: [ RUN ] NbnxmSetupTest.CheckKernelSetupThrowsAuto 7: [ OK ] NbnxmSetupTest.CheckKernelSetupThrowsAuto (0 ms) 7: [ RUN ] NbnxmSetupTest.CheckKernelSetupThrowsCount 7: [ OK ] NbnxmSetupTest.CheckKernelSetupThrowsCount (0 ms) 7: [ RUN ] NbnxmSetupTest.canCreateKernelSetupPlain 7: [ OK ] NbnxmSetupTest.canCreateKernelSetupPlain (0 ms) 7: [ RUN ] NbnxmSetupTest.canCreateParticleInfoAllVdv 7: [ OK ] NbnxmSetupTest.canCreateParticleInfoAllVdv (0 ms) 7: [ RUN ] NbnxmSetupTest.ewaldCoeffWorks 7: [ OK ] NbnxmSetupTest.ewaldCoeffWorks (0 ms) 7: [ RUN ] NbnxmSetupTest.updateForcerecWorks 7: [ OK ] NbnxmSetupTest.updateForcerecWorks (0 ms) 7: [ RUN ] NbnxmSetupTest.canCheckKernelSetup 7: [ OK ] NbnxmSetupTest.canCheckKernelSetup (0 ms) 7: [ RUN ] NbnxmSetupTest.cannotCreateKernelSetupCPU2XM 7: [ OK ] NbnxmSetupTest.cannotCreateKernelSetupCPU2XM (0 ms) 7: [ RUN ] NbnxmSetupTest.cannotCreateKernelSetupCPU4XM 7: [ OK ] NbnxmSetupTest.cannotCreateKernelSetupCPU4XM (0 ms) 7: [ RUN ] NbnxmSetupTest.CanCreateNbnxmCPU 7: [ OK ] NbnxmSetupTest.CanCreateNbnxmCPU (0 ms) 7: [----------] 15 tests from NbnxmSetupTest (0 ms total) 7: 7: [----------] 1 test from VirialsTest 7: [ RUN ] VirialsTest.computeVirialTensorWorks 7: [ OK ] VirialsTest.computeVirialTensorWorks (0 ms) 7: [----------] 1 test from VirialsTest (0 ms total) 7: 7: [----------] Global test environment tear-down 7: [==========] 57 tests from 3 test suites ran. (11 ms total) 7: [ PASSED ] 57 tests. 7/92 Test #7: NbLibSetupTests ........................... Passed 0.16 sec test 8 Start 8: NbLibTprTests 8: Test command: /build/reproducible-path/gromacs-2025.1/build/basic-dp/bin/nblib-tpr-test "--gtest_output=xml:/build/reproducible-path/gromacs-2025.1/build/basic-dp/Testing/Temporary/NbLibTprTests.xml" 8: Working Directory: /build/reproducible-path/gromacs-2025.1/build/basic-dp/api/nblib/tests 8: Test timeout computed to be: 30 8: [==========] Running 4 tests from 1 test suite. 8: [----------] Global test environment set-up. 8: [----------] 4 tests from TprReaderTest 8: [ RUN ] TprReaderTest.SimDBTprIsCreated 8: 8: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/api/nblib/tests/Testing/Temporary/TprReaderTest_SimDBTprIsCreated_input.mdp]: 8: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 8: that with the Verlet scheme, nstlist has no effect on the accuracy of 8: your simulation. 8: 8: 8: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/api/nblib/tests/Testing/Temporary/TprReaderTest_SimDBTprIsCreated_input.mdp]: 8: Setting nstcalcenergy (100) equal to nstenergy (4) 8: 8: Number of degrees of freedom in T-Coupling group System is 33.00 8: 8: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/api/nblib/tests/Testing/Temporary/TprReaderTest_SimDBTprIsCreated_input.mdp]: 8: NVE simulation: will use the initial temperature of 68.810 K for 8: determining the Verlet buffer size 8: 8: 8: There were 3 NOTEs 8: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/api/nblib/tests/Testing/Temporary/TprReaderTest_SimDBTprIsCreated.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 8: Generated 1 of the 1 non-bonded parameter combinations 8: 8: Excluding 1 bonded neighbours molecule type 'Argon' 8: 8: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 8: 8: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 8: 8: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 8: 8: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 8: 8: Note that mdrun will redetermine rlist based on the actual pair-list setup 8: 8: This run will generate roughly 0 Mb of data 8: [ OK ] TprReaderTest.SimDBTprIsCreated (40 ms) 8: [ RUN ] TprReaderTest.Spc2Reads 8: 8: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/api/nblib/tests/Testing/Temporary/TprReaderTest_Spc2Reads_input.mdp]: 8: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 8: that with the Verlet scheme, nstlist has no effect on the accuracy of 8: your simulation. 8: 8: 8: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/api/nblib/tests/Testing/Temporary/TprReaderTest_Spc2Reads_input.mdp]: 8: Setting nstcalcenergy (100) equal to nstenergy (4) 8: 8: Generating 1-4 interactions: fudge = 0.5 8: Number of degrees of freedom in T-Coupling group System is 9.00 8: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 8: 8: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/api/nblib/tests/Testing/Temporary/TprReaderTest_Spc2Reads_input.mdp]: 8: NVE simulation: will use the initial temperature of 2573.591 K for 8: determining the Verlet buffer size 8: 8: 8: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/api/nblib/tests/Testing/Temporary/TprReaderTest_Spc2Reads_input.mdp]: 8: You are using a plain Coulomb cut-off, which might produce artifacts. 8: You might want to consider using PME electrostatics. 8: 8: 8: 8: There were 4 NOTEs 8: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/api/nblib/tests/Testing/Temporary/TprReaderTest_Spc2Reads.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 8: Generated 3 of the 3 non-bonded parameter combinations 8: 8: Generated 3 of the 3 1-4 parameter combinations 8: 8: Excluding 2 bonded neighbours molecule type 'SOL' 8: 8: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/spc2.gro' 8: 8: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 2573.59 K 8: 8: Calculated rlist for 1x1 atom pair-list as 0.906 nm, buffer size 0.206 nm 8: 8: Set rlist, assuming 4x4 atom pair-list, to 0.892 nm, buffer size 0.192 nm 8: 8: Note that mdrun will redetermine rlist based on the actual pair-list setup 8: 8: This run will generate roughly 0 Mb of data 8: [ OK ] TprReaderTest.Spc2Reads (32 ms) 8: [ RUN ] TprReaderTest.ArgonImportedDataIsCorrect 8: 8: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/api/nblib/tests/Testing/Temporary/TprReaderTest_ArgonImportedDataIsCorrect_input.mdp]: 8: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 8: that with the Verlet scheme, nstlist has no effect on the accuracy of 8: your simulation. 8: 8: 8: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/api/nblib/tests/Testing/Temporary/TprReaderTest_ArgonImportedDataIsCorrect_input.mdp]: 8: Setting nstcalcenergy (100) equal to nstenergy (4) 8: 8: Number of degrees of freedom in T-Coupling group System is 33.00 8: 8: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/api/nblib/tests/Testing/Temporary/TprReaderTest_ArgonImportedDataIsCorrect_input.mdp]: 8: NVE simulation: will use the initial temperature of 68.810 K for 8: determining the Verlet buffer size 8: 8: 8: There were 3 NOTEs 8: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/api/nblib/tests/Testing/Temporary/TprReaderTest_ArgonImportedDataIsCorrect.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 8: Generated 1 of the 1 non-bonded parameter combinations 8: 8: Excluding 1 bonded neighbours molecule type 'Argon' 8: 8: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 8: 8: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 8: 8: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 8: 8: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 8: 8: Note that mdrun will redetermine rlist based on the actual pair-list setup 8: 8: This run will generate roughly 0 Mb of data 8: [ OK ] TprReaderTest.ArgonImportedDataIsCorrect (31 ms) 8: [ RUN ] TprReaderTest.FCfromTprDataWorks 8: 8: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/api/nblib/tests/Testing/Temporary/TprReaderTest_FCfromTprDataWorks_input.mdp]: 8: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 8: that with the Verlet scheme, nstlist has no effect on the accuracy of 8: your simulation. 8: 8: 8: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/api/nblib/tests/Testing/Temporary/TprReaderTest_FCfromTprDataWorks_input.mdp]: 8: Setting nstcalcenergy (100) equal to nstenergy (4) 8: 8: Number of degrees of freedom in T-Coupling group System is 33.00 8: 8: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/api/nblib/tests/Testing/Temporary/TprReaderTest_FCfromTprDataWorks_input.mdp]: 8: NVE simulation: will use the initial temperature of 68.810 K for 8: determining the Verlet buffer size 8: 8: 8: There were 3 NOTEs 8: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/api/nblib/tests/Testing/Temporary/TprReaderTest_FCfromTprDataWorks.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 8: Generated 1 of the 1 non-bonded parameter combinations 8: 8: Excluding 1 bonded neighbours molecule type 'Argon' 8: 8: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 8: 8: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 8: 8: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 8: 8: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 8: 8: Note that mdrun will redetermine rlist based on the actual pair-list setup 8: 8: This run will generate roughly 0 Mb of data 8: [ OK ] TprReaderTest.FCfromTprDataWorks (34 ms) 8: [----------] 4 tests from TprReaderTest (139 ms total) 8: 8: [----------] Global test environment tear-down 8: [==========] 4 tests from 1 test suite ran. (184 ms total) 8: [ PASSED ] 4 tests. 8/92 Test #8: NbLibTprTests ............................. Passed 0.27 sec test 9 Start 9: NbLibIntegrationTests 9: Test command: /build/reproducible-path/gromacs-2025.1/build/basic-dp/bin/nblib-integration-test "--gtest_output=xml:/build/reproducible-path/gromacs-2025.1/build/basic-dp/Testing/Temporary/NbLibIntegrationTests.xml" 9: Working Directory: /build/reproducible-path/gromacs-2025.1/build/basic-dp/api/nblib/tests 9: Test timeout computed to be: 600 9: [==========] Running 20 tests from 1 test suite. 9: [----------] Global test environment set-up. 9: [----------] 20 tests from NBlibTest 9: [ RUN ] NBlibTest.GmxForceCalculatorCanCompute 9: [ OK ] NBlibTest.GmxForceCalculatorCanCompute (5 ms) 9: [ RUN ] NBlibTest.ArgonVirialsAreCorrect 9: [ OK ] NBlibTest.ArgonVirialsAreCorrect (3 ms) 9: [ RUN ] NBlibTest.ArgonEnergiesAreCorrect 9: [ OK ] NBlibTest.ArgonEnergiesAreCorrect (3 ms) 9: [ RUN ] NBlibTest.SpcMethanolEnergiesAreCorrect 9: [ OK ] NBlibTest.SpcMethanolEnergiesAreCorrect (3 ms) 9: [ RUN ] NBlibTest.SpcMethanolForcesAreCorrect 9: [ OK ] NBlibTest.SpcMethanolForcesAreCorrect (1 ms) 9: [ RUN ] NBlibTest.ExpectedNumberOfForces 9: [ OK ] NBlibTest.ExpectedNumberOfForces (3 ms) 9: [ RUN ] NBlibTest.CanIntegrateSystem 9: [ OK ] NBlibTest.CanIntegrateSystem (3 ms) 9: [ RUN ] NBlibTest.UpdateChangesForces 9: [ OK ] NBlibTest.UpdateChangesForces (3 ms) 9: [ RUN ] NBlibTest.ArgonOplsaForcesAreCorrect 9: [ OK ] NBlibTest.ArgonOplsaForcesAreCorrect (1 ms) 9: [ RUN ] NBlibTest.ArgonGromos43A1ForcesAreCorrect 9: [ OK ] NBlibTest.ArgonGromos43A1ForcesAreCorrect (1 ms) 9: [ RUN ] NBlibTest.CanConstructSimulationState 9: [ OK ] NBlibTest.CanConstructSimulationState (0 ms) 9: [ RUN ] NBlibTest.SimulationStateThrowsCoordinateNAN 9: [ OK ] NBlibTest.SimulationStateThrowsCoordinateNAN (0 ms) 9: [ RUN ] NBlibTest.SimulationStateThrowsCoordinateINF 9: [ OK ] NBlibTest.SimulationStateThrowsCoordinateINF (0 ms) 9: [ RUN ] NBlibTest.SimulationStateThrowsVelocityNAN 9: [ OK ] NBlibTest.SimulationStateThrowsVelocityNAN (0 ms) 9: [ RUN ] NBlibTest.SimulationStateThrowsVelocityINF 9: [ OK ] NBlibTest.SimulationStateThrowsVelocityINF (0 ms) 9: [ RUN ] NBlibTest.SimulationStateCanMove 9: [ OK ] NBlibTest.SimulationStateCanMove (0 ms) 9: [ RUN ] NBlibTest.SimulationStateCanAssign 9: [ OK ] NBlibTest.SimulationStateCanAssign (0 ms) 9: [ RUN ] NBlibTest.SimulationStateHasBox 9: [ OK ] NBlibTest.SimulationStateHasBox (0 ms) 9: [ RUN ] NBlibTest.SimulationStateHasCorrectCoordinates 9: [ OK ] NBlibTest.SimulationStateHasCorrectCoordinates (0 ms) 9: [ RUN ] NBlibTest.SimulationStateHasCorrectVelocities 9: [ OK ] NBlibTest.SimulationStateHasCorrectVelocities (0 ms) 9: [----------] 20 tests from NBlibTest (37 ms total) 9: 9: [----------] Global test environment tear-down 9: [==========] 20 tests from 1 test suite ran. (37 ms total) 9: [ PASSED ] 20 tests. 9/92 Test #9: NbLibIntegrationTests ..................... Passed 0.12 sec test 10 Start 10: NbLibIntegratorTests 10: Test command: /build/reproducible-path/gromacs-2025.1/build/basic-dp/bin/nblib-integrator-test "--gtest_output=xml:/build/reproducible-path/gromacs-2025.1/build/basic-dp/Testing/Temporary/NbLibIntegratorTests.xml" 10: Working Directory: /build/reproducible-path/gromacs-2025.1/build/basic-dp/api/nblib/tests 10: Test timeout computed to be: 600 10: [==========] Running 1 test from 1 test suite. 10: [----------] Global test environment set-up. 10: [----------] 1 test from NBlibTest 10: [ RUN ] NBlibTest.IntegratorWorks 10: [ OK ] NBlibTest.IntegratorWorks (0 ms) 10: [----------] 1 test from NBlibTest (1 ms total) 10: 10: [----------] Global test environment tear-down 10: [==========] 1 test from 1 test suite ran. (1 ms total) 10: [ PASSED ] 1 test. 10/92 Test #10: NbLibIntegratorTests ...................... Passed 0.08 sec test 11 Start 11: TestUtilsUnitTests 11: Test command: /build/reproducible-path/gromacs-2025.1/build/basic-dp/bin/testutils-test "--gtest_output=xml:/build/reproducible-path/gromacs-2025.1/build/basic-dp/Testing/Temporary/TestUtilsUnitTests.xml" 11: Working Directory: /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/testutils/tests 11: Test timeout computed to be: 30 11: [==========] Running 75 tests from 7 test suites. 11: [----------] Global test environment set-up. 11: [----------] 10 tests from InteractiveTestHelperTest 11: [ RUN ] InteractiveTestHelperTest.ChecksSimpleSession 11: [ OK ] InteractiveTestHelperTest.ChecksSimpleSession (2 ms) 11: [ RUN ] InteractiveTestHelperTest.ChecksSessionWithoutLastNewline 11: [ OK ] InteractiveTestHelperTest.ChecksSessionWithoutLastNewline (1 ms) 11: [ RUN ] InteractiveTestHelperTest.ChecksSessionWithMissingOutput 11: [ OK ] InteractiveTestHelperTest.ChecksSessionWithMissingOutput (1 ms) 11: [ RUN ] InteractiveTestHelperTest.ChecksSessionWithEquivalentOutput 11: [ OK ] InteractiveTestHelperTest.ChecksSessionWithEquivalentOutput (1 ms) 11: [ RUN ] InteractiveTestHelperTest.DetectsIncorrectOutput 11: [ OK ] InteractiveTestHelperTest.DetectsIncorrectOutput (1 ms) 11: [ RUN ] InteractiveTestHelperTest.DetectsMissingOutput 11: [ OK ] InteractiveTestHelperTest.DetectsMissingOutput (1 ms) 11: [ RUN ] InteractiveTestHelperTest.DetectsMissingFinalOutput 11: [ OK ] InteractiveTestHelperTest.DetectsMissingFinalOutput (1 ms) 11: [ RUN ] InteractiveTestHelperTest.DetectsExtraOutput 11: [ OK ] InteractiveTestHelperTest.DetectsExtraOutput (1 ms) 11: [ RUN ] InteractiveTestHelperTest.DetectsMissingInput 11: [ OK ] InteractiveTestHelperTest.DetectsMissingInput (1 ms) 11: [ RUN ] InteractiveTestHelperTest.DetectsExtraInput 11: [ OK ] InteractiveTestHelperTest.DetectsExtraInput (1 ms) 11: [----------] 10 tests from InteractiveTestHelperTest (14 ms total) 11: 11: [----------] 10 tests from NameOfTestFromTupleTest 11: [ RUN ] NameOfTestFromTupleTest.WorksWithEmptyTuple 11: [ OK ] NameOfTestFromTupleTest.WorksWithEmptyTuple (0 ms) 11: [ RUN ] NameOfTestFromTupleTest.WorksWithFormatFunction 11: [ OK ] NameOfTestFromTupleTest.WorksWithFormatFunction (0 ms) 11: [ RUN ] NameOfTestFromTupleTest.WorksWithFormatFunctionOfEnumVariable 11: [ OK ] NameOfTestFromTupleTest.WorksWithFormatFunctionOfEnumVariable (0 ms) 11: [ RUN ] NameOfTestFromTupleTest.RejectsNullptrFormatFunction 11: [ OK ] NameOfTestFromTupleTest.RejectsNullptrFormatFunction (0 ms) 11: [ RUN ] NameOfTestFromTupleTest.WorksWithFormatLambda 11: [ OK ] NameOfTestFromTupleTest.WorksWithFormatLambda (0 ms) 11: [ RUN ] NameOfTestFromTupleTest.WorksWithUseStringFormat 11: [ OK ] NameOfTestFromTupleTest.WorksWithUseStringFormat (0 ms) 11: [ RUN ] NameOfTestFromTupleTest.WorksWithPrefixFormatter 11: [ OK ] NameOfTestFromTupleTest.WorksWithPrefixFormatter (0 ms) 11: [ RUN ] NameOfTestFromTupleTest.WorksWithFormatFunctor 11: [ OK ] NameOfTestFromTupleTest.WorksWithFormatFunctor (0 ms) 11: [ RUN ] NameOfTestFromTupleTest.WorksWithFormatFromEnumerationArray 11: [ OK ] NameOfTestFromTupleTest.WorksWithFormatFromEnumerationArray (0 ms) 11: [ RUN ] NameOfTestFromTupleTest.WorksWithMixtureOfFormatters 11: [ OK ] NameOfTestFromTupleTest.WorksWithMixtureOfFormatters (0 ms) 11: [----------] 10 tests from NameOfTestFromTupleTest (0 ms total) 11: 11: [----------] 3 tests from RefDataFilenameMakerTest 11: [ RUN ] RefDataFilenameMakerTest.WorksWithFormatFunction 11: [ OK ] RefDataFilenameMakerTest.WorksWithFormatFunction (0 ms) 11: [ RUN ] RefDataFilenameMakerTest.WorksWithMixtureOfFormatters 11: [ OK ] RefDataFilenameMakerTest.WorksWithMixtureOfFormatters (0 ms) 11: [ RUN ] RefDataFilenameMakerTest.WorksWithToEmpty 11: [ OK ] RefDataFilenameMakerTest.WorksWithToEmpty (0 ms) 11: [----------] 3 tests from RefDataFilenameMakerTest (0 ms total) 11: 11: [----------] 37 tests from ReferenceDataTest 11: [ RUN ] ReferenceDataTest.HandlesSimpleData 11: [ OK ] ReferenceDataTest.HandlesSimpleData (0 ms) 11: [ RUN ] ReferenceDataTest.HandlesFloatingPointData 11: [ OK ] ReferenceDataTest.HandlesFloatingPointData (0 ms) 11: [ RUN ] ReferenceDataTest.HandlesPresenceChecks 11: [ OK ] ReferenceDataTest.HandlesPresenceChecks (0 ms) 11: [ RUN ] ReferenceDataTest.HandlesStringBlockData 11: [ OK ] ReferenceDataTest.HandlesStringBlockData (0 ms) 11: [ RUN ] ReferenceDataTest.HandlesVectorData 11: [ OK ] ReferenceDataTest.HandlesVectorData (0 ms) 11: [ RUN ] ReferenceDataTest.HandlesSequenceData 11: [ OK ] ReferenceDataTest.HandlesSequenceData (0 ms) 11: [ RUN ] ReferenceDataTest.HandlesSequenceOfCustomData 11: [ OK ] ReferenceDataTest.HandlesSequenceOfCustomData (0 ms) 11: [ RUN ] ReferenceDataTest.CheckSequenceArrayRef 11: [ OK ] ReferenceDataTest.CheckSequenceArrayRef (0 ms) 11: [ RUN ] ReferenceDataTest.CheckSequenceArrayRefHandlesIncorrectData 11: [ OK ] ReferenceDataTest.CheckSequenceArrayRefHandlesIncorrectData (1 ms) 11: [ RUN ] ReferenceDataTest.CheckSequenceArrayRefHandlesSequenceOfCustomData 11: [ OK ] ReferenceDataTest.CheckSequenceArrayRefHandlesSequenceOfCustomData (1 ms) 11: [ RUN ] ReferenceDataTest.HandlesIncorrectData 11: [ OK ] ReferenceDataTest.HandlesIncorrectData (1 ms) 11: [ RUN ] ReferenceDataTest.HandlesIncorrectDataType 11: [ OK ] ReferenceDataTest.HandlesIncorrectDataType (0 ms) 11: [ RUN ] ReferenceDataTest.HandlesMissingData 11: [ OK ] ReferenceDataTest.HandlesMissingData (0 ms) 11: [ RUN ] ReferenceDataTest.HandlesUncheckedData 11: [ OK ] ReferenceDataTest.HandlesUncheckedData (0 ms) 11: [ RUN ] ReferenceDataTest.HandlesUncheckedDataInSequence 11: [ OK ] ReferenceDataTest.HandlesUncheckedDataInSequence (0 ms) 11: [ RUN ] ReferenceDataTest.HandlesUncheckedDataInCompound 11: [ OK ] ReferenceDataTest.HandlesUncheckedDataInCompound (0 ms) 11: [ RUN ] ReferenceDataTest.HandlesAnys 11: [ OK ] ReferenceDataTest.HandlesAnys (0 ms) 11: [ RUN ] ReferenceDataTest.HandlesKeyValueTree 11: [ OK ] ReferenceDataTest.HandlesKeyValueTree (0 ms) 11: [ RUN ] ReferenceDataTest.HandlesKeyValueTreeExtraKey 11: [ OK ] ReferenceDataTest.HandlesKeyValueTreeExtraKey (0 ms) 11: [ RUN ] ReferenceDataTest.HandlesKeyValueTreeMissingKey 11: [ OK ] ReferenceDataTest.HandlesKeyValueTreeMissingKey (1 ms) 11: [ RUN ] ReferenceDataTest.HandlesAnysWithIncorrectValue 11: [ OK ] ReferenceDataTest.HandlesAnysWithIncorrectValue (1 ms) 11: [ RUN ] ReferenceDataTest.HandlesAnysWithIncorrectType 11: [ OK ] ReferenceDataTest.HandlesAnysWithIncorrectType (0 ms) 11: [ RUN ] ReferenceDataTest.HandlesMissingReferenceDataFile 11: [ OK ] ReferenceDataTest.HandlesMissingReferenceDataFile (0 ms) 11: [ RUN ] ReferenceDataTest.HandlesSpecialCharactersInStrings 11: [ OK ] ReferenceDataTest.HandlesSpecialCharactersInStrings (0 ms) 11: [ RUN ] ReferenceDataTest.HandlesStringsWithTextAndWhitespace 11: [ OK ] ReferenceDataTest.HandlesStringsWithTextAndWhitespace (1 ms) 11: [ RUN ] ReferenceDataTest.HandlesEmptyStrings 11: [ OK ] ReferenceDataTest.HandlesEmptyStrings (1 ms) 11: [ RUN ] ReferenceDataTest.HandlesEmbeddedCdataEndTagInTextBlock 11: [ OK ] ReferenceDataTest.HandlesEmbeddedCdataEndTagInTextBlock (0 ms) 11: [ RUN ] ReferenceDataTest.HandlesSequenceItemIndices 11: [ OK ] ReferenceDataTest.HandlesSequenceItemIndices (1 ms) 11: [ RUN ] ReferenceDataTest.HandlesMultipleChecksAgainstSameData 11: [ OK ] ReferenceDataTest.HandlesMultipleChecksAgainstSameData (1 ms) 11: [ RUN ] ReferenceDataTest.HandlesMultipleNullIds 11: [ OK ] ReferenceDataTest.HandlesMultipleNullIds (0 ms) 11: [ RUN ] ReferenceDataTest.HandlesMultipleComparisonsAgainstNullIds 11: [ OK ] ReferenceDataTest.HandlesMultipleComparisonsAgainstNullIds (1 ms) 11: [ RUN ] ReferenceDataTest.HandlesReadingValues 11: [ OK ] ReferenceDataTest.HandlesReadingValues (0 ms) 11: [ RUN ] ReferenceDataTest.HandlesUpdateChangedWithoutChanges 11: [ OK ] ReferenceDataTest.HandlesUpdateChangedWithoutChanges (1 ms) 11: [ RUN ] ReferenceDataTest.HandlesUpdateChangedWithValueChanges 11: [ OK ] ReferenceDataTest.HandlesUpdateChangedWithValueChanges (1 ms) 11: [ RUN ] ReferenceDataTest.HandlesUpdateChangedWithTypeChanges 11: [ OK ] ReferenceDataTest.HandlesUpdateChangedWithTypeChanges (1 ms) 11: [ RUN ] ReferenceDataTest.HandlesUpdateChangedWithCompoundChanges 11: [ OK ] ReferenceDataTest.HandlesUpdateChangedWithCompoundChanges (1 ms) 11: [ RUN ] ReferenceDataTest.HandlesUpdateChangedWithRemovedEntries 11: [ OK ] ReferenceDataTest.HandlesUpdateChangedWithRemovedEntries (1 ms) 11: [----------] 37 tests from ReferenceDataTest (38 ms total) 11: 11: [----------] 7 tests from FloatingPointDifferenceTest 11: [ RUN ] FloatingPointDifferenceTest.HandlesEqualValues 11: [ OK ] FloatingPointDifferenceTest.HandlesEqualValues (0 ms) 11: [ RUN ] FloatingPointDifferenceTest.HandlesFloatValues 11: [ OK ] FloatingPointDifferenceTest.HandlesFloatValues (0 ms) 11: [ RUN ] FloatingPointDifferenceTest.HandlesZerosOfDifferentSign 11: [ OK ] FloatingPointDifferenceTest.HandlesZerosOfDifferentSign (0 ms) 11: [ RUN ] FloatingPointDifferenceTest.HandlesSignComparisonWithZero 11: [ OK ] FloatingPointDifferenceTest.HandlesSignComparisonWithZero (0 ms) 11: [ RUN ] FloatingPointDifferenceTest.HandlesUlpDifferences 11: [ OK ] FloatingPointDifferenceTest.HandlesUlpDifferences (0 ms) 11: [ RUN ] FloatingPointDifferenceTest.HandlesUlpDifferenceAcrossZero 11: [ OK ] FloatingPointDifferenceTest.HandlesUlpDifferenceAcrossZero (0 ms) 11: [ RUN ] FloatingPointDifferenceTest.HandlesNaN 11: [ OK ] FloatingPointDifferenceTest.HandlesNaN (0 ms) 11: [----------] 7 tests from FloatingPointDifferenceTest (0 ms total) 11: 11: [----------] 4 tests from FloatingPointToleranceTest 11: [ RUN ] FloatingPointToleranceTest.UlpTolerance 11: [ OK ] FloatingPointToleranceTest.UlpTolerance (0 ms) 11: [ RUN ] FloatingPointToleranceTest.RelativeToleranceAsFloatingPoint 11: [ OK ] FloatingPointToleranceTest.RelativeToleranceAsFloatingPoint (0 ms) 11: [ RUN ] FloatingPointToleranceTest.RelativeToleranceAsUlp 11: [ OK ] FloatingPointToleranceTest.RelativeToleranceAsUlp (0 ms) 11: [ RUN ] FloatingPointToleranceTest.DefaultFloatTolerance 11: [ OK ] FloatingPointToleranceTest.DefaultFloatTolerance (0 ms) 11: [----------] 4 tests from FloatingPointToleranceTest (0 ms total) 11: 11: [----------] 4 tests from XvgTests 11: [ RUN ] XvgTests.CreateFile 11: [ OK ] XvgTests.CreateFile (1 ms) 11: [ RUN ] XvgTests.CheckMissing 11: [ OK ] XvgTests.CheckMissing (1 ms) 11: [ RUN ] XvgTests.CheckExtra 11: [ OK ] XvgTests.CheckExtra (1 ms) 11: [ RUN ] XvgTests.ReadIncorrect 11: [ OK ] XvgTests.ReadIncorrect (1 ms) 11: [----------] 4 tests from XvgTests (6 ms total) 11: 11: [----------] Global test environment tear-down 11: [==========] 75 tests from 7 test suites ran. (61 ms total) 11: [ PASSED ] 75 tests. 11/92 Test #11: TestUtilsUnitTests ........................ Passed 0.15 sec test 12 Start 12: TestUtilsMpiUnitTests 12: Test command: /build/reproducible-path/gromacs-2025.1/build/basic-dp/bin/testutils-mpi-test "-ntmpi" "2" "--gtest_output=xml:/build/reproducible-path/gromacs-2025.1/build/basic-dp/Testing/Temporary/TestUtilsMpiUnitTests.xml" 12: Working Directory: /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/testutils/tests 12: Test timeout computed to be: 30 12: [==========] Running 1 test from 1 test suite. 12: [----------] Global test environment set-up. 12: [----------] 1 test from MpiSelfTest 12: [ RUN ] MpiSelfTest.Runs 12: [ OK ] MpiSelfTest.Runs (5 ms) 12: [----------] 1 test from MpiSelfTest (5 ms total) 12: 12: [----------] Global test environment tear-down 12: [==========] 1 test from 1 test suite ran. (5 ms total) 12: [ PASSED ] 1 test. 12/92 Test #12: TestUtilsMpiUnitTests ..................... Passed 0.07 sec test 13 Start 13: UtilityUnitTests 13: Test command: /build/reproducible-path/gromacs-2025.1/build/basic-dp/bin/utility-test "--gtest_output=xml:/build/reproducible-path/gromacs-2025.1/build/basic-dp/Testing/Temporary/UtilityUnitTests.xml" 13: Working Directory: /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/utility/tests 13: Test timeout computed to be: 30 13: [==========] Running 420 tests from 65 test suites. 13: [----------] Global test environment set-up. 13: [----------] 6 tests from AllocatorTest/0, where TypeParam = gmx::Allocator 13: [ RUN ] AllocatorTest/0.AllocatorAlignAllocatesWithAlignment 13: [ OK ] AllocatorTest/0.AllocatorAlignAllocatesWithAlignment (0 ms) 13: [ RUN ] AllocatorTest/0.VectorAllocatesAndResizesWithAlignment 13: [ OK ] AllocatorTest/0.VectorAllocatesAndResizesWithAlignment (1 ms) 13: [ RUN ] AllocatorTest/0.VectorAllocatesAndReservesWithAlignment 13: [ OK ] AllocatorTest/0.VectorAllocatesAndReservesWithAlignment (0 ms) 13: [ RUN ] AllocatorTest/0.Move 13: [ OK ] AllocatorTest/0.Move (0 ms) 13: [ RUN ] AllocatorTest/0.StatelessAllocatorUsesNoMemory 13: [ OK ] AllocatorTest/0.StatelessAllocatorUsesNoMemory (0 ms) 13: [ RUN ] AllocatorTest/0.Comparison 13: [ OK ] AllocatorTest/0.Comparison (0 ms) 13: [----------] 6 tests from AllocatorTest/0 (1 ms total) 13: 13: [----------] 6 tests from AllocatorTest/1, where TypeParam = gmx::Allocator 13: [ RUN ] AllocatorTest/1.AllocatorAlignAllocatesWithAlignment 13: [ OK ] AllocatorTest/1.AllocatorAlignAllocatesWithAlignment (0 ms) 13: [ RUN ] AllocatorTest/1.VectorAllocatesAndResizesWithAlignment 13: [ OK ] AllocatorTest/1.VectorAllocatesAndResizesWithAlignment (0 ms) 13: [ RUN ] AllocatorTest/1.VectorAllocatesAndReservesWithAlignment 13: [ OK ] AllocatorTest/1.VectorAllocatesAndReservesWithAlignment (0 ms) 13: [ RUN ] AllocatorTest/1.Move 13: [ OK ] AllocatorTest/1.Move (0 ms) 13: [ RUN ] AllocatorTest/1.StatelessAllocatorUsesNoMemory 13: [ OK ] AllocatorTest/1.StatelessAllocatorUsesNoMemory (0 ms) 13: [ RUN ] AllocatorTest/1.Comparison 13: [ OK ] AllocatorTest/1.Comparison (0 ms) 13: [----------] 6 tests from AllocatorTest/1 (0 ms total) 13: 13: [----------] 6 tests from AllocatorTest/2, where TypeParam = gmx::Allocator 13: [ RUN ] AllocatorTest/2.AllocatorAlignAllocatesWithAlignment 13: [ OK ] AllocatorTest/2.AllocatorAlignAllocatesWithAlignment (0 ms) 13: [ RUN ] AllocatorTest/2.VectorAllocatesAndResizesWithAlignment 13: [ OK ] AllocatorTest/2.VectorAllocatesAndResizesWithAlignment (0 ms) 13: [ RUN ] AllocatorTest/2.VectorAllocatesAndReservesWithAlignment 13: [ OK ] AllocatorTest/2.VectorAllocatesAndReservesWithAlignment (0 ms) 13: [ RUN ] AllocatorTest/2.Move 13: [ OK ] AllocatorTest/2.Move (0 ms) 13: [ RUN ] AllocatorTest/2.StatelessAllocatorUsesNoMemory 13: [ OK ] AllocatorTest/2.StatelessAllocatorUsesNoMemory (0 ms) 13: [ RUN ] AllocatorTest/2.Comparison 13: [ OK ] AllocatorTest/2.Comparison (0 ms) 13: [----------] 6 tests from AllocatorTest/2 (0 ms total) 13: 13: [----------] 6 tests from AllocatorTest/3, where TypeParam = gmx::Allocator 13: [ RUN ] AllocatorTest/3.AllocatorAlignAllocatesWithAlignment 13: [ OK ] AllocatorTest/3.AllocatorAlignAllocatesWithAlignment (0 ms) 13: [ RUN ] AllocatorTest/3.VectorAllocatesAndResizesWithAlignment 13: [ OK ] AllocatorTest/3.VectorAllocatesAndResizesWithAlignment (0 ms) 13: [ RUN ] AllocatorTest/3.VectorAllocatesAndReservesWithAlignment 13: [ OK ] AllocatorTest/3.VectorAllocatesAndReservesWithAlignment (0 ms) 13: [ RUN ] AllocatorTest/3.Move 13: [ OK ] AllocatorTest/3.Move (0 ms) 13: [ RUN ] AllocatorTest/3.StatelessAllocatorUsesNoMemory 13: [ OK ] AllocatorTest/3.StatelessAllocatorUsesNoMemory (0 ms) 13: [ RUN ] AllocatorTest/3.Comparison 13: [ OK ] AllocatorTest/3.Comparison (0 ms) 13: [----------] 6 tests from AllocatorTest/3 (0 ms total) 13: 13: [----------] 6 tests from AllocatorTest/4, where TypeParam = gmx::Allocator, gmx::AlignedAllocationPolicy> 13: [ RUN ] AllocatorTest/4.AllocatorAlignAllocatesWithAlignment 13: [ OK ] AllocatorTest/4.AllocatorAlignAllocatesWithAlignment (0 ms) 13: [ RUN ] AllocatorTest/4.VectorAllocatesAndResizesWithAlignment 13: [ OK ] AllocatorTest/4.VectorAllocatesAndResizesWithAlignment (1 ms) 13: [ RUN ] AllocatorTest/4.VectorAllocatesAndReservesWithAlignment 13: [ OK ] AllocatorTest/4.VectorAllocatesAndReservesWithAlignment (0 ms) 13: [ RUN ] AllocatorTest/4.Move 13: [ OK ] AllocatorTest/4.Move (0 ms) 13: [ RUN ] AllocatorTest/4.StatelessAllocatorUsesNoMemory 13: [ OK ] AllocatorTest/4.StatelessAllocatorUsesNoMemory (0 ms) 13: [ RUN ] AllocatorTest/4.Comparison 13: [ OK ] AllocatorTest/4.Comparison (0 ms) 13: [----------] 6 tests from AllocatorTest/4 (2 ms total) 13: 13: [----------] 6 tests from AllocatorTest/5, where TypeParam = gmx::Allocator, gmx::PageAlignedAllocationPolicy> 13: [ RUN ] AllocatorTest/5.AllocatorAlignAllocatesWithAlignment 13: [ OK ] AllocatorTest/5.AllocatorAlignAllocatesWithAlignment (0 ms) 13: [ RUN ] AllocatorTest/5.VectorAllocatesAndResizesWithAlignment 13: [ OK ] AllocatorTest/5.VectorAllocatesAndResizesWithAlignment (1 ms) 13: [ RUN ] AllocatorTest/5.VectorAllocatesAndReservesWithAlignment 13: [ OK ] AllocatorTest/5.VectorAllocatesAndReservesWithAlignment (0 ms) 13: [ RUN ] AllocatorTest/5.Move 13: [ OK ] AllocatorTest/5.Move (0 ms) 13: [ RUN ] AllocatorTest/5.StatelessAllocatorUsesNoMemory 13: [ OK ] AllocatorTest/5.StatelessAllocatorUsesNoMemory (0 ms) 13: [ RUN ] AllocatorTest/5.Comparison 13: [ OK ] AllocatorTest/5.Comparison (0 ms) 13: [----------] 6 tests from AllocatorTest/5 (1 ms total) 13: 13: [----------] 1 test from AllocatorUntypedTest 13: [ RUN ] AllocatorUntypedTest.Comparison 13: [ OK ] AllocatorUntypedTest.Comparison (0 ms) 13: [----------] 1 test from AllocatorUntypedTest (0 ms total) 13: 13: [----------] 4 tests from EmptyArrayRefTest 13: [ RUN ] EmptyArrayRefTest.IsEmpty 13: [ OK ] EmptyArrayRefTest.IsEmpty (0 ms) 13: [ RUN ] EmptyArrayRefTest.ConstructFromNullptrIsEmpty 13: [ OK ] EmptyArrayRefTest.ConstructFromNullptrIsEmpty (0 ms) 13: [ RUN ] EmptyArrayRefTest.arrayRefFromArrayIsEmptyForNullptr 13: [ OK ] EmptyArrayRefTest.arrayRefFromArrayIsEmptyForNullptr (0 ms) 13: [ RUN ] EmptyArrayRefTest.arrayRefFromArrayIsEmptyForSizeNull 13: [ OK ] EmptyArrayRefTest.arrayRefFromArrayIsEmptyForSizeNull (0 ms) 13: [----------] 4 tests from EmptyArrayRefTest (0 ms total) 13: 13: [----------] 1 test from EmptyConstArrayRefTest 13: [ RUN ] EmptyConstArrayRefTest.IsEmpty 13: [ OK ] EmptyConstArrayRefTest.IsEmpty (0 ms) 13: [----------] 1 test from EmptyConstArrayRefTest (0 ms total) 13: 13: [----------] 9 tests from ArrayRefTest/0, where TypeParam = gmx::ArrayRef 13: [ RUN ] ArrayRefTest/0.MakeWithAssignmentWorks 13: [ OK ] ArrayRefTest/0.MakeWithAssignmentWorks (0 ms) 13: [ RUN ] ArrayRefTest/0.MakeWithNonConstAssignmentWorks 13: [ OK ] ArrayRefTest/0.MakeWithNonConstAssignmentWorks (0 ms) 13: [ RUN ] ArrayRefTest/0.ConstructWithTemplateConstructorWorks 13: [ OK ] ArrayRefTest/0.ConstructWithTemplateConstructorWorks (0 ms) 13: [ RUN ] ArrayRefTest/0.ConstructWithNonConstTemplateConstructorWorks 13: [ OK ] ArrayRefTest/0.ConstructWithNonConstTemplateConstructorWorks (0 ms) 13: [ RUN ] ArrayRefTest/0.ConstructFromPointersWorks 13: [ OK ] ArrayRefTest/0.ConstructFromPointersWorks (0 ms) 13: [ RUN ] ArrayRefTest/0.ConstructFromNonConstPointersWorks 13: [ OK ] ArrayRefTest/0.ConstructFromNonConstPointersWorks (0 ms) 13: [ RUN ] ArrayRefTest/0.ConstructFromVectorWorks 13: [ OK ] ArrayRefTest/0.ConstructFromVectorWorks (0 ms) 13: [ RUN ] ArrayRefTest/0.ConstructFromNonConstVectorWorks 13: [ OK ] ArrayRefTest/0.ConstructFromNonConstVectorWorks (0 ms) 13: [ RUN ] ArrayRefTest/0.ConstructFromStructFieldWithTemplateConstructorWorks 13: [ OK ] ArrayRefTest/0.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms) 13: [----------] 9 tests from ArrayRefTest/0 (0 ms total) 13: 13: [----------] 9 tests from ArrayRefTest/1, where TypeParam = gmx::ArrayRef 13: [ RUN ] ArrayRefTest/1.MakeWithAssignmentWorks 13: [ OK ] ArrayRefTest/1.MakeWithAssignmentWorks (0 ms) 13: [ RUN ] ArrayRefTest/1.MakeWithNonConstAssignmentWorks 13: [ OK ] ArrayRefTest/1.MakeWithNonConstAssignmentWorks (0 ms) 13: [ RUN ] ArrayRefTest/1.ConstructWithTemplateConstructorWorks 13: [ OK ] ArrayRefTest/1.ConstructWithTemplateConstructorWorks (0 ms) 13: [ RUN ] ArrayRefTest/1.ConstructWithNonConstTemplateConstructorWorks 13: [ OK ] ArrayRefTest/1.ConstructWithNonConstTemplateConstructorWorks (0 ms) 13: [ RUN ] ArrayRefTest/1.ConstructFromPointersWorks 13: [ OK ] ArrayRefTest/1.ConstructFromPointersWorks (0 ms) 13: [ RUN ] ArrayRefTest/1.ConstructFromNonConstPointersWorks 13: [ OK ] ArrayRefTest/1.ConstructFromNonConstPointersWorks (0 ms) 13: [ RUN ] ArrayRefTest/1.ConstructFromVectorWorks 13: [ OK ] ArrayRefTest/1.ConstructFromVectorWorks (0 ms) 13: [ RUN ] ArrayRefTest/1.ConstructFromNonConstVectorWorks 13: [ OK ] ArrayRefTest/1.ConstructFromNonConstVectorWorks (0 ms) 13: [ RUN ] ArrayRefTest/1.ConstructFromStructFieldWithTemplateConstructorWorks 13: [ OK ] ArrayRefTest/1.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms) 13: [----------] 9 tests from ArrayRefTest/1 (0 ms total) 13: 13: [----------] 9 tests from ArrayRefTest/2, where TypeParam = gmx::ArrayRef 13: [ RUN ] ArrayRefTest/2.MakeWithAssignmentWorks 13: [ OK ] ArrayRefTest/2.MakeWithAssignmentWorks (0 ms) 13: [ RUN ] ArrayRefTest/2.MakeWithNonConstAssignmentWorks 13: [ OK ] ArrayRefTest/2.MakeWithNonConstAssignmentWorks (0 ms) 13: [ RUN ] ArrayRefTest/2.ConstructWithTemplateConstructorWorks 13: [ OK ] ArrayRefTest/2.ConstructWithTemplateConstructorWorks (0 ms) 13: [ RUN ] ArrayRefTest/2.ConstructWithNonConstTemplateConstructorWorks 13: [ OK ] ArrayRefTest/2.ConstructWithNonConstTemplateConstructorWorks (0 ms) 13: [ RUN ] ArrayRefTest/2.ConstructFromPointersWorks 13: [ OK ] ArrayRefTest/2.ConstructFromPointersWorks (0 ms) 13: [ RUN ] ArrayRefTest/2.ConstructFromNonConstPointersWorks 13: [ OK ] ArrayRefTest/2.ConstructFromNonConstPointersWorks (0 ms) 13: [ RUN ] ArrayRefTest/2.ConstructFromVectorWorks 13: [ OK ] ArrayRefTest/2.ConstructFromVectorWorks (0 ms) 13: [ RUN ] ArrayRefTest/2.ConstructFromNonConstVectorWorks 13: [ OK ] ArrayRefTest/2.ConstructFromNonConstVectorWorks (0 ms) 13: [ RUN ] ArrayRefTest/2.ConstructFromStructFieldWithTemplateConstructorWorks 13: [ OK ] ArrayRefTest/2.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms) 13: [----------] 9 tests from ArrayRefTest/2 (0 ms total) 13: 13: [----------] 9 tests from ArrayRefTest/3, where TypeParam = gmx::ArrayRef 13: [ RUN ] ArrayRefTest/3.MakeWithAssignmentWorks 13: [ OK ] ArrayRefTest/3.MakeWithAssignmentWorks (0 ms) 13: [ RUN ] ArrayRefTest/3.MakeWithNonConstAssignmentWorks 13: [ OK ] ArrayRefTest/3.MakeWithNonConstAssignmentWorks (0 ms) 13: [ RUN ] ArrayRefTest/3.ConstructWithTemplateConstructorWorks 13: [ OK ] ArrayRefTest/3.ConstructWithTemplateConstructorWorks (0 ms) 13: [ RUN ] ArrayRefTest/3.ConstructWithNonConstTemplateConstructorWorks 13: [ OK ] ArrayRefTest/3.ConstructWithNonConstTemplateConstructorWorks (0 ms) 13: [ RUN ] ArrayRefTest/3.ConstructFromPointersWorks 13: [ OK ] ArrayRefTest/3.ConstructFromPointersWorks (0 ms) 13: [ RUN ] ArrayRefTest/3.ConstructFromNonConstPointersWorks 13: [ OK ] ArrayRefTest/3.ConstructFromNonConstPointersWorks (0 ms) 13: [ RUN ] ArrayRefTest/3.ConstructFromVectorWorks 13: [ OK ] ArrayRefTest/3.ConstructFromVectorWorks (0 ms) 13: [ RUN ] ArrayRefTest/3.ConstructFromNonConstVectorWorks 13: [ OK ] ArrayRefTest/3.ConstructFromNonConstVectorWorks (0 ms) 13: [ RUN ] ArrayRefTest/3.ConstructFromStructFieldWithTemplateConstructorWorks 13: [ OK ] ArrayRefTest/3.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms) 13: [----------] 9 tests from ArrayRefTest/3 (0 ms total) 13: 13: [----------] 9 tests from ArrayRefTest/4, where TypeParam = gmx::ArrayRef 13: [ RUN ] ArrayRefTest/4.MakeWithAssignmentWorks 13: [ OK ] ArrayRefTest/4.MakeWithAssignmentWorks (0 ms) 13: [ RUN ] ArrayRefTest/4.MakeWithNonConstAssignmentWorks 13: [ OK ] ArrayRefTest/4.MakeWithNonConstAssignmentWorks (0 ms) 13: [ RUN ] ArrayRefTest/4.ConstructWithTemplateConstructorWorks 13: [ OK ] ArrayRefTest/4.ConstructWithTemplateConstructorWorks (0 ms) 13: [ RUN ] ArrayRefTest/4.ConstructWithNonConstTemplateConstructorWorks 13: [ OK ] ArrayRefTest/4.ConstructWithNonConstTemplateConstructorWorks (0 ms) 13: [ RUN ] ArrayRefTest/4.ConstructFromPointersWorks 13: [ OK ] ArrayRefTest/4.ConstructFromPointersWorks (0 ms) 13: [ RUN ] ArrayRefTest/4.ConstructFromNonConstPointersWorks 13: [ OK ] ArrayRefTest/4.ConstructFromNonConstPointersWorks (0 ms) 13: [ RUN ] ArrayRefTest/4.ConstructFromVectorWorks 13: [ OK ] ArrayRefTest/4.ConstructFromVectorWorks (0 ms) 13: [ RUN ] ArrayRefTest/4.ConstructFromNonConstVectorWorks 13: [ OK ] ArrayRefTest/4.ConstructFromNonConstVectorWorks (0 ms) 13: [ RUN ] ArrayRefTest/4.ConstructFromStructFieldWithTemplateConstructorWorks 13: [ OK ] ArrayRefTest/4.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms) 13: [----------] 9 tests from ArrayRefTest/4 (0 ms total) 13: 13: [----------] 9 tests from ArrayRefTest/5, where TypeParam = gmx::ArrayRef 13: [ RUN ] ArrayRefTest/5.MakeWithAssignmentWorks 13: [ OK ] ArrayRefTest/5.MakeWithAssignmentWorks (0 ms) 13: [ RUN ] ArrayRefTest/5.MakeWithNonConstAssignmentWorks 13: [ OK ] ArrayRefTest/5.MakeWithNonConstAssignmentWorks (0 ms) 13: [ RUN ] ArrayRefTest/5.ConstructWithTemplateConstructorWorks 13: [ OK ] ArrayRefTest/5.ConstructWithTemplateConstructorWorks (0 ms) 13: [ RUN ] ArrayRefTest/5.ConstructWithNonConstTemplateConstructorWorks 13: [ OK ] ArrayRefTest/5.ConstructWithNonConstTemplateConstructorWorks (0 ms) 13: [ RUN ] ArrayRefTest/5.ConstructFromPointersWorks 13: [ OK ] ArrayRefTest/5.ConstructFromPointersWorks (0 ms) 13: [ RUN ] ArrayRefTest/5.ConstructFromNonConstPointersWorks 13: [ OK ] ArrayRefTest/5.ConstructFromNonConstPointersWorks (0 ms) 13: [ RUN ] ArrayRefTest/5.ConstructFromVectorWorks 13: [ OK ] ArrayRefTest/5.ConstructFromVectorWorks (0 ms) 13: [ RUN ] ArrayRefTest/5.ConstructFromNonConstVectorWorks 13: [ OK ] ArrayRefTest/5.ConstructFromNonConstVectorWorks (0 ms) 13: [ RUN ] ArrayRefTest/5.ConstructFromStructFieldWithTemplateConstructorWorks 13: [ OK ] ArrayRefTest/5.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms) 13: [----------] 9 tests from ArrayRefTest/5 (0 ms total) 13: 13: [----------] 9 tests from ArrayRefTest/6, where TypeParam = gmx::ArrayRef 13: [ RUN ] ArrayRefTest/6.MakeWithAssignmentWorks 13: [ OK ] ArrayRefTest/6.MakeWithAssignmentWorks (0 ms) 13: [ RUN ] ArrayRefTest/6.MakeWithNonConstAssignmentWorks 13: [ OK ] ArrayRefTest/6.MakeWithNonConstAssignmentWorks (0 ms) 13: [ RUN ] ArrayRefTest/6.ConstructWithTemplateConstructorWorks 13: [ OK ] ArrayRefTest/6.ConstructWithTemplateConstructorWorks (0 ms) 13: [ RUN ] ArrayRefTest/6.ConstructWithNonConstTemplateConstructorWorks 13: [ OK ] ArrayRefTest/6.ConstructWithNonConstTemplateConstructorWorks (0 ms) 13: [ RUN ] ArrayRefTest/6.ConstructFromPointersWorks 13: [ OK ] ArrayRefTest/6.ConstructFromPointersWorks (0 ms) 13: [ RUN ] ArrayRefTest/6.ConstructFromNonConstPointersWorks 13: [ OK ] ArrayRefTest/6.ConstructFromNonConstPointersWorks (0 ms) 13: [ RUN ] ArrayRefTest/6.ConstructFromVectorWorks 13: [ OK ] ArrayRefTest/6.ConstructFromVectorWorks (0 ms) 13: [ RUN ] ArrayRefTest/6.ConstructFromNonConstVectorWorks 13: [ OK ] ArrayRefTest/6.ConstructFromNonConstVectorWorks (0 ms) 13: [ RUN ] ArrayRefTest/6.ConstructFromStructFieldWithTemplateConstructorWorks 13: [ OK ] ArrayRefTest/6.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms) 13: [----------] 9 tests from ArrayRefTest/6 (0 ms total) 13: 13: [----------] 9 tests from ArrayRefTest/7, where TypeParam = gmx::ArrayRef 13: [ RUN ] ArrayRefTest/7.MakeWithAssignmentWorks 13: [ OK ] ArrayRefTest/7.MakeWithAssignmentWorks (0 ms) 13: [ RUN ] ArrayRefTest/7.MakeWithNonConstAssignmentWorks 13: [ OK ] ArrayRefTest/7.MakeWithNonConstAssignmentWorks (0 ms) 13: [ RUN ] ArrayRefTest/7.ConstructWithTemplateConstructorWorks 13: [ OK ] ArrayRefTest/7.ConstructWithTemplateConstructorWorks (0 ms) 13: [ RUN ] ArrayRefTest/7.ConstructWithNonConstTemplateConstructorWorks 13: [ OK ] ArrayRefTest/7.ConstructWithNonConstTemplateConstructorWorks (0 ms) 13: [ RUN ] ArrayRefTest/7.ConstructFromPointersWorks 13: [ OK ] ArrayRefTest/7.ConstructFromPointersWorks (0 ms) 13: [ RUN ] ArrayRefTest/7.ConstructFromNonConstPointersWorks 13: [ OK ] ArrayRefTest/7.ConstructFromNonConstPointersWorks (0 ms) 13: [ RUN ] ArrayRefTest/7.ConstructFromVectorWorks 13: [ OK ] ArrayRefTest/7.ConstructFromVectorWorks (0 ms) 13: [ RUN ] ArrayRefTest/7.ConstructFromNonConstVectorWorks 13: [ OK ] ArrayRefTest/7.ConstructFromNonConstVectorWorks (0 ms) 13: [ RUN ] ArrayRefTest/7.ConstructFromStructFieldWithTemplateConstructorWorks 13: [ OK ] ArrayRefTest/7.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms) 13: [----------] 9 tests from ArrayRefTest/7 (0 ms total) 13: 13: [----------] 9 tests from ArrayRefTest/8, where TypeParam = gmx::ArrayRef 13: [ RUN ] ArrayRefTest/8.MakeWithAssignmentWorks 13: [ OK ] ArrayRefTest/8.MakeWithAssignmentWorks (0 ms) 13: [ RUN ] ArrayRefTest/8.MakeWithNonConstAssignmentWorks 13: [ OK ] ArrayRefTest/8.MakeWithNonConstAssignmentWorks (0 ms) 13: [ RUN ] ArrayRefTest/8.ConstructWithTemplateConstructorWorks 13: [ OK ] ArrayRefTest/8.ConstructWithTemplateConstructorWorks (0 ms) 13: [ RUN ] ArrayRefTest/8.ConstructWithNonConstTemplateConstructorWorks 13: [ OK ] ArrayRefTest/8.ConstructWithNonConstTemplateConstructorWorks (0 ms) 13: [ RUN ] ArrayRefTest/8.ConstructFromPointersWorks 13: [ OK ] ArrayRefTest/8.ConstructFromPointersWorks (0 ms) 13: [ RUN ] ArrayRefTest/8.ConstructFromNonConstPointersWorks 13: [ OK ] ArrayRefTest/8.ConstructFromNonConstPointersWorks (0 ms) 13: [ RUN ] ArrayRefTest/8.ConstructFromVectorWorks 13: [ OK ] ArrayRefTest/8.ConstructFromVectorWorks (0 ms) 13: [ RUN ] ArrayRefTest/8.ConstructFromNonConstVectorWorks 13: [ OK ] ArrayRefTest/8.ConstructFromNonConstVectorWorks (0 ms) 13: [ RUN ] ArrayRefTest/8.ConstructFromStructFieldWithTemplateConstructorWorks 13: [ OK ] ArrayRefTest/8.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms) 13: [----------] 9 tests from ArrayRefTest/8 (0 ms total) 13: 13: [----------] 9 tests from ArrayRefTest/9, where TypeParam = gmx::ArrayRef 13: [ RUN ] ArrayRefTest/9.MakeWithAssignmentWorks 13: [ OK ] ArrayRefTest/9.MakeWithAssignmentWorks (0 ms) 13: [ RUN ] ArrayRefTest/9.MakeWithNonConstAssignmentWorks 13: [ OK ] ArrayRefTest/9.MakeWithNonConstAssignmentWorks (0 ms) 13: [ RUN ] ArrayRefTest/9.ConstructWithTemplateConstructorWorks 13: [ OK ] ArrayRefTest/9.ConstructWithTemplateConstructorWorks (0 ms) 13: [ RUN ] ArrayRefTest/9.ConstructWithNonConstTemplateConstructorWorks 13: [ OK ] ArrayRefTest/9.ConstructWithNonConstTemplateConstructorWorks (0 ms) 13: [ RUN ] ArrayRefTest/9.ConstructFromPointersWorks 13: [ OK ] ArrayRefTest/9.ConstructFromPointersWorks (0 ms) 13: [ RUN ] ArrayRefTest/9.ConstructFromNonConstPointersWorks 13: [ OK ] ArrayRefTest/9.ConstructFromNonConstPointersWorks (0 ms) 13: [ RUN ] ArrayRefTest/9.ConstructFromVectorWorks 13: [ OK ] ArrayRefTest/9.ConstructFromVectorWorks (0 ms) 13: [ RUN ] ArrayRefTest/9.ConstructFromNonConstVectorWorks 13: [ OK ] ArrayRefTest/9.ConstructFromNonConstVectorWorks (0 ms) 13: [ RUN ] ArrayRefTest/9.ConstructFromStructFieldWithTemplateConstructorWorks 13: [ OK ] ArrayRefTest/9.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms) 13: [----------] 9 tests from ArrayRefTest/9 (0 ms total) 13: 13: [----------] 9 tests from ArrayRefTest/10, where TypeParam = gmx::ArrayRef 13: [ RUN ] ArrayRefTest/10.MakeWithAssignmentWorks 13: [ OK ] ArrayRefTest/10.MakeWithAssignmentWorks (0 ms) 13: [ RUN ] ArrayRefTest/10.MakeWithNonConstAssignmentWorks 13: [ OK ] ArrayRefTest/10.MakeWithNonConstAssignmentWorks (0 ms) 13: [ RUN ] ArrayRefTest/10.ConstructWithTemplateConstructorWorks 13: [ OK ] ArrayRefTest/10.ConstructWithTemplateConstructorWorks (0 ms) 13: [ RUN ] ArrayRefTest/10.ConstructWithNonConstTemplateConstructorWorks 13: [ OK ] ArrayRefTest/10.ConstructWithNonConstTemplateConstructorWorks (0 ms) 13: [ RUN ] ArrayRefTest/10.ConstructFromPointersWorks 13: [ OK ] ArrayRefTest/10.ConstructFromPointersWorks (0 ms) 13: [ RUN ] ArrayRefTest/10.ConstructFromNonConstPointersWorks 13: [ OK ] ArrayRefTest/10.ConstructFromNonConstPointersWorks (0 ms) 13: [ RUN ] ArrayRefTest/10.ConstructFromVectorWorks 13: [ OK ] ArrayRefTest/10.ConstructFromVectorWorks (0 ms) 13: [ RUN ] ArrayRefTest/10.ConstructFromNonConstVectorWorks 13: [ OK ] ArrayRefTest/10.ConstructFromNonConstVectorWorks (0 ms) 13: [ RUN ] ArrayRefTest/10.ConstructFromStructFieldWithTemplateConstructorWorks 13: [ OK ] ArrayRefTest/10.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms) 13: [----------] 9 tests from ArrayRefTest/10 (0 ms total) 13: 13: [----------] 9 tests from ArrayRefTest/11, where TypeParam = gmx::ArrayRef 13: [ RUN ] ArrayRefTest/11.MakeWithAssignmentWorks 13: [ OK ] ArrayRefTest/11.MakeWithAssignmentWorks (0 ms) 13: [ RUN ] ArrayRefTest/11.MakeWithNonConstAssignmentWorks 13: [ OK ] ArrayRefTest/11.MakeWithNonConstAssignmentWorks (0 ms) 13: [ RUN ] ArrayRefTest/11.ConstructWithTemplateConstructorWorks 13: [ OK ] ArrayRefTest/11.ConstructWithTemplateConstructorWorks (0 ms) 13: [ RUN ] ArrayRefTest/11.ConstructWithNonConstTemplateConstructorWorks 13: [ OK ] ArrayRefTest/11.ConstructWithNonConstTemplateConstructorWorks (0 ms) 13: [ RUN ] ArrayRefTest/11.ConstructFromPointersWorks 13: [ OK ] ArrayRefTest/11.ConstructFromPointersWorks (0 ms) 13: [ RUN ] ArrayRefTest/11.ConstructFromNonConstPointersWorks 13: [ OK ] ArrayRefTest/11.ConstructFromNonConstPointersWorks (0 ms) 13: [ RUN ] ArrayRefTest/11.ConstructFromVectorWorks 13: [ OK ] ArrayRefTest/11.ConstructFromVectorWorks (0 ms) 13: [ RUN ] ArrayRefTest/11.ConstructFromNonConstVectorWorks 13: [ OK ] ArrayRefTest/11.ConstructFromNonConstVectorWorks (0 ms) 13: [ RUN ] ArrayRefTest/11.ConstructFromStructFieldWithTemplateConstructorWorks 13: [ OK ] ArrayRefTest/11.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms) 13: [----------] 9 tests from ArrayRefTest/11 (0 ms total) 13: 13: [----------] 9 tests from ArrayRefTest/12, where TypeParam = gmx::ArrayRef 13: [ RUN ] ArrayRefTest/12.MakeWithAssignmentWorks 13: [ OK ] ArrayRefTest/12.MakeWithAssignmentWorks (0 ms) 13: [ RUN ] ArrayRefTest/12.MakeWithNonConstAssignmentWorks 13: [ OK ] ArrayRefTest/12.MakeWithNonConstAssignmentWorks (0 ms) 13: [ RUN ] ArrayRefTest/12.ConstructWithTemplateConstructorWorks 13: [ OK ] ArrayRefTest/12.ConstructWithTemplateConstructorWorks (0 ms) 13: [ RUN ] ArrayRefTest/12.ConstructWithNonConstTemplateConstructorWorks 13: [ OK ] ArrayRefTest/12.ConstructWithNonConstTemplateConstructorWorks (0 ms) 13: [ RUN ] ArrayRefTest/12.ConstructFromPointersWorks 13: [ OK ] ArrayRefTest/12.ConstructFromPointersWorks (0 ms) 13: [ RUN ] ArrayRefTest/12.ConstructFromNonConstPointersWorks 13: [ OK ] ArrayRefTest/12.ConstructFromNonConstPointersWorks (0 ms) 13: [ RUN ] ArrayRefTest/12.ConstructFromVectorWorks 13: [ OK ] ArrayRefTest/12.ConstructFromVectorWorks (0 ms) 13: [ RUN ] ArrayRefTest/12.ConstructFromNonConstVectorWorks 13: [ OK ] ArrayRefTest/12.ConstructFromNonConstVectorWorks (0 ms) 13: [ RUN ] ArrayRefTest/12.ConstructFromStructFieldWithTemplateConstructorWorks 13: [ OK ] ArrayRefTest/12.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms) 13: [----------] 9 tests from ArrayRefTest/12 (0 ms total) 13: 13: [----------] 9 tests from ArrayRefTest/13, where TypeParam = gmx::ArrayRef 13: [ RUN ] ArrayRefTest/13.MakeWithAssignmentWorks 13: [ OK ] ArrayRefTest/13.MakeWithAssignmentWorks (0 ms) 13: [ RUN ] ArrayRefTest/13.MakeWithNonConstAssignmentWorks 13: [ OK ] ArrayRefTest/13.MakeWithNonConstAssignmentWorks (0 ms) 13: [ RUN ] ArrayRefTest/13.ConstructWithTemplateConstructorWorks 13: [ OK ] ArrayRefTest/13.ConstructWithTemplateConstructorWorks (0 ms) 13: [ RUN ] ArrayRefTest/13.ConstructWithNonConstTemplateConstructorWorks 13: [ OK ] ArrayRefTest/13.ConstructWithNonConstTemplateConstructorWorks (0 ms) 13: [ RUN ] ArrayRefTest/13.ConstructFromPointersWorks 13: [ OK ] ArrayRefTest/13.ConstructFromPointersWorks (0 ms) 13: [ RUN ] ArrayRefTest/13.ConstructFromNonConstPointersWorks 13: [ OK ] ArrayRefTest/13.ConstructFromNonConstPointersWorks (0 ms) 13: [ RUN ] ArrayRefTest/13.ConstructFromVectorWorks 13: [ OK ] ArrayRefTest/13.ConstructFromVectorWorks (0 ms) 13: [ RUN ] ArrayRefTest/13.ConstructFromNonConstVectorWorks 13: [ OK ] ArrayRefTest/13.ConstructFromNonConstVectorWorks (0 ms) 13: [ RUN ] ArrayRefTest/13.ConstructFromStructFieldWithTemplateConstructorWorks 13: [ OK ] ArrayRefTest/13.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms) 13: [----------] 9 tests from ArrayRefTest/13 (0 ms total) 13: 13: [----------] 9 tests from ArrayRefTest/14, where TypeParam = gmx::ArrayRef 13: [ RUN ] ArrayRefTest/14.MakeWithAssignmentWorks 13: [ OK ] ArrayRefTest/14.MakeWithAssignmentWorks (0 ms) 13: [ RUN ] ArrayRefTest/14.MakeWithNonConstAssignmentWorks 13: [ OK ] ArrayRefTest/14.MakeWithNonConstAssignmentWorks (0 ms) 13: [ RUN ] ArrayRefTest/14.ConstructWithTemplateConstructorWorks 13: [ OK ] ArrayRefTest/14.ConstructWithTemplateConstructorWorks (0 ms) 13: [ RUN ] ArrayRefTest/14.ConstructWithNonConstTemplateConstructorWorks 13: [ OK ] ArrayRefTest/14.ConstructWithNonConstTemplateConstructorWorks (0 ms) 13: [ RUN ] ArrayRefTest/14.ConstructFromPointersWorks 13: [ OK ] ArrayRefTest/14.ConstructFromPointersWorks (0 ms) 13: [ RUN ] ArrayRefTest/14.ConstructFromNonConstPointersWorks 13: [ OK ] ArrayRefTest/14.ConstructFromNonConstPointersWorks (0 ms) 13: [ RUN ] ArrayRefTest/14.ConstructFromVectorWorks 13: [ OK ] ArrayRefTest/14.ConstructFromVectorWorks (0 ms) 13: [ RUN ] ArrayRefTest/14.ConstructFromNonConstVectorWorks 13: [ OK ] ArrayRefTest/14.ConstructFromNonConstVectorWorks (0 ms) 13: [ RUN ] ArrayRefTest/14.ConstructFromStructFieldWithTemplateConstructorWorks 13: [ OK ] ArrayRefTest/14.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms) 13: [----------] 9 tests from ArrayRefTest/14 (0 ms total) 13: 13: [----------] 9 tests from ArrayRefTest/15, where TypeParam = gmx::ArrayRef 13: [ RUN ] ArrayRefTest/15.MakeWithAssignmentWorks 13: [ OK ] ArrayRefTest/15.MakeWithAssignmentWorks (0 ms) 13: [ RUN ] ArrayRefTest/15.MakeWithNonConstAssignmentWorks 13: [ OK ] ArrayRefTest/15.MakeWithNonConstAssignmentWorks (0 ms) 13: [ RUN ] ArrayRefTest/15.ConstructWithTemplateConstructorWorks 13: [ OK ] ArrayRefTest/15.ConstructWithTemplateConstructorWorks (0 ms) 13: [ RUN ] ArrayRefTest/15.ConstructWithNonConstTemplateConstructorWorks 13: [ OK ] ArrayRefTest/15.ConstructWithNonConstTemplateConstructorWorks (0 ms) 13: [ RUN ] ArrayRefTest/15.ConstructFromPointersWorks 13: [ OK ] ArrayRefTest/15.ConstructFromPointersWorks (0 ms) 13: [ RUN ] ArrayRefTest/15.ConstructFromNonConstPointersWorks 13: [ OK ] ArrayRefTest/15.ConstructFromNonConstPointersWorks (0 ms) 13: [ RUN ] ArrayRefTest/15.ConstructFromVectorWorks 13: [ OK ] ArrayRefTest/15.ConstructFromVectorWorks (0 ms) 13: [ RUN ] ArrayRefTest/15.ConstructFromNonConstVectorWorks 13: [ OK ] ArrayRefTest/15.ConstructFromNonConstVectorWorks (0 ms) 13: [ RUN ] ArrayRefTest/15.ConstructFromStructFieldWithTemplateConstructorWorks 13: [ OK ] ArrayRefTest/15.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms) 13: [----------] 9 tests from ArrayRefTest/15 (0 ms total) 13: 13: [----------] 9 tests from ArrayRefTest/16, where TypeParam = gmx::ArrayRef 13: [ RUN ] ArrayRefTest/16.MakeWithAssignmentWorks 13: [ OK ] ArrayRefTest/16.MakeWithAssignmentWorks (0 ms) 13: [ RUN ] ArrayRefTest/16.MakeWithNonConstAssignmentWorks 13: [ OK ] ArrayRefTest/16.MakeWithNonConstAssignmentWorks (0 ms) 13: [ RUN ] ArrayRefTest/16.ConstructWithTemplateConstructorWorks 13: [ OK ] ArrayRefTest/16.ConstructWithTemplateConstructorWorks (0 ms) 13: [ RUN ] ArrayRefTest/16.ConstructWithNonConstTemplateConstructorWorks 13: [ OK ] ArrayRefTest/16.ConstructWithNonConstTemplateConstructorWorks (0 ms) 13: [ RUN ] ArrayRefTest/16.ConstructFromPointersWorks 13: [ OK ] ArrayRefTest/16.ConstructFromPointersWorks (0 ms) 13: [ RUN ] ArrayRefTest/16.ConstructFromNonConstPointersWorks 13: [ OK ] ArrayRefTest/16.ConstructFromNonConstPointersWorks (0 ms) 13: [ RUN ] ArrayRefTest/16.ConstructFromVectorWorks 13: [ OK ] ArrayRefTest/16.ConstructFromVectorWorks (0 ms) 13: [ RUN ] ArrayRefTest/16.ConstructFromNonConstVectorWorks 13: [ OK ] ArrayRefTest/16.ConstructFromNonConstVectorWorks (0 ms) 13: [ RUN ] ArrayRefTest/16.ConstructFromStructFieldWithTemplateConstructorWorks 13: [ OK ] ArrayRefTest/16.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms) 13: [----------] 9 tests from ArrayRefTest/16 (0 ms total) 13: 13: [----------] 9 tests from ArrayRefTest/17, where TypeParam = gmx::ArrayRef 13: [ RUN ] ArrayRefTest/17.MakeWithAssignmentWorks 13: [ OK ] ArrayRefTest/17.MakeWithAssignmentWorks (0 ms) 13: [ RUN ] ArrayRefTest/17.MakeWithNonConstAssignmentWorks 13: [ OK ] ArrayRefTest/17.MakeWithNonConstAssignmentWorks (0 ms) 13: [ RUN ] ArrayRefTest/17.ConstructWithTemplateConstructorWorks 13: [ OK ] ArrayRefTest/17.ConstructWithTemplateConstructorWorks (0 ms) 13: [ RUN ] ArrayRefTest/17.ConstructWithNonConstTemplateConstructorWorks 13: [ OK ] ArrayRefTest/17.ConstructWithNonConstTemplateConstructorWorks (0 ms) 13: [ RUN ] ArrayRefTest/17.ConstructFromPointersWorks 13: [ OK ] ArrayRefTest/17.ConstructFromPointersWorks (0 ms) 13: [ RUN ] ArrayRefTest/17.ConstructFromNonConstPointersWorks 13: [ OK ] ArrayRefTest/17.ConstructFromNonConstPointersWorks (0 ms) 13: [ RUN ] ArrayRefTest/17.ConstructFromVectorWorks 13: [ OK ] ArrayRefTest/17.ConstructFromVectorWorks (0 ms) 13: [ RUN ] ArrayRefTest/17.ConstructFromNonConstVectorWorks 13: [ OK ] ArrayRefTest/17.ConstructFromNonConstVectorWorks (0 ms) 13: [ RUN ] ArrayRefTest/17.ConstructFromStructFieldWithTemplateConstructorWorks 13: [ OK ] ArrayRefTest/17.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms) 13: [----------] 9 tests from ArrayRefTest/17 (0 ms total) 13: 13: [----------] 9 tests from ArrayRefTest/18, where TypeParam = gmx::ArrayRef 13: [ RUN ] ArrayRefTest/18.MakeWithAssignmentWorks 13: [ OK ] ArrayRefTest/18.MakeWithAssignmentWorks (0 ms) 13: [ RUN ] ArrayRefTest/18.MakeWithNonConstAssignmentWorks 13: [ OK ] ArrayRefTest/18.MakeWithNonConstAssignmentWorks (0 ms) 13: [ RUN ] ArrayRefTest/18.ConstructWithTemplateConstructorWorks 13: [ OK ] ArrayRefTest/18.ConstructWithTemplateConstructorWorks (0 ms) 13: [ RUN ] ArrayRefTest/18.ConstructWithNonConstTemplateConstructorWorks 13: [ OK ] ArrayRefTest/18.ConstructWithNonConstTemplateConstructorWorks (0 ms) 13: [ RUN ] ArrayRefTest/18.ConstructFromPointersWorks 13: [ OK ] ArrayRefTest/18.ConstructFromPointersWorks (0 ms) 13: [ RUN ] ArrayRefTest/18.ConstructFromNonConstPointersWorks 13: [ OK ] ArrayRefTest/18.ConstructFromNonConstPointersWorks (0 ms) 13: [ RUN ] ArrayRefTest/18.ConstructFromVectorWorks 13: [ OK ] ArrayRefTest/18.ConstructFromVectorWorks (0 ms) 13: [ RUN ] ArrayRefTest/18.ConstructFromNonConstVectorWorks 13: [ OK ] ArrayRefTest/18.ConstructFromNonConstVectorWorks (0 ms) 13: [ RUN ] ArrayRefTest/18.ConstructFromStructFieldWithTemplateConstructorWorks 13: [ OK ] ArrayRefTest/18.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms) 13: [----------] 9 tests from ArrayRefTest/18 (0 ms total) 13: 13: [----------] 9 tests from ArrayRefTest/19, where TypeParam = gmx::ArrayRef 13: [ RUN ] ArrayRefTest/19.MakeWithAssignmentWorks 13: [ OK ] ArrayRefTest/19.MakeWithAssignmentWorks (0 ms) 13: [ RUN ] ArrayRefTest/19.MakeWithNonConstAssignmentWorks 13: [ OK ] ArrayRefTest/19.MakeWithNonConstAssignmentWorks (0 ms) 13: [ RUN ] ArrayRefTest/19.ConstructWithTemplateConstructorWorks 13: [ OK ] ArrayRefTest/19.ConstructWithTemplateConstructorWorks (0 ms) 13: [ RUN ] ArrayRefTest/19.ConstructWithNonConstTemplateConstructorWorks 13: [ OK ] ArrayRefTest/19.ConstructWithNonConstTemplateConstructorWorks (0 ms) 13: [ RUN ] ArrayRefTest/19.ConstructFromPointersWorks 13: [ OK ] ArrayRefTest/19.ConstructFromPointersWorks (0 ms) 13: [ RUN ] ArrayRefTest/19.ConstructFromNonConstPointersWorks 13: [ OK ] ArrayRefTest/19.ConstructFromNonConstPointersWorks (0 ms) 13: [ RUN ] ArrayRefTest/19.ConstructFromVectorWorks 13: [ OK ] ArrayRefTest/19.ConstructFromVectorWorks (0 ms) 13: [ RUN ] ArrayRefTest/19.ConstructFromNonConstVectorWorks 13: [ OK ] ArrayRefTest/19.ConstructFromNonConstVectorWorks (0 ms) 13: [ RUN ] ArrayRefTest/19.ConstructFromStructFieldWithTemplateConstructorWorks 13: [ OK ] ArrayRefTest/19.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms) 13: [----------] 9 tests from ArrayRefTest/19 (0 ms total) 13: 13: [----------] 8 tests from BoolType 13: [ RUN ] BoolType.ImplicitConversion 13: [ OK ] BoolType.ImplicitConversion (0 ms) 13: [ RUN ] BoolType.FalseByDefault 13: [ OK ] BoolType.FalseByDefault (0 ms) 13: [ RUN ] BoolType.Assignment 13: [ OK ] BoolType.Assignment (0 ms) 13: [ RUN ] BoolType.Copy 13: [ OK ] BoolType.Copy (0 ms) 13: [ RUN ] BoolType.ArrayRefCanBeCreated 13: [ OK ] BoolType.ArrayRefCanBeCreated (0 ms) 13: [ RUN ] BoolType.CanBeCastToBool 13: [ OK ] BoolType.CanBeCastToBool (0 ms) 13: [ RUN ] BoolType.HasSizeOfBool 13: [ OK ] BoolType.HasSizeOfBool (0 ms) 13: [ RUN ] BoolType.HasAlignmentOfBool 13: [ OK ] BoolType.HasAlignmentOfBool (0 ms) 13: [----------] 8 tests from BoolType (0 ms total) 13: 13: [----------] 4 tests from ArrayRefFromBoolTypeVector 13: [ RUN ] ArrayRefFromBoolTypeVector.CanConstructEmpty 13: [ OK ] ArrayRefFromBoolTypeVector.CanConstructEmpty (0 ms) 13: [ RUN ] ArrayRefFromBoolTypeVector.Works 13: [ OK ] ArrayRefFromBoolTypeVector.Works (0 ms) 13: [ RUN ] ArrayRefFromBoolTypeVector.CanConstructConstEmpty 13: [ OK ] ArrayRefFromBoolTypeVector.CanConstructConstEmpty (0 ms) 13: [ RUN ] ArrayRefFromBoolTypeVector.ConstWorks 13: [ OK ] ArrayRefFromBoolTypeVector.ConstWorks (0 ms) 13: [----------] 4 tests from ArrayRefFromBoolTypeVector (0 ms total) 13: 13: [----------] 7 tests from CStringUtilityTest 13: [ RUN ] CStringUtilityTest.CaseInsensitiveComparison 13: [ OK ] CStringUtilityTest.CaseInsensitiveComparison (0 ms) 13: [ RUN ] CStringUtilityTest.CaseInsensitiveComparisonInLength 13: [ OK ] CStringUtilityTest.CaseInsensitiveComparisonInLength (0 ms) 13: [ RUN ] CStringUtilityTest.strip_comment 13: [ OK ] CStringUtilityTest.strip_comment (0 ms) 13: [ RUN ] CStringUtilityTest.upstring 13: [ OK ] CStringUtilityTest.upstring (0 ms) 13: [ RUN ] CStringUtilityTest.ltrim 13: [ OK ] CStringUtilityTest.ltrim (0 ms) 13: [ RUN ] CStringUtilityTest.rtrim 13: [ OK ] CStringUtilityTest.rtrim (0 ms) 13: [ RUN ] CStringUtilityTest.trim 13: [ OK ] CStringUtilityTest.trim (0 ms) 13: [----------] 7 tests from CStringUtilityTest (0 ms total) 13: 13: [----------] 2 tests from DefaultInitializationAllocator 13: [ RUN ] DefaultInitializationAllocator.PerformsValueInitialization 13: [ OK ] DefaultInitializationAllocator.PerformsValueInitialization (0 ms) 13: [ RUN ] DefaultInitializationAllocator.PerformsNoInitialization 13: [ OK ] DefaultInitializationAllocator.PerformsNoInitialization (0 ms) 13: [----------] 2 tests from DefaultInitializationAllocator (0 ms total) 13: 13: [----------] 4 tests from EnumerationHelpersTest 13: [ RUN ] EnumerationHelpersTest.EnumerationWrapperWorks 13: [ OK ] EnumerationHelpersTest.EnumerationWrapperWorks (0 ms) 13: [ RUN ] EnumerationHelpersTest.EnumerationArrayWorks 13: [ OK ] EnumerationHelpersTest.EnumerationArrayWorks (0 ms) 13: [ RUN ] EnumerationHelpersTest.EnumerationArrayCountIsSafe 13: [ OK ] EnumerationHelpersTest.EnumerationArrayCountIsSafe (0 ms) 13: [ RUN ] EnumerationHelpersTest.ArrayRefOfEnumerationArrayWorks 13: [ OK ] EnumerationHelpersTest.ArrayRefOfEnumerationArrayWorks (0 ms) 13: [----------] 4 tests from EnumerationHelpersTest (0 ms total) 13: 13: [----------] 1 test from EnumClassSuitsEnumerationArray 13: [ RUN ] EnumClassSuitsEnumerationArray.Works 13: [ OK ] EnumClassSuitsEnumerationArray.Works (0 ms) 13: [----------] 1 test from EnumClassSuitsEnumerationArray (0 ms total) 13: 13: [----------] 18 tests from FixedCapacityVectorTest 13: [ RUN ] FixedCapacityVectorTest.IsEmpty 13: [ OK ] FixedCapacityVectorTest.IsEmpty (0 ms) 13: [ RUN ] FixedCapacityVectorTest.ConstructorWorks 13: [ OK ] FixedCapacityVectorTest.ConstructorWorks (0 ms) 13: [ RUN ] FixedCapacityVectorTest.PushWorks 13: [ OK ] FixedCapacityVectorTest.PushWorks (0 ms) 13: [ RUN ] FixedCapacityVectorTest.PopWorks 13: [ OK ] FixedCapacityVectorTest.PopWorks (0 ms) 13: [ RUN ] FixedCapacityVectorTest.ResizeWorks 13: [ OK ] FixedCapacityVectorTest.ResizeWorks (0 ms) 13: [ RUN ] FixedCapacityVectorTest.ClearWorks 13: [ OK ] FixedCapacityVectorTest.ClearWorks (0 ms) 13: [ RUN ] FixedCapacityVectorTest.EmplaceBackWorks 13: [ OK ] FixedCapacityVectorTest.EmplaceBackWorks (0 ms) 13: [ RUN ] FixedCapacityVectorTest.AtThrows 13: [ OK ] FixedCapacityVectorTest.AtThrows (0 ms) 13: [ RUN ] FixedCapacityVectorTest.IteratorWorks 13: [ OK ] FixedCapacityVectorTest.IteratorWorks (0 ms) 13: [ RUN ] FixedCapacityVectorTest.ReverseIteratorWorks 13: [ OK ] FixedCapacityVectorTest.ReverseIteratorWorks (0 ms) 13: [ RUN ] FixedCapacityVectorTest.ZeroCapacityWorks 13: [ OK ] FixedCapacityVectorTest.ZeroCapacityWorks (0 ms) 13: [ RUN ] FixedCapacityVectorTest.CopyConstructorWorks 13: [ OK ] FixedCapacityVectorTest.CopyConstructorWorks (0 ms) 13: [ RUN ] FixedCapacityVectorTest.CopyAssignmentWorks 13: [ OK ] FixedCapacityVectorTest.CopyAssignmentWorks (0 ms) 13: [ RUN ] FixedCapacityVectorTest.MoveConstructorWorks 13: [ OK ] FixedCapacityVectorTest.MoveConstructorWorks (0 ms) 13: [ RUN ] FixedCapacityVectorTest.MoveAssignmentWorks 13: [ OK ] FixedCapacityVectorTest.MoveAssignmentWorks (0 ms) 13: [ RUN ] FixedCapacityVectorTest.ElementAssignmentWorks 13: [ OK ] FixedCapacityVectorTest.ElementAssignmentWorks (0 ms) 13: [ RUN ] FixedCapacityVectorTest.DataWorks 13: [ OK ] FixedCapacityVectorTest.DataWorks (0 ms) 13: [ RUN ] FixedCapacityVectorTest.ConstMethodsWork 13: [ OK ] FixedCapacityVectorTest.ConstMethodsWork (0 ms) 13: [----------] 18 tests from FixedCapacityVectorTest (0 ms total) 13: 13: [----------] 5 tests from InMemorySerializerTest 13: [ RUN ] InMemorySerializerTest.Roundtrip 13: [ OK ] InMemorySerializerTest.Roundtrip (0 ms) 13: [ RUN ] InMemorySerializerTest.RoundtripWithEndianessSwap 13: [ OK ] InMemorySerializerTest.RoundtripWithEndianessSwap (0 ms) 13: [ RUN ] InMemorySerializerTest.SerializerExplicitEndianessSwap 13: [ OK ] InMemorySerializerTest.SerializerExplicitEndianessSwap (0 ms) 13: [ RUN ] InMemorySerializerTest.DeserializerExplicitEndianessSwap 13: [ OK ] InMemorySerializerTest.DeserializerExplicitEndianessSwap (0 ms) 13: [ RUN ] InMemorySerializerTest.SizeIsCorrect 13: [ OK ] InMemorySerializerTest.SizeIsCorrect (0 ms) 13: [----------] 5 tests from InMemorySerializerTest (0 ms total) 13: 13: [----------] 4 tests from KeyValueTreeSerializerTest 13: [ RUN ] KeyValueTreeSerializerTest.EmptyTree 13: [ OK ] KeyValueTreeSerializerTest.EmptyTree (0 ms) 13: [ RUN ] KeyValueTreeSerializerTest.SimpleObject 13: [ OK ] KeyValueTreeSerializerTest.SimpleObject (0 ms) 13: [ RUN ] KeyValueTreeSerializerTest.ObjectWithArrays 13: [ OK ] KeyValueTreeSerializerTest.ObjectWithArrays (0 ms) 13: [ RUN ] KeyValueTreeSerializerTest.ObjectWithObjects 13: [ OK ] KeyValueTreeSerializerTest.ObjectWithObjects (0 ms) 13: [----------] 4 tests from KeyValueTreeSerializerTest (3 ms total) 13: 13: [----------] 7 tests from TreeValueTransformTest 13: [ RUN ] TreeValueTransformTest.SimpleTransforms 13: [ OK ] TreeValueTransformTest.SimpleTransforms (0 ms) 13: [ RUN ] TreeValueTransformTest.SimpleTransformsCaseAndDashInsensitive 13: [ OK ] TreeValueTransformTest.SimpleTransformsCaseAndDashInsensitive (0 ms) 13: [ RUN ] TreeValueTransformTest.SimpleTransformsToObject 13: [ OK ] TreeValueTransformTest.SimpleTransformsToObject (0 ms) 13: [ RUN ] TreeValueTransformTest.ObjectFromString 13: [ OK ] TreeValueTransformTest.ObjectFromString (0 ms) 13: [ RUN ] TreeValueTransformTest.ObjectFromMultipleStrings 13: [ OK ] TreeValueTransformTest.ObjectFromMultipleStrings (0 ms) 13: [ RUN ] TreeValueTransformTest.ScopedTransformRules 13: [ OK ] TreeValueTransformTest.ScopedTransformRules (0 ms) 13: [ RUN ] TreeValueTransformTest.CanAssignUserMultiValue 13: [ OK ] TreeValueTransformTest.CanAssignUserMultiValue (0 ms) 13: [----------] 7 tests from TreeValueTransformTest (4 ms total) 13: 13: [----------] 1 test from TreeValueTransformErrorTest 13: [ RUN ] TreeValueTransformErrorTest.ConversionError 13: [ OK ] TreeValueTransformErrorTest.ConversionError (1 ms) 13: [----------] 1 test from TreeValueTransformErrorTest (1 ms total) 13: 13: [----------] 9 tests from ListOfLists 13: [ RUN ] ListOfLists.EmptyListOfListsWorks 13: [ OK ] ListOfLists.EmptyListOfListsWorks (0 ms) 13: [ RUN ] ListOfLists.AppendWorks 13: [ OK ] ListOfLists.AppendWorks (0 ms) 13: [ RUN ] ListOfLists.EmptyListWorks 13: [ OK ] ListOfLists.EmptyListWorks (0 ms) 13: [ RUN ] ListOfLists.AppendAccessWorks 13: [ OK ] ListOfLists.AppendAccessWorks (0 ms) 13: [ RUN ] ListOfLists.ClearWorks 13: [ OK ] ListOfLists.ClearWorks (0 ms) 13: [ RUN ] ListOfLists.OutOfRangeAccessThrows 13: [ OK ] ListOfLists.OutOfRangeAccessThrows (0 ms) 13: [ RUN ] ListOfLists.FrontAndBackWork 13: [ OK ] ListOfLists.FrontAndBackWork (0 ms) 13: [ RUN ] ListOfLists.ExtractsAndRestores 13: [ OK ] ListOfLists.ExtractsAndRestores (0 ms) 13: [ RUN ] ListOfLists.AppendsListOfListsWithOffset 13: [ OK ] ListOfLists.AppendsListOfListsWithOffset (0 ms) 13: [----------] 9 tests from ListOfLists (0 ms total) 13: 13: [----------] 7 tests from LoggerTest 13: [ RUN ] LoggerTest.EmptyLoggerWorks 13: [ OK ] LoggerTest.EmptyLoggerWorks (0 ms) 13: [ RUN ] LoggerTest.LogsToStream 13: [ OK ] LoggerTest.LogsToStream (0 ms) 13: [ RUN ] LoggerTest.LogsToFile 13: [ OK ] LoggerTest.LogsToFile (1 ms) 13: [ RUN ] LoggerTest.LevelFilteringWorks 13: [ OK ] LoggerTest.LevelFilteringWorks (0 ms) 13: [ RUN ] LoggerTest.LogsToMultipleStreams 13: [ OK ] LoggerTest.LogsToMultipleStreams (0 ms) 13: [ RUN ] LoggerTest.LogsToMultipleFiles 13: [ OK ] LoggerTest.LogsToMultipleFiles (3 ms) 13: [ RUN ] LoggerTest.LogsToStreamAndFile 13: [ OK ] LoggerTest.LogsToStreamAndFile (0 ms) 13: [----------] 7 tests from LoggerTest (6 ms total) 13: 13: [----------] 7 tests from MessageStringCollectorTest 13: [ RUN ] MessageStringCollectorTest.CanAddAndClearMessagesNoContext 13: [ OK ] MessageStringCollectorTest.CanAddAndClearMessagesNoContext (0 ms) 13: [ RUN ] MessageStringCollectorTest.CanAddAndClearMessagesWithContext 13: [ OK ] MessageStringCollectorTest.CanAddAndClearMessagesWithContext (0 ms) 13: [ RUN ] MessageStringCollectorTest.CanAddStringMessages 13: [ OK ] MessageStringCollectorTest.CanAddStringMessages (0 ms) 13: [ RUN ] MessageStringCollectorTest.CanAddCharMessagesConditionally 13: [ OK ] MessageStringCollectorTest.CanAddCharMessagesConditionally (0 ms) 13: [ RUN ] MessageStringCollectorTest.CanAddStringMessagesConditionally 13: [ OK ] MessageStringCollectorTest.CanAddStringMessagesConditionally (0 ms) 13: [ RUN ] MessageStringCollectorTest.CanMoveConstruct 13: [ OK ] MessageStringCollectorTest.CanMoveConstruct (0 ms) 13: [ RUN ] MessageStringCollectorTest.CanMoveAssign 13: [ OK ] MessageStringCollectorTest.CanMoveAssign (0 ms) 13: [----------] 7 tests from MessageStringCollectorTest (0 ms total) 13: 13: [----------] 1 test from PathTest 13: [ RUN ] PathTest.StripSourcePrefixWorks 13: [ OK ] PathTest.StripSourcePrefixWorks (0 ms) 13: [----------] 1 test from PathTest (0 ms total) 13: 13: [----------] 2 tests from PhysicalNodeCommunicatorTest 13: [ RUN ] PhysicalNodeCommunicatorTest.CanConstruct 13: [ OK ] PhysicalNodeCommunicatorTest.CanConstruct (0 ms) 13: [ RUN ] PhysicalNodeCommunicatorTest.CanCallBarrier 13: [ OK ] PhysicalNodeCommunicatorTest.CanCallBarrier (0 ms) 13: [----------] 2 tests from PhysicalNodeCommunicatorTest (0 ms total) 13: 13: [----------] 5 tests from Range 13: [ RUN ] Range.EmptyRangeWorks 13: [ OK ] Range.EmptyRangeWorks (0 ms) 13: [ RUN ] Range.NonEmptyRangeWorks 13: [ OK ] Range.NonEmptyRangeWorks (0 ms) 13: [ RUN ] Range.BeginEnd 13: [ OK ] Range.BeginEnd (0 ms) 13: [ RUN ] Range.IsInRangeWorks 13: [ OK ] Range.IsInRangeWorks (0 ms) 13: [ RUN ] Range.IteratorWorks 13: [ OK ] Range.IteratorWorks (0 ms) 13: [----------] 5 tests from Range (0 ms total) 13: 13: [----------] 3 tests from ScopeGuardTest 13: [ RUN ] ScopeGuardTest.ScopeGuardExecutesCallbackOnExit 13: [ OK ] ScopeGuardTest.ScopeGuardExecutesCallbackOnExit (0 ms) 13: [ RUN ] ScopeGuardTest.ScopeGuardCanFreePointers 13: [ OK ] ScopeGuardTest.ScopeGuardCanFreePointers (0 ms) 13: [ RUN ] ScopeGuardTest.ScopeGuardsCanBeCreatedByHelperFunctions 13: [ OK ] ScopeGuardTest.ScopeGuardsCanBeCreatedByHelperFunctions (0 ms) 13: [----------] 3 tests from ScopeGuardTest (0 ms total) 13: 13: [----------] 7 tests from StringConvert 13: [ RUN ] StringConvert.NoResultFromEptyString 13: [ OK ] StringConvert.NoResultFromEptyString (0 ms) 13: [ RUN ] StringConvert.ThreeFloatsSuccessfully 13: [ OK ] StringConvert.ThreeFloatsSuccessfully (0 ms) 13: [ RUN ] StringConvert.OneIntSucessfully 13: [ OK ] StringConvert.OneIntSucessfully (0 ms) 13: [ RUN ] StringConvert.FloatAsStringToIntArrayThrows 13: [ OK ] StringConvert.FloatAsStringToIntArrayThrows (0 ms) 13: [ RUN ] StringConvert.ThrowsWhenWrongSize 13: [ OK ] StringConvert.ThrowsWhenWrongSize (0 ms) 13: [ RUN ] StringConvert.StringIdentityTransformWithArrayThrows 13: [ OK ] StringConvert.StringIdentityTransformWithArrayThrows (0 ms) 13: [ RUN ] StringConvert.StringIdentityTransformWithArrayOkay 13: [ OK ] StringConvert.StringIdentityTransformWithArrayOkay (0 ms) 13: [----------] 7 tests from StringConvert (0 ms total) 13: 13: [----------] 7 tests from StringToEnumValueConverterTest 13: [ RUN ] StringToEnumValueConverterTest.ExactStringComparisonWorksWithoutStripping 13: [ OK ] StringToEnumValueConverterTest.ExactStringComparisonWorksWithoutStripping (0 ms) 13: [ RUN ] StringToEnumValueConverterTest.CaseInsensitiveStringComparisonWorksWithoutStripping 13: [ OK ] StringToEnumValueConverterTest.CaseInsensitiveStringComparisonWorksWithoutStripping (0 ms) 13: [ RUN ] StringToEnumValueConverterTest.CaseAndDashInsensitiveStringComparisonWorksWithoutStripping 13: [ OK ] StringToEnumValueConverterTest.CaseAndDashInsensitiveStringComparisonWorksWithoutStripping (0 ms) 13: [ RUN ] StringToEnumValueConverterTest.ExactStringComparisonWorksWithStripping 13: [ OK ] StringToEnumValueConverterTest.ExactStringComparisonWorksWithStripping (0 ms) 13: [ RUN ] StringToEnumValueConverterTest.CaseInsensitiveStringComparisonWorksWithStripping 13: [ OK ] StringToEnumValueConverterTest.CaseInsensitiveStringComparisonWorksWithStripping (0 ms) 13: [ RUN ] StringToEnumValueConverterTest.CaseAndDashInsensitiveStringComparisonWorksWithStripping 13: [ OK ] StringToEnumValueConverterTest.CaseAndDashInsensitiveStringComparisonWorksWithStripping (0 ms) 13: [ RUN ] StringToEnumValueConverterTest.CustomConverterWorks 13: [ OK ] StringToEnumValueConverterTest.CustomConverterWorks (0 ms) 13: [----------] 7 tests from StringToEnumValueConverterTest (0 ms total) 13: 13: [----------] 9 tests from StringUtilityTest 13: [ RUN ] StringUtilityTest.StartsWith 13: [ OK ] StringUtilityTest.StartsWith (0 ms) 13: [ RUN ] StringUtilityTest.EndsWith 13: [ OK ] StringUtilityTest.EndsWith (0 ms) 13: [ RUN ] StringUtilityTest.StripSuffixIfPresent 13: [ OK ] StringUtilityTest.StripSuffixIfPresent (0 ms) 13: [ RUN ] StringUtilityTest.StripString 13: [ OK ] StringUtilityTest.StripString (0 ms) 13: [ RUN ] StringUtilityTest.SplitString 13: [ OK ] StringUtilityTest.SplitString (0 ms) 13: [ RUN ] StringUtilityTest.SplitDelimitedString 13: [ OK ] StringUtilityTest.SplitDelimitedString (0 ms) 13: [ RUN ] StringUtilityTest.SplitAndTrimDelimitedString 13: [ OK ] StringUtilityTest.SplitAndTrimDelimitedString (0 ms) 13: [ RUN ] StringUtilityTest.CanCompareCaseInsensitive 13: [ OK ] StringUtilityTest.CanCompareCaseInsensitive (0 ms) 13: [ RUN ] StringUtilityTest.CanCompareCaseInsensitiveInLength 13: [ OK ] StringUtilityTest.CanCompareCaseInsensitiveInLength (0 ms) 13: [----------] 9 tests from StringUtilityTest (0 ms total) 13: 13: [----------] 2 tests from FormatStringTest 13: [ RUN ] FormatStringTest.HandlesBasicFormatting 13: [ OK ] FormatStringTest.HandlesBasicFormatting (0 ms) 13: [ RUN ] FormatStringTest.HandlesLongStrings 13: [ OK ] FormatStringTest.HandlesLongStrings (0 ms) 13: [----------] 2 tests from FormatStringTest (0 ms total) 13: 13: [----------] 1 test from StringFormatterTest 13: [ RUN ] StringFormatterTest.HandlesBasicFormatting 13: [ OK ] StringFormatterTest.HandlesBasicFormatting (0 ms) 13: [----------] 1 test from StringFormatterTest (0 ms total) 13: 13: [----------] 1 test from formatAndJoinTest 13: [ RUN ] formatAndJoinTest.Works 13: [ OK ] formatAndJoinTest.Works (0 ms) 13: [----------] 1 test from formatAndJoinTest (0 ms total) 13: 13: [----------] 1 test from JoinStringsTest 13: [ RUN ] JoinStringsTest.Works 13: [ OK ] JoinStringsTest.Works (0 ms) 13: [----------] 1 test from JoinStringsTest (0 ms total) 13: 13: [----------] 6 tests from ReplaceAllTest 13: [ RUN ] ReplaceAllTest.HandlesEmptyStrings 13: [ OK ] ReplaceAllTest.HandlesEmptyStrings (0 ms) 13: [ RUN ] ReplaceAllTest.HandlesNoMatches 13: [ OK ] ReplaceAllTest.HandlesNoMatches (0 ms) 13: [ RUN ] ReplaceAllTest.HandlesMatchesAtEnds 13: [ OK ] ReplaceAllTest.HandlesMatchesAtEnds (0 ms) 13: [ RUN ] ReplaceAllTest.HandlesMultipleMatches 13: [ OK ] ReplaceAllTest.HandlesMultipleMatches (0 ms) 13: [ RUN ] ReplaceAllTest.HandlesWordBoundaries 13: [ OK ] ReplaceAllTest.HandlesWordBoundaries (0 ms) 13: [ RUN ] ReplaceAllTest.HandlesPossibleRecursiveMatches 13: [ OK ] ReplaceAllTest.HandlesPossibleRecursiveMatches (0 ms) 13: [----------] 6 tests from ReplaceAllTest (0 ms total) 13: 13: [----------] 10 tests from TextLineWrapperTest 13: [ RUN ] TextLineWrapperTest.HandlesEmptyStrings 13: [ OK ] TextLineWrapperTest.HandlesEmptyStrings (0 ms) 13: [ RUN ] TextLineWrapperTest.HandlesTrailingWhitespace 13: [ OK ] TextLineWrapperTest.HandlesTrailingWhitespace (0 ms) 13: [ RUN ] TextLineWrapperTest.HandlesTrailingNewlines 13: [ OK ] TextLineWrapperTest.HandlesTrailingNewlines (0 ms) 13: [ RUN ] TextLineWrapperTest.WrapsCorrectly 13: [ OK ] TextLineWrapperTest.WrapsCorrectly (0 ms) 13: [ RUN ] TextLineWrapperTest.WrapsCorrectlyWithExistingBreaks 13: [ OK ] TextLineWrapperTest.WrapsCorrectlyWithExistingBreaks (0 ms) 13: [ RUN ] TextLineWrapperTest.HandlesIndent 13: [ OK ] TextLineWrapperTest.HandlesIndent (0 ms) 13: [ RUN ] TextLineWrapperTest.HandlesIndentWithEmptyLines 13: [ OK ] TextLineWrapperTest.HandlesIndentWithEmptyLines (0 ms) 13: [ RUN ] TextLineWrapperTest.HandlesHangingIndent 13: [ OK ] TextLineWrapperTest.HandlesHangingIndent (0 ms) 13: [ RUN ] TextLineWrapperTest.HandlesContinuationCharacter 13: [ OK ] TextLineWrapperTest.HandlesContinuationCharacter (0 ms) 13: [ RUN ] TextLineWrapperTest.WrapsCorrectlyWithExtraWhitespace 13: [ OK ] TextLineWrapperTest.WrapsCorrectlyWithExtraWhitespace (0 ms) 13: [----------] 10 tests from TextLineWrapperTest (4 ms total) 13: 13: [----------] 1 test from CompileTimeStringJoin 13: [ RUN ] CompileTimeStringJoin.Works 13: [ OK ] CompileTimeStringJoin.Works (0 ms) 13: [----------] 1 test from CompileTimeStringJoin (0 ms total) 13: 13: [----------] 3 tests from TemplateMPTest 13: [ RUN ] TemplateMPTest.DispatchTemplatedFunctionEnum 13: [ OK ] TemplateMPTest.DispatchTemplatedFunctionEnum (0 ms) 13: [ RUN ] TemplateMPTest.DispatchTemplatedFunctionBool 13: [ OK ] TemplateMPTest.DispatchTemplatedFunctionBool (0 ms) 13: [ RUN ] TemplateMPTest.DispatchTemplatedFunctionEnumBool 13: [ OK ] TemplateMPTest.DispatchTemplatedFunctionEnumBool (0 ms) 13: [----------] 3 tests from TemplateMPTest (0 ms total) 13: 13: [----------] 6 tests from TextWriterTest 13: [ RUN ] TextWriterTest.WritesLines 13: [ OK ] TextWriterTest.WritesLines (0 ms) 13: [ RUN ] TextWriterTest.WritesLinesInParts 13: [ OK ] TextWriterTest.WritesLinesInParts (0 ms) 13: [ RUN ] TextWriterTest.WritesWrappedLines 13: [ OK ] TextWriterTest.WritesWrappedLines (0 ms) 13: [ RUN ] TextWriterTest.WritesLinesInPartsWithWrapper 13: [ OK ] TextWriterTest.WritesLinesInPartsWithWrapper (0 ms) 13: [ RUN ] TextWriterTest.TracksNewlines 13: [ OK ] TextWriterTest.TracksNewlines (0 ms) 13: [ RUN ] TextWriterTest.PreservesTrailingWhitespace 13: [ OK ] TextWriterTest.PreservesTrailingWhitespace (0 ms) 13: [----------] 6 tests from TextWriterTest (1 ms total) 13: 13: [----------] 1 test from TypeTraitsTest 13: [ RUN ] TypeTraitsTest.IsIntegralConstant 13: [ OK ] TypeTraitsTest.IsIntegralConstant (0 ms) 13: [----------] 1 test from TypeTraitsTest (0 ms total) 13: 13: [----------] 6 tests from BitmaskTest32_11/BitmaskTest32 13: [ RUN ] BitmaskTest32_11/BitmaskTest32.SetAndClear/0 13: [ OK ] BitmaskTest32_11/BitmaskTest32.SetAndClear/0 (0 ms) 13: [ RUN ] BitmaskTest32_11/BitmaskTest32.InitBit/0 13: [ OK ] BitmaskTest32_11/BitmaskTest32.InitBit/0 (0 ms) 13: [ RUN ] BitmaskTest32_11/BitmaskTest32.InitLowBits/0 13: [ OK ] BitmaskTest32_11/BitmaskTest32.InitLowBits/0 (0 ms) 13: [ RUN ] BitmaskTest32_11/BitmaskTest32.Disjoint/0 13: [ OK ] BitmaskTest32_11/BitmaskTest32.Disjoint/0 (0 ms) 13: [ RUN ] BitmaskTest32_11/BitmaskTest32.Union/0 13: [ OK ] BitmaskTest32_11/BitmaskTest32.Union/0 (0 ms) 13: [ RUN ] BitmaskTest32_11/BitmaskTest32.ToHex/0 13: [ OK ] BitmaskTest32_11/BitmaskTest32.ToHex/0 (0 ms) 13: [----------] 6 tests from BitmaskTest32_11/BitmaskTest32 (0 ms total) 13: 13: [----------] 12 tests from BitmaskTest64_10_42/BitmaskTest64 13: [ RUN ] BitmaskTest64_10_42/BitmaskTest64.SetAndClear/0 13: [ OK ] BitmaskTest64_10_42/BitmaskTest64.SetAndClear/0 (0 ms) 13: [ RUN ] BitmaskTest64_10_42/BitmaskTest64.SetAndClear/1 13: [ OK ] BitmaskTest64_10_42/BitmaskTest64.SetAndClear/1 (0 ms) 13: [ RUN ] BitmaskTest64_10_42/BitmaskTest64.InitBit/0 13: [ OK ] BitmaskTest64_10_42/BitmaskTest64.InitBit/0 (0 ms) 13: [ RUN ] BitmaskTest64_10_42/BitmaskTest64.InitBit/1 13: [ OK ] BitmaskTest64_10_42/BitmaskTest64.InitBit/1 (0 ms) 13: [ RUN ] BitmaskTest64_10_42/BitmaskTest64.InitLowBits/0 13: [ OK ] BitmaskTest64_10_42/BitmaskTest64.InitLowBits/0 (0 ms) 13: [ RUN ] BitmaskTest64_10_42/BitmaskTest64.InitLowBits/1 13: [ OK ] BitmaskTest64_10_42/BitmaskTest64.InitLowBits/1 (0 ms) 13: [ RUN ] BitmaskTest64_10_42/BitmaskTest64.Disjoint/0 13: [ OK ] BitmaskTest64_10_42/BitmaskTest64.Disjoint/0 (0 ms) 13: [ RUN ] BitmaskTest64_10_42/BitmaskTest64.Disjoint/1 13: [ OK ] BitmaskTest64_10_42/BitmaskTest64.Disjoint/1 (0 ms) 13: [ RUN ] BitmaskTest64_10_42/BitmaskTest64.Union/0 13: [ OK ] BitmaskTest64_10_42/BitmaskTest64.Union/0 (0 ms) 13: [ RUN ] BitmaskTest64_10_42/BitmaskTest64.Union/1 13: [ OK ] BitmaskTest64_10_42/BitmaskTest64.Union/1 (0 ms) 13: [ RUN ] BitmaskTest64_10_42/BitmaskTest64.ToHex/0 13: [ OK ] BitmaskTest64_10_42/BitmaskTest64.ToHex/0 (0 ms) 13: [ RUN ] BitmaskTest64_10_42/BitmaskTest64.ToHex/1 13: [ OK ] BitmaskTest64_10_42/BitmaskTest64.ToHex/1 (0 ms) 13: [----------] 12 tests from BitmaskTest64_10_42/BitmaskTest64 (0 ms total) 13: 13: [----------] 12 tests from BitmaskTest128_9_78/BitmaskTest128 13: [ RUN ] BitmaskTest128_9_78/BitmaskTest128.SetAndClear/0 13: [ OK ] BitmaskTest128_9_78/BitmaskTest128.SetAndClear/0 (0 ms) 13: [ RUN ] BitmaskTest128_9_78/BitmaskTest128.SetAndClear/1 13: [ OK ] BitmaskTest128_9_78/BitmaskTest128.SetAndClear/1 (0 ms) 13: [ RUN ] BitmaskTest128_9_78/BitmaskTest128.InitBit/0 13: [ OK ] BitmaskTest128_9_78/BitmaskTest128.InitBit/0 (0 ms) 13: [ RUN ] BitmaskTest128_9_78/BitmaskTest128.InitBit/1 13: [ OK ] BitmaskTest128_9_78/BitmaskTest128.InitBit/1 (0 ms) 13: [ RUN ] BitmaskTest128_9_78/BitmaskTest128.InitLowBits/0 13: [ OK ] BitmaskTest128_9_78/BitmaskTest128.InitLowBits/0 (0 ms) 13: [ RUN ] BitmaskTest128_9_78/BitmaskTest128.InitLowBits/1 13: [ OK ] BitmaskTest128_9_78/BitmaskTest128.InitLowBits/1 (0 ms) 13: [ RUN ] BitmaskTest128_9_78/BitmaskTest128.Disjoint/0 13: [ OK ] BitmaskTest128_9_78/BitmaskTest128.Disjoint/0 (0 ms) 13: [ RUN ] BitmaskTest128_9_78/BitmaskTest128.Disjoint/1 13: [ OK ] BitmaskTest128_9_78/BitmaskTest128.Disjoint/1 (0 ms) 13: [ RUN ] BitmaskTest128_9_78/BitmaskTest128.Union/0 13: [ OK ] BitmaskTest128_9_78/BitmaskTest128.Union/0 (0 ms) 13: [ RUN ] BitmaskTest128_9_78/BitmaskTest128.Union/1 13: [ OK ] BitmaskTest128_9_78/BitmaskTest128.Union/1 (0 ms) 13: [ RUN ] BitmaskTest128_9_78/BitmaskTest128.ToHex/0 13: [ OK ] BitmaskTest128_9_78/BitmaskTest128.ToHex/0 (0 ms) 13: [ RUN ] BitmaskTest128_9_78/BitmaskTest128.ToHex/1 13: [ OK ] BitmaskTest128_9_78/BitmaskTest128.ToHex/1 (0 ms) 13: [----------] 12 tests from BitmaskTest128_9_78/BitmaskTest128 (0 ms total) 13: 13: [----------] 11 tests from WithInputPaths/PathSearchTest 13: [ RUN ] WithInputPaths/PathSearchTest.SearchOperationsWork/0 13: [ OK ] WithInputPaths/PathSearchTest.SearchOperationsWork/0 (0 ms) 13: [ RUN ] WithInputPaths/PathSearchTest.SearchOperationsWork/1 13: [ OK ] WithInputPaths/PathSearchTest.SearchOperationsWork/1 (0 ms) 13: [ RUN ] WithInputPaths/PathSearchTest.SearchOperationsWork/2 13: [ OK ] WithInputPaths/PathSearchTest.SearchOperationsWork/2 (0 ms) 13: [ RUN ] WithInputPaths/PathSearchTest.SearchOperationsWork/3 13: [ OK ] WithInputPaths/PathSearchTest.SearchOperationsWork/3 (2 ms) 13: [ RUN ] WithInputPaths/PathSearchTest.SearchOperationsWork/4 13: [ OK ] WithInputPaths/PathSearchTest.SearchOperationsWork/4 (0 ms) 13: [ RUN ] WithInputPaths/PathSearchTest.SearchOperationsWork/5 13: [ OK ] WithInputPaths/PathSearchTest.SearchOperationsWork/5 (0 ms) 13: [ RUN ] WithInputPaths/PathSearchTest.SearchOperationsWork/6 13: [ OK ] WithInputPaths/PathSearchTest.SearchOperationsWork/6 (0 ms) 13: [ RUN ] WithInputPaths/PathSearchTest.SearchOperationsWork/7 13: [ OK ] WithInputPaths/PathSearchTest.SearchOperationsWork/7 (0 ms) 13: [ RUN ] WithInputPaths/PathSearchTest.SearchOperationsWork/8 13: [ OK ] WithInputPaths/PathSearchTest.SearchOperationsWork/8 (0 ms) 13: [ RUN ] WithInputPaths/PathSearchTest.SearchOperationsWork/9 13: [ OK ] WithInputPaths/PathSearchTest.SearchOperationsWork/9 (0 ms) 13: [ RUN ] WithInputPaths/PathSearchTest.SearchOperationsWork/10 13: [ OK ] WithInputPaths/PathSearchTest.SearchOperationsWork/10 (0 ms) 13: [----------] 11 tests from WithInputPaths/PathSearchTest (6 ms total) 13: 13: [----------] 7 tests from ParsesLinesDifferently/TextReaderTest 13: [ RUN ] ParsesLinesDifferently/TextReaderTest.UsingDifferentConfigurations/0 13: [ OK ] ParsesLinesDifferently/TextReaderTest.UsingDifferentConfigurations/0 (0 ms) 13: [ RUN ] ParsesLinesDifferently/TextReaderTest.UsingDifferentConfigurations/1 13: [ OK ] ParsesLinesDifferently/TextReaderTest.UsingDifferentConfigurations/1 (0 ms) 13: [ RUN ] ParsesLinesDifferently/TextReaderTest.UsingDifferentConfigurations/2 13: [ OK ] ParsesLinesDifferently/TextReaderTest.UsingDifferentConfigurations/2 (0 ms) 13: [ RUN ] ParsesLinesDifferently/TextReaderTest.UsingDifferentConfigurations/3 13: [ OK ] ParsesLinesDifferently/TextReaderTest.UsingDifferentConfigurations/3 (0 ms) 13: [ RUN ] ParsesLinesDifferently/TextReaderTest.UsingDifferentConfigurations/4 13: [ OK ] ParsesLinesDifferently/TextReaderTest.UsingDifferentConfigurations/4 (0 ms) 13: [ RUN ] ParsesLinesDifferently/TextReaderTest.UsingDifferentConfigurations/5 13: [ OK ] ParsesLinesDifferently/TextReaderTest.UsingDifferentConfigurations/5 (0 ms) 13: [ RUN ] ParsesLinesDifferently/TextReaderTest.UsingDifferentConfigurations/6 13: [ OK ] ParsesLinesDifferently/TextReaderTest.UsingDifferentConfigurations/6 (0 ms) 13: [----------] 7 tests from ParsesLinesDifferently/TextReaderTest (0 ms total) 13: 13: [----------] Global test environment tear-down 13: [==========] 420 tests from 65 test suites ran. (51 ms total) 13: [ PASSED ] 420 tests. 13: 13: YOU HAVE 1 DISABLED TEST 13: 13/92 Test #13: UtilityUnitTests .......................... Passed 0.20 sec test 14 Start 14: UtilityMpiUnitTests 14: Test command: /build/reproducible-path/gromacs-2025.1/build/basic-dp/bin/utility-mpi-test "-ntmpi" "2" "--gtest_output=xml:/build/reproducible-path/gromacs-2025.1/build/basic-dp/Testing/Temporary/UtilityMpiUnitTests.xml" 14: Working Directory: /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/utility/tests 14: Test timeout computed to be: 30 14: [==========] Running 2 tests from 1 test suite. 14: [----------] Global test environment set-up. 14: [----------] 2 tests from PhysicalNodeCommunicatorTest 14: [ RUN ] PhysicalNodeCommunicatorTest.CanConstruct 14: [ OK ] PhysicalNodeCommunicatorTest.CanConstruct (2 ms) 14: [ RUN ] PhysicalNodeCommunicatorTest.CanCallBarrier 14: [ OK ] PhysicalNodeCommunicatorTest.CanCallBarrier (5 ms) 14: [----------] 2 tests from PhysicalNodeCommunicatorTest (7 ms total) 14: 14: [----------] Global test environment tear-down 14: [==========] 2 tests from 1 test suite ran. (8 ms total) 14: [ PASSED ] 2 tests. 14/92 Test #14: UtilityMpiUnitTests ....................... Passed 0.10 sec test 15 Start 15: GmxlibTests 15: Test command: /build/reproducible-path/gromacs-2025.1/build/basic-dp/bin/nonbonded-fep-test "--gtest_output=xml:/build/reproducible-path/gromacs-2025.1/build/basic-dp/Testing/Temporary/GmxlibTests.xml" 15: Working Directory: /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/gmxlib/nonbonded/tests 15: Test timeout computed to be: 30 15: [==========] Running 78 tests from 2 test suites. 15: [----------] Global test environment set-up. 15: [----------] 72 tests from NBInteraction/NonbondedFepTest 15: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/0 15: [ OK ] NBInteraction/NonbondedFepTest.testKernel/0 (2 ms) 15: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/1 15: [ OK ] NBInteraction/NonbondedFepTest.testKernel/1 (0 ms) 15: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/2 15: [ OK ] NBInteraction/NonbondedFepTest.testKernel/2 (1 ms) 15: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/3 15: [ OK ] NBInteraction/NonbondedFepTest.testKernel/3 (0 ms) 15: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/4 15: [ OK ] NBInteraction/NonbondedFepTest.testKernel/4 (0 ms) 15: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/5 15: [ OK ] NBInteraction/NonbondedFepTest.testKernel/5 (0 ms) 15: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/6 15: [ OK ] NBInteraction/NonbondedFepTest.testKernel/6 (0 ms) 15: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/7 15: [ OK ] NBInteraction/NonbondedFepTest.testKernel/7 (0 ms) 15: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/8 15: [ OK ] NBInteraction/NonbondedFepTest.testKernel/8 (0 ms) 15: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/9 15: [ OK ] NBInteraction/NonbondedFepTest.testKernel/9 (1 ms) 15: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/10 15: [ OK ] NBInteraction/NonbondedFepTest.testKernel/10 (0 ms) 15: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/11 15: [ OK ] NBInteraction/NonbondedFepTest.testKernel/11 (0 ms) 15: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/12 15: [ OK ] NBInteraction/NonbondedFepTest.testKernel/12 (0 ms) 15: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/13 15: [ OK ] NBInteraction/NonbondedFepTest.testKernel/13 (0 ms) 15: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/14 15: [ OK ] NBInteraction/NonbondedFepTest.testKernel/14 (0 ms) 15: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/15 15: [ OK ] NBInteraction/NonbondedFepTest.testKernel/15 (0 ms) 15: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/16 15: [ OK ] NBInteraction/NonbondedFepTest.testKernel/16 (0 ms) 15: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/17 15: [ OK ] NBInteraction/NonbondedFepTest.testKernel/17 (0 ms) 15: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/18 15: [ OK ] NBInteraction/NonbondedFepTest.testKernel/18 (0 ms) 15: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/19 15: [ OK ] NBInteraction/NonbondedFepTest.testKernel/19 (0 ms) 15: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/20 15: [ OK ] NBInteraction/NonbondedFepTest.testKernel/20 (0 ms) 15: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/21 15: [ OK ] NBInteraction/NonbondedFepTest.testKernel/21 (0 ms) 15: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/22 15: [ OK ] NBInteraction/NonbondedFepTest.testKernel/22 (0 ms) 15: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/23 15: [ OK ] NBInteraction/NonbondedFepTest.testKernel/23 (0 ms) 15: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/24 15: [ OK ] NBInteraction/NonbondedFepTest.testKernel/24 (1 ms) 15: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/25 15: [ OK ] NBInteraction/NonbondedFepTest.testKernel/25 (1 ms) 15: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/26 15: [ OK ] NBInteraction/NonbondedFepTest.testKernel/26 (1 ms) 15: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/27 15: [ OK ] NBInteraction/NonbondedFepTest.testKernel/27 (1 ms) 15: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/28 15: [ OK ] NBInteraction/NonbondedFepTest.testKernel/28 (1 ms) 15: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/29 15: [ OK ] NBInteraction/NonbondedFepTest.testKernel/29 (1 ms) 15: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/30 15: [ OK ] NBInteraction/NonbondedFepTest.testKernel/30 (1 ms) 15: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/31 15: [ OK ] NBInteraction/NonbondedFepTest.testKernel/31 (1 ms) 15: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/32 15: [ OK ] NBInteraction/NonbondedFepTest.testKernel/32 (1 ms) 15: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/33 15: [ OK ] NBInteraction/NonbondedFepTest.testKernel/33 (1 ms) 15: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/34 15: [ OK ] NBInteraction/NonbondedFepTest.testKernel/34 (1 ms) 15: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/35 15: [ OK ] NBInteraction/NonbondedFepTest.testKernel/35 (1 ms) 15: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/36 15: [ OK ] NBInteraction/NonbondedFepTest.testKernel/36 (0 ms) 15: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/37 15: [ OK ] NBInteraction/NonbondedFepTest.testKernel/37 (0 ms) 15: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/38 15: [ OK ] NBInteraction/NonbondedFepTest.testKernel/38 (0 ms) 15: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/39 15: [ OK ] NBInteraction/NonbondedFepTest.testKernel/39 (0 ms) 15: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/40 15: [ OK ] NBInteraction/NonbondedFepTest.testKernel/40 (0 ms) 15: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/41 15: [ OK ] NBInteraction/NonbondedFepTest.testKernel/41 (0 ms) 15: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/42 15: [ OK ] NBInteraction/NonbondedFepTest.testKernel/42 (0 ms) 15: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/43 15: [ OK ] NBInteraction/NonbondedFepTest.testKernel/43 (0 ms) 15: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/44 15: [ OK ] NBInteraction/NonbondedFepTest.testKernel/44 (0 ms) 15: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/45 15: [ OK ] NBInteraction/NonbondedFepTest.testKernel/45 (0 ms) 15: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/46 15: [ OK ] NBInteraction/NonbondedFepTest.testKernel/46 (0 ms) 15: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/47 15: [ OK ] NBInteraction/NonbondedFepTest.testKernel/47 (0 ms) 15: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/48 15: [ OK ] NBInteraction/NonbondedFepTest.testKernel/48 (0 ms) 15: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/49 15: [ OK ] NBInteraction/NonbondedFepTest.testKernel/49 (0 ms) 15: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/50 15: [ OK ] NBInteraction/NonbondedFepTest.testKernel/50 (0 ms) 15: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/51 15: [ OK ] NBInteraction/NonbondedFepTest.testKernel/51 (0 ms) 15: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/52 15: [ OK ] NBInteraction/NonbondedFepTest.testKernel/52 (0 ms) 15: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/53 15: [ OK ] NBInteraction/NonbondedFepTest.testKernel/53 (0 ms) 15: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/54 15: [ OK ] NBInteraction/NonbondedFepTest.testKernel/54 (0 ms) 15: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/55 15: [ OK ] NBInteraction/NonbondedFepTest.testKernel/55 (0 ms) 15: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/56 15: [ OK ] NBInteraction/NonbondedFepTest.testKernel/56 (0 ms) 15: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/57 15: [ OK ] NBInteraction/NonbondedFepTest.testKernel/57 (0 ms) 15: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/58 15: [ OK ] NBInteraction/NonbondedFepTest.testKernel/58 (0 ms) 15: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/59 15: [ OK ] NBInteraction/NonbondedFepTest.testKernel/59 (0 ms) 15: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/60 15: [ OK ] NBInteraction/NonbondedFepTest.testKernel/60 (1 ms) 15: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/61 15: [ OK ] NBInteraction/NonbondedFepTest.testKernel/61 (1 ms) 15: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/62 15: [ OK ] NBInteraction/NonbondedFepTest.testKernel/62 (2 ms) 15: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/63 15: [ OK ] NBInteraction/NonbondedFepTest.testKernel/63 (1 ms) 15: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/64 15: [ OK ] NBInteraction/NonbondedFepTest.testKernel/64 (1 ms) 15: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/65 15: [ OK ] NBInteraction/NonbondedFepTest.testKernel/65 (1 ms) 15: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/66 15: [ OK ] NBInteraction/NonbondedFepTest.testKernel/66 (1 ms) 15: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/67 15: [ OK ] NBInteraction/NonbondedFepTest.testKernel/67 (1 ms) 15: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/68 15: [ OK ] NBInteraction/NonbondedFepTest.testKernel/68 (1 ms) 15: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/69 15: [ OK ] NBInteraction/NonbondedFepTest.testKernel/69 (1 ms) 15: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/70 15: [ OK ] NBInteraction/NonbondedFepTest.testKernel/70 (1 ms) 15: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/71 15: [ OK ] NBInteraction/NonbondedFepTest.testKernel/71 (1 ms) 15: [----------] 72 tests from NBInteraction/NonbondedFepTest (76 ms total) 15: 15: [----------] 6 tests from NBInteractionShortDistance/NonbondedFepTest 15: [ RUN ] NBInteractionShortDistance/NonbondedFepTest.testKernel/0 15: [ OK ] NBInteractionShortDistance/NonbondedFepTest.testKernel/0 (0 ms) 15: [ RUN ] NBInteractionShortDistance/NonbondedFepTest.testKernel/1 15: [ OK ] NBInteractionShortDistance/NonbondedFepTest.testKernel/1 (0 ms) 15: [ RUN ] NBInteractionShortDistance/NonbondedFepTest.testKernel/2 15: [ OK ] NBInteractionShortDistance/NonbondedFepTest.testKernel/2 (1 ms) 15: [ RUN ] NBInteractionShortDistance/NonbondedFepTest.testKernel/3 15: [ OK ] NBInteractionShortDistance/NonbondedFepTest.testKernel/3 (1 ms) 15: [ RUN ] NBInteractionShortDistance/NonbondedFepTest.testKernel/4 15: [ OK ] NBInteractionShortDistance/NonbondedFepTest.testKernel/4 (0 ms) 15: [ RUN ] NBInteractionShortDistance/NonbondedFepTest.testKernel/5 15: [ OK ] NBInteractionShortDistance/NonbondedFepTest.testKernel/5 (1 ms) 15: [----------] 6 tests from NBInteractionShortDistance/NonbondedFepTest (6 ms total) 15: 15: [----------] Global test environment tear-down 15: [==========] 78 tests from 2 test suites ran. (83 ms total) 15: [ PASSED ] 78 tests. 15/92 Test #15: GmxlibTests ............................... Passed 0.25 sec test 16 Start 16: MdlibUnitTest 16: Test command: /build/reproducible-path/gromacs-2025.1/build/basic-dp/bin/mdlib-test "--gtest_output=xml:/build/reproducible-path/gromacs-2025.1/build/basic-dp/Testing/Temporary/MdlibUnitTest.xml" 16: Working Directory: /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/mdlib/tests 16: Test timeout computed to be: 30 16: [==========] Running 1032 tests from 27 test suites. 16: [----------] Global test environment set-up. 16: [----------] 3 tests from EffectiveAtomDensity 16: [ RUN ] EffectiveAtomDensity.VolumeIndependence 16: [ OK ] EffectiveAtomDensity.VolumeIndependence (0 ms) 16: [ RUN ] EffectiveAtomDensity.WeightingWorks 16: [ OK ] EffectiveAtomDensity.WeightingWorks (0 ms) 16: [ RUN ] EffectiveAtomDensity.LargeValuesHandledWell 16: [ OK ] EffectiveAtomDensity.LargeValuesHandledWell (0 ms) 16: [----------] 3 tests from EffectiveAtomDensity (0 ms total) 16: 16: [----------] 2 tests from AtomNonbondedAndKineticProperties 16: [ RUN ] AtomNonbondedAndKineticProperties.IsAccurate 16: [ OK ] AtomNonbondedAndKineticProperties.IsAccurate (0 ms) 16: [ RUN ] AtomNonbondedAndKineticProperties.ConstraintsWork 16: [ OK ] AtomNonbondedAndKineticProperties.ConstraintsWork (0 ms) 16: [----------] 2 tests from AtomNonbondedAndKineticProperties (0 ms total) 16: 16: [----------] 1 test from VerletBufferConstraintTest 16: [ RUN ] VerletBufferConstraintTest.EqualMasses 16: [ OK ] VerletBufferConstraintTest.EqualMasses (0 ms) 16: [----------] 1 test from VerletBufferConstraintTest (0 ms total) 16: 16: [----------] 1 test from VerletBufferSize 16: [ RUN ] VerletBufferSize.SizeAboveFourIsEquivalent 16: [ OK ] VerletBufferSize.SizeAboveFourIsEquivalent (1 ms) 16: [----------] 1 test from VerletBufferSize (1 ms total) 16: 16: [----------] 6 tests from CalcvirTest 16: [ RUN ] CalcvirTest.CanCalculateVirialAllAtomsInBox 16: [ OK ] CalcvirTest.CanCalculateVirialAllAtomsInBox (0 ms) 16: [ RUN ] CalcvirTest.CanCalculateVirialAllAtomsInBoxScrew 16: [ OK ] CalcvirTest.CanCalculateVirialAllAtomsInBoxScrew (0 ms) 16: [ RUN ] CalcvirTest.CanCalculateVirialAtomsOutOfBoxScrewX 16: [ OK ] CalcvirTest.CanCalculateVirialAtomsOutOfBoxScrewX (0 ms) 16: [ RUN ] CalcvirTest.CanCalculateVirialAtomsOutOfBoxScrewY 16: [ OK ] CalcvirTest.CanCalculateVirialAtomsOutOfBoxScrewY (0 ms) 16: [ RUN ] CalcvirTest.CanCalculateVirialAtomsOutOfBoxScrewZ 16: [ OK ] CalcvirTest.CanCalculateVirialAtomsOutOfBoxScrewZ (0 ms) 16: [ RUN ] CalcvirTest.CanCalculateVirialAtomsOutOfBoxScrewXYZ 16: [ OK ] CalcvirTest.CanCalculateVirialAtomsOutOfBoxScrewXYZ (0 ms) 16: [----------] 6 tests from CalcvirTest (3 ms total) 16: 16: [----------] 2 tests from PrEbinTest 16: [ RUN ] PrEbinTest.HandlesAverages 16: [ OK ] PrEbinTest.HandlesAverages (1 ms) 16: [ RUN ] PrEbinTest.HandlesEmptyAverages 16: [ OK ] PrEbinTest.HandlesEmptyAverages (1 ms) 16: [----------] 2 tests from PrEbinTest (2 ms total) 16: 16: [----------] 3 tests from EnergyDriftTracker 16: [ RUN ] EnergyDriftTracker.emptyWorks 16: [ OK ] EnergyDriftTracker.emptyWorks (0 ms) 16: [ RUN ] EnergyDriftTracker.onePointWorks 16: [ OK ] EnergyDriftTracker.onePointWorks (0 ms) 16: [ RUN ] EnergyDriftTracker.manyPointsWorks 16: [ OK ] EnergyDriftTracker.manyPointsWorks (0 ms) 16: [----------] 3 tests from EnergyDriftTracker (0 ms total) 16: 16: [----------] 4 tests from ShakeTest 16: [ RUN ] ShakeTest.ConstrainsOneBond 16: [ OK ] ShakeTest.ConstrainsOneBond (0 ms) 16: [ RUN ] ShakeTest.ConstrainsTwoDisjointBonds 16: [ OK ] ShakeTest.ConstrainsTwoDisjointBonds (0 ms) 16: [ RUN ] ShakeTest.ConstrainsTwoBondsWithACommonAtom 16: [ OK ] ShakeTest.ConstrainsTwoBondsWithACommonAtom (0 ms) 16: [ RUN ] ShakeTest.ConstrainsThreeBondsWithCommonAtoms 16: [ OK ] ShakeTest.ConstrainsThreeBondsWithCommonAtoms (0 ms) 16: [----------] 4 tests from ShakeTest (0 ms total) 16: 16: [----------] 1 test from NullSignalTest 16: [ RUN ] NullSignalTest.NullSignallerWorks 16: [ OK ] NullSignalTest.NullSignallerWorks (0 ms) 16: [----------] 1 test from NullSignalTest (0 ms total) 16: 16: [----------] 7 tests from SignalTest 16: [ RUN ] SignalTest.NoSignalPropagatesIfNoSignallingTakesPlace 16: [ OK ] SignalTest.NoSignalPropagatesIfNoSignallingTakesPlace (0 ms) 16: [ RUN ] SignalTest.LocalIntraSimSignalPropagatesWhenIntraSimSignalTakesPlace 16: [ OK ] SignalTest.LocalIntraSimSignalPropagatesWhenIntraSimSignalTakesPlace (0 ms) 16: [ RUN ] SignalTest.LocalIntraSimSignalPropagatesWhenInterSimTakesPlace 16: [ OK ] SignalTest.LocalIntraSimSignalPropagatesWhenInterSimTakesPlace (0 ms) 16: [ RUN ] SignalTest.LocalIntraSimSignalPropagatesWhenBothTakePlace 16: [ OK ] SignalTest.LocalIntraSimSignalPropagatesWhenBothTakePlace (0 ms) 16: [ RUN ] SignalTest.NonLocalSignalDoesntPropagateWhenIntraSimSignalTakesPlace 16: [ OK ] SignalTest.NonLocalSignalDoesntPropagateWhenIntraSimSignalTakesPlace (0 ms) 16: [ RUN ] SignalTest.NonLocalSignalPropagatesWhenInterSimSignalTakesPlace 16: [ OK ] SignalTest.NonLocalSignalPropagatesWhenInterSimSignalTakesPlace (0 ms) 16: [ RUN ] SignalTest.NonLocalSignalPropagatesWhenBothTakePlace 16: [ OK ] SignalTest.NonLocalSignalPropagatesWhenBothTakePlace (0 ms) 16: [----------] 7 tests from SignalTest (0 ms total) 16: 16: [----------] 13 tests from UpdateGroupsTest 16: [ RUN ] UpdateGroupsTest.WithEthaneUA 16: [ OK ] UpdateGroupsTest.WithEthaneUA (0 ms) 16: [ RUN ] UpdateGroupsTest.WithMethane 16: [ OK ] UpdateGroupsTest.WithMethane (0 ms) 16: [ RUN ] UpdateGroupsTest.WithEthane 16: [ OK ] UpdateGroupsTest.WithEthane (0 ms) 16: [ RUN ] UpdateGroupsTest.CheckRadiusCalculationAtDifferentTemperaturesWithEthane 16: [ OK ] UpdateGroupsTest.CheckRadiusCalculationAtDifferentTemperaturesWithEthane (0 ms) 16: [ RUN ] UpdateGroupsTest.WithButaneUALogsThatUnsuitableForUpdateGroups 16: [ OK ] UpdateGroupsTest.WithButaneUALogsThatUnsuitableForUpdateGroups (0 ms) 16: [ RUN ] UpdateGroupsTest.WithWaterThreeSite 16: [ OK ] UpdateGroupsTest.WithWaterThreeSite (0 ms) 16: [ RUN ] UpdateGroupsTest.WithWaterFourSite 16: [ OK ] UpdateGroupsTest.WithWaterFourSite (0 ms) 16: [ RUN ] UpdateGroupsTest.WithFourAtomsWithSettle 16: [ OK ] UpdateGroupsTest.WithFourAtomsWithSettle (0 ms) 16: [ RUN ] UpdateGroupsTest.WithWaterFlexAngle 16: [ OK ] UpdateGroupsTest.WithWaterFlexAngle (0 ms) 16: [ RUN ] UpdateGroupsTest.CheckRadiusCalculationAtDifferentTemperaturesWithWaterFlexAngle 16: [ OK ] UpdateGroupsTest.CheckRadiusCalculationAtDifferentTemperaturesWithWaterFlexAngle (0 ms) 16: [ RUN ] UpdateGroupsTest.WithTwoMoltypes 16: [ OK ] UpdateGroupsTest.WithTwoMoltypes (0 ms) 16: [ RUN ] UpdateGroupsTest.LogsWhenSizesAreInvalid 16: [ OK ] UpdateGroupsTest.LogsWhenSizesAreInvalid (1 ms) 16: [ RUN ] UpdateGroupsTest.LogsWhenUpdateGroupsAreNotUseful 16: [ OK ] UpdateGroupsTest.LogsWhenUpdateGroupsAreNotUseful (0 ms) 16: [----------] 13 tests from UpdateGroupsTest (3 ms total) 16: 16: [----------] 1 test from UpdateGroupsCog 16: [ RUN ] UpdateGroupsCog.ComputesCogs 16: [ OK ] UpdateGroupsCog.ComputesCogs (2 ms) 16: [----------] 1 test from UpdateGroupsCog (3 ms total) 16: 16: [----------] 2 tests from WholeMoleculeTransform 16: [ RUN ] WholeMoleculeTransform.MakesMoleculesWhole 16: [ OK ] WholeMoleculeTransform.MakesMoleculesWhole (0 ms) 16: [ RUN ] WholeMoleculeTransform.HandlesReordering 16: [ OK ] WholeMoleculeTransform.HandlesReordering (0 ms) 16: [----------] 2 tests from WholeMoleculeTransform (0 ms total) 16: 16: [----------] 28 tests from WithParameters/ConstraintsTest 16: [ RUN ] WithParameters/ConstraintsTest.SatisfiesConstraints/0 16: [ OK ] WithParameters/ConstraintsTest.SatisfiesConstraints/0 (1 ms) 16: [ RUN ] WithParameters/ConstraintsTest.SatisfiesConstraints/1 16: [ OK ] WithParameters/ConstraintsTest.SatisfiesConstraints/1 (0 ms) 16: [ RUN ] WithParameters/ConstraintsTest.SatisfiesConstraints/2 16: [ OK ] WithParameters/ConstraintsTest.SatisfiesConstraints/2 (1 ms) 16: [ RUN ] WithParameters/ConstraintsTest.SatisfiesConstraints/3 16: [ OK ] WithParameters/ConstraintsTest.SatisfiesConstraints/3 (1 ms) 16: [ RUN ] WithParameters/ConstraintsTest.SatisfiesConstraints/4 16: [ OK ] WithParameters/ConstraintsTest.SatisfiesConstraints/4 (1 ms) 16: [ RUN ] WithParameters/ConstraintsTest.SatisfiesConstraints/5 16: [ OK ] WithParameters/ConstraintsTest.SatisfiesConstraints/5 (1 ms) 16: [ RUN ] WithParameters/ConstraintsTest.SatisfiesConstraints/6 16: [ OK ] WithParameters/ConstraintsTest.SatisfiesConstraints/6 (1 ms) 16: [ RUN ] WithParameters/ConstraintsTest.SatisfiesConstraints/7 16: [ OK ] WithParameters/ConstraintsTest.SatisfiesConstraints/7 (1 ms) 16: [ RUN ] WithParameters/ConstraintsTest.SatisfiesConstraints/8 16: [ OK ] WithParameters/ConstraintsTest.SatisfiesConstraints/8 (1 ms) 16: [ RUN ] WithParameters/ConstraintsTest.SatisfiesConstraints/9 16: [ OK ] WithParameters/ConstraintsTest.SatisfiesConstraints/9 (1 ms) 16: [ RUN ] WithParameters/ConstraintsTest.SatisfiesConstraints/10 16: [ OK ] WithParameters/ConstraintsTest.SatisfiesConstraints/10 (1 ms) 16: [ RUN ] WithParameters/ConstraintsTest.SatisfiesConstraints/11 16: [ OK ] WithParameters/ConstraintsTest.SatisfiesConstraints/11 (1 ms) 16: [ RUN ] WithParameters/ConstraintsTest.SatisfiesConstraints/12 16: [ OK ] WithParameters/ConstraintsTest.SatisfiesConstraints/12 (66 ms) 16: [ RUN ] WithParameters/ConstraintsTest.SatisfiesConstraints/13 16: [ OK ] WithParameters/ConstraintsTest.SatisfiesConstraints/13 (67 ms) 16: [ RUN ] WithParameters/ConstraintsTest.TriangleDetectionWorks/0 16: [ OK ] WithParameters/ConstraintsTest.TriangleDetectionWorks/0 (0 ms) 16: [ RUN ] WithParameters/ConstraintsTest.TriangleDetectionWorks/1 16: [ OK ] WithParameters/ConstraintsTest.TriangleDetectionWorks/1 (0 ms) 16: [ RUN ] WithParameters/ConstraintsTest.TriangleDetectionWorks/2 16: [ OK ] WithParameters/ConstraintsTest.TriangleDetectionWorks/2 (0 ms) 16: [ RUN ] WithParameters/ConstraintsTest.TriangleDetectionWorks/3 16: [ OK ] WithParameters/ConstraintsTest.TriangleDetectionWorks/3 (0 ms) 16: [ RUN ] WithParameters/ConstraintsTest.TriangleDetectionWorks/4 16: [ OK ] WithParameters/ConstraintsTest.TriangleDetectionWorks/4 (0 ms) 16: [ RUN ] WithParameters/ConstraintsTest.TriangleDetectionWorks/5 16: [ OK ] WithParameters/ConstraintsTest.TriangleDetectionWorks/5 (0 ms) 16: [ RUN ] WithParameters/ConstraintsTest.TriangleDetectionWorks/6 16: [ OK ] WithParameters/ConstraintsTest.TriangleDetectionWorks/6 (0 ms) 16: [ RUN ] WithParameters/ConstraintsTest.TriangleDetectionWorks/7 16: [ OK ] WithParameters/ConstraintsTest.TriangleDetectionWorks/7 (0 ms) 16: [ RUN ] WithParameters/ConstraintsTest.TriangleDetectionWorks/8 16: [ OK ] WithParameters/ConstraintsTest.TriangleDetectionWorks/8 (0 ms) 16: [ RUN ] WithParameters/ConstraintsTest.TriangleDetectionWorks/9 16: [ OK ] WithParameters/ConstraintsTest.TriangleDetectionWorks/9 (0 ms) 16: [ RUN ] WithParameters/ConstraintsTest.TriangleDetectionWorks/10 16: [ OK ] WithParameters/ConstraintsTest.TriangleDetectionWorks/10 (0 ms) 16: [ RUN ] WithParameters/ConstraintsTest.TriangleDetectionWorks/11 16: [ OK ] WithParameters/ConstraintsTest.TriangleDetectionWorks/11 (0 ms) 16: [ RUN ] WithParameters/ConstraintsTest.TriangleDetectionWorks/12 16: [ OK ] WithParameters/ConstraintsTest.TriangleDetectionWorks/12 (0 ms) 16: [ RUN ] WithParameters/ConstraintsTest.TriangleDetectionWorks/13 16: [ OK ] WithParameters/ConstraintsTest.TriangleDetectionWorks/13 (0 ms) 16: [----------] 28 tests from WithParameters/ConstraintsTest (166 ms total) 16: 16: [----------] 11 tests from WithParameters/EnergyOutputTest 16: [ RUN ] WithParameters/EnergyOutputTest.CheckOutput/0 16: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/mdlib/tests/Testing/Temporary/WithParameters_EnergyOutputTest_CheckOutput_0.edr as double precision energy file 16: Reading energy frame 0 time 10.100 [ OK ] WithParameters/EnergyOutputTest.CheckOutput/0 (9 ms) 16: [ RUN ] WithParameters/EnergyOutputTest.CheckOutput/1 16: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/mdlib/tests/Testing/Temporary/WithParameters_EnergyOutputTest_CheckOutput_1.edr as double precision energy file 16: Reading energy frame 0 time 10.100 [ OK ] WithParameters/EnergyOutputTest.CheckOutput/1 (7 ms) 16: [ RUN ] WithParameters/EnergyOutputTest.CheckOutput/2 16: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/mdlib/tests/Testing/Temporary/WithParameters_EnergyOutputTest_CheckOutput_2.edr as double precision energy file 16: Reading energy frame 0 time 10.100 [ OK ] WithParameters/EnergyOutputTest.CheckOutput/2 (9 ms) 16: [ RUN ] WithParameters/EnergyOutputTest.CheckOutput/3 16: [ OK ] WithParameters/EnergyOutputTest.CheckOutput/3 (3 ms) 16: [ RUN ] WithParameters/EnergyOutputTest.CheckOutput/4 16: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/mdlib/tests/Testing/Temporary/WithParameters_EnergyOutputTest_CheckOutput_4.edr as double precision energy file 16: Reading energy frame 0 time 10.100 Reading energy frame 1 time 27.500 Reading energy frame 2 time 44.900 Reading energy frame 3 time 62.300 Reading energy frame 4 time 79.700 Reading energy frame 5 time 97.100 Reading energy frame 6 time 114.500 Reading energy frame 7 time 131.900 Reading energy frame 8 time 149.300 Reading energy frame 9 time 166.700 [ OK ] WithParameters/EnergyOutputTest.CheckOutput/4 (42 ms) 16: [ RUN ] WithParameters/EnergyOutputTest.CheckOutput/5 16: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/mdlib/tests/Testing/Temporary/WithParameters_EnergyOutputTest_CheckOutput_5.edr as double precision energy file 16: Reading energy frame 0 time 10.100 [ OK ] WithParameters/EnergyOutputTest.CheckOutput/5 (11 ms) 16: [ RUN ] WithParameters/EnergyOutputTest.CheckOutput/6 16: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/mdlib/tests/Testing/Temporary/WithParameters_EnergyOutputTest_CheckOutput_6.edr as double precision energy file 16: Reading energy frame 0 time 10.100 [ OK ] WithParameters/EnergyOutputTest.CheckOutput/6 (11 ms) 16: [ RUN ] WithParameters/EnergyOutputTest.CheckOutput/7 16: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/mdlib/tests/Testing/Temporary/WithParameters_EnergyOutputTest_CheckOutput_7.edr as double precision energy file 16: Reading energy frame 0 time 10.100 [ OK ] WithParameters/EnergyOutputTest.CheckOutput/7 (12 ms) 16: [ RUN ] WithParameters/EnergyOutputTest.CheckOutput/8 16: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/mdlib/tests/Testing/Temporary/WithParameters_EnergyOutputTest_CheckOutput_8.edr as double precision energy file 16: Reading energy frame 0 time 10.100 [ OK ] WithParameters/EnergyOutputTest.CheckOutput/8 (12 ms) 16: [ RUN ] WithParameters/EnergyOutputTest.CheckOutput/9 16: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/mdlib/tests/Testing/Temporary/WithParameters_EnergyOutputTest_CheckOutput_9.edr as double precision energy file 16: Reading energy frame 0 time 10.100 [ OK ] WithParameters/EnergyOutputTest.CheckOutput/9 (10 ms) 16: [ RUN ] WithParameters/EnergyOutputTest.CheckOutput/10 16: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/mdlib/tests/Testing/Temporary/WithParameters_EnergyOutputTest_CheckOutput_10.edr as double precision energy file 16: Reading energy frame 0 time 10.100 [ OK ] WithParameters/EnergyOutputTest.CheckOutput/10 (11 ms) 16: [----------] 11 tests from WithParameters/EnergyOutputTest (161 ms total) 16: 16: [----------] 24 tests from SimpleTests/CalculateAcceptanceWeightSimple 16: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.UnknownCalculationModeThrows/0 16: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.UnknownCalculationModeThrows/0 (2 ms) 16: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.UnknownCalculationModeThrows/1 16: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.UnknownCalculationModeThrows/1 (0 ms) 16: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.UnknownCalculationModeThrows/2 16: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.UnknownCalculationModeThrows/2 (0 ms) 16: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.UnknownCalculationModeThrows/3 16: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.UnknownCalculationModeThrows/3 (0 ms) 16: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.UnknownCalculationModeThrows/4 16: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.UnknownCalculationModeThrows/4 (0 ms) 16: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.UnknownCalculationModeThrows/5 16: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.UnknownCalculationModeThrows/5 (0 ms) 16: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.UnknownCalculationModeThrows/6 16: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.UnknownCalculationModeThrows/6 (0 ms) 16: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.UnknownCalculationModeThrows/7 16: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.UnknownCalculationModeThrows/7 (0 ms) 16: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.KnownCalculationModeDoesNotThrow/0 16: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.KnownCalculationModeDoesNotThrow/0 (0 ms) 16: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.KnownCalculationModeDoesNotThrow/1 16: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.KnownCalculationModeDoesNotThrow/1 (0 ms) 16: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.KnownCalculationModeDoesNotThrow/2 16: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.KnownCalculationModeDoesNotThrow/2 (0 ms) 16: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.KnownCalculationModeDoesNotThrow/3 16: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.KnownCalculationModeDoesNotThrow/3 (0 ms) 16: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.KnownCalculationModeDoesNotThrow/4 16: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.KnownCalculationModeDoesNotThrow/4 (0 ms) 16: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.KnownCalculationModeDoesNotThrow/5 16: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.KnownCalculationModeDoesNotThrow/5 (0 ms) 16: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.KnownCalculationModeDoesNotThrow/6 16: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.KnownCalculationModeDoesNotThrow/6 (0 ms) 16: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.KnownCalculationModeDoesNotThrow/7 16: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.KnownCalculationModeDoesNotThrow/7 (0 ms) 16: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.BarkerAndMinVarAreIdentical/0 16: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.BarkerAndMinVarAreIdentical/0 (0 ms) 16: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.BarkerAndMinVarAreIdentical/1 16: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.BarkerAndMinVarAreIdentical/1 (0 ms) 16: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.BarkerAndMinVarAreIdentical/2 16: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.BarkerAndMinVarAreIdentical/2 (0 ms) 16: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.BarkerAndMinVarAreIdentical/3 16: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.BarkerAndMinVarAreIdentical/3 (0 ms) 16: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.BarkerAndMinVarAreIdentical/4 16: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.BarkerAndMinVarAreIdentical/4 (0 ms) 16: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.BarkerAndMinVarAreIdentical/5 16: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.BarkerAndMinVarAreIdentical/5 (0 ms) 16: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.BarkerAndMinVarAreIdentical/6 16: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.BarkerAndMinVarAreIdentical/6 (0 ms) 16: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.BarkerAndMinVarAreIdentical/7 16: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.BarkerAndMinVarAreIdentical/7 (0 ms) 16: [----------] 24 tests from SimpleTests/CalculateAcceptanceWeightSimple (4 ms total) 16: 16: [----------] 14 tests from RegressionTests/CalculateAcceptanceWeightRangeRegression 16: [ RUN ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/0 16: [ OK ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/0 (0 ms) 16: [ RUN ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/1 16: [ OK ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/1 (0 ms) 16: [ RUN ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/2 16: [ OK ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/2 (0 ms) 16: [ RUN ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/3 16: [ OK ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/3 (0 ms) 16: [ RUN ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/4 16: [ OK ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/4 (0 ms) 16: [ RUN ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/5 16: [ OK ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/5 (0 ms) 16: [ RUN ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/6 16: [ OK ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/6 (0 ms) 16: [ RUN ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/7 16: [ OK ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/7 (0 ms) 16: [ RUN ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/8 16: [ OK ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/8 (0 ms) 16: [ RUN ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/9 16: [ OK ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/9 (0 ms) 16: [ RUN ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/10 16: [ OK ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/10 (0 ms) 16: [ RUN ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/11 16: [ OK ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/11 (0 ms) 16: [ RUN ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/12 16: [ OK ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/12 (0 ms) 16: [ RUN ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/13 16: [ OK ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/13 (0 ms) 16: [----------] 14 tests from RegressionTests/CalculateAcceptanceWeightRangeRegression (0 ms total) 16: 16: [----------] 23 tests from WithParameters/FreeEnergyParameterTest 16: [ RUN ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/0 16: [ OK ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/0 (0 ms) 16: [ RUN ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/1 16: [ OK ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/1 (0 ms) 16: [ RUN ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/2 16: [ OK ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/2 (0 ms) 16: [ RUN ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/3 16: [ OK ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/3 (0 ms) 16: [ RUN ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/4 16: [ OK ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/4 (0 ms) 16: [ RUN ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/5 16: [ OK ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/5 (0 ms) 16: [ RUN ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/6 16: [ OK ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/6 (0 ms) 16: [ RUN ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/7 16: [ OK ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/7 (0 ms) 16: [ RUN ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/8 16: [ OK ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/8 (0 ms) 16: [ RUN ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/9 16: [ OK ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/9 (0 ms) 16: [ RUN ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/10 16: [ OK ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/10 (0 ms) 16: [ RUN ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/11 16: [ OK ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/11 (0 ms) 16: [ RUN ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/12 16: [ OK ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/12 (0 ms) 16: [ RUN ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/13 16: [ OK ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/13 (0 ms) 16: [ RUN ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/14 16: [ OK ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/14 (0 ms) 16: [ RUN ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/15 16: [ OK ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/15 (0 ms) 16: [ RUN ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/16 16: [ OK ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/16 (0 ms) 16: [ RUN ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/17 16: [ OK ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/17 (0 ms) 16: [ RUN ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/18 16: [ OK ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/18 (0 ms) 16: [ RUN ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/19 16: [ OK ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/19 (0 ms) 16: [ RUN ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/20 16: [ OK ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/20 (0 ms) 16: [ RUN ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/21 16: [ OK ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/21 (0 ms) 16: [ RUN ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/22 16: [ OK ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/22 (0 ms) 16: [----------] 23 tests from WithParameters/FreeEnergyParameterTest (1 ms total) 16: 16: [----------] 17 tests from WithParameters/LangevinTest 16: [ RUN ] WithParameters/LangevinTest.SimpleIntegration/0 16: [ OK ] WithParameters/LangevinTest.SimpleIntegration/0 (1 ms) 16: [ RUN ] WithParameters/LangevinTest.SimpleIntegration/1 16: [ OK ] WithParameters/LangevinTest.SimpleIntegration/1 (1 ms) 16: [ RUN ] WithParameters/LangevinTest.SimpleIntegration/2 16: [ OK ] WithParameters/LangevinTest.SimpleIntegration/2 (0 ms) 16: [ RUN ] WithParameters/LangevinTest.SimpleIntegration/3 16: [ OK ] WithParameters/LangevinTest.SimpleIntegration/3 (0 ms) 16: [ RUN ] WithParameters/LangevinTest.SimpleIntegration/4 16: [ OK ] WithParameters/LangevinTest.SimpleIntegration/4 (0 ms) 16: [ RUN ] WithParameters/LangevinTest.SimpleIntegration/5 16: [ OK ] WithParameters/LangevinTest.SimpleIntegration/5 (0 ms) 16: [ RUN ] WithParameters/LangevinTest.SimpleIntegration/6 16: [ OK ] WithParameters/LangevinTest.SimpleIntegration/6 (0 ms) 16: [ RUN ] WithParameters/LangevinTest.SimpleIntegration/7 16: [ OK ] WithParameters/LangevinTest.SimpleIntegration/7 (0 ms) 16: [ RUN ] WithParameters/LangevinTest.SimpleIntegration/8 16: [ OK ] WithParameters/LangevinTest.SimpleIntegration/8 (0 ms) 16: [ RUN ] WithParameters/LangevinTest.SimpleIntegration/9 16: [ OK ] WithParameters/LangevinTest.SimpleIntegration/9 (0 ms) 16: [ RUN ] WithParameters/LangevinTest.SimpleIntegration/10 16: [ OK ] WithParameters/LangevinTest.SimpleIntegration/10 (0 ms) 16: [ RUN ] WithParameters/LangevinTest.SimpleIntegration/11 16: [ OK ] WithParameters/LangevinTest.SimpleIntegration/11 (0 ms) 16: [ RUN ] WithParameters/LangevinTest.SimpleIntegration/12 16: [ OK ] WithParameters/LangevinTest.SimpleIntegration/12 (1 ms) 16: [ RUN ] WithParameters/LangevinTest.SimpleIntegration/13 16: [ OK ] WithParameters/LangevinTest.SimpleIntegration/13 (1 ms) 16: [ RUN ] WithParameters/LangevinTest.SimpleIntegration/14 16: [ OK ] WithParameters/LangevinTest.SimpleIntegration/14 (1 ms) 16: [ RUN ] WithParameters/LangevinTest.SimpleIntegration/15 16: [ OK ] WithParameters/LangevinTest.SimpleIntegration/15 (1 ms) 16: [ RUN ] WithParameters/LangevinTest.SimpleIntegration/16 16: [ OK ] WithParameters/LangevinTest.SimpleIntegration/16 (1 ms) 16: [----------] 17 tests from WithParameters/LangevinTest (19 ms total) 16: 16: [----------] 16 tests from WithParameters/LeapFrogTest 16: [ RUN ] WithParameters/LeapFrogTest.SimpleIntegration/0 16: [ OK ] WithParameters/LeapFrogTest.SimpleIntegration/0 (0 ms) 16: [ RUN ] WithParameters/LeapFrogTest.SimpleIntegration/1 16: [ OK ] WithParameters/LeapFrogTest.SimpleIntegration/1 (0 ms) 16: [ RUN ] WithParameters/LeapFrogTest.SimpleIntegration/2 16: [ OK ] WithParameters/LeapFrogTest.SimpleIntegration/2 (0 ms) 16: [ RUN ] WithParameters/LeapFrogTest.SimpleIntegration/3 16: [ OK ] WithParameters/LeapFrogTest.SimpleIntegration/3 (0 ms) 16: [ RUN ] WithParameters/LeapFrogTest.SimpleIntegration/4 16: [ OK ] WithParameters/LeapFrogTest.SimpleIntegration/4 (1 ms) 16: [ RUN ] WithParameters/LeapFrogTest.SimpleIntegration/5 16: [ OK ] WithParameters/LeapFrogTest.SimpleIntegration/5 (10 ms) 16: [ RUN ] WithParameters/LeapFrogTest.SimpleIntegration/6 16: [ OK ] WithParameters/LeapFrogTest.SimpleIntegration/6 (33 ms) 16: [ RUN ] WithParameters/LeapFrogTest.SimpleIntegration/7 16: [ OK ] WithParameters/LeapFrogTest.SimpleIntegration/7 (1 ms) 16: [ RUN ] WithParameters/LeapFrogTest.SimpleIntegration/8 16: [ OK ] WithParameters/LeapFrogTest.SimpleIntegration/8 (0 ms) 16: [ RUN ] WithParameters/LeapFrogTest.SimpleIntegration/9 16: [ OK ] WithParameters/LeapFrogTest.SimpleIntegration/9 (1 ms) 16: [ RUN ] WithParameters/LeapFrogTest.SimpleIntegration/10 16: [ OK ] WithParameters/LeapFrogTest.SimpleIntegration/10 (11 ms) 16: [ RUN ] WithParameters/LeapFrogTest.SimpleIntegration/11 16: [ OK ] WithParameters/LeapFrogTest.SimpleIntegration/11 (11 ms) 16: [ RUN ] WithParameters/LeapFrogTest.SimpleIntegration/12 16: [ OK ] WithParameters/LeapFrogTest.SimpleIntegration/12 (10 ms) 16: [ RUN ] WithParameters/LeapFrogTest.SimpleIntegration/13 16: [ OK ] WithParameters/LeapFrogTest.SimpleIntegration/13 (10 ms) 16: [ RUN ] WithParameters/LeapFrogTest.SimpleIntegration/14 16: [ OK ] WithParameters/LeapFrogTest.SimpleIntegration/14 (10 ms) 16: [ RUN ] WithParameters/LeapFrogTest.SimpleIntegration/15 16: [ OK ] WithParameters/LeapFrogTest.SimpleIntegration/15 (9 ms) 16: [----------] 16 tests from WithParameters/LeapFrogTest (135 ms total) 16: 16: [----------] 140 tests from Cubic/ParrRahmTest 16: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_cubic_box_2_5_boxv__100 16: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_cubic_box_2_5_boxv__100 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_cubic_box_2_5_boxv__1 16: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_cubic_box_2_5_boxv__1 (2 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_cubic_box_2_5_boxv__1e_07 16: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_cubic_box_2_5_boxv__1e_07 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_cubic_box_2_5_boxv_0 16: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_cubic_box_2_5_boxv_0 (1 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_cubic_box_2_5_boxv_1e_07 16: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_cubic_box_2_5_boxv_1e_07 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_cubic_box_2_5_boxv_1 16: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_cubic_box_2_5_boxv_1 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_cubic_box_2_5_boxv_100 16: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_cubic_box_2_5_boxv_100 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_cubic_box_10000_boxv__100 16: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_cubic_box_10000_boxv__100 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_cubic_box_10000_boxv__1 16: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_cubic_box_10000_boxv__1 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_cubic_box_10000_boxv__1e_07 16: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_cubic_box_10000_boxv__1e_07 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_cubic_box_10000_boxv_0 16: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_cubic_box_10000_boxv_0 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_cubic_box_10000_boxv_1e_07 16: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_cubic_box_10000_boxv_1e_07 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_cubic_box_10000_boxv_1 16: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_cubic_box_10000_boxv_1 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_cubic_box_10000_boxv_100 16: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_cubic_box_10000_boxv_100 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_cubic_box_2_5_boxv__100 16: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_cubic_box_2_5_boxv__100 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_cubic_box_2_5_boxv__1 16: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_cubic_box_2_5_boxv__1 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_cubic_box_2_5_boxv__1e_07 16: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_cubic_box_2_5_boxv__1e_07 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_cubic_box_2_5_boxv_0 16: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_cubic_box_2_5_boxv_0 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_cubic_box_2_5_boxv_1e_07 16: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_cubic_box_2_5_boxv_1e_07 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_cubic_box_2_5_boxv_1 16: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_cubic_box_2_5_boxv_1 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_cubic_box_2_5_boxv_100 16: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_cubic_box_2_5_boxv_100 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_cubic_box_10000_boxv__100 16: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_cubic_box_10000_boxv__100 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_cubic_box_10000_boxv__1 16: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_cubic_box_10000_boxv__1 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_cubic_box_10000_boxv__1e_07 16: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_cubic_box_10000_boxv__1e_07 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_cubic_box_10000_boxv_0 16: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_cubic_box_10000_boxv_0 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_cubic_box_10000_boxv_1e_07 16: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_cubic_box_10000_boxv_1e_07 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_cubic_box_10000_boxv_1 16: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_cubic_box_10000_boxv_1 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_cubic_box_10000_boxv_100 16: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_cubic_box_10000_boxv_100 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_cubic_box_2_5_boxv__100 16: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_cubic_box_2_5_boxv__100 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_cubic_box_2_5_boxv__1 16: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_cubic_box_2_5_boxv__1 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_cubic_box_2_5_boxv__1e_07 16: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_cubic_box_2_5_boxv__1e_07 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_cubic_box_2_5_boxv_0 16: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_cubic_box_2_5_boxv_0 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_cubic_box_2_5_boxv_1e_07 16: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_cubic_box_2_5_boxv_1e_07 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_cubic_box_2_5_boxv_1 16: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_cubic_box_2_5_boxv_1 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_cubic_box_2_5_boxv_100 16: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_cubic_box_2_5_boxv_100 (1 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_cubic_box_10000_boxv__100 16: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_cubic_box_10000_boxv__100 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_cubic_box_10000_boxv__1 16: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_cubic_box_10000_boxv__1 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_cubic_box_10000_boxv__1e_07 16: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_cubic_box_10000_boxv__1e_07 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_cubic_box_10000_boxv_0 16: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_cubic_box_10000_boxv_0 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_cubic_box_10000_boxv_1e_07 16: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_cubic_box_10000_boxv_1e_07 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_cubic_box_10000_boxv_1 16: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_cubic_box_10000_boxv_1 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_cubic_box_10000_boxv_100 16: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_cubic_box_10000_boxv_100 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_general_shape_cubic_box_2_5_boxv__100 16: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_general_shape_cubic_box_2_5_boxv__100 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_general_shape_cubic_box_2_5_boxv__1 16: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_general_shape_cubic_box_2_5_boxv__1 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_general_shape_cubic_box_2_5_boxv__1e_07 16: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_general_shape_cubic_box_2_5_boxv__1e_07 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_general_shape_cubic_box_2_5_boxv_0 16: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_general_shape_cubic_box_2_5_boxv_0 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_general_shape_cubic_box_2_5_boxv_1e_07 16: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_general_shape_cubic_box_2_5_boxv_1e_07 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_general_shape_cubic_box_2_5_boxv_1 16: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_general_shape_cubic_box_2_5_boxv_1 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_general_shape_cubic_box_2_5_boxv_100 16: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_general_shape_cubic_box_2_5_boxv_100 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_general_shape_cubic_box_10000_boxv__100 16: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_general_shape_cubic_box_10000_boxv__100 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_general_shape_cubic_box_10000_boxv__1 16: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_general_shape_cubic_box_10000_boxv__1 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_general_shape_cubic_box_10000_boxv__1e_07 16: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_general_shape_cubic_box_10000_boxv__1e_07 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_general_shape_cubic_box_10000_boxv_0 16: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_general_shape_cubic_box_10000_boxv_0 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_general_shape_cubic_box_10000_boxv_1e_07 16: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_general_shape_cubic_box_10000_boxv_1e_07 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_general_shape_cubic_box_10000_boxv_1 16: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_general_shape_cubic_box_10000_boxv_1 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_general_shape_cubic_box_10000_boxv_100 16: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_general_shape_cubic_box_10000_boxv_100 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_cubic_box_2_5_boxv__100 16: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_cubic_box_2_5_boxv__100 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_cubic_box_2_5_boxv__1 16: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_cubic_box_2_5_boxv__1 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_cubic_box_2_5_boxv__1e_07 16: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_cubic_box_2_5_boxv__1e_07 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_cubic_box_2_5_boxv_0 16: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_cubic_box_2_5_boxv_0 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_cubic_box_2_5_boxv_1e_07 16: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_cubic_box_2_5_boxv_1e_07 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_cubic_box_2_5_boxv_1 16: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_cubic_box_2_5_boxv_1 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_cubic_box_2_5_boxv_100 16: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_cubic_box_2_5_boxv_100 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_cubic_box_10000_boxv__100 16: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_cubic_box_10000_boxv__100 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_cubic_box_10000_boxv__1 16: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_cubic_box_10000_boxv__1 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_cubic_box_10000_boxv__1e_07 16: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_cubic_box_10000_boxv__1e_07 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_cubic_box_10000_boxv_0 16: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_cubic_box_10000_boxv_0 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_cubic_box_10000_boxv_1e_07 16: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_cubic_box_10000_boxv_1e_07 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_cubic_box_10000_boxv_1 16: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_cubic_box_10000_boxv_1 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_cubic_box_10000_boxv_100 16: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_cubic_box_10000_boxv_100 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_cubic_box_2_5_boxv__100 16: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_cubic_box_2_5_boxv__100 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_cubic_box_2_5_boxv__1 16: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_cubic_box_2_5_boxv__1 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_cubic_box_2_5_boxv__1e_07 16: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_cubic_box_2_5_boxv__1e_07 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_cubic_box_2_5_boxv_0 16: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_cubic_box_2_5_boxv_0 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_cubic_box_2_5_boxv_1e_07 16: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_cubic_box_2_5_boxv_1e_07 (1 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_cubic_box_2_5_boxv_1 16: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_cubic_box_2_5_boxv_1 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_cubic_box_2_5_boxv_100 16: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_cubic_box_2_5_boxv_100 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_cubic_box_10000_boxv__100 16: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_cubic_box_10000_boxv__100 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_cubic_box_10000_boxv__1 16: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_cubic_box_10000_boxv__1 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_cubic_box_10000_boxv__1e_07 16: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_cubic_box_10000_boxv__1e_07 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_cubic_box_10000_boxv_0 16: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_cubic_box_10000_boxv_0 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_cubic_box_10000_boxv_1e_07 16: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_cubic_box_10000_boxv_1e_07 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_cubic_box_10000_boxv_1 16: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_cubic_box_10000_boxv_1 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_cubic_box_10000_boxv_100 16: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_cubic_box_10000_boxv_100 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_cubic_box_2_5_boxv__100 16: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_cubic_box_2_5_boxv__100 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_cubic_box_2_5_boxv__1 16: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_cubic_box_2_5_boxv__1 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_cubic_box_2_5_boxv__1e_07 16: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_cubic_box_2_5_boxv__1e_07 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_cubic_box_2_5_boxv_0 16: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_cubic_box_2_5_boxv_0 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_cubic_box_2_5_boxv_1e_07 16: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_cubic_box_2_5_boxv_1e_07 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_cubic_box_2_5_boxv_1 16: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_cubic_box_2_5_boxv_1 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_cubic_box_2_5_boxv_100 16: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_cubic_box_2_5_boxv_100 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_cubic_box_10000_boxv__100 16: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_cubic_box_10000_boxv__100 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_cubic_box_10000_boxv__1 16: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_cubic_box_10000_boxv__1 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_cubic_box_10000_boxv__1e_07 16: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_cubic_box_10000_boxv__1e_07 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_cubic_box_10000_boxv_0 16: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_cubic_box_10000_boxv_0 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_cubic_box_10000_boxv_1e_07 16: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_cubic_box_10000_boxv_1e_07 (1 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_cubic_box_10000_boxv_1 16: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_cubic_box_10000_boxv_1 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_cubic_box_10000_boxv_100 16: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_cubic_box_10000_boxv_100 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_cubic_box_2_5_boxv__100 16: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_cubic_box_2_5_boxv__100 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_cubic_box_2_5_boxv__1 16: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_cubic_box_2_5_boxv__1 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_cubic_box_2_5_boxv__1e_07 16: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_cubic_box_2_5_boxv__1e_07 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_cubic_box_2_5_boxv_0 16: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_cubic_box_2_5_boxv_0 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_cubic_box_2_5_boxv_1e_07 16: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_cubic_box_2_5_boxv_1e_07 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_cubic_box_2_5_boxv_1 16: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_cubic_box_2_5_boxv_1 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_cubic_box_2_5_boxv_100 16: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_cubic_box_2_5_boxv_100 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_cubic_box_10000_boxv__100 16: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_cubic_box_10000_boxv__100 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_cubic_box_10000_boxv__1 16: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_cubic_box_10000_boxv__1 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_cubic_box_10000_boxv__1e_07 16: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_cubic_box_10000_boxv__1e_07 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_cubic_box_10000_boxv_0 16: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_cubic_box_10000_boxv_0 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_cubic_box_10000_boxv_1e_07 16: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_cubic_box_10000_boxv_1e_07 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_cubic_box_10000_boxv_1 16: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_cubic_box_10000_boxv_1 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_cubic_box_10000_boxv_100 16: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_cubic_box_10000_boxv_100 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_general_shape_cubic_box_2_5_boxv__100 16: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_general_shape_cubic_box_2_5_boxv__100 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_general_shape_cubic_box_2_5_boxv__1 16: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_general_shape_cubic_box_2_5_boxv__1 (8 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_general_shape_cubic_box_2_5_boxv__1e_07 16: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_general_shape_cubic_box_2_5_boxv__1e_07 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_general_shape_cubic_box_2_5_boxv_0 16: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_general_shape_cubic_box_2_5_boxv_0 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_general_shape_cubic_box_2_5_boxv_1e_07 16: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_general_shape_cubic_box_2_5_boxv_1e_07 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_general_shape_cubic_box_2_5_boxv_1 16: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_general_shape_cubic_box_2_5_boxv_1 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_general_shape_cubic_box_2_5_boxv_100 16: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_general_shape_cubic_box_2_5_boxv_100 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_general_shape_cubic_box_10000_boxv__100 16: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_general_shape_cubic_box_10000_boxv__100 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_general_shape_cubic_box_10000_boxv__1 16: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_general_shape_cubic_box_10000_boxv__1 (5 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_general_shape_cubic_box_10000_boxv__1e_07 16: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_general_shape_cubic_box_10000_boxv__1e_07 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_general_shape_cubic_box_10000_boxv_0 16: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_general_shape_cubic_box_10000_boxv_0 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_general_shape_cubic_box_10000_boxv_1e_07 16: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_general_shape_cubic_box_10000_boxv_1e_07 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_general_shape_cubic_box_10000_boxv_1 16: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_general_shape_cubic_box_10000_boxv_1 (6 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_general_shape_cubic_box_10000_boxv_100 16: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_general_shape_cubic_box_10000_boxv_100 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_cubic_box_2_5_boxv__100 16: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_cubic_box_2_5_boxv__100 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_cubic_box_2_5_boxv__1 16: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_cubic_box_2_5_boxv__1 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_cubic_box_2_5_boxv__1e_07 16: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_cubic_box_2_5_boxv__1e_07 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_cubic_box_2_5_boxv_0 16: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_cubic_box_2_5_boxv_0 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_cubic_box_2_5_boxv_1e_07 16: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_cubic_box_2_5_boxv_1e_07 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_cubic_box_2_5_boxv_1 16: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_cubic_box_2_5_boxv_1 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_cubic_box_2_5_boxv_100 16: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_cubic_box_2_5_boxv_100 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_cubic_box_10000_boxv__100 16: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_cubic_box_10000_boxv__100 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_cubic_box_10000_boxv__1 16: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_cubic_box_10000_boxv__1 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_cubic_box_10000_boxv__1e_07 16: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_cubic_box_10000_boxv__1e_07 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_cubic_box_10000_boxv_0 16: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_cubic_box_10000_boxv_0 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_cubic_box_10000_boxv_1e_07 16: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_cubic_box_10000_boxv_1e_07 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_cubic_box_10000_boxv_1 16: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_cubic_box_10000_boxv_1 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_cubic_box_10000_boxv_100 16: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_cubic_box_10000_boxv_100 (0 ms) 16: [----------] 140 tests from Cubic/ParrRahmTest (88 ms total) 16: 16: [----------] 140 tests from Rectilinear/ParrRahmTest 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rect_box_2_5_boxv__100 16: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rect_box_2_5_boxv__100 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rect_box_2_5_boxv__1 16: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rect_box_2_5_boxv__1 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rect_box_2_5_boxv__1e_07 16: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rect_box_2_5_boxv__1e_07 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rect_box_2_5_boxv_0 16: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rect_box_2_5_boxv_0 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rect_box_2_5_boxv_1e_07 16: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rect_box_2_5_boxv_1e_07 (1 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rect_box_2_5_boxv_1 16: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rect_box_2_5_boxv_1 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rect_box_2_5_boxv_100 16: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rect_box_2_5_boxv_100 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rect_box_10000_boxv__100 16: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rect_box_10000_boxv__100 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rect_box_10000_boxv__1 16: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rect_box_10000_boxv__1 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rect_box_10000_boxv__1e_07 16: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rect_box_10000_boxv__1e_07 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rect_box_10000_boxv_0 16: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rect_box_10000_boxv_0 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rect_box_10000_boxv_1e_07 16: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rect_box_10000_boxv_1e_07 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rect_box_10000_boxv_1 16: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rect_box_10000_boxv_1 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rect_box_10000_boxv_100 16: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rect_box_10000_boxv_100 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rect_box_2_5_boxv__100 16: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rect_box_2_5_boxv__100 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rect_box_2_5_boxv__1 16: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rect_box_2_5_boxv__1 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rect_box_2_5_boxv__1e_07 16: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rect_box_2_5_boxv__1e_07 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rect_box_2_5_boxv_0 16: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rect_box_2_5_boxv_0 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rect_box_2_5_boxv_1e_07 16: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rect_box_2_5_boxv_1e_07 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rect_box_2_5_boxv_1 16: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rect_box_2_5_boxv_1 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rect_box_2_5_boxv_100 16: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rect_box_2_5_boxv_100 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rect_box_10000_boxv__100 16: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rect_box_10000_boxv__100 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rect_box_10000_boxv__1 16: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rect_box_10000_boxv__1 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rect_box_10000_boxv__1e_07 16: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rect_box_10000_boxv__1e_07 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rect_box_10000_boxv_0 16: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rect_box_10000_boxv_0 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rect_box_10000_boxv_1e_07 16: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rect_box_10000_boxv_1e_07 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rect_box_10000_boxv_1 16: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rect_box_10000_boxv_1 (1 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rect_box_10000_boxv_100 16: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rect_box_10000_boxv_100 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rect_box_2_5_boxv__100 16: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rect_box_2_5_boxv__100 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rect_box_2_5_boxv__1 16: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rect_box_2_5_boxv__1 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rect_box_2_5_boxv__1e_07 16: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rect_box_2_5_boxv__1e_07 (12 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rect_box_2_5_boxv_0 16: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rect_box_2_5_boxv_0 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rect_box_2_5_boxv_1e_07 16: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rect_box_2_5_boxv_1e_07 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rect_box_2_5_boxv_1 16: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rect_box_2_5_boxv_1 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rect_box_2_5_boxv_100 16: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rect_box_2_5_boxv_100 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rect_box_10000_boxv__100 16: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rect_box_10000_boxv__100 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rect_box_10000_boxv__1 16: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rect_box_10000_boxv__1 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rect_box_10000_boxv__1e_07 16: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rect_box_10000_boxv__1e_07 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rect_box_10000_boxv_0 16: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rect_box_10000_boxv_0 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rect_box_10000_boxv_1e_07 16: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rect_box_10000_boxv_1e_07 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rect_box_10000_boxv_1 16: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rect_box_10000_boxv_1 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rect_box_10000_boxv_100 16: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rect_box_10000_boxv_100 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_general_shape_rect_box_2_5_boxv__100 16: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_general_shape_rect_box_2_5_boxv__100 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_general_shape_rect_box_2_5_boxv__1 16: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_general_shape_rect_box_2_5_boxv__1 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_general_shape_rect_box_2_5_boxv__1e_07 16: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_general_shape_rect_box_2_5_boxv__1e_07 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_general_shape_rect_box_2_5_boxv_0 16: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_general_shape_rect_box_2_5_boxv_0 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_general_shape_rect_box_2_5_boxv_1e_07 16: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_general_shape_rect_box_2_5_boxv_1e_07 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_general_shape_rect_box_2_5_boxv_1 16: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_general_shape_rect_box_2_5_boxv_1 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_general_shape_rect_box_2_5_boxv_100 16: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_general_shape_rect_box_2_5_boxv_100 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_general_shape_rect_box_10000_boxv__100 16: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_general_shape_rect_box_10000_boxv__100 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_general_shape_rect_box_10000_boxv__1 16: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_general_shape_rect_box_10000_boxv__1 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_general_shape_rect_box_10000_boxv__1e_07 16: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_general_shape_rect_box_10000_boxv__1e_07 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_general_shape_rect_box_10000_boxv_0 16: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_general_shape_rect_box_10000_boxv_0 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_general_shape_rect_box_10000_boxv_1e_07 16: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_general_shape_rect_box_10000_boxv_1e_07 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_general_shape_rect_box_10000_boxv_1 16: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_general_shape_rect_box_10000_boxv_1 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_general_shape_rect_box_10000_boxv_100 16: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_general_shape_rect_box_10000_boxv_100 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rect_box_2_5_boxv__100 16: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rect_box_2_5_boxv__100 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rect_box_2_5_boxv__1 16: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rect_box_2_5_boxv__1 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rect_box_2_5_boxv__1e_07 16: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rect_box_2_5_boxv__1e_07 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rect_box_2_5_boxv_0 16: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rect_box_2_5_boxv_0 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rect_box_2_5_boxv_1e_07 16: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rect_box_2_5_boxv_1e_07 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rect_box_2_5_boxv_1 16: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rect_box_2_5_boxv_1 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rect_box_2_5_boxv_100 16: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rect_box_2_5_boxv_100 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rect_box_10000_boxv__100 16: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rect_box_10000_boxv__100 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rect_box_10000_boxv__1 16: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rect_box_10000_boxv__1 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rect_box_10000_boxv__1e_07 16: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rect_box_10000_boxv__1e_07 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rect_box_10000_boxv_0 16: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rect_box_10000_boxv_0 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rect_box_10000_boxv_1e_07 16: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rect_box_10000_boxv_1e_07 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rect_box_10000_boxv_1 16: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rect_box_10000_boxv_1 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rect_box_10000_boxv_100 16: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rect_box_10000_boxv_100 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rect_box_2_5_boxv__100 16: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rect_box_2_5_boxv__100 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rect_box_2_5_boxv__1 16: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rect_box_2_5_boxv__1 (1 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rect_box_2_5_boxv__1e_07 16: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rect_box_2_5_boxv__1e_07 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rect_box_2_5_boxv_0 16: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rect_box_2_5_boxv_0 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rect_box_2_5_boxv_1e_07 16: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rect_box_2_5_boxv_1e_07 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rect_box_2_5_boxv_1 16: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rect_box_2_5_boxv_1 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rect_box_2_5_boxv_100 16: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rect_box_2_5_boxv_100 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rect_box_10000_boxv__100 16: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rect_box_10000_boxv__100 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rect_box_10000_boxv__1 16: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rect_box_10000_boxv__1 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rect_box_10000_boxv__1e_07 16: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rect_box_10000_boxv__1e_07 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rect_box_10000_boxv_0 16: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rect_box_10000_boxv_0 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rect_box_10000_boxv_1e_07 16: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rect_box_10000_boxv_1e_07 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rect_box_10000_boxv_1 16: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rect_box_10000_boxv_1 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rect_box_10000_boxv_100 16: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rect_box_10000_boxv_100 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rect_box_2_5_boxv__100 16: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rect_box_2_5_boxv__100 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rect_box_2_5_boxv__1 16: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rect_box_2_5_boxv__1 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rect_box_2_5_boxv__1e_07 16: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rect_box_2_5_boxv__1e_07 (2 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rect_box_2_5_boxv_0 16: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rect_box_2_5_boxv_0 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rect_box_2_5_boxv_1e_07 16: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rect_box_2_5_boxv_1e_07 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rect_box_2_5_boxv_1 16: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rect_box_2_5_boxv_1 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rect_box_2_5_boxv_100 16: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rect_box_2_5_boxv_100 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rect_box_10000_boxv__100 16: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rect_box_10000_boxv__100 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rect_box_10000_boxv__1 16: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rect_box_10000_boxv__1 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rect_box_10000_boxv__1e_07 16: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rect_box_10000_boxv__1e_07 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rect_box_10000_boxv_0 16: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rect_box_10000_boxv_0 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rect_box_10000_boxv_1e_07 16: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rect_box_10000_boxv_1e_07 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rect_box_10000_boxv_1 16: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rect_box_10000_boxv_1 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rect_box_10000_boxv_100 16: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rect_box_10000_boxv_100 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rect_box_2_5_boxv__100 16: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rect_box_2_5_boxv__100 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rect_box_2_5_boxv__1 16: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rect_box_2_5_boxv__1 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rect_box_2_5_boxv__1e_07 16: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rect_box_2_5_boxv__1e_07 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rect_box_2_5_boxv_0 16: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rect_box_2_5_boxv_0 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rect_box_2_5_boxv_1e_07 16: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rect_box_2_5_boxv_1e_07 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rect_box_2_5_boxv_1 16: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rect_box_2_5_boxv_1 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rect_box_2_5_boxv_100 16: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rect_box_2_5_boxv_100 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rect_box_10000_boxv__100 16: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rect_box_10000_boxv__100 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rect_box_10000_boxv__1 16: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rect_box_10000_boxv__1 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rect_box_10000_boxv__1e_07 16: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rect_box_10000_boxv__1e_07 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rect_box_10000_boxv_0 16: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rect_box_10000_boxv_0 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rect_box_10000_boxv_1e_07 16: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rect_box_10000_boxv_1e_07 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rect_box_10000_boxv_1 16: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rect_box_10000_boxv_1 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rect_box_10000_boxv_100 16: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rect_box_10000_boxv_100 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rect_box_2_5_boxv__100 16: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rect_box_2_5_boxv__100 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rect_box_2_5_boxv__1 16: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rect_box_2_5_boxv__1 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rect_box_2_5_boxv__1e_07 16: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rect_box_2_5_boxv__1e_07 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rect_box_2_5_boxv_0 16: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rect_box_2_5_boxv_0 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rect_box_2_5_boxv_1e_07 16: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rect_box_2_5_boxv_1e_07 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rect_box_2_5_boxv_1 16: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rect_box_2_5_boxv_1 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rect_box_2_5_boxv_100 16: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rect_box_2_5_boxv_100 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rect_box_10000_boxv__100 16: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rect_box_10000_boxv__100 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rect_box_10000_boxv__1 16: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rect_box_10000_boxv__1 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rect_box_10000_boxv__1e_07 16: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rect_box_10000_boxv__1e_07 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rect_box_10000_boxv_0 16: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rect_box_10000_boxv_0 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rect_box_10000_boxv_1e_07 16: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rect_box_10000_boxv_1e_07 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rect_box_10000_boxv_1 16: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rect_box_10000_boxv_1 (2 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rect_box_10000_boxv_100 16: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rect_box_10000_boxv_100 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rect_box_2_5_boxv__100 16: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rect_box_2_5_boxv__100 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rect_box_2_5_boxv__1 16: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rect_box_2_5_boxv__1 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rect_box_2_5_boxv__1e_07 16: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rect_box_2_5_boxv__1e_07 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rect_box_2_5_boxv_0 16: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rect_box_2_5_boxv_0 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rect_box_2_5_boxv_1e_07 16: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rect_box_2_5_boxv_1e_07 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rect_box_2_5_boxv_1 16: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rect_box_2_5_boxv_1 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rect_box_2_5_boxv_100 16: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rect_box_2_5_boxv_100 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rect_box_10000_boxv__100 16: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rect_box_10000_boxv__100 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rect_box_10000_boxv__1 16: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rect_box_10000_boxv__1 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rect_box_10000_boxv__1e_07 16: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rect_box_10000_boxv__1e_07 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rect_box_10000_boxv_0 16: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rect_box_10000_boxv_0 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rect_box_10000_boxv_1e_07 16: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rect_box_10000_boxv_1e_07 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rect_box_10000_boxv_1 16: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rect_box_10000_boxv_1 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rect_box_10000_boxv_100 16: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rect_box_10000_boxv_100 (0 ms) 16: [----------] 140 tests from Rectilinear/ParrRahmTest (78 ms total) 16: 16: [----------] 140 tests from RhombDodecXYSquare/ParrRahmTest 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rds_box_2_5_boxv__100 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rds_box_2_5_boxv__100 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rds_box_2_5_boxv__1 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rds_box_2_5_boxv__1 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rds_box_2_5_boxv__1e_07 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rds_box_2_5_boxv__1e_07 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rds_box_2_5_boxv_0 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rds_box_2_5_boxv_0 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rds_box_2_5_boxv_1e_07 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rds_box_2_5_boxv_1e_07 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rds_box_2_5_boxv_1 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rds_box_2_5_boxv_1 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rds_box_2_5_boxv_100 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rds_box_2_5_boxv_100 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rds_box_10000_boxv__100 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rds_box_10000_boxv__100 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rds_box_10000_boxv__1 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rds_box_10000_boxv__1 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rds_box_10000_boxv__1e_07 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rds_box_10000_boxv__1e_07 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rds_box_10000_boxv_0 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rds_box_10000_boxv_0 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rds_box_10000_boxv_1e_07 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rds_box_10000_boxv_1e_07 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rds_box_10000_boxv_1 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rds_box_10000_boxv_1 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rds_box_10000_boxv_100 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rds_box_10000_boxv_100 (2 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rds_box_2_5_boxv__100 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rds_box_2_5_boxv__100 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rds_box_2_5_boxv__1 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rds_box_2_5_boxv__1 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rds_box_2_5_boxv__1e_07 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rds_box_2_5_boxv__1e_07 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rds_box_2_5_boxv_0 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rds_box_2_5_boxv_0 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rds_box_2_5_boxv_1e_07 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rds_box_2_5_boxv_1e_07 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rds_box_2_5_boxv_1 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rds_box_2_5_boxv_1 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rds_box_2_5_boxv_100 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rds_box_2_5_boxv_100 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rds_box_10000_boxv__100 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rds_box_10000_boxv__100 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rds_box_10000_boxv__1 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rds_box_10000_boxv__1 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rds_box_10000_boxv__1e_07 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rds_box_10000_boxv__1e_07 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rds_box_10000_boxv_0 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rds_box_10000_boxv_0 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rds_box_10000_boxv_1e_07 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rds_box_10000_boxv_1e_07 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rds_box_10000_boxv_1 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rds_box_10000_boxv_1 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rds_box_10000_boxv_100 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rds_box_10000_boxv_100 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rds_box_2_5_boxv__100 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rds_box_2_5_boxv__100 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rds_box_2_5_boxv__1 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rds_box_2_5_boxv__1 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rds_box_2_5_boxv__1e_07 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rds_box_2_5_boxv__1e_07 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rds_box_2_5_boxv_0 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rds_box_2_5_boxv_0 (1 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rds_box_2_5_boxv_1e_07 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rds_box_2_5_boxv_1e_07 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rds_box_2_5_boxv_1 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rds_box_2_5_boxv_1 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rds_box_2_5_boxv_100 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rds_box_2_5_boxv_100 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rds_box_10000_boxv__100 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rds_box_10000_boxv__100 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rds_box_10000_boxv__1 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rds_box_10000_boxv__1 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rds_box_10000_boxv__1e_07 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rds_box_10000_boxv__1e_07 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rds_box_10000_boxv_0 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rds_box_10000_boxv_0 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rds_box_10000_boxv_1e_07 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rds_box_10000_boxv_1e_07 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rds_box_10000_boxv_1 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rds_box_10000_boxv_1 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rds_box_10000_boxv_100 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rds_box_10000_boxv_100 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_general_shape_rds_box_2_5_boxv__100 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_general_shape_rds_box_2_5_boxv__100 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_general_shape_rds_box_2_5_boxv__1 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_general_shape_rds_box_2_5_boxv__1 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_general_shape_rds_box_2_5_boxv__1e_07 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_general_shape_rds_box_2_5_boxv__1e_07 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_general_shape_rds_box_2_5_boxv_0 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_general_shape_rds_box_2_5_boxv_0 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_general_shape_rds_box_2_5_boxv_1e_07 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_general_shape_rds_box_2_5_boxv_1e_07 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_general_shape_rds_box_2_5_boxv_1 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_general_shape_rds_box_2_5_boxv_1 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_general_shape_rds_box_2_5_boxv_100 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_general_shape_rds_box_2_5_boxv_100 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_general_shape_rds_box_10000_boxv__100 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_general_shape_rds_box_10000_boxv__100 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_general_shape_rds_box_10000_boxv__1 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_general_shape_rds_box_10000_boxv__1 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_general_shape_rds_box_10000_boxv__1e_07 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_general_shape_rds_box_10000_boxv__1e_07 (1 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_general_shape_rds_box_10000_boxv_0 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_general_shape_rds_box_10000_boxv_0 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_general_shape_rds_box_10000_boxv_1e_07 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_general_shape_rds_box_10000_boxv_1e_07 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_general_shape_rds_box_10000_boxv_1 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_general_shape_rds_box_10000_boxv_1 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_general_shape_rds_box_10000_boxv_100 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_general_shape_rds_box_10000_boxv_100 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rds_box_2_5_boxv__100 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rds_box_2_5_boxv__100 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rds_box_2_5_boxv__1 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rds_box_2_5_boxv__1 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rds_box_2_5_boxv__1e_07 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rds_box_2_5_boxv__1e_07 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rds_box_2_5_boxv_0 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rds_box_2_5_boxv_0 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rds_box_2_5_boxv_1e_07 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rds_box_2_5_boxv_1e_07 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rds_box_2_5_boxv_1 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rds_box_2_5_boxv_1 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rds_box_2_5_boxv_100 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rds_box_2_5_boxv_100 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rds_box_10000_boxv__100 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rds_box_10000_boxv__100 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rds_box_10000_boxv__1 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rds_box_10000_boxv__1 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rds_box_10000_boxv__1e_07 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rds_box_10000_boxv__1e_07 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rds_box_10000_boxv_0 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rds_box_10000_boxv_0 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rds_box_10000_boxv_1e_07 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rds_box_10000_boxv_1e_07 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rds_box_10000_boxv_1 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rds_box_10000_boxv_1 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rds_box_10000_boxv_100 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rds_box_10000_boxv_100 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rds_box_2_5_boxv__100 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rds_box_2_5_boxv__100 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rds_box_2_5_boxv__1 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rds_box_2_5_boxv__1 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rds_box_2_5_boxv__1e_07 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rds_box_2_5_boxv__1e_07 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rds_box_2_5_boxv_0 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rds_box_2_5_boxv_0 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rds_box_2_5_boxv_1e_07 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rds_box_2_5_boxv_1e_07 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rds_box_2_5_boxv_1 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rds_box_2_5_boxv_1 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rds_box_2_5_boxv_100 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rds_box_2_5_boxv_100 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rds_box_10000_boxv__100 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rds_box_10000_boxv__100 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rds_box_10000_boxv__1 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rds_box_10000_boxv__1 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rds_box_10000_boxv__1e_07 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rds_box_10000_boxv__1e_07 (1 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rds_box_10000_boxv_0 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rds_box_10000_boxv_0 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rds_box_10000_boxv_1e_07 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rds_box_10000_boxv_1e_07 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rds_box_10000_boxv_1 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rds_box_10000_boxv_1 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rds_box_10000_boxv_100 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rds_box_10000_boxv_100 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rds_box_2_5_boxv__100 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rds_box_2_5_boxv__100 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rds_box_2_5_boxv__1 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rds_box_2_5_boxv__1 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rds_box_2_5_boxv__1e_07 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rds_box_2_5_boxv__1e_07 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rds_box_2_5_boxv_0 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rds_box_2_5_boxv_0 (1 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rds_box_2_5_boxv_1e_07 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rds_box_2_5_boxv_1e_07 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rds_box_2_5_boxv_1 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rds_box_2_5_boxv_1 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rds_box_2_5_boxv_100 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rds_box_2_5_boxv_100 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rds_box_10000_boxv__100 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rds_box_10000_boxv__100 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rds_box_10000_boxv__1 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rds_box_10000_boxv__1 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rds_box_10000_boxv__1e_07 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rds_box_10000_boxv__1e_07 (3 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rds_box_10000_boxv_0 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rds_box_10000_boxv_0 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rds_box_10000_boxv_1e_07 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rds_box_10000_boxv_1e_07 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rds_box_10000_boxv_1 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rds_box_10000_boxv_1 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rds_box_10000_boxv_100 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rds_box_10000_boxv_100 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rds_box_2_5_boxv__100 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rds_box_2_5_boxv__100 (1 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rds_box_2_5_boxv__1 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rds_box_2_5_boxv__1 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rds_box_2_5_boxv__1e_07 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rds_box_2_5_boxv__1e_07 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rds_box_2_5_boxv_0 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rds_box_2_5_boxv_0 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rds_box_2_5_boxv_1e_07 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rds_box_2_5_boxv_1e_07 (8 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rds_box_2_5_boxv_1 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rds_box_2_5_boxv_1 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rds_box_2_5_boxv_100 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rds_box_2_5_boxv_100 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rds_box_10000_boxv__100 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rds_box_10000_boxv__100 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rds_box_10000_boxv__1 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rds_box_10000_boxv__1 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rds_box_10000_boxv__1e_07 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rds_box_10000_boxv__1e_07 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rds_box_10000_boxv_0 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rds_box_10000_boxv_0 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rds_box_10000_boxv_1e_07 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rds_box_10000_boxv_1e_07 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rds_box_10000_boxv_1 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rds_box_10000_boxv_1 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rds_box_10000_boxv_100 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rds_box_10000_boxv_100 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rds_box_2_5_boxv__100 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rds_box_2_5_boxv__100 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rds_box_2_5_boxv__1 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rds_box_2_5_boxv__1 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rds_box_2_5_boxv__1e_07 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rds_box_2_5_boxv__1e_07 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rds_box_2_5_boxv_0 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rds_box_2_5_boxv_0 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rds_box_2_5_boxv_1e_07 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rds_box_2_5_boxv_1e_07 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rds_box_2_5_boxv_1 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rds_box_2_5_boxv_1 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rds_box_2_5_boxv_100 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rds_box_2_5_boxv_100 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rds_box_10000_boxv__100 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rds_box_10000_boxv__100 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rds_box_10000_boxv__1 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rds_box_10000_boxv__1 (1 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rds_box_10000_boxv__1e_07 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rds_box_10000_boxv__1e_07 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rds_box_10000_boxv_0 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rds_box_10000_boxv_0 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rds_box_10000_boxv_1e_07 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rds_box_10000_boxv_1e_07 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rds_box_10000_boxv_1 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rds_box_10000_boxv_1 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rds_box_10000_boxv_100 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rds_box_10000_boxv_100 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rds_box_2_5_boxv__100 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rds_box_2_5_boxv__100 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rds_box_2_5_boxv__1 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rds_box_2_5_boxv__1 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rds_box_2_5_boxv__1e_07 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rds_box_2_5_boxv__1e_07 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rds_box_2_5_boxv_0 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rds_box_2_5_boxv_0 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rds_box_2_5_boxv_1e_07 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rds_box_2_5_boxv_1e_07 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rds_box_2_5_boxv_1 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rds_box_2_5_boxv_1 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rds_box_2_5_boxv_100 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rds_box_2_5_boxv_100 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rds_box_10000_boxv__100 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rds_box_10000_boxv__100 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rds_box_10000_boxv__1 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rds_box_10000_boxv__1 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rds_box_10000_boxv__1e_07 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rds_box_10000_boxv__1e_07 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rds_box_10000_boxv_0 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rds_box_10000_boxv_0 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rds_box_10000_boxv_1e_07 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rds_box_10000_boxv_1e_07 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rds_box_10000_boxv_1 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rds_box_10000_boxv_1 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rds_box_10000_boxv_100 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rds_box_10000_boxv_100 (0 ms) 16: [----------] 140 tests from RhombDodecXYSquare/ParrRahmTest (86 ms total) 16: 16: [----------] 140 tests from RhombDodecXYHex/ParrRahmTest 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rdh_box_2_5_boxv__100 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rdh_box_2_5_boxv__100 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rdh_box_2_5_boxv__1 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rdh_box_2_5_boxv__1 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rdh_box_2_5_boxv__1e_07 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rdh_box_2_5_boxv__1e_07 (1 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rdh_box_2_5_boxv_0 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rdh_box_2_5_boxv_0 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rdh_box_2_5_boxv_1e_07 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rdh_box_2_5_boxv_1e_07 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rdh_box_2_5_boxv_1 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rdh_box_2_5_boxv_1 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rdh_box_2_5_boxv_100 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rdh_box_2_5_boxv_100 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rdh_box_10000_boxv__100 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rdh_box_10000_boxv__100 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rdh_box_10000_boxv__1 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rdh_box_10000_boxv__1 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rdh_box_10000_boxv__1e_07 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rdh_box_10000_boxv__1e_07 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rdh_box_10000_boxv_0 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rdh_box_10000_boxv_0 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rdh_box_10000_boxv_1e_07 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rdh_box_10000_boxv_1e_07 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rdh_box_10000_boxv_1 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rdh_box_10000_boxv_1 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rdh_box_10000_boxv_100 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rdh_box_10000_boxv_100 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rdh_box_2_5_boxv__100 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rdh_box_2_5_boxv__100 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rdh_box_2_5_boxv__1 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rdh_box_2_5_boxv__1 (1 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rdh_box_2_5_boxv__1e_07 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rdh_box_2_5_boxv__1e_07 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rdh_box_2_5_boxv_0 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rdh_box_2_5_boxv_0 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rdh_box_2_5_boxv_1e_07 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rdh_box_2_5_boxv_1e_07 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rdh_box_2_5_boxv_1 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rdh_box_2_5_boxv_1 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rdh_box_2_5_boxv_100 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rdh_box_2_5_boxv_100 (1 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rdh_box_10000_boxv__100 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rdh_box_10000_boxv__100 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rdh_box_10000_boxv__1 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rdh_box_10000_boxv__1 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rdh_box_10000_boxv__1e_07 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rdh_box_10000_boxv__1e_07 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rdh_box_10000_boxv_0 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rdh_box_10000_boxv_0 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rdh_box_10000_boxv_1e_07 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rdh_box_10000_boxv_1e_07 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rdh_box_10000_boxv_1 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rdh_box_10000_boxv_1 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rdh_box_10000_boxv_100 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rdh_box_10000_boxv_100 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rdh_box_2_5_boxv__100 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rdh_box_2_5_boxv__100 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rdh_box_2_5_boxv__1 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rdh_box_2_5_boxv__1 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rdh_box_2_5_boxv__1e_07 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rdh_box_2_5_boxv__1e_07 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rdh_box_2_5_boxv_0 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rdh_box_2_5_boxv_0 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rdh_box_2_5_boxv_1e_07 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rdh_box_2_5_boxv_1e_07 (1 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rdh_box_2_5_boxv_1 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rdh_box_2_5_boxv_1 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rdh_box_2_5_boxv_100 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rdh_box_2_5_boxv_100 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rdh_box_10000_boxv__100 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rdh_box_10000_boxv__100 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rdh_box_10000_boxv__1 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rdh_box_10000_boxv__1 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rdh_box_10000_boxv__1e_07 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rdh_box_10000_boxv__1e_07 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rdh_box_10000_boxv_0 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rdh_box_10000_boxv_0 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rdh_box_10000_boxv_1e_07 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rdh_box_10000_boxv_1e_07 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rdh_box_10000_boxv_1 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rdh_box_10000_boxv_1 (2 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rdh_box_10000_boxv_100 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rdh_box_10000_boxv_100 (1 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_general_shape_rdh_box_2_5_boxv__100 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_general_shape_rdh_box_2_5_boxv__100 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_general_shape_rdh_box_2_5_boxv__1 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_general_shape_rdh_box_2_5_boxv__1 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_general_shape_rdh_box_2_5_boxv__1e_07 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_general_shape_rdh_box_2_5_boxv__1e_07 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_general_shape_rdh_box_2_5_boxv_0 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_general_shape_rdh_box_2_5_boxv_0 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_general_shape_rdh_box_2_5_boxv_1e_07 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_general_shape_rdh_box_2_5_boxv_1e_07 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_general_shape_rdh_box_2_5_boxv_1 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_general_shape_rdh_box_2_5_boxv_1 (2 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_general_shape_rdh_box_2_5_boxv_100 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_general_shape_rdh_box_2_5_boxv_100 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_general_shape_rdh_box_10000_boxv__100 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_general_shape_rdh_box_10000_boxv__100 (1 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_general_shape_rdh_box_10000_boxv__1 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_general_shape_rdh_box_10000_boxv__1 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_general_shape_rdh_box_10000_boxv__1e_07 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_general_shape_rdh_box_10000_boxv__1e_07 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_general_shape_rdh_box_10000_boxv_0 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_general_shape_rdh_box_10000_boxv_0 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_general_shape_rdh_box_10000_boxv_1e_07 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_general_shape_rdh_box_10000_boxv_1e_07 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_general_shape_rdh_box_10000_boxv_1 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_general_shape_rdh_box_10000_boxv_1 (1 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_general_shape_rdh_box_10000_boxv_100 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_general_shape_rdh_box_10000_boxv_100 (1 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rdh_box_2_5_boxv__100 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rdh_box_2_5_boxv__100 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rdh_box_2_5_boxv__1 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rdh_box_2_5_boxv__1 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rdh_box_2_5_boxv__1e_07 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rdh_box_2_5_boxv__1e_07 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rdh_box_2_5_boxv_0 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rdh_box_2_5_boxv_0 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rdh_box_2_5_boxv_1e_07 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rdh_box_2_5_boxv_1e_07 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rdh_box_2_5_boxv_1 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rdh_box_2_5_boxv_1 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rdh_box_2_5_boxv_100 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rdh_box_2_5_boxv_100 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rdh_box_10000_boxv__100 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rdh_box_10000_boxv__100 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rdh_box_10000_boxv__1 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rdh_box_10000_boxv__1 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rdh_box_10000_boxv__1e_07 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rdh_box_10000_boxv__1e_07 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rdh_box_10000_boxv_0 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rdh_box_10000_boxv_0 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rdh_box_10000_boxv_1e_07 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rdh_box_10000_boxv_1e_07 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rdh_box_10000_boxv_1 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rdh_box_10000_boxv_1 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rdh_box_10000_boxv_100 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rdh_box_10000_boxv_100 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rdh_box_2_5_boxv__100 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rdh_box_2_5_boxv__100 (1 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rdh_box_2_5_boxv__1 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rdh_box_2_5_boxv__1 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rdh_box_2_5_boxv__1e_07 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rdh_box_2_5_boxv__1e_07 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rdh_box_2_5_boxv_0 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rdh_box_2_5_boxv_0 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rdh_box_2_5_boxv_1e_07 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rdh_box_2_5_boxv_1e_07 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rdh_box_2_5_boxv_1 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rdh_box_2_5_boxv_1 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rdh_box_2_5_boxv_100 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rdh_box_2_5_boxv_100 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rdh_box_10000_boxv__100 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rdh_box_10000_boxv__100 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rdh_box_10000_boxv__1 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rdh_box_10000_boxv__1 (2 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rdh_box_10000_boxv__1e_07 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rdh_box_10000_boxv__1e_07 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rdh_box_10000_boxv_0 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rdh_box_10000_boxv_0 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rdh_box_10000_boxv_1e_07 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rdh_box_10000_boxv_1e_07 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rdh_box_10000_boxv_1 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rdh_box_10000_boxv_1 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rdh_box_10000_boxv_100 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rdh_box_10000_boxv_100 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rdh_box_2_5_boxv__100 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rdh_box_2_5_boxv__100 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rdh_box_2_5_boxv__1 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rdh_box_2_5_boxv__1 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rdh_box_2_5_boxv__1e_07 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rdh_box_2_5_boxv__1e_07 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rdh_box_2_5_boxv_0 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rdh_box_2_5_boxv_0 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rdh_box_2_5_boxv_1e_07 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rdh_box_2_5_boxv_1e_07 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rdh_box_2_5_boxv_1 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rdh_box_2_5_boxv_1 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rdh_box_2_5_boxv_100 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rdh_box_2_5_boxv_100 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rdh_box_10000_boxv__100 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rdh_box_10000_boxv__100 (1 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rdh_box_10000_boxv__1 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rdh_box_10000_boxv__1 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rdh_box_10000_boxv__1e_07 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rdh_box_10000_boxv__1e_07 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rdh_box_10000_boxv_0 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rdh_box_10000_boxv_0 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rdh_box_10000_boxv_1e_07 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rdh_box_10000_boxv_1e_07 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rdh_box_10000_boxv_1 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rdh_box_10000_boxv_1 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rdh_box_10000_boxv_100 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rdh_box_10000_boxv_100 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rdh_box_2_5_boxv__100 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rdh_box_2_5_boxv__100 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rdh_box_2_5_boxv__1 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rdh_box_2_5_boxv__1 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rdh_box_2_5_boxv__1e_07 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rdh_box_2_5_boxv__1e_07 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rdh_box_2_5_boxv_0 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rdh_box_2_5_boxv_0 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rdh_box_2_5_boxv_1e_07 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rdh_box_2_5_boxv_1e_07 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rdh_box_2_5_boxv_1 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rdh_box_2_5_boxv_1 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rdh_box_2_5_boxv_100 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rdh_box_2_5_boxv_100 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rdh_box_10000_boxv__100 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rdh_box_10000_boxv__100 (1 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rdh_box_10000_boxv__1 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rdh_box_10000_boxv__1 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rdh_box_10000_boxv__1e_07 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rdh_box_10000_boxv__1e_07 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rdh_box_10000_boxv_0 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rdh_box_10000_boxv_0 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rdh_box_10000_boxv_1e_07 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rdh_box_10000_boxv_1e_07 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rdh_box_10000_boxv_1 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rdh_box_10000_boxv_1 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rdh_box_10000_boxv_100 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rdh_box_10000_boxv_100 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rdh_box_2_5_boxv__100 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rdh_box_2_5_boxv__100 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rdh_box_2_5_boxv__1 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rdh_box_2_5_boxv__1 (1 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rdh_box_2_5_boxv__1e_07 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rdh_box_2_5_boxv__1e_07 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rdh_box_2_5_boxv_0 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rdh_box_2_5_boxv_0 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rdh_box_2_5_boxv_1e_07 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rdh_box_2_5_boxv_1e_07 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rdh_box_2_5_boxv_1 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rdh_box_2_5_boxv_1 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rdh_box_2_5_boxv_100 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rdh_box_2_5_boxv_100 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rdh_box_10000_boxv__100 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rdh_box_10000_boxv__100 (1 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rdh_box_10000_boxv__1 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rdh_box_10000_boxv__1 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rdh_box_10000_boxv__1e_07 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rdh_box_10000_boxv__1e_07 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rdh_box_10000_boxv_0 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rdh_box_10000_boxv_0 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rdh_box_10000_boxv_1e_07 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rdh_box_10000_boxv_1e_07 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rdh_box_10000_boxv_1 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rdh_box_10000_boxv_1 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rdh_box_10000_boxv_100 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rdh_box_10000_boxv_100 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rdh_box_2_5_boxv__100 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rdh_box_2_5_boxv__100 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rdh_box_2_5_boxv__1 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rdh_box_2_5_boxv__1 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rdh_box_2_5_boxv__1e_07 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rdh_box_2_5_boxv__1e_07 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rdh_box_2_5_boxv_0 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rdh_box_2_5_boxv_0 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rdh_box_2_5_boxv_1e_07 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rdh_box_2_5_boxv_1e_07 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rdh_box_2_5_boxv_1 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rdh_box_2_5_boxv_1 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rdh_box_2_5_boxv_100 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rdh_box_2_5_boxv_100 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rdh_box_10000_boxv__100 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rdh_box_10000_boxv__100 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rdh_box_10000_boxv__1 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rdh_box_10000_boxv__1 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rdh_box_10000_boxv__1e_07 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rdh_box_10000_boxv__1e_07 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rdh_box_10000_boxv_0 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rdh_box_10000_boxv_0 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rdh_box_10000_boxv_1e_07 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rdh_box_10000_boxv_1e_07 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rdh_box_10000_boxv_1 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rdh_box_10000_boxv_1 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rdh_box_10000_boxv_100 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rdh_box_10000_boxv_100 (0 ms) 16: [----------] 140 tests from RhombDodecXYHex/ParrRahmTest (83 ms total) 16: 16: [----------] 140 tests from TruncOct/ParrRahmTest 16: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_to_box_2_5_boxv__100 16: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_to_box_2_5_boxv__100 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_to_box_2_5_boxv__1 16: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_to_box_2_5_boxv__1 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_to_box_2_5_boxv__1e_07 16: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_to_box_2_5_boxv__1e_07 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_to_box_2_5_boxv_0 16: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_to_box_2_5_boxv_0 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_to_box_2_5_boxv_1e_07 16: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_to_box_2_5_boxv_1e_07 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_to_box_2_5_boxv_1 16: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_to_box_2_5_boxv_1 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_to_box_2_5_boxv_100 16: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_to_box_2_5_boxv_100 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_to_box_10000_boxv__100 16: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_to_box_10000_boxv__100 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_to_box_10000_boxv__1 16: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_to_box_10000_boxv__1 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_to_box_10000_boxv__1e_07 16: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_to_box_10000_boxv__1e_07 (3 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_to_box_10000_boxv_0 16: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_to_box_10000_boxv_0 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_to_box_10000_boxv_1e_07 16: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_to_box_10000_boxv_1e_07 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_to_box_10000_boxv_1 16: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_to_box_10000_boxv_1 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_to_box_10000_boxv_100 16: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_to_box_10000_boxv_100 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_to_box_2_5_boxv__100 16: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_to_box_2_5_boxv__100 (1 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_to_box_2_5_boxv__1 16: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_to_box_2_5_boxv__1 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_to_box_2_5_boxv__1e_07 16: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_to_box_2_5_boxv__1e_07 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_to_box_2_5_boxv_0 16: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_to_box_2_5_boxv_0 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_to_box_2_5_boxv_1e_07 16: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_to_box_2_5_boxv_1e_07 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_to_box_2_5_boxv_1 16: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_to_box_2_5_boxv_1 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_to_box_2_5_boxv_100 16: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_to_box_2_5_boxv_100 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_to_box_10000_boxv__100 16: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_to_box_10000_boxv__100 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_to_box_10000_boxv__1 16: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_to_box_10000_boxv__1 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_to_box_10000_boxv__1e_07 16: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_to_box_10000_boxv__1e_07 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_to_box_10000_boxv_0 16: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_to_box_10000_boxv_0 (1 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_to_box_10000_boxv_1e_07 16: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_to_box_10000_boxv_1e_07 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_to_box_10000_boxv_1 16: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_to_box_10000_boxv_1 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_to_box_10000_boxv_100 16: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_to_box_10000_boxv_100 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_to_box_2_5_boxv__100 16: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_to_box_2_5_boxv__100 (1 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_to_box_2_5_boxv__1 16: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_to_box_2_5_boxv__1 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_to_box_2_5_boxv__1e_07 16: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_to_box_2_5_boxv__1e_07 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_to_box_2_5_boxv_0 16: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_to_box_2_5_boxv_0 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_to_box_2_5_boxv_1e_07 16: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_to_box_2_5_boxv_1e_07 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_to_box_2_5_boxv_1 16: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_to_box_2_5_boxv_1 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_to_box_2_5_boxv_100 16: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_to_box_2_5_boxv_100 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_to_box_10000_boxv__100 16: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_to_box_10000_boxv__100 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_to_box_10000_boxv__1 16: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_to_box_10000_boxv__1 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_to_box_10000_boxv__1e_07 16: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_to_box_10000_boxv__1e_07 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_to_box_10000_boxv_0 16: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_to_box_10000_boxv_0 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_to_box_10000_boxv_1e_07 16: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_to_box_10000_boxv_1e_07 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_to_box_10000_boxv_1 16: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_to_box_10000_boxv_1 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_to_box_10000_boxv_100 16: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_to_box_10000_boxv_100 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_general_shape_to_box_2_5_boxv__100 16: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_general_shape_to_box_2_5_boxv__100 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_general_shape_to_box_2_5_boxv__1 16: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_general_shape_to_box_2_5_boxv__1 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_general_shape_to_box_2_5_boxv__1e_07 16: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_general_shape_to_box_2_5_boxv__1e_07 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_general_shape_to_box_2_5_boxv_0 16: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_general_shape_to_box_2_5_boxv_0 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_general_shape_to_box_2_5_boxv_1e_07 16: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_general_shape_to_box_2_5_boxv_1e_07 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_general_shape_to_box_2_5_boxv_1 16: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_general_shape_to_box_2_5_boxv_1 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_general_shape_to_box_2_5_boxv_100 16: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_general_shape_to_box_2_5_boxv_100 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_general_shape_to_box_10000_boxv__100 16: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_general_shape_to_box_10000_boxv__100 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_general_shape_to_box_10000_boxv__1 16: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_general_shape_to_box_10000_boxv__1 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_general_shape_to_box_10000_boxv__1e_07 16: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_general_shape_to_box_10000_boxv__1e_07 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_general_shape_to_box_10000_boxv_0 16: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_general_shape_to_box_10000_boxv_0 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_general_shape_to_box_10000_boxv_1e_07 16: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_general_shape_to_box_10000_boxv_1e_07 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_general_shape_to_box_10000_boxv_1 16: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_general_shape_to_box_10000_boxv_1 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_general_shape_to_box_10000_boxv_100 16: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_general_shape_to_box_10000_boxv_100 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_to_box_2_5_boxv__100 16: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_to_box_2_5_boxv__100 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_to_box_2_5_boxv__1 16: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_to_box_2_5_boxv__1 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_to_box_2_5_boxv__1e_07 16: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_to_box_2_5_boxv__1e_07 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_to_box_2_5_boxv_0 16: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_to_box_2_5_boxv_0 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_to_box_2_5_boxv_1e_07 16: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_to_box_2_5_boxv_1e_07 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_to_box_2_5_boxv_1 16: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_to_box_2_5_boxv_1 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_to_box_2_5_boxv_100 16: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_to_box_2_5_boxv_100 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_to_box_10000_boxv__100 16: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_to_box_10000_boxv__100 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_to_box_10000_boxv__1 16: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_to_box_10000_boxv__1 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_to_box_10000_boxv__1e_07 16: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_to_box_10000_boxv__1e_07 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_to_box_10000_boxv_0 16: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_to_box_10000_boxv_0 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_to_box_10000_boxv_1e_07 16: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_to_box_10000_boxv_1e_07 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_to_box_10000_boxv_1 16: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_to_box_10000_boxv_1 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_to_box_10000_boxv_100 16: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_to_box_10000_boxv_100 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_to_box_2_5_boxv__100 16: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_to_box_2_5_boxv__100 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_to_box_2_5_boxv__1 16: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_to_box_2_5_boxv__1 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_to_box_2_5_boxv__1e_07 16: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_to_box_2_5_boxv__1e_07 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_to_box_2_5_boxv_0 16: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_to_box_2_5_boxv_0 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_to_box_2_5_boxv_1e_07 16: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_to_box_2_5_boxv_1e_07 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_to_box_2_5_boxv_1 16: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_to_box_2_5_boxv_1 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_to_box_2_5_boxv_100 16: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_to_box_2_5_boxv_100 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_to_box_10000_boxv__100 16: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_to_box_10000_boxv__100 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_to_box_10000_boxv__1 16: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_to_box_10000_boxv__1 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_to_box_10000_boxv__1e_07 16: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_to_box_10000_boxv__1e_07 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_to_box_10000_boxv_0 16: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_to_box_10000_boxv_0 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_to_box_10000_boxv_1e_07 16: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_to_box_10000_boxv_1e_07 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_to_box_10000_boxv_1 16: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_to_box_10000_boxv_1 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_to_box_10000_boxv_100 16: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_to_box_10000_boxv_100 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_to_box_2_5_boxv__100 16: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_to_box_2_5_boxv__100 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_to_box_2_5_boxv__1 16: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_to_box_2_5_boxv__1 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_to_box_2_5_boxv__1e_07 16: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_to_box_2_5_boxv__1e_07 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_to_box_2_5_boxv_0 16: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_to_box_2_5_boxv_0 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_to_box_2_5_boxv_1e_07 16: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_to_box_2_5_boxv_1e_07 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_to_box_2_5_boxv_1 16: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_to_box_2_5_boxv_1 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_to_box_2_5_boxv_100 16: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_to_box_2_5_boxv_100 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_to_box_10000_boxv__100 16: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_to_box_10000_boxv__100 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_to_box_10000_boxv__1 16: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_to_box_10000_boxv__1 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_to_box_10000_boxv__1e_07 16: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_to_box_10000_boxv__1e_07 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_to_box_10000_boxv_0 16: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_to_box_10000_boxv_0 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_to_box_10000_boxv_1e_07 16: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_to_box_10000_boxv_1e_07 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_to_box_10000_boxv_1 16: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_to_box_10000_boxv_1 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_to_box_10000_boxv_100 16: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_to_box_10000_boxv_100 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_to_box_2_5_boxv__100 16: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_to_box_2_5_boxv__100 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_to_box_2_5_boxv__1 16: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_to_box_2_5_boxv__1 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_to_box_2_5_boxv__1e_07 16: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_to_box_2_5_boxv__1e_07 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_to_box_2_5_boxv_0 16: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_to_box_2_5_boxv_0 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_to_box_2_5_boxv_1e_07 16: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_to_box_2_5_boxv_1e_07 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_to_box_2_5_boxv_1 16: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_to_box_2_5_boxv_1 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_to_box_2_5_boxv_100 16: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_to_box_2_5_boxv_100 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_to_box_10000_boxv__100 16: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_to_box_10000_boxv__100 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_to_box_10000_boxv__1 16: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_to_box_10000_boxv__1 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_to_box_10000_boxv__1e_07 16: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_to_box_10000_boxv__1e_07 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_to_box_10000_boxv_0 16: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_to_box_10000_boxv_0 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_to_box_10000_boxv_1e_07 16: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_to_box_10000_boxv_1e_07 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_to_box_10000_boxv_1 16: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_to_box_10000_boxv_1 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_to_box_10000_boxv_100 16: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_to_box_10000_boxv_100 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_general_shape_to_box_2_5_boxv__100 16: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_general_shape_to_box_2_5_boxv__100 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_general_shape_to_box_2_5_boxv__1 16: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_general_shape_to_box_2_5_boxv__1 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_general_shape_to_box_2_5_boxv__1e_07 16: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_general_shape_to_box_2_5_boxv__1e_07 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_general_shape_to_box_2_5_boxv_0 16: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_general_shape_to_box_2_5_boxv_0 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_general_shape_to_box_2_5_boxv_1e_07 16: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_general_shape_to_box_2_5_boxv_1e_07 (1 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_general_shape_to_box_2_5_boxv_1 16: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_general_shape_to_box_2_5_boxv_1 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_general_shape_to_box_2_5_boxv_100 16: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_general_shape_to_box_2_5_boxv_100 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_general_shape_to_box_10000_boxv__100 16: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_general_shape_to_box_10000_boxv__100 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_general_shape_to_box_10000_boxv__1 16: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_general_shape_to_box_10000_boxv__1 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_general_shape_to_box_10000_boxv__1e_07 16: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_general_shape_to_box_10000_boxv__1e_07 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_general_shape_to_box_10000_boxv_0 16: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_general_shape_to_box_10000_boxv_0 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_general_shape_to_box_10000_boxv_1e_07 16: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_general_shape_to_box_10000_boxv_1e_07 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_general_shape_to_box_10000_boxv_1 16: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_general_shape_to_box_10000_boxv_1 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_general_shape_to_box_10000_boxv_100 16: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_general_shape_to_box_10000_boxv_100 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_to_box_2_5_boxv__100 16: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_to_box_2_5_boxv__100 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_to_box_2_5_boxv__1 16: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_to_box_2_5_boxv__1 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_to_box_2_5_boxv__1e_07 16: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_to_box_2_5_boxv__1e_07 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_to_box_2_5_boxv_0 16: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_to_box_2_5_boxv_0 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_to_box_2_5_boxv_1e_07 16: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_to_box_2_5_boxv_1e_07 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_to_box_2_5_boxv_1 16: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_to_box_2_5_boxv_1 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_to_box_2_5_boxv_100 16: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_to_box_2_5_boxv_100 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_to_box_10000_boxv__100 16: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_to_box_10000_boxv__100 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_to_box_10000_boxv__1 16: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_to_box_10000_boxv__1 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_to_box_10000_boxv__1e_07 16: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_to_box_10000_boxv__1e_07 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_to_box_10000_boxv_0 16: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_to_box_10000_boxv_0 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_to_box_10000_boxv_1e_07 16: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_to_box_10000_boxv_1e_07 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_to_box_10000_boxv_1 16: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_to_box_10000_boxv_1 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_to_box_10000_boxv_100 16: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_to_box_10000_boxv_100 (0 ms) 16: [----------] 140 tests from TruncOct/ParrRahmTest (72 ms total) 16: 16: [----------] 140 tests from Other/ParrRahmTest 16: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_other_box_2_5_boxv__100 16: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_other_box_2_5_boxv__100 (2 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_other_box_2_5_boxv__1 16: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_other_box_2_5_boxv__1 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_other_box_2_5_boxv__1e_07 16: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_other_box_2_5_boxv__1e_07 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_other_box_2_5_boxv_0 16: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_other_box_2_5_boxv_0 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_other_box_2_5_boxv_1e_07 16: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_other_box_2_5_boxv_1e_07 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_other_box_2_5_boxv_1 16: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_other_box_2_5_boxv_1 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_other_box_2_5_boxv_100 16: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_other_box_2_5_boxv_100 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_other_box_10000_boxv__100 16: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_other_box_10000_boxv__100 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_other_box_10000_boxv__1 16: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_other_box_10000_boxv__1 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_other_box_10000_boxv__1e_07 16: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_other_box_10000_boxv__1e_07 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_other_box_10000_boxv_0 16: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_other_box_10000_boxv_0 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_other_box_10000_boxv_1e_07 16: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_other_box_10000_boxv_1e_07 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_other_box_10000_boxv_1 16: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_other_box_10000_boxv_1 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_other_box_10000_boxv_100 16: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_other_box_10000_boxv_100 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_other_box_2_5_boxv__100 16: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_other_box_2_5_boxv__100 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_other_box_2_5_boxv__1 16: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_other_box_2_5_boxv__1 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_other_box_2_5_boxv__1e_07 16: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_other_box_2_5_boxv__1e_07 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_other_box_2_5_boxv_0 16: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_other_box_2_5_boxv_0 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_other_box_2_5_boxv_1e_07 16: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_other_box_2_5_boxv_1e_07 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_other_box_2_5_boxv_1 16: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_other_box_2_5_boxv_1 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_other_box_2_5_boxv_100 16: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_other_box_2_5_boxv_100 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_other_box_10000_boxv__100 16: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_other_box_10000_boxv__100 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_other_box_10000_boxv__1 16: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_other_box_10000_boxv__1 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_other_box_10000_boxv__1e_07 16: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_other_box_10000_boxv__1e_07 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_other_box_10000_boxv_0 16: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_other_box_10000_boxv_0 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_other_box_10000_boxv_1e_07 16: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_other_box_10000_boxv_1e_07 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_other_box_10000_boxv_1 16: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_other_box_10000_boxv_1 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_other_box_10000_boxv_100 16: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_other_box_10000_boxv_100 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_other_box_2_5_boxv__100 16: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_other_box_2_5_boxv__100 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_other_box_2_5_boxv__1 16: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_other_box_2_5_boxv__1 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_other_box_2_5_boxv__1e_07 16: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_other_box_2_5_boxv__1e_07 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_other_box_2_5_boxv_0 16: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_other_box_2_5_boxv_0 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_other_box_2_5_boxv_1e_07 16: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_other_box_2_5_boxv_1e_07 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_other_box_2_5_boxv_1 16: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_other_box_2_5_boxv_1 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_other_box_2_5_boxv_100 16: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_other_box_2_5_boxv_100 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_other_box_10000_boxv__100 16: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_other_box_10000_boxv__100 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_other_box_10000_boxv__1 16: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_other_box_10000_boxv__1 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_other_box_10000_boxv__1e_07 16: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_other_box_10000_boxv__1e_07 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_other_box_10000_boxv_0 16: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_other_box_10000_boxv_0 (1 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_other_box_10000_boxv_1e_07 16: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_other_box_10000_boxv_1e_07 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_other_box_10000_boxv_1 16: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_other_box_10000_boxv_1 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_other_box_10000_boxv_100 16: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_other_box_10000_boxv_100 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_general_shape_other_box_2_5_boxv__100 16: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_general_shape_other_box_2_5_boxv__100 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_general_shape_other_box_2_5_boxv__1 16: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_general_shape_other_box_2_5_boxv__1 (1 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_general_shape_other_box_2_5_boxv__1e_07 16: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_general_shape_other_box_2_5_boxv__1e_07 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_general_shape_other_box_2_5_boxv_0 16: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_general_shape_other_box_2_5_boxv_0 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_general_shape_other_box_2_5_boxv_1e_07 16: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_general_shape_other_box_2_5_boxv_1e_07 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_general_shape_other_box_2_5_boxv_1 16: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_general_shape_other_box_2_5_boxv_1 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_general_shape_other_box_2_5_boxv_100 16: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_general_shape_other_box_2_5_boxv_100 (1 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_general_shape_other_box_10000_boxv__100 16: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_general_shape_other_box_10000_boxv__100 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_general_shape_other_box_10000_boxv__1 16: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_general_shape_other_box_10000_boxv__1 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_general_shape_other_box_10000_boxv__1e_07 16: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_general_shape_other_box_10000_boxv__1e_07 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_general_shape_other_box_10000_boxv_0 16: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_general_shape_other_box_10000_boxv_0 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_general_shape_other_box_10000_boxv_1e_07 16: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_general_shape_other_box_10000_boxv_1e_07 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_general_shape_other_box_10000_boxv_1 16: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_general_shape_other_box_10000_boxv_1 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_general_shape_other_box_10000_boxv_100 16: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_general_shape_other_box_10000_boxv_100 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_other_box_2_5_boxv__100 16: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_other_box_2_5_boxv__100 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_other_box_2_5_boxv__1 16: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_other_box_2_5_boxv__1 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_other_box_2_5_boxv__1e_07 16: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_other_box_2_5_boxv__1e_07 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_other_box_2_5_boxv_0 16: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_other_box_2_5_boxv_0 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_other_box_2_5_boxv_1e_07 16: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_other_box_2_5_boxv_1e_07 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_other_box_2_5_boxv_1 16: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_other_box_2_5_boxv_1 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_other_box_2_5_boxv_100 16: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_other_box_2_5_boxv_100 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_other_box_10000_boxv__100 16: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_other_box_10000_boxv__100 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_other_box_10000_boxv__1 16: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_other_box_10000_boxv__1 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_other_box_10000_boxv__1e_07 16: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_other_box_10000_boxv__1e_07 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_other_box_10000_boxv_0 16: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_other_box_10000_boxv_0 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_other_box_10000_boxv_1e_07 16: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_other_box_10000_boxv_1e_07 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_other_box_10000_boxv_1 16: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_other_box_10000_boxv_1 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_other_box_10000_boxv_100 16: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_other_box_10000_boxv_100 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_other_box_2_5_boxv__100 16: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_other_box_2_5_boxv__100 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_other_box_2_5_boxv__1 16: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_other_box_2_5_boxv__1 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_other_box_2_5_boxv__1e_07 16: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_other_box_2_5_boxv__1e_07 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_other_box_2_5_boxv_0 16: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_other_box_2_5_boxv_0 (1 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_other_box_2_5_boxv_1e_07 16: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_other_box_2_5_boxv_1e_07 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_other_box_2_5_boxv_1 16: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_other_box_2_5_boxv_1 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_other_box_2_5_boxv_100 16: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_other_box_2_5_boxv_100 (1 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_other_box_10000_boxv__100 16: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_other_box_10000_boxv__100 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_other_box_10000_boxv__1 16: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_other_box_10000_boxv__1 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_other_box_10000_boxv__1e_07 16: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_other_box_10000_boxv__1e_07 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_other_box_10000_boxv_0 16: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_other_box_10000_boxv_0 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_other_box_10000_boxv_1e_07 16: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_other_box_10000_boxv_1e_07 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_other_box_10000_boxv_1 16: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_other_box_10000_boxv_1 (2 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_other_box_10000_boxv_100 16: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_other_box_10000_boxv_100 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_other_box_2_5_boxv__100 16: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_other_box_2_5_boxv__100 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_other_box_2_5_boxv__1 16: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_other_box_2_5_boxv__1 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_other_box_2_5_boxv__1e_07 16: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_other_box_2_5_boxv__1e_07 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_other_box_2_5_boxv_0 16: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_other_box_2_5_boxv_0 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_other_box_2_5_boxv_1e_07 16: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_other_box_2_5_boxv_1e_07 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_other_box_2_5_boxv_1 16: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_other_box_2_5_boxv_1 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_other_box_2_5_boxv_100 16: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_other_box_2_5_boxv_100 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_other_box_10000_boxv__100 16: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_other_box_10000_boxv__100 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_other_box_10000_boxv__1 16: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_other_box_10000_boxv__1 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_other_box_10000_boxv__1e_07 16: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_other_box_10000_boxv__1e_07 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_other_box_10000_boxv_0 16: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_other_box_10000_boxv_0 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_other_box_10000_boxv_1e_07 16: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_other_box_10000_boxv_1e_07 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_other_box_10000_boxv_1 16: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_other_box_10000_boxv_1 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_other_box_10000_boxv_100 16: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_other_box_10000_boxv_100 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_other_box_2_5_boxv__100 16: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_other_box_2_5_boxv__100 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_other_box_2_5_boxv__1 16: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_other_box_2_5_boxv__1 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_other_box_2_5_boxv__1e_07 16: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_other_box_2_5_boxv__1e_07 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_other_box_2_5_boxv_0 16: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_other_box_2_5_boxv_0 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_other_box_2_5_boxv_1e_07 16: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_other_box_2_5_boxv_1e_07 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_other_box_2_5_boxv_1 16: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_other_box_2_5_boxv_1 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_other_box_2_5_boxv_100 16: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_other_box_2_5_boxv_100 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_other_box_10000_boxv__100 16: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_other_box_10000_boxv__100 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_other_box_10000_boxv__1 16: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_other_box_10000_boxv__1 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_other_box_10000_boxv__1e_07 16: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_other_box_10000_boxv__1e_07 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_other_box_10000_boxv_0 16: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_other_box_10000_boxv_0 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_other_box_10000_boxv_1e_07 16: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_other_box_10000_boxv_1e_07 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_other_box_10000_boxv_1 16: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_other_box_10000_boxv_1 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_other_box_10000_boxv_100 16: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_other_box_10000_boxv_100 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_general_shape_other_box_2_5_boxv__100 16: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_general_shape_other_box_2_5_boxv__100 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_general_shape_other_box_2_5_boxv__1 16: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_general_shape_other_box_2_5_boxv__1 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_general_shape_other_box_2_5_boxv__1e_07 16: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_general_shape_other_box_2_5_boxv__1e_07 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_general_shape_other_box_2_5_boxv_0 16: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_general_shape_other_box_2_5_boxv_0 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_general_shape_other_box_2_5_boxv_1e_07 16: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_general_shape_other_box_2_5_boxv_1e_07 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_general_shape_other_box_2_5_boxv_1 16: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_general_shape_other_box_2_5_boxv_1 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_general_shape_other_box_2_5_boxv_100 16: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_general_shape_other_box_2_5_boxv_100 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_general_shape_other_box_10000_boxv__100 16: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_general_shape_other_box_10000_boxv__100 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_general_shape_other_box_10000_boxv__1 16: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_general_shape_other_box_10000_boxv__1 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_general_shape_other_box_10000_boxv__1e_07 16: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_general_shape_other_box_10000_boxv__1e_07 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_general_shape_other_box_10000_boxv_0 16: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_general_shape_other_box_10000_boxv_0 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_general_shape_other_box_10000_boxv_1e_07 16: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_general_shape_other_box_10000_boxv_1e_07 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_general_shape_other_box_10000_boxv_1 16: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_general_shape_other_box_10000_boxv_1 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_general_shape_other_box_10000_boxv_100 16: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_general_shape_other_box_10000_boxv_100 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_other_box_2_5_boxv__100 16: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_other_box_2_5_boxv__100 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_other_box_2_5_boxv__1 16: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_other_box_2_5_boxv__1 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_other_box_2_5_boxv__1e_07 16: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_other_box_2_5_boxv__1e_07 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_other_box_2_5_boxv_0 16: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_other_box_2_5_boxv_0 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_other_box_2_5_boxv_1e_07 16: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_other_box_2_5_boxv_1e_07 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_other_box_2_5_boxv_1 16: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_other_box_2_5_boxv_1 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_other_box_2_5_boxv_100 16: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_other_box_2_5_boxv_100 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_other_box_10000_boxv__100 16: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_other_box_10000_boxv__100 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_other_box_10000_boxv__1 16: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_other_box_10000_boxv__1 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_other_box_10000_boxv__1e_07 16: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_other_box_10000_boxv__1e_07 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_other_box_10000_boxv_0 16: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_other_box_10000_boxv_0 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_other_box_10000_boxv_1e_07 16: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_other_box_10000_boxv_1e_07 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_other_box_10000_boxv_1 16: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_other_box_10000_boxv_1 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_other_box_10000_boxv_100 16: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_other_box_10000_boxv_100 (0 ms) 16: [----------] 140 tests from Other/ParrRahmTest (74 ms total) 16: 16: [----------] 13 tests from WithParameters/SettleTest 16: [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/0 16: [ OK ] WithParameters/SettleTest.SatisfiesConstraints/0 (0 ms) 16: [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/1 16: [ OK ] WithParameters/SettleTest.SatisfiesConstraints/1 (1 ms) 16: [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/2 16: [ OK ] WithParameters/SettleTest.SatisfiesConstraints/2 (1 ms) 16: [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/3 16: [ OK ] WithParameters/SettleTest.SatisfiesConstraints/3 (1 ms) 16: [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/4 16: [ OK ] WithParameters/SettleTest.SatisfiesConstraints/4 (1 ms) 16: [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/5 16: [ OK ] WithParameters/SettleTest.SatisfiesConstraints/5 (2 ms) 16: [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/6 16: [ OK ] WithParameters/SettleTest.SatisfiesConstraints/6 (2 ms) 16: [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/7 16: [ OK ] WithParameters/SettleTest.SatisfiesConstraints/7 (2 ms) 16: [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/8 16: [ OK ] WithParameters/SettleTest.SatisfiesConstraints/8 (6 ms) 16: [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/9 16: [ OK ] WithParameters/SettleTest.SatisfiesConstraints/9 (3 ms) 16: [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/10 16: [ OK ] WithParameters/SettleTest.SatisfiesConstraints/10 (4 ms) 16: [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/11 16: [ OK ] WithParameters/SettleTest.SatisfiesConstraints/11 (7 ms) 16: [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/12 16: [ OK ] WithParameters/SettleTest.SatisfiesConstraints/12 (6 ms) 16: [----------] 13 tests from WithParameters/SettleTest (51 ms total) 16: 16: [----------] Global test environment tear-down 16: [==========] 1032 tests from 27 test suites ran. (1040 ms total) 16: [ PASSED ] 1032 tests. 16/92 Test #16: MdlibUnitTest ............................. Passed 1.83 sec test 17 Start 17: AwhTest 17: Test command: /build/reproducible-path/gromacs-2025.1/build/basic-dp/bin/awh-test "--gtest_output=xml:/build/reproducible-path/gromacs-2025.1/build/basic-dp/Testing/Temporary/AwhTest.xml" 17: Working Directory: /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/applied_forces/awh/tests 17: Test timeout computed to be: 30 17: [==========] Running 27 tests from 10 test suites. 17: [----------] Global test environment set-up. 17: [----------] 3 tests from SerializationTest 17: [ RUN ] SerializationTest.CanSerializeDimParams 17: [ OK ] SerializationTest.CanSerializeDimParams (0 ms) 17: [ RUN ] SerializationTest.CanSerializeBiasParams 17: [ OK ] SerializationTest.CanSerializeBiasParams (0 ms) 17: [ RUN ] SerializationTest.CanSerializeAwhParams 17: [ OK ] SerializationTest.CanSerializeAwhParams (0 ms) 17: [----------] 3 tests from SerializationTest (0 ms total) 17: 17: [----------] 1 test from BiasTest 17: [ RUN ] BiasTest.DetectsCovering 17: [ OK ] BiasTest.DetectsCovering (7 ms) 17: [----------] 1 test from BiasTest (7 ms total) 17: 17: [----------] 1 test from biasGridTest 17: [ RUN ] biasGridTest.neighborhood 17: [ OK ] biasGridTest.neighborhood (7 ms) 17: [----------] 1 test from biasGridTest (7 ms total) 17: 17: [----------] 2 tests from BiasSharingTest 17: [ RUN ] BiasSharingTest.SharingWorks 17: [ OK ] BiasSharingTest.SharingWorks (59 ms) 17: [ RUN ] BiasSharingTest.SharingScalingByMetricWorks 17: [ OK ] BiasSharingTest.SharingScalingByMetricWorks (93 ms) 17: [----------] 2 tests from BiasSharingTest (154 ms total) 17: 17: [----------] 2 tests from BiasFepLambdaStateTest 17: [ RUN ] BiasFepLambdaStateTest.DetectsCovering 17: [ OK ] BiasFepLambdaStateTest.DetectsCovering (24 ms) 17: [ RUN ] BiasFepLambdaStateTest.DetectsLargeNegativeForeignEnergy 17: [ OK ] BiasFepLambdaStateTest.DetectsLargeNegativeForeignEnergy (1 ms) 17: [----------] 2 tests from BiasFepLambdaStateTest (26 ms total) 17: 17: [----------] 8 tests from WithParameters/BiasTest 17: [ RUN ] WithParameters/BiasTest.ForcesBiasPmfWeightSum/0 17: [ OK ] WithParameters/BiasTest.ForcesBiasPmfWeightSum/0 (3 ms) 17: [ RUN ] WithParameters/BiasTest.ForcesBiasPmfWeightSum/1 17: [ OK ] WithParameters/BiasTest.ForcesBiasPmfWeightSum/1 (3 ms) 17: [ RUN ] WithParameters/BiasTest.ForcesBiasPmfWeightSum/2 17: [ OK ] WithParameters/BiasTest.ForcesBiasPmfWeightSum/2 (3 ms) 17: [ RUN ] WithParameters/BiasTest.ForcesBiasPmfWeightSum/3 17: [ OK ] WithParameters/BiasTest.ForcesBiasPmfWeightSum/3 (3 ms) 17: [ RUN ] WithParameters/BiasTest.ForcesBiasPmfWeightSum/4 17: [ OK ] WithParameters/BiasTest.ForcesBiasPmfWeightSum/4 (3 ms) 17: [ RUN ] WithParameters/BiasTest.ForcesBiasPmfWeightSum/5 17: [ OK ] WithParameters/BiasTest.ForcesBiasPmfWeightSum/5 (2 ms) 17: [ RUN ] WithParameters/BiasTest.ForcesBiasPmfWeightSum/6 17: [ OK ] WithParameters/BiasTest.ForcesBiasPmfWeightSum/6 (2 ms) 17: [ RUN ] WithParameters/BiasTest.ForcesBiasPmfWeightSum/7 17: [ OK ] WithParameters/BiasTest.ForcesBiasPmfWeightSum/7 (2 ms) 17: [----------] 8 tests from WithParameters/BiasTest (28 ms total) 17: 17: [----------] 2 tests from WithParameters/BiasStateTest 17: [ RUN ] WithParameters/BiasStateTest.InitializesFromFile/0 17: [ OK ] WithParameters/BiasStateTest.InitializesFromFile/0 (1 ms) 17: [ RUN ] WithParameters/BiasStateTest.InitializesFromFile/1 17: [ OK ] WithParameters/BiasStateTest.InitializesFromFile/1 (1 ms) 17: [----------] 2 tests from WithParameters/BiasStateTest (2 ms total) 17: 17: [----------] 1 test from WithParameters/UserInputTest 17: [ RUN ] WithParameters/UserInputTest.ParsesUser3DInput/0 17: [ OK ] WithParameters/UserInputTest.ParsesUser3DInput/0 (1 ms) 17: [----------] 1 test from WithParameters/UserInputTest (1 ms total) 17: 17: [----------] 4 tests from WithParameters/BiasFepLambdaStateTest 17: [ RUN ] WithParameters/BiasFepLambdaStateTest.ForcesBiasPmf/0 17: [ OK ] WithParameters/BiasFepLambdaStateTest.ForcesBiasPmf/0 (48 ms) 17: [ RUN ] WithParameters/BiasFepLambdaStateTest.ForcesBiasPmf/1 17: [ OK ] WithParameters/BiasFepLambdaStateTest.ForcesBiasPmf/1 (45 ms) 17: [ RUN ] WithParameters/BiasFepLambdaStateTest.ForcesBiasPmf/2 17: [ OK ] WithParameters/BiasFepLambdaStateTest.ForcesBiasPmf/2 (45 ms) 17: [ RUN ] WithParameters/BiasFepLambdaStateTest.ForcesBiasPmf/3 17: [ OK ] WithParameters/BiasFepLambdaStateTest.ForcesBiasPmf/3 (48 ms) 17: [----------] 4 tests from WithParameters/BiasFepLambdaStateTest (197 ms total) 17: 17: [----------] 3 tests from WithParameters/FrictionMetricTest 17: [ RUN ] WithParameters/FrictionMetricTest.FrictionMetric/0 17: [ OK ] WithParameters/FrictionMetricTest.FrictionMetric/0 (1 ms) 17: [ RUN ] WithParameters/FrictionMetricTest.FrictionMetric/1 17: [ OK ] WithParameters/FrictionMetricTest.FrictionMetric/1 (7 ms) 17: [ RUN ] WithParameters/FrictionMetricTest.FrictionMetric/2 17: [ OK ] WithParameters/FrictionMetricTest.FrictionMetric/2 (187 ms) 17: [----------] 3 tests from WithParameters/FrictionMetricTest (217 ms total) 17: 17: [----------] Global test environment tear-down 17: [==========] 27 tests from 10 test suites ran. (645 ms total) 17: [ PASSED ] 27 tests. 17/92 Test #17: AwhTest ................................... Passed 0.74 sec test 18 Start 18: DensityFittingAppliedForcesUnitTest 18: Test command: /build/reproducible-path/gromacs-2025.1/build/basic-dp/bin/density_fitting_applied_forces-test "--gtest_output=xml:/build/reproducible-path/gromacs-2025.1/build/basic-dp/Testing/Temporary/DensityFittingAppliedForcesUnitTest.xml" 18: Working Directory: /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/applied_forces/densityfitting/tests 18: Test timeout computed to be: 30 18: [==========] Running 18 tests from 4 test suites. 18: [----------] Global test environment set-up. 18: [----------] 2 tests from DensityFittingTest 18: [ RUN ] DensityFittingTest.ForceProviderLackingInputThrows 18: [ OK ] DensityFittingTest.ForceProviderLackingInputThrows (2 ms) 18: [ RUN ] DensityFittingTest.SingleAtom 18: [ OK ] DensityFittingTest.SingleAtom (2 ms) 18: [----------] 2 tests from DensityFittingTest (4 ms total) 18: 18: [----------] 7 tests from DensityFittingAmplitudeLookupTest 18: [ RUN ] DensityFittingAmplitudeLookupTest.Unity 18: [ OK ] DensityFittingAmplitudeLookupTest.Unity (0 ms) 18: [ RUN ] DensityFittingAmplitudeLookupTest.Charge 18: [ OK ] DensityFittingAmplitudeLookupTest.Charge (0 ms) 18: [ RUN ] DensityFittingAmplitudeLookupTest.Masses 18: [ OK ] DensityFittingAmplitudeLookupTest.Masses (0 ms) 18: [ RUN ] DensityFittingAmplitudeLookupTest.CanCopyAssign 18: [ OK ] DensityFittingAmplitudeLookupTest.CanCopyAssign (0 ms) 18: [ RUN ] DensityFittingAmplitudeLookupTest.CanCopyConstruct 18: [ OK ] DensityFittingAmplitudeLookupTest.CanCopyConstruct (0 ms) 18: [ RUN ] DensityFittingAmplitudeLookupTest.CanMoveAssign 18: [ OK ] DensityFittingAmplitudeLookupTest.CanMoveAssign (0 ms) 18: [ RUN ] DensityFittingAmplitudeLookupTest.CanMoveConstruct 18: [ OK ] DensityFittingAmplitudeLookupTest.CanMoveConstruct (0 ms) 18: [----------] 7 tests from DensityFittingAmplitudeLookupTest (0 ms total) 18: 18: [----------] 1 test from DensityFittingForceProviderState 18: [ RUN ] DensityFittingForceProviderState.RoundTripSaving 18: [ OK ] DensityFittingForceProviderState.RoundTripSaving (0 ms) 18: [----------] 1 test from DensityFittingForceProviderState (0 ms total) 18: 18: [----------] 8 tests from DensityFittingOptionsTest 18: [ RUN ] DensityFittingOptionsTest.DefaultParameters 18: [ OK ] DensityFittingOptionsTest.DefaultParameters (0 ms) 18: [ RUN ] DensityFittingOptionsTest.OptionSetsActive 18: [ OK ] DensityFittingOptionsTest.OptionSetsActive (0 ms) 18: [ RUN ] DensityFittingOptionsTest.OutputNoDefaultValuesWhenInactive 18: [ OK ] DensityFittingOptionsTest.OutputNoDefaultValuesWhenInactive (0 ms) 18: [ RUN ] DensityFittingOptionsTest.OutputDefaultValuesWhenActive 18: [ OK ] DensityFittingOptionsTest.OutputDefaultValuesWhenActive (1 ms) 18: [ RUN ] DensityFittingOptionsTest.CanConvertGroupStringToIndexGroup 18: [ OK ] DensityFittingOptionsTest.CanConvertGroupStringToIndexGroup (1 ms) 18: [ RUN ] DensityFittingOptionsTest.InternalsToKvt 18: [ OK ] DensityFittingOptionsTest.InternalsToKvt (0 ms) 18: [ RUN ] DensityFittingOptionsTest.KvtToInternal 18: [ OK ] DensityFittingOptionsTest.KvtToInternal (1 ms) 18: [ RUN ] DensityFittingOptionsTest.RoundTripForInternalsIsIdempotent 18: [ OK ] DensityFittingOptionsTest.RoundTripForInternalsIsIdempotent (0 ms) 18: [----------] 8 tests from DensityFittingOptionsTest (6 ms total) 18: 18: [----------] Global test environment tear-down 18: [==========] 18 tests from 4 test suites ran. (11 ms total) 18: [ PASSED ] 18 tests. 18/92 Test #18: DensityFittingAppliedForcesUnitTest ....... Passed 0.09 sec test 19 Start 19: QMMMAppliedForcesUnitTest 19: Test command: /build/reproducible-path/gromacs-2025.1/build/basic-dp/bin/qmmm_applied_forces-test "--gtest_output=xml:/build/reproducible-path/gromacs-2025.1/build/basic-dp/Testing/Temporary/QMMMAppliedForcesUnitTest.xml" 19: Working Directory: /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/applied_forces/qmmm/tests 19: Test timeout computed to be: 30 19: [==========] Running 21 tests from 5 test suites. 19: [----------] Global test environment set-up. 19: [----------] 3 tests from QMMMInputGeneratorTest 19: [ RUN ] QMMMInputGeneratorTest.CanConstruct 19: [ OK ] QMMMInputGeneratorTest.CanConstruct (0 ms) 19: [ RUN ] QMMMInputGeneratorTest.TwoWatersPBENoLink 19: [ OK ] QMMMInputGeneratorTest.TwoWatersPBENoLink (1 ms) 19: [ RUN ] QMMMInputGeneratorTest.TwoWatersPBEWithLink 19: [ OK ] QMMMInputGeneratorTest.TwoWatersPBEWithLink (1 ms) 19: [----------] 3 tests from QMMMInputGeneratorTest (3 ms total) 19: 19: [----------] 7 tests from QMMMTopologyPreprocessorTest 19: [ RUN ] QMMMTopologyPreprocessorTest.CanConstruct 19: [ OK ] QMMMTopologyPreprocessorTest.CanConstruct (0 ms) 19: [ RUN ] QMMMTopologyPreprocessorTest.FourWatersFirstQMNoLink 19: 19: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary/QMMMTopologyPreprocessorTest_FourWatersFirstQMNoLink_4water.mdp]: 19: For a correct single-point energy evaluation with nsteps = 0, use 19: continuation = yes to avoid constraining the input coordinates. 19: 19: Generating 1-4 interactions: fudge = 0.5 19: Number of degrees of freedom in T-Coupling group rest is 21.00 19: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 19: 19: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary/QMMMTopologyPreprocessorTest_FourWatersFirstQMNoLink_4water.mdp]: 19: NVE simulation with an initial temperature of zero: will use a Verlet 19: buffer of 10%. Check your energy drift! 19: 19: 19: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary/QMMMTopologyPreprocessorTest_FourWatersFirstQMNoLink_4water.mdp]: 19: You are using a plain Coulomb cut-off, which might produce artifacts. 19: You might want to consider using PME electrostatics. 19: 19: 19: 19: There were 3 NOTEs 19: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary/QMMMTopologyPreprocessorTest_FourWatersFirstQMNoLink_4water.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 19: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary/QMMMTopologyPreprocessorTest_FourWatersFirstQMNoLink_4water.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 19: Setting the LD random seed to -1929712737 19: 19: Generated 10 of the 10 non-bonded parameter combinations 19: 19: Generated 10 of the 10 1-4 parameter combinations 19: 19: Excluding 2 bonded neighbours molecule type 'SOL' 19: 19: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/4water.gro', all velocities are zero 19: Analysing residue names: 19: There are: 4 Water residues 19: 19: This run will generate roughly 0 Mb of data 19: [ OK ] QMMMTopologyPreprocessorTest.FourWatersFirstQMNoLink (31 ms) 19: [ RUN ] QMMMTopologyPreprocessorTest.FourWatersSeondAndForthQMNoLink 19: 19: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary/QMMMTopologyPreprocessorTest_FourWatersSeondAndForthQMNoLink_4water.mdp]: 19: For a correct single-point energy evaluation with nsteps = 0, use 19: continuation = yes to avoid constraining the input coordinates. 19: 19: Generating 1-4 interactions: fudge = 0.5 19: Number of degrees of freedom in T-Coupling group rest is 21.00 19: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 19: 19: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary/QMMMTopologyPreprocessorTest_FourWatersSeondAndForthQMNoLink_4water.mdp]: 19: NVE simulation with an initial temperature of zero: will use a Verlet 19: buffer of 10%. Check your energy drift! 19: 19: 19: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary/QMMMTopologyPreprocessorTest_FourWatersSeondAndForthQMNoLink_4water.mdp]: 19: You are using a plain Coulomb cut-off, which might produce artifacts. 19: You might want to consider using PME electrostatics. 19: 19: 19: 19: There were 3 NOTEs 19: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary/QMMMTopologyPreprocessorTest_FourWatersSeondAndForthQMNoLink_4water.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 19: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary/QMMMTopologyPreprocessorTest_FourWatersSeondAndForthQMNoLink_4water.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 19: Setting the LD random seed to -615850017 19: 19: Generated 10 of the 10 non-bonded parameter combinations 19: 19: Generated 10 of the 10 1-4 parameter combinations 19: 19: Excluding 2 bonded neighbours molecule type 'SOL' 19: 19: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/4water.gro', all velocities are zero 19: Analysing residue names: 19: There are: 4 Water residues 19: 19: This run will generate roughly 0 Mb of data 19: [ OK ] QMMMTopologyPreprocessorTest.FourWatersSeondAndForthQMNoLink (27 ms) 19: [ RUN ] QMMMTopologyPreprocessorTest.FourWatersFirstQMWithLink 19: 19: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary/QMMMTopologyPreprocessorTest_FourWatersFirstQMWithLink_4water.mdp]: 19: For a correct single-point energy evaluation with nsteps = 0, use 19: continuation = yes to avoid constraining the input coordinates. 19: 19: Generating 1-4 interactions: fudge = 0.5 19: Number of degrees of freedom in T-Coupling group rest is 21.00 19: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 19: 19: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary/QMMMTopologyPreprocessorTest_FourWatersFirstQMWithLink_4water.mdp]: 19: NVE simulation with an initial temperature of zero: will use a Verlet 19: buffer of 10%. Check your energy drift! 19: 19: 19: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary/QMMMTopologyPreprocessorTest_FourWatersFirstQMWithLink_4water.mdp]: 19: You are using a plain Coulomb cut-off, which might produce artifacts. 19: You might want to consider using PME electrostatics. 19: 19: 19: 19: There were 3 NOTEs 19: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary/QMMMTopologyPreprocessorTest_FourWatersFirstQMWithLink_4water.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 19: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary/QMMMTopologyPreprocessorTest_FourWatersFirstQMWithLink_4water.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 19: Setting the LD random seed to -1459662981 19: 19: Generated 10 of the 10 non-bonded parameter combinations 19: 19: Generated 10 of the 10 1-4 parameter combinations 19: 19: Excluding 2 bonded neighbours molecule type 'SOL' 19: 19: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/4water.gro', all velocities are zero 19: Analysing residue names: 19: There are: 4 Water residues 19: 19: This run will generate roughly 0 Mb of data 19: [ OK ] QMMMTopologyPreprocessorTest.FourWatersFirstQMWithLink (27 ms) 19: [ RUN ] QMMMTopologyPreprocessorTest.AlanineDipeptideWithLinksNoConstraints 19: 19: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary/QMMMTopologyPreprocessorTest_AlanineDipeptideWithLinksNoConstraints_alanine_vacuo.mdp]: 19: For a correct single-point energy evaluation with nsteps = 0, use 19: continuation = yes to avoid constraining the input coordinates. 19: 19: Generating 1-4 interactions: fudge = 0.5 19: Number of degrees of freedom in T-Coupling group rest is 63.00 19: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 19: 19: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary/QMMMTopologyPreprocessorTest_AlanineDipeptideWithLinksNoConstraints_alanine_vacuo.mdp]: 19: NVE simulation: will use the initial temperature of 129.093 K for 19: determining the Verlet buffer size 19: 19: 19: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary/QMMMTopologyPreprocessorTest_AlanineDipeptideWithLinksNoConstraints_alanine_vacuo.mdp]: 19: You are using a plain Coulomb cut-off, which might produce artifacts. 19: You might want to consider using PME electrostatics. 19: 19: 19: 19: There were 3 NOTEs 19: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary/QMMMTopologyPreprocessorTest_AlanineDipeptideWithLinksNoConstraints_alanine_vacuo.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 19: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary/QMMMTopologyPreprocessorTest_AlanineDipeptideWithLinksNoConstraints_alanine_vacuo.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 19: Setting the LD random seed to 1879039331 19: 19: Generated 2145 of the 2145 non-bonded parameter combinations 19: 19: Generated 2145 of the 2145 1-4 parameter combinations 19: 19: Excluding 3 bonded neighbours molecule type 'ALANINEDIPEPTIDE' 19: 19: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/alanine_vacuo.gro' 19: Analysing residue names: 19: There are: 3 Protein residues 19: Analysing Protein... 19: 19: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 129.093 K 19: 19: Calculated rlist for 1x1 atom pair-list as 1.021 nm, buffer size 0.021 nm 19: 19: Set rlist, assuming 4x4 atom pair-list, to 1.013 nm, buffer size 0.013 nm 19: 19: Note that mdrun will redetermine rlist based on the actual pair-list setup 19: 19: This run will generate roughly 0 Mb of data 19: [ OK ] QMMMTopologyPreprocessorTest.AlanineDipeptideWithLinksNoConstraints (98 ms) 19: [ RUN ] QMMMTopologyPreprocessorTest.AlanineDipeptideWithLinksWithConstraints 19: 19: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary/QMMMTopologyPreprocessorTest_AlanineDipeptideWithLinksWithConstraints_alanine_vacuo.mdp]: 19: For a correct single-point energy evaluation with nsteps = 0, use 19: continuation = yes to avoid constraining the input coordinates. 19: 19: Generating 1-4 interactions: fudge = 0.5 19: 19: NOTE 2 [file unknown]: 19: You are using constraints on all bonds, whereas the forcefield has been 19: parametrized only with constraints involving hydrogen atoms. We suggest 19: using constraints = h-bonds instead, this will also improve performance. 19: 19: 19: NOTE 3 [file unknown]: 19: For energy conservation with LINCS, lincs_iter should be 2 or larger. 19: 19: 19: Number of degrees of freedom in T-Coupling group rest is 42.00 19: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 19: 19: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary/QMMMTopologyPreprocessorTest_AlanineDipeptideWithLinksWithConstraints_alanine_vacuo.mdp]: 19: NVE simulation: will use the initial temperature of 193.640 K for 19: determining the Verlet buffer size 19: 19: 19: NOTE 5 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary/QMMMTopologyPreprocessorTest_AlanineDipeptideWithLinksWithConstraints_alanine_vacuo.mdp]: 19: You are using a plain Coulomb cut-off, which might produce artifacts. 19: You might want to consider using PME electrostatics. 19: 19: 19: 19: There were 5 NOTEs 19: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary/QMMMTopologyPreprocessorTest_AlanineDipeptideWithLinksWithConstraints_alanine_vacuo.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 19: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary/QMMMTopologyPreprocessorTest_AlanineDipeptideWithLinksWithConstraints_alanine_vacuo.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 19: Setting the LD random seed to -1082392619 19: 19: Generated 2145 of the 2145 non-bonded parameter combinations 19: 19: Generated 2145 of the 2145 1-4 parameter combinations 19: 19: Excluding 3 bonded neighbours molecule type 'ALANINEDIPEPTIDE' 19: 19: turning all bonds into constraints... 19: 19: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/alanine_vacuo.gro' 19: Analysing residue names: 19: There are: 3 Protein residues 19: Analysing Protein... 19: 19: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 193.64 K 19: 19: Calculated rlist for 1x1 atom pair-list as 1.023 nm, buffer size 0.023 nm 19: 19: Set rlist, assuming 4x4 atom pair-list, to 1.015 nm, buffer size 0.015 nm 19: 19: Note that mdrun will redetermine rlist based on the actual pair-list setup 19: 19: This run will generate roughly 0 Mb of data 19: [ OK ] QMMMTopologyPreprocessorTest.AlanineDipeptideWithLinksWithConstraints (113 ms) 19: [ RUN ] QMMMTopologyPreprocessorTest.RemovingQMVsites 19: 19: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary/QMMMTopologyPreprocessorTest_RemovingQMVsites_vsite_test.mdp]: 19: For a correct single-point energy evaluation with nsteps = 0, use 19: continuation = yes to avoid constraining the input coordinates. 19: 19: Number of degrees of freedom in T-Coupling group rest is 45.00 19: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 19: 19: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary/QMMMTopologyPreprocessorTest_RemovingQMVsites_vsite_test.mdp]: 19: NVE simulation with an initial temperature of zero: will use a Verlet 19: buffer of 10%. Check your energy drift! 19: 19: 19: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary/QMMMTopologyPreprocessorTest_RemovingQMVsites_vsite_test.mdp]: 19: You are using a plain Coulomb cut-off, which might produce artifacts. 19: You might want to consider using PME electrostatics. 19: 19: 19: 19: There were 3 NOTEs 19: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary/QMMMTopologyPreprocessorTest_RemovingQMVsites_vsite_test.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 19: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary/QMMMTopologyPreprocessorTest_RemovingQMVsites_vsite_test.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 19: Setting the LD random seed to 2143010287 19: 19: Generated 3 of the 6 non-bonded parameter combinations 19: 19: Excluding 3 bonded neighbours molecule type 'VSTEST' 19: 19: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/vsite_test.gro', all velocities are zero 19: 19: Cleaning up constraints and constant bonded interactions with virtual sites 19: Analysing residue names: 19: There are: 1 Other residues 19: Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups... 19: 19: This run will generate roughly 0 Mb of data 19: [ OK ] QMMMTopologyPreprocessorTest.RemovingQMVsites (34 ms) 19: [----------] 7 tests from QMMMTopologyPreprocessorTest (333 ms total) 19: 19: [----------] 9 tests from QMMMOptionsTest 19: [ RUN ] QMMMOptionsTest.DefaultParameters 19: [ OK ] QMMMOptionsTest.DefaultParameters (0 ms) 19: [ RUN ] QMMMOptionsTest.OptionSetsActive 19: [ OK ] QMMMOptionsTest.OptionSetsActive (0 ms) 19: [ RUN ] QMMMOptionsTest.OutputNoDefaultValuesWhenInactive 19: [ OK ] QMMMOptionsTest.OutputNoDefaultValuesWhenInactive (0 ms) 19: [ RUN ] QMMMOptionsTest.OutputDefaultValuesWhenActive 19: [ OK ] QMMMOptionsTest.OutputDefaultValuesWhenActive (1 ms) 19: [ RUN ] QMMMOptionsTest.CanConvertGroupStringToIndexGroup 19: [ OK ] QMMMOptionsTest.CanConvertGroupStringToIndexGroup (0 ms) 19: [ RUN ] QMMMOptionsTest.NoQMGroupConvertGroupStringToIndexGroup 19: [ OK ] QMMMOptionsTest.NoQMGroupConvertGroupStringToIndexGroup (0 ms) 19: [ RUN ] QMMMOptionsTest.EmptyQMGroupConvertGroupStringToIndexGroup 19: [ OK ] QMMMOptionsTest.EmptyQMGroupConvertGroupStringToIndexGroup (0 ms) 19: [ RUN ] QMMMOptionsTest.InternalsToKvtAndBack 19: [ OK ] QMMMOptionsTest.InternalsToKvtAndBack (0 ms) 19: [ RUN ] QMMMOptionsTest.CP2KInputProcessing 19: [ OK ] QMMMOptionsTest.CP2KInputProcessing (2 ms) 19: [----------] 9 tests from QMMMOptionsTest (9 ms total) 19: 19: [----------] 1 test from QMMMForceProviderTest 19: [ RUN ] QMMMForceProviderTest.CanConstructOrNot 19: [ OK ] QMMMForceProviderTest.CanConstructOrNot (0 ms) 19: [----------] 1 test from QMMMForceProviderTest (0 ms total) 19: 19: [----------] 1 test from QMMMTest 19: [ RUN ] QMMMTest.ForceProviderLackingInputThrows 19: [ OK ] QMMMTest.ForceProviderLackingInputThrows (0 ms) 19: [----------] 1 test from QMMMTest (0 ms total) 19: 19: [----------] Global test environment tear-down 19: [==========] 21 tests from 5 test suites ran. (347 ms total) 19: [ PASSED ] 21 tests. 19/92 Test #19: QMMMAppliedForcesUnitTest ................. Passed 0.42 sec test 20 Start 20: ColvarsAppliedForcesUnitTest 20: Test command: /build/reproducible-path/gromacs-2025.1/build/basic-dp/bin/colvars_applied_forces-test "--gtest_output=xml:/build/reproducible-path/gromacs-2025.1/build/basic-dp/Testing/Temporary/ColvarsAppliedForcesUnitTest.xml" 20: Working Directory: /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/applied_forces/colvars/tests 20: Test timeout computed to be: 30 20: [==========] Running 16 tests from 4 test suites. 20: [----------] Global test environment set-up. 20: [----------] 1 test from ColvarsTest 20: [ RUN ] ColvarsTest.ForceProviderLackingInputThrows 20: [ OK ] ColvarsTest.ForceProviderLackingInputThrows (0 ms) 20: [----------] 1 test from ColvarsTest (0 ms total) 20: 20: [----------] 6 tests from ColvarsOptionsTest 20: [ RUN ] ColvarsOptionsTest.OutputNoDefaultValuesWhenInactive 20: [ OK ] ColvarsOptionsTest.OutputNoDefaultValuesWhenInactive (0 ms) 20: [ RUN ] ColvarsOptionsTest.OutputDefaultValuesWhenActive 20: [ OK ] ColvarsOptionsTest.OutputDefaultValuesWhenActive (1 ms) 20: [ RUN ] ColvarsOptionsTest.OutputValuesWhenActive 20: [ OK ] ColvarsOptionsTest.OutputValuesWhenActive (0 ms) 20: [ RUN ] ColvarsOptionsTest.OptionSetsActive 20: [ OK ] ColvarsOptionsTest.OptionSetsActive (0 ms) 20: [ RUN ] ColvarsOptionsTest.InternalsToKvtAndBack 20: 20: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsOptionsTest_InternalsToKvtAndBack_4water.mdp]: 20: For a correct single-point energy evaluation with nsteps = 0, use 20: continuation = yes to avoid constraining the input coordinates. 20: 20: Generating 1-4 interactions: fudge = 0.5 20: Number of degrees of freedom in T-Coupling group rest is 21.00 20: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 20: 20: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsOptionsTest_InternalsToKvtAndBack_4water.mdp]: 20: NVE simulation with an initial temperature of zero: will use a Verlet 20: buffer of 10%. Check your energy drift! 20: 20: 20: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsOptionsTest_InternalsToKvtAndBack_4water.mdp]: 20: You are using a plain Coulomb cut-off, which might produce artifacts. 20: You might want to consider using PME electrostatics. 20: 20: 20: 20: There were 3 NOTEs 20: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsOptionsTest_InternalsToKvtAndBack_4water.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 20: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsOptionsTest_InternalsToKvtAndBack_4water.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 20: Setting the LD random seed to -526817 20: 20: Generated 10 of the 10 non-bonded parameter combinations 20: 20: Generated 10 of the 10 1-4 parameter combinations 20: 20: Excluding 2 bonded neighbours molecule type 'SOL' 20: 20: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/4water.gro', all velocities are zero 20: Analysing residue names: 20: There are: 4 Water residues 20: 20: This run will generate roughly 0 Mb of data 20: [ OK ] ColvarsOptionsTest.InternalsToKvtAndBack (44 ms) 20: [ RUN ] ColvarsOptionsTest.RetrieveEdrFilename 20: [ OK ] ColvarsOptionsTest.RetrieveEdrFilename (0 ms) 20: [----------] 6 tests from ColvarsOptionsTest (48 ms total) 20: 20: [----------] 4 tests from ColvarsPreProcessorTest 20: [ RUN ] ColvarsPreProcessorTest.CanConstructColvarsPreProcess 20: 20: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsPreProcessorTest_CanConstructColvarsPreProcess_4water.mdp]: 20: For a correct single-point energy evaluation with nsteps = 0, use 20: continuation = yes to avoid constraining the input coordinates. 20: 20: Generating 1-4 interactions: fudge = 0.5 20: Number of degrees of freedom in T-Coupling group rest is 21.00 20: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 20: 20: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsPreProcessorTest_CanConstructColvarsPreProcess_4water.mdp]: 20: NVE simulation with an initial temperature of zero: will use a Verlet 20: buffer of 10%. Check your energy drift! 20: 20: 20: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsPreProcessorTest_CanConstructColvarsPreProcess_4water.mdp]: 20: You are using a plain Coulomb cut-off, which might produce artifacts. 20: You might want to consider using PME electrostatics. 20: 20: 20: 20: There were 3 NOTEs 20: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsPreProcessorTest_CanConstructColvarsPreProcess_4water.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 20: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsPreProcessorTest_CanConstructColvarsPreProcess_4water.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 20: Setting the LD random seed to 2147480279 20: 20: Generated 10 of the 10 non-bonded parameter combinations 20: 20: Generated 10 of the 10 1-4 parameter combinations 20: 20: Excluding 2 bonded neighbours molecule type 'SOL' 20: 20: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/4water.gro', all velocities are zero 20: Analysing residue names: 20: There are: 4 Water residues 20: 20: This run will generate roughly 0 Mb of data 20: [ OK ] ColvarsPreProcessorTest.CanConstructColvarsPreProcess (34 ms) 20: [ RUN ] ColvarsPreProcessorTest.CheckValuesFourWaters 20: 20: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsPreProcessorTest_CheckValuesFourWaters_4water.mdp]: 20: For a correct single-point energy evaluation with nsteps = 0, use 20: continuation = yes to avoid constraining the input coordinates. 20: 20: Generating 1-4 interactions: fudge = 0.5 20: Number of degrees of freedom in T-Coupling group rest is 21.00 20: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 20: 20: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsPreProcessorTest_CheckValuesFourWaters_4water.mdp]: 20: NVE simulation with an initial temperature of zero: will use a Verlet 20: buffer of 10%. Check your energy drift! 20: 20: 20: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsPreProcessorTest_CheckValuesFourWaters_4water.mdp]: 20: You are using a plain Coulomb cut-off, which might produce artifacts. 20: You might want to consider using PME electrostatics. 20: 20: 20: 20: There were 3 NOTEs 20: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsPreProcessorTest_CheckValuesFourWaters_4water.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 20: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsPreProcessorTest_CheckValuesFourWaters_4water.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 20: Setting the LD random seed to -71958663 20: 20: Generated 10 of the 10 non-bonded parameter combinations 20: 20: Generated 10 of the 10 1-4 parameter combinations 20: 20: Excluding 2 bonded neighbours molecule type 'SOL' 20: 20: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/4water.gro', all velocities are zero 20: Analysing residue names: 20: There are: 4 Water residues 20: 20: This run will generate roughly 0 Mb of data 20: [ OK ] ColvarsPreProcessorTest.CheckValuesFourWaters (42 ms) 20: [ RUN ] ColvarsPreProcessorTest.CheckNestedInputFiles 20: 20: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsPreProcessorTest_CheckNestedInputFiles_4water.mdp]: 20: For a correct single-point energy evaluation with nsteps = 0, use 20: continuation = yes to avoid constraining the input coordinates. 20: 20: Generating 1-4 interactions: fudge = 0.5 20: Number of degrees of freedom in T-Coupling group rest is 21.00 20: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 20: 20: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsPreProcessorTest_CheckNestedInputFiles_4water.mdp]: 20: NVE simulation with an initial temperature of zero: will use a Verlet 20: buffer of 10%. Check your energy drift! 20: 20: 20: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsPreProcessorTest_CheckNestedInputFiles_4water.mdp]: 20: You are using a plain Coulomb cut-off, which might produce artifacts. 20: You might want to consider using PME electrostatics. 20: 20: 20: 20: There were 3 NOTEs 20: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsPreProcessorTest_CheckNestedInputFiles_4water.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 20: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsPreProcessorTest_CheckNestedInputFiles_4water.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 20: Setting the LD random seed to -1612742917 20: 20: Generated 10 of the 10 non-bonded parameter combinations 20: 20: Generated 10 of the 10 1-4 parameter combinations 20: 20: Excluding 2 bonded neighbours molecule type 'SOL' 20: 20: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/4water.gro', all velocities are zero 20: Analysing residue names: 20: There are: 4 Water residues 20: 20: This run will generate roughly 0 Mb of data 20: [ OK ] ColvarsPreProcessorTest.CheckNestedInputFiles (41 ms) 20: [ RUN ] ColvarsPreProcessorTest.WrongColvarsInput 20: 20: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsPreProcessorTest_WrongColvarsInput_4water.mdp]: 20: For a correct single-point energy evaluation with nsteps = 0, use 20: continuation = yes to avoid constraining the input coordinates. 20: 20: Generating 1-4 interactions: fudge = 0.5 20: Number of degrees of freedom in T-Coupling group rest is 21.00 20: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 20: 20: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsPreProcessorTest_WrongColvarsInput_4water.mdp]: 20: NVE simulation with an initial temperature of zero: will use a Verlet 20: buffer of 10%. Check your energy drift! 20: 20: 20: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsPreProcessorTest_WrongColvarsInput_4water.mdp]: 20: You are using a plain Coulomb cut-off, which might produce artifacts. 20: You might want to consider using PME electrostatics. 20: 20: 20: 20: There were 3 NOTEs 20: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsPreProcessorTest_WrongColvarsInput_4water.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 20: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsPreProcessorTest_WrongColvarsInput_4water.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 20: Setting the LD random seed to -143788549 20: 20: Generated 10 of the 10 non-bonded parameter combinations 20: 20: Generated 10 of the 10 1-4 parameter combinations 20: 20: Excluding 2 bonded neighbours molecule type 'SOL' 20: 20: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/4water.gro', all velocities are zero 20: Analysing residue names: 20: There are: 4 Water residues 20: 20: This run will generate roughly 0 Mb of data 20: [ OK ] ColvarsPreProcessorTest.WrongColvarsInput (37 ms) 20: [----------] 4 tests from ColvarsPreProcessorTest (156 ms total) 20: 20: [----------] 5 tests from ColvarsForceProviderTest 20: [ RUN ] ColvarsForceProviderTest.CanConstructOrNot 20: [ OK ] ColvarsForceProviderTest.CanConstructOrNot (3 ms) 20: [ RUN ] ColvarsForceProviderTest.SimpleInputs 20: 20: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsForceProviderTest_SimpleInputs_4water.mdp]: 20: For a correct single-point energy evaluation with nsteps = 0, use 20: continuation = yes to avoid constraining the input coordinates. 20: 20: Generating 1-4 interactions: fudge = 0.5 20: Number of degrees of freedom in T-Coupling group rest is 21.00 20: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 20: 20: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsForceProviderTest_SimpleInputs_4water.mdp]: 20: NVE simulation with an initial temperature of zero: will use a Verlet 20: buffer of 10%. Check your energy drift! 20: 20: 20: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsForceProviderTest_SimpleInputs_4water.mdp]: 20: You are using a plain Coulomb cut-off, which might produce artifacts. 20: You might want to consider using PME electrostatics. 20: 20: 20: 20: There were 3 NOTEs 20: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsForceProviderTest_SimpleInputs_4water.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 20: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsForceProviderTest_SimpleInputs_4water.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 20: Setting the LD random seed to -635507713 20: 20: Generated 10 of the 10 non-bonded parameter combinations 20: 20: Generated 10 of the 10 1-4 parameter combinations 20: 20: Excluding 2 bonded neighbours molecule type 'SOL' 20: 20: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/4water.gro', all velocities are zero 20: Analysing residue names: 20: There are: 4 Water residues 20: 20: This run will generate roughly 0 Mb of data 20: [ OK ] ColvarsForceProviderTest.SimpleInputs (37 ms) 20: [ RUN ] ColvarsForceProviderTest.WrongColvarsInput 20: 20: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsForceProviderTest_WrongColvarsInput_4water.mdp]: 20: For a correct single-point energy evaluation with nsteps = 0, use 20: continuation = yes to avoid constraining the input coordinates. 20: 20: Generating 1-4 interactions: fudge = 0.5 20: Number of degrees of freedom in T-Coupling group rest is 21.00 20: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 20: 20: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsForceProviderTest_WrongColvarsInput_4water.mdp]: 20: NVE simulation with an initial temperature of zero: will use a Verlet 20: buffer of 10%. Check your energy drift! 20: 20: 20: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsForceProviderTest_WrongColvarsInput_4water.mdp]: 20: You are using a plain Coulomb cut-off, which might produce artifacts. 20: You might want to consider using PME electrostatics. 20: 20: 20: 20: There were 3 NOTEs 20: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsForceProviderTest_WrongColvarsInput_4water.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 20: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsForceProviderTest_WrongColvarsInput_4water.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 20: Setting the LD random seed to -536977995 20: 20: Generated 10 of the 10 non-bonded parameter combinations 20: 20: Generated 10 of the 10 1-4 parameter combinations 20: 20: Excluding 2 bonded neighbours molecule type 'SOL' 20: 20: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/4water.gro', all velocities are zero 20: Analysing residue names: 20: There are: 4 Water residues 20: 20: This run will generate roughly 0 Mb of data 20: [ OK ] ColvarsForceProviderTest.WrongColvarsInput (34 ms) 20: [ RUN ] ColvarsForceProviderTest.CalculateForces4water 20: 20: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsForceProviderTest_CalculateForces4water_4water.mdp]: 20: For a correct single-point energy evaluation with nsteps = 0, use 20: continuation = yes to avoid constraining the input coordinates. 20: 20: Generating 1-4 interactions: fudge = 0.5 20: Number of degrees of freedom in T-Coupling group rest is 21.00 20: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 20: 20: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsForceProviderTest_CalculateForces4water_4water.mdp]: 20: NVE simulation with an initial temperature of zero: will use a Verlet 20: buffer of 10%. Check your energy drift! 20: 20: 20: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsForceProviderTest_CalculateForces4water_4water.mdp]: 20: You are using a plain Coulomb cut-off, which might produce artifacts. 20: You might want to consider using PME electrostatics. 20: 20: 20: 20: There were 3 NOTEs 20: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsForceProviderTest_CalculateForces4water_4water.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 20: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsForceProviderTest_CalculateForces4water_4water.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 20: Setting the LD random seed to -1111566433 20: 20: Generated 10 of the 10 non-bonded parameter combinations 20: 20: Generated 10 of the 10 1-4 parameter combinations 20: 20: Excluding 2 bonded neighbours molecule type 'SOL' 20: 20: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/4water.gro', all velocities are zero 20: Analysing residue names: 20: There are: 4 Water residues 20: 20: This run will generate roughly 0 Mb of data 20: [ OK ] ColvarsForceProviderTest.CalculateForces4water (54 ms) 20: [ RUN ] ColvarsForceProviderTest.CalculateForcesAlanine 20: 20: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsForceProviderTest_CalculateForcesAlanine_ala.mdp]: 20: For a correct single-point energy evaluation with nsteps = 0, use 20: continuation = yes to avoid constraining the input coordinates. 20: 20: Generating 1-4 interactions: fudge = 0.5 20: Number of degrees of freedom in T-Coupling group rest is 66.00 20: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 20: 20: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsForceProviderTest_CalculateForcesAlanine_ala.mdp]: 20: NVE simulation: will use the initial temperature of 300.368 K for 20: determining the Verlet buffer size 20: 20: 20: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsForceProviderTest_CalculateForcesAlanine_ala.mdp]: 20: You are using a plain Coulomb cut-off, which might produce artifacts. 20: You might want to consider using PME electrostatics. 20: 20: 20: 20: There were 3 NOTEs 20: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsForceProviderTest_CalculateForcesAlanine_ala.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 20: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsForceProviderTest_CalculateForcesAlanine_ala.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 20: Setting the LD random seed to -1211251209 20: 20: Generated 2211 of the 2211 non-bonded parameter combinations 20: 20: Generated 2211 of the 2211 1-4 parameter combinations 20: 20: Excluding 3 bonded neighbours molecule type 'Protein_chain_A' 20: 20: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/ala.gro' 20: Analysing residue names: 20: There are: 2 Protein residues 20: Analysing Protein... 20: 20: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 300.368 K 20: 20: Calculated rlist for 1x1 atom pair-list as 1.048 nm, buffer size 0.048 nm 20: 20: Set rlist, assuming 4x4 atom pair-list, to 1.036 nm, buffer size 0.036 nm 20: 20: Note that mdrun will redetermine rlist based on the actual pair-list setup 20: 20: This run will generate roughly 0 Mb of data 20: [ OK ] ColvarsForceProviderTest.CalculateForcesAlanine (132 ms) 20: [----------] 5 tests from ColvarsForceProviderTest (262 ms total) 20: 20: [----------] Global test environment tear-down 20: [==========] 16 tests from 4 test suites ran. (468 ms total) 20: [ PASSED ] 16 tests. 20/92 Test #20: ColvarsAppliedForcesUnitTest .............. Passed 0.56 sec test 21 Start 21: PlumedAppliedForcesUnitTests 21: Test command: /build/reproducible-path/gromacs-2025.1/build/basic-dp/bin/plumed_applied_forces-test "--gtest_output=xml:/build/reproducible-path/gromacs-2025.1/build/basic-dp/Testing/Temporary/PlumedAppliedForcesUnitTests.xml" 21: Working Directory: /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/applied_forces/plumed/tests 21: Test timeout computed to be: 30 21: [==========] Running 8 tests from 1 test suite. 21: [----------] Global test environment set-up. 21: [----------] 8 tests from PlumedOptionsTest 21: [ RUN ] PlumedOptionsTest.defaultConstructor 21: [ OK ] PlumedOptionsTest.defaultConstructor (0 ms) 21: [ RUN ] PlumedOptionsTest.setTimeStep 21: [ OK ] PlumedOptionsTest.setTimeStep (0 ms) 21: [ RUN ] PlumedOptionsTest.setStartingBehavior 21: [ OK ] PlumedOptionsTest.setStartingBehavior (0 ms) 21: [ RUN ] PlumedOptionsTest.setPlumedFile 21: [ OK ] PlumedOptionsTest.setPlumedFile (0 ms) 21: [ RUN ] PlumedOptionsTest.setPlumedFileNotSet 21: [ OK ] PlumedOptionsTest.setPlumedFileNotSet (0 ms) 21: [ RUN ] PlumedOptionsTest.setEnsembleTemperature_data 21: [ OK ] PlumedOptionsTest.setEnsembleTemperature_data (0 ms) 21: [ RUN ] PlumedOptionsTest.setEnsembleTemperature_notConstant 21: [ OK ] PlumedOptionsTest.setEnsembleTemperature_notConstant (0 ms) 21: [ RUN ] PlumedOptionsTest.setTopology 21: 21: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/applied_forces/plumed/tests/Testing/Temporary/PlumedOptionsTest_setTopology_4water.mdp]: 21: For a correct single-point energy evaluation with nsteps = 0, use 21: continuation = yes to avoid constraining the input coordinates. 21: 21: Generating 1-4 interactions: fudge = 0.5 21: Number of degrees of freedom in T-Coupling group rest is 21.00 21: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 21: 21: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/applied_forces/plumed/tests/Testing/Temporary/PlumedOptionsTest_setTopology_4water.mdp]: 21: NVE simulation with an initial temperature of zero: will use a Verlet 21: buffer of 10%. Check your energy drift! 21: 21: 21: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/applied_forces/plumed/tests/Testing/Temporary/PlumedOptionsTest_setTopology_4water.mdp]: 21: You are using a plain Coulomb cut-off, which might produce artifacts. 21: You might want to consider using PME electrostatics. 21: 21: 21: 21: There were 3 NOTEs 21: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/applied_forces/plumed/tests/Testing/Temporary/PlumedOptionsTest_setTopology_4water.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 21: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/applied_forces/plumed/tests/Testing/Temporary/PlumedOptionsTest_setTopology_4water.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 21: 21: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/applied_forces/plumed/tests/Testing/Temporary/PlumedOptionsTest_setTopology_angles1.mdp]: 21: For a correct single-point energy evaluation with nsteps = 0, use 21: continuation = yes to avoid constraining the input coordinates. 21: 21: 21: NOTE 2 [file angles1.top, line 72]: 21: In moleculetype 'butane' 4 atoms are not bound by a potential or 21: constraint to any other atom in the same moleculetype. Although 21: technically this might not cause issues in a simulation, this often means 21: that the user forgot to add a bond/potential/constraint or put multiple 21: molecules in the same moleculetype definition by mistake. Run with -v to 21: get information for each atom. 21: 21: Number of degrees of freedom in T-Coupling group rest is 9.00 21: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 21: 21: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/applied_forces/plumed/tests/Testing/Temporary/PlumedOptionsTest_setTopology_angles1.mdp]: 21: NVE simulation: will use the initial temperature of 238.919 K for 21: determining the Verlet buffer size 21: 21: 21: There were 3 NOTEs 21: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/applied_forces/plumed/tests/Testing/Temporary/PlumedOptionsTest_setTopology_angles1.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 21: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/applied_forces/plumed/tests/Testing/Temporary/PlumedOptionsTest_setTopology_angles1.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 21: 21: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/applied_forces/plumed/tests/Testing/Temporary/PlumedOptionsTest_setTopology_argon5832.mdp]: 21: For a correct single-point energy evaluation with nsteps = 0, use 21: continuation = yes to avoid constraining the input coordinates. 21: 21: Number of degrees of freedom in T-Coupling group rest is 17493.00 21: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 21: 21: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/applied_forces/plumed/tests/Testing/Temporary/PlumedOptionsTest_setTopology_argon5832.mdp]: 21: NVE simulation: will use the initial temperature of 67.983 K for 21: determining the Verlet buffer size 21: 21: 21: There were 2 NOTEs 21: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/applied_forces/plumed/tests/Testing/Temporary/PlumedOptionsTest_setTopology_argon5832.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 21: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/applied_forces/plumed/tests/Testing/Temporary/PlumedOptionsTest_setTopology_argon5832.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 21: 21: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/applied_forces/plumed/tests/Testing/Temporary/PlumedOptionsTest_setTopology_argon4.mdp]: 21: For a correct single-point energy evaluation with nsteps = 0, use 21: continuation = yes to avoid constraining the input coordinates. 21: 21: Number of degrees of freedom in T-Coupling group rest is 9.00 21: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 21: 21: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/applied_forces/plumed/tests/Testing/Temporary/PlumedOptionsTest_setTopology_argon4.mdp]: 21: NVE simulation with an initial temperature of zero: will use a Verlet 21: buffer of 10%. Check your energy drift! 21: 21: 21: There were 2 NOTEs 21: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/applied_forces/plumed/tests/Testing/Temporary/PlumedOptionsTest_setTopology_argon4.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 21: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/applied_forces/plumed/tests/Testing/Temporary/PlumedOptionsTest_setTopology_argon4.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 21: 21: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/applied_forces/plumed/tests/Testing/Temporary/PlumedOptionsTest_setTopology_dipoles.mdp]: 21: For a correct single-point energy evaluation with nsteps = 0, use 21: continuation = yes to avoid constraining the input coordinates. 21: 21: Number of degrees of freedom in T-Coupling group rest is 9.00 21: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 21: 21: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/applied_forces/plumed/tests/Testing/Temporary/PlumedOptionsTest_setTopology_dipoles.mdp]: 21: NVE simulation with an initial temperature of zero: will use a Verlet 21: buffer of 10%. Check your energy drift! 21: 21: 21: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/applied_forces/plumed/tests/Testing/Temporary/PlumedOptionsTest_setTopology_dipoles.mdp]: 21: You are using a plain Coulomb cut-off, which might produce artifacts. 21: You might want to consider using PME electrostatics. 21: 21: 21: 21: There were 3 NOTEs 21: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/applied_forces/plumed/tests/Testing/Temporary/PlumedOptionsTest_setTopology_dipoles.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 21: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/applied_forces/plumed/tests/Testing/Temporary/PlumedOptionsTest_setTopology_dipoles.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 21: 21: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/applied_forces/plumed/tests/Testing/Temporary/PlumedOptionsTest_setTopology_spc_and_methane.mdp]: 21: For a correct single-point energy evaluation with nsteps = 0, use 21: continuation = yes to avoid constraining the input coordinates. 21: 21: Generating 1-4 interactions: fudge = 0.5 21: Number of degrees of freedom in T-Coupling group rest is 18.00 21: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 21: 21: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/applied_forces/plumed/tests/Testing/Temporary/PlumedOptionsTest_setTopology_spc_and_methane.mdp]: 21: NVE simulation: will use the initial temperature of 135.187 K for 21: determining the Verlet buffer size 21: 21: 21: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/applied_forces/plumed/tests/Testing/Temporary/PlumedOptionsTest_setTopology_spc_and_methane.mdp]: 21: You are using a plain Coulomb cut-off, which might produce artifacts. 21: You might want to consider using PME electrostatics. 21: 21: 21: 21: There were 3 NOTEs 21: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/applied_forces/plumed/tests/Testing/Temporary/PlumedOptionsTest_setTopology_spc_and_methane.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 21: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/applied_forces/plumed/tests/Testing/Temporary/PlumedOptionsTest_setTopology_spc_and_methane.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 21: Setting the LD random seed to -274745377 21: 21: Generated 10 of the 10 non-bonded parameter combinations 21: 21: Generated 10 of the 10 1-4 parameter combinations 21: 21: Excluding 2 bonded neighbours molecule type 'SOL' 21: 21: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/4water.gro', all velocities are zero 21: Analysing residue names: 21: There are: 4 Water residues 21: 21: This run will generate roughly 0 Mb of data 21: Setting the LD random seed to -173057 21: 21: Generated 3 of the 3 non-bonded parameter combinations 21: 21: Excluding 3 bonded neighbours molecule type 'butane' 21: 21: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/angles1.gro' 21: Analysing residue names: 21: There are: 1 Other residues 21: Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups... 21: 21: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 238.919 K 21: 21: Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm 21: 21: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm 21: 21: Note that mdrun will redetermine rlist based on the actual pair-list setup 21: 21: This run will generate roughly 0 Mb of data 21: Setting the LD random seed to -592291 21: 21: Generated 1 of the 1 non-bonded parameter combinations 21: 21: Excluding 1 bonded neighbours molecule type 'Argon' 21: 21: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon5832.gro' 21: Analysing residue names: 21: There are: 5832 Other residues 21: Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups... 21: 21: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 67.9831 K 21: 21: Calculated rlist for 1x1 atom pair-list as 1.001 nm, buffer size 0.001 nm 21: 21: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm 21: 21: Note that mdrun will redetermine rlist based on the actual pair-list setup 21: 21: This run will generate roughly 0 Mb of data 21: Setting the LD random seed to -176984582 21: 21: Generated 1 of the 1 non-bonded parameter combinations 21: 21: Excluding 1 bonded neighbours molecule type 'ArgonA' 21: 21: Excluding 1 bonded neighbours molecule type 'ArgonB' 21: 21: Excluding 1 bonded neighbours molecule type 'ArgonC' 21: 21: Excluding 1 bonded neighbours molecule type 'ArgonD' 21: 21: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon4.gro', all velocities are zero 21: Analysing residue names: 21: There are: 4 Other residues 21: Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups... 21: 21: This run will generate roughly 0 Mb of data 21: Setting the LD random seed to -117972997 21: 21: Generated 1 of the 1 non-bonded parameter combinations 21: 21: Excluding 1 bonded neighbours molecule type 'Dipole' 21: 21: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/dipoles.gro', all velocities are zero 21: Analysing residue names: 21: There are: 2 Other residues 21: Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups... 21: 21: This run will generate roughly 0 Mb of data 21: Setting the LD random seed to -12649505 21: 21: Generated 331705 of the 331705 non-bonded parameter combinations 21: 21: Generated 331705 of the 331705 1-4 parameter combinations 21: 21: Excluding 2 bonded neighbours molecule type 'SOL' 21: 21: Excluding 3 bonded neighbours molecule type 'methane' 21: 21: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/spc_and_methane.gro' 21: Analysing residue names: 21: There are: 1 Water residues 21: There are: 1 Other residues 21: Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups... 21: 21: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 135.187 K 21: 21: Calculated rlist for 1x1 atom pair-list as 1.020 nm, buffer size 0.020 nm 21: 21: Set rlist, assuming 4x4 atom pair-list, to 1.013 nm, buffer size 0.013 nm 21: 21: Note that mdrun will redetermine rlist based on the actual pair-list setup 21: 21: This run will generate roughly 0 Mb of data 21: [ OK ] PlumedOptionsTest.setTopology (6200 ms) 21: [----------] 8 tests from PlumedOptionsTest (6203 ms total) 21: 21: [----------] Global test environment tear-down 21: [==========] 8 tests from 1 test suite ran. (6203 ms total) 21: [ PASSED ] 8 tests. 21/92 Test #21: PlumedAppliedForcesUnitTests .............. Passed 6.30 sec test 22 Start 22: PlumedMDTests 22: Test command: /build/reproducible-path/gromacs-2025.1/build/basic-dp/bin/plumed_md-test "--gtest_output=xml:/build/reproducible-path/gromacs-2025.1/build/basic-dp/Testing/Temporary/PlumedMDTests.xml" 22: Working Directory: /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/applied_forces/plumed/tests 22: Test timeout computed to be: 600 22: [==========] Running 2 tests from 1 test suite. 22: [----------] Global test environment set-up. 22: [----------] 2 tests from SimplePlumedMD/PlumedRun 22: [ RUN ] SimplePlumedMD/PlumedRun.PlumedSees/0 22: ./src/gromacs/applied_forces/plumed/tests/plumed_md_test.cpp:92: Skipped 22: The GMX_TEST_PLUMED_KERNEL_IS_AVAILABLE environment variable is not set, and the PLUMED kernel was not found. 22: [ SKIPPED ] SimplePlumedMD/PlumedRun.PlumedSees/0 (0 ms) 22: [ RUN ] SimplePlumedMD/PlumedRun.PlumedDoes/0 22: ./src/gromacs/applied_forces/plumed/tests/plumed_md_test.cpp:92: Skipped 22: The GMX_TEST_PLUMED_KERNEL_IS_AVAILABLE environment variable is not set, and the PLUMED kernel was not found. 22: [ SKIPPED ] SimplePlumedMD/PlumedRun.PlumedDoes/0 (0 ms) 22: [----------] 2 tests from SimplePlumedMD/PlumedRun (1 ms total) 22: 22: [----------] Global test environment tear-down 22: [==========] 2 tests from 1 test suite ran. (53 ms total) 22: [ PASSED ] 0 tests. 22: [ SKIPPED ] 2 tests, listed below: 22: [ SKIPPED ] SimplePlumedMD/PlumedRun.PlumedSees/0 22: [ SKIPPED ] SimplePlumedMD/PlumedRun.PlumedDoes/0 22/92 Test #22: PlumedMDTests ............................. Passed 0.13 sec test 23 Start 23: NNPotAppliedForcesUnitTest 23: Test command: /build/reproducible-path/gromacs-2025.1/build/basic-dp/bin/nnpot_applied_forces-test "--gtest_output=xml:/build/reproducible-path/gromacs-2025.1/build/basic-dp/Testing/Temporary/NNPotAppliedForcesUnitTest.xml" 23: Working Directory: /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/applied_forces/nnpot/tests 23: Test timeout computed to be: 30 23: [==========] Running 12 tests from 4 test suites. 23: [----------] Global test environment set-up. 23: [----------] 1 test from NNPotTest 23: [ RUN ] NNPotTest.ForceProviderLackingInputThrows 23: [ OK ] NNPotTest.ForceProviderLackingInputThrows (0 ms) 23: [----------] 1 test from NNPotTest (1 ms total) 23: 23: [----------] 5 tests from NNPotOptionsTest 23: [ RUN ] NNPotOptionsTest.DefaultParameters 23: [ OK ] NNPotOptionsTest.DefaultParameters (0 ms) 23: [ RUN ] NNPotOptionsTest.OptionSetsActive 23: [ OK ] NNPotOptionsTest.OptionSetsActive (0 ms) 23: [ RUN ] NNPotOptionsTest.OutputNoDefaultValuesWhenInactive 23: [ OK ] NNPotOptionsTest.OutputNoDefaultValuesWhenInactive (0 ms) 23: [ RUN ] NNPotOptionsTest.OutputDefaultValuesWhenActive 23: [ OK ] NNPotOptionsTest.OutputDefaultValuesWhenActive (0 ms) 23: [ RUN ] NNPotOptionsTest.InternalsToKvtAndBack 23: [ OK ] NNPotOptionsTest.InternalsToKvtAndBack (0 ms) 23: [----------] 5 tests from NNPotOptionsTest (3 ms total) 23: 23: [----------] 5 tests from NNPotTopologyPreprocessorTest 23: [ RUN ] NNPotTopologyPreprocessorTest.CanConstruct 23: [ OK ] NNPotTopologyPreprocessorTest.CanConstruct (0 ms) 23: [ RUN ] NNPotTopologyPreprocessorTest.FourWatersFirstInQMRegion 23: 23: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/applied_forces/nnpot/tests/Testing/Temporary/NNPotTopologyPreprocessorTest_FourWatersFirstInQMRegion_4water.mdp]: 23: For a correct single-point energy evaluation with nsteps = 0, use 23: continuation = yes to avoid constraining the input coordinates. 23: 23: Generating 1-4 interactions: fudge = 0.5 23: Number of degrees of freedom in T-Coupling group rest is 21.00 23: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 23: 23: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/applied_forces/nnpot/tests/Testing/Temporary/NNPotTopologyPreprocessorTest_FourWatersFirstInQMRegion_4water.mdp]: 23: NVE simulation with an initial temperature of zero: will use a Verlet 23: buffer of 10%. Check your energy drift! 23: 23: 23: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/applied_forces/nnpot/tests/Testing/Temporary/NNPotTopologyPreprocessorTest_FourWatersFirstInQMRegion_4water.mdp]: 23: You are using a plain Coulomb cut-off, which might produce artifacts. 23: You might want to consider using PME electrostatics. 23: 23: 23: 23: There were 3 NOTEs 23: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/applied_forces/nnpot/tests/Testing/Temporary/NNPotTopologyPreprocessorTest_FourWatersFirstInQMRegion_4water.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 23: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/applied_forces/nnpot/tests/Testing/Temporary/NNPotTopologyPreprocessorTest_FourWatersFirstInQMRegion_4water.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 23: Setting the LD random seed to -708870753 23: 23: Generated 10 of the 10 non-bonded parameter combinations 23: 23: Generated 10 of the 10 1-4 parameter combinations 23: 23: Excluding 2 bonded neighbours molecule type 'SOL' 23: 23: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/4water.gro', all velocities are zero 23: Analysing residue names: 23: There are: 4 Water residues 23: 23: This run will generate roughly 0 Mb of data 23: [ OK ] NNPotTopologyPreprocessorTest.FourWatersFirstInQMRegion (33 ms) 23: [ RUN ] NNPotTopologyPreprocessorTest.FourWatersSecondAndFourthInQMRegion 23: 23: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/applied_forces/nnpot/tests/Testing/Temporary/NNPotTopologyPreprocessorTest_FourWatersSecondAndFourthInQMRegion_4water.mdp]: 23: For a correct single-point energy evaluation with nsteps = 0, use 23: continuation = yes to avoid constraining the input coordinates. 23: 23: Generating 1-4 interactions: fudge = 0.5 23: Number of degrees of freedom in T-Coupling group rest is 21.00 23: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 23: 23: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/applied_forces/nnpot/tests/Testing/Temporary/NNPotTopologyPreprocessorTest_FourWatersSecondAndFourthInQMRegion_4water.mdp]: 23: NVE simulation with an initial temperature of zero: will use a Verlet 23: buffer of 10%. Check your energy drift! 23: 23: 23: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/applied_forces/nnpot/tests/Testing/Temporary/NNPotTopologyPreprocessorTest_FourWatersSecondAndFourthInQMRegion_4water.mdp]: 23: You are using a plain Coulomb cut-off, which might produce artifacts. 23: You might want to consider using PME electrostatics. 23: 23: 23: 23: There were 3 NOTEs 23: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/applied_forces/nnpot/tests/Testing/Temporary/NNPotTopologyPreprocessorTest_FourWatersSecondAndFourthInQMRegion_4water.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 23: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/applied_forces/nnpot/tests/Testing/Temporary/NNPotTopologyPreprocessorTest_FourWatersSecondAndFourthInQMRegion_4water.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 23: Setting the LD random seed to -1645490817 23: 23: Generated 10 of the 10 non-bonded parameter combinations 23: 23: Generated 10 of the 10 1-4 parameter combinations 23: 23: Excluding 2 bonded neighbours molecule type 'SOL' 23: 23: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/4water.gro', all velocities are zero 23: Analysing residue names: 23: There are: 4 Water residues 23: 23: This run will generate roughly 0 Mb of data 23: [ OK ] NNPotTopologyPreprocessorTest.FourWatersSecondAndFourthInQMRegion (32 ms) 23: [ RUN ] NNPotTopologyPreprocessorTest.AlanineDipeptideWithLinkAtomsNoConstraints 23: 23: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/applied_forces/nnpot/tests/Testing/Temporary/NNPotTopologyPreprocessorTest_AlanineDipeptideWithLinkAtomsNoConstraints_alanine_vacuo.mdp]: 23: For a correct single-point energy evaluation with nsteps = 0, use 23: continuation = yes to avoid constraining the input coordinates. 23: 23: Generating 1-4 interactions: fudge = 0.5 23: Number of degrees of freedom in T-Coupling group rest is 63.00 23: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 23: 23: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/applied_forces/nnpot/tests/Testing/Temporary/NNPotTopologyPreprocessorTest_AlanineDipeptideWithLinkAtomsNoConstraints_alanine_vacuo.mdp]: 23: NVE simulation: will use the initial temperature of 129.093 K for 23: determining the Verlet buffer size 23: 23: 23: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/applied_forces/nnpot/tests/Testing/Temporary/NNPotTopologyPreprocessorTest_AlanineDipeptideWithLinkAtomsNoConstraints_alanine_vacuo.mdp]: 23: You are using a plain Coulomb cut-off, which might produce artifacts. 23: You might want to consider using PME electrostatics. 23: 23: 23: 23: There were 3 NOTEs 23: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/applied_forces/nnpot/tests/Testing/Temporary/NNPotTopologyPreprocessorTest_AlanineDipeptideWithLinkAtomsNoConstraints_alanine_vacuo.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 23: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/applied_forces/nnpot/tests/Testing/Temporary/NNPotTopologyPreprocessorTest_AlanineDipeptideWithLinkAtomsNoConstraints_alanine_vacuo.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 23: Setting the LD random seed to -221790257 23: 23: Generated 2145 of the 2145 non-bonded parameter combinations 23: 23: Generated 2145 of the 2145 1-4 parameter combinations 23: 23: Excluding 3 bonded neighbours molecule type 'ALANINEDIPEPTIDE' 23: 23: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/alanine_vacuo.gro' 23: Analysing residue names: 23: There are: 3 Protein residues 23: Analysing Protein... 23: 23: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 129.093 K 23: 23: Calculated rlist for 1x1 atom pair-list as 1.021 nm, buffer size 0.021 nm 23: 23: Set rlist, assuming 4x4 atom pair-list, to 1.013 nm, buffer size 0.013 nm 23: 23: Note that mdrun will redetermine rlist based on the actual pair-list setup 23: 23: This run will generate roughly 0 Mb of data 23: [ OK ] NNPotTopologyPreprocessorTest.AlanineDipeptideWithLinkAtomsNoConstraints (101 ms) 23: [ RUN ] NNPotTopologyPreprocessorTest.AlanineDipeptideWithLinkAtomsWithConstraints 23: 23: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/applied_forces/nnpot/tests/Testing/Temporary/NNPotTopologyPreprocessorTest_AlanineDipeptideWithLinkAtomsWithConstraints_alanine_vacuo.mdp]: 23: For a correct single-point energy evaluation with nsteps = 0, use 23: continuation = yes to avoid constraining the input coordinates. 23: 23: Generating 1-4 interactions: fudge = 0.5 23: 23: NOTE 2 [file unknown]: 23: You are using constraints on all bonds, whereas the forcefield has been 23: parametrized only with constraints involving hydrogen atoms. We suggest 23: using constraints = h-bonds instead, this will also improve performance. 23: 23: 23: NOTE 3 [file unknown]: 23: For energy conservation with LINCS, lincs_iter should be 2 or larger. 23: 23: 23: Number of degrees of freedom in T-Coupling group rest is 42.00 23: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 23: 23: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/applied_forces/nnpot/tests/Testing/Temporary/NNPotTopologyPreprocessorTest_AlanineDipeptideWithLinkAtomsWithConstraints_alanine_vacuo.mdp]: 23: NVE simulation: will use the initial temperature of 193.640 K for 23: determining the Verlet buffer size 23: 23: 23: NOTE 5 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/applied_forces/nnpot/tests/Testing/Temporary/NNPotTopologyPreprocessorTest_AlanineDipeptideWithLinkAtomsWithConstraints_alanine_vacuo.mdp]: 23: You are using a plain Coulomb cut-off, which might produce artifacts. 23: You might want to consider using PME electrostatics. 23: 23: 23: 23: There were 5 NOTEs 23: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/applied_forces/nnpot/tests/Testing/Temporary/NNPotTopologyPreprocessorTest_AlanineDipeptideWithLinkAtomsWithConstraints_alanine_vacuo.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 23: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/applied_forces/nnpot/tests/Testing/Temporary/NNPotTopologyPreprocessorTest_AlanineDipeptideWithLinkAtomsWithConstraints_alanine_vacuo.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 23: Setting the LD random seed to -1216913413 23: 23: Generated 2145 of the 2145 non-bonded parameter combinations 23: 23: Generated 2145 of the 2145 1-4 parameter combinations 23: 23: Excluding 3 bonded neighbours molecule type 'ALANINEDIPEPTIDE' 23: 23: turning all bonds into constraints... 23: 23: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/alanine_vacuo.gro' 23: Analysing residue names: 23: There are: 3 Protein residues 23: Analysing Protein... 23: 23: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 193.64 K 23: 23: Calculated rlist for 1x1 atom pair-list as 1.023 nm, buffer size 0.023 nm 23: 23: Set rlist, assuming 4x4 atom pair-list, to 1.015 nm, buffer size 0.015 nm 23: 23: Note that mdrun will redetermine rlist based on the actual pair-list setup 23: 23: This run will generate roughly 0 Mb of data 23: [ OK ] NNPotTopologyPreprocessorTest.AlanineDipeptideWithLinkAtomsWithConstraints (114 ms) 23: [----------] 5 tests from NNPotTopologyPreprocessorTest (283 ms total) 23: 23: [----------] 1 test from NNPotForceProviderTest 23: [ RUN ] NNPotForceProviderTest.CanConstruct 23: [ OK ] NNPotForceProviderTest.CanConstruct (0 ms) 23: [----------] 1 test from NNPotForceProviderTest (0 ms total) 23: 23: [----------] Global test environment tear-down 23: [==========] 12 tests from 4 test suites ran. (288 ms total) 23: [ PASSED ] 12 tests. 23/92 Test #23: NNPotAppliedForcesUnitTest ................ Passed 0.42 sec test 24 Start 24: AppliedForcesUnitTest 24: Test command: /build/reproducible-path/gromacs-2025.1/build/basic-dp/bin/applied_forces-test "--gtest_output=xml:/build/reproducible-path/gromacs-2025.1/build/basic-dp/Testing/Temporary/AppliedForcesUnitTest.xml" 24: Working Directory: /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/applied_forces/tests 24: Test timeout computed to be: 30 24: [==========] Running 3 tests from 1 test suite. 24: [----------] Global test environment set-up. 24: [----------] 3 tests from ElectricFieldTest 24: [ RUN ] ElectricFieldTest.Static 24: [ OK ] ElectricFieldTest.Static (0 ms) 24: [ RUN ] ElectricFieldTest.Oscillating 24: [ OK ] ElectricFieldTest.Oscillating (0 ms) 24: [ RUN ] ElectricFieldTest.Pulsed 24: [ OK ] ElectricFieldTest.Pulsed (0 ms) 24: [----------] 3 tests from ElectricFieldTest (1 ms total) 24: 24: [----------] Global test environment tear-down 24: [==========] 3 tests from 1 test suite ran. (1 ms total) 24: [ PASSED ] 3 tests. 24/92 Test #24: AppliedForcesUnitTest ..................... Passed 0.08 sec test 25 Start 25: ListedForcesTest 25: Test command: /build/reproducible-path/gromacs-2025.1/build/basic-dp/bin/listed_forces-test "--gtest_output=xml:/build/reproducible-path/gromacs-2025.1/build/basic-dp/Testing/Temporary/ListedForcesTest.xml" 25: Working Directory: /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/listed_forces/tests 25: Test timeout computed to be: 30 25: [==========] Running 132 tests from 9 test suites. 25: [----------] Global test environment set-up. 25: [----------] 24 tests from Bond/ListedForcesTest 25: [ RUN ] Bond/ListedForcesTest.Ifunc/0 25: [ OK ] Bond/ListedForcesTest.Ifunc/0 (1 ms) 25: [ RUN ] Bond/ListedForcesTest.Ifunc/1 25: [ OK ] Bond/ListedForcesTest.Ifunc/1 (0 ms) 25: [ RUN ] Bond/ListedForcesTest.Ifunc/2 25: [ OK ] Bond/ListedForcesTest.Ifunc/2 (0 ms) 25: [ RUN ] Bond/ListedForcesTest.Ifunc/3 25: [ OK ] Bond/ListedForcesTest.Ifunc/3 (1 ms) 25: [ RUN ] Bond/ListedForcesTest.Ifunc/4 25: [ OK ] Bond/ListedForcesTest.Ifunc/4 (1 ms) 25: [ RUN ] Bond/ListedForcesTest.Ifunc/5 25: [ OK ] Bond/ListedForcesTest.Ifunc/5 (1 ms) 25: [ RUN ] Bond/ListedForcesTest.Ifunc/6 25: [ OK ] Bond/ListedForcesTest.Ifunc/6 (0 ms) 25: [ RUN ] Bond/ListedForcesTest.Ifunc/7 25: [ OK ] Bond/ListedForcesTest.Ifunc/7 (0 ms) 25: [ RUN ] Bond/ListedForcesTest.Ifunc/8 25: [ OK ] Bond/ListedForcesTest.Ifunc/8 (0 ms) 25: [ RUN ] Bond/ListedForcesTest.Ifunc/9 25: [ OK ] Bond/ListedForcesTest.Ifunc/9 (1 ms) 25: [ RUN ] Bond/ListedForcesTest.Ifunc/10 25: [ OK ] Bond/ListedForcesTest.Ifunc/10 (1 ms) 25: [ RUN ] Bond/ListedForcesTest.Ifunc/11 25: [ OK ] Bond/ListedForcesTest.Ifunc/11 (1 ms) 25: [ RUN ] Bond/ListedForcesTest.Ifunc/12 25: [ OK ] Bond/ListedForcesTest.Ifunc/12 (0 ms) 25: [ RUN ] Bond/ListedForcesTest.Ifunc/13 25: [ OK ] Bond/ListedForcesTest.Ifunc/13 (0 ms) 25: [ RUN ] Bond/ListedForcesTest.Ifunc/14 25: [ OK ] Bond/ListedForcesTest.Ifunc/14 (0 ms) 25: [ RUN ] Bond/ListedForcesTest.Ifunc/15 25: [ OK ] Bond/ListedForcesTest.Ifunc/15 (1 ms) 25: [ RUN ] Bond/ListedForcesTest.Ifunc/16 25: [ OK ] Bond/ListedForcesTest.Ifunc/16 (1 ms) 25: [ RUN ] Bond/ListedForcesTest.Ifunc/17 25: [ OK ] Bond/ListedForcesTest.Ifunc/17 (1 ms) 25: [ RUN ] Bond/ListedForcesTest.Ifunc/18 25: [ OK ] Bond/ListedForcesTest.Ifunc/18 (0 ms) 25: [ RUN ] Bond/ListedForcesTest.Ifunc/19 25: [ OK ] Bond/ListedForcesTest.Ifunc/19 (0 ms) 25: [ RUN ] Bond/ListedForcesTest.Ifunc/20 25: [ OK ] Bond/ListedForcesTest.Ifunc/20 (0 ms) 25: [ RUN ] Bond/ListedForcesTest.Ifunc/21 25: [ OK ] Bond/ListedForcesTest.Ifunc/21 (0 ms) 25: [ RUN ] Bond/ListedForcesTest.Ifunc/22 25: [ OK ] Bond/ListedForcesTest.Ifunc/22 (0 ms) 25: [ RUN ] Bond/ListedForcesTest.Ifunc/23 25: [ OK ] Bond/ListedForcesTest.Ifunc/23 (0 ms) 25: [----------] 24 tests from Bond/ListedForcesTest (28 ms total) 25: 25: [----------] 33 tests from Angle/ListedForcesTest 25: [ RUN ] Angle/ListedForcesTest.Ifunc/0 25: [ OK ] Angle/ListedForcesTest.Ifunc/0 (0 ms) 25: [ RUN ] Angle/ListedForcesTest.Ifunc/1 25: [ OK ] Angle/ListedForcesTest.Ifunc/1 (0 ms) 25: [ RUN ] Angle/ListedForcesTest.Ifunc/2 25: [ OK ] Angle/ListedForcesTest.Ifunc/2 (0 ms) 25: [ RUN ] Angle/ListedForcesTest.Ifunc/3 25: [ OK ] Angle/ListedForcesTest.Ifunc/3 (1 ms) 25: [ RUN ] Angle/ListedForcesTest.Ifunc/4 25: [ OK ] Angle/ListedForcesTest.Ifunc/4 (1 ms) 25: [ RUN ] Angle/ListedForcesTest.Ifunc/5 25: [ OK ] Angle/ListedForcesTest.Ifunc/5 (1 ms) 25: [ RUN ] Angle/ListedForcesTest.Ifunc/6 25: [ OK ] Angle/ListedForcesTest.Ifunc/6 (0 ms) 25: [ RUN ] Angle/ListedForcesTest.Ifunc/7 25: [ OK ] Angle/ListedForcesTest.Ifunc/7 (0 ms) 25: [ RUN ] Angle/ListedForcesTest.Ifunc/8 25: [ OK ] Angle/ListedForcesTest.Ifunc/8 (0 ms) 25: [ RUN ] Angle/ListedForcesTest.Ifunc/9 25: [ OK ] Angle/ListedForcesTest.Ifunc/9 (1 ms) 25: [ RUN ] Angle/ListedForcesTest.Ifunc/10 25: [ OK ] Angle/ListedForcesTest.Ifunc/10 (1 ms) 25: [ RUN ] Angle/ListedForcesTest.Ifunc/11 25: [ OK ] Angle/ListedForcesTest.Ifunc/11 (1 ms) 25: [ RUN ] Angle/ListedForcesTest.Ifunc/12 25: [ OK ] Angle/ListedForcesTest.Ifunc/12 (0 ms) 25: [ RUN ] Angle/ListedForcesTest.Ifunc/13 25: [ OK ] Angle/ListedForcesTest.Ifunc/13 (0 ms) 25: [ RUN ] Angle/ListedForcesTest.Ifunc/14 25: [ OK ] Angle/ListedForcesTest.Ifunc/14 (0 ms) 25: [ RUN ] Angle/ListedForcesTest.Ifunc/15 25: [ OK ] Angle/ListedForcesTest.Ifunc/15 (5 ms) 25: [ RUN ] Angle/ListedForcesTest.Ifunc/16 25: [ OK ] Angle/ListedForcesTest.Ifunc/16 (1 ms) 25: [ RUN ] Angle/ListedForcesTest.Ifunc/17 25: [ OK ] Angle/ListedForcesTest.Ifunc/17 (2 ms) 25: [ RUN ] Angle/ListedForcesTest.Ifunc/18 25: [ OK ] Angle/ListedForcesTest.Ifunc/18 (0 ms) 25: [ RUN ] Angle/ListedForcesTest.Ifunc/19 25: [ OK ] Angle/ListedForcesTest.Ifunc/19 (0 ms) 25: [ RUN ] Angle/ListedForcesTest.Ifunc/20 25: [ OK ] Angle/ListedForcesTest.Ifunc/20 (0 ms) 25: [ RUN ] Angle/ListedForcesTest.Ifunc/21 25: [ OK ] Angle/ListedForcesTest.Ifunc/21 (0 ms) 25: [ RUN ] Angle/ListedForcesTest.Ifunc/22 25: [ OK ] Angle/ListedForcesTest.Ifunc/22 (0 ms) 25: [ RUN ] Angle/ListedForcesTest.Ifunc/23 25: [ OK ] Angle/ListedForcesTest.Ifunc/23 (0 ms) 25: [ RUN ] Angle/ListedForcesTest.Ifunc/24 25: [ OK ] Angle/ListedForcesTest.Ifunc/24 (0 ms) 25: [ RUN ] Angle/ListedForcesTest.Ifunc/25 25: [ OK ] Angle/ListedForcesTest.Ifunc/25 (0 ms) 25: [ RUN ] Angle/ListedForcesTest.Ifunc/26 25: [ OK ] Angle/ListedForcesTest.Ifunc/26 (0 ms) 25: [ RUN ] Angle/ListedForcesTest.Ifunc/27 25: [ OK ] Angle/ListedForcesTest.Ifunc/27 (1 ms) 25: [ RUN ] Angle/ListedForcesTest.Ifunc/28 25: [ OK ] Angle/ListedForcesTest.Ifunc/28 (1 ms) 25: [ RUN ] Angle/ListedForcesTest.Ifunc/29 25: [ OK ] Angle/ListedForcesTest.Ifunc/29 (1 ms) 25: [ RUN ] Angle/ListedForcesTest.Ifunc/30 25: [ OK ] Angle/ListedForcesTest.Ifunc/30 (1 ms) 25: [ RUN ] Angle/ListedForcesTest.Ifunc/31 25: [ OK ] Angle/ListedForcesTest.Ifunc/31 (0 ms) 25: [ RUN ] Angle/ListedForcesTest.Ifunc/32 25: [ OK ] Angle/ListedForcesTest.Ifunc/32 (0 ms) 25: [----------] 33 tests from Angle/ListedForcesTest (45 ms total) 25: 25: [----------] 18 tests from Dihedral/ListedForcesTest 25: [ RUN ] Dihedral/ListedForcesTest.Ifunc/0 25: [ OK ] Dihedral/ListedForcesTest.Ifunc/0 (1 ms) 25: [ RUN ] Dihedral/ListedForcesTest.Ifunc/1 25: [ OK ] Dihedral/ListedForcesTest.Ifunc/1 (1 ms) 25: [ RUN ] Dihedral/ListedForcesTest.Ifunc/2 25: [ OK ] Dihedral/ListedForcesTest.Ifunc/2 (1 ms) 25: [ RUN ] Dihedral/ListedForcesTest.Ifunc/3 25: [ OK ] Dihedral/ListedForcesTest.Ifunc/3 (1 ms) 25: [ RUN ] Dihedral/ListedForcesTest.Ifunc/4 25: [ OK ] Dihedral/ListedForcesTest.Ifunc/4 (0 ms) 25: [ RUN ] Dihedral/ListedForcesTest.Ifunc/5 25: [ OK ] Dihedral/ListedForcesTest.Ifunc/5 (0 ms) 25: [ RUN ] Dihedral/ListedForcesTest.Ifunc/6 25: [ OK ] Dihedral/ListedForcesTest.Ifunc/6 (0 ms) 25: [ RUN ] Dihedral/ListedForcesTest.Ifunc/7 25: [ OK ] Dihedral/ListedForcesTest.Ifunc/7 (0 ms) 25: [ RUN ] Dihedral/ListedForcesTest.Ifunc/8 25: [ OK ] Dihedral/ListedForcesTest.Ifunc/8 (0 ms) 25: [ RUN ] Dihedral/ListedForcesTest.Ifunc/9 25: [ OK ] Dihedral/ListedForcesTest.Ifunc/9 (1 ms) 25: [ RUN ] Dihedral/ListedForcesTest.Ifunc/10 25: [ OK ] Dihedral/ListedForcesTest.Ifunc/10 (1 ms) 25: [ RUN ] Dihedral/ListedForcesTest.Ifunc/11 25: [ OK ] Dihedral/ListedForcesTest.Ifunc/11 (1 ms) 25: [ RUN ] Dihedral/ListedForcesTest.Ifunc/12 25: [ OK ] Dihedral/ListedForcesTest.Ifunc/12 (1 ms) 25: [ RUN ] Dihedral/ListedForcesTest.Ifunc/13 25: [ OK ] Dihedral/ListedForcesTest.Ifunc/13 (1 ms) 25: [ RUN ] Dihedral/ListedForcesTest.Ifunc/14 25: [ OK ] Dihedral/ListedForcesTest.Ifunc/14 (1 ms) 25: [ RUN ] Dihedral/ListedForcesTest.Ifunc/15 25: [ OK ] Dihedral/ListedForcesTest.Ifunc/15 (0 ms) 25: [ RUN ] Dihedral/ListedForcesTest.Ifunc/16 25: [ OK ] Dihedral/ListedForcesTest.Ifunc/16 (0 ms) 25: [ RUN ] Dihedral/ListedForcesTest.Ifunc/17 25: [ OK ] Dihedral/ListedForcesTest.Ifunc/17 (0 ms) 25: [----------] 18 tests from Dihedral/ListedForcesTest (23 ms total) 25: 25: [----------] 12 tests from Polarize/ListedForcesTest 25: [ RUN ] Polarize/ListedForcesTest.Ifunc/0 25: [ OK ] Polarize/ListedForcesTest.Ifunc/0 (0 ms) 25: [ RUN ] Polarize/ListedForcesTest.Ifunc/1 25: [ OK ] Polarize/ListedForcesTest.Ifunc/1 (0 ms) 25: [ RUN ] Polarize/ListedForcesTest.Ifunc/2 25: [ OK ] Polarize/ListedForcesTest.Ifunc/2 (0 ms) 25: [ RUN ] Polarize/ListedForcesTest.Ifunc/3 25: [ OK ] Polarize/ListedForcesTest.Ifunc/3 (0 ms) 25: [ RUN ] Polarize/ListedForcesTest.Ifunc/4 25: [ OK ] Polarize/ListedForcesTest.Ifunc/4 (0 ms) 25: [ RUN ] Polarize/ListedForcesTest.Ifunc/5 25: [ OK ] Polarize/ListedForcesTest.Ifunc/5 (0 ms) 25: [ RUN ] Polarize/ListedForcesTest.Ifunc/6 25: [ OK ] Polarize/ListedForcesTest.Ifunc/6 (2 ms) 25: [ RUN ] Polarize/ListedForcesTest.Ifunc/7 25: [ OK ] Polarize/ListedForcesTest.Ifunc/7 (0 ms) 25: [ RUN ] Polarize/ListedForcesTest.Ifunc/8 25: [ OK ] Polarize/ListedForcesTest.Ifunc/8 (0 ms) 25: [ RUN ] Polarize/ListedForcesTest.Ifunc/9 25: [ OK ] Polarize/ListedForcesTest.Ifunc/9 (0 ms) 25: [ RUN ] Polarize/ListedForcesTest.Ifunc/10 25: [ OK ] Polarize/ListedForcesTest.Ifunc/10 (0 ms) 25: [ RUN ] Polarize/ListedForcesTest.Ifunc/11 25: [ OK ] Polarize/ListedForcesTest.Ifunc/11 (0 ms) 25: [----------] 12 tests from Polarize/ListedForcesTest (12 ms total) 25: 25: [----------] 18 tests from Restraints/ListedForcesTest 25: [ RUN ] Restraints/ListedForcesTest.Ifunc/0 25: [ OK ] Restraints/ListedForcesTest.Ifunc/0 (1 ms) 25: [ RUN ] Restraints/ListedForcesTest.Ifunc/1 25: [ OK ] Restraints/ListedForcesTest.Ifunc/1 (1 ms) 25: [ RUN ] Restraints/ListedForcesTest.Ifunc/2 25: [ OK ] Restraints/ListedForcesTest.Ifunc/2 (1 ms) 25: [ RUN ] Restraints/ListedForcesTest.Ifunc/3 25: [ OK ] Restraints/ListedForcesTest.Ifunc/3 (0 ms) 25: [ RUN ] Restraints/ListedForcesTest.Ifunc/4 25: [ OK ] Restraints/ListedForcesTest.Ifunc/4 (0 ms) 25: [ RUN ] Restraints/ListedForcesTest.Ifunc/5 25: [ OK ] Restraints/ListedForcesTest.Ifunc/5 (0 ms) 25: [ RUN ] Restraints/ListedForcesTest.Ifunc/6 25: [ OK ] Restraints/ListedForcesTest.Ifunc/6 (1 ms) 25: [ RUN ] Restraints/ListedForcesTest.Ifunc/7 25: [ OK ] Restraints/ListedForcesTest.Ifunc/7 (1 ms) 25: [ RUN ] Restraints/ListedForcesTest.Ifunc/8 25: [ OK ] Restraints/ListedForcesTest.Ifunc/8 (1 ms) 25: [ RUN ] Restraints/ListedForcesTest.Ifunc/9 25: [ OK ] Restraints/ListedForcesTest.Ifunc/9 (0 ms) 25: [ RUN ] Restraints/ListedForcesTest.Ifunc/10 25: [ OK ] Restraints/ListedForcesTest.Ifunc/10 (0 ms) 25: [ RUN ] Restraints/ListedForcesTest.Ifunc/11 25: [ OK ] Restraints/ListedForcesTest.Ifunc/11 (0 ms) 25: [ RUN ] Restraints/ListedForcesTest.Ifunc/12 25: [ OK ] Restraints/ListedForcesTest.Ifunc/12 (0 ms) 25: [ RUN ] Restraints/ListedForcesTest.Ifunc/13 25: [ OK ] Restraints/ListedForcesTest.Ifunc/13 (0 ms) 25: [ RUN ] Restraints/ListedForcesTest.Ifunc/14 25: [ OK ] Restraints/ListedForcesTest.Ifunc/14 (0 ms) 25: [ RUN ] Restraints/ListedForcesTest.Ifunc/15 25: [ OK ] Restraints/ListedForcesTest.Ifunc/15 (2 ms) 25: [ RUN ] Restraints/ListedForcesTest.Ifunc/16 25: [ OK ] Restraints/ListedForcesTest.Ifunc/16 (1 ms) 25: [ RUN ] Restraints/ListedForcesTest.Ifunc/17 25: [ OK ] Restraints/ListedForcesTest.Ifunc/17 (1 ms) 25: [----------] 18 tests from Restraints/ListedForcesTest (25 ms total) 25: 25: [----------] 3 tests from BondZeroLength/ListedForcesTest 25: [ RUN ] BondZeroLength/ListedForcesTest.Ifunc/0 25: [ OK ] BondZeroLength/ListedForcesTest.Ifunc/0 (0 ms) 25: [ RUN ] BondZeroLength/ListedForcesTest.Ifunc/1 25: [ OK ] BondZeroLength/ListedForcesTest.Ifunc/1 (0 ms) 25: [ RUN ] BondZeroLength/ListedForcesTest.Ifunc/2 25: [ OK ] BondZeroLength/ListedForcesTest.Ifunc/2 (0 ms) 25: [----------] 3 tests from BondZeroLength/ListedForcesTest (2 ms total) 25: 25: [----------] 3 tests from AngleZero/ListedForcesTest 25: [ RUN ] AngleZero/ListedForcesTest.Ifunc/0 25: [ OK ] AngleZero/ListedForcesTest.Ifunc/0 (1 ms) 25: [ RUN ] AngleZero/ListedForcesTest.Ifunc/1 25: [ OK ] AngleZero/ListedForcesTest.Ifunc/1 (0 ms) 25: [ RUN ] AngleZero/ListedForcesTest.Ifunc/2 25: [ OK ] AngleZero/ListedForcesTest.Ifunc/2 (0 ms) 25: [----------] 3 tests from AngleZero/ListedForcesTest (3 ms total) 25: 25: [----------] 12 tests from 14Interaction/ListedForcesPairsTest 25: [ RUN ] 14Interaction/ListedForcesPairsTest.Ifunc/0 25: [ OK ] 14Interaction/ListedForcesPairsTest.Ifunc/0 (3 ms) 25: [ RUN ] 14Interaction/ListedForcesPairsTest.Ifunc/1 25: [ OK ] 14Interaction/ListedForcesPairsTest.Ifunc/1 (2 ms) 25: [ RUN ] 14Interaction/ListedForcesPairsTest.Ifunc/2 25: [ OK ] 14Interaction/ListedForcesPairsTest.Ifunc/2 (6 ms) 25: [ RUN ] 14Interaction/ListedForcesPairsTest.Ifunc/3 25: [ OK ] 14Interaction/ListedForcesPairsTest.Ifunc/3 (1 ms) 25: [ RUN ] 14Interaction/ListedForcesPairsTest.Ifunc/4 25: [ OK ] 14Interaction/ListedForcesPairsTest.Ifunc/4 (0 ms) 25: [ RUN ] 14Interaction/ListedForcesPairsTest.Ifunc/5 25: [ OK ] 14Interaction/ListedForcesPairsTest.Ifunc/5 (0 ms) 25: [ RUN ] 14Interaction/ListedForcesPairsTest.Ifunc/6 25: [ OK ] 14Interaction/ListedForcesPairsTest.Ifunc/6 (0 ms) 25: [ RUN ] 14Interaction/ListedForcesPairsTest.Ifunc/7 25: [ OK ] 14Interaction/ListedForcesPairsTest.Ifunc/7 (0 ms) 25: [ RUN ] 14Interaction/ListedForcesPairsTest.Ifunc/8 25: [ OK ] 14Interaction/ListedForcesPairsTest.Ifunc/8 (0 ms) 25: [ RUN ] 14Interaction/ListedForcesPairsTest.Ifunc/9 25: [ OK ] 14Interaction/ListedForcesPairsTest.Ifunc/9 (0 ms) 25: [ RUN ] 14Interaction/ListedForcesPairsTest.Ifunc/10 25: [ OK ] 14Interaction/ListedForcesPairsTest.Ifunc/10 (0 ms) 25: [ RUN ] 14Interaction/ListedForcesPairsTest.Ifunc/11 25: [ OK ] 14Interaction/ListedForcesPairsTest.Ifunc/11 (0 ms) 25: [----------] 12 tests from 14Interaction/ListedForcesPairsTest (22 ms total) 25: 25: [----------] 9 tests from PosResBasicTest/PositionRestraintsTest 25: [ RUN ] PosResBasicTest/PositionRestraintsTest.BasicPosResNoFreeEnergy/0 25: [ OK ] PosResBasicTest/PositionRestraintsTest.BasicPosResNoFreeEnergy/0 (0 ms) 25: [ RUN ] PosResBasicTest/PositionRestraintsTest.BasicPosResNoFreeEnergy/1 25: [ OK ] PosResBasicTest/PositionRestraintsTest.BasicPosResNoFreeEnergy/1 (0 ms) 25: [ RUN ] PosResBasicTest/PositionRestraintsTest.BasicPosResNoFreeEnergy/2 25: [ OK ] PosResBasicTest/PositionRestraintsTest.BasicPosResNoFreeEnergy/2 (2 ms) 25: [ RUN ] PosResBasicTest/PositionRestraintsTest.BasicPosResNoFreeEnergy/3 25: [ OK ] PosResBasicTest/PositionRestraintsTest.BasicPosResNoFreeEnergy/3 (0 ms) 25: [ RUN ] PosResBasicTest/PositionRestraintsTest.BasicPosResNoFreeEnergy/4 25: [ OK ] PosResBasicTest/PositionRestraintsTest.BasicPosResNoFreeEnergy/4 (0 ms) 25: [ RUN ] PosResBasicTest/PositionRestraintsTest.BasicPosResNoFreeEnergy/5 25: [ OK ] PosResBasicTest/PositionRestraintsTest.BasicPosResNoFreeEnergy/5 (0 ms) 25: [ RUN ] PosResBasicTest/PositionRestraintsTest.BasicPosResNoFreeEnergy/6 25: [ OK ] PosResBasicTest/PositionRestraintsTest.BasicPosResNoFreeEnergy/6 (0 ms) 25: [ RUN ] PosResBasicTest/PositionRestraintsTest.BasicPosResNoFreeEnergy/7 25: [ OK ] PosResBasicTest/PositionRestraintsTest.BasicPosResNoFreeEnergy/7 (0 ms) 25: [ RUN ] PosResBasicTest/PositionRestraintsTest.BasicPosResNoFreeEnergy/8 25: [ OK ] PosResBasicTest/PositionRestraintsTest.BasicPosResNoFreeEnergy/8 (0 ms) 25: [----------] 9 tests from PosResBasicTest/PositionRestraintsTest (9 ms total) 25: 25: [----------] Global test environment tear-down 25: [==========] 132 tests from 9 test suites ran. (174 ms total) 25: [ PASSED ] 132 tests. 25/92 Test #25: ListedForcesTest .......................... Passed 0.34 sec test 26 Start 26: NbnxmTests 26: Test command: /build/reproducible-path/gromacs-2025.1/build/basic-dp/bin/nbnxm-test "--gtest_output=xml:/build/reproducible-path/gromacs-2025.1/build/basic-dp/Testing/Temporary/NbnxmTests.xml" 26: Working Directory: /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/nbnxm/tests 26: Test timeout computed to be: 30 26: [==========] Running 380 tests from 3 test suites. 26: [----------] Global test environment set-up. 26: [----------] 18 tests from KernelSetupTest 26: [ RUN ] KernelSetupTest.getCoulombKernelTypeRF 26: [ OK ] KernelSetupTest.getCoulombKernelTypeRF (0 ms) 26: [ RUN ] KernelSetupTest.getCoulombKernelTypeCut 26: [ OK ] KernelSetupTest.getCoulombKernelTypeCut (0 ms) 26: [ RUN ] KernelSetupTest.getCoulombKernelTypeTable 26: [ OK ] KernelSetupTest.getCoulombKernelTypeTable (0 ms) 26: [ RUN ] KernelSetupTest.getCoulombKernelTypeTableTwin 26: [ OK ] KernelSetupTest.getCoulombKernelTypeTableTwin (0 ms) 26: [ RUN ] KernelSetupTest.getCoulombKernelTypeEwald 26: [ OK ] KernelSetupTest.getCoulombKernelTypeEwald (0 ms) 26: [ RUN ] KernelSetupTest.getCoulombKernelTypeEwaldTwin 26: [ OK ] KernelSetupTest.getCoulombKernelTypeEwaldTwin (0 ms) 26: [ RUN ] KernelSetupTest.getVdwKernelTypeLjCutCombGeomNone 26: [ OK ] KernelSetupTest.getVdwKernelTypeLjCutCombGeomNone (0 ms) 26: [ RUN ] KernelSetupTest.getVdwKernelTypeLjCutCombGeomPotShift 26: [ OK ] KernelSetupTest.getVdwKernelTypeLjCutCombGeomPotShift (0 ms) 26: [ RUN ] KernelSetupTest.getVdwKernelTypeLjCutCombLBNone 26: [ OK ] KernelSetupTest.getVdwKernelTypeLjCutCombLBNone (0 ms) 26: [ RUN ] KernelSetupTest.getVdwKernelTypeLjCutCombLBPotShift 26: [ OK ] KernelSetupTest.getVdwKernelTypeLjCutCombLBPotShift (0 ms) 26: [ RUN ] KernelSetupTest.getVdwKernelTypeLjCutCombNoneNone 26: [ OK ] KernelSetupTest.getVdwKernelTypeLjCutCombNoneNone (0 ms) 26: [ RUN ] KernelSetupTest.getVdwKernelTypeLjCutCombNonePotShift 26: [ OK ] KernelSetupTest.getVdwKernelTypeLjCutCombNonePotShift (0 ms) 26: [ RUN ] KernelSetupTest.getVdwKernelTypeLjCutThrows 26: [ OK ] KernelSetupTest.getVdwKernelTypeLjCutThrows (0 ms) 26: [ RUN ] KernelSetupTest.getVdwKernelTypeLjCutForceSwitch 26: [ OK ] KernelSetupTest.getVdwKernelTypeLjCutForceSwitch (0 ms) 26: [ RUN ] KernelSetupTest.getVdwKernelTypePmeGeom 26: [ OK ] KernelSetupTest.getVdwKernelTypePmeGeom (0 ms) 26: [ RUN ] KernelSetupTest.getVdwKernelTypePmeNone 26: [ OK ] KernelSetupTest.getVdwKernelTypePmeNone (0 ms) 26: [ RUN ] KernelSetupTest.getVdwKernelTypeLjCutPotSwitch 26: [ OK ] KernelSetupTest.getVdwKernelTypeLjCutPotSwitch (0 ms) 26: [ RUN ] KernelSetupTest.getVdwKernelTypeAllCountThrows 26: [ OK ] KernelSetupTest.getVdwKernelTypeAllCountThrows (0 ms) 26: [----------] 18 tests from KernelSetupTest (1 ms total) 26: 26: [----------] 2 tests from WithParameters/CpuListDiagonalExclusionsTest 26: [ RUN ] WithParameters/CpuListDiagonalExclusionsTest.CheckMask/0 26: [ OK ] WithParameters/CpuListDiagonalExclusionsTest.CheckMask/0 (0 ms) 26: [ RUN ] WithParameters/CpuListDiagonalExclusionsTest.CheckMask/1 26: [ OK ] WithParameters/CpuListDiagonalExclusionsTest.CheckMask/1 (0 ms) 26: [----------] 2 tests from WithParameters/CpuListDiagonalExclusionsTest (0 ms total) 26: 26: [----------] 360 tests from Combinations/NbnxmKernelTest 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombReactionField_VdwCutCombGeom 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:540: Skipped 26: There are no combination rule versions of the plain-C kernel 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombReactionField_VdwCutCombGeom (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombReactionField_VdwCutCombGeom 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:540: Skipped 26: There are no combination rule versions of the plain-C kernel 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombReactionField_VdwCutCombGeom (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwCutCombGeom 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:540: Skipped 26: There are no combination rule versions of the plain-C kernel 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwCutCombGeom (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombReactionField_VdwCutCombLB 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:540: Skipped 26: There are no combination rule versions of the plain-C kernel 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombReactionField_VdwCutCombLB (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombReactionField_VdwCutCombLB 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:540: Skipped 26: There are no combination rule versions of the plain-C kernel 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombReactionField_VdwCutCombLB (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwCutCombLB 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:540: Skipped 26: There are no combination rule versions of the plain-C kernel 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwCutCombLB (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombReactionField_VdwCutCombNone 26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombReactionField_VdwCutCombNone (31 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombReactionField_VdwCutCombNone 26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombReactionField_VdwCutCombNone (23 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwCutCombNone 26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwCutCombNone (24 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombReactionField_VdwForceSwitch 26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombReactionField_VdwForceSwitch (23 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombReactionField_VdwForceSwitch 26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombReactionField_VdwForceSwitch (24 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwForceSwitch 26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwForceSwitch (23 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombReactionField_VdwPotSwitch 26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombReactionField_VdwPotSwitch (26 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombReactionField_VdwPotSwitch 26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombReactionField_VdwPotSwitch (24 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwPotSwitch 26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwPotSwitch (25 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombReactionField_VdwEwaldCombGeom 26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombReactionField_VdwEwaldCombGeom (26 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombReactionField_VdwEwaldCombGeom 26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombReactionField_VdwEwaldCombGeom (26 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwEwaldCombGeom 26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwEwaldCombGeom (26 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombEwald_VdwCutCombGeom 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 26: Analytical Ewald is not implemented for the plain-C kernel, skip this test 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombEwald_VdwCutCombGeom (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombEwald_VdwCutCombGeom 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 26: Analytical Ewald is not implemented for the plain-C kernel, skip this test 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombEwald_VdwCutCombGeom (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombEwald_VdwCutCombGeom 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 26: Analytical Ewald is not implemented for the plain-C kernel, skip this test 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombEwald_VdwCutCombGeom (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombEwald_VdwCutCombLB 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 26: Analytical Ewald is not implemented for the plain-C kernel, skip this test 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombEwald_VdwCutCombLB (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombEwald_VdwCutCombLB 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 26: Analytical Ewald is not implemented for the plain-C kernel, skip this test 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombEwald_VdwCutCombLB (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombEwald_VdwCutCombLB 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 26: Analytical Ewald is not implemented for the plain-C kernel, skip this test 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombEwald_VdwCutCombLB (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombEwald_VdwCutCombNone 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 26: Analytical Ewald is not implemented for the plain-C kernel, skip this test 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombEwald_VdwCutCombNone (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombEwald_VdwCutCombNone 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 26: Analytical Ewald is not implemented for the plain-C kernel, skip this test 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombEwald_VdwCutCombNone (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombEwald_VdwCutCombNone 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 26: Analytical Ewald is not implemented for the plain-C kernel, skip this test 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombEwald_VdwCutCombNone (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombEwald_VdwForceSwitch 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 26: Analytical Ewald is not implemented for the plain-C kernel, skip this test 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombEwald_VdwForceSwitch (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombEwald_VdwForceSwitch 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 26: Analytical Ewald is not implemented for the plain-C kernel, skip this test 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombEwald_VdwForceSwitch (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombEwald_VdwForceSwitch 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 26: Analytical Ewald is not implemented for the plain-C kernel, skip this test 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombEwald_VdwForceSwitch (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombEwald_VdwPotSwitch 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 26: Analytical Ewald is not implemented for the plain-C kernel, skip this test 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombEwald_VdwPotSwitch (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombEwald_VdwPotSwitch 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 26: Analytical Ewald is not implemented for the plain-C kernel, skip this test 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombEwald_VdwPotSwitch (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombEwald_VdwPotSwitch 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 26: Analytical Ewald is not implemented for the plain-C kernel, skip this test 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombEwald_VdwPotSwitch (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombEwald_VdwEwaldCombGeom 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 26: Analytical Ewald is not implemented for the plain-C kernel, skip this test 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombEwald_VdwEwaldCombGeom (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombEwald_VdwEwaldCombGeom 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 26: Analytical Ewald is not implemented for the plain-C kernel, skip this test 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombEwald_VdwEwaldCombGeom (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombEwald_VdwEwaldCombGeom 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 26: Analytical Ewald is not implemented for the plain-C kernel, skip this test 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombEwald_VdwEwaldCombGeom (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombEwaldTwin_VdwCutCombGeom 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 26: Analytical Ewald is not implemented for the plain-C kernel, skip this test 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombEwaldTwin_VdwCutCombGeom (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombEwaldTwin_VdwCutCombGeom 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 26: Analytical Ewald is not implemented for the plain-C kernel, skip this test 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombEwaldTwin_VdwCutCombGeom (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombGeom 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 26: Analytical Ewald is not implemented for the plain-C kernel, skip this test 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombGeom (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombEwaldTwin_VdwCutCombLB 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 26: Analytical Ewald is not implemented for the plain-C kernel, skip this test 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombEwaldTwin_VdwCutCombLB (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombEwaldTwin_VdwCutCombLB 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 26: Analytical Ewald is not implemented for the plain-C kernel, skip this test 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombEwaldTwin_VdwCutCombLB (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombLB 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 26: Analytical Ewald is not implemented for the plain-C kernel, skip this test 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombLB (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombEwaldTwin_VdwCutCombNone 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 26: Analytical Ewald is not implemented for the plain-C kernel, skip this test 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombEwaldTwin_VdwCutCombNone (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombEwaldTwin_VdwCutCombNone 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 26: Analytical Ewald is not implemented for the plain-C kernel, skip this test 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombEwaldTwin_VdwCutCombNone (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombNone 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 26: Analytical Ewald is not implemented for the plain-C kernel, skip this test 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombNone (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombEwaldTwin_VdwForceSwitch 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 26: Analytical Ewald is not implemented for the plain-C kernel, skip this test 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombEwaldTwin_VdwForceSwitch (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombEwaldTwin_VdwForceSwitch 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 26: Analytical Ewald is not implemented for the plain-C kernel, skip this test 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombEwaldTwin_VdwForceSwitch (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwForceSwitch 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 26: Analytical Ewald is not implemented for the plain-C kernel, skip this test 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwForceSwitch (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombEwaldTwin_VdwPotSwitch 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 26: Analytical Ewald is not implemented for the plain-C kernel, skip this test 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombEwaldTwin_VdwPotSwitch (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombEwaldTwin_VdwPotSwitch 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 26: Analytical Ewald is not implemented for the plain-C kernel, skip this test 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombEwaldTwin_VdwPotSwitch (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwPotSwitch 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 26: Analytical Ewald is not implemented for the plain-C kernel, skip this test 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwPotSwitch (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombEwaldTwin_VdwEwaldCombGeom 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 26: Analytical Ewald is not implemented for the plain-C kernel, skip this test 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombEwaldTwin_VdwEwaldCombGeom (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombEwaldTwin_VdwEwaldCombGeom 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 26: Analytical Ewald is not implemented for the plain-C kernel, skip this test 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombEwaldTwin_VdwEwaldCombGeom (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwEwaldCombGeom 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 26: Analytical Ewald is not implemented for the plain-C kernel, skip this test 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwEwaldCombGeom (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_NoEnergies_CoulombEwald_VdwCutCombGeom 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:540: Skipped 26: There are no combination rule versions of the plain-C kernel 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_NoEnergies_CoulombEwald_VdwCutCombGeom (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_Energies_CoulombEwald_VdwCutCombGeom 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:540: Skipped 26: There are no combination rule versions of the plain-C kernel 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_Energies_CoulombEwald_VdwCutCombGeom (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_ThreeEnergyGroups_CoulombEwald_VdwCutCombGeom 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:540: Skipped 26: There are no combination rule versions of the plain-C kernel 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_ThreeEnergyGroups_CoulombEwald_VdwCutCombGeom (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_NoEnergies_CoulombEwald_VdwCutCombLB 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:540: Skipped 26: There are no combination rule versions of the plain-C kernel 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_NoEnergies_CoulombEwald_VdwCutCombLB (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_Energies_CoulombEwald_VdwCutCombLB 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:540: Skipped 26: There are no combination rule versions of the plain-C kernel 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_Energies_CoulombEwald_VdwCutCombLB (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_ThreeEnergyGroups_CoulombEwald_VdwCutCombLB 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:540: Skipped 26: There are no combination rule versions of the plain-C kernel 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_ThreeEnergyGroups_CoulombEwald_VdwCutCombLB (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_NoEnergies_CoulombEwald_VdwCutCombNone 26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_NoEnergies_CoulombEwald_VdwCutCombNone (27 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_Energies_CoulombEwald_VdwCutCombNone 26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_Energies_CoulombEwald_VdwCutCombNone (26 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_ThreeEnergyGroups_CoulombEwald_VdwCutCombNone 26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_ThreeEnergyGroups_CoulombEwald_VdwCutCombNone (25 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_NoEnergies_CoulombEwald_VdwForceSwitch 26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_NoEnergies_CoulombEwald_VdwForceSwitch (26 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_Energies_CoulombEwald_VdwForceSwitch 26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_Energies_CoulombEwald_VdwForceSwitch (26 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_ThreeEnergyGroups_CoulombEwald_VdwForceSwitch 26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_ThreeEnergyGroups_CoulombEwald_VdwForceSwitch (25 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_NoEnergies_CoulombEwald_VdwPotSwitch 26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_NoEnergies_CoulombEwald_VdwPotSwitch (26 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_Energies_CoulombEwald_VdwPotSwitch 26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_Energies_CoulombEwald_VdwPotSwitch (25 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_ThreeEnergyGroups_CoulombEwald_VdwPotSwitch 26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_ThreeEnergyGroups_CoulombEwald_VdwPotSwitch (25 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_NoEnergies_CoulombEwald_VdwEwaldCombGeom 26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_NoEnergies_CoulombEwald_VdwEwaldCombGeom (29 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_Energies_CoulombEwald_VdwEwaldCombGeom 26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_Energies_CoulombEwald_VdwEwaldCombGeom (28 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_ThreeEnergyGroups_CoulombEwald_VdwEwaldCombGeom 26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_ThreeEnergyGroups_CoulombEwald_VdwEwaldCombGeom (28 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_NoEnergies_CoulombEwaldTwin_VdwCutCombGeom 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:540: Skipped 26: There are no combination rule versions of the plain-C kernel 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_NoEnergies_CoulombEwaldTwin_VdwCutCombGeom (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_Energies_CoulombEwaldTwin_VdwCutCombGeom 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:540: Skipped 26: There are no combination rule versions of the plain-C kernel 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_Energies_CoulombEwaldTwin_VdwCutCombGeom (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombGeom 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:540: Skipped 26: There are no combination rule versions of the plain-C kernel 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombGeom (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_NoEnergies_CoulombEwaldTwin_VdwCutCombLB 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:540: Skipped 26: There are no combination rule versions of the plain-C kernel 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_NoEnergies_CoulombEwaldTwin_VdwCutCombLB (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_Energies_CoulombEwaldTwin_VdwCutCombLB 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:540: Skipped 26: There are no combination rule versions of the plain-C kernel 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_Energies_CoulombEwaldTwin_VdwCutCombLB (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombLB 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:540: Skipped 26: There are no combination rule versions of the plain-C kernel 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombLB (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_NoEnergies_CoulombEwaldTwin_VdwCutCombNone 26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_NoEnergies_CoulombEwaldTwin_VdwCutCombNone (25 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_Energies_CoulombEwaldTwin_VdwCutCombNone 26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_Energies_CoulombEwaldTwin_VdwCutCombNone (25 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombNone 26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombNone (27 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_NoEnergies_CoulombEwaldTwin_VdwForceSwitch 26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_NoEnergies_CoulombEwaldTwin_VdwForceSwitch (27 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_Energies_CoulombEwaldTwin_VdwForceSwitch 26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_Energies_CoulombEwaldTwin_VdwForceSwitch (26 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwForceSwitch 26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwForceSwitch (27 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_NoEnergies_CoulombEwaldTwin_VdwPotSwitch 26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_NoEnergies_CoulombEwaldTwin_VdwPotSwitch (27 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_Energies_CoulombEwaldTwin_VdwPotSwitch 26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_Energies_CoulombEwaldTwin_VdwPotSwitch (28 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwPotSwitch 26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwPotSwitch (26 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_NoEnergies_CoulombEwaldTwin_VdwEwaldCombGeom 26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_NoEnergies_CoulombEwaldTwin_VdwEwaldCombGeom (30 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_Energies_CoulombEwaldTwin_VdwEwaldCombGeom 26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_Energies_CoulombEwaldTwin_VdwEwaldCombGeom (26 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwEwaldCombGeom 26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwEwaldCombGeom (28 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombReactionField_VdwCutCombGeom 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:540: Skipped 26: There are no combination rule versions of the plain-C kernel 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombReactionField_VdwCutCombGeom (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombReactionField_VdwCutCombGeom 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:540: Skipped 26: There are no combination rule versions of the plain-C kernel 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombReactionField_VdwCutCombGeom (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwCutCombGeom 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:540: Skipped 26: There are no combination rule versions of the plain-C kernel 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwCutCombGeom (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombReactionField_VdwCutCombLB 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:540: Skipped 26: There are no combination rule versions of the plain-C kernel 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombReactionField_VdwCutCombLB (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombReactionField_VdwCutCombLB 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:540: Skipped 26: There are no combination rule versions of the plain-C kernel 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombReactionField_VdwCutCombLB (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwCutCombLB 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:540: Skipped 26: There are no combination rule versions of the plain-C kernel 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwCutCombLB (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombReactionField_VdwCutCombNone 26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombReactionField_VdwCutCombNone (20 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombReactionField_VdwCutCombNone 26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombReactionField_VdwCutCombNone (21 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwCutCombNone 26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwCutCombNone (21 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombReactionField_VdwForceSwitch 26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombReactionField_VdwForceSwitch (22 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombReactionField_VdwForceSwitch 26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombReactionField_VdwForceSwitch (23 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwForceSwitch 26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwForceSwitch (22 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombReactionField_VdwPotSwitch 26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombReactionField_VdwPotSwitch (21 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombReactionField_VdwPotSwitch 26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombReactionField_VdwPotSwitch (22 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwPotSwitch 26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwPotSwitch (23 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombReactionField_VdwEwaldCombGeom 26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombReactionField_VdwEwaldCombGeom (25 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombReactionField_VdwEwaldCombGeom 26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombReactionField_VdwEwaldCombGeom (25 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwEwaldCombGeom 26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwEwaldCombGeom (24 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombEwald_VdwCutCombGeom 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 26: Analytical Ewald is not implemented for the plain-C kernel, skip this test 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombEwald_VdwCutCombGeom (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombEwald_VdwCutCombGeom 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 26: Analytical Ewald is not implemented for the plain-C kernel, skip this test 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombEwald_VdwCutCombGeom (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombEwald_VdwCutCombGeom 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 26: Analytical Ewald is not implemented for the plain-C kernel, skip this test 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombEwald_VdwCutCombGeom (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombEwald_VdwCutCombLB 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 26: Analytical Ewald is not implemented for the plain-C kernel, skip this test 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombEwald_VdwCutCombLB (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombEwald_VdwCutCombLB 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 26: Analytical Ewald is not implemented for the plain-C kernel, skip this test 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombEwald_VdwCutCombLB (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombEwald_VdwCutCombLB 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 26: Analytical Ewald is not implemented for the plain-C kernel, skip this test 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombEwald_VdwCutCombLB (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombEwald_VdwCutCombNone 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 26: Analytical Ewald is not implemented for the plain-C kernel, skip this test 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombEwald_VdwCutCombNone (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombEwald_VdwCutCombNone 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 26: Analytical Ewald is not implemented for the plain-C kernel, skip this test 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombEwald_VdwCutCombNone (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombEwald_VdwCutCombNone 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 26: Analytical Ewald is not implemented for the plain-C kernel, skip this test 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombEwald_VdwCutCombNone (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombEwald_VdwForceSwitch 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 26: Analytical Ewald is not implemented for the plain-C kernel, skip this test 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombEwald_VdwForceSwitch (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombEwald_VdwForceSwitch 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 26: Analytical Ewald is not implemented for the plain-C kernel, skip this test 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombEwald_VdwForceSwitch (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombEwald_VdwForceSwitch 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 26: Analytical Ewald is not implemented for the plain-C kernel, skip this test 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombEwald_VdwForceSwitch (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombEwald_VdwPotSwitch 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 26: Analytical Ewald is not implemented for the plain-C kernel, skip this test 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombEwald_VdwPotSwitch (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombEwald_VdwPotSwitch 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 26: Analytical Ewald is not implemented for the plain-C kernel, skip this test 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombEwald_VdwPotSwitch (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombEwald_VdwPotSwitch 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 26: Analytical Ewald is not implemented for the plain-C kernel, skip this test 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombEwald_VdwPotSwitch (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombEwald_VdwEwaldCombGeom 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 26: Analytical Ewald is not implemented for the plain-C kernel, skip this test 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombEwald_VdwEwaldCombGeom (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombEwald_VdwEwaldCombGeom 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 26: Analytical Ewald is not implemented for the plain-C kernel, skip this test 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombEwald_VdwEwaldCombGeom (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombEwald_VdwEwaldCombGeom 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 26: Analytical Ewald is not implemented for the plain-C kernel, skip this test 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombEwald_VdwEwaldCombGeom (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombEwaldTwin_VdwCutCombGeom 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 26: Analytical Ewald is not implemented for the plain-C kernel, skip this test 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombEwaldTwin_VdwCutCombGeom (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombEwaldTwin_VdwCutCombGeom 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 26: Analytical Ewald is not implemented for the plain-C kernel, skip this test 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombEwaldTwin_VdwCutCombGeom (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombGeom 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 26: Analytical Ewald is not implemented for the plain-C kernel, skip this test 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombGeom (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombEwaldTwin_VdwCutCombLB 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 26: Analytical Ewald is not implemented for the plain-C kernel, skip this test 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombEwaldTwin_VdwCutCombLB (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombEwaldTwin_VdwCutCombLB 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 26: Analytical Ewald is not implemented for the plain-C kernel, skip this test 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombEwaldTwin_VdwCutCombLB (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombLB 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 26: Analytical Ewald is not implemented for the plain-C kernel, skip this test 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombLB (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombEwaldTwin_VdwCutCombNone 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 26: Analytical Ewald is not implemented for the plain-C kernel, skip this test 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombEwaldTwin_VdwCutCombNone (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombEwaldTwin_VdwCutCombNone 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 26: Analytical Ewald is not implemented for the plain-C kernel, skip this test 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombEwaldTwin_VdwCutCombNone (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombNone 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 26: Analytical Ewald is not implemented for the plain-C kernel, skip this test 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombNone (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombEwaldTwin_VdwForceSwitch 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 26: Analytical Ewald is not implemented for the plain-C kernel, skip this test 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombEwaldTwin_VdwForceSwitch (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombEwaldTwin_VdwForceSwitch 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 26: Analytical Ewald is not implemented for the plain-C kernel, skip this test 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombEwaldTwin_VdwForceSwitch (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwForceSwitch 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 26: Analytical Ewald is not implemented for the plain-C kernel, skip this test 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwForceSwitch (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombEwaldTwin_VdwPotSwitch 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 26: Analytical Ewald is not implemented for the plain-C kernel, skip this test 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombEwaldTwin_VdwPotSwitch (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombEwaldTwin_VdwPotSwitch 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 26: Analytical Ewald is not implemented for the plain-C kernel, skip this test 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombEwaldTwin_VdwPotSwitch (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwPotSwitch 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 26: Analytical Ewald is not implemented for the plain-C kernel, skip this test 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwPotSwitch (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombEwaldTwin_VdwEwaldCombGeom 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 26: Analytical Ewald is not implemented for the plain-C kernel, skip this test 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombEwaldTwin_VdwEwaldCombGeom (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombEwaldTwin_VdwEwaldCombGeom 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 26: Analytical Ewald is not implemented for the plain-C kernel, skip this test 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombEwaldTwin_VdwEwaldCombGeom (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwEwaldCombGeom 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 26: Analytical Ewald is not implemented for the plain-C kernel, skip this test 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwEwaldCombGeom (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_NoEnergies_CoulombEwald_VdwCutCombGeom 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:540: Skipped 26: There are no combination rule versions of the plain-C kernel 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_NoEnergies_CoulombEwald_VdwCutCombGeom (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_Energies_CoulombEwald_VdwCutCombGeom 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:540: Skipped 26: There are no combination rule versions of the plain-C kernel 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_Energies_CoulombEwald_VdwCutCombGeom (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_ThreeEnergyGroups_CoulombEwald_VdwCutCombGeom 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:540: Skipped 26: There are no combination rule versions of the plain-C kernel 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_ThreeEnergyGroups_CoulombEwald_VdwCutCombGeom (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_NoEnergies_CoulombEwald_VdwCutCombLB 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:540: Skipped 26: There are no combination rule versions of the plain-C kernel 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_NoEnergies_CoulombEwald_VdwCutCombLB (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_Energies_CoulombEwald_VdwCutCombLB 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:540: Skipped 26: There are no combination rule versions of the plain-C kernel 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_Energies_CoulombEwald_VdwCutCombLB (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_ThreeEnergyGroups_CoulombEwald_VdwCutCombLB 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:540: Skipped 26: There are no combination rule versions of the plain-C kernel 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_ThreeEnergyGroups_CoulombEwald_VdwCutCombLB (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_NoEnergies_CoulombEwald_VdwCutCombNone 26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_NoEnergies_CoulombEwald_VdwCutCombNone (24 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_Energies_CoulombEwald_VdwCutCombNone 26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_Energies_CoulombEwald_VdwCutCombNone (24 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_ThreeEnergyGroups_CoulombEwald_VdwCutCombNone 26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_ThreeEnergyGroups_CoulombEwald_VdwCutCombNone (23 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_NoEnergies_CoulombEwald_VdwForceSwitch 26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_NoEnergies_CoulombEwald_VdwForceSwitch (26 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_Energies_CoulombEwald_VdwForceSwitch 26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_Energies_CoulombEwald_VdwForceSwitch (24 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_ThreeEnergyGroups_CoulombEwald_VdwForceSwitch 26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_ThreeEnergyGroups_CoulombEwald_VdwForceSwitch (24 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_NoEnergies_CoulombEwald_VdwPotSwitch 26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_NoEnergies_CoulombEwald_VdwPotSwitch (28 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_Energies_CoulombEwald_VdwPotSwitch 26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_Energies_CoulombEwald_VdwPotSwitch (26 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_ThreeEnergyGroups_CoulombEwald_VdwPotSwitch 26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_ThreeEnergyGroups_CoulombEwald_VdwPotSwitch (25 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_NoEnergies_CoulombEwald_VdwEwaldCombGeom 26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_NoEnergies_CoulombEwald_VdwEwaldCombGeom (30 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_Energies_CoulombEwald_VdwEwaldCombGeom 26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_Energies_CoulombEwald_VdwEwaldCombGeom (29 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_ThreeEnergyGroups_CoulombEwald_VdwEwaldCombGeom 26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_ThreeEnergyGroups_CoulombEwald_VdwEwaldCombGeom (29 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_NoEnergies_CoulombEwaldTwin_VdwCutCombGeom 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:540: Skipped 26: There are no combination rule versions of the plain-C kernel 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_NoEnergies_CoulombEwaldTwin_VdwCutCombGeom (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_Energies_CoulombEwaldTwin_VdwCutCombGeom 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:540: Skipped 26: There are no combination rule versions of the plain-C kernel 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_Energies_CoulombEwaldTwin_VdwCutCombGeom (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombGeom 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:540: Skipped 26: There are no combination rule versions of the plain-C kernel 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombGeom (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_NoEnergies_CoulombEwaldTwin_VdwCutCombLB 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:540: Skipped 26: There are no combination rule versions of the plain-C kernel 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_NoEnergies_CoulombEwaldTwin_VdwCutCombLB (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_Energies_CoulombEwaldTwin_VdwCutCombLB 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:540: Skipped 26: There are no combination rule versions of the plain-C kernel 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_Energies_CoulombEwaldTwin_VdwCutCombLB (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombLB 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:540: Skipped 26: There are no combination rule versions of the plain-C kernel 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombLB (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_NoEnergies_CoulombEwaldTwin_VdwCutCombNone 26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_NoEnergies_CoulombEwaldTwin_VdwCutCombNone (24 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_Energies_CoulombEwaldTwin_VdwCutCombNone 26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_Energies_CoulombEwaldTwin_VdwCutCombNone (24 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombNone 26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombNone (24 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_NoEnergies_CoulombEwaldTwin_VdwForceSwitch 26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_NoEnergies_CoulombEwaldTwin_VdwForceSwitch (24 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_Energies_CoulombEwaldTwin_VdwForceSwitch 26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_Energies_CoulombEwaldTwin_VdwForceSwitch (25 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwForceSwitch 26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwForceSwitch (26 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_NoEnergies_CoulombEwaldTwin_VdwPotSwitch 26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_NoEnergies_CoulombEwaldTwin_VdwPotSwitch (28 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_Energies_CoulombEwaldTwin_VdwPotSwitch 26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_Energies_CoulombEwaldTwin_VdwPotSwitch (26 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwPotSwitch 26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwPotSwitch (25 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_NoEnergies_CoulombEwaldTwin_VdwEwaldCombGeom 26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_NoEnergies_CoulombEwaldTwin_VdwEwaldCombGeom (29 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_Energies_CoulombEwaldTwin_VdwEwaldCombGeom 26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_Energies_CoulombEwaldTwin_VdwEwaldCombGeom (29 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwEwaldCombGeom 26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwEwaldCombGeom (28 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_NoEnergies_CoulombReactionField_VdwCutCombGeom 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:514: Skipped 26: Cannot test or generate data for 4xN kernels without suitable SIMD support 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_NoEnergies_CoulombReactionField_VdwCutCombGeom (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_Energies_CoulombReactionField_VdwCutCombGeom 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:514: Skipped 26: Cannot test or generate data for 4xN kernels without suitable SIMD support 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_Energies_CoulombReactionField_VdwCutCombGeom (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwCutCombGeom 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:514: Skipped 26: Cannot test or generate data for 4xN kernels without suitable SIMD support 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwCutCombGeom (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_NoEnergies_CoulombReactionField_VdwCutCombLB 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:514: Skipped 26: Cannot test or generate data for 4xN kernels without suitable SIMD support 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_NoEnergies_CoulombReactionField_VdwCutCombLB (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_Energies_CoulombReactionField_VdwCutCombLB 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:514: Skipped 26: Cannot test or generate data for 4xN kernels without suitable SIMD support 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_Energies_CoulombReactionField_VdwCutCombLB (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwCutCombLB 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:514: Skipped 26: Cannot test or generate data for 4xN kernels without suitable SIMD support 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwCutCombLB (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_NoEnergies_CoulombReactionField_VdwCutCombNone 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:514: Skipped 26: Cannot test or generate data for 4xN kernels without suitable SIMD support 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_NoEnergies_CoulombReactionField_VdwCutCombNone (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_Energies_CoulombReactionField_VdwCutCombNone 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:514: Skipped 26: Cannot test or generate data for 4xN kernels without suitable SIMD support 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_Energies_CoulombReactionField_VdwCutCombNone (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwCutCombNone 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:514: Skipped 26: Cannot test or generate data for 4xN kernels without suitable SIMD support 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwCutCombNone (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_NoEnergies_CoulombReactionField_VdwForceSwitch 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:514: Skipped 26: Cannot test or generate data for 4xN kernels without suitable SIMD support 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_NoEnergies_CoulombReactionField_VdwForceSwitch (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_Energies_CoulombReactionField_VdwForceSwitch 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:514: Skipped 26: Cannot test or generate data for 4xN kernels without suitable SIMD support 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_Energies_CoulombReactionField_VdwForceSwitch (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwForceSwitch 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:514: Skipped 26: Cannot test or generate data for 4xN kernels without suitable SIMD support 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwForceSwitch (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_NoEnergies_CoulombReactionField_VdwPotSwitch 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:514: Skipped 26: Cannot test or generate data for 4xN kernels without suitable SIMD support 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_NoEnergies_CoulombReactionField_VdwPotSwitch (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_Energies_CoulombReactionField_VdwPotSwitch 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:514: Skipped 26: Cannot test or generate data for 4xN kernels without suitable SIMD support 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_Energies_CoulombReactionField_VdwPotSwitch (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwPotSwitch 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:514: Skipped 26: Cannot test or generate data for 4xN kernels without suitable SIMD support 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwPotSwitch (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_NoEnergies_CoulombReactionField_VdwEwaldCombGeom 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:514: Skipped 26: Cannot test or generate data for 4xN kernels without suitable SIMD support 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_NoEnergies_CoulombReactionField_VdwEwaldCombGeom (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_Energies_CoulombReactionField_VdwEwaldCombGeom 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:514: Skipped 26: Cannot test or generate data for 4xN kernels without suitable SIMD support 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_Energies_CoulombReactionField_VdwEwaldCombGeom (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwEwaldCombGeom 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:514: Skipped 26: Cannot test or generate data for 4xN kernels without suitable SIMD support 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwEwaldCombGeom (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_NoEnergies_CoulombEwald_VdwCutCombGeom 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:514: Skipped 26: Cannot test or generate data for 4xN kernels without suitable SIMD support 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_NoEnergies_CoulombEwald_VdwCutCombGeom (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_Energies_CoulombEwald_VdwCutCombGeom 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:514: Skipped 26: Cannot test or generate data for 4xN kernels without suitable SIMD support 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_Energies_CoulombEwald_VdwCutCombGeom (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_ThreeEnergyGroups_CoulombEwald_VdwCutCombGeom 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:514: Skipped 26: Cannot test or generate data for 4xN kernels without suitable SIMD support 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_ThreeEnergyGroups_CoulombEwald_VdwCutCombGeom (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_NoEnergies_CoulombEwald_VdwCutCombLB 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:514: Skipped 26: Cannot test or generate data for 4xN kernels without suitable SIMD support 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_NoEnergies_CoulombEwald_VdwCutCombLB (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_Energies_CoulombEwald_VdwCutCombLB 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:514: Skipped 26: Cannot test or generate data for 4xN kernels without suitable SIMD support 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_Energies_CoulombEwald_VdwCutCombLB (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_ThreeEnergyGroups_CoulombEwald_VdwCutCombLB 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:514: Skipped 26: Cannot test or generate data for 4xN kernels without suitable SIMD support 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_ThreeEnergyGroups_CoulombEwald_VdwCutCombLB (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_NoEnergies_CoulombEwald_VdwCutCombNone 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:514: Skipped 26: Cannot test or generate data for 4xN kernels without suitable SIMD support 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_NoEnergies_CoulombEwald_VdwCutCombNone (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_Energies_CoulombEwald_VdwCutCombNone 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:514: Skipped 26: Cannot test or generate data for 4xN kernels without suitable SIMD support 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_Energies_CoulombEwald_VdwCutCombNone (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_ThreeEnergyGroups_CoulombEwald_VdwCutCombNone 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:514: Skipped 26: Cannot test or generate data for 4xN kernels without suitable SIMD support 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_ThreeEnergyGroups_CoulombEwald_VdwCutCombNone (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_NoEnergies_CoulombEwald_VdwForceSwitch 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:514: Skipped 26: Cannot test or generate data for 4xN kernels without suitable SIMD support 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_NoEnergies_CoulombEwald_VdwForceSwitch (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_Energies_CoulombEwald_VdwForceSwitch 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:514: Skipped 26: Cannot test or generate data for 4xN kernels without suitable SIMD support 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_Energies_CoulombEwald_VdwForceSwitch (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_ThreeEnergyGroups_CoulombEwald_VdwForceSwitch 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:514: Skipped 26: Cannot test or generate data for 4xN kernels without suitable SIMD support 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_ThreeEnergyGroups_CoulombEwald_VdwForceSwitch (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_NoEnergies_CoulombEwald_VdwPotSwitch 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:514: Skipped 26: Cannot test or generate data for 4xN kernels without suitable SIMD support 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_NoEnergies_CoulombEwald_VdwPotSwitch (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_Energies_CoulombEwald_VdwPotSwitch 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:514: Skipped 26: Cannot test or generate data for 4xN kernels without suitable SIMD support 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_Energies_CoulombEwald_VdwPotSwitch (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_ThreeEnergyGroups_CoulombEwald_VdwPotSwitch 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:514: Skipped 26: Cannot test or generate data for 4xN kernels without suitable SIMD support 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_ThreeEnergyGroups_CoulombEwald_VdwPotSwitch (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_NoEnergies_CoulombEwald_VdwEwaldCombGeom 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:514: Skipped 26: Cannot test or generate data for 4xN kernels without suitable SIMD support 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_NoEnergies_CoulombEwald_VdwEwaldCombGeom (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_Energies_CoulombEwald_VdwEwaldCombGeom 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:514: Skipped 26: Cannot test or generate data for 4xN kernels without suitable SIMD support 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_Energies_CoulombEwald_VdwEwaldCombGeom (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_ThreeEnergyGroups_CoulombEwald_VdwEwaldCombGeom 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:514: Skipped 26: Cannot test or generate data for 4xN kernels without suitable SIMD support 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_ThreeEnergyGroups_CoulombEwald_VdwEwaldCombGeom (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_NoEnergies_CoulombEwaldTwin_VdwCutCombGeom 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:514: Skipped 26: Cannot test or generate data for 4xN kernels without suitable SIMD support 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_NoEnergies_CoulombEwaldTwin_VdwCutCombGeom (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_Energies_CoulombEwaldTwin_VdwCutCombGeom 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:514: Skipped 26: Cannot test or generate data for 4xN kernels without suitable SIMD support 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_Energies_CoulombEwaldTwin_VdwCutCombGeom (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombGeom 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:514: Skipped 26: Cannot test or generate data for 4xN kernels without suitable SIMD support 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombGeom (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_NoEnergies_CoulombEwaldTwin_VdwCutCombLB 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:514: Skipped 26: Cannot test or generate data for 4xN kernels without suitable SIMD support 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_NoEnergies_CoulombEwaldTwin_VdwCutCombLB (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_Energies_CoulombEwaldTwin_VdwCutCombLB 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:514: Skipped 26: Cannot test or generate data for 4xN kernels without suitable SIMD support 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_Energies_CoulombEwaldTwin_VdwCutCombLB (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombLB 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:514: Skipped 26: Cannot test or generate data for 4xN kernels without suitable SIMD support 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombLB (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_NoEnergies_CoulombEwaldTwin_VdwCutCombNone 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:514: Skipped 26: Cannot test or generate data for 4xN kernels without suitable SIMD support 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_NoEnergies_CoulombEwaldTwin_VdwCutCombNone (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_Energies_CoulombEwaldTwin_VdwCutCombNone 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:514: Skipped 26: Cannot test or generate data for 4xN kernels without suitable SIMD support 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_Energies_CoulombEwaldTwin_VdwCutCombNone (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombNone 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:514: Skipped 26: Cannot test or generate data for 4xN kernels without suitable SIMD support 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombNone (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_NoEnergies_CoulombEwaldTwin_VdwForceSwitch 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:514: Skipped 26: Cannot test or generate data for 4xN kernels without suitable SIMD support 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_NoEnergies_CoulombEwaldTwin_VdwForceSwitch (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_Energies_CoulombEwaldTwin_VdwForceSwitch 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:514: Skipped 26: Cannot test or generate data for 4xN kernels without suitable SIMD support 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_Energies_CoulombEwaldTwin_VdwForceSwitch (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwForceSwitch 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:514: Skipped 26: Cannot test or generate data for 4xN kernels without suitable SIMD support 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwForceSwitch (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_NoEnergies_CoulombEwaldTwin_VdwPotSwitch 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:514: Skipped 26: Cannot test or generate data for 4xN kernels without suitable SIMD support 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_NoEnergies_CoulombEwaldTwin_VdwPotSwitch (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_Energies_CoulombEwaldTwin_VdwPotSwitch 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:514: Skipped 26: Cannot test or generate data for 4xN kernels without suitable SIMD support 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_Energies_CoulombEwaldTwin_VdwPotSwitch (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwPotSwitch 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:514: Skipped 26: Cannot test or generate data for 4xN kernels without suitable SIMD support 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwPotSwitch (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_NoEnergies_CoulombEwaldTwin_VdwEwaldCombGeom 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:514: Skipped 26: Cannot test or generate data for 4xN kernels without suitable SIMD support 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_NoEnergies_CoulombEwaldTwin_VdwEwaldCombGeom (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_Energies_CoulombEwaldTwin_VdwEwaldCombGeom 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:514: Skipped 26: Cannot test or generate data for 4xN kernels without suitable SIMD support 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_Energies_CoulombEwaldTwin_VdwEwaldCombGeom (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwEwaldCombGeom 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:514: Skipped 26: Cannot test or generate data for 4xN kernels without suitable SIMD support 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwEwaldCombGeom (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_NoEnergies_CoulombEwald_VdwCutCombGeom 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:514: Skipped 26: Cannot test or generate data for 4xN kernels without suitable SIMD support 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_NoEnergies_CoulombEwald_VdwCutCombGeom (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_Energies_CoulombEwald_VdwCutCombGeom 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:514: Skipped 26: Cannot test or generate data for 4xN kernels without suitable SIMD support 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_Energies_CoulombEwald_VdwCutCombGeom (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_ThreeEnergyGroups_CoulombEwald_VdwCutCombGeom 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:514: Skipped 26: Cannot test or generate data for 4xN kernels without suitable SIMD support 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_ThreeEnergyGroups_CoulombEwald_VdwCutCombGeom (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_NoEnergies_CoulombEwald_VdwCutCombLB 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:514: Skipped 26: Cannot test or generate data for 4xN kernels without suitable SIMD support 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_NoEnergies_CoulombEwald_VdwCutCombLB (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_Energies_CoulombEwald_VdwCutCombLB 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:514: Skipped 26: Cannot test or generate data for 4xN kernels without suitable SIMD support 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_Energies_CoulombEwald_VdwCutCombLB (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_ThreeEnergyGroups_CoulombEwald_VdwCutCombLB 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:514: Skipped 26: Cannot test or generate data for 4xN kernels without suitable SIMD support 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_ThreeEnergyGroups_CoulombEwald_VdwCutCombLB (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_NoEnergies_CoulombEwald_VdwCutCombNone 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:514: Skipped 26: Cannot test or generate data for 4xN kernels without suitable SIMD support 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_NoEnergies_CoulombEwald_VdwCutCombNone (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_Energies_CoulombEwald_VdwCutCombNone 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:514: Skipped 26: Cannot test or generate data for 4xN kernels without suitable SIMD support 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_Energies_CoulombEwald_VdwCutCombNone (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_ThreeEnergyGroups_CoulombEwald_VdwCutCombNone 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:514: Skipped 26: Cannot test or generate data for 4xN kernels without suitable SIMD support 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_ThreeEnergyGroups_CoulombEwald_VdwCutCombNone (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_NoEnergies_CoulombEwald_VdwForceSwitch 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:514: Skipped 26: Cannot test or generate data for 4xN kernels without suitable SIMD support 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_NoEnergies_CoulombEwald_VdwForceSwitch (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_Energies_CoulombEwald_VdwForceSwitch 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:514: Skipped 26: Cannot test or generate data for 4xN kernels without suitable SIMD support 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_Energies_CoulombEwald_VdwForceSwitch (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_ThreeEnergyGroups_CoulombEwald_VdwForceSwitch 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:514: Skipped 26: Cannot test or generate data for 4xN kernels without suitable SIMD support 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_ThreeEnergyGroups_CoulombEwald_VdwForceSwitch (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_NoEnergies_CoulombEwald_VdwPotSwitch 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:514: Skipped 26: Cannot test or generate data for 4xN kernels without suitable SIMD support 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_NoEnergies_CoulombEwald_VdwPotSwitch (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_Energies_CoulombEwald_VdwPotSwitch 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:514: Skipped 26: Cannot test or generate data for 4xN kernels without suitable SIMD support 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_Energies_CoulombEwald_VdwPotSwitch (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_ThreeEnergyGroups_CoulombEwald_VdwPotSwitch 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:514: Skipped 26: Cannot test or generate data for 4xN kernels without suitable SIMD support 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_ThreeEnergyGroups_CoulombEwald_VdwPotSwitch (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_NoEnergies_CoulombEwald_VdwEwaldCombGeom 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:514: Skipped 26: Cannot test or generate data for 4xN kernels without suitable SIMD support 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_NoEnergies_CoulombEwald_VdwEwaldCombGeom (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_Energies_CoulombEwald_VdwEwaldCombGeom 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:514: Skipped 26: Cannot test or generate data for 4xN kernels without suitable SIMD support 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_Energies_CoulombEwald_VdwEwaldCombGeom (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_ThreeEnergyGroups_CoulombEwald_VdwEwaldCombGeom 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:514: Skipped 26: Cannot test or generate data for 4xN kernels without suitable SIMD support 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_ThreeEnergyGroups_CoulombEwald_VdwEwaldCombGeom (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_NoEnergies_CoulombEwaldTwin_VdwCutCombGeom 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:514: Skipped 26: Cannot test or generate data for 4xN kernels without suitable SIMD support 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_NoEnergies_CoulombEwaldTwin_VdwCutCombGeom (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_Energies_CoulombEwaldTwin_VdwCutCombGeom 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:514: Skipped 26: Cannot test or generate data for 4xN kernels without suitable SIMD support 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_Energies_CoulombEwaldTwin_VdwCutCombGeom (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombGeom 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:514: Skipped 26: Cannot test or generate data for 4xN kernels without suitable SIMD support 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombGeom (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_NoEnergies_CoulombEwaldTwin_VdwCutCombLB 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:514: Skipped 26: Cannot test or generate data for 4xN kernels without suitable SIMD support 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_NoEnergies_CoulombEwaldTwin_VdwCutCombLB (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_Energies_CoulombEwaldTwin_VdwCutCombLB 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:514: Skipped 26: Cannot test or generate data for 4xN kernels without suitable SIMD support 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_Energies_CoulombEwaldTwin_VdwCutCombLB (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombLB 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:514: Skipped 26: Cannot test or generate data for 4xN kernels without suitable SIMD support 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombLB (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_NoEnergies_CoulombEwaldTwin_VdwCutCombNone 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:514: Skipped 26: Cannot test or generate data for 4xN kernels without suitable SIMD support 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_NoEnergies_CoulombEwaldTwin_VdwCutCombNone (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_Energies_CoulombEwaldTwin_VdwCutCombNone 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:514: Skipped 26: Cannot test or generate data for 4xN kernels without suitable SIMD support 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_Energies_CoulombEwaldTwin_VdwCutCombNone (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombNone 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:514: Skipped 26: Cannot test or generate data for 4xN kernels without suitable SIMD support 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombNone (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_NoEnergies_CoulombEwaldTwin_VdwForceSwitch 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:514: Skipped 26: Cannot test or generate data for 4xN kernels without suitable SIMD support 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_NoEnergies_CoulombEwaldTwin_VdwForceSwitch (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_Energies_CoulombEwaldTwin_VdwForceSwitch 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:514: Skipped 26: Cannot test or generate data for 4xN kernels without suitable SIMD support 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_Energies_CoulombEwaldTwin_VdwForceSwitch (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwForceSwitch 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:514: Skipped 26: Cannot test or generate data for 4xN kernels without suitable SIMD support 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwForceSwitch (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_NoEnergies_CoulombEwaldTwin_VdwPotSwitch 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:514: Skipped 26: Cannot test or generate data for 4xN kernels without suitable SIMD support 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_NoEnergies_CoulombEwaldTwin_VdwPotSwitch (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_Energies_CoulombEwaldTwin_VdwPotSwitch 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:514: Skipped 26: Cannot test or generate data for 4xN kernels without suitable SIMD support 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_Energies_CoulombEwaldTwin_VdwPotSwitch (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwPotSwitch 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:514: Skipped 26: Cannot test or generate data for 4xN kernels without suitable SIMD support 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwPotSwitch (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_NoEnergies_CoulombEwaldTwin_VdwEwaldCombGeom 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:514: Skipped 26: Cannot test or generate data for 4xN kernels without suitable SIMD support 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_NoEnergies_CoulombEwaldTwin_VdwEwaldCombGeom (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_Energies_CoulombEwaldTwin_VdwEwaldCombGeom 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:514: Skipped 26: Cannot test or generate data for 4xN kernels without suitable SIMD support 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_Energies_CoulombEwaldTwin_VdwEwaldCombGeom (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwEwaldCombGeom 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:514: Skipped 26: Cannot test or generate data for 4xN kernels without suitable SIMD support 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwEwaldCombGeom (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombReactionField_VdwCutCombGeom 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped 26: Cannot test or generate data for 2xNN kernels without suitable SIMD support 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombReactionField_VdwCutCombGeom (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombReactionField_VdwCutCombGeom 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped 26: Cannot test or generate data for 2xNN kernels without suitable SIMD support 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombReactionField_VdwCutCombGeom (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwCutCombGeom 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped 26: Cannot test or generate data for 2xNN kernels without suitable SIMD support 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwCutCombGeom (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombReactionField_VdwCutCombLB 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped 26: Cannot test or generate data for 2xNN kernels without suitable SIMD support 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombReactionField_VdwCutCombLB (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombReactionField_VdwCutCombLB 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped 26: Cannot test or generate data for 2xNN kernels without suitable SIMD support 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombReactionField_VdwCutCombLB (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwCutCombLB 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped 26: Cannot test or generate data for 2xNN kernels without suitable SIMD support 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwCutCombLB (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombReactionField_VdwCutCombNone 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped 26: Cannot test or generate data for 2xNN kernels without suitable SIMD support 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombReactionField_VdwCutCombNone (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombReactionField_VdwCutCombNone 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped 26: Cannot test or generate data for 2xNN kernels without suitable SIMD support 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombReactionField_VdwCutCombNone (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwCutCombNone 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped 26: Cannot test or generate data for 2xNN kernels without suitable SIMD support 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwCutCombNone (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombReactionField_VdwForceSwitch 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped 26: Cannot test or generate data for 2xNN kernels without suitable SIMD support 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombReactionField_VdwForceSwitch (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombReactionField_VdwForceSwitch 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped 26: Cannot test or generate data for 2xNN kernels without suitable SIMD support 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombReactionField_VdwForceSwitch (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwForceSwitch 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped 26: Cannot test or generate data for 2xNN kernels without suitable SIMD support 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwForceSwitch (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombReactionField_VdwPotSwitch 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped 26: Cannot test or generate data for 2xNN kernels without suitable SIMD support 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombReactionField_VdwPotSwitch (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombReactionField_VdwPotSwitch 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped 26: Cannot test or generate data for 2xNN kernels without suitable SIMD support 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombReactionField_VdwPotSwitch (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwPotSwitch 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped 26: Cannot test or generate data for 2xNN kernels without suitable SIMD support 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwPotSwitch (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombReactionField_VdwEwaldCombGeom 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped 26: Cannot test or generate data for 2xNN kernels without suitable SIMD support 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombReactionField_VdwEwaldCombGeom (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombReactionField_VdwEwaldCombGeom 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped 26: Cannot test or generate data for 2xNN kernels without suitable SIMD support 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombReactionField_VdwEwaldCombGeom (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwEwaldCombGeom 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped 26: Cannot test or generate data for 2xNN kernels without suitable SIMD support 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwEwaldCombGeom (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombEwald_VdwCutCombGeom 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped 26: Cannot test or generate data for 2xNN kernels without suitable SIMD support 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombEwald_VdwCutCombGeom (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombEwald_VdwCutCombGeom 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped 26: Cannot test or generate data for 2xNN kernels without suitable SIMD support 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombEwald_VdwCutCombGeom (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombEwald_VdwCutCombGeom 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped 26: Cannot test or generate data for 2xNN kernels without suitable SIMD support 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombEwald_VdwCutCombGeom (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombEwald_VdwCutCombLB 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped 26: Cannot test or generate data for 2xNN kernels without suitable SIMD support 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombEwald_VdwCutCombLB (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombEwald_VdwCutCombLB 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped 26: Cannot test or generate data for 2xNN kernels without suitable SIMD support 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombEwald_VdwCutCombLB (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombEwald_VdwCutCombLB 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped 26: Cannot test or generate data for 2xNN kernels without suitable SIMD support 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombEwald_VdwCutCombLB (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombEwald_VdwCutCombNone 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped 26: Cannot test or generate data for 2xNN kernels without suitable SIMD support 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombEwald_VdwCutCombNone (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombEwald_VdwCutCombNone 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped 26: Cannot test or generate data for 2xNN kernels without suitable SIMD support 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombEwald_VdwCutCombNone (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombEwald_VdwCutCombNone 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped 26: Cannot test or generate data for 2xNN kernels without suitable SIMD support 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombEwald_VdwCutCombNone (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombEwald_VdwForceSwitch 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped 26: Cannot test or generate data for 2xNN kernels without suitable SIMD support 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombEwald_VdwForceSwitch (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombEwald_VdwForceSwitch 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped 26: Cannot test or generate data for 2xNN kernels without suitable SIMD support 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombEwald_VdwForceSwitch (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombEwald_VdwForceSwitch 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped 26: Cannot test or generate data for 2xNN kernels without suitable SIMD support 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombEwald_VdwForceSwitch (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombEwald_VdwPotSwitch 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped 26: Cannot test or generate data for 2xNN kernels without suitable SIMD support 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombEwald_VdwPotSwitch (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombEwald_VdwPotSwitch 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped 26: Cannot test or generate data for 2xNN kernels without suitable SIMD support 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombEwald_VdwPotSwitch (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombEwald_VdwPotSwitch 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped 26: Cannot test or generate data for 2xNN kernels without suitable SIMD support 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombEwald_VdwPotSwitch (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombEwald_VdwEwaldCombGeom 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped 26: Cannot test or generate data for 2xNN kernels without suitable SIMD support 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombEwald_VdwEwaldCombGeom (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombEwald_VdwEwaldCombGeom 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped 26: Cannot test or generate data for 2xNN kernels without suitable SIMD support 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombEwald_VdwEwaldCombGeom (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombEwald_VdwEwaldCombGeom 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped 26: Cannot test or generate data for 2xNN kernels without suitable SIMD support 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombEwald_VdwEwaldCombGeom (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombEwaldTwin_VdwCutCombGeom 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped 26: Cannot test or generate data for 2xNN kernels without suitable SIMD support 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombEwaldTwin_VdwCutCombGeom (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombEwaldTwin_VdwCutCombGeom 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped 26: Cannot test or generate data for 2xNN kernels without suitable SIMD support 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombEwaldTwin_VdwCutCombGeom (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombGeom 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped 26: Cannot test or generate data for 2xNN kernels without suitable SIMD support 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombGeom (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombEwaldTwin_VdwCutCombLB 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped 26: Cannot test or generate data for 2xNN kernels without suitable SIMD support 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombEwaldTwin_VdwCutCombLB (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombEwaldTwin_VdwCutCombLB 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped 26: Cannot test or generate data for 2xNN kernels without suitable SIMD support 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombEwaldTwin_VdwCutCombLB (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombLB 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped 26: Cannot test or generate data for 2xNN kernels without suitable SIMD support 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombLB (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombEwaldTwin_VdwCutCombNone 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped 26: Cannot test or generate data for 2xNN kernels without suitable SIMD support 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombEwaldTwin_VdwCutCombNone (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombEwaldTwin_VdwCutCombNone 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped 26: Cannot test or generate data for 2xNN kernels without suitable SIMD support 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombEwaldTwin_VdwCutCombNone (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombNone 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped 26: Cannot test or generate data for 2xNN kernels without suitable SIMD support 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombNone (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombEwaldTwin_VdwForceSwitch 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped 26: Cannot test or generate data for 2xNN kernels without suitable SIMD support 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombEwaldTwin_VdwForceSwitch (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombEwaldTwin_VdwForceSwitch 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped 26: Cannot test or generate data for 2xNN kernels without suitable SIMD support 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombEwaldTwin_VdwForceSwitch (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwForceSwitch 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped 26: Cannot test or generate data for 2xNN kernels without suitable SIMD support 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwForceSwitch (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombEwaldTwin_VdwPotSwitch 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped 26: Cannot test or generate data for 2xNN kernels without suitable SIMD support 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombEwaldTwin_VdwPotSwitch (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombEwaldTwin_VdwPotSwitch 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped 26: Cannot test or generate data for 2xNN kernels without suitable SIMD support 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombEwaldTwin_VdwPotSwitch (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwPotSwitch 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped 26: Cannot test or generate data for 2xNN kernels without suitable SIMD support 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwPotSwitch (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombEwaldTwin_VdwEwaldCombGeom 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped 26: Cannot test or generate data for 2xNN kernels without suitable SIMD support 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombEwaldTwin_VdwEwaldCombGeom (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombEwaldTwin_VdwEwaldCombGeom 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped 26: Cannot test or generate data for 2xNN kernels without suitable SIMD support 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombEwaldTwin_VdwEwaldCombGeom (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwEwaldCombGeom 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped 26: Cannot test or generate data for 2xNN kernels without suitable SIMD support 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwEwaldCombGeom (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_NoEnergies_CoulombEwald_VdwCutCombGeom 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped 26: Cannot test or generate data for 2xNN kernels without suitable SIMD support 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_NoEnergies_CoulombEwald_VdwCutCombGeom (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_Energies_CoulombEwald_VdwCutCombGeom 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped 26: Cannot test or generate data for 2xNN kernels without suitable SIMD support 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_Energies_CoulombEwald_VdwCutCombGeom (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_ThreeEnergyGroups_CoulombEwald_VdwCutCombGeom 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped 26: Cannot test or generate data for 2xNN kernels without suitable SIMD support 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_ThreeEnergyGroups_CoulombEwald_VdwCutCombGeom (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_NoEnergies_CoulombEwald_VdwCutCombLB 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped 26: Cannot test or generate data for 2xNN kernels without suitable SIMD support 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_NoEnergies_CoulombEwald_VdwCutCombLB (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_Energies_CoulombEwald_VdwCutCombLB 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped 26: Cannot test or generate data for 2xNN kernels without suitable SIMD support 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_Energies_CoulombEwald_VdwCutCombLB (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_ThreeEnergyGroups_CoulombEwald_VdwCutCombLB 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped 26: Cannot test or generate data for 2xNN kernels without suitable SIMD support 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_ThreeEnergyGroups_CoulombEwald_VdwCutCombLB (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_NoEnergies_CoulombEwald_VdwCutCombNone 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped 26: Cannot test or generate data for 2xNN kernels without suitable SIMD support 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_NoEnergies_CoulombEwald_VdwCutCombNone (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_Energies_CoulombEwald_VdwCutCombNone 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped 26: Cannot test or generate data for 2xNN kernels without suitable SIMD support 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_Energies_CoulombEwald_VdwCutCombNone (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_ThreeEnergyGroups_CoulombEwald_VdwCutCombNone 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped 26: Cannot test or generate data for 2xNN kernels without suitable SIMD support 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_ThreeEnergyGroups_CoulombEwald_VdwCutCombNone (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_NoEnergies_CoulombEwald_VdwForceSwitch 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped 26: Cannot test or generate data for 2xNN kernels without suitable SIMD support 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_NoEnergies_CoulombEwald_VdwForceSwitch (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_Energies_CoulombEwald_VdwForceSwitch 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped 26: Cannot test or generate data for 2xNN kernels without suitable SIMD support 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_Energies_CoulombEwald_VdwForceSwitch (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_ThreeEnergyGroups_CoulombEwald_VdwForceSwitch 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped 26: Cannot test or generate data for 2xNN kernels without suitable SIMD support 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_ThreeEnergyGroups_CoulombEwald_VdwForceSwitch (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_NoEnergies_CoulombEwald_VdwPotSwitch 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped 26: Cannot test or generate data for 2xNN kernels without suitable SIMD support 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_NoEnergies_CoulombEwald_VdwPotSwitch (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_Energies_CoulombEwald_VdwPotSwitch 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped 26: Cannot test or generate data for 2xNN kernels without suitable SIMD support 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_Energies_CoulombEwald_VdwPotSwitch (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_ThreeEnergyGroups_CoulombEwald_VdwPotSwitch 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped 26: Cannot test or generate data for 2xNN kernels without suitable SIMD support 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_ThreeEnergyGroups_CoulombEwald_VdwPotSwitch (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_NoEnergies_CoulombEwald_VdwEwaldCombGeom 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped 26: Cannot test or generate data for 2xNN kernels without suitable SIMD support 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_NoEnergies_CoulombEwald_VdwEwaldCombGeom (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_Energies_CoulombEwald_VdwEwaldCombGeom 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped 26: Cannot test or generate data for 2xNN kernels without suitable SIMD support 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_Energies_CoulombEwald_VdwEwaldCombGeom (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_ThreeEnergyGroups_CoulombEwald_VdwEwaldCombGeom 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped 26: Cannot test or generate data for 2xNN kernels without suitable SIMD support 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_ThreeEnergyGroups_CoulombEwald_VdwEwaldCombGeom (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_NoEnergies_CoulombEwaldTwin_VdwCutCombGeom 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped 26: Cannot test or generate data for 2xNN kernels without suitable SIMD support 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_NoEnergies_CoulombEwaldTwin_VdwCutCombGeom (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_Energies_CoulombEwaldTwin_VdwCutCombGeom 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped 26: Cannot test or generate data for 2xNN kernels without suitable SIMD support 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_Energies_CoulombEwaldTwin_VdwCutCombGeom (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombGeom 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped 26: Cannot test or generate data for 2xNN kernels without suitable SIMD support 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombGeom (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_NoEnergies_CoulombEwaldTwin_VdwCutCombLB 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped 26: Cannot test or generate data for 2xNN kernels without suitable SIMD support 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_NoEnergies_CoulombEwaldTwin_VdwCutCombLB (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_Energies_CoulombEwaldTwin_VdwCutCombLB 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped 26: Cannot test or generate data for 2xNN kernels without suitable SIMD support 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_Energies_CoulombEwaldTwin_VdwCutCombLB (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombLB 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped 26: Cannot test or generate data for 2xNN kernels without suitable SIMD support 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombLB (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_NoEnergies_CoulombEwaldTwin_VdwCutCombNone 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped 26: Cannot test or generate data for 2xNN kernels without suitable SIMD support 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_NoEnergies_CoulombEwaldTwin_VdwCutCombNone (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_Energies_CoulombEwaldTwin_VdwCutCombNone 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped 26: Cannot test or generate data for 2xNN kernels without suitable SIMD support 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_Energies_CoulombEwaldTwin_VdwCutCombNone (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombNone 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped 26: Cannot test or generate data for 2xNN kernels without suitable SIMD support 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombNone (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_NoEnergies_CoulombEwaldTwin_VdwForceSwitch 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped 26: Cannot test or generate data for 2xNN kernels without suitable SIMD support 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_NoEnergies_CoulombEwaldTwin_VdwForceSwitch (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_Energies_CoulombEwaldTwin_VdwForceSwitch 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped 26: Cannot test or generate data for 2xNN kernels without suitable SIMD support 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_Energies_CoulombEwaldTwin_VdwForceSwitch (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwForceSwitch 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped 26: Cannot test or generate data for 2xNN kernels without suitable SIMD support 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwForceSwitch (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_NoEnergies_CoulombEwaldTwin_VdwPotSwitch 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped 26: Cannot test or generate data for 2xNN kernels without suitable SIMD support 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_NoEnergies_CoulombEwaldTwin_VdwPotSwitch (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_Energies_CoulombEwaldTwin_VdwPotSwitch 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped 26: Cannot test or generate data for 2xNN kernels without suitable SIMD support 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_Energies_CoulombEwaldTwin_VdwPotSwitch (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwPotSwitch 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped 26: Cannot test or generate data for 2xNN kernels without suitable SIMD support 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwPotSwitch (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_NoEnergies_CoulombEwaldTwin_VdwEwaldCombGeom 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped 26: Cannot test or generate data for 2xNN kernels without suitable SIMD support 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_NoEnergies_CoulombEwaldTwin_VdwEwaldCombGeom (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_Energies_CoulombEwaldTwin_VdwEwaldCombGeom 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped 26: Cannot test or generate data for 2xNN kernels without suitable SIMD support 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_Energies_CoulombEwaldTwin_VdwEwaldCombGeom (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwEwaldCombGeom 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped 26: Cannot test or generate data for 2xNN kernels without suitable SIMD support 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwEwaldCombGeom (0 ms) 26: [----------] 360 tests from Combinations/NbnxmKernelTest (2026 ms total) 26: 26: [----------] Global test environment tear-down 26: [==========] 380 tests from 3 test suites ran. (2029 ms total) 26: [ PASSED ] 92 tests. 26: [ SKIPPED ] 288 tests, listed below: 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombReactionField_VdwCutCombGeom 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombReactionField_VdwCutCombGeom 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwCutCombGeom 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombReactionField_VdwCutCombLB 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombReactionField_VdwCutCombLB 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwCutCombLB 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombEwald_VdwCutCombGeom 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombEwald_VdwCutCombGeom 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombEwald_VdwCutCombGeom 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombEwald_VdwCutCombLB 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombEwald_VdwCutCombLB 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombEwald_VdwCutCombLB 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombEwald_VdwCutCombNone 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombEwald_VdwCutCombNone 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombEwald_VdwCutCombNone 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombEwald_VdwForceSwitch 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombEwald_VdwForceSwitch 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombEwald_VdwForceSwitch 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombEwald_VdwPotSwitch 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombEwald_VdwPotSwitch 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombEwald_VdwPotSwitch 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombEwald_VdwEwaldCombGeom 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombEwald_VdwEwaldCombGeom 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombEwald_VdwEwaldCombGeom 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombEwaldTwin_VdwCutCombGeom 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombEwaldTwin_VdwCutCombGeom 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombGeom 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombEwaldTwin_VdwCutCombLB 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombEwaldTwin_VdwCutCombLB 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombLB 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombEwaldTwin_VdwCutCombNone 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombEwaldTwin_VdwCutCombNone 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombNone 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombEwaldTwin_VdwForceSwitch 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombEwaldTwin_VdwForceSwitch 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwForceSwitch 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombEwaldTwin_VdwPotSwitch 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombEwaldTwin_VdwPotSwitch 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwPotSwitch 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombEwaldTwin_VdwEwaldCombGeom 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombEwaldTwin_VdwEwaldCombGeom 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwEwaldCombGeom 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_NoEnergies_CoulombEwald_VdwCutCombGeom 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_Energies_CoulombEwald_VdwCutCombGeom 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_ThreeEnergyGroups_CoulombEwald_VdwCutCombGeom 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_NoEnergies_CoulombEwald_VdwCutCombLB 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_Energies_CoulombEwald_VdwCutCombLB 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_ThreeEnergyGroups_CoulombEwald_VdwCutCombLB 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_NoEnergies_CoulombEwaldTwin_VdwCutCombGeom 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_Energies_CoulombEwaldTwin_VdwCutCombGeom 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombGeom 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_NoEnergies_CoulombEwaldTwin_VdwCutCombLB 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_Energies_CoulombEwaldTwin_VdwCutCombLB 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombLB 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombReactionField_VdwCutCombGeom 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombReactionField_VdwCutCombGeom 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwCutCombGeom 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombReactionField_VdwCutCombLB 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombReactionField_VdwCutCombLB 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwCutCombLB 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombEwald_VdwCutCombGeom 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombEwald_VdwCutCombGeom 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombEwald_VdwCutCombGeom 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombEwald_VdwCutCombLB 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombEwald_VdwCutCombLB 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombEwald_VdwCutCombLB 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombEwald_VdwCutCombNone 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombEwald_VdwCutCombNone 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombEwald_VdwCutCombNone 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombEwald_VdwForceSwitch 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombEwald_VdwForceSwitch 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombEwald_VdwForceSwitch 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombEwald_VdwPotSwitch 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombEwald_VdwPotSwitch 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombEwald_VdwPotSwitch 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombEwald_VdwEwaldCombGeom 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombEwald_VdwEwaldCombGeom 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombEwald_VdwEwaldCombGeom 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombEwaldTwin_VdwCutCombGeom 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombEwaldTwin_VdwCutCombGeom 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombGeom 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombEwaldTwin_VdwCutCombLB 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombEwaldTwin_VdwCutCombLB 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombLB 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombEwaldTwin_VdwCutCombNone 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombEwaldTwin_VdwCutCombNone 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombNone 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombEwaldTwin_VdwForceSwitch 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombEwaldTwin_VdwForceSwitch 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwForceSwitch 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombEwaldTwin_VdwPotSwitch 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombEwaldTwin_VdwPotSwitch 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwPotSwitch 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombEwaldTwin_VdwEwaldCombGeom 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombEwaldTwin_VdwEwaldCombGeom 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwEwaldCombGeom 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_NoEnergies_CoulombEwald_VdwCutCombGeom 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_Energies_CoulombEwald_VdwCutCombGeom 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_ThreeEnergyGroups_CoulombEwald_VdwCutCombGeom 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_NoEnergies_CoulombEwald_VdwCutCombLB 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_Energies_CoulombEwald_VdwCutCombLB 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_ThreeEnergyGroups_CoulombEwald_VdwCutCombLB 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_NoEnergies_CoulombEwaldTwin_VdwCutCombGeom 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_Energies_CoulombEwaldTwin_VdwCutCombGeom 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombGeom 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_NoEnergies_CoulombEwaldTwin_VdwCutCombLB 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_Energies_CoulombEwaldTwin_VdwCutCombLB 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombLB 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_NoEnergies_CoulombReactionField_VdwCutCombGeom 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_Energies_CoulombReactionField_VdwCutCombGeom 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwCutCombGeom 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_NoEnergies_CoulombReactionField_VdwCutCombLB 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_Energies_CoulombReactionField_VdwCutCombLB 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwCutCombLB 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_NoEnergies_CoulombReactionField_VdwCutCombNone 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_Energies_CoulombReactionField_VdwCutCombNone 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwCutCombNone 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_NoEnergies_CoulombReactionField_VdwForceSwitch 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_Energies_CoulombReactionField_VdwForceSwitch 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwForceSwitch 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_NoEnergies_CoulombReactionField_VdwPotSwitch 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_Energies_CoulombReactionField_VdwPotSwitch 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwPotSwitch 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_NoEnergies_CoulombReactionField_VdwEwaldCombGeom 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_Energies_CoulombReactionField_VdwEwaldCombGeom 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwEwaldCombGeom 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_NoEnergies_CoulombEwald_VdwCutCombGeom 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_Energies_CoulombEwald_VdwCutCombGeom 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_ThreeEnergyGroups_CoulombEwald_VdwCutCombGeom 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_NoEnergies_CoulombEwald_VdwCutCombLB 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_Energies_CoulombEwald_VdwCutCombLB 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_ThreeEnergyGroups_CoulombEwald_VdwCutCombLB 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_NoEnergies_CoulombEwald_VdwCutCombNone 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_Energies_CoulombEwald_VdwCutCombNone 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_ThreeEnergyGroups_CoulombEwald_VdwCutCombNone 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_NoEnergies_CoulombEwald_VdwForceSwitch 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_Energies_CoulombEwald_VdwForceSwitch 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_ThreeEnergyGroups_CoulombEwald_VdwForceSwitch 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_NoEnergies_CoulombEwald_VdwPotSwitch 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_Energies_CoulombEwald_VdwPotSwitch 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_ThreeEnergyGroups_CoulombEwald_VdwPotSwitch 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_NoEnergies_CoulombEwald_VdwEwaldCombGeom 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_Energies_CoulombEwald_VdwEwaldCombGeom 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_ThreeEnergyGroups_CoulombEwald_VdwEwaldCombGeom 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_NoEnergies_CoulombEwaldTwin_VdwCutCombGeom 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_Energies_CoulombEwaldTwin_VdwCutCombGeom 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombGeom 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_NoEnergies_CoulombEwaldTwin_VdwCutCombLB 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_Energies_CoulombEwaldTwin_VdwCutCombLB 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombLB 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_NoEnergies_CoulombEwaldTwin_VdwCutCombNone 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_Energies_CoulombEwaldTwin_VdwCutCombNone 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombNone 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_NoEnergies_CoulombEwaldTwin_VdwForceSwitch 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_Energies_CoulombEwaldTwin_VdwForceSwitch 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwForceSwitch 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_NoEnergies_CoulombEwaldTwin_VdwPotSwitch 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_Energies_CoulombEwaldTwin_VdwPotSwitch 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwPotSwitch 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_NoEnergies_CoulombEwaldTwin_VdwEwaldCombGeom 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_Energies_CoulombEwaldTwin_VdwEwaldCombGeom 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwEwaldCombGeom 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_NoEnergies_CoulombEwald_VdwCutCombGeom 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_Energies_CoulombEwald_VdwCutCombGeom 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_ThreeEnergyGroups_CoulombEwald_VdwCutCombGeom 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_NoEnergies_CoulombEwald_VdwCutCombLB 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_Energies_CoulombEwald_VdwCutCombLB 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_ThreeEnergyGroups_CoulombEwald_VdwCutCombLB 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_NoEnergies_CoulombEwald_VdwCutCombNone 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_Energies_CoulombEwald_VdwCutCombNone 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_ThreeEnergyGroups_CoulombEwald_VdwCutCombNone 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_NoEnergies_CoulombEwald_VdwForceSwitch 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_Energies_CoulombEwald_VdwForceSwitch 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_ThreeEnergyGroups_CoulombEwald_VdwForceSwitch 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_NoEnergies_CoulombEwald_VdwPotSwitch 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_Energies_CoulombEwald_VdwPotSwitch 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_ThreeEnergyGroups_CoulombEwald_VdwPotSwitch 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_NoEnergies_CoulombEwald_VdwEwaldCombGeom 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_Energies_CoulombEwald_VdwEwaldCombGeom 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_ThreeEnergyGroups_CoulombEwald_VdwEwaldCombGeom 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_NoEnergies_CoulombEwaldTwin_VdwCutCombGeom 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_Energies_CoulombEwaldTwin_VdwCutCombGeom 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombGeom 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_NoEnergies_CoulombEwaldTwin_VdwCutCombLB 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_Energies_CoulombEwaldTwin_VdwCutCombLB 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombLB 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_NoEnergies_CoulombEwaldTwin_VdwCutCombNone 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_Energies_CoulombEwaldTwin_VdwCutCombNone 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombNone 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_NoEnergies_CoulombEwaldTwin_VdwForceSwitch 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_Energies_CoulombEwaldTwin_VdwForceSwitch 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwForceSwitch 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_NoEnergies_CoulombEwaldTwin_VdwPotSwitch 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_Energies_CoulombEwaldTwin_VdwPotSwitch 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwPotSwitch 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_NoEnergies_CoulombEwaldTwin_VdwEwaldCombGeom 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_Energies_CoulombEwaldTwin_VdwEwaldCombGeom 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwEwaldCombGeom 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombReactionField_VdwCutCombGeom 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombReactionField_VdwCutCombGeom 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwCutCombGeom 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombReactionField_VdwCutCombLB 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombReactionField_VdwCutCombLB 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwCutCombLB 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombReactionField_VdwCutCombNone 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombReactionField_VdwCutCombNone 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwCutCombNone 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombReactionField_VdwForceSwitch 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombReactionField_VdwForceSwitch 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwForceSwitch 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombReactionField_VdwPotSwitch 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombReactionField_VdwPotSwitch 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwPotSwitch 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombReactionField_VdwEwaldCombGeom 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombReactionField_VdwEwaldCombGeom 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwEwaldCombGeom 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombEwald_VdwCutCombGeom 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombEwald_VdwCutCombGeom 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombEwald_VdwCutCombGeom 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombEwald_VdwCutCombLB 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombEwald_VdwCutCombLB 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombEwald_VdwCutCombLB 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombEwald_VdwCutCombNone 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombEwald_VdwCutCombNone 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombEwald_VdwCutCombNone 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombEwald_VdwForceSwitch 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombEwald_VdwForceSwitch 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombEwald_VdwForceSwitch 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombEwald_VdwPotSwitch 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombEwald_VdwPotSwitch 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombEwald_VdwPotSwitch 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombEwald_VdwEwaldCombGeom 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombEwald_VdwEwaldCombGeom 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombEwald_VdwEwaldCombGeom 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombEwaldTwin_VdwCutCombGeom 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombEwaldTwin_VdwCutCombGeom 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombGeom 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombEwaldTwin_VdwCutCombLB 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombEwaldTwin_VdwCutCombLB 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombLB 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombEwaldTwin_VdwCutCombNone 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombEwaldTwin_VdwCutCombNone 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombNone 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombEwaldTwin_VdwForceSwitch 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombEwaldTwin_VdwForceSwitch 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwForceSwitch 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombEwaldTwin_VdwPotSwitch 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombEwaldTwin_VdwPotSwitch 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwPotSwitch 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombEwaldTwin_VdwEwaldCombGeom 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombEwaldTwin_VdwEwaldCombGeom 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwEwaldCombGeom 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_NoEnergies_CoulombEwald_VdwCutCombGeom 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_Energies_CoulombEwald_VdwCutCombGeom 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_ThreeEnergyGroups_CoulombEwald_VdwCutCombGeom 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_NoEnergies_CoulombEwald_VdwCutCombLB 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_Energies_CoulombEwald_VdwCutCombLB 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_ThreeEnergyGroups_CoulombEwald_VdwCutCombLB 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_NoEnergies_CoulombEwald_VdwCutCombNone 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_Energies_CoulombEwald_VdwCutCombNone 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_ThreeEnergyGroups_CoulombEwald_VdwCutCombNone 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_NoEnergies_CoulombEwald_VdwForceSwitch 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_Energies_CoulombEwald_VdwForceSwitch 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_ThreeEnergyGroups_CoulombEwald_VdwForceSwitch 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_NoEnergies_CoulombEwald_VdwPotSwitch 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_Energies_CoulombEwald_VdwPotSwitch 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_ThreeEnergyGroups_CoulombEwald_VdwPotSwitch 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_NoEnergies_CoulombEwald_VdwEwaldCombGeom 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_Energies_CoulombEwald_VdwEwaldCombGeom 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_ThreeEnergyGroups_CoulombEwald_VdwEwaldCombGeom 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_NoEnergies_CoulombEwaldTwin_VdwCutCombGeom 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_Energies_CoulombEwaldTwin_VdwCutCombGeom 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombGeom 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_NoEnergies_CoulombEwaldTwin_VdwCutCombLB 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_Energies_CoulombEwaldTwin_VdwCutCombLB 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombLB 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_NoEnergies_CoulombEwaldTwin_VdwCutCombNone 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_Energies_CoulombEwaldTwin_VdwCutCombNone 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombNone 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_NoEnergies_CoulombEwaldTwin_VdwForceSwitch 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_Energies_CoulombEwaldTwin_VdwForceSwitch 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwForceSwitch 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_NoEnergies_CoulombEwaldTwin_VdwPotSwitch 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_Energies_CoulombEwaldTwin_VdwPotSwitch 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwPotSwitch 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_NoEnergies_CoulombEwaldTwin_VdwEwaldCombGeom 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_Energies_CoulombEwaldTwin_VdwEwaldCombGeom 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwEwaldCombGeom 26/92 Test #26: NbnxmTests ................................ Passed 2.24 sec test 27 Start 27: NbnxmGpuTests 27: Test command: /build/reproducible-path/gromacs-2025.1/build/basic-dp/bin/nbnxm-gpu-test "--gtest_output=xml:/build/reproducible-path/gromacs-2025.1/build/basic-dp/Testing/Temporary/NbnxmGpuTests.xml" 27: Working Directory: /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/nbnxm/tests 27: Test timeout computed to be: 30 27: [==========] Running 0 tests from 0 test suites. 27: [==========] 0 tests from 0 test suites ran. (0 ms total) 27: [ PASSED ] 0 tests. 27/92 Test #27: NbnxmGpuTests ............................. Passed 0.12 sec test 28 Start 28: CommandLineUnitTests 28: Test command: /build/reproducible-path/gromacs-2025.1/build/basic-dp/bin/commandline-test "--gtest_output=xml:/build/reproducible-path/gromacs-2025.1/build/basic-dp/Testing/Temporary/CommandLineUnitTests.xml" 28: Working Directory: /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/commandline/tests 28: Test timeout computed to be: 30 28: [==========] Running 60 tests from 7 test suites. 28: [----------] Global test environment set-up. 28: [----------] 3 tests from CommandLineHelpModuleTest 28: [ RUN ] CommandLineHelpModuleTest.PrintsGeneralHelp 28: [ OK ] CommandLineHelpModuleTest.PrintsGeneralHelp (3 ms) 28: [ RUN ] CommandLineHelpModuleTest.PrintsHelpOnTopic 28: [ OK ] CommandLineHelpModuleTest.PrintsHelpOnTopic (1 ms) 28: [ RUN ] CommandLineHelpModuleTest.ExportsHelp 28: [ OK ] CommandLineHelpModuleTest.ExportsHelp (4 ms) 28: [----------] 3 tests from CommandLineHelpModuleTest (9 ms total) 28: 28: [----------] 7 tests from CommandLineHelpWriterTest 28: [ RUN ] CommandLineHelpWriterTest.HandlesOptionTypes 28: [ OK ] CommandLineHelpWriterTest.HandlesOptionTypes (2 ms) 28: [ RUN ] CommandLineHelpWriterTest.HandlesDefaultValuesFromVariables 28: [ OK ] CommandLineHelpWriterTest.HandlesDefaultValuesFromVariables (0 ms) 28: [ RUN ] CommandLineHelpWriterTest.HandlesLongFileOptions 28: [ OK ] CommandLineHelpWriterTest.HandlesLongFileOptions (1 ms) 28: [ RUN ] CommandLineHelpWriterTest.HandlesLongOptions 28: [ OK ] CommandLineHelpWriterTest.HandlesLongOptions (0 ms) 28: [ RUN ] CommandLineHelpWriterTest.HandlesOptionGroups 28: [ OK ] CommandLineHelpWriterTest.HandlesOptionGroups (0 ms) 28: [ RUN ] CommandLineHelpWriterTest.HandlesHelpText 28: [ OK ] CommandLineHelpWriterTest.HandlesHelpText (0 ms) 28: [ RUN ] CommandLineHelpWriterTest.HandlesKnownIssues 28: [ OK ] CommandLineHelpWriterTest.HandlesKnownIssues (0 ms) 28: [----------] 7 tests from CommandLineHelpWriterTest (8 ms total) 28: 28: [----------] 6 tests from CommandLineModuleManagerTest 28: [ RUN ] CommandLineModuleManagerTest.RunsModule 28: [ OK ] CommandLineModuleManagerTest.RunsModule (0 ms) 28: [ RUN ] CommandLineModuleManagerTest.RunsModuleHelp 28: [ OK ] CommandLineModuleManagerTest.RunsModuleHelp (0 ms) 28: [ RUN ] CommandLineModuleManagerTest.RunsModuleHelpAfterQuiet 28: [ OK ] CommandLineModuleManagerTest.RunsModuleHelpAfterQuiet (0 ms) 28: [ RUN ] CommandLineModuleManagerTest.RunsModuleHelpWithDashH 28: [ OK ] CommandLineModuleManagerTest.RunsModuleHelpWithDashH (0 ms) 28: [ RUN ] CommandLineModuleManagerTest.RunsModuleHelpWithDashHWithSingleModule 28: [ OK ] CommandLineModuleManagerTest.RunsModuleHelpWithDashHWithSingleModule (0 ms) 28: [ RUN ] CommandLineModuleManagerTest.HandlesConflictingBinaryAndModuleNames 28: [ OK ] CommandLineModuleManagerTest.HandlesConflictingBinaryAndModuleNames (0 ms) 28: [----------] 6 tests from CommandLineModuleManagerTest (3 ms total) 28: 28: [----------] 13 tests from CommandLineParserTest 28: [ RUN ] CommandLineParserTest.HandlesSingleValues 28: [ OK ] CommandLineParserTest.HandlesSingleValues (0 ms) 28: [ RUN ] CommandLineParserTest.HandlesBooleanWithoutArgument 28: [ OK ] CommandLineParserTest.HandlesBooleanWithoutArgument (0 ms) 28: [ RUN ] CommandLineParserTest.HandlesBooleanAsNoWithoutArgument 28: [ OK ] CommandLineParserTest.HandlesBooleanAsNoWithoutArgument (0 ms) 28: [ RUN ] CommandLineParserTest.ThrowsWithBooleanAsNoWithArgument 28: [ OK ] CommandLineParserTest.ThrowsWithBooleanAsNoWithArgument (0 ms) 28: [ RUN ] CommandLineParserTest.HandlesNegativeNumbers 28: [ OK ] CommandLineParserTest.HandlesNegativeNumbers (0 ms) 28: [ RUN ] CommandLineParserTest.HandlesString 28: [ OK ] CommandLineParserTest.HandlesString (0 ms) 28: [ RUN ] CommandLineParserTest.RejectsStringWithMultipleValues 28: [ OK ] CommandLineParserTest.RejectsStringWithMultipleValues (0 ms) 28: [ RUN ] CommandLineParserTest.HandlesDoubleDashOptionPrefix 28: [ OK ] CommandLineParserTest.HandlesDoubleDashOptionPrefix (0 ms) 28: [ RUN ] CommandLineParserTest.HandlesOptionsStartingWithNumbers 28: [ OK ] CommandLineParserTest.HandlesOptionsStartingWithNumbers (0 ms) 28: [ RUN ] CommandLineParserTest.HandlesSkipUnknown 28: [ OK ] CommandLineParserTest.HandlesSkipUnknown (0 ms) 28: [ RUN ] CommandLineParserTest.RejectsPositionalArgumentsByDefault 28: [ OK ] CommandLineParserTest.RejectsPositionalArgumentsByDefault (0 ms) 28: [ RUN ] CommandLineParserTest.CanAllowPositionalArguments 28: [ OK ] CommandLineParserTest.CanAllowPositionalArguments (0 ms) 28: [ RUN ] CommandLineParserTest.CannotHavePositionalArgumentsAfterOptions 28: [ OK ] CommandLineParserTest.CannotHavePositionalArgumentsAfterOptions (0 ms) 28: [----------] 13 tests from CommandLineParserTest (3 ms total) 28: 28: [----------] 6 tests from CommandLineProgramContextTest 28: [ RUN ] CommandLineProgramContextTest.FindsBinaryWithAbsolutePath 28: [ OK ] CommandLineProgramContextTest.FindsBinaryWithAbsolutePath (0 ms) 28: [ RUN ] CommandLineProgramContextTest.FindsBinaryWithRelativePath 28: [ OK ] CommandLineProgramContextTest.FindsBinaryWithRelativePath (0 ms) 28: [ RUN ] CommandLineProgramContextTest.FindsBinaryFromPath 28: [ OK ] CommandLineProgramContextTest.FindsBinaryFromPath (0 ms) 28: [ RUN ] CommandLineProgramContextTest.FindsBinaryFromCurrentDirectory 28: [ OK ] CommandLineProgramContextTest.FindsBinaryFromCurrentDirectory (0 ms) 28: [ RUN ] CommandLineProgramContextTest.FindsBinaryFromAbsoluteSymLink 28: [ OK ] CommandLineProgramContextTest.FindsBinaryFromAbsoluteSymLink (0 ms) 28: [ RUN ] CommandLineProgramContextTest.FindsBinaryFromRelativeSymLink 28: [ OK ] CommandLineProgramContextTest.FindsBinaryFromRelativeSymLink (0 ms) 28: [----------] 6 tests from CommandLineProgramContextTest (1 ms total) 28: 28: [----------] 3 tests from OutputNamesTest 28: [ RUN ] OutputNamesTest.CanBeSuffixed 28: [ OK ] OutputNamesTest.CanBeSuffixed (0 ms) 28: [ RUN ] OutputNamesTest.HasSuffixFromNoAppend 28: [ OK ] OutputNamesTest.HasSuffixFromNoAppend (0 ms) 28: [ RUN ] OutputNamesTest.CanHavePartNumberAdded 28: [ OK ] OutputNamesTest.CanHavePartNumberAdded (0 ms) 28: [----------] 3 tests from OutputNamesTest (0 ms total) 28: 28: [----------] 22 tests from ParseCommonArgsTest 28: [ RUN ] ParseCommonArgsTest.ParsesIntegerArgs 28: [ OK ] ParseCommonArgsTest.ParsesIntegerArgs (0 ms) 28: [ RUN ] ParseCommonArgsTest.ParsesInt64Args 28: [ OK ] ParseCommonArgsTest.ParsesInt64Args (0 ms) 28: [ RUN ] ParseCommonArgsTest.ParsesRealArgs 28: [ OK ] ParseCommonArgsTest.ParsesRealArgs (0 ms) 28: [ RUN ] ParseCommonArgsTest.ParsesStringArgs 28: [ OK ] ParseCommonArgsTest.ParsesStringArgs (0 ms) 28: [ RUN ] ParseCommonArgsTest.ParsesBooleanArgs 28: [ OK ] ParseCommonArgsTest.ParsesBooleanArgs (0 ms) 28: [ RUN ] ParseCommonArgsTest.ParsesBooleanArgsToValuesOfSuitableEnum 28: [ OK ] ParseCommonArgsTest.ParsesBooleanArgsToValuesOfSuitableEnum (0 ms) 28: [ RUN ] ParseCommonArgsTest.ParsesVectorArgs 28: [ OK ] ParseCommonArgsTest.ParsesVectorArgs (0 ms) 28: [ RUN ] ParseCommonArgsTest.ParsesTimeArgs 28: [ OK ] ParseCommonArgsTest.ParsesTimeArgs (0 ms) 28: [ RUN ] ParseCommonArgsTest.ParsesTimeArgsWithTimeUnit 28: [ OK ] ParseCommonArgsTest.ParsesTimeArgsWithTimeUnit (0 ms) 28: [ RUN ] ParseCommonArgsTest.ParsesEnumArgs 28: [ OK ] ParseCommonArgsTest.ParsesEnumArgs (0 ms) 28: [ RUN ] ParseCommonArgsTest.ParsesFileArgs 28: [ OK ] ParseCommonArgsTest.ParsesFileArgs (0 ms) 28: [ RUN ] ParseCommonArgsTest.ParsesFileArgsWithDefaults 28: [ OK ] ParseCommonArgsTest.ParsesFileArgsWithDefaults (0 ms) 28: [ RUN ] ParseCommonArgsTest.ParsesFileArgsWithDefaultFileName 28: [ OK ] ParseCommonArgsTest.ParsesFileArgsWithDefaultFileName (0 ms) 28: [ RUN ] ParseCommonArgsTest.ParseFileArgsWithCustomDefaultExtension 28: [ OK ] ParseCommonArgsTest.ParseFileArgsWithCustomDefaultExtension (0 ms) 28: [ RUN ] ParseCommonArgsTest.HandlesNonExistentInputFiles 28: [ OK ] ParseCommonArgsTest.HandlesNonExistentInputFiles (0 ms) 28: [ RUN ] ParseCommonArgsTest.HandlesNonExistentOptionalInputFiles 28: [ OK ] ParseCommonArgsTest.HandlesNonExistentOptionalInputFiles (0 ms) 28: [ RUN ] ParseCommonArgsTest.AcceptsNonExistentInputFilesIfSpecified 28: [ OK ] ParseCommonArgsTest.AcceptsNonExistentInputFilesIfSpecified (0 ms) 28: [ RUN ] ParseCommonArgsTest.HandlesCompressedFiles 28: [ OK ] ParseCommonArgsTest.HandlesCompressedFiles (2 ms) 28: [ RUN ] ParseCommonArgsTest.AcceptsUnknownTrajectoryExtension 28: Value is /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/commandline/tests/Testing/Temporary/ParseCommonArgsTest_AcceptsUnknownTrajectoryExtension.foo 28: [ OK ] ParseCommonArgsTest.AcceptsUnknownTrajectoryExtension (0 ms) 28: [ RUN ] ParseCommonArgsTest.CompletesExtensionFromExistingFile 28: [ OK ] ParseCommonArgsTest.CompletesExtensionFromExistingFile (3 ms) 28: [ RUN ] ParseCommonArgsTest.CompletesExtensionFromExistingFileWithDefaultFileName 28: [ OK ] ParseCommonArgsTest.CompletesExtensionFromExistingFileWithDefaultFileName (3 ms) 28: [ RUN ] ParseCommonArgsTest.CanKeepUnknownArgs 28: [ OK ] ParseCommonArgsTest.CanKeepUnknownArgs (0 ms) 28: [----------] 22 tests from ParseCommonArgsTest (16 ms total) 28: 28: [----------] Global test environment tear-down 28: [==========] 60 tests from 7 test suites ran. (42 ms total) 28: [ PASSED ] 60 tests. 28/92 Test #28: CommandLineUnitTests ...................... Passed 0.14 sec test 29 Start 29: DomDecTests 29: Test command: /build/reproducible-path/gromacs-2025.1/build/basic-dp/bin/domdec-test "--gtest_output=xml:/build/reproducible-path/gromacs-2025.1/build/basic-dp/Testing/Temporary/DomDecTests.xml" 29: Working Directory: /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/domdec/tests 29: Test timeout computed to be: 30 29: [==========] Running 9 tests from 2 test suites. 29: [----------] Global test environment set-up. 29: [----------] 7 tests from HashedMap 29: [ RUN ] HashedMap.InsertsFinds 29: [ OK ] HashedMap.InsertsFinds (0 ms) 29: [ RUN ] HashedMap.NegativeKeysWork 29: [ OK ] HashedMap.NegativeKeysWork (0 ms) 29: [ RUN ] HashedMap.InsertsErases 29: [ OK ] HashedMap.InsertsErases (0 ms) 29: [ RUN ] HashedMap.InsertsOrAssigns 29: [ OK ] HashedMap.InsertsOrAssigns (0 ms) 29: [ RUN ] HashedMap.Clears 29: [ OK ] HashedMap.Clears (0 ms) 29: [ RUN ] HashedMap.LinkedEntries 29: [ OK ] HashedMap.LinkedEntries (0 ms) 29: [ RUN ] HashedMap.ResizesTable 29: [ OK ] HashedMap.ResizesTable (0 ms) 29: [----------] 7 tests from HashedMap (0 ms total) 29: 29: [----------] 2 tests from LocalAtomSetManager 29: [ RUN ] LocalAtomSetManager.CanAddEmptyLocalAtomSet 29: [ OK ] LocalAtomSetManager.CanAddEmptyLocalAtomSet (0 ms) 29: [ RUN ] LocalAtomSetManager.CanAddandReadLocalAtomSetIndices 29: [ OK ] LocalAtomSetManager.CanAddandReadLocalAtomSetIndices (0 ms) 29: [----------] 2 tests from LocalAtomSetManager (0 ms total) 29: 29: [----------] Global test environment tear-down 29: [==========] 9 tests from 2 test suites ran. (0 ms total) 29: [ PASSED ] 9 tests. 29/92 Test #29: DomDecTests ............................... Passed 0.07 sec test 30 Start 30: DomDecMpiTests 30: Test command: /build/reproducible-path/gromacs-2025.1/build/basic-dp/bin/domdec-mpi-test "-ntmpi" "4" "--gtest_output=xml:/build/reproducible-path/gromacs-2025.1/build/basic-dp/Testing/Temporary/DomDecMpiTests.xml" 30: Working Directory: /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/domdec/tests 30: Test timeout computed to be: 30 30: [==========] Running 4 tests from 1 test suite. 30: [----------] Global test environment set-up. 30: [----------] 4 tests from HaloExchangeTest 30: [ RUN ] HaloExchangeTest.Coordinates1dHaloWith1Pulse 30: [ OK ] HaloExchangeTest.Coordinates1dHaloWith1Pulse (19 ms) 30: [ RUN ] HaloExchangeTest.Coordinates1dHaloWith2Pulses 30: [ OK ] HaloExchangeTest.Coordinates1dHaloWith2Pulses (27 ms) 30: [ RUN ] HaloExchangeTest.Coordinates2dHaloWith1PulseInEachDim 30: [ OK ] HaloExchangeTest.Coordinates2dHaloWith1PulseInEachDim (16 ms) 30: [ RUN ] HaloExchangeTest.Coordinates2dHaloWith2PulsesInDim1 30: [ OK ] HaloExchangeTest.Coordinates2dHaloWith2PulsesInDim1 (27 ms) 30: [----------] 4 tests from HaloExchangeTest (91 ms total) 30: 30: [----------] Global test environment tear-down 30: [==========] 4 tests from 1 test suite ran. (91 ms total) 30: [ PASSED ] 4 tests. 30/92 Test #30: DomDecMpiTests ............................ Passed 0.21 sec test 31 Start 31: EwaldUnitTests 31: Test command: /build/reproducible-path/gromacs-2025.1/build/basic-dp/bin/ewald-test "--gtest_output=xml:/build/reproducible-path/gromacs-2025.1/build/basic-dp/Testing/Temporary/EwaldUnitTests.xml" 31: Working Directory: /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/ewald/tests 31: Test timeout computed to be: 30 31: [==========] Running 407 tests from 9 test suites. 31: [----------] Global test environment set-up. 31: [----------] 6 tests from SeparatePmeRanksPermittedTest 31: [ RUN ] SeparatePmeRanksPermittedTest.ZeroPmeDisableReasons 31: [ OK ] SeparatePmeRanksPermittedTest.ZeroPmeDisableReasons (0 ms) 31: [ RUN ] SeparatePmeRanksPermittedTest.CanBeDisabled 31: [ OK ] SeparatePmeRanksPermittedTest.CanBeDisabled (0 ms) 31: [ RUN ] SeparatePmeRanksPermittedTest.OneDisableReasonFlag 31: [ OK ] SeparatePmeRanksPermittedTest.OneDisableReasonFlag (0 ms) 31: [ RUN ] SeparatePmeRanksPermittedTest.OneDisableReasonText 31: [ OK ] SeparatePmeRanksPermittedTest.OneDisableReasonText (0 ms) 31: [ RUN ] SeparatePmeRanksPermittedTest.TwoDisableReasonText 31: [ OK ] SeparatePmeRanksPermittedTest.TwoDisableReasonText (0 ms) 31: [ RUN ] SeparatePmeRanksPermittedTest.EmptyDisableReasonText 31: [ OK ] SeparatePmeRanksPermittedTest.EmptyDisableReasonText (0 ms) 31: [----------] 6 tests from SeparatePmeRanksPermittedTest (0 ms total) 31: 31: [----------] 108 tests from Pme_SplineAndSpreadTest 31: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_16_12_14_system_1_atom_spline 31: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_16_12_14_system_1_atom_spline (9 ms) 31: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_16_12_14_system_1_atom_spread 31: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_16_12_14_system_1_atom_spread (2 ms) 31: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_16_12_14_system_1_atom_fused spline and spread 31: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_16_12_14_system_1_atom_fused spline and spread (2 ms) 31: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_16_12_14_system_2_atoms_spline 31: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_16_12_14_system_2_atoms_spline (2 ms) 31: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_16_12_14_system_2_atoms_spread 31: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_16_12_14_system_2_atoms_spread (2 ms) 31: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_16_12_14_system_2_atoms_fused spline and spread 31: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_16_12_14_system_2_atoms_fused spline and spread (2 ms) 31: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_16_12_14_system_13_atoms_spline 31: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_16_12_14_system_13_atoms_spline (7 ms) 31: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_16_12_14_system_13_atoms_spread 31: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_16_12_14_system_13_atoms_spread (8 ms) 31: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_16_12_14_system_13_atoms_fused spline and spread 31: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_16_12_14_system_13_atoms_fused spline and spread (8 ms) 31: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_19_17_11_system_1_atom_spline 31: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_19_17_11_system_1_atom_spline (6 ms) 31: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_19_17_11_system_1_atom_spread 31: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_19_17_11_system_1_atom_spread (2 ms) 31: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_19_17_11_system_1_atom_fused spline and spread 31: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_19_17_11_system_1_atom_fused spline and spread (2 ms) 31: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_19_17_11_system_2_atoms_spline 31: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_19_17_11_system_2_atoms_spline (2 ms) 31: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_19_17_11_system_2_atoms_spread 31: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_19_17_11_system_2_atoms_spread (2 ms) 31: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_19_17_11_system_2_atoms_fused spline and spread 31: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_19_17_11_system_2_atoms_fused spline and spread (2 ms) 31: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_19_17_11_system_13_atoms_spline 31: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_19_17_11_system_13_atoms_spline (7 ms) 31: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_19_17_11_system_13_atoms_spread 31: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_19_17_11_system_13_atoms_spread (8 ms) 31: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_19_17_11_system_13_atoms_fused spline and spread 31: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_19_17_11_system_13_atoms_fused spline and spread (9 ms) 31: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_16_12_14_system_1_atom_spline 31: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_16_12_14_system_1_atom_spline (2 ms) 31: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_16_12_14_system_1_atom_spread 31: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_16_12_14_system_1_atom_spread (2 ms) 31: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_16_12_14_system_1_atom_fused spline and spread 31: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_16_12_14_system_1_atom_fused spline and spread (2 ms) 31: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_16_12_14_system_2_atoms_spline 31: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_16_12_14_system_2_atoms_spline (3 ms) 31: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_16_12_14_system_2_atoms_spread 31: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_16_12_14_system_2_atoms_spread (3 ms) 31: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_16_12_14_system_2_atoms_fused spline and spread 31: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_16_12_14_system_2_atoms_fused spline and spread (3 ms) 31: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_16_12_14_system_13_atoms_spline 31: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_16_12_14_system_13_atoms_spline (10 ms) 31: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_16_12_14_system_13_atoms_spread 31: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_16_12_14_system_13_atoms_spread (13 ms) 31: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_16_12_14_system_13_atoms_fused spline and spread 31: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_16_12_14_system_13_atoms_fused spline and spread (14 ms) 31: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_19_17_11_system_1_atom_spline 31: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_19_17_11_system_1_atom_spline (2 ms) 31: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_19_17_11_system_1_atom_spread 31: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_19_17_11_system_1_atom_spread (2 ms) 31: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_19_17_11_system_1_atom_fused spline and spread 31: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_19_17_11_system_1_atom_fused spline and spread (3 ms) 31: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_19_17_11_system_2_atoms_spline 31: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_19_17_11_system_2_atoms_spline (3 ms) 31: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_19_17_11_system_2_atoms_spread 31: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_19_17_11_system_2_atoms_spread (3 ms) 31: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_19_17_11_system_2_atoms_fused spline and spread 31: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_19_17_11_system_2_atoms_fused spline and spread (4 ms) 31: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_19_17_11_system_13_atoms_spline 31: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_19_17_11_system_13_atoms_spline (11 ms) 31: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_19_17_11_system_13_atoms_spread 31: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_19_17_11_system_13_atoms_spread (13 ms) 31: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_19_17_11_system_13_atoms_fused spline and spread 31: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_19_17_11_system_13_atoms_fused spline and spread (15 ms) 31: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_16_12_14_system_1_atom_spline 31: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_16_12_14_system_1_atom_spline (3 ms) 31: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_16_12_14_system_1_atom_spread 31: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_16_12_14_system_1_atom_spread (3 ms) 31: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_16_12_14_system_1_atom_fused spline and spread 31: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_16_12_14_system_1_atom_fused spline and spread (4 ms) 31: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_16_12_14_system_2_atoms_spline 31: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_16_12_14_system_2_atoms_spline (4 ms) 31: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_16_12_14_system_2_atoms_spread 31: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_16_12_14_system_2_atoms_spread (4 ms) 31: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_16_12_14_system_2_atoms_fused spline and spread 31: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_16_12_14_system_2_atoms_fused spline and spread (4 ms) 31: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_16_12_14_system_13_atoms_spline 31: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_16_12_14_system_13_atoms_spline (15 ms) 31: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_16_12_14_system_13_atoms_spread 31: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_16_12_14_system_13_atoms_spread (20 ms) 31: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_16_12_14_system_13_atoms_fused spline and spread 31: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_16_12_14_system_13_atoms_fused spline and spread (20 ms) 31: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_19_17_11_system_1_atom_spline 31: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_19_17_11_system_1_atom_spline (4 ms) 31: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_19_17_11_system_1_atom_spread 31: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_19_17_11_system_1_atom_spread (4 ms) 31: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_19_17_11_system_1_atom_fused spline and spread 31: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_19_17_11_system_1_atom_fused spline and spread (4 ms) 31: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_19_17_11_system_2_atoms_spline 31: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_19_17_11_system_2_atoms_spline (4 ms) 31: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_19_17_11_system_2_atoms_spread 31: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_19_17_11_system_2_atoms_spread (5 ms) 31: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_19_17_11_system_2_atoms_fused spline and spread 31: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_19_17_11_system_2_atoms_fused spline and spread (5 ms) 31: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_19_17_11_system_13_atoms_spline 31: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_19_17_11_system_13_atoms_spline (15 ms) 31: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_19_17_11_system_13_atoms_spread 31: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_19_17_11_system_13_atoms_spread (21 ms) 31: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_19_17_11_system_13_atoms_fused spline and spread 31: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_19_17_11_system_13_atoms_fused spline and spread (23 ms) 31: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_16_12_14_system_1_atom_spline 31: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_16_12_14_system_1_atom_spline (2 ms) 31: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_16_12_14_system_1_atom_spread 31: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_16_12_14_system_1_atom_spread (2 ms) 31: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_16_12_14_system_1_atom_fused spline and spread 31: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_16_12_14_system_1_atom_fused spline and spread (2 ms) 31: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_16_12_14_system_2_atoms_spline 31: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_16_12_14_system_2_atoms_spline (2 ms) 31: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_16_12_14_system_2_atoms_spread 31: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_16_12_14_system_2_atoms_spread (2 ms) 31: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_16_12_14_system_2_atoms_fused spline and spread 31: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_16_12_14_system_2_atoms_fused spline and spread (3 ms) 31: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_16_12_14_system_13_atoms_spline 31: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_16_12_14_system_13_atoms_spline (7 ms) 31: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_16_12_14_system_13_atoms_spread 31: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_16_12_14_system_13_atoms_spread (8 ms) 31: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_16_12_14_system_13_atoms_fused spline and spread 31: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_16_12_14_system_13_atoms_fused spline and spread (8 ms) 31: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_19_17_11_system_1_atom_spline 31: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_19_17_11_system_1_atom_spline (2 ms) 31: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_19_17_11_system_1_atom_spread 31: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_19_17_11_system_1_atom_spread (2 ms) 31: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_19_17_11_system_1_atom_fused spline and spread 31: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_19_17_11_system_1_atom_fused spline and spread (2 ms) 31: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_19_17_11_system_2_atoms_spline 31: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_19_17_11_system_2_atoms_spline (2 ms) 31: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_19_17_11_system_2_atoms_spread 31: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_19_17_11_system_2_atoms_spread (2 ms) 31: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_19_17_11_system_2_atoms_fused spline and spread 31: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_19_17_11_system_2_atoms_fused spline and spread (2 ms) 31: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_19_17_11_system_13_atoms_spline 31: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_19_17_11_system_13_atoms_spline (7 ms) 31: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_19_17_11_system_13_atoms_spread 31: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_19_17_11_system_13_atoms_spread (8 ms) 31: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_19_17_11_system_13_atoms_fused spline and spread 31: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_19_17_11_system_13_atoms_fused spline and spread (9 ms) 31: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_16_12_14_system_1_atom_spline 31: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_16_12_14_system_1_atom_spline (2 ms) 31: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_16_12_14_system_1_atom_spread 31: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_16_12_14_system_1_atom_spread (2 ms) 31: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_16_12_14_system_1_atom_fused spline and spread 31: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_16_12_14_system_1_atom_fused spline and spread (2 ms) 31: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_16_12_14_system_2_atoms_spline 31: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_16_12_14_system_2_atoms_spline (2 ms) 31: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_16_12_14_system_2_atoms_spread 31: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_16_12_14_system_2_atoms_spread (3 ms) 31: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_16_12_14_system_2_atoms_fused spline and spread 31: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_16_12_14_system_2_atoms_fused spline and spread (3 ms) 31: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_16_12_14_system_13_atoms_spline 31: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_16_12_14_system_13_atoms_spline (9 ms) 31: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_16_12_14_system_13_atoms_spread 31: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_16_12_14_system_13_atoms_spread (10 ms) 31: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_16_12_14_system_13_atoms_fused spline and spread 31: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_16_12_14_system_13_atoms_fused spline and spread (12 ms) 31: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_19_17_11_system_1_atom_spline 31: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_19_17_11_system_1_atom_spline (3 ms) 31: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_19_17_11_system_1_atom_spread 31: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_19_17_11_system_1_atom_spread (2 ms) 31: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_19_17_11_system_1_atom_fused spline and spread 31: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_19_17_11_system_1_atom_fused spline and spread (3 ms) 31: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_19_17_11_system_2_atoms_spline 31: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_19_17_11_system_2_atoms_spline (3 ms) 31: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_19_17_11_system_2_atoms_spread 31: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_19_17_11_system_2_atoms_spread (3 ms) 31: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_19_17_11_system_2_atoms_fused spline and spread 31: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_19_17_11_system_2_atoms_fused spline and spread (4 ms) 31: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_19_17_11_system_13_atoms_spline 31: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_19_17_11_system_13_atoms_spline (11 ms) 31: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_19_17_11_system_13_atoms_spread 31: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_19_17_11_system_13_atoms_spread (13 ms) 31: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_19_17_11_system_13_atoms_fused spline and spread 31: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_19_17_11_system_13_atoms_fused spline and spread (14 ms) 31: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_16_12_14_system_1_atom_spline 31: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_16_12_14_system_1_atom_spline (3 ms) 31: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_16_12_14_system_1_atom_spread 31: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_16_12_14_system_1_atom_spread (4 ms) 31: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_16_12_14_system_1_atom_fused spline and spread 31: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_16_12_14_system_1_atom_fused spline and spread (4 ms) 31: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_16_12_14_system_2_atoms_spline 31: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_16_12_14_system_2_atoms_spline (5 ms) 31: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_16_12_14_system_2_atoms_spread 31: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_16_12_14_system_2_atoms_spread (5 ms) 31: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_16_12_14_system_2_atoms_fused spline and spread 31: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_16_12_14_system_2_atoms_fused spline and spread (6 ms) 31: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_16_12_14_system_13_atoms_spline 31: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_16_12_14_system_13_atoms_spline (13 ms) 31: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_16_12_14_system_13_atoms_spread 31: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_16_12_14_system_13_atoms_spread (17 ms) 31: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_16_12_14_system_13_atoms_fused spline and spread 31: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_16_12_14_system_13_atoms_fused spline and spread (19 ms) 31: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_19_17_11_system_1_atom_spline 31: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_19_17_11_system_1_atom_spline (3 ms) 31: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_19_17_11_system_1_atom_spread 31: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_19_17_11_system_1_atom_spread (3 ms) 31: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_19_17_11_system_1_atom_fused spline and spread 31: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_19_17_11_system_1_atom_fused spline and spread (3 ms) 31: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_19_17_11_system_2_atoms_spline 31: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_19_17_11_system_2_atoms_spline (4 ms) 31: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_19_17_11_system_2_atoms_spread 31: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_19_17_11_system_2_atoms_spread (5 ms) 31: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_19_17_11_system_2_atoms_fused spline and spread 31: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_19_17_11_system_2_atoms_fused spline and spread (6 ms) 31: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_19_17_11_system_13_atoms_spline 31: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_19_17_11_system_13_atoms_spline (15 ms) 31: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_19_17_11_system_13_atoms_spread 31: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_19_17_11_system_13_atoms_spread (19 ms) 31: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_19_17_11_system_13_atoms_fused spline and spread 31: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_19_17_11_system_13_atoms_fused spline and spread (22 ms) 31: [----------] 108 tests from Pme_SplineAndSpreadTest (824 ms total) 31: 31: [----------] 64 tests from Pme_SolveTest 31: [ RUN ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ 31: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 31: Test is being skipped because: 31: CPU PME solve does not implement XYZ grid ordering 31: 31: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ (0 ms) 31: [ RUN ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy 31: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 31: Test is being skipped because: 31: CPU PME solve does not implement XYZ grid ordering 31: 31: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy (0 ms) 31: [ RUN ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_ 31: [ OK ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_ (4 ms) 31: [ RUN ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_energy 31: [ OK ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_energy (3 ms) 31: [ RUN ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ 31: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 31: Test is being skipped because: 31: CPU PME solve does not implement XYZ grid ordering 31: 31: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ (0 ms) 31: [ RUN ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy 31: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 31: Test is being skipped because: 31: CPU PME solve does not implement XYZ grid ordering 31: 31: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy (0 ms) 31: [ RUN ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_ 31: [ OK ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_ (4 ms) 31: [ RUN ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_energy 31: [ OK ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_energy (5 ms) 31: [ RUN ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ 31: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 31: Test is being skipped because: 31: CPU PME solve does not implement XYZ grid ordering 31: 31: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ (0 ms) 31: [ RUN ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy 31: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 31: Test is being skipped because: 31: CPU PME solve does not implement XYZ grid ordering 31: 31: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy (0 ms) 31: [ RUN ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_ 31: [ OK ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_ (2 ms) 31: [ RUN ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_energy 31: [ OK ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_energy (2 ms) 31: [ RUN ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ 31: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 31: Test is being skipped because: 31: CPU PME solve does not implement XYZ grid ordering 31: 31: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ (0 ms) 31: [ RUN ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy 31: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 31: Test is being skipped because: 31: CPU PME solve does not implement XYZ grid ordering 31: 31: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy (0 ms) 31: [ RUN ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_ 31: [ OK ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_ (4 ms) 31: [ RUN ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_energy 31: [ OK ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_energy (5 ms) 31: [ RUN ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ 31: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 31: Test is being skipped because: 31: CPU PME solve does not implement XYZ grid ordering 31: 31: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ (0 ms) 31: [ RUN ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy 31: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 31: Test is being skipped because: 31: CPU PME solve does not implement XYZ grid ordering 31: 31: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy (0 ms) 31: [ RUN ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_ 31: [ OK ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_ (6 ms) 31: [ RUN ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_energy 31: [ OK ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_energy (1 ms) 31: [ RUN ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ 31: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 31: Test is being skipped because: 31: CPU PME solve does not implement XYZ grid ordering 31: 31: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ (0 ms) 31: [ RUN ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy 31: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 31: Test is being skipped because: 31: CPU PME solve does not implement XYZ grid ordering 31: 31: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy (0 ms) 31: [ RUN ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_ 31: [ OK ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_ (2 ms) 31: [ RUN ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_energy 31: [ OK ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_energy (2 ms) 31: [ RUN ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ 31: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 31: Test is being skipped because: 31: CPU PME solve does not implement XYZ grid ordering 31: 31: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ (0 ms) 31: [ RUN ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy 31: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 31: Test is being skipped because: 31: CPU PME solve does not implement XYZ grid ordering 31: 31: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy (0 ms) 31: [ RUN ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_ 31: [ OK ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_ (1 ms) 31: [ RUN ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_energy 31: [ OK ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_energy (1 ms) 31: [ RUN ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ 31: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 31: Test is being skipped because: 31: CPU PME solve does not implement XYZ grid ordering 31: 31: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ (0 ms) 31: [ RUN ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy 31: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 31: Test is being skipped because: 31: CPU PME solve does not implement XYZ grid ordering 31: 31: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy (0 ms) 31: [ RUN ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_ 31: [ OK ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_ (2 ms) 31: [ RUN ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_energy 31: [ OK ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_energy (2 ms) 31: [ RUN ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ 31: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 31: Test is being skipped because: 31: CPU PME solve does not implement XYZ grid ordering 31: 31: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ (0 ms) 31: [ RUN ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy 31: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 31: Test is being skipped because: 31: CPU PME solve does not implement XYZ grid ordering 31: 31: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy (0 ms) 31: [ RUN ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_ 31: [ OK ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_ (2 ms) 31: [ RUN ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_energy 31: [ OK ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_energy (3 ms) 31: [ RUN ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ 31: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 31: Test is being skipped because: 31: CPU PME solve does not implement XYZ grid ordering 31: 31: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ (0 ms) 31: [ RUN ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy 31: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 31: Test is being skipped because: 31: CPU PME solve does not implement XYZ grid ordering 31: 31: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy (0 ms) 31: [ RUN ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_ 31: [ OK ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_ (5 ms) 31: [ RUN ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_energy 31: [ OK ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_energy (6 ms) 31: [ RUN ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ 31: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 31: Test is being skipped because: 31: CPU PME solve does not implement XYZ grid ordering 31: 31: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ (0 ms) 31: [ RUN ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy 31: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 31: Test is being skipped because: 31: CPU PME solve does not implement XYZ grid ordering 31: 31: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy (0 ms) 31: [ RUN ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_ 31: [ OK ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_ (2 ms) 31: [ RUN ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_energy 31: [ OK ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_energy (2 ms) 31: [ RUN ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ 31: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 31: Test is being skipped because: 31: CPU PME solve does not implement XYZ grid ordering 31: 31: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ (0 ms) 31: [ RUN ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy 31: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 31: Test is being skipped because: 31: CPU PME solve does not implement XYZ grid ordering 31: 31: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy (0 ms) 31: [ RUN ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_ 31: [ OK ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_ (5 ms) 31: [ RUN ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_energy 31: [ OK ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_energy (5 ms) 31: [ RUN ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ 31: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 31: Test is being skipped because: 31: CPU PME solve does not implement XYZ grid ordering 31: 31: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ (0 ms) 31: [ RUN ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy 31: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 31: Test is being skipped because: 31: CPU PME solve does not implement XYZ grid ordering 31: 31: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy (0 ms) 31: [ RUN ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_ 31: [ OK ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_ (2 ms) 31: [ RUN ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_energy 31: [ OK ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_energy (1 ms) 31: [ RUN ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ 31: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 31: Test is being skipped because: 31: CPU PME solve does not implement XYZ grid ordering 31: 31: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ (0 ms) 31: [ RUN ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy 31: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 31: Test is being skipped because: 31: CPU PME solve does not implement XYZ grid ordering 31: 31: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy (0 ms) 31: [ RUN ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_ 31: [ OK ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_ (2 ms) 31: [ RUN ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_energy 31: [ OK ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_energy (2 ms) 31: [ RUN ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ 31: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 31: Test is being skipped because: 31: CPU PME solve does not implement XYZ grid ordering 31: 31: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ (0 ms) 31: [ RUN ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy 31: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 31: Test is being skipped because: 31: CPU PME solve does not implement XYZ grid ordering 31: 31: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy (0 ms) 31: [ RUN ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_ 31: [ OK ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_ (1 ms) 31: [ RUN ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_energy 31: [ OK ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_energy (1 ms) 31: [ RUN ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ 31: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 31: Test is being skipped because: 31: CPU PME solve does not implement XYZ grid ordering 31: 31: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ (0 ms) 31: [ RUN ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy 31: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 31: Test is being skipped because: 31: CPU PME solve does not implement XYZ grid ordering 31: 31: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy (0 ms) 31: [ RUN ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_ 31: [ OK ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_ (2 ms) 31: [ RUN ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_energy 31: [ OK ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_energy (2 ms) 31: [----------] 64 tests from Pme_SolveTest (116 ms total) 31: 31: [----------] 32 tests from PmeDiffEwaldQ_SolveTest 31: [ RUN ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_ 31: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 31: Test is being skipped because: 31: CPU PME solve does not implement XYZ grid ordering 31: 31: [ SKIPPED ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_ (0 ms) 31: [ RUN ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_energy 31: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 31: Test is being skipped because: 31: CPU PME solve does not implement XYZ grid ordering 31: 31: [ SKIPPED ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_energy (0 ms) 31: [ RUN ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_YZX_ 31: [ OK ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_YZX_ (2 ms) 31: [ RUN ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_YZX_energy 31: [ OK ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_YZX_energy (3 ms) 31: [ RUN ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_ 31: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 31: Test is being skipped because: 31: CPU PME solve does not implement XYZ grid ordering 31: 31: [ SKIPPED ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_ (0 ms) 31: [ RUN ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_energy 31: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 31: Test is being skipped because: 31: CPU PME solve does not implement XYZ grid ordering 31: 31: [ SKIPPED ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_energy (0 ms) 31: [ RUN ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_YZX_ 31: [ OK ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_YZX_ (3 ms) 31: [ RUN ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_YZX_energy 31: [ OK ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_YZX_energy (2 ms) 31: [ RUN ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_ 31: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 31: Test is being skipped because: 31: CPU PME solve does not implement XYZ grid ordering 31: 31: [ SKIPPED ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_ (0 ms) 31: [ RUN ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_energy 31: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 31: Test is being skipped because: 31: CPU PME solve does not implement XYZ grid ordering 31: 31: [ SKIPPED ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_energy (0 ms) 31: [ RUN ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_YZX_ 31: [ OK ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_YZX_ (1 ms) 31: [ RUN ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_YZX_energy 31: [ OK ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_YZX_energy (1 ms) 31: [ RUN ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_ 31: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 31: Test is being skipped because: 31: CPU PME solve does not implement XYZ grid ordering 31: 31: [ SKIPPED ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_ (0 ms) 31: [ RUN ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_energy 31: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 31: Test is being skipped because: 31: CPU PME solve does not implement XYZ grid ordering 31: 31: [ SKIPPED ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_energy (0 ms) 31: [ RUN ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_YZX_ 31: [ OK ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_YZX_ (1 ms) 31: [ RUN ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_YZX_energy 31: [ OK ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_YZX_energy (1 ms) 31: [ RUN ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_ 31: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 31: Test is being skipped because: 31: CPU PME solve does not implement XYZ grid ordering 31: 31: [ SKIPPED ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_ (0 ms) 31: [ RUN ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_energy 31: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 31: Test is being skipped because: 31: CPU PME solve does not implement XYZ grid ordering 31: 31: [ SKIPPED ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_energy (0 ms) 31: [ RUN ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_YZX_ 31: [ OK ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_YZX_ (2 ms) 31: [ RUN ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_YZX_energy 31: [ OK ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_YZX_energy (3 ms) 31: [ RUN ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_ 31: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 31: Test is being skipped because: 31: CPU PME solve does not implement XYZ grid ordering 31: 31: [ SKIPPED ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_ (0 ms) 31: [ RUN ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_energy 31: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 31: Test is being skipped because: 31: CPU PME solve does not implement XYZ grid ordering 31: 31: [ SKIPPED ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_energy (0 ms) 31: [ RUN ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_YZX_ 31: [ OK ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_YZX_ (2 ms) 31: [ RUN ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_YZX_energy 31: [ OK ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_YZX_energy (3 ms) 31: [ RUN ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_ 31: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 31: Test is being skipped because: 31: CPU PME solve does not implement XYZ grid ordering 31: 31: [ SKIPPED ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_ (0 ms) 31: [ RUN ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_energy 31: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 31: Test is being skipped because: 31: CPU PME solve does not implement XYZ grid ordering 31: 31: [ SKIPPED ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_energy (0 ms) 31: [ RUN ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_YZX_ 31: [ OK ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_YZX_ (1 ms) 31: [ RUN ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_YZX_energy 31: [ OK ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_YZX_energy (1 ms) 31: [ RUN ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_ 31: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 31: Test is being skipped because: 31: CPU PME solve does not implement XYZ grid ordering 31: 31: [ SKIPPED ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_ (0 ms) 31: [ RUN ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_energy 31: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 31: Test is being skipped because: 31: CPU PME solve does not implement XYZ grid ordering 31: 31: [ SKIPPED ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_energy (0 ms) 31: [ RUN ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_YZX_ 31: [ OK ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_YZX_ (1 ms) 31: [ RUN ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_YZX_energy 31: [ OK ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_YZX_energy (2 ms) 31: [----------] 32 tests from PmeDiffEwaldQ_SolveTest (42 ms total) 31: 31: [----------] 32 tests from PmeDiffEwaldLJ_SolveTest 31: [ RUN ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_ 31: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 31: Test is being skipped because: 31: CPU PME solve does not implement XYZ grid ordering 31: 31: [ SKIPPED ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_ (0 ms) 31: [ RUN ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_energy 31: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 31: Test is being skipped because: 31: CPU PME solve does not implement XYZ grid ordering 31: 31: [ SKIPPED ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_energy (0 ms) 31: [ RUN ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_YZX_ 31: [ OK ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_YZX_ (8 ms) 31: [ RUN ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_YZX_energy 31: [ OK ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_YZX_energy (6 ms) 31: [ RUN ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_ 31: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 31: Test is being skipped because: 31: CPU PME solve does not implement XYZ grid ordering 31: 31: [ SKIPPED ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_ (0 ms) 31: [ RUN ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_energy 31: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 31: Test is being skipped because: 31: CPU PME solve does not implement XYZ grid ordering 31: 31: [ SKIPPED ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_energy (0 ms) 31: [ RUN ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_YZX_ 31: [ OK ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_YZX_ (7 ms) 31: [ RUN ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_YZX_energy 31: [ OK ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_YZX_energy (5 ms) 31: [ RUN ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_ 31: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 31: Test is being skipped because: 31: CPU PME solve does not implement XYZ grid ordering 31: 31: [ SKIPPED ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_ (0 ms) 31: [ RUN ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_energy 31: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 31: Test is being skipped because: 31: CPU PME solve does not implement XYZ grid ordering 31: 31: [ SKIPPED ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_energy (0 ms) 31: [ RUN ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_YZX_ 31: [ OK ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_YZX_ (3 ms) 31: [ RUN ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_YZX_energy 31: [ OK ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_YZX_energy (2 ms) 31: [ RUN ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_ 31: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 31: Test is being skipped because: 31: CPU PME solve does not implement XYZ grid ordering 31: 31: [ SKIPPED ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_ (0 ms) 31: [ RUN ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_energy 31: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 31: Test is being skipped because: 31: CPU PME solve does not implement XYZ grid ordering 31: 31: [ SKIPPED ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_energy (0 ms) 31: [ RUN ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_YZX_ 31: [ OK ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_YZX_ (4 ms) 31: [ RUN ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_YZX_energy 31: [ OK ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_YZX_energy (3 ms) 31: [ RUN ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_ 31: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 31: Test is being skipped because: 31: CPU PME solve does not implement XYZ grid ordering 31: 31: [ SKIPPED ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_ (0 ms) 31: [ RUN ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_energy 31: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 31: Test is being skipped because: 31: CPU PME solve does not implement XYZ grid ordering 31: 31: [ SKIPPED ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_energy (0 ms) 31: [ RUN ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_YZX_ 31: [ OK ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_YZX_ (5 ms) 31: [ RUN ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_YZX_energy 31: [ OK ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_YZX_energy (4 ms) 31: [ RUN ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_ 31: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 31: Test is being skipped because: 31: CPU PME solve does not implement XYZ grid ordering 31: 31: [ SKIPPED ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_ (0 ms) 31: [ RUN ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_energy 31: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 31: Test is being skipped because: 31: CPU PME solve does not implement XYZ grid ordering 31: 31: [ SKIPPED ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_energy (0 ms) 31: [ RUN ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_YZX_ 31: [ OK ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_YZX_ (4 ms) 31: [ RUN ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_YZX_energy 31: [ OK ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_YZX_energy (4 ms) 31: [ RUN ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_ 31: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 31: Test is being skipped because: 31: CPU PME solve does not implement XYZ grid ordering 31: 31: [ SKIPPED ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_ (0 ms) 31: [ RUN ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_energy 31: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 31: Test is being skipped because: 31: CPU PME solve does not implement XYZ grid ordering 31: 31: [ SKIPPED ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_energy (0 ms) 31: [ RUN ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_YZX_ 31: [ OK ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_YZX_ (2 ms) 31: [ RUN ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_YZX_energy 31: [ OK ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_YZX_energy (2 ms) 31: [ RUN ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_ 31: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 31: Test is being skipped because: 31: CPU PME solve does not implement XYZ grid ordering 31: 31: [ SKIPPED ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_ (0 ms) 31: [ RUN ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_energy 31: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 31: Test is being skipped because: 31: CPU PME solve does not implement XYZ grid ordering 31: 31: [ SKIPPED ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_energy (0 ms) 31: [ RUN ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_YZX_ 31: [ OK ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_YZX_ (2 ms) 31: [ RUN ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_YZX_energy 31: [ OK ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_YZX_energy (2 ms) 31: [----------] 32 tests from PmeDiffEwaldLJ_SolveTest (74 ms total) 31: 31: [----------] 64 tests from PmeDiffEps_SolveTest 31: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ 31: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 31: Test is being skipped because: 31: CPU PME solve does not implement XYZ grid ordering 31: 31: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ (0 ms) 31: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy 31: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 31: Test is being skipped because: 31: CPU PME solve does not implement XYZ grid ordering 31: 31: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy (0 ms) 31: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_ 31: [ OK ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_ (2 ms) 31: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_energy 31: [ OK ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_energy (2 ms) 31: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ 31: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 31: Test is being skipped because: 31: CPU PME solve does not implement XYZ grid ordering 31: 31: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ (0 ms) 31: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy 31: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 31: Test is being skipped because: 31: CPU PME solve does not implement XYZ grid ordering 31: 31: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy (0 ms) 31: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_ 31: [ OK ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_ (7 ms) 31: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_energy 31: [ OK ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_energy (5 ms) 31: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ 31: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 31: Test is being skipped because: 31: CPU PME solve does not implement XYZ grid ordering 31: 31: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ (0 ms) 31: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy 31: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 31: Test is being skipped because: 31: CPU PME solve does not implement XYZ grid ordering 31: 31: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy (0 ms) 31: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_ 31: [ OK ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_ (2 ms) 31: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_energy 31: [ OK ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_energy (2 ms) 31: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ 31: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 31: Test is being skipped because: 31: CPU PME solve does not implement XYZ grid ordering 31: 31: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ (0 ms) 31: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy 31: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 31: Test is being skipped because: 31: CPU PME solve does not implement XYZ grid ordering 31: 31: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy (0 ms) 31: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_ 31: [ OK ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_ (4 ms) 31: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_energy 31: [ OK ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_energy (4 ms) 31: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ 31: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 31: Test is being skipped because: 31: CPU PME solve does not implement XYZ grid ordering 31: 31: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ (0 ms) 31: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy 31: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 31: Test is being skipped because: 31: CPU PME solve does not implement XYZ grid ordering 31: 31: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy (0 ms) 31: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_ 31: [ OK ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_ (1 ms) 31: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_energy 31: [ OK ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_energy (1 ms) 31: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ 31: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 31: Test is being skipped because: 31: CPU PME solve does not implement XYZ grid ordering 31: 31: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ (0 ms) 31: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy 31: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 31: Test is being skipped because: 31: CPU PME solve does not implement XYZ grid ordering 31: 31: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy (0 ms) 31: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_ 31: [ OK ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_ (2 ms) 31: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_energy 31: [ OK ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_energy (2 ms) 31: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ 31: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 31: Test is being skipped because: 31: CPU PME solve does not implement XYZ grid ordering 31: 31: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ (0 ms) 31: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy 31: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 31: Test is being skipped because: 31: CPU PME solve does not implement XYZ grid ordering 31: 31: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy (0 ms) 31: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_ 31: [ OK ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_ (1 ms) 31: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_energy 31: [ OK ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_energy (1 ms) 31: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ 31: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 31: Test is being skipped because: 31: CPU PME solve does not implement XYZ grid ordering 31: 31: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ (0 ms) 31: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy 31: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 31: Test is being skipped because: 31: CPU PME solve does not implement XYZ grid ordering 31: 31: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy (0 ms) 31: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_ 31: [ OK ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_ (3 ms) 31: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_energy 31: [ OK ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_energy (2 ms) 31: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ 31: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 31: Test is being skipped because: 31: CPU PME solve does not implement XYZ grid ordering 31: 31: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ (0 ms) 31: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy 31: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 31: Test is being skipped because: 31: CPU PME solve does not implement XYZ grid ordering 31: 31: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy (0 ms) 31: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_ 31: [ OK ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_ (2 ms) 31: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_energy 31: [ OK ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_energy (2 ms) 31: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ 31: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 31: Test is being skipped because: 31: CPU PME solve does not implement XYZ grid ordering 31: 31: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ (0 ms) 31: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy 31: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 31: Test is being skipped because: 31: CPU PME solve does not implement XYZ grid ordering 31: 31: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy (0 ms) 31: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_ 31: [ OK ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_ (5 ms) 31: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_energy 31: [ OK ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_energy (5 ms) 31: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ 31: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 31: Test is being skipped because: 31: CPU PME solve does not implement XYZ grid ordering 31: 31: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ (0 ms) 31: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy 31: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 31: Test is being skipped because: 31: CPU PME solve does not implement XYZ grid ordering 31: 31: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy (0 ms) 31: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_ 31: [ OK ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_ (2 ms) 31: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_energy 31: [ OK ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_energy (2 ms) 31: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ 31: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 31: Test is being skipped because: 31: CPU PME solve does not implement XYZ grid ordering 31: 31: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ (0 ms) 31: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy 31: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 31: Test is being skipped because: 31: CPU PME solve does not implement XYZ grid ordering 31: 31: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy (0 ms) 31: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_ 31: [ OK ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_ (4 ms) 31: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_energy 31: [ OK ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_energy (5 ms) 31: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ 31: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 31: Test is being skipped because: 31: CPU PME solve does not implement XYZ grid ordering 31: 31: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ (0 ms) 31: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy 31: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 31: Test is being skipped because: 31: CPU PME solve does not implement XYZ grid ordering 31: 31: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy (0 ms) 31: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_ 31: [ OK ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_ (1 ms) 31: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_energy 31: [ OK ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_energy (1 ms) 31: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ 31: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 31: Test is being skipped because: 31: CPU PME solve does not implement XYZ grid ordering 31: 31: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ (0 ms) 31: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy 31: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 31: Test is being skipped because: 31: CPU PME solve does not implement XYZ grid ordering 31: 31: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy (0 ms) 31: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_ 31: [ OK ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_ (2 ms) 31: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_energy 31: [ OK ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_energy (2 ms) 31: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ 31: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 31: Test is being skipped because: 31: CPU PME solve does not implement XYZ grid ordering 31: 31: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ (0 ms) 31: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy 31: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 31: Test is being skipped because: 31: CPU PME solve does not implement XYZ grid ordering 31: 31: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy (0 ms) 31: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_ 31: [ OK ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_ (1 ms) 31: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_energy 31: [ OK ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_energy (1 ms) 31: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ 31: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 31: Test is being skipped because: 31: CPU PME solve does not implement XYZ grid ordering 31: 31: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ (0 ms) 31: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy 31: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 31: Test is being skipped because: 31: CPU PME solve does not implement XYZ grid ordering 31: 31: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy (0 ms) 31: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_ 31: [ OK ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_ (2 ms) 31: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_energy 31: [ OK ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_energy (2 ms) 31: [----------] 64 tests from PmeDiffEps_SolveTest (107 ms total) 31: 31: [----------] 72 tests from Pme_GatherTest 31: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_3_grid_16_12_14_gridvalues_first_system_1_atom 31: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_3_grid_16_12_14_gridvalues_first_system_1_atom (1 ms) 31: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_3_grid_16_12_14_gridvalues_first_system_2_atoms 31: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_3_grid_16_12_14_gridvalues_first_system_2_atoms (1 ms) 31: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_3_grid_16_12_14_gridvalues_first_system_13_atoms 31: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_3_grid_16_12_14_gridvalues_first_system_13_atoms (1 ms) 31: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_3_grid_16_12_14_gridvalues_second_system_1_atom 31: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_3_grid_16_12_14_gridvalues_second_system_1_atom (1 ms) 31: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_3_grid_16_12_14_gridvalues_second_system_2_atoms 31: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_3_grid_16_12_14_gridvalues_second_system_2_atoms (1 ms) 31: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_3_grid_16_12_14_gridvalues_second_system_13_atoms 31: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_3_grid_16_12_14_gridvalues_second_system_13_atoms (1 ms) 31: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_3_grid_13_15_11_gridvalues_first_system_1_atom 31: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_3_grid_13_15_11_gridvalues_first_system_1_atom (1 ms) 31: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_3_grid_13_15_11_gridvalues_first_system_2_atoms 31: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_3_grid_13_15_11_gridvalues_first_system_2_atoms (1 ms) 31: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_3_grid_13_15_11_gridvalues_first_system_13_atoms 31: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_3_grid_13_15_11_gridvalues_first_system_13_atoms (1 ms) 31: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_3_grid_13_15_11_gridvalues_second_system_1_atom 31: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_3_grid_13_15_11_gridvalues_second_system_1_atom (1 ms) 31: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_3_grid_13_15_11_gridvalues_second_system_2_atoms 31: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_3_grid_13_15_11_gridvalues_second_system_2_atoms (1 ms) 31: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_3_grid_13_15_11_gridvalues_second_system_13_atoms 31: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_3_grid_13_15_11_gridvalues_second_system_13_atoms (1 ms) 31: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_4_grid_16_12_14_gridvalues_first_system_1_atom 31: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_4_grid_16_12_14_gridvalues_first_system_1_atom (1 ms) 31: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_4_grid_16_12_14_gridvalues_first_system_2_atoms 31: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_4_grid_16_12_14_gridvalues_first_system_2_atoms (1 ms) 31: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_4_grid_16_12_14_gridvalues_first_system_13_atoms 31: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_4_grid_16_12_14_gridvalues_first_system_13_atoms (1 ms) 31: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_4_grid_16_12_14_gridvalues_second_system_1_atom 31: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_4_grid_16_12_14_gridvalues_second_system_1_atom (1 ms) 31: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_4_grid_16_12_14_gridvalues_second_system_2_atoms 31: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_4_grid_16_12_14_gridvalues_second_system_2_atoms (1 ms) 31: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_4_grid_16_12_14_gridvalues_second_system_13_atoms 31: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_4_grid_16_12_14_gridvalues_second_system_13_atoms (1 ms) 31: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_4_grid_13_15_11_gridvalues_first_system_1_atom 31: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_4_grid_13_15_11_gridvalues_first_system_1_atom (1 ms) 31: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_4_grid_13_15_11_gridvalues_first_system_2_atoms 31: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_4_grid_13_15_11_gridvalues_first_system_2_atoms (1 ms) 31: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_4_grid_13_15_11_gridvalues_first_system_13_atoms 31: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_4_grid_13_15_11_gridvalues_first_system_13_atoms (1 ms) 31: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_4_grid_13_15_11_gridvalues_second_system_1_atom 31: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_4_grid_13_15_11_gridvalues_second_system_1_atom (1 ms) 31: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_4_grid_13_15_11_gridvalues_second_system_2_atoms 31: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_4_grid_13_15_11_gridvalues_second_system_2_atoms (1 ms) 31: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_4_grid_13_15_11_gridvalues_second_system_13_atoms 31: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_4_grid_13_15_11_gridvalues_second_system_13_atoms (1 ms) 31: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_5_grid_16_12_14_gridvalues_first_system_1_atom 31: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_5_grid_16_12_14_gridvalues_first_system_1_atom (1 ms) 31: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_5_grid_16_12_14_gridvalues_first_system_2_atoms 31: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_5_grid_16_12_14_gridvalues_first_system_2_atoms (1 ms) 31: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_5_grid_16_12_14_gridvalues_first_system_13_atoms 31: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_5_grid_16_12_14_gridvalues_first_system_13_atoms (1 ms) 31: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_5_grid_16_12_14_gridvalues_second_system_1_atom 31: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_5_grid_16_12_14_gridvalues_second_system_1_atom (1 ms) 31: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_5_grid_16_12_14_gridvalues_second_system_2_atoms 31: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_5_grid_16_12_14_gridvalues_second_system_2_atoms (1 ms) 31: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_5_grid_16_12_14_gridvalues_second_system_13_atoms 31: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_5_grid_16_12_14_gridvalues_second_system_13_atoms (1 ms) 31: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_5_grid_13_15_11_gridvalues_first_system_1_atom 31: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_5_grid_13_15_11_gridvalues_first_system_1_atom (1 ms) 31: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_5_grid_13_15_11_gridvalues_first_system_2_atoms 31: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_5_grid_13_15_11_gridvalues_first_system_2_atoms (1 ms) 31: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_5_grid_13_15_11_gridvalues_first_system_13_atoms 31: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_5_grid_13_15_11_gridvalues_first_system_13_atoms (1 ms) 31: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_5_grid_13_15_11_gridvalues_second_system_1_atom 31: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_5_grid_13_15_11_gridvalues_second_system_1_atom (1 ms) 31: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_5_grid_13_15_11_gridvalues_second_system_2_atoms 31: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_5_grid_13_15_11_gridvalues_second_system_2_atoms (1 ms) 31: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_5_grid_13_15_11_gridvalues_second_system_13_atoms 31: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_5_grid_13_15_11_gridvalues_second_system_13_atoms (1 ms) 31: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_3_grid_16_12_14_gridvalues_first_system_1_atom 31: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_3_grid_16_12_14_gridvalues_first_system_1_atom (1 ms) 31: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_3_grid_16_12_14_gridvalues_first_system_2_atoms 31: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_3_grid_16_12_14_gridvalues_first_system_2_atoms (1 ms) 31: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_3_grid_16_12_14_gridvalues_first_system_13_atoms 31: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_3_grid_16_12_14_gridvalues_first_system_13_atoms (1 ms) 31: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_3_grid_16_12_14_gridvalues_second_system_1_atom 31: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_3_grid_16_12_14_gridvalues_second_system_1_atom (1 ms) 31: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_3_grid_16_12_14_gridvalues_second_system_2_atoms 31: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_3_grid_16_12_14_gridvalues_second_system_2_atoms (1 ms) 31: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_3_grid_16_12_14_gridvalues_second_system_13_atoms 31: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_3_grid_16_12_14_gridvalues_second_system_13_atoms (1 ms) 31: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_3_grid_13_15_11_gridvalues_first_system_1_atom 31: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_3_grid_13_15_11_gridvalues_first_system_1_atom (1 ms) 31: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_3_grid_13_15_11_gridvalues_first_system_2_atoms 31: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_3_grid_13_15_11_gridvalues_first_system_2_atoms (1 ms) 31: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_3_grid_13_15_11_gridvalues_first_system_13_atoms 31: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_3_grid_13_15_11_gridvalues_first_system_13_atoms (1 ms) 31: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_3_grid_13_15_11_gridvalues_second_system_1_atom 31: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_3_grid_13_15_11_gridvalues_second_system_1_atom (1 ms) 31: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_3_grid_13_15_11_gridvalues_second_system_2_atoms 31: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_3_grid_13_15_11_gridvalues_second_system_2_atoms (0 ms) 31: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_3_grid_13_15_11_gridvalues_second_system_13_atoms 31: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_3_grid_13_15_11_gridvalues_second_system_13_atoms (1 ms) 31: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_4_grid_16_12_14_gridvalues_first_system_1_atom 31: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_4_grid_16_12_14_gridvalues_first_system_1_atom (1 ms) 31: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_4_grid_16_12_14_gridvalues_first_system_2_atoms 31: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_4_grid_16_12_14_gridvalues_first_system_2_atoms (1 ms) 31: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_4_grid_16_12_14_gridvalues_first_system_13_atoms 31: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_4_grid_16_12_14_gridvalues_first_system_13_atoms (1 ms) 31: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_4_grid_16_12_14_gridvalues_second_system_1_atom 31: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_4_grid_16_12_14_gridvalues_second_system_1_atom (1 ms) 31: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_4_grid_16_12_14_gridvalues_second_system_2_atoms 31: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_4_grid_16_12_14_gridvalues_second_system_2_atoms (1 ms) 31: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_4_grid_16_12_14_gridvalues_second_system_13_atoms 31: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_4_grid_16_12_14_gridvalues_second_system_13_atoms (1 ms) 31: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_4_grid_13_15_11_gridvalues_first_system_1_atom 31: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_4_grid_13_15_11_gridvalues_first_system_1_atom (1 ms) 31: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_4_grid_13_15_11_gridvalues_first_system_2_atoms 31: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_4_grid_13_15_11_gridvalues_first_system_2_atoms (1 ms) 31: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_4_grid_13_15_11_gridvalues_first_system_13_atoms 31: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_4_grid_13_15_11_gridvalues_first_system_13_atoms (1 ms) 31: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_4_grid_13_15_11_gridvalues_second_system_1_atom 31: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_4_grid_13_15_11_gridvalues_second_system_1_atom (1 ms) 31: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_4_grid_13_15_11_gridvalues_second_system_2_atoms 31: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_4_grid_13_15_11_gridvalues_second_system_2_atoms (1 ms) 31: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_4_grid_13_15_11_gridvalues_second_system_13_atoms 31: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_4_grid_13_15_11_gridvalues_second_system_13_atoms (1 ms) 31: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_5_grid_16_12_14_gridvalues_first_system_1_atom 31: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_5_grid_16_12_14_gridvalues_first_system_1_atom (1 ms) 31: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_5_grid_16_12_14_gridvalues_first_system_2_atoms 31: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_5_grid_16_12_14_gridvalues_first_system_2_atoms (1 ms) 31: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_5_grid_16_12_14_gridvalues_first_system_13_atoms 31: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_5_grid_16_12_14_gridvalues_first_system_13_atoms (1 ms) 31: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_5_grid_16_12_14_gridvalues_second_system_1_atom 31: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_5_grid_16_12_14_gridvalues_second_system_1_atom (1 ms) 31: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_5_grid_16_12_14_gridvalues_second_system_2_atoms 31: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_5_grid_16_12_14_gridvalues_second_system_2_atoms (1 ms) 31: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_5_grid_16_12_14_gridvalues_second_system_13_atoms 31: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_5_grid_16_12_14_gridvalues_second_system_13_atoms (1 ms) 31: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_5_grid_13_15_11_gridvalues_first_system_1_atom 31: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_5_grid_13_15_11_gridvalues_first_system_1_atom (1 ms) 31: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_5_grid_13_15_11_gridvalues_first_system_2_atoms 31: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_5_grid_13_15_11_gridvalues_first_system_2_atoms (1 ms) 31: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_5_grid_13_15_11_gridvalues_first_system_13_atoms 31: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_5_grid_13_15_11_gridvalues_first_system_13_atoms (1 ms) 31: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_5_grid_13_15_11_gridvalues_second_system_1_atom 31: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_5_grid_13_15_11_gridvalues_second_system_1_atom (1 ms) 31: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_5_grid_13_15_11_gridvalues_second_system_2_atoms 31: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_5_grid_13_15_11_gridvalues_second_system_2_atoms (1 ms) 31: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_5_grid_13_15_11_gridvalues_second_system_13_atoms 31: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_5_grid_13_15_11_gridvalues_second_system_13_atoms (1 ms) 31: [----------] 72 tests from Pme_GatherTest (100 ms total) 31: 31: [----------] 5 tests from InsaneInput/PmeBSplineModuliFailureTest 31: [ RUN ] InsaneInput/PmeBSplineModuliFailureTest.Throws/0 31: [ OK ] InsaneInput/PmeBSplineModuliFailureTest.Throws/0 (0 ms) 31: [ RUN ] InsaneInput/PmeBSplineModuliFailureTest.Throws/1 31: [ OK ] InsaneInput/PmeBSplineModuliFailureTest.Throws/1 (0 ms) 31: [ RUN ] InsaneInput/PmeBSplineModuliFailureTest.Throws/2 31: [ OK ] InsaneInput/PmeBSplineModuliFailureTest.Throws/2 (0 ms) 31: [ RUN ] InsaneInput/PmeBSplineModuliFailureTest.Throws/3 31: [ OK ] InsaneInput/PmeBSplineModuliFailureTest.Throws/3 (14 ms) 31: [ RUN ] InsaneInput/PmeBSplineModuliFailureTest.Throws/4 31: [ OK ] InsaneInput/PmeBSplineModuliFailureTest.Throws/4 (0 ms) 31: [----------] 5 tests from InsaneInput/PmeBSplineModuliFailureTest (15 ms total) 31: 31: [----------] 24 tests from SaneInput1/PmeBSplineModuliCorrectnessTest 31: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/0 31: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/0 (21 ms) 31: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/1 31: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/1 (19 ms) 31: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/2 31: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/2 (21 ms) 31: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/3 31: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/3 (16 ms) 31: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/4 31: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/4 (17 ms) 31: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/5 31: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/5 (21 ms) 31: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/6 31: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/6 (20 ms) 31: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/7 31: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/7 (22 ms) 31: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/8 31: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/8 (20 ms) 31: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/9 31: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/9 (19 ms) 31: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/10 31: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/10 (19 ms) 31: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/11 31: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/11 (18 ms) 31: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/12 31: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/12 (31 ms) 31: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/13 31: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/13 (21 ms) 31: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/14 31: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/14 (19 ms) 31: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/15 31: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/15 (21 ms) 31: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/16 31: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/16 (21 ms) 31: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/17 31: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/17 (22 ms) 31: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/18 31: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/18 (21 ms) 31: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/19 31: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/19 (18 ms) 31: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/20 31: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/20 (22 ms) 31: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/21 31: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/21 (22 ms) 31: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/22 31: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/22 (20 ms) 31: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/23 31: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/23 (22 ms) 31: [----------] 24 tests from SaneInput1/PmeBSplineModuliCorrectnessTest (521 ms total) 31: 31: [----------] Global test environment tear-down 31: [==========] 407 tests from 9 test suites ran. (1804 ms total) 31: [ PASSED ] 311 tests. 31: [ SKIPPED ] 96 tests, listed below: 31: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ 31: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy 31: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ 31: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy 31: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ 31: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy 31: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ 31: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy 31: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ 31: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy 31: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ 31: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy 31: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ 31: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy 31: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ 31: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy 31: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ 31: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy 31: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ 31: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy 31: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ 31: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy 31: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ 31: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy 31: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ 31: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy 31: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ 31: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy 31: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ 31: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy 31: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ 31: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy 31: [ SKIPPED ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_ 31: [ SKIPPED ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_energy 31: [ SKIPPED ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_ 31: [ SKIPPED ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_energy 31: [ SKIPPED ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_ 31: [ SKIPPED ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_energy 31: [ SKIPPED ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_ 31: [ SKIPPED ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_energy 31: [ SKIPPED ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_ 31: [ SKIPPED ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_energy 31: [ SKIPPED ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_ 31: [ SKIPPED ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_energy 31: [ SKIPPED ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_ 31: [ SKIPPED ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_energy 31: [ SKIPPED ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_ 31: [ SKIPPED ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_energy 31: [ SKIPPED ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_ 31: [ SKIPPED ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_energy 31: [ SKIPPED ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_ 31: [ SKIPPED ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_energy 31: [ SKIPPED ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_ 31: [ SKIPPED ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_energy 31: [ SKIPPED ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_ 31: [ SKIPPED ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_energy 31: [ SKIPPED ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_ 31: [ SKIPPED ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_energy 31: [ SKIPPED ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_ 31: [ SKIPPED ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_energy 31: [ SKIPPED ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_ 31: [ SKIPPED ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_energy 31: [ SKIPPED ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_ 31: [ SKIPPED ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_energy 31: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ 31: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy 31: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ 31: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy 31: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ 31: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy 31: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ 31: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy 31: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ 31: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy 31: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ 31: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy 31: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ 31: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy 31: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ 31: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy 31: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ 31: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy 31: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ 31: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy 31: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ 31: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy 31: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ 31: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy 31: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ 31: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy 31: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ 31: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy 31: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ 31: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy 31: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ 31: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy 31/92 Test #31: EwaldUnitTests ............................ Passed 2.01 sec test 32 Start 32: FFTUnitTests 32: Test command: /build/reproducible-path/gromacs-2025.1/build/basic-dp/bin/fft-test "--gtest_output=xml:/build/reproducible-path/gromacs-2025.1/build/basic-dp/Testing/Temporary/FFTUnitTests.xml" 32: Working Directory: /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/fft/tests 32: Test timeout computed to be: 1920 32: [==========] Running 15 tests from 4 test suites. 32: [----------] Global test environment set-up. 32: [----------] 2 tests from ManyFFTTest 32: [ RUN ] ManyFFTTest.Complex1DLength48Multi5Test 32: [ OK ] ManyFFTTest.Complex1DLength48Multi5Test (18 ms) 32: [ RUN ] ManyFFTTest.Real1DLength48Multi5Test 32: [ OK ] ManyFFTTest.Real1DLength48Multi5Test (28 ms) 32: [----------] 2 tests from ManyFFTTest (50 ms total) 32: 32: [----------] 1 test from FFTTest 32: [ RUN ] FFTTest.Real2DLength18_15Test 32: [ OK ] FFTTest.Real2DLength18_15Test (9 ms) 32: [----------] 1 test from FFTTest (10 ms total) 32: 32: [----------] 10 tests from 7_8_25_36_60/FFTTest1D 32: [ RUN ] 7_8_25_36_60/FFTTest1D.Complex/0 32: [ OK ] 7_8_25_36_60/FFTTest1D.Complex/0 (1 ms) 32: [ RUN ] 7_8_25_36_60/FFTTest1D.Complex/1 32: [ OK ] 7_8_25_36_60/FFTTest1D.Complex/1 (1 ms) 32: [ RUN ] 7_8_25_36_60/FFTTest1D.Complex/2 32: [ OK ] 7_8_25_36_60/FFTTest1D.Complex/2 (3 ms) 32: [ RUN ] 7_8_25_36_60/FFTTest1D.Complex/3 32: [ OK ] 7_8_25_36_60/FFTTest1D.Complex/3 (5 ms) 32: [ RUN ] 7_8_25_36_60/FFTTest1D.Complex/4 32: [ OK ] 7_8_25_36_60/FFTTest1D.Complex/4 (6 ms) 32: [ RUN ] 7_8_25_36_60/FFTTest1D.Real/0 32: [ OK ] 7_8_25_36_60/FFTTest1D.Real/0 (1 ms) 32: [ RUN ] 7_8_25_36_60/FFTTest1D.Real/1 32: [ OK ] 7_8_25_36_60/FFTTest1D.Real/1 (1 ms) 32: [ RUN ] 7_8_25_36_60/FFTTest1D.Real/2 32: [ OK ] 7_8_25_36_60/FFTTest1D.Real/2 (1 ms) 32: [ RUN ] 7_8_25_36_60/FFTTest1D.Real/3 32: [ OK ] 7_8_25_36_60/FFTTest1D.Real/3 (16 ms) 32: [ RUN ] 7_8_25_36_60/FFTTest1D.Real/4 32: [ OK ] 7_8_25_36_60/FFTTest1D.Real/4 (25 ms) 32: [----------] 10 tests from 7_8_25_36_60/FFTTest1D (67 ms total) 32: 32: [----------] 2 tests from Works/ParameterizedFFTTest3D 32: [ RUN ] Works/ParameterizedFFTTest3D.RunsOnHost/5_6_9 32: [ OK ] Works/ParameterizedFFTTest3D.RunsOnHost/5_6_9 (5 ms) 32: [ RUN ] Works/ParameterizedFFTTest3D.RunsOnHost/5_5_10 32: [ OK ] Works/ParameterizedFFTTest3D.RunsOnHost/5_5_10 (5 ms) 32: [----------] 2 tests from Works/ParameterizedFFTTest3D (12 ms total) 32: 32: [----------] Global test environment tear-down 32: [==========] 15 tests from 4 test suites ran. (141 ms total) 32: [ PASSED ] 15 tests. 32/92 Test #32: FFTUnitTests .............................. Passed 0.27 sec test 33 Start 33: GpuUtilsUnitTests 33: Test command: /build/reproducible-path/gromacs-2025.1/build/basic-dp/bin/gpu_utils-test "--gtest_output=xml:/build/reproducible-path/gromacs-2025.1/build/basic-dp/Testing/Temporary/GpuUtilsUnitTests.xml" 33: Working Directory: /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/gpu_utils/tests 33: Test timeout computed to be: 30 33: [==========] Running 67 tests from 22 test suites. 33: [----------] Global test environment set-up. 33: [----------] 2 tests from ClfftInitializer 33: [ RUN ] ClfftInitializer.SingleInitializationWorks 33: [ OK ] ClfftInitializer.SingleInitializationWorks (0 ms) 33: [ RUN ] ClfftInitializer.TwoInitializationsWork 33: [ OK ] ClfftInitializer.TwoInitializationsWork (0 ms) 33: [----------] 2 tests from ClfftInitializer (0 ms total) 33: 33: [----------] 1 test from DevicesAvailable 33: [ RUN ] DevicesAvailable.ShouldBeAbleToRunOnDevice 33: [ OK ] DevicesAvailable.ShouldBeAbleToRunOnDevice (0 ms) 33: [----------] 1 test from DevicesAvailable (0 ms total) 33: 33: [----------] 1 test from DeviceStreamManagerTest 33: [ RUN ] DeviceStreamManagerTest.CorrectStreamsAreReturnedOnNonbondedDevice 33: [ OK ] DeviceStreamManagerTest.CorrectStreamsAreReturnedOnNonbondedDevice (0 ms) 33: [----------] 1 test from DeviceStreamManagerTest (0 ms total) 33: 33: [----------] 2 tests from HostAllocatorTest/0, where TypeParam = int 33: [ RUN ] HostAllocatorTest/0.EmptyMemoryAlwaysWorks 33: [ OK ] HostAllocatorTest/0.EmptyMemoryAlwaysWorks (0 ms) 33: [ RUN ] HostAllocatorTest/0.StatefulAllocatorUsesMemory 33: [ OK ] HostAllocatorTest/0.StatefulAllocatorUsesMemory (0 ms) 33: [----------] 2 tests from HostAllocatorTest/0 (0 ms total) 33: 33: [----------] 2 tests from HostAllocatorTest/1, where TypeParam = double 33: [ RUN ] HostAllocatorTest/1.EmptyMemoryAlwaysWorks 33: [ OK ] HostAllocatorTest/1.EmptyMemoryAlwaysWorks (0 ms) 33: [ RUN ] HostAllocatorTest/1.StatefulAllocatorUsesMemory 33: [ OK ] HostAllocatorTest/1.StatefulAllocatorUsesMemory (0 ms) 33: [----------] 2 tests from HostAllocatorTest/1 (0 ms total) 33: 33: [----------] 2 tests from HostAllocatorTest/2, where TypeParam = gmx::BasicVector 33: [ RUN ] HostAllocatorTest/2.EmptyMemoryAlwaysWorks 33: [ OK ] HostAllocatorTest/2.EmptyMemoryAlwaysWorks (0 ms) 33: [ RUN ] HostAllocatorTest/2.StatefulAllocatorUsesMemory 33: [ OK ] HostAllocatorTest/2.StatefulAllocatorUsesMemory (0 ms) 33: [----------] 2 tests from HostAllocatorTest/2 (0 ms total) 33: 33: [----------] 2 tests from HostAllocatorTest/3, where TypeParam = gmx::test::MoveOnly 33: [ RUN ] HostAllocatorTest/3.EmptyMemoryAlwaysWorks 33: [ OK ] HostAllocatorTest/3.EmptyMemoryAlwaysWorks (0 ms) 33: [ RUN ] HostAllocatorTest/3.StatefulAllocatorUsesMemory 33: [ OK ] HostAllocatorTest/3.StatefulAllocatorUsesMemory (0 ms) 33: [----------] 2 tests from HostAllocatorTest/3 (0 ms total) 33: 33: [----------] 3 tests from HostAllocatorTestCopyable/0, where TypeParam = int 33: [ RUN ] HostAllocatorTestCopyable/0.VectorsWithDefaultHostAllocatorAlwaysWorks 33: [ OK ] HostAllocatorTestCopyable/0.VectorsWithDefaultHostAllocatorAlwaysWorks (0 ms) 33: [ RUN ] HostAllocatorTestCopyable/0.TransfersWithoutPinningWork 33: [ OK ] HostAllocatorTestCopyable/0.TransfersWithoutPinningWork (0 ms) 33: [ RUN ] HostAllocatorTestCopyable/0.FillInputAlsoWorksAfterCallingReserve 33: [ OK ] HostAllocatorTestCopyable/0.FillInputAlsoWorksAfterCallingReserve (0 ms) 33: [----------] 3 tests from HostAllocatorTestCopyable/0 (0 ms total) 33: 33: [----------] 3 tests from HostAllocatorTestCopyable/1, where TypeParam = double 33: [ RUN ] HostAllocatorTestCopyable/1.VectorsWithDefaultHostAllocatorAlwaysWorks 33: [ OK ] HostAllocatorTestCopyable/1.VectorsWithDefaultHostAllocatorAlwaysWorks (0 ms) 33: [ RUN ] HostAllocatorTestCopyable/1.TransfersWithoutPinningWork 33: [ OK ] HostAllocatorTestCopyable/1.TransfersWithoutPinningWork (0 ms) 33: [ RUN ] HostAllocatorTestCopyable/1.FillInputAlsoWorksAfterCallingReserve 33: [ OK ] HostAllocatorTestCopyable/1.FillInputAlsoWorksAfterCallingReserve (0 ms) 33: [----------] 3 tests from HostAllocatorTestCopyable/1 (0 ms total) 33: 33: [----------] 3 tests from HostAllocatorTestCopyable/2, where TypeParam = gmx::BasicVector 33: [ RUN ] HostAllocatorTestCopyable/2.VectorsWithDefaultHostAllocatorAlwaysWorks 33: [ OK ] HostAllocatorTestCopyable/2.VectorsWithDefaultHostAllocatorAlwaysWorks (0 ms) 33: [ RUN ] HostAllocatorTestCopyable/2.TransfersWithoutPinningWork 33: [ OK ] HostAllocatorTestCopyable/2.TransfersWithoutPinningWork (0 ms) 33: [ RUN ] HostAllocatorTestCopyable/2.FillInputAlsoWorksAfterCallingReserve 33: [ OK ] HostAllocatorTestCopyable/2.FillInputAlsoWorksAfterCallingReserve (0 ms) 33: [----------] 3 tests from HostAllocatorTestCopyable/2 (0 ms total) 33: 33: [----------] 5 tests from HostAllocatorTestNoMem/0, where TypeParam = int 33: [ RUN ] HostAllocatorTestNoMem/0.CreateVector 33: [ OK ] HostAllocatorTestNoMem/0.CreateVector (0 ms) 33: [ RUN ] HostAllocatorTestNoMem/0.MoveAssignment 33: [ OK ] HostAllocatorTestNoMem/0.MoveAssignment (0 ms) 33: [ RUN ] HostAllocatorTestNoMem/0.MoveConstruction 33: [ OK ] HostAllocatorTestNoMem/0.MoveConstruction (0 ms) 33: [ RUN ] HostAllocatorTestNoMem/0.Swap 33: [ OK ] HostAllocatorTestNoMem/0.Swap (0 ms) 33: [ RUN ] HostAllocatorTestNoMem/0.Comparison 33: [ OK ] HostAllocatorTestNoMem/0.Comparison (0 ms) 33: [----------] 5 tests from HostAllocatorTestNoMem/0 (0 ms total) 33: 33: [----------] 5 tests from HostAllocatorTestNoMem/1, where TypeParam = double 33: [ RUN ] HostAllocatorTestNoMem/1.CreateVector 33: [ OK ] HostAllocatorTestNoMem/1.CreateVector (0 ms) 33: [ RUN ] HostAllocatorTestNoMem/1.MoveAssignment 33: [ OK ] HostAllocatorTestNoMem/1.MoveAssignment (0 ms) 33: [ RUN ] HostAllocatorTestNoMem/1.MoveConstruction 33: [ OK ] HostAllocatorTestNoMem/1.MoveConstruction (0 ms) 33: [ RUN ] HostAllocatorTestNoMem/1.Swap 33: [ OK ] HostAllocatorTestNoMem/1.Swap (0 ms) 33: [ RUN ] HostAllocatorTestNoMem/1.Comparison 33: [ OK ] HostAllocatorTestNoMem/1.Comparison (0 ms) 33: [----------] 5 tests from HostAllocatorTestNoMem/1 (0 ms total) 33: 33: [----------] 5 tests from HostAllocatorTestNoMem/2, where TypeParam = gmx::BasicVector 33: [ RUN ] HostAllocatorTestNoMem/2.CreateVector 33: [ OK ] HostAllocatorTestNoMem/2.CreateVector (0 ms) 33: [ RUN ] HostAllocatorTestNoMem/2.MoveAssignment 33: [ OK ] HostAllocatorTestNoMem/2.MoveAssignment (0 ms) 33: [ RUN ] HostAllocatorTestNoMem/2.MoveConstruction 33: [ OK ] HostAllocatorTestNoMem/2.MoveConstruction (0 ms) 33: [ RUN ] HostAllocatorTestNoMem/2.Swap 33: [ OK ] HostAllocatorTestNoMem/2.Swap (0 ms) 33: [ RUN ] HostAllocatorTestNoMem/2.Comparison 33: [ OK ] HostAllocatorTestNoMem/2.Comparison (0 ms) 33: [----------] 5 tests from HostAllocatorTestNoMem/2 (0 ms total) 33: 33: [----------] 5 tests from HostAllocatorTestNoMem/3, where TypeParam = gmx::test::MoveOnly 33: [ RUN ] HostAllocatorTestNoMem/3.CreateVector 33: [ OK ] HostAllocatorTestNoMem/3.CreateVector (0 ms) 33: [ RUN ] HostAllocatorTestNoMem/3.MoveAssignment 33: [ OK ] HostAllocatorTestNoMem/3.MoveAssignment (0 ms) 33: [ RUN ] HostAllocatorTestNoMem/3.MoveConstruction 33: [ OK ] HostAllocatorTestNoMem/3.MoveConstruction (0 ms) 33: [ RUN ] HostAllocatorTestNoMem/3.Swap 33: [ OK ] HostAllocatorTestNoMem/3.Swap (0 ms) 33: [ RUN ] HostAllocatorTestNoMem/3.Comparison 33: [ OK ] HostAllocatorTestNoMem/3.Comparison (0 ms) 33: [----------] 5 tests from HostAllocatorTestNoMem/3 (0 ms total) 33: 33: [----------] 3 tests from HostAllocatorTestNoMemCopyable/0, where TypeParam = int 33: [ RUN ] HostAllocatorTestNoMemCopyable/0.CopyAssignment 33: [ OK ] HostAllocatorTestNoMemCopyable/0.CopyAssignment (0 ms) 33: [ RUN ] HostAllocatorTestNoMemCopyable/0.CopyConstruction 33: [ OK ] HostAllocatorTestNoMemCopyable/0.CopyConstruction (0 ms) 33: [ RUN ] HostAllocatorTestNoMemCopyable/0.CopyConstructionOfStructHoldingAHostVectorDoesNotCopyTheAllocator 33: [ OK ] HostAllocatorTestNoMemCopyable/0.CopyConstructionOfStructHoldingAHostVectorDoesNotCopyTheAllocator (0 ms) 33: [----------] 3 tests from HostAllocatorTestNoMemCopyable/0 (0 ms total) 33: 33: [----------] 3 tests from HostAllocatorTestNoMemCopyable/1, where TypeParam = double 33: [ RUN ] HostAllocatorTestNoMemCopyable/1.CopyAssignment 33: [ OK ] HostAllocatorTestNoMemCopyable/1.CopyAssignment (0 ms) 33: [ RUN ] HostAllocatorTestNoMemCopyable/1.CopyConstruction 33: [ OK ] HostAllocatorTestNoMemCopyable/1.CopyConstruction (0 ms) 33: [ RUN ] HostAllocatorTestNoMemCopyable/1.CopyConstructionOfStructHoldingAHostVectorDoesNotCopyTheAllocator 33: [ OK ] HostAllocatorTestNoMemCopyable/1.CopyConstructionOfStructHoldingAHostVectorDoesNotCopyTheAllocator (0 ms) 33: [----------] 3 tests from HostAllocatorTestNoMemCopyable/1 (0 ms total) 33: 33: [----------] 3 tests from HostAllocatorTestNoMemCopyable/2, where TypeParam = gmx::BasicVector 33: [ RUN ] HostAllocatorTestNoMemCopyable/2.CopyAssignment 33: [ OK ] HostAllocatorTestNoMemCopyable/2.CopyAssignment (0 ms) 33: [ RUN ] HostAllocatorTestNoMemCopyable/2.CopyConstruction 33: [ OK ] HostAllocatorTestNoMemCopyable/2.CopyConstruction (0 ms) 33: [ RUN ] HostAllocatorTestNoMemCopyable/2.CopyConstructionOfStructHoldingAHostVectorDoesNotCopyTheAllocator 33: [ OK ] HostAllocatorTestNoMemCopyable/2.CopyConstructionOfStructHoldingAHostVectorDoesNotCopyTheAllocator (0 ms) 33: [----------] 3 tests from HostAllocatorTestNoMemCopyable/2 (0 ms total) 33: 33: [----------] 1 test from HostAllocatorUntypedTest 33: [ RUN ] HostAllocatorUntypedTest.Comparison 33: [ OK ] HostAllocatorUntypedTest.Comparison (0 ms) 33: [----------] 1 test from HostAllocatorUntypedTest (0 ms total) 33: 33: [----------] 4 tests from AllocatorTest/0, where TypeParam = gmx::Allocator 33: [ RUN ] AllocatorTest/0.AllocatorAlignAllocatesWithAlignment 33: [ OK ] AllocatorTest/0.AllocatorAlignAllocatesWithAlignment (0 ms) 33: [ RUN ] AllocatorTest/0.VectorAllocatesAndResizesWithAlignment 33: [ OK ] AllocatorTest/0.VectorAllocatesAndResizesWithAlignment (1 ms) 33: [ RUN ] AllocatorTest/0.VectorAllocatesAndReservesWithAlignment 33: [ OK ] AllocatorTest/0.VectorAllocatesAndReservesWithAlignment (0 ms) 33: [ RUN ] AllocatorTest/0.Move 33: [ OK ] AllocatorTest/0.Move (0 ms) 33: [----------] 4 tests from AllocatorTest/0 (1 ms total) 33: 33: [----------] 4 tests from AllocatorTest/1, where TypeParam = gmx::Allocator 33: [ RUN ] AllocatorTest/1.AllocatorAlignAllocatesWithAlignment 33: [ OK ] AllocatorTest/1.AllocatorAlignAllocatesWithAlignment (0 ms) 33: [ RUN ] AllocatorTest/1.VectorAllocatesAndResizesWithAlignment 33: [ OK ] AllocatorTest/1.VectorAllocatesAndResizesWithAlignment (0 ms) 33: [ RUN ] AllocatorTest/1.VectorAllocatesAndReservesWithAlignment 33: [ OK ] AllocatorTest/1.VectorAllocatesAndReservesWithAlignment (0 ms) 33: [ RUN ] AllocatorTest/1.Move 33: [ OK ] AllocatorTest/1.Move (0 ms) 33: [----------] 4 tests from AllocatorTest/1 (0 ms total) 33: 33: [----------] 4 tests from AllocatorTest/2, where TypeParam = gmx::Allocator, gmx::HostAllocationPolicy> 33: [ RUN ] AllocatorTest/2.AllocatorAlignAllocatesWithAlignment 33: [ OK ] AllocatorTest/2.AllocatorAlignAllocatesWithAlignment (0 ms) 33: [ RUN ] AllocatorTest/2.VectorAllocatesAndResizesWithAlignment 33: [ OK ] AllocatorTest/2.VectorAllocatesAndResizesWithAlignment (1 ms) 33: [ RUN ] AllocatorTest/2.VectorAllocatesAndReservesWithAlignment 33: [ OK ] AllocatorTest/2.VectorAllocatesAndReservesWithAlignment (0 ms) 33: [ RUN ] AllocatorTest/2.Move 33: [ OK ] AllocatorTest/2.Move (0 ms) 33: [----------] 4 tests from AllocatorTest/2 (2 ms total) 33: 33: [----------] 4 tests from AllocatorTest/3, where TypeParam = gmx::Allocator 33: [ RUN ] AllocatorTest/3.AllocatorAlignAllocatesWithAlignment 33: [ OK ] AllocatorTest/3.AllocatorAlignAllocatesWithAlignment (0 ms) 33: [ RUN ] AllocatorTest/3.VectorAllocatesAndResizesWithAlignment 33: [ OK ] AllocatorTest/3.VectorAllocatesAndResizesWithAlignment (0 ms) 33: [ RUN ] AllocatorTest/3.VectorAllocatesAndReservesWithAlignment 33: [ OK ] AllocatorTest/3.VectorAllocatesAndReservesWithAlignment (0 ms) 33: [ RUN ] AllocatorTest/3.Move 33: [ OK ] AllocatorTest/3.Move (0 ms) 33: [----------] 4 tests from AllocatorTest/3 (0 ms total) 33: 33: [----------] Global test environment tear-down 33: [==========] 67 tests from 22 test suites ran. (7 ms total) 33: [ PASSED ] 67 tests. 33/92 Test #33: GpuUtilsUnitTests ......................... Passed 0.14 sec test 34 Start 34: HardwareUnitTests 34: Test command: /build/reproducible-path/gromacs-2025.1/build/basic-dp/bin/hardware-test "--gtest_output=xml:/build/reproducible-path/gromacs-2025.1/build/basic-dp/Testing/Temporary/HardwareUnitTests.xml" 34: Working Directory: /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/hardware/tests 34: Test timeout computed to be: 30 34: [==========] Running 22 tests from 10 test suites. 34: [----------] Global test environment set-up. 34: [----------] 1 test from CpuInfoTest 34: [ RUN ] CpuInfoTest.SupportLevel 34: [ OK ] CpuInfoTest.SupportLevel (0 ms) 34: [----------] 1 test from CpuInfoTest (0 ms total) 34: 34: [----------] 4 tests from HardwareTopologyTest 34: [ RUN ] HardwareTopologyTest.Execute 34: [ OK ] HardwareTopologyTest.Execute (48 ms) 34: [ RUN ] HardwareTopologyTest.HwlocExecute 34: [ OK ] HardwareTopologyTest.HwlocExecute (45 ms) 34: [ RUN ] HardwareTopologyTest.ProcessorSelfconsistency 34: [ OK ] HardwareTopologyTest.ProcessorSelfconsistency (48 ms) 34: [ RUN ] HardwareTopologyTest.NumaCacheSelfconsistency 34: [ OK ] HardwareTopologyTest.NumaCacheSelfconsistency (43 ms) 34: [----------] 4 tests from HardwareTopologyTest (186 ms total) 34: 34: [----------] 1 test from DevicesManagerTest 34: [ RUN ] DevicesManagerTest.Serialization 34: [ OK ] DevicesManagerTest.Serialization (0 ms) 34: [ DISABLED ] DevicesManagerTest.DISABLED_DetectsUuid 34: [----------] 1 test from DevicesManagerTest (0 ms total) 34: 34: [----------] 1 test from UuidStringTest 34: [ RUN ] UuidStringTest.Works 34: [ OK ] UuidStringTest.Works (0 ms) 34: [----------] 1 test from UuidStringTest (0 ms total) 34: 34: [----------] 5 tests from XeonE52620/MockHardwareTopologyTest 34: [ RUN ] XeonE52620/MockHardwareTopologyTest.DetectsHardware/0 34: [ OK ] XeonE52620/MockHardwareTopologyTest.DetectsHardware/0 (9 ms) 34: [ RUN ] XeonE52620/MockHardwareTopologyTest.DetectsHardware/1 34: [ OK ] XeonE52620/MockHardwareTopologyTest.DetectsHardware/1 (4 ms) 34: [ RUN ] XeonE52620/MockHardwareTopologyTest.DetectsHardware/2 34: [ OK ] XeonE52620/MockHardwareTopologyTest.DetectsHardware/2 (3 ms) 34: [ RUN ] XeonE52620/MockHardwareTopologyTest.DetectsHardware/3 34: [ OK ] XeonE52620/MockHardwareTopologyTest.DetectsHardware/3 (4 ms) 34: [ RUN ] XeonE52620/MockHardwareTopologyTest.DetectsHardware/4 34: [ OK ] XeonE52620/MockHardwareTopologyTest.DetectsHardware/4 (3 ms) 34: [----------] 5 tests from XeonE52620/MockHardwareTopologyTest (28 ms total) 34: 34: [----------] 5 tests from Xeon4116/MockHardwareTopologyTest 34: [ RUN ] Xeon4116/MockHardwareTopologyTest.DetectsHardware/0 34: [ OK ] Xeon4116/MockHardwareTopologyTest.DetectsHardware/0 (9 ms) 34: [ RUN ] Xeon4116/MockHardwareTopologyTest.DetectsHardware/1 34: [ OK ] Xeon4116/MockHardwareTopologyTest.DetectsHardware/1 (3 ms) 34: [ RUN ] Xeon4116/MockHardwareTopologyTest.DetectsHardware/2 34: [ OK ] Xeon4116/MockHardwareTopologyTest.DetectsHardware/2 (3 ms) 34: [ RUN ] Xeon4116/MockHardwareTopologyTest.DetectsHardware/3 34: [ OK ] Xeon4116/MockHardwareTopologyTest.DetectsHardware/3 (3 ms) 34: [ RUN ] Xeon4116/MockHardwareTopologyTest.DetectsHardware/4 34: [ OK ] Xeon4116/MockHardwareTopologyTest.DetectsHardware/4 (3 ms) 34: [----------] 5 tests from Xeon4116/MockHardwareTopologyTest (27 ms total) 34: 34: [----------] 2 tests from Core12900K/MockHardwareTopologyTest 34: [ RUN ] Core12900K/MockHardwareTopologyTest.DetectsHardware/0 34: [ OK ] Core12900K/MockHardwareTopologyTest.DetectsHardware/0 (4 ms) 34: [ RUN ] Core12900K/MockHardwareTopologyTest.DetectsHardware/1 34: [ OK ] Core12900K/MockHardwareTopologyTest.DetectsHardware/1 (4 ms) 34: [----------] 2 tests from Core12900K/MockHardwareTopologyTest (11 ms total) 34: 34: [----------] 1 test from Core12900K/MockHardwareTopologySpecialSystemTest 34: [ RUN ] Core12900K/MockHardwareTopologySpecialSystemTest.DetectsHardware/0 34: [ OK ] Core12900K/MockHardwareTopologySpecialSystemTest.DetectsHardware/0 (9 ms) 34: [----------] 1 test from Core12900K/MockHardwareTopologySpecialSystemTest (10 ms total) 34: 34: [----------] 1 test from Power9/MockHardwareTopologySpecialSystemTest 34: [ RUN ] Power9/MockHardwareTopologySpecialSystemTest.DetectsHardware/0 34: [ OK ] Power9/MockHardwareTopologySpecialSystemTest.DetectsHardware/0 (12 ms) 34: [----------] 1 test from Power9/MockHardwareTopologySpecialSystemTest (13 ms total) 34: 34: [----------] 1 test from A64fx/MockHardwareTopologySpecialSystemTest 34: [ RUN ] A64fx/MockHardwareTopologySpecialSystemTest.DetectsHardware/0 34: [ OK ] A64fx/MockHardwareTopologySpecialSystemTest.DetectsHardware/0 (20 ms) 34: [----------] 1 test from A64fx/MockHardwareTopologySpecialSystemTest (21 ms total) 34: 34: [----------] Global test environment tear-down 34: [==========] 22 tests from 10 test suites ran. (300 ms total) 34: [ PASSED ] 22 tests. 34: 34: YOU HAVE 1 DISABLED TEST 34: 34/92 Test #34: HardwareUnitTests ......................... Passed 0.38 sec test 35 Start 35: MathUnitTests 35: Test command: /build/reproducible-path/gromacs-2025.1/build/basic-dp/bin/math-test "--gtest_output=xml:/build/reproducible-path/gromacs-2025.1/build/basic-dp/Testing/Temporary/MathUnitTests.xml" 35: Working Directory: /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/math/tests 35: Test timeout computed to be: 30 35: [==========] Running 328 tests from 41 test suites. 35: [----------] Global test environment set-up. 35: [----------] 1 test from EmptyArrayRefWithPaddingTest 35: [ RUN ] EmptyArrayRefWithPaddingTest.IsEmpty 35: [ OK ] EmptyArrayRefWithPaddingTest.IsEmpty (0 ms) 35: [----------] 1 test from EmptyArrayRefWithPaddingTest (0 ms total) 35: 35: [----------] 1 test from EmptyConstArrayRefWithPaddingTest 35: [ RUN ] EmptyConstArrayRefWithPaddingTest.IsEmpty 35: [ OK ] EmptyConstArrayRefWithPaddingTest.IsEmpty (0 ms) 35: [----------] 1 test from EmptyConstArrayRefWithPaddingTest (0 ms total) 35: 35: [----------] 2 tests from ArrayRefWithPaddingTest/0, where TypeParam = gmx::ArrayRefWithPadding 35: [ RUN ] ArrayRefWithPaddingTest/0.AssignFromPaddedVectorWorks 35: [ OK ] ArrayRefWithPaddingTest/0.AssignFromPaddedVectorWorks (0 ms) 35: [ RUN ] ArrayRefWithPaddingTest/0.ConstructFromPointersWorks 35: [ OK ] ArrayRefWithPaddingTest/0.ConstructFromPointersWorks (0 ms) 35: [----------] 2 tests from ArrayRefWithPaddingTest/0 (0 ms total) 35: 35: [----------] 2 tests from ArrayRefWithPaddingTest/1, where TypeParam = gmx::ArrayRefWithPadding 35: [ RUN ] ArrayRefWithPaddingTest/1.AssignFromPaddedVectorWorks 35: [ OK ] ArrayRefWithPaddingTest/1.AssignFromPaddedVectorWorks (0 ms) 35: [ RUN ] ArrayRefWithPaddingTest/1.ConstructFromPointersWorks 35: [ OK ] ArrayRefWithPaddingTest/1.ConstructFromPointersWorks (0 ms) 35: [----------] 2 tests from ArrayRefWithPaddingTest/1 (0 ms total) 35: 35: [----------] 2 tests from ArrayRefWithPaddingTest/2, where TypeParam = gmx::ArrayRefWithPadding 35: [ RUN ] ArrayRefWithPaddingTest/2.AssignFromPaddedVectorWorks 35: [ OK ] ArrayRefWithPaddingTest/2.AssignFromPaddedVectorWorks (0 ms) 35: [ RUN ] ArrayRefWithPaddingTest/2.ConstructFromPointersWorks 35: [ OK ] ArrayRefWithPaddingTest/2.ConstructFromPointersWorks (0 ms) 35: [----------] 2 tests from ArrayRefWithPaddingTest/2 (0 ms total) 35: 35: [----------] 2 tests from InvertBoxMatrixTest 35: [ RUN ] InvertBoxMatrixTest.IdentityIsImpotent 35: [ OK ] InvertBoxMatrixTest.IdentityIsImpotent (0 ms) 35: [ RUN ] InvertBoxMatrixTest.ComputesInverseInPlace 35: [ OK ] InvertBoxMatrixTest.ComputesInverseInPlace (0 ms) 35: [----------] 2 tests from InvertBoxMatrixTest (0 ms total) 35: 35: [----------] 8 tests from ComplexNumberTest 35: [ RUN ] ComplexNumberTest.RealComplexMultiply 35: [ OK ] ComplexNumberTest.RealComplexMultiply (0 ms) 35: [ RUN ] ComplexNumberTest.RealComplexExp 35: [ OK ] ComplexNumberTest.RealComplexExp (0 ms) 35: [ RUN ] ComplexNumberTest.ComplexAdd 35: [ OK ] ComplexNumberTest.ComplexAdd (0 ms) 35: [ RUN ] ComplexNumberTest.ComplexSubtract 35: [ OK ] ComplexNumberTest.ComplexSubtract (0 ms) 35: [ RUN ] ComplexNumberTest.ComplexMultiply 35: [ OK ] ComplexNumberTest.ComplexMultiply (0 ms) 35: [ RUN ] ComplexNumberTest.ComplexDivision 35: [ OK ] ComplexNumberTest.ComplexDivision (0 ms) 35: [ RUN ] ComplexNumberTest.ComplexConjugate 35: [ OK ] ComplexNumberTest.ComplexConjugate (8 ms) 35: [ RUN ] ComplexNumberTest.ComplexAbs2 35: [ OK ] ComplexNumberTest.ComplexAbs2 (0 ms) 35: [----------] 8 tests from ComplexNumberTest (12 ms total) 35: 35: [----------] 11 tests from TranslateAndScaleTest 35: [ RUN ] TranslateAndScaleTest.identityTransformation 35: [ OK ] TranslateAndScaleTest.identityTransformation (0 ms) 35: [ RUN ] TranslateAndScaleTest.translationWithIdentityScaling 35: [ OK ] TranslateAndScaleTest.translationWithIdentityScaling (0 ms) 35: [ RUN ] TranslateAndScaleTest.scalingWithZeroTranslation 35: [ OK ] TranslateAndScaleTest.scalingWithZeroTranslation (0 ms) 35: [ RUN ] TranslateAndScaleTest.translationAndScalingNonTrivial 35: [ OK ] TranslateAndScaleTest.translationAndScalingNonTrivial (0 ms) 35: [ RUN ] TranslateAndScaleTest.translationAndScalingNonTrivialSingeVector 35: [ OK ] TranslateAndScaleTest.translationAndScalingNonTrivialSingeVector (0 ms) 35: [ RUN ] TranslateAndScaleTest.scalingIdentity 35: [ OK ] TranslateAndScaleTest.scalingIdentity (0 ms) 35: [ RUN ] TranslateAndScaleTest.scalingNonTrivial 35: [ OK ] TranslateAndScaleTest.scalingNonTrivial (0 ms) 35: [ RUN ] TranslateAndScaleTest.scalingNonTrivialSingleVector 35: [ OK ] TranslateAndScaleTest.scalingNonTrivialSingleVector (0 ms) 35: [ RUN ] TranslateAndScaleTest.scalingInverseNoZero 35: [ OK ] TranslateAndScaleTest.scalingInverseNoZero (0 ms) 35: [ RUN ] TranslateAndScaleTest.scalingInverseWithOneScaleDimensionZero 35: [ OK ] TranslateAndScaleTest.scalingInverseWithOneScaleDimensionZero (0 ms) 35: [ RUN ] TranslateAndScaleTest.scalingInverseWithOneScaleDimensionZeroSingleVector 35: [ OK ] TranslateAndScaleTest.scalingInverseWithOneScaleDimensionZeroSingleVector (0 ms) 35: [----------] 11 tests from TranslateAndScaleTest (0 ms total) 35: 35: [----------] 3 tests from AffineTransformationTest 35: [ RUN ] AffineTransformationTest.identityTransformYieldsSameVectors 35: [ OK ] AffineTransformationTest.identityTransformYieldsSameVectors (0 ms) 35: [ RUN ] AffineTransformationTest.applyTransformationToVectors 35: [ OK ] AffineTransformationTest.applyTransformationToVectors (0 ms) 35: [ RUN ] AffineTransformationTest.retrieveGradient 35: [ OK ] AffineTransformationTest.retrieveGradient (0 ms) 35: [----------] 3 tests from AffineTransformationTest (0 ms total) 35: 35: [----------] 14 tests from DensitySimilarityTest 35: [ RUN ] DensitySimilarityTest.InnerProductIsCorrect 35: [ OK ] DensitySimilarityTest.InnerProductIsCorrect (0 ms) 35: [ RUN ] DensitySimilarityTest.InnerProductGradientIsCorrect 35: [ OK ] DensitySimilarityTest.InnerProductGradientIsCorrect (0 ms) 35: [ RUN ] DensitySimilarityTest.GradientThrowsIfDensitiesDontMatch 35: [ OK ] DensitySimilarityTest.GradientThrowsIfDensitiesDontMatch (0 ms) 35: [ RUN ] DensitySimilarityTest.SimilarityThrowsIfDensitiesDontMatch 35: [ OK ] DensitySimilarityTest.SimilarityThrowsIfDensitiesDontMatch (0 ms) 35: [ RUN ] DensitySimilarityTest.CopiedMeasureInnerProductIsCorrect 35: [ OK ] DensitySimilarityTest.CopiedMeasureInnerProductIsCorrect (0 ms) 35: [ RUN ] DensitySimilarityTest.RelativeEntropyOfSameDensityIsZero 35: [ OK ] DensitySimilarityTest.RelativeEntropyOfSameDensityIsZero (0 ms) 35: [ RUN ] DensitySimilarityTest.RelativeEntropyIsCorrect 35: [ OK ] DensitySimilarityTest.RelativeEntropyIsCorrect (0 ms) 35: [ RUN ] DensitySimilarityTest.RelativeEntropyGradientIsCorrect 35: [ OK ] DensitySimilarityTest.RelativeEntropyGradientIsCorrect (0 ms) 35: [ RUN ] DensitySimilarityTest.CrossCorrelationIsOne 35: [ OK ] DensitySimilarityTest.CrossCorrelationIsOne (406 ms) 35: [ RUN ] DensitySimilarityTest.CrossCorrelationIsMinusOneWhenAntiCorrelated 35: [ OK ] DensitySimilarityTest.CrossCorrelationIsMinusOneWhenAntiCorrelated (419 ms) 35: [ RUN ] DensitySimilarityTest.CrossCorrelationGradientIsZeroWhenCorrelated 35: [ OK ] DensitySimilarityTest.CrossCorrelationGradientIsZeroWhenCorrelated (14 ms) 35: [ RUN ] DensitySimilarityTest.CrossCorrelationGradientIsCorrect 35: [ OK ] DensitySimilarityTest.CrossCorrelationGradientIsCorrect (0 ms) 35: [ RUN ] DensitySimilarityTest.NormalizationCorrect 35: [ OK ] DensitySimilarityTest.NormalizationCorrect (0 ms) 35: [ RUN ] DensitySimilarityTest.NormalizationAllNonPositive 35: [ OK ] DensitySimilarityTest.NormalizationAllNonPositive (0 ms) 35: [----------] 14 tests from DensitySimilarityTest (844 ms total) 35: 35: [----------] 6 tests from StructureSimilarityTest 35: [ RUN ] StructureSimilarityTest.StructureComparedToSelfHasZeroRMSD 35: [ OK ] StructureSimilarityTest.StructureComparedToSelfHasZeroRMSD (0 ms) 35: [ RUN ] StructureSimilarityTest.StructureComparedToSelfHasZeroRho 35: [ OK ] StructureSimilarityTest.StructureComparedToSelfHasZeroRho (0 ms) 35: [ RUN ] StructureSimilarityTest.YieldsCorrectRMSD 35: [ OK ] StructureSimilarityTest.YieldsCorrectRMSD (0 ms) 35: [ RUN ] StructureSimilarityTest.YieldsCorrectRho 35: [ OK ] StructureSimilarityTest.YieldsCorrectRho (0 ms) 35: [ RUN ] StructureSimilarityTest.YieldsCorrectRMSDWithIndex 35: [ OK ] StructureSimilarityTest.YieldsCorrectRMSDWithIndex (0 ms) 35: [ RUN ] StructureSimilarityTest.YieldsCorrectRhoWidthIndex 35: [ OK ] StructureSimilarityTest.YieldsCorrectRhoWidthIndex (0 ms) 35: [----------] 6 tests from StructureSimilarityTest (0 ms total) 35: 35: [----------] 8 tests from ExponentialMovingAverage 35: [ RUN ] ExponentialMovingAverage.ThrowsWhenLagTimeIsZero 35: [ OK ] ExponentialMovingAverage.ThrowsWhenLagTimeIsZero (0 ms) 35: [ RUN ] ExponentialMovingAverage.ThrowsWhenLagTimeIsNegative 35: [ OK ] ExponentialMovingAverage.ThrowsWhenLagTimeIsNegative (0 ms) 35: [ RUN ] ExponentialMovingAverage.LagTimeOneYieldsInstantaneousValue 35: [ OK ] ExponentialMovingAverage.LagTimeOneYieldsInstantaneousValue (0 ms) 35: [ RUN ] ExponentialMovingAverage.YieldsCorrectValue 35: [ OK ] ExponentialMovingAverage.YieldsCorrectValue (0 ms) 35: [ RUN ] ExponentialMovingAverage.SetAverageCorrectly 35: [ OK ] ExponentialMovingAverage.SetAverageCorrectly (0 ms) 35: [ RUN ] ExponentialMovingAverage.DeterminesCorrectlyIfIncreasing 35: [ OK ] ExponentialMovingAverage.DeterminesCorrectlyIfIncreasing (0 ms) 35: [ RUN ] ExponentialMovingAverage.InverseLagTimeCorrect 35: [ OK ] ExponentialMovingAverage.InverseLagTimeCorrect (0 ms) 35: [ RUN ] ExponentialMovingAverage.RoundTripAsKeyValueTree 35: [ OK ] ExponentialMovingAverage.RoundTripAsKeyValueTree (0 ms) 35: [----------] 8 tests from ExponentialMovingAverage (0 ms total) 35: 35: [----------] 21 tests from FunctionTest 35: [ RUN ] FunctionTest.StaticLog2 35: [ OK ] FunctionTest.StaticLog2 (0 ms) 35: [ RUN ] FunctionTest.Log2I32Bit 35: [ OK ] FunctionTest.Log2I32Bit (0 ms) 35: [ RUN ] FunctionTest.Log2I64Bit 35: [ OK ] FunctionTest.Log2I64Bit (0 ms) 35: [ RUN ] FunctionTest.GreatestCommonDivisor 35: [ OK ] FunctionTest.GreatestCommonDivisor (0 ms) 35: [ RUN ] FunctionTest.InvsqrtFloat 35: [ OK ] FunctionTest.InvsqrtFloat (0 ms) 35: [ RUN ] FunctionTest.InvsqrtDouble 35: [ OK ] FunctionTest.InvsqrtDouble (0 ms) 35: [ RUN ] FunctionTest.InvsqrtInteger 35: [ OK ] FunctionTest.InvsqrtInteger (0 ms) 35: [ RUN ] FunctionTest.InvcbrtFloat 35: [ OK ] FunctionTest.InvcbrtFloat (0 ms) 35: [ RUN ] FunctionTest.InvcbrtDouble 35: [ OK ] FunctionTest.InvcbrtDouble (0 ms) 35: [ RUN ] FunctionTest.InvcbrtInteger 35: [ OK ] FunctionTest.InvcbrtInteger (0 ms) 35: [ RUN ] FunctionTest.SixthrootFloat 35: [ OK ] FunctionTest.SixthrootFloat (0 ms) 35: [ RUN ] FunctionTest.SixthrootDouble 35: [ OK ] FunctionTest.SixthrootDouble (0 ms) 35: [ RUN ] FunctionTest.SixthrootInteger 35: [ OK ] FunctionTest.SixthrootInteger (0 ms) 35: [ RUN ] FunctionTest.InvsixthrootFloat 35: [ OK ] FunctionTest.InvsixthrootFloat (0 ms) 35: [ RUN ] FunctionTest.InvsixthrootDouble 35: [ OK ] FunctionTest.InvsixthrootDouble (0 ms) 35: [ RUN ] FunctionTest.InvsixthrootInteger 35: [ OK ] FunctionTest.InvsixthrootInteger (0 ms) 35: [ RUN ] FunctionTest.Powers 35: [ OK ] FunctionTest.Powers (0 ms) 35: [ RUN ] FunctionTest.ErfInvFloat 35: [ OK ] FunctionTest.ErfInvFloat (0 ms) 35: [ RUN ] FunctionTest.ErfInvDouble 35: [ OK ] FunctionTest.ErfInvDouble (0 ms) 35: [ RUN ] FunctionTest.ErfAndErfInvAreInversesFloat 35: [ OK ] FunctionTest.ErfAndErfInvAreInversesFloat (0 ms) 35: [ RUN ] FunctionTest.ErfAndErfInvAreInversesDouble 35: [ OK ] FunctionTest.ErfAndErfInvAreInversesDouble (0 ms) 35: [----------] 21 tests from FunctionTest (9 ms total) 35: 35: [----------] 2 tests from FunctionTestIntegerTypes/0, where TypeParam = signed char 35: [ RUN ] FunctionTestIntegerTypes/0.IsPowerOfTwo 35: [ OK ] FunctionTestIntegerTypes/0.IsPowerOfTwo (0 ms) 35: [ RUN ] FunctionTestIntegerTypes/0.DivideRoundUp 35: [ OK ] FunctionTestIntegerTypes/0.DivideRoundUp (0 ms) 35: [----------] 2 tests from FunctionTestIntegerTypes/0 (0 ms total) 35: 35: [----------] 2 tests from FunctionTestIntegerTypes/1, where TypeParam = unsigned char 35: [ RUN ] FunctionTestIntegerTypes/1.IsPowerOfTwo 35: [ OK ] FunctionTestIntegerTypes/1.IsPowerOfTwo (0 ms) 35: [ RUN ] FunctionTestIntegerTypes/1.DivideRoundUp 35: [ OK ] FunctionTestIntegerTypes/1.DivideRoundUp (0 ms) 35: [----------] 2 tests from FunctionTestIntegerTypes/1 (0 ms total) 35: 35: [----------] 2 tests from FunctionTestIntegerTypes/2, where TypeParam = short 35: [ RUN ] FunctionTestIntegerTypes/2.IsPowerOfTwo 35: [ OK ] FunctionTestIntegerTypes/2.IsPowerOfTwo (0 ms) 35: [ RUN ] FunctionTestIntegerTypes/2.DivideRoundUp 35: [ OK ] FunctionTestIntegerTypes/2.DivideRoundUp (0 ms) 35: [----------] 2 tests from FunctionTestIntegerTypes/2 (0 ms total) 35: 35: [----------] 2 tests from FunctionTestIntegerTypes/3, where TypeParam = unsigned short 35: [ RUN ] FunctionTestIntegerTypes/3.IsPowerOfTwo 35: [ OK ] FunctionTestIntegerTypes/3.IsPowerOfTwo (0 ms) 35: [ RUN ] FunctionTestIntegerTypes/3.DivideRoundUp 35: [ OK ] FunctionTestIntegerTypes/3.DivideRoundUp (0 ms) 35: [----------] 2 tests from FunctionTestIntegerTypes/3 (0 ms total) 35: 35: [----------] 2 tests from FunctionTestIntegerTypes/4, where TypeParam = int 35: [ RUN ] FunctionTestIntegerTypes/4.IsPowerOfTwo 35: [ OK ] FunctionTestIntegerTypes/4.IsPowerOfTwo (0 ms) 35: [ RUN ] FunctionTestIntegerTypes/4.DivideRoundUp 35: [ OK ] FunctionTestIntegerTypes/4.DivideRoundUp (0 ms) 35: [----------] 2 tests from FunctionTestIntegerTypes/4 (0 ms total) 35: 35: [----------] 2 tests from FunctionTestIntegerTypes/5, where TypeParam = unsigned int 35: [ RUN ] FunctionTestIntegerTypes/5.IsPowerOfTwo 35: [ OK ] FunctionTestIntegerTypes/5.IsPowerOfTwo (0 ms) 35: [ RUN ] FunctionTestIntegerTypes/5.DivideRoundUp 35: [ OK ] FunctionTestIntegerTypes/5.DivideRoundUp (0 ms) 35: [----------] 2 tests from FunctionTestIntegerTypes/5 (0 ms total) 35: 35: [----------] 2 tests from FunctionTestIntegerTypes/6, where TypeParam = long 35: [ RUN ] FunctionTestIntegerTypes/6.IsPowerOfTwo 35: [ OK ] FunctionTestIntegerTypes/6.IsPowerOfTwo (0 ms) 35: [ RUN ] FunctionTestIntegerTypes/6.DivideRoundUp 35: [ OK ] FunctionTestIntegerTypes/6.DivideRoundUp (0 ms) 35: [----------] 2 tests from FunctionTestIntegerTypes/6 (0 ms total) 35: 35: [----------] 2 tests from FunctionTestIntegerTypes/7, where TypeParam = unsigned long 35: [ RUN ] FunctionTestIntegerTypes/7.IsPowerOfTwo 35: [ OK ] FunctionTestIntegerTypes/7.IsPowerOfTwo (0 ms) 35: [ RUN ] FunctionTestIntegerTypes/7.DivideRoundUp 35: [ OK ] FunctionTestIntegerTypes/7.DivideRoundUp (0 ms) 35: [----------] 2 tests from FunctionTestIntegerTypes/7 (0 ms total) 35: 35: [----------] 4 tests from GaussianOn1DLattice 35: [ RUN ] GaussianOn1DLattice.sumsCloseToOne 35: [ OK ] GaussianOn1DLattice.sumsCloseToOne (0 ms) 35: [ RUN ] GaussianOn1DLattice.isCorrect 35: [ OK ] GaussianOn1DLattice.isCorrect (0 ms) 35: [ RUN ] GaussianOn1DLattice.complementaryAmplitudesSumToZero 35: [ OK ] GaussianOn1DLattice.complementaryAmplitudesSumToZero (0 ms) 35: [ RUN ] GaussianOn1DLattice.doesNotOverflowForLargeRange 35: [ OK ] GaussianOn1DLattice.doesNotOverflowForLargeRange (0 ms) 35: [----------] 4 tests from GaussianOn1DLattice (0 ms total) 35: 35: [----------] 9 tests from GaussTransformTest 35: [ RUN ] GaussTransformTest.isZeroUponConstruction 35: [ OK ] GaussTransformTest.isZeroUponConstruction (0 ms) 35: [ RUN ] GaussTransformTest.isZeroAddingZeroAmplitudeGauss 35: [ OK ] GaussTransformTest.isZeroAddingZeroAmplitudeGauss (0 ms) 35: [ RUN ] GaussTransformTest.isZeroAfterSettingZero 35: [ OK ] GaussTransformTest.isZeroAfterSettingZero (0 ms) 35: [ RUN ] GaussTransformTest.isZeroWhenOutsideRangeinX 35: [ OK ] GaussTransformTest.isZeroWhenOutsideRangeinX (0 ms) 35: [ RUN ] GaussTransformTest.isZeroWhenOutsideRangeinY 35: [ OK ] GaussTransformTest.isZeroWhenOutsideRangeinY (0 ms) 35: [ RUN ] GaussTransformTest.isZeroWhenOutsideRangeinZ 35: [ OK ] GaussTransformTest.isZeroWhenOutsideRangeinZ (0 ms) 35: [ RUN ] GaussTransformTest.complementaryGaussAddToZero 35: [ OK ] GaussTransformTest.complementaryGaussAddToZero (0 ms) 35: [ RUN ] GaussTransformTest.centerGaussianInCubeHasExpectedValues 35: [ OK ] GaussTransformTest.centerGaussianInCubeHasExpectedValues (0 ms) 35: [ RUN ] GaussTransformTest.view 35: [ OK ] GaussTransformTest.view (0 ms) 35: [----------] 9 tests from GaussTransformTest (0 ms total) 35: 35: [----------] 3 tests from DensityFittingForce 35: [ RUN ] DensityFittingForce.isZeroWhenMatchingDensity 35: [ OK ] DensityFittingForce.isZeroWhenMatchingDensity (0 ms) 35: [ RUN ] DensityFittingForce.isZeroWhenMismatchingSameAllDirections 35: [ OK ] DensityFittingForce.isZeroWhenMismatchingSameAllDirections (0 ms) 35: [ RUN ] DensityFittingForce.pullsTowardsDerivative 35: [ OK ] DensityFittingForce.pullsTowardsDerivative (0 ms) 35: [----------] 3 tests from DensityFittingForce (0 ms total) 35: 35: [----------] 2 tests from InvertMatrixTest 35: [ RUN ] InvertMatrixTest.IdentityIsImpotent 35: [ OK ] InvertMatrixTest.IdentityIsImpotent (0 ms) 35: [ RUN ] InvertMatrixTest.ComputesInverse 35: [ OK ] InvertMatrixTest.ComputesInverse (0 ms) 35: [----------] 2 tests from InvertMatrixTest (0 ms total) 35: 35: [----------] 22 tests from MatrixTest 35: [ RUN ] MatrixTest.canSetFromArray 35: [ OK ] MatrixTest.canSetFromArray (0 ms) 35: [ RUN ] MatrixTest.canSetStaticallyFromList 35: [ OK ] MatrixTest.canSetStaticallyFromList (0 ms) 35: [ RUN ] MatrixTest.canConstructAndFill 35: [ OK ] MatrixTest.canConstructAndFill (0 ms) 35: [ RUN ] MatrixTest.canSetValues 35: [ OK ] MatrixTest.canSetValues (0 ms) 35: [ RUN ] MatrixTest.canCopyAssign 35: [ OK ] MatrixTest.canCopyAssign (0 ms) 35: [ RUN ] MatrixTest.canSwap 35: [ OK ] MatrixTest.canSwap (0 ms) 35: [ RUN ] MatrixTest.staticMultiDimArrayExtent 35: [ OK ] MatrixTest.staticMultiDimArrayExtent (0 ms) 35: [ RUN ] MatrixTest.canAddMatrix 35: [ OK ] MatrixTest.canAddMatrix (0 ms) 35: [ RUN ] MatrixTest.canSubstractMatrix 35: [ OK ] MatrixTest.canSubstractMatrix (0 ms) 35: [ RUN ] MatrixTest.canNegateMatrix 35: [ OK ] MatrixTest.canNegateMatrix (0 ms) 35: [ RUN ] MatrixTest.determinantWorks 35: [ OK ] MatrixTest.determinantWorks (0 ms) 35: [ RUN ] MatrixTest.noninvertableDeterminantIsZero 35: [ OK ] MatrixTest.noninvertableDeterminantIsZero (0 ms) 35: [ RUN ] MatrixTest.determinantOfDiagonalMatrix 35: [ OK ] MatrixTest.determinantOfDiagonalMatrix (0 ms) 35: [ RUN ] MatrixTest.traceWorks 35: [ OK ] MatrixTest.traceWorks (0 ms) 35: [ RUN ] MatrixTest.transposeWorks 35: [ OK ] MatrixTest.transposeWorks (0 ms) 35: [ RUN ] MatrixTest.transposeOfSymmetricMatrix 35: [ OK ] MatrixTest.transposeOfSymmetricMatrix (0 ms) 35: [ RUN ] MatrixTest.canCreateFromLegacyMatrix 35: [ OK ] MatrixTest.canCreateFromLegacyMatrix (0 ms) 35: [ RUN ] MatrixTest.canFillLegacyMatrix 35: [ OK ] MatrixTest.canFillLegacyMatrix (0 ms) 35: [ RUN ] MatrixTest.IdentityMatrix 35: [ OK ] MatrixTest.IdentityMatrix (0 ms) 35: [ RUN ] MatrixTest.MatrixMatrixInnerProduct 35: [ OK ] MatrixTest.MatrixMatrixInnerProduct (0 ms) 35: [ RUN ] MatrixTest.MatrixMatrixMultiplication 35: [ OK ] MatrixTest.MatrixMatrixMultiplication (0 ms) 35: [ RUN ] MatrixTest.MatrixVectorMultiplication 35: [ OK ] MatrixTest.MatrixVectorMultiplication (0 ms) 35: [----------] 22 tests from MatrixTest (0 ms total) 35: 35: [----------] 25 tests from MultiDimArrayTest 35: [ RUN ] MultiDimArrayTest.canConstructAndFillStatic 35: [ OK ] MultiDimArrayTest.canConstructAndFillStatic (0 ms) 35: [ RUN ] MultiDimArrayTest.canConstructAndFillDynamic 35: [ OK ] MultiDimArrayTest.canConstructAndFillDynamic (0 ms) 35: [ RUN ] MultiDimArrayTest.canSetValuesInStatic 35: [ OK ] MultiDimArrayTest.canSetValuesInStatic (0 ms) 35: [ RUN ] MultiDimArrayTest.canSetValuesInDynamic 35: [ OK ] MultiDimArrayTest.canSetValuesInDynamic (0 ms) 35: [ RUN ] MultiDimArrayTest.canMoveConstructStatic 35: [ OK ] MultiDimArrayTest.canMoveConstructStatic (0 ms) 35: [ RUN ] MultiDimArrayTest.canMoveConstructDynamic 35: [ OK ] MultiDimArrayTest.canMoveConstructDynamic (0 ms) 35: [ RUN ] MultiDimArrayTest.canMoveAssignStatic 35: [ OK ] MultiDimArrayTest.canMoveAssignStatic (0 ms) 35: [ RUN ] MultiDimArrayTest.canMoveAssignDynamic 35: [ OK ] MultiDimArrayTest.canMoveAssignDynamic (0 ms) 35: [ RUN ] MultiDimArrayTest.canCopyConstructStatic 35: [ OK ] MultiDimArrayTest.canCopyConstructStatic (0 ms) 35: [ RUN ] MultiDimArrayTest.canCopyConstructDynamic 35: [ OK ] MultiDimArrayTest.canCopyConstructDynamic (0 ms) 35: [ RUN ] MultiDimArrayTest.canCopyAssignStatic 35: [ OK ] MultiDimArrayTest.canCopyAssignStatic (0 ms) 35: [ RUN ] MultiDimArrayTest.canCopyAssignDynamic 35: [ OK ] MultiDimArrayTest.canCopyAssignDynamic (0 ms) 35: [ RUN ] MultiDimArrayTest.canSwapStatic 35: [ OK ] MultiDimArrayTest.canSwapStatic (0 ms) 35: [ RUN ] MultiDimArrayTest.canSwapDynamic 35: [ OK ] MultiDimArrayTest.canSwapDynamic (0 ms) 35: [ RUN ] MultiDimArrayTest.staticMultiDimArrayExtent 35: [ OK ] MultiDimArrayTest.staticMultiDimArrayExtent (0 ms) 35: [ RUN ] MultiDimArrayTest.dynamicMultiDimArrayExtent 35: [ OK ] MultiDimArrayTest.dynamicMultiDimArrayExtent (0 ms) 35: [ RUN ] MultiDimArrayTest.dynamicMultiDimArrayResizesToCorrectExtent 35: [ OK ] MultiDimArrayTest.dynamicMultiDimArrayResizesToCorrectExtent (0 ms) 35: [ RUN ] MultiDimArrayTest.dynamicMultiDimArrayResizeAndSetValue 35: [ OK ] MultiDimArrayTest.dynamicMultiDimArrayResizeAndSetValue (0 ms) 35: [ RUN ] MultiDimArrayTest.staticMultiDimArrayFromArray 35: [ OK ] MultiDimArrayTest.staticMultiDimArrayFromArray (0 ms) 35: [ RUN ] MultiDimArrayTest.conversionToView 35: [ OK ] MultiDimArrayTest.conversionToView (0 ms) 35: [ RUN ] MultiDimArrayTest.conversionToConstView 35: [ OK ] MultiDimArrayTest.conversionToConstView (0 ms) 35: [ RUN ] MultiDimArrayTest.viewBegin 35: [ OK ] MultiDimArrayTest.viewBegin (0 ms) 35: [ RUN ] MultiDimArrayTest.viewEnd 35: [ OK ] MultiDimArrayTest.viewEnd (0 ms) 35: [ RUN ] MultiDimArrayTest.constViewConstBegin 35: [ OK ] MultiDimArrayTest.constViewConstBegin (0 ms) 35: [ RUN ] MultiDimArrayTest.constViewConstEnd 35: [ OK ] MultiDimArrayTest.constViewConstEnd (0 ms) 35: [----------] 25 tests from MultiDimArrayTest (0 ms total) 35: 35: [----------] 4 tests from MultiDimArrayToMdSpanTest 35: [ RUN ] MultiDimArrayToMdSpanTest.convertsToMdSpan 35: [ OK ] MultiDimArrayToMdSpanTest.convertsToMdSpan (0 ms) 35: [ RUN ] MultiDimArrayToMdSpanTest.constArrayToMdSpan 35: [ OK ] MultiDimArrayToMdSpanTest.constArrayToMdSpan (0 ms) 35: [ RUN ] MultiDimArrayToMdSpanTest.nonConstArrayToConstMdSpan 35: [ OK ] MultiDimArrayToMdSpanTest.nonConstArrayToConstMdSpan (0 ms) 35: [ RUN ] MultiDimArrayToMdSpanTest.implicitConversionToMdSpan 35: [ OK ] MultiDimArrayToMdSpanTest.implicitConversionToMdSpan (0 ms) 35: [----------] 4 tests from MultiDimArrayToMdSpanTest (0 ms total) 35: 35: [----------] 9 tests from NelderMeadSimplexTest 35: [ RUN ] NelderMeadSimplexTest.BestVertex 35: [ OK ] NelderMeadSimplexTest.BestVertex (0 ms) 35: [ RUN ] NelderMeadSimplexTest.WorstVertex 35: [ OK ] NelderMeadSimplexTest.WorstVertex (0 ms) 35: [ RUN ] NelderMeadSimplexTest.SecondWorstValue 35: [ OK ] NelderMeadSimplexTest.SecondWorstValue (0 ms) 35: [ RUN ] NelderMeadSimplexTest.ReflectionPoint 35: [ OK ] NelderMeadSimplexTest.ReflectionPoint (0 ms) 35: [ RUN ] NelderMeadSimplexTest.EvaluateExpansionPoint 35: [ OK ] NelderMeadSimplexTest.EvaluateExpansionPoint (0 ms) 35: [ RUN ] NelderMeadSimplexTest.EvaluateContractionPoint 35: [ OK ] NelderMeadSimplexTest.EvaluateContractionPoint (0 ms) 35: [ RUN ] NelderMeadSimplexTest.SwapOutWorst 35: [ OK ] NelderMeadSimplexTest.SwapOutWorst (0 ms) 35: [ RUN ] NelderMeadSimplexTest.ShrinkSimplexPointsExceptBest 35: [ OK ] NelderMeadSimplexTest.ShrinkSimplexPointsExceptBest (0 ms) 35: [ RUN ] NelderMeadSimplexTest.OrientedLength 35: [ OK ] NelderMeadSimplexTest.OrientedLength (0 ms) 35: [----------] 9 tests from NelderMeadSimplexTest (0 ms total) 35: 35: [----------] 2 tests from NelderMead 35: [ RUN ] NelderMead.Optimizes2DFunctionCorrectly 35: [ OK ] NelderMead.Optimizes2DFunctionCorrectly (1 ms) 35: [ RUN ] NelderMead.Optimizes3DFunctorCorrectly 35: [ OK ] NelderMead.Optimizes3DFunctorCorrectly (1 ms) 35: [----------] 2 tests from NelderMead (2 ms total) 35: 35: [----------] 11 tests from PaddedVectorTest/0, where TypeParam = std::allocator 35: [ RUN ] PaddedVectorTest/0.DefaultConstructorWorks 35: [ OK ] PaddedVectorTest/0.DefaultConstructorWorks (0 ms) 35: [ RUN ] PaddedVectorTest/0.ResizeWorks 35: [ OK ] PaddedVectorTest/0.ResizeWorks (0 ms) 35: [ RUN ] PaddedVectorTest/0.ReserveWorks 35: [ OK ] PaddedVectorTest/0.ReserveWorks (0 ms) 35: [ RUN ] PaddedVectorTest/0.ReserveWorksTheSameAsNoReserve 35: [ OK ] PaddedVectorTest/0.ReserveWorksTheSameAsNoReserve (0 ms) 35: [ RUN ] PaddedVectorTest/0.MoveConstructorWorks 35: [ OK ] PaddedVectorTest/0.MoveConstructorWorks (0 ms) 35: [ RUN ] PaddedVectorTest/0.MoveConstructorWithAllocatorWorks 35: [ OK ] PaddedVectorTest/0.MoveConstructorWithAllocatorWorks (0 ms) 35: [ RUN ] PaddedVectorTest/0.MoveAssignmentWorks 35: [ OK ] PaddedVectorTest/0.MoveAssignmentWorks (0 ms) 35: [ RUN ] PaddedVectorTest/0.ArrayRefConversionsAreIdentical 35: [ OK ] PaddedVectorTest/0.ArrayRefConversionsAreIdentical (0 ms) 35: [ RUN ] PaddedVectorTest/0.CanCopyAssign 35: [ OK ] PaddedVectorTest/0.CanCopyAssign (0 ms) 35: [ RUN ] PaddedVectorTest/0.CanMoveAssign 35: [ OK ] PaddedVectorTest/0.CanMoveAssign (0 ms) 35: [ RUN ] PaddedVectorTest/0.CanSwap 35: [ OK ] PaddedVectorTest/0.CanSwap (0 ms) 35: [----------] 11 tests from PaddedVectorTest/0 (0 ms total) 35: 35: [----------] 11 tests from PaddedVectorTest/1, where TypeParam = std::allocator 35: [ RUN ] PaddedVectorTest/1.DefaultConstructorWorks 35: [ OK ] PaddedVectorTest/1.DefaultConstructorWorks (0 ms) 35: [ RUN ] PaddedVectorTest/1.ResizeWorks 35: [ OK ] PaddedVectorTest/1.ResizeWorks (0 ms) 35: [ RUN ] PaddedVectorTest/1.ReserveWorks 35: [ OK ] PaddedVectorTest/1.ReserveWorks (0 ms) 35: [ RUN ] PaddedVectorTest/1.ReserveWorksTheSameAsNoReserve 35: [ OK ] PaddedVectorTest/1.ReserveWorksTheSameAsNoReserve (0 ms) 35: [ RUN ] PaddedVectorTest/1.MoveConstructorWorks 35: [ OK ] PaddedVectorTest/1.MoveConstructorWorks (0 ms) 35: [ RUN ] PaddedVectorTest/1.MoveConstructorWithAllocatorWorks 35: [ OK ] PaddedVectorTest/1.MoveConstructorWithAllocatorWorks (0 ms) 35: [ RUN ] PaddedVectorTest/1.MoveAssignmentWorks 35: [ OK ] PaddedVectorTest/1.MoveAssignmentWorks (0 ms) 35: [ RUN ] PaddedVectorTest/1.ArrayRefConversionsAreIdentical 35: [ OK ] PaddedVectorTest/1.ArrayRefConversionsAreIdentical (0 ms) 35: [ RUN ] PaddedVectorTest/1.CanCopyAssign 35: [ OK ] PaddedVectorTest/1.CanCopyAssign (0 ms) 35: [ RUN ] PaddedVectorTest/1.CanMoveAssign 35: [ OK ] PaddedVectorTest/1.CanMoveAssign (0 ms) 35: [ RUN ] PaddedVectorTest/1.CanSwap 35: [ OK ] PaddedVectorTest/1.CanSwap (0 ms) 35: [----------] 11 tests from PaddedVectorTest/1 (0 ms total) 35: 35: [----------] 11 tests from PaddedVectorTest/2, where TypeParam = std::allocator 35: [ RUN ] PaddedVectorTest/2.DefaultConstructorWorks 35: [ OK ] PaddedVectorTest/2.DefaultConstructorWorks (0 ms) 35: [ RUN ] PaddedVectorTest/2.ResizeWorks 35: [ OK ] PaddedVectorTest/2.ResizeWorks (0 ms) 35: [ RUN ] PaddedVectorTest/2.ReserveWorks 35: [ OK ] PaddedVectorTest/2.ReserveWorks (0 ms) 35: [ RUN ] PaddedVectorTest/2.ReserveWorksTheSameAsNoReserve 35: [ OK ] PaddedVectorTest/2.ReserveWorksTheSameAsNoReserve (0 ms) 35: [ RUN ] PaddedVectorTest/2.MoveConstructorWorks 35: [ OK ] PaddedVectorTest/2.MoveConstructorWorks (0 ms) 35: [ RUN ] PaddedVectorTest/2.MoveConstructorWithAllocatorWorks 35: [ OK ] PaddedVectorTest/2.MoveConstructorWithAllocatorWorks (0 ms) 35: [ RUN ] PaddedVectorTest/2.MoveAssignmentWorks 35: [ OK ] PaddedVectorTest/2.MoveAssignmentWorks (0 ms) 35: [ RUN ] PaddedVectorTest/2.ArrayRefConversionsAreIdentical 35: [ OK ] PaddedVectorTest/2.ArrayRefConversionsAreIdentical (0 ms) 35: [ RUN ] PaddedVectorTest/2.CanCopyAssign 35: [ OK ] PaddedVectorTest/2.CanCopyAssign (0 ms) 35: [ RUN ] PaddedVectorTest/2.CanMoveAssign 35: [ OK ] PaddedVectorTest/2.CanMoveAssign (0 ms) 35: [ RUN ] PaddedVectorTest/2.CanSwap 35: [ OK ] PaddedVectorTest/2.CanSwap (0 ms) 35: [----------] 11 tests from PaddedVectorTest/2 (0 ms total) 35: 35: [----------] 11 tests from PaddedVectorTest/3, where TypeParam = std::allocator > 35: [ RUN ] PaddedVectorTest/3.DefaultConstructorWorks 35: [ OK ] PaddedVectorTest/3.DefaultConstructorWorks (0 ms) 35: [ RUN ] PaddedVectorTest/3.ResizeWorks 35: [ OK ] PaddedVectorTest/3.ResizeWorks (0 ms) 35: [ RUN ] PaddedVectorTest/3.ReserveWorks 35: [ OK ] PaddedVectorTest/3.ReserveWorks (0 ms) 35: [ RUN ] PaddedVectorTest/3.ReserveWorksTheSameAsNoReserve 35: [ OK ] PaddedVectorTest/3.ReserveWorksTheSameAsNoReserve (0 ms) 35: [ RUN ] PaddedVectorTest/3.MoveConstructorWorks 35: [ OK ] PaddedVectorTest/3.MoveConstructorWorks (0 ms) 35: [ RUN ] PaddedVectorTest/3.MoveConstructorWithAllocatorWorks 35: [ OK ] PaddedVectorTest/3.MoveConstructorWithAllocatorWorks (0 ms) 35: [ RUN ] PaddedVectorTest/3.MoveAssignmentWorks 35: [ OK ] PaddedVectorTest/3.MoveAssignmentWorks (0 ms) 35: [ RUN ] PaddedVectorTest/3.ArrayRefConversionsAreIdentical 35: [ OK ] PaddedVectorTest/3.ArrayRefConversionsAreIdentical (0 ms) 35: [ RUN ] PaddedVectorTest/3.CanCopyAssign 35: [ OK ] PaddedVectorTest/3.CanCopyAssign (0 ms) 35: [ RUN ] PaddedVectorTest/3.CanMoveAssign 35: [ OK ] PaddedVectorTest/3.CanMoveAssign (0 ms) 35: [ RUN ] PaddedVectorTest/3.CanSwap 35: [ OK ] PaddedVectorTest/3.CanSwap (0 ms) 35: [----------] 11 tests from PaddedVectorTest/3 (0 ms total) 35: 35: [----------] 11 tests from PaddedVectorTest/4, where TypeParam = std::allocator > 35: [ RUN ] PaddedVectorTest/4.DefaultConstructorWorks 35: [ OK ] PaddedVectorTest/4.DefaultConstructorWorks (0 ms) 35: [ RUN ] PaddedVectorTest/4.ResizeWorks 35: [ OK ] PaddedVectorTest/4.ResizeWorks (0 ms) 35: [ RUN ] PaddedVectorTest/4.ReserveWorks 35: [ OK ] PaddedVectorTest/4.ReserveWorks (0 ms) 35: [ RUN ] PaddedVectorTest/4.ReserveWorksTheSameAsNoReserve 35: [ OK ] PaddedVectorTest/4.ReserveWorksTheSameAsNoReserve (0 ms) 35: [ RUN ] PaddedVectorTest/4.MoveConstructorWorks 35: [ OK ] PaddedVectorTest/4.MoveConstructorWorks (0 ms) 35: [ RUN ] PaddedVectorTest/4.MoveConstructorWithAllocatorWorks 35: [ OK ] PaddedVectorTest/4.MoveConstructorWithAllocatorWorks (0 ms) 35: [ RUN ] PaddedVectorTest/4.MoveAssignmentWorks 35: [ OK ] PaddedVectorTest/4.MoveAssignmentWorks (0 ms) 35: [ RUN ] PaddedVectorTest/4.ArrayRefConversionsAreIdentical 35: [ OK ] PaddedVectorTest/4.ArrayRefConversionsAreIdentical (0 ms) 35: [ RUN ] PaddedVectorTest/4.CanCopyAssign 35: [ OK ] PaddedVectorTest/4.CanCopyAssign (0 ms) 35: [ RUN ] PaddedVectorTest/4.CanMoveAssign 35: [ OK ] PaddedVectorTest/4.CanMoveAssign (0 ms) 35: [ RUN ] PaddedVectorTest/4.CanSwap 35: [ OK ] PaddedVectorTest/4.CanSwap (0 ms) 35: [----------] 11 tests from PaddedVectorTest/4 (0 ms total) 35: 35: [----------] 11 tests from PaddedVectorTest/5, where TypeParam = gmx::Allocator 35: [ RUN ] PaddedVectorTest/5.DefaultConstructorWorks 35: [ OK ] PaddedVectorTest/5.DefaultConstructorWorks (0 ms) 35: [ RUN ] PaddedVectorTest/5.ResizeWorks 35: [ OK ] PaddedVectorTest/5.ResizeWorks (0 ms) 35: [ RUN ] PaddedVectorTest/5.ReserveWorks 35: [ OK ] PaddedVectorTest/5.ReserveWorks (0 ms) 35: [ RUN ] PaddedVectorTest/5.ReserveWorksTheSameAsNoReserve 35: [ OK ] PaddedVectorTest/5.ReserveWorksTheSameAsNoReserve (0 ms) 35: [ RUN ] PaddedVectorTest/5.MoveConstructorWorks 35: [ OK ] PaddedVectorTest/5.MoveConstructorWorks (0 ms) 35: [ RUN ] PaddedVectorTest/5.MoveConstructorWithAllocatorWorks 35: [ OK ] PaddedVectorTest/5.MoveConstructorWithAllocatorWorks (0 ms) 35: [ RUN ] PaddedVectorTest/5.MoveAssignmentWorks 35: [ OK ] PaddedVectorTest/5.MoveAssignmentWorks (0 ms) 35: [ RUN ] PaddedVectorTest/5.ArrayRefConversionsAreIdentical 35: [ OK ] PaddedVectorTest/5.ArrayRefConversionsAreIdentical (0 ms) 35: [ RUN ] PaddedVectorTest/5.CanCopyAssign 35: [ OK ] PaddedVectorTest/5.CanCopyAssign (0 ms) 35: [ RUN ] PaddedVectorTest/5.CanMoveAssign 35: [ OK ] PaddedVectorTest/5.CanMoveAssign (0 ms) 35: [ RUN ] PaddedVectorTest/5.CanSwap 35: [ OK ] PaddedVectorTest/5.CanSwap (0 ms) 35: [----------] 11 tests from PaddedVectorTest/5 (0 ms total) 35: 35: [----------] 11 tests from PaddedVectorTest/6, where TypeParam = gmx::Allocator 35: [ RUN ] PaddedVectorTest/6.DefaultConstructorWorks 35: [ OK ] PaddedVectorTest/6.DefaultConstructorWorks (0 ms) 35: [ RUN ] PaddedVectorTest/6.ResizeWorks 35: [ OK ] PaddedVectorTest/6.ResizeWorks (0 ms) 35: [ RUN ] PaddedVectorTest/6.ReserveWorks 35: [ OK ] PaddedVectorTest/6.ReserveWorks (0 ms) 35: [ RUN ] PaddedVectorTest/6.ReserveWorksTheSameAsNoReserve 35: [ OK ] PaddedVectorTest/6.ReserveWorksTheSameAsNoReserve (0 ms) 35: [ RUN ] PaddedVectorTest/6.MoveConstructorWorks 35: [ OK ] PaddedVectorTest/6.MoveConstructorWorks (0 ms) 35: [ RUN ] PaddedVectorTest/6.MoveConstructorWithAllocatorWorks 35: [ OK ] PaddedVectorTest/6.MoveConstructorWithAllocatorWorks (0 ms) 35: [ RUN ] PaddedVectorTest/6.MoveAssignmentWorks 35: [ OK ] PaddedVectorTest/6.MoveAssignmentWorks (0 ms) 35: [ RUN ] PaddedVectorTest/6.ArrayRefConversionsAreIdentical 35: [ OK ] PaddedVectorTest/6.ArrayRefConversionsAreIdentical (0 ms) 35: [ RUN ] PaddedVectorTest/6.CanCopyAssign 35: [ OK ] PaddedVectorTest/6.CanCopyAssign (0 ms) 35: [ RUN ] PaddedVectorTest/6.CanMoveAssign 35: [ OK ] PaddedVectorTest/6.CanMoveAssign (0 ms) 35: [ RUN ] PaddedVectorTest/6.CanSwap 35: [ OK ] PaddedVectorTest/6.CanSwap (0 ms) 35: [----------] 11 tests from PaddedVectorTest/6 (0 ms total) 35: 35: [----------] 11 tests from PaddedVectorTest/7, where TypeParam = gmx::Allocator 35: [ RUN ] PaddedVectorTest/7.DefaultConstructorWorks 35: [ OK ] PaddedVectorTest/7.DefaultConstructorWorks (0 ms) 35: [ RUN ] PaddedVectorTest/7.ResizeWorks 35: [ OK ] PaddedVectorTest/7.ResizeWorks (0 ms) 35: [ RUN ] PaddedVectorTest/7.ReserveWorks 35: [ OK ] PaddedVectorTest/7.ReserveWorks (0 ms) 35: [ RUN ] PaddedVectorTest/7.ReserveWorksTheSameAsNoReserve 35: [ OK ] PaddedVectorTest/7.ReserveWorksTheSameAsNoReserve (0 ms) 35: [ RUN ] PaddedVectorTest/7.MoveConstructorWorks 35: [ OK ] PaddedVectorTest/7.MoveConstructorWorks (0 ms) 35: [ RUN ] PaddedVectorTest/7.MoveConstructorWithAllocatorWorks 35: [ OK ] PaddedVectorTest/7.MoveConstructorWithAllocatorWorks (0 ms) 35: [ RUN ] PaddedVectorTest/7.MoveAssignmentWorks 35: [ OK ] PaddedVectorTest/7.MoveAssignmentWorks (0 ms) 35: [ RUN ] PaddedVectorTest/7.ArrayRefConversionsAreIdentical 35: [ OK ] PaddedVectorTest/7.ArrayRefConversionsAreIdentical (0 ms) 35: [ RUN ] PaddedVectorTest/7.CanCopyAssign 35: [ OK ] PaddedVectorTest/7.CanCopyAssign (0 ms) 35: [ RUN ] PaddedVectorTest/7.CanMoveAssign 35: [ OK ] PaddedVectorTest/7.CanMoveAssign (0 ms) 35: [ RUN ] PaddedVectorTest/7.CanSwap 35: [ OK ] PaddedVectorTest/7.CanSwap (0 ms) 35: [----------] 11 tests from PaddedVectorTest/7 (0 ms total) 35: 35: [----------] 11 tests from PaddedVectorTest/8, where TypeParam = gmx::Allocator, gmx::AlignedAllocationPolicy> 35: [ RUN ] PaddedVectorTest/8.DefaultConstructorWorks 35: [ OK ] PaddedVectorTest/8.DefaultConstructorWorks (0 ms) 35: [ RUN ] PaddedVectorTest/8.ResizeWorks 35: [ OK ] PaddedVectorTest/8.ResizeWorks (0 ms) 35: [ RUN ] PaddedVectorTest/8.ReserveWorks 35: [ OK ] PaddedVectorTest/8.ReserveWorks (0 ms) 35: [ RUN ] PaddedVectorTest/8.ReserveWorksTheSameAsNoReserve 35: [ OK ] PaddedVectorTest/8.ReserveWorksTheSameAsNoReserve (0 ms) 35: [ RUN ] PaddedVectorTest/8.MoveConstructorWorks 35: [ OK ] PaddedVectorTest/8.MoveConstructorWorks (0 ms) 35: [ RUN ] PaddedVectorTest/8.MoveConstructorWithAllocatorWorks 35: [ OK ] PaddedVectorTest/8.MoveConstructorWithAllocatorWorks (0 ms) 35: [ RUN ] PaddedVectorTest/8.MoveAssignmentWorks 35: [ OK ] PaddedVectorTest/8.MoveAssignmentWorks (0 ms) 35: [ RUN ] PaddedVectorTest/8.ArrayRefConversionsAreIdentical 35: [ OK ] PaddedVectorTest/8.ArrayRefConversionsAreIdentical (0 ms) 35: [ RUN ] PaddedVectorTest/8.CanCopyAssign 35: [ OK ] PaddedVectorTest/8.CanCopyAssign (0 ms) 35: [ RUN ] PaddedVectorTest/8.CanMoveAssign 35: [ OK ] PaddedVectorTest/8.CanMoveAssign (0 ms) 35: [ RUN ] PaddedVectorTest/8.CanSwap 35: [ OK ] PaddedVectorTest/8.CanSwap (0 ms) 35: [----------] 11 tests from PaddedVectorTest/8 (0 ms total) 35: 35: [----------] 11 tests from PaddedVectorTest/9, where TypeParam = gmx::Allocator, gmx::AlignedAllocationPolicy> 35: [ RUN ] PaddedVectorTest/9.DefaultConstructorWorks 35: [ OK ] PaddedVectorTest/9.DefaultConstructorWorks (0 ms) 35: [ RUN ] PaddedVectorTest/9.ResizeWorks 35: [ OK ] PaddedVectorTest/9.ResizeWorks (0 ms) 35: [ RUN ] PaddedVectorTest/9.ReserveWorks 35: [ OK ] PaddedVectorTest/9.ReserveWorks (0 ms) 35: [ RUN ] PaddedVectorTest/9.ReserveWorksTheSameAsNoReserve 35: [ OK ] PaddedVectorTest/9.ReserveWorksTheSameAsNoReserve (0 ms) 35: [ RUN ] PaddedVectorTest/9.MoveConstructorWorks 35: [ OK ] PaddedVectorTest/9.MoveConstructorWorks (0 ms) 35: [ RUN ] PaddedVectorTest/9.MoveConstructorWithAllocatorWorks 35: [ OK ] PaddedVectorTest/9.MoveConstructorWithAllocatorWorks (0 ms) 35: [ RUN ] PaddedVectorTest/9.MoveAssignmentWorks 35: [ OK ] PaddedVectorTest/9.MoveAssignmentWorks (0 ms) 35: [ RUN ] PaddedVectorTest/9.ArrayRefConversionsAreIdentical 35: [ OK ] PaddedVectorTest/9.ArrayRefConversionsAreIdentical (0 ms) 35: [ RUN ] PaddedVectorTest/9.CanCopyAssign 35: [ OK ] PaddedVectorTest/9.CanCopyAssign (0 ms) 35: [ RUN ] PaddedVectorTest/9.CanMoveAssign 35: [ OK ] PaddedVectorTest/9.CanMoveAssign (0 ms) 35: [ RUN ] PaddedVectorTest/9.CanSwap 35: [ OK ] PaddedVectorTest/9.CanSwap (0 ms) 35: [----------] 11 tests from PaddedVectorTest/9 (0 ms total) 35: 35: [----------] 41 tests from RVecTest 35: [ RUN ] RVecTest.CanBeStoredInVector 35: [ OK ] RVecTest.CanBeStoredInVector (0 ms) 35: [ RUN ] RVecTest.ConvertsImplicitlyFrom_rvec 35: [ OK ] RVecTest.ConvertsImplicitlyFrom_rvec (0 ms) 35: [ RUN ] RVecTest.ConvertsImplicitlyTo_rvec 35: [ OK ] RVecTest.ConvertsImplicitlyTo_rvec (0 ms) 35: [ RUN ] RVecTest.WorksAsMutable_rvec 35: [ OK ] RVecTest.WorksAsMutable_rvec (0 ms) 35: [ RUN ] RVecTest.WorksAs_rvec_Array 35: [ OK ] RVecTest.WorksAs_rvec_Array (0 ms) 35: [ RUN ] RVecTest.ComparesEqual 35: [ OK ] RVecTest.ComparesEqual (0 ms) 35: [ RUN ] RVecTest.ComparesUnequal 35: [ OK ] RVecTest.ComparesUnequal (0 ms) 35: [ RUN ] RVecTest.CanAddRVecToRvec 35: [ OK ] RVecTest.CanAddRVecToRvec (0 ms) 35: [ RUN ] RVecTest.CanAddAssignRVecToRvec 35: [ OK ] RVecTest.CanAddAssignRVecToRvec (0 ms) 35: [ RUN ] RVecTest.CanSubtractRVecFromRvec 35: [ OK ] RVecTest.CanSubtractRVecFromRvec (0 ms) 35: [ RUN ] RVecTest.CanSubtractAssignRVecFromRvec 35: [ OK ] RVecTest.CanSubtractAssignRVecFromRvec (0 ms) 35: [ RUN ] RVecTest.CanDotProductRVecByRvec 35: [ OK ] RVecTest.CanDotProductRVecByRvec (0 ms) 35: [ RUN ] RVecTest.CanCrossProductRVecByRvec 35: [ OK ] RVecTest.CanCrossProductRVecByRvec (0 ms) 35: [ RUN ] RVecTest.CanDivideRVecInplace 35: [ OK ] RVecTest.CanDivideRVecInplace (0 ms) 35: [ RUN ] RVecTest.CanScaleRVec 35: [ OK ] RVecTest.CanScaleRVec (0 ms) 35: [ RUN ] RVecTest.CanDivideRVec 35: [ OK ] RVecTest.CanDivideRVec (0 ms) 35: [ RUN ] RVecTest.CanDoUnitvFromRVec 35: [ OK ] RVecTest.CanDoUnitvFromRVec (0 ms) 35: [ RUN ] RVecTest.CanSqLengthOfRVec 35: [ OK ] RVecTest.CanSqLengthOfRVec (0 ms) 35: [ RUN ] RVecTest.CanLengthOfRVec 35: [ OK ] RVecTest.CanLengthOfRVec (0 ms) 35: [ RUN ] RVecTest.CanCastToRVec 35: [ OK ] RVecTest.CanCastToRVec (0 ms) 35: [ RUN ] RVecTest.CanCastToDVec 35: [ OK ] RVecTest.CanCastToDVec (0 ms) 35: [ RUN ] RVecTest.CanLeftScalarMultiply 35: [ OK ] RVecTest.CanLeftScalarMultiply (0 ms) 35: [ RUN ] RVecTest.CanRightScalarMultiply 35: [ OK ] RVecTest.CanRightScalarMultiply (0 ms) 35: [ RUN ] RVecTest.CanGetUnitvFromRVec 35: [ OK ] RVecTest.CanGetUnitvFromRVec (0 ms) 35: [ RUN ] RVecTest.CanGetSqLengthOfRVec 35: [ OK ] RVecTest.CanGetSqLengthOfRVec (0 ms) 35: [ RUN ] RVecTest.CanGetLengthOfRVec 35: [ OK ] RVecTest.CanGetLengthOfRVec (0 ms) 35: [ RUN ] RVecTest.CanDoCrossProductOfRVec 35: [ OK ] RVecTest.CanDoCrossProductOfRVec (0 ms) 35: [ RUN ] RVecTest.CanDoDotProductOfRVec 35: [ OK ] RVecTest.CanDoDotProductOfRVec (0 ms) 35: [ RUN ] RVecTest.CanScaleByVector 35: [ OK ] RVecTest.CanScaleByVector (0 ms) 35: [ RUN ] RVecTest.CanNegate 35: [ OK ] RVecTest.CanNegate (0 ms) 35: [ RUN ] RVecTest.asIVec 35: [ OK ] RVecTest.asIVec (0 ms) 35: [ RUN ] RVecTest.elementWiseMin 35: [ OK ] RVecTest.elementWiseMin (0 ms) 35: [ RUN ] RVecTest.elementWiseMax 35: [ OK ] RVecTest.elementWiseMax (0 ms) 35: [ RUN ] RVecTest.WorksAs_dvec_Reference 35: [ OK ] RVecTest.WorksAs_dvec_Reference (0 ms) 35: [ RUN ] RVecTest.WorksAs_ivec_Reference 35: [ OK ] RVecTest.WorksAs_ivec_Reference (0 ms) 35: [ RUN ] RVecTest.WorksAs_rvec_Reference 35: [ OK ] RVecTest.WorksAs_rvec_Reference (0 ms) 35: [ RUN ] RVecTest.CopyConstructorWorks 35: [ OK ] RVecTest.CopyConstructorWorks (0 ms) 35: [ RUN ] RVecTest.CopyAssignmentWorks 35: [ OK ] RVecTest.CopyAssignmentWorks (0 ms) 35: [ RUN ] RVecTest.MoveConstructorWorks 35: [ OK ] RVecTest.MoveConstructorWorks (0 ms) 35: [ RUN ] RVecTest.MoveAssignmentWorks 35: [ OK ] RVecTest.MoveAssignmentWorks (0 ms) 35: [ RUN ] RVecTest.UsableInConstexpr 35: [ OK ] RVecTest.UsableInConstexpr (0 ms) 35: [----------] 41 tests from RVecTest (1 ms total) 35: 35: [----------] Global test environment tear-down 35: [==========] 328 tests from 41 test suites ran. (881 ms total) 35: [ PASSED ] 328 tests. 35/92 Test #35: MathUnitTests ............................. Passed 1.01 sec test 36 Start 36: MdrunUtilityUnitTests 36: Test command: /build/reproducible-path/gromacs-2025.1/build/basic-dp/bin/mdrunutility-test "--gtest_output=xml:/build/reproducible-path/gromacs-2025.1/build/basic-dp/Testing/Temporary/MdrunUtilityUnitTests.xml" 36: Working Directory: /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/mdrunutility/tests 36: Test timeout computed to be: 30 36: [==========] Running 21 tests from 2 test suites. 36: [----------] Global test environment set-up. 36: [----------] 4 tests from MDModulesNotifierTest 36: [ RUN ] MDModulesNotifierTest.AddConsumer 36: [ OK ] MDModulesNotifierTest.AddConsumer (0 ms) 36: [ RUN ] MDModulesNotifierTest.AddConsumerWithPointerParameter 36: [ OK ] MDModulesNotifierTest.AddConsumerWithPointerParameter (0 ms) 36: [ RUN ] MDModulesNotifierTest.AddTwoDifferentConsumers 36: [ OK ] MDModulesNotifierTest.AddTwoDifferentConsumers (0 ms) 36: [ RUN ] MDModulesNotifierTest.AddConsumerOfTwoResources 36: [ OK ] MDModulesNotifierTest.AddConsumerOfTwoResources (0 ms) 36: [----------] 4 tests from MDModulesNotifierTest (0 ms total) 36: 36: [----------] 17 tests from ThreadAffinityTest 36: [ RUN ] ThreadAffinityTest.DoesNothingWhenDisabled 36: [ OK ] ThreadAffinityTest.DoesNothingWhenDisabled (0 ms) 36: [ RUN ] ThreadAffinityTest.DoesNothingWhenNotSupported 36: [ OK ] ThreadAffinityTest.DoesNothingWhenNotSupported (0 ms) 36: [ RUN ] ThreadAffinityTest.DoesNothingWithAutoAndTooFewUserSetThreads 36: [ OK ] ThreadAffinityTest.DoesNothingWithAutoAndTooFewUserSetThreads (1 ms) 36: [ RUN ] ThreadAffinityTest.DoesNothingWithAutoAndTooManyUserSetThreads 36: [ OK ] ThreadAffinityTest.DoesNothingWithAutoAndTooManyUserSetThreads (0 ms) 36: [ RUN ] ThreadAffinityTest.DoesNothingWithAutoAndTooManyAutoSetThreads 36: [ OK ] ThreadAffinityTest.DoesNothingWithAutoAndTooManyAutoSetThreads (0 ms) 36: [ RUN ] ThreadAffinityTest.DoesNothingWithUnknownHardware 36: [ OK ] ThreadAffinityTest.DoesNothingWithUnknownHardware (0 ms) 36: [ RUN ] ThreadAffinityTest.DoesNothingWithTooManyThreads 36: [ OK ] ThreadAffinityTest.DoesNothingWithTooManyThreads (0 ms) 36: [ RUN ] ThreadAffinityTest.DoesNothingWithTooLargeOffset 36: [ OK ] ThreadAffinityTest.DoesNothingWithTooLargeOffset (0 ms) 36: [ RUN ] ThreadAffinityTest.DoesNothingWithTooLargeStride 36: [ OK ] ThreadAffinityTest.DoesNothingWithTooLargeStride (0 ms) 36: [ RUN ] ThreadAffinityTest.PinsSingleThreadWithAuto 36: [ OK ] ThreadAffinityTest.PinsSingleThreadWithAuto (0 ms) 36: [ RUN ] ThreadAffinityTest.PinsSingleThreadWhenForced 36: [ OK ] ThreadAffinityTest.PinsSingleThreadWhenForced (0 ms) 36: [ RUN ] ThreadAffinityTest.PinsSingleThreadWithOffsetWhenForced 36: [ OK ] ThreadAffinityTest.PinsSingleThreadWithOffsetWhenForced (1 ms) 36: [ RUN ] ThreadAffinityTest.HandlesPinningFailureWithSingleThread 36: NOTE: Affinity setting failed. 36: [ OK ] ThreadAffinityTest.HandlesPinningFailureWithSingleThread (0 ms) 36: [ RUN ] ThreadAffinityTest.PinsMultipleThreadsWithAuto 36: [ OK ] ThreadAffinityTest.PinsMultipleThreadsWithAuto (2 ms) 36: [ RUN ] ThreadAffinityTest.PinsMultipleThreadsWithStrideWhenForced 36: [ OK ] ThreadAffinityTest.PinsMultipleThreadsWithStrideWhenForced (4 ms) 36: [ RUN ] ThreadAffinityTest.PinsWithAutoAndFewerAutoSetThreads 36: [ OK ] ThreadAffinityTest.PinsWithAutoAndFewerAutoSetThreads (2 ms) 36: [ RUN ] ThreadAffinityTest.HandlesPinningFailureWithOneThreadFailing 36: NOTE: Affinity setting for 1/2 threads failed. 36: [ OK ] ThreadAffinityTest.HandlesPinningFailureWithOneThreadFailing (3 ms) 36: [----------] 17 tests from ThreadAffinityTest (22 ms total) 36: 36: [----------] Global test environment tear-down 36: [==========] 21 tests from 2 test suites ran. (23 ms total) 36: [ PASSED ] 21 tests. 36/92 Test #36: MdrunUtilityUnitTests ..................... Passed 0.12 sec test 37 Start 37: MdrunUtilityMpiUnitTests 37: Test command: /build/reproducible-path/gromacs-2025.1/build/basic-dp/bin/mdrunutility-mpi-test "-ntmpi" "4" "--gtest_output=xml:/build/reproducible-path/gromacs-2025.1/build/basic-dp/Testing/Temporary/MdrunUtilityMpiUnitTests.xml" 37: Working Directory: /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/mdrunutility/tests 37: Test timeout computed to be: 30 37: [==========] Running 13 tests from 2 test suites. 37: [----------] Global test environment set-up. 37: [----------] 6 tests from ThreadAffinityMultiRankTest 37: [ RUN ] ThreadAffinityMultiRankTest.PinsWholeNode 37: [ OK ] ThreadAffinityMultiRankTest.PinsWholeNode (46 ms) 37: [ RUN ] ThreadAffinityMultiRankTest.PinsWithOffsetAndStride 37: [ OK ] ThreadAffinityMultiRankTest.PinsWithOffsetAndStride (34 ms) 37: [ RUN ] ThreadAffinityMultiRankTest.PinsTwoNodes 37: [ OK ] ThreadAffinityMultiRankTest.PinsTwoNodes (16 ms) 37: [ RUN ] ThreadAffinityMultiRankTest.DoesNothingWhenDisabled 37: [ OK ] ThreadAffinityMultiRankTest.DoesNothingWhenDisabled (68 ms) 37: [ RUN ] ThreadAffinityMultiRankTest.HandlesTooManyThreadsWithAuto 37: [ OK ] ThreadAffinityMultiRankTest.HandlesTooManyThreadsWithAuto (87 ms) 37: [ RUN ] ThreadAffinityMultiRankTest.HandlesTooManyThreadsWithForce 37: [ OK ] ThreadAffinityMultiRankTest.HandlesTooManyThreadsWithForce (120 ms) 37: [----------] 6 tests from ThreadAffinityMultiRankTest (373 ms total) 37: 37: [----------] 7 tests from ThreadAffinityHeterogeneousNodesTest 37: [ RUN ] ThreadAffinityHeterogeneousNodesTest.PinsOnMainOnly 37: [ OK ] ThreadAffinityHeterogeneousNodesTest.PinsOnMainOnly (75 ms) 37: [ RUN ] ThreadAffinityHeterogeneousNodesTest.PinsOnNonMainOnly 37: [ OK ] ThreadAffinityHeterogeneousNodesTest.PinsOnNonMainOnly (56 ms) 37: [ RUN ] ThreadAffinityHeterogeneousNodesTest.HandlesUnknownHardwareOnNonMain 37: [ OK ] ThreadAffinityHeterogeneousNodesTest.HandlesUnknownHardwareOnNonMain (53 ms) 37: [ RUN ] ThreadAffinityHeterogeneousNodesTest.PinsAutomaticallyOnMainOnly 37: [ OK ] ThreadAffinityHeterogeneousNodesTest.PinsAutomaticallyOnMainOnly (51 ms) 37: [ RUN ] ThreadAffinityHeterogeneousNodesTest.PinsAutomaticallyOnNonMainOnly 37: [ OK ] ThreadAffinityHeterogeneousNodesTest.PinsAutomaticallyOnNonMainOnly (43 ms) 37: [ RUN ] ThreadAffinityHeterogeneousNodesTest.HandlesInvalidOffsetOnNonMainOnly 37: [ OK ] ThreadAffinityHeterogeneousNodesTest.HandlesInvalidOffsetOnNonMainOnly (18 ms) 37: [ RUN ] ThreadAffinityHeterogeneousNodesTest.HandlesInvalidStrideOnNonMainOnly 37: [ OK ] ThreadAffinityHeterogeneousNodesTest.HandlesInvalidStrideOnNonMainOnly (44 ms) 37: [----------] 7 tests from ThreadAffinityHeterogeneousNodesTest (343 ms total) 37: 37: [----------] Global test environment tear-down 37: [==========] 13 tests from 2 test suites ran. (717 ms total) 37: [ PASSED ] 13 tests. 37/92 Test #37: MdrunUtilityMpiUnitTests .................. Passed 0.80 sec test 38 Start 38: MDSpanTests 38: Test command: /build/reproducible-path/gromacs-2025.1/build/basic-dp/bin/mdspan-test "--gtest_output=xml:/build/reproducible-path/gromacs-2025.1/build/basic-dp/Testing/Temporary/MDSpanTests.xml" 38: Working Directory: /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/mdspan/tests 38: Test timeout computed to be: 30 38: [==========] Running 32 tests from 7 test suites. 38: [----------] Global test environment set-up. 38: [----------] 4 tests from BasicAccessorPolicy 38: [ RUN ] BasicAccessorPolicy.Decay 38: [ OK ] BasicAccessorPolicy.Decay (0 ms) 38: [ RUN ] BasicAccessorPolicy.Access 38: [ OK ] BasicAccessorPolicy.Access (0 ms) 38: [ RUN ] BasicAccessorPolicy.Offset 38: [ OK ] BasicAccessorPolicy.Offset (0 ms) 38: [ RUN ] BasicAccessorPolicy.CopyAccessor 38: [ OK ] BasicAccessorPolicy.CopyAccessor (0 ms) 38: [----------] 4 tests from BasicAccessorPolicy (0 ms total) 38: 38: [----------] 4 tests from ExtentsTest 38: [ RUN ] ExtentsTest.Construction 38: [ OK ] ExtentsTest.Construction (0 ms) 38: [ RUN ] ExtentsTest.PurelyStatic 38: [ OK ] ExtentsTest.PurelyStatic (0 ms) 38: [ RUN ] ExtentsTest.RankNought 38: [ OK ] ExtentsTest.RankNought (0 ms) 38: [ RUN ] ExtentsTest.Assignment 38: [ OK ] ExtentsTest.Assignment (0 ms) 38: [----------] 4 tests from ExtentsTest (0 ms total) 38: 38: [----------] 8 tests from MdSpanExtension 38: [ RUN ] MdSpanExtension.SlicingAllStatic 38: [ OK ] MdSpanExtension.SlicingAllStatic (0 ms) 38: [ RUN ] MdSpanExtension.SlicingDynamic 38: [ OK ] MdSpanExtension.SlicingDynamic (0 ms) 38: [ RUN ] MdSpanExtension.SlicingAllStatic3D 38: [ OK ] MdSpanExtension.SlicingAllStatic3D (0 ms) 38: [ RUN ] MdSpanExtension.SlicingEqualsView3D 38: [ OK ] MdSpanExtension.SlicingEqualsView3D (0 ms) 38: [ RUN ] MdSpanExtension.additionWorks 38: [ OK ] MdSpanExtension.additionWorks (0 ms) 38: [ RUN ] MdSpanExtension.subtractionWorks 38: [ OK ] MdSpanExtension.subtractionWorks (0 ms) 38: [ RUN ] MdSpanExtension.multiplicationWorks 38: [ OK ] MdSpanExtension.multiplicationWorks (0 ms) 38: [ RUN ] MdSpanExtension.divisionWorks 38: [ OK ] MdSpanExtension.divisionWorks (0 ms) 38: [----------] 8 tests from MdSpanExtension (0 ms total) 38: 38: [----------] 3 tests from LayoutTests 38: [ RUN ] LayoutTests.LayoutRightConstruction 38: [ OK ] LayoutTests.LayoutRightConstruction (0 ms) 38: [ RUN ] LayoutTests.LayoutRightProperties 38: [ OK ] LayoutTests.LayoutRightProperties (0 ms) 38: [ RUN ] LayoutTests.LayoutRightOperator 38: [ OK ] LayoutTests.LayoutRightOperator (0 ms) 38: [----------] 3 tests from LayoutTests (0 ms total) 38: 38: [----------] 1 test from MdSpanTest 38: [ RUN ] MdSpanTest.MdSpanWrapsBasicMdSpanCorrectly 38: [ OK ] MdSpanTest.MdSpanWrapsBasicMdSpanCorrectly (0 ms) 38: [----------] 1 test from MdSpanTest (0 ms total) 38: 38: [----------] 6 tests from MdSpanTest/0, where TypeParam = gmx::basic_mdspan, gmx::layout_right, gmx::accessor_basic > 38: [ RUN ] MdSpanTest/0.Rank 38: [ OK ] MdSpanTest/0.Rank (0 ms) 38: [ RUN ] MdSpanTest/0.DynamicRank 38: [ OK ] MdSpanTest/0.DynamicRank (0 ms) 38: [ RUN ] MdSpanTest/0.Extents 38: [ OK ] MdSpanTest/0.Extents (0 ms) 38: [ RUN ] MdSpanTest/0.Strides 38: [ OK ] MdSpanTest/0.Strides (0 ms) 38: [ RUN ] MdSpanTest/0.Properties 38: [ OK ] MdSpanTest/0.Properties (0 ms) 38: [ RUN ] MdSpanTest/0.Operator 38: [ OK ] MdSpanTest/0.Operator (0 ms) 38: [----------] 6 tests from MdSpanTest/0 (0 ms total) 38: 38: [----------] 6 tests from MdSpanTest/1, where TypeParam = gmx::basic_mdspan, gmx::layout_right, gmx::accessor_basic > 38: [ RUN ] MdSpanTest/1.Rank 38: [ OK ] MdSpanTest/1.Rank (0 ms) 38: [ RUN ] MdSpanTest/1.DynamicRank 38: [ OK ] MdSpanTest/1.DynamicRank (0 ms) 38: [ RUN ] MdSpanTest/1.Extents 38: [ OK ] MdSpanTest/1.Extents (0 ms) 38: [ RUN ] MdSpanTest/1.Strides 38: [ OK ] MdSpanTest/1.Strides (0 ms) 38: [ RUN ] MdSpanTest/1.Properties 38: [ OK ] MdSpanTest/1.Properties (0 ms) 38: [ RUN ] MdSpanTest/1.Operator 38: [ OK ] MdSpanTest/1.Operator (0 ms) 38: [----------] 6 tests from MdSpanTest/1 (0 ms total) 38: 38: [----------] Global test environment tear-down 38: [==========] 32 tests from 7 test suites ran. (1 ms total) 38: [ PASSED ] 32 tests. 38/92 Test #38: MDSpanTests ............................... Passed 0.08 sec test 39 Start 39: MdtypesUnitTest 39: Test command: /build/reproducible-path/gromacs-2025.1/build/basic-dp/bin/mdtypes-test "--gtest_output=xml:/build/reproducible-path/gromacs-2025.1/build/basic-dp/Testing/Temporary/MdtypesUnitTest.xml" 39: Working Directory: /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/mdtypes/tests 39: Test timeout computed to be: 30 39: [==========] Running 97 tests from 7 test suites. 39: [----------] Global test environment set-up. 39: [----------] 4 tests from ForeingLambdaTermsDhdl 39: [ RUN ] ForeingLambdaTermsDhdl.RateCheckWorks 39: [ OK ] ForeingLambdaTermsDhdl.RateCheckWorks (0 ms) 39: [ RUN ] ForeingLambdaTermsDhdl.AllLinear 39: [ OK ] ForeingLambdaTermsDhdl.AllLinear (0 ms) 39: [ RUN ] ForeingLambdaTermsDhdl.AllLinearNegative 39: [ OK ] ForeingLambdaTermsDhdl.AllLinearNegative (0 ms) 39: [ RUN ] ForeingLambdaTermsDhdl.SeparateVdwCoul 39: [ OK ] ForeingLambdaTermsDhdl.SeparateVdwCoul (0 ms) 39: [----------] 4 tests from ForeingLambdaTermsDhdl (0 ms total) 39: 39: [----------] 4 tests from ObservablesReducerTest 39: [ RUN ] ObservablesReducerTest.CanMoveAssign 39: [ OK ] ObservablesReducerTest.CanMoveAssign (0 ms) 39: [ RUN ] ObservablesReducerTest.CanMoveConstruct 39: [ OK ] ObservablesReducerTest.CanMoveConstruct (0 ms) 39: [ RUN ] ObservablesReducerTest.CanBuildAndUseWithNoSubscribers 39: [ OK ] ObservablesReducerTest.CanBuildAndUseWithNoSubscribers (0 ms) 39: [ RUN ] ObservablesReducerTest.CanBuildAndUseWithOneSubscriber 39: [ OK ] ObservablesReducerTest.CanBuildAndUseWithOneSubscriber (0 ms) 39: [----------] 4 tests from ObservablesReducerTest (0 ms total) 39: 39: [----------] 2 tests from CheckpointDataTest 39: [ RUN ] CheckpointDataTest.SingleDataTest 39: [ OK ] CheckpointDataTest.SingleDataTest (12 ms) 39: [ RUN ] CheckpointDataTest.MultiDataTest 39: [ OK ] CheckpointDataTest.MultiDataTest (61 ms) 39: [----------] 2 tests from CheckpointDataTest (73 ms total) 39: 39: [----------] 7 tests from ForceBuffers 39: [ RUN ] ForceBuffers.ConstructsUnpinned 39: [ OK ] ForceBuffers.ConstructsUnpinned (0 ms) 39: [ RUN ] ForceBuffers.ConstructsPinned 39: [ OK ] ForceBuffers.ConstructsPinned (0 ms) 39: [ RUN ] ForceBuffers.ConstructsEmpty 39: [ OK ] ForceBuffers.ConstructsEmpty (0 ms) 39: [ RUN ] ForceBuffers.ResizeWorks 39: [ OK ] ForceBuffers.ResizeWorks (0 ms) 39: [ RUN ] ForceBuffers.PaddingWorks 39: [ OK ] ForceBuffers.PaddingWorks (0 ms) 39: [ RUN ] ForceBuffers.CopyWorks 39: [ OK ] ForceBuffers.CopyWorks (0 ms) 39: [ RUN ] ForceBuffers.CopyDoesNotPin 39: [ OK ] ForceBuffers.CopyDoesNotPin (0 ms) 39: [----------] 7 tests from ForceBuffers (0 ms total) 39: 39: [----------] 5 tests from MultipleTimeStepping 39: [ RUN ] MultipleTimeStepping.ChecksNumLevels 39: [ OK ] MultipleTimeStepping.ChecksNumLevels (0 ms) 39: [ RUN ] MultipleTimeStepping.SelectsForceGroups 39: [ OK ] MultipleTimeStepping.SelectsForceGroups (0 ms) 39: [ RUN ] MultipleTimeStepping.ChecksStepFactor 39: [ OK ] MultipleTimeStepping.ChecksStepFactor (0 ms) 39: [ RUN ] MultipleTimeStepping.ChecksPmeIsAtLastLevel 39: [ OK ] MultipleTimeStepping.ChecksPmeIsAtLastLevel (0 ms) 39: [ RUN ] MultipleTimeStepping.ChecksIntegrator 39: [ OK ] MultipleTimeStepping.ChecksIntegrator (0 ms) 39: [----------] 5 tests from MultipleTimeStepping (0 ms total) 39: 39: [----------] 60 tests from WithVariousSubscriberCounts/ObservablesReducerIntegrationTest 39: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseSimply/numSubscribers0numRanks1 39: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseSimply/numSubscribers0numRanks1 (0 ms) 39: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseSimply/numSubscribers0numRanks2 39: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseSimply/numSubscribers0numRanks2 (0 ms) 39: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseSimply/numSubscribers0numRanks3 39: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseSimply/numSubscribers0numRanks3 (0 ms) 39: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseSimply/numSubscribers1numRanks1 39: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseSimply/numSubscribers1numRanks1 (0 ms) 39: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseSimply/numSubscribers1numRanks2 39: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseSimply/numSubscribers1numRanks2 (0 ms) 39: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseSimply/numSubscribers1numRanks3 39: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseSimply/numSubscribers1numRanks3 (0 ms) 39: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseSimply/numSubscribers2numRanks1 39: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseSimply/numSubscribers2numRanks1 (0 ms) 39: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseSimply/numSubscribers2numRanks2 39: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseSimply/numSubscribers2numRanks2 (0 ms) 39: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseSimply/numSubscribers2numRanks3 39: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseSimply/numSubscribers2numRanks3 (0 ms) 39: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseSimply/numSubscribers3numRanks1 39: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseSimply/numSubscribers3numRanks1 (0 ms) 39: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseSimply/numSubscribers3numRanks2 39: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseSimply/numSubscribers3numRanks2 (0 ms) 39: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseSimply/numSubscribers3numRanks3 39: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseSimply/numSubscribers3numRanks3 (0 ms) 39: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseOverMultipleSteps/numSubscribers0numRanks1 39: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseOverMultipleSteps/numSubscribers0numRanks1 (0 ms) 39: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseOverMultipleSteps/numSubscribers0numRanks2 39: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseOverMultipleSteps/numSubscribers0numRanks2 (0 ms) 39: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseOverMultipleSteps/numSubscribers0numRanks3 39: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseOverMultipleSteps/numSubscribers0numRanks3 (0 ms) 39: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseOverMultipleSteps/numSubscribers1numRanks1 39: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseOverMultipleSteps/numSubscribers1numRanks1 (0 ms) 39: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseOverMultipleSteps/numSubscribers1numRanks2 39: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseOverMultipleSteps/numSubscribers1numRanks2 (0 ms) 39: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseOverMultipleSteps/numSubscribers1numRanks3 39: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseOverMultipleSteps/numSubscribers1numRanks3 (0 ms) 39: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseOverMultipleSteps/numSubscribers2numRanks1 39: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseOverMultipleSteps/numSubscribers2numRanks1 (0 ms) 39: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseOverMultipleSteps/numSubscribers2numRanks2 39: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseOverMultipleSteps/numSubscribers2numRanks2 (0 ms) 39: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseOverMultipleSteps/numSubscribers2numRanks3 39: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseOverMultipleSteps/numSubscribers2numRanks3 (0 ms) 39: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseOverMultipleSteps/numSubscribers3numRanks1 39: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseOverMultipleSteps/numSubscribers3numRanks1 (0 ms) 39: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseOverMultipleSteps/numSubscribers3numRanks2 39: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseOverMultipleSteps/numSubscribers3numRanks2 (0 ms) 39: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseOverMultipleSteps/numSubscribers3numRanks3 39: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseOverMultipleSteps/numSubscribers3numRanks3 (0 ms) 39: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWithoutAllNeedingReduction/numSubscribers0numRanks1 39: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWithoutAllNeedingReduction/numSubscribers0numRanks1 (0 ms) 39: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWithoutAllNeedingReduction/numSubscribers0numRanks2 39: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWithoutAllNeedingReduction/numSubscribers0numRanks2 (0 ms) 39: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWithoutAllNeedingReduction/numSubscribers0numRanks3 39: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWithoutAllNeedingReduction/numSubscribers0numRanks3 (0 ms) 39: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWithoutAllNeedingReduction/numSubscribers1numRanks1 39: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWithoutAllNeedingReduction/numSubscribers1numRanks1 (0 ms) 39: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWithoutAllNeedingReduction/numSubscribers1numRanks2 39: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWithoutAllNeedingReduction/numSubscribers1numRanks2 (0 ms) 39: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWithoutAllNeedingReduction/numSubscribers1numRanks3 39: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWithoutAllNeedingReduction/numSubscribers1numRanks3 (0 ms) 39: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWithoutAllNeedingReduction/numSubscribers2numRanks1 39: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWithoutAllNeedingReduction/numSubscribers2numRanks1 (0 ms) 39: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWithoutAllNeedingReduction/numSubscribers2numRanks2 39: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWithoutAllNeedingReduction/numSubscribers2numRanks2 (0 ms) 39: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWithoutAllNeedingReduction/numSubscribers2numRanks3 39: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWithoutAllNeedingReduction/numSubscribers2numRanks3 (0 ms) 39: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWithoutAllNeedingReduction/numSubscribers3numRanks1 39: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWithoutAllNeedingReduction/numSubscribers3numRanks1 (0 ms) 39: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWithoutAllNeedingReduction/numSubscribers3numRanks2 39: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWithoutAllNeedingReduction/numSubscribers3numRanks2 (0 ms) 39: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWithoutAllNeedingReduction/numSubscribers3numRanks3 39: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWithoutAllNeedingReduction/numSubscribers3numRanks3 (0 ms) 39: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenASubscriberUsesEventually/numSubscribers0numRanks1 39: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenASubscriberUsesEventually/numSubscribers0numRanks1 (0 ms) 39: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenASubscriberUsesEventually/numSubscribers0numRanks2 39: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenASubscriberUsesEventually/numSubscribers0numRanks2 (0 ms) 39: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenASubscriberUsesEventually/numSubscribers0numRanks3 39: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenASubscriberUsesEventually/numSubscribers0numRanks3 (0 ms) 39: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenASubscriberUsesEventually/numSubscribers1numRanks1 39: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenASubscriberUsesEventually/numSubscribers1numRanks1 (0 ms) 39: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenASubscriberUsesEventually/numSubscribers1numRanks2 39: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenASubscriberUsesEventually/numSubscribers1numRanks2 (0 ms) 39: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenASubscriberUsesEventually/numSubscribers1numRanks3 39: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenASubscriberUsesEventually/numSubscribers1numRanks3 (0 ms) 39: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenASubscriberUsesEventually/numSubscribers2numRanks1 39: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenASubscriberUsesEventually/numSubscribers2numRanks1 (0 ms) 39: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenASubscriberUsesEventually/numSubscribers2numRanks2 39: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenASubscriberUsesEventually/numSubscribers2numRanks2 (0 ms) 39: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenASubscriberUsesEventually/numSubscribers2numRanks3 39: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenASubscriberUsesEventually/numSubscribers2numRanks3 (0 ms) 39: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenASubscriberUsesEventually/numSubscribers3numRanks1 39: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenASubscriberUsesEventually/numSubscribers3numRanks1 (0 ms) 39: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenASubscriberUsesEventually/numSubscribers3numRanks2 39: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenASubscriberUsesEventually/numSubscribers3numRanks2 (0 ms) 39: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenASubscriberUsesEventually/numSubscribers3numRanks3 39: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenASubscriberUsesEventually/numSubscribers3numRanks3 (0 ms) 39: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenAllSubscribersUseEventually/numSubscribers0numRanks1 39: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenAllSubscribersUseEventually/numSubscribers0numRanks1 (0 ms) 39: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenAllSubscribersUseEventually/numSubscribers0numRanks2 39: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenAllSubscribersUseEventually/numSubscribers0numRanks2 (0 ms) 39: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenAllSubscribersUseEventually/numSubscribers0numRanks3 39: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenAllSubscribersUseEventually/numSubscribers0numRanks3 (0 ms) 39: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenAllSubscribersUseEventually/numSubscribers1numRanks1 39: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenAllSubscribersUseEventually/numSubscribers1numRanks1 (0 ms) 39: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenAllSubscribersUseEventually/numSubscribers1numRanks2 39: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenAllSubscribersUseEventually/numSubscribers1numRanks2 (0 ms) 39: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenAllSubscribersUseEventually/numSubscribers1numRanks3 39: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenAllSubscribersUseEventually/numSubscribers1numRanks3 (0 ms) 39: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenAllSubscribersUseEventually/numSubscribers2numRanks1 39: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenAllSubscribersUseEventually/numSubscribers2numRanks1 (0 ms) 39: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenAllSubscribersUseEventually/numSubscribers2numRanks2 39: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenAllSubscribersUseEventually/numSubscribers2numRanks2 (0 ms) 39: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenAllSubscribersUseEventually/numSubscribers2numRanks3 39: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenAllSubscribersUseEventually/numSubscribers2numRanks3 (0 ms) 39: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenAllSubscribersUseEventually/numSubscribers3numRanks1 39: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenAllSubscribersUseEventually/numSubscribers3numRanks1 (0 ms) 39: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenAllSubscribersUseEventually/numSubscribers3numRanks2 39: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenAllSubscribersUseEventually/numSubscribers3numRanks2 (0 ms) 39: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenAllSubscribersUseEventually/numSubscribers3numRanks3 39: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenAllSubscribersUseEventually/numSubscribers3numRanks3 (0 ms) 39: [----------] 60 tests from WithVariousSubscriberCounts/ObservablesReducerIntegrationTest (8 ms total) 39: 39: [----------] 15 tests from ChecksStepInterval/MtsIntervalTest 39: [ RUN ] ChecksStepInterval/MtsIntervalTest.Works/0 39: [ OK ] ChecksStepInterval/MtsIntervalTest.Works/0 (0 ms) 39: [ RUN ] ChecksStepInterval/MtsIntervalTest.Works/1 39: [ OK ] ChecksStepInterval/MtsIntervalTest.Works/1 (0 ms) 39: [ RUN ] ChecksStepInterval/MtsIntervalTest.Works/2 39: [ OK ] ChecksStepInterval/MtsIntervalTest.Works/2 (0 ms) 39: [ RUN ] ChecksStepInterval/MtsIntervalTest.Works/3 39: [ OK ] ChecksStepInterval/MtsIntervalTest.Works/3 (0 ms) 39: [ RUN ] ChecksStepInterval/MtsIntervalTest.Works/4 39: [ OK ] ChecksStepInterval/MtsIntervalTest.Works/4 (0 ms) 39: [ RUN ] ChecksStepInterval/MtsIntervalTest.Works/5 39: [ OK ] ChecksStepInterval/MtsIntervalTest.Works/5 (0 ms) 39: [ RUN ] ChecksStepInterval/MtsIntervalTest.Works/6 39: [ OK ] ChecksStepInterval/MtsIntervalTest.Works/6 (0 ms) 39: [ RUN ] ChecksStepInterval/MtsIntervalTest.Works/7 39: [ OK ] ChecksStepInterval/MtsIntervalTest.Works/7 (0 ms) 39: [ RUN ] ChecksStepInterval/MtsIntervalTest.Works/8 39: [ OK ] ChecksStepInterval/MtsIntervalTest.Works/8 (0 ms) 39: [ RUN ] ChecksStepInterval/MtsIntervalTest.Works/9 39: [ OK ] ChecksStepInterval/MtsIntervalTest.Works/9 (0 ms) 39: [ RUN ] ChecksStepInterval/MtsIntervalTest.Works/10 39: [ OK ] ChecksStepInterval/MtsIntervalTest.Works/10 (0 ms) 39: [ RUN ] ChecksStepInterval/MtsIntervalTest.Works/11 39: [ OK ] ChecksStepInterval/MtsIntervalTest.Works/11 (0 ms) 39: [ RUN ] ChecksStepInterval/MtsIntervalTest.Works/12 39: [ OK ] ChecksStepInterval/MtsIntervalTest.Works/12 (0 ms) 39: [ RUN ] ChecksStepInterval/MtsIntervalTest.Works/13 39: [ OK ] ChecksStepInterval/MtsIntervalTest.Works/13 (0 ms) 39: [ RUN ] ChecksStepInterval/MtsIntervalTest.Works/14 39: [ OK ] ChecksStepInterval/MtsIntervalTest.Works/14 (0 ms) 39: [----------] 15 tests from ChecksStepInterval/MtsIntervalTest (0 ms total) 39: 39: [----------] Global test environment tear-down 39: [==========] 97 tests from 7 test suites ran. (84 ms total) 39: [ PASSED ] 97 tests. 39/92 Test #39: MdtypesUnitTest ........................... Passed 0.18 sec test 40 Start 40: OnlineHelpUnitTests 40: Test command: /build/reproducible-path/gromacs-2025.1/build/basic-dp/bin/onlinehelp-test "--gtest_output=xml:/build/reproducible-path/gromacs-2025.1/build/basic-dp/Testing/Temporary/OnlineHelpUnitTests.xml" 40: Working Directory: /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/onlinehelp/tests 40: Test timeout computed to be: 30 40: [==========] Running 22 tests from 4 test suites. 40: [----------] Global test environment set-up. 40: [----------] 6 tests from TextTableFormatterTest 40: [ RUN ] TextTableFormatterTest.HandlesBasicCase 40: [ OK ] TextTableFormatterTest.HandlesBasicCase (0 ms) 40: [ RUN ] TextTableFormatterTest.HandlesEmptyColumnTitles 40: [ OK ] TextTableFormatterTest.HandlesEmptyColumnTitles (0 ms) 40: [ RUN ] TextTableFormatterTest.HandlesIndentation 40: [ OK ] TextTableFormatterTest.HandlesIndentation (0 ms) 40: [ RUN ] TextTableFormatterTest.HandlesOverflowingLines 40: [ OK ] TextTableFormatterTest.HandlesOverflowingLines (0 ms) 40: [ RUN ] TextTableFormatterTest.HandlesLastColumnFolding 40: [ OK ] TextTableFormatterTest.HandlesLastColumnFolding (0 ms) 40: [ RUN ] TextTableFormatterTest.HandlesEmptyColumns 40: [ OK ] TextTableFormatterTest.HandlesEmptyColumns (0 ms) 40: [----------] 6 tests from TextTableFormatterTest (3 ms total) 40: 40: [----------] 3 tests from HelpManagerTest 40: [ RUN ] HelpManagerTest.HandlesRootTopic 40: [ OK ] HelpManagerTest.HandlesRootTopic (0 ms) 40: [ RUN ] HelpManagerTest.HandlesSubTopics 40: [ OK ] HelpManagerTest.HandlesSubTopics (0 ms) 40: [ RUN ] HelpManagerTest.HandlesInvalidTopics 40: [ OK ] HelpManagerTest.HandlesInvalidTopics (2 ms) 40: [----------] 3 tests from HelpManagerTest (3 ms total) 40: 40: [----------] 2 tests from HelpTopicFormattingTest 40: [ RUN ] HelpTopicFormattingTest.FormatsSimpleTopic 40: [ OK ] HelpTopicFormattingTest.FormatsSimpleTopic (0 ms) 40: [ RUN ] HelpTopicFormattingTest.FormatsCompositeTopicWithSubTopics 40: [ OK ] HelpTopicFormattingTest.FormatsCompositeTopicWithSubTopics (0 ms) 40: [----------] 2 tests from HelpTopicFormattingTest (1 ms total) 40: 40: [----------] 11 tests from HelpWriterContextTest 40: [ RUN ] HelpWriterContextTest.FormatsParagraphs 40: [ OK ] HelpWriterContextTest.FormatsParagraphs (0 ms) 40: [ RUN ] HelpWriterContextTest.FormatsRstStyleParagraphs 40: [ OK ] HelpWriterContextTest.FormatsRstStyleParagraphs (0 ms) 40: [ RUN ] HelpWriterContextTest.CleansUpExtraWhitespace 40: [ OK ] HelpWriterContextTest.CleansUpExtraWhitespace (0 ms) 40: [ RUN ] HelpWriterContextTest.FormatsLiteralText 40: [ OK ] HelpWriterContextTest.FormatsLiteralText (0 ms) 40: [ RUN ] HelpWriterContextTest.FormatsLiteralTextAtBeginning 40: [ OK ] HelpWriterContextTest.FormatsLiteralTextAtBeginning (0 ms) 40: [ RUN ] HelpWriterContextTest.FormatsLiteralTextWithIndentation 40: [ OK ] HelpWriterContextTest.FormatsLiteralTextWithIndentation (0 ms) 40: [ RUN ] HelpWriterContextTest.FormatsBulletList 40: [ OK ] HelpWriterContextTest.FormatsBulletList (0 ms) 40: [ RUN ] HelpWriterContextTest.FormatsEnumeratedList 40: [ OK ] HelpWriterContextTest.FormatsEnumeratedList (0 ms) 40: [ RUN ] HelpWriterContextTest.FormatsSimpleTable 40: [ OK ] HelpWriterContextTest.FormatsSimpleTable (0 ms) 40: [ RUN ] HelpWriterContextTest.FormatsGridTable 40: [ OK ] HelpWriterContextTest.FormatsGridTable (0 ms) 40: [ RUN ] HelpWriterContextTest.FormatsTitles 40: [ OK ] HelpWriterContextTest.FormatsTitles (0 ms) 40: [----------] 11 tests from HelpWriterContextTest (6 ms total) 40: 40: [----------] Global test environment tear-down 40: [==========] 22 tests from 4 test suites ran. (14 ms total) 40: [ PASSED ] 22 tests. 40/92 Test #40: OnlineHelpUnitTests ....................... Passed 0.09 sec test 41 Start 41: OptionsUnitTests 41: Test command: /build/reproducible-path/gromacs-2025.1/build/basic-dp/bin/options-test "--gtest_output=xml:/build/reproducible-path/gromacs-2025.1/build/basic-dp/Testing/Temporary/OptionsUnitTests.xml" 41: Working Directory: /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/options/tests 41: Test timeout computed to be: 30 41: [==========] Running 112 tests from 18 test suites. 41: [----------] Global test environment set-up. 41: [----------] 5 tests from AbstractOptionStorageTest 41: [ RUN ] AbstractOptionStorageTest.HandlesSetInFinish 41: [ OK ] AbstractOptionStorageTest.HandlesSetInFinish (0 ms) 41: [ RUN ] AbstractOptionStorageTest.HandlesValueRemoval 41: [ OK ] AbstractOptionStorageTest.HandlesValueRemoval (0 ms) 41: [ RUN ] AbstractOptionStorageTest.HandlesValueAddition 41: [ OK ] AbstractOptionStorageTest.HandlesValueAddition (0 ms) 41: [ RUN ] AbstractOptionStorageTest.HandlesTooManyValueAddition 41: [ OK ] AbstractOptionStorageTest.HandlesTooManyValueAddition (0 ms) 41: [ RUN ] AbstractOptionStorageTest.AllowsEmptyValues 41: [ OK ] AbstractOptionStorageTest.AllowsEmptyValues (0 ms) 41: [----------] 5 tests from AbstractOptionStorageTest (2 ms total) 41: 41: [----------] 10 tests from FileNameOptionTest 41: [ RUN ] FileNameOptionTest.HandlesRequiredDefaultValueWithoutExtension 41: [ OK ] FileNameOptionTest.HandlesRequiredDefaultValueWithoutExtension (0 ms) 41: [ RUN ] FileNameOptionTest.HandlesRequiredOptionWithoutValue 41: [ OK ] FileNameOptionTest.HandlesRequiredOptionWithoutValue (0 ms) 41: [ RUN ] FileNameOptionTest.HandlesOptionalUnsetOption 41: [ OK ] FileNameOptionTest.HandlesOptionalUnsetOption (0 ms) 41: [ RUN ] FileNameOptionTest.HandlesOptionalDefaultValueWithoutExtension 41: [ OK ] FileNameOptionTest.HandlesOptionalDefaultValueWithoutExtension (0 ms) 41: [ RUN ] FileNameOptionTest.HandlesRequiredCustomDefaultExtension 41: [ OK ] FileNameOptionTest.HandlesRequiredCustomDefaultExtension (0 ms) 41: [ RUN ] FileNameOptionTest.HandlesOptionalCustomDefaultExtension 41: [ OK ] FileNameOptionTest.HandlesOptionalCustomDefaultExtension (0 ms) 41: [ RUN ] FileNameOptionTest.GivesErrorOnUnknownFileSuffix 41: [ OK ] FileNameOptionTest.GivesErrorOnUnknownFileSuffix (0 ms) 41: [ RUN ] FileNameOptionTest.GivesErrorOnInvalidFileSuffix 41: [ OK ] FileNameOptionTest.GivesErrorOnInvalidFileSuffix (0 ms) 41: [ RUN ] FileNameOptionTest.HandlesRequiredCsvValueWithoutExtension 41: [ OK ] FileNameOptionTest.HandlesRequiredCsvValueWithoutExtension (0 ms) 41: [ RUN ] FileNameOptionTest.HandlesRequiredCsvOptionWithoutValue 41: [ OK ] FileNameOptionTest.HandlesRequiredCsvOptionWithoutValue (0 ms) 41: [----------] 10 tests from FileNameOptionTest (1 ms total) 41: 41: [----------] 16 tests from FileNameOptionManagerTest 41: [ RUN ] FileNameOptionManagerTest.AddsMissingExtension 41: [ OK ] FileNameOptionManagerTest.AddsMissingExtension (0 ms) 41: [ RUN ] FileNameOptionManagerTest.AddsMissingCustomDefaultExtension 41: [ OK ] FileNameOptionManagerTest.AddsMissingCustomDefaultExtension (0 ms) 41: [ RUN ] FileNameOptionManagerTest.GivesErrorOnMissingInputFile 41: [ OK ] FileNameOptionManagerTest.GivesErrorOnMissingInputFile (0 ms) 41: [ RUN ] FileNameOptionManagerTest.GivesErrorOnMissingGenericInputFile 41: [ OK ] FileNameOptionManagerTest.GivesErrorOnMissingGenericInputFile (0 ms) 41: [ RUN ] FileNameOptionManagerTest.GivesErrorOnMissingDefaultInputFile 41: [ OK ] FileNameOptionManagerTest.GivesErrorOnMissingDefaultInputFile (0 ms) 41: [ RUN ] FileNameOptionManagerTest.GivesErrorOnMissingRequiredInputFile 41: [ OK ] FileNameOptionManagerTest.GivesErrorOnMissingRequiredInputFile (0 ms) 41: [ RUN ] FileNameOptionManagerTest.AcceptsMissingInputFileIfSpecified 41: [ OK ] FileNameOptionManagerTest.AcceptsMissingInputFileIfSpecified (0 ms) 41: [ RUN ] FileNameOptionManagerTest.AcceptsMissingDefaultInputFileIfSpecified 41: [ OK ] FileNameOptionManagerTest.AcceptsMissingDefaultInputFileIfSpecified (0 ms) 41: [ RUN ] FileNameOptionManagerTest.AcceptsMissingRequiredInputFileIfSpecified 41: [ OK ] FileNameOptionManagerTest.AcceptsMissingRequiredInputFileIfSpecified (0 ms) 41: [ RUN ] FileNameOptionManagerTest.AddsMissingExtensionBasedOnExistingFile 41: [ OK ] FileNameOptionManagerTest.AddsMissingExtensionBasedOnExistingFile (0 ms) 41: [ RUN ] FileNameOptionManagerTest.AddsMissingExtensionForRequiredDefaultNameBasedOnExistingFile 41: [ OK ] FileNameOptionManagerTest.AddsMissingExtensionForRequiredDefaultNameBasedOnExistingFile (0 ms) 41: [ RUN ] FileNameOptionManagerTest.AddsMissingExtensionForOptionalDefaultNameBasedOnExistingFile 41: [ OK ] FileNameOptionManagerTest.AddsMissingExtensionForOptionalDefaultNameBasedOnExistingFile (0 ms) 41: [ RUN ] FileNameOptionManagerTest.AddsMissingExtensionForRequiredFromDefaultNameOptionBasedOnExistingFile 41: [ OK ] FileNameOptionManagerTest.AddsMissingExtensionForRequiredFromDefaultNameOptionBasedOnExistingFile (0 ms) 41: [ RUN ] FileNameOptionManagerTest.AddsMissingExtensionForOptionalFromDefaultNameOptionBasedOnExistingFile 41: [ OK ] FileNameOptionManagerTest.AddsMissingExtensionForOptionalFromDefaultNameOptionBasedOnExistingFile (0 ms) 41: [ RUN ] FileNameOptionManagerTest.DefaultNameOptionWorksWithoutInputChecking 41: [ OK ] FileNameOptionManagerTest.DefaultNameOptionWorksWithoutInputChecking (0 ms) 41: [ RUN ] FileNameOptionManagerTest.AcceptsCompressedInputFile 41: [ OK ] FileNameOptionManagerTest.AcceptsCompressedInputFile (0 ms) 41: [----------] 16 tests from FileNameOptionManagerTest (2 ms total) 41: 41: [----------] 1 test from OptionsTest 41: [ RUN ] OptionsTest.FailsOnNonsafeStorage 41: [ OK ] OptionsTest.FailsOnNonsafeStorage (0 ms) 41: [----------] 1 test from OptionsTest (0 ms total) 41: 41: [----------] 9 tests from OptionsAssignerTest 41: [ RUN ] OptionsAssignerTest.HandlesMissingRequiredParameter 41: [ OK ] OptionsAssignerTest.HandlesMissingRequiredParameter (0 ms) 41: [ RUN ] OptionsAssignerTest.HandlesRequiredParameterWithDefaultValue 41: [ OK ] OptionsAssignerTest.HandlesRequiredParameterWithDefaultValue (0 ms) 41: [ RUN ] OptionsAssignerTest.HandlesInvalidMultipleParameter 41: [ OK ] OptionsAssignerTest.HandlesInvalidMultipleParameter (0 ms) 41: [ RUN ] OptionsAssignerTest.HandlesMultipleParameter 41: [ OK ] OptionsAssignerTest.HandlesMultipleParameter (0 ms) 41: [ RUN ] OptionsAssignerTest.HandlesMissingValue 41: [ OK ] OptionsAssignerTest.HandlesMissingValue (0 ms) 41: [ RUN ] OptionsAssignerTest.HandlesExtraValue 41: [ OK ] OptionsAssignerTest.HandlesExtraValue (0 ms) 41: [ RUN ] OptionsAssignerTest.HandlesGroups 41: [ OK ] OptionsAssignerTest.HandlesGroups (0 ms) 41: [ RUN ] OptionsAssignerTest.HandlesSections 41: [ OK ] OptionsAssignerTest.HandlesSections (0 ms) 41: [ RUN ] OptionsAssignerTest.HandlesMultipleSources 41: [ OK ] OptionsAssignerTest.HandlesMultipleSources (0 ms) 41: [----------] 9 tests from OptionsAssignerTest (1 ms total) 41: 41: [----------] 4 tests from OptionsAssignerBooleanTest 41: [ RUN ] OptionsAssignerBooleanTest.StoresYesValue 41: [ OK ] OptionsAssignerBooleanTest.StoresYesValue (0 ms) 41: [ RUN ] OptionsAssignerBooleanTest.SetsBooleanWithoutExplicitValue 41: [ OK ] OptionsAssignerBooleanTest.SetsBooleanWithoutExplicitValue (0 ms) 41: [ RUN ] OptionsAssignerBooleanTest.ClearsBooleanWithPrefixNo 41: [ OK ] OptionsAssignerBooleanTest.ClearsBooleanWithPrefixNo (0 ms) 41: [ RUN ] OptionsAssignerBooleanTest.HandlesBooleanWithPrefixAndValue 41: [ OK ] OptionsAssignerBooleanTest.HandlesBooleanWithPrefixAndValue (0 ms) 41: [----------] 4 tests from OptionsAssignerBooleanTest (0 ms total) 41: 41: [----------] 13 tests from OptionsAssignerIntegerTest 41: [ RUN ] OptionsAssignerIntegerTest.StoresSingleValue 41: [ OK ] OptionsAssignerIntegerTest.StoresSingleValue (0 ms) 41: [ RUN ] OptionsAssignerIntegerTest.HandlesEmptyValue 41: [ OK ] OptionsAssignerIntegerTest.HandlesEmptyValue (0 ms) 41: [ RUN ] OptionsAssignerIntegerTest.HandlesInvalidValue 41: [ OK ] OptionsAssignerIntegerTest.HandlesInvalidValue (0 ms) 41: [ RUN ] OptionsAssignerIntegerTest.HandlesOverflow 41: [ OK ] OptionsAssignerIntegerTest.HandlesOverflow (0 ms) 41: [ RUN ] OptionsAssignerIntegerTest.StoresDefaultValue 41: [ OK ] OptionsAssignerIntegerTest.StoresDefaultValue (0 ms) 41: [ RUN ] OptionsAssignerIntegerTest.StoresDefaultValueIfSet 41: [ OK ] OptionsAssignerIntegerTest.StoresDefaultValueIfSet (0 ms) 41: [ RUN ] OptionsAssignerIntegerTest.HandlesDefaultValueIfSetWhenNotSet 41: [ OK ] OptionsAssignerIntegerTest.HandlesDefaultValueIfSetWhenNotSet (0 ms) 41: [ RUN ] OptionsAssignerIntegerTest.HandlesBothDefaultValues 41: [ OK ] OptionsAssignerIntegerTest.HandlesBothDefaultValues (0 ms) 41: [ RUN ] OptionsAssignerIntegerTest.StoresToVector 41: [ OK ] OptionsAssignerIntegerTest.StoresToVector (0 ms) 41: [ RUN ] OptionsAssignerIntegerTest.HandlesVectors 41: [ OK ] OptionsAssignerIntegerTest.HandlesVectors (0 ms) 41: [ RUN ] OptionsAssignerIntegerTest.HandlesVectorFromSingleValue 41: [ OK ] OptionsAssignerIntegerTest.HandlesVectorFromSingleValue (0 ms) 41: [ RUN ] OptionsAssignerIntegerTest.HandlesVectorsWithDefaultValue 41: [ OK ] OptionsAssignerIntegerTest.HandlesVectorsWithDefaultValue (0 ms) 41: [ RUN ] OptionsAssignerIntegerTest.HandlesVectorsWithDefaultValueWithInvalidAssignment 41: [ OK ] OptionsAssignerIntegerTest.HandlesVectorsWithDefaultValueWithInvalidAssignment (0 ms) 41: [----------] 13 tests from OptionsAssignerIntegerTest (1 ms total) 41: 41: [----------] 5 tests from OptionsAssignerDoubleTest 41: [ RUN ] OptionsAssignerDoubleTest.StoresSingleValue 41: [ OK ] OptionsAssignerDoubleTest.StoresSingleValue (0 ms) 41: [ RUN ] OptionsAssignerDoubleTest.StoresValueFromFloat 41: [ OK ] OptionsAssignerDoubleTest.StoresValueFromFloat (0 ms) 41: [ RUN ] OptionsAssignerDoubleTest.HandlesEmptyValue 41: [ OK ] OptionsAssignerDoubleTest.HandlesEmptyValue (0 ms) 41: [ RUN ] OptionsAssignerDoubleTest.HandlesPreSetScaleValue 41: [ OK ] OptionsAssignerDoubleTest.HandlesPreSetScaleValue (0 ms) 41: [ RUN ] OptionsAssignerDoubleTest.HandlesPostSetScaleValue 41: [ OK ] OptionsAssignerDoubleTest.HandlesPostSetScaleValue (0 ms) 41: [----------] 5 tests from OptionsAssignerDoubleTest (0 ms total) 41: 41: [----------] 9 tests from OptionsAssignerStringTest 41: [ RUN ] OptionsAssignerStringTest.StoresSingleValue 41: [ OK ] OptionsAssignerStringTest.StoresSingleValue (0 ms) 41: [ RUN ] OptionsAssignerStringTest.HandlesEnumValue 41: [ OK ] OptionsAssignerStringTest.HandlesEnumValue (0 ms) 41: [ RUN ] OptionsAssignerStringTest.HandlesEnumValueFromNullTerminatedArray 41: [ OK ] OptionsAssignerStringTest.HandlesEnumValueFromNullTerminatedArray (0 ms) 41: [ RUN ] OptionsAssignerStringTest.HandlesIncorrectEnumValue 41: [ OK ] OptionsAssignerStringTest.HandlesIncorrectEnumValue (0 ms) 41: [ RUN ] OptionsAssignerStringTest.CompletesEnumValue 41: [ OK ] OptionsAssignerStringTest.CompletesEnumValue (0 ms) 41: [ RUN ] OptionsAssignerStringTest.HandlesEnumWithNoValue 41: [ OK ] OptionsAssignerStringTest.HandlesEnumWithNoValue (0 ms) 41: [ RUN ] OptionsAssignerStringTest.HandlesEnumDefaultValue 41: [ OK ] OptionsAssignerStringTest.HandlesEnumDefaultValue (0 ms) 41: [ RUN ] OptionsAssignerStringTest.HandlesEnumDefaultValueFromVariable 41: [ OK ] OptionsAssignerStringTest.HandlesEnumDefaultValueFromVariable (0 ms) 41: [ RUN ] OptionsAssignerStringTest.HandlesEnumDefaultValueFromVector 41: [ OK ] OptionsAssignerStringTest.HandlesEnumDefaultValueFromVector (0 ms) 41: [----------] 9 tests from OptionsAssignerStringTest (0 ms total) 41: 41: [----------] 6 tests from OptionsAssignerEnumTest 41: [ RUN ] OptionsAssignerEnumTest.StoresSingleValue 41: [ OK ] OptionsAssignerEnumTest.StoresSingleValue (0 ms) 41: [ RUN ] OptionsAssignerEnumTest.StoresVectorValues 41: [ OK ] OptionsAssignerEnumTest.StoresVectorValues (0 ms) 41: [ RUN ] OptionsAssignerEnumTest.HandlesInitialValueOutOfRange 41: [ OK ] OptionsAssignerEnumTest.HandlesInitialValueOutOfRange (0 ms) 41: [ RUN ] OptionsAssignerEnumTest.HandlesEnumDefaultValue 41: [ OK ] OptionsAssignerEnumTest.HandlesEnumDefaultValue (0 ms) 41: [ RUN ] OptionsAssignerEnumTest.HandlesEnumDefaultValueFromVariable 41: [ OK ] OptionsAssignerEnumTest.HandlesEnumDefaultValueFromVariable (0 ms) 41: [ RUN ] OptionsAssignerEnumTest.HandlesEnumDefaultValueFromVector 41: [ OK ] OptionsAssignerEnumTest.HandlesEnumDefaultValueFromVector (0 ms) 41: [----------] 6 tests from OptionsAssignerEnumTest (0 ms total) 41: 41: [----------] 8 tests from RepeatingOptionSectionTest 41: [ RUN ] RepeatingOptionSectionTest.HandlesNoInstance 41: [ OK ] RepeatingOptionSectionTest.HandlesNoInstance (0 ms) 41: [ RUN ] RepeatingOptionSectionTest.HandlesNoInstanceWithRequiredOption 41: [ OK ] RepeatingOptionSectionTest.HandlesNoInstanceWithRequiredOption (0 ms) 41: [ RUN ] RepeatingOptionSectionTest.HandlesSingleInstance 41: [ OK ] RepeatingOptionSectionTest.HandlesSingleInstance (0 ms) 41: [ RUN ] RepeatingOptionSectionTest.HandlesDefaultValue 41: [ OK ] RepeatingOptionSectionTest.HandlesDefaultValue (0 ms) 41: [ RUN ] RepeatingOptionSectionTest.HandlesTwoInstances 41: [ OK ] RepeatingOptionSectionTest.HandlesTwoInstances (0 ms) 41: [ RUN ] RepeatingOptionSectionTest.HandlesUnsetOptionWithImplicitDefault 41: [ OK ] RepeatingOptionSectionTest.HandlesUnsetOptionWithImplicitDefault (0 ms) 41: [ RUN ] RepeatingOptionSectionTest.HandlesUnsetOptionWithExplicitDefault 41: [ OK ] RepeatingOptionSectionTest.HandlesUnsetOptionWithExplicitDefault (0 ms) 41: [ RUN ] RepeatingOptionSectionTest.HandlesNestedSections 41: [ OK ] RepeatingOptionSectionTest.HandlesNestedSections (0 ms) 41: [----------] 8 tests from RepeatingOptionSectionTest (0 ms total) 41: 41: [----------] 1 test from TimeUnitManagerTest 41: [ RUN ] TimeUnitManagerTest.BasicOperations 41: [ OK ] TimeUnitManagerTest.BasicOperations (0 ms) 41: [----------] 1 test from TimeUnitManagerTest (0 ms total) 41: 41: [----------] 4 tests from TimeUnitBehaviorTest 41: [ RUN ] TimeUnitBehaviorTest.ScalesAssignedOptionValue 41: [ OK ] TimeUnitBehaviorTest.ScalesAssignedOptionValue (0 ms) 41: [ RUN ] TimeUnitBehaviorTest.DoesNotScaleDefaultValues 41: [ OK ] TimeUnitBehaviorTest.DoesNotScaleDefaultValues (0 ms) 41: [ RUN ] TimeUnitBehaviorTest.ScalesUserInputWithMultipleSources 41: [ OK ] TimeUnitBehaviorTest.ScalesUserInputWithMultipleSources (0 ms) 41: [ RUN ] TimeUnitBehaviorTest.TimeUnitOptionWorks 41: [ OK ] TimeUnitBehaviorTest.TimeUnitOptionWorks (0 ms) 41: [----------] 4 tests from TimeUnitBehaviorTest (0 ms total) 41: 41: [----------] 2 tests from TreeValueSupportAssignTest 41: [ RUN ] TreeValueSupportAssignTest.AssignsFromTree 41: [ OK ] TreeValueSupportAssignTest.AssignsFromTree (0 ms) 41: [ RUN ] TreeValueSupportAssignTest.AssignsFromTreeWithArrays 41: [ OK ] TreeValueSupportAssignTest.AssignsFromTreeWithArrays (0 ms) 41: [----------] 2 tests from TreeValueSupportAssignTest (0 ms total) 41: 41: [----------] 1 test from TreeValueSupportAssignErrorTest 41: [ RUN ] TreeValueSupportAssignErrorTest.HandlesInvalidValue 41: [ OK ] TreeValueSupportAssignErrorTest.HandlesInvalidValue (0 ms) 41: [----------] 1 test from TreeValueSupportAssignErrorTest (0 ms total) 41: 41: [----------] 5 tests from TreeValueSupportCheckTest 41: [ RUN ] TreeValueSupportCheckTest.HandlesEmpty 41: [ OK ] TreeValueSupportCheckTest.HandlesEmpty (0 ms) 41: [ RUN ] TreeValueSupportCheckTest.HandlesMatchingTree 41: [ OK ] TreeValueSupportCheckTest.HandlesMatchingTree (0 ms) 41: [ RUN ] TreeValueSupportCheckTest.HandlesSmallerTree1 41: [ OK ] TreeValueSupportCheckTest.HandlesSmallerTree1 (0 ms) 41: [ RUN ] TreeValueSupportCheckTest.HandlesSmallerTree2 41: [ OK ] TreeValueSupportCheckTest.HandlesSmallerTree2 (0 ms) 41: [ RUN ] TreeValueSupportCheckTest.DetectsExtraValue 41: [ OK ] TreeValueSupportCheckTest.DetectsExtraValue (0 ms) 41: [----------] 5 tests from TreeValueSupportCheckTest (0 ms total) 41: 41: [----------] 6 tests from TreeValueSupportAdjustTest 41: [ RUN ] TreeValueSupportAdjustTest.FillsDefaultValues 41: [ OK ] TreeValueSupportAdjustTest.FillsDefaultValues (0 ms) 41: [ RUN ] TreeValueSupportAdjustTest.FillsDefaultVectorValues 41: [ OK ] TreeValueSupportAdjustTest.FillsDefaultVectorValues (0 ms) 41: [ RUN ] TreeValueSupportAdjustTest.FillsDefaultObjectValues 41: [ OK ] TreeValueSupportAdjustTest.FillsDefaultObjectValues (0 ms) 41: [ RUN ] TreeValueSupportAdjustTest.NormalizesValues 41: [ OK ] TreeValueSupportAdjustTest.NormalizesValues (0 ms) 41: [ RUN ] TreeValueSupportAdjustTest.MergesDefaultValues 41: [ OK ] TreeValueSupportAdjustTest.MergesDefaultValues (0 ms) 41: [ RUN ] TreeValueSupportAdjustTest.OrdersValues 41: [ OK ] TreeValueSupportAdjustTest.OrdersValues (0 ms) 41: [----------] 6 tests from TreeValueSupportAdjustTest (3 ms total) 41: 41: [----------] 7 tests from TreeValueSupportTest 41: [ RUN ] TreeValueSupportTest.SupportsBooleanOption 41: [ OK ] TreeValueSupportTest.SupportsBooleanOption (0 ms) 41: [ RUN ] TreeValueSupportTest.SupportsIntegerOption 41: [ OK ] TreeValueSupportTest.SupportsIntegerOption (0 ms) 41: [ RUN ] TreeValueSupportTest.SupportsInt64Option 41: [ OK ] TreeValueSupportTest.SupportsInt64Option (0 ms) 41: [ RUN ] TreeValueSupportTest.SupportsStringOption 41: [ OK ] TreeValueSupportTest.SupportsStringOption (0 ms) 41: [ RUN ] TreeValueSupportTest.SupportsFloatOption 41: [ OK ] TreeValueSupportTest.SupportsFloatOption (0 ms) 41: [ RUN ] TreeValueSupportTest.SupportsDoubleOption 41: [ OK ] TreeValueSupportTest.SupportsDoubleOption (0 ms) 41: [ RUN ] TreeValueSupportTest.SupportsEnumOption 41: [ OK ] TreeValueSupportTest.SupportsEnumOption (0 ms) 41: [----------] 7 tests from TreeValueSupportTest (3 ms total) 41: 41: [----------] Global test environment tear-down 41: [==========] 112 tests from 18 test suites ran. (20 ms total) 41: [ PASSED ] 112 tests. 41/92 Test #41: OptionsUnitTests .......................... Passed 0.11 sec test 42 Start 42: PbcutilUnitTest 42: Test command: /build/reproducible-path/gromacs-2025.1/build/basic-dp/bin/pbcutil-test "--gtest_output=xml:/build/reproducible-path/gromacs-2025.1/build/basic-dp/Testing/Temporary/PbcutilUnitTest.xml" 42: Working Directory: /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/pbcutil/tests 42: Test timeout computed to be: 30 42: [==========] Running 36 tests from 5 test suites. 42: [----------] Global test environment set-up. 42: [----------] 1 test from ShiftTest 42: [ RUN ] ShiftTest.CoordinateShiftWorks 42: [ OK ] ShiftTest.CoordinateShiftWorks (0 ms) 42: [----------] 1 test from ShiftTest (0 ms total) 42: 42: [----------] 2 tests from MShift 42: [ RUN ] MShift.shiftsAndUnshifts 42: [ OK ] MShift.shiftsAndUnshifts (0 ms) 42: [ RUN ] MShift.shiftsAndUnshiftsSelf 42: [ OK ] MShift.shiftsAndUnshiftsSelf (0 ms) 42: [----------] 2 tests from MShift (0 ms total) 42: 42: [----------] 4 tests from PbcTest 42: [ RUN ] PbcTest.CalcShiftsWorks 42: [ OK ] PbcTest.CalcShiftsWorks (3 ms) 42: [ RUN ] PbcTest.PutAtomsInCubicBoxAlreadyInBox 42: [ OK ] PbcTest.PutAtomsInCubicBoxAlreadyInBox (0 ms) 42: [ RUN ] PbcTest.PutAtomsInCubicBoxFromOutsideBox 42: [ OK ] PbcTest.PutAtomsInCubicBoxFromOutsideBox (0 ms) 42: [ RUN ] PbcTest.PutAtomsInTriclinicBoxFromOutsideBox 42: [ OK ] PbcTest.PutAtomsInTriclinicBoxFromOutsideBox (0 ms) 42: [----------] 4 tests from PbcTest (4 ms total) 42: 42: [----------] 2 tests from PbcEnumsTest 42: [ RUN ] PbcEnumsTest.CenteringTypeNamesAreCorrect 42: [ OK ] PbcEnumsTest.CenteringTypeNamesAreCorrect (0 ms) 42: [ RUN ] PbcEnumsTest.UnitCellTypeNamesAreCorrect 42: [ OK ] PbcEnumsTest.UnitCellTypeNamesAreCorrect (0 ms) 42: [----------] 2 tests from PbcEnumsTest (0 ms total) 42: 42: [----------] 27 tests from CorrectCoordinates/COMInPlaceTest 42: [ RUN ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/0 42: [ OK ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/0 (2 ms) 42: [ RUN ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/1 42: [ OK ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/1 (1 ms) 42: [ RUN ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/2 42: [ OK ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/2 (1 ms) 42: [ RUN ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/3 42: [ OK ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/3 (1 ms) 42: [ RUN ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/4 42: [ OK ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/4 (1 ms) 42: [ RUN ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/5 42: [ OK ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/5 (1 ms) 42: [ RUN ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/6 42: [ OK ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/6 (1 ms) 42: [ RUN ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/7 42: [ OK ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/7 (1 ms) 42: [ RUN ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/8 42: [ OK ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/8 (1 ms) 42: [ RUN ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/9 42: [ OK ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/9 (1 ms) 42: [ RUN ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/10 42: [ OK ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/10 (1 ms) 42: [ RUN ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/11 42: [ OK ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/11 (2 ms) 42: [ RUN ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/12 42: [ OK ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/12 (1 ms) 42: [ RUN ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/13 42: [ OK ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/13 (1 ms) 42: [ RUN ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/14 42: [ OK ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/14 (1 ms) 42: [ RUN ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/15 42: [ OK ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/15 (1 ms) 42: [ RUN ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/16 42: [ OK ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/16 (1 ms) 42: [ RUN ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/17 42: [ OK ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/17 (1 ms) 42: [ RUN ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/18 42: [ OK ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/18 (1 ms) 42: [ RUN ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/19 42: [ OK ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/19 (1 ms) 42: [ RUN ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/20 42: [ OK ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/20 (1 ms) 42: [ RUN ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/21 42: [ OK ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/21 (1 ms) 42: [ RUN ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/22 42: [ OK ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/22 (2 ms) 42: [ RUN ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/23 42: [ OK ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/23 (2 ms) 42: [ RUN ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/24 42: [ OK ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/24 (1 ms) 42: [ RUN ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/25 42: [ OK ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/25 (1 ms) 42: [ RUN ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/26 42: [ OK ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/26 (1 ms) 42: [----------] 27 tests from CorrectCoordinates/COMInPlaceTest (48 ms total) 42: 42: [----------] Global test environment tear-down 42: [==========] 36 tests from 5 test suites ran. (53 ms total) 42: [ PASSED ] 36 tests. 42/92 Test #42: PbcutilUnitTest ........................... Passed 0.14 sec test 43 Start 43: RandomUnitTests 43: Test command: /build/reproducible-path/gromacs-2025.1/build/basic-dp/bin/random-test "--gtest_output=xml:/build/reproducible-path/gromacs-2025.1/build/basic-dp/Testing/Temporary/RandomUnitTests.xml" 43: Working Directory: /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/random/tests 43: Test timeout computed to be: 30 43: [==========] Running 44 tests from 10 test suites. 43: [----------] Global test environment set-up. 43: [----------] 4 tests from ExponentialDistributionTest 43: [ RUN ] ExponentialDistributionTest.Output 43: [ OK ] ExponentialDistributionTest.Output (1 ms) 43: [ RUN ] ExponentialDistributionTest.Logical 43: [ OK ] ExponentialDistributionTest.Logical (0 ms) 43: [ RUN ] ExponentialDistributionTest.Reset 43: [ OK ] ExponentialDistributionTest.Reset (0 ms) 43: [ RUN ] ExponentialDistributionTest.AltParam 43: [ OK ] ExponentialDistributionTest.AltParam (0 ms) 43: [----------] 4 tests from ExponentialDistributionTest (1 ms total) 43: 43: [----------] 4 tests from GammaDistributionTest 43: [ RUN ] GammaDistributionTest.Output 43: [ OK ] GammaDistributionTest.Output (0 ms) 43: [ RUN ] GammaDistributionTest.Logical 43: [ OK ] GammaDistributionTest.Logical (0 ms) 43: [ RUN ] GammaDistributionTest.Reset 43: [ OK ] GammaDistributionTest.Reset (0 ms) 43: [ RUN ] GammaDistributionTest.AltParam 43: [ OK ] GammaDistributionTest.AltParam (0 ms) 43: [----------] 4 tests from GammaDistributionTest (1 ms total) 43: 43: [----------] 4 tests from NormalDistributionTest 43: [ RUN ] NormalDistributionTest.Output 43: [ OK ] NormalDistributionTest.Output (0 ms) 43: [ RUN ] NormalDistributionTest.Logical 43: [ OK ] NormalDistributionTest.Logical (0 ms) 43: [ RUN ] NormalDistributionTest.Reset 43: [ OK ] NormalDistributionTest.Reset (0 ms) 43: [ RUN ] NormalDistributionTest.AltParam 43: [ OK ] NormalDistributionTest.AltParam (0 ms) 43: [----------] 4 tests from NormalDistributionTest (0 ms total) 43: 43: [----------] 1 test from SeedTest 43: [ RUN ] SeedTest.makeRandomSeed 43: [ OK ] SeedTest.makeRandomSeed (0 ms) 43: [----------] 1 test from SeedTest (0 ms total) 43: 43: [----------] 6 tests from TabulatedNormalDistributionTest 43: [ RUN ] TabulatedNormalDistributionTest.Output14 43: [ OK ] TabulatedNormalDistributionTest.Output14 (0 ms) 43: [ RUN ] TabulatedNormalDistributionTest.Output16 43: [ OK ] TabulatedNormalDistributionTest.Output16 (0 ms) 43: [ RUN ] TabulatedNormalDistributionTest.OutputDouble14 43: [ OK ] TabulatedNormalDistributionTest.OutputDouble14 (0 ms) 43: [ RUN ] TabulatedNormalDistributionTest.Logical 43: [ OK ] TabulatedNormalDistributionTest.Logical (0 ms) 43: [ RUN ] TabulatedNormalDistributionTest.Reset 43: [ OK ] TabulatedNormalDistributionTest.Reset (0 ms) 43: [ RUN ] TabulatedNormalDistributionTest.AltParam 43: [ OK ] TabulatedNormalDistributionTest.AltParam (0 ms) 43: [----------] 6 tests from TabulatedNormalDistributionTest (1 ms total) 43: 43: [----------] 1 test from TabulatedNormalDistributionTableTest 43: [ RUN ] TabulatedNormalDistributionTableTest.HasValidProperties 43: [ OK ] TabulatedNormalDistributionTableTest.HasValidProperties (3 ms) 43: [----------] 1 test from TabulatedNormalDistributionTableTest (4 ms total) 43: 43: [----------] 6 tests from ThreeFry2x64Test 43: [ RUN ] ThreeFry2x64Test.Logical 43: [ OK ] ThreeFry2x64Test.Logical (0 ms) 43: [ RUN ] ThreeFry2x64Test.InternalCounterSequence 43: [ OK ] ThreeFry2x64Test.InternalCounterSequence (0 ms) 43: [ RUN ] ThreeFry2x64Test.Reseed 43: [ OK ] ThreeFry2x64Test.Reseed (0 ms) 43: [ RUN ] ThreeFry2x64Test.Discard 43: [ OK ] ThreeFry2x64Test.Discard (0 ms) 43: [ RUN ] ThreeFry2x64Test.InvalidCounter 43: [ OK ] ThreeFry2x64Test.InvalidCounter (0 ms) 43: [ RUN ] ThreeFry2x64Test.ExhaustInternalCounter 43: [ OK ] ThreeFry2x64Test.ExhaustInternalCounter (0 ms) 43: [----------] 6 tests from ThreeFry2x64Test (1 ms total) 43: 43: [----------] 4 tests from UniformIntDistributionTest 43: [ RUN ] UniformIntDistributionTest.Output 43: [ OK ] UniformIntDistributionTest.Output (0 ms) 43: [ RUN ] UniformIntDistributionTest.Logical 43: [ OK ] UniformIntDistributionTest.Logical (0 ms) 43: [ RUN ] UniformIntDistributionTest.Reset 43: [ OK ] UniformIntDistributionTest.Reset (0 ms) 43: [ RUN ] UniformIntDistributionTest.AltParam 43: [ OK ] UniformIntDistributionTest.AltParam (0 ms) 43: [----------] 4 tests from UniformIntDistributionTest (0 ms total) 43: 43: [----------] 5 tests from UniformRealDistributionTest 43: [ RUN ] UniformRealDistributionTest.GenerateCanonical 43: [ OK ] UniformRealDistributionTest.GenerateCanonical (0 ms) 43: [ RUN ] UniformRealDistributionTest.Output 43: [ OK ] UniformRealDistributionTest.Output (0 ms) 43: [ RUN ] UniformRealDistributionTest.Logical 43: [ OK ] UniformRealDistributionTest.Logical (0 ms) 43: [ RUN ] UniformRealDistributionTest.Reset 43: [ OK ] UniformRealDistributionTest.Reset (0 ms) 43: [ RUN ] UniformRealDistributionTest.AltParam 43: [ OK ] UniformRealDistributionTest.AltParam (0 ms) 43: [----------] 5 tests from UniformRealDistributionTest (1 ms total) 43: 43: [----------] 9 tests from KnownAnswersTest/ThreeFry2x64Test 43: [ RUN ] KnownAnswersTest/ThreeFry2x64Test.Default/0 43: [ OK ] KnownAnswersTest/ThreeFry2x64Test.Default/0 (0 ms) 43: [ RUN ] KnownAnswersTest/ThreeFry2x64Test.Default/1 43: [ OK ] KnownAnswersTest/ThreeFry2x64Test.Default/1 (0 ms) 43: [ RUN ] KnownAnswersTest/ThreeFry2x64Test.Default/2 43: [ OK ] KnownAnswersTest/ThreeFry2x64Test.Default/2 (0 ms) 43: [ RUN ] KnownAnswersTest/ThreeFry2x64Test.Fast/0 43: [ OK ] KnownAnswersTest/ThreeFry2x64Test.Fast/0 (0 ms) 43: [ RUN ] KnownAnswersTest/ThreeFry2x64Test.Fast/1 43: [ OK ] KnownAnswersTest/ThreeFry2x64Test.Fast/1 (0 ms) 43: [ RUN ] KnownAnswersTest/ThreeFry2x64Test.Fast/2 43: [ OK ] KnownAnswersTest/ThreeFry2x64Test.Fast/2 (0 ms) 43: [ RUN ] KnownAnswersTest/ThreeFry2x64Test.Using40Rounds/0 43: [ OK ] KnownAnswersTest/ThreeFry2x64Test.Using40Rounds/0 (0 ms) 43: [ RUN ] KnownAnswersTest/ThreeFry2x64Test.Using40Rounds/1 43: [ OK ] KnownAnswersTest/ThreeFry2x64Test.Using40Rounds/1 (0 ms) 43: [ RUN ] KnownAnswersTest/ThreeFry2x64Test.Using40Rounds/2 43: [ OK ] KnownAnswersTest/ThreeFry2x64Test.Using40Rounds/2 (0 ms) 43: [----------] 9 tests from KnownAnswersTest/ThreeFry2x64Test (3 ms total) 43: 43: [----------] Global test environment tear-down 43: [==========] 44 tests from 10 test suites ran. (16 ms total) 43: [ PASSED ] 44 tests. 43/92 Test #43: RandomUnitTests ........................... Passed 0.11 sec test 44 Start 44: RestraintTests 44: Test command: /build/reproducible-path/gromacs-2025.1/build/basic-dp/bin/restraintpotential-test "--gtest_output=xml:/build/reproducible-path/gromacs-2025.1/build/basic-dp/Testing/Temporary/RestraintTests.xml" 44: Working Directory: /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/restraint/tests 44: Test timeout computed to be: 30 44: [==========] Running 1 test from 1 test suite. 44: [----------] Global test environment set-up. 44: [----------] 1 test from RestraintManager 44: [ RUN ] RestraintManager.restraintList 44: [ OK ] RestraintManager.restraintList (0 ms) 44: [----------] 1 test from RestraintManager (0 ms total) 44: 44: [----------] Global test environment tear-down 44: [==========] 1 test from 1 test suite ran. (0 ms total) 44: [ PASSED ] 1 test. 44/92 Test #44: RestraintTests ............................ Passed 0.07 sec test 45 Start 45: TableUnitTests 45: Test command: /build/reproducible-path/gromacs-2025.1/build/basic-dp/bin/table-test "--gtest_output=xml:/build/reproducible-path/gromacs-2025.1/build/basic-dp/Testing/Temporary/TableUnitTests.xml" 45: Working Directory: /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/tables/tests 45: Test timeout computed to be: 30 45: [==========] Running 16 tests from 2 test suites. 45: [----------] Global test environment set-up. 45: [----------] 8 tests from SplineTableTest/0, where TypeParam = gmx::QuadraticSplineTable 45: [ RUN ] SplineTableTest/0.HandlesIncorrectInput 45: [ OK ] SplineTableTest/0.HandlesIncorrectInput (5 ms) 45: [ RUN ] SplineTableTest/0.Sinc 45: [ OK ] SplineTableTest/0.Sinc (4 ms) 45: [ RUN ] SplineTableTest/0.LJ12 45: [ OK ] SplineTableTest/0.LJ12 (86 ms) 45: [ RUN ] SplineTableTest/0.PmeCorrection 45: [ OK ] SplineTableTest/0.PmeCorrection (7 ms) 45: [ RUN ] SplineTableTest/0.HandlesIncorrectNumericalInput 45: [ OK ] SplineTableTest/0.HandlesIncorrectNumericalInput (1 ms) 45: [ RUN ] SplineTableTest/0.NumericalInputPmeCorr 45: [ OK ] SplineTableTest/0.NumericalInputPmeCorr (7 ms) 45: [ RUN ] SplineTableTest/0.TwoFunctions 45: [ OK ] SplineTableTest/0.TwoFunctions (172 ms) 45: [ RUN ] SplineTableTest/0.ThreeFunctions 45: [ OK ] SplineTableTest/0.ThreeFunctions (236 ms) 45: [----------] 8 tests from SplineTableTest/0 (522 ms total) 45: 45: [----------] 8 tests from SplineTableTest/1, where TypeParam = gmx::CubicSplineTable 45: [ RUN ] SplineTableTest/1.HandlesIncorrectInput 45: [ OK ] SplineTableTest/1.HandlesIncorrectInput (4 ms) 45: [ RUN ] SplineTableTest/1.Sinc 45: [ OK ] SplineTableTest/1.Sinc (10 ms) 45: [ RUN ] SplineTableTest/1.LJ12 45: [ OK ] SplineTableTest/1.LJ12 (229 ms) 45: [ RUN ] SplineTableTest/1.PmeCorrection 45: [ OK ] SplineTableTest/1.PmeCorrection (7 ms) 45: [ RUN ] SplineTableTest/1.HandlesIncorrectNumericalInput 45: [ OK ] SplineTableTest/1.HandlesIncorrectNumericalInput (1 ms) 45: [ RUN ] SplineTableTest/1.NumericalInputPmeCorr 45: [ OK ] SplineTableTest/1.NumericalInputPmeCorr (6 ms) 45: [ RUN ] SplineTableTest/1.TwoFunctions 45: [ OK ] SplineTableTest/1.TwoFunctions (514 ms) 45: [ RUN ] SplineTableTest/1.ThreeFunctions 45: [ OK ] SplineTableTest/1.ThreeFunctions (643 ms) 45: [----------] 8 tests from SplineTableTest/1 (1419 ms total) 45: 45: [----------] Global test environment tear-down 45: [==========] 16 tests from 2 test suites ran. (1942 ms total) 45: [ PASSED ] 16 tests. 45/92 Test #45: TableUnitTests ............................ Passed 2.02 sec test 46 Start 46: TaskAssignmentUnitTests 46: Test command: /build/reproducible-path/gromacs-2025.1/build/basic-dp/bin/taskassignment-test "--gtest_output=xml:/build/reproducible-path/gromacs-2025.1/build/basic-dp/Testing/Temporary/TaskAssignmentUnitTests.xml" 46: Working Directory: /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/taskassignment/tests 46: Test timeout computed to be: 30 46: [==========] Running 3 tests from 2 test suites. 46: [----------] Global test environment set-up. 46: [----------] 2 tests from UserTaskAssignmentStringHandlingTest 46: [ RUN ] UserTaskAssignmentStringHandlingTest.ParsingAndReconstructionWork 46: [ OK ] UserTaskAssignmentStringHandlingTest.ParsingAndReconstructionWork (0 ms) 46: [ RUN ] UserTaskAssignmentStringHandlingTest.EmptyStringCanBeValid 46: [ OK ] UserTaskAssignmentStringHandlingTest.EmptyStringCanBeValid (0 ms) 46: [----------] 2 tests from UserTaskAssignmentStringHandlingTest (0 ms total) 46: 46: [----------] 1 test from GpuIdAndAssignmentStringHandlingTest 46: [ RUN ] GpuIdAndAssignmentStringHandlingTest.InvalidInputsThrow 46: [ OK ] GpuIdAndAssignmentStringHandlingTest.InvalidInputsThrow (2 ms) 46: [----------] 1 test from GpuIdAndAssignmentStringHandlingTest (2 ms total) 46: 46: [----------] Global test environment tear-down 46: [==========] 3 tests from 2 test suites ran. (2 ms total) 46: [ PASSED ] 3 tests. 46/92 Test #46: TaskAssignmentUnitTests ................... Passed 0.07 sec test 47 Start 47: GmxTimingTests 47: Test command: /build/reproducible-path/gromacs-2025.1/build/basic-dp/bin/timing-test "--gtest_output=xml:/build/reproducible-path/gromacs-2025.1/build/basic-dp/Testing/Temporary/GmxTimingTests.xml" 47: Working Directory: /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/timing/tests 47: Test timeout computed to be: 30 47: [==========] Running 6 tests from 1 test suite. 47: [----------] Global test environment set-up. 47: [----------] 6 tests from TimingTest 47: [ RUN ] TimingTest.ElementCountingWorks 47: [ OK ] TimingTest.ElementCountingWorks (0 ms) 47: [ RUN ] TimingTest.ElementNoCountingWorks 47: [ OK ] TimingTest.ElementNoCountingWorks (0 ms) 47: [ RUN ] TimingTest.SubElementCountingWorks 47: [ OK ] TimingTest.SubElementCountingWorks (0 ms) 47: [ RUN ] TimingTest.SubElementNoCountingWorks 47: [ OK ] TimingTest.SubElementNoCountingWorks (0 ms) 47: [ RUN ] TimingTest.RunWallCycle 47: [ OK ] TimingTest.RunWallCycle (1 ms) 47: [ RUN ] TimingTest.RunWallCycleSub 47: [ OK ] TimingTest.RunWallCycleSub (0 ms) 47: [----------] 6 tests from TimingTest (1 ms total) 47: 47: [----------] Global test environment tear-down 47: [==========] 6 tests from 1 test suite ran. (1 ms total) 47: [ PASSED ] 6 tests. 47/92 Test #47: GmxTimingTests ............................ Passed 0.07 sec test 48 Start 48: TopologyTest 48: Test command: /build/reproducible-path/gromacs-2025.1/build/basic-dp/bin/topology-test "--gtest_output=xml:/build/reproducible-path/gromacs-2025.1/build/basic-dp/Testing/Temporary/TopologyTest.xml" 48: Working Directory: /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/topology/tests 48: Test timeout computed to be: 30 48: [==========] Running 153 tests from 10 test suites. 48: [----------] Global test environment set-up. 48: [----------] 3 tests from PdbAtomEntryTest 48: [ RUN ] PdbAtomEntryTest.CanCreateBasicEntry 48: [ OK ] PdbAtomEntryTest.CanCreateBasicEntry (0 ms) 48: [ RUN ] PdbAtomEntryTest.CanCreateEntryWithOccupAndBfac 48: [ OK ] PdbAtomEntryTest.CanCreateEntryWithOccupAndBfac (0 ms) 48: [ RUN ] PdbAtomEntryTest.CanCreateFullEntry 48: [ OK ] PdbAtomEntryTest.CanCreateFullEntry (0 ms) 48: [----------] 3 tests from PdbAtomEntryTest (0 ms total) 48: 48: [----------] 3 tests from ExclusionBlockTest 48: [ RUN ] ExclusionBlockTest.ConvertBlockAToExclusionBlocks 48: [ OK ] ExclusionBlockTest.ConvertBlockAToExclusionBlocks (0 ms) 48: [ RUN ] ExclusionBlockTest.ConvertExclusionBlockToBlocka 48: [ OK ] ExclusionBlockTest.ConvertExclusionBlockToBlocka (0 ms) 48: [ RUN ] ExclusionBlockTest.MergeExclusions 48: [ OK ] ExclusionBlockTest.MergeExclusions (0 ms) 48: [----------] 3 tests from ExclusionBlockTest (0 ms total) 48: 48: [----------] 6 tests from InteractionListTest 48: [ RUN ] InteractionListTest.EmptyWorks 48: [ OK ] InteractionListTest.EmptyWorks (0 ms) 48: [ RUN ] InteractionListTest.CanAddInteractionArray 48: [ OK ] InteractionListTest.CanAddInteractionArray (0 ms) 48: [ RUN ] InteractionListTest.CanAddInteractionArrayMultipleAtoms 48: [ OK ] InteractionListTest.CanAddInteractionArrayMultipleAtoms (0 ms) 48: [ RUN ] InteractionListTest.CanAddInteractionPointer 48: [ OK ] InteractionListTest.CanAddInteractionPointer (0 ms) 48: [ RUN ] InteractionListTest.CanAddListToOtherList 48: [ OK ] InteractionListTest.CanAddListToOtherList (0 ms) 48: [ RUN ] InteractionListTest.ClearingWorks 48: [ OK ] InteractionListTest.ClearingWorks (0 ms) 48: [----------] 6 tests from InteractionListTest (0 ms total) 48: 48: [----------] 3 tests from IndexTest 48: [ RUN ] IndexTest.AnalyseWorksDefaultGroups 48: 48: WARNING: Masses and atomic (Van der Waals) radii will be guessed 48: based on residue and atom names, since they could not be 48: definitively assigned from the information in your input 48: files. These guessed numbers might deviate from the mass 48: and radius of the atom type. Please check the output 48: files if necessary. Note, that this functionality may 48: be removed in a future GROMACS version. Please, consider 48: using another file format for your input. 48: 48: [ OK ] IndexTest.AnalyseWorksDefaultGroups (24 ms) 48: [ RUN ] IndexTest.WriteIndexWorks 48: 48: WARNING: Masses and atomic (Van der Waals) radii will be guessed 48: based on residue and atom names, since they could not be 48: definitively assigned from the information in your input 48: files. These guessed numbers might deviate from the mass 48: and radius of the atom type. Please check the output 48: files if necessary. Note, that this functionality may 48: be removed in a future GROMACS version. Please, consider 48: using another file format for your input. 48: 48: [ OK ] IndexTest.WriteIndexWorks (18 ms) 48: [ RUN ] IndexTest.WriteAndReadIndexWorks 48: 48: WARNING: Masses and atomic (Van der Waals) radii will be guessed 48: based on residue and atom names, since they could not be 48: definitively assigned from the information in your input 48: files. These guessed numbers might deviate from the mass 48: and radius of the atom type. Please check the output 48: files if necessary. Note, that this functionality may 48: be removed in a future GROMACS version. Please, consider 48: using another file format for your input. 48: 48: [ OK ] IndexTest.WriteAndReadIndexWorks (19 ms) 48: [----------] 3 tests from IndexTest (64 ms total) 48: 48: [----------] 4 tests from MtopTest 48: [ RUN ] MtopTest.RangeBasedLoop 48: [ OK ] MtopTest.RangeBasedLoop (0 ms) 48: [ RUN ] MtopTest.Operators 48: [ OK ] MtopTest.Operators (0 ms) 48: [ RUN ] MtopTest.CanFindResidueStartAndEndAtoms 48: [ OK ] MtopTest.CanFindResidueStartAndEndAtoms (0 ms) 48: [ RUN ] MtopTest.CanSortPerturbedInteractionsCorrectly 48: [ OK ] MtopTest.CanSortPerturbedInteractionsCorrectly (0 ms) 48: [----------] 4 tests from MtopTest (0 ms total) 48: 48: [----------] 2 tests from IListRangeTest 48: [ RUN ] IListRangeTest.RangeBasedLoopWorks 48: [ OK ] IListRangeTest.RangeBasedLoopWorks (0 ms) 48: [ RUN ] IListRangeTest.RangeBasedLoopWithIntermolecularInteraction 48: [ OK ] IListRangeTest.RangeBasedLoopWithIntermolecularInteraction (0 ms) 48: [----------] 2 tests from IListRangeTest (0 ms total) 48: 48: [----------] 13 tests from StringTableTest 48: [ RUN ] StringTableTest.AddSingleEntry 48: [ OK ] StringTableTest.AddSingleEntry (1 ms) 48: [ RUN ] StringTableTest.CanAccessWithAt 48: [ OK ] StringTableTest.CanAccessWithAt (1 ms) 48: [ RUN ] StringTableTest.CanAccessWithBracket 48: [ OK ] StringTableTest.CanAccessWithBracket (1 ms) 48: [ RUN ] StringTableTest.ThrowsOutOfRange 48: [ OK ] StringTableTest.ThrowsOutOfRange (1 ms) 48: [ RUN ] StringTableTest.StringCompareIsCorrect 48: [ OK ] StringTableTest.StringCompareIsCorrect (1 ms) 48: [ RUN ] StringTableTest.AddTwoDistinctEntries 48: [ OK ] StringTableTest.AddTwoDistinctEntries (1 ms) 48: [ RUN ] StringTableTest.TryToAddDuplicates 48: [ OK ] StringTableTest.TryToAddDuplicates (0 ms) 48: [ RUN ] StringTableTest.AddLargeNumberOfEntries 48: [ OK ] StringTableTest.AddLargeNumberOfEntries (1 ms) 48: [ RUN ] StringTableTest.NoDuplicatesInLargeTable 48: [ OK ] StringTableTest.NoDuplicatesInLargeTable (1 ms) 48: [ RUN ] StringTableTest.CanWriteToBuffer 48: [ OK ] StringTableTest.CanWriteToBuffer (0 ms) 48: [ RUN ] StringTableTest.Roundtrip 48: [ OK ] StringTableTest.Roundtrip (0 ms) 48: [ RUN ] StringTableTest.RoundtripWithCorrectStringIndices 48: [ OK ] StringTableTest.RoundtripWithCorrectStringIndices (0 ms) 48: [ RUN ] StringTableTest.CanCopyToLegacyTable 48: [ OK ] StringTableTest.CanCopyToLegacyTable (0 ms) 48: [----------] 13 tests from StringTableTest (11 ms total) 48: 48: [----------] 6 tests from LegacySymtabTest 48: [ RUN ] LegacySymtabTest.EmptyOnOpen 48: [ OK ] LegacySymtabTest.EmptyOnOpen (0 ms) 48: [ RUN ] LegacySymtabTest.AddSingleEntry 48: [ OK ] LegacySymtabTest.AddSingleEntry (0 ms) 48: [ RUN ] LegacySymtabTest.AddTwoDistinctEntries 48: [ OK ] LegacySymtabTest.AddTwoDistinctEntries (0 ms) 48: [ RUN ] LegacySymtabTest.TryToAddDuplicates 48: [ OK ] LegacySymtabTest.TryToAddDuplicates (0 ms) 48: [ RUN ] LegacySymtabTest.AddLargeNumberOfEntries 48: [ OK ] LegacySymtabTest.AddLargeNumberOfEntries (0 ms) 48: [ RUN ] LegacySymtabTest.NoDuplicatesInLargeTable 48: [ OK ] LegacySymtabTest.NoDuplicatesInLargeTable (0 ms) 48: [----------] 6 tests from LegacySymtabTest (1 ms total) 48: 48: [----------] 5 tests from TopSortTest 48: [ RUN ] TopSortTest.WorksOnEmptyIdef 48: [ OK ] TopSortTest.WorksOnEmptyIdef (0 ms) 48: [ RUN ] TopSortTest.WorksOnIdefWithNoPerturbedInteraction 48: [ OK ] TopSortTest.WorksOnIdefWithNoPerturbedInteraction (0 ms) 48: [ RUN ] TopSortTest.WorksOnIdefWithPerturbedInteractions 48: [ OK ] TopSortTest.WorksOnIdefWithPerturbedInteractions (0 ms) 48: [ RUN ] TopSortTest.SortsIdefWithPerturbedInteractions 48: [ OK ] TopSortTest.SortsIdefWithPerturbedInteractions (0 ms) 48: [ RUN ] TopSortTest.SortsMoreComplexIdefWithPerturbedInteractions 48: [ OK ] TopSortTest.SortsMoreComplexIdefWithPerturbedInteractions (0 ms) 48: [----------] 5 tests from TopSortTest (0 ms total) 48: 48: [----------] 108 tests from BuildsValidDataStructure/SimulationParticleTest 48: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/0 48: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/0 (0 ms) 48: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/1 48: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/1 (0 ms) 48: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/2 48: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/2 (0 ms) 48: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/3 48: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/3 (0 ms) 48: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/4 48: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/4 (0 ms) 48: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/5 48: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/5 (0 ms) 48: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/6 48: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/6 (0 ms) 48: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/7 48: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/7 (0 ms) 48: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/8 48: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/8 (0 ms) 48: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/9 48: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/9 (0 ms) 48: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/10 48: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/10 (0 ms) 48: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/11 48: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/11 (0 ms) 48: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/12 48: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/12 (0 ms) 48: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/13 48: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/13 (0 ms) 48: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/14 48: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/14 (0 ms) 48: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/15 48: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/15 (0 ms) 48: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/16 48: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/16 (0 ms) 48: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/17 48: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/17 (0 ms) 48: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/18 48: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/18 (0 ms) 48: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/19 48: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/19 (0 ms) 48: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/20 48: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/20 (0 ms) 48: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/21 48: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/21 (0 ms) 48: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/22 48: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/22 (0 ms) 48: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/23 48: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/23 (0 ms) 48: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/24 48: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/24 (0 ms) 48: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/25 48: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/25 (0 ms) 48: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/26 48: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/26 (0 ms) 48: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/27 48: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/27 (0 ms) 48: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/28 48: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/28 (0 ms) 48: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/29 48: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/29 (0 ms) 48: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/30 48: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/30 (0 ms) 48: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/31 48: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/31 (0 ms) 48: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/32 48: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/32 (0 ms) 48: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/33 48: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/33 (0 ms) 48: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/34 48: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/34 (0 ms) 48: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/35 48: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/35 (0 ms) 48: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/36 48: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/36 (0 ms) 48: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/37 48: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/37 (0 ms) 48: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/38 48: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/38 (0 ms) 48: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/39 48: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/39 (0 ms) 48: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/40 48: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/40 (0 ms) 48: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/41 48: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/41 (0 ms) 48: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/42 48: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/42 (0 ms) 48: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/43 48: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/43 (0 ms) 48: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/44 48: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/44 (0 ms) 48: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/45 48: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/45 (0 ms) 48: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/46 48: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/46 (0 ms) 48: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/47 48: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/47 (0 ms) 48: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/48 48: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/48 (0 ms) 48: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/49 48: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/49 (0 ms) 48: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/50 48: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/50 (0 ms) 48: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/51 48: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/51 (0 ms) 48: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/52 48: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/52 (0 ms) 48: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/53 48: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/53 (0 ms) 48: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/0 48: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/0 (0 ms) 48: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/1 48: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/1 (0 ms) 48: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/2 48: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/2 (0 ms) 48: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/3 48: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/3 (0 ms) 48: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/4 48: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/4 (0 ms) 48: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/5 48: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/5 (0 ms) 48: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/6 48: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/6 (0 ms) 48: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/7 48: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/7 (0 ms) 48: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/8 48: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/8 (0 ms) 48: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/9 48: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/9 (0 ms) 48: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/10 48: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/10 (0 ms) 48: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/11 48: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/11 (0 ms) 48: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/12 48: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/12 (0 ms) 48: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/13 48: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/13 (0 ms) 48: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/14 48: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/14 (0 ms) 48: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/15 48: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/15 (0 ms) 48: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/16 48: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/16 (0 ms) 48: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/17 48: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/17 (0 ms) 48: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/18 48: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/18 (0 ms) 48: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/19 48: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/19 (0 ms) 48: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/20 48: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/20 (0 ms) 48: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/21 48: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/21 (0 ms) 48: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/22 48: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/22 (0 ms) 48: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/23 48: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/23 (0 ms) 48: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/24 48: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/24 (0 ms) 48: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/25 48: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/25 (0 ms) 48: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/26 48: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/26 (0 ms) 48: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/27 48: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/27 (0 ms) 48: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/28 48: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/28 (0 ms) 48: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/29 48: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/29 (0 ms) 48: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/30 48: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/30 (0 ms) 48: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/31 48: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/31 (0 ms) 48: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/32 48: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/32 (0 ms) 48: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/33 48: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/33 (0 ms) 48: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/34 48: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/34 (0 ms) 48: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/35 48: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/35 (0 ms) 48: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/36 48: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/36 (0 ms) 48: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/37 48: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/37 (0 ms) 48: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/38 48: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/38 (0 ms) 48: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/39 48: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/39 (0 ms) 48: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/40 48: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/40 (0 ms) 48: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/41 48: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/41 (0 ms) 48: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/42 48: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/42 (0 ms) 48: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/43 48: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/43 (0 ms) 48: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/44 48: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/44 (0 ms) 48: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/45 48: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/45 (0 ms) 48: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/46 48: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/46 (0 ms) 48: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/47 48: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/47 (0 ms) 48: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/48 48: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/48 (0 ms) 48: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/49 48: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/49 (0 ms) 48: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/50 48: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/50 (0 ms) 48: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/51 48: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/51 (0 ms) 48: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/52 48: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/52 (0 ms) 48: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/53 48: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/53 (0 ms) 48: [----------] 108 tests from BuildsValidDataStructure/SimulationParticleTest (69 ms total) 48: 48: [----------] Global test environment tear-down 48: [==========] 153 tests from 10 test suites ran. (149 ms total) 48: [ PASSED ] 153 tests. 48: 48: YOU HAVE 1 DISABLED TEST 48: 48/92 Test #48: TopologyTest .............................. Passed 0.26 sec test 49 Start 49: PullTest 49: Test command: /build/reproducible-path/gromacs-2025.1/build/basic-dp/bin/pull-test "--gtest_output=xml:/build/reproducible-path/gromacs-2025.1/build/basic-dp/Testing/Temporary/PullTest.xml" 49: Working Directory: /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/pulling/tests 49: Test timeout computed to be: 30 49: [==========] Running 10 tests from 1 test suite. 49: [----------] Global test environment set-up. 49: [----------] 10 tests from PullTest 49: [ RUN ] PullTest.MaxPullDistanceXyzScrewBox 49: [ OK ] PullTest.MaxPullDistanceXyzScrewBox (0 ms) 49: [ RUN ] PullTest.MaxPullDistanceXyzCubicBox 49: [ OK ] PullTest.MaxPullDistanceXyzCubicBox (0 ms) 49: [ RUN ] PullTest.MaxPullDistanceXyzTricBox 49: [ OK ] PullTest.MaxPullDistanceXyzTricBox (0 ms) 49: [ RUN ] PullTest.MaxPullDistanceXyzLongBox 49: [ OK ] PullTest.MaxPullDistanceXyzLongBox (0 ms) 49: [ RUN ] PullTest.MaxPullDistanceXySkewedBox 49: [ OK ] PullTest.MaxPullDistanceXySkewedBox (0 ms) 49: [ RUN ] PullTest.TransformationCoordSimple 49: [ OK ] PullTest.TransformationCoordSimple (0 ms) 49: [ RUN ] PullTest.TransformationCoordAdvanced 49: [ OK ] PullTest.TransformationCoordAdvanced (0 ms) 49: [ RUN ] PullTest.TransformationCoordTime 49: [ OK ] PullTest.TransformationCoordTime (0 ms) 49: [ RUN ] PullTest.TransformationCoordTimeNotAllowed 49: [ OK ] PullTest.TransformationCoordTimeNotAllowed (0 ms) 49: [ RUN ] PullTest.TransformationCoordDummyExpression 49: [ OK ] PullTest.TransformationCoordDummyExpression (0 ms) 49: [----------] 10 tests from PullTest (3 ms total) 49: 49: [----------] Global test environment tear-down 49: [==========] 10 tests from 1 test suite ran. (3 ms total) 49: [ PASSED ] 10 tests. 49/92 Test #49: PullTest .................................. Passed 0.08 sec test 50 Start 50: SimdUnitTests 50: Test command: /build/reproducible-path/gromacs-2025.1/build/basic-dp/bin/simd-test "--gtest_output=xml:/build/reproducible-path/gromacs-2025.1/build/basic-dp/Testing/Temporary/SimdUnitTests.xml" 50: Working Directory: /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/simd/tests 50: Test timeout computed to be: 30 50: [==========] Running 86 tests from 3 test suites. 50: [----------] Global test environment set-up. 50: [----------] 41 tests from SimdScalarTest 50: [ RUN ] SimdScalarTest.load 50: [ OK ] SimdScalarTest.load (0 ms) 50: [ RUN ] SimdScalarTest.loadU 50: [ OK ] SimdScalarTest.loadU (0 ms) 50: [ RUN ] SimdScalarTest.store 50: [ OK ] SimdScalarTest.store (0 ms) 50: [ RUN ] SimdScalarTest.storeU 50: [ OK ] SimdScalarTest.storeU (0 ms) 50: [ RUN ] SimdScalarTest.setZero 50: [ OK ] SimdScalarTest.setZero (0 ms) 50: [ RUN ] SimdScalarTest.andNot 50: [ OK ] SimdScalarTest.andNot (0 ms) 50: [ RUN ] SimdScalarTest.fma 50: [ OK ] SimdScalarTest.fma (0 ms) 50: [ RUN ] SimdScalarTest.fms 50: [ OK ] SimdScalarTest.fms (0 ms) 50: [ RUN ] SimdScalarTest.fnma 50: [ OK ] SimdScalarTest.fnma (0 ms) 50: [ RUN ] SimdScalarTest.fnms 50: [ OK ] SimdScalarTest.fnms (0 ms) 50: [ RUN ] SimdScalarTest.maskAdd 50: [ OK ] SimdScalarTest.maskAdd (0 ms) 50: [ RUN ] SimdScalarTest.maskzMul 50: [ OK ] SimdScalarTest.maskzMul (0 ms) 50: [ RUN ] SimdScalarTest.maskzFma 50: [ OK ] SimdScalarTest.maskzFma (0 ms) 50: [ RUN ] SimdScalarTest.abs 50: [ OK ] SimdScalarTest.abs (0 ms) 50: [ RUN ] SimdScalarTest.max 50: [ OK ] SimdScalarTest.max (0 ms) 50: [ RUN ] SimdScalarTest.min 50: [ OK ] SimdScalarTest.min (0 ms) 50: [ RUN ] SimdScalarTest.round 50: [ OK ] SimdScalarTest.round (0 ms) 50: [ RUN ] SimdScalarTest.trunc 50: [ OK ] SimdScalarTest.trunc (0 ms) 50: [ RUN ] SimdScalarTest.reduce 50: [ OK ] SimdScalarTest.reduce (0 ms) 50: [ RUN ] SimdScalarTest.testBits 50: [ OK ] SimdScalarTest.testBits (0 ms) 50: [ RUN ] SimdScalarTest.anyTrue 50: [ OK ] SimdScalarTest.anyTrue (0 ms) 50: [ RUN ] SimdScalarTest.selectByMask 50: [ OK ] SimdScalarTest.selectByMask (0 ms) 50: [ RUN ] SimdScalarTest.selectByNotMask 50: [ OK ] SimdScalarTest.selectByNotMask (0 ms) 50: [ RUN ] SimdScalarTest.blend 50: [ OK ] SimdScalarTest.blend (0 ms) 50: [ RUN ] SimdScalarTest.cvtR2I 50: [ OK ] SimdScalarTest.cvtR2I (0 ms) 50: [ RUN ] SimdScalarTest.cvttR2I 50: [ OK ] SimdScalarTest.cvttR2I (0 ms) 50: [ RUN ] SimdScalarTest.cvtI2R 50: [ OK ] SimdScalarTest.cvtI2R (0 ms) 50: [ RUN ] SimdScalarTest.cvtF2D 50: [ OK ] SimdScalarTest.cvtF2D (0 ms) 50: [ RUN ] SimdScalarTest.cvtD2D 50: [ OK ] SimdScalarTest.cvtD2D (0 ms) 50: [ RUN ] SimdScalarTest.loadI 50: [ OK ] SimdScalarTest.loadI (0 ms) 50: [ RUN ] SimdScalarTest.loadUI 50: [ OK ] SimdScalarTest.loadUI (0 ms) 50: [ RUN ] SimdScalarTest.storeI 50: [ OK ] SimdScalarTest.storeI (0 ms) 50: [ RUN ] SimdScalarTest.storeUI 50: [ OK ] SimdScalarTest.storeUI (0 ms) 50: [ RUN ] SimdScalarTest.andNotI 50: [ OK ] SimdScalarTest.andNotI (0 ms) 50: [ RUN ] SimdScalarTest.testBitsI 50: [ OK ] SimdScalarTest.testBitsI (0 ms) 50: [ RUN ] SimdScalarTest.selectByMaskI 50: [ OK ] SimdScalarTest.selectByMaskI (0 ms) 50: [ RUN ] SimdScalarTest.selectByNotMaskI 50: [ OK ] SimdScalarTest.selectByNotMaskI (0 ms) 50: [ RUN ] SimdScalarTest.blendI 50: [ OK ] SimdScalarTest.blendI (0 ms) 50: [ RUN ] SimdScalarTest.cvtB2IB 50: [ OK ] SimdScalarTest.cvtB2IB (0 ms) 50: [ RUN ] SimdScalarTest.cvtIB2B 50: [ OK ] SimdScalarTest.cvtIB2B (0 ms) 50: [ RUN ] SimdScalarTest.expandScalarsToTriplets 50: [ OK ] SimdScalarTest.expandScalarsToTriplets (0 ms) 50: [----------] 41 tests from SimdScalarTest (1 ms total) 50: 50: [----------] 8 tests from SimdScalarUtilTest 50: [ RUN ] SimdScalarUtilTest.gatherLoadTranspose 50: [ OK ] SimdScalarUtilTest.gatherLoadTranspose (0 ms) 50: [ RUN ] SimdScalarUtilTest.gatherLoadUTranspose 50: [ OK ] SimdScalarUtilTest.gatherLoadUTranspose (0 ms) 50: [ RUN ] SimdScalarUtilTest.transposeScatterStoreU 50: [ OK ] SimdScalarUtilTest.transposeScatterStoreU (0 ms) 50: [ RUN ] SimdScalarUtilTest.transposeScatterIncrU 50: [ OK ] SimdScalarUtilTest.transposeScatterIncrU (0 ms) 50: [ RUN ] SimdScalarUtilTest.transposeScatterDecrU 50: [ OK ] SimdScalarUtilTest.transposeScatterDecrU (0 ms) 50: [ RUN ] SimdScalarUtilTest.gatherLoadBySimdIntTranspose 50: [ OK ] SimdScalarUtilTest.gatherLoadBySimdIntTranspose (0 ms) 50: [ RUN ] SimdScalarUtilTest.gatherLoadUBySimdIntTranspose 50: [ OK ] SimdScalarUtilTest.gatherLoadUBySimdIntTranspose (0 ms) 50: [ RUN ] SimdScalarUtilTest.reduceIncr4ReturnSum 50: [ OK ] SimdScalarUtilTest.reduceIncr4ReturnSum (0 ms) 50: [----------] 8 tests from SimdScalarUtilTest (0 ms total) 50: 50: [----------] 37 tests from SimdScalarMathTest 50: [ RUN ] SimdScalarMathTest.copysign 50: [ OK ] SimdScalarMathTest.copysign (0 ms) 50: [ RUN ] SimdScalarMathTest.invsqrtPair 50: [ OK ] SimdScalarMathTest.invsqrtPair (0 ms) 50: [ RUN ] SimdScalarMathTest.inv 50: [ OK ] SimdScalarMathTest.inv (0 ms) 50: [ RUN ] SimdScalarMathTest.maskzInvsqrt 50: [ OK ] SimdScalarMathTest.maskzInvsqrt (0 ms) 50: [ RUN ] SimdScalarMathTest.log 50: [ OK ] SimdScalarMathTest.log (0 ms) 50: [ RUN ] SimdScalarMathTest.exp2 50: [ OK ] SimdScalarMathTest.exp2 (0 ms) 50: [ RUN ] SimdScalarMathTest.exp 50: [ OK ] SimdScalarMathTest.exp (0 ms) 50: [ RUN ] SimdScalarMathTest.erf 50: [ OK ] SimdScalarMathTest.erf (0 ms) 50: [ RUN ] SimdScalarMathTest.erfc 50: [ OK ] SimdScalarMathTest.erfc (0 ms) 50: [ RUN ] SimdScalarMathTest.sincos 50: [ OK ] SimdScalarMathTest.sincos (0 ms) 50: [ RUN ] SimdScalarMathTest.sin 50: [ OK ] SimdScalarMathTest.sin (0 ms) 50: [ RUN ] SimdScalarMathTest.cos 50: [ OK ] SimdScalarMathTest.cos (0 ms) 50: [ RUN ] SimdScalarMathTest.tan 50: [ OK ] SimdScalarMathTest.tan (0 ms) 50: [ RUN ] SimdScalarMathTest.asin 50: [ OK ] SimdScalarMathTest.asin (0 ms) 50: [ RUN ] SimdScalarMathTest.acos 50: [ OK ] SimdScalarMathTest.acos (0 ms) 50: [ RUN ] SimdScalarMathTest.atan 50: [ OK ] SimdScalarMathTest.atan (0 ms) 50: [ RUN ] SimdScalarMathTest.atan2 50: [ OK ] SimdScalarMathTest.atan2 (0 ms) 50: [ RUN ] SimdScalarMathTest.pmeForceCorrection 50: [ OK ] SimdScalarMathTest.pmeForceCorrection (0 ms) 50: [ RUN ] SimdScalarMathTest.pmePotentialCorrection 50: [ OK ] SimdScalarMathTest.pmePotentialCorrection (0 ms) 50: [ RUN ] SimdScalarMathTest.invsqrtPairSingleAccuracy 50: [ OK ] SimdScalarMathTest.invsqrtPairSingleAccuracy (0 ms) 50: [ RUN ] SimdScalarMathTest.invSingleAccuracy 50: [ OK ] SimdScalarMathTest.invSingleAccuracy (0 ms) 50: [ RUN ] SimdScalarMathTest.maskzInvsqrtSingleAccuracy 50: [ OK ] SimdScalarMathTest.maskzInvsqrtSingleAccuracy (0 ms) 50: [ RUN ] SimdScalarMathTest.logSingleAccuracy 50: [ OK ] SimdScalarMathTest.logSingleAccuracy (0 ms) 50: [ RUN ] SimdScalarMathTest.exp2SingleAccuracy 50: [ OK ] SimdScalarMathTest.exp2SingleAccuracy (0 ms) 50: [ RUN ] SimdScalarMathTest.expSingleAccuracy 50: [ OK ] SimdScalarMathTest.expSingleAccuracy (0 ms) 50: [ RUN ] SimdScalarMathTest.erfSingleAccuracy 50: [ OK ] SimdScalarMathTest.erfSingleAccuracy (0 ms) 50: [ RUN ] SimdScalarMathTest.erfcSingleAccuracy 50: [ OK ] SimdScalarMathTest.erfcSingleAccuracy (0 ms) 50: [ RUN ] SimdScalarMathTest.sincosSingleAccuracy 50: [ OK ] SimdScalarMathTest.sincosSingleAccuracy (0 ms) 50: [ RUN ] SimdScalarMathTest.sinSingleAccuracy 50: [ OK ] SimdScalarMathTest.sinSingleAccuracy (0 ms) 50: [ RUN ] SimdScalarMathTest.cosSingleAccuracy 50: [ OK ] SimdScalarMathTest.cosSingleAccuracy (0 ms) 50: [ RUN ] SimdScalarMathTest.tanSingleAccuracy 50: [ OK ] SimdScalarMathTest.tanSingleAccuracy (0 ms) 50: [ RUN ] SimdScalarMathTest.asinSingleAccuracy 50: [ OK ] SimdScalarMathTest.asinSingleAccuracy (0 ms) 50: [ RUN ] SimdScalarMathTest.acosSingleAccuracy 50: [ OK ] SimdScalarMathTest.acosSingleAccuracy (0 ms) 50: [ RUN ] SimdScalarMathTest.atanSingleAccuracy 50: [ OK ] SimdScalarMathTest.atanSingleAccuracy (0 ms) 50: [ RUN ] SimdScalarMathTest.atan2SingleAccuracy 50: [ OK ] SimdScalarMathTest.atan2SingleAccuracy (0 ms) 50: [ RUN ] SimdScalarMathTest.pmeForceCorrectionSingleAccuracy 50: [ OK ] SimdScalarMathTest.pmeForceCorrectionSingleAccuracy (0 ms) 50: [ RUN ] SimdScalarMathTest.pmePotentialCorrectionSingleAccuracy 50: [ OK ] SimdScalarMathTest.pmePotentialCorrectionSingleAccuracy (0 ms) 50: [----------] 37 tests from SimdScalarMathTest (0 ms total) 50: 50: [----------] Global test environment tear-down 50: [==========] 86 tests from 3 test suites ran. (2 ms total) 50: [ PASSED ] 86 tests. 50/92 Test #50: SimdUnitTests ............................. Passed 0.10 sec test 51 Start 51: CompatibilityHelpersTests 51: Test command: /build/reproducible-path/gromacs-2025.1/build/basic-dp/bin/compat-test "--gtest_output=xml:/build/reproducible-path/gromacs-2025.1/build/basic-dp/Testing/Temporary/CompatibilityHelpersTests.xml" 51: Working Directory: /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/compat/tests 51: Test timeout computed to be: 30 51: [==========] Running 9 tests from 6 test suites. 51: [----------] Global test environment set-up. 51: [----------] 4 tests from TemplateMPTest 51: [ RUN ] TemplateMPTest.MpWithIndexInt 51: [ OK ] TemplateMPTest.MpWithIndexInt (0 ms) 51: [ RUN ] TemplateMPTest.MpWithIndexIntBad 51: [ OK ] TemplateMPTest.MpWithIndexIntBad (0 ms) 51: [ RUN ] TemplateMPTest.MpWithIndexBool 51: [ OK ] TemplateMPTest.MpWithIndexBool (0 ms) 51: [ RUN ] TemplateMPTest.MpWithIndexEnum 51: [ OK ] TemplateMPTest.MpWithIndexEnum (0 ms) 51: [----------] 4 tests from TemplateMPTest (0 ms total) 51: 51: [----------] 1 test from NotNullConstruction 51: [ RUN ] NotNullConstruction.Works 51: [ OK ] NotNullConstruction.Works (0 ms) 51: [----------] 1 test from NotNullConstruction (0 ms total) 51: 51: [----------] 1 test from NotNullCasting 51: [ RUN ] NotNullCasting.Works 51: [ OK ] NotNullCasting.Works (0 ms) 51: [----------] 1 test from NotNullCasting (0 ms total) 51: 51: [----------] 1 test from NotNullAssignment 51: [ RUN ] NotNullAssignment.Works 51: [ OK ] NotNullAssignment.Works (0 ms) 51: [----------] 1 test from NotNullAssignment (0 ms total) 51: 51: [----------] 1 test from MakeNotNull 51: [ RUN ] MakeNotNull.Works 51: [ OK ] MakeNotNull.Works (0 ms) 51: [----------] 1 test from MakeNotNull (0 ms total) 51: 51: [----------] 1 test from NotNull 51: [ RUN ] NotNull.WorksInContainers 51: [ OK ] NotNull.WorksInContainers (0 ms) 51: [----------] 1 test from NotNull (0 ms total) 51: 51: [----------] Global test environment tear-down 51: [==========] 9 tests from 6 test suites ran. (0 ms total) 51: [ PASSED ] 9 tests. 51/92 Test #51: CompatibilityHelpersTests ................. Passed 0.08 sec test 52 Start 52: GmxAnaTest 52: Test command: /build/reproducible-path/gromacs-2025.1/build/basic-dp/bin/gmxana-test "--gtest_output=xml:/build/reproducible-path/gromacs-2025.1/build/basic-dp/Testing/Temporary/GmxAnaTest.xml" 52: Working Directory: /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/gmxana/tests 52: Test timeout computed to be: 600 52: [==========] Running 31 tests from 4 test suites. 52: [----------] Global test environment set-up. 52: [----------] 7 tests from Entropy 52: [ RUN ] Entropy.Schlitter_300_NoLinear 52: [ OK ] Entropy.Schlitter_300_NoLinear (0 ms) 52: [ RUN ] Entropy.Schlitter_300_Linear 52: [ OK ] Entropy.Schlitter_300_Linear (0 ms) 52: [ RUN ] Entropy.QuasiHarmonic_300_NoLinear 52: [ OK ] Entropy.QuasiHarmonic_300_NoLinear (0 ms) 52: [ RUN ] Entropy.QuasiHarmonic_200_NoLinear 52: [ OK ] Entropy.QuasiHarmonic_200_NoLinear (0 ms) 52: [ RUN ] Entropy.QuasiHarmonic_200_Linear 52: [ OK ] Entropy.QuasiHarmonic_200_Linear (0 ms) 52: [ RUN ] Entropy.EntropyCompare_200_Linear 52: [ OK ] Entropy.EntropyCompare_200_Linear (0 ms) 52: [ RUN ] Entropy.EntropyCompare_300_Linear 52: [ OK ] Entropy.EntropyCompare_300_Linear (0 ms) 52: [----------] 7 tests from Entropy (2 ms total) 52: 52: [----------] 2 tests from GmxChiTest 52: [ RUN ] GmxChiTest.gmxchiWorksWithAll 52: Analyzing from residue 1 to residue 11 52: 10 residues with dihedrals found 52: 46 dihedrals found 52: Reading frames from gro file 'First 10 residues from 1AKI t= 0.00000 step= 0', 156 atoms. 52: Reading frame 0 time 0.000 Reading frame 1 time 0.020 Reading frame 2 time 0.040 Last frame 2 time 0.040 52: j after resetting (nr. active dihedrals) = 46 52: Printing phiLYS1.xvg Printing phiVAL2.xvg Printing phiPHE3.xvg Printing phiGLY4.xvg Printing phiARG5.xvg Printing phiCYS6.xvg Printing phiGLU7.xvg Printing phiLEU8.xvg Printing phiALA9.xvg Printing phiALA10.xvg Printing psiLYS1.xvg Printing psiVAL2.xvg Printing psiPHE3.xvg Printing psiGLY4.xvg Printing psiARG5.xvg Printing psiCYS6.xvg Printing psiGLU7.xvg Printing psiLEU8.xvg Printing psiALA9.xvg Printing psiALA10.xvg Printing omegaVAL2.xvg Printing omegaPHE3.xvg Printing omegaGLY4.xvg Printing omegaARG5.xvg Printing omegaCYS6.xvg Printing omegaGLU7.xvg Printing omegaLEU8.xvg Printing omegaALA9.xvg Printing omegaALA10.xvg Printing chi1LYS1.xvg Printing chi1VAL2.xvg Printing chi1PHE3.xvg Printing chi1ARG5.xvg Printing chi1CYS6.xvg Printing chi1GLU7.xvg Printing chi1LEU8.xvg Printing chi2LYS1.xvg Printing chi2PHE3.xvg Printing chi2ARG5.xvg Printing chi2GLU7.xvg Printing chi2LEU8.xvg Printing chi3LYS1.xvg Printing chi3ARG5.xvg Printing chi3GLU7.xvg Printing chi4LYS1.xvg Printing chi4ARG5.xvg 52: Now calculating transitions... 52: Total number of transitions: 0 52: Now printing out transitions and OPs... 52: Now printing out rotamer occupancies... 52: Now calculating Chi product trajectories... 52: Printing chiproductLYS1.xvg and histo-chiprodLYS1.xvg Printing chiproductVAL2.xvg and histo-chiprodVAL2.xvg Printing chiproductPHE3.xvg and histo-chiprodPHE3.xvg Printing chiproductARG5.xvg and histo-chiprodARG5.xvg Printing chiproductCYS6.xvg and histo-chiprodCYS6.xvg Printing chiproductGLU7.xvg and histo-chiprodGLU7.xvg Printing chiproductLEU8.xvg and histo-chiprodLEU8.xvg 52: [ OK ] GmxChiTest.gmxchiWorksWithAll (5177 ms) 52: [ RUN ] GmxChiTest.gmxchiWorksWithr0AndrN 52: Analyzing from residue 2 to residue 6 52: 5 residues with dihedrals found 52: 23 dihedrals found 52: Reading frames from gro file 'First 10 residues from 1AKI t= 0.00000 step= 0', 156 atoms. 52: Reading frame 0 time 0.000 Reading frame 1 time 0.020 Reading frame 2 time 0.040 Last frame 2 time 0.040 52: j after resetting (nr. active dihedrals) = 23 52: Printing phiVAL2.xvg Printing phiPHE3.xvg Printing phiGLY4.xvg Printing phiARG5.xvg Printing phiCYS6.xvg Printing psiVAL2.xvg Printing psiPHE3.xvg Printing psiGLY4.xvg Printing psiARG5.xvg Printing psiCYS6.xvg Printing omegaVAL2.xvg Printing omegaPHE3.xvg Printing omegaGLY4.xvg Printing omegaARG5.xvg Printing omegaCYS6.xvg Printing chi1VAL2.xvg Printing chi1PHE3.xvg Printing chi1ARG5.xvg Printing chi1CYS6.xvg Printing chi2PHE3.xvg Printing chi2ARG5.xvg Printing chi3ARG5.xvg Printing chi4ARG5.xvg 52: Now calculating transitions... 52: Total number of transitions: 0 52: Now printing out transitions and OPs... 52: Now printing out rotamer occupancies... 52: Now calculating Chi product trajectories... 52: Printing chiproductVAL2.xvg and histo-chiprodVAL2.xvg Printing chiproductPHE3.xvg and histo-chiprodPHE3.xvg Printing chiproductARG5.xvg and histo-chiprodARG5.xvg Printing chiproductCYS6.xvg and histo-chiprodCYS6.xvg 52: [ OK ] GmxChiTest.gmxchiWorksWithr0AndrN (2616 ms) 52: [----------] 2 tests from GmxChiTest (8927 ms total) 52: 52: [----------] 10 tests from MindistTest 52: [ RUN ] MindistTest.mindistWorksWithSingleAtoms 52: Group 0 ( atom1) has 1 elements 52: Group 1 ( atom2) has 1 elements 52: Group 2 ( atom3) has 1 elements 52: Group 3 ( atoms12) has 2 elements 52: Group 4 ( atoms23) has 2 elements 52: Group 5 ( atoms123) has 3 elements 52: Select a group: Select a group: Reading frames from gro file 'mindist_beads', 3 atoms. 52: Reading frame 0 time 0.000 Last frame 0 time 0.000 52: Selected 0: 'atom1' 52: Selected 1: 'atom2' 52: [ OK ] MindistTest.mindistWorksWithSingleAtoms (61 ms) 52: [ RUN ] MindistTest.mindistWorksWithMultipleAtoms 52: Group 0 ( atom1) has 1 elements 52: Group 1 ( atom2) has 1 elements 52: Group 2 ( atom3) has 1 elements 52: Group 3 ( atoms12) has 2 elements 52: Group 4 ( atoms23) has 2 elements 52: Group 5 ( atoms123) has 3 elements 52: Select a group: Select a group: Reading frames from gro file 'mindist_beads', 3 atoms. 52: Reading frame 0 time 0.000 Last frame 0 time 0.000 52: Selected 2: 'atom3' 52: Selected 3: 'atoms12' 52: [ OK ] MindistTest.mindistWorksWithMultipleAtoms (10 ms) 52: [ RUN ] MindistTest.mindistDoesNotPickUpContacts 52: Group 0 ( atom1) has 1 elements 52: Group 1 ( atom2) has 1 elements 52: Group 2 ( atom3) has 1 elements 52: Group 3 ( atoms12) has 2 elements 52: Group 4 ( atoms23) has 2 elements 52: Group 5 ( atoms123) has 3 elements 52: Select a group: Select a group: Reading frames from gro file 'mindist_beads', 3 atoms. 52: Reading frame 0 time 0.000 Last frame 0 time 0.000 52: Selected 0: 'atom1' 52: Selected 1: 'atom2' 52: [ OK ] MindistTest.mindistDoesNotPickUpContacts (7 ms) 52: [ RUN ] MindistTest.mindistPicksUpContacts 52: Group 0 ( atom1) has 1 elements 52: Group 1 ( atom2) has 1 elements 52: Group 2 ( atom3) has 1 elements 52: Group 3 ( atoms12) has 2 elements 52: Group 4 ( atoms23) has 2 elements 52: Group 5 ( atoms123) has 3 elements 52: Select a group: Select a group: Reading frames from gro file 'mindist_beads', 3 atoms. 52: Reading frame 0 time 0.000 Last frame 0 time 0.000 52: Selected 0: 'atom1' 52: Selected 1: 'atom2' 52: [ OK ] MindistTest.mindistPicksUpContacts (8 ms) 52: [ RUN ] MindistTest.ngWorks 52: Group 0 ( atom1) has 1 elements 52: Group 1 ( atom2) has 1 elements 52: Group 2 ( atom3) has 1 elements 52: Group 3 ( atoms12) has 2 elements 52: Group 4 ( atoms23) has 2 elements 52: Group 5 ( atoms123) has 3 elements 52: Select a group: Select a group: Select a group: Reading frames from gro file 'mindist_beads', 3 atoms. 52: Reading frame 0 time 0.000 Last frame 0 time 0.000 52: Selected 0: 'atom1' 52: Selected 1: 'atom2' 52: Selected 2: 'atom3' 52: [ OK ] MindistTest.ngWorks (6 ms) 52: [ RUN ] MindistTest.groupWorks 52: Group 0 ( atom1) has 1 elements 52: Group 1 ( atom2) has 1 elements 52: Group 2 ( atom3) has 1 elements 52: Group 3 ( atoms12) has 2 elements 52: Group 4 ( atoms23) has 2 elements 52: Group 5 ( atoms123) has 3 elements 52: Select a group: Select a group: Reading frames from gro file 'mindist_beads', 3 atoms. 52: Reading frame 0 time 0.000 Last frame 0 time 0.000 52: Selected 3: 'atoms12' 52: Selected 2: 'atom3' 52: [ OK ] MindistTest.groupWorks (15 ms) 52: [ RUN ] MindistTest.maxDistWorks 52: Group 0 ( atom1) has 1 elements 52: Group 1 ( atom2) has 1 elements 52: Group 2 ( atom3) has 1 elements 52: Group 3 ( atoms12) has 2 elements 52: Group 4 ( atoms23) has 2 elements 52: Group 5 ( atoms123) has 3 elements 52: Select a group: Select a group: Reading frames from gro file 'mindist_beads', 3 atoms. 52: Reading frame 0 time 0.000 Last frame 0 time 0.000 52: Selected 2: 'atom3' 52: Selected 3: 'atoms12' 52: [ OK ] MindistTest.maxDistWorks (8 ms) 52: [ RUN ] MindistTest.noPbcWorks 52: Group 0 ( atom1) has 1 elements 52: Group 1 ( atom2) has 1 elements 52: Group 2 ( atom3) has 1 elements 52: Group 3 ( atoms12) has 2 elements 52: Group 4 ( atoms23) has 2 elements 52: Group 5 ( atoms123) has 3 elements 52: Select a group: Select a group: Reading frames from gro file 'mindist_beads', 3 atoms. 52: Reading frame 0 time 0.000 Last frame 0 time 0.000 52: Selected 0: 'atom1' 52: Selected 1: 'atom2' 52: [ OK ] MindistTest.noPbcWorks (9 ms) 52: [ RUN ] MindistTest.resPerTimeWorks 52: Group 0 ( atom1) has 1 elements 52: Group 1 ( atom2) has 1 elements 52: Group 2 ( atom3) has 1 elements 52: Group 3 ( atoms12) has 2 elements 52: Group 4 ( atoms23) has 2 elements 52: Group 5 ( atoms123) has 3 elements 52: Select a group: Select a group: Reading frames from gro file 'mindist_beads', 3 atoms. 52: Reading frame 0 time 0.000 Last frame 0 time 0.000 52: Selected 3: 'atoms12' 52: Selected 2: 'atom3' 52: [ OK ] MindistTest.resPerTimeWorks (11 ms) 52: [ RUN ] MindistTest.matrixWorks 52: Group 0 ( atom1) has 1 elements 52: Group 1 ( atom2) has 1 elements 52: Group 2 ( atom3) has 1 elements 52: Group 3 ( atoms12) has 2 elements 52: Group 4 ( atoms23) has 2 elements 52: Group 5 ( atoms123) has 3 elements 52: Select a group: Reading frames from gro file 'mindist_beads', 3 atoms. 52: Reading frame 0 time 0.000 Last frame 0 time 0.000 52: Selected 5: 'atoms123' 52: Special case: making distance matrix between all atoms in group atoms123 52: [ OK ] MindistTest.matrixWorks (9 ms) 52: [----------] 10 tests from MindistTest (151 ms total) 52: 52: [----------] 12 tests from NoFatalErrorWhenWritingFrom/GmxTraj 52: [ RUN ] NoFatalErrorWhenWritingFrom/GmxTraj.WithDifferentInputFormats/0 52: Group 0 ( System) has 6 elements 52: Group 1 ( Water) has 6 elements 52: Group 2 ( SOL) has 6 elements 52: Select a group: trr version: GMX_trn_file (single precision) 52: Reading frame 0 time 0.000 Reading frame 1 time 1.000 Last frame 1 time 1.000 52: Selected 0: 'System' 52: [ OK ] NoFatalErrorWhenWritingFrom/GmxTraj.WithDifferentInputFormats/0 (13 ms) 52: [ RUN ] NoFatalErrorWhenWritingFrom/GmxTraj.WithDifferentInputFormats/1 52: Group 0 ( System) has 6 elements 52: Group 1 ( Water) has 6 elements 52: Group 2 ( SOL) has 6 elements 52: Select a group: Reading frame 0 time 0.000 Reading frame 1 time 1.000 Last frame 1 time 1.000 52: Selected 0: 'System' 52: [ OK ] NoFatalErrorWhenWritingFrom/GmxTraj.WithDifferentInputFormats/1 (12 ms) 52: [ RUN ] NoFatalErrorWhenWritingFrom/GmxTraj.WithDifferentInputFormats/2 52: Group 0 ( System) has 6 elements 52: Group 1 ( Water) has 6 elements 52: Group 2 ( SOL) has 6 elements 52: Select a group: Reading frames from gro file 'Generated by trjconv t= 0.00000 step= 0', 6 atoms. 52: Reading frame 0 time 0.000 Reading frame 1 time 1.000 Last frame 1 time 1.000 52: Selected 0: 'System' 52: [ OK ] NoFatalErrorWhenWritingFrom/GmxTraj.WithDifferentInputFormats/2 (7 ms) 52: [ RUN ] NoFatalErrorWhenWritingFrom/GmxTraj.WithDifferentInputFormats/3 52: Group 0 ( System) has 6 elements 52: Group 1 ( Water) has 6 elements 52: Group 2 ( SOL) has 6 elements 52: Select a group: Reading frames from pdb file Reading frame 0 time 0.000 'Generated by trjconv t= 1.00000 step= 1', 6 atoms 52: Reading frame 1 time 1.000 Last frame 1 time 1.000 52: Selected 0: 'System' 52: [ OK ] NoFatalErrorWhenWritingFrom/GmxTraj.WithDifferentInputFormats/3 (7 ms) 52: [ RUN ] NoFatalErrorWhenWritingFrom/GmxTraj.WithDifferentInputFormats/4 52: Group 0 ( System) has 6 elements 52: Group 1 ( Water) has 6 elements 52: Group 2 ( SOL) has 6 elements 52: Select a group: Reading frame 0 time 0.000 Reading frame 1 time 1.000 Last frame 1 time 1.000 52: Selected 0: 'System' 52: [ OK ] NoFatalErrorWhenWritingFrom/GmxTraj.WithDifferentInputFormats/4 (12 ms) 52: [ RUN ] NoFatalErrorWhenWritingFrom/GmxTraj.WithDifferentInputFormats/5 52: Group 0 ( System) has 6 elements 52: Group 1 ( Water) has 6 elements 52: Group 2 ( SOL) has 6 elements 52: Select a group: Reading frame 0 time 0.000 Reading frame 1 time 1.000 Last frame 1 time 1.000 52: Selected 0: 'System' 52: [ OK ] NoFatalErrorWhenWritingFrom/GmxTraj.WithDifferentInputFormats/5 (10 ms) 52: [ RUN ] NoFatalErrorWhenWritingFrom/GmxTraj.RotationalKineticEnergy/0 52: Group 0 ( System) has 6 elements 52: Group 1 ( Water) has 6 elements 52: Group 2 ( SOL) has 6 elements 52: Select a group: Reading frame 0 time 0.000 52: WARNING: If there are molecules in the input trajectory file 52: that are broken across periodic boundaries, they 52: cannot be made whole (or treated as whole) without 52: you providing a run input file. 52: 52: Reading frame 1 time 1.000 Last frame 1 time 1.000 52: 52: WARNING: Masses and atomic (Van der Waals) radii will be guessed 52: based on residue and atom names, since they could not be 52: definitively assigned from the information in your input 52: files. These guessed numbers might deviate from the mass 52: and radius of the atom type. Please check the output 52: files if necessary. Note, that this functionality may 52: be removed in a future GROMACS version. Please, consider 52: using another file format for your input. 52: 52: Selected 0: 'System' 52: [ OK ] NoFatalErrorWhenWritingFrom/GmxTraj.RotationalKineticEnergy/0 (13 ms) 52: [ RUN ] NoFatalErrorWhenWritingFrom/GmxTraj.RotationalKineticEnergy/1 52: Group 0 ( System) has 6 elements 52: Group 1 ( Water) has 6 elements 52: Group 2 ( SOL) has 6 elements 52: Select a group: Reading frame 0 time 0.000 52: WARNING: If there are molecules in the input trajectory file 52: that are broken across periodic boundaries, they 52: cannot be made whole (or treated as whole) without 52: you providing a run input file. 52: 52: Reading frame 1 time 1.000 Last frame 1 time 1.000 52: 52: WARNING: Masses and atomic (Van der Waals) radii will be guessed 52: based on residue and atom names, since they could not be 52: definitively assigned from the information in your input 52: files. These guessed numbers might deviate from the mass 52: and radius of the atom type. Please check the output 52: files if necessary. Note, that this functionality may 52: be removed in a future GROMACS version. Please, consider 52: using another file format for your input. 52: 52: Selected 0: 'System' 52: [ OK ] NoFatalErrorWhenWritingFrom/GmxTraj.RotationalKineticEnergy/1 (19 ms) 52: [ RUN ] NoFatalErrorWhenWritingFrom/GmxTraj.RotationalKineticEnergy/2 52: Group 0 ( System) has 6 elements 52: Group 1 ( Water) has 6 elements 52: Group 2 ( SOL) has 6 elements 52: Select a group: Reading frames from gro file 'Generated by trjconv t= 0.00000 step= 0', 6 atoms. 52: Reading frame 0 time 0.000 52: WARNING: If there are molecules in the input trajectory file 52: that are broken across periodic boundaries, they 52: cannot be made whole (or treated as whole) without 52: you providing a run input file. 52: 52: Reading frame 1 time 1.000 Last frame 1 time 1.000 52: 52: WARNING: Masses and atomic (Van der Waals) radii will be guessed 52: based on residue and atom names, since they could not be 52: definitively assigned from the information in your input 52: files. These guessed numbers might deviate from the mass 52: and radius of the atom type. Please check the output 52: files if necessary. Note, that this functionality may 52: be removed in a future GROMACS version. Please, consider 52: using another file format for your input. 52: 52: Selected 0: 'System' 52: [ OK ] NoFatalErrorWhenWritingFrom/GmxTraj.RotationalKineticEnergy/2 (17 ms) 52: [ RUN ] NoFatalErrorWhenWritingFrom/GmxTraj.RotationalKineticEnergy/3 52: Group 0 ( System) has 6 elements 52: Group 1 ( Water) has 6 elements 52: Group 2 ( SOL) has 6 elements 52: Select a group: Reading frames from pdb file Reading frame 0 time 0.000 52: WARNING: If there are molecules in the input trajectory file 52: that are broken across periodic boundaries, they 52: cannot be made whole (or treated as whole) without 52: you providing a run input file. 52: 52: 'Generated by trjconv t= 1.00000 step= 1', 6 atoms 52: Reading frame 1 time 1.000 Last frame 1 time 1.000 52: 52: WARNING: Masses and atomic (Van der Waals) radii will be guessed 52: based on residue and atom names, since they could not be 52: definitively assigned from the information in your input 52: files. These guessed numbers might deviate from the mass 52: and radius of the atom type. Please check the output 52: files if necessary. Note, that this functionality may 52: be removed in a future GROMACS version. Please, consider 52: using another file format for your input. 52: 52: Selected 0: 'System' 52: [ OK ] NoFatalErrorWhenWritingFrom/GmxTraj.RotationalKineticEnergy/3 (17 ms) 52: [ RUN ] NoFatalErrorWhenWritingFrom/GmxTraj.RotationalKineticEnergy/4 52: Group 0 ( System) has 6 elements 52: Group 1 ( Water) has 6 elements 52: Group 2 ( SOL) has 6 elements 52: Select a group: Reading frame 0 time 0.000 52: WARNING: If there are molecules in the input trajectory file 52: that are broken across periodic boundaries, they 52: cannot be made whole (or treated as whole) without 52: you providing a run input file. 52: 52: Reading frame 1 time 1.000 Last frame 1 time 1.000 52: 52: WARNING: Masses and atomic (Van der Waals) radii will be guessed 52: based on residue and atom names, since they could not be 52: definitively assigned from the information in your input 52: files. These guessed numbers might deviate from the mass 52: and radius of the atom type. Please check the output 52: files if necessary. Note, that this functionality may 52: be removed in a future GROMACS version. Please, consider 52: using another file format for your input. 52: 52: Selected 0: 'System' 52: [ OK ] NoFatalErrorWhenWritingFrom/GmxTraj.RotationalKineticEnergy/4 (16 ms) 52: [ RUN ] NoFatalErrorWhenWritingFrom/GmxTraj.RotationalKineticEnergy/5 52: Group 0 ( System) has 6 elements 52: Group 1 ( Water) has 6 elements 52: Group 2 ( SOL) has 6 elements 52: Select a group: Reading frame 0 time 0.000 52: WARNING: If there are molecules in the input trajectory file 52: that are broken across periodic boundaries, they 52: cannot be made whole (or treated as whole) without 52: you providing a run input file. 52: 52: Reading frame 1 time 1.000 Last frame 1 time 1.000 52: 52: WARNING: Masses and atomic (Van der Waals) radii will be guessed 52: based on residue and atom names, since they could not be 52: definitively assigned from the information in your input 52: files. These guessed numbers might deviate from the mass 52: and radius of the atom type. Please check the output 52: files if necessary. Note, that this functionality may 52: be removed in a future GROMACS version. Please, consider 52: using another file format for your input. 52: 52: Selected 0: 'System' 52: [ OK ] NoFatalErrorWhenWritingFrom/GmxTraj.RotationalKineticEnergy/5 (20 ms) 52: [----------] 12 tests from NoFatalErrorWhenWritingFrom/GmxTraj (171 ms total) 52: 52: [----------] Global test environment tear-down 52: [==========] 31 tests from 4 test suites ran. (9253 ms total) 52: [ PASSED ] 31 tests. 52/92 Test #52: GmxAnaTest ................................ Passed 9.37 sec test 53 Start 53: GmxPreprocessTests 53: Test command: /build/reproducible-path/gromacs-2025.1/build/basic-dp/bin/gmxpreprocess-test "--gtest_output=xml:/build/reproducible-path/gromacs-2025.1/build/basic-dp/Testing/Temporary/GmxPreprocessTests.xml" 53: Working Directory: /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/gmxpreprocess/tests 53: Test timeout computed to be: 1920 53: [==========] Running 215 tests from 15 test suites. 53: [----------] Global test environment set-up. 53: [----------] 1 test from ConvertInteractionsTest 53: [ RUN ] ConvertInteractionsTest.DoingNothingWorks 53: [ OK ] ConvertInteractionsTest.DoingNothingWorks (0 ms) 53: [----------] 1 test from ConvertInteractionsTest (0 ms total) 53: 53: [----------] 4 tests from GenconfTest 53: [ RUN ] GenconfTest.nbox_Works 53: [ OK ] GenconfTest.nbox_Works (6 ms) 53: [ RUN ] GenconfTest.nbox_norenumber_Works 53: [ OK ] GenconfTest.nbox_norenumber_Works (2 ms) 53: [ RUN ] GenconfTest.nbox_dist_Works 53: [ OK ] GenconfTest.nbox_dist_Works (3 ms) 53: [ RUN ] GenconfTest.nbox_rot_Works 53: center of geometry: 1.733667, 1.477000, 0.905167 53: center of geometry: 1.733667, 1.477000, 0.905167 53: center of geometry: 1.733667, 1.477000, 0.905167 53: center of geometry: 1.733667, 1.477000, 0.905167 53: center of geometry: 1.733667, 1.477000, 0.905167 53: center of geometry: 1.733667, 1.477000, 0.905167 53: center of geometry: 1.733667, 1.477000, 0.905167 53: center of geometry: 1.733667, 1.477000, 0.905167 53: center of geometry: 1.733667, 1.477000, 0.905167 53: center of geometry: 1.733667, 1.477000, 0.905167 53: center of geometry: 1.733667, 1.477000, 0.905167 53: center of geometry: 1.733667, 1.477000, 0.905167 53: [ OK ] GenconfTest.nbox_rot_Works (4 ms) 53: [----------] 4 tests from GenconfTest (17 ms total) 53: 53: [----------] 2 tests from GenionTest 53: [ RUN ] GenionTest.HighConcentrationIonPlacement 53: 53: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GenionTest_HighConcentrationIonPlacement_input.mdp]: 53: rlist is equal to rvdw and/or rcoulomb: there is no explicit Verlet 53: buffer. The cluster pair list does have a buffering effect, but choosing 53: a larger rlist might be necessary for good energy conservation. 53: 53: 53: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GenionTest_HighConcentrationIonPlacement_input.mdp]: 53: verlet-buffer-pressure-tolerance is ignored when verlet-buffer-tolerance 53: < 0 53: 53: 53: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GenionTest_HighConcentrationIonPlacement_input.mdp]: 53: For a correct single-point energy evaluation with nsteps = 0, use 53: continuation = yes to avoid constraining the input coordinates. 53: 53: Generating 1-4 interactions: fudge = 0.5 53: Number of degrees of freedom in T-Coupling group rest is 1308.00 53: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 53: 53: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GenionTest_HighConcentrationIonPlacement_input.mdp]: 53: You are using a plain Coulomb cut-off, which might produce artifacts. 53: You might want to consider using PME electrostatics. 53: 53: 53: 53: There were 4 NOTEs 53: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GenionTest_HighConcentrationIonPlacement_spc216_with_methane.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 53: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GenionTest_HighConcentrationIonPlacement_spc216_with_methane.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 53: Group 0 ( System) has 653 elements 53: Group 1 ( Water) has 648 elements 53: Group 2 ( SOL) has 648 elements 53: Group 3 ( non-Water) has 5 elements 53: Group 4 ( Other) has 5 elements 53: Group 5 ( METH) has 5 elements 53: Select a group: Number of (3-atomic) solvent molecules: 216 53: Using random seed 1997. 53: Replacing solvent molecule 56 (atom 168) with NA 53: Replacing solvent molecule 120 (atom 360) with NA 53: Replacing solvent molecule 182 (atom 546) with NA 53: Replacing solvent molecule 71 (atom 213) with NA 53: Replacing solvent molecule 189 (atom 567) with CL 53: Replacing solvent molecule 54 (atom 162) with CL 53: Replacing solvent molecule 155 (atom 465) with CL 53: Replacing solvent molecule 99 (atom 297) with CL 53: 53: Setting the LD random seed to 2130443166 53: 53: Generated 331705 of the 331705 non-bonded parameter combinations 53: 53: Generated 331705 of the 331705 1-4 parameter combinations 53: 53: Excluding 2 bonded neighbours molecule type 'SOL' 53: 53: Excluding 3 bonded neighbours molecule type 'methane' 53: 53: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/spc216_with_methane.gro' 53: Analysing residue names: 53: There are: 216 Water residues 53: There are: 1 Other residues 53: Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups... 53: 53: This run will generate roughly 0 Mb of data 53: Will try to add 4 NA ions and 4 CL ions. 53: Select a continuous group of solvent molecules 53: Selected 1: 'Water' 53: [ OK ] GenionTest.HighConcentrationIonPlacement (5921 ms) 53: [ RUN ] GenionTest.NoIonPlacement 53: 53: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GenionTest_NoIonPlacement_input.mdp]: 53: rlist is equal to rvdw and/or rcoulomb: there is no explicit Verlet 53: buffer. The cluster pair list does have a buffering effect, but choosing 53: a larger rlist might be necessary for good energy conservation. 53: 53: 53: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GenionTest_NoIonPlacement_input.mdp]: 53: verlet-buffer-pressure-tolerance is ignored when verlet-buffer-tolerance 53: < 0 53: 53: 53: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GenionTest_NoIonPlacement_input.mdp]: 53: For a correct single-point energy evaluation with nsteps = 0, use 53: continuation = yes to avoid constraining the input coordinates. 53: 53: Generating 1-4 interactions: fudge = 0.5 53: Number of degrees of freedom in T-Coupling group rest is 1308.00 53: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 53: 53: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GenionTest_NoIonPlacement_input.mdp]: 53: You are using a plain Coulomb cut-off, which might produce artifacts. 53: You might want to consider using PME electrostatics. 53: 53: 53: 53: There were 4 NOTEs 53: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GenionTest_NoIonPlacement_spc216_with_methane.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 53: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GenionTest_NoIonPlacement_spc216_with_methane.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 53: No ions to add, will just copy input configuration. 53: Setting the LD random seed to -809763881 53: 53: Generated 331705 of the 331705 non-bonded parameter combinations 53: 53: Generated 331705 of the 331705 1-4 parameter combinations 53: 53: Excluding 2 bonded neighbours molecule type 'SOL' 53: 53: Excluding 3 bonded neighbours molecule type 'methane' 53: 53: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/spc216_with_methane.gro' 53: Analysing residue names: 53: There are: 216 Water residues 53: There are: 1 Other residues 53: Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups... 53: 53: This run will generate roughly 0 Mb of data 53: [ OK ] GenionTest.NoIonPlacement (5804 ms) 53: [----------] 2 tests from GenionTest (11725 ms total) 53: 53: [----------] 1 test from GenRestrTest 53: [ RUN ] GenRestrTest.SimpleRestraintsGenerated 53: 53: Reading structure file 53: Group 0 ( System) has 156 elements 53: Group 1 ( Protein) has 156 elements 53: Group 2 ( Protein-H) has 75 elements 53: Group 3 ( C-alpha) has 10 elements 53: Group 4 ( Backbone) has 30 elements 53: Group 5 ( MainChain) has 40 elements 53: Group 6 ( MainChain+Cb) has 49 elements 53: Group 7 ( MainChain+H) has 52 elements 53: Group 8 ( SideChain) has 104 elements 53: Group 9 ( SideChain-H) has 35 elements 53: Select a group: Select group to position restrain 53: Selected 3: 'C-alpha' 53: [ OK ] GenRestrTest.SimpleRestraintsGenerated (12 ms) 53: [----------] 1 test from GenRestrTest (12 ms total) 53: 53: [----------] 9 tests from PreprocessingAtomTypesTest 53: [ RUN ] PreprocessingAtomTypesTest.EmptyOnCreate 53: [ OK ] PreprocessingAtomTypesTest.EmptyOnCreate (0 ms) 53: [ RUN ] PreprocessingAtomTypesTest.IndexOutOfRangeInvalid 53: [ OK ] PreprocessingAtomTypesTest.IndexOutOfRangeInvalid (0 ms) 53: [ RUN ] PreprocessingAtomTypesTest.AddTypeWorks 53: [ OK ] PreprocessingAtomTypesTest.AddTypeWorks (0 ms) 53: [ RUN ] PreprocessingAtomTypesTest.AddMultipleTypesWorks 53: [ OK ] PreprocessingAtomTypesTest.AddMultipleTypesWorks (0 ms) 53: [ RUN ] PreprocessingAtomTypesTest.CannotAddDuplicateEntry 53: [ OK ] PreprocessingAtomTypesTest.CannotAddDuplicateEntry (0 ms) 53: [ RUN ] PreprocessingAtomTypesTest.CorrectNameFound 53: [ OK ] PreprocessingAtomTypesTest.CorrectNameFound (0 ms) 53: [ RUN ] PreprocessingAtomTypesTest.WrongNameNotFound 53: [ OK ] PreprocessingAtomTypesTest.WrongNameNotFound (0 ms) 53: [ RUN ] PreprocessingAtomTypesTest.CorrectNameFromTypeNumber 53: [ OK ] PreprocessingAtomTypesTest.CorrectNameFromTypeNumber (0 ms) 53: [ RUN ] PreprocessingAtomTypesTest.NoNameFromIncorrectTypeNumber 53: [ OK ] PreprocessingAtomTypesTest.NoNameFromIncorrectTypeNumber (0 ms) 53: [----------] 9 tests from PreprocessingAtomTypesTest (0 ms total) 53: 53: [----------] 10 tests from PreprocessingBondAtomTypeTest 53: [ RUN ] PreprocessingBondAtomTypeTest.EmptyOnCreate 53: [ OK ] PreprocessingBondAtomTypeTest.EmptyOnCreate (0 ms) 53: [ RUN ] PreprocessingBondAtomTypeTest.IndexOutOfRangeInvalid 53: [ OK ] PreprocessingBondAtomTypeTest.IndexOutOfRangeInvalid (0 ms) 53: [ RUN ] PreprocessingBondAtomTypeTest.AddTypeWorks 53: [ OK ] PreprocessingBondAtomTypeTest.AddTypeWorks (0 ms) 53: [ RUN ] PreprocessingBondAtomTypeTest.AddMultipleTypesWorks 53: [ OK ] PreprocessingBondAtomTypeTest.AddMultipleTypesWorks (0 ms) 53: [ RUN ] PreprocessingBondAtomTypeTest.CannotAddDuplicateEntry 53: [ OK ] PreprocessingBondAtomTypeTest.CannotAddDuplicateEntry (0 ms) 53: [ RUN ] PreprocessingBondAtomTypeTest.ReturnsCorrectIndexOnDuplicateType 53: [ OK ] PreprocessingBondAtomTypeTest.ReturnsCorrectIndexOnDuplicateType (0 ms) 53: [ RUN ] PreprocessingBondAtomTypeTest.CorrectNameFound 53: [ OK ] PreprocessingBondAtomTypeTest.CorrectNameFound (0 ms) 53: [ RUN ] PreprocessingBondAtomTypeTest.WrongNameNotFound 53: [ OK ] PreprocessingBondAtomTypeTest.WrongNameNotFound (0 ms) 53: [ RUN ] PreprocessingBondAtomTypeTest.CorrectNameFromTypeNumber 53: [ OK ] PreprocessingBondAtomTypeTest.CorrectNameFromTypeNumber (0 ms) 53: [ RUN ] PreprocessingBondAtomTypeTest.NoNameFromIncorrectTypeNumber 53: [ OK ] PreprocessingBondAtomTypeTest.NoNameFromIncorrectTypeNumber (0 ms) 53: [----------] 10 tests from PreprocessingBondAtomTypeTest (0 ms total) 53: 53: [----------] 3 tests from GromppDirectiveTest 53: [ RUN ] GromppDirectiveTest.edgeCaseAtomTypeNames 53: Ignoring obsolete mdp entry 'title' 53: Generating 1-4 interactions: fudge = 0.5 53: 53: NOTE 1 [file directives.top, line 59]: 53: In moleculetype 'A' 2 atoms are not bound by a potential or constraint to 53: any other atom in the same moleculetype. Although technically this might 53: not cause issues in a simulation, this often means that the user forgot 53: to add a bond/potential/constraint or put multiple molecules in the same 53: moleculetype definition by mistake. Run with -v to get information for 53: each atom. 53: 53: Number of degrees of freedom in T-Coupling group rest is 9.00 53: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 53: 53: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GromppDirectiveTest_edgeCaseAtomTypeNames_directives.mdp]: 53: NVE simulation: will use the initial temperature of 300.000 K for 53: determining the Verlet buffer size 53: 53: 53: There were 2 NOTEs 53: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GromppDirectiveTest_edgeCaseAtomTypeNames_directives.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 53: Setting the LD random seed to 1607974395 53: 53: Generated 10 of the 10 non-bonded parameter combinations 53: 53: Generated 10 of the 10 1-4 parameter combinations 53: 53: Excluding 0 bonded neighbours molecule type 'A' 53: 53: Setting gen_seed to -92551683 53: 53: Velocities were taken from a Maxwell distribution at 300 K 53: Analysing residue names: 53: There are: 1 Other residues 53: Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups... 53: 53: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 300 K 53: 53: Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm 53: 53: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm 53: 53: Note that mdrun will redetermine rlist based on the actual pair-list setup 53: 53: This run will generate roughly 0 Mb of data 53: [ OK ] GromppDirectiveTest.edgeCaseAtomTypeNames (31 ms) 53: [ RUN ] GromppDirectiveTest.NoteOnDihedralNotSumToZero 53: Ignoring obsolete mdp entry 'title' 53: Generating 1-4 interactions: fudge = 0.5 53: 53: NOTE 1 [file directives.top, line 59]: 53: 1 dihedrals with function type 3 (Ryckaert-Bellemans or Fourier) have 53: coefficients that do not sum to zero. This does not affect the simulation 53: and can be ignored, unless you are comparing potential energy values with 53: other force field ports and/or MD software. 53: First such dihedral in molecule A, involving atoms 0 2 1 3 53: 53: 53: NOTE 2 [file directives.top, line 59]: 53: In moleculetype 'A' 2 atoms are not bound by a potential or constraint to 53: any other atom in the same moleculetype. Although technically this might 53: not cause issues in a simulation, this often means that the user forgot 53: to add a bond/potential/constraint or put multiple molecules in the same 53: moleculetype definition by mistake. Run with -v to get information for 53: each atom. 53: 53: Number of degrees of freedom in T-Coupling group rest is 9.00 53: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 53: 53: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GromppDirectiveTest_NoteOnDihedralNotSumToZero_directives.mdp]: 53: NVE simulation: will use the initial temperature of 300.000 K for 53: determining the Verlet buffer size 53: 53: 53: There were 3 NOTEs 53: Setting the LD random seed to 2112815067 53: 53: Generated 10 of the 10 non-bonded parameter combinations 53: 53: Generated 10 of the 10 1-4 parameter combinations 53: 53: Excluding 0 bonded neighbours molecule type 'A' 53: 53: Setting gen_seed to -277873217 53: 53: Velocities were taken from a Maxwell distribution at 300 K 53: Analysing residue names: 53: There are: 1 Other residues 53: Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups... 53: 53: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 300 K 53: 53: Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm 53: 53: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm 53: 53: Note that mdrun will redetermine rlist based on the actual pair-list setup 53: 53: This run will generate roughly 0 Mb of data 53: [ OK ] GromppDirectiveTest.NoteOnDihedralNotSumToZero (31 ms) 53: [ RUN ] GromppDirectiveTest.WarnOnDihedralSumDifferentForFreeEnergy 53: Setting the LD random seed to 1859059133 53: 53: Generated 10 of the 10 non-bonded parameter combinations 53: 53: Generated 10 of the 10 1-4 parameter combinations 53: 53: Excluding 0 bonded neighbours molecule type 'A' 53: 53: Setting gen_seed to -16954132 53: 53: Velocities were taken from a Maxwell distribution at 300 K 53: Analysing residue names: 53: There are: 1 Other residues 53: Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups... 53: 53: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 300 K 53: 53: Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm 53: 53: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm 53: 53: Note that mdrun will redetermine rlist based on the actual pair-list setup 53: 53: This run will generate roughly 0 Mb of data 53: [ OK ] GromppDirectiveTest.WarnOnDihedralSumDifferentForFreeEnergy (64 ms) 53: [----------] 3 tests from GromppDirectiveTest (126 ms total) 53: 53: [----------] 6 tests from InsertMoleculesTest 53: [ RUN ] InsertMoleculesTest.InsertsMoleculesIntoExistingConfiguration 53: Reading solute configuration 53: Initialising inter-atomic distances... 53: 53: WARNING: Masses and atomic (Van der Waals) radii will be guessed 53: based on residue and atom names, since they could not be 53: definitively assigned from the information in your input 53: files. These guessed numbers might deviate from the mass 53: and radius of the atom type. Please check the output 53: files if necessary. Note, that this functionality may 53: be removed in a future GROMACS version. Please, consider 53: using another file format for your input. 53: 53: NOTE: From version 5.0 gmxpreprocess-test uses the Van der Waals radii 53: from the source below. This means the results may be different 53: compared to previous GROMACS versions. 53: 53: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 53: A. Bondi 53: van der Waals Volumes and Radii 53: J. Phys. Chem. (1964) 53: DOI: 10.1021/j100785a001 53: -------- -------- --- Thank You --- -------- -------- 53: 53: Using random seed 1997 53: Try 1 success (now 8 atoms)! 53: 53: Added 1 molecules (out of 1 requested) 53: Writing generated configuration to /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/InsertMoleculesTest_InsertsMoleculesIntoExistingConfiguration_out.gro 53: 53: Output configuration contains 8 atoms in 4 residues 53: [ OK ] InsertMoleculesTest.InsertsMoleculesIntoExistingConfiguration (10 ms) 53: [ RUN ] InsertMoleculesTest.InsertsMoleculesIntoEmptyBox 53: Initialising inter-atomic distances... 53: 53: WARNING: Masses and atomic (Van der Waals) radii will be guessed 53: based on residue and atom names, since they could not be 53: definitively assigned from the information in your input 53: files. These guessed numbers might deviate from the mass 53: and radius of the atom type. Please check the output 53: files if necessary. Note, that this functionality may 53: be removed in a future GROMACS version. Please, consider 53: using another file format for your input. 53: 53: NOTE: From version 5.0 gmxpreprocess-test uses the Van der Waals radii 53: from the source below. This means the results may be different 53: compared to previous GROMACS versions. 53: 53: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 53: A. Bondi 53: van der Waals Volumes and Radii 53: J. Phys. Chem. (1964) 53: DOI: 10.1021/j100785a001 53: -------- -------- --- Thank You --- -------- -------- 53: 53: Using random seed 1997 53: Try 1 success (now 2 atoms)! 53: Try 2 success (now 4 atoms)! 53: Try 3 success (now 6 atoms)! 53: Try 4 success (now 8 atoms)! 53: Try 5 success (now 10 atoms)! 53: 53: Added 5 molecules (out of 5 requested) 53: Writing generated configuration to /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/InsertMoleculesTest_InsertsMoleculesIntoEmptyBox_out.gro 53: 53: Output configuration contains 10 atoms in 10 residues 53: [ OK ] InsertMoleculesTest.InsertsMoleculesIntoEmptyBox (10 ms) 53: [ RUN ] InsertMoleculesTest.InsertsMoleculesIntoEmptyBoxConcentration 53: Initialising inter-atomic distances... 53: 53: WARNING: Masses and atomic (Van der Waals) radii will be guessed 53: based on residue and atom names, since they could not be 53: definitively assigned from the information in your input 53: files. These guessed numbers might deviate from the mass 53: and radius of the atom type. Please check the output 53: files if necessary. Note, that this functionality may 53: be removed in a future GROMACS version. Please, consider 53: using another file format for your input. 53: 53: NOTE: From version 5.0 gmxpreprocess-test uses the Van der Waals radii 53: from the source below. This means the results may be different 53: compared to previous GROMACS versions. 53: 53: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 53: A. Bondi 53: van der Waals Volumes and Radii 53: J. Phys. Chem. (1964) 53: DOI: 10.1021/j100785a001 53: -------- -------- --- Thank You --- -------- -------- 53: 53: Using random seed 1997 53: Try 1 success (now 2 atoms)! 53: Try 2 success (now 4 atoms)! 53: Try 3 success (now 6 atoms)! 53: Try 4 success (now 8 atoms)! 53: Try 5 success (now 10 atoms)! 53: 53: Added 5 molecules (out of 5 requested) 53: Writing generated configuration to /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/InsertMoleculesTest_InsertsMoleculesIntoEmptyBoxConcentration_out.gro 53: 53: Output configuration contains 10 atoms in 10 residues 53: [ OK ] InsertMoleculesTest.InsertsMoleculesIntoEmptyBoxConcentration (8 ms) 53: [ RUN ] InsertMoleculesTest.InsertsMoleculesIntoEnlargedBox 53: Reading solute configuration 53: Initialising inter-atomic distances... 53: 53: WARNING: Masses and atomic (Van der Waals) radii will be guessed 53: based on residue and atom names, since they could not be 53: definitively assigned from the information in your input 53: files. These guessed numbers might deviate from the mass 53: and radius of the atom type. Please check the output 53: files if necessary. Note, that this functionality may 53: be removed in a future GROMACS version. Please, consider 53: using another file format for your input. 53: 53: NOTE: From version 5.0 gmxpreprocess-test uses the Van der Waals radii 53: from the source below. This means the results may be different 53: compared to previous GROMACS versions. 53: 53: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 53: A. Bondi 53: van der Waals Volumes and Radii 53: J. Phys. Chem. (1964) 53: DOI: 10.1021/j100785a001 53: -------- -------- --- Thank You --- -------- -------- 53: 53: Using random seed 1997 53: Try 1 success (now 8 atoms)! 53: Try 2 success (now 10 atoms)! 53: 53: Added 2 molecules (out of 2 requested) 53: Writing generated configuration to /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/InsertMoleculesTest_InsertsMoleculesIntoEnlargedBox_out.gro 53: 53: Output configuration contains 10 atoms in 4 residues 53: [ OK ] InsertMoleculesTest.InsertsMoleculesIntoEnlargedBox (8 ms) 53: [ RUN ] InsertMoleculesTest.InsertsMoleculesWithReplacement 53: Reading solute configuration 53: Initialising inter-atomic distances... 53: 53: WARNING: Masses and atomic (Van der Waals) radii will be guessed 53: based on residue and atom names, since they could not be 53: definitively assigned from the information in your input 53: files. These guessed numbers might deviate from the mass 53: and radius of the atom type. Please check the output 53: files if necessary. Note, that this functionality may 53: be removed in a future GROMACS version. Please, consider 53: using another file format for your input. 53: 53: NOTE: From version 5.0 gmxpreprocess-test uses the Van der Waals radii 53: from the source below. This means the results may be different 53: compared to previous GROMACS versions. 53: 53: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 53: A. Bondi 53: van der Waals Volumes and Radii 53: J. Phys. Chem. (1964) 53: DOI: 10.1021/j100785a001 53: -------- -------- --- Thank You --- -------- -------- 53: 53: Using random seed 1997 53: Try 1 success (now 650 atoms)! 53: Try 2 success (now 652 atoms)! 53: Try 3 success (now 654 atoms)! 53: Try 4 success (now 656 atoms)! 53: 53: Added 4 molecules (out of 4 requested) 53: Replaced 8 residues (24 atoms) 53: Writing generated configuration to /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/InsertMoleculesTest_InsertsMoleculesWithReplacement_out.gro 53: 53: Output configuration contains 632 atoms in 212 residues 53: [ OK ] InsertMoleculesTest.InsertsMoleculesWithReplacement (29 ms) 53: [ RUN ] InsertMoleculesTest.InsertsMoleculesIntoFixedPositions 53: Initialising inter-atomic distances... 53: 53: WARNING: Masses and atomic (Van der Waals) radii will be guessed 53: based on residue and atom names, since they could not be 53: definitively assigned from the information in your input 53: files. These guessed numbers might deviate from the mass 53: and radius of the atom type. Please check the output 53: files if necessary. Note, that this functionality may 53: be removed in a future GROMACS version. Please, consider 53: using another file format for your input. 53: 53: NOTE: From version 5.0 gmxpreprocess-test uses the Van der Waals radii 53: from the source below. This means the results may be different 53: compared to previous GROMACS versions. 53: 53: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 53: A. Bondi 53: van der Waals Volumes and Radii 53: J. Phys. Chem. (1964) 53: DOI: 10.1021/j100785a001 53: -------- -------- --- Thank You --- -------- -------- 53: 53: Using random seed 1997 53: Read 4 positions from file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/InsertMoleculesTest_InsertsMoleculesIntoFixedPositions_5.dat 53: 53: Try 1 success (now 2 atoms)! 53: Try 2 success (now 4 atoms)! 53: Try 3 Try 4 Try 5 Try 6 Try 7 Try 8 Try 9 Try 10 Try 11 Try 12 skipped position (0.990, 2.010, 3.000) 53: Try 13 success (now 6 atoms)! 53: 53: Added 3 molecules (out of 4 requested) 53: Writing generated configuration to /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/InsertMoleculesTest_InsertsMoleculesIntoFixedPositions_out.gro 53: 53: Output configuration contains 6 atoms in 3 residues 53: [ OK ] InsertMoleculesTest.InsertsMoleculesIntoFixedPositions (9 ms) 53: [----------] 6 tests from InsertMoleculesTest (79 ms total) 53: 53: [----------] 3 tests from MassRepartitioning 53: [ RUN ] MassRepartitioning.ValidCaseWorks 53: The smallest mass in the system is 2, setting the minimum mass to 6 53: [ OK ] MassRepartitioning.ValidCaseWorks (0 ms) 53: [ RUN ] MassRepartitioning.UnboundGivesWarning 53: 53: WARNING 1 [file unknown]: 53: The are 1 atoms that have a mass below the mass repartitioning limit but 53: are not bound. These masses cannot be repartitioned. 53: 53: The smallest mass in the system is 2, setting the minimum mass to 6 53: [ OK ] MassRepartitioning.UnboundGivesWarning (0 ms) 53: [ RUN ] MassRepartitioning.LightPartnerGivesError 53: 53: ERROR 1 [file unknown]: 53: Light atoms are bound to at least one atom that has a too low mass for 53: repartitioning 53: 53: The smallest mass in the system is 2, setting the minimum mass to 6 53: [ OK ] MassRepartitioning.LightPartnerGivesError (0 ms) 53: [----------] 3 tests from MassRepartitioning (0 ms total) 53: 53: [----------] 35 tests from GetIrTest 53: [ RUN ] GetIrTest.HandlesDifferentKindsOfMdpLines 53: Ignoring obsolete mdp entry 'title' 53: Replacing old mdp entry 'xtc_grps' by 'compressed-x-grps' 53: 53: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_HandlesDifferentKindsOfMdpLines_input.mdp]: 53: For a correct single-point energy evaluation with nsteps = 0, use 53: continuation = yes to avoid constraining the input coordinates. 53: 53: [ OK ] GetIrTest.HandlesDifferentKindsOfMdpLines (23 ms) 53: [ RUN ] GetIrTest.RejectsNonCommentLineWithNoEquals 53: [ OK ] GetIrTest.RejectsNonCommentLineWithNoEquals (39 ms) 53: [ RUN ] GetIrTest.AcceptsKeyWithoutValue 53: 53: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_AcceptsKeyWithoutValue_input.mdp]: 53: For a correct single-point energy evaluation with nsteps = 0, use 53: continuation = yes to avoid constraining the input coordinates. 53: 53: [ OK ] GetIrTest.AcceptsKeyWithoutValue (22 ms) 53: [ RUN ] GetIrTest.RejectsValueWithoutKey 53: [ OK ] GetIrTest.RejectsValueWithoutKey (45 ms) 53: [ RUN ] GetIrTest.RejectsEmptyKeyAndEmptyValue 53: [ OK ] GetIrTest.RejectsEmptyKeyAndEmptyValue (37 ms) 53: [ RUN ] GetIrTest.AcceptsDefineParametersWithValuesIncludingAssignment 53: 53: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_AcceptsDefineParametersWithValuesIncludingAssignment_input.mdp]: 53: For a correct single-point energy evaluation with nsteps = 0, use 53: continuation = yes to avoid constraining the input coordinates. 53: 53: [ OK ] GetIrTest.AcceptsDefineParametersWithValuesIncludingAssignment (22 ms) 53: [ RUN ] GetIrTest.AcceptsEmptyLines 53: 53: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_AcceptsEmptyLines_input.mdp]: 53: For a correct single-point energy evaluation with nsteps = 0, use 53: continuation = yes to avoid constraining the input coordinates. 53: 53: [ OK ] GetIrTest.AcceptsEmptyLines (23 ms) 53: [ RUN ] GetIrTest.MtsCheckNstcalcenergy 53: 53: ERROR 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_MtsCheckNstcalcenergy_input.mdp]: 53: With MTS, nstcalcenergy = 5 should be a multiple of mts-factor = 2 53: 53: 53: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_MtsCheckNstcalcenergy_input.mdp]: 53: For a correct single-point energy evaluation with nsteps = 0, use 53: continuation = yes to avoid constraining the input coordinates. 53: 53: [ OK ] GetIrTest.MtsCheckNstcalcenergy (17 ms) 53: [ RUN ] GetIrTest.MtsCheckNstenergy 53: 53: ERROR 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_MtsCheckNstenergy_input.mdp]: 53: With MTS, nstenergy = 5 should be a multiple of mts-factor = 2 53: 53: 53: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_MtsCheckNstenergy_input.mdp]: 53: Setting nstcalcenergy (100) equal to nstenergy (5) 53: 53: 53: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_MtsCheckNstenergy_input.mdp]: 53: For a correct single-point energy evaluation with nsteps = 0, use 53: continuation = yes to avoid constraining the input coordinates. 53: 53: [ OK ] GetIrTest.MtsCheckNstenergy (17 ms) 53: [ RUN ] GetIrTest.MtsCheckNstpcouple 53: 53: ERROR 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_MtsCheckNstpcouple_input.mdp, line 7]: 53: Pressure coupling incorrect number of values (I need exactly 1) 53: 53: 53: ERROR 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_MtsCheckNstpcouple_input.mdp, line 7]: 53: Pressure coupling incorrect number of values (I need exactly 1) 53: 53: 53: ERROR 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_MtsCheckNstpcouple_input.mdp]: 53: With multiple time stepping, nstpcouple should be a multiple of 53: mts-factor 53: 53: 53: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_MtsCheckNstpcouple_input.mdp]: 53: For a correct single-point energy evaluation with nsteps = 0, use 53: continuation = yes to avoid constraining the input coordinates. 53: 53: 53: ERROR 4 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_MtsCheckNstpcouple_input.mdp]: 53: The Berendsen barostat does not generate any strictly correct ensemble, 53: and should not be used for new production simulations (in our opinion). 53: We recommend using the C-rescale barostat instead. 53: 53: 53: ERROR 5 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_MtsCheckNstpcouple_input.mdp]: 53: compressibility must be > 0 when using pressure coupling Berendsen 53: 53: 53: [ OK ] GetIrTest.MtsCheckNstpcouple (18 ms) 53: [ RUN ] GetIrTest.MtsCheckNstdhdl 53: 53: ERROR 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_MtsCheckNstdhdl_input.mdp]: 53: With MTS, nstdhdl = 5 should be a multiple of mts-factor = 2 53: 53: 53: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_MtsCheckNstdhdl_input.mdp]: 53: Setting nstcalcenergy (100) equal to nstdhdl (5) 53: 53: 53: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_MtsCheckNstdhdl_input.mdp]: 53: For a correct single-point energy evaluation with nsteps = 0, use 53: continuation = yes to avoid constraining the input coordinates. 53: 53: 53: ERROR 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_MtsCheckNstdhdl_input.mdp]: 53: Lambda state must be set, either with init-lambda-state or with 53: init-lambda 53: 53: [ OK ] GetIrTest.MtsCheckNstdhdl (17 ms) 53: [ RUN ] GetIrTest.MtsCheckSDNotSupported 53: 53: ERROR 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_MtsCheckSDNotSupported_input.mdp]: 53: Multiple time stepping is only supported with integrator md 53: 53: 53: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_MtsCheckSDNotSupported_input.mdp]: 53: For a correct single-point energy evaluation with nsteps = 0, use 53: continuation = yes to avoid constraining the input coordinates. 53: 53: [ OK ] GetIrTest.MtsCheckSDNotSupported (17 ms) 53: [ RUN ] GetIrTest.AcceptsElectricField 53: 53: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_AcceptsElectricField_input.mdp]: 53: For a correct single-point energy evaluation with nsteps = 0, use 53: continuation = yes to avoid constraining the input coordinates. 53: 53: [ OK ] GetIrTest.AcceptsElectricField (22 ms) 53: [ RUN ] GetIrTest.AcceptsElectricFieldPulsed 53: 53: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_AcceptsElectricFieldPulsed_input.mdp]: 53: For a correct single-point energy evaluation with nsteps = 0, use 53: continuation = yes to avoid constraining the input coordinates. 53: 53: [ OK ] GetIrTest.AcceptsElectricFieldPulsed (23 ms) 53: [ RUN ] GetIrTest.AcceptsElectricFieldOscillating 53: 53: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_AcceptsElectricFieldOscillating_input.mdp]: 53: For a correct single-point energy evaluation with nsteps = 0, use 53: continuation = yes to avoid constraining the input coordinates. 53: 53: [ OK ] GetIrTest.AcceptsElectricFieldOscillating (23 ms) 53: [ RUN ] GetIrTest.RejectsDuplicateOldAndNewKeys 53: [ OK ] GetIrTest.RejectsDuplicateOldAndNewKeys (18 ms) 53: [ RUN ] GetIrTest.AcceptsImplicitSolventNo 53: 53: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_AcceptsImplicitSolventNo_input.mdp]: 53: For a correct single-point energy evaluation with nsteps = 0, use 53: continuation = yes to avoid constraining the input coordinates. 53: 53: [ OK ] GetIrTest.AcceptsImplicitSolventNo (23 ms) 53: [ RUN ] GetIrTest.RejectsImplicitSolventYes 53: [ OK ] GetIrTest.RejectsImplicitSolventYes (40 ms) 53: [ RUN ] GetIrTest.AcceptsMimic 53: 53: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_AcceptsMimic_input.mdp]: 53: For a correct single-point energy evaluation with nsteps = 0, use 53: continuation = yes to avoid constraining the input coordinates. 53: 53: [ OK ] GetIrTest.AcceptsMimic (23 ms) 53: [ RUN ] GetIrTest.AcceptsTransformationCoord 53: 53: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_AcceptsTransformationCoord_input.mdp, line 11]: 53: pull-coord2 has a non-zero force constant and is also referenced in 53: pull-coord1-expression. Make sure that this is intended. In most use 53: cases, the pull coordinates referenced by a transformation coordinate 53: should have their force constant set to zero. 53: 53: 53: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_AcceptsTransformationCoord_input.mdp]: 53: For a correct single-point energy evaluation with nsteps = 0, use 53: continuation = yes to avoid constraining the input coordinates. 53: 53: [ OK ] GetIrTest.AcceptsTransformationCoord (23 ms) 53: [ RUN ] GetIrTest.InvalidTransformationCoordWithConstraint 53: 53: ERROR 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_InvalidTransformationCoordWithConstraint_input.mdp, line 7]: 53: pull-coord1 cannot have type 'constraint' and geometry 'transformation' 53: 53: 53: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_InvalidTransformationCoordWithConstraint_input.mdp]: 53: For a correct single-point energy evaluation with nsteps = 0, use 53: continuation = yes to avoid constraining the input coordinates. 53: 53: [ OK ] GetIrTest.InvalidTransformationCoordWithConstraint (20 ms) 53: [ RUN ] GetIrTest.InvalidPullCoordWithConstraintInTransformationExpression 53: 53: ERROR 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_InvalidPullCoordWithConstraintInTransformationExpression_input.mdp, line 10]: 53: pull-coord2 can not use pull-coord1 in the transformation since this is a 53: constraint 53: 53: 53: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_InvalidPullCoordWithConstraintInTransformationExpression_input.mdp]: 53: For a correct single-point energy evaluation with nsteps = 0, use 53: continuation = yes to avoid constraining the input coordinates. 53: 53: [ OK ] GetIrTest.InvalidPullCoordWithConstraintInTransformationExpression (20 ms) 53: [ RUN ] GetIrTest.InvalidTransformationCoordDxValue 53: 53: ERROR 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_InvalidTransformationCoordDxValue_input.mdp, line 7]: 53: pull-coord1-dx cannot be set to zero for pull coordinate of geometry 53: 'transformation' 53: 53: 53: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_InvalidTransformationCoordDxValue_input.mdp]: 53: For a correct single-point energy evaluation with nsteps = 0, use 53: continuation = yes to avoid constraining the input coordinates. 53: 53: [ OK ] GetIrTest.InvalidTransformationCoordDxValue (18 ms) 53: [ RUN ] GetIrTest.MissingTransformationCoordExpression 53: 53: ERROR 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_MissingTransformationCoordExpression_input.mdp, line 5]: 53: pull-coord1-expression not set for pull coordinate of geometry 53: 'transformation' 53: 53: 53: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_MissingTransformationCoordExpression_input.mdp]: 53: For a correct single-point energy evaluation with nsteps = 0, use 53: continuation = yes to avoid constraining the input coordinates. 53: 53: [ OK ] GetIrTest.MissingTransformationCoordExpression (18 ms) 53: [ RUN ] GetIrTest.lambdaOverOneCheck_SC_And_ExactlyAsManyStep 53: [ OK ] GetIrTest.lambdaOverOneCheck_SC_And_ExactlyAsManyStep (16 ms) 53: [ RUN ] GetIrTest.lambdaOverOneCheck_SC_And_ExactlyAsManyStep_negativeDelta 53: [ OK ] GetIrTest.lambdaOverOneCheck_SC_And_ExactlyAsManyStep_negativeDelta (17 ms) 53: [ RUN ] GetIrTest.lambdaOverOneCheck_NoSC_And_ExactlyAsManyStep 53: [ OK ] GetIrTest.lambdaOverOneCheck_NoSC_And_ExactlyAsManyStep (17 ms) 53: [ RUN ] GetIrTest.lambdaOverOneCheck_NoSC_And_ExactlyAsManyStep_negativeDelta 53: [ OK ] GetIrTest.lambdaOverOneCheck_NoSC_And_ExactlyAsManyStep_negativeDelta (18 ms) 53: [ RUN ] GetIrTest.lambdaOverOneCheck_SC_And_OneStepTooMuch 53: 53: ERROR 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_lambdaOverOneCheck_SC_And_OneStepTooMuch_input.mdp]: 53: With init-lambda = 0 and delta_lambda = 1e-05 and no explicit input, 53: coul-lambdas and vdw-lambdas will be greater than 1 after step 100000 of 53: in total 100001 steps. This is not compatible with using soft-core 53: potentials. 53: 53: 53: [ OK ] GetIrTest.lambdaOverOneCheck_SC_And_OneStepTooMuch (17 ms) 53: [ RUN ] GetIrTest.lambdaOverOneCheck_SC_And_OneStepTooMuch_negativeDelta 53: 53: ERROR 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_lambdaOverOneCheck_SC_And_OneStepTooMuch_negativeDelta_input.mdp]: 53: With init-lambda = 1 and delta_lambda = -1e-05, the lambda components 53: won't change anymore after step 100000 until the end of the simulation 53: after 100001 steps. 53: 53: 53: [ OK ] GetIrTest.lambdaOverOneCheck_SC_And_OneStepTooMuch_negativeDelta (18 ms) 53: [ RUN ] GetIrTest.lambdaOverOneCheck_NoSC_And_OneStepTooMuch_negativeDelta 53: 53: ERROR 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_lambdaOverOneCheck_NoSC_And_OneStepTooMuch_negativeDelta_input.mdp]: 53: With init-lambda = 1 and delta_lambda = -1e-05, the lambda components 53: won't change anymore after step 100000 until the end of the simulation 53: after 100001 steps. 53: 53: 53: [ OK ] GetIrTest.lambdaOverOneCheck_NoSC_And_OneStepTooMuch_negativeDelta (17 ms) 53: [ RUN ] GetIrTest.lambdaOverOneCheck_LambdaVector_And_OneStepTooMuch 53: 53: ERROR 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_lambdaOverOneCheck_LambdaVector_And_OneStepTooMuch_input.mdp]: 53: With init-lambda-state = 0 and delta_lambda = 1e-05, the lambda 53: components won't change anymore after step 100000 until the end of the 53: simulation after 100001 steps. 53: 53: 53: [ OK ] GetIrTest.lambdaOverOneCheck_LambdaVector_And_OneStepTooMuch (17 ms) 53: [ RUN ] GetIrTest.lambdaOverOneCheck_LambdaVector_And_OneStepTooMuch_negativeDelta 53: 53: ERROR 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_lambdaOverOneCheck_LambdaVector_And_OneStepTooMuch_negativeDelta_input.mdp]: 53: With init-lambda-state = 2 and delta_lambda = -1e-05, the lambda 53: components won't change anymore after step 100000 until the end of the 53: simulation after 100001 steps. 53: 53: 53: [ OK ] GetIrTest.lambdaOverOneCheck_LambdaVector_And_OneStepTooMuch_negativeDelta (17 ms) 53: [ RUN ] GetIrTest.lambdaOverOneCheck_LambdaVector_And_ExactlyAsManyStep 53: [ OK ] GetIrTest.lambdaOverOneCheck_LambdaVector_And_ExactlyAsManyStep (17 ms) 53: [ RUN ] GetIrTest.lambdaOverOneCheck_LambdaVector_And_ExactlyAsManyStep_negativeDelta 53: [ OK ] GetIrTest.lambdaOverOneCheck_LambdaVector_And_ExactlyAsManyStep_negativeDelta (17 ms) 53: [----------] 35 tests from GetIrTest (780 ms total) 53: 53: [----------] 6 tests from SolvateTest 53: [ RUN ] SolvateTest.cs_box_Works 53: Reading solvent configuration 53: 53: Initialising inter-atomic distances... 53: 53: WARNING: Masses and atomic (Van der Waals) radii will be guessed 53: based on residue and atom names, since they could not be 53: definitively assigned from the information in your input 53: files. These guessed numbers might deviate from the mass 53: and radius of the atom type. Please check the output 53: files if necessary. Note, that this functionality may 53: be removed in a future GROMACS version. Please, consider 53: using another file format for your input. 53: 53: NOTE: From version 5.0 gmxpreprocess-test uses the Van der Waals radii 53: from the source below. This means the results may be different 53: compared to previous GROMACS versions. 53: 53: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 53: A. Bondi 53: van der Waals Volumes and Radii 53: J. Phys. Chem. (1964) 53: DOI: 10.1021/j100785a001 53: -------- -------- --- Thank You --- -------- -------- 53: 53: Generating solvent configuration 53: Will generate new solvent configuration of 1x1x1 boxes 53: Solvent box contains 270 atoms in 90 residues 53: Removed 129 solvent atoms due to solvent-solvent overlap 53: Sorting configuration 53: Found 1 molecule type: 53: SOL ( 3 atoms): 47 residues 53: Generated solvent containing 141 atoms in 47 residues 53: Writing generated configuration to /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/SolvateTest_cs_box_Works_out.gro 53: 53: Output configuration contains 141 atoms in 47 residues 53: Volume : 1.331 (nm^3) 53: Density : 1056.36 (g/l) 53: Number of solvent molecules: 47 53: 53: [ OK ] SolvateTest.cs_box_Works (22 ms) 53: [ RUN ] SolvateTest.cs_cp_Works 53: Reading solute configuration 53: Reading solvent configuration 53: 53: Initialising inter-atomic distances... 53: 53: WARNING: Masses and atomic (Van der Waals) radii will be guessed 53: based on residue and atom names, since they could not be 53: definitively assigned from the information in your input 53: files. These guessed numbers might deviate from the mass 53: and radius of the atom type. Please check the output 53: files if necessary. Note, that this functionality may 53: be removed in a future GROMACS version. Please, consider 53: using another file format for your input. 53: 53: NOTE: From version 5.0 gmxpreprocess-test uses the Van der Waals radii 53: from the source below. This means the results may be different 53: compared to previous GROMACS versions. 53: 53: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 53: A. Bondi 53: van der Waals Volumes and Radii 53: J. Phys. Chem. (1964) 53: DOI: 10.1021/j100785a001 53: -------- -------- --- Thank You --- -------- -------- 53: 53: Generating solvent configuration 53: Will generate new solvent configuration of 2x2x2 boxes 53: Solvent box contains 3660 atoms in 1220 residues 53: Removed 987 solvent atoms due to solvent-solvent overlap 53: Removed 15 solvent atoms due to solute-solvent overlap 53: Sorting configuration 53: Found 1 molecule type: 53: SOL ( 3 atoms): 886 residues 53: Generated solvent containing 2658 atoms in 886 residues 53: Writing generated configuration to /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/SolvateTest_cs_cp_Works_out.gro 53: 53: Output configuration contains 2664 atoms in 888 residues 53: Volume : 27.2709 (nm^3) 53: Density : 974.777 (g/l) 53: Number of solvent molecules: 886 53: 53: [ OK ] SolvateTest.cs_cp_Works (112 ms) 53: [ RUN ] SolvateTest.cs_cp_p_Works 53: Reading solute configuration 53: Reading solvent configuration 53: 53: Initialising inter-atomic distances... 53: 53: WARNING: Masses and atomic (Van der Waals) radii will be guessed 53: based on residue and atom names, since they could not be 53: definitively assigned from the information in your input 53: files. These guessed numbers might deviate from the mass 53: and radius of the atom type. Please check the output 53: files if necessary. Note, that this functionality may 53: be removed in a future GROMACS version. Please, consider 53: using another file format for your input. 53: 53: NOTE: From version 5.0 gmxpreprocess-test uses the Van der Waals radii 53: from the source below. This means the results may be different 53: compared to previous GROMACS versions. 53: 53: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 53: A. Bondi 53: van der Waals Volumes and Radii 53: J. Phys. Chem. (1964) 53: DOI: 10.1021/j100785a001 53: -------- -------- --- Thank You --- -------- -------- 53: 53: Generating solvent configuration 53: Will generate new solvent configuration of 2x2x2 boxes 53: Solvent box contains 3660 atoms in 1220 residues 53: Removed 987 solvent atoms due to solvent-solvent overlap 53: Removed 15 solvent atoms due to solute-solvent overlap 53: Sorting configuration 53: Found 1 molecule type: 53: SOL ( 3 atoms): 886 residues 53: Generated solvent containing 2658 atoms in 886 residues 53: Writing generated configuration to /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/SolvateTest_cs_cp_p_Works_out.gro 53: 53: Output configuration contains 2664 atoms in 888 residues 53: Volume : 27.2709 (nm^3) 53: Density : 974.777 (g/l) 53: Number of solvent molecules: 886 53: 53: Processing topology 53: Adding line for 886 solvent molecules with resname (SOL) to topology file (/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/SolvateTest_cs_cp_p_Works_spc-and-methanol.top) 53: [ OK ] SolvateTest.cs_cp_p_Works (116 ms) 53: [ RUN ] SolvateTest.shell_Works 53: Reading solute configuration 53: Reading solvent configuration 53: 53: Initialising inter-atomic distances... 53: 53: WARNING: Masses and atomic (Van der Waals) radii will be guessed 53: based on residue and atom names, since they could not be 53: definitively assigned from the information in your input 53: files. These guessed numbers might deviate from the mass 53: and radius of the atom type. Please check the output 53: files if necessary. Note, that this functionality may 53: be removed in a future GROMACS version. Please, consider 53: using another file format for your input. 53: 53: NOTE: From version 5.0 gmxpreprocess-test uses the Van der Waals radii 53: from the source below. This means the results may be different 53: compared to previous GROMACS versions. 53: 53: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 53: A. Bondi 53: van der Waals Volumes and Radii 53: J. Phys. Chem. (1964) 53: DOI: 10.1021/j100785a001 53: -------- -------- --- Thank You --- -------- -------- 53: 53: Generating solvent configuration 53: Will generate new solvent configuration of 2x2x2 boxes 53: Solvent box contains 3660 atoms in 1220 residues 53: Removed 987 solvent atoms due to solvent-solvent overlap 53: Removed 1902 solvent atoms more than 1.000000 nm from solute. 53: Removed 15 solvent atoms due to solute-solvent overlap 53: Sorting configuration 53: Found 1 molecule type: 53: SOL ( 3 atoms): 252 residues 53: Generated solvent containing 756 atoms in 252 residues 53: Writing generated configuration to /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/SolvateTest_shell_Works_out.gro 53: 53: Output configuration contains 762 atoms in 254 residues 53: Volume : 27.2709 (nm^3) 53: Density : 279.3 (g/l) 53: Number of solvent molecules: 252 53: 53: [ OK ] SolvateTest.shell_Works (77 ms) 53: [ RUN ] SolvateTest.update_Topology_Works 53: Reading solute configuration 53: Reading solvent configuration 53: 53: Initialising inter-atomic distances... 53: 53: WARNING: Masses and atomic (Van der Waals) radii will be guessed 53: based on residue and atom names, since they could not be 53: definitively assigned from the information in your input 53: files. These guessed numbers might deviate from the mass 53: and radius of the atom type. Please check the output 53: files if necessary. Note, that this functionality may 53: be removed in a future GROMACS version. Please, consider 53: using another file format for your input. 53: 53: NOTE: From version 5.0 gmxpreprocess-test uses the Van der Waals radii 53: from the source below. This means the results may be different 53: compared to previous GROMACS versions. 53: 53: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 53: A. Bondi 53: van der Waals Volumes and Radii 53: J. Phys. Chem. (1964) 53: DOI: 10.1021/j100785a001 53: -------- -------- --- Thank You --- -------- -------- 53: 53: Generating solvent configuration 53: Will generate new solvent configuration of 3x3x3 boxes 53: Solvent box contains 14952 atoms in 4984 residues 53: Removed 2787 solvent atoms due to solvent-solvent overlap 53: Removed 30 solvent atoms due to solute-solvent overlap 53: Sorting configuration 53: Found 2 different molecule types: 53: HOH ( 3 atoms): 1876 residues 53: SOL ( 3 atoms): 2169 residues 53: Generated solvent containing 0 atoms in 0 residues 53: Writing generated configuration to /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/SolvateTest_update_Topology_Works_out.gro 53: 53: Output configuration contains 12141 atoms in 4047 residues 53: Volume : 125 (nm^3) 53: Density : 968.963 (g/l) 53: Number of solvent molecules: 4045 53: 53: Processing topology 53: Adding line for 1876 solvent molecules with resname (HOH) to topology file (/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/SolvateTest_update_Topology_Works_simple.top) 53: Adding line for 2169 solvent molecules with resname (SOL) to topology file (/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/SolvateTest_update_Topology_Works_simple.top) 53: [ OK ] SolvateTest.update_Topology_Works (467 ms) 53: [ RUN ] SolvateTest.cs_pdb_big_box_Works 53: Reading solvent configuration 53: 53: Initialising inter-atomic distances... 53: 53: WARNING: Masses and atomic (Van der Waals) radii will be guessed 53: based on residue and atom names, since they could not be 53: definitively assigned from the information in your input 53: files. These guessed numbers might deviate from the mass 53: and radius of the atom type. Please check the output 53: files if necessary. Note, that this functionality may 53: be removed in a future GROMACS version. Please, consider 53: using another file format for your input. 53: 53: NOTE: From version 5.0 gmxpreprocess-test uses the Van der Waals radii 53: from the source below. This means the results may be different 53: compared to previous GROMACS versions. 53: 53: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 53: A. Bondi 53: van der Waals Volumes and Radii 53: J. Phys. Chem. (1964) 53: DOI: 10.1021/j100785a001 53: -------- -------- --- Thank You --- -------- -------- 53: 53: Generating solvent configuration 53: Will generate new solvent configuration of 2x2x2 boxes 53: Solvent box contains 1218 atoms in 406 residues 53: Removed 555 solvent atoms due to solvent-solvent overlap 53: Sorting configuration 53: Found 1 molecule type: 53: SOL ( 3 atoms): 221 residues 53: Generated solvent containing 663 atoms in 221 residues 53: Writing generated configuration to /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/SolvateTest_cs_pdb_big_box_Works_out.gro 53: 53: Output configuration contains 663 atoms in 221 residues 53: Volume : 8 (nm^3) 53: Density : 826.409 (g/l) 53: Number of solvent molecules: 221 53: 53: [ OK ] SolvateTest.cs_pdb_big_box_Works (46 ms) 53: [----------] 6 tests from SolvateTest (843 ms total) 53: 53: [----------] 1 test from TopDirTests 53: [ RUN ] TopDirTests.NamesArrayHasCorrectSize 53: [ OK ] TopDirTests.NamesArrayHasCorrectSize (0 ms) 53: [----------] 1 test from TopDirTests (0 ms total) 53: 53: [----------] 95 tests from InteractionFunctionKind/ConvertInteractionsTest 53: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Bond 53: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/Bond (0 ms) 53: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/G96Bond 53: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/G96Bond (0 ms) 53: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Morse 53: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/Morse (0 ms) 53: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Cubic_Bonds 53: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/Cubic_Bonds (0 ms) 53: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Connect_Bonds 53: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/Connect_Bonds (0 ms) 53: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Harmonic_Pot_ 53: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/Harmonic_Pot_ (0 ms) 53: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/FENE_Bonds 53: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/FENE_Bonds (0 ms) 53: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Tab__Bonds 53: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/Tab__Bonds (0 ms) 53: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Tab__Bonds_NC 53: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/Tab__Bonds_NC (0 ms) 53: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Restraint_Pot_ 53: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/Restraint_Pot_ (0 ms) 53: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Angle 53: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/Angle (0 ms) 53: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/G96Angle 53: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/G96Angle (0 ms) 53: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Restr__Angles 53: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/Restr__Angles (0 ms) 53: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Lin__Angle 53: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/Lin__Angle (0 ms) 53: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Bond_Cross 53: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/Bond_Cross (0 ms) 53: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/BA_Cross 53: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/BA_Cross (0 ms) 53: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/U_B 53: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/U_B (0 ms) 53: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Quartic_Angles 53: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/Quartic_Angles (0 ms) 53: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Tab__Angles 53: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/Tab__Angles (0 ms) 53: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Proper_Dih_ 53: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/Proper_Dih_ (0 ms) 53: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Ryckaert_Bell_ 53: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/Ryckaert_Bell_ (0 ms) 53: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Restr__Dih_ 53: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/Restr__Dih_ (0 ms) 53: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/CBT_Dih_ 53: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/CBT_Dih_ (0 ms) 53: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Fourier_Dih_ 53: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/Fourier_Dih_ (0 ms) 53: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Improper_Dih_ 53: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/Improper_Dih_ (0 ms) 53: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Per__Imp__Dih_ 53: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/Per__Imp__Dih_ (0 ms) 53: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Tab__Dih_ 53: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/Tab__Dih_ (0 ms) 53: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/CMAP_Dih_ 53: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/CMAP_Dih_ (0 ms) 53: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/GB_1_2_Pol_ 53: ./src/gromacs/gmxpreprocess/tests/convparm.cpp:132: Skipped 53: Skipping interaction type that does not represent a interaction with parameters converted in grompp 53: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/GB_1_2_Pol_ (0 ms) 53: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/GB_1_3_Pol_ 53: ./src/gromacs/gmxpreprocess/tests/convparm.cpp:132: Skipped 53: Skipping interaction type that does not represent a interaction with parameters converted in grompp 53: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/GB_1_3_Pol_ (0 ms) 53: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/GB_1_4_Pol_ 53: ./src/gromacs/gmxpreprocess/tests/convparm.cpp:132: Skipped 53: Skipping interaction type that does not represent a interaction with parameters converted in grompp 53: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/GB_1_4_Pol_ (0 ms) 53: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/GB_Polariz_ 53: ./src/gromacs/gmxpreprocess/tests/convparm.cpp:132: Skipped 53: Skipping interaction type that does not represent a interaction with parameters converted in grompp 53: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/GB_Polariz_ (0 ms) 53: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Nonpolar_Sol_ 53: ./src/gromacs/gmxpreprocess/tests/convparm.cpp:132: Skipped 53: Skipping interaction type that does not represent a interaction with parameters converted in grompp 53: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/Nonpolar_Sol_ (0 ms) 53: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/LJ_14 53: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/LJ_14 (0 ms) 53: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Coulomb_14 53: ./src/gromacs/gmxpreprocess/tests/convparm.cpp:132: Skipped 53: Skipping interaction type that does not represent a interaction with parameters converted in grompp 53: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/Coulomb_14 (0 ms) 53: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/LJC_14_q 53: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/LJC_14_q (0 ms) 53: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/LJC_Pairs_NB 53: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/LJC_Pairs_NB (0 ms) 53: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/LJ__SR_ 53: ./src/gromacs/gmxpreprocess/tests/convparm.cpp:132: Skipped 53: Skipping interaction type that does not represent a interaction with parameters converted in grompp 53: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/LJ__SR_ (0 ms) 53: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Buck_ham__SR_ 53: ./src/gromacs/gmxpreprocess/tests/convparm.cpp:132: Skipped 53: Skipping interaction type that does not represent a interaction with parameters converted in grompp 53: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/Buck_ham__SR_ (0 ms) 53: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/LJ 53: ./src/gromacs/gmxpreprocess/tests/convparm.cpp:132: Skipped 53: Skipping interaction type that does not represent a interaction with parameters converted in grompp 53: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/LJ (0 ms) 53: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/B_ham 53: ./src/gromacs/gmxpreprocess/tests/convparm.cpp:132: Skipped 53: Skipping interaction type that does not represent a interaction with parameters converted in grompp 53: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/B_ham (0 ms) 53: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Disper__corr_ 53: ./src/gromacs/gmxpreprocess/tests/convparm.cpp:132: Skipped 53: Skipping interaction type that does not represent a interaction with parameters converted in grompp 53: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/Disper__corr_ (0 ms) 53: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Coulomb__SR_ 53: ./src/gromacs/gmxpreprocess/tests/convparm.cpp:132: Skipped 53: Skipping interaction type that does not represent a interaction with parameters converted in grompp 53: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/Coulomb__SR_ (0 ms) 53: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Coul 53: ./src/gromacs/gmxpreprocess/tests/convparm.cpp:132: Skipped 53: Skipping interaction type that does not represent a interaction with parameters converted in grompp 53: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/Coul (0 ms) 53: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/RF_excl_ 53: ./src/gromacs/gmxpreprocess/tests/convparm.cpp:132: Skipped 53: Skipping interaction type that does not represent a interaction with parameters converted in grompp 53: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/RF_excl_ (0 ms) 53: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Coul__recip_ 53: ./src/gromacs/gmxpreprocess/tests/convparm.cpp:132: Skipped 53: Skipping interaction type that does not represent a interaction with parameters converted in grompp 53: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/Coul__recip_ (0 ms) 53: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/LJ_recip_ 53: ./src/gromacs/gmxpreprocess/tests/convparm.cpp:132: Skipped 53: Skipping interaction type that does not represent a interaction with parameters converted in grompp 53: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/LJ_recip_ (0 ms) 53: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/DPD 53: ./src/gromacs/gmxpreprocess/tests/convparm.cpp:132: Skipped 53: Skipping interaction type that does not represent a interaction with parameters converted in grompp 53: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/DPD (0 ms) 53: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Polarization 53: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/Polarization (0 ms) 53: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Water_Pol_ 53: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/Water_Pol_ (0 ms) 53: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Thole_Pol_ 53: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/Thole_Pol_ (0 ms) 53: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Anharm__Pol_ 53: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/Anharm__Pol_ (0 ms) 53: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Position_Rest_ 53: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/Position_Rest_ (0 ms) 53: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Flat_b__P_R_ 53: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/Flat_b__P_R_ (0 ms) 53: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Dis__Rest_ 53: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/Dis__Rest_ (0 ms) 53: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/D_R_Viol___nm_ 53: ./src/gromacs/gmxpreprocess/tests/convparm.cpp:132: Skipped 53: Skipping interaction type that does not represent a interaction with parameters converted in grompp 53: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/D_R_Viol___nm_ (0 ms) 53: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Orient__Rest_ 53: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/Orient__Rest_ (0 ms) 53: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Ori__R__RMSD 53: ./src/gromacs/gmxpreprocess/tests/convparm.cpp:132: Skipped 53: Skipping interaction type that does not represent a interaction with parameters converted in grompp 53: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/Ori__R__RMSD (0 ms) 53: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Angle_Rest_ 53: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/Angle_Rest_ (0 ms) 53: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Angle_Rest__Z 53: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/Angle_Rest__Z (0 ms) 53: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Dih__Rest_ 53: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/Dih__Rest_ (0 ms) 53: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Dih__Rest__Vi_ 53: ./src/gromacs/gmxpreprocess/tests/convparm.cpp:132: Skipped 53: Skipping interaction type that does not represent a interaction with parameters converted in grompp 53: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/Dih__Rest__Vi_ (0 ms) 53: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Constraint 53: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/Constraint (0 ms) 53: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Constr__No_Co_ 53: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/Constr__No_Co_ (0 ms) 53: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Settle 53: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/Settle (0 ms) 53: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Virtual_site_1 53: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/Virtual_site_1 (0 ms) 53: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Virtual_site_2 53: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/Virtual_site_2 (0 ms) 53: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Virt__site_2fd 53: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/Virt__site_2fd (0 ms) 53: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Virtual_site_3 53: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/Virtual_site_3 (0 ms) 53: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Virt__site_3fd 53: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/Virt__site_3fd (0 ms) 53: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Vir__site_3fad 53: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/Vir__site_3fad (0 ms) 53: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Vir__site_3out 53: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/Vir__site_3out (0 ms) 53: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Virt__site_4fd 53: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/Virt__site_4fd (0 ms) 53: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Vir__site_4fdn 53: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/Vir__site_4fdn (0 ms) 53: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Virtual_site_N 53: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/Virtual_site_N (0 ms) 53: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/COM_Pull_En_ 53: ./src/gromacs/gmxpreprocess/tests/convparm.cpp:132: Skipped 53: Skipping interaction type that does not represent a interaction with parameters converted in grompp 53: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/COM_Pull_En_ (0 ms) 53: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Dens__fitting 53: ./src/gromacs/gmxpreprocess/tests/convparm.cpp:132: Skipped 53: Skipping interaction type that does not represent a interaction with parameters converted in grompp 53: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/Dens__fitting (0 ms) 53: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Quantum_En_ 53: ./src/gromacs/gmxpreprocess/tests/convparm.cpp:132: Skipped 53: Skipping interaction type that does not represent a interaction with parameters converted in grompp 53: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/Quantum_En_ (0 ms) 53: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/NN_Potential 53: ./src/gromacs/gmxpreprocess/tests/convparm.cpp:132: Skipped 53: Skipping interaction type that does not represent a interaction with parameters converted in grompp 53: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/NN_Potential (0 ms) 53: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Potential 53: ./src/gromacs/gmxpreprocess/tests/convparm.cpp:132: Skipped 53: Skipping interaction type that does not represent a interaction with parameters converted in grompp 53: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/Potential (0 ms) 53: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Kinetic_En_ 53: ./src/gromacs/gmxpreprocess/tests/convparm.cpp:132: Skipped 53: Skipping interaction type that does not represent a interaction with parameters converted in grompp 53: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/Kinetic_En_ (0 ms) 53: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Total_Energy 53: ./src/gromacs/gmxpreprocess/tests/convparm.cpp:132: Skipped 53: Skipping interaction type that does not represent a interaction with parameters converted in grompp 53: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/Total_Energy (0 ms) 53: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Conserved_En_ 53: ./src/gromacs/gmxpreprocess/tests/convparm.cpp:132: Skipped 53: Skipping interaction type that does not represent a interaction with parameters converted in grompp 53: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/Conserved_En_ (0 ms) 53: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Temperature 53: ./src/gromacs/gmxpreprocess/tests/convparm.cpp:132: Skipped 53: Skipping interaction type that does not represent a interaction with parameters converted in grompp 53: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/Temperature (0 ms) 53: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Vir__Temp_ 53: ./src/gromacs/gmxpreprocess/tests/convparm.cpp:132: Skipped 53: Skipping interaction type that does not represent a interaction with parameters converted in grompp 53: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/Vir__Temp_ (0 ms) 53: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Pres__DC 53: ./src/gromacs/gmxpreprocess/tests/convparm.cpp:132: Skipped 53: Skipping interaction type that does not represent a interaction with parameters converted in grompp 53: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/Pres__DC (0 ms) 53: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Pressure 53: ./src/gromacs/gmxpreprocess/tests/convparm.cpp:132: Skipped 53: Skipping interaction type that does not represent a interaction with parameters converted in grompp 53: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/Pressure (0 ms) 53: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/dH_dl_constr_ 53: ./src/gromacs/gmxpreprocess/tests/convparm.cpp:132: Skipped 53: Skipping interaction type that does not represent a interaction with parameters converted in grompp 53: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/dH_dl_constr_ (0 ms) 53: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/dVremain_dl 53: ./src/gromacs/gmxpreprocess/tests/convparm.cpp:132: Skipped 53: Skipping interaction type that does not represent a interaction with parameters converted in grompp 53: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/dVremain_dl (0 ms) 53: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/dEkin_dl 53: ./src/gromacs/gmxpreprocess/tests/convparm.cpp:132: Skipped 53: Skipping interaction type that does not represent a interaction with parameters converted in grompp 53: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/dEkin_dl (0 ms) 53: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/dVcoul_dl 53: ./src/gromacs/gmxpreprocess/tests/convparm.cpp:132: Skipped 53: Skipping interaction type that does not represent a interaction with parameters converted in grompp 53: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/dVcoul_dl (0 ms) 53: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/dVvdw_dl 53: ./src/gromacs/gmxpreprocess/tests/convparm.cpp:132: Skipped 53: Skipping interaction type that does not represent a interaction with parameters converted in grompp 53: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/dVvdw_dl (0 ms) 53: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/dVbonded_dl 53: ./src/gromacs/gmxpreprocess/tests/convparm.cpp:132: Skipped 53: Skipping interaction type that does not represent a interaction with parameters converted in grompp 53: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/dVbonded_dl (0 ms) 53: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/dVrestraint_dl 53: ./src/gromacs/gmxpreprocess/tests/convparm.cpp:132: Skipped 53: Skipping interaction type that does not represent a interaction with parameters converted in grompp 53: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/dVrestraint_dl (0 ms) 53: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/dVtemp_dl 53: ./src/gromacs/gmxpreprocess/tests/convparm.cpp:132: Skipped 53: Skipping interaction type that does not represent a interaction with parameters converted in grompp 53: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/dVtemp_dl (0 ms) 53: [----------] 95 tests from InteractionFunctionKind/ConvertInteractionsTest (11 ms total) 53: 53: [----------] 16 tests from CorrectVelocity/MaxwellTest 53: [ RUN ] CorrectVelocity/MaxwellTest.CreationWorks/0 53: [ OK ] CorrectVelocity/MaxwellTest.CreationWorks/0 (4 ms) 53: [ RUN ] CorrectVelocity/MaxwellTest.CreationWorks/1 53: [ OK ] CorrectVelocity/MaxwellTest.CreationWorks/1 (6 ms) 53: [ RUN ] CorrectVelocity/MaxwellTest.CreationWorks/2 53: [ OK ] CorrectVelocity/MaxwellTest.CreationWorks/2 (3 ms) 53: [ RUN ] CorrectVelocity/MaxwellTest.CreationWorks/3 53: [ OK ] CorrectVelocity/MaxwellTest.CreationWorks/3 (6 ms) 53: [ RUN ] CorrectVelocity/MaxwellTest.CreationWorks/4 53: [ OK ] CorrectVelocity/MaxwellTest.CreationWorks/4 (8 ms) 53: [ RUN ] CorrectVelocity/MaxwellTest.CreationWorks/5 53: [ OK ] CorrectVelocity/MaxwellTest.CreationWorks/5 (7 ms) 53: [ RUN ] CorrectVelocity/MaxwellTest.CreationWorks/6 53: [ OK ] CorrectVelocity/MaxwellTest.CreationWorks/6 (4 ms) 53: [ RUN ] CorrectVelocity/MaxwellTest.CreationWorks/7 53: [ OK ] CorrectVelocity/MaxwellTest.CreationWorks/7 (7 ms) 53: [ RUN ] CorrectVelocity/MaxwellTest.CreationWorks/8 53: [ OK ] CorrectVelocity/MaxwellTest.CreationWorks/8 (4 ms) 53: [ RUN ] CorrectVelocity/MaxwellTest.CreationWorks/9 53: [ OK ] CorrectVelocity/MaxwellTest.CreationWorks/9 (7 ms) 53: [ RUN ] CorrectVelocity/MaxwellTest.CreationWorks/10 53: [ OK ] CorrectVelocity/MaxwellTest.CreationWorks/10 (4 ms) 53: [ RUN ] CorrectVelocity/MaxwellTest.CreationWorks/11 53: [ OK ] CorrectVelocity/MaxwellTest.CreationWorks/11 (6 ms) 53: [ RUN ] CorrectVelocity/MaxwellTest.CreationWorks/12 53: [ OK ] CorrectVelocity/MaxwellTest.CreationWorks/12 (4 ms) 53: [ RUN ] CorrectVelocity/MaxwellTest.CreationWorks/13 53: [ OK ] CorrectVelocity/MaxwellTest.CreationWorks/13 (7 ms) 53: [ RUN ] CorrectVelocity/MaxwellTest.CreationWorks/14 53: [ OK ] CorrectVelocity/MaxwellTest.CreationWorks/14 (4 ms) 53: [ RUN ] CorrectVelocity/MaxwellTest.CreationWorks/15 53: [ OK ] CorrectVelocity/MaxwellTest.CreationWorks/15 (7 ms) 53: [----------] 16 tests from CorrectVelocity/MaxwellTest (108 ms total) 53: 53: [----------] 23 tests from CMAPDefinesAndErrors/GromppDirectiveTest 53: [ RUN ] CMAPDefinesAndErrors/GromppDirectiveTest.AcceptValidAndErrorOnInvalidCMAP/0 53: Setting the LD random seed to -951233282 53: 53: Generated 3 of the 3 non-bonded parameter combinations 53: 53: Generated 3 of the 3 1-4 parameter combinations 53: [ OK ] CMAPDefinesAndErrors/GromppDirectiveTest.AcceptValidAndErrorOnInvalidCMAP/0 (47 ms) 53: [ RUN ] CMAPDefinesAndErrors/GromppDirectiveTest.AcceptValidAndErrorOnInvalidCMAP/1 53: Setting the LD random seed to -1687446017 53: [ OK ] CMAPDefinesAndErrors/GromppDirectiveTest.AcceptValidAndErrorOnInvalidCMAP/1 (45 ms) 53: [ RUN ] CMAPDefinesAndErrors/GromppDirectiveTest.AcceptValidAndErrorOnInvalidCMAP/2 53: Ignoring obsolete mdp entry 'title' 53: Generating 1-4 interactions: fudge = 0.5 53: 53: NOTE 1 [file directives-cmap.top, line 114]: 53: In moleculetype 'A' 5 atoms are not bound by a potential or constraint to 53: any other atom in the same moleculetype. Although technically this might 53: not cause issues in a simulation, this often means that the user forgot 53: to add a bond/potential/constraint or put multiple molecules in the same 53: moleculetype definition by mistake. Run with -v to get information for 53: each atom. 53: 53: Number of degrees of freedom in T-Coupling group rest is 12.00 53: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 53: 53: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/CMAPDefinesAndErrors_GromppDirectiveTest_AcceptValidAndErrorOnInvalidCMAP_2_directives-cmap.mdp]: 53: NVE simulation: will use the initial temperature of 300.000 K for 53: determining the Verlet buffer size 53: 53: 53: There were 2 NOTEs 53: Setting the LD random seed to -2134193 53: 53: Generated 3 of the 3 non-bonded parameter combinations 53: 53: Generated 3 of the 3 1-4 parameter combinations 53: 53: Excluding 0 bonded neighbours molecule type 'A' 53: 53: Setting gen_seed to 1533001719 53: 53: Velocities were taken from a Maxwell distribution at 300 K 53: Analysing residue names: 53: There are: 1 Other residues 53: Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups... 53: 53: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 300 K 53: 53: Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm 53: 53: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm 53: 53: Note that mdrun will redetermine rlist based on the actual pair-list setup 53: 53: This run will generate roughly 0 Mb of data 53: [ OK ] CMAPDefinesAndErrors/GromppDirectiveTest.AcceptValidAndErrorOnInvalidCMAP/2 (30 ms) 53: [ RUN ] CMAPDefinesAndErrors/GromppDirectiveTest.AcceptValidAndErrorOnInvalidCMAP/3 53: Ignoring obsolete mdp entry 'title' 53: Generating 1-4 interactions: fudge = 0.5 53: 53: NOTE 1 [file directives-cmap.top, line 114]: 53: In moleculetype 'A' 5 atoms are not bound by a potential or constraint to 53: any other atom in the same moleculetype. Although technically this might 53: not cause issues in a simulation, this often means that the user forgot 53: to add a bond/potential/constraint or put multiple molecules in the same 53: moleculetype definition by mistake. Run with -v to get information for 53: each atom. 53: 53: Number of degrees of freedom in T-Coupling group rest is 12.00 53: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 53: 53: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/CMAPDefinesAndErrors_GromppDirectiveTest_AcceptValidAndErrorOnInvalidCMAP_3_directives-cmap.mdp]: 53: NVE simulation: will use the initial temperature of 300.000 K for 53: determining the Verlet buffer size 53: 53: 53: There were 2 NOTEs 53: Setting the LD random seed to -630481478 53: 53: Generated 3 of the 3 non-bonded parameter combinations 53: 53: Generated 3 of the 3 1-4 parameter combinations 53: 53: Excluding 0 bonded neighbours molecule type 'A' 53: 53: Setting gen_seed to -1026576577 53: 53: Velocities were taken from a Maxwell distribution at 300 K 53: Analysing residue names: 53: There are: 1 Other residues 53: Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups... 53: 53: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 300 K 53: 53: Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm 53: 53: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm 53: 53: Note that mdrun will redetermine rlist based on the actual pair-list setup 53: 53: This run will generate roughly 0 Mb of data 53: [ OK ] CMAPDefinesAndErrors/GromppDirectiveTest.AcceptValidAndErrorOnInvalidCMAP/3 (28 ms) 53: [ RUN ] CMAPDefinesAndErrors/GromppDirectiveTest.AcceptValidAndErrorOnInvalidCMAP/4 53: Ignoring obsolete mdp entry 'title' 53: Generating 1-4 interactions: fudge = 0.5 53: 53: NOTE 1 [file directives-cmap.top, line 114]: 53: In moleculetype 'A' 5 atoms are not bound by a potential or constraint to 53: any other atom in the same moleculetype. Although technically this might 53: not cause issues in a simulation, this often means that the user forgot 53: to add a bond/potential/constraint or put multiple molecules in the same 53: moleculetype definition by mistake. Run with -v to get information for 53: each atom. 53: 53: Number of degrees of freedom in T-Coupling group rest is 12.00 53: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 53: 53: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/CMAPDefinesAndErrors_GromppDirectiveTest_AcceptValidAndErrorOnInvalidCMAP_4_directives-cmap.mdp]: 53: NVE simulation: will use the initial temperature of 300.000 K for 53: determining the Verlet buffer size 53: 53: 53: There were 2 NOTEs 53: Setting the LD random seed to -413428813 53: 53: Generated 3 of the 3 non-bonded parameter combinations 53: 53: Generated 3 of the 3 1-4 parameter combinations 53: 53: Excluding 0 bonded neighbours molecule type 'A' 53: 53: Setting gen_seed to -1962934562 53: 53: Velocities were taken from a Maxwell distribution at 300 K 53: Analysing residue names: 53: There are: 1 Other residues 53: Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups... 53: 53: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 300 K 53: 53: Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm 53: 53: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm 53: 53: Note that mdrun will redetermine rlist based on the actual pair-list setup 53: 53: This run will generate roughly 0 Mb of data 53: [ OK ] CMAPDefinesAndErrors/GromppDirectiveTest.AcceptValidAndErrorOnInvalidCMAP/4 (28 ms) 53: [ RUN ] CMAPDefinesAndErrors/GromppDirectiveTest.AcceptValidAndErrorOnInvalidCMAP/5 53: Ignoring obsolete mdp entry 'title' 53: Generating 1-4 interactions: fudge = 0.5 53: 53: NOTE 1 [file directives-cmap.top, line 114]: 53: In moleculetype 'A' 5 atoms are not bound by a potential or constraint to 53: any other atom in the same moleculetype. Although technically this might 53: not cause issues in a simulation, this often means that the user forgot 53: to add a bond/potential/constraint or put multiple molecules in the same 53: moleculetype definition by mistake. Run with -v to get information for 53: each atom. 53: 53: Number of degrees of freedom in T-Coupling group rest is 12.00 53: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 53: 53: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/CMAPDefinesAndErrors_GromppDirectiveTest_AcceptValidAndErrorOnInvalidCMAP_5_directives-cmap.mdp]: 53: NVE simulation: will use the initial temperature of 300.000 K for 53: determining the Verlet buffer size 53: 53: 53: There were 2 NOTEs 53: Setting the LD random seed to -71320073 53: 53: Generated 3 of the 3 non-bonded parameter combinations 53: 53: Generated 3 of the 3 1-4 parameter combinations 53: 53: Excluding 0 bonded neighbours molecule type 'A' 53: 53: Setting gen_seed to -1087702037 53: 53: Velocities were taken from a Maxwell distribution at 300 K 53: Analysing residue names: 53: There are: 1 Other residues 53: Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups... 53: 53: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 300 K 53: 53: Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm 53: 53: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm 53: 53: Note that mdrun will redetermine rlist based on the actual pair-list setup 53: 53: This run will generate roughly 0 Mb of data 53: [ OK ] CMAPDefinesAndErrors/GromppDirectiveTest.AcceptValidAndErrorOnInvalidCMAP/5 (29 ms) 53: [ RUN ] CMAPDefinesAndErrors/GromppDirectiveTest.AcceptValidAndErrorOnInvalidCMAP/6 53: Setting the LD random seed to -1141432545 53: [ OK ] CMAPDefinesAndErrors/GromppDirectiveTest.AcceptValidAndErrorOnInvalidCMAP/6 (48 ms) 53: [ RUN ] CMAPDefinesAndErrors/GromppDirectiveTest.AcceptValidAndErrorOnInvalidCMAP/7 53: Setting the LD random seed to -56887297 53: 53: Generated 3 of the 3 non-bonded parameter combinations 53: 53: Generated 3 of the 3 1-4 parameter combinations 53: 53: Excluding 0 bonded neighbours molecule type 'A' 53: 53: Setting gen_seed to -573055489 53: 53: Velocities were taken from a Maxwell distribution at 300 K 53: [ OK ] CMAPDefinesAndErrors/GromppDirectiveTest.AcceptValidAndErrorOnInvalidCMAP/7 (51 ms) 53: [ RUN ] CMAPDefinesAndErrors/GromppDirectiveTest.AcceptValidAndErrorOnInvalidCMAP/8 53: Setting the LD random seed to -1076986181 53: [ OK ] CMAPDefinesAndErrors/GromppDirectiveTest.AcceptValidAndErrorOnInvalidCMAP/8 (43 ms) 53: [ RUN ] CMAPDefinesAndErrors/GromppDirectiveTest.AcceptValidAndErrorOnInvalidCMAP/9 53: Setting the LD random seed to -67960851 53: 53: Generated 3 of the 3 non-bonded parameter combinations 53: 53: Generated 3 of the 3 1-4 parameter combinations 53: 53: Excluding 0 bonded neighbours molecule type 'A' 53: 53: Setting gen_seed to -87097537 53: 53: Velocities were taken from a Maxwell distribution at 300 K 53: [ OK ] CMAPDefinesAndErrors/GromppDirectiveTest.AcceptValidAndErrorOnInvalidCMAP/9 (49 ms) 53: [ RUN ] CMAPDefinesAndErrors/GromppDirectiveTest.AcceptValidAndErrorOnInvalidCMAP/10 53: Setting the LD random seed to 2088173406 53: 53: Generated 3 of the 3 non-bonded parameter combinations 53: 53: Generated 3 of the 3 1-4 parameter combinations 53: 53: Excluding 0 bonded neighbours molecule type 'A' 53: 53: Setting gen_seed to -1212973441 53: 53: Velocities were taken from a Maxwell distribution at 300 K 53: [ OK ] CMAPDefinesAndErrors/GromppDirectiveTest.AcceptValidAndErrorOnInvalidCMAP/10 (55 ms) 53: [ RUN ] CMAPDefinesAndErrors/GromppDirectiveTest.AcceptValidAndErrorOnInvalidCMAP/11 53: Setting the LD random seed to -480413699 53: 53: Generated 3 of the 3 non-bonded parameter combinations 53: 53: Generated 3 of the 3 1-4 parameter combinations 53: 53: Excluding 0 bonded neighbours molecule type 'A' 53: 53: Setting gen_seed to -534817 53: 53: Velocities were taken from a Maxwell distribution at 300 K 53: [ OK ] CMAPDefinesAndErrors/GromppDirectiveTest.AcceptValidAndErrorOnInvalidCMAP/11 (50 ms) 53: [ RUN ] CMAPDefinesAndErrors/GromppDirectiveTest.AcceptValidAndErrorOnInvalidCMAP/12 53: Setting the LD random seed to 1541926911 53: 53: Generated 3 of the 3 non-bonded parameter combinations 53: 53: Generated 3 of the 3 1-4 parameter combinations 53: 53: Excluding 0 bonded neighbours molecule type 'A' 53: 53: Setting gen_seed to -1477542065 53: 53: Velocities were taken from a Maxwell distribution at 300 K 53: [ OK ] CMAPDefinesAndErrors/GromppDirectiveTest.AcceptValidAndErrorOnInvalidCMAP/12 (50 ms) 53: [ RUN ] CMAPDefinesAndErrors/GromppDirectiveTest.AcceptValidAndErrorOnInvalidCMAP/13 53: Setting the LD random seed to 1740232367 53: 53: Generated 3 of the 3 non-bonded parameter combinations 53: 53: Generated 3 of the 3 1-4 parameter combinations 53: 53: Excluding 0 bonded neighbours molecule type 'A' 53: 53: Setting gen_seed to -157714 53: 53: Velocities were taken from a Maxwell distribution at 300 K 53: [ OK ] CMAPDefinesAndErrors/GromppDirectiveTest.AcceptValidAndErrorOnInvalidCMAP/13 (50 ms) 53: [ RUN ] CMAPDefinesAndErrors/GromppDirectiveTest.AcceptValidAndErrorOnInvalidCMAP/14 53: Setting the LD random seed to -1050645 53: 53: Generated 3 of the 3 non-bonded parameter combinations 53: 53: Generated 3 of the 3 1-4 parameter combinations 53: 53: Excluding 0 bonded neighbours molecule type 'A' 53: 53: Setting gen_seed to -33850452 53: 53: Velocities were taken from a Maxwell distribution at 300 K 53: [ OK ] CMAPDefinesAndErrors/GromppDirectiveTest.AcceptValidAndErrorOnInvalidCMAP/14 (50 ms) 53: [ RUN ] CMAPDefinesAndErrors/GromppDirectiveTest.AcceptValidAndErrorOnInvalidCMAP/15 53: Setting the LD random seed to -319029617 53: 53: Generated 3 of the 3 non-bonded parameter combinations 53: 53: Generated 3 of the 3 1-4 parameter combinations 53: 53: Excluding 0 bonded neighbours molecule type 'A' 53: 53: Setting gen_seed to -33 53: 53: Velocities were taken from a Maxwell distribution at 300 K 53: [ OK ] CMAPDefinesAndErrors/GromppDirectiveTest.AcceptValidAndErrorOnInvalidCMAP/15 (47 ms) 53: [ RUN ] CMAPDefinesAndErrors/GromppDirectiveTest.AcceptValidAndErrorOnInvalidCMAP/16 53: Ignoring obsolete mdp entry 'title' 53: Generating 1-4 interactions: fudge = 0.5 53: 53: NOTE 1 [file directives-cmap.top, line 114]: 53: In moleculetype 'A' 5 atoms are not bound by a potential or constraint to 53: any other atom in the same moleculetype. Although technically this might 53: not cause issues in a simulation, this often means that the user forgot 53: to add a bond/potential/constraint or put multiple molecules in the same 53: moleculetype definition by mistake. Run with -v to get information for 53: each atom. 53: 53: Number of degrees of freedom in T-Coupling group rest is 12.00 53: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 53: 53: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/CMAPDefinesAndErrors_GromppDirectiveTest_AcceptValidAndErrorOnInvalidCMAP_16_directives-cmap.mdp]: 53: NVE simulation: will use the initial temperature of 300.000 K for 53: determining the Verlet buffer size 53: 53: 53: There were 2 NOTEs 53: Setting the LD random seed to -615711907 53: 53: Generated 3 of the 3 non-bonded parameter combinations 53: 53: Generated 3 of the 3 1-4 parameter combinations 53: 53: Excluding 0 bonded neighbours molecule type 'A' 53: 53: Setting gen_seed to -607331081 53: 53: Velocities were taken from a Maxwell distribution at 300 K 53: Analysing residue names: 53: There are: 1 Other residues 53: Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups... 53: 53: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 300 K 53: 53: Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm 53: 53: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm 53: 53: Note that mdrun will redetermine rlist based on the actual pair-list setup 53: 53: This run will generate roughly 0 Mb of data 53: [ OK ] CMAPDefinesAndErrors/GromppDirectiveTest.AcceptValidAndErrorOnInvalidCMAP/16 (42 ms) 53: [ RUN ] CMAPDefinesAndErrors/GromppDirectiveTest.AcceptValidAndErrorOnInvalidCMAP/17 53: Ignoring obsolete mdp entry 'title' 53: Generating 1-4 interactions: fudge = 0.5 53: 53: NOTE 1 [file directives-cmap.top, line 114]: 53: In moleculetype 'A' 5 atoms are not bound by a potential or constraint to 53: any other atom in the same moleculetype. Although technically this might 53: not cause issues in a simulation, this often means that the user forgot 53: to add a bond/potential/constraint or put multiple molecules in the same 53: moleculetype definition by mistake. Run with -v to get information for 53: each atom. 53: 53: Number of degrees of freedom in T-Coupling group rest is 12.00 53: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 53: 53: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/CMAPDefinesAndErrors_GromppDirectiveTest_AcceptValidAndErrorOnInvalidCMAP_17_directives-cmap.mdp]: 53: NVE simulation: will use the initial temperature of 300.000 K for 53: determining the Verlet buffer size 53: 53: 53: There were 2 NOTEs 53: Setting the LD random seed to -1719722138 53: 53: Generated 3 of the 3 non-bonded parameter combinations 53: 53: Generated 3 of the 3 1-4 parameter combinations 53: 53: Excluding 0 bonded neighbours molecule type 'A' 53: 53: Setting gen_seed to 2147416509 53: 53: Velocities were taken from a Maxwell distribution at 300 K 53: Analysing residue names: 53: There are: 1 Other residues 53: Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups... 53: 53: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 300 K 53: 53: Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm 53: 53: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm 53: 53: Note that mdrun will redetermine rlist based on the actual pair-list setup 53: 53: This run will generate roughly 0 Mb of data 53: [ OK ] CMAPDefinesAndErrors/GromppDirectiveTest.AcceptValidAndErrorOnInvalidCMAP/17 (34 ms) 53: [ RUN ] CMAPDefinesAndErrors/GromppDirectiveTest.AcceptValidAndErrorOnInvalidCMAP/18 53: Setting the LD random seed to -33849411 53: 53: Generated 3 of the 3 non-bonded parameter combinations 53: 53: Generated 3 of the 3 1-4 parameter combinations 53: [ OK ] CMAPDefinesAndErrors/GromppDirectiveTest.AcceptValidAndErrorOnInvalidCMAP/18 (42 ms) 53: [ RUN ] CMAPDefinesAndErrors/GromppDirectiveTest.AcceptValidAndErrorOnInvalidCMAP/19 53: Setting the LD random seed to -1074003974 53: 53: Generated 3 of the 3 non-bonded parameter combinations 53: 53: Generated 3 of the 3 1-4 parameter combinations 53: 53: Excluding 0 bonded neighbours molecule type 'A' 53: 53: Setting gen_seed to -153616390 53: 53: Velocities were taken from a Maxwell distribution at 300 K 53: Analysing residue names: 53: There are: 1 Other residues 53: Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups... 53: 53: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 300 K 53: 53: Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm 53: 53: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm 53: 53: Note that mdrun will redetermine rlist based on the actual pair-list setup 53: 53: This run will generate roughly 0 Mb of data 53: [ OK ] CMAPDefinesAndErrors/GromppDirectiveTest.AcceptValidAndErrorOnInvalidCMAP/19 (49 ms) 53: [ RUN ] CMAPDefinesAndErrors/GromppDirectiveTest.AcceptValidAndErrorOnInvalidCMAP/20 53: Setting the LD random seed to -268705798 53: 53: Generated 3 of the 3 non-bonded parameter combinations 53: 53: Generated 3 of the 3 1-4 parameter combinations 53: [ OK ] CMAPDefinesAndErrors/GromppDirectiveTest.AcceptValidAndErrorOnInvalidCMAP/20 (44 ms) 53: [ RUN ] CMAPDefinesAndErrors/GromppDirectiveTest.AcceptValidAndErrorOnInvalidCMAP/21 53: Ignoring obsolete mdp entry 'title' 53: Generating 1-4 interactions: fudge = 0.5 53: 53: NOTE 1 [file directives-cmap.top, line 114]: 53: In moleculetype 'A' 5 atoms are not bound by a potential or constraint to 53: any other atom in the same moleculetype. Although technically this might 53: not cause issues in a simulation, this often means that the user forgot 53: to add a bond/potential/constraint or put multiple molecules in the same 53: moleculetype definition by mistake. Run with -v to get information for 53: each atom. 53: 53: Number of degrees of freedom in T-Coupling group rest is 12.00 53: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 53: 53: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/CMAPDefinesAndErrors_GromppDirectiveTest_AcceptValidAndErrorOnInvalidCMAP_21_directives-cmap.mdp]: 53: NVE simulation: will use the initial temperature of 300.000 K for 53: determining the Verlet buffer size 53: 53: 53: There were 2 NOTEs 53: Setting the LD random seed to -51203 53: 53: Generated 3 of the 3 non-bonded parameter combinations 53: 53: Generated 3 of the 3 1-4 parameter combinations 53: 53: Excluding 0 bonded neighbours molecule type 'A' 53: 53: Setting gen_seed to -25430725 53: 53: Velocities were taken from a Maxwell distribution at 300 K 53: Analysing residue names: 53: There are: 1 Other residues 53: Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups... 53: 53: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 300 K 53: 53: Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm 53: 53: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm 53: 53: Note that mdrun will redetermine rlist based on the actual pair-list setup 53: 53: This run will generate roughly 0 Mb of data 53: [ OK ] CMAPDefinesAndErrors/GromppDirectiveTest.AcceptValidAndErrorOnInvalidCMAP/21 (35 ms) 53: [ RUN ] CMAPDefinesAndErrors/GromppDirectiveTest.AcceptValidAndErrorOnInvalidCMAP/22 53: Setting the LD random seed to -67158041 53: 53: Generated 3 of the 3 non-bonded parameter combinations 53: 53: Generated 3 of the 3 1-4 parameter combinations 53: [ OK ] CMAPDefinesAndErrors/GromppDirectiveTest.AcceptValidAndErrorOnInvalidCMAP/22 (47 ms) 53: [----------] 23 tests from CMAPDefinesAndErrors/GromppDirectiveTest (1005 ms total) 53: 53: [----------] Global test environment tear-down 53: [==========] 215 tests from 15 test suites ran. (14713 ms total) 53: [ PASSED ] 175 tests. 53: [ SKIPPED ] 40 tests, listed below: 53: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/GB_1_2_Pol_ 53: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/GB_1_3_Pol_ 53: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/GB_1_4_Pol_ 53: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/GB_Polariz_ 53: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/Nonpolar_Sol_ 53: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/Coulomb_14 53: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/LJ__SR_ 53: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/Buck_ham__SR_ 53: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/LJ 53: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/B_ham 53: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/Disper__corr_ 53: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/Coulomb__SR_ 53: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/Coul 53: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/RF_excl_ 53: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/Coul__recip_ 53: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/LJ_recip_ 53: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/DPD 53: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/D_R_Viol___nm_ 53: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/Ori__R__RMSD 53: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/Dih__Rest__Vi_ 53: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/COM_Pull_En_ 53: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/Dens__fitting 53: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/Quantum_En_ 53: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/NN_Potential 53: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/Potential 53: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/Kinetic_En_ 53: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/Total_Energy 53: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/Conserved_En_ 53: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/Temperature 53: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/Vir__Temp_ 53: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/Pres__DC 53: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/Pressure 53: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/dH_dl_constr_ 53: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/dVremain_dl 53: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/dEkin_dl 53: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/dVcoul_dl 53: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/dVvdw_dl 53: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/dVbonded_dl 53: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/dVrestraint_dl 53: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/dVtemp_dl 53/92 Test #53: GmxPreprocessTests ........................ Passed 14.85 sec test 54 Start 54: Pdb2gmx1Test 54: Test command: /build/reproducible-path/gromacs-2025.1/build/basic-dp/bin/pdb2gmx1-test "--gtest_output=xml:/build/reproducible-path/gromacs-2025.1/build/basic-dp/Testing/Temporary/Pdb2gmx1Test.xml" 54: Working Directory: /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/gmxpreprocess/tests 54: Test timeout computed to be: 1920 54: [==========] Running 30 tests from 1 test suite. 54: [----------] Global test environment set-up. 54: [----------] 30 tests from Oplsaa/Pdb2gmxTest 54: [ RUN ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip3p_vsite_none_id_or_ter_merge_no_Apdb_format_gro_match_file 54: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/oplsaa.ff/aminoacids.r2b 54: All occupancies are one 54: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/oplsaa.ff/atomtypes.atp 54: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/oplsaa.ff/aminoacids.rtp 54: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/oplsaa.ff/aminoacids.hdb 54: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/oplsaa.ff/aminoacids.n.tdb 54: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/oplsaa.ff/aminoacids.c.tdb 54: Analysing hydrogen-bonding network for automated assignment of histidine 54: protonation. 25 donors and 23 acceptors were found. 54: There are 41 hydrogen bonds 54: Will use HISE for residue 8 54: 9 out of 9 lines of specbond.dat converted successfully 54: Special Atom Distance matrix: 54: CYS3 HIS8 54: SG9 NE251 54: HIS8 NE251 1.055 54: MET12 SD83 0.763 0.990 54: Before cleaning: 653 pairs 54: Before cleaning: 663 dihedrals 54: Using the Oplsaa force field in directory oplsaa.ff 54: 54: going to rename oplsaa.ff/aminoacids.r2b 54: Reading /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/A.pdb... 54: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms 54: 54: Analyzing pdb file 54: Splitting chemical chains based on TER records or chain id changing. 54: 54: There are 1 chains and 0 blocks of water and 16 residues with 128 atoms 54: 54: chain #res #atoms 54: 54: 1 ' ' 16 128 54: 54: All occupancies are one 54: 54: Reading residue database... (Oplsaa) 54: 54: Processing chain 1 (128 atoms, 16 residues) 54: 54: Identified residue ALA2 as a starting terminus. 54: 54: Identified residue SER17 as a ending terminus. 54: Start terminus ALA-2: NH3+ 54: End terminus SER-17: COO- 54: 54: Checking for duplicate atoms.... 54: 54: Generating any missing hydrogen atoms and/or adding termini. 54: 54: Now there are 16 residues with 252 atoms 54: 54: Making bonds... 54: 54: Number of bonds was 254, now 254 54: 54: Generating angles, dihedrals and pairs... 54: 54: Making cmap torsions... 54: 54: There are 663 dihedrals, 51 impropers, 457 angles 54: 650 pairs, 254 bonds and 0 virtual sites 54: 54: Total mass 1846.112 a.m.u. 54: 54: Total charge 0.000 e 54: 54: Writing topology 54: 54: Writing coordinate file... 54: 54: --------- PLEASE NOTE ------------ 54: 54: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/A.pdb. 54: 54: The Oplsaa force field and the tip3p water model are used. 54: 54: --------- ETON ESAELP ------------ 54: [ OK ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip3p_vsite_none_id_or_ter_merge_no_Apdb_format_gro_match_file (206 ms) 54: [ RUN ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip3p_vsite_none_id_or_ter_merge_no_Bpdb_format_gro_match_file 54: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/oplsaa.ff/aminoacids.r2b 54: All occupancies are one 54: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/oplsaa.ff/atomtypes.atp 54: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/oplsaa.ff/aminoacids.rtp 54: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/oplsaa.ff/aminoacids.hdb 54: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/oplsaa.ff/aminoacids.n.tdb 54: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/oplsaa.ff/aminoacids.c.tdb 54: Analysing hydrogen-bonding network for automated assignment of histidine 54: protonation. 30 donors and 22 acceptors were found. 54: There are 36 hydrogen bonds 54: Will use HISE for residue 29 54: Will use HISE for residue 32 54: 9 out of 9 lines of specbond.dat converted successfully 54: Special Atom Distance matrix: 54: CYS27 HIS29 54: SG90 NE2111 54: HIS29 NE2111 0.987 54: HIS32 NE2135 1.590 1.155 54: Before cleaning: 748 pairs 54: Before cleaning: 778 dihedrals 54: Using the Oplsaa force field in directory oplsaa.ff 54: 54: going to rename oplsaa.ff/aminoacids.r2b 54: Reading /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/B.pdb... 54: Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms 54: 54: Analyzing pdb file 54: Splitting chemical chains based on TER records or chain id changing. 54: 54: There are 1 chains and 0 blocks of water and 16 residues with 149 atoms 54: 54: chain #res #atoms 54: 54: 1 ' ' 16 149 54: 54: All occupancies are one 54: 54: Reading residue database... (Oplsaa) 54: 54: Processing chain 1 (149 atoms, 16 residues) 54: 54: Replaced 1 residue named GLUH to the default GLU. Use interactive selection of protonated residues if that is what you need. 54: 54: Identified residue THR18 as a starting terminus. 54: 54: Identified residue PHE33 as a ending terminus. 54: Start terminus THR-18: NH3+ 54: End terminus PHE-33: COO- 54: 54: Checking for duplicate atoms.... 54: 54: Generating any missing hydrogen atoms and/or adding termini. 54: 54: Now there are 16 residues with 281 atoms 54: 54: Making bonds... 54: 54: Number of bonds was 290, now 290 54: 54: Generating angles, dihedrals and pairs... 54: 54: Making cmap torsions... 54: 54: There are 778 dihedrals, 72 impropers, 516 angles 54: 736 pairs, 290 bonds and 0 virtual sites 54: 54: Total mass 2088.357 a.m.u. 54: 54: Total charge 1.000 e 54: 54: Writing topology 54: 54: Writing coordinate file... 54: 54: --------- PLEASE NOTE ------------ 54: 54: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/B.pdb. 54: 54: The Oplsaa force field and the tip3p water model are used. 54: 54: --------- ETON ESAELP ------------ 54: [ OK ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip3p_vsite_none_id_or_ter_merge_no_Bpdb_format_gro_match_file (221 ms) 54: [ RUN ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip3p_vsite_none_id_or_ter_merge_no_Cpdb_format_gro_match_file 54: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/oplsaa.ff/aminoacids.r2b 54: All occupancies are one 54: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/oplsaa.ff/atomtypes.atp 54: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/oplsaa.ff/aminoacids.rtp 54: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/oplsaa.ff/aminoacids.hdb 54: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/oplsaa.ff/aminoacids.n.tdb 54: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/oplsaa.ff/aminoacids.c.tdb 54: Analysing hydrogen-bonding network for automated assignment of histidine 54: protonation. 22 donors and 22 acceptors were found. 54: There are 26 hydrogen bonds 54: Will use HISE for residue 45 54: 9 out of 9 lines of specbond.dat converted successfully 54: Special Atom Distance matrix: 54: HIS45 54: NE295 54: MET46 SD102 1.078 54: Before cleaning: 676 pairs 54: Before cleaning: 696 dihedrals 54: Using the Oplsaa force field in directory oplsaa.ff 54: 54: going to rename oplsaa.ff/aminoacids.r2b 54: Reading /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/C.pdb... 54: Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms 54: 54: Analyzing pdb file 54: Splitting chemical chains based on TER records or chain id changing. 54: 54: There are 1 chains and 0 blocks of water and 16 residues with 132 atoms 54: 54: chain #res #atoms 54: 54: 1 ' ' 16 132 54: 54: All occupancies are one 54: 54: Reading residue database... (Oplsaa) 54: 54: Processing chain 1 (132 atoms, 16 residues) 54: 54: Identified residue ALA34 as a starting terminus. 54: 54: Identified residue ALA49 as a ending terminus. 54: Start terminus ALA-34: NH3+ 54: End terminus ALA-49: COO- 54: 54: Checking for duplicate atoms.... 54: 54: Generating any missing hydrogen atoms and/or adding termini. 54: 54: Now there are 16 residues with 255 atoms 54: 54: Making bonds... 54: 54: Number of bonds was 261, now 261 54: 54: Generating angles, dihedrals and pairs... 54: 54: Making cmap torsions... 54: 54: There are 696 dihedrals, 56 impropers, 472 angles 54: 667 pairs, 261 bonds and 0 virtual sites 54: 54: Total mass 1861.128 a.m.u. 54: 54: Total charge -1.000 e 54: 54: Writing topology 54: 54: Writing coordinate file... 54: 54: --------- PLEASE NOTE ------------ 54: 54: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/C.pdb. 54: 54: The Oplsaa force field and the tip3p water model are used. 54: 54: --------- ETON ESAELP ------------ 54: [ OK ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip3p_vsite_none_id_or_ter_merge_no_Cpdb_format_gro_match_file (205 ms) 54: [ RUN ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip3p_vsite_none_id_or_ter_merge_no_Dpdb_format_gro_match_file 54: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/oplsaa.ff/aminoacids.r2b 54: All occupancies are one 54: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/oplsaa.ff/atomtypes.atp 54: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/oplsaa.ff/aminoacids.rtp 54: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/oplsaa.ff/aminoacids.hdb 54: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/oplsaa.ff/aminoacids.n.tdb 54: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/oplsaa.ff/aminoacids.c.tdb 54: Analysing hydrogen-bonding network for automated assignment of histidine 54: protonation. 22 donors and 21 acceptors were found. 54: There are 30 hydrogen bonds 54: Will use HISE for residue 60 54: 9 out of 9 lines of specbond.dat converted successfully 54: Special Atom Distance matrix: 54: HIS60 54: NE285 54: CYS62 SG98 0.803 54: Before cleaning: 603 pairs 54: Before cleaning: 618 dihedrals 54: Using the Oplsaa force field in directory oplsaa.ff 54: 54: going to rename oplsaa.ff/aminoacids.r2b 54: Reading /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/D.pdb... 54: Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms 54: 54: Analyzing pdb file 54: Splitting chemical chains based on TER records or chain id changing. 54: 54: There are 1 chains and 0 blocks of water and 16 residues with 117 atoms 54: 54: chain #res #atoms 54: 54: 1 ' ' 16 117 54: 54: All occupancies are one 54: 54: Reading residue database... (Oplsaa) 54: 54: Processing chain 1 (117 atoms, 16 residues) 54: 54: Replaced 1 residue named ASPH to the default ASP. Use interactive selection of protonated residues if that is what you need. 54: 54: Identified residue LYS50 as a starting terminus. 54: 54: Identified residue PRO65 as a ending terminus. 54: Start terminus LYS-50: NH3+ 54: End terminus PRO-65: PRO-COO- 54: 54: Checking for duplicate atoms.... 54: 54: Generating any missing hydrogen atoms and/or adding termini. 54: 54: Now there are 16 residues with 228 atoms 54: 54: Making bonds... 54: 54: Number of bonds was 232, now 232 54: 54: Generating angles, dihedrals and pairs... 54: 54: Making cmap torsions... 54: 54: There are 618 dihedrals, 48 impropers, 419 angles 54: 597 pairs, 232 bonds and 0 virtual sites 54: 54: Total mass 1662.883 a.m.u. 54: 54: Total charge 0.000 e 54: 54: Writing topology 54: 54: Writing coordinate file... 54: 54: --------- PLEASE NOTE ------------ 54: 54: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/D.pdb. 54: 54: The Oplsaa force field and the tip3p water model are used. 54: 54: --------- ETON ESAELP ------------ 54: [ OK ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip3p_vsite_none_id_or_ter_merge_no_Dpdb_format_gro_match_file (189 ms) 54: [ RUN ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip3p_vsite_none_id_or_ter_merge_no_Epdb_format_gro_match_file 54: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/oplsaa.ff/aminoacids.r2b 54: All occupancies are one 54: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/oplsaa.ff/atomtypes.atp 54: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/oplsaa.ff/aminoacids.rtp 54: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/oplsaa.ff/aminoacids.hdb 54: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/oplsaa.ff/aminoacids.n.tdb 54: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/oplsaa.ff/aminoacids.c.tdb 54: Analysing hydrogen-bonding network for automated assignment of histidine 54: protonation. 89 donors and 98 acceptors were found. 54: There are 129 hydrogen bonds 54: Will use HISE for residue 31 54: Will use HISE for residue 51 54: 9 out of 9 lines of specbond.dat converted successfully 54: Special Atom Distance matrix: 54: CYS25 HIS31 HIS51 54: SG14 NE264 NE2226 54: HIS31 NE264 1.921 54: HIS51 NE2226 1.498 2.650 54: CYS80 SG477 0.207 1.984 1.570 54: Linking CYS-25 SG-14 and CYS-80 SG-477... 54: Before cleaning: 2499 pairs 54: Before cleaning: 2524 dihedrals 54: Using the Oplsaa force field in directory oplsaa.ff 54: 54: going to rename oplsaa.ff/aminoacids.r2b 54: Reading /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/E.pdb... 54: Read 'This is a fragment of 2d4f for testing a disulfide bridge', 488 atoms 54: 54: Analyzing pdb file 54: Splitting chemical chains based on TER records or chain id changing. 54: 54: There are 1 chains and 0 blocks of water and 58 residues with 488 atoms 54: 54: chain #res #atoms 54: 54: 1 'A' 58 488 54: 54: All occupancies are one 54: 54: Reading residue database... (Oplsaa) 54: 54: Processing chain 1 'A' (488 atoms, 58 residues) 54: 54: Identified residue ASN24 as a starting terminus. 54: 54: Identified residue ARG81 as a ending terminus. 54: Start terminus ASN-24: NH3+ 54: End terminus ARG-81: COO- 54: 54: Checking for duplicate atoms.... 54: 54: Generating any missing hydrogen atoms and/or adding termini. 54: 54: Now there are 58 residues with 936 atoms 54: 54: Making bonds... 54: 54: Number of bonds was 951, now 951 54: 54: Generating angles, dihedrals and pairs... 54: 54: Making cmap torsions... 54: 54: There are 2524 dihedrals, 208 impropers, 1704 angles 54: 2469 pairs, 951 bonds and 0 virtual sites 54: 54: Total mass 6908.578 a.m.u. 54: 54: Total charge -6.000 e 54: 54: Writing topology 54: 54: Writing coordinate file... 54: 54: --------- PLEASE NOTE ------------ 54: 54: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/E.pdb. 54: 54: The Oplsaa force field and the tip3p water model are used. 54: 54: --------- ETON ESAELP ------------ 54: [ OK ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip3p_vsite_none_id_or_ter_merge_no_Epdb_format_gro_match_file (618 ms) 54: [ RUN ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip3p_vsite_h_id_or_ter_merge_no_Apdb_format_gro_match_file 54: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/oplsaa.ff/aminoacids.r2b 54: All occupancies are one 54: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/oplsaa.ff/atomtypes.atp 54: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/oplsaa.ff/aminoacids.rtp 54: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/oplsaa.ff/aminoacids.hdb 54: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/oplsaa.ff/aminoacids.n.tdb 54: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/oplsaa.ff/aminoacids.c.tdb 54: Analysing hydrogen-bonding network for automated assignment of histidine 54: protonation. 25 donors and 23 acceptors were found. 54: There are 41 hydrogen bonds 54: Will use HISE for residue 8 54: 9 out of 9 lines of specbond.dat converted successfully 54: Special Atom Distance matrix: 54: CYS3 HIS8 54: SG9 NE251 54: HIS8 NE251 1.055 54: MET12 SD83 0.763 0.990 54: Marked 124 virtual sites 54: Added 16 dummy masses 54: Added 26 new constraints 54: Before cleaning: 653 pairs 54: Before cleaning: 663 dihedrals 54: Using the Oplsaa force field in directory oplsaa.ff 54: 54: going to rename oplsaa.ff/aminoacids.r2b 54: Reading /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/A.pdb... 54: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms 54: 54: Analyzing pdb file 54: Splitting chemical chains based on TER records or chain id changing. 54: 54: There are 1 chains and 0 blocks of water and 16 residues with 128 atoms 54: 54: chain #res #atoms 54: 54: 1 ' ' 16 128 54: 54: All occupancies are one 54: 54: Reading residue database... (Oplsaa) 54: 54: Processing chain 1 (128 atoms, 16 residues) 54: 54: Identified residue ALA2 as a starting terminus. 54: 54: Identified residue SER17 as a ending terminus. 54: Start terminus ALA-2: NH3+ 54: End terminus SER-17: COO- 54: 54: Checking for duplicate atoms.... 54: 54: Generating any missing hydrogen atoms and/or adding termini. 54: 54: Now there are 16 residues with 252 atoms 54: 54: Making bonds... 54: 54: Number of bonds was 254, now 254 54: 54: Generating angles, dihedrals and pairs... 54: 54: Making cmap torsions... 54: 54: There are 663 dihedrals, 51 impropers, 457 angles 54: 650 pairs, 254 bonds and 130 virtual sites 54: 54: Total mass 1846.112 a.m.u. 54: 54: Total charge 0.000 e 54: 54: Writing topology 54: 54: Writing coordinate file... 54: 54: --------- PLEASE NOTE ------------ 54: 54: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/A.pdb. 54: 54: The Oplsaa force field and the tip3p water model are used. 54: 54: --------- ETON ESAELP ------------ 54: [ OK ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip3p_vsite_h_id_or_ter_merge_no_Apdb_format_gro_match_file (221 ms) 54: [ RUN ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip3p_vsite_h_id_or_ter_merge_no_Bpdb_format_gro_match_file 54: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/oplsaa.ff/aminoacids.r2b 54: All occupancies are one 54: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/oplsaa.ff/atomtypes.atp 54: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/oplsaa.ff/aminoacids.rtp 54: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/oplsaa.ff/aminoacids.hdb 54: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/oplsaa.ff/aminoacids.n.tdb 54: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/oplsaa.ff/aminoacids.c.tdb 54: Analysing hydrogen-bonding network for automated assignment of histidine 54: protonation. 30 donors and 22 acceptors were found. 54: There are 36 hydrogen bonds 54: Will use HISE for residue 29 54: Will use HISE for residue 32 54: 9 out of 9 lines of specbond.dat converted successfully 54: Special Atom Distance matrix: 54: CYS27 HIS29 54: SG90 NE2111 54: HIS29 NE2111 0.987 54: HIS32 NE2135 1.590 1.155 54: Marked 132 virtual sites 54: Added 10 dummy masses 54: Added 19 new constraints 54: Before cleaning: 748 pairs 54: Before cleaning: 778 dihedrals 54: Using the Oplsaa force field in directory oplsaa.ff 54: 54: going to rename oplsaa.ff/aminoacids.r2b 54: Reading /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/B.pdb... 54: Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms 54: 54: Analyzing pdb file 54: Splitting chemical chains based on TER records or chain id changing. 54: 54: There are 1 chains and 0 blocks of water and 16 residues with 149 atoms 54: 54: chain #res #atoms 54: 54: 1 ' ' 16 149 54: 54: All occupancies are one 54: 54: Reading residue database... (Oplsaa) 54: 54: Processing chain 1 (149 atoms, 16 residues) 54: 54: Replaced 1 residue named GLUH to the default GLU. Use interactive selection of protonated residues if that is what you need. 54: 54: Identified residue THR18 as a starting terminus. 54: 54: Identified residue PHE33 as a ending terminus. 54: Start terminus THR-18: NH3+ 54: End terminus PHE-33: COO- 54: 54: Checking for duplicate atoms.... 54: 54: Generating any missing hydrogen atoms and/or adding termini. 54: 54: Now there are 16 residues with 281 atoms 54: 54: Making bonds... 54: 54: Number of bonds was 290, now 290 54: 54: Generating angles, dihedrals and pairs... 54: 54: Making cmap torsions... 54: 54: There are 778 dihedrals, 72 impropers, 516 angles 54: 736 pairs, 290 bonds and 133 virtual sites 54: 54: Total mass 2088.357 a.m.u. 54: 54: Total charge 1.000 e 54: 54: Writing topology 54: 54: Writing coordinate file... 54: 54: --------- PLEASE NOTE ------------ 54: 54: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/B.pdb. 54: 54: The Oplsaa force field and the tip3p water model are used. 54: 54: --------- ETON ESAELP ------------ 54: [ OK ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip3p_vsite_h_id_or_ter_merge_no_Bpdb_format_gro_match_file (251 ms) 54: [ RUN ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip3p_vsite_h_id_or_ter_merge_no_Cpdb_format_gro_match_file 54: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/oplsaa.ff/aminoacids.r2b 54: All occupancies are one 54: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/oplsaa.ff/atomtypes.atp 54: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/oplsaa.ff/aminoacids.rtp 54: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/oplsaa.ff/aminoacids.hdb 54: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/oplsaa.ff/aminoacids.n.tdb 54: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/oplsaa.ff/aminoacids.c.tdb 54: Analysing hydrogen-bonding network for automated assignment of histidine 54: protonation. 22 donors and 22 acceptors were found. 54: There are 26 hydrogen bonds 54: Will use HISE for residue 45 54: 9 out of 9 lines of specbond.dat converted successfully 54: Special Atom Distance matrix: 54: HIS45 54: NE295 54: MET46 SD102 1.078 54: Marked 123 virtual sites 54: Added 22 dummy masses 54: Added 35 new constraints 54: Before cleaning: 676 pairs 54: Before cleaning: 696 dihedrals 54: Using the Oplsaa force field in directory oplsaa.ff 54: 54: going to rename oplsaa.ff/aminoacids.r2b 54: Reading /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/C.pdb... 54: Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms 54: 54: Analyzing pdb file 54: Splitting chemical chains based on TER records or chain id changing. 54: 54: There are 1 chains and 0 blocks of water and 16 residues with 132 atoms 54: 54: chain #res #atoms 54: 54: 1 ' ' 16 132 54: 54: All occupancies are one 54: 54: Reading residue database... (Oplsaa) 54: 54: Processing chain 1 (132 atoms, 16 residues) 54: 54: Identified residue ALA34 as a starting terminus. 54: 54: Identified residue ALA49 as a ending terminus. 54: Start terminus ALA-34: NH3+ 54: End terminus ALA-49: COO- 54: 54: Checking for duplicate atoms.... 54: 54: Generating any missing hydrogen atoms and/or adding termini. 54: 54: Now there are 16 residues with 255 atoms 54: 54: Making bonds... 54: 54: Number of bonds was 261, now 261 54: 54: Generating angles, dihedrals and pairs... 54: 54: Making cmap torsions... 54: 54: There are 696 dihedrals, 56 impropers, 472 angles 54: 667 pairs, 261 bonds and 132 virtual sites 54: 54: Total mass 1861.128 a.m.u. 54: 54: Total charge -1.000 e 54: 54: Writing topology 54: 54: Writing coordinate file... 54: 54: --------- PLEASE NOTE ------------ 54: 54: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/C.pdb. 54: 54: The Oplsaa force field and the tip3p water model are used. 54: 54: --------- ETON ESAELP ------------ 54: [ OK ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip3p_vsite_h_id_or_ter_merge_no_Cpdb_format_gro_match_file (233 ms) 54: [ RUN ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip3p_vsite_h_id_or_ter_merge_no_Dpdb_format_gro_match_file 54: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/oplsaa.ff/aminoacids.r2b 54: All occupancies are one 54: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/oplsaa.ff/atomtypes.atp 54: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/oplsaa.ff/aminoacids.rtp 54: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/oplsaa.ff/aminoacids.hdb 54: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/oplsaa.ff/aminoacids.n.tdb 54: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/oplsaa.ff/aminoacids.c.tdb 54: Analysing hydrogen-bonding network for automated assignment of histidine 54: protonation. 22 donors and 21 acceptors were found. 54: There are 30 hydrogen bonds 54: Will use HISE for residue 60 54: 9 out of 9 lines of specbond.dat converted successfully 54: Special Atom Distance matrix: 54: HIS60 54: NE285 54: CYS62 SG98 0.803 54: Marked 111 virtual sites 54: Added 18 dummy masses 54: Added 31 new constraints 54: Before cleaning: 603 pairs 54: Before cleaning: 618 dihedrals 54: Using the Oplsaa force field in directory oplsaa.ff 54: 54: going to rename oplsaa.ff/aminoacids.r2b 54: Reading /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/D.pdb... 54: Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms 54: 54: Analyzing pdb file 54: Splitting chemical chains based on TER records or chain id changing. 54: 54: There are 1 chains and 0 blocks of water and 16 residues with 117 atoms 54: 54: chain #res #atoms 54: 54: 1 ' ' 16 117 54: 54: All occupancies are one 54: 54: Reading residue database... (Oplsaa) 54: 54: Processing chain 1 (117 atoms, 16 residues) 54: 54: Replaced 1 residue named ASPH to the default ASP. Use interactive selection of protonated residues if that is what you need. 54: 54: Identified residue LYS50 as a starting terminus. 54: 54: Identified residue PRO65 as a ending terminus. 54: Start terminus LYS-50: NH3+ 54: End terminus PRO-65: PRO-COO- 54: 54: Checking for duplicate atoms.... 54: 54: Generating any missing hydrogen atoms and/or adding termini. 54: 54: Now there are 16 residues with 228 atoms 54: 54: Making bonds... 54: 54: Number of bonds was 232, now 232 54: 54: Generating angles, dihedrals and pairs... 54: 54: Making cmap torsions... 54: 54: There are 618 dihedrals, 48 impropers, 419 angles 54: 597 pairs, 232 bonds and 116 virtual sites 54: 54: Total mass 1662.883 a.m.u. 54: 54: Total charge 0.000 e 54: 54: Writing topology 54: 54: Writing coordinate file... 54: 54: --------- PLEASE NOTE ------------ 54: 54: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/D.pdb. 54: 54: The Oplsaa force field and the tip3p water model are used. 54: 54: --------- ETON ESAELP ------------ 54: [ OK ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip3p_vsite_h_id_or_ter_merge_no_Dpdb_format_gro_match_file (193 ms) 54: [ RUN ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip3p_vsite_h_id_or_ter_merge_no_Epdb_format_gro_match_file 54: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/oplsaa.ff/aminoacids.r2b 54: All occupancies are one 54: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/oplsaa.ff/atomtypes.atp 54: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/oplsaa.ff/aminoacids.rtp 54: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/oplsaa.ff/aminoacids.hdb 54: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/oplsaa.ff/aminoacids.n.tdb 54: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/oplsaa.ff/aminoacids.c.tdb 54: Analysing hydrogen-bonding network for automated assignment of histidine 54: protonation. 89 donors and 98 acceptors were found. 54: There are 129 hydrogen bonds 54: Will use HISE for residue 31 54: Will use HISE for residue 51 54: 9 out of 9 lines of specbond.dat converted successfully 54: Special Atom Distance matrix: 54: CYS25 HIS31 HIS51 54: SG14 NE264 NE2226 54: HIS31 NE264 1.921 54: HIS51 NE2226 1.498 2.650 54: CYS80 SG477 0.207 1.984 1.570 54: Linking CYS-25 SG-14 and CYS-80 SG-477... 54: Marked 447 virtual sites 54: Added 58 dummy masses 54: Added 101 new constraints 54: Before cleaning: 2499 pairs 54: Before cleaning: 2524 dihedrals 54: Using the Oplsaa force field in directory oplsaa.ff 54: 54: going to rename oplsaa.ff/aminoacids.r2b 54: Reading /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/E.pdb... 54: Read 'This is a fragment of 2d4f for testing a disulfide bridge', 488 atoms 54: 54: Analyzing pdb file 54: Splitting chemical chains based on TER records or chain id changing. 54: 54: There are 1 chains and 0 blocks of water and 58 residues with 488 atoms 54: 54: chain #res #atoms 54: 54: 1 'A' 58 488 54: 54: All occupancies are one 54: 54: Reading residue database... (Oplsaa) 54: 54: Processing chain 1 'A' (488 atoms, 58 residues) 54: 54: Identified residue ASN24 as a starting terminus. 54: 54: Identified residue ARG81 as a ending terminus. 54: Start terminus ASN-24: NH3+ 54: End terminus ARG-81: COO- 54: 54: Checking for duplicate atoms.... 54: 54: Generating any missing hydrogen atoms and/or adding termini. 54: 54: Now there are 58 residues with 936 atoms 54: 54: Making bonds... 54: 54: Number of bonds was 951, now 951 54: 54: Generating angles, dihedrals and pairs... 54: 54: Making cmap torsions... 54: 54: There are 2524 dihedrals, 208 impropers, 1704 angles 54: 2469 pairs, 951 bonds and 462 virtual sites 54: 54: Total mass 6908.578 a.m.u. 54: 54: Total charge -6.000 e 54: 54: Writing topology 54: 54: Writing coordinate file... 54: 54: --------- PLEASE NOTE ------------ 54: 54: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/E.pdb. 54: 54: The Oplsaa force field and the tip3p water model are used. 54: 54: --------- ETON ESAELP ------------ 54: [ OK ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip3p_vsite_h_id_or_ter_merge_no_Epdb_format_gro_match_file (668 ms) 54: [ RUN ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip4p_vsite_none_id_or_ter_merge_no_Apdb_format_gro_match_file 54: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/oplsaa.ff/aminoacids.r2b 54: All occupancies are one 54: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/oplsaa.ff/atomtypes.atp 54: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/oplsaa.ff/aminoacids.rtp 54: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/oplsaa.ff/aminoacids.hdb 54: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/oplsaa.ff/aminoacids.n.tdb 54: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/oplsaa.ff/aminoacids.c.tdb 54: Analysing hydrogen-bonding network for automated assignment of histidine 54: protonation. 25 donors and 23 acceptors were found. 54: There are 41 hydrogen bonds 54: Will use HISE for residue 8 54: 9 out of 9 lines of specbond.dat converted successfully 54: Special Atom Distance matrix: 54: CYS3 HIS8 54: SG9 NE251 54: HIS8 NE251 1.055 54: MET12 SD83 0.763 0.990 54: Before cleaning: 653 pairs 54: Before cleaning: 663 dihedrals 54: Using the Oplsaa force field in directory oplsaa.ff 54: 54: going to rename oplsaa.ff/aminoacids.r2b 54: Reading /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/A.pdb... 54: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms 54: 54: Analyzing pdb file 54: Splitting chemical chains based on TER records or chain id changing. 54: 54: There are 1 chains and 0 blocks of water and 16 residues with 128 atoms 54: 54: chain #res #atoms 54: 54: 1 ' ' 16 128 54: 54: All occupancies are one 54: 54: Reading residue database... (Oplsaa) 54: 54: Processing chain 1 (128 atoms, 16 residues) 54: 54: Identified residue ALA2 as a starting terminus. 54: 54: Identified residue SER17 as a ending terminus. 54: Start terminus ALA-2: NH3+ 54: End terminus SER-17: COO- 54: 54: Checking for duplicate atoms.... 54: 54: Generating any missing hydrogen atoms and/or adding termini. 54: 54: Now there are 16 residues with 252 atoms 54: 54: Making bonds... 54: 54: Number of bonds was 254, now 254 54: 54: Generating angles, dihedrals and pairs... 54: 54: Making cmap torsions... 54: 54: There are 663 dihedrals, 51 impropers, 457 angles 54: 650 pairs, 254 bonds and 0 virtual sites 54: 54: Total mass 1846.112 a.m.u. 54: 54: Total charge 0.000 e 54: 54: Writing topology 54: 54: Writing coordinate file... 54: 54: --------- PLEASE NOTE ------------ 54: 54: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/A.pdb. 54: 54: The Oplsaa force field and the tip4p water model are used. 54: 54: --------- ETON ESAELP ------------ 54: [ OK ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip4p_vsite_none_id_or_ter_merge_no_Apdb_format_gro_match_file (203 ms) 54: [ RUN ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip4p_vsite_none_id_or_ter_merge_no_Bpdb_format_gro_match_file 54: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/oplsaa.ff/aminoacids.r2b 54: All occupancies are one 54: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/oplsaa.ff/atomtypes.atp 54: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/oplsaa.ff/aminoacids.rtp 54: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/oplsaa.ff/aminoacids.hdb 54: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/oplsaa.ff/aminoacids.n.tdb 54: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/oplsaa.ff/aminoacids.c.tdb 54: Analysing hydrogen-bonding network for automated assignment of histidine 54: protonation. 30 donors and 22 acceptors were found. 54: There are 36 hydrogen bonds 54: Will use HISE for residue 29 54: Will use HISE for residue 32 54: 9 out of 9 lines of specbond.dat converted successfully 54: Special Atom Distance matrix: 54: CYS27 HIS29 54: SG90 NE2111 54: HIS29 NE2111 0.987 54: HIS32 NE2135 1.590 1.155 54: Before cleaning: 748 pairs 54: Before cleaning: 778 dihedrals 54: Using the Oplsaa force field in directory oplsaa.ff 54: 54: going to rename oplsaa.ff/aminoacids.r2b 54: Reading /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/B.pdb... 54: Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms 54: 54: Analyzing pdb file 54: Splitting chemical chains based on TER records or chain id changing. 54: 54: There are 1 chains and 0 blocks of water and 16 residues with 149 atoms 54: 54: chain #res #atoms 54: 54: 1 ' ' 16 149 54: 54: All occupancies are one 54: 54: Reading residue database... (Oplsaa) 54: 54: Processing chain 1 (149 atoms, 16 residues) 54: 54: Replaced 1 residue named GLUH to the default GLU. Use interactive selection of protonated residues if that is what you need. 54: 54: Identified residue THR18 as a starting terminus. 54: 54: Identified residue PHE33 as a ending terminus. 54: Start terminus THR-18: NH3+ 54: End terminus PHE-33: COO- 54: 54: Checking for duplicate atoms.... 54: 54: Generating any missing hydrogen atoms and/or adding termini. 54: 54: Now there are 16 residues with 281 atoms 54: 54: Making bonds... 54: 54: Number of bonds was 290, now 290 54: 54: Generating angles, dihedrals and pairs... 54: 54: Making cmap torsions... 54: 54: There are 778 dihedrals, 72 impropers, 516 angles 54: 736 pairs, 290 bonds and 0 virtual sites 54: 54: Total mass 2088.357 a.m.u. 54: 54: Total charge 1.000 e 54: 54: Writing topology 54: 54: Writing coordinate file... 54: 54: --------- PLEASE NOTE ------------ 54: 54: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/B.pdb. 54: 54: The Oplsaa force field and the tip4p water model are used. 54: 54: --------- ETON ESAELP ------------ 54: [ OK ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip4p_vsite_none_id_or_ter_merge_no_Bpdb_format_gro_match_file (229 ms) 54: [ RUN ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip4p_vsite_none_id_or_ter_merge_no_Cpdb_format_gro_match_file 54: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/oplsaa.ff/aminoacids.r2b 54: All occupancies are one 54: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/oplsaa.ff/atomtypes.atp 54: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/oplsaa.ff/aminoacids.rtp 54: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/oplsaa.ff/aminoacids.hdb 54: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/oplsaa.ff/aminoacids.n.tdb 54: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/oplsaa.ff/aminoacids.c.tdb 54: Analysing hydrogen-bonding network for automated assignment of histidine 54: protonation. 22 donors and 22 acceptors were found. 54: There are 26 hydrogen bonds 54: Will use HISE for residue 45 54: 9 out of 9 lines of specbond.dat converted successfully 54: Special Atom Distance matrix: 54: HIS45 54: NE295 54: MET46 SD102 1.078 54: Before cleaning: 676 pairs 54: Before cleaning: 696 dihedrals 54: Using the Oplsaa force field in directory oplsaa.ff 54: 54: going to rename oplsaa.ff/aminoacids.r2b 54: Reading /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/C.pdb... 54: Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms 54: 54: Analyzing pdb file 54: Splitting chemical chains based on TER records or chain id changing. 54: 54: There are 1 chains and 0 blocks of water and 16 residues with 132 atoms 54: 54: chain #res #atoms 54: 54: 1 ' ' 16 132 54: 54: All occupancies are one 54: 54: Reading residue database... (Oplsaa) 54: 54: Processing chain 1 (132 atoms, 16 residues) 54: 54: Identified residue ALA34 as a starting terminus. 54: 54: Identified residue ALA49 as a ending terminus. 54: Start terminus ALA-34: NH3+ 54: End terminus ALA-49: COO- 54: 54: Checking for duplicate atoms.... 54: 54: Generating any missing hydrogen atoms and/or adding termini. 54: 54: Now there are 16 residues with 255 atoms 54: 54: Making bonds... 54: 54: Number of bonds was 261, now 261 54: 54: Generating angles, dihedrals and pairs... 54: 54: Making cmap torsions... 54: 54: There are 696 dihedrals, 56 impropers, 472 angles 54: 667 pairs, 261 bonds and 0 virtual sites 54: 54: Total mass 1861.128 a.m.u. 54: 54: Total charge -1.000 e 54: 54: Writing topology 54: 54: Writing coordinate file... 54: 54: --------- PLEASE NOTE ------------ 54: 54: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/C.pdb. 54: 54: The Oplsaa force field and the tip4p water model are used. 54: 54: --------- ETON ESAELP ------------ 54: [ OK ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip4p_vsite_none_id_or_ter_merge_no_Cpdb_format_gro_match_file (203 ms) 54: [ RUN ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip4p_vsite_none_id_or_ter_merge_no_Dpdb_format_gro_match_file 54: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/oplsaa.ff/aminoacids.r2b 54: All occupancies are one 54: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/oplsaa.ff/atomtypes.atp 54: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/oplsaa.ff/aminoacids.rtp 54: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/oplsaa.ff/aminoacids.hdb 54: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/oplsaa.ff/aminoacids.n.tdb 54: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/oplsaa.ff/aminoacids.c.tdb 54: Analysing hydrogen-bonding network for automated assignment of histidine 54: protonation. 22 donors and 21 acceptors were found. 54: There are 30 hydrogen bonds 54: Will use HISE for residue 60 54: 9 out of 9 lines of specbond.dat converted successfully 54: Special Atom Distance matrix: 54: HIS60 54: NE285 54: CYS62 SG98 0.803 54: Before cleaning: 603 pairs 54: Before cleaning: 618 dihedrals 54: Using the Oplsaa force field in directory oplsaa.ff 54: 54: going to rename oplsaa.ff/aminoacids.r2b 54: Reading /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/D.pdb... 54: Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms 54: 54: Analyzing pdb file 54: Splitting chemical chains based on TER records or chain id changing. 54: 54: There are 1 chains and 0 blocks of water and 16 residues with 117 atoms 54: 54: chain #res #atoms 54: 54: 1 ' ' 16 117 54: 54: All occupancies are one 54: 54: Reading residue database... (Oplsaa) 54: 54: Processing chain 1 (117 atoms, 16 residues) 54: 54: Replaced 1 residue named ASPH to the default ASP. Use interactive selection of protonated residues if that is what you need. 54: 54: Identified residue LYS50 as a starting terminus. 54: 54: Identified residue PRO65 as a ending terminus. 54: Start terminus LYS-50: NH3+ 54: End terminus PRO-65: PRO-COO- 54: 54: Checking for duplicate atoms.... 54: 54: Generating any missing hydrogen atoms and/or adding termini. 54: 54: Now there are 16 residues with 228 atoms 54: 54: Making bonds... 54: 54: Number of bonds was 232, now 232 54: 54: Generating angles, dihedrals and pairs... 54: 54: Making cmap torsions... 54: 54: There are 618 dihedrals, 48 impropers, 419 angles 54: 597 pairs, 232 bonds and 0 virtual sites 54: 54: Total mass 1662.883 a.m.u. 54: 54: Total charge 0.000 e 54: 54: Writing topology 54: 54: Writing coordinate file... 54: 54: --------- PLEASE NOTE ------------ 54: 54: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/D.pdb. 54: 54: The Oplsaa force field and the tip4p water model are used. 54: 54: --------- ETON ESAELP ------------ 54: [ OK ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip4p_vsite_none_id_or_ter_merge_no_Dpdb_format_gro_match_file (186 ms) 54: [ RUN ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip4p_vsite_none_id_or_ter_merge_no_Epdb_format_gro_match_file 54: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/oplsaa.ff/aminoacids.r2b 54: All occupancies are one 54: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/oplsaa.ff/atomtypes.atp 54: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/oplsaa.ff/aminoacids.rtp 54: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/oplsaa.ff/aminoacids.hdb 54: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/oplsaa.ff/aminoacids.n.tdb 54: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/oplsaa.ff/aminoacids.c.tdb 54: Analysing hydrogen-bonding network for automated assignment of histidine 54: protonation. 89 donors and 98 acceptors were found. 54: There are 129 hydrogen bonds 54: Will use HISE for residue 31 54: Will use HISE for residue 51 54: 9 out of 9 lines of specbond.dat converted successfully 54: Special Atom Distance matrix: 54: CYS25 HIS31 HIS51 54: SG14 NE264 NE2226 54: HIS31 NE264 1.921 54: HIS51 NE2226 1.498 2.650 54: CYS80 SG477 0.207 1.984 1.570 54: Linking CYS-25 SG-14 and CYS-80 SG-477... 54: Before cleaning: 2499 pairs 54: Before cleaning: 2524 dihedrals 54: Using the Oplsaa force field in directory oplsaa.ff 54: 54: going to rename oplsaa.ff/aminoacids.r2b 54: Reading /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/E.pdb... 54: Read 'This is a fragment of 2d4f for testing a disulfide bridge', 488 atoms 54: 54: Analyzing pdb file 54: Splitting chemical chains based on TER records or chain id changing. 54: 54: There are 1 chains and 0 blocks of water and 58 residues with 488 atoms 54: 54: chain #res #atoms 54: 54: 1 'A' 58 488 54: 54: All occupancies are one 54: 54: Reading residue database... (Oplsaa) 54: 54: Processing chain 1 'A' (488 atoms, 58 residues) 54: 54: Identified residue ASN24 as a starting terminus. 54: 54: Identified residue ARG81 as a ending terminus. 54: Start terminus ASN-24: NH3+ 54: End terminus ARG-81: COO- 54: 54: Checking for duplicate atoms.... 54: 54: Generating any missing hydrogen atoms and/or adding termini. 54: 54: Now there are 58 residues with 936 atoms 54: 54: Making bonds... 54: 54: Number of bonds was 951, now 951 54: 54: Generating angles, dihedrals and pairs... 54: 54: Making cmap torsions... 54: 54: There are 2524 dihedrals, 208 impropers, 1704 angles 54: 2469 pairs, 951 bonds and 0 virtual sites 54: 54: Total mass 6908.578 a.m.u. 54: 54: Total charge -6.000 e 54: 54: Writing topology 54: 54: Writing coordinate file... 54: 54: --------- PLEASE NOTE ------------ 54: 54: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/E.pdb. 54: 54: The Oplsaa force field and the tip4p water model are used. 54: 54: --------- ETON ESAELP ------------ 54: [ OK ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip4p_vsite_none_id_or_ter_merge_no_Epdb_format_gro_match_file (612 ms) 54: [ RUN ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip4p_vsite_h_id_or_ter_merge_no_Apdb_format_gro_match_file 54: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/oplsaa.ff/aminoacids.r2b 54: All occupancies are one 54: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/oplsaa.ff/atomtypes.atp 54: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/oplsaa.ff/aminoacids.rtp 54: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/oplsaa.ff/aminoacids.hdb 54: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/oplsaa.ff/aminoacids.n.tdb 54: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/oplsaa.ff/aminoacids.c.tdb 54: Analysing hydrogen-bonding network for automated assignment of histidine 54: protonation. 25 donors and 23 acceptors were found. 54: There are 41 hydrogen bonds 54: Will use HISE for residue 8 54: 9 out of 9 lines of specbond.dat converted successfully 54: Special Atom Distance matrix: 54: CYS3 HIS8 54: SG9 NE251 54: HIS8 NE251 1.055 54: MET12 SD83 0.763 0.990 54: Marked 124 virtual sites 54: Added 16 dummy masses 54: Added 26 new constraints 54: Before cleaning: 653 pairs 54: Before cleaning: 663 dihedrals 54: Using the Oplsaa force field in directory oplsaa.ff 54: 54: going to rename oplsaa.ff/aminoacids.r2b 54: Reading /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/A.pdb... 54: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms 54: 54: Analyzing pdb file 54: Splitting chemical chains based on TER records or chain id changing. 54: 54: There are 1 chains and 0 blocks of water and 16 residues with 128 atoms 54: 54: chain #res #atoms 54: 54: 1 ' ' 16 128 54: 54: All occupancies are one 54: 54: Reading residue database... (Oplsaa) 54: 54: Processing chain 1 (128 atoms, 16 residues) 54: 54: Identified residue ALA2 as a starting terminus. 54: 54: Identified residue SER17 as a ending terminus. 54: Start terminus ALA-2: NH3+ 54: End terminus SER-17: COO- 54: 54: Checking for duplicate atoms.... 54: 54: Generating any missing hydrogen atoms and/or adding termini. 54: 54: Now there are 16 residues with 252 atoms 54: 54: Making bonds... 54: 54: Number of bonds was 254, now 254 54: 54: Generating angles, dihedrals and pairs... 54: 54: Making cmap torsions... 54: 54: There are 663 dihedrals, 51 impropers, 457 angles 54: 650 pairs, 254 bonds and 130 virtual sites 54: 54: Total mass 1846.112 a.m.u. 54: 54: Total charge 0.000 e 54: 54: Writing topology 54: 54: Writing coordinate file... 54: 54: --------- PLEASE NOTE ------------ 54: 54: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/A.pdb. 54: 54: The Oplsaa force field and the tip4p water model are used. 54: 54: --------- ETON ESAELP ------------ 54: [ OK ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip4p_vsite_h_id_or_ter_merge_no_Apdb_format_gro_match_file (214 ms) 54: [ RUN ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip4p_vsite_h_id_or_ter_merge_no_Bpdb_format_gro_match_file 54: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/oplsaa.ff/aminoacids.r2b 54: All occupancies are one 54: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/oplsaa.ff/atomtypes.atp 54: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/oplsaa.ff/aminoacids.rtp 54: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/oplsaa.ff/aminoacids.hdb 54: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/oplsaa.ff/aminoacids.n.tdb 54: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/oplsaa.ff/aminoacids.c.tdb 54: Analysing hydrogen-bonding network for automated assignment of histidine 54: protonation. 30 donors and 22 acceptors were found. 54: There are 36 hydrogen bonds 54: Will use HISE for residue 29 54: Will use HISE for residue 32 54: 9 out of 9 lines of specbond.dat converted successfully 54: Special Atom Distance matrix: 54: CYS27 HIS29 54: SG90 NE2111 54: HIS29 NE2111 0.987 54: HIS32 NE2135 1.590 1.155 54: Marked 132 virtual sites 54: Added 10 dummy masses 54: Added 19 new constraints 54: Before cleaning: 748 pairs 54: Before cleaning: 778 dihedrals 54: Using the Oplsaa force field in directory oplsaa.ff 54: 54: going to rename oplsaa.ff/aminoacids.r2b 54: Reading /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/B.pdb... 54: Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms 54: 54: Analyzing pdb file 54: Splitting chemical chains based on TER records or chain id changing. 54: 54: There are 1 chains and 0 blocks of water and 16 residues with 149 atoms 54: 54: chain #res #atoms 54: 54: 1 ' ' 16 149 54: 54: All occupancies are one 54: 54: Reading residue database... (Oplsaa) 54: 54: Processing chain 1 (149 atoms, 16 residues) 54: 54: Replaced 1 residue named GLUH to the default GLU. Use interactive selection of protonated residues if that is what you need. 54: 54: Identified residue THR18 as a starting terminus. 54: 54: Identified residue PHE33 as a ending terminus. 54: Start terminus THR-18: NH3+ 54: End terminus PHE-33: COO- 54: 54: Checking for duplicate atoms.... 54: 54: Generating any missing hydrogen atoms and/or adding termini. 54: 54: Now there are 16 residues with 281 atoms 54: 54: Making bonds... 54: 54: Number of bonds was 290, now 290 54: 54: Generating angles, dihedrals and pairs... 54: 54: Making cmap torsions... 54: 54: There are 778 dihedrals, 72 impropers, 516 angles 54: 736 pairs, 290 bonds and 133 virtual sites 54: 54: Total mass 2088.357 a.m.u. 54: 54: Total charge 1.000 e 54: 54: Writing topology 54: 54: Writing coordinate file... 54: 54: --------- PLEASE NOTE ------------ 54: 54: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/B.pdb. 54: 54: The Oplsaa force field and the tip4p water model are used. 54: 54: --------- ETON ESAELP ------------ 54: [ OK ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip4p_vsite_h_id_or_ter_merge_no_Bpdb_format_gro_match_file (235 ms) 54: [ RUN ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip4p_vsite_h_id_or_ter_merge_no_Cpdb_format_gro_match_file 54: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/oplsaa.ff/aminoacids.r2b 54: All occupancies are one 54: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/oplsaa.ff/atomtypes.atp 54: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/oplsaa.ff/aminoacids.rtp 54: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/oplsaa.ff/aminoacids.hdb 54: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/oplsaa.ff/aminoacids.n.tdb 54: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/oplsaa.ff/aminoacids.c.tdb 54: Analysing hydrogen-bonding network for automated assignment of histidine 54: protonation. 22 donors and 22 acceptors were found. 54: There are 26 hydrogen bonds 54: Will use HISE for residue 45 54: 9 out of 9 lines of specbond.dat converted successfully 54: Special Atom Distance matrix: 54: HIS45 54: NE295 54: MET46 SD102 1.078 54: Marked 123 virtual sites 54: Added 22 dummy masses 54: Added 35 new constraints 54: Before cleaning: 676 pairs 54: Before cleaning: 696 dihedrals 54: Using the Oplsaa force field in directory oplsaa.ff 54: 54: going to rename oplsaa.ff/aminoacids.r2b 54: Reading /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/C.pdb... 54: Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms 54: 54: Analyzing pdb file 54: Splitting chemical chains based on TER records or chain id changing. 54: 54: There are 1 chains and 0 blocks of water and 16 residues with 132 atoms 54: 54: chain #res #atoms 54: 54: 1 ' ' 16 132 54: 54: All occupancies are one 54: 54: Reading residue database... (Oplsaa) 54: 54: Processing chain 1 (132 atoms, 16 residues) 54: 54: Identified residue ALA34 as a starting terminus. 54: 54: Identified residue ALA49 as a ending terminus. 54: Start terminus ALA-34: NH3+ 54: End terminus ALA-49: COO- 54: 54: Checking for duplicate atoms.... 54: 54: Generating any missing hydrogen atoms and/or adding termini. 54: 54: Now there are 16 residues with 255 atoms 54: 54: Making bonds... 54: 54: Number of bonds was 261, now 261 54: 54: Generating angles, dihedrals and pairs... 54: 54: Making cmap torsions... 54: 54: There are 696 dihedrals, 56 impropers, 472 angles 54: 667 pairs, 261 bonds and 132 virtual sites 54: 54: Total mass 1861.128 a.m.u. 54: 54: Total charge -1.000 e 54: 54: Writing topology 54: 54: Writing coordinate file... 54: 54: --------- PLEASE NOTE ------------ 54: 54: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/C.pdb. 54: 54: The Oplsaa force field and the tip4p water model are used. 54: 54: --------- ETON ESAELP ------------ 54: [ OK ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip4p_vsite_h_id_or_ter_merge_no_Cpdb_format_gro_match_file (225 ms) 54: [ RUN ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip4p_vsite_h_id_or_ter_merge_no_Dpdb_format_gro_match_file 54: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/oplsaa.ff/aminoacids.r2b 54: All occupancies are one 54: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/oplsaa.ff/atomtypes.atp 54: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/oplsaa.ff/aminoacids.rtp 54: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/oplsaa.ff/aminoacids.hdb 54: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/oplsaa.ff/aminoacids.n.tdb 54: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/oplsaa.ff/aminoacids.c.tdb 54: Analysing hydrogen-bonding network for automated assignment of histidine 54: protonation. 22 donors and 21 acceptors were found. 54: There are 30 hydrogen bonds 54: Will use HISE for residue 60 54: 9 out of 9 lines of specbond.dat converted successfully 54: Special Atom Distance matrix: 54: HIS60 54: NE285 54: CYS62 SG98 0.803 54: Marked 111 virtual sites 54: Added 18 dummy masses 54: Added 31 new constraints 54: Before cleaning: 603 pairs 54: Before cleaning: 618 dihedrals 54: Using the Oplsaa force field in directory oplsaa.ff 54: 54: going to rename oplsaa.ff/aminoacids.r2b 54: Reading /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/D.pdb... 54: Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms 54: 54: Analyzing pdb file 54: Splitting chemical chains based on TER records or chain id changing. 54: 54: There are 1 chains and 0 blocks of water and 16 residues with 117 atoms 54: 54: chain #res #atoms 54: 54: 1 ' ' 16 117 54: 54: All occupancies are one 54: 54: Reading residue database... (Oplsaa) 54: 54: Processing chain 1 (117 atoms, 16 residues) 54: 54: Replaced 1 residue named ASPH to the default ASP. Use interactive selection of protonated residues if that is what you need. 54: 54: Identified residue LYS50 as a starting terminus. 54: 54: Identified residue PRO65 as a ending terminus. 54: Start terminus LYS-50: NH3+ 54: End terminus PRO-65: PRO-COO- 54: 54: Checking for duplicate atoms.... 54: 54: Generating any missing hydrogen atoms and/or adding termini. 54: 54: Now there are 16 residues with 228 atoms 54: 54: Making bonds... 54: 54: Number of bonds was 232, now 232 54: 54: Generating angles, dihedrals and pairs... 54: 54: Making cmap torsions... 54: 54: There are 618 dihedrals, 48 impropers, 419 angles 54: 597 pairs, 232 bonds and 116 virtual sites 54: 54: Total mass 1662.883 a.m.u. 54: 54: Total charge 0.000 e 54: 54: Writing topology 54: 54: Writing coordinate file... 54: 54: --------- PLEASE NOTE ------------ 54: 54: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/D.pdb. 54: 54: The Oplsaa force field and the tip4p water model are used. 54: 54: --------- ETON ESAELP ------------ 54: [ OK ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip4p_vsite_h_id_or_ter_merge_no_Dpdb_format_gro_match_file (200 ms) 54: [ RUN ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip4p_vsite_h_id_or_ter_merge_no_Epdb_format_gro_match_file 54: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/oplsaa.ff/aminoacids.r2b 54: All occupancies are one 54: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/oplsaa.ff/atomtypes.atp 54: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/oplsaa.ff/aminoacids.rtp 54: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/oplsaa.ff/aminoacids.hdb 54: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/oplsaa.ff/aminoacids.n.tdb 54: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/oplsaa.ff/aminoacids.c.tdb 54: Analysing hydrogen-bonding network for automated assignment of histidine 54: protonation. 89 donors and 98 acceptors were found. 54: There are 129 hydrogen bonds 54: Will use HISE for residue 31 54: Will use HISE for residue 51 54: 9 out of 9 lines of specbond.dat converted successfully 54: Special Atom Distance matrix: 54: CYS25 HIS31 HIS51 54: SG14 NE264 NE2226 54: HIS31 NE264 1.921 54: HIS51 NE2226 1.498 2.650 54: CYS80 SG477 0.207 1.984 1.570 54: Linking CYS-25 SG-14 and CYS-80 SG-477... 54: Marked 447 virtual sites 54: Added 58 dummy masses 54: Added 101 new constraints 54: Before cleaning: 2499 pairs 54: Before cleaning: 2524 dihedrals 54: Using the Oplsaa force field in directory oplsaa.ff 54: 54: going to rename oplsaa.ff/aminoacids.r2b 54: Reading /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/E.pdb... 54: Read 'This is a fragment of 2d4f for testing a disulfide bridge', 488 atoms 54: 54: Analyzing pdb file 54: Splitting chemical chains based on TER records or chain id changing. 54: 54: There are 1 chains and 0 blocks of water and 58 residues with 488 atoms 54: 54: chain #res #atoms 54: 54: 1 'A' 58 488 54: 54: All occupancies are one 54: 54: Reading residue database... (Oplsaa) 54: 54: Processing chain 1 'A' (488 atoms, 58 residues) 54: 54: Identified residue ASN24 as a starting terminus. 54: 54: Identified residue ARG81 as a ending terminus. 54: Start terminus ASN-24: NH3+ 54: End terminus ARG-81: COO- 54: 54: Checking for duplicate atoms.... 54: 54: Generating any missing hydrogen atoms and/or adding termini. 54: 54: Now there are 58 residues with 936 atoms 54: 54: Making bonds... 54: 54: Number of bonds was 951, now 951 54: 54: Generating angles, dihedrals and pairs... 54: 54: Making cmap torsions... 54: 54: There are 2524 dihedrals, 208 impropers, 1704 angles 54: 2469 pairs, 951 bonds and 462 virtual sites 54: 54: Total mass 6908.578 a.m.u. 54: 54: Total charge -6.000 e 54: 54: Writing topology 54: 54: Writing coordinate file... 54: 54: --------- PLEASE NOTE ------------ 54: 54: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/E.pdb. 54: 54: The Oplsaa force field and the tip4p water model are used. 54: 54: --------- ETON ESAELP ------------ 54: [ OK ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip4p_vsite_h_id_or_ter_merge_no_Epdb_format_gro_match_file (730 ms) 54: [ RUN ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip5p_vsite_none_id_or_ter_merge_no_Apdb_format_gro_match_file 54: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/oplsaa.ff/aminoacids.r2b 54: All occupancies are one 54: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/oplsaa.ff/atomtypes.atp 54: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/oplsaa.ff/aminoacids.rtp 54: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/oplsaa.ff/aminoacids.hdb 54: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/oplsaa.ff/aminoacids.n.tdb 54: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/oplsaa.ff/aminoacids.c.tdb 54: Analysing hydrogen-bonding network for automated assignment of histidine 54: protonation. 25 donors and 23 acceptors were found. 54: There are 41 hydrogen bonds 54: Will use HISE for residue 8 54: 9 out of 9 lines of specbond.dat converted successfully 54: Special Atom Distance matrix: 54: CYS3 HIS8 54: SG9 NE251 54: HIS8 NE251 1.055 54: MET12 SD83 0.763 0.990 54: Before cleaning: 653 pairs 54: Before cleaning: 663 dihedrals 54: Using the Oplsaa force field in directory oplsaa.ff 54: 54: going to rename oplsaa.ff/aminoacids.r2b 54: Reading /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/A.pdb... 54: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms 54: 54: Analyzing pdb file 54: Splitting chemical chains based on TER records or chain id changing. 54: 54: There are 1 chains and 0 blocks of water and 16 residues with 128 atoms 54: 54: chain #res #atoms 54: 54: 1 ' ' 16 128 54: 54: All occupancies are one 54: 54: Reading residue database... (Oplsaa) 54: 54: Processing chain 1 (128 atoms, 16 residues) 54: 54: Identified residue ALA2 as a starting terminus. 54: 54: Identified residue SER17 as a ending terminus. 54: Start terminus ALA-2: NH3+ 54: End terminus SER-17: COO- 54: 54: Checking for duplicate atoms.... 54: 54: Generating any missing hydrogen atoms and/or adding termini. 54: 54: Now there are 16 residues with 252 atoms 54: 54: Making bonds... 54: 54: Number of bonds was 254, now 254 54: 54: Generating angles, dihedrals and pairs... 54: 54: Making cmap torsions... 54: 54: There are 663 dihedrals, 51 impropers, 457 angles 54: 650 pairs, 254 bonds and 0 virtual sites 54: 54: Total mass 1846.112 a.m.u. 54: 54: Total charge 0.000 e 54: 54: Writing topology 54: 54: Writing coordinate file... 54: 54: --------- PLEASE NOTE ------------ 54: 54: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/A.pdb. 54: 54: The Oplsaa force field and the tip5p water model are used. 54: 54: --------- ETON ESAELP ------------ 54: [ OK ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip5p_vsite_none_id_or_ter_merge_no_Apdb_format_gro_match_file (211 ms) 54: [ RUN ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip5p_vsite_none_id_or_ter_merge_no_Bpdb_format_gro_match_file 54: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/oplsaa.ff/aminoacids.r2b 54: All occupancies are one 54: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/oplsaa.ff/atomtypes.atp 54: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/oplsaa.ff/aminoacids.rtp 54: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/oplsaa.ff/aminoacids.hdb 54: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/oplsaa.ff/aminoacids.n.tdb 54: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/oplsaa.ff/aminoacids.c.tdb 54: Analysing hydrogen-bonding network for automated assignment of histidine 54: protonation. 30 donors and 22 acceptors were found. 54: There are 36 hydrogen bonds 54: Will use HISE for residue 29 54: Will use HISE for residue 32 54: 9 out of 9 lines of specbond.dat converted successfully 54: Special Atom Distance matrix: 54: CYS27 HIS29 54: SG90 NE2111 54: HIS29 NE2111 0.987 54: HIS32 NE2135 1.590 1.155 54: Before cleaning: 748 pairs 54: Before cleaning: 778 dihedrals 54: Using the Oplsaa force field in directory oplsaa.ff 54: 54: going to rename oplsaa.ff/aminoacids.r2b 54: Reading /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/B.pdb... 54: Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms 54: 54: Analyzing pdb file 54: Splitting chemical chains based on TER records or chain id changing. 54: 54: There are 1 chains and 0 blocks of water and 16 residues with 149 atoms 54: 54: chain #res #atoms 54: 54: 1 ' ' 16 149 54: 54: All occupancies are one 54: 54: Reading residue database... (Oplsaa) 54: 54: Processing chain 1 (149 atoms, 16 residues) 54: 54: Replaced 1 residue named GLUH to the default GLU. Use interactive selection of protonated residues if that is what you need. 54: 54: Identified residue THR18 as a starting terminus. 54: 54: Identified residue PHE33 as a ending terminus. 54: Start terminus THR-18: NH3+ 54: End terminus PHE-33: COO- 54: 54: Checking for duplicate atoms.... 54: 54: Generating any missing hydrogen atoms and/or adding termini. 54: 54: Now there are 16 residues with 281 atoms 54: 54: Making bonds... 54: 54: Number of bonds was 290, now 290 54: 54: Generating angles, dihedrals and pairs... 54: 54: Making cmap torsions... 54: 54: There are 778 dihedrals, 72 impropers, 516 angles 54: 736 pairs, 290 bonds and 0 virtual sites 54: 54: Total mass 2088.357 a.m.u. 54: 54: Total charge 1.000 e 54: 54: Writing topology 54: 54: Writing coordinate file... 54: 54: --------- PLEASE NOTE ------------ 54: 54: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/B.pdb. 54: 54: The Oplsaa force field and the tip5p water model are used. 54: 54: --------- ETON ESAELP ------------ 54: [ OK ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip5p_vsite_none_id_or_ter_merge_no_Bpdb_format_gro_match_file (226 ms) 54: [ RUN ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip5p_vsite_none_id_or_ter_merge_no_Cpdb_format_gro_match_file 54: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/oplsaa.ff/aminoacids.r2b 54: All occupancies are one 54: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/oplsaa.ff/atomtypes.atp 54: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/oplsaa.ff/aminoacids.rtp 54: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/oplsaa.ff/aminoacids.hdb 54: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/oplsaa.ff/aminoacids.n.tdb 54: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/oplsaa.ff/aminoacids.c.tdb 54: Analysing hydrogen-bonding network for automated assignment of histidine 54: protonation. 22 donors and 22 acceptors were found. 54: There are 26 hydrogen bonds 54: Will use HISE for residue 45 54: 9 out of 9 lines of specbond.dat converted successfully 54: Special Atom Distance matrix: 54: HIS45 54: NE295 54: MET46 SD102 1.078 54: Before cleaning: 676 pairs 54: Before cleaning: 696 dihedrals 54: Using the Oplsaa force field in directory oplsaa.ff 54: 54: going to rename oplsaa.ff/aminoacids.r2b 54: Reading /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/C.pdb... 54: Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms 54: 54: Analyzing pdb file 54: Splitting chemical chains based on TER records or chain id changing. 54: 54: There are 1 chains and 0 blocks of water and 16 residues with 132 atoms 54: 54: chain #res #atoms 54: 54: 1 ' ' 16 132 54: 54: All occupancies are one 54: 54: Reading residue database... (Oplsaa) 54: 54: Processing chain 1 (132 atoms, 16 residues) 54: 54: Identified residue ALA34 as a starting terminus. 54: 54: Identified residue ALA49 as a ending terminus. 54: Start terminus ALA-34: NH3+ 54: End terminus ALA-49: COO- 54: 54: Checking for duplicate atoms.... 54: 54: Generating any missing hydrogen atoms and/or adding termini. 54: 54: Now there are 16 residues with 255 atoms 54: 54: Making bonds... 54: 54: Number of bonds was 261, now 261 54: 54: Generating angles, dihedrals and pairs... 54: 54: Making cmap torsions... 54: 54: There are 696 dihedrals, 56 impropers, 472 angles 54: 667 pairs, 261 bonds and 0 virtual sites 54: 54: Total mass 1861.128 a.m.u. 54: 54: Total charge -1.000 e 54: 54: Writing topology 54: 54: Writing coordinate file... 54: 54: --------- PLEASE NOTE ------------ 54: 54: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/C.pdb. 54: 54: The Oplsaa force field and the tip5p water model are used. 54: 54: --------- ETON ESAELP ------------ 54: [ OK ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip5p_vsite_none_id_or_ter_merge_no_Cpdb_format_gro_match_file (211 ms) 54: [ RUN ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip5p_vsite_none_id_or_ter_merge_no_Dpdb_format_gro_match_file 54: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/oplsaa.ff/aminoacids.r2b 54: All occupancies are one 54: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/oplsaa.ff/atomtypes.atp 54: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/oplsaa.ff/aminoacids.rtp 54: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/oplsaa.ff/aminoacids.hdb 54: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/oplsaa.ff/aminoacids.n.tdb 54: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/oplsaa.ff/aminoacids.c.tdb 54: Analysing hydrogen-bonding network for automated assignment of histidine 54: protonation. 22 donors and 21 acceptors were found. 54: There are 30 hydrogen bonds 54: Will use HISE for residue 60 54: 9 out of 9 lines of specbond.dat converted successfully 54: Special Atom Distance matrix: 54: HIS60 54: NE285 54: CYS62 SG98 0.803 54: Before cleaning: 603 pairs 54: Before cleaning: 618 dihedrals 54: Using the Oplsaa force field in directory oplsaa.ff 54: 54: going to rename oplsaa.ff/aminoacids.r2b 54: Reading /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/D.pdb... 54: Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms 54: 54: Analyzing pdb file 54: Splitting chemical chains based on TER records or chain id changing. 54: 54: There are 1 chains and 0 blocks of water and 16 residues with 117 atoms 54: 54: chain #res #atoms 54: 54: 1 ' ' 16 117 54: 54: All occupancies are one 54: 54: Reading residue database... (Oplsaa) 54: 54: Processing chain 1 (117 atoms, 16 residues) 54: 54: Replaced 1 residue named ASPH to the default ASP. Use interactive selection of protonated residues if that is what you need. 54: 54: Identified residue LYS50 as a starting terminus. 54: 54: Identified residue PRO65 as a ending terminus. 54: Start terminus LYS-50: NH3+ 54: End terminus PRO-65: PRO-COO- 54: 54: Checking for duplicate atoms.... 54: 54: Generating any missing hydrogen atoms and/or adding termini. 54: 54: Now there are 16 residues with 228 atoms 54: 54: Making bonds... 54: 54: Number of bonds was 232, now 232 54: 54: Generating angles, dihedrals and pairs... 54: 54: Making cmap torsions... 54: 54: There are 618 dihedrals, 48 impropers, 419 angles 54: 597 pairs, 232 bonds and 0 virtual sites 54: 54: Total mass 1662.883 a.m.u. 54: 54: Total charge 0.000 e 54: 54: Writing topology 54: 54: Writing coordinate file... 54: 54: --------- PLEASE NOTE ------------ 54: 54: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/D.pdb. 54: 54: The Oplsaa force field and the tip5p water model are used. 54: 54: --------- ETON ESAELP ------------ 54: [ OK ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip5p_vsite_none_id_or_ter_merge_no_Dpdb_format_gro_match_file (197 ms) 54: [ RUN ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip5p_vsite_none_id_or_ter_merge_no_Epdb_format_gro_match_file 54: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/oplsaa.ff/aminoacids.r2b 54: All occupancies are one 54: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/oplsaa.ff/atomtypes.atp 54: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/oplsaa.ff/aminoacids.rtp 54: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/oplsaa.ff/aminoacids.hdb 54: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/oplsaa.ff/aminoacids.n.tdb 54: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/oplsaa.ff/aminoacids.c.tdb 54: Analysing hydrogen-bonding network for automated assignment of histidine 54: protonation. 89 donors and 98 acceptors were found. 54: There are 129 hydrogen bonds 54: Will use HISE for residue 31 54: Will use HISE for residue 51 54: 9 out of 9 lines of specbond.dat converted successfully 54: Special Atom Distance matrix: 54: CYS25 HIS31 HIS51 54: SG14 NE264 NE2226 54: HIS31 NE264 1.921 54: HIS51 NE2226 1.498 2.650 54: CYS80 SG477 0.207 1.984 1.570 54: Linking CYS-25 SG-14 and CYS-80 SG-477... 54: Before cleaning: 2499 pairs 54: Before cleaning: 2524 dihedrals 54: Using the Oplsaa force field in directory oplsaa.ff 54: 54: going to rename oplsaa.ff/aminoacids.r2b 54: Reading /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/E.pdb... 54: Read 'This is a fragment of 2d4f for testing a disulfide bridge', 488 atoms 54: 54: Analyzing pdb file 54: Splitting chemical chains based on TER records or chain id changing. 54: 54: There are 1 chains and 0 blocks of water and 58 residues with 488 atoms 54: 54: chain #res #atoms 54: 54: 1 'A' 58 488 54: 54: All occupancies are one 54: 54: Reading residue database... (Oplsaa) 54: 54: Processing chain 1 'A' (488 atoms, 58 residues) 54: 54: Identified residue ASN24 as a starting terminus. 54: 54: Identified residue ARG81 as a ending terminus. 54: Start terminus ASN-24: NH3+ 54: End terminus ARG-81: COO- 54: 54: Checking for duplicate atoms.... 54: 54: Generating any missing hydrogen atoms and/or adding termini. 54: 54: Now there are 58 residues with 936 atoms 54: 54: Making bonds... 54: 54: Number of bonds was 951, now 951 54: 54: Generating angles, dihedrals and pairs... 54: 54: Making cmap torsions... 54: 54: There are 2524 dihedrals, 208 impropers, 1704 angles 54: 2469 pairs, 951 bonds and 0 virtual sites 54: 54: Total mass 6908.578 a.m.u. 54: 54: Total charge -6.000 e 54: 54: Writing topology 54: 54: Writing coordinate file... 54: 54: --------- PLEASE NOTE ------------ 54: 54: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/E.pdb. 54: 54: The Oplsaa force field and the tip5p water model are used. 54: 54: --------- ETON ESAELP ------------ 54: [ OK ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip5p_vsite_none_id_or_ter_merge_no_Epdb_format_gro_match_file (613 ms) 54: [ RUN ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip5p_vsite_h_id_or_ter_merge_no_Apdb_format_gro_match_file 54: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/oplsaa.ff/aminoacids.r2b 54: All occupancies are one 54: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/oplsaa.ff/atomtypes.atp 54: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/oplsaa.ff/aminoacids.rtp 54: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/oplsaa.ff/aminoacids.hdb 54: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/oplsaa.ff/aminoacids.n.tdb 54: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/oplsaa.ff/aminoacids.c.tdb 54: Analysing hydrogen-bonding network for automated assignment of histidine 54: protonation. 25 donors and 23 acceptors were found. 54: There are 41 hydrogen bonds 54: Will use HISE for residue 8 54: 9 out of 9 lines of specbond.dat converted successfully 54: Special Atom Distance matrix: 54: CYS3 HIS8 54: SG9 NE251 54: HIS8 NE251 1.055 54: MET12 SD83 0.763 0.990 54: Marked 124 virtual sites 54: Added 16 dummy masses 54: Added 26 new constraints 54: Before cleaning: 653 pairs 54: Before cleaning: 663 dihedrals 54: Using the Oplsaa force field in directory oplsaa.ff 54: 54: going to rename oplsaa.ff/aminoacids.r2b 54: Reading /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/A.pdb... 54: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms 54: 54: Analyzing pdb file 54: Splitting chemical chains based on TER records or chain id changing. 54: 54: There are 1 chains and 0 blocks of water and 16 residues with 128 atoms 54: 54: chain #res #atoms 54: 54: 1 ' ' 16 128 54: 54: All occupancies are one 54: 54: Reading residue database... (Oplsaa) 54: 54: Processing chain 1 (128 atoms, 16 residues) 54: 54: Identified residue ALA2 as a starting terminus. 54: 54: Identified residue SER17 as a ending terminus. 54: Start terminus ALA-2: NH3+ 54: End terminus SER-17: COO- 54: 54: Checking for duplicate atoms.... 54: 54: Generating any missing hydrogen atoms and/or adding termini. 54: 54: Now there are 16 residues with 252 atoms 54: 54: Making bonds... 54: 54: Number of bonds was 254, now 254 54: 54: Generating angles, dihedrals and pairs... 54: 54: Making cmap torsions... 54: 54: There are 663 dihedrals, 51 impropers, 457 angles 54: 650 pairs, 254 bonds and 130 virtual sites 54: 54: Total mass 1846.112 a.m.u. 54: 54: Total charge 0.000 e 54: 54: Writing topology 54: 54: Writing coordinate file... 54: 54: --------- PLEASE NOTE ------------ 54: 54: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/A.pdb. 54: 54: The Oplsaa force field and the tip5p water model are used. 54: 54: --------- ETON ESAELP ------------ 54: [ OK ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip5p_vsite_h_id_or_ter_merge_no_Apdb_format_gro_match_file (225 ms) 54: [ RUN ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip5p_vsite_h_id_or_ter_merge_no_Bpdb_format_gro_match_file 54: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/oplsaa.ff/aminoacids.r2b 54: All occupancies are one 54: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/oplsaa.ff/atomtypes.atp 54: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/oplsaa.ff/aminoacids.rtp 54: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/oplsaa.ff/aminoacids.hdb 54: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/oplsaa.ff/aminoacids.n.tdb 54: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/oplsaa.ff/aminoacids.c.tdb 54: Analysing hydrogen-bonding network for automated assignment of histidine 54: protonation. 30 donors and 22 acceptors were found. 54: There are 36 hydrogen bonds 54: Will use HISE for residue 29 54: Will use HISE for residue 32 54: 9 out of 9 lines of specbond.dat converted successfully 54: Special Atom Distance matrix: 54: CYS27 HIS29 54: SG90 NE2111 54: HIS29 NE2111 0.987 54: HIS32 NE2135 1.590 1.155 54: Marked 132 virtual sites 54: Added 10 dummy masses 54: Added 19 new constraints 54: Before cleaning: 748 pairs 54: Before cleaning: 778 dihedrals 54: Using the Oplsaa force field in directory oplsaa.ff 54: 54: going to rename oplsaa.ff/aminoacids.r2b 54: Reading /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/B.pdb... 54: Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms 54: 54: Analyzing pdb file 54: Splitting chemical chains based on TER records or chain id changing. 54: 54: There are 1 chains and 0 blocks of water and 16 residues with 149 atoms 54: 54: chain #res #atoms 54: 54: 1 ' ' 16 149 54: 54: All occupancies are one 54: 54: Reading residue database... (Oplsaa) 54: 54: Processing chain 1 (149 atoms, 16 residues) 54: 54: Replaced 1 residue named GLUH to the default GLU. Use interactive selection of protonated residues if that is what you need. 54: 54: Identified residue THR18 as a starting terminus. 54: 54: Identified residue PHE33 as a ending terminus. 54: Start terminus THR-18: NH3+ 54: End terminus PHE-33: COO- 54: 54: Checking for duplicate atoms.... 54: 54: Generating any missing hydrogen atoms and/or adding termini. 54: 54: Now there are 16 residues with 281 atoms 54: 54: Making bonds... 54: 54: Number of bonds was 290, now 290 54: 54: Generating angles, dihedrals and pairs... 54: 54: Making cmap torsions... 54: 54: There are 778 dihedrals, 72 impropers, 516 angles 54: 736 pairs, 290 bonds and 133 virtual sites 54: 54: Total mass 2088.357 a.m.u. 54: 54: Total charge 1.000 e 54: 54: Writing topology 54: 54: Writing coordinate file... 54: 54: --------- PLEASE NOTE ------------ 54: 54: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/B.pdb. 54: 54: The Oplsaa force field and the tip5p water model are used. 54: 54: --------- ETON ESAELP ------------ 54: [ OK ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip5p_vsite_h_id_or_ter_merge_no_Bpdb_format_gro_match_file (246 ms) 54: [ RUN ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip5p_vsite_h_id_or_ter_merge_no_Cpdb_format_gro_match_file 54: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/oplsaa.ff/aminoacids.r2b 54: All occupancies are one 54: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/oplsaa.ff/atomtypes.atp 54: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/oplsaa.ff/aminoacids.rtp 54: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/oplsaa.ff/aminoacids.hdb 54: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/oplsaa.ff/aminoacids.n.tdb 54: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/oplsaa.ff/aminoacids.c.tdb 54: Analysing hydrogen-bonding network for automated assignment of histidine 54: protonation. 22 donors and 22 acceptors were found. 54: There are 26 hydrogen bonds 54: Will use HISE for residue 45 54: 9 out of 9 lines of specbond.dat converted successfully 54: Special Atom Distance matrix: 54: HIS45 54: NE295 54: MET46 SD102 1.078 54: Marked 123 virtual sites 54: Added 22 dummy masses 54: Added 35 new constraints 54: Before cleaning: 676 pairs 54: Before cleaning: 696 dihedrals 54: Using the Oplsaa force field in directory oplsaa.ff 54: 54: going to rename oplsaa.ff/aminoacids.r2b 54: Reading /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/C.pdb... 54: Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms 54: 54: Analyzing pdb file 54: Splitting chemical chains based on TER records or chain id changing. 54: 54: There are 1 chains and 0 blocks of water and 16 residues with 132 atoms 54: 54: chain #res #atoms 54: 54: 1 ' ' 16 132 54: 54: All occupancies are one 54: 54: Reading residue database... (Oplsaa) 54: 54: Processing chain 1 (132 atoms, 16 residues) 54: 54: Identified residue ALA34 as a starting terminus. 54: 54: Identified residue ALA49 as a ending terminus. 54: Start terminus ALA-34: NH3+ 54: End terminus ALA-49: COO- 54: 54: Checking for duplicate atoms.... 54: 54: Generating any missing hydrogen atoms and/or adding termini. 54: 54: Now there are 16 residues with 255 atoms 54: 54: Making bonds... 54: 54: Number of bonds was 261, now 261 54: 54: Generating angles, dihedrals and pairs... 54: 54: Making cmap torsions... 54: 54: There are 696 dihedrals, 56 impropers, 472 angles 54: 667 pairs, 261 bonds and 132 virtual sites 54: 54: Total mass 1861.128 a.m.u. 54: 54: Total charge -1.000 e 54: 54: Writing topology 54: 54: Writing coordinate file... 54: 54: --------- PLEASE NOTE ------------ 54: 54: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/C.pdb. 54: 54: The Oplsaa force field and the tip5p water model are used. 54: 54: --------- ETON ESAELP ------------ 54: [ OK ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip5p_vsite_h_id_or_ter_merge_no_Cpdb_format_gro_match_file (234 ms) 54: [ RUN ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip5p_vsite_h_id_or_ter_merge_no_Dpdb_format_gro_match_file 54: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/oplsaa.ff/aminoacids.r2b 54: All occupancies are one 54: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/oplsaa.ff/atomtypes.atp 54: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/oplsaa.ff/aminoacids.rtp 54: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/oplsaa.ff/aminoacids.hdb 54: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/oplsaa.ff/aminoacids.n.tdb 54: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/oplsaa.ff/aminoacids.c.tdb 54: Analysing hydrogen-bonding network for automated assignment of histidine 54: protonation. 22 donors and 21 acceptors were found. 54: There are 30 hydrogen bonds 54: Will use HISE for residue 60 54: 9 out of 9 lines of specbond.dat converted successfully 54: Special Atom Distance matrix: 54: HIS60 54: NE285 54: CYS62 SG98 0.803 54: Marked 111 virtual sites 54: Added 18 dummy masses 54: Added 31 new constraints 54: Before cleaning: 603 pairs 54: Before cleaning: 618 dihedrals 54: Using the Oplsaa force field in directory oplsaa.ff 54: 54: going to rename oplsaa.ff/aminoacids.r2b 54: Reading /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/D.pdb... 54: Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms 54: 54: Analyzing pdb file 54: Splitting chemical chains based on TER records or chain id changing. 54: 54: There are 1 chains and 0 blocks of water and 16 residues with 117 atoms 54: 54: chain #res #atoms 54: 54: 1 ' ' 16 117 54: 54: All occupancies are one 54: 54: Reading residue database... (Oplsaa) 54: 54: Processing chain 1 (117 atoms, 16 residues) 54: 54: Replaced 1 residue named ASPH to the default ASP. Use interactive selection of protonated residues if that is what you need. 54: 54: Identified residue LYS50 as a starting terminus. 54: 54: Identified residue PRO65 as a ending terminus. 54: Start terminus LYS-50: NH3+ 54: End terminus PRO-65: PRO-COO- 54: 54: Checking for duplicate atoms.... 54: 54: Generating any missing hydrogen atoms and/or adding termini. 54: 54: Now there are 16 residues with 228 atoms 54: 54: Making bonds... 54: 54: Number of bonds was 232, now 232 54: 54: Generating angles, dihedrals and pairs... 54: 54: Making cmap torsions... 54: 54: There are 618 dihedrals, 48 impropers, 419 angles 54: 597 pairs, 232 bonds and 116 virtual sites 54: 54: Total mass 1662.883 a.m.u. 54: 54: Total charge 0.000 e 54: 54: Writing topology 54: 54: Writing coordinate file... 54: 54: --------- PLEASE NOTE ------------ 54: 54: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/D.pdb. 54: 54: The Oplsaa force field and the tip5p water model are used. 54: 54: --------- ETON ESAELP ------------ 54: [ OK ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip5p_vsite_h_id_or_ter_merge_no_Dpdb_format_gro_match_file (203 ms) 54: [ RUN ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip5p_vsite_h_id_or_ter_merge_no_Epdb_format_gro_match_file 54: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/oplsaa.ff/aminoacids.r2b 54: All occupancies are one 54: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/oplsaa.ff/atomtypes.atp 54: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/oplsaa.ff/aminoacids.rtp 54: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/oplsaa.ff/aminoacids.hdb 54: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/oplsaa.ff/aminoacids.n.tdb 54: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/oplsaa.ff/aminoacids.c.tdb 54: Analysing hydrogen-bonding network for automated assignment of histidine 54: protonation. 89 donors and 98 acceptors were found. 54: There are 129 hydrogen bonds 54: Will use HISE for residue 31 54: Will use HISE for residue 51 54: 9 out of 9 lines of specbond.dat converted successfully 54: Special Atom Distance matrix: 54: CYS25 HIS31 HIS51 54: SG14 NE264 NE2226 54: HIS31 NE264 1.921 54: HIS51 NE2226 1.498 2.650 54: CYS80 SG477 0.207 1.984 1.570 54: Linking CYS-25 SG-14 and CYS-80 SG-477... 54: Marked 447 virtual sites 54: Added 58 dummy masses 54: Added 101 new constraints 54: Before cleaning: 2499 pairs 54: Before cleaning: 2524 dihedrals 54: Using the Oplsaa force field in directory oplsaa.ff 54: 54: going to rename oplsaa.ff/aminoacids.r2b 54: Reading /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/E.pdb... 54: Read 'This is a fragment of 2d4f for testing a disulfide bridge', 488 atoms 54: 54: Analyzing pdb file 54: Splitting chemical chains based on TER records or chain id changing. 54: 54: There are 1 chains and 0 blocks of water and 58 residues with 488 atoms 54: 54: chain #res #atoms 54: 54: 1 'A' 58 488 54: 54: All occupancies are one 54: 54: Reading residue database... (Oplsaa) 54: 54: Processing chain 1 'A' (488 atoms, 58 residues) 54: 54: Identified residue ASN24 as a starting terminus. 54: 54: Identified residue ARG81 as a ending terminus. 54: Start terminus ASN-24: NH3+ 54: End terminus ARG-81: COO- 54: 54: Checking for duplicate atoms.... 54: 54: Generating any missing hydrogen atoms and/or adding termini. 54: 54: Now there are 58 residues with 936 atoms 54: 54: Making bonds... 54: 54: Number of bonds was 951, now 951 54: 54: Generating angles, dihedrals and pairs... 54: 54: Making cmap torsions... 54: 54: There are 2524 dihedrals, 208 impropers, 1704 angles 54: 2469 pairs, 951 bonds and 462 virtual sites 54: 54: Total mass 6908.578 a.m.u. 54: 54: Total charge -6.000 e 54: 54: Writing topology 54: 54: Writing coordinate file... 54: 54: --------- PLEASE NOTE ------------ 54: 54: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/E.pdb. 54: 54: The Oplsaa force field and the tip5p water model are used. 54: 54: --------- ETON ESAELP ------------ 54: [ OK ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip5p_vsite_h_id_or_ter_merge_no_Epdb_format_gro_match_file (697 ms) 54: [----------] 30 tests from Oplsaa/Pdb2gmxTest (9127 ms total) 54: 54: [----------] Global test environment tear-down 54: [==========] 30 tests from 1 test suite ran. (9127 ms total) 54: [ PASSED ] 30 tests. 54/92 Test #54: Pdb2gmx1Test .............................. Passed 9.21 sec test 55 Start 55: Pdb2gmx2Test 55: Test command: /build/reproducible-path/gromacs-2025.1/build/basic-dp/bin/pdb2gmx2-test "--gtest_output=xml:/build/reproducible-path/gromacs-2025.1/build/basic-dp/Testing/Temporary/Pdb2gmx2Test.xml" 55: Working Directory: /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/gmxpreprocess/tests 55: Test timeout computed to be: 1920 55: [==========] Running 40 tests from 2 test suites. 55: [----------] Global test environment set-up. 55: [----------] 20 tests from G43a1/Pdb2gmxTest 55: [ RUN ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spc_vsite_none_id_or_ter_merge_no_Apdb_format_gro_match_file 55: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos43a1.ff/aminoacids.r2b 55: All occupancies are one 55: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos43a1.ff/atomtypes.atp 55: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos43a1.ff/aminoacids.rtp 55: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos43a1.ff/aminoacids.hdb 55: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos43a1.ff/aminoacids.n.tdb 55: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos43a1.ff/aminoacids.c.tdb 55: Analysing hydrogen-bonding network for automated assignment of histidine 55: protonation. 25 donors and 23 acceptors were found. 55: There are 41 hydrogen bonds 55: Will use HISE for residue 8 55: 9 out of 9 lines of specbond.dat converted successfully 55: Special Atom Distance matrix: 55: CYS3 HIS8 55: SG9 NE251 55: HIS8 NE251 1.055 55: MET12 SD83 0.763 0.990 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: WARNING: Residue 1 named ALA of a molecule in the input file was mapped 55: to an entry in the topology database, but the atom H used in 55: an interaction of type angle in that entry is not found in the 55: input file. Perhaps your atom and/or residue naming needs to be 55: fixed. 55: 55: 55: 55: WARNING: WARNING: Residue 16 named SER of a molecule in the input file was mapped 55: to an entry in the topology database, but the atom O used in 55: an interaction of type angle in that entry is not found in the 55: input file. Perhaps your atom and/or residue naming needs to be 55: fixed. 55: 55: 55: Before cleaning: 267 pairs 55: Before cleaning: 305 dihedrals 55: Using the Gromos43a1 force field in directory gromos43a1.ff 55: 55: going to rename gromos43a1.ff/aminoacids.r2b 55: Reading /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/A.pdb... 55: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms 55: 55: Analyzing pdb file 55: Splitting chemical chains based on TER records or chain id changing. 55: 55: There are 1 chains and 0 blocks of water and 16 residues with 128 atoms 55: 55: chain #res #atoms 55: 55: 1 ' ' 16 128 55: 55: All occupancies are one 55: 55: Reading residue database... (Gromos43a1) 55: 55: Processing chain 1 (128 atoms, 16 residues) 55: 55: Identified residue ALA2 as a starting terminus. 55: 55: Identified residue SER17 as a ending terminus. 55: Start terminus ALA-2: NH3+ 55: End terminus SER-17: COO- 55: 55: Checking for duplicate atoms.... 55: 55: Generating any missing hydrogen atoms and/or adding termini. 55: 55: Now there are 16 residues with 165 atoms 55: 55: Making bonds... 55: 55: Number of bonds was 172, now 167 55: 55: Generating angles, dihedrals and pairs... 55: 55: Making cmap torsions... 55: 55: There are 90 dihedrals, 77 impropers, 241 angles 55: 267 pairs, 167 bonds and 0 virtual sites 55: 55: Total mass 1846.116 a.m.u. 55: 55: Total charge 0.000 e 55: 55: Writing topology 55: 55: Writing coordinate file... 55: 55: --------- PLEASE NOTE ------------ 55: 55: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/A.pdb. 55: 55: The Gromos43a1 force field and the spc water model are used. 55: 55: --------- ETON ESAELP ------------ 55: [ OK ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spc_vsite_none_id_or_ter_merge_no_Apdb_format_gro_match_file (248 ms) 55: [ RUN ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spc_vsite_none_id_or_ter_merge_no_Bpdb_format_gro_match_file 55: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos43a1.ff/aminoacids.r2b 55: All occupancies are one 55: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos43a1.ff/atomtypes.atp 55: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos43a1.ff/aminoacids.rtp 55: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos43a1.ff/aminoacids.hdb 55: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos43a1.ff/aminoacids.n.tdb 55: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos43a1.ff/aminoacids.c.tdb 55: Analysing hydrogen-bonding network for automated assignment of histidine 55: protonation. 30 donors and 22 acceptors were found. 55: There are 36 hydrogen bonds 55: Will use HISE for residue 29 55: Will use HISE for residue 32 55: 9 out of 9 lines of specbond.dat converted successfully 55: Special Atom Distance matrix: 55: CYS27 HIS29 55: SG90 NE2111 55: HIS29 NE2111 0.987 55: HIS32 NE2135 1.590 1.155 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: WARNING: Residue 1 named THR of a molecule in the input file was mapped 55: to an entry in the topology database, but the atom H used in 55: an interaction of type angle in that entry is not found in the 55: input file. Perhaps your atom and/or residue naming needs to be 55: fixed. 55: 55: 55: 55: WARNING: WARNING: Residue 16 named PHE of a molecule in the input file was mapped 55: to an entry in the topology database, but the atom O used in 55: an interaction of type angle in that entry is not found in the 55: input file. Perhaps your atom and/or residue naming needs to be 55: fixed. 55: 55: 55: Before cleaning: 273 pairs 55: Before cleaning: 429 dihedrals 55: Using the Gromos43a1 force field in directory gromos43a1.ff 55: 55: going to rename gromos43a1.ff/aminoacids.r2b 55: Reading /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/B.pdb... 55: Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms 55: 55: Analyzing pdb file 55: Splitting chemical chains based on TER records or chain id changing. 55: 55: There are 1 chains and 0 blocks of water and 16 residues with 149 atoms 55: 55: chain #res #atoms 55: 55: 1 ' ' 16 149 55: 55: All occupancies are one 55: 55: Reading residue database... (Gromos43a1) 55: 55: Processing chain 1 (149 atoms, 16 residues) 55: 55: Replaced 1 residue named GLUH to the default GLU. Use interactive selection of protonated residues if that is what you need. 55: 55: Identified residue THR18 as a starting terminus. 55: 55: Identified residue PHE33 as a ending terminus. 55: Start terminus THR-18: NH3+ 55: End terminus PHE-33: COO- 55: 55: Checking for duplicate atoms.... 55: 55: Generating any missing hydrogen atoms and/or adding termini. 55: 55: Now there are 16 residues with 202 atoms 55: 55: Making bonds... 55: 55: Number of bonds was 216, now 211 55: 55: Generating angles, dihedrals and pairs... 55: 55: Making cmap torsions... 55: 55: There are 93 dihedrals, 134 impropers, 316 angles 55: 273 pairs, 211 bonds and 0 virtual sites 55: 55: Total mass 2088.361 a.m.u. 55: 55: Total charge 1.000 e 55: 55: Writing topology 55: 55: Writing coordinate file... 55: 55: --------- PLEASE NOTE ------------ 55: 55: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/B.pdb. 55: 55: The Gromos43a1 force field and the spc water model are used. 55: 55: --------- ETON ESAELP ------------ 55: [ OK ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spc_vsite_none_id_or_ter_merge_no_Bpdb_format_gro_match_file (255 ms) 55: [ RUN ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spc_vsite_none_id_or_ter_merge_no_Cpdb_format_gro_match_file 55: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos43a1.ff/aminoacids.r2b 55: All occupancies are one 55: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos43a1.ff/atomtypes.atp 55: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos43a1.ff/aminoacids.rtp 55: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos43a1.ff/aminoacids.hdb 55: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos43a1.ff/aminoacids.n.tdb 55: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos43a1.ff/aminoacids.c.tdb 55: Analysing hydrogen-bonding network for automated assignment of histidine 55: protonation. 22 donors and 22 acceptors were found. 55: There are 26 hydrogen bonds 55: Will use HISE for residue 45 55: 9 out of 9 lines of specbond.dat converted successfully 55: Special Atom Distance matrix: 55: HIS45 55: NE295 55: MET46 SD102 1.078 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: WARNING: Residue 1 named ALA of a molecule in the input file was mapped 55: to an entry in the topology database, but the atom H used in 55: an interaction of type angle in that entry is not found in the 55: input file. Perhaps your atom and/or residue naming needs to be 55: fixed. 55: 55: 55: 55: WARNING: WARNING: Residue 16 named ALA of a molecule in the input file was mapped 55: to an entry in the topology database, but the atom O used in 55: an interaction of type angle in that entry is not found in the 55: input file. Perhaps your atom and/or residue naming needs to be 55: fixed. 55: 55: 55: Before cleaning: 242 pairs 55: Before cleaning: 349 dihedrals 55: Using the Gromos43a1 force field in directory gromos43a1.ff 55: 55: going to rename gromos43a1.ff/aminoacids.r2b 55: Reading /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/C.pdb... 55: Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms 55: 55: Analyzing pdb file 55: Splitting chemical chains based on TER records or chain id changing. 55: 55: There are 1 chains and 0 blocks of water and 16 residues with 132 atoms 55: 55: chain #res #atoms 55: 55: 1 ' ' 16 132 55: 55: All occupancies are one 55: 55: Reading residue database... (Gromos43a1) 55: 55: Processing chain 1 (132 atoms, 16 residues) 55: 55: Identified residue ALA34 as a starting terminus. 55: 55: Identified residue ALA49 as a ending terminus. 55: Start terminus ALA-34: NH3+ 55: End terminus ALA-49: COO- 55: 55: Checking for duplicate atoms.... 55: 55: Generating any missing hydrogen atoms and/or adding termini. 55: 55: Now there are 16 residues with 168 atoms 55: 55: Making bonds... 55: 55: Number of bonds was 179, now 174 55: 55: Generating angles, dihedrals and pairs... 55: 55: Making cmap torsions... 55: 55: There are 81 dihedrals, 102 impropers, 260 angles 55: 242 pairs, 174 bonds and 0 virtual sites 55: 55: Total mass 1861.132 a.m.u. 55: 55: Total charge -1.000 e 55: 55: Writing topology 55: 55: Writing coordinate file... 55: 55: --------- PLEASE NOTE ------------ 55: 55: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/C.pdb. 55: 55: The Gromos43a1 force field and the spc water model are used. 55: 55: --------- ETON ESAELP ------------ 55: [ OK ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spc_vsite_none_id_or_ter_merge_no_Cpdb_format_gro_match_file (238 ms) 55: [ RUN ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spc_vsite_none_id_or_ter_merge_no_Dpdb_format_gro_match_file 55: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos43a1.ff/aminoacids.r2b 55: All occupancies are one 55: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos43a1.ff/atomtypes.atp 55: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos43a1.ff/aminoacids.rtp 55: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos43a1.ff/aminoacids.hdb 55: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos43a1.ff/aminoacids.n.tdb 55: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos43a1.ff/aminoacids.c.tdb 55: Analysing hydrogen-bonding network for automated assignment of histidine 55: protonation. 22 donors and 21 acceptors were found. 55: There are 30 hydrogen bonds 55: Will use HISE for residue 60 55: 9 out of 9 lines of specbond.dat converted successfully 55: Special Atom Distance matrix: 55: HIS60 55: NE285 55: CYS62 SG98 0.803 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: WARNING: Residue 1 named LYS of a molecule in the input file was mapped 55: to an entry in the topology database, but the atom H used in 55: an interaction of type angle in that entry is not found in the 55: input file. Perhaps your atom and/or residue naming needs to be 55: fixed. 55: 55: 55: 55: WARNING: WARNING: Residue 16 named PRO of a molecule in the input file was mapped 55: to an entry in the topology database, but the atom O used in 55: an interaction of type angle in that entry is not found in the 55: input file. Perhaps your atom and/or residue naming needs to be 55: fixed. 55: 55: 55: Before cleaning: 232 pairs 55: Before cleaning: 299 dihedrals 55: Using the Gromos43a1 force field in directory gromos43a1.ff 55: 55: going to rename gromos43a1.ff/aminoacids.r2b 55: Reading /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/D.pdb... 55: Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms 55: 55: Analyzing pdb file 55: Splitting chemical chains based on TER records or chain id changing. 55: 55: There are 1 chains and 0 blocks of water and 16 residues with 117 atoms 55: 55: chain #res #atoms 55: 55: 1 ' ' 16 117 55: 55: All occupancies are one 55: 55: Reading residue database... (Gromos43a1) 55: 55: Processing chain 1 (117 atoms, 16 residues) 55: 55: Replaced 1 residue named ASPH to the default ASP. Use interactive selection of protonated residues if that is what you need. 55: 55: Identified residue LYS50 as a starting terminus. 55: 55: Identified residue PRO65 as a ending terminus. 55: Start terminus LYS-50: NH3+ 55: End terminus PRO-65: COO- 55: 55: Checking for duplicate atoms.... 55: 55: Generating any missing hydrogen atoms and/or adding termini. 55: 55: Now there are 16 residues with 150 atoms 55: 55: Making bonds... 55: 55: Number of bonds was 159, now 154 55: 55: Generating angles, dihedrals and pairs... 55: 55: Making cmap torsions... 55: 55: There are 78 dihedrals, 80 impropers, 227 angles 55: 232 pairs, 154 bonds and 0 virtual sites 55: 55: Total mass 1662.887 a.m.u. 55: 55: Total charge 0.000 e 55: 55: Writing topology 55: 55: Writing coordinate file... 55: 55: --------- PLEASE NOTE ------------ 55: 55: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/D.pdb. 55: 55: The Gromos43a1 force field and the spc water model are used. 55: 55: --------- ETON ESAELP ------------ 55: [ OK ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spc_vsite_none_id_or_ter_merge_no_Dpdb_format_gro_match_file (228 ms) 55: [ RUN ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spc_vsite_none_id_or_ter_merge_no_Epdb_format_gro_match_file 55: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos43a1.ff/aminoacids.r2b 55: All occupancies are one 55: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos43a1.ff/atomtypes.atp 55: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos43a1.ff/aminoacids.rtp 55: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos43a1.ff/aminoacids.hdb 55: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos43a1.ff/aminoacids.n.tdb 55: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos43a1.ff/aminoacids.c.tdb 55: Analysing hydrogen-bonding network for automated assignment of histidine 55: protonation. 89 donors and 98 acceptors were found. 55: There are 129 hydrogen bonds 55: Will use HISE for residue 31 55: Will use HISE for residue 51 55: 9 out of 9 lines of specbond.dat converted successfully 55: Special Atom Distance matrix: 55: CYS25 HIS31 HIS51 55: SG14 NE264 NE2226 55: HIS31 NE264 1.921 55: HIS51 NE2226 1.498 2.650 55: CYS80 SG477 0.207 1.984 1.570 55: Linking CYS-25 SG-14 and CYS-80 SG-477... 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: WARNING: Residue 1 named ASN of a molecule in the input file was mapped 55: to an entry in the topology database, but the atom H used in 55: an interaction of type angle in that entry is not found in the 55: input file. Perhaps your atom and/or residue naming needs to be 55: fixed. 55: 55: 55: 55: WARNING: WARNING: Residue 58 named ARG of a molecule in the input file was mapped 55: to an entry in the topology database, but the atom O used in 55: an interaction of type angle in that entry is not found in the 55: input file. Perhaps your atom and/or residue naming needs to be 55: fixed. 55: 55: 55: Before cleaning: 972 pairs 55: Before cleaning: 1256 dihedrals 55: Using the Gromos43a1 force field in directory gromos43a1.ff 55: 55: going to rename gromos43a1.ff/aminoacids.r2b 55: Reading /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/E.pdb... 55: Read 'This is a fragment of 2d4f for testing a disulfide bridge', 488 atoms 55: 55: Analyzing pdb file 55: Splitting chemical chains based on TER records or chain id changing. 55: 55: There are 1 chains and 0 blocks of water and 58 residues with 488 atoms 55: 55: chain #res #atoms 55: 55: 1 'A' 58 488 55: 55: All occupancies are one 55: 55: Reading residue database... (Gromos43a1) 55: 55: Processing chain 1 'A' (488 atoms, 58 residues) 55: 55: Identified residue ASN24 as a starting terminus. 55: 55: Identified residue ARG81 as a ending terminus. 55: Start terminus ASN-24: NH3+ 55: End terminus ARG-81: COO- 55: 55: Checking for duplicate atoms.... 55: 55: Generating any missing hydrogen atoms and/or adding termini. 55: 55: Now there are 58 residues with 635 atoms 55: 55: Making bonds... 55: 55: Number of bonds was 655, now 650 55: 55: Generating angles, dihedrals and pairs... 55: 55: Making cmap torsions... 55: 55: There are 321 dihedrals, 350 impropers, 955 angles 55: 972 pairs, 650 bonds and 0 virtual sites 55: 55: Total mass 6908.582 a.m.u. 55: 55: Total charge -6.000 e 55: 55: Writing topology 55: 55: Writing coordinate file... 55: 55: --------- PLEASE NOTE ------------ 55: 55: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/E.pdb. 55: 55: The Gromos43a1 force field and the spc water model are used. 55: 55: --------- ETON ESAELP ------------ 55: [ OK ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spc_vsite_none_id_or_ter_merge_no_Epdb_format_gro_match_file (485 ms) 55: [ RUN ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spc_vsite_h_id_or_ter_merge_no_Apdb_format_gro_match_file 55: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos43a1.ff/aminoacids.r2b 55: All occupancies are one 55: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos43a1.ff/atomtypes.atp 55: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos43a1.ff/aminoacids.rtp 55: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos43a1.ff/aminoacids.hdb 55: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos43a1.ff/aminoacids.n.tdb 55: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos43a1.ff/aminoacids.c.tdb 55: Analysing hydrogen-bonding network for automated assignment of histidine 55: protonation. 25 donors and 23 acceptors were found. 55: There are 41 hydrogen bonds 55: Will use HISE for residue 8 55: 9 out of 9 lines of specbond.dat converted successfully 55: Special Atom Distance matrix: 55: CYS3 HIS8 55: SG9 NE251 55: HIS8 NE251 1.055 55: MET12 SD83 0.763 0.990 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: Marked 37 virtual sites 55: Added 4 dummy masses 55: Added 8 new constraints 55: 55: WARNING: WARNING: Residue 1 named ALA of a molecule in the input file was mapped 55: to an entry in the topology database, but the atom H used in 55: an interaction of type angle in that entry is not found in the 55: input file. Perhaps your atom and/or residue naming needs to be 55: fixed. 55: 55: 55: 55: WARNING: WARNING: Residue 16 named SER of a molecule in the input file was mapped 55: to an entry in the topology database, but the atom O used in 55: an interaction of type angle in that entry is not found in the 55: input file. Perhaps your atom and/or residue naming needs to be 55: fixed. 55: 55: 55: Before cleaning: 267 pairs 55: Before cleaning: 305 dihedrals 55: Using the Gromos43a1 force field in directory gromos43a1.ff 55: 55: going to rename gromos43a1.ff/aminoacids.r2b 55: Reading /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/A.pdb... 55: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms 55: 55: Analyzing pdb file 55: Splitting chemical chains based on TER records or chain id changing. 55: 55: There are 1 chains and 0 blocks of water and 16 residues with 128 atoms 55: 55: chain #res #atoms 55: 55: 1 ' ' 16 128 55: 55: All occupancies are one 55: 55: Reading residue database... (Gromos43a1) 55: 55: Processing chain 1 (128 atoms, 16 residues) 55: 55: Identified residue ALA2 as a starting terminus. 55: 55: Identified residue SER17 as a ending terminus. 55: Start terminus ALA-2: NH3+ 55: End terminus SER-17: COO- 55: 55: Checking for duplicate atoms.... 55: 55: Generating any missing hydrogen atoms and/or adding termini. 55: 55: Now there are 16 residues with 165 atoms 55: 55: Making bonds... 55: 55: Number of bonds was 172, now 167 55: 55: Generating angles, dihedrals and pairs... 55: 55: Making cmap torsions... 55: 55: There are 90 dihedrals, 77 impropers, 241 angles 55: 267 pairs, 167 bonds and 37 virtual sites 55: 55: Total mass 1846.116 a.m.u. 55: 55: Total charge 0.000 e 55: 55: Writing topology 55: 55: Writing coordinate file... 55: 55: --------- PLEASE NOTE ------------ 55: 55: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/A.pdb. 55: 55: The Gromos43a1 force field and the spc water model are used. 55: 55: --------- ETON ESAELP ------------ 55: [ OK ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spc_vsite_h_id_or_ter_merge_no_Apdb_format_gro_match_file (241 ms) 55: [ RUN ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spc_vsite_h_id_or_ter_merge_no_Bpdb_format_gro_match_file 55: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos43a1.ff/aminoacids.r2b 55: All occupancies are one 55: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos43a1.ff/atomtypes.atp 55: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos43a1.ff/aminoacids.rtp 55: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos43a1.ff/aminoacids.hdb 55: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos43a1.ff/aminoacids.n.tdb 55: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos43a1.ff/aminoacids.c.tdb 55: Analysing hydrogen-bonding network for automated assignment of histidine 55: protonation. 30 donors and 22 acceptors were found. 55: There are 36 hydrogen bonds 55: Will use HISE for residue 29 55: Will use HISE for residue 32 55: 9 out of 9 lines of specbond.dat converted successfully 55: Special Atom Distance matrix: 55: CYS27 HIS29 55: SG90 NE2111 55: HIS29 NE2111 0.987 55: HIS32 NE2135 1.590 1.155 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: Marked 53 virtual sites 55: Added 4 dummy masses 55: Added 10 new constraints 55: 55: WARNING: WARNING: Residue 1 named THR of a molecule in the input file was mapped 55: to an entry in the topology database, but the atom H used in 55: an interaction of type angle in that entry is not found in the 55: input file. Perhaps your atom and/or residue naming needs to be 55: fixed. 55: 55: 55: 55: WARNING: WARNING: Residue 16 named PHE of a molecule in the input file was mapped 55: to an entry in the topology database, but the atom O used in 55: an interaction of type angle in that entry is not found in the 55: input file. Perhaps your atom and/or residue naming needs to be 55: fixed. 55: 55: 55: Before cleaning: 273 pairs 55: Before cleaning: 429 dihedrals 55: Using the Gromos43a1 force field in directory gromos43a1.ff 55: 55: going to rename gromos43a1.ff/aminoacids.r2b 55: Reading /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/B.pdb... 55: Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms 55: 55: Analyzing pdb file 55: Splitting chemical chains based on TER records or chain id changing. 55: 55: There are 1 chains and 0 blocks of water and 16 residues with 149 atoms 55: 55: chain #res #atoms 55: 55: 1 ' ' 16 149 55: 55: All occupancies are one 55: 55: Reading residue database... (Gromos43a1) 55: 55: Processing chain 1 (149 atoms, 16 residues) 55: 55: Replaced 1 residue named GLUH to the default GLU. Use interactive selection of protonated residues if that is what you need. 55: 55: Identified residue THR18 as a starting terminus. 55: 55: Identified residue PHE33 as a ending terminus. 55: Start terminus THR-18: NH3+ 55: End terminus PHE-33: COO- 55: 55: Checking for duplicate atoms.... 55: 55: Generating any missing hydrogen atoms and/or adding termini. 55: 55: Now there are 16 residues with 202 atoms 55: 55: Making bonds... 55: 55: Number of bonds was 216, now 211 55: 55: Generating angles, dihedrals and pairs... 55: 55: Making cmap torsions... 55: 55: There are 93 dihedrals, 134 impropers, 316 angles 55: 273 pairs, 211 bonds and 51 virtual sites 55: 55: Total mass 2088.361 a.m.u. 55: 55: Total charge 1.000 e 55: 55: Writing topology 55: 55: Writing coordinate file... 55: 55: --------- PLEASE NOTE ------------ 55: 55: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/B.pdb. 55: 55: The Gromos43a1 force field and the spc water model are used. 55: 55: --------- ETON ESAELP ------------ 55: [ OK ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spc_vsite_h_id_or_ter_merge_no_Bpdb_format_gro_match_file (265 ms) 55: [ RUN ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spc_vsite_h_id_or_ter_merge_no_Cpdb_format_gro_match_file 55: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos43a1.ff/aminoacids.r2b 55: All occupancies are one 55: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos43a1.ff/atomtypes.atp 55: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos43a1.ff/aminoacids.rtp 55: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos43a1.ff/aminoacids.hdb 55: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos43a1.ff/aminoacids.n.tdb 55: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos43a1.ff/aminoacids.c.tdb 55: Analysing hydrogen-bonding network for automated assignment of histidine 55: protonation. 22 donors and 22 acceptors were found. 55: There are 26 hydrogen bonds 55: Will use HISE for residue 45 55: 9 out of 9 lines of specbond.dat converted successfully 55: Special Atom Distance matrix: 55: HIS45 55: NE295 55: MET46 SD102 1.078 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: Marked 36 virtual sites 55: Added 4 dummy masses 55: Added 8 new constraints 55: 55: WARNING: WARNING: Residue 1 named ALA of a molecule in the input file was mapped 55: to an entry in the topology database, but the atom H used in 55: an interaction of type angle in that entry is not found in the 55: input file. Perhaps your atom and/or residue naming needs to be 55: fixed. 55: 55: 55: 55: WARNING: WARNING: Residue 16 named ALA of a molecule in the input file was mapped 55: to an entry in the topology database, but the atom O used in 55: an interaction of type angle in that entry is not found in the 55: input file. Perhaps your atom and/or residue naming needs to be 55: fixed. 55: 55: 55: Before cleaning: 242 pairs 55: Before cleaning: 349 dihedrals 55: Using the Gromos43a1 force field in directory gromos43a1.ff 55: 55: going to rename gromos43a1.ff/aminoacids.r2b 55: Reading /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/C.pdb... 55: Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms 55: 55: Analyzing pdb file 55: Splitting chemical chains based on TER records or chain id changing. 55: 55: There are 1 chains and 0 blocks of water and 16 residues with 132 atoms 55: 55: chain #res #atoms 55: 55: 1 ' ' 16 132 55: 55: All occupancies are one 55: 55: Reading residue database... (Gromos43a1) 55: 55: Processing chain 1 (132 atoms, 16 residues) 55: 55: Identified residue ALA34 as a starting terminus. 55: 55: Identified residue ALA49 as a ending terminus. 55: Start terminus ALA-34: NH3+ 55: End terminus ALA-49: COO- 55: 55: Checking for duplicate atoms.... 55: 55: Generating any missing hydrogen atoms and/or adding termini. 55: 55: Now there are 16 residues with 168 atoms 55: 55: Making bonds... 55: 55: Number of bonds was 179, now 174 55: 55: Generating angles, dihedrals and pairs... 55: 55: Making cmap torsions... 55: 55: There are 81 dihedrals, 102 impropers, 260 angles 55: 242 pairs, 174 bonds and 36 virtual sites 55: 55: Total mass 1861.132 a.m.u. 55: 55: Total charge -1.000 e 55: 55: Writing topology 55: 55: Writing coordinate file... 55: 55: --------- PLEASE NOTE ------------ 55: 55: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/C.pdb. 55: 55: The Gromos43a1 force field and the spc water model are used. 55: 55: --------- ETON ESAELP ------------ 55: [ OK ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spc_vsite_h_id_or_ter_merge_no_Cpdb_format_gro_match_file (264 ms) 55: [ RUN ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spc_vsite_h_id_or_ter_merge_no_Dpdb_format_gro_match_file 55: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos43a1.ff/aminoacids.r2b 55: All occupancies are one 55: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos43a1.ff/atomtypes.atp 55: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos43a1.ff/aminoacids.rtp 55: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos43a1.ff/aminoacids.hdb 55: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos43a1.ff/aminoacids.n.tdb 55: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos43a1.ff/aminoacids.c.tdb 55: Analysing hydrogen-bonding network for automated assignment of histidine 55: protonation. 22 donors and 21 acceptors were found. 55: There are 30 hydrogen bonds 55: Will use HISE for residue 60 55: 9 out of 9 lines of specbond.dat converted successfully 55: Special Atom Distance matrix: 55: HIS60 55: NE285 55: CYS62 SG98 0.803 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: Marked 33 virtual sites 55: Added 4 dummy masses 55: Added 10 new constraints 55: 55: WARNING: WARNING: Residue 1 named LYS of a molecule in the input file was mapped 55: to an entry in the topology database, but the atom H used in 55: an interaction of type angle in that entry is not found in the 55: input file. Perhaps your atom and/or residue naming needs to be 55: fixed. 55: 55: 55: 55: WARNING: WARNING: Residue 16 named PRO of a molecule in the input file was mapped 55: to an entry in the topology database, but the atom O used in 55: an interaction of type angle in that entry is not found in the 55: input file. Perhaps your atom and/or residue naming needs to be 55: fixed. 55: 55: 55: Before cleaning: 232 pairs 55: Before cleaning: 299 dihedrals 55: Using the Gromos43a1 force field in directory gromos43a1.ff 55: 55: going to rename gromos43a1.ff/aminoacids.r2b 55: Reading /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/D.pdb... 55: Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms 55: 55: Analyzing pdb file 55: Splitting chemical chains based on TER records or chain id changing. 55: 55: There are 1 chains and 0 blocks of water and 16 residues with 117 atoms 55: 55: chain #res #atoms 55: 55: 1 ' ' 16 117 55: 55: All occupancies are one 55: 55: Reading residue database... (Gromos43a1) 55: 55: Processing chain 1 (117 atoms, 16 residues) 55: 55: Replaced 1 residue named ASPH to the default ASP. Use interactive selection of protonated residues if that is what you need. 55: 55: Identified residue LYS50 as a starting terminus. 55: 55: Identified residue PRO65 as a ending terminus. 55: Start terminus LYS-50: NH3+ 55: End terminus PRO-65: COO- 55: 55: Checking for duplicate atoms.... 55: 55: Generating any missing hydrogen atoms and/or adding termini. 55: 55: Now there are 16 residues with 150 atoms 55: 55: Making bonds... 55: 55: Number of bonds was 159, now 154 55: 55: Generating angles, dihedrals and pairs... 55: 55: Making cmap torsions... 55: 55: There are 78 dihedrals, 80 impropers, 227 angles 55: 232 pairs, 154 bonds and 31 virtual sites 55: 55: Total mass 1662.887 a.m.u. 55: 55: Total charge 0.000 e 55: 55: Writing topology 55: 55: Writing coordinate file... 55: 55: --------- PLEASE NOTE ------------ 55: 55: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/D.pdb. 55: 55: The Gromos43a1 force field and the spc water model are used. 55: 55: --------- ETON ESAELP ------------ 55: [ OK ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spc_vsite_h_id_or_ter_merge_no_Dpdb_format_gro_match_file (237 ms) 55: [ RUN ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spc_vsite_h_id_or_ter_merge_no_Epdb_format_gro_match_file 55: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos43a1.ff/aminoacids.r2b 55: All occupancies are one 55: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos43a1.ff/atomtypes.atp 55: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos43a1.ff/aminoacids.rtp 55: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos43a1.ff/aminoacids.hdb 55: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos43a1.ff/aminoacids.n.tdb 55: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos43a1.ff/aminoacids.c.tdb 55: Analysing hydrogen-bonding network for automated assignment of histidine 55: protonation. 89 donors and 98 acceptors were found. 55: There are 129 hydrogen bonds 55: Will use HISE for residue 31 55: Will use HISE for residue 51 55: 9 out of 9 lines of specbond.dat converted successfully 55: Special Atom Distance matrix: 55: CYS25 HIS31 HIS51 55: SG14 NE264 NE2226 55: HIS31 NE264 1.921 55: HIS51 NE2226 1.498 2.650 55: CYS80 SG477 0.207 1.984 1.570 55: Linking CYS-25 SG-14 and CYS-80 SG-477... 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: Marked 146 virtual sites 55: Added 10 dummy masses 55: Added 29 new constraints 55: 55: WARNING: WARNING: Residue 1 named ASN of a molecule in the input file was mapped 55: to an entry in the topology database, but the atom H used in 55: an interaction of type angle in that entry is not found in the 55: input file. Perhaps your atom and/or residue naming needs to be 55: fixed. 55: 55: 55: 55: WARNING: WARNING: Residue 58 named ARG of a molecule in the input file was mapped 55: to an entry in the topology database, but the atom O used in 55: an interaction of type angle in that entry is not found in the 55: input file. Perhaps your atom and/or residue naming needs to be 55: fixed. 55: 55: 55: Before cleaning: 972 pairs 55: Before cleaning: 1256 dihedrals 55: Using the Gromos43a1 force field in directory gromos43a1.ff 55: 55: going to rename gromos43a1.ff/aminoacids.r2b 55: Reading /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/E.pdb... 55: Read 'This is a fragment of 2d4f for testing a disulfide bridge', 488 atoms 55: 55: Analyzing pdb file 55: Splitting chemical chains based on TER records or chain id changing. 55: 55: There are 1 chains and 0 blocks of water and 58 residues with 488 atoms 55: 55: chain #res #atoms 55: 55: 1 'A' 58 488 55: 55: All occupancies are one 55: 55: Reading residue database... (Gromos43a1) 55: 55: Processing chain 1 'A' (488 atoms, 58 residues) 55: 55: Identified residue ASN24 as a starting terminus. 55: 55: Identified residue ARG81 as a ending terminus. 55: Start terminus ASN-24: NH3+ 55: End terminus ARG-81: COO- 55: 55: Checking for duplicate atoms.... 55: 55: Generating any missing hydrogen atoms and/or adding termini. 55: 55: Now there are 58 residues with 635 atoms 55: 55: Making bonds... 55: 55: Number of bonds was 655, now 650 55: 55: Generating angles, dihedrals and pairs... 55: 55: Making cmap torsions... 55: 55: There are 321 dihedrals, 350 impropers, 955 angles 55: 972 pairs, 650 bonds and 137 virtual sites 55: 55: Total mass 6908.582 a.m.u. 55: 55: Total charge -6.000 e 55: 55: Writing topology 55: 55: Writing coordinate file... 55: 55: --------- PLEASE NOTE ------------ 55: 55: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/E.pdb. 55: 55: The Gromos43a1 force field and the spc water model are used. 55: 55: --------- ETON ESAELP ------------ 55: [ OK ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spc_vsite_h_id_or_ter_merge_no_Epdb_format_gro_match_file (511 ms) 55: [ RUN ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spce_vsite_none_id_or_ter_merge_no_Apdb_format_gro_match_file 55: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos43a1.ff/aminoacids.r2b 55: All occupancies are one 55: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos43a1.ff/atomtypes.atp 55: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos43a1.ff/aminoacids.rtp 55: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos43a1.ff/aminoacids.hdb 55: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos43a1.ff/aminoacids.n.tdb 55: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos43a1.ff/aminoacids.c.tdb 55: Analysing hydrogen-bonding network for automated assignment of histidine 55: protonation. 25 donors and 23 acceptors were found. 55: There are 41 hydrogen bonds 55: Will use HISE for residue 8 55: 9 out of 9 lines of specbond.dat converted successfully 55: Special Atom Distance matrix: 55: CYS3 HIS8 55: SG9 NE251 55: HIS8 NE251 1.055 55: MET12 SD83 0.763 0.990 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: WARNING: Residue 1 named ALA of a molecule in the input file was mapped 55: to an entry in the topology database, but the atom H used in 55: an interaction of type angle in that entry is not found in the 55: input file. Perhaps your atom and/or residue naming needs to be 55: fixed. 55: 55: 55: 55: WARNING: WARNING: Residue 16 named SER of a molecule in the input file was mapped 55: to an entry in the topology database, but the atom O used in 55: an interaction of type angle in that entry is not found in the 55: input file. Perhaps your atom and/or residue naming needs to be 55: fixed. 55: 55: 55: Before cleaning: 267 pairs 55: Before cleaning: 305 dihedrals 55: Using the Gromos43a1 force field in directory gromos43a1.ff 55: 55: going to rename gromos43a1.ff/aminoacids.r2b 55: Reading /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/A.pdb... 55: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms 55: 55: Analyzing pdb file 55: Splitting chemical chains based on TER records or chain id changing. 55: 55: There are 1 chains and 0 blocks of water and 16 residues with 128 atoms 55: 55: chain #res #atoms 55: 55: 1 ' ' 16 128 55: 55: All occupancies are one 55: 55: Reading residue database... (Gromos43a1) 55: 55: Processing chain 1 (128 atoms, 16 residues) 55: 55: Identified residue ALA2 as a starting terminus. 55: 55: Identified residue SER17 as a ending terminus. 55: Start terminus ALA-2: NH3+ 55: End terminus SER-17: COO- 55: 55: Checking for duplicate atoms.... 55: 55: Generating any missing hydrogen atoms and/or adding termini. 55: 55: Now there are 16 residues with 165 atoms 55: 55: Making bonds... 55: 55: Number of bonds was 172, now 167 55: 55: Generating angles, dihedrals and pairs... 55: 55: Making cmap torsions... 55: 55: There are 90 dihedrals, 77 impropers, 241 angles 55: 267 pairs, 167 bonds and 0 virtual sites 55: 55: Total mass 1846.116 a.m.u. 55: 55: Total charge 0.000 e 55: 55: Writing topology 55: 55: Writing coordinate file... 55: 55: --------- PLEASE NOTE ------------ 55: 55: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/A.pdb. 55: 55: The Gromos43a1 force field and the spce water model are used. 55: 55: --------- ETON ESAELP ------------ 55: [ OK ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spce_vsite_none_id_or_ter_merge_no_Apdb_format_gro_match_file (235 ms) 55: [ RUN ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spce_vsite_none_id_or_ter_merge_no_Bpdb_format_gro_match_file 55: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos43a1.ff/aminoacids.r2b 55: All occupancies are one 55: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos43a1.ff/atomtypes.atp 55: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos43a1.ff/aminoacids.rtp 55: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos43a1.ff/aminoacids.hdb 55: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos43a1.ff/aminoacids.n.tdb 55: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos43a1.ff/aminoacids.c.tdb 55: Analysing hydrogen-bonding network for automated assignment of histidine 55: protonation. 30 donors and 22 acceptors were found. 55: There are 36 hydrogen bonds 55: Will use HISE for residue 29 55: Will use HISE for residue 32 55: 9 out of 9 lines of specbond.dat converted successfully 55: Special Atom Distance matrix: 55: CYS27 HIS29 55: SG90 NE2111 55: HIS29 NE2111 0.987 55: HIS32 NE2135 1.590 1.155 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: WARNING: Residue 1 named THR of a molecule in the input file was mapped 55: to an entry in the topology database, but the atom H used in 55: an interaction of type angle in that entry is not found in the 55: input file. Perhaps your atom and/or residue naming needs to be 55: fixed. 55: 55: 55: 55: WARNING: WARNING: Residue 16 named PHE of a molecule in the input file was mapped 55: to an entry in the topology database, but the atom O used in 55: an interaction of type angle in that entry is not found in the 55: input file. Perhaps your atom and/or residue naming needs to be 55: fixed. 55: 55: 55: Before cleaning: 273 pairs 55: Before cleaning: 429 dihedrals 55: Using the Gromos43a1 force field in directory gromos43a1.ff 55: 55: going to rename gromos43a1.ff/aminoacids.r2b 55: Reading /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/B.pdb... 55: Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms 55: 55: Analyzing pdb file 55: Splitting chemical chains based on TER records or chain id changing. 55: 55: There are 1 chains and 0 blocks of water and 16 residues with 149 atoms 55: 55: chain #res #atoms 55: 55: 1 ' ' 16 149 55: 55: All occupancies are one 55: 55: Reading residue database... (Gromos43a1) 55: 55: Processing chain 1 (149 atoms, 16 residues) 55: 55: Replaced 1 residue named GLUH to the default GLU. Use interactive selection of protonated residues if that is what you need. 55: 55: Identified residue THR18 as a starting terminus. 55: 55: Identified residue PHE33 as a ending terminus. 55: Start terminus THR-18: NH3+ 55: End terminus PHE-33: COO- 55: 55: Checking for duplicate atoms.... 55: 55: Generating any missing hydrogen atoms and/or adding termini. 55: 55: Now there are 16 residues with 202 atoms 55: 55: Making bonds... 55: 55: Number of bonds was 216, now 211 55: 55: Generating angles, dihedrals and pairs... 55: 55: Making cmap torsions... 55: 55: There are 93 dihedrals, 134 impropers, 316 angles 55: 273 pairs, 211 bonds and 0 virtual sites 55: 55: Total mass 2088.361 a.m.u. 55: 55: Total charge 1.000 e 55: 55: Writing topology 55: 55: Writing coordinate file... 55: 55: --------- PLEASE NOTE ------------ 55: 55: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/B.pdb. 55: 55: The Gromos43a1 force field and the spce water model are used. 55: 55: --------- ETON ESAELP ------------ 55: [ OK ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spce_vsite_none_id_or_ter_merge_no_Bpdb_format_gro_match_file (257 ms) 55: [ RUN ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spce_vsite_none_id_or_ter_merge_no_Cpdb_format_gro_match_file 55: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos43a1.ff/aminoacids.r2b 55: All occupancies are one 55: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos43a1.ff/atomtypes.atp 55: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos43a1.ff/aminoacids.rtp 55: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos43a1.ff/aminoacids.hdb 55: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos43a1.ff/aminoacids.n.tdb 55: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos43a1.ff/aminoacids.c.tdb 55: Analysing hydrogen-bonding network for automated assignment of histidine 55: protonation. 22 donors and 22 acceptors were found. 55: There are 26 hydrogen bonds 55: Will use HISE for residue 45 55: 9 out of 9 lines of specbond.dat converted successfully 55: Special Atom Distance matrix: 55: HIS45 55: NE295 55: MET46 SD102 1.078 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: WARNING: Residue 1 named ALA of a molecule in the input file was mapped 55: to an entry in the topology database, but the atom H used in 55: an interaction of type angle in that entry is not found in the 55: input file. Perhaps your atom and/or residue naming needs to be 55: fixed. 55: 55: 55: 55: WARNING: WARNING: Residue 16 named ALA of a molecule in the input file was mapped 55: to an entry in the topology database, but the atom O used in 55: an interaction of type angle in that entry is not found in the 55: input file. Perhaps your atom and/or residue naming needs to be 55: fixed. 55: 55: 55: Before cleaning: 242 pairs 55: Before cleaning: 349 dihedrals 55: Using the Gromos43a1 force field in directory gromos43a1.ff 55: 55: going to rename gromos43a1.ff/aminoacids.r2b 55: Reading /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/C.pdb... 55: Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms 55: 55: Analyzing pdb file 55: Splitting chemical chains based on TER records or chain id changing. 55: 55: There are 1 chains and 0 blocks of water and 16 residues with 132 atoms 55: 55: chain #res #atoms 55: 55: 1 ' ' 16 132 55: 55: All occupancies are one 55: 55: Reading residue database... (Gromos43a1) 55: 55: Processing chain 1 (132 atoms, 16 residues) 55: 55: Identified residue ALA34 as a starting terminus. 55: 55: Identified residue ALA49 as a ending terminus. 55: Start terminus ALA-34: NH3+ 55: End terminus ALA-49: COO- 55: 55: Checking for duplicate atoms.... 55: 55: Generating any missing hydrogen atoms and/or adding termini. 55: 55: Now there are 16 residues with 168 atoms 55: 55: Making bonds... 55: 55: Number of bonds was 179, now 174 55: 55: Generating angles, dihedrals and pairs... 55: 55: Making cmap torsions... 55: 55: There are 81 dihedrals, 102 impropers, 260 angles 55: 242 pairs, 174 bonds and 0 virtual sites 55: 55: Total mass 1861.132 a.m.u. 55: 55: Total charge -1.000 e 55: 55: Writing topology 55: 55: Writing coordinate file... 55: 55: --------- PLEASE NOTE ------------ 55: 55: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/C.pdb. 55: 55: The Gromos43a1 force field and the spce water model are used. 55: 55: --------- ETON ESAELP ------------ 55: [ OK ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spce_vsite_none_id_or_ter_merge_no_Cpdb_format_gro_match_file (241 ms) 55: [ RUN ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spce_vsite_none_id_or_ter_merge_no_Dpdb_format_gro_match_file 55: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos43a1.ff/aminoacids.r2b 55: All occupancies are one 55: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos43a1.ff/atomtypes.atp 55: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos43a1.ff/aminoacids.rtp 55: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos43a1.ff/aminoacids.hdb 55: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos43a1.ff/aminoacids.n.tdb 55: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos43a1.ff/aminoacids.c.tdb 55: Analysing hydrogen-bonding network for automated assignment of histidine 55: protonation. 22 donors and 21 acceptors were found. 55: There are 30 hydrogen bonds 55: Will use HISE for residue 60 55: 9 out of 9 lines of specbond.dat converted successfully 55: Special Atom Distance matrix: 55: HIS60 55: NE285 55: CYS62 SG98 0.803 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: WARNING: Residue 1 named LYS of a molecule in the input file was mapped 55: to an entry in the topology database, but the atom H used in 55: an interaction of type angle in that entry is not found in the 55: input file. Perhaps your atom and/or residue naming needs to be 55: fixed. 55: 55: 55: 55: WARNING: WARNING: Residue 16 named PRO of a molecule in the input file was mapped 55: to an entry in the topology database, but the atom O used in 55: an interaction of type angle in that entry is not found in the 55: input file. Perhaps your atom and/or residue naming needs to be 55: fixed. 55: 55: 55: Before cleaning: 232 pairs 55: Before cleaning: 299 dihedrals 55: Using the Gromos43a1 force field in directory gromos43a1.ff 55: 55: going to rename gromos43a1.ff/aminoacids.r2b 55: Reading /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/D.pdb... 55: Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms 55: 55: Analyzing pdb file 55: Splitting chemical chains based on TER records or chain id changing. 55: 55: There are 1 chains and 0 blocks of water and 16 residues with 117 atoms 55: 55: chain #res #atoms 55: 55: 1 ' ' 16 117 55: 55: All occupancies are one 55: 55: Reading residue database... (Gromos43a1) 55: 55: Processing chain 1 (117 atoms, 16 residues) 55: 55: Replaced 1 residue named ASPH to the default ASP. Use interactive selection of protonated residues if that is what you need. 55: 55: Identified residue LYS50 as a starting terminus. 55: 55: Identified residue PRO65 as a ending terminus. 55: Start terminus LYS-50: NH3+ 55: End terminus PRO-65: COO- 55: 55: Checking for duplicate atoms.... 55: 55: Generating any missing hydrogen atoms and/or adding termini. 55: 55: Now there are 16 residues with 150 atoms 55: 55: Making bonds... 55: 55: Number of bonds was 159, now 154 55: 55: Generating angles, dihedrals and pairs... 55: 55: Making cmap torsions... 55: 55: There are 78 dihedrals, 80 impropers, 227 angles 55: 232 pairs, 154 bonds and 0 virtual sites 55: 55: Total mass 1662.887 a.m.u. 55: 55: Total charge 0.000 e 55: 55: Writing topology 55: 55: Writing coordinate file... 55: 55: --------- PLEASE NOTE ------------ 55: 55: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/D.pdb. 55: 55: The Gromos43a1 force field and the spce water model are used. 55: 55: --------- ETON ESAELP ------------ 55: [ OK ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spce_vsite_none_id_or_ter_merge_no_Dpdb_format_gro_match_file (227 ms) 55: [ RUN ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spce_vsite_none_id_or_ter_merge_no_Epdb_format_gro_match_file 55: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos43a1.ff/aminoacids.r2b 55: All occupancies are one 55: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos43a1.ff/atomtypes.atp 55: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos43a1.ff/aminoacids.rtp 55: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos43a1.ff/aminoacids.hdb 55: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos43a1.ff/aminoacids.n.tdb 55: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos43a1.ff/aminoacids.c.tdb 55: Analysing hydrogen-bonding network for automated assignment of histidine 55: protonation. 89 donors and 98 acceptors were found. 55: There are 129 hydrogen bonds 55: Will use HISE for residue 31 55: Will use HISE for residue 51 55: 9 out of 9 lines of specbond.dat converted successfully 55: Special Atom Distance matrix: 55: CYS25 HIS31 HIS51 55: SG14 NE264 NE2226 55: HIS31 NE264 1.921 55: HIS51 NE2226 1.498 2.650 55: CYS80 SG477 0.207 1.984 1.570 55: Linking CYS-25 SG-14 and CYS-80 SG-477... 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: WARNING: Residue 1 named ASN of a molecule in the input file was mapped 55: to an entry in the topology database, but the atom H used in 55: an interaction of type angle in that entry is not found in the 55: input file. Perhaps your atom and/or residue naming needs to be 55: fixed. 55: 55: 55: 55: WARNING: WARNING: Residue 58 named ARG of a molecule in the input file was mapped 55: to an entry in the topology database, but the atom O used in 55: an interaction of type angle in that entry is not found in the 55: input file. Perhaps your atom and/or residue naming needs to be 55: fixed. 55: 55: 55: Before cleaning: 972 pairs 55: Before cleaning: 1256 dihedrals 55: Using the Gromos43a1 force field in directory gromos43a1.ff 55: 55: going to rename gromos43a1.ff/aminoacids.r2b 55: Reading /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/E.pdb... 55: Read 'This is a fragment of 2d4f for testing a disulfide bridge', 488 atoms 55: 55: Analyzing pdb file 55: Splitting chemical chains based on TER records or chain id changing. 55: 55: There are 1 chains and 0 blocks of water and 58 residues with 488 atoms 55: 55: chain #res #atoms 55: 55: 1 'A' 58 488 55: 55: All occupancies are one 55: 55: Reading residue database... (Gromos43a1) 55: 55: Processing chain 1 'A' (488 atoms, 58 residues) 55: 55: Identified residue ASN24 as a starting terminus. 55: 55: Identified residue ARG81 as a ending terminus. 55: Start terminus ASN-24: NH3+ 55: End terminus ARG-81: COO- 55: 55: Checking for duplicate atoms.... 55: 55: Generating any missing hydrogen atoms and/or adding termini. 55: 55: Now there are 58 residues with 635 atoms 55: 55: Making bonds... 55: 55: Number of bonds was 655, now 650 55: 55: Generating angles, dihedrals and pairs... 55: 55: Making cmap torsions... 55: 55: There are 321 dihedrals, 350 impropers, 955 angles 55: 972 pairs, 650 bonds and 0 virtual sites 55: 55: Total mass 6908.582 a.m.u. 55: 55: Total charge -6.000 e 55: 55: Writing topology 55: 55: Writing coordinate file... 55: 55: --------- PLEASE NOTE ------------ 55: 55: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/E.pdb. 55: 55: The Gromos43a1 force field and the spce water model are used. 55: 55: --------- ETON ESAELP ------------ 55: [ OK ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spce_vsite_none_id_or_ter_merge_no_Epdb_format_gro_match_file (488 ms) 55: [ RUN ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spce_vsite_h_id_or_ter_merge_no_Apdb_format_gro_match_file 55: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos43a1.ff/aminoacids.r2b 55: All occupancies are one 55: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos43a1.ff/atomtypes.atp 55: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos43a1.ff/aminoacids.rtp 55: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos43a1.ff/aminoacids.hdb 55: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos43a1.ff/aminoacids.n.tdb 55: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos43a1.ff/aminoacids.c.tdb 55: Analysing hydrogen-bonding network for automated assignment of histidine 55: protonation. 25 donors and 23 acceptors were found. 55: There are 41 hydrogen bonds 55: Will use HISE for residue 8 55: 9 out of 9 lines of specbond.dat converted successfully 55: Special Atom Distance matrix: 55: CYS3 HIS8 55: SG9 NE251 55: HIS8 NE251 1.055 55: MET12 SD83 0.763 0.990 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: Marked 37 virtual sites 55: Added 4 dummy masses 55: Added 8 new constraints 55: 55: WARNING: WARNING: Residue 1 named ALA of a molecule in the input file was mapped 55: to an entry in the topology database, but the atom H used in 55: an interaction of type angle in that entry is not found in the 55: input file. Perhaps your atom and/or residue naming needs to be 55: fixed. 55: 55: 55: 55: WARNING: WARNING: Residue 16 named SER of a molecule in the input file was mapped 55: to an entry in the topology database, but the atom O used in 55: an interaction of type angle in that entry is not found in the 55: input file. Perhaps your atom and/or residue naming needs to be 55: fixed. 55: 55: 55: Before cleaning: 267 pairs 55: Before cleaning: 305 dihedrals 55: Using the Gromos43a1 force field in directory gromos43a1.ff 55: 55: going to rename gromos43a1.ff/aminoacids.r2b 55: Reading /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/A.pdb... 55: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms 55: 55: Analyzing pdb file 55: Splitting chemical chains based on TER records or chain id changing. 55: 55: There are 1 chains and 0 blocks of water and 16 residues with 128 atoms 55: 55: chain #res #atoms 55: 55: 1 ' ' 16 128 55: 55: All occupancies are one 55: 55: Reading residue database... (Gromos43a1) 55: 55: Processing chain 1 (128 atoms, 16 residues) 55: 55: Identified residue ALA2 as a starting terminus. 55: 55: Identified residue SER17 as a ending terminus. 55: Start terminus ALA-2: NH3+ 55: End terminus SER-17: COO- 55: 55: Checking for duplicate atoms.... 55: 55: Generating any missing hydrogen atoms and/or adding termini. 55: 55: Now there are 16 residues with 165 atoms 55: 55: Making bonds... 55: 55: Number of bonds was 172, now 167 55: 55: Generating angles, dihedrals and pairs... 55: 55: Making cmap torsions... 55: 55: There are 90 dihedrals, 77 impropers, 241 angles 55: 267 pairs, 167 bonds and 37 virtual sites 55: 55: Total mass 1846.116 a.m.u. 55: 55: Total charge 0.000 e 55: 55: Writing topology 55: 55: Writing coordinate file... 55: 55: --------- PLEASE NOTE ------------ 55: 55: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/A.pdb. 55: 55: The Gromos43a1 force field and the spce water model are used. 55: 55: --------- ETON ESAELP ------------ 55: [ OK ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spce_vsite_h_id_or_ter_merge_no_Apdb_format_gro_match_file (261 ms) 55: [ RUN ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spce_vsite_h_id_or_ter_merge_no_Bpdb_format_gro_match_file 55: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos43a1.ff/aminoacids.r2b 55: All occupancies are one 55: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos43a1.ff/atomtypes.atp 55: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos43a1.ff/aminoacids.rtp 55: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos43a1.ff/aminoacids.hdb 55: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos43a1.ff/aminoacids.n.tdb 55: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos43a1.ff/aminoacids.c.tdb 55: Analysing hydrogen-bonding network for automated assignment of histidine 55: protonation. 30 donors and 22 acceptors were found. 55: There are 36 hydrogen bonds 55: Will use HISE for residue 29 55: Will use HISE for residue 32 55: 9 out of 9 lines of specbond.dat converted successfully 55: Special Atom Distance matrix: 55: CYS27 HIS29 55: SG90 NE2111 55: HIS29 NE2111 0.987 55: HIS32 NE2135 1.590 1.155 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: Marked 53 virtual sites 55: Added 4 dummy masses 55: Added 10 new constraints 55: 55: WARNING: WARNING: Residue 1 named THR of a molecule in the input file was mapped 55: to an entry in the topology database, but the atom H used in 55: an interaction of type angle in that entry is not found in the 55: input file. Perhaps your atom and/or residue naming needs to be 55: fixed. 55: 55: 55: 55: WARNING: WARNING: Residue 16 named PHE of a molecule in the input file was mapped 55: to an entry in the topology database, but the atom O used in 55: an interaction of type angle in that entry is not found in the 55: input file. Perhaps your atom and/or residue naming needs to be 55: fixed. 55: 55: 55: Before cleaning: 273 pairs 55: Before cleaning: 429 dihedrals 55: Using the Gromos43a1 force field in directory gromos43a1.ff 55: 55: going to rename gromos43a1.ff/aminoacids.r2b 55: Reading /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/B.pdb... 55: Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms 55: 55: Analyzing pdb file 55: Splitting chemical chains based on TER records or chain id changing. 55: 55: There are 1 chains and 0 blocks of water and 16 residues with 149 atoms 55: 55: chain #res #atoms 55: 55: 1 ' ' 16 149 55: 55: All occupancies are one 55: 55: Reading residue database... (Gromos43a1) 55: 55: Processing chain 1 (149 atoms, 16 residues) 55: 55: Replaced 1 residue named GLUH to the default GLU. Use interactive selection of protonated residues if that is what you need. 55: 55: Identified residue THR18 as a starting terminus. 55: 55: Identified residue PHE33 as a ending terminus. 55: Start terminus THR-18: NH3+ 55: End terminus PHE-33: COO- 55: 55: Checking for duplicate atoms.... 55: 55: Generating any missing hydrogen atoms and/or adding termini. 55: 55: Now there are 16 residues with 202 atoms 55: 55: Making bonds... 55: 55: Number of bonds was 216, now 211 55: 55: Generating angles, dihedrals and pairs... 55: 55: Making cmap torsions... 55: 55: There are 93 dihedrals, 134 impropers, 316 angles 55: 273 pairs, 211 bonds and 51 virtual sites 55: 55: Total mass 2088.361 a.m.u. 55: 55: Total charge 1.000 e 55: 55: Writing topology 55: 55: Writing coordinate file... 55: 55: --------- PLEASE NOTE ------------ 55: 55: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/B.pdb. 55: 55: The Gromos43a1 force field and the spce water model are used. 55: 55: --------- ETON ESAELP ------------ 55: [ OK ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spce_vsite_h_id_or_ter_merge_no_Bpdb_format_gro_match_file (255 ms) 55: [ RUN ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spce_vsite_h_id_or_ter_merge_no_Cpdb_format_gro_match_file 55: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos43a1.ff/aminoacids.r2b 55: All occupancies are one 55: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos43a1.ff/atomtypes.atp 55: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos43a1.ff/aminoacids.rtp 55: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos43a1.ff/aminoacids.hdb 55: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos43a1.ff/aminoacids.n.tdb 55: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos43a1.ff/aminoacids.c.tdb 55: Analysing hydrogen-bonding network for automated assignment of histidine 55: protonation. 22 donors and 22 acceptors were found. 55: There are 26 hydrogen bonds 55: Will use HISE for residue 45 55: 9 out of 9 lines of specbond.dat converted successfully 55: Special Atom Distance matrix: 55: HIS45 55: NE295 55: MET46 SD102 1.078 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: Marked 36 virtual sites 55: Added 4 dummy masses 55: Added 8 new constraints 55: 55: WARNING: WARNING: Residue 1 named ALA of a molecule in the input file was mapped 55: to an entry in the topology database, but the atom H used in 55: an interaction of type angle in that entry is not found in the 55: input file. Perhaps your atom and/or residue naming needs to be 55: fixed. 55: 55: 55: 55: WARNING: WARNING: Residue 16 named ALA of a molecule in the input file was mapped 55: to an entry in the topology database, but the atom O used in 55: an interaction of type angle in that entry is not found in the 55: input file. Perhaps your atom and/or residue naming needs to be 55: fixed. 55: 55: 55: Before cleaning: 242 pairs 55: Before cleaning: 349 dihedrals 55: Using the Gromos43a1 force field in directory gromos43a1.ff 55: 55: going to rename gromos43a1.ff/aminoacids.r2b 55: Reading /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/C.pdb... 55: Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms 55: 55: Analyzing pdb file 55: Splitting chemical chains based on TER records or chain id changing. 55: 55: There are 1 chains and 0 blocks of water and 16 residues with 132 atoms 55: 55: chain #res #atoms 55: 55: 1 ' ' 16 132 55: 55: All occupancies are one 55: 55: Reading residue database... (Gromos43a1) 55: 55: Processing chain 1 (132 atoms, 16 residues) 55: 55: Identified residue ALA34 as a starting terminus. 55: 55: Identified residue ALA49 as a ending terminus. 55: Start terminus ALA-34: NH3+ 55: End terminus ALA-49: COO- 55: 55: Checking for duplicate atoms.... 55: 55: Generating any missing hydrogen atoms and/or adding termini. 55: 55: Now there are 16 residues with 168 atoms 55: 55: Making bonds... 55: 55: Number of bonds was 179, now 174 55: 55: Generating angles, dihedrals and pairs... 55: 55: Making cmap torsions... 55: 55: There are 81 dihedrals, 102 impropers, 260 angles 55: 242 pairs, 174 bonds and 36 virtual sites 55: 55: Total mass 1861.132 a.m.u. 55: 55: Total charge -1.000 e 55: 55: Writing topology 55: 55: Writing coordinate file... 55: 55: --------- PLEASE NOTE ------------ 55: 55: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/C.pdb. 55: 55: The Gromos43a1 force field and the spce water model are used. 55: 55: --------- ETON ESAELP ------------ 55: [ OK ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spce_vsite_h_id_or_ter_merge_no_Cpdb_format_gro_match_file (244 ms) 55: [ RUN ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spce_vsite_h_id_or_ter_merge_no_Dpdb_format_gro_match_file 55: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos43a1.ff/aminoacids.r2b 55: All occupancies are one 55: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos43a1.ff/atomtypes.atp 55: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos43a1.ff/aminoacids.rtp 55: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos43a1.ff/aminoacids.hdb 55: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos43a1.ff/aminoacids.n.tdb 55: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos43a1.ff/aminoacids.c.tdb 55: Analysing hydrogen-bonding network for automated assignment of histidine 55: protonation. 22 donors and 21 acceptors were found. 55: There are 30 hydrogen bonds 55: Will use HISE for residue 60 55: 9 out of 9 lines of specbond.dat converted successfully 55: Special Atom Distance matrix: 55: HIS60 55: NE285 55: CYS62 SG98 0.803 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: Marked 33 virtual sites 55: Added 4 dummy masses 55: Added 10 new constraints 55: 55: WARNING: WARNING: Residue 1 named LYS of a molecule in the input file was mapped 55: to an entry in the topology database, but the atom H used in 55: an interaction of type angle in that entry is not found in the 55: input file. Perhaps your atom and/or residue naming needs to be 55: fixed. 55: 55: 55: 55: WARNING: WARNING: Residue 16 named PRO of a molecule in the input file was mapped 55: to an entry in the topology database, but the atom O used in 55: an interaction of type angle in that entry is not found in the 55: input file. Perhaps your atom and/or residue naming needs to be 55: fixed. 55: 55: 55: Before cleaning: 232 pairs 55: Before cleaning: 299 dihedrals 55: Using the Gromos43a1 force field in directory gromos43a1.ff 55: 55: going to rename gromos43a1.ff/aminoacids.r2b 55: Reading /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/D.pdb... 55: Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms 55: 55: Analyzing pdb file 55: Splitting chemical chains based on TER records or chain id changing. 55: 55: There are 1 chains and 0 blocks of water and 16 residues with 117 atoms 55: 55: chain #res #atoms 55: 55: 1 ' ' 16 117 55: 55: All occupancies are one 55: 55: Reading residue database... (Gromos43a1) 55: 55: Processing chain 1 (117 atoms, 16 residues) 55: 55: Replaced 1 residue named ASPH to the default ASP. Use interactive selection of protonated residues if that is what you need. 55: 55: Identified residue LYS50 as a starting terminus. 55: 55: Identified residue PRO65 as a ending terminus. 55: Start terminus LYS-50: NH3+ 55: End terminus PRO-65: COO- 55: 55: Checking for duplicate atoms.... 55: 55: Generating any missing hydrogen atoms and/or adding termini. 55: 55: Now there are 16 residues with 150 atoms 55: 55: Making bonds... 55: 55: Number of bonds was 159, now 154 55: 55: Generating angles, dihedrals and pairs... 55: 55: Making cmap torsions... 55: 55: There are 78 dihedrals, 80 impropers, 227 angles 55: 232 pairs, 154 bonds and 31 virtual sites 55: 55: Total mass 1662.887 a.m.u. 55: 55: Total charge 0.000 e 55: 55: Writing topology 55: 55: Writing coordinate file... 55: 55: --------- PLEASE NOTE ------------ 55: 55: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/D.pdb. 55: 55: The Gromos43a1 force field and the spce water model are used. 55: 55: --------- ETON ESAELP ------------ 55: [ OK ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spce_vsite_h_id_or_ter_merge_no_Dpdb_format_gro_match_file (221 ms) 55: [ RUN ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spce_vsite_h_id_or_ter_merge_no_Epdb_format_gro_match_file 55: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos43a1.ff/aminoacids.r2b 55: All occupancies are one 55: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos43a1.ff/atomtypes.atp 55: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos43a1.ff/aminoacids.rtp 55: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos43a1.ff/aminoacids.hdb 55: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos43a1.ff/aminoacids.n.tdb 55: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos43a1.ff/aminoacids.c.tdb 55: Analysing hydrogen-bonding network for automated assignment of histidine 55: protonation. 89 donors and 98 acceptors were found. 55: There are 129 hydrogen bonds 55: Will use HISE for residue 31 55: Will use HISE for residue 51 55: 9 out of 9 lines of specbond.dat converted successfully 55: Special Atom Distance matrix: 55: CYS25 HIS31 HIS51 55: SG14 NE264 NE2226 55: HIS31 NE264 1.921 55: HIS51 NE2226 1.498 2.650 55: CYS80 SG477 0.207 1.984 1.570 55: Linking CYS-25 SG-14 and CYS-80 SG-477... 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: Marked 146 virtual sites 55: Added 10 dummy masses 55: Added 29 new constraints 55: 55: WARNING: WARNING: Residue 1 named ASN of a molecule in the input file was mapped 55: to an entry in the topology database, but the atom H used in 55: an interaction of type angle in that entry is not found in the 55: input file. Perhaps your atom and/or residue naming needs to be 55: fixed. 55: 55: 55: 55: WARNING: WARNING: Residue 58 named ARG of a molecule in the input file was mapped 55: to an entry in the topology database, but the atom O used in 55: an interaction of type angle in that entry is not found in the 55: input file. Perhaps your atom and/or residue naming needs to be 55: fixed. 55: 55: 55: Before cleaning: 972 pairs 55: Before cleaning: 1256 dihedrals 55: Using the Gromos43a1 force field in directory gromos43a1.ff 55: 55: going to rename gromos43a1.ff/aminoacids.r2b 55: Reading /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/E.pdb... 55: Read 'This is a fragment of 2d4f for testing a disulfide bridge', 488 atoms 55: 55: Analyzing pdb file 55: Splitting chemical chains based on TER records or chain id changing. 55: 55: There are 1 chains and 0 blocks of water and 58 residues with 488 atoms 55: 55: chain #res #atoms 55: 55: 1 'A' 58 488 55: 55: All occupancies are one 55: 55: Reading residue database... (Gromos43a1) 55: 55: Processing chain 1 'A' (488 atoms, 58 residues) 55: 55: Identified residue ASN24 as a starting terminus. 55: 55: Identified residue ARG81 as a ending terminus. 55: Start terminus ASN-24: NH3+ 55: End terminus ARG-81: COO- 55: 55: Checking for duplicate atoms.... 55: 55: Generating any missing hydrogen atoms and/or adding termini. 55: 55: Now there are 58 residues with 635 atoms 55: 55: Making bonds... 55: 55: Number of bonds was 655, now 650 55: 55: Generating angles, dihedrals and pairs... 55: 55: Making cmap torsions... 55: 55: There are 321 dihedrals, 350 impropers, 955 angles 55: 972 pairs, 650 bonds and 137 virtual sites 55: 55: Total mass 6908.582 a.m.u. 55: 55: Total charge -6.000 e 55: 55: Writing topology 55: 55: Writing coordinate file... 55: 55: --------- PLEASE NOTE ------------ 55: 55: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/E.pdb. 55: 55: The Gromos43a1 force field and the spce water model are used. 55: 55: --------- ETON ESAELP ------------ 55: [ OK ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spce_vsite_h_id_or_ter_merge_no_Epdb_format_gro_match_file (487 ms) 55: [----------] 20 tests from G43a1/Pdb2gmxTest (5900 ms total) 55: 55: [----------] 20 tests from G53a6/Pdb2gmxTest 55: [ RUN ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spc_vsite_none_id_or_ter_merge_no_Apdb_format_gro_match_file 55: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos53a6.ff/aminoacids.r2b 55: All occupancies are one 55: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos53a6.ff/atomtypes.atp 55: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos53a6.ff/aminoacids.rtp 55: 55: Using default: removing proper dihedrals found on the same bond as a proper dihedral 55: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos53a6.ff/aminoacids.hdb 55: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos53a6.ff/aminoacids.n.tdb 55: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos53a6.ff/aminoacids.c.tdb 55: Analysing hydrogen-bonding network for automated assignment of histidine 55: protonation. 25 donors and 23 acceptors were found. 55: There are 41 hydrogen bonds 55: Will use HISE for residue 8 55: 9 out of 9 lines of specbond.dat converted successfully 55: Special Atom Distance matrix: 55: CYS3 HIS8 55: SG9 NE251 55: HIS8 NE251 1.055 55: MET12 SD83 0.763 0.990 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: WARNING: Residue 1 named ALA of a molecule in the input file was mapped 55: to an entry in the topology database, but the atom H used in 55: an interaction of type angle in that entry is not found in the 55: input file. Perhaps your atom and/or residue naming needs to be 55: fixed. 55: 55: 55: 55: WARNING: WARNING: Residue 16 named SER of a molecule in the input file was mapped 55: to an entry in the topology database, but the atom O used in 55: an interaction of type angle in that entry is not found in the 55: input file. Perhaps your atom and/or residue naming needs to be 55: fixed. 55: 55: 55: Before cleaning: 267 pairs 55: Before cleaning: 312 dihedrals 55: Using the Gromos53a6 force field in directory gromos53a6.ff 55: 55: going to rename gromos53a6.ff/aminoacids.r2b 55: Reading /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/A.pdb... 55: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms 55: 55: Analyzing pdb file 55: Splitting chemical chains based on TER records or chain id changing. 55: 55: There are 1 chains and 0 blocks of water and 16 residues with 128 atoms 55: 55: chain #res #atoms 55: 55: 1 ' ' 16 128 55: 55: All occupancies are one 55: 55: Reading residue database... (Gromos53a6) 55: 55: Using default: not generating all possible dihedrals 55: 55: Using default: excluding 3 bonded neighbors 55: 55: Using default: generating 1,4 H--H interactions 55: 55: Using default: removing proper dihedrals found on the same bond as a proper dihedral 55: 55: Processing chain 1 (128 atoms, 16 residues) 55: 55: Identified residue ALA2 as a starting terminus. 55: 55: Identified residue SER17 as a ending terminus. 55: Start terminus ALA-2: NH3+ 55: End terminus SER-17: COO- 55: 55: Checking for duplicate atoms.... 55: 55: Generating any missing hydrogen atoms and/or adding termini. 55: 55: Now there are 16 residues with 167 atoms 55: 55: Making bonds... 55: 55: Number of bonds was 174, now 169 55: 55: Generating angles, dihedrals and pairs... 55: 55: Making cmap torsions... 55: 55: There are 90 dihedrals, 79 impropers, 245 angles 55: 267 pairs, 169 bonds and 0 virtual sites 55: 55: Total mass 1846.116 a.m.u. 55: 55: Total charge 0.000 e 55: 55: Writing topology 55: 55: Writing coordinate file... 55: 55: --------- PLEASE NOTE ------------ 55: 55: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/A.pdb. 55: 55: The Gromos53a6 force field and the spc water model are used. 55: 55: --------- ETON ESAELP ------------ 55: [ OK ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spc_vsite_none_id_or_ter_merge_no_Apdb_format_gro_match_file (264 ms) 55: [ RUN ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spc_vsite_none_id_or_ter_merge_no_Bpdb_format_gro_match_file 55: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos53a6.ff/aminoacids.r2b 55: All occupancies are one 55: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos53a6.ff/atomtypes.atp 55: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos53a6.ff/aminoacids.rtp 55: 55: Using default: removing proper dihedrals found on the same bond as a proper dihedral 55: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos53a6.ff/aminoacids.hdb 55: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos53a6.ff/aminoacids.n.tdb 55: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos53a6.ff/aminoacids.c.tdb 55: Analysing hydrogen-bonding network for automated assignment of histidine 55: protonation. 30 donors and 22 acceptors were found. 55: There are 36 hydrogen bonds 55: Will use HISE for residue 29 55: Will use HISE for residue 32 55: 9 out of 9 lines of specbond.dat converted successfully 55: Special Atom Distance matrix: 55: CYS27 HIS29 55: SG90 NE2111 55: HIS29 NE2111 0.987 55: HIS32 NE2135 1.590 1.155 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: WARNING: Residue 1 named THR of a molecule in the input file was mapped 55: to an entry in the topology database, but the atom H used in 55: an interaction of type angle in that entry is not found in the 55: input file. Perhaps your atom and/or residue naming needs to be 55: fixed. 55: 55: 55: 55: WARNING: WARNING: Residue 16 named PHE of a molecule in the input file was mapped 55: to an entry in the topology database, but the atom O used in 55: an interaction of type angle in that entry is not found in the 55: input file. Perhaps your atom and/or residue naming needs to be 55: fixed. 55: 55: 55: Before cleaning: 273 pairs 55: Before cleaning: 443 dihedrals 55: Using the Gromos53a6 force field in directory gromos53a6.ff 55: 55: going to rename gromos53a6.ff/aminoacids.r2b 55: Reading /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/B.pdb... 55: Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms 55: 55: Analyzing pdb file 55: Splitting chemical chains based on TER records or chain id changing. 55: 55: There are 1 chains and 0 blocks of water and 16 residues with 149 atoms 55: 55: chain #res #atoms 55: 55: 1 ' ' 16 149 55: 55: All occupancies are one 55: 55: Reading residue database... (Gromos53a6) 55: 55: Using default: not generating all possible dihedrals 55: 55: Using default: excluding 3 bonded neighbors 55: 55: Using default: generating 1,4 H--H interactions 55: 55: Using default: removing proper dihedrals found on the same bond as a proper dihedral 55: 55: Processing chain 1 (149 atoms, 16 residues) 55: 55: Replaced 1 residue named GLUH to the default GLU. Use interactive selection of protonated residues if that is what you need. 55: 55: Identified residue THR18 as a starting terminus. 55: 55: Identified residue PHE33 as a ending terminus. 55: Start terminus THR-18: NH3+ 55: End terminus PHE-33: COO- 55: 55: Checking for duplicate atoms.... 55: 55: Generating any missing hydrogen atoms and/or adding termini. 55: 55: Now there are 16 residues with 206 atoms 55: 55: Making bonds... 55: 55: Number of bonds was 220, now 215 55: 55: Generating angles, dihedrals and pairs... 55: 55: Making cmap torsions... 55: 55: There are 93 dihedrals, 138 impropers, 324 angles 55: 273 pairs, 215 bonds and 0 virtual sites 55: 55: Total mass 2088.361 a.m.u. 55: 55: Total charge 1.000 e 55: 55: Writing topology 55: 55: Writing coordinate file... 55: 55: --------- PLEASE NOTE ------------ 55: 55: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/B.pdb. 55: 55: The Gromos53a6 force field and the spc water model are used. 55: 55: --------- ETON ESAELP ------------ 55: [ OK ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spc_vsite_none_id_or_ter_merge_no_Bpdb_format_gro_match_file (287 ms) 55: [ RUN ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spc_vsite_none_id_or_ter_merge_no_Cpdb_format_gro_match_file 55: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos53a6.ff/aminoacids.r2b 55: All occupancies are one 55: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos53a6.ff/atomtypes.atp 55: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos53a6.ff/aminoacids.rtp 55: 55: Using default: removing proper dihedrals found on the same bond as a proper dihedral 55: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos53a6.ff/aminoacids.hdb 55: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos53a6.ff/aminoacids.n.tdb 55: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos53a6.ff/aminoacids.c.tdb 55: Analysing hydrogen-bonding network for automated assignment of histidine 55: protonation. 22 donors and 22 acceptors were found. 55: There are 26 hydrogen bonds 55: Will use HISE for residue 45 55: 9 out of 9 lines of specbond.dat converted successfully 55: Special Atom Distance matrix: 55: HIS45 55: NE295 55: MET46 SD102 1.078 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: WARNING: Residue 1 named ALA of a molecule in the input file was mapped 55: to an entry in the topology database, but the atom H used in 55: an interaction of type angle in that entry is not found in the 55: input file. Perhaps your atom and/or residue naming needs to be 55: fixed. 55: 55: 55: 55: WARNING: WARNING: Residue 16 named ALA of a molecule in the input file was mapped 55: to an entry in the topology database, but the atom O used in 55: an interaction of type angle in that entry is not found in the 55: input file. Perhaps your atom and/or residue naming needs to be 55: fixed. 55: 55: 55: Before cleaning: 242 pairs 55: Before cleaning: 356 dihedrals 55: Using the Gromos53a6 force field in directory gromos53a6.ff 55: 55: going to rename gromos53a6.ff/aminoacids.r2b 55: Reading /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/C.pdb... 55: Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms 55: 55: Analyzing pdb file 55: Splitting chemical chains based on TER records or chain id changing. 55: 55: There are 1 chains and 0 blocks of water and 16 residues with 132 atoms 55: 55: chain #res #atoms 55: 55: 1 ' ' 16 132 55: 55: All occupancies are one 55: 55: Reading residue database... (Gromos53a6) 55: 55: Using default: not generating all possible dihedrals 55: 55: Using default: excluding 3 bonded neighbors 55: 55: Using default: generating 1,4 H--H interactions 55: 55: Using default: removing proper dihedrals found on the same bond as a proper dihedral 55: 55: Processing chain 1 (132 atoms, 16 residues) 55: 55: Identified residue ALA34 as a starting terminus. 55: 55: Identified residue ALA49 as a ending terminus. 55: Start terminus ALA-34: NH3+ 55: End terminus ALA-49: COO- 55: 55: Checking for duplicate atoms.... 55: 55: Generating any missing hydrogen atoms and/or adding termini. 55: 55: Now there are 16 residues with 170 atoms 55: 55: Making bonds... 55: 55: Number of bonds was 181, now 176 55: 55: Generating angles, dihedrals and pairs... 55: 55: Making cmap torsions... 55: 55: There are 81 dihedrals, 104 impropers, 264 angles 55: 242 pairs, 176 bonds and 0 virtual sites 55: 55: Total mass 1861.132 a.m.u. 55: 55: Total charge -1.000 e 55: 55: Writing topology 55: 55: Writing coordinate file... 55: 55: --------- PLEASE NOTE ------------ 55: 55: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/C.pdb. 55: 55: The Gromos53a6 force field and the spc water model are used. 55: 55: --------- ETON ESAELP ------------ 55: [ OK ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spc_vsite_none_id_or_ter_merge_no_Cpdb_format_gro_match_file (262 ms) 55: [ RUN ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spc_vsite_none_id_or_ter_merge_no_Dpdb_format_gro_match_file 55: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos53a6.ff/aminoacids.r2b 55: All occupancies are one 55: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos53a6.ff/atomtypes.atp 55: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos53a6.ff/aminoacids.rtp 55: 55: Using default: removing proper dihedrals found on the same bond as a proper dihedral 55: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos53a6.ff/aminoacids.hdb 55: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos53a6.ff/aminoacids.n.tdb 55: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos53a6.ff/aminoacids.c.tdb 55: Analysing hydrogen-bonding network for automated assignment of histidine 55: protonation. 22 donors and 21 acceptors were found. 55: There are 30 hydrogen bonds 55: Will use HISE for residue 60 55: 9 out of 9 lines of specbond.dat converted successfully 55: Special Atom Distance matrix: 55: HIS60 55: NE285 55: CYS62 SG98 0.803 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: WARNING: Residue 1 named LYS of a molecule in the input file was mapped 55: to an entry in the topology database, but the atom H used in 55: an interaction of type angle in that entry is not found in the 55: input file. Perhaps your atom and/or residue naming needs to be 55: fixed. 55: 55: 55: 55: WARNING: WARNING: Residue 16 named PRO of a molecule in the input file was mapped 55: to an entry in the topology database, but the atom O used in 55: an interaction of type angle in that entry is not found in the 55: input file. Perhaps your atom and/or residue naming needs to be 55: fixed. 55: 55: 55: Before cleaning: 232 pairs 55: Before cleaning: 306 dihedrals 55: Using the Gromos53a6 force field in directory gromos53a6.ff 55: 55: going to rename gromos53a6.ff/aminoacids.r2b 55: Reading /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/D.pdb... 55: Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms 55: 55: Analyzing pdb file 55: Splitting chemical chains based on TER records or chain id changing. 55: 55: There are 1 chains and 0 blocks of water and 16 residues with 117 atoms 55: 55: chain #res #atoms 55: 55: 1 ' ' 16 117 55: 55: All occupancies are one 55: 55: Reading residue database... (Gromos53a6) 55: 55: Using default: not generating all possible dihedrals 55: 55: Using default: excluding 3 bonded neighbors 55: 55: Using default: generating 1,4 H--H interactions 55: 55: Using default: removing proper dihedrals found on the same bond as a proper dihedral 55: 55: Processing chain 1 (117 atoms, 16 residues) 55: 55: Replaced 1 residue named ASPH to the default ASP. Use interactive selection of protonated residues if that is what you need. 55: 55: Identified residue LYS50 as a starting terminus. 55: 55: Identified residue PRO65 as a ending terminus. 55: Start terminus LYS-50: NH3+ 55: End terminus PRO-65: COO- 55: 55: Checking for duplicate atoms.... 55: 55: Generating any missing hydrogen atoms and/or adding termini. 55: 55: Now there are 16 residues with 152 atoms 55: 55: Making bonds... 55: 55: Number of bonds was 161, now 156 55: 55: Generating angles, dihedrals and pairs... 55: 55: Making cmap torsions... 55: 55: There are 78 dihedrals, 82 impropers, 231 angles 55: 232 pairs, 156 bonds and 0 virtual sites 55: 55: Total mass 1662.887 a.m.u. 55: 55: Total charge -0.000 e 55: 55: Writing topology 55: 55: Writing coordinate file... 55: 55: --------- PLEASE NOTE ------------ 55: 55: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/D.pdb. 55: 55: The Gromos53a6 force field and the spc water model are used. 55: 55: --------- ETON ESAELP ------------ 55: [ OK ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spc_vsite_none_id_or_ter_merge_no_Dpdb_format_gro_match_file (252 ms) 55: [ RUN ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spc_vsite_none_id_or_ter_merge_no_Epdb_format_gro_match_file 55: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos53a6.ff/aminoacids.r2b 55: All occupancies are one 55: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos53a6.ff/atomtypes.atp 55: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos53a6.ff/aminoacids.rtp 55: 55: Using default: removing proper dihedrals found on the same bond as a proper dihedral 55: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos53a6.ff/aminoacids.hdb 55: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos53a6.ff/aminoacids.n.tdb 55: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos53a6.ff/aminoacids.c.tdb 55: Analysing hydrogen-bonding network for automated assignment of histidine 55: protonation. 89 donors and 98 acceptors were found. 55: There are 129 hydrogen bonds 55: Will use HISE for residue 31 55: Will use HISE for residue 51 55: 9 out of 9 lines of specbond.dat converted successfully 55: Special Atom Distance matrix: 55: CYS25 HIS31 HIS51 55: SG14 NE264 NE2226 55: HIS31 NE264 1.921 55: HIS51 NE2226 1.498 2.650 55: CYS80 SG477 0.207 1.984 1.570 55: Linking CYS-25 SG-14 and CYS-80 SG-477... 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: WARNING: Residue 1 named ASN of a molecule in the input file was mapped 55: to an entry in the topology database, but the atom H used in 55: an interaction of type angle in that entry is not found in the 55: input file. Perhaps your atom and/or residue naming needs to be 55: fixed. 55: 55: 55: 55: WARNING: WARNING: Residue 58 named ARG of a molecule in the input file was mapped 55: to an entry in the topology database, but the atom O used in 55: an interaction of type angle in that entry is not found in the 55: input file. Perhaps your atom and/or residue naming needs to be 55: fixed. 55: 55: 55: Before cleaning: 972 pairs 55: Before cleaning: 1270 dihedrals 55: Using the Gromos53a6 force field in directory gromos53a6.ff 55: 55: going to rename gromos53a6.ff/aminoacids.r2b 55: Reading /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/E.pdb... 55: Read 'This is a fragment of 2d4f for testing a disulfide bridge', 488 atoms 55: 55: Analyzing pdb file 55: Splitting chemical chains based on TER records or chain id changing. 55: 55: There are 1 chains and 0 blocks of water and 58 residues with 488 atoms 55: 55: chain #res #atoms 55: 55: 1 'A' 58 488 55: 55: All occupancies are one 55: 55: Reading residue database... (Gromos53a6) 55: 55: Using default: not generating all possible dihedrals 55: 55: Using default: excluding 3 bonded neighbors 55: 55: Using default: generating 1,4 H--H interactions 55: 55: Using default: removing proper dihedrals found on the same bond as a proper dihedral 55: 55: Processing chain 1 'A' (488 atoms, 58 residues) 55: 55: Identified residue ASN24 as a starting terminus. 55: 55: Identified residue ARG81 as a ending terminus. 55: Start terminus ASN-24: NH3+ 55: End terminus ARG-81: COO- 55: 55: Checking for duplicate atoms.... 55: 55: Generating any missing hydrogen atoms and/or adding termini. 55: 55: Now there are 58 residues with 639 atoms 55: 55: Making bonds... 55: 55: Number of bonds was 659, now 654 55: 55: Generating angles, dihedrals and pairs... 55: 55: Making cmap torsions... 55: 55: There are 321 dihedrals, 354 impropers, 963 angles 55: 972 pairs, 654 bonds and 0 virtual sites 55: 55: Total mass 6908.582 a.m.u. 55: 55: Total charge -6.000 e 55: 55: Writing topology 55: 55: Writing coordinate file... 55: 55: --------- PLEASE NOTE ------------ 55: 55: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/E.pdb. 55: 55: The Gromos53a6 force field and the spc water model are used. 55: 55: --------- ETON ESAELP ------------ 55: [ OK ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spc_vsite_none_id_or_ter_merge_no_Epdb_format_gro_match_file (530 ms) 55: [ RUN ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spc_vsite_h_id_or_ter_merge_no_Apdb_format_gro_match_file 55: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos53a6.ff/aminoacids.r2b 55: All occupancies are one 55: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos53a6.ff/atomtypes.atp 55: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos53a6.ff/aminoacids.rtp 55: 55: Using default: removing proper dihedrals found on the same bond as a proper dihedral 55: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos53a6.ff/aminoacids.hdb 55: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos53a6.ff/aminoacids.n.tdb 55: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos53a6.ff/aminoacids.c.tdb 55: Analysing hydrogen-bonding network for automated assignment of histidine 55: protonation. 25 donors and 23 acceptors were found. 55: There are 41 hydrogen bonds 55: Will use HISE for residue 8 55: 9 out of 9 lines of specbond.dat converted successfully 55: Special Atom Distance matrix: 55: CYS3 HIS8 55: SG9 NE251 55: HIS8 NE251 1.055 55: MET12 SD83 0.763 0.990 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: Marked 39 virtual sites 55: Added 4 dummy masses 55: Added 8 new constraints 55: 55: WARNING: WARNING: Residue 1 named ALA of a molecule in the input file was mapped 55: to an entry in the topology database, but the atom H used in 55: an interaction of type angle in that entry is not found in the 55: input file. Perhaps your atom and/or residue naming needs to be 55: fixed. 55: 55: 55: 55: WARNING: WARNING: Residue 16 named SER of a molecule in the input file was mapped 55: to an entry in the topology database, but the atom O used in 55: an interaction of type angle in that entry is not found in the 55: input file. Perhaps your atom and/or residue naming needs to be 55: fixed. 55: 55: 55: Before cleaning: 267 pairs 55: Before cleaning: 312 dihedrals 55: Using the Gromos53a6 force field in directory gromos53a6.ff 55: 55: going to rename gromos53a6.ff/aminoacids.r2b 55: Reading /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/A.pdb... 55: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms 55: 55: Analyzing pdb file 55: Splitting chemical chains based on TER records or chain id changing. 55: 55: There are 1 chains and 0 blocks of water and 16 residues with 128 atoms 55: 55: chain #res #atoms 55: 55: 1 ' ' 16 128 55: 55: All occupancies are one 55: 55: Reading residue database... (Gromos53a6) 55: 55: Using default: not generating all possible dihedrals 55: 55: Using default: excluding 3 bonded neighbors 55: 55: Using default: generating 1,4 H--H interactions 55: 55: Using default: removing proper dihedrals found on the same bond as a proper dihedral 55: 55: Processing chain 1 (128 atoms, 16 residues) 55: 55: Identified residue ALA2 as a starting terminus. 55: 55: Identified residue SER17 as a ending terminus. 55: Start terminus ALA-2: NH3+ 55: End terminus SER-17: COO- 55: 55: Checking for duplicate atoms.... 55: 55: Generating any missing hydrogen atoms and/or adding termini. 55: 55: Now there are 16 residues with 167 atoms 55: 55: Making bonds... 55: 55: Number of bonds was 174, now 169 55: 55: Generating angles, dihedrals and pairs... 55: 55: Making cmap torsions... 55: 55: There are 90 dihedrals, 79 impropers, 245 angles 55: 267 pairs, 169 bonds and 39 virtual sites 55: 55: Total mass 1846.116 a.m.u. 55: 55: Total charge 0.000 e 55: 55: Writing topology 55: 55: Writing coordinate file... 55: 55: --------- PLEASE NOTE ------------ 55: 55: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/A.pdb. 55: 55: The Gromos53a6 force field and the spc water model are used. 55: 55: --------- ETON ESAELP ------------ 55: [ OK ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spc_vsite_h_id_or_ter_merge_no_Apdb_format_gro_match_file (260 ms) 55: [ RUN ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spc_vsite_h_id_or_ter_merge_no_Bpdb_format_gro_match_file 55: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos53a6.ff/aminoacids.r2b 55: All occupancies are one 55: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos53a6.ff/atomtypes.atp 55: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos53a6.ff/aminoacids.rtp 55: 55: Using default: removing proper dihedrals found on the same bond as a proper dihedral 55: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos53a6.ff/aminoacids.hdb 55: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos53a6.ff/aminoacids.n.tdb 55: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos53a6.ff/aminoacids.c.tdb 55: Analysing hydrogen-bonding network for automated assignment of histidine 55: protonation. 30 donors and 22 acceptors were found. 55: There are 36 hydrogen bonds 55: Will use HISE for residue 29 55: Will use HISE for residue 32 55: 9 out of 9 lines of specbond.dat converted successfully 55: Special Atom Distance matrix: 55: CYS27 HIS29 55: SG90 NE2111 55: HIS29 NE2111 0.987 55: HIS32 NE2135 1.590 1.155 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: Marked 57 virtual sites 55: Added 4 dummy masses 55: Added 10 new constraints 55: 55: WARNING: WARNING: Residue 1 named THR of a molecule in the input file was mapped 55: to an entry in the topology database, but the atom H used in 55: an interaction of type angle in that entry is not found in the 55: input file. Perhaps your atom and/or residue naming needs to be 55: fixed. 55: 55: 55: 55: WARNING: WARNING: Residue 16 named PHE of a molecule in the input file was mapped 55: to an entry in the topology database, but the atom O used in 55: an interaction of type angle in that entry is not found in the 55: input file. Perhaps your atom and/or residue naming needs to be 55: fixed. 55: 55: 55: Before cleaning: 273 pairs 55: Before cleaning: 443 dihedrals 55: Using the Gromos53a6 force field in directory gromos53a6.ff 55: 55: going to rename gromos53a6.ff/aminoacids.r2b 55: Reading /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/B.pdb... 55: Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms 55: 55: Analyzing pdb file 55: Splitting chemical chains based on TER records or chain id changing. 55: 55: There are 1 chains and 0 blocks of water and 16 residues with 149 atoms 55: 55: chain #res #atoms 55: 55: 1 ' ' 16 149 55: 55: All occupancies are one 55: 55: Reading residue database... (Gromos53a6) 55: 55: Using default: not generating all possible dihedrals 55: 55: Using default: excluding 3 bonded neighbors 55: 55: Using default: generating 1,4 H--H interactions 55: 55: Using default: removing proper dihedrals found on the same bond as a proper dihedral 55: 55: Processing chain 1 (149 atoms, 16 residues) 55: 55: Replaced 1 residue named GLUH to the default GLU. Use interactive selection of protonated residues if that is what you need. 55: 55: Identified residue THR18 as a starting terminus. 55: 55: Identified residue PHE33 as a ending terminus. 55: Start terminus THR-18: NH3+ 55: End terminus PHE-33: COO- 55: 55: Checking for duplicate atoms.... 55: 55: Generating any missing hydrogen atoms and/or adding termini. 55: 55: Now there are 16 residues with 206 atoms 55: 55: Making bonds... 55: 55: Number of bonds was 220, now 215 55: 55: Generating angles, dihedrals and pairs... 55: 55: Making cmap torsions... 55: 55: There are 93 dihedrals, 138 impropers, 324 angles 55: 273 pairs, 215 bonds and 55 virtual sites 55: 55: Total mass 2088.361 a.m.u. 55: 55: Total charge 1.000 e 55: 55: Writing topology 55: 55: Writing coordinate file... 55: 55: --------- PLEASE NOTE ------------ 55: 55: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/B.pdb. 55: 55: The Gromos53a6 force field and the spc water model are used. 55: 55: --------- ETON ESAELP ------------ 55: [ OK ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spc_vsite_h_id_or_ter_merge_no_Bpdb_format_gro_match_file (294 ms) 55: [ RUN ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spc_vsite_h_id_or_ter_merge_no_Cpdb_format_gro_match_file 55: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos53a6.ff/aminoacids.r2b 55: All occupancies are one 55: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos53a6.ff/atomtypes.atp 55: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos53a6.ff/aminoacids.rtp 55: 55: Using default: removing proper dihedrals found on the same bond as a proper dihedral 55: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos53a6.ff/aminoacids.hdb 55: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos53a6.ff/aminoacids.n.tdb 55: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos53a6.ff/aminoacids.c.tdb 55: Analysing hydrogen-bonding network for automated assignment of histidine 55: protonation. 22 donors and 22 acceptors were found. 55: There are 26 hydrogen bonds 55: Will use HISE for residue 45 55: 9 out of 9 lines of specbond.dat converted successfully 55: Special Atom Distance matrix: 55: HIS45 55: NE295 55: MET46 SD102 1.078 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: Marked 38 virtual sites 55: Added 4 dummy masses 55: Added 8 new constraints 55: 55: WARNING: WARNING: Residue 1 named ALA of a molecule in the input file was mapped 55: to an entry in the topology database, but the atom H used in 55: an interaction of type angle in that entry is not found in the 55: input file. Perhaps your atom and/or residue naming needs to be 55: fixed. 55: 55: 55: 55: WARNING: WARNING: Residue 16 named ALA of a molecule in the input file was mapped 55: to an entry in the topology database, but the atom O used in 55: an interaction of type angle in that entry is not found in the 55: input file. Perhaps your atom and/or residue naming needs to be 55: fixed. 55: 55: 55: Before cleaning: 242 pairs 55: Before cleaning: 356 dihedrals 55: Using the Gromos53a6 force field in directory gromos53a6.ff 55: 55: going to rename gromos53a6.ff/aminoacids.r2b 55: Reading /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/C.pdb... 55: Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms 55: 55: Analyzing pdb file 55: Splitting chemical chains based on TER records or chain id changing. 55: 55: There are 1 chains and 0 blocks of water and 16 residues with 132 atoms 55: 55: chain #res #atoms 55: 55: 1 ' ' 16 132 55: 55: All occupancies are one 55: 55: Reading residue database... (Gromos53a6) 55: 55: Using default: not generating all possible dihedrals 55: 55: Using default: excluding 3 bonded neighbors 55: 55: Using default: generating 1,4 H--H interactions 55: 55: Using default: removing proper dihedrals found on the same bond as a proper dihedral 55: 55: Processing chain 1 (132 atoms, 16 residues) 55: 55: Identified residue ALA34 as a starting terminus. 55: 55: Identified residue ALA49 as a ending terminus. 55: Start terminus ALA-34: NH3+ 55: End terminus ALA-49: COO- 55: 55: Checking for duplicate atoms.... 55: 55: Generating any missing hydrogen atoms and/or adding termini. 55: 55: Now there are 16 residues with 170 atoms 55: 55: Making bonds... 55: 55: Number of bonds was 181, now 176 55: 55: Generating angles, dihedrals and pairs... 55: 55: Making cmap torsions... 55: 55: There are 81 dihedrals, 104 impropers, 264 angles 55: 242 pairs, 176 bonds and 38 virtual sites 55: 55: Total mass 1861.132 a.m.u. 55: 55: Total charge -1.000 e 55: 55: Writing topology 55: 55: Writing coordinate file... 55: 55: --------- PLEASE NOTE ------------ 55: 55: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/C.pdb. 55: 55: The Gromos53a6 force field and the spc water model are used. 55: 55: --------- ETON ESAELP ------------ 55: [ OK ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spc_vsite_h_id_or_ter_merge_no_Cpdb_format_gro_match_file (275 ms) 55: [ RUN ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spc_vsite_h_id_or_ter_merge_no_Dpdb_format_gro_match_file 55: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos53a6.ff/aminoacids.r2b 55: All occupancies are one 55: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos53a6.ff/atomtypes.atp 55: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos53a6.ff/aminoacids.rtp 55: 55: Using default: removing proper dihedrals found on the same bond as a proper dihedral 55: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos53a6.ff/aminoacids.hdb 55: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos53a6.ff/aminoacids.n.tdb 55: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos53a6.ff/aminoacids.c.tdb 55: Analysing hydrogen-bonding network for automated assignment of histidine 55: protonation. 22 donors and 21 acceptors were found. 55: There are 30 hydrogen bonds 55: Will use HISE for residue 60 55: 9 out of 9 lines of specbond.dat converted successfully 55: Special Atom Distance matrix: 55: HIS60 55: NE285 55: CYS62 SG98 0.803 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: Marked 35 virtual sites 55: Added 4 dummy masses 55: Added 10 new constraints 55: 55: WARNING: WARNING: Residue 1 named LYS of a molecule in the input file was mapped 55: to an entry in the topology database, but the atom H used in 55: an interaction of type angle in that entry is not found in the 55: input file. Perhaps your atom and/or residue naming needs to be 55: fixed. 55: 55: 55: 55: WARNING: WARNING: Residue 16 named PRO of a molecule in the input file was mapped 55: to an entry in the topology database, but the atom O used in 55: an interaction of type angle in that entry is not found in the 55: input file. Perhaps your atom and/or residue naming needs to be 55: fixed. 55: 55: 55: Before cleaning: 232 pairs 55: Before cleaning: 306 dihedrals 55: Using the Gromos53a6 force field in directory gromos53a6.ff 55: 55: going to rename gromos53a6.ff/aminoacids.r2b 55: Reading /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/D.pdb... 55: Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms 55: 55: Analyzing pdb file 55: Splitting chemical chains based on TER records or chain id changing. 55: 55: There are 1 chains and 0 blocks of water and 16 residues with 117 atoms 55: 55: chain #res #atoms 55: 55: 1 ' ' 16 117 55: 55: All occupancies are one 55: 55: Reading residue database... (Gromos53a6) 55: 55: Using default: not generating all possible dihedrals 55: 55: Using default: excluding 3 bonded neighbors 55: 55: Using default: generating 1,4 H--H interactions 55: 55: Using default: removing proper dihedrals found on the same bond as a proper dihedral 55: 55: Processing chain 1 (117 atoms, 16 residues) 55: 55: Replaced 1 residue named ASPH to the default ASP. Use interactive selection of protonated residues if that is what you need. 55: 55: Identified residue LYS50 as a starting terminus. 55: 55: Identified residue PRO65 as a ending terminus. 55: Start terminus LYS-50: NH3+ 55: End terminus PRO-65: COO- 55: 55: Checking for duplicate atoms.... 55: 55: Generating any missing hydrogen atoms and/or adding termini. 55: 55: Now there are 16 residues with 152 atoms 55: 55: Making bonds... 55: 55: Number of bonds was 161, now 156 55: 55: Generating angles, dihedrals and pairs... 55: 55: Making cmap torsions... 55: 55: There are 78 dihedrals, 82 impropers, 231 angles 55: 232 pairs, 156 bonds and 33 virtual sites 55: 55: Total mass 1662.887 a.m.u. 55: 55: Total charge -0.000 e 55: 55: Writing topology 55: 55: Writing coordinate file... 55: 55: --------- PLEASE NOTE ------------ 55: 55: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/D.pdb. 55: 55: The Gromos53a6 force field and the spc water model are used. 55: 55: --------- ETON ESAELP ------------ 55: [ OK ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spc_vsite_h_id_or_ter_merge_no_Dpdb_format_gro_match_file (252 ms) 55: [ RUN ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spc_vsite_h_id_or_ter_merge_no_Epdb_format_gro_match_file 55: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos53a6.ff/aminoacids.r2b 55: All occupancies are one 55: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos53a6.ff/atomtypes.atp 55: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos53a6.ff/aminoacids.rtp 55: 55: Using default: removing proper dihedrals found on the same bond as a proper dihedral 55: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos53a6.ff/aminoacids.hdb 55: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos53a6.ff/aminoacids.n.tdb 55: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos53a6.ff/aminoacids.c.tdb 55: Analysing hydrogen-bonding network for automated assignment of histidine 55: protonation. 89 donors and 98 acceptors were found. 55: There are 129 hydrogen bonds 55: Will use HISE for residue 31 55: Will use HISE for residue 51 55: 9 out of 9 lines of specbond.dat converted successfully 55: Special Atom Distance matrix: 55: CYS25 HIS31 HIS51 55: SG14 NE264 NE2226 55: HIS31 NE264 1.921 55: HIS51 NE2226 1.498 2.650 55: CYS80 SG477 0.207 1.984 1.570 55: Linking CYS-25 SG-14 and CYS-80 SG-477... 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: Marked 150 virtual sites 55: Added 10 dummy masses 55: Added 29 new constraints 55: 55: WARNING: WARNING: Residue 1 named ASN of a molecule in the input file was mapped 55: to an entry in the topology database, but the atom H used in 55: an interaction of type angle in that entry is not found in the 55: input file. Perhaps your atom and/or residue naming needs to be 55: fixed. 55: 55: 55: 55: WARNING: WARNING: Residue 58 named ARG of a molecule in the input file was mapped 55: to an entry in the topology database, but the atom O used in 55: an interaction of type angle in that entry is not found in the 55: input file. Perhaps your atom and/or residue naming needs to be 55: fixed. 55: 55: 55: Before cleaning: 972 pairs 55: Before cleaning: 1270 dihedrals 55: Using the Gromos53a6 force field in directory gromos53a6.ff 55: 55: going to rename gromos53a6.ff/aminoacids.r2b 55: Reading /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/E.pdb... 55: Read 'This is a fragment of 2d4f for testing a disulfide bridge', 488 atoms 55: 55: Analyzing pdb file 55: Splitting chemical chains based on TER records or chain id changing. 55: 55: There are 1 chains and 0 blocks of water and 58 residues with 488 atoms 55: 55: chain #res #atoms 55: 55: 1 'A' 58 488 55: 55: All occupancies are one 55: 55: Reading residue database... (Gromos53a6) 55: 55: Using default: not generating all possible dihedrals 55: 55: Using default: excluding 3 bonded neighbors 55: 55: Using default: generating 1,4 H--H interactions 55: 55: Using default: removing proper dihedrals found on the same bond as a proper dihedral 55: 55: Processing chain 1 'A' (488 atoms, 58 residues) 55: 55: Identified residue ASN24 as a starting terminus. 55: 55: Identified residue ARG81 as a ending terminus. 55: Start terminus ASN-24: NH3+ 55: End terminus ARG-81: COO- 55: 55: Checking for duplicate atoms.... 55: 55: Generating any missing hydrogen atoms and/or adding termini. 55: 55: Now there are 58 residues with 639 atoms 55: 55: Making bonds... 55: 55: Number of bonds was 659, now 654 55: 55: Generating angles, dihedrals and pairs... 55: 55: Making cmap torsions... 55: 55: There are 321 dihedrals, 354 impropers, 963 angles 55: 972 pairs, 654 bonds and 141 virtual sites 55: 55: Total mass 6908.582 a.m.u. 55: 55: Total charge -6.000 e 55: 55: Writing topology 55: 55: Writing coordinate file... 55: 55: --------- PLEASE NOTE ------------ 55: 55: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/E.pdb. 55: 55: The Gromos53a6 force field and the spc water model are used. 55: 55: --------- ETON ESAELP ------------ 55: [ OK ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spc_vsite_h_id_or_ter_merge_no_Epdb_format_gro_match_file (524 ms) 55: [ RUN ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spce_vsite_none_id_or_ter_merge_no_Apdb_format_gro_match_file 55: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos53a6.ff/aminoacids.r2b 55: All occupancies are one 55: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos53a6.ff/atomtypes.atp 55: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos53a6.ff/aminoacids.rtp 55: 55: Using default: removing proper dihedrals found on the same bond as a proper dihedral 55: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos53a6.ff/aminoacids.hdb 55: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos53a6.ff/aminoacids.n.tdb 55: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos53a6.ff/aminoacids.c.tdb 55: Analysing hydrogen-bonding network for automated assignment of histidine 55: protonation. 25 donors and 23 acceptors were found. 55: There are 41 hydrogen bonds 55: Will use HISE for residue 8 55: 9 out of 9 lines of specbond.dat converted successfully 55: Special Atom Distance matrix: 55: CYS3 HIS8 55: SG9 NE251 55: HIS8 NE251 1.055 55: MET12 SD83 0.763 0.990 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: WARNING: Residue 1 named ALA of a molecule in the input file was mapped 55: to an entry in the topology database, but the atom H used in 55: an interaction of type angle in that entry is not found in the 55: input file. Perhaps your atom and/or residue naming needs to be 55: fixed. 55: 55: 55: 55: WARNING: WARNING: Residue 16 named SER of a molecule in the input file was mapped 55: to an entry in the topology database, but the atom O used in 55: an interaction of type angle in that entry is not found in the 55: input file. Perhaps your atom and/or residue naming needs to be 55: fixed. 55: 55: 55: Before cleaning: 267 pairs 55: Before cleaning: 312 dihedrals 55: Using the Gromos53a6 force field in directory gromos53a6.ff 55: 55: going to rename gromos53a6.ff/aminoacids.r2b 55: Reading /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/A.pdb... 55: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms 55: 55: Analyzing pdb file 55: Splitting chemical chains based on TER records or chain id changing. 55: 55: There are 1 chains and 0 blocks of water and 16 residues with 128 atoms 55: 55: chain #res #atoms 55: 55: 1 ' ' 16 128 55: 55: All occupancies are one 55: 55: Reading residue database... (Gromos53a6) 55: 55: Using default: not generating all possible dihedrals 55: 55: Using default: excluding 3 bonded neighbors 55: 55: Using default: generating 1,4 H--H interactions 55: 55: Using default: removing proper dihedrals found on the same bond as a proper dihedral 55: 55: Processing chain 1 (128 atoms, 16 residues) 55: 55: Identified residue ALA2 as a starting terminus. 55: 55: Identified residue SER17 as a ending terminus. 55: Start terminus ALA-2: NH3+ 55: End terminus SER-17: COO- 55: 55: Checking for duplicate atoms.... 55: 55: Generating any missing hydrogen atoms and/or adding termini. 55: 55: Now there are 16 residues with 167 atoms 55: 55: Making bonds... 55: 55: Number of bonds was 174, now 169 55: 55: Generating angles, dihedrals and pairs... 55: 55: Making cmap torsions... 55: 55: There are 90 dihedrals, 79 impropers, 245 angles 55: 267 pairs, 169 bonds and 0 virtual sites 55: 55: Total mass 1846.116 a.m.u. 55: 55: Total charge 0.000 e 55: 55: Writing topology 55: 55: Writing coordinate file... 55: 55: --------- PLEASE NOTE ------------ 55: 55: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/A.pdb. 55: 55: The Gromos53a6 force field and the spce water model are used. 55: 55: --------- ETON ESAELP ------------ 55: [ OK ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spce_vsite_none_id_or_ter_merge_no_Apdb_format_gro_match_file (258 ms) 55: [ RUN ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spce_vsite_none_id_or_ter_merge_no_Bpdb_format_gro_match_file 55: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos53a6.ff/aminoacids.r2b 55: All occupancies are one 55: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos53a6.ff/atomtypes.atp 55: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos53a6.ff/aminoacids.rtp 55: 55: Using default: removing proper dihedrals found on the same bond as a proper dihedral 55: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos53a6.ff/aminoacids.hdb 55: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos53a6.ff/aminoacids.n.tdb 55: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos53a6.ff/aminoacids.c.tdb 55: Analysing hydrogen-bonding network for automated assignment of histidine 55: protonation. 30 donors and 22 acceptors were found. 55: There are 36 hydrogen bonds 55: Will use HISE for residue 29 55: Will use HISE for residue 32 55: 9 out of 9 lines of specbond.dat converted successfully 55: Special Atom Distance matrix: 55: CYS27 HIS29 55: SG90 NE2111 55: HIS29 NE2111 0.987 55: HIS32 NE2135 1.590 1.155 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: WARNING: Residue 1 named THR of a molecule in the input file was mapped 55: to an entry in the topology database, but the atom H used in 55: an interaction of type angle in that entry is not found in the 55: input file. Perhaps your atom and/or residue naming needs to be 55: fixed. 55: 55: 55: 55: WARNING: WARNING: Residue 16 named PHE of a molecule in the input file was mapped 55: to an entry in the topology database, but the atom O used in 55: an interaction of type angle in that entry is not found in the 55: input file. Perhaps your atom and/or residue naming needs to be 55: fixed. 55: 55: 55: Before cleaning: 273 pairs 55: Before cleaning: 443 dihedrals 55: Using the Gromos53a6 force field in directory gromos53a6.ff 55: 55: going to rename gromos53a6.ff/aminoacids.r2b 55: Reading /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/B.pdb... 55: Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms 55: 55: Analyzing pdb file 55: Splitting chemical chains based on TER records or chain id changing. 55: 55: There are 1 chains and 0 blocks of water and 16 residues with 149 atoms 55: 55: chain #res #atoms 55: 55: 1 ' ' 16 149 55: 55: All occupancies are one 55: 55: Reading residue database... (Gromos53a6) 55: 55: Using default: not generating all possible dihedrals 55: 55: Using default: excluding 3 bonded neighbors 55: 55: Using default: generating 1,4 H--H interactions 55: 55: Using default: removing proper dihedrals found on the same bond as a proper dihedral 55: 55: Processing chain 1 (149 atoms, 16 residues) 55: 55: Replaced 1 residue named GLUH to the default GLU. Use interactive selection of protonated residues if that is what you need. 55: 55: Identified residue THR18 as a starting terminus. 55: 55: Identified residue PHE33 as a ending terminus. 55: Start terminus THR-18: NH3+ 55: End terminus PHE-33: COO- 55: 55: Checking for duplicate atoms.... 55: 55: Generating any missing hydrogen atoms and/or adding termini. 55: 55: Now there are 16 residues with 206 atoms 55: 55: Making bonds... 55: 55: Number of bonds was 220, now 215 55: 55: Generating angles, dihedrals and pairs... 55: 55: Making cmap torsions... 55: 55: There are 93 dihedrals, 138 impropers, 324 angles 55: 273 pairs, 215 bonds and 0 virtual sites 55: 55: Total mass 2088.361 a.m.u. 55: 55: Total charge 1.000 e 55: 55: Writing topology 55: 55: Writing coordinate file... 55: 55: --------- PLEASE NOTE ------------ 55: 55: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/B.pdb. 55: 55: The Gromos53a6 force field and the spce water model are used. 55: 55: --------- ETON ESAELP ------------ 55: [ OK ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spce_vsite_none_id_or_ter_merge_no_Bpdb_format_gro_match_file (284 ms) 55: [ RUN ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spce_vsite_none_id_or_ter_merge_no_Cpdb_format_gro_match_file 55: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos53a6.ff/aminoacids.r2b 55: All occupancies are one 55: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos53a6.ff/atomtypes.atp 55: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos53a6.ff/aminoacids.rtp 55: 55: Using default: removing proper dihedrals found on the same bond as a proper dihedral 55: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos53a6.ff/aminoacids.hdb 55: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos53a6.ff/aminoacids.n.tdb 55: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos53a6.ff/aminoacids.c.tdb 55: Analysing hydrogen-bonding network for automated assignment of histidine 55: protonation. 22 donors and 22 acceptors were found. 55: There are 26 hydrogen bonds 55: Will use HISE for residue 45 55: 9 out of 9 lines of specbond.dat converted successfully 55: Special Atom Distance matrix: 55: HIS45 55: NE295 55: MET46 SD102 1.078 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: WARNING: Residue 1 named ALA of a molecule in the input file was mapped 55: to an entry in the topology database, but the atom H used in 55: an interaction of type angle in that entry is not found in the 55: input file. Perhaps your atom and/or residue naming needs to be 55: fixed. 55: 55: 55: 55: WARNING: WARNING: Residue 16 named ALA of a molecule in the input file was mapped 55: to an entry in the topology database, but the atom O used in 55: an interaction of type angle in that entry is not found in the 55: input file. Perhaps your atom and/or residue naming needs to be 55: fixed. 55: 55: 55: Before cleaning: 242 pairs 55: Before cleaning: 356 dihedrals 55: Using the Gromos53a6 force field in directory gromos53a6.ff 55: 55: going to rename gromos53a6.ff/aminoacids.r2b 55: Reading /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/C.pdb... 55: Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms 55: 55: Analyzing pdb file 55: Splitting chemical chains based on TER records or chain id changing. 55: 55: There are 1 chains and 0 blocks of water and 16 residues with 132 atoms 55: 55: chain #res #atoms 55: 55: 1 ' ' 16 132 55: 55: All occupancies are one 55: 55: Reading residue database... (Gromos53a6) 55: 55: Using default: not generating all possible dihedrals 55: 55: Using default: excluding 3 bonded neighbors 55: 55: Using default: generating 1,4 H--H interactions 55: 55: Using default: removing proper dihedrals found on the same bond as a proper dihedral 55: 55: Processing chain 1 (132 atoms, 16 residues) 55: 55: Identified residue ALA34 as a starting terminus. 55: 55: Identified residue ALA49 as a ending terminus. 55: Start terminus ALA-34: NH3+ 55: End terminus ALA-49: COO- 55: 55: Checking for duplicate atoms.... 55: 55: Generating any missing hydrogen atoms and/or adding termini. 55: 55: Now there are 16 residues with 170 atoms 55: 55: Making bonds... 55: 55: Number of bonds was 181, now 176 55: 55: Generating angles, dihedrals and pairs... 55: 55: Making cmap torsions... 55: 55: There are 81 dihedrals, 104 impropers, 264 angles 55: 242 pairs, 176 bonds and 0 virtual sites 55: 55: Total mass 1861.132 a.m.u. 55: 55: Total charge -1.000 e 55: 55: Writing topology 55: 55: Writing coordinate file... 55: 55: --------- PLEASE NOTE ------------ 55: 55: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/C.pdb. 55: 55: The Gromos53a6 force field and the spce water model are used. 55: 55: --------- ETON ESAELP ------------ 55: [ OK ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spce_vsite_none_id_or_ter_merge_no_Cpdb_format_gro_match_file (249 ms) 55: [ RUN ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spce_vsite_none_id_or_ter_merge_no_Dpdb_format_gro_match_file 55: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos53a6.ff/aminoacids.r2b 55: All occupancies are one 55: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos53a6.ff/atomtypes.atp 55: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos53a6.ff/aminoacids.rtp 55: 55: Using default: removing proper dihedrals found on the same bond as a proper dihedral 55: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos53a6.ff/aminoacids.hdb 55: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos53a6.ff/aminoacids.n.tdb 55: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos53a6.ff/aminoacids.c.tdb 55: Analysing hydrogen-bonding network for automated assignment of histidine 55: protonation. 22 donors and 21 acceptors were found. 55: There are 30 hydrogen bonds 55: Will use HISE for residue 60 55: 9 out of 9 lines of specbond.dat converted successfully 55: Special Atom Distance matrix: 55: HIS60 55: NE285 55: CYS62 SG98 0.803 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: WARNING: Residue 1 named LYS of a molecule in the input file was mapped 55: to an entry in the topology database, but the atom H used in 55: an interaction of type angle in that entry is not found in the 55: input file. Perhaps your atom and/or residue naming needs to be 55: fixed. 55: 55: 55: 55: WARNING: WARNING: Residue 16 named PRO of a molecule in the input file was mapped 55: to an entry in the topology database, but the atom O used in 55: an interaction of type angle in that entry is not found in the 55: input file. Perhaps your atom and/or residue naming needs to be 55: fixed. 55: 55: 55: Before cleaning: 232 pairs 55: Before cleaning: 306 dihedrals 55: Using the Gromos53a6 force field in directory gromos53a6.ff 55: 55: going to rename gromos53a6.ff/aminoacids.r2b 55: Reading /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/D.pdb... 55: Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms 55: 55: Analyzing pdb file 55: Splitting chemical chains based on TER records or chain id changing. 55: 55: There are 1 chains and 0 blocks of water and 16 residues with 117 atoms 55: 55: chain #res #atoms 55: 55: 1 ' ' 16 117 55: 55: All occupancies are one 55: 55: Reading residue database... (Gromos53a6) 55: 55: Using default: not generating all possible dihedrals 55: 55: Using default: excluding 3 bonded neighbors 55: 55: Using default: generating 1,4 H--H interactions 55: 55: Using default: removing proper dihedrals found on the same bond as a proper dihedral 55: 55: Processing chain 1 (117 atoms, 16 residues) 55: 55: Replaced 1 residue named ASPH to the default ASP. Use interactive selection of protonated residues if that is what you need. 55: 55: Identified residue LYS50 as a starting terminus. 55: 55: Identified residue PRO65 as a ending terminus. 55: Start terminus LYS-50: NH3+ 55: End terminus PRO-65: COO- 55: 55: Checking for duplicate atoms.... 55: 55: Generating any missing hydrogen atoms and/or adding termini. 55: 55: Now there are 16 residues with 152 atoms 55: 55: Making bonds... 55: 55: Number of bonds was 161, now 156 55: 55: Generating angles, dihedrals and pairs... 55: 55: Making cmap torsions... 55: 55: There are 78 dihedrals, 82 impropers, 231 angles 55: 232 pairs, 156 bonds and 0 virtual sites 55: 55: Total mass 1662.887 a.m.u. 55: 55: Total charge -0.000 e 55: 55: Writing topology 55: 55: Writing coordinate file... 55: 55: --------- PLEASE NOTE ------------ 55: 55: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/D.pdb. 55: 55: The Gromos53a6 force field and the spce water model are used. 55: 55: --------- ETON ESAELP ------------ 55: [ OK ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spce_vsite_none_id_or_ter_merge_no_Dpdb_format_gro_match_file (242 ms) 55: [ RUN ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spce_vsite_none_id_or_ter_merge_no_Epdb_format_gro_match_file 55: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos53a6.ff/aminoacids.r2b 55: All occupancies are one 55: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos53a6.ff/atomtypes.atp 55: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos53a6.ff/aminoacids.rtp 55: 55: Using default: removing proper dihedrals found on the same bond as a proper dihedral 55: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos53a6.ff/aminoacids.hdb 55: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos53a6.ff/aminoacids.n.tdb 55: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos53a6.ff/aminoacids.c.tdb 55: Analysing hydrogen-bonding network for automated assignment of histidine 55: protonation. 89 donors and 98 acceptors were found. 55: There are 129 hydrogen bonds 55: Will use HISE for residue 31 55: Will use HISE for residue 51 55: 9 out of 9 lines of specbond.dat converted successfully 55: Special Atom Distance matrix: 55: CYS25 HIS31 HIS51 55: SG14 NE264 NE2226 55: HIS31 NE264 1.921 55: HIS51 NE2226 1.498 2.650 55: CYS80 SG477 0.207 1.984 1.570 55: Linking CYS-25 SG-14 and CYS-80 SG-477... 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: WARNING: Residue 1 named ASN of a molecule in the input file was mapped 55: to an entry in the topology database, but the atom H used in 55: an interaction of type angle in that entry is not found in the 55: input file. Perhaps your atom and/or residue naming needs to be 55: fixed. 55: 55: 55: 55: WARNING: WARNING: Residue 58 named ARG of a molecule in the input file was mapped 55: to an entry in the topology database, but the atom O used in 55: an interaction of type angle in that entry is not found in the 55: input file. Perhaps your atom and/or residue naming needs to be 55: fixed. 55: 55: 55: Before cleaning: 972 pairs 55: Before cleaning: 1270 dihedrals 55: Using the Gromos53a6 force field in directory gromos53a6.ff 55: 55: going to rename gromos53a6.ff/aminoacids.r2b 55: Reading /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/E.pdb... 55: Read 'This is a fragment of 2d4f for testing a disulfide bridge', 488 atoms 55: 55: Analyzing pdb file 55: Splitting chemical chains based on TER records or chain id changing. 55: 55: There are 1 chains and 0 blocks of water and 58 residues with 488 atoms 55: 55: chain #res #atoms 55: 55: 1 'A' 58 488 55: 55: All occupancies are one 55: 55: Reading residue database... (Gromos53a6) 55: 55: Using default: not generating all possible dihedrals 55: 55: Using default: excluding 3 bonded neighbors 55: 55: Using default: generating 1,4 H--H interactions 55: 55: Using default: removing proper dihedrals found on the same bond as a proper dihedral 55: 55: Processing chain 1 'A' (488 atoms, 58 residues) 55: 55: Identified residue ASN24 as a starting terminus. 55: 55: Identified residue ARG81 as a ending terminus. 55: Start terminus ASN-24: NH3+ 55: End terminus ARG-81: COO- 55: 55: Checking for duplicate atoms.... 55: 55: Generating any missing hydrogen atoms and/or adding termini. 55: 55: Now there are 58 residues with 639 atoms 55: 55: Making bonds... 55: 55: Number of bonds was 659, now 654 55: 55: Generating angles, dihedrals and pairs... 55: 55: Making cmap torsions... 55: 55: There are 321 dihedrals, 354 impropers, 963 angles 55: 972 pairs, 654 bonds and 0 virtual sites 55: 55: Total mass 6908.582 a.m.u. 55: 55: Total charge -6.000 e 55: 55: Writing topology 55: 55: Writing coordinate file... 55: 55: --------- PLEASE NOTE ------------ 55: 55: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/E.pdb. 55: 55: The Gromos53a6 force field and the spce water model are used. 55: 55: --------- ETON ESAELP ------------ 55: [ OK ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spce_vsite_none_id_or_ter_merge_no_Epdb_format_gro_match_file (513 ms) 55: [ RUN ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spce_vsite_h_id_or_ter_merge_no_Apdb_format_gro_match_file 55: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos53a6.ff/aminoacids.r2b 55: All occupancies are one 55: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos53a6.ff/atomtypes.atp 55: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos53a6.ff/aminoacids.rtp 55: 55: Using default: removing proper dihedrals found on the same bond as a proper dihedral 55: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos53a6.ff/aminoacids.hdb 55: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos53a6.ff/aminoacids.n.tdb 55: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos53a6.ff/aminoacids.c.tdb 55: Analysing hydrogen-bonding network for automated assignment of histidine 55: protonation. 25 donors and 23 acceptors were found. 55: There are 41 hydrogen bonds 55: Will use HISE for residue 8 55: 9 out of 9 lines of specbond.dat converted successfully 55: Special Atom Distance matrix: 55: CYS3 HIS8 55: SG9 NE251 55: HIS8 NE251 1.055 55: MET12 SD83 0.763 0.990 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: Marked 39 virtual sites 55: Added 4 dummy masses 55: Added 8 new constraints 55: 55: WARNING: WARNING: Residue 1 named ALA of a molecule in the input file was mapped 55: to an entry in the topology database, but the atom H used in 55: an interaction of type angle in that entry is not found in the 55: input file. Perhaps your atom and/or residue naming needs to be 55: fixed. 55: 55: 55: 55: WARNING: WARNING: Residue 16 named SER of a molecule in the input file was mapped 55: to an entry in the topology database, but the atom O used in 55: an interaction of type angle in that entry is not found in the 55: input file. Perhaps your atom and/or residue naming needs to be 55: fixed. 55: 55: 55: Before cleaning: 267 pairs 55: Before cleaning: 312 dihedrals 55: Using the Gromos53a6 force field in directory gromos53a6.ff 55: 55: going to rename gromos53a6.ff/aminoacids.r2b 55: Reading /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/A.pdb... 55: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms 55: 55: Analyzing pdb file 55: Splitting chemical chains based on TER records or chain id changing. 55: 55: There are 1 chains and 0 blocks of water and 16 residues with 128 atoms 55: 55: chain #res #atoms 55: 55: 1 ' ' 16 128 55: 55: All occupancies are one 55: 55: Reading residue database... (Gromos53a6) 55: 55: Using default: not generating all possible dihedrals 55: 55: Using default: excluding 3 bonded neighbors 55: 55: Using default: generating 1,4 H--H interactions 55: 55: Using default: removing proper dihedrals found on the same bond as a proper dihedral 55: 55: Processing chain 1 (128 atoms, 16 residues) 55: 55: Identified residue ALA2 as a starting terminus. 55: 55: Identified residue SER17 as a ending terminus. 55: Start terminus ALA-2: NH3+ 55: End terminus SER-17: COO- 55: 55: Checking for duplicate atoms.... 55: 55: Generating any missing hydrogen atoms and/or adding termini. 55: 55: Now there are 16 residues with 167 atoms 55: 55: Making bonds... 55: 55: Number of bonds was 174, now 169 55: 55: Generating angles, dihedrals and pairs... 55: 55: Making cmap torsions... 55: 55: There are 90 dihedrals, 79 impropers, 245 angles 55: 267 pairs, 169 bonds and 39 virtual sites 55: 55: Total mass 1846.116 a.m.u. 55: 55: Total charge 0.000 e 55: 55: Writing topology 55: 55: Writing coordinate file... 55: 55: --------- PLEASE NOTE ------------ 55: 55: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/A.pdb. 55: 55: The Gromos53a6 force field and the spce water model are used. 55: 55: --------- ETON ESAELP ------------ 55: [ OK ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spce_vsite_h_id_or_ter_merge_no_Apdb_format_gro_match_file (283 ms) 55: [ RUN ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spce_vsite_h_id_or_ter_merge_no_Bpdb_format_gro_match_file 55: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos53a6.ff/aminoacids.r2b 55: All occupancies are one 55: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos53a6.ff/atomtypes.atp 55: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos53a6.ff/aminoacids.rtp 55: 55: Using default: removing proper dihedrals found on the same bond as a proper dihedral 55: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos53a6.ff/aminoacids.hdb 55: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos53a6.ff/aminoacids.n.tdb 55: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos53a6.ff/aminoacids.c.tdb 55: Analysing hydrogen-bonding network for automated assignment of histidine 55: protonation. 30 donors and 22 acceptors were found. 55: There are 36 hydrogen bonds 55: Will use HISE for residue 29 55: Will use HISE for residue 32 55: 9 out of 9 lines of specbond.dat converted successfully 55: Special Atom Distance matrix: 55: CYS27 HIS29 55: SG90 NE2111 55: HIS29 NE2111 0.987 55: HIS32 NE2135 1.590 1.155 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: Marked 57 virtual sites 55: Added 4 dummy masses 55: Added 10 new constraints 55: 55: WARNING: WARNING: Residue 1 named THR of a molecule in the input file was mapped 55: to an entry in the topology database, but the atom H used in 55: an interaction of type angle in that entry is not found in the 55: input file. Perhaps your atom and/or residue naming needs to be 55: fixed. 55: 55: 55: 55: WARNING: WARNING: Residue 16 named PHE of a molecule in the input file was mapped 55: to an entry in the topology database, but the atom O used in 55: an interaction of type angle in that entry is not found in the 55: input file. Perhaps your atom and/or residue naming needs to be 55: fixed. 55: 55: 55: Before cleaning: 273 pairs 55: Before cleaning: 443 dihedrals 55: Using the Gromos53a6 force field in directory gromos53a6.ff 55: 55: going to rename gromos53a6.ff/aminoacids.r2b 55: Reading /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/B.pdb... 55: Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms 55: 55: Analyzing pdb file 55: Splitting chemical chains based on TER records or chain id changing. 55: 55: There are 1 chains and 0 blocks of water and 16 residues with 149 atoms 55: 55: chain #res #atoms 55: 55: 1 ' ' 16 149 55: 55: All occupancies are one 55: 55: Reading residue database... (Gromos53a6) 55: 55: Using default: not generating all possible dihedrals 55: 55: Using default: excluding 3 bonded neighbors 55: 55: Using default: generating 1,4 H--H interactions 55: 55: Using default: removing proper dihedrals found on the same bond as a proper dihedral 55: 55: Processing chain 1 (149 atoms, 16 residues) 55: 55: Replaced 1 residue named GLUH to the default GLU. Use interactive selection of protonated residues if that is what you need. 55: 55: Identified residue THR18 as a starting terminus. 55: 55: Identified residue PHE33 as a ending terminus. 55: Start terminus THR-18: NH3+ 55: End terminus PHE-33: COO- 55: 55: Checking for duplicate atoms.... 55: 55: Generating any missing hydrogen atoms and/or adding termini. 55: 55: Now there are 16 residues with 206 atoms 55: 55: Making bonds... 55: 55: Number of bonds was 220, now 215 55: 55: Generating angles, dihedrals and pairs... 55: 55: Making cmap torsions... 55: 55: There are 93 dihedrals, 138 impropers, 324 angles 55: 273 pairs, 215 bonds and 55 virtual sites 55: 55: Total mass 2088.361 a.m.u. 55: 55: Total charge 1.000 e 55: 55: Writing topology 55: 55: Writing coordinate file... 55: 55: --------- PLEASE NOTE ------------ 55: 55: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/B.pdb. 55: 55: The Gromos53a6 force field and the spce water model are used. 55: 55: --------- ETON ESAELP ------------ 55: [ OK ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spce_vsite_h_id_or_ter_merge_no_Bpdb_format_gro_match_file (290 ms) 55: [ RUN ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spce_vsite_h_id_or_ter_merge_no_Cpdb_format_gro_match_file 55: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos53a6.ff/aminoacids.r2b 55: All occupancies are one 55: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos53a6.ff/atomtypes.atp 55: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos53a6.ff/aminoacids.rtp 55: 55: Using default: removing proper dihedrals found on the same bond as a proper dihedral 55: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos53a6.ff/aminoacids.hdb 55: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos53a6.ff/aminoacids.n.tdb 55: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos53a6.ff/aminoacids.c.tdb 55: Analysing hydrogen-bonding network for automated assignment of histidine 55: protonation. 22 donors and 22 acceptors were found. 55: There are 26 hydrogen bonds 55: Will use HISE for residue 45 55: 9 out of 9 lines of specbond.dat converted successfully 55: Special Atom Distance matrix: 55: HIS45 55: NE295 55: MET46 SD102 1.078 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: Marked 38 virtual sites 55: Added 4 dummy masses 55: Added 8 new constraints 55: 55: WARNING: WARNING: Residue 1 named ALA of a molecule in the input file was mapped 55: to an entry in the topology database, but the atom H used in 55: an interaction of type angle in that entry is not found in the 55: input file. Perhaps your atom and/or residue naming needs to be 55: fixed. 55: 55: 55: 55: WARNING: WARNING: Residue 16 named ALA of a molecule in the input file was mapped 55: to an entry in the topology database, but the atom O used in 55: an interaction of type angle in that entry is not found in the 55: input file. Perhaps your atom and/or residue naming needs to be 55: fixed. 55: 55: 55: Before cleaning: 242 pairs 55: Before cleaning: 356 dihedrals 55: Using the Gromos53a6 force field in directory gromos53a6.ff 55: 55: going to rename gromos53a6.ff/aminoacids.r2b 55: Reading /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/C.pdb... 55: Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms 55: 55: Analyzing pdb file 55: Splitting chemical chains based on TER records or chain id changing. 55: 55: There are 1 chains and 0 blocks of water and 16 residues with 132 atoms 55: 55: chain #res #atoms 55: 55: 1 ' ' 16 132 55: 55: All occupancies are one 55: 55: Reading residue database... (Gromos53a6) 55: 55: Using default: not generating all possible dihedrals 55: 55: Using default: excluding 3 bonded neighbors 55: 55: Using default: generating 1,4 H--H interactions 55: 55: Using default: removing proper dihedrals found on the same bond as a proper dihedral 55: 55: Processing chain 1 (132 atoms, 16 residues) 55: 55: Identified residue ALA34 as a starting terminus. 55: 55: Identified residue ALA49 as a ending terminus. 55: Start terminus ALA-34: NH3+ 55: End terminus ALA-49: COO- 55: 55: Checking for duplicate atoms.... 55: 55: Generating any missing hydrogen atoms and/or adding termini. 55: 55: Now there are 16 residues with 170 atoms 55: 55: Making bonds... 55: 55: Number of bonds was 181, now 176 55: 55: Generating angles, dihedrals and pairs... 55: 55: Making cmap torsions... 55: 55: There are 81 dihedrals, 104 impropers, 264 angles 55: 242 pairs, 176 bonds and 38 virtual sites 55: 55: Total mass 1861.132 a.m.u. 55: 55: Total charge -1.000 e 55: 55: Writing topology 55: 55: Writing coordinate file... 55: 55: --------- PLEASE NOTE ------------ 55: 55: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/C.pdb. 55: 55: The Gromos53a6 force field and the spce water model are used. 55: 55: --------- ETON ESAELP ------------ 55: [ OK ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spce_vsite_h_id_or_ter_merge_no_Cpdb_format_gro_match_file (304 ms) 55: [ RUN ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spce_vsite_h_id_or_ter_merge_no_Dpdb_format_gro_match_file 55: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos53a6.ff/aminoacids.r2b 55: All occupancies are one 55: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos53a6.ff/atomtypes.atp 55: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos53a6.ff/aminoacids.rtp 55: 55: Using default: removing proper dihedrals found on the same bond as a proper dihedral 55: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos53a6.ff/aminoacids.hdb 55: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos53a6.ff/aminoacids.n.tdb 55: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos53a6.ff/aminoacids.c.tdb 55: Analysing hydrogen-bonding network for automated assignment of histidine 55: protonation. 22 donors and 21 acceptors were found. 55: There are 30 hydrogen bonds 55: Will use HISE for residue 60 55: 9 out of 9 lines of specbond.dat converted successfully 55: Special Atom Distance matrix: 55: HIS60 55: NE285 55: CYS62 SG98 0.803 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: Marked 35 virtual sites 55: Added 4 dummy masses 55: Added 10 new constraints 55: 55: WARNING: WARNING: Residue 1 named LYS of a molecule in the input file was mapped 55: to an entry in the topology database, but the atom H used in 55: an interaction of type angle in that entry is not found in the 55: input file. Perhaps your atom and/or residue naming needs to be 55: fixed. 55: 55: 55: 55: WARNING: WARNING: Residue 16 named PRO of a molecule in the input file was mapped 55: to an entry in the topology database, but the atom O used in 55: an interaction of type angle in that entry is not found in the 55: input file. Perhaps your atom and/or residue naming needs to be 55: fixed. 55: 55: 55: Before cleaning: 232 pairs 55: Before cleaning: 306 dihedrals 55: Using the Gromos53a6 force field in directory gromos53a6.ff 55: 55: going to rename gromos53a6.ff/aminoacids.r2b 55: Reading /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/D.pdb... 55: Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms 55: 55: Analyzing pdb file 55: Splitting chemical chains based on TER records or chain id changing. 55: 55: There are 1 chains and 0 blocks of water and 16 residues with 117 atoms 55: 55: chain #res #atoms 55: 55: 1 ' ' 16 117 55: 55: All occupancies are one 55: 55: Reading residue database... (Gromos53a6) 55: 55: Using default: not generating all possible dihedrals 55: 55: Using default: excluding 3 bonded neighbors 55: 55: Using default: generating 1,4 H--H interactions 55: 55: Using default: removing proper dihedrals found on the same bond as a proper dihedral 55: 55: Processing chain 1 (117 atoms, 16 residues) 55: 55: Replaced 1 residue named ASPH to the default ASP. Use interactive selection of protonated residues if that is what you need. 55: 55: Identified residue LYS50 as a starting terminus. 55: 55: Identified residue PRO65 as a ending terminus. 55: Start terminus LYS-50: NH3+ 55: End terminus PRO-65: COO- 55: 55: Checking for duplicate atoms.... 55: 55: Generating any missing hydrogen atoms and/or adding termini. 55: 55: Now there are 16 residues with 152 atoms 55: 55: Making bonds... 55: 55: Number of bonds was 161, now 156 55: 55: Generating angles, dihedrals and pairs... 55: 55: Making cmap torsions... 55: 55: There are 78 dihedrals, 82 impropers, 231 angles 55: 232 pairs, 156 bonds and 33 virtual sites 55: 55: Total mass 1662.887 a.m.u. 55: 55: Total charge -0.000 e 55: 55: Writing topology 55: 55: Writing coordinate file... 55: 55: --------- PLEASE NOTE ------------ 55: 55: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/D.pdb. 55: 55: The Gromos53a6 force field and the spce water model are used. 55: 55: --------- ETON ESAELP ------------ 55: [ OK ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spce_vsite_h_id_or_ter_merge_no_Dpdb_format_gro_match_file (295 ms) 55: [ RUN ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spce_vsite_h_id_or_ter_merge_no_Epdb_format_gro_match_file 55: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos53a6.ff/aminoacids.r2b 55: All occupancies are one 55: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos53a6.ff/atomtypes.atp 55: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos53a6.ff/aminoacids.rtp 55: 55: Using default: removing proper dihedrals found on the same bond as a proper dihedral 55: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos53a6.ff/aminoacids.hdb 55: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos53a6.ff/aminoacids.n.tdb 55: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos53a6.ff/aminoacids.c.tdb 55: Analysing hydrogen-bonding network for automated assignment of histidine 55: protonation. 89 donors and 98 acceptors were found. 55: There are 129 hydrogen bonds 55: Will use HISE for residue 31 55: Will use HISE for residue 51 55: 9 out of 9 lines of specbond.dat converted successfully 55: Special Atom Distance matrix: 55: CYS25 HIS31 HIS51 55: SG14 NE264 NE2226 55: HIS31 NE264 1.921 55: HIS51 NE2226 1.498 2.650 55: CYS80 SG477 0.207 1.984 1.570 55: Linking CYS-25 SG-14 and CYS-80 SG-477... 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: Marked 150 virtual sites 55: Added 10 dummy masses 55: Added 29 new constraints 55: 55: WARNING: WARNING: Residue 1 named ASN of a molecule in the input file was mapped 55: to an entry in the topology database, but the atom H used in 55: an interaction of type angle in that entry is not found in the 55: input file. Perhaps your atom and/or residue naming needs to be 55: fixed. 55: 55: 55: 55: WARNING: WARNING: Residue 58 named ARG of a molecule in the input file was mapped 55: to an entry in the topology database, but the atom O used in 55: an interaction of type angle in that entry is not found in the 55: input file. Perhaps your atom and/or residue naming needs to be 55: fixed. 55: 55: 55: Before cleaning: 972 pairs 55: Before cleaning: 1270 dihedrals 55: Using the Gromos53a6 force field in directory gromos53a6.ff 55: 55: going to rename gromos53a6.ff/aminoacids.r2b 55: Reading /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/E.pdb... 55: Read 'This is a fragment of 2d4f for testing a disulfide bridge', 488 atoms 55: 55: Analyzing pdb file 55: Splitting chemical chains based on TER records or chain id changing. 55: 55: There are 1 chains and 0 blocks of water and 58 residues with 488 atoms 55: 55: chain #res #atoms 55: 55: 1 'A' 58 488 55: 55: All occupancies are one 55: 55: Reading residue database... (Gromos53a6) 55: 55: Using default: not generating all possible dihedrals 55: 55: Using default: excluding 3 bonded neighbors 55: 55: Using default: generating 1,4 H--H interactions 55: 55: Using default: removing proper dihedrals found on the same bond as a proper dihedral 55: 55: Processing chain 1 'A' (488 atoms, 58 residues) 55: 55: Identified residue ASN24 as a starting terminus. 55: 55: Identified residue ARG81 as a ending terminus. 55: Start terminus ASN-24: NH3+ 55: End terminus ARG-81: COO- 55: 55: Checking for duplicate atoms.... 55: 55: Generating any missing hydrogen atoms and/or adding termini. 55: 55: Now there are 58 residues with 639 atoms 55: 55: Making bonds... 55: 55: Number of bonds was 659, now 654 55: 55: Generating angles, dihedrals and pairs... 55: 55: Making cmap torsions... 55: 55: There are 321 dihedrals, 354 impropers, 963 angles 55: 972 pairs, 654 bonds and 141 virtual sites 55: 55: Total mass 6908.582 a.m.u. 55: 55: Total charge -6.000 e 55: 55: Writing topology 55: 55: Writing coordinate file... 55: 55: --------- PLEASE NOTE ------------ 55: 55: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/E.pdb. 55: 55: The Gromos53a6 force field and the spce water model are used. 55: 55: --------- ETON ESAELP ------------ 55: [ OK ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spce_vsite_h_id_or_ter_merge_no_Epdb_format_gro_match_file (600 ms) 55: [----------] 20 tests from G53a6/Pdb2gmxTest (6531 ms total) 55: 55: [----------] Global test environment tear-down 55: [==========] 40 tests from 2 test suites ran. (12431 ms total) 55: [ PASSED ] 40 tests. 55/92 Test #55: Pdb2gmx2Test .............................. Passed 12.53 sec test 56 Start 56: Pdb2gmx3Test 56: Test command: /build/reproducible-path/gromacs-2025.1/build/basic-dp/bin/pdb2gmx3-test "--gtest_output=xml:/build/reproducible-path/gromacs-2025.1/build/basic-dp/Testing/Temporary/Pdb2gmx3Test.xml" 56: Working Directory: /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/gmxpreprocess/tests 56: Test timeout computed to be: 1920 56: [==========] Running 39 tests from 6 test suites. 56: [----------] Global test environment set-up. 56: [----------] 10 tests from Amber/Pdb2gmxTest 56: [ RUN ] Amber/Pdb2gmxTest.Runs/ff_amber99sbildn_tip3p_vsite_none_id_or_ter_merge_no_Apdb_format_gro_match_file 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/amber99sb-ildn.ff/aminoacids.r2b 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/amber99sb-ildn.ff/dna.r2b 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/amber99sb-ildn.ff/rna.r2b 56: All occupancies are one 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/amber99sb-ildn.ff/atomtypes.atp 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/amber99sb-ildn.ff/aminoacids.rtp 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/amber99sb-ildn.ff/dna.rtp 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/amber99sb-ildn.ff/rna.rtp 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/amber99sb-ildn.ff/aminoacids.hdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/amber99sb-ildn.ff/dna.hdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/amber99sb-ildn.ff/rna.hdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/amber99sb-ildn.ff/aminoacids.n.tdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/amber99sb-ildn.ff/aminoacids.c.tdb 56: Analysing hydrogen-bonding network for automated assignment of histidine 56: protonation. 25 donors and 23 acceptors were found. 56: There are 41 hydrogen bonds 56: Will use HISE for residue 8 56: 9 out of 9 lines of specbond.dat converted successfully 56: Special Atom Distance matrix: 56: CYS3 HIS8 56: SG9 NE251 56: HIS8 NE251 1.055 56: MET12 SD83 0.763 0.990 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/amber99sb-ildn.ff/aminoacids.arn 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/amber99sb-ildn.ff/dna.arn 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/amber99sb-ildn.ff/rna.arn 56: Before cleaning: 653 pairs 56: Before cleaning: 691 dihedrals 56: Using the Amber99sb-ildn force field in directory amber99sb-ildn.ff 56: 56: going to rename amber99sb-ildn.ff/aminoacids.r2b 56: 56: going to rename amber99sb-ildn.ff/dna.r2b 56: 56: going to rename amber99sb-ildn.ff/rna.r2b 56: Reading /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/A.pdb... 56: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms 56: 56: Analyzing pdb file 56: Splitting chemical chains based on TER records or chain id changing. 56: 56: There are 1 chains and 0 blocks of water and 16 residues with 128 atoms 56: 56: chain #res #atoms 56: 56: 1 ' ' 16 128 56: 56: All occupancies are one 56: 56: Reading residue database... (Amber99sb-ildn) 56: 56: Processing chain 1 (128 atoms, 16 residues) 56: 56: Identified residue ALA2 as a starting terminus. 56: 56: Identified residue SER17 as a ending terminus. 56: 56: Checking for duplicate atoms.... 56: 56: Generating any missing hydrogen atoms and/or adding termini. 56: 56: Now there are 16 residues with 252 atoms 56: 56: Making bonds... 56: 56: Number of bonds was 255, now 254 56: 56: Generating angles, dihedrals and pairs... 56: 56: Making cmap torsions... 56: 56: There are 691 dihedrals, 51 impropers, 457 angles 56: 650 pairs, 254 bonds and 0 virtual sites 56: 56: Total mass 1846.132 a.m.u. 56: 56: Total charge 0.000 e 56: 56: Writing topology 56: 56: Writing coordinate file... 56: 56: --------- PLEASE NOTE ------------ 56: 56: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/A.pdb. 56: 56: The Amber99sb-ildn force field and the tip3p water model are used. 56: 56: --------- ETON ESAELP ------------ 56: [ OK ] Amber/Pdb2gmxTest.Runs/ff_amber99sbildn_tip3p_vsite_none_id_or_ter_merge_no_Apdb_format_gro_match_file (283 ms) 56: [ RUN ] Amber/Pdb2gmxTest.Runs/ff_amber99sbildn_tip3p_vsite_none_id_or_ter_merge_no_Bpdb_format_gro_match_file 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/amber99sb-ildn.ff/aminoacids.r2b 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/amber99sb-ildn.ff/dna.r2b 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/amber99sb-ildn.ff/rna.r2b 56: All occupancies are one 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/amber99sb-ildn.ff/atomtypes.atp 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/amber99sb-ildn.ff/aminoacids.rtp 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/amber99sb-ildn.ff/dna.rtp 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/amber99sb-ildn.ff/rna.rtp 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/amber99sb-ildn.ff/aminoacids.hdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/amber99sb-ildn.ff/dna.hdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/amber99sb-ildn.ff/rna.hdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/amber99sb-ildn.ff/aminoacids.n.tdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/amber99sb-ildn.ff/aminoacids.c.tdb 56: Analysing hydrogen-bonding network for automated assignment of histidine 56: protonation. 30 donors and 22 acceptors were found. 56: There are 36 hydrogen bonds 56: Will use HISE for residue 29 56: Will use HISE for residue 32 56: 9 out of 9 lines of specbond.dat converted successfully 56: Special Atom Distance matrix: 56: CYS27 HIS29 56: SG90 NE2111 56: HIS29 NE2111 0.987 56: HIS32 NE2135 1.590 1.155 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/amber99sb-ildn.ff/aminoacids.arn 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/amber99sb-ildn.ff/dna.arn 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/amber99sb-ildn.ff/rna.arn 56: Before cleaning: 748 pairs 56: Before cleaning: 788 dihedrals 56: Using the Amber99sb-ildn force field in directory amber99sb-ildn.ff 56: 56: going to rename amber99sb-ildn.ff/aminoacids.r2b 56: 56: going to rename amber99sb-ildn.ff/dna.r2b 56: 56: going to rename amber99sb-ildn.ff/rna.r2b 56: Reading /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/B.pdb... 56: Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms 56: 56: Analyzing pdb file 56: Splitting chemical chains based on TER records or chain id changing. 56: 56: There are 1 chains and 0 blocks of water and 16 residues with 149 atoms 56: 56: chain #res #atoms 56: 56: 1 ' ' 16 149 56: 56: All occupancies are one 56: 56: Reading residue database... (Amber99sb-ildn) 56: 56: Processing chain 1 (149 atoms, 16 residues) 56: 56: Replaced 1 residue named GLUH to the default GLU. Use interactive selection of protonated residues if that is what you need. 56: 56: Identified residue THR18 as a starting terminus. 56: 56: Identified residue PHE33 as a ending terminus. 56: 56: Checking for duplicate atoms.... 56: 56: Generating any missing hydrogen atoms and/or adding termini. 56: 56: Now there are 16 residues with 281 atoms 56: 56: Making bonds... 56: 56: Number of bonds was 291, now 290 56: 56: Generating angles, dihedrals and pairs... 56: 56: Making cmap torsions... 56: 56: There are 788 dihedrals, 72 impropers, 516 angles 56: 736 pairs, 290 bonds and 0 virtual sites 56: 56: Total mass 2088.366 a.m.u. 56: 56: Total charge 1.000 e 56: 56: Writing topology 56: 56: Writing coordinate file... 56: 56: --------- PLEASE NOTE ------------ 56: 56: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/B.pdb. 56: 56: The Amber99sb-ildn force field and the tip3p water model are used. 56: 56: --------- ETON ESAELP ------------ 56: [ OK ] Amber/Pdb2gmxTest.Runs/ff_amber99sbildn_tip3p_vsite_none_id_or_ter_merge_no_Bpdb_format_gro_match_file (304 ms) 56: [ RUN ] Amber/Pdb2gmxTest.Runs/ff_amber99sbildn_tip3p_vsite_none_id_or_ter_merge_no_Cpdb_format_gro_match_file 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/amber99sb-ildn.ff/aminoacids.r2b 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/amber99sb-ildn.ff/dna.r2b 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/amber99sb-ildn.ff/rna.r2b 56: All occupancies are one 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/amber99sb-ildn.ff/atomtypes.atp 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/amber99sb-ildn.ff/aminoacids.rtp 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/amber99sb-ildn.ff/dna.rtp 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/amber99sb-ildn.ff/rna.rtp 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/amber99sb-ildn.ff/aminoacids.hdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/amber99sb-ildn.ff/dna.hdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/amber99sb-ildn.ff/rna.hdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/amber99sb-ildn.ff/aminoacids.n.tdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/amber99sb-ildn.ff/aminoacids.c.tdb 56: Analysing hydrogen-bonding network for automated assignment of histidine 56: protonation. 22 donors and 22 acceptors were found. 56: There are 26 hydrogen bonds 56: Will use HISE for residue 45 56: 9 out of 9 lines of specbond.dat converted successfully 56: Special Atom Distance matrix: 56: HIS45 56: NE295 56: MET46 SD102 1.078 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/amber99sb-ildn.ff/aminoacids.arn 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/amber99sb-ildn.ff/dna.arn 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/amber99sb-ildn.ff/rna.arn 56: Before cleaning: 676 pairs 56: Before cleaning: 727 dihedrals 56: Using the Amber99sb-ildn force field in directory amber99sb-ildn.ff 56: 56: going to rename amber99sb-ildn.ff/aminoacids.r2b 56: 56: going to rename amber99sb-ildn.ff/dna.r2b 56: 56: going to rename amber99sb-ildn.ff/rna.r2b 56: Reading /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/C.pdb... 56: Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms 56: 56: Analyzing pdb file 56: Splitting chemical chains based on TER records or chain id changing. 56: 56: There are 1 chains and 0 blocks of water and 16 residues with 132 atoms 56: 56: chain #res #atoms 56: 56: 1 ' ' 16 132 56: 56: All occupancies are one 56: 56: Reading residue database... (Amber99sb-ildn) 56: 56: Processing chain 1 (132 atoms, 16 residues) 56: 56: Identified residue ALA34 as a starting terminus. 56: 56: Identified residue ALA49 as a ending terminus. 56: 56: Checking for duplicate atoms.... 56: 56: Generating any missing hydrogen atoms and/or adding termini. 56: 56: Now there are 16 residues with 255 atoms 56: 56: Making bonds... 56: 56: Number of bonds was 262, now 261 56: 56: Generating angles, dihedrals and pairs... 56: 56: Making cmap torsions... 56: 56: There are 727 dihedrals, 56 impropers, 472 angles 56: 667 pairs, 261 bonds and 0 virtual sites 56: 56: Total mass 1861.124 a.m.u. 56: 56: Total charge -1.000 e 56: 56: Writing topology 56: 56: Writing coordinate file... 56: 56: --------- PLEASE NOTE ------------ 56: 56: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/C.pdb. 56: 56: The Amber99sb-ildn force field and the tip3p water model are used. 56: 56: --------- ETON ESAELP ------------ 56: [ OK ] Amber/Pdb2gmxTest.Runs/ff_amber99sbildn_tip3p_vsite_none_id_or_ter_merge_no_Cpdb_format_gro_match_file (300 ms) 56: [ RUN ] Amber/Pdb2gmxTest.Runs/ff_amber99sbildn_tip3p_vsite_none_id_or_ter_merge_no_Dpdb_format_gro_match_file 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/amber99sb-ildn.ff/aminoacids.r2b 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/amber99sb-ildn.ff/dna.r2b 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/amber99sb-ildn.ff/rna.r2b 56: All occupancies are one 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/amber99sb-ildn.ff/atomtypes.atp 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/amber99sb-ildn.ff/aminoacids.rtp 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/amber99sb-ildn.ff/dna.rtp 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/amber99sb-ildn.ff/rna.rtp 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/amber99sb-ildn.ff/aminoacids.hdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/amber99sb-ildn.ff/dna.hdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/amber99sb-ildn.ff/rna.hdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/amber99sb-ildn.ff/aminoacids.n.tdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/amber99sb-ildn.ff/aminoacids.c.tdb 56: Analysing hydrogen-bonding network for automated assignment of histidine 56: protonation. 22 donors and 21 acceptors were found. 56: There are 30 hydrogen bonds 56: Will use HISE for residue 60 56: 9 out of 9 lines of specbond.dat converted successfully 56: Special Atom Distance matrix: 56: HIS60 56: NE285 56: CYS62 SG98 0.803 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/amber99sb-ildn.ff/aminoacids.arn 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/amber99sb-ildn.ff/dna.arn 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/amber99sb-ildn.ff/rna.arn 56: Before cleaning: 603 pairs 56: Before cleaning: 634 dihedrals 56: Using the Amber99sb-ildn force field in directory amber99sb-ildn.ff 56: 56: going to rename amber99sb-ildn.ff/aminoacids.r2b 56: 56: going to rename amber99sb-ildn.ff/dna.r2b 56: 56: going to rename amber99sb-ildn.ff/rna.r2b 56: Reading /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/D.pdb... 56: Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms 56: 56: Analyzing pdb file 56: Splitting chemical chains based on TER records or chain id changing. 56: 56: There are 1 chains and 0 blocks of water and 16 residues with 117 atoms 56: 56: chain #res #atoms 56: 56: 1 ' ' 16 117 56: 56: All occupancies are one 56: 56: Reading residue database... (Amber99sb-ildn) 56: 56: Processing chain 1 (117 atoms, 16 residues) 56: 56: Replaced 1 residue named ASPH to the default ASP. Use interactive selection of protonated residues if that is what you need. 56: 56: Identified residue LYS50 as a starting terminus. 56: 56: Identified residue PRO65 as a ending terminus. 56: 56: Checking for duplicate atoms.... 56: 56: Generating any missing hydrogen atoms and/or adding termini. 56: 56: Now there are 16 residues with 228 atoms 56: 56: Making bonds... 56: 56: Number of bonds was 233, now 232 56: 56: Generating angles, dihedrals and pairs... 56: 56: Making cmap torsions... 56: 56: There are 634 dihedrals, 48 impropers, 419 angles 56: 597 pairs, 232 bonds and 0 virtual sites 56: 56: Total mass 1662.888 a.m.u. 56: 56: Total charge 0.000 e 56: 56: Writing topology 56: 56: Writing coordinate file... 56: 56: --------- PLEASE NOTE ------------ 56: 56: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/D.pdb. 56: 56: The Amber99sb-ildn force field and the tip3p water model are used. 56: 56: --------- ETON ESAELP ------------ 56: [ OK ] Amber/Pdb2gmxTest.Runs/ff_amber99sbildn_tip3p_vsite_none_id_or_ter_merge_no_Dpdb_format_gro_match_file (286 ms) 56: [ RUN ] Amber/Pdb2gmxTest.Runs/ff_amber99sbildn_tip3p_vsite_none_id_or_ter_merge_no_Epdb_format_gro_match_file 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/amber99sb-ildn.ff/aminoacids.r2b 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/amber99sb-ildn.ff/dna.r2b 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/amber99sb-ildn.ff/rna.r2b 56: All occupancies are one 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/amber99sb-ildn.ff/atomtypes.atp 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/amber99sb-ildn.ff/aminoacids.rtp 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/amber99sb-ildn.ff/dna.rtp 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/amber99sb-ildn.ff/rna.rtp 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/amber99sb-ildn.ff/aminoacids.hdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/amber99sb-ildn.ff/dna.hdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/amber99sb-ildn.ff/rna.hdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/amber99sb-ildn.ff/aminoacids.n.tdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/amber99sb-ildn.ff/aminoacids.c.tdb 56: Analysing hydrogen-bonding network for automated assignment of histidine 56: protonation. 89 donors and 98 acceptors were found. 56: There are 129 hydrogen bonds 56: Will use HISE for residue 31 56: Will use HISE for residue 51 56: 9 out of 9 lines of specbond.dat converted successfully 56: Special Atom Distance matrix: 56: CYS25 HIS31 HIS51 56: SG14 NE264 NE2226 56: HIS31 NE264 1.921 56: HIS51 NE2226 1.498 2.650 56: CYS80 SG477 0.207 1.984 1.570 56: Linking CYS-25 SG-14 and CYS-80 SG-477... 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/amber99sb-ildn.ff/aminoacids.arn 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/amber99sb-ildn.ff/dna.arn 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/amber99sb-ildn.ff/rna.arn 56: Before cleaning: 2499 pairs 56: Before cleaning: 2631 dihedrals 56: Using the Amber99sb-ildn force field in directory amber99sb-ildn.ff 56: 56: going to rename amber99sb-ildn.ff/aminoacids.r2b 56: 56: going to rename amber99sb-ildn.ff/dna.r2b 56: 56: going to rename amber99sb-ildn.ff/rna.r2b 56: Reading /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/E.pdb... 56: Read 'This is a fragment of 2d4f for testing a disulfide bridge', 488 atoms 56: 56: Analyzing pdb file 56: Splitting chemical chains based on TER records or chain id changing. 56: 56: There are 1 chains and 0 blocks of water and 58 residues with 488 atoms 56: 56: chain #res #atoms 56: 56: 1 'A' 58 488 56: 56: All occupancies are one 56: 56: Reading residue database... (Amber99sb-ildn) 56: 56: Processing chain 1 'A' (488 atoms, 58 residues) 56: 56: Identified residue ASN24 as a starting terminus. 56: 56: Identified residue ARG81 as a ending terminus. 56: 56: Checking for duplicate atoms.... 56: 56: Generating any missing hydrogen atoms and/or adding termini. 56: 56: Now there are 58 residues with 936 atoms 56: 56: Making bonds... 56: 56: Number of bonds was 952, now 951 56: 56: Generating angles, dihedrals and pairs... 56: 56: Making cmap torsions... 56: 56: There are 2631 dihedrals, 208 impropers, 1704 angles 56: 2469 pairs, 951 bonds and 0 virtual sites 56: 56: Total mass 6908.576 a.m.u. 56: 56: Total charge -6.000 e 56: 56: Writing topology 56: 56: Writing coordinate file... 56: 56: --------- PLEASE NOTE ------------ 56: 56: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/E.pdb. 56: 56: The Amber99sb-ildn force field and the tip3p water model are used. 56: 56: --------- ETON ESAELP ------------ 56: [ OK ] Amber/Pdb2gmxTest.Runs/ff_amber99sbildn_tip3p_vsite_none_id_or_ter_merge_no_Epdb_format_gro_match_file (795 ms) 56: [ RUN ] Amber/Pdb2gmxTest.Runs/ff_amber99sbildn_tip3p_vsite_h_id_or_ter_merge_no_Apdb_format_gro_match_file 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/amber99sb-ildn.ff/aminoacids.r2b 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/amber99sb-ildn.ff/dna.r2b 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/amber99sb-ildn.ff/rna.r2b 56: All occupancies are one 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/amber99sb-ildn.ff/atomtypes.atp 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/amber99sb-ildn.ff/aminoacids.rtp 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/amber99sb-ildn.ff/dna.rtp 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/amber99sb-ildn.ff/rna.rtp 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/amber99sb-ildn.ff/aminoacids.hdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/amber99sb-ildn.ff/dna.hdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/amber99sb-ildn.ff/rna.hdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/amber99sb-ildn.ff/aminoacids.n.tdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/amber99sb-ildn.ff/aminoacids.c.tdb 56: Analysing hydrogen-bonding network for automated assignment of histidine 56: protonation. 25 donors and 23 acceptors were found. 56: There are 41 hydrogen bonds 56: Will use HISE for residue 8 56: 9 out of 9 lines of specbond.dat converted successfully 56: Special Atom Distance matrix: 56: CYS3 HIS8 56: SG9 NE251 56: HIS8 NE251 1.055 56: MET12 SD83 0.763 0.990 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/amber99sb-ildn.ff/aminoacids.arn 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/amber99sb-ildn.ff/dna.arn 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/amber99sb-ildn.ff/rna.arn 56: Marked 124 virtual sites 56: Added 16 dummy masses 56: Added 26 new constraints 56: Before cleaning: 653 pairs 56: Before cleaning: 691 dihedrals 56: Using the Amber99sb-ildn force field in directory amber99sb-ildn.ff 56: 56: going to rename amber99sb-ildn.ff/aminoacids.r2b 56: 56: going to rename amber99sb-ildn.ff/dna.r2b 56: 56: going to rename amber99sb-ildn.ff/rna.r2b 56: Reading /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/A.pdb... 56: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms 56: 56: Analyzing pdb file 56: Splitting chemical chains based on TER records or chain id changing. 56: 56: There are 1 chains and 0 blocks of water and 16 residues with 128 atoms 56: 56: chain #res #atoms 56: 56: 1 ' ' 16 128 56: 56: All occupancies are one 56: 56: Reading residue database... (Amber99sb-ildn) 56: 56: Processing chain 1 (128 atoms, 16 residues) 56: 56: Identified residue ALA2 as a starting terminus. 56: 56: Identified residue SER17 as a ending terminus. 56: 56: Checking for duplicate atoms.... 56: 56: Generating any missing hydrogen atoms and/or adding termini. 56: 56: Now there are 16 residues with 252 atoms 56: 56: Making bonds... 56: 56: Number of bonds was 255, now 254 56: 56: Generating angles, dihedrals and pairs... 56: 56: Making cmap torsions... 56: 56: There are 691 dihedrals, 51 impropers, 457 angles 56: 650 pairs, 254 bonds and 130 virtual sites 56: 56: Total mass 1846.132 a.m.u. 56: 56: Total charge 0.000 e 56: 56: Writing topology 56: 56: Writing coordinate file... 56: 56: --------- PLEASE NOTE ------------ 56: 56: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/A.pdb. 56: 56: The Amber99sb-ildn force field and the tip3p water model are used. 56: 56: --------- ETON ESAELP ------------ 56: [ OK ] Amber/Pdb2gmxTest.Runs/ff_amber99sbildn_tip3p_vsite_h_id_or_ter_merge_no_Apdb_format_gro_match_file (301 ms) 56: [ RUN ] Amber/Pdb2gmxTest.Runs/ff_amber99sbildn_tip3p_vsite_h_id_or_ter_merge_no_Bpdb_format_gro_match_file 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/amber99sb-ildn.ff/aminoacids.r2b 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/amber99sb-ildn.ff/dna.r2b 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/amber99sb-ildn.ff/rna.r2b 56: All occupancies are one 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/amber99sb-ildn.ff/atomtypes.atp 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/amber99sb-ildn.ff/aminoacids.rtp 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/amber99sb-ildn.ff/dna.rtp 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/amber99sb-ildn.ff/rna.rtp 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/amber99sb-ildn.ff/aminoacids.hdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/amber99sb-ildn.ff/dna.hdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/amber99sb-ildn.ff/rna.hdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/amber99sb-ildn.ff/aminoacids.n.tdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/amber99sb-ildn.ff/aminoacids.c.tdb 56: Analysing hydrogen-bonding network for automated assignment of histidine 56: protonation. 30 donors and 22 acceptors were found. 56: There are 36 hydrogen bonds 56: Will use HISE for residue 29 56: Will use HISE for residue 32 56: 9 out of 9 lines of specbond.dat converted successfully 56: Special Atom Distance matrix: 56: CYS27 HIS29 56: SG90 NE2111 56: HIS29 NE2111 0.987 56: HIS32 NE2135 1.590 1.155 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/amber99sb-ildn.ff/aminoacids.arn 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/amber99sb-ildn.ff/dna.arn 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/amber99sb-ildn.ff/rna.arn 56: Marked 132 virtual sites 56: Added 10 dummy masses 56: Added 19 new constraints 56: Before cleaning: 748 pairs 56: Before cleaning: 788 dihedrals 56: Using the Amber99sb-ildn force field in directory amber99sb-ildn.ff 56: 56: going to rename amber99sb-ildn.ff/aminoacids.r2b 56: 56: going to rename amber99sb-ildn.ff/dna.r2b 56: 56: going to rename amber99sb-ildn.ff/rna.r2b 56: Reading /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/B.pdb... 56: Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms 56: 56: Analyzing pdb file 56: Splitting chemical chains based on TER records or chain id changing. 56: 56: There are 1 chains and 0 blocks of water and 16 residues with 149 atoms 56: 56: chain #res #atoms 56: 56: 1 ' ' 16 149 56: 56: All occupancies are one 56: 56: Reading residue database... (Amber99sb-ildn) 56: 56: Processing chain 1 (149 atoms, 16 residues) 56: 56: Replaced 1 residue named GLUH to the default GLU. Use interactive selection of protonated residues if that is what you need. 56: 56: Identified residue THR18 as a starting terminus. 56: 56: Identified residue PHE33 as a ending terminus. 56: 56: Checking for duplicate atoms.... 56: 56: Generating any missing hydrogen atoms and/or adding termini. 56: 56: Now there are 16 residues with 281 atoms 56: 56: Making bonds... 56: 56: Number of bonds was 291, now 290 56: 56: Generating angles, dihedrals and pairs... 56: 56: Making cmap torsions... 56: 56: There are 788 dihedrals, 72 impropers, 516 angles 56: 736 pairs, 290 bonds and 133 virtual sites 56: 56: Total mass 2088.366 a.m.u. 56: 56: Total charge 1.000 e 56: 56: Writing topology 56: 56: Writing coordinate file... 56: 56: --------- PLEASE NOTE ------------ 56: 56: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/B.pdb. 56: 56: The Amber99sb-ildn force field and the tip3p water model are used. 56: 56: --------- ETON ESAELP ------------ 56: [ OK ] Amber/Pdb2gmxTest.Runs/ff_amber99sbildn_tip3p_vsite_h_id_or_ter_merge_no_Bpdb_format_gro_match_file (310 ms) 56: [ RUN ] Amber/Pdb2gmxTest.Runs/ff_amber99sbildn_tip3p_vsite_h_id_or_ter_merge_no_Cpdb_format_gro_match_file 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/amber99sb-ildn.ff/aminoacids.r2b 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/amber99sb-ildn.ff/dna.r2b 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/amber99sb-ildn.ff/rna.r2b 56: All occupancies are one 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/amber99sb-ildn.ff/atomtypes.atp 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/amber99sb-ildn.ff/aminoacids.rtp 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/amber99sb-ildn.ff/dna.rtp 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/amber99sb-ildn.ff/rna.rtp 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/amber99sb-ildn.ff/aminoacids.hdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/amber99sb-ildn.ff/dna.hdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/amber99sb-ildn.ff/rna.hdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/amber99sb-ildn.ff/aminoacids.n.tdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/amber99sb-ildn.ff/aminoacids.c.tdb 56: Analysing hydrogen-bonding network for automated assignment of histidine 56: protonation. 22 donors and 22 acceptors were found. 56: There are 26 hydrogen bonds 56: Will use HISE for residue 45 56: 9 out of 9 lines of specbond.dat converted successfully 56: Special Atom Distance matrix: 56: HIS45 56: NE295 56: MET46 SD102 1.078 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/amber99sb-ildn.ff/aminoacids.arn 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/amber99sb-ildn.ff/dna.arn 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/amber99sb-ildn.ff/rna.arn 56: Marked 123 virtual sites 56: Added 22 dummy masses 56: Added 35 new constraints 56: Before cleaning: 676 pairs 56: Before cleaning: 727 dihedrals 56: Using the Amber99sb-ildn force field in directory amber99sb-ildn.ff 56: 56: going to rename amber99sb-ildn.ff/aminoacids.r2b 56: 56: going to rename amber99sb-ildn.ff/dna.r2b 56: 56: going to rename amber99sb-ildn.ff/rna.r2b 56: Reading /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/C.pdb... 56: Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms 56: 56: Analyzing pdb file 56: Splitting chemical chains based on TER records or chain id changing. 56: 56: There are 1 chains and 0 blocks of water and 16 residues with 132 atoms 56: 56: chain #res #atoms 56: 56: 1 ' ' 16 132 56: 56: All occupancies are one 56: 56: Reading residue database... (Amber99sb-ildn) 56: 56: Processing chain 1 (132 atoms, 16 residues) 56: 56: Identified residue ALA34 as a starting terminus. 56: 56: Identified residue ALA49 as a ending terminus. 56: 56: Checking for duplicate atoms.... 56: 56: Generating any missing hydrogen atoms and/or adding termini. 56: 56: Now there are 16 residues with 255 atoms 56: 56: Making bonds... 56: 56: Number of bonds was 262, now 261 56: 56: Generating angles, dihedrals and pairs... 56: 56: Making cmap torsions... 56: 56: There are 727 dihedrals, 56 impropers, 472 angles 56: 667 pairs, 261 bonds and 132 virtual sites 56: 56: Total mass 1861.124 a.m.u. 56: 56: Total charge -1.000 e 56: 56: Writing topology 56: 56: Writing coordinate file... 56: 56: --------- PLEASE NOTE ------------ 56: 56: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/C.pdb. 56: 56: The Amber99sb-ildn force field and the tip3p water model are used. 56: 56: --------- ETON ESAELP ------------ 56: [ OK ] Amber/Pdb2gmxTest.Runs/ff_amber99sbildn_tip3p_vsite_h_id_or_ter_merge_no_Cpdb_format_gro_match_file (296 ms) 56: [ RUN ] Amber/Pdb2gmxTest.Runs/ff_amber99sbildn_tip3p_vsite_h_id_or_ter_merge_no_Dpdb_format_gro_match_file 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/amber99sb-ildn.ff/aminoacids.r2b 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/amber99sb-ildn.ff/dna.r2b 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/amber99sb-ildn.ff/rna.r2b 56: All occupancies are one 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/amber99sb-ildn.ff/atomtypes.atp 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/amber99sb-ildn.ff/aminoacids.rtp 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/amber99sb-ildn.ff/dna.rtp 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/amber99sb-ildn.ff/rna.rtp 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/amber99sb-ildn.ff/aminoacids.hdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/amber99sb-ildn.ff/dna.hdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/amber99sb-ildn.ff/rna.hdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/amber99sb-ildn.ff/aminoacids.n.tdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/amber99sb-ildn.ff/aminoacids.c.tdb 56: Analysing hydrogen-bonding network for automated assignment of histidine 56: protonation. 22 donors and 21 acceptors were found. 56: There are 30 hydrogen bonds 56: Will use HISE for residue 60 56: 9 out of 9 lines of specbond.dat converted successfully 56: Special Atom Distance matrix: 56: HIS60 56: NE285 56: CYS62 SG98 0.803 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/amber99sb-ildn.ff/aminoacids.arn 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/amber99sb-ildn.ff/dna.arn 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/amber99sb-ildn.ff/rna.arn 56: Marked 111 virtual sites 56: Added 18 dummy masses 56: Added 31 new constraints 56: Before cleaning: 603 pairs 56: Before cleaning: 634 dihedrals 56: Using the Amber99sb-ildn force field in directory amber99sb-ildn.ff 56: 56: going to rename amber99sb-ildn.ff/aminoacids.r2b 56: 56: going to rename amber99sb-ildn.ff/dna.r2b 56: 56: going to rename amber99sb-ildn.ff/rna.r2b 56: Reading /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/D.pdb... 56: Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms 56: 56: Analyzing pdb file 56: Splitting chemical chains based on TER records or chain id changing. 56: 56: There are 1 chains and 0 blocks of water and 16 residues with 117 atoms 56: 56: chain #res #atoms 56: 56: 1 ' ' 16 117 56: 56: All occupancies are one 56: 56: Reading residue database... (Amber99sb-ildn) 56: 56: Processing chain 1 (117 atoms, 16 residues) 56: 56: Replaced 1 residue named ASPH to the default ASP. Use interactive selection of protonated residues if that is what you need. 56: 56: Identified residue LYS50 as a starting terminus. 56: 56: Identified residue PRO65 as a ending terminus. 56: 56: Checking for duplicate atoms.... 56: 56: Generating any missing hydrogen atoms and/or adding termini. 56: 56: Now there are 16 residues with 228 atoms 56: 56: Making bonds... 56: 56: Number of bonds was 233, now 232 56: 56: Generating angles, dihedrals and pairs... 56: 56: Making cmap torsions... 56: 56: There are 634 dihedrals, 48 impropers, 419 angles 56: 597 pairs, 232 bonds and 116 virtual sites 56: 56: Total mass 1662.888 a.m.u. 56: 56: Total charge 0.000 e 56: 56: Writing topology 56: 56: Writing coordinate file... 56: 56: --------- PLEASE NOTE ------------ 56: 56: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/D.pdb. 56: 56: The Amber99sb-ildn force field and the tip3p water model are used. 56: 56: --------- ETON ESAELP ------------ 56: [ OK ] Amber/Pdb2gmxTest.Runs/ff_amber99sbildn_tip3p_vsite_h_id_or_ter_merge_no_Dpdb_format_gro_match_file (279 ms) 56: [ RUN ] Amber/Pdb2gmxTest.Runs/ff_amber99sbildn_tip3p_vsite_h_id_or_ter_merge_no_Epdb_format_gro_match_file 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/amber99sb-ildn.ff/aminoacids.r2b 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/amber99sb-ildn.ff/dna.r2b 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/amber99sb-ildn.ff/rna.r2b 56: All occupancies are one 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/amber99sb-ildn.ff/atomtypes.atp 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/amber99sb-ildn.ff/aminoacids.rtp 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/amber99sb-ildn.ff/dna.rtp 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/amber99sb-ildn.ff/rna.rtp 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/amber99sb-ildn.ff/aminoacids.hdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/amber99sb-ildn.ff/dna.hdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/amber99sb-ildn.ff/rna.hdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/amber99sb-ildn.ff/aminoacids.n.tdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/amber99sb-ildn.ff/aminoacids.c.tdb 56: Analysing hydrogen-bonding network for automated assignment of histidine 56: protonation. 89 donors and 98 acceptors were found. 56: There are 129 hydrogen bonds 56: Will use HISE for residue 31 56: Will use HISE for residue 51 56: 9 out of 9 lines of specbond.dat converted successfully 56: Special Atom Distance matrix: 56: CYS25 HIS31 HIS51 56: SG14 NE264 NE2226 56: HIS31 NE264 1.921 56: HIS51 NE2226 1.498 2.650 56: CYS80 SG477 0.207 1.984 1.570 56: Linking CYS-25 SG-14 and CYS-80 SG-477... 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/amber99sb-ildn.ff/aminoacids.arn 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/amber99sb-ildn.ff/dna.arn 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/amber99sb-ildn.ff/rna.arn 56: Marked 447 virtual sites 56: Added 58 dummy masses 56: Added 101 new constraints 56: Before cleaning: 2499 pairs 56: Before cleaning: 2631 dihedrals 56: Using the Amber99sb-ildn force field in directory amber99sb-ildn.ff 56: 56: going to rename amber99sb-ildn.ff/aminoacids.r2b 56: 56: going to rename amber99sb-ildn.ff/dna.r2b 56: 56: going to rename amber99sb-ildn.ff/rna.r2b 56: Reading /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/E.pdb... 56: Read 'This is a fragment of 2d4f for testing a disulfide bridge', 488 atoms 56: 56: Analyzing pdb file 56: Splitting chemical chains based on TER records or chain id changing. 56: 56: There are 1 chains and 0 blocks of water and 58 residues with 488 atoms 56: 56: chain #res #atoms 56: 56: 1 'A' 58 488 56: 56: All occupancies are one 56: 56: Reading residue database... (Amber99sb-ildn) 56: 56: Processing chain 1 'A' (488 atoms, 58 residues) 56: 56: Identified residue ASN24 as a starting terminus. 56: 56: Identified residue ARG81 as a ending terminus. 56: 56: Checking for duplicate atoms.... 56: 56: Generating any missing hydrogen atoms and/or adding termini. 56: 56: Now there are 58 residues with 936 atoms 56: 56: Making bonds... 56: 56: Number of bonds was 952, now 951 56: 56: Generating angles, dihedrals and pairs... 56: 56: Making cmap torsions... 56: 56: There are 2631 dihedrals, 208 impropers, 1704 angles 56: 2469 pairs, 951 bonds and 462 virtual sites 56: 56: Total mass 6908.576 a.m.u. 56: 56: Total charge -6.000 e 56: 56: Writing topology 56: 56: Writing coordinate file... 56: 56: --------- PLEASE NOTE ------------ 56: 56: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/E.pdb. 56: 56: The Amber99sb-ildn force field and the tip3p water model are used. 56: 56: --------- ETON ESAELP ------------ 56: [ OK ] Amber/Pdb2gmxTest.Runs/ff_amber99sbildn_tip3p_vsite_h_id_or_ter_merge_no_Epdb_format_gro_match_file (826 ms) 56: [----------] 10 tests from Amber/Pdb2gmxTest (3986 ms total) 56: 56: [----------] 1 test from AmberTip4p/Pdb2gmxTest 56: [ RUN ] AmberTip4p/Pdb2gmxTest.Runs/ff_amber99sbildn_tip4p_vsite_none_id_or_ter_merge_no_tip4ppdb_format_gro_match_full 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/amber99sb-ildn.ff/aminoacids.r2b 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/amber99sb-ildn.ff/dna.r2b 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/amber99sb-ildn.ff/rna.r2b 56: All occupancies are one 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/amber99sb-ildn.ff/atomtypes.atp 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/amber99sb-ildn.ff/aminoacids.rtp 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/amber99sb-ildn.ff/dna.rtp 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/amber99sb-ildn.ff/rna.rtp 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/amber99sb-ildn.ff/aminoacids.hdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/amber99sb-ildn.ff/dna.hdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/amber99sb-ildn.ff/rna.hdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/amber99sb-ildn.ff/aminoacids.n.tdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/amber99sb-ildn.ff/aminoacids.c.tdb 56: 9 out of 9 lines of specbond.dat converted successfully 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/amber99sb-ildn.ff/aminoacids.arn 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/amber99sb-ildn.ff/dna.arn 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/amber99sb-ildn.ff/rna.arn 56: Using the Amber99sb-ildn force field in directory amber99sb-ildn.ff 56: 56: going to rename amber99sb-ildn.ff/aminoacids.r2b 56: 56: going to rename amber99sb-ildn.ff/dna.r2b 56: 56: going to rename amber99sb-ildn.ff/rna.r2b 56: Reading /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/tip4p.pdb... 56: Read 'TIP4p ice to test that MW is handled correctly', 4 atoms 56: 56: Analyzing pdb file 56: Splitting chemical chains based on TER records or chain id changing. 56: 56: There are 0 chains and 1 blocks of water and 2 residues with 4 atoms 56: 56: chain #res #atoms 56: 56: 1 ' ' 2 4 (only water) 56: 56: All occupancies are one 56: 56: Reading residue database... (Amber99sb-ildn) 56: 56: Processing chain 1 (4 atoms, 2 residues) 56: 56: Problem with chain definition, or missing terminal residues. This chain does not appear to contain a recognized chain molecule. If this is incorrect, you can edit residuetypes.dat to modify the behavior. 56: 56: Checking for duplicate atoms.... 56: 56: Generating any missing hydrogen atoms and/or adding termini. 56: 56: Now there are 2 residues with 8 atoms 56: 56: Making bonds... 56: 56: Number of bonds was 4, now 4 56: 56: Generating angles, dihedrals and pairs... 56: 56: Making cmap torsions... 56: 56: There are 0 dihedrals, 0 impropers, 2 angles 56: 0 pairs, 4 bonds and 0 virtual sites 56: 56: Total mass 36.032 a.m.u. 56: 56: Total charge 0.000 e 56: 56: Writing coordinate file... 56: 56: --------- PLEASE NOTE ------------ 56: 56: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/tip4p.pdb. 56: 56: The Amber99sb-ildn force field and the tip4p water model are used. 56: 56: --------- ETON ESAELP ------------ 56: [ OK ] AmberTip4p/Pdb2gmxTest.Runs/ff_amber99sbildn_tip4p_vsite_none_id_or_ter_merge_no_tip4ppdb_format_gro_match_full (120 ms) 56: [----------] 1 test from AmberTip4p/Pdb2gmxTest (120 ms total) 56: 56: [----------] 12 tests from Charmm/Pdb2gmxTest 56: [ RUN ] Charmm/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_or_ter_merge_no_Apdb_format_gro_match_file 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/aminoacids.r2b 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/rna.r2b 56: All occupancies are one 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/atomtypes.atp 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/aminoacids.rtp 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/dna.rtp 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/lipids.rtp 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/rna.rtp 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/aminoacids.hdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/dna.hdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/lipids.hdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/rna.hdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/aminoacids.n.tdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/dna.n.tdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/rna.n.tdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/aminoacids.c.tdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/dna.c.tdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/rna.c.tdb 56: Analysing hydrogen-bonding network for automated assignment of histidine 56: protonation. 25 donors and 23 acceptors were found. 56: There are 41 hydrogen bonds 56: Will use HISE for residue 8 56: 9 out of 9 lines of specbond.dat converted successfully 56: Special Atom Distance matrix: 56: CYS3 HIS8 56: SG9 NE251 56: HIS8 NE251 1.055 56: MET12 SD83 0.763 0.990 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/aminoacids.arn 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/dna.arn 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/rna.arn 56: Before cleaning: 653 pairs 56: Before cleaning: 663 dihedrals 56: Using the Charmm27 force field in directory charmm27.ff 56: 56: going to rename charmm27.ff/aminoacids.r2b 56: 56: going to rename charmm27.ff/rna.r2b 56: Reading /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/A.pdb... 56: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms 56: 56: Analyzing pdb file 56: Splitting chemical chains based on TER records or chain id changing. 56: 56: There are 1 chains and 0 blocks of water and 16 residues with 128 atoms 56: 56: chain #res #atoms 56: 56: 1 ' ' 16 128 56: 56: All occupancies are one 56: 56: Reading residue database... (Charmm27) 56: 56: Processing chain 1 (128 atoms, 16 residues) 56: 56: Identified residue ALA2 as a starting terminus. 56: 56: Identified residue SER17 as a ending terminus. 56: Start terminus ALA-2: NH3+ 56: End terminus SER-17: COO- 56: 56: Checking for duplicate atoms.... 56: 56: Generating any missing hydrogen atoms and/or adding termini. 56: 56: Now there are 16 residues with 252 atoms 56: 56: Making bonds... 56: 56: Number of bonds was 254, now 254 56: 56: Generating angles, dihedrals and pairs... 56: 56: Making cmap torsions... 56: 56: There are 14 cmap torsion pairs 56: 56: There are 663 dihedrals, 48 impropers, 457 angles 56: 650 pairs, 254 bonds and 0 virtual sites 56: 56: Total mass 1846.115 a.m.u. 56: 56: Total charge 0.000 e 56: 56: Writing topology 56: 56: Writing coordinate file... 56: 56: --------- PLEASE NOTE ------------ 56: 56: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/A.pdb. 56: 56: The Charmm27 force field and the tip3p water model are used. 56: 56: --------- ETON ESAELP ------------ 56: [ OK ] Charmm/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_or_ter_merge_no_Apdb_format_gro_match_file (255 ms) 56: [ RUN ] Charmm/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_or_ter_merge_no_Bpdb_format_gro_match_file 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/aminoacids.r2b 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/rna.r2b 56: All occupancies are one 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/atomtypes.atp 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/aminoacids.rtp 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/dna.rtp 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/lipids.rtp 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/rna.rtp 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/aminoacids.hdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/dna.hdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/lipids.hdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/rna.hdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/aminoacids.n.tdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/dna.n.tdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/rna.n.tdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/aminoacids.c.tdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/dna.c.tdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/rna.c.tdb 56: Analysing hydrogen-bonding network for automated assignment of histidine 56: protonation. 30 donors and 22 acceptors were found. 56: There are 36 hydrogen bonds 56: Will use HISE for residue 29 56: Will use HISE for residue 32 56: 9 out of 9 lines of specbond.dat converted successfully 56: Special Atom Distance matrix: 56: CYS27 HIS29 56: SG90 NE2111 56: HIS29 NE2111 0.987 56: HIS32 NE2135 1.590 1.155 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/aminoacids.arn 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/dna.arn 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/rna.arn 56: Before cleaning: 748 pairs 56: Before cleaning: 778 dihedrals 56: Using the Charmm27 force field in directory charmm27.ff 56: 56: going to rename charmm27.ff/aminoacids.r2b 56: 56: going to rename charmm27.ff/rna.r2b 56: Reading /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/B.pdb... 56: Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms 56: 56: Analyzing pdb file 56: Splitting chemical chains based on TER records or chain id changing. 56: 56: There are 1 chains and 0 blocks of water and 16 residues with 149 atoms 56: 56: chain #res #atoms 56: 56: 1 ' ' 16 149 56: 56: All occupancies are one 56: 56: Reading residue database... (Charmm27) 56: 56: Processing chain 1 (149 atoms, 16 residues) 56: 56: Replaced 1 residue named GLUH to the default GLU. Use interactive selection of protonated residues if that is what you need. 56: 56: Identified residue THR18 as a starting terminus. 56: 56: Identified residue PHE33 as a ending terminus. 56: Start terminus THR-18: NH3+ 56: End terminus PHE-33: COO- 56: 56: Checking for duplicate atoms.... 56: 56: Generating any missing hydrogen atoms and/or adding termini. 56: 56: Now there are 16 residues with 281 atoms 56: 56: Making bonds... 56: 56: Number of bonds was 290, now 290 56: 56: Generating angles, dihedrals and pairs... 56: 56: Making cmap torsions... 56: 56: There are 14 cmap torsion pairs 56: 56: There are 778 dihedrals, 49 impropers, 516 angles 56: 736 pairs, 290 bonds and 0 virtual sites 56: 56: Total mass 2088.361 a.m.u. 56: 56: Total charge 1.000 e 56: 56: Writing topology 56: 56: Writing coordinate file... 56: 56: --------- PLEASE NOTE ------------ 56: 56: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/B.pdb. 56: 56: The Charmm27 force field and the tip3p water model are used. 56: 56: --------- ETON ESAELP ------------ 56: [ OK ] Charmm/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_or_ter_merge_no_Bpdb_format_gro_match_file (278 ms) 56: [ RUN ] Charmm/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_or_ter_merge_no_Cpdb_format_gro_match_file 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/aminoacids.r2b 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/rna.r2b 56: All occupancies are one 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/atomtypes.atp 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/aminoacids.rtp 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/dna.rtp 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/lipids.rtp 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/rna.rtp 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/aminoacids.hdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/dna.hdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/lipids.hdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/rna.hdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/aminoacids.n.tdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/dna.n.tdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/rna.n.tdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/aminoacids.c.tdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/dna.c.tdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/rna.c.tdb 56: Analysing hydrogen-bonding network for automated assignment of histidine 56: protonation. 22 donors and 22 acceptors were found. 56: There are 26 hydrogen bonds 56: Will use HISE for residue 45 56: 9 out of 9 lines of specbond.dat converted successfully 56: Special Atom Distance matrix: 56: HIS45 56: NE295 56: MET46 SD102 1.078 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/aminoacids.arn 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/dna.arn 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/rna.arn 56: Before cleaning: 676 pairs 56: Before cleaning: 696 dihedrals 56: Using the Charmm27 force field in directory charmm27.ff 56: 56: going to rename charmm27.ff/aminoacids.r2b 56: 56: going to rename charmm27.ff/rna.r2b 56: Reading /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/C.pdb... 56: Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms 56: 56: Analyzing pdb file 56: Splitting chemical chains based on TER records or chain id changing. 56: 56: There are 1 chains and 0 blocks of water and 16 residues with 132 atoms 56: 56: chain #res #atoms 56: 56: 1 ' ' 16 132 56: 56: All occupancies are one 56: 56: Reading residue database... (Charmm27) 56: 56: Processing chain 1 (132 atoms, 16 residues) 56: 56: Identified residue ALA34 as a starting terminus. 56: 56: Identified residue ALA49 as a ending terminus. 56: Start terminus ALA-34: NH3+ 56: End terminus ALA-49: COO- 56: 56: Checking for duplicate atoms.... 56: 56: Generating any missing hydrogen atoms and/or adding termini. 56: 56: Now there are 16 residues with 255 atoms 56: 56: Making bonds... 56: 56: Number of bonds was 261, now 261 56: 56: Generating angles, dihedrals and pairs... 56: 56: Making cmap torsions... 56: 56: There are 14 cmap torsion pairs 56: 56: There are 696 dihedrals, 39 impropers, 472 angles 56: 667 pairs, 261 bonds and 0 virtual sites 56: 56: Total mass 1861.130 a.m.u. 56: 56: Total charge -1.000 e 56: 56: Writing topology 56: 56: Writing coordinate file... 56: 56: --------- PLEASE NOTE ------------ 56: 56: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/C.pdb. 56: 56: The Charmm27 force field and the tip3p water model are used. 56: 56: --------- ETON ESAELP ------------ 56: [ OK ] Charmm/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_or_ter_merge_no_Cpdb_format_gro_match_file (254 ms) 56: [ RUN ] Charmm/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_or_ter_merge_no_Dpdb_format_gro_match_file 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/aminoacids.r2b 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/rna.r2b 56: All occupancies are one 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/atomtypes.atp 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/aminoacids.rtp 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/dna.rtp 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/lipids.rtp 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/rna.rtp 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/aminoacids.hdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/dna.hdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/lipids.hdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/rna.hdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/aminoacids.n.tdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/dna.n.tdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/rna.n.tdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/aminoacids.c.tdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/dna.c.tdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/rna.c.tdb 56: Analysing hydrogen-bonding network for automated assignment of histidine 56: protonation. 22 donors and 21 acceptors were found. 56: There are 30 hydrogen bonds 56: Will use HISE for residue 60 56: 9 out of 9 lines of specbond.dat converted successfully 56: Special Atom Distance matrix: 56: HIS60 56: NE285 56: CYS62 SG98 0.803 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/aminoacids.arn 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/dna.arn 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/rna.arn 56: Before cleaning: 603 pairs 56: Before cleaning: 618 dihedrals 56: Using the Charmm27 force field in directory charmm27.ff 56: 56: going to rename charmm27.ff/aminoacids.r2b 56: 56: going to rename charmm27.ff/rna.r2b 56: Reading /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/D.pdb... 56: Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms 56: 56: Analyzing pdb file 56: Splitting chemical chains based on TER records or chain id changing. 56: 56: There are 1 chains and 0 blocks of water and 16 residues with 117 atoms 56: 56: chain #res #atoms 56: 56: 1 ' ' 16 117 56: 56: All occupancies are one 56: 56: Reading residue database... (Charmm27) 56: 56: Processing chain 1 (117 atoms, 16 residues) 56: 56: Replaced 1 residue named ASPH to the default ASP. Use interactive selection of protonated residues if that is what you need. 56: 56: Identified residue LYS50 as a starting terminus. 56: 56: Identified residue PRO65 as a ending terminus. 56: Start terminus LYS-50: NH3+ 56: End terminus PRO-65: COO- 56: 56: Checking for duplicate atoms.... 56: 56: Generating any missing hydrogen atoms and/or adding termini. 56: 56: Now there are 16 residues with 228 atoms 56: 56: Making bonds... 56: 56: Number of bonds was 232, now 232 56: 56: Generating angles, dihedrals and pairs... 56: 56: Making cmap torsions... 56: 56: There are 14 cmap torsion pairs 56: 56: There are 618 dihedrals, 38 impropers, 419 angles 56: 597 pairs, 232 bonds and 0 virtual sites 56: 56: Total mass 1662.885 a.m.u. 56: 56: Total charge 0.000 e 56: 56: Writing topology 56: 56: Writing coordinate file... 56: 56: --------- PLEASE NOTE ------------ 56: 56: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/D.pdb. 56: 56: The Charmm27 force field and the tip3p water model are used. 56: 56: --------- ETON ESAELP ------------ 56: [ OK ] Charmm/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_or_ter_merge_no_Dpdb_format_gro_match_file (232 ms) 56: [ RUN ] Charmm/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_or_ter_merge_no_Epdb_format_gro_match_file 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/aminoacids.r2b 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/rna.r2b 56: All occupancies are one 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/atomtypes.atp 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/aminoacids.rtp 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/dna.rtp 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/lipids.rtp 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/rna.rtp 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/aminoacids.hdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/dna.hdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/lipids.hdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/rna.hdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/aminoacids.n.tdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/dna.n.tdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/rna.n.tdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/aminoacids.c.tdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/dna.c.tdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/rna.c.tdb 56: Analysing hydrogen-bonding network for automated assignment of histidine 56: protonation. 89 donors and 98 acceptors were found. 56: There are 129 hydrogen bonds 56: Will use HISE for residue 31 56: Will use HISE for residue 51 56: 9 out of 9 lines of specbond.dat converted successfully 56: Special Atom Distance matrix: 56: CYS25 HIS31 HIS51 56: SG14 NE264 NE2226 56: HIS31 NE264 1.921 56: HIS51 NE2226 1.498 2.650 56: CYS80 SG477 0.207 1.984 1.570 56: Linking CYS-25 SG-14 and CYS-80 SG-477... 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/aminoacids.arn 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/dna.arn 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/rna.arn 56: Before cleaning: 2499 pairs 56: Before cleaning: 2524 dihedrals 56: Using the Charmm27 force field in directory charmm27.ff 56: 56: going to rename charmm27.ff/aminoacids.r2b 56: 56: going to rename charmm27.ff/rna.r2b 56: Reading /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/E.pdb... 56: Read 'This is a fragment of 2d4f for testing a disulfide bridge', 488 atoms 56: 56: Analyzing pdb file 56: Splitting chemical chains based on TER records or chain id changing. 56: 56: There are 1 chains and 0 blocks of water and 58 residues with 488 atoms 56: 56: chain #res #atoms 56: 56: 1 'A' 58 488 56: 56: All occupancies are one 56: 56: Reading residue database... (Charmm27) 56: 56: Processing chain 1 'A' (488 atoms, 58 residues) 56: 56: Identified residue ASN24 as a starting terminus. 56: 56: Identified residue ARG81 as a ending terminus. 56: Start terminus ASN-24: NH3+ 56: End terminus ARG-81: COO- 56: 56: Checking for duplicate atoms.... 56: 56: Generating any missing hydrogen atoms and/or adding termini. 56: 56: Now there are 58 residues with 936 atoms 56: 56: Making bonds... 56: 56: Number of bonds was 951, now 951 56: 56: Generating angles, dihedrals and pairs... 56: 56: Making cmap torsions... 56: 56: There are 56 cmap torsion pairs 56: 56: There are 2524 dihedrals, 149 impropers, 1704 angles 56: 2469 pairs, 951 bonds and 0 virtual sites 56: 56: Total mass 6908.566 a.m.u. 56: 56: Total charge -6.000 e 56: 56: Writing topology 56: 56: Writing coordinate file... 56: 56: --------- PLEASE NOTE ------------ 56: 56: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/E.pdb. 56: 56: The Charmm27 force field and the tip3p water model are used. 56: 56: --------- ETON ESAELP ------------ 56: [ OK ] Charmm/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_or_ter_merge_no_Epdb_format_gro_match_file (669 ms) 56: [ RUN ] Charmm/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_or_ter_merge_no_monomerpdb_format_gro_match_file 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/aminoacids.r2b 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/rna.r2b 56: All occupancies are one 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/atomtypes.atp 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/aminoacids.rtp 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/dna.rtp 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/lipids.rtp 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/rna.rtp 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/aminoacids.hdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/dna.hdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/lipids.hdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/rna.hdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/aminoacids.n.tdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/dna.n.tdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/rna.n.tdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/aminoacids.c.tdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/dna.c.tdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/rna.c.tdb 56: 9 out of 9 lines of specbond.dat converted successfully 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/aminoacids.arn 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/dna.arn 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/rna.arn 56: Before cleaning: 39 pairs 56: Before cleaning: 39 dihedrals 56: Using the Charmm27 force field in directory charmm27.ff 56: 56: going to rename charmm27.ff/aminoacids.r2b 56: 56: going to rename charmm27.ff/rna.r2b 56: Reading /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/monomer.pdb... 56: Read 'GLU', 9 atoms 56: 56: Analyzing pdb file 56: Splitting chemical chains based on TER records or chain id changing. 56: 56: There are 1 chains and 0 blocks of water and 1 residues with 9 atoms 56: 56: chain #res #atoms 56: 56: 1 'X' 1 9 56: 56: All occupancies are one 56: 56: Reading residue database... (Charmm27) 56: 56: Processing chain 1 'X' (9 atoms, 1 residues) 56: 56: Identified residue GLU1 as a starting terminus. 56: 56: Identified residue GLU1 as a ending terminus. 56: Start terminus GLU-1: NH3+ 56: End terminus GLU-1: COO- 56: 56: Checking for duplicate atoms.... 56: 56: Generating any missing hydrogen atoms and/or adding termini. 56: 56: Now there are 1 residues with 18 atoms 56: 56: Making bonds... 56: 56: Number of bonds was 17, now 17 56: 56: Generating angles, dihedrals and pairs... 56: 56: Making cmap torsions... 56: 56: There are 39 dihedrals, 2 impropers, 30 angles 56: 39 pairs, 17 bonds and 0 virtual sites 56: 56: Total mass 146.123 a.m.u. 56: 56: Total charge -1.000 e 56: 56: Writing topology 56: 56: Writing coordinate file... 56: 56: --------- PLEASE NOTE ------------ 56: 56: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/monomer.pdb. 56: 56: The Charmm27 force field and the tip3p water model are used. 56: 56: --------- ETON ESAELP ------------ 56: [ OK ] Charmm/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_or_ter_merge_no_monomerpdb_format_gro_match_file (126 ms) 56: [ RUN ] Charmm/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_h_id_or_ter_merge_no_Apdb_format_gro_match_file 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/aminoacids.r2b 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/rna.r2b 56: All occupancies are one 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/atomtypes.atp 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/aminoacids.rtp 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/dna.rtp 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/lipids.rtp 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/rna.rtp 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/aminoacids.hdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/dna.hdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/lipids.hdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/rna.hdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/aminoacids.n.tdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/dna.n.tdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/rna.n.tdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/aminoacids.c.tdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/dna.c.tdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/rna.c.tdb 56: Analysing hydrogen-bonding network for automated assignment of histidine 56: protonation. 25 donors and 23 acceptors were found. 56: There are 41 hydrogen bonds 56: Will use HISE for residue 8 56: 9 out of 9 lines of specbond.dat converted successfully 56: Special Atom Distance matrix: 56: CYS3 HIS8 56: SG9 NE251 56: HIS8 NE251 1.055 56: MET12 SD83 0.763 0.990 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/aminoacids.arn 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/dna.arn 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/rna.arn 56: Marked 124 virtual sites 56: Added 16 dummy masses 56: Added 26 new constraints 56: Before cleaning: 653 pairs 56: Before cleaning: 663 dihedrals 56: Using the Charmm27 force field in directory charmm27.ff 56: 56: going to rename charmm27.ff/aminoacids.r2b 56: 56: going to rename charmm27.ff/rna.r2b 56: Reading /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/A.pdb... 56: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms 56: 56: Analyzing pdb file 56: Splitting chemical chains based on TER records or chain id changing. 56: 56: There are 1 chains and 0 blocks of water and 16 residues with 128 atoms 56: 56: chain #res #atoms 56: 56: 1 ' ' 16 128 56: 56: All occupancies are one 56: 56: Reading residue database... (Charmm27) 56: 56: Processing chain 1 (128 atoms, 16 residues) 56: 56: Identified residue ALA2 as a starting terminus. 56: 56: Identified residue SER17 as a ending terminus. 56: Start terminus ALA-2: NH3+ 56: End terminus SER-17: COO- 56: 56: Checking for duplicate atoms.... 56: 56: Generating any missing hydrogen atoms and/or adding termini. 56: 56: Now there are 16 residues with 252 atoms 56: 56: Making bonds... 56: 56: Number of bonds was 254, now 254 56: 56: Generating angles, dihedrals and pairs... 56: 56: Making cmap torsions... 56: 56: There are 14 cmap torsion pairs 56: 56: There are 663 dihedrals, 48 impropers, 457 angles 56: 650 pairs, 254 bonds and 130 virtual sites 56: 56: Total mass 1846.115 a.m.u. 56: 56: Total charge 0.000 e 56: 56: Writing topology 56: 56: Writing coordinate file... 56: 56: --------- PLEASE NOTE ------------ 56: 56: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/A.pdb. 56: 56: The Charmm27 force field and the tip3p water model are used. 56: 56: --------- ETON ESAELP ------------ 56: [ OK ] Charmm/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_h_id_or_ter_merge_no_Apdb_format_gro_match_file (283 ms) 56: [ RUN ] Charmm/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_h_id_or_ter_merge_no_Bpdb_format_gro_match_file 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/aminoacids.r2b 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/rna.r2b 56: All occupancies are one 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/atomtypes.atp 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/aminoacids.rtp 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/dna.rtp 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/lipids.rtp 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/rna.rtp 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/aminoacids.hdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/dna.hdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/lipids.hdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/rna.hdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/aminoacids.n.tdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/dna.n.tdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/rna.n.tdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/aminoacids.c.tdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/dna.c.tdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/rna.c.tdb 56: Analysing hydrogen-bonding network for automated assignment of histidine 56: protonation. 30 donors and 22 acceptors were found. 56: There are 36 hydrogen bonds 56: Will use HISE for residue 29 56: Will use HISE for residue 32 56: 9 out of 9 lines of specbond.dat converted successfully 56: Special Atom Distance matrix: 56: CYS27 HIS29 56: SG90 NE2111 56: HIS29 NE2111 0.987 56: HIS32 NE2135 1.590 1.155 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/aminoacids.arn 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/dna.arn 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/rna.arn 56: Marked 132 virtual sites 56: Added 10 dummy masses 56: Added 19 new constraints 56: Before cleaning: 748 pairs 56: Before cleaning: 778 dihedrals 56: Using the Charmm27 force field in directory charmm27.ff 56: 56: going to rename charmm27.ff/aminoacids.r2b 56: 56: going to rename charmm27.ff/rna.r2b 56: Reading /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/B.pdb... 56: Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms 56: 56: Analyzing pdb file 56: Splitting chemical chains based on TER records or chain id changing. 56: 56: There are 1 chains and 0 blocks of water and 16 residues with 149 atoms 56: 56: chain #res #atoms 56: 56: 1 ' ' 16 149 56: 56: All occupancies are one 56: 56: Reading residue database... (Charmm27) 56: 56: Processing chain 1 (149 atoms, 16 residues) 56: 56: Replaced 1 residue named GLUH to the default GLU. Use interactive selection of protonated residues if that is what you need. 56: 56: Identified residue THR18 as a starting terminus. 56: 56: Identified residue PHE33 as a ending terminus. 56: Start terminus THR-18: NH3+ 56: End terminus PHE-33: COO- 56: 56: Checking for duplicate atoms.... 56: 56: Generating any missing hydrogen atoms and/or adding termini. 56: 56: Now there are 16 residues with 281 atoms 56: 56: Making bonds... 56: 56: Number of bonds was 290, now 290 56: 56: Generating angles, dihedrals and pairs... 56: 56: Making cmap torsions... 56: 56: There are 14 cmap torsion pairs 56: 56: There are 778 dihedrals, 49 impropers, 516 angles 56: 736 pairs, 290 bonds and 133 virtual sites 56: 56: Total mass 2088.361 a.m.u. 56: 56: Total charge 1.000 e 56: 56: Writing topology 56: 56: Writing coordinate file... 56: 56: --------- PLEASE NOTE ------------ 56: 56: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/B.pdb. 56: 56: The Charmm27 force field and the tip3p water model are used. 56: 56: --------- ETON ESAELP ------------ 56: [ OK ] Charmm/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_h_id_or_ter_merge_no_Bpdb_format_gro_match_file (299 ms) 56: [ RUN ] Charmm/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_h_id_or_ter_merge_no_Cpdb_format_gro_match_file 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/aminoacids.r2b 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/rna.r2b 56: All occupancies are one 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/atomtypes.atp 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/aminoacids.rtp 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/dna.rtp 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/lipids.rtp 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/rna.rtp 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/aminoacids.hdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/dna.hdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/lipids.hdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/rna.hdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/aminoacids.n.tdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/dna.n.tdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/rna.n.tdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/aminoacids.c.tdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/dna.c.tdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/rna.c.tdb 56: Analysing hydrogen-bonding network for automated assignment of histidine 56: protonation. 22 donors and 22 acceptors were found. 56: There are 26 hydrogen bonds 56: Will use HISE for residue 45 56: 9 out of 9 lines of specbond.dat converted successfully 56: Special Atom Distance matrix: 56: HIS45 56: NE295 56: MET46 SD102 1.078 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/aminoacids.arn 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/dna.arn 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/rna.arn 56: Marked 123 virtual sites 56: Added 22 dummy masses 56: Added 35 new constraints 56: Before cleaning: 676 pairs 56: Before cleaning: 696 dihedrals 56: Using the Charmm27 force field in directory charmm27.ff 56: 56: going to rename charmm27.ff/aminoacids.r2b 56: 56: going to rename charmm27.ff/rna.r2b 56: Reading /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/C.pdb... 56: Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms 56: 56: Analyzing pdb file 56: Splitting chemical chains based on TER records or chain id changing. 56: 56: There are 1 chains and 0 blocks of water and 16 residues with 132 atoms 56: 56: chain #res #atoms 56: 56: 1 ' ' 16 132 56: 56: All occupancies are one 56: 56: Reading residue database... (Charmm27) 56: 56: Processing chain 1 (132 atoms, 16 residues) 56: 56: Identified residue ALA34 as a starting terminus. 56: 56: Identified residue ALA49 as a ending terminus. 56: Start terminus ALA-34: NH3+ 56: End terminus ALA-49: COO- 56: 56: Checking for duplicate atoms.... 56: 56: Generating any missing hydrogen atoms and/or adding termini. 56: 56: Now there are 16 residues with 255 atoms 56: 56: Making bonds... 56: 56: Number of bonds was 261, now 261 56: 56: Generating angles, dihedrals and pairs... 56: 56: Making cmap torsions... 56: 56: There are 14 cmap torsion pairs 56: 56: There are 696 dihedrals, 39 impropers, 472 angles 56: 667 pairs, 261 bonds and 132 virtual sites 56: 56: Total mass 1861.130 a.m.u. 56: 56: Total charge -1.000 e 56: 56: Writing topology 56: 56: Writing coordinate file... 56: 56: --------- PLEASE NOTE ------------ 56: 56: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/C.pdb. 56: 56: The Charmm27 force field and the tip3p water model are used. 56: 56: --------- ETON ESAELP ------------ 56: [ OK ] Charmm/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_h_id_or_ter_merge_no_Cpdb_format_gro_match_file (286 ms) 56: [ RUN ] Charmm/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_h_id_or_ter_merge_no_Dpdb_format_gro_match_file 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/aminoacids.r2b 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/rna.r2b 56: All occupancies are one 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/atomtypes.atp 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/aminoacids.rtp 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/dna.rtp 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/lipids.rtp 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/rna.rtp 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/aminoacids.hdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/dna.hdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/lipids.hdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/rna.hdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/aminoacids.n.tdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/dna.n.tdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/rna.n.tdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/aminoacids.c.tdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/dna.c.tdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/rna.c.tdb 56: Analysing hydrogen-bonding network for automated assignment of histidine 56: protonation. 22 donors and 21 acceptors were found. 56: There are 30 hydrogen bonds 56: Will use HISE for residue 60 56: 9 out of 9 lines of specbond.dat converted successfully 56: Special Atom Distance matrix: 56: HIS60 56: NE285 56: CYS62 SG98 0.803 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/aminoacids.arn 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/dna.arn 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/rna.arn 56: Marked 111 virtual sites 56: Added 18 dummy masses 56: Added 31 new constraints 56: Before cleaning: 603 pairs 56: Before cleaning: 618 dihedrals 56: Using the Charmm27 force field in directory charmm27.ff 56: 56: going to rename charmm27.ff/aminoacids.r2b 56: 56: going to rename charmm27.ff/rna.r2b 56: Reading /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/D.pdb... 56: Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms 56: 56: Analyzing pdb file 56: Splitting chemical chains based on TER records or chain id changing. 56: 56: There are 1 chains and 0 blocks of water and 16 residues with 117 atoms 56: 56: chain #res #atoms 56: 56: 1 ' ' 16 117 56: 56: All occupancies are one 56: 56: Reading residue database... (Charmm27) 56: 56: Processing chain 1 (117 atoms, 16 residues) 56: 56: Replaced 1 residue named ASPH to the default ASP. Use interactive selection of protonated residues if that is what you need. 56: 56: Identified residue LYS50 as a starting terminus. 56: 56: Identified residue PRO65 as a ending terminus. 56: Start terminus LYS-50: NH3+ 56: End terminus PRO-65: COO- 56: 56: Checking for duplicate atoms.... 56: 56: Generating any missing hydrogen atoms and/or adding termini. 56: 56: Now there are 16 residues with 228 atoms 56: 56: Making bonds... 56: 56: Number of bonds was 232, now 232 56: 56: Generating angles, dihedrals and pairs... 56: 56: Making cmap torsions... 56: 56: There are 14 cmap torsion pairs 56: 56: There are 618 dihedrals, 38 impropers, 419 angles 56: 597 pairs, 232 bonds and 116 virtual sites 56: 56: Total mass 1662.885 a.m.u. 56: 56: Total charge 0.000 e 56: 56: Writing topology 56: 56: Writing coordinate file... 56: 56: --------- PLEASE NOTE ------------ 56: 56: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/D.pdb. 56: 56: The Charmm27 force field and the tip3p water model are used. 56: 56: --------- ETON ESAELP ------------ 56: [ OK ] Charmm/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_h_id_or_ter_merge_no_Dpdb_format_gro_match_file (263 ms) 56: [ RUN ] Charmm/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_h_id_or_ter_merge_no_Epdb_format_gro_match_file 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/aminoacids.r2b 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/rna.r2b 56: All occupancies are one 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/atomtypes.atp 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/aminoacids.rtp 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/dna.rtp 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/lipids.rtp 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/rna.rtp 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/aminoacids.hdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/dna.hdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/lipids.hdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/rna.hdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/aminoacids.n.tdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/dna.n.tdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/rna.n.tdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/aminoacids.c.tdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/dna.c.tdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/rna.c.tdb 56: Analysing hydrogen-bonding network for automated assignment of histidine 56: protonation. 89 donors and 98 acceptors were found. 56: There are 129 hydrogen bonds 56: Will use HISE for residue 31 56: Will use HISE for residue 51 56: 9 out of 9 lines of specbond.dat converted successfully 56: Special Atom Distance matrix: 56: CYS25 HIS31 HIS51 56: SG14 NE264 NE2226 56: HIS31 NE264 1.921 56: HIS51 NE2226 1.498 2.650 56: CYS80 SG477 0.207 1.984 1.570 56: Linking CYS-25 SG-14 and CYS-80 SG-477... 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/aminoacids.arn 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/dna.arn 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/rna.arn 56: Marked 447 virtual sites 56: Added 58 dummy masses 56: Added 101 new constraints 56: Before cleaning: 2499 pairs 56: Before cleaning: 2524 dihedrals 56: Using the Charmm27 force field in directory charmm27.ff 56: 56: going to rename charmm27.ff/aminoacids.r2b 56: 56: going to rename charmm27.ff/rna.r2b 56: Reading /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/E.pdb... 56: Read 'This is a fragment of 2d4f for testing a disulfide bridge', 488 atoms 56: 56: Analyzing pdb file 56: Splitting chemical chains based on TER records or chain id changing. 56: 56: There are 1 chains and 0 blocks of water and 58 residues with 488 atoms 56: 56: chain #res #atoms 56: 56: 1 'A' 58 488 56: 56: All occupancies are one 56: 56: Reading residue database... (Charmm27) 56: 56: Processing chain 1 'A' (488 atoms, 58 residues) 56: 56: Identified residue ASN24 as a starting terminus. 56: 56: Identified residue ARG81 as a ending terminus. 56: Start terminus ASN-24: NH3+ 56: End terminus ARG-81: COO- 56: 56: Checking for duplicate atoms.... 56: 56: Generating any missing hydrogen atoms and/or adding termini. 56: 56: Now there are 58 residues with 936 atoms 56: 56: Making bonds... 56: 56: Number of bonds was 951, now 951 56: 56: Generating angles, dihedrals and pairs... 56: 56: Making cmap torsions... 56: 56: There are 56 cmap torsion pairs 56: 56: There are 2524 dihedrals, 149 impropers, 1704 angles 56: 2469 pairs, 951 bonds and 462 virtual sites 56: 56: Total mass 6908.566 a.m.u. 56: 56: Total charge -6.000 e 56: 56: Writing topology 56: 56: Writing coordinate file... 56: 56: --------- PLEASE NOTE ------------ 56: 56: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/E.pdb. 56: 56: The Charmm27 force field and the tip3p water model are used. 56: 56: --------- ETON ESAELP ------------ 56: [ OK ] Charmm/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_h_id_or_ter_merge_no_Epdb_format_gro_match_file (743 ms) 56: [ RUN ] Charmm/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_h_id_or_ter_merge_no_monomerpdb_format_gro_match_file 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/aminoacids.r2b 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/rna.r2b 56: All occupancies are one 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/atomtypes.atp 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/aminoacids.rtp 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/dna.rtp 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/lipids.rtp 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/rna.rtp 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/aminoacids.hdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/dna.hdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/lipids.hdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/rna.hdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/aminoacids.n.tdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/dna.n.tdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/rna.n.tdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/aminoacids.c.tdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/dna.c.tdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/rna.c.tdb 56: 9 out of 9 lines of specbond.dat converted successfully 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/aminoacids.arn 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/dna.arn 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/rna.arn 56: Marked 8 virtual sites 56: Added 2 dummy masses 56: Added 3 new constraints 56: Before cleaning: 39 pairs 56: Before cleaning: 39 dihedrals 56: Using the Charmm27 force field in directory charmm27.ff 56: 56: going to rename charmm27.ff/aminoacids.r2b 56: 56: going to rename charmm27.ff/rna.r2b 56: Reading /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/monomer.pdb... 56: Read 'GLU', 9 atoms 56: 56: Analyzing pdb file 56: Splitting chemical chains based on TER records or chain id changing. 56: 56: There are 1 chains and 0 blocks of water and 1 residues with 9 atoms 56: 56: chain #res #atoms 56: 56: 1 'X' 1 9 56: 56: All occupancies are one 56: 56: Reading residue database... (Charmm27) 56: 56: Processing chain 1 'X' (9 atoms, 1 residues) 56: 56: Identified residue GLU1 as a starting terminus. 56: 56: Identified residue GLU1 as a ending terminus. 56: Start terminus GLU-1: NH3+ 56: End terminus GLU-1: COO- 56: 56: Checking for duplicate atoms.... 56: 56: Generating any missing hydrogen atoms and/or adding termini. 56: 56: Now there are 1 residues with 18 atoms 56: 56: Making bonds... 56: 56: Number of bonds was 17, now 17 56: 56: Generating angles, dihedrals and pairs... 56: 56: Making cmap torsions... 56: 56: There are 39 dihedrals, 2 impropers, 30 angles 56: 39 pairs, 17 bonds and 9 virtual sites 56: 56: Total mass 146.123 a.m.u. 56: 56: Total charge -1.000 e 56: 56: Writing topology 56: 56: Writing coordinate file... 56: 56: --------- PLEASE NOTE ------------ 56: 56: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/monomer.pdb. 56: 56: The Charmm27 force field and the tip3p water model are used. 56: 56: --------- ETON ESAELP ------------ 56: [ OK ] Charmm/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_h_id_or_ter_merge_no_monomerpdb_format_gro_match_file (131 ms) 56: [----------] 12 tests from Charmm/Pdb2gmxTest (3827 ms total) 56: 56: [----------] 8 tests from ChainSep/Pdb2gmxTest 56: [ RUN ] ChainSep/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_merge_all_chainTerpdb_format_gro_match_file 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/aminoacids.r2b 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/rna.r2b 56: All occupancies are one 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/atomtypes.atp 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/aminoacids.rtp 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/dna.rtp 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/lipids.rtp 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/rna.rtp 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/aminoacids.hdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/dna.hdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/lipids.hdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/rna.hdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/aminoacids.n.tdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/dna.n.tdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/rna.n.tdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/aminoacids.c.tdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/dna.c.tdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/rna.c.tdb 56: Analysing hydrogen-bonding network for automated assignment of histidine 56: protonation. 25 donors and 23 acceptors were found. 56: There are 41 hydrogen bonds 56: Will use HISE for residue 8 56: 9 out of 9 lines of specbond.dat converted successfully 56: Special Atom Distance matrix: 56: CYS3 HIS8 56: SG9 NE251 56: HIS8 NE251 1.055 56: MET12 SD83 0.763 0.990 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/aminoacids.arn 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/dna.arn 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/rna.arn 56: Before cleaning: 651 pairs 56: Before cleaning: 661 dihedrals 56: Using the Charmm27 force field in directory charmm27.ff 56: 56: going to rename charmm27.ff/aminoacids.r2b 56: 56: going to rename charmm27.ff/rna.r2b 56: Reading /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/chainTer.pdb... 56: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 127 atoms 56: 56: Analyzing pdb file 56: Splitting chemical chains based on changing chain id only (ignoring TER records). 56: 56: Merged chains into joint molecule definitions at 2 places. 56: 56: There are 1 chains and 0 blocks of water and 16 residues with 127 atoms 56: 56: chain #res #atoms 56: 56: 1 'A' 16 127 56: 56: All occupancies are one 56: 56: Reading residue database... (Charmm27) 56: 56: Processing chain 1 'A' (127 atoms, 16 residues) 56: 56: Identified residue ALA2 as a starting terminus. 56: 56: Identified residue GLU5 as a ending terminus. 56: 56: Identified residue PHE6 as a starting terminus. 56: 56: Identified residue MET12 as a ending terminus. 56: 56: Identified residue ASN13 as a starting terminus. 56: 56: Identified residue SER17 as a ending terminus. 56: Start terminus ALA-2: NH3+ 56: End terminus GLU-5: COO- 56: Start terminus PHE-6: NH3+ 56: End terminus MET-12: COO- 56: Start terminus ASN-13: NH3+ 56: End terminus SER-17: COO- 56: 56: Checking for duplicate atoms.... 56: 56: Generating any missing hydrogen atoms and/or adding termini. 56: 56: Now there are 16 residues with 258 atoms 56: 56: Making bonds... 56: 56: Number of bonds was 258, now 258 56: 56: Generating angles, dihedrals and pairs... 56: 56: Making cmap torsions... 56: 56: There are 10 cmap torsion pairs 56: 56: There are 661 dihedrals, 46 impropers, 463 angles 56: 648 pairs, 258 bonds and 0 virtual sites 56: 56: Total mass 1882.146 a.m.u. 56: 56: Total charge 0.000 e 56: 56: Writing topology 56: 56: Writing coordinate file... 56: 56: --------- PLEASE NOTE ------------ 56: 56: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/chainTer.pdb. 56: 56: The Charmm27 force field and the tip3p water model are used. 56: 56: --------- ETON ESAELP ------------ 56: [ OK ] ChainSep/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_merge_all_chainTerpdb_format_gro_match_file (255 ms) 56: [ RUN ] ChainSep/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_merge_no_chainTerpdb_format_gro_match_file 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/aminoacids.r2b 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/rna.r2b 56: All occupancies are one 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/atomtypes.atp 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/aminoacids.rtp 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/dna.rtp 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/lipids.rtp 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/rna.rtp 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/aminoacids.hdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/dna.hdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/lipids.hdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/rna.hdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/aminoacids.n.tdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/dna.n.tdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/rna.n.tdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/aminoacids.c.tdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/dna.c.tdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/rna.c.tdb 56: 9 out of 9 lines of specbond.dat converted successfully 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/aminoacids.arn 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/dna.arn 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/rna.arn 56: Before cleaning: 123 pairs 56: Before cleaning: 123 dihedrals 56: Analysing hydrogen-bonding network for automated assignment of histidine 56: protonation. 10 donors and 7 acceptors were found. 56: There are 7 hydrogen bonds 56: Will use HISE for residue 8 56: 9 out of 9 lines of specbond.dat converted successfully 56: Special Atom Distance matrix: 56: HIS8 56: NE223 56: MET12 SD55 0.990 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/aminoacids.arn 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/dna.arn 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/rna.arn 56: Before cleaning: 317 pairs 56: Before cleaning: 322 dihedrals 56: 9 out of 9 lines of specbond.dat converted successfully 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/aminoacids.arn 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/dna.arn 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/rna.arn 56: Before cleaning: 211 pairs 56: Before cleaning: 216 dihedrals 56: Using the Charmm27 force field in directory charmm27.ff 56: 56: going to rename charmm27.ff/aminoacids.r2b 56: 56: going to rename charmm27.ff/rna.r2b 56: Reading /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/chainTer.pdb... 56: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 127 atoms 56: 56: Analyzing pdb file 56: Splitting chemical chains based on changing chain id only (ignoring TER records). 56: 56: There are 3 chains and 0 blocks of water and 16 residues with 127 atoms 56: 56: chain #res #atoms 56: 56: 1 'A' 4 28 56: 56: 2 'B' 7 58 56: 56: 3 'C' 5 41 56: 56: All occupancies are one 56: 56: Reading residue database... (Charmm27) 56: 56: Processing chain 1 'A' (28 atoms, 4 residues) 56: 56: Identified residue ALA2 as a starting terminus. 56: 56: Identified residue GLU5 as a ending terminus. 56: Start terminus ALA-2: NH3+ 56: End terminus GLU-5: COO- 56: 56: Checking for duplicate atoms.... 56: 56: Generating any missing hydrogen atoms and/or adding termini. 56: 56: Now there are 4 residues with 51 atoms 56: Chain time... 56: 56: Making bonds... 56: 56: Number of bonds was 50, now 50 56: 56: Generating angles, dihedrals and pairs... 56: 56: Making cmap torsions... 56: 56: There are 2 cmap torsion pairs 56: 56: There are 123 dihedrals, 9 impropers, 88 angles 56: 123 pairs, 50 bonds and 0 virtual sites 56: 56: Total mass 434.421 a.m.u. 56: 56: Total charge -2.000 e 56: 56: Writing topology 56: 56: Processing chain 2 'B' (58 atoms, 7 residues) 56: 56: Identified residue PHE6 as a starting terminus. 56: 56: Identified residue MET12 as a ending terminus. 56: Start terminus PHE-6: NH3+ 56: End terminus MET-12: COO- 56: 56: Checking for duplicate atoms.... 56: 56: Generating any missing hydrogen atoms and/or adding termini. 56: 56: Now there are 7 residues with 124 atoms 56: Chain time... 56: 56: Making bonds... 56: 56: Number of bonds was 125, now 125 56: 56: Generating angles, dihedrals and pairs... 56: 56: Making cmap torsions... 56: 56: There are 5 cmap torsion pairs 56: 56: There are 322 dihedrals, 19 impropers, 227 angles 56: 314 pairs, 125 bonds and 0 virtual sites 56: 56: Total mass 846.083 a.m.u. 56: 56: Total charge 1.000 e 56: 56: Writing topology 56: 56: Processing chain 3 'C' (41 atoms, 5 residues) 56: 56: Identified residue ASN13 as a starting terminus. 56: 56: Identified residue SER17 as a ending terminus. 56: Start terminus ASN-13: NH3+ 56: End terminus SER-17: COO- 56: 56: Checking for duplicate atoms.... 56: 56: Generating any missing hydrogen atoms and/or adding termini. 56: 56: Now there are 5 residues with 83 atoms 56: Chain time... 56: 56: Making bonds... 56: 56: Number of bonds was 83, now 83 56: 56: Generating angles, dihedrals and pairs... 56: 56: Making cmap torsions... 56: 56: There are 3 cmap torsion pairs 56: 56: There are 216 dihedrals, 18 impropers, 148 angles 56: 211 pairs, 83 bonds and 0 virtual sites 56: 56: Total mass 601.643 a.m.u. 56: 56: Total charge 1.000 e 56: 56: Writing topology 56: 56: Including chain 1 in system: 51 atoms 4 residues 56: 56: Including chain 2 in system: 124 atoms 7 residues 56: 56: Including chain 3 in system: 83 atoms 5 residues 56: 56: Now there are 258 atoms and 16 residues 56: 56: Total mass in system 1882.146 a.m.u. 56: 56: Total charge in system 0.000 e 56: 56: Writing coordinate file... 56: 56: --------- PLEASE NOTE ------------ 56: 56: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/chainTer.pdb. 56: 56: The Charmm27 force field and the tip3p water model are used. 56: 56: --------- ETON ESAELP ------------ 56: [ OK ] ChainSep/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_merge_no_chainTerpdb_format_gro_match_file (215 ms) 56: [ RUN ] ChainSep/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_ter_merge_all_chainTerpdb_format_gro_match_file 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/aminoacids.r2b 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/rna.r2b 56: All occupancies are one 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/atomtypes.atp 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/aminoacids.rtp 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/dna.rtp 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/lipids.rtp 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/rna.rtp 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/aminoacids.hdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/dna.hdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/lipids.hdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/rna.hdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/aminoacids.n.tdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/dna.n.tdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/rna.n.tdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/aminoacids.c.tdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/dna.c.tdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/rna.c.tdb 56: Analysing hydrogen-bonding network for automated assignment of histidine 56: protonation. 25 donors and 23 acceptors were found. 56: There are 41 hydrogen bonds 56: Will use HISE for residue 8 56: 9 out of 9 lines of specbond.dat converted successfully 56: Special Atom Distance matrix: 56: CYS3 HIS8 56: SG9 NE251 56: HIS8 NE251 1.055 56: MET12 SD83 0.763 0.990 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/aminoacids.arn 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/dna.arn 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/rna.arn 56: Before cleaning: 651 pairs 56: Before cleaning: 661 dihedrals 56: Using the Charmm27 force field in directory charmm27.ff 56: 56: going to rename charmm27.ff/aminoacids.r2b 56: 56: going to rename charmm27.ff/rna.r2b 56: Reading /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/chainTer.pdb... 56: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 127 atoms 56: 56: Analyzing pdb file 56: Splitting chemical chains based on TER records only (ignoring chain id). 56: 56: Merged chains into joint molecule definitions at 2 places. 56: 56: There are 1 chains and 0 blocks of water and 16 residues with 127 atoms 56: 56: chain #res #atoms 56: 56: 1 'A' 16 127 56: 56: All occupancies are one 56: 56: Reading residue database... (Charmm27) 56: 56: Processing chain 1 'A' (127 atoms, 16 residues) 56: 56: Identified residue ALA2 as a starting terminus. 56: 56: Identified residue ILE9 as a ending terminus. 56: 56: Identified residue LYS10 as a starting terminus. 56: 56: Identified residue MET12 as a ending terminus. 56: 56: Identified residue ASN13 as a starting terminus. 56: 56: Identified residue SER17 as a ending terminus. 56: Start terminus ALA-2: NH3+ 56: End terminus ILE-9: COO- 56: Start terminus LYS-10: NH3+ 56: End terminus MET-12: COO- 56: Start terminus ASN-13: NH3+ 56: End terminus SER-17: COO- 56: 56: Checking for duplicate atoms.... 56: 56: Generating any missing hydrogen atoms and/or adding termini. 56: 56: Now there are 16 residues with 258 atoms 56: 56: Making bonds... 56: 56: Number of bonds was 258, now 258 56: 56: Generating angles, dihedrals and pairs... 56: 56: Making cmap torsions... 56: 56: There are 10 cmap torsion pairs 56: 56: There are 661 dihedrals, 46 impropers, 463 angles 56: 648 pairs, 258 bonds and 0 virtual sites 56: 56: Total mass 1882.146 a.m.u. 56: 56: Total charge 0.000 e 56: 56: Writing topology 56: 56: Writing coordinate file... 56: 56: --------- PLEASE NOTE ------------ 56: 56: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/chainTer.pdb. 56: 56: The Charmm27 force field and the tip3p water model are used. 56: 56: --------- ETON ESAELP ------------ 56: [ OK ] ChainSep/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_ter_merge_all_chainTerpdb_format_gro_match_file (252 ms) 56: [ RUN ] ChainSep/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_ter_merge_no_chainTerpdb_format_gro_match_file 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/aminoacids.r2b 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/rna.r2b 56: All occupancies are one 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/atomtypes.atp 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/aminoacids.rtp 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/dna.rtp 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/lipids.rtp 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/rna.rtp 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/aminoacids.hdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/dna.hdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/lipids.hdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/rna.hdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/aminoacids.n.tdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/dna.n.tdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/rna.n.tdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/aminoacids.c.tdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/dna.c.tdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/rna.c.tdb 56: Analysing hydrogen-bonding network for automated assignment of histidine 56: protonation. 10 donors and 12 acceptors were found. 56: There are 13 hydrogen bonds 56: Will use HISE for residue 8 56: 9 out of 9 lines of specbond.dat converted successfully 56: Special Atom Distance matrix: 56: CYS3 56: SG9 56: HIS8 NE251 1.055 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/aminoacids.arn 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/dna.arn 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/rna.arn 56: Before cleaning: 288 pairs 56: Before cleaning: 293 dihedrals 56: 9 out of 9 lines of specbond.dat converted successfully 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/aminoacids.arn 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/dna.arn 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/rna.arn 56: Before cleaning: 152 pairs 56: Before cleaning: 152 dihedrals 56: 9 out of 9 lines of specbond.dat converted successfully 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/aminoacids.arn 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/dna.arn 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/rna.arn 56: Before cleaning: 211 pairs 56: Before cleaning: 216 dihedrals 56: Using the Charmm27 force field in directory charmm27.ff 56: 56: going to rename charmm27.ff/aminoacids.r2b 56: 56: going to rename charmm27.ff/rna.r2b 56: Reading /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/chainTer.pdb... 56: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 127 atoms 56: 56: Analyzing pdb file 56: Splitting chemical chains based on TER records only (ignoring chain id). 56: 56: There are 3 chains and 0 blocks of water and 16 residues with 127 atoms 56: 56: chain #res #atoms 56: 56: 1 'A' 8 61 56: 56: 2 'B' 3 25 56: 56: 3 'C' 5 41 56: 56: All occupancies are one 56: 56: Reading residue database... (Charmm27) 56: 56: Processing chain 1 'A' (61 atoms, 8 residues) 56: 56: Identified residue ALA2 as a starting terminus. 56: 56: Identified residue ILE9 as a ending terminus. 56: Start terminus ALA-2: NH3+ 56: End terminus ILE-9: COO- 56: 56: Checking for duplicate atoms.... 56: 56: Generating any missing hydrogen atoms and/or adding termini. 56: 56: Now there are 8 residues with 114 atoms 56: Chain time... 56: 56: Making bonds... 56: 56: Number of bonds was 115, now 115 56: 56: Generating angles, dihedrals and pairs... 56: 56: Making cmap torsions... 56: 56: There are 6 cmap torsion pairs 56: 56: There are 293 dihedrals, 23 impropers, 203 angles 56: 285 pairs, 115 bonds and 0 virtual sites 56: 56: Total mass 888.952 a.m.u. 56: 56: Total charge -2.000 e 56: 56: Writing topology 56: 56: Processing chain 2 'B' (25 atoms, 3 residues) 56: 56: Identified residue LYS10 as a starting terminus. 56: 56: Identified residue MET12 as a ending terminus. 56: Start terminus LYS-10: NH3+ 56: End terminus MET-12: COO- 56: 56: Checking for duplicate atoms.... 56: 56: Generating any missing hydrogen atoms and/or adding termini. 56: 56: Now there are 3 residues with 61 atoms 56: Chain time... 56: 56: Making bonds... 56: 56: Number of bonds was 60, now 60 56: 56: Generating angles, dihedrals and pairs... 56: 56: Making cmap torsions... 56: 56: There are 1 cmap torsion pairs 56: 56: There are 152 dihedrals, 5 impropers, 112 angles 56: 152 pairs, 60 bonds and 0 virtual sites 56: 56: Total mass 391.552 a.m.u. 56: 56: Total charge 1.000 e 56: 56: Writing topology 56: 56: Processing chain 3 'C' (41 atoms, 5 residues) 56: 56: Identified residue ASN13 as a starting terminus. 56: 56: Identified residue SER17 as a ending terminus. 56: Start terminus ASN-13: NH3+ 56: End terminus SER-17: COO- 56: 56: Checking for duplicate atoms.... 56: 56: Generating any missing hydrogen atoms and/or adding termini. 56: 56: Now there are 5 residues with 83 atoms 56: Chain time... 56: 56: Making bonds... 56: 56: Number of bonds was 83, now 83 56: 56: Generating angles, dihedrals and pairs... 56: 56: Making cmap torsions... 56: 56: There are 3 cmap torsion pairs 56: 56: There are 216 dihedrals, 18 impropers, 148 angles 56: 211 pairs, 83 bonds and 0 virtual sites 56: 56: Total mass 601.643 a.m.u. 56: 56: Total charge 1.000 e 56: 56: Writing topology 56: 56: Including chain 1 in system: 114 atoms 8 residues 56: 56: Including chain 2 in system: 61 atoms 3 residues 56: 56: Including chain 3 in system: 83 atoms 5 residues 56: 56: Now there are 258 atoms and 16 residues 56: 56: Total mass in system 1882.146 a.m.u. 56: 56: Total charge in system 0.000 e 56: 56: Writing coordinate file... 56: 56: --------- PLEASE NOTE ------------ 56: 56: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/chainTer.pdb. 56: 56: The Charmm27 force field and the tip3p water model are used. 56: 56: --------- ETON ESAELP ------------ 56: [ OK ] ChainSep/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_ter_merge_no_chainTerpdb_format_gro_match_file (218 ms) 56: [ RUN ] ChainSep/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_or_ter_merge_all_chainTerpdb_format_gro_match_file 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/aminoacids.r2b 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/rna.r2b 56: All occupancies are one 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/atomtypes.atp 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/aminoacids.rtp 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/dna.rtp 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/lipids.rtp 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/rna.rtp 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/aminoacids.hdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/dna.hdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/lipids.hdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/rna.hdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/aminoacids.n.tdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/dna.n.tdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/rna.n.tdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/aminoacids.c.tdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/dna.c.tdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/rna.c.tdb 56: Analysing hydrogen-bonding network for automated assignment of histidine 56: protonation. 25 donors and 23 acceptors were found. 56: There are 41 hydrogen bonds 56: Will use HISE for residue 8 56: 9 out of 9 lines of specbond.dat converted successfully 56: Special Atom Distance matrix: 56: CYS3 HIS8 56: SG9 NE251 56: HIS8 NE251 1.055 56: MET12 SD83 0.763 0.990 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/aminoacids.arn 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/dna.arn 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/rna.arn 56: Before cleaning: 650 pairs 56: Before cleaning: 660 dihedrals 56: Using the Charmm27 force field in directory charmm27.ff 56: 56: going to rename charmm27.ff/aminoacids.r2b 56: 56: going to rename charmm27.ff/rna.r2b 56: Reading /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/chainTer.pdb... 56: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 127 atoms 56: 56: Analyzing pdb file 56: Splitting chemical chains based on TER records or chain id changing. 56: 56: Merged chains into joint molecule definitions at 3 places. 56: 56: There are 1 chains and 0 blocks of water and 16 residues with 127 atoms 56: 56: chain #res #atoms 56: 56: 1 'A' 16 127 56: 56: All occupancies are one 56: 56: Reading residue database... (Charmm27) 56: 56: Processing chain 1 'A' (127 atoms, 16 residues) 56: 56: Identified residue ALA2 as a starting terminus. 56: 56: Identified residue GLU5 as a ending terminus. 56: 56: Identified residue PHE6 as a starting terminus. 56: 56: Identified residue ILE9 as a ending terminus. 56: 56: Identified residue LYS10 as a starting terminus. 56: 56: Identified residue MET12 as a ending terminus. 56: 56: Identified residue ASN13 as a starting terminus. 56: 56: Identified residue SER17 as a ending terminus. 56: Start terminus ALA-2: NH3+ 56: End terminus GLU-5: COO- 56: Start terminus PHE-6: NH3+ 56: End terminus ILE-9: COO- 56: Start terminus LYS-10: NH3+ 56: End terminus MET-12: COO- 56: Start terminus ASN-13: NH3+ 56: End terminus SER-17: COO- 56: 56: Checking for duplicate atoms.... 56: 56: Generating any missing hydrogen atoms and/or adding termini. 56: 56: Now there are 16 residues with 261 atoms 56: 56: Making bonds... 56: 56: Number of bonds was 260, now 260 56: 56: Generating angles, dihedrals and pairs... 56: 56: Making cmap torsions... 56: 56: There are 8 cmap torsion pairs 56: 56: There are 660 dihedrals, 45 impropers, 466 angles 56: 647 pairs, 260 bonds and 0 virtual sites 56: 56: Total mass 1900.162 a.m.u. 56: 56: Total charge 0.000 e 56: 56: Writing topology 56: 56: Writing coordinate file... 56: 56: --------- PLEASE NOTE ------------ 56: 56: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/chainTer.pdb. 56: 56: The Charmm27 force field and the tip3p water model are used. 56: 56: --------- ETON ESAELP ------------ 56: [ OK ] ChainSep/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_or_ter_merge_all_chainTerpdb_format_gro_match_file (255 ms) 56: [ RUN ] ChainSep/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_or_ter_merge_no_chainTerpdb_format_gro_match_file 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/aminoacids.r2b 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/rna.r2b 56: Chain identifier 'B' is used in two non-sequential blocks. They will be treated as separate chains unless you reorder your file. 56: 56: All occupancies are one 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/atomtypes.atp 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/aminoacids.rtp 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/dna.rtp 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/lipids.rtp 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/rna.rtp 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/aminoacids.hdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/dna.hdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/lipids.hdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/rna.hdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/aminoacids.n.tdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/dna.n.tdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/rna.n.tdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/aminoacids.c.tdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/dna.c.tdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/rna.c.tdb 56: 9 out of 9 lines of specbond.dat converted successfully 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/aminoacids.arn 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/dna.arn 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/rna.arn 56: Before cleaning: 123 pairs 56: Before cleaning: 123 dihedrals 56: Analysing hydrogen-bonding network for automated assignment of histidine 56: protonation. 6 donors and 4 acceptors were found. 56: There are 3 hydrogen bonds 56: Will use HISE for residue 8 56: 9 out of 9 lines of specbond.dat converted successfully 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/aminoacids.arn 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/dna.arn 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/rna.arn 56: Before cleaning: 164 pairs 56: Before cleaning: 169 dihedrals 56: 9 out of 9 lines of specbond.dat converted successfully 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/aminoacids.arn 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/dna.arn 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/rna.arn 56: Before cleaning: 152 pairs 56: Before cleaning: 152 dihedrals 56: 9 out of 9 lines of specbond.dat converted successfully 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/aminoacids.arn 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/dna.arn 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/rna.arn 56: Before cleaning: 211 pairs 56: Before cleaning: 216 dihedrals 56: Using the Charmm27 force field in directory charmm27.ff 56: 56: going to rename charmm27.ff/aminoacids.r2b 56: 56: going to rename charmm27.ff/rna.r2b 56: Reading /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/chainTer.pdb... 56: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 127 atoms 56: 56: Analyzing pdb file 56: Splitting chemical chains based on TER records or chain id changing. 56: 56: Chain identifier 'B' is used in two non-sequential blocks. They will be treated as separate chains unless you reorder your file. 56: 56: There are 4 chains and 0 blocks of water and 16 residues with 127 atoms 56: 56: chain #res #atoms 56: 56: 1 'A' 4 28 56: 56: 2 'B' 4 33 56: 56: 3 'B' 3 25 56: 56: 4 'C' 5 41 56: 56: All occupancies are one 56: 56: Reading residue database... (Charmm27) 56: 56: Processing chain 1 'A' (28 atoms, 4 residues) 56: 56: Identified residue ALA2 as a starting terminus. 56: 56: Identified residue GLU5 as a ending terminus. 56: Start terminus ALA-2: NH3+ 56: End terminus GLU-5: COO- 56: 56: Checking for duplicate atoms.... 56: 56: Generating any missing hydrogen atoms and/or adding termini. 56: 56: Now there are 4 residues with 51 atoms 56: Chain time... 56: 56: Making bonds... 56: 56: Number of bonds was 50, now 50 56: 56: Generating angles, dihedrals and pairs... 56: 56: Making cmap torsions... 56: 56: There are 2 cmap torsion pairs 56: 56: There are 123 dihedrals, 9 impropers, 88 angles 56: 123 pairs, 50 bonds and 0 virtual sites 56: 56: Total mass 434.421 a.m.u. 56: 56: Total charge -2.000 e 56: 56: Writing topology 56: 56: Processing chain 2 'B' (33 atoms, 4 residues) 56: 56: Identified residue PHE6 as a starting terminus. 56: 56: Identified residue ILE9 as a ending terminus. 56: Start terminus PHE-6: NH3+ 56: End terminus ILE-9: COO- 56: 56: Checking for duplicate atoms.... 56: 56: Generating any missing hydrogen atoms and/or adding termini. 56: 56: Now there are 4 residues with 66 atoms 56: Chain time... 56: 56: Making bonds... 56: 56: Number of bonds was 67, now 67 56: 56: Generating angles, dihedrals and pairs... 56: 56: Making cmap torsions... 56: 56: There are 2 cmap torsion pairs 56: 56: There are 169 dihedrals, 13 impropers, 118 angles 56: 161 pairs, 67 bonds and 0 virtual sites 56: 56: Total mass 472.547 a.m.u. 56: 56: Total charge 0.000 e 56: 56: Writing topology 56: 56: Processing chain 3 'B' (25 atoms, 3 residues) 56: 56: Identified residue LYS10 as a starting terminus. 56: 56: Identified residue MET12 as a ending terminus. 56: Start terminus LYS-10: NH3+ 56: End terminus MET-12: COO- 56: 56: Checking for duplicate atoms.... 56: 56: Generating any missing hydrogen atoms and/or adding termini. 56: 56: Now there are 3 residues with 61 atoms 56: Chain time... 56: 56: Making bonds... 56: 56: Number of bonds was 60, now 60 56: 56: Generating angles, dihedrals and pairs... 56: 56: Making cmap torsions... 56: 56: There are 1 cmap torsion pairs 56: 56: There are 152 dihedrals, 5 impropers, 112 angles 56: 152 pairs, 60 bonds and 0 virtual sites 56: 56: Total mass 391.552 a.m.u. 56: 56: Total charge 1.000 e 56: 56: Writing topology 56: 56: Processing chain 4 'C' (41 atoms, 5 residues) 56: 56: Identified residue ASN13 as a starting terminus. 56: 56: Identified residue SER17 as a ending terminus. 56: Start terminus ASN-13: NH3+ 56: End terminus SER-17: COO- 56: 56: Checking for duplicate atoms.... 56: 56: Generating any missing hydrogen atoms and/or adding termini. 56: 56: Now there are 5 residues with 83 atoms 56: Chain time... 56: 56: Making bonds... 56: 56: Number of bonds was 83, now 83 56: 56: Generating angles, dihedrals and pairs... 56: 56: Making cmap torsions... 56: 56: There are 3 cmap torsion pairs 56: 56: There are 216 dihedrals, 18 impropers, 148 angles 56: 211 pairs, 83 bonds and 0 virtual sites 56: 56: Total mass 601.643 a.m.u. 56: 56: Total charge 1.000 e 56: 56: Writing topology 56: 56: Including chain 1 in system: 51 atoms 4 residues 56: 56: Including chain 2 in system: 66 atoms 4 residues 56: 56: Including chain 3 in system: 61 atoms 3 residues 56: 56: Including chain 4 in system: 83 atoms 5 residues 56: 56: Now there are 261 atoms and 16 residues 56: 56: Total mass in system 1900.162 a.m.u. 56: 56: Total charge in system 0.000 e 56: 56: Writing coordinate file... 56: 56: --------- PLEASE NOTE ------------ 56: 56: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/chainTer.pdb. 56: 56: The Charmm27 force field and the tip3p water model are used. 56: 56: --------- ETON ESAELP ------------ 56: [ OK ] ChainSep/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_or_ter_merge_no_chainTerpdb_format_gro_match_file (223 ms) 56: [ RUN ] ChainSep/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_and_ter_merge_all_chainTerpdb_format_gro_match_file 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/aminoacids.r2b 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/rna.r2b 56: All occupancies are one 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/atomtypes.atp 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/aminoacids.rtp 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/dna.rtp 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/lipids.rtp 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/rna.rtp 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/aminoacids.hdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/dna.hdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/lipids.hdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/rna.hdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/aminoacids.n.tdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/dna.n.tdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/rna.n.tdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/aminoacids.c.tdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/dna.c.tdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/rna.c.tdb 56: Analysing hydrogen-bonding network for automated assignment of histidine 56: protonation. 25 donors and 23 acceptors were found. 56: There are 41 hydrogen bonds 56: Will use HISE for residue 8 56: 9 out of 9 lines of specbond.dat converted successfully 56: Special Atom Distance matrix: 56: CYS3 HIS8 56: SG9 NE251 56: HIS8 NE251 1.055 56: MET12 SD83 0.763 0.990 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/aminoacids.arn 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/dna.arn 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/rna.arn 56: Before cleaning: 652 pairs 56: Before cleaning: 662 dihedrals 56: Using the Charmm27 force field in directory charmm27.ff 56: 56: going to rename charmm27.ff/aminoacids.r2b 56: 56: going to rename charmm27.ff/rna.r2b 56: Reading /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/chainTer.pdb... 56: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 127 atoms 56: 56: Analyzing pdb file 56: Splitting chemical chains based on TER records and chain id changing. 56: 56: Merged chains into joint molecule definitions at 1 places. 56: 56: There are 1 chains and 0 blocks of water and 16 residues with 127 atoms 56: 56: chain #res #atoms 56: 56: 1 'A' 16 127 56: 56: All occupancies are one 56: 56: Reading residue database... (Charmm27) 56: 56: Processing chain 1 'A' (127 atoms, 16 residues) 56: 56: Identified residue ALA2 as a starting terminus. 56: 56: Identified residue MET12 as a ending terminus. 56: 56: Identified residue ASN13 as a starting terminus. 56: 56: Identified residue SER17 as a ending terminus. 56: Start terminus ALA-2: NH3+ 56: End terminus MET-12: COO- 56: Start terminus ASN-13: NH3+ 56: End terminus SER-17: COO- 56: 56: Checking for duplicate atoms.... 56: 56: Generating any missing hydrogen atoms and/or adding termini. 56: 56: Now there are 16 residues with 255 atoms 56: 56: Making bonds... 56: 56: Number of bonds was 256, now 256 56: 56: Generating angles, dihedrals and pairs... 56: 56: Making cmap torsions... 56: 56: There are 12 cmap torsion pairs 56: 56: There are 662 dihedrals, 47 impropers, 460 angles 56: 649 pairs, 256 bonds and 0 virtual sites 56: 56: Total mass 1864.131 a.m.u. 56: 56: Total charge 0.000 e 56: 56: Writing topology 56: 56: Writing coordinate file... 56: 56: --------- PLEASE NOTE ------------ 56: 56: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/chainTer.pdb. 56: 56: The Charmm27 force field and the tip3p water model are used. 56: 56: --------- ETON ESAELP ------------ 56: [ OK ] ChainSep/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_and_ter_merge_all_chainTerpdb_format_gro_match_file (248 ms) 56: [ RUN ] ChainSep/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_and_ter_merge_no_chainTerpdb_format_gro_match_file 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/aminoacids.r2b 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/rna.r2b 56: All occupancies are one 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/atomtypes.atp 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/aminoacids.rtp 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/dna.rtp 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/lipids.rtp 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/rna.rtp 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/aminoacids.hdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/dna.hdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/lipids.hdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/rna.hdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/aminoacids.n.tdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/dna.n.tdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/rna.n.tdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/aminoacids.c.tdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/dna.c.tdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/rna.c.tdb 56: Analysing hydrogen-bonding network for automated assignment of histidine 56: protonation. 14 donors and 15 acceptors were found. 56: There are 20 hydrogen bonds 56: Will use HISE for residue 8 56: 9 out of 9 lines of specbond.dat converted successfully 56: Special Atom Distance matrix: 56: CYS3 HIS8 56: SG9 NE251 56: HIS8 NE251 1.055 56: MET12 SD83 0.763 0.990 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/aminoacids.arn 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/dna.arn 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/rna.arn 56: Before cleaning: 441 pairs 56: Before cleaning: 446 dihedrals 56: 9 out of 9 lines of specbond.dat converted successfully 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/aminoacids.arn 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/dna.arn 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/rna.arn 56: Before cleaning: 211 pairs 56: Before cleaning: 216 dihedrals 56: Using the Charmm27 force field in directory charmm27.ff 56: 56: going to rename charmm27.ff/aminoacids.r2b 56: 56: going to rename charmm27.ff/rna.r2b 56: Reading /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/chainTer.pdb... 56: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 127 atoms 56: 56: Analyzing pdb file 56: Splitting chemical chains based on TER records and chain id changing. 56: 56: There are 2 chains and 0 blocks of water and 16 residues with 127 atoms 56: 56: chain #res #atoms 56: 56: 1 'A' 11 86 56: 56: 2 'C' 5 41 56: 56: All occupancies are one 56: 56: Reading residue database... (Charmm27) 56: 56: Processing chain 1 'A' (86 atoms, 11 residues) 56: 56: Identified residue ALA2 as a starting terminus. 56: 56: Identified residue MET12 as a ending terminus. 56: Start terminus ALA-2: NH3+ 56: End terminus MET-12: COO- 56: 56: Checking for duplicate atoms.... 56: 56: Generating any missing hydrogen atoms and/or adding termini. 56: 56: Now there are 11 residues with 172 atoms 56: Chain time... 56: 56: Making bonds... 56: 56: Number of bonds was 173, now 173 56: 56: Generating angles, dihedrals and pairs... 56: 56: Making cmap torsions... 56: 56: There are 9 cmap torsion pairs 56: 56: There are 446 dihedrals, 29 impropers, 312 angles 56: 438 pairs, 173 bonds and 0 virtual sites 56: 56: Total mass 1262.488 a.m.u. 56: 56: Total charge -1.000 e 56: 56: Writing topology 56: 56: Processing chain 2 'C' (41 atoms, 5 residues) 56: 56: Identified residue ASN13 as a starting terminus. 56: 56: Identified residue SER17 as a ending terminus. 56: Start terminus ASN-13: NH3+ 56: End terminus SER-17: COO- 56: 56: Checking for duplicate atoms.... 56: 56: Generating any missing hydrogen atoms and/or adding termini. 56: 56: Now there are 5 residues with 83 atoms 56: Chain time... 56: 56: Making bonds... 56: 56: Number of bonds was 83, now 83 56: 56: Generating angles, dihedrals and pairs... 56: 56: Making cmap torsions... 56: 56: There are 3 cmap torsion pairs 56: 56: There are 216 dihedrals, 18 impropers, 148 angles 56: 211 pairs, 83 bonds and 0 virtual sites 56: 56: Total mass 601.643 a.m.u. 56: 56: Total charge 1.000 e 56: 56: Writing topology 56: 56: Including chain 1 in system: 172 atoms 11 residues 56: 56: Including chain 2 in system: 83 atoms 5 residues 56: 56: Now there are 255 atoms and 16 residues 56: 56: Total mass in system 1864.131 a.m.u. 56: 56: Total charge in system 0.000 e 56: 56: Writing coordinate file... 56: 56: --------- PLEASE NOTE ------------ 56: 56: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/chainTer.pdb. 56: 56: The Charmm27 force field and the tip3p water model are used. 56: 56: --------- ETON ESAELP ------------ 56: [ OK ] ChainSep/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_and_ter_merge_no_chainTerpdb_format_gro_match_file (211 ms) 56: [----------] 8 tests from ChainSep/Pdb2gmxTest (1882 ms total) 56: 56: [----------] 4 tests from ChainChanges/Pdb2gmxTest 56: [ RUN ] ChainChanges/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_merge_no_fragmentspdb_format_pdb_match_file 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/aminoacids.r2b 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/rna.r2b 56: All occupancies are one 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/atomtypes.atp 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/aminoacids.rtp 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/dna.rtp 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/lipids.rtp 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/rna.rtp 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/aminoacids.hdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/dna.hdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/lipids.hdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/rna.hdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/aminoacids.n.tdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/dna.n.tdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/rna.n.tdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/aminoacids.c.tdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/dna.c.tdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/rna.c.tdb 56: 9 out of 9 lines of specbond.dat converted successfully 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/aminoacids.arn 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/dna.arn 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/rna.arn 56: Before cleaning: 83 pairs 56: Before cleaning: 83 dihedrals 56: 9 out of 9 lines of specbond.dat converted successfully 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/aminoacids.arn 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/dna.arn 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/rna.arn 56: Before cleaning: 145 pairs 56: Before cleaning: 150 dihedrals 56: Using the Charmm27 force field in directory charmm27.ff 56: 56: going to rename charmm27.ff/aminoacids.r2b 56: 56: going to rename charmm27.ff/rna.r2b 56: Reading /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/fragments.pdb... 56: Read 'Fragments of peptides and ions', 47 atoms 56: 56: Analyzing pdb file 56: Splitting chemical chains based on changing chain id only (ignoring TER records). 56: 56: There are 2 chains and 0 blocks of water and 6 residues with 47 atoms 56: 56: chain #res #atoms 56: 56: 1 'A' 3 19 56: 56: 2 'B' 3 28 56: 56: All occupancies are one 56: 56: Reading residue database... (Charmm27) 56: 56: Processing chain 1 'A' (19 atoms, 3 residues) 56: 56: Identified residue ALA2 as a starting terminus. 56: 56: Identified residue ASP4 as a ending terminus. 56: Start terminus ALA-2: NH3+ 56: End terminus ASP-4: COO- 56: 56: Checking for duplicate atoms.... 56: 56: Generating any missing hydrogen atoms and/or adding termini. 56: 56: Now there are 3 residues with 36 atoms 56: Chain time... 56: 56: Making bonds... 56: 56: Number of bonds was 35, now 35 56: 56: Generating angles, dihedrals and pairs... 56: 56: Making cmap torsions... 56: 56: There are 1 cmap torsion pairs 56: 56: There are 83 dihedrals, 6 impropers, 61 angles 56: 83 pairs, 35 bonds and 0 virtual sites 56: 56: Total mass 306.314 a.m.u. 56: 56: Total charge -1.000 e 56: 56: Writing topology 56: 56: Processing chain 2 'B' (28 atoms, 3 residues) 56: 56: Identified residue THR18 as a starting terminus. 56: 56: Identified residue TRP20 as a ending terminus. 56: Start terminus THR-18: NH3+ 56: End terminus TRP-20: COO- 56: 56: Checking for duplicate atoms.... 56: 56: Generating any missing hydrogen atoms and/or adding termini. 56: 56: Now there are 3 residues with 57 atoms 56: Chain time... 56: 56: Making bonds... 56: 56: Number of bonds was 58, now 58 56: 56: Generating angles, dihedrals and pairs... 56: 56: Making cmap torsions... 56: 56: There are 1 cmap torsion pairs 56: 56: There are 150 dihedrals, 5 impropers, 103 angles 56: 142 pairs, 58 bonds and 0 virtual sites 56: 56: Total mass 404.468 a.m.u. 56: 56: Total charge 0.000 e 56: 56: Writing topology 56: 56: Including chain 1 in system: 36 atoms 3 residues 56: 56: Including chain 2 in system: 57 atoms 3 residues 56: 56: Now there are 93 atoms and 6 residues 56: 56: Total mass in system 710.782 a.m.u. 56: 56: Total charge in system -1.000 e 56: 56: Writing coordinate file... 56: 56: --------- PLEASE NOTE ------------ 56: 56: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/fragments.pdb. 56: 56: The Charmm27 force field and the tip3p water model are used. 56: 56: --------- ETON ESAELP ------------ 56: [ OK ] ChainChanges/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_merge_no_fragmentspdb_format_pdb_match_file (154 ms) 56: [ RUN ] ChainChanges/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_ter_merge_no_fragmentspdb_format_pdb_match_file 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/aminoacids.r2b 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/rna.r2b 56: All occupancies are one 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/atomtypes.atp 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/aminoacids.rtp 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/dna.rtp 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/lipids.rtp 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/rna.rtp 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/aminoacids.hdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/dna.hdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/lipids.hdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/rna.hdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/aminoacids.n.tdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/dna.n.tdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/rna.n.tdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/aminoacids.c.tdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/dna.c.tdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/rna.c.tdb 56: 9 out of 9 lines of specbond.dat converted successfully 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/aminoacids.arn 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/dna.arn 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/rna.arn 56: Before cleaning: 83 pairs 56: Before cleaning: 83 dihedrals 56: 9 out of 9 lines of specbond.dat converted successfully 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/aminoacids.arn 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/dna.arn 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/rna.arn 56: Before cleaning: 145 pairs 56: Before cleaning: 150 dihedrals 56: Using the Charmm27 force field in directory charmm27.ff 56: 56: going to rename charmm27.ff/aminoacids.r2b 56: 56: going to rename charmm27.ff/rna.r2b 56: Reading /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/fragments.pdb... 56: Read 'Fragments of peptides and ions', 47 atoms 56: 56: Analyzing pdb file 56: Splitting chemical chains based on TER records only (ignoring chain id). 56: 56: There are 2 chains and 0 blocks of water and 6 residues with 47 atoms 56: 56: chain #res #atoms 56: 56: 1 'A' 3 19 56: 56: 2 'B' 3 28 56: 56: All occupancies are one 56: 56: Reading residue database... (Charmm27) 56: 56: Processing chain 1 'A' (19 atoms, 3 residues) 56: 56: Identified residue ALA2 as a starting terminus. 56: 56: Identified residue ASP4 as a ending terminus. 56: Start terminus ALA-2: NH3+ 56: End terminus ASP-4: COO- 56: 56: Checking for duplicate atoms.... 56: 56: Generating any missing hydrogen atoms and/or adding termini. 56: 56: Now there are 3 residues with 36 atoms 56: Chain time... 56: 56: Making bonds... 56: 56: Number of bonds was 35, now 35 56: 56: Generating angles, dihedrals and pairs... 56: 56: Making cmap torsions... 56: 56: There are 1 cmap torsion pairs 56: 56: There are 83 dihedrals, 6 impropers, 61 angles 56: 83 pairs, 35 bonds and 0 virtual sites 56: 56: Total mass 306.314 a.m.u. 56: 56: Total charge -1.000 e 56: 56: Writing topology 56: 56: Processing chain 2 'B' (28 atoms, 3 residues) 56: 56: Identified residue THR18 as a starting terminus. 56: 56: Identified residue TRP20 as a ending terminus. 56: Start terminus THR-18: NH3+ 56: End terminus TRP-20: COO- 56: 56: Checking for duplicate atoms.... 56: 56: Generating any missing hydrogen atoms and/or adding termini. 56: 56: Now there are 3 residues with 57 atoms 56: Chain time... 56: 56: Making bonds... 56: 56: Number of bonds was 58, now 58 56: 56: Generating angles, dihedrals and pairs... 56: 56: Making cmap torsions... 56: 56: There are 1 cmap torsion pairs 56: 56: There are 150 dihedrals, 5 impropers, 103 angles 56: 142 pairs, 58 bonds and 0 virtual sites 56: 56: Total mass 404.468 a.m.u. 56: 56: Total charge 0.000 e 56: 56: Writing topology 56: 56: Including chain 1 in system: 36 atoms 3 residues 56: 56: Including chain 2 in system: 57 atoms 3 residues 56: 56: Now there are 93 atoms and 6 residues 56: 56: Total mass in system 710.782 a.m.u. 56: 56: Total charge in system -1.000 e 56: 56: Writing coordinate file... 56: 56: --------- PLEASE NOTE ------------ 56: 56: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/fragments.pdb. 56: 56: The Charmm27 force field and the tip3p water model are used. 56: 56: --------- ETON ESAELP ------------ 56: [ OK ] ChainChanges/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_ter_merge_no_fragmentspdb_format_pdb_match_file (152 ms) 56: [ RUN ] ChainChanges/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_or_ter_merge_no_fragmentspdb_format_pdb_match_file 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/aminoacids.r2b 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/rna.r2b 56: All occupancies are one 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/atomtypes.atp 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/aminoacids.rtp 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/dna.rtp 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/lipids.rtp 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/rna.rtp 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/aminoacids.hdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/dna.hdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/lipids.hdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/rna.hdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/aminoacids.n.tdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/dna.n.tdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/rna.n.tdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/aminoacids.c.tdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/dna.c.tdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/rna.c.tdb 56: 9 out of 9 lines of specbond.dat converted successfully 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/aminoacids.arn 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/dna.arn 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/rna.arn 56: Before cleaning: 83 pairs 56: Before cleaning: 83 dihedrals 56: 9 out of 9 lines of specbond.dat converted successfully 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/aminoacids.arn 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/dna.arn 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/rna.arn 56: Before cleaning: 145 pairs 56: Before cleaning: 150 dihedrals 56: Using the Charmm27 force field in directory charmm27.ff 56: 56: going to rename charmm27.ff/aminoacids.r2b 56: 56: going to rename charmm27.ff/rna.r2b 56: Reading /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/fragments.pdb... 56: Read 'Fragments of peptides and ions', 47 atoms 56: 56: Analyzing pdb file 56: Splitting chemical chains based on TER records or chain id changing. 56: 56: There are 2 chains and 0 blocks of water and 6 residues with 47 atoms 56: 56: chain #res #atoms 56: 56: 1 'A' 3 19 56: 56: 2 'B' 3 28 56: 56: All occupancies are one 56: 56: Reading residue database... (Charmm27) 56: 56: Processing chain 1 'A' (19 atoms, 3 residues) 56: 56: Identified residue ALA2 as a starting terminus. 56: 56: Identified residue ASP4 as a ending terminus. 56: Start terminus ALA-2: NH3+ 56: End terminus ASP-4: COO- 56: 56: Checking for duplicate atoms.... 56: 56: Generating any missing hydrogen atoms and/or adding termini. 56: 56: Now there are 3 residues with 36 atoms 56: Chain time... 56: 56: Making bonds... 56: 56: Number of bonds was 35, now 35 56: 56: Generating angles, dihedrals and pairs... 56: 56: Making cmap torsions... 56: 56: There are 1 cmap torsion pairs 56: 56: There are 83 dihedrals, 6 impropers, 61 angles 56: 83 pairs, 35 bonds and 0 virtual sites 56: 56: Total mass 306.314 a.m.u. 56: 56: Total charge -1.000 e 56: 56: Writing topology 56: 56: Processing chain 2 'B' (28 atoms, 3 residues) 56: 56: Identified residue THR18 as a starting terminus. 56: 56: Identified residue TRP20 as a ending terminus. 56: Start terminus THR-18: NH3+ 56: End terminus TRP-20: COO- 56: 56: Checking for duplicate atoms.... 56: 56: Generating any missing hydrogen atoms and/or adding termini. 56: 56: Now there are 3 residues with 57 atoms 56: Chain time... 56: 56: Making bonds... 56: 56: Number of bonds was 58, now 58 56: 56: Generating angles, dihedrals and pairs... 56: 56: Making cmap torsions... 56: 56: There are 1 cmap torsion pairs 56: 56: There are 150 dihedrals, 5 impropers, 103 angles 56: 142 pairs, 58 bonds and 0 virtual sites 56: 56: Total mass 404.468 a.m.u. 56: 56: Total charge 0.000 e 56: 56: Writing topology 56: 56: Including chain 1 in system: 36 atoms 3 residues 56: 56: Including chain 2 in system: 57 atoms 3 residues 56: 56: Now there are 93 atoms and 6 residues 56: 56: Total mass in system 710.782 a.m.u. 56: 56: Total charge in system -1.000 e 56: 56: Writing coordinate file... 56: 56: --------- PLEASE NOTE ------------ 56: 56: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/fragments.pdb. 56: 56: The Charmm27 force field and the tip3p water model are used. 56: 56: --------- ETON ESAELP ------------ 56: [ OK ] ChainChanges/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_or_ter_merge_no_fragmentspdb_format_pdb_match_file (152 ms) 56: [ RUN ] ChainChanges/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_and_ter_merge_no_fragmentspdb_format_pdb_match_file 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/aminoacids.r2b 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/rna.r2b 56: All occupancies are one 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/atomtypes.atp 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/aminoacids.rtp 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/dna.rtp 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/lipids.rtp 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/rna.rtp 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/aminoacids.hdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/dna.hdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/lipids.hdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/rna.hdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/aminoacids.n.tdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/dna.n.tdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/rna.n.tdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/aminoacids.c.tdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/dna.c.tdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/rna.c.tdb 56: 9 out of 9 lines of specbond.dat converted successfully 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/aminoacids.arn 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/dna.arn 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/rna.arn 56: Before cleaning: 83 pairs 56: Before cleaning: 83 dihedrals 56: 9 out of 9 lines of specbond.dat converted successfully 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/aminoacids.arn 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/dna.arn 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/rna.arn 56: Before cleaning: 145 pairs 56: Before cleaning: 150 dihedrals 56: Using the Charmm27 force field in directory charmm27.ff 56: 56: going to rename charmm27.ff/aminoacids.r2b 56: 56: going to rename charmm27.ff/rna.r2b 56: Reading /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/fragments.pdb... 56: Read 'Fragments of peptides and ions', 47 atoms 56: 56: Analyzing pdb file 56: Splitting chemical chains based on TER records and chain id changing. 56: 56: There are 2 chains and 0 blocks of water and 6 residues with 47 atoms 56: 56: chain #res #atoms 56: 56: 1 'A' 3 19 56: 56: 2 'B' 3 28 56: 56: All occupancies are one 56: 56: Reading residue database... (Charmm27) 56: 56: Processing chain 1 'A' (19 atoms, 3 residues) 56: 56: Identified residue ALA2 as a starting terminus. 56: 56: Identified residue ASP4 as a ending terminus. 56: Start terminus ALA-2: NH3+ 56: End terminus ASP-4: COO- 56: 56: Checking for duplicate atoms.... 56: 56: Generating any missing hydrogen atoms and/or adding termini. 56: 56: Now there are 3 residues with 36 atoms 56: Chain time... 56: 56: Making bonds... 56: 56: Number of bonds was 35, now 35 56: 56: Generating angles, dihedrals and pairs... 56: 56: Making cmap torsions... 56: 56: There are 1 cmap torsion pairs 56: 56: There are 83 dihedrals, 6 impropers, 61 angles 56: 83 pairs, 35 bonds and 0 virtual sites 56: 56: Total mass 306.314 a.m.u. 56: 56: Total charge -1.000 e 56: 56: Writing topology 56: 56: Processing chain 2 'B' (28 atoms, 3 residues) 56: 56: Identified residue THR18 as a starting terminus. 56: 56: Identified residue TRP20 as a ending terminus. 56: Start terminus THR-18: NH3+ 56: End terminus TRP-20: COO- 56: 56: Checking for duplicate atoms.... 56: 56: Generating any missing hydrogen atoms and/or adding termini. 56: 56: Now there are 3 residues with 57 atoms 56: Chain time... 56: 56: Making bonds... 56: 56: Number of bonds was 58, now 58 56: 56: Generating angles, dihedrals and pairs... 56: 56: Making cmap torsions... 56: 56: There are 1 cmap torsion pairs 56: 56: There are 150 dihedrals, 5 impropers, 103 angles 56: 142 pairs, 58 bonds and 0 virtual sites 56: 56: Total mass 404.468 a.m.u. 56: 56: Total charge 0.000 e 56: 56: Writing topology 56: 56: Including chain 1 in system: 36 atoms 3 residues 56: 56: Including chain 2 in system: 57 atoms 3 residues 56: 56: Now there are 93 atoms and 6 residues 56: 56: Total mass in system 710.782 a.m.u. 56: 56: Total charge in system -1.000 e 56: 56: Writing coordinate file... 56: 56: --------- PLEASE NOTE ------------ 56: 56: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/fragments.pdb. 56: 56: The Charmm27 force field and the tip3p water model are used. 56: 56: --------- ETON ESAELP ------------ 56: [ OK ] ChainChanges/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_and_ter_merge_no_fragmentspdb_format_pdb_match_file (153 ms) 56: [----------] 4 tests from ChainChanges/Pdb2gmxTest (614 ms total) 56: 56: [----------] 4 tests from Cyclic/Pdb2gmxTest 56: [ RUN ] Cyclic/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_or_ter_merge_no_cycrnapdb_format_gro_match_file 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/aminoacids.r2b 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/rna.r2b 56: WARNING: all CONECT records are ignored 56: Chain identifier 'Q' is used in two non-sequential blocks. They will be treated as separate chains unless you reorder your file. 56: 56: All occupancies are one 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/atomtypes.atp 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/aminoacids.rtp 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/dna.rtp 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/lipids.rtp 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/rna.rtp 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/aminoacids.hdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/dna.hdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/lipids.hdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/rna.hdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/aminoacids.n.tdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/dna.n.tdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/rna.n.tdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/aminoacids.c.tdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/dna.c.tdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/rna.c.tdb 56: 9 out of 9 lines of specbond.dat converted successfully 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/aminoacids.arn 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/dna.arn 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/rna.arn 56: Before cleaning: 6040 pairs 56: Before cleaning: 6605 dihedrals 56: 9 out of 9 lines of specbond.dat converted successfully 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/aminoacids.arn 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/dna.arn 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/rna.arn 56: Before cleaning: 6040 pairs 56: Before cleaning: 6605 dihedrals 56: 9 out of 9 lines of specbond.dat converted successfully 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/aminoacids.arn 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/dna.arn 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/rna.arn 56: 9 out of 9 lines of specbond.dat converted successfully 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/aminoacids.arn 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/dna.arn 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/rna.arn 56: 9 out of 9 lines of specbond.dat converted successfully 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/aminoacids.arn 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/dna.arn 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/rna.arn 56: Using the Charmm27 force field in directory charmm27.ff 56: 56: going to rename charmm27.ff/aminoacids.r2b 56: 56: going to rename charmm27.ff/rna.r2b 56: Reading /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/cyc-rna.pdb... 56: Read 'L1 RIBOZYME RNA LIGASE', 3087 atoms 56: 56: Analyzing pdb file 56: Splitting chemical chains based on TER records or chain id changing. 56: 56: Chain identifier 'Q' is used in two non-sequential blocks. They will be treated as separate chains unless you reorder your file. 56: 56: Moved all the water blocks to the end 56: 56: There are 3 chains and 2 blocks of water and 175 residues with 3087 atoms 56: 56: chain #res #atoms 56: 56: 1 'P' 71 1527 56: 56: 2 'Q' 71 1527 56: 56: 3 'Q' 7 7 56: 56: 4 ' ' 10 10 (only water) 56: 56: 5 ' ' 16 16 (only water) 56: 56: All occupancies are one 56: 56: Reading residue database... (Charmm27) 56: 56: Processing chain 1 'P' (1527 atoms, 71 residues) 56: 56: Identified residue G1 as a starting terminus. 56: 56: Identified residue U71 as a ending terminus. 56: 56: Checking for duplicate atoms.... 56: 56: Generating any missing hydrogen atoms and/or adding termini. 56: 56: Now there are 71 residues with 2297 atoms 56: Chain time... 56: 56: Making bonds... 56: 56: Number of bonds was 2481, now 2481 56: 56: Generating angles, dihedrals and pairs... 56: 56: Making cmap torsions... 56: 56: There are 6605 dihedrals, 183 impropers, 4434 angles 56: 5827 pairs, 2481 bonds and 0 virtual sites 56: 56: Total mass 22984.514 a.m.u. 56: 56: Total charge -71.000 e 56: 56: Writing topology 56: 56: Processing chain 2 'Q' (1527 atoms, 71 residues) 56: 56: Identified residue G1 as a starting terminus. 56: 56: Identified residue U71 as a ending terminus. 56: 56: Checking for duplicate atoms.... 56: 56: Generating any missing hydrogen atoms and/or adding termini. 56: 56: Now there are 71 residues with 2297 atoms 56: Chain time... 56: 56: Making bonds... 56: 56: Number of bonds was 2481, now 2481 56: 56: Generating angles, dihedrals and pairs... 56: 56: Making cmap torsions... 56: 56: There are 6605 dihedrals, 183 impropers, 4434 angles 56: 5827 pairs, 2481 bonds and 0 virtual sites 56: 56: Total mass 22984.514 a.m.u. 56: 56: Total charge -71.000 e 56: 56: Writing topology 56: 56: Processing chain 3 'Q' (7 atoms, 7 residues) 56: 56: Residue MG72 has type 'Ion', assuming it is not linked into a chain. 56: 56: Residue MG73 has type 'Ion', assuming it is not linked into a chain. 56: 56: Residue MG74 has type 'Ion', assuming it is not linked into a chain. 56: 56: Residue MG75 has type 'Ion', assuming it is not linked into a chain. 56: 56: Residue MG76 has type 'Ion', assuming it is not linked into a chain. 56: 56: Disabling further notes about ions. 56: 56: Problem with chain definition, or missing terminal residues. This chain does not appear to contain a recognized chain molecule. If this is incorrect, you can edit residuetypes.dat to modify the behavior. 56: 56: Checking for duplicate atoms.... 56: 56: Generating any missing hydrogen atoms and/or adding termini. 56: 56: Now there are 7 residues with 7 atoms 56: Chain time... 56: 56: Making bonds... 56: 56: No bonds 56: 56: Generating angles, dihedrals and pairs... 56: 56: Making cmap torsions... 56: 56: There are 0 dihedrals, 0 impropers, 0 angles 56: 0 pairs, 0 bonds and 0 virtual sites 56: 56: Total mass 170.135 a.m.u. 56: 56: Total charge 14.000 e 56: 56: Writing topology 56: 56: Processing chain 4 (10 atoms, 10 residues) 56: 56: Problem with chain definition, or missing terminal residues. This chain does not appear to contain a recognized chain molecule. If this is incorrect, you can edit residuetypes.dat to modify the behavior. 56: 56: Checking for duplicate atoms.... 56: 56: Generating any missing hydrogen atoms and/or adding termini. 56: 56: Now there are 10 residues with 30 atoms 56: 56: Making bonds... 56: 56: Number of bonds was 30, now 30 56: 56: Generating angles, dihedrals and pairs... 56: 56: Making cmap torsions... 56: 56: There are 0 dihedrals, 0 impropers, 30 angles 56: 0 pairs, 30 bonds and 0 virtual sites 56: 56: Total mass 180.154 a.m.u. 56: 56: Total charge 0.000 e 56: 56: Processing chain 5 (16 atoms, 16 residues) 56: 56: Problem with chain definition, or missing terminal residues. This chain does not appear to contain a recognized chain molecule. If this is incorrect, you can edit residuetypes.dat to modify the behavior. 56: 56: Checking for duplicate atoms.... 56: 56: Generating any missing hydrogen atoms and/or adding termini. 56: 56: Now there are 16 residues with 48 atoms 56: 56: Making bonds... 56: 56: Number of bonds was 48, now 48 56: 56: Generating angles, dihedrals and pairs... 56: 56: Making cmap torsions... 56: 56: There are 0 dihedrals, 0 impropers, 48 angles 56: 0 pairs, 48 bonds and 0 virtual sites 56: 56: Total mass 288.246 a.m.u. 56: 56: Total charge 0.000 e 56: 56: Including chain 1 in system: 2297 atoms 71 residues 56: 56: Including chain 2 in system: 2297 atoms 71 residues 56: 56: Including chain 3 in system: 7 atoms 7 residues 56: 56: Including chain 4 in system: 30 atoms 10 residues 56: 56: Including chain 5 in system: 48 atoms 16 residues 56: 56: Now there are 4679 atoms and 175 residues 56: 56: Total mass in system 46607.563 a.m.u. 56: 56: Total charge in system -128.000 e 56: 56: Writing coordinate file... 56: 56: --------- PLEASE NOTE ------------ 56: 56: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/cyc-rna.pdb. 56: 56: The Charmm27 force field and the tip3p water model are used. 56: 56: --------- ETON ESAELP ------------ 56: [ OK ] Cyclic/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_or_ter_merge_no_cycrnapdb_format_gro_match_file (2993 ms) 56: [ RUN ] Cyclic/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_or_ter_merge_no_cycprotpdb_format_gro_match_file 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/aminoacids.r2b 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/rna.r2b 56: All occupancies are one 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/atomtypes.atp 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/aminoacids.rtp 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/dna.rtp 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/lipids.rtp 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/rna.rtp 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/aminoacids.hdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/dna.hdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/lipids.hdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/rna.hdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/aminoacids.n.tdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/dna.n.tdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/rna.n.tdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/aminoacids.c.tdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/dna.c.tdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/rna.c.tdb 56: 9 out of 9 lines of specbond.dat converted successfully 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/aminoacids.arn 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/dna.arn 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/rna.arn 56: Before cleaning: 2325 pairs 56: Before cleaning: 2325 dihedrals 56: Using the Charmm27 force field in directory charmm27.ff 56: 56: going to rename charmm27.ff/aminoacids.r2b 56: 56: going to rename charmm27.ff/rna.r2b 56: Reading /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/cyc-prot.pdb... 56: Read 'CARNOCYCLIN-A', 413 atoms 56: 56: Analyzing pdb file 56: Splitting chemical chains based on TER records or chain id changing. 56: 56: There are 1 chains and 0 blocks of water and 60 residues with 413 atoms 56: 56: chain #res #atoms 56: 56: 1 'A' 60 413 56: 56: All occupancies are one 56: 56: Reading residue database... (Charmm27) 56: 56: Processing chain 1 'A' (413 atoms, 60 residues) 56: 56: Identified residue LEU1 as a starting terminus. 56: 56: Identified residue LEU60 as a ending terminus. 56: 56: Checking for duplicate atoms.... 56: 56: Generating any missing hydrogen atoms and/or adding termini. 56: 56: Now there are 60 residues with 878 atoms 56: 56: Making bonds... 56: 56: Number of bonds was 880, now 880 56: 56: Generating angles, dihedrals and pairs... 56: 56: Making cmap torsions... 56: 56: There are 60 cmap torsion pairs 56: 56: There are 2325 dihedrals, 137 impropers, 1614 angles 56: 2319 pairs, 880 bonds and 0 virtual sites 56: 56: Total mass 5866.087 a.m.u. 56: 56: Total charge 4.000 e 56: 56: Writing topology 56: 56: Writing coordinate file... 56: 56: --------- PLEASE NOTE ------------ 56: 56: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/cyc-prot.pdb. 56: 56: The Charmm27 force field and the tip3p water model are used. 56: 56: --------- ETON ESAELP ------------ 56: [ OK ] Cyclic/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_or_ter_merge_no_cycprotpdb_format_gro_match_file (661 ms) 56: [ RUN ] Cyclic/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_or_ter_merge_all_cycrnapdb_format_gro_match_file 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/aminoacids.r2b 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/rna.r2b 56: WARNING: all CONECT records are ignored 56: All occupancies are one 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/atomtypes.atp 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/aminoacids.rtp 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/dna.rtp 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/lipids.rtp 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/rna.rtp 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/aminoacids.hdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/dna.hdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/lipids.hdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/rna.hdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/aminoacids.n.tdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/dna.n.tdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/rna.n.tdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/aminoacids.c.tdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/dna.c.tdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/rna.c.tdb 56: 9 out of 9 lines of specbond.dat converted successfully 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/aminoacids.arn 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/dna.arn 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/rna.arn 56: Before cleaning: 12080 pairs 56: Before cleaning: 13210 dihedrals 56: 9 out of 9 lines of specbond.dat converted successfully 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/aminoacids.arn 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/dna.arn 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/rna.arn 56: 9 out of 9 lines of specbond.dat converted successfully 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/aminoacids.arn 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/dna.arn 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/rna.arn 56: Using the Charmm27 force field in directory charmm27.ff 56: 56: going to rename charmm27.ff/aminoacids.r2b 56: 56: going to rename charmm27.ff/rna.r2b 56: Reading /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/cyc-rna.pdb... 56: Read 'L1 RIBOZYME RNA LIGASE', 3087 atoms 56: 56: Analyzing pdb file 56: Splitting chemical chains based on TER records or chain id changing. 56: 56: Moved all the water blocks to the end 56: 56: Merged chains into joint molecule definitions at 2 places. 56: 56: There are 1 chains and 2 blocks of water and 175 residues with 3087 atoms 56: 56: chain #res #atoms 56: 56: 1 'P' 149 3061 56: 56: 2 ' ' 10 10 (only water) 56: 56: 3 ' ' 16 16 (only water) 56: 56: All occupancies are one 56: 56: Reading residue database... (Charmm27) 56: 56: Processing chain 1 'P' (3061 atoms, 149 residues) 56: 56: Identified residue G1 as a starting terminus. 56: 56: Identified residue U71 as a ending terminus. 56: 56: Identified residue G1 as a starting terminus. 56: 56: Identified residue U71 as a ending terminus. 56: 56: Residue MG72 has type 'Ion', assuming it is not linked into a chain. 56: 56: Residue MG73 has type 'Ion', assuming it is not linked into a chain. 56: 56: Residue MG74 has type 'Ion', assuming it is not linked into a chain. 56: 56: Residue MG75 has type 'Ion', assuming it is not linked into a chain. 56: 56: Residue MG76 has type 'Ion', assuming it is not linked into a chain. 56: 56: Disabling further notes about ions. 56: 56: Checking for duplicate atoms.... 56: 56: Generating any missing hydrogen atoms and/or adding termini. 56: 56: Now there are 149 residues with 4601 atoms 56: 56: Making bonds... 56: 56: Number of bonds was 4962, now 4962 56: 56: Generating angles, dihedrals and pairs... 56: 56: Making cmap torsions... 56: 56: There are 13210 dihedrals, 366 impropers, 8868 angles 56: 11654 pairs, 4962 bonds and 0 virtual sites 56: 56: Total mass 46139.162 a.m.u. 56: 56: Total charge -128.000 e 56: 56: Writing topology 56: 56: Processing chain 2 (10 atoms, 10 residues) 56: 56: Problem with chain definition, or missing terminal residues. This chain does not appear to contain a recognized chain molecule. If this is incorrect, you can edit residuetypes.dat to modify the behavior. 56: 56: Checking for duplicate atoms.... 56: 56: Generating any missing hydrogen atoms and/or adding termini. 56: 56: Now there are 10 residues with 30 atoms 56: 56: Making bonds... 56: 56: Number of bonds was 30, now 30 56: 56: Generating angles, dihedrals and pairs... 56: 56: Making cmap torsions... 56: 56: There are 0 dihedrals, 0 impropers, 30 angles 56: 0 pairs, 30 bonds and 0 virtual sites 56: 56: Total mass 180.154 a.m.u. 56: 56: Total charge 0.000 e 56: 56: Processing chain 3 (16 atoms, 16 residues) 56: 56: Problem with chain definition, or missing terminal residues. This chain does not appear to contain a recognized chain molecule. If this is incorrect, you can edit residuetypes.dat to modify the behavior. 56: 56: Checking for duplicate atoms.... 56: 56: Generating any missing hydrogen atoms and/or adding termini. 56: 56: Now there are 16 residues with 48 atoms 56: 56: Making bonds... 56: 56: Number of bonds was 48, now 48 56: 56: Generating angles, dihedrals and pairs... 56: 56: Making cmap torsions... 56: 56: There are 0 dihedrals, 0 impropers, 48 angles 56: 0 pairs, 48 bonds and 0 virtual sites 56: 56: Total mass 288.246 a.m.u. 56: 56: Total charge 0.000 e 56: 56: Including chain 1 in system: 4601 atoms 149 residues 56: 56: Including chain 2 in system: 30 atoms 10 residues 56: 56: Including chain 3 in system: 48 atoms 16 residues 56: 56: Now there are 4679 atoms and 175 residues 56: 56: Total mass in system 46607.563 a.m.u. 56: 56: Total charge in system -128.000 e 56: 56: Writing coordinate file... 56: 56: --------- PLEASE NOTE ------------ 56: 56: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/cyc-rna.pdb. 56: 56: The Charmm27 force field and the tip3p water model are used. 56: 56: --------- ETON ESAELP ------------ 56: [ OK ] Cyclic/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_or_ter_merge_all_cycrnapdb_format_gro_match_file (4752 ms) 56: [ RUN ] Cyclic/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_or_ter_merge_all_cycprotpdb_format_gro_match_file 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/aminoacids.r2b 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/rna.r2b 56: All occupancies are one 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/atomtypes.atp 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/aminoacids.rtp 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/dna.rtp 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/lipids.rtp 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/rna.rtp 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/aminoacids.hdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/dna.hdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/lipids.hdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/rna.hdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/aminoacids.n.tdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/dna.n.tdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/rna.n.tdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/aminoacids.c.tdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/dna.c.tdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/rna.c.tdb 56: 9 out of 9 lines of specbond.dat converted successfully 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/aminoacids.arn 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/dna.arn 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/rna.arn 56: Before cleaning: 2325 pairs 56: Before cleaning: 2325 dihedrals 56: Using the Charmm27 force field in directory charmm27.ff 56: 56: going to rename charmm27.ff/aminoacids.r2b 56: 56: going to rename charmm27.ff/rna.r2b 56: Reading /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/cyc-prot.pdb... 56: Read 'CARNOCYCLIN-A', 413 atoms 56: 56: Analyzing pdb file 56: Splitting chemical chains based on TER records or chain id changing. 56: 56: There are 1 chains and 0 blocks of water and 60 residues with 413 atoms 56: 56: chain #res #atoms 56: 56: 1 'A' 60 413 56: 56: All occupancies are one 56: 56: Reading residue database... (Charmm27) 56: 56: Processing chain 1 'A' (413 atoms, 60 residues) 56: 56: Identified residue LEU1 as a starting terminus. 56: 56: Identified residue LEU60 as a ending terminus. 56: 56: Checking for duplicate atoms.... 56: 56: Generating any missing hydrogen atoms and/or adding termini. 56: 56: Now there are 60 residues with 878 atoms 56: 56: Making bonds... 56: 56: Number of bonds was 880, now 880 56: 56: Generating angles, dihedrals and pairs... 56: 56: Making cmap torsions... 56: 56: There are 60 cmap torsion pairs 56: 56: There are 2325 dihedrals, 137 impropers, 1614 angles 56: 2319 pairs, 880 bonds and 0 virtual sites 56: 56: Total mass 5866.087 a.m.u. 56: 56: Total charge 4.000 e 56: 56: Writing topology 56: 56: Writing coordinate file... 56: 56: --------- PLEASE NOTE ------------ 56: 56: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/cyc-prot.pdb. 56: 56: The Charmm27 force field and the tip3p water model are used. 56: 56: --------- ETON ESAELP ------------ 56: [ OK ] Cyclic/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_or_ter_merge_all_cycprotpdb_format_gro_match_file (599 ms) 56: [----------] 4 tests from Cyclic/Pdb2gmxTest (9007 ms total) 56: 56: [----------] Global test environment tear-down 56: [==========] 39 tests from 6 test suites ran. (19439 ms total) 56: [ PASSED ] 39 tests. 56/92 Test #56: Pdb2gmx3Test .............................. Passed 19.53 sec test 57 Start 57: CorrelationsTest 57: Test command: /build/reproducible-path/gromacs-2025.1/build/basic-dp/bin/correlations-test "--gtest_output=xml:/build/reproducible-path/gromacs-2025.1/build/basic-dp/Testing/Temporary/CorrelationsTest.xml" 57: Working Directory: /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/correlationfunctions/tests 57: Test timeout computed to be: 30 57: [==========] Running 21 tests from 3 test suites. 57: [----------] Global test environment set-up. 57: [----------] 10 tests from AutocorrTest 57: [ RUN ] AutocorrTest.EacNormal 57: [ OK ] AutocorrTest.EacNormal (17 ms) 57: [ RUN ] AutocorrTest.EacNoNormalize 57: [ OK ] AutocorrTest.EacNoNormalize (9 ms) 57: [ RUN ] AutocorrTest.EacCos 57: [ OK ] AutocorrTest.EacCos (16 ms) 57: [ RUN ] AutocorrTest.EacVector 57: [ OK ] AutocorrTest.EacVector (24 ms) 57: [ RUN ] AutocorrTest.EacRcross 57: [ OK ] AutocorrTest.EacRcross (9 ms) 57: [ RUN ] AutocorrTest.EacP0 57: [ OK ] AutocorrTest.EacP0 (23 ms) 57: [ RUN ] AutocorrTest.EacP1 57: [ OK ] AutocorrTest.EacP1 (24 ms) 57: [ RUN ] AutocorrTest.EacP2 57: [ OK ] AutocorrTest.EacP2 (41 ms) 57: [ RUN ] AutocorrTest.EacP3 57: [ OK ] AutocorrTest.EacP3 (28 ms) 57: [ RUN ] AutocorrTest.EacP4 57: [ OK ] AutocorrTest.EacP4 (24 ms) 57: [----------] 10 tests from AutocorrTest (226 ms total) 57: 57: [----------] 10 tests from ExpfitTest 57: [ RUN ] ExpfitTest.EffnEXP1 57: [ OK ] ExpfitTest.EffnEXP1 (5 ms) 57: [ RUN ] ExpfitTest.EffnEXP2 57: [ OK ] ExpfitTest.EffnEXP2 (7 ms) 57: [ RUN ] ExpfitTest.EffnEXPEXP 57: [ OK ] ExpfitTest.EffnEXPEXP (11 ms) 57: [ RUN ] ExpfitTest.EffnEXP5 57: [ OK ] ExpfitTest.EffnEXP5 (37 ms) 57: [ RUN ] ExpfitTest.EffnEXP7 57: [ OK ] ExpfitTest.EffnEXP7 (32 ms) 57: [ RUN ] ExpfitTest.EffnEXP9 57: [ OK ] ExpfitTest.EffnEXP9 (128 ms) 57: [ RUN ] ExpfitTest.EffnERF 57: [ OK ] ExpfitTest.EffnERF (18 ms) 57: [ RUN ] ExpfitTest.EffnERREST 57: [ OK ] ExpfitTest.EffnERREST (29 ms) 57: [ RUN ] ExpfitTest.EffnVAC 57: [ OK ] ExpfitTest.EffnVAC (64 ms) 57: [ RUN ] ExpfitTest.EffnPRES 57: [ OK ] ExpfitTest.EffnPRES (91 ms) 57: [----------] 10 tests from ExpfitTest (427 ms total) 57: 57: [----------] 1 test from ManyAutocorrelationTest 57: [ RUN ] ManyAutocorrelationTest.Empty 57: [ OK ] ManyAutocorrelationTest.Empty (0 ms) 57: [----------] 1 test from ManyAutocorrelationTest (0 ms total) 57: 57: [----------] Global test environment tear-down 57: [==========] 21 tests from 3 test suites ran. (684 ms total) 57: [ PASSED ] 21 tests. 57/92 Test #57: CorrelationsTest .......................... Passed 0.76 sec test 58 Start 58: AnalysisDataUnitTests 58: Test command: /build/reproducible-path/gromacs-2025.1/build/basic-dp/bin/analysisdata-test "--gtest_output=xml:/build/reproducible-path/gromacs-2025.1/build/basic-dp/Testing/Temporary/AnalysisDataUnitTests.xml" 58: Working Directory: /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/analysisdata/tests 58: Test timeout computed to be: 30 58: [==========] Running 69 tests from 14 test suites. 58: [----------] Global test environment set-up. 58: [----------] 3 tests from AnalysisDataInitializationTest 58: [ RUN ] AnalysisDataInitializationTest.BasicInitialization 58: [ OK ] AnalysisDataInitializationTest.BasicInitialization (0 ms) 58: [ RUN ] AnalysisDataInitializationTest.ChecksMultiColumnModules 58: [ OK ] AnalysisDataInitializationTest.ChecksMultiColumnModules (0 ms) 58: [ RUN ] AnalysisDataInitializationTest.ChecksMultipointModules 58: [ OK ] AnalysisDataInitializationTest.ChecksMultipointModules (0 ms) 58: [----------] 3 tests from AnalysisDataInitializationTest (0 ms total) 58: 58: [----------] 8 tests from AnalysisDataCommonTest/0, where TypeParam = gmx::test::(anonymous namespace)::SimpleInputData 58: [ RUN ] AnalysisDataCommonTest/0.CallsModuleCorrectly 58: [ OK ] AnalysisDataCommonTest/0.CallsModuleCorrectly (2 ms) 58: [ RUN ] AnalysisDataCommonTest/0.CallsParallelModuleCorrectly 58: [ OK ] AnalysisDataCommonTest/0.CallsParallelModuleCorrectly (1 ms) 58: [ RUN ] AnalysisDataCommonTest/0.CallsMixedModulesCorrectly 58: [ OK ] AnalysisDataCommonTest/0.CallsMixedModulesCorrectly (1 ms) 58: [ RUN ] AnalysisDataCommonTest/0.CallsColumnModuleCorrectly 58: [ OK ] AnalysisDataCommonTest/0.CallsColumnModuleCorrectly (1 ms) 58: [ RUN ] AnalysisDataCommonTest/0.CallsModuleCorrectlyWithOutOfOrderFrames 58: [ OK ] AnalysisDataCommonTest/0.CallsModuleCorrectlyWithOutOfOrderFrames (2 ms) 58: [ RUN ] AnalysisDataCommonTest/0.FullStorageWorks 58: [ OK ] AnalysisDataCommonTest/0.FullStorageWorks (0 ms) 58: [ RUN ] AnalysisDataCommonTest/0.CanAddModuleAfterStoredData 58: [ OK ] AnalysisDataCommonTest/0.CanAddModuleAfterStoredData (0 ms) 58: [ RUN ] AnalysisDataCommonTest/0.LimitedStorageWorks 58: [ OK ] AnalysisDataCommonTest/0.LimitedStorageWorks (0 ms) 58: [----------] 8 tests from AnalysisDataCommonTest/0 (12 ms total) 58: 58: [----------] 8 tests from AnalysisDataCommonTest/1, where TypeParam = gmx::test::(anonymous namespace)::DataSetsInputData 58: [ RUN ] AnalysisDataCommonTest/1.CallsModuleCorrectly 58: [ OK ] AnalysisDataCommonTest/1.CallsModuleCorrectly (1 ms) 58: [ RUN ] AnalysisDataCommonTest/1.CallsParallelModuleCorrectly 58: [ OK ] AnalysisDataCommonTest/1.CallsParallelModuleCorrectly (1 ms) 58: [ RUN ] AnalysisDataCommonTest/1.CallsMixedModulesCorrectly 58: [ OK ] AnalysisDataCommonTest/1.CallsMixedModulesCorrectly (1 ms) 58: [ RUN ] AnalysisDataCommonTest/1.CallsColumnModuleCorrectly 58: [ OK ] AnalysisDataCommonTest/1.CallsColumnModuleCorrectly (1 ms) 58: [ RUN ] AnalysisDataCommonTest/1.CallsModuleCorrectlyWithOutOfOrderFrames 58: [ OK ] AnalysisDataCommonTest/1.CallsModuleCorrectlyWithOutOfOrderFrames (2 ms) 58: [ RUN ] AnalysisDataCommonTest/1.FullStorageWorks 58: [ OK ] AnalysisDataCommonTest/1.FullStorageWorks (1 ms) 58: [ RUN ] AnalysisDataCommonTest/1.CanAddModuleAfterStoredData 58: [ OK ] AnalysisDataCommonTest/1.CanAddModuleAfterStoredData (0 ms) 58: [ RUN ] AnalysisDataCommonTest/1.LimitedStorageWorks 58: [ OK ] AnalysisDataCommonTest/1.LimitedStorageWorks (1 ms) 58: [----------] 8 tests from AnalysisDataCommonTest/1 (13 ms total) 58: 58: [----------] 8 tests from AnalysisDataCommonTest/2, where TypeParam = gmx::test::(anonymous namespace)::MultipointInputData 58: [ RUN ] AnalysisDataCommonTest/2.CallsModuleCorrectly 58: [ OK ] AnalysisDataCommonTest/2.CallsModuleCorrectly (2 ms) 58: [ RUN ] AnalysisDataCommonTest/2.CallsParallelModuleCorrectly 58: [ OK ] AnalysisDataCommonTest/2.CallsParallelModuleCorrectly (2 ms) 58: [ RUN ] AnalysisDataCommonTest/2.CallsMixedModulesCorrectly 58: [ OK ] AnalysisDataCommonTest/2.CallsMixedModulesCorrectly (2 ms) 58: [ RUN ] AnalysisDataCommonTest/2.CallsColumnModuleCorrectly 58: [ OK ] AnalysisDataCommonTest/2.CallsColumnModuleCorrectly (2 ms) 58: [ RUN ] AnalysisDataCommonTest/2.CallsModuleCorrectlyWithOutOfOrderFrames 58: [ OK ] AnalysisDataCommonTest/2.CallsModuleCorrectlyWithOutOfOrderFrames (3 ms) 58: [ RUN ] AnalysisDataCommonTest/2.FullStorageWorks 58: [ OK ] AnalysisDataCommonTest/2.FullStorageWorks (1 ms) 58: [ RUN ] AnalysisDataCommonTest/2.CanAddModuleAfterStoredData 58: [ OK ] AnalysisDataCommonTest/2.CanAddModuleAfterStoredData (1 ms) 58: [ RUN ] AnalysisDataCommonTest/2.LimitedStorageWorks 58: [ OK ] AnalysisDataCommonTest/2.LimitedStorageWorks (1 ms) 58: [----------] 8 tests from AnalysisDataCommonTest/2 (16 ms total) 58: 58: [----------] 8 tests from AnalysisDataCommonTest/3, where TypeParam = gmx::test::(anonymous namespace)::MultipointDataSetsInputData 58: [ RUN ] AnalysisDataCommonTest/3.CallsModuleCorrectly 58: [ OK ] AnalysisDataCommonTest/3.CallsModuleCorrectly (2 ms) 58: [ RUN ] AnalysisDataCommonTest/3.CallsParallelModuleCorrectly 58: [ OK ] AnalysisDataCommonTest/3.CallsParallelModuleCorrectly (2 ms) 58: [ RUN ] AnalysisDataCommonTest/3.CallsMixedModulesCorrectly 58: [ OK ] AnalysisDataCommonTest/3.CallsMixedModulesCorrectly (2 ms) 58: [ RUN ] AnalysisDataCommonTest/3.CallsColumnModuleCorrectly 58: [ OK ] AnalysisDataCommonTest/3.CallsColumnModuleCorrectly (2 ms) 58: [ RUN ] AnalysisDataCommonTest/3.CallsModuleCorrectlyWithOutOfOrderFrames 58: [ OK ] AnalysisDataCommonTest/3.CallsModuleCorrectlyWithOutOfOrderFrames (3 ms) 58: [ RUN ] AnalysisDataCommonTest/3.FullStorageWorks 58: [ OK ] AnalysisDataCommonTest/3.FullStorageWorks (1 ms) 58: [ RUN ] AnalysisDataCommonTest/3.CanAddModuleAfterStoredData 58: [ OK ] AnalysisDataCommonTest/3.CanAddModuleAfterStoredData (1 ms) 58: [ RUN ] AnalysisDataCommonTest/3.LimitedStorageWorks 58: [ OK ] AnalysisDataCommonTest/3.LimitedStorageWorks (1 ms) 58: [----------] 8 tests from AnalysisDataCommonTest/3 (16 ms total) 58: 58: [----------] 4 tests from AnalysisArrayDataTest 58: [ RUN ] AnalysisArrayDataTest.CallsModuleCorrectly 58: [ OK ] AnalysisArrayDataTest.CallsModuleCorrectly (1 ms) 58: [ RUN ] AnalysisArrayDataTest.StorageWorks 58: [ OK ] AnalysisArrayDataTest.StorageWorks (1 ms) 58: [ RUN ] AnalysisArrayDataTest.CanSetXAxis 58: [ OK ] AnalysisArrayDataTest.CanSetXAxis (0 ms) 58: [ RUN ] AnalysisArrayDataTest.CanSetXAxisBeforeRowCount 58: [ OK ] AnalysisArrayDataTest.CanSetXAxisBeforeRowCount (0 ms) 58: [----------] 4 tests from AnalysisArrayDataTest (3 ms total) 58: 58: [----------] 6 tests from AverageModuleTest 58: [ RUN ] AverageModuleTest.BasicTest 58: [ OK ] AverageModuleTest.BasicTest (3 ms) 58: [ RUN ] AverageModuleTest.HandlesMultipointData 58: [ OK ] AverageModuleTest.HandlesMultipointData (3 ms) 58: [ RUN ] AverageModuleTest.HandlesMultipleDataSets 58: [ OK ] AverageModuleTest.HandlesMultipleDataSets (3 ms) 58: [ RUN ] AverageModuleTest.HandlesDataSetAveraging 58: [ OK ] AverageModuleTest.HandlesDataSetAveraging (3 ms) 58: [ RUN ] AverageModuleTest.CanCustomizeXAxis 58: [ OK ] AverageModuleTest.CanCustomizeXAxis (2 ms) 58: [ RUN ] AverageModuleTest.CanCustomizeNonUniformXAxis 58: [ OK ] AverageModuleTest.CanCustomizeNonUniformXAxis (2 ms) 58: [----------] 6 tests from AverageModuleTest (20 ms total) 58: 58: [----------] 2 tests from FrameAverageModuleTest 58: [ RUN ] FrameAverageModuleTest.BasicTest 58: [ OK ] FrameAverageModuleTest.BasicTest (2 ms) 58: [ RUN ] FrameAverageModuleTest.HandlesMultipleDataSets 58: [ OK ] FrameAverageModuleTest.HandlesMultipleDataSets (3 ms) 58: [----------] 2 tests from FrameAverageModuleTest (6 ms total) 58: 58: [----------] 7 tests from AnalysisHistogramSettingsTest 58: [ RUN ] AnalysisHistogramSettingsTest.InitializesFromBins 58: [ OK ] AnalysisHistogramSettingsTest.InitializesFromBins (0 ms) 58: [ RUN ] AnalysisHistogramSettingsTest.InitializesFromBinsWithIntegerBins 58: [ OK ] AnalysisHistogramSettingsTest.InitializesFromBinsWithIntegerBins (0 ms) 58: [ RUN ] AnalysisHistogramSettingsTest.InitializesFromRangeWithBinCount 58: [ OK ] AnalysisHistogramSettingsTest.InitializesFromRangeWithBinCount (0 ms) 58: [ RUN ] AnalysisHistogramSettingsTest.InitializesFromRangeWithBinWidth 58: [ OK ] AnalysisHistogramSettingsTest.InitializesFromRangeWithBinWidth (0 ms) 58: [ RUN ] AnalysisHistogramSettingsTest.InitializesFromRangeWithBinCountAndIntegerBins 58: [ OK ] AnalysisHistogramSettingsTest.InitializesFromRangeWithBinCountAndIntegerBins (0 ms) 58: [ RUN ] AnalysisHistogramSettingsTest.InitializesFromRangeWithBinWidthAndIntegerBins 58: [ OK ] AnalysisHistogramSettingsTest.InitializesFromRangeWithBinWidthAndIntegerBins (0 ms) 58: [ RUN ] AnalysisHistogramSettingsTest.InitializesFromRangeWithRoundedRange 58: [ OK ] AnalysisHistogramSettingsTest.InitializesFromRangeWithRoundedRange (0 ms) 58: [----------] 7 tests from AnalysisHistogramSettingsTest (0 ms total) 58: 58: [----------] 2 tests from SimpleHistogramModuleTest 58: [ RUN ] SimpleHistogramModuleTest.ComputesCorrectly 58: [ OK ] SimpleHistogramModuleTest.ComputesCorrectly (4 ms) 58: [ RUN ] SimpleHistogramModuleTest.ComputesCorrectlyWithAll 58: [ OK ] SimpleHistogramModuleTest.ComputesCorrectlyWithAll (4 ms) 58: [----------] 2 tests from SimpleHistogramModuleTest (9 ms total) 58: 58: [----------] 3 tests from WeightedHistogramModuleTest 58: [ RUN ] WeightedHistogramModuleTest.ComputesCorrectly 58: [ OK ] WeightedHistogramModuleTest.ComputesCorrectly (4 ms) 58: [ RUN ] WeightedHistogramModuleTest.ComputesCorrectlyWithAll 58: [ OK ] WeightedHistogramModuleTest.ComputesCorrectlyWithAll (4 ms) 58: [ RUN ] WeightedHistogramModuleTest.HandlesMultipleDataSets 58: [ OK ] WeightedHistogramModuleTest.HandlesMultipleDataSets (5 ms) 58: [----------] 3 tests from WeightedHistogramModuleTest (15 ms total) 58: 58: [----------] 3 tests from BinAverageModuleTest 58: [ RUN ] BinAverageModuleTest.ComputesCorrectly 58: [ OK ] BinAverageModuleTest.ComputesCorrectly (3 ms) 58: [ RUN ] BinAverageModuleTest.ComputesCorrectlyWithAll 58: [ OK ] BinAverageModuleTest.ComputesCorrectlyWithAll (3 ms) 58: [ RUN ] BinAverageModuleTest.HandlesMultipleDataSets 58: [ OK ] BinAverageModuleTest.HandlesMultipleDataSets (3 ms) 58: [----------] 3 tests from BinAverageModuleTest (12 ms total) 58: 58: [----------] 4 tests from AbstractAverageHistogramTest 58: [ RUN ] AbstractAverageHistogramTest.ClonesCorrectly 58: [ OK ] AbstractAverageHistogramTest.ClonesCorrectly (5 ms) 58: [ RUN ] AbstractAverageHistogramTest.ComputesCumulativeHistogram 58: [ OK ] AbstractAverageHistogramTest.ComputesCumulativeHistogram (4 ms) 58: [ RUN ] AbstractAverageHistogramTest.ResamplesAtDoubleBinWidth 58: [ OK ] AbstractAverageHistogramTest.ResamplesAtDoubleBinWidth (3 ms) 58: [ RUN ] AbstractAverageHistogramTest.ResamplesAtDoubleBinWidthWithIntegerBins 58: [ OK ] AbstractAverageHistogramTest.ResamplesAtDoubleBinWidthWithIntegerBins (4 ms) 58: [----------] 4 tests from AbstractAverageHistogramTest (18 ms total) 58: 58: [----------] 3 tests from LifetimeModuleTest 58: [ RUN ] LifetimeModuleTest.BasicTest 58: [ OK ] LifetimeModuleTest.BasicTest (2 ms) 58: [ RUN ] LifetimeModuleTest.CumulativeTest 58: [ OK ] LifetimeModuleTest.CumulativeTest (2 ms) 58: [ RUN ] LifetimeModuleTest.HandlesMultipleDataSets 58: [ OK ] LifetimeModuleTest.HandlesMultipleDataSets (3 ms) 58: [----------] 3 tests from LifetimeModuleTest (8 ms total) 58: 58: [----------] Global test environment tear-down 58: [==========] 69 tests from 14 test suites ran. (155 ms total) 58: [ PASSED ] 69 tests. 58/92 Test #58: AnalysisDataUnitTests ..................... Passed 0.24 sec test 59 Start 59: CoordinateIOTests 59: Test command: /build/reproducible-path/gromacs-2025.1/build/basic-dp/bin/coordinateio-test "--gtest_output=xml:/build/reproducible-path/gromacs-2025.1/build/basic-dp/Testing/Temporary/CoordinateIOTests.xml" 59: Working Directory: /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/coordinateio/tests 59: Test timeout computed to be: 30 59: [==========] Running 67 tests from 20 test suites. 59: [----------] Global test environment set-up. 59: [----------] 1 test from OutputSelectorDeathTest 59: [ RUN ] OutputSelectorDeathTest.RejectsBadSelection 59: 59: WARNING: Masses and atomic (Van der Waals) radii will be guessed 59: based on residue and atom names, since they could not be 59: definitively assigned from the information in your input 59: files. These guessed numbers might deviate from the mass 59: and radius of the atom type. Please check the output 59: files if necessary. Note, that this functionality may 59: be removed in a future GROMACS version. Please, consider 59: using another file format for your input. 59: 59: [ OK ] OutputSelectorDeathTest.RejectsBadSelection (20 ms) 59: [----------] 1 test from OutputSelectorDeathTest (20 ms total) 59: 59: [----------] 5 tests from TrajectoryFrameWriterTest 59: [ RUN ] TrajectoryFrameWriterTest.RejectsWrongFiletype 59: 59: WARNING: Masses and atomic (Van der Waals) radii will be guessed 59: based on residue and atom names, since they could not be 59: definitively assigned from the information in your input 59: files. These guessed numbers might deviate from the mass 59: and radius of the atom type. Please check the output 59: files if necessary. Note, that this functionality may 59: be removed in a future GROMACS version. Please, consider 59: using another file format for your input. 59: 59: [ OK ] TrajectoryFrameWriterTest.RejectsWrongFiletype (10 ms) 59: [ RUN ] TrajectoryFrameWriterTest.BuilderFailsWithPdbAndNoAtoms 59: 59: WARNING: Masses and atomic (Van der Waals) radii will be guessed 59: based on residue and atom names, since they could not be 59: definitively assigned from the information in your input 59: files. These guessed numbers might deviate from the mass 59: and radius of the atom type. Please check the output 59: files if necessary. Note, that this functionality may 59: be removed in a future GROMACS version. Please, consider 59: using another file format for your input. 59: 59: [ OK ] TrajectoryFrameWriterTest.BuilderFailsWithPdbAndNoAtoms (9 ms) 59: [ RUN ] TrajectoryFrameWriterTest.BuilderFailsWithGroAndNoAtoms 59: 59: WARNING: Masses and atomic (Van der Waals) radii will be guessed 59: based on residue and atom names, since they could not be 59: definitively assigned from the information in your input 59: files. These guessed numbers might deviate from the mass 59: and radius of the atom type. Please check the output 59: files if necessary. Note, that this functionality may 59: be removed in a future GROMACS version. Please, consider 59: using another file format for your input. 59: 59: [ OK ] TrajectoryFrameWriterTest.BuilderFailsWithGroAndNoAtoms (8 ms) 59: [ RUN ] TrajectoryFrameWriterTest.BuilderImplictlyAddsAtoms 59: 59: WARNING: Masses and atomic (Van der Waals) radii will be guessed 59: based on residue and atom names, since they could not be 59: definitively assigned from the information in your input 59: files. These guessed numbers might deviate from the mass 59: and radius of the atom type. Please check the output 59: files if necessary. Note, that this functionality may 59: be removed in a future GROMACS version. Please, consider 59: using another file format for your input. 59: 59: 59: WARNING: Masses and atomic (Van der Waals) radii will be guessed 59: based on residue and atom names, since they could not be 59: definitively assigned from the information in your input 59: files. These guessed numbers might deviate from the mass 59: and radius of the atom type. Please check the output 59: files if necessary. Note, that this functionality may 59: be removed in a future GROMACS version. Please, consider 59: using another file format for your input. 59: 59: [ OK ] TrajectoryFrameWriterTest.BuilderImplictlyAddsAtoms (16 ms) 59: [ RUN ] TrajectoryFrameWriterTest.TNGOutputWorks 59: [ OK ] TrajectoryFrameWriterTest.TNGOutputWorks (0 ms) 59: [----------] 5 tests from TrajectoryFrameWriterTest (45 ms total) 59: 59: [----------] 5 tests from OutputAdapterContainer 59: [ RUN ] OutputAdapterContainer.MakeEmpty 59: [ OK ] OutputAdapterContainer.MakeEmpty (0 ms) 59: [ RUN ] OutputAdapterContainer.AddAdapter 59: [ OK ] OutputAdapterContainer.AddAdapter (0 ms) 59: [ RUN ] OutputAdapterContainer.RejectBadAdapter 59: [ OK ] OutputAdapterContainer.RejectBadAdapter (0 ms) 59: [ RUN ] OutputAdapterContainer.RejectDuplicateAdapter 59: [ OK ] OutputAdapterContainer.RejectDuplicateAdapter (0 ms) 59: [ RUN ] OutputAdapterContainer.AcceptMultipleAdapters 59: [ OK ] OutputAdapterContainer.AcceptMultipleAdapters (0 ms) 59: [----------] 5 tests from OutputAdapterContainer (0 ms total) 59: 59: [----------] 3 tests from RegisterFrameConverterTest 59: [ RUN ] RegisterFrameConverterTest.NoConverterWorks 59: [ OK ] RegisterFrameConverterTest.NoConverterWorks (0 ms) 59: [ RUN ] RegisterFrameConverterTest.RegistrationWorks 59: [ OK ] RegisterFrameConverterTest.RegistrationWorks (0 ms) 59: [ RUN ] RegisterFrameConverterTest.NewConverterCanInvalidateGuarantees 59: [ OK ] RegisterFrameConverterTest.NewConverterCanInvalidateGuarantees (0 ms) 59: [----------] 3 tests from RegisterFrameConverterTest (0 ms total) 59: 59: [----------] 5 tests from FlagTest 59: [ RUN ] FlagTest.CanSetSimpleFlag 59: [ OK ] FlagTest.CanSetSimpleFlag (0 ms) 59: [ RUN ] FlagTest.CanAddNewBox 59: [ OK ] FlagTest.CanAddNewBox (0 ms) 59: [ RUN ] FlagTest.SetsImplicitPrecisionChange 59: [ OK ] FlagTest.SetsImplicitPrecisionChange (0 ms) 59: [ RUN ] FlagTest.SetsImplicitStartTimeChange 59: [ OK ] FlagTest.SetsImplicitStartTimeChange (0 ms) 59: [ RUN ] FlagTest.SetsImplicitTimeStepChange 59: [ OK ] FlagTest.SetsImplicitTimeStepChange (0 ms) 59: [----------] 5 tests from FlagTest (1 ms total) 59: 59: [----------] 5 tests from SetAtomsTest 59: [ RUN ] SetAtomsTest.RemovesExistingAtoms 59: 59: WARNING: Masses and atomic (Van der Waals) radii will be guessed 59: based on residue and atom names, since they could not be 59: definitively assigned from the information in your input 59: files. These guessed numbers might deviate from the mass 59: and radius of the atom type. Please check the output 59: files if necessary. Note, that this functionality may 59: be removed in a future GROMACS version. Please, consider 59: using another file format for your input. 59: 59: [ OK ] SetAtomsTest.RemovesExistingAtoms (8 ms) 59: [ RUN ] SetAtomsTest.AddsNewAtoms 59: 59: WARNING: Masses and atomic (Van der Waals) radii will be guessed 59: based on residue and atom names, since they could not be 59: definitively assigned from the information in your input 59: files. These guessed numbers might deviate from the mass 59: and radius of the atom type. Please check the output 59: files if necessary. Note, that this functionality may 59: be removed in a future GROMACS version. Please, consider 59: using another file format for your input. 59: 59: [ OK ] SetAtomsTest.AddsNewAtoms (8 ms) 59: [ RUN ] SetAtomsTest.ThrowsOnRequiredAtomsNotAvailable 59: 59: WARNING: Masses and atomic (Van der Waals) radii will be guessed 59: based on residue and atom names, since they could not be 59: definitively assigned from the information in your input 59: files. These guessed numbers might deviate from the mass 59: and radius of the atom type. Please check the output 59: files if necessary. Note, that this functionality may 59: be removed in a future GROMACS version. Please, consider 59: using another file format for your input. 59: 59: [ OK ] SetAtomsTest.ThrowsOnRequiredAtomsNotAvailable (8 ms) 59: [ RUN ] SetAtomsTest.WillUseOldAtomsWhenNoNewAvailable 59: 59: WARNING: Masses and atomic (Van der Waals) radii will be guessed 59: based on residue and atom names, since they could not be 59: definitively assigned from the information in your input 59: files. These guessed numbers might deviate from the mass 59: and radius of the atom type. Please check the output 59: files if necessary. Note, that this functionality may 59: be removed in a future GROMACS version. Please, consider 59: using another file format for your input. 59: 59: [ OK ] SetAtomsTest.WillUseOldAtomsWhenNoNewAvailable (8 ms) 59: [ RUN ] SetAtomsTest.ThrowsWhenUserAtomReplacementNotPossible 59: 59: WARNING: Masses and atomic (Van der Waals) radii will be guessed 59: based on residue and atom names, since they could not be 59: definitively assigned from the information in your input 59: files. These guessed numbers might deviate from the mass 59: and radius of the atom type. Please check the output 59: files if necessary. Note, that this functionality may 59: be removed in a future GROMACS version. Please, consider 59: using another file format for your input. 59: 59: [ OK ] SetAtomsTest.ThrowsWhenUserAtomReplacementNotPossible (8 ms) 59: [----------] 5 tests from SetAtomsTest (43 ms total) 59: 59: [----------] 2 tests from SetBothTimeTest 59: [ RUN ] SetBothTimeTest.StartTimeZeroWorks 59: [ OK ] SetBothTimeTest.StartTimeZeroWorks (0 ms) 59: [ RUN ] SetBothTimeTest.SetStartTimeNonZeroWorks 59: [ OK ] SetBothTimeTest.SetStartTimeNonZeroWorks (0 ms) 59: [----------] 2 tests from SetBothTimeTest (0 ms total) 59: 59: [----------] 2 tests from SetStartTimeTest 59: [ RUN ] SetStartTimeTest.WorksWithNonZeroStart 59: [ OK ] SetStartTimeTest.WorksWithNonZeroStart (0 ms) 59: [ RUN ] SetStartTimeTest.WorksWithZeroStart 59: [ OK ] SetStartTimeTest.WorksWithZeroStart (0 ms) 59: [----------] 2 tests from SetStartTimeTest (0 ms total) 59: 59: [----------] 1 test from SetTimeStepTest 59: [ RUN ] SetTimeStepTest.SetTimeStepWorks 59: [ OK ] SetTimeStepTest.SetTimeStepWorks (0 ms) 59: [----------] 1 test from SetTimeStepTest (0 ms total) 59: 59: [----------] 6 tests from CoordinateFileFileFormats/TrajectoryFrameWriterTest 59: [ RUN ] CoordinateFileFileFormats/TrajectoryFrameWriterTest.WorksWithFormats/0 59: 59: WARNING: Masses and atomic (Van der Waals) radii will be guessed 59: based on residue and atom names, since they could not be 59: definitively assigned from the information in your input 59: files. These guessed numbers might deviate from the mass 59: and radius of the atom type. Please check the output 59: files if necessary. Note, that this functionality may 59: be removed in a future GROMACS version. Please, consider 59: using another file format for your input. 59: 59: [ OK ] CoordinateFileFileFormats/TrajectoryFrameWriterTest.WorksWithFormats/0 (8 ms) 59: [ RUN ] CoordinateFileFileFormats/TrajectoryFrameWriterTest.WorksWithFormats/1 59: 59: WARNING: Masses and atomic (Van der Waals) radii will be guessed 59: based on residue and atom names, since they could not be 59: definitively assigned from the information in your input 59: files. These guessed numbers might deviate from the mass 59: and radius of the atom type. Please check the output 59: files if necessary. Note, that this functionality may 59: be removed in a future GROMACS version. Please, consider 59: using another file format for your input. 59: 59: [ OK ] CoordinateFileFileFormats/TrajectoryFrameWriterTest.WorksWithFormats/1 (8 ms) 59: [ RUN ] CoordinateFileFileFormats/TrajectoryFrameWriterTest.WorksWithFormats/2 59: 59: WARNING: Masses and atomic (Van der Waals) radii will be guessed 59: based on residue and atom names, since they could not be 59: definitively assigned from the information in your input 59: files. These guessed numbers might deviate from the mass 59: and radius of the atom type. Please check the output 59: files if necessary. Note, that this functionality may 59: be removed in a future GROMACS version. Please, consider 59: using another file format for your input. 59: 59: [ OK ] CoordinateFileFileFormats/TrajectoryFrameWriterTest.WorksWithFormats/2 (8 ms) 59: [ RUN ] CoordinateFileFileFormats/TrajectoryFrameWriterTest.WorksWithFormats/3 59: 59: WARNING: Masses and atomic (Van der Waals) radii will be guessed 59: based on residue and atom names, since they could not be 59: definitively assigned from the information in your input 59: files. These guessed numbers might deviate from the mass 59: and radius of the atom type. Please check the output 59: files if necessary. Note, that this functionality may 59: be removed in a future GROMACS version. Please, consider 59: using another file format for your input. 59: 59: [ OK ] CoordinateFileFileFormats/TrajectoryFrameWriterTest.WorksWithFormats/3 (8 ms) 59: [ RUN ] CoordinateFileFileFormats/TrajectoryFrameWriterTest.WorksWithFormats/4 59: 59: WARNING: Masses and atomic (Van der Waals) radii will be guessed 59: based on residue and atom names, since they could not be 59: definitively assigned from the information in your input 59: files. These guessed numbers might deviate from the mass 59: and radius of the atom type. Please check the output 59: files if necessary. Note, that this functionality may 59: be removed in a future GROMACS version. Please, consider 59: using another file format for your input. 59: 59: [ OK ] CoordinateFileFileFormats/TrajectoryFrameWriterTest.WorksWithFormats/4 (8 ms) 59: [ RUN ] CoordinateFileFileFormats/TrajectoryFrameWriterTest.WorksWithFormats/5 59: 59: WARNING: Masses and atomic (Van der Waals) radii will be guessed 59: based on residue and atom names, since they could not be 59: definitively assigned from the information in your input 59: files. These guessed numbers might deviate from the mass 59: and radius of the atom type. Please check the output 59: files if necessary. Note, that this functionality may 59: be removed in a future GROMACS version. Please, consider 59: using another file format for your input. 59: 59: [ OK ] CoordinateFileFileFormats/TrajectoryFrameWriterTest.WorksWithFormats/5 (8 ms) 59: [----------] 6 tests from CoordinateFileFileFormats/TrajectoryFrameWriterTest (51 ms total) 59: 59: [----------] 3 tests from ModuleSupported/SetAtomsSupportedFiles 59: [ RUN ] ModuleSupported/SetAtomsSupportedFiles.Works/0 59: 59: WARNING: Masses and atomic (Van der Waals) radii will be guessed 59: based on residue and atom names, since they could not be 59: definitively assigned from the information in your input 59: files. These guessed numbers might deviate from the mass 59: and radius of the atom type. Please check the output 59: files if necessary. Note, that this functionality may 59: be removed in a future GROMACS version. Please, consider 59: using another file format for your input. 59: 59: [ OK ] ModuleSupported/SetAtomsSupportedFiles.Works/0 (8 ms) 59: [ RUN ] ModuleSupported/SetAtomsSupportedFiles.Works/1 59: 59: WARNING: Masses and atomic (Van der Waals) radii will be guessed 59: based on residue and atom names, since they could not be 59: definitively assigned from the information in your input 59: files. These guessed numbers might deviate from the mass 59: and radius of the atom type. Please check the output 59: files if necessary. Note, that this functionality may 59: be removed in a future GROMACS version. Please, consider 59: using another file format for your input. 59: 59: [ OK ] ModuleSupported/SetAtomsSupportedFiles.Works/1 (8 ms) 59: [ RUN ] ModuleSupported/SetAtomsSupportedFiles.Works/2 59: 59: WARNING: Masses and atomic (Van der Waals) radii will be guessed 59: based on residue and atom names, since they could not be 59: definitively assigned from the information in your input 59: files. These guessed numbers might deviate from the mass 59: and radius of the atom type. Please check the output 59: files if necessary. Note, that this functionality may 59: be removed in a future GROMACS version. Please, consider 59: using another file format for your input. 59: 59: [ OK ] ModuleSupported/SetAtomsSupportedFiles.Works/2 (8 ms) 59: [----------] 3 tests from ModuleSupported/SetAtomsSupportedFiles (25 ms total) 59: 59: [----------] 3 tests from ModuleUnSupported/SetAtomsUnSupportedFiles 59: [ RUN ] ModuleUnSupported/SetAtomsUnSupportedFiles.Works/0 59: [ OK ] ModuleUnSupported/SetAtomsUnSupportedFiles.Works/0 (0 ms) 59: [ RUN ] ModuleUnSupported/SetAtomsUnSupportedFiles.Works/1 59: [ OK ] ModuleUnSupported/SetAtomsUnSupportedFiles.Works/1 (0 ms) 59: [ RUN ] ModuleUnSupported/SetAtomsUnSupportedFiles.Works/2 59: [ OK ] ModuleUnSupported/SetAtomsUnSupportedFiles.Works/2 (0 ms) 59: [----------] 3 tests from ModuleUnSupported/SetAtomsUnSupportedFiles (0 ms total) 59: 59: [----------] 4 tests from ModuleSupported/AnyOutputSupportedFiles 59: [ RUN ] ModuleSupported/AnyOutputSupportedFiles.Works/0 59: 59: WARNING: Masses and atomic (Van der Waals) radii will be guessed 59: based on residue and atom names, since they could not be 59: definitively assigned from the information in your input 59: files. These guessed numbers might deviate from the mass 59: and radius of the atom type. Please check the output 59: files if necessary. Note, that this functionality may 59: be removed in a future GROMACS version. Please, consider 59: using another file format for your input. 59: 59: 59: WARNING: Masses and atomic (Van der Waals) radii will be guessed 59: based on residue and atom names, since they could not be 59: definitively assigned from the information in your input 59: files. These guessed numbers might deviate from the mass 59: and radius of the atom type. Please check the output 59: files if necessary. Note, that this functionality may 59: be removed in a future GROMACS version. Please, consider 59: using another file format for your input. 59: 59: [ OK ] ModuleSupported/AnyOutputSupportedFiles.Works/0 (18 ms) 59: [ RUN ] ModuleSupported/AnyOutputSupportedFiles.Works/1 59: 59: WARNING: Masses and atomic (Van der Waals) radii will be guessed 59: based on residue and atom names, since they could not be 59: definitively assigned from the information in your input 59: files. These guessed numbers might deviate from the mass 59: and radius of the atom type. Please check the output 59: files if necessary. Note, that this functionality may 59: be removed in a future GROMACS version. Please, consider 59: using another file format for your input. 59: 59: 59: WARNING: Masses and atomic (Van der Waals) radii will be guessed 59: based on residue and atom names, since they could not be 59: definitively assigned from the information in your input 59: files. These guessed numbers might deviate from the mass 59: and radius of the atom type. Please check the output 59: files if necessary. Note, that this functionality may 59: be removed in a future GROMACS version. Please, consider 59: using another file format for your input. 59: 59: [ OK ] ModuleSupported/AnyOutputSupportedFiles.Works/1 (18 ms) 59: [ RUN ] ModuleSupported/AnyOutputSupportedFiles.Works/2 59: 59: WARNING: Masses and atomic (Van der Waals) radii will be guessed 59: based on residue and atom names, since they could not be 59: definitively assigned from the information in your input 59: files. These guessed numbers might deviate from the mass 59: and radius of the atom type. Please check the output 59: files if necessary. Note, that this functionality may 59: be removed in a future GROMACS version. Please, consider 59: using another file format for your input. 59: 59: 59: WARNING: Masses and atomic (Van der Waals) radii will be guessed 59: based on residue and atom names, since they could not be 59: definitively assigned from the information in your input 59: files. These guessed numbers might deviate from the mass 59: and radius of the atom type. Please check the output 59: files if necessary. Note, that this functionality may 59: be removed in a future GROMACS version. Please, consider 59: using another file format for your input. 59: 59: [ OK ] ModuleSupported/AnyOutputSupportedFiles.Works/2 (18 ms) 59: [ RUN ] ModuleSupported/AnyOutputSupportedFiles.Works/3 59: 59: WARNING: Masses and atomic (Van der Waals) radii will be guessed 59: based on residue and atom names, since they could not be 59: definitively assigned from the information in your input 59: files. These guessed numbers might deviate from the mass 59: and radius of the atom type. Please check the output 59: files if necessary. Note, that this functionality may 59: be removed in a future GROMACS version. Please, consider 59: using another file format for your input. 59: 59: 59: WARNING: Masses and atomic (Van der Waals) radii will be guessed 59: based on residue and atom names, since they could not be 59: definitively assigned from the information in your input 59: files. These guessed numbers might deviate from the mass 59: and radius of the atom type. Please check the output 59: files if necessary. Note, that this functionality may 59: be removed in a future GROMACS version. Please, consider 59: using another file format for your input. 59: 59: [ OK ] ModuleSupported/AnyOutputSupportedFiles.Works/3 (18 ms) 59: [----------] 4 tests from ModuleSupported/AnyOutputSupportedFiles (75 ms total) 59: 59: [----------] 3 tests from ModuleSupported/SetVelocitySupportedFiles 59: [ RUN ] ModuleSupported/SetVelocitySupportedFiles.Works/0 59: 59: WARNING: Masses and atomic (Van der Waals) radii will be guessed 59: based on residue and atom names, since they could not be 59: definitively assigned from the information in your input 59: files. These guessed numbers might deviate from the mass 59: and radius of the atom type. Please check the output 59: files if necessary. Note, that this functionality may 59: be removed in a future GROMACS version. Please, consider 59: using another file format for your input. 59: 59: [ OK ] ModuleSupported/SetVelocitySupportedFiles.Works/0 (8 ms) 59: [ RUN ] ModuleSupported/SetVelocitySupportedFiles.Works/1 59: 59: WARNING: Masses and atomic (Van der Waals) radii will be guessed 59: based on residue and atom names, since they could not be 59: definitively assigned from the information in your input 59: files. These guessed numbers might deviate from the mass 59: and radius of the atom type. Please check the output 59: files if necessary. Note, that this functionality may 59: be removed in a future GROMACS version. Please, consider 59: using another file format for your input. 59: 59: [ OK ] ModuleSupported/SetVelocitySupportedFiles.Works/1 (8 ms) 59: [ RUN ] ModuleSupported/SetVelocitySupportedFiles.Works/2 59: 59: WARNING: Masses and atomic (Van der Waals) radii will be guessed 59: based on residue and atom names, since they could not be 59: definitively assigned from the information in your input 59: files. These guessed numbers might deviate from the mass 59: and radius of the atom type. Please check the output 59: files if necessary. Note, that this functionality may 59: be removed in a future GROMACS version. Please, consider 59: using another file format for your input. 59: 59: [ OK ] ModuleSupported/SetVelocitySupportedFiles.Works/2 (8 ms) 59: [----------] 3 tests from ModuleSupported/SetVelocitySupportedFiles (26 ms total) 59: 59: [----------] 3 tests from ModuleUnSupported/SetVelocityUnSupportedFiles 59: [ RUN ] ModuleUnSupported/SetVelocityUnSupportedFiles.Works/0 59: [ OK ] ModuleUnSupported/SetVelocityUnSupportedFiles.Works/0 (0 ms) 59: [ RUN ] ModuleUnSupported/SetVelocityUnSupportedFiles.Works/1 59: [ OK ] ModuleUnSupported/SetVelocityUnSupportedFiles.Works/1 (0 ms) 59: [ RUN ] ModuleUnSupported/SetVelocityUnSupportedFiles.Works/2 59: [ OK ] ModuleUnSupported/SetVelocityUnSupportedFiles.Works/2 (0 ms) 59: [----------] 3 tests from ModuleUnSupported/SetVelocityUnSupportedFiles (1 ms total) 59: 59: [----------] 2 tests from ModuleSupported/SetForceSupportedFiles 59: [ RUN ] ModuleSupported/SetForceSupportedFiles.Works/0 59: 59: WARNING: Masses and atomic (Van der Waals) radii will be guessed 59: based on residue and atom names, since they could not be 59: definitively assigned from the information in your input 59: files. These guessed numbers might deviate from the mass 59: and radius of the atom type. Please check the output 59: files if necessary. Note, that this functionality may 59: be removed in a future GROMACS version. Please, consider 59: using another file format for your input. 59: 59: [ OK ] ModuleSupported/SetForceSupportedFiles.Works/0 (8 ms) 59: [ RUN ] ModuleSupported/SetForceSupportedFiles.Works/1 59: 59: WARNING: Masses and atomic (Van der Waals) radii will be guessed 59: based on residue and atom names, since they could not be 59: definitively assigned from the information in your input 59: files. These guessed numbers might deviate from the mass 59: and radius of the atom type. Please check the output 59: files if necessary. Note, that this functionality may 59: be removed in a future GROMACS version. Please, consider 59: using another file format for your input. 59: 59: [ OK ] ModuleSupported/SetForceSupportedFiles.Works/1 (8 ms) 59: [----------] 2 tests from ModuleSupported/SetForceSupportedFiles (17 ms total) 59: 59: [----------] 4 tests from ModuleUnSupported/SetForceUnSupportedFiles 59: [ RUN ] ModuleUnSupported/SetForceUnSupportedFiles.Works/0 59: [ OK ] ModuleUnSupported/SetForceUnSupportedFiles.Works/0 (0 ms) 59: [ RUN ] ModuleUnSupported/SetForceUnSupportedFiles.Works/1 59: [ OK ] ModuleUnSupported/SetForceUnSupportedFiles.Works/1 (0 ms) 59: [ RUN ] ModuleUnSupported/SetForceUnSupportedFiles.Works/2 59: [ OK ] ModuleUnSupported/SetForceUnSupportedFiles.Works/2 (0 ms) 59: [ RUN ] ModuleUnSupported/SetForceUnSupportedFiles.Works/3 59: [ OK ] ModuleUnSupported/SetForceUnSupportedFiles.Works/3 (0 ms) 59: [----------] 4 tests from ModuleUnSupported/SetForceUnSupportedFiles (1 ms total) 59: 59: [----------] 2 tests from ModuleSupported/SetPrecisionSupportedFiles 59: [ RUN ] ModuleSupported/SetPrecisionSupportedFiles.Works/0 59: 59: WARNING: Masses and atomic (Van der Waals) radii will be guessed 59: based on residue and atom names, since they could not be 59: definitively assigned from the information in your input 59: files. These guessed numbers might deviate from the mass 59: and radius of the atom type. Please check the output 59: files if necessary. Note, that this functionality may 59: be removed in a future GROMACS version. Please, consider 59: using another file format for your input. 59: 59: [ OK ] ModuleSupported/SetPrecisionSupportedFiles.Works/0 (8 ms) 59: [ RUN ] ModuleSupported/SetPrecisionSupportedFiles.Works/1 59: 59: WARNING: Masses and atomic (Van der Waals) radii will be guessed 59: based on residue and atom names, since they could not be 59: definitively assigned from the information in your input 59: files. These guessed numbers might deviate from the mass 59: and radius of the atom type. Please check the output 59: files if necessary. Note, that this functionality may 59: be removed in a future GROMACS version. Please, consider 59: using another file format for your input. 59: 59: [ OK ] ModuleSupported/SetPrecisionSupportedFiles.Works/1 (8 ms) 59: [----------] 2 tests from ModuleSupported/SetPrecisionSupportedFiles (17 ms total) 59: 59: [----------] 4 tests from ModuleUnSupported/SetPrecisionUnSupportedFiles 59: [ RUN ] ModuleUnSupported/SetPrecisionUnSupportedFiles.Works/0 59: [ OK ] ModuleUnSupported/SetPrecisionUnSupportedFiles.Works/0 (0 ms) 59: [ RUN ] ModuleUnSupported/SetPrecisionUnSupportedFiles.Works/1 59: [ OK ] ModuleUnSupported/SetPrecisionUnSupportedFiles.Works/1 (0 ms) 59: [ RUN ] ModuleUnSupported/SetPrecisionUnSupportedFiles.Works/2 59: [ OK ] ModuleUnSupported/SetPrecisionUnSupportedFiles.Works/2 (0 ms) 59: [ RUN ] ModuleUnSupported/SetPrecisionUnSupportedFiles.Works/3 59: [ OK ] ModuleUnSupported/SetPrecisionUnSupportedFiles.Works/3 (0 ms) 59: [----------] 4 tests from ModuleUnSupported/SetPrecisionUnSupportedFiles (1 ms total) 59: 59: [----------] 4 tests from ModuleSupported/NoOptionalOutput 59: [ RUN ] ModuleSupported/NoOptionalOutput.Works/0 59: 59: WARNING: Masses and atomic (Van der Waals) radii will be guessed 59: based on residue and atom names, since they could not be 59: definitively assigned from the information in your input 59: files. These guessed numbers might deviate from the mass 59: and radius of the atom type. Please check the output 59: files if necessary. Note, that this functionality may 59: be removed in a future GROMACS version. Please, consider 59: using another file format for your input. 59: 59: [ OK ] ModuleSupported/NoOptionalOutput.Works/0 (8 ms) 59: [ RUN ] ModuleSupported/NoOptionalOutput.Works/1 59: 59: WARNING: Masses and atomic (Van der Waals) radii will be guessed 59: based on residue and atom names, since they could not be 59: definitively assigned from the information in your input 59: files. These guessed numbers might deviate from the mass 59: and radius of the atom type. Please check the output 59: files if necessary. Note, that this functionality may 59: be removed in a future GROMACS version. Please, consider 59: using another file format for your input. 59: 59: [ OK ] ModuleSupported/NoOptionalOutput.Works/1 (8 ms) 59: [ RUN ] ModuleSupported/NoOptionalOutput.Works/2 59: 59: WARNING: Masses and atomic (Van der Waals) radii will be guessed 59: based on residue and atom names, since they could not be 59: definitively assigned from the information in your input 59: files. These guessed numbers might deviate from the mass 59: and radius of the atom type. Please check the output 59: files if necessary. Note, that this functionality may 59: be removed in a future GROMACS version. Please, consider 59: using another file format for your input. 59: 59: [ OK ] ModuleSupported/NoOptionalOutput.Works/2 (8 ms) 59: [ RUN ] ModuleSupported/NoOptionalOutput.Works/3 59: 59: WARNING: Masses and atomic (Van der Waals) radii will be guessed 59: based on residue and atom names, since they could not be 59: definitively assigned from the information in your input 59: files. These guessed numbers might deviate from the mass 59: and radius of the atom type. Please check the output 59: files if necessary. Note, that this functionality may 59: be removed in a future GROMACS version. Please, consider 59: using another file format for your input. 59: 59: [ OK ] ModuleSupported/NoOptionalOutput.Works/3 (8 ms) 59: [----------] 4 tests from ModuleSupported/NoOptionalOutput (34 ms total) 59: 59: [----------] Global test environment tear-down 59: [==========] 67 tests from 20 test suites ran. (364 ms total) 59: [ PASSED ] 67 tests. 59/92 Test #59: CoordinateIOTests ......................... Passed 0.45 sec test 60 Start 60: TrajectoryAnalysisUnitTests 60: Test command: /build/reproducible-path/gromacs-2025.1/build/basic-dp/bin/trajectoryanalysis-test "--gtest_output=xml:/build/reproducible-path/gromacs-2025.1/build/basic-dp/Testing/Temporary/TrajectoryAnalysisUnitTests.xml" 60: Working Directory: /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/trajectoryanalysis/tests 60: Test timeout computed to be: 1920 60: [==========] Running 393 tests from 21 test suites. 60: [----------] Global test environment set-up. 60: [----------] 11 tests from AngleModuleTest 60: [ RUN ] AngleModuleTest.ComputesSimpleAngles 60: Analyzed topology coordinates 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: [ OK ] AngleModuleTest.ComputesSimpleAngles (12 ms) 60: [ RUN ] AngleModuleTest.ComputesDihedrals 60: Analyzed topology coordinates 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: [ OK ] AngleModuleTest.ComputesDihedrals (10 ms) 60: [ RUN ] AngleModuleTest.ComputesVectorPairAngles 60: Analyzed topology coordinates 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: [ OK ] AngleModuleTest.ComputesVectorPairAngles (10 ms) 60: [ RUN ] AngleModuleTest.ComputesVectorPlanePairAngles 60: Analyzed topology coordinates 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: [ OK ] AngleModuleTest.ComputesVectorPlanePairAngles (10 ms) 60: [ RUN ] AngleModuleTest.ComputesPlaneZAxisAngles 60: Analyzed topology coordinates 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: [ OK ] AngleModuleTest.ComputesPlaneZAxisAngles (10 ms) 60: [ RUN ] AngleModuleTest.ComputesVectorSphereNormalZAxisAngles 60: Analyzed topology coordinates 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: [ OK ] AngleModuleTest.ComputesVectorSphereNormalZAxisAngles (10 ms) 60: [ RUN ] AngleModuleTest.ComputesVectorTimeZeroAngles 60: Reading frames from gro file 'Test system for different angles', 33 atoms. 60: Reading frame 0 time 0.000 Reading frame 1 time 0.000 Last frame 1 time 0.000 60: Analyzed 2 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: [ OK ] AngleModuleTest.ComputesVectorTimeZeroAngles (11 ms) 60: [ RUN ] AngleModuleTest.ComputesMultipleAngles 60: Analyzed topology coordinates 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: [ OK ] AngleModuleTest.ComputesMultipleAngles (11 ms) 60: [ RUN ] AngleModuleTest.HandlesDynamicSelections 60: Analyzed topology coordinates 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: [ OK ] AngleModuleTest.HandlesDynamicSelections (11 ms) 60: [ RUN ] AngleModuleTest.HandlesOneVsMultipleVectorAngles 60: Analyzed topology coordinates 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: [ OK ] AngleModuleTest.HandlesOneVsMultipleVectorAngles (10 ms) 60: [ RUN ] AngleModuleTest.HandlesOneVsMultipleVectorGroupsAngles 60: Analyzed topology coordinates 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: [ OK ] AngleModuleTest.HandlesOneVsMultipleVectorGroupsAngles (11 ms) 60: [----------] 11 tests from AngleModuleTest (123 ms total) 60: 60: [----------] 5 tests from ClustsizeTest 60: [ RUN ] ClustsizeTest.NoMolDefaultCutoff 60: Reading frames from pdb file Reading frame 0 time 0.000 Group 0 ( SOL) has 24 elements 60: There is one group in the index 60: '', 24 atoms 60: Reading frame 1 time 0.000 Last frame 1 time 0.000 60: Total number of atoms in clusters = 24 60: cmid: 2, cmax: 4, max_size: 6 60: 16% 33% 50% 66% 83%100%cmid: 6, cmax: 18, max_size: 6 60: 16% 33% 50% 66% 83%100%[ OK ] ClustsizeTest.NoMolDefaultCutoff (10 ms) 60: [ RUN ] ClustsizeTest.NoMolShortCutoff 60: Reading frames from pdb file Reading frame 0 time 0.000 Group 0 ( SOL) has 24 elements 60: There is one group in the index 60: '', 24 atoms 60: Reading frame 1 time 0.000 Last frame 1 time 0.000 60: Total number of atoms in clusters = 24 60: cmid: 1, cmax: 6, max_size: 6 60: 16% 33% 50% 66% 83%100%cmid: 6, cmax: 18, max_size: 6 60: 16% 33% 50% 66% 83%100%[ OK ] ClustsizeTest.NoMolShortCutoff (9 ms) 60: [ RUN ] ClustsizeTest.MolDefaultCutoff 60: Reading frames from pdb file Reading frame 0 time 0.000 Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/clustsize.tpr, VERSION 2016 (single precision) 60: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/clustsize.tpr, VERSION 2016 (single precision) 60: '', 24 atoms 60: Reading frame 1 time 0.000 Last frame 1 time 0.000 60: Total number of atoms in clusters = 8 60: cmid: 2, cmax: 4, max_size: 2 60: 50%100%cmid: 2, cmax: 6, max_size: 2 60: 50%100%[ OK ] ClustsizeTest.MolDefaultCutoff (13 ms) 60: [ RUN ] ClustsizeTest.MolShortCutoff 60: Reading frames from pdb file Reading frame 0 time 0.000 Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/clustsize.tpr, VERSION 2016 (single precision) 60: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/clustsize.tpr, VERSION 2016 (single precision) 60: '', 24 atoms 60: Reading frame 1 time 0.000 Last frame 1 time 0.000 60: Total number of atoms in clusters = 8 60: cmid: 1, cmax: 6, max_size: 2 60: 50%100%cmid: 2, cmax: 6, max_size: 2 60: 50%100%[ OK ] ClustsizeTest.MolShortCutoff (13 ms) 60: [ RUN ] ClustsizeTest.MolCSize 60: Reading frames from pdb file Reading frame 0 time 0.000 Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/clustsize.tpr, VERSION 2016 (single precision) 60: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/clustsize.tpr, VERSION 2016 (single precision) 60: '', 24 atoms 60: Reading frame 1 time 0.000 Last frame 1 time 0.000 60: Total number of atoms in clusters = 8 60: cmid: 2, cmax: 4, max_size: 2 60: 50%100%cmid: 2, cmax: 6, max_size: 2 60: 50%100%[ OK ] ClustsizeTest.MolCSize (13 ms) 60: [----------] 5 tests from ClustsizeTest (62 ms total) 60: 60: [----------] 4 tests from TrajectoryAnalysisCommandLineRunnerTest 60: [ RUN ] TrajectoryAnalysisCommandLineRunnerTest.WritesHelp 60: [ OK ] TrajectoryAnalysisCommandLineRunnerTest.WritesHelp (4 ms) 60: [ RUN ] TrajectoryAnalysisCommandLineRunnerTest.RunsWithSubsetTrajectory 60: Reading frames from gro file 'Test system', 8 atoms. 60: Reading frame 0 time 0.000 Reading frame 1 time 0.000 Last frame 1 time 0.000 60: Analyzed 2 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: [ OK ] TrajectoryAnalysisCommandLineRunnerTest.RunsWithSubsetTrajectory (9 ms) 60: [ RUN ] TrajectoryAnalysisCommandLineRunnerTest.DetectsIncorrectTrajectorySubset 60: Reading frames from gro file 'Test system', 8 atoms. 60: Reading frame 0 time 0.000 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: [ OK ] TrajectoryAnalysisCommandLineRunnerTest.DetectsIncorrectTrajectorySubset (9 ms) 60: [ RUN ] TrajectoryAnalysisCommandLineRunnerTest.FailsWithTrajectorySubsetWithoutTrajectory 60: [ OK ] TrajectoryAnalysisCommandLineRunnerTest.FailsWithTrajectorySubsetWithoutTrajectory (3 ms) 60: [----------] 4 tests from TrajectoryAnalysisCommandLineRunnerTest (26 ms total) 60: 60: [----------] 4 tests from ConvertTrjModuleTest 60: [ RUN ] ConvertTrjModuleTest.WritesNormalOutput 60: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/freevolume.tpr, VERSION 4.5.5 (single precision) 60: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/freevolume.tpr, VERSION 4.5.5 (single precision) 60: Reading frame 0 time 0.000 Last frame 0 time 0.000 60: Analyzed 1 frames, last time 0.000 60: [ OK ] ConvertTrjModuleTest.WritesNormalOutput (62 ms) 60: [ RUN ] ConvertTrjModuleTest.WritesAtomSubset 60: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/freevolume.tpr, VERSION 4.5.5 (single precision) 60: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/freevolume.tpr, VERSION 4.5.5 (single precision) 60: Reading frame 0 time 0.000 Last frame 0 time 0.000 60: Analyzed 1 frames, last time 0.000 60: [ OK ] ConvertTrjModuleTest.WritesAtomSubset (69 ms) 60: [ RUN ] ConvertTrjModuleTest.WorksWithAtomAdding 60: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/clustsize.tpr, VERSION 2016 (single precision) 60: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/clustsize.tpr, VERSION 2016 (single precision) 60: Reading frames from pdb file Reading frame 0 time 0.000 '', 24 atoms 60: Reading frame 1 time 0.000 Last frame 1 time 0.000 60: Analyzed 2 frames, last time 0.000 60: [ OK ] ConvertTrjModuleTest.WorksWithAtomAdding (10 ms) 60: [ RUN ] ConvertTrjModuleTest.WorksWithAtomsAndSelection 60: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/clustsize.tpr, VERSION 2016 (single precision) 60: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/clustsize.tpr, VERSION 2016 (single precision) 60: Reading frames from pdb file Reading frame 0 time 0.000 '', 24 atoms 60: Reading frame 1 time 0.000 Last frame 1 time 0.000 60: Analyzed 2 frames, last time 0.000 60: [ OK ] ConvertTrjModuleTest.WorksWithAtomsAndSelection (10 ms) 60: [----------] 4 tests from ConvertTrjModuleTest (153 ms total) 60: 60: [----------] 6 tests from DistanceModuleTest 60: [ RUN ] DistanceModuleTest.ComputesDistances 60: Analyzed topology coordinates 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: atomname S1 S2: 60: Number of samples: 5 60: Average distance: 1.43246 nm 60: Standard deviation: 0.96700 nm 60: [ OK ] DistanceModuleTest.ComputesDistances (13 ms) 60: [ RUN ] DistanceModuleTest.ComputesMultipleDistances 60: Analyzed topology coordinates 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: atomname S1 S2: 60: Number of samples: 5 60: Average distance: 1.43246 nm 60: Standard deviation: 0.96700 nm 60: resindex 1 to 4 and atomname CB merge resindex 2 to 5 and atomname CB: 60: Number of samples: 4 60: Average distance: 1.81066 nm 60: Standard deviation: 0.79289 nm 60: [ OK ] DistanceModuleTest.ComputesMultipleDistances (15 ms) 60: [ RUN ] DistanceModuleTest.HandlesDynamicSelections 60: Analyzed topology coordinates 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: atomname S1 S2 and res_cog x < 2.8: 60: Number of samples: 3 60: Average distance: 1.72076 nm 60: Standard deviation: 1.24839 nm 60: [ OK ] DistanceModuleTest.HandlesDynamicSelections (14 ms) 60: [ RUN ] DistanceModuleTest.HandlesSelectionFromGroup 60: Analyzed topology coordinates 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: Contacts: 60: Number of samples: 2 60: Average distance: 1.00000 nm 60: Standard deviation: 0.00000 nm 60: [ OK ] DistanceModuleTest.HandlesSelectionFromGroup (39 ms) 60: [ RUN ] DistanceModuleTest.HandlesSelectionFromGroupWithSuccessiveIndices 60: Analyzed topology coordinates 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: SuccessiveContacts: 60: Number of samples: 2 60: Average distance: 1.00000 nm 60: Standard deviation: 0.00000 nm 60: [ OK ] DistanceModuleTest.HandlesSelectionFromGroupWithSuccessiveIndices (38 ms) 60: [ RUN ] DistanceModuleTest.HandlesSelectionFromLargeGroup 60: Analyzed topology coordinates 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: ManyContacts: 60: Number of samples: 10 60: Average distance: 1.82913 nm 60: Standard deviation: 0.78478 nm 60: [ OK ] DistanceModuleTest.HandlesSelectionFromLargeGroup (40 ms) 60: [----------] 6 tests from DistanceModuleTest (172 ms total) 60: 60: [----------] 2 tests from ExtractClusterModuleTest 60: [ RUN ] ExtractClusterModuleTest.WorksWithAllAtoms 60: trr version: GMX_trn_file (single precision) 60: Reading frame 0 time 0.000 Reading frame 1 time 0.002 Reading frame 2 time 0.004 Reading frame 3 time 0.006 Reading frame 4 time 0.008 Reading frame 5 time 0.010 Reading frame 6 time 0.012 Reading frame 7 time 0.014 Reading frame 8 time 0.016 Reading frame 9 time 0.018 Reading frame 10 time 0.020 Reading frame 11 time 0.022 Reading frame 12 time 0.024 Reading frame 13 time 0.026 Reading frame 14 time 0.028 Reading frame 15 time 0.030 Reading frame 16 time 0.032 Reading frame 17 time 0.034 Reading frame 18 time 0.036 Reading frame 19 time 0.038 Reading frame 20 time 0.040 60: Analyzed 26 frames, last time 0.050 60: There are 8 clusters containing 26 structures, highest framenr is 25 60: [ OK ] ExtractClusterModuleTest.WorksWithAllAtoms (15 ms) 60: [ RUN ] ExtractClusterModuleTest.WorksWithAtomSubset 60: Reading frame 0 time 0.000 Reading frame 1 time 0.002 Reading frame 2 time 0.004 Reading frame 3 time 0.006 Reading frame 4 time 0.008 Reading frame 5 time 0.010 Reading frame 6 time 0.012 Reading frame 7 time 0.014 Reading frame 8 time 0.016 Reading frame 9 time 0.018 Reading frame 10 time 0.020 Reading frame 11 time 0.022 Reading frame 12 time 0.024 Reading frame 13 time 0.026 Reading frame 14 time 0.028 Reading frame 15 time 0.030 Reading frame 16 time 0.032 Reading frame 17 time 0.034 Reading frame 18 time 0.036 Reading frame 19 time 0.038 Reading frame 20 time 0.040 60: Analyzed 26 frames, last time 0.050 60: There are 8 clusters containing 26 structures, highest framenr is 25 60: [ OK ] ExtractClusterModuleTest.WorksWithAtomSubset (13 ms) 60: [----------] 2 tests from ExtractClusterModuleTest (29 ms total) 60: 60: [----------] 2 tests from FreeVolumeModuleTest 60: [ RUN ] FreeVolumeModuleTest.ComputesFreeVolume 60: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/freevolume.tpr, VERSION 4.5.5 (single precision) 60: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/freevolume.tpr, VERSION 4.5.5 (single precision) 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: NOTE: From version 5.0 trajectoryanalysis-test uses the Van der Waals radii 60: from the source below. This means the results may be different 60: compared to previous GROMACS versions. 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: A. Bondi 60: van der Waals Volumes and Radii 60: J. Phys. Chem. (1964) 60: DOI: 10.1021/j100785a001 60: -------- -------- --- Thank You --- -------- -------- 60: 60: Could not determine VDW radius for CO2-RM. Set to zero. 60: Could not determine VDW radius for CO2-RM. Set to zero. 60: Could not determine VDW radius for CO2-RM. Set to zero. 60: Could not determine VDW radius for CO2-RM. Set to zero. 60: Could not determine VDW radius for CO2-RM. Set to zero. 60: Could not determine VDW radius for CO2-RM. Set to zero. 60: Could not determine VDW radius for CO2-RM. Set to zero. 60: Could not determine VDW radius for CO2-RM. Set to zero. 60: Could not determine VDW radius for CO2-RM. Set to zero. 60: Could not determine VDW radius for 40 particles. These were set to zero. 60: Reading frame 0 time 0.000 Last frame 0 time 0.000 60: Analyzed 1 frames, last time 0.000 60: cutoff = 0.18 nm 60: probe_radius = 0 nm 60: seed = 13 60: ninsert = 1000 probes per nm^3 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: A. Bondi 60: van der Waals Volumes and Radii 60: J. Phys. Chem. (1964) 60: DOI: 10.1021/j100785a001 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: Tuanan C. Lourenco, Mariny F. C. Coelho, Teodorico C. Ramalho, David van der 60: Spoel, Luciano T. Costa 60: Insights on the Solubility of CO2 in 1-Ethyl-3-methylimidazolium 60: Bis(trifluoromethylsulfonyl)imide from the Microscopic Point of View 60: Environ. Sci. Technol. (2013) 60: DOI: 10.1021/es4020986 60: -------- -------- --- Thank You --- -------- -------- 60: 60: Free volume 38.02 +/- 0.00 % 60: Total volume 68.92 +/- 0.00 nm^3 60: Number of molecules 340 total mass 63491.38 Dalton 60: Average molar mass: 186.74 Dalton 60: Density rho: 1529.71 +/- 0.00 nm^3 60: Molecular volume Vm assuming homogeneity: 0.2027 +/- 0.0000 nm^3 60: Molecular van der Waals volume assuming homogeneity: 0.1256 +/- 0.0000 nm^3 60: Fractional free volume 0.194 +/- 0.000 60: [ OK ] FreeVolumeModuleTest.ComputesFreeVolume (518 ms) 60: [ RUN ] FreeVolumeModuleTest.ComputesFreeVolumeSelection 60: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/freevolume.tpr, VERSION 4.5.5 (single precision) 60: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/freevolume.tpr, VERSION 4.5.5 (single precision) 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: NOTE: From version 5.0 trajectoryanalysis-test uses the Van der Waals radii 60: from the source below. This means the results may be different 60: compared to previous GROMACS versions. 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: A. Bondi 60: van der Waals Volumes and Radii 60: J. Phys. Chem. (1964) 60: DOI: 10.1021/j100785a001 60: -------- -------- --- Thank You --- -------- -------- 60: 60: Reading frame 0 time 0.000 Last frame 0 time 0.000 60: Analyzed 1 frames, last time 0.000 60: cutoff = 0.18 nm 60: probe_radius = 0 nm 60: seed = 17 60: ninsert = 1000 probes per nm^3 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: A. Bondi 60: van der Waals Volumes and Radii 60: J. Phys. Chem. (1964) 60: DOI: 10.1021/j100785a001 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: Tuanan C. Lourenco, Mariny F. C. Coelho, Teodorico C. Ramalho, David van der 60: Spoel, Luciano T. Costa 60: Insights on the Solubility of CO2 in 1-Ethyl-3-methylimidazolium 60: Bis(trifluoromethylsulfonyl)imide from the Microscopic Point of View 60: Environ. Sci. Technol. (2013) 60: DOI: 10.1021/es4020986 60: -------- -------- --- Thank You --- -------- -------- 60: 60: Free volume 38.48 +/- 0.00 % 60: Total volume 68.92 +/- 0.00 nm^3 60: Number of molecules 340 total mass 63491.38 Dalton 60: Average molar mass: 186.74 Dalton 60: Density rho: 1529.71 +/- 0.00 nm^3 60: Molecular volume Vm assuming homogeneity: 0.2027 +/- 0.0000 nm^3 60: Molecular van der Waals volume assuming homogeneity: 0.1247 +/- 0.0000 nm^3 60: Fractional free volume 0.200 +/- 0.000 60: [ OK ] FreeVolumeModuleTest.ComputesFreeVolumeSelection (557 ms) 60: [----------] 2 tests from FreeVolumeModuleTest (1076 ms total) 60: 60: [----------] 13 tests from MsdModuleTest 60: [ RUN ] MsdModuleTest.threeDimensionalDiffusion 60: Reading frame 0 time 0.000 Reading frame 1 time 1.000 Reading frame 2 time 2.000 Reading frame 3 time 3.000 Reading frame 4 time 4.000 Reading frame 5 time 5.000 Reading frame 6 time 6.000 Reading frame 7 time 7.000 Reading frame 8 time 8.000 Reading frame 9 time 9.000 Last frame 9 time 9.000 60: Analyzed 10 frames, last time 9.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: [ OK ] MsdModuleTest.threeDimensionalDiffusion (13 ms) 60: [ RUN ] MsdModuleTest.twoDimensionalDiffusion 60: Reading frame 0 time 0.000 Reading frame 1 time 1.000 Reading frame 2 time 2.000 Reading frame 3 time 3.000 Reading frame 4 time 4.000 Reading frame 5 time 5.000 Reading frame 6 time 6.000 Reading frame 7 time 7.000 Reading frame 8 time 8.000 Reading frame 9 time 9.000 Last frame 9 time 9.000 60: Analyzed 10 frames, last time 9.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: [ OK ] MsdModuleTest.twoDimensionalDiffusion (13 ms) 60: [ RUN ] MsdModuleTest.oneDimensionalDiffusion 60: Reading frame 0 time 0.000 Reading frame 1 time 1.000 Reading frame 2 time 2.000 Reading frame 3 time 3.000 Reading frame 4 time 4.000 Reading frame 5 time 5.000 Reading frame 6 time 6.000 Reading frame 7 time 7.000 Reading frame 8 time 8.000 Reading frame 9 time 9.000 Last frame 9 time 9.000 60: Analyzed 10 frames, last time 9.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: [ OK ] MsdModuleTest.oneDimensionalDiffusion (12 ms) 60: [ RUN ] MsdModuleTest.oneDimensionalDiffusionWithMaxTau 60: Reading frame 0 time 0.000 Reading frame 1 time 1.000 Reading frame 2 time 2.000 Reading frame 3 time 3.000 Reading frame 4 time 4.000 Reading frame 5 time 5.000 Reading frame 6 time 6.000 Reading frame 7 time 7.000 Reading frame 8 time 8.000 Reading frame 9 time 9.000 Last frame 9 time 9.000 60: Analyzed 10 frames, last time 9.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: [ OK ] MsdModuleTest.oneDimensionalDiffusionWithMaxTau (12 ms) 60: [ RUN ] MsdModuleTest.multipleGroupsWork 60: 60: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_multipleGroupsWork.mdp]: 60: For a correct single-point energy evaluation with nsteps = 0, use 60: continuation = yes to avoid constraining the input coordinates. 60: 60: Generating 1-4 interactions: fudge = 0.5 60: 60: NOTE 2 [file alanine_vsite_solvated.top, line 28]: 60: For energy conservation with LINCS, lincs_iter should be 2 or larger. 60: 60: 60: Number of degrees of freedom in T-Coupling group rest is 1818.00 60: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 60: 60: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_multipleGroupsWork.mdp]: 60: NVE simulation: will use the initial temperature of 288.764 K for 60: determining the Verlet buffer size 60: 60: 60: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_multipleGroupsWork.mdp]: 60: There are 9 non-linear virtual site constructions. Their contribution to 60: the energy error is approximated. In most cases this does not affect the 60: error significantly. 60: 60: 60: NOTE 5 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_multipleGroupsWork.mdp]: 60: You are using a plain Coulomb cut-off, which might produce artifacts. 60: You might want to consider using PME electrostatics. 60: 60: 60: 60: There were 5 NOTEs 60: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_multipleGroupsWork.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 60: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_multipleGroupsWork.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 60: Reading frame 0 time 0.000 Reading frame 1 time 2.000 60: WARNING: -dt and -trestart are equal. Statistics for each tau data point will not be independent. 60: Reading frame 2 time 4.000 Reading frame 3 time 6.000 Reading frame 4 time 8.000 Reading frame 5 time 10.000 Reading frame 6 time 12.000 Reading frame 7 time 14.000 Reading frame 8 time 16.000 Reading frame 9 time 18.000 Reading frame 10 time 20.000 Reading frame 11 time 22.000 Reading frame 12 time 24.000 Reading frame 13 time 26.000 Reading frame 14 time 28.000 Reading frame 15 time 30.000 Reading frame 16 time 32.000 Reading frame 17 time 34.000 Reading frame 18 time 36.000 Reading frame 19 time 38.000 Reading frame 20 time 40.000 Last frame 20 time 40.000 60: Analyzed 21 frames, last time 40.000 60: Setting the LD random seed to -22549732 60: 60: Generated 2145 of the 2145 non-bonded parameter combinations 60: 60: Generated 2145 of the 2145 1-4 parameter combinations 60: 60: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' 60: 60: Excluding 2 bonded neighbours molecule type 'SOL' 60: 60: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/alanine_vsite_solvated.gro' 60: 60: Cleaning up constraints and constant bonded interactions with virtual sites 60: 60: Converted 15 Bonds with virtual sites to connections, 7 left 60: 60: Removed 18 Angles with virtual sites, 21 left 60: 60: Removed 10 Proper Dih.s with virtual sites, 44 left 60: 60: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 288.764 K 60: 60: Calculated rlist for 1x1 atom pair-list as 0.910 nm, buffer size 0.060 nm 60: 60: Set rlist, assuming 4x4 atom pair-list, to 0.898 nm, buffer size 0.048 nm 60: 60: Note that mdrun will redetermine rlist based on the actual pair-list setup 60: 60: This run will generate roughly 0 Mb of data 60: [ OK ] MsdModuleTest.multipleGroupsWork (188 ms) 60: [ RUN ] MsdModuleTest.subPicosecondTrajectoryWorks 60: 60: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_subPicosecondTrajectoryWorks.mdp]: 60: For a correct single-point energy evaluation with nsteps = 0, use 60: continuation = yes to avoid constraining the input coordinates. 60: 60: Generating 1-4 interactions: fudge = 0.5 60: 60: NOTE 2 [file alanine_vsite_solvated.top, line 28]: 60: For energy conservation with LINCS, lincs_iter should be 2 or larger. 60: 60: 60: Number of degrees of freedom in T-Coupling group rest is 1818.00 60: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 60: 60: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_subPicosecondTrajectoryWorks.mdp]: 60: NVE simulation: will use the initial temperature of 288.764 K for 60: determining the Verlet buffer size 60: 60: 60: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_subPicosecondTrajectoryWorks.mdp]: 60: There are 9 non-linear virtual site constructions. Their contribution to 60: the energy error is approximated. In most cases this does not affect the 60: error significantly. 60: 60: 60: NOTE 5 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_subPicosecondTrajectoryWorks.mdp]: 60: You are using a plain Coulomb cut-off, which might produce artifacts. 60: You might want to consider using PME electrostatics. 60: 60: 60: 60: There were 5 NOTEs 60: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_subPicosecondTrajectoryWorks.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 60: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_subPicosecondTrajectoryWorks.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 60: Reading frame 0 time 0.000 Reading frame 1 time 0.100 60: WARNING: -dt and -trestart are equal. Statistics for each tau data point will not be independent. 60: Reading frame 2 time 0.200 Reading frame 3 time 0.300 Reading frame 4 time 0.400 Reading frame 5 time 0.500 Reading frame 6 time 0.600 Reading frame 7 time 0.700 Reading frame 8 time 0.800 Reading frame 9 time 0.900 Reading frame 10 time 1.000 Reading frame 11 time 1.100 Reading frame 12 time 1.200 Reading frame 13 time 1.300 Reading frame 14 time 1.400 Reading frame 15 time 1.500 Reading frame 16 time 1.600 Reading frame 17 time 1.700 Reading frame 18 time 1.800 Reading frame 19 time 1.900 Reading frame 20 time 2.000 Last frame 20 time 2.000 60: Analyzed 21 frames, last time 2.000 60: Setting the LD random seed to -149759555 60: 60: Generated 2145 of the 2145 non-bonded parameter combinations 60: 60: Generated 2145 of the 2145 1-4 parameter combinations 60: 60: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' 60: 60: Excluding 2 bonded neighbours molecule type 'SOL' 60: 60: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/alanine_vsite_solvated.gro' 60: 60: Cleaning up constraints and constant bonded interactions with virtual sites 60: 60: Converted 15 Bonds with virtual sites to connections, 7 left 60: 60: Removed 18 Angles with virtual sites, 21 left 60: 60: Removed 10 Proper Dih.s with virtual sites, 44 left 60: 60: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 288.764 K 60: 60: Calculated rlist for 1x1 atom pair-list as 0.910 nm, buffer size 0.060 nm 60: 60: Set rlist, assuming 4x4 atom pair-list, to 0.898 nm, buffer size 0.048 nm 60: 60: Note that mdrun will redetermine rlist based on the actual pair-list setup 60: 60: This run will generate roughly 0 Mb of data 60: [ OK ] MsdModuleTest.subPicosecondTrajectoryWorks (190 ms) 60: [ RUN ] MsdModuleTest.trestartLessThanDt 60: 60: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_trestartLessThanDt.mdp]: 60: For a correct single-point energy evaluation with nsteps = 0, use 60: continuation = yes to avoid constraining the input coordinates. 60: 60: Generating 1-4 interactions: fudge = 0.5 60: 60: NOTE 2 [file alanine_vsite_solvated.top, line 28]: 60: For energy conservation with LINCS, lincs_iter should be 2 or larger. 60: 60: 60: Number of degrees of freedom in T-Coupling group rest is 1818.00 60: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 60: 60: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_trestartLessThanDt.mdp]: 60: NVE simulation: will use the initial temperature of 288.764 K for 60: determining the Verlet buffer size 60: 60: 60: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_trestartLessThanDt.mdp]: 60: There are 9 non-linear virtual site constructions. Their contribution to 60: the energy error is approximated. In most cases this does not affect the 60: error significantly. 60: 60: 60: NOTE 5 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_trestartLessThanDt.mdp]: 60: You are using a plain Coulomb cut-off, which might produce artifacts. 60: You might want to consider using PME electrostatics. 60: 60: 60: 60: There were 5 NOTEs 60: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_trestartLessThanDt.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 60: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_trestartLessThanDt.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 60: Reading frame 0 time 0.000 Reading frame 1 time 2.000 Setting the LD random seed to -1179691 60: 60: Generated 2145 of the 2145 non-bonded parameter combinations 60: 60: Generated 2145 of the 2145 1-4 parameter combinations 60: 60: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' 60: 60: Excluding 2 bonded neighbours molecule type 'SOL' 60: 60: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/alanine_vsite_solvated.gro' 60: 60: Cleaning up constraints and constant bonded interactions with virtual sites 60: 60: Converted 15 Bonds with virtual sites to connections, 7 left 60: 60: Removed 18 Angles with virtual sites, 21 left 60: 60: Removed 10 Proper Dih.s with virtual sites, 44 left 60: 60: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 288.764 K 60: 60: Calculated rlist for 1x1 atom pair-list as 0.910 nm, buffer size 0.060 nm 60: 60: Set rlist, assuming 4x4 atom pair-list, to 0.898 nm, buffer size 0.048 nm 60: 60: Note that mdrun will redetermine rlist based on the actual pair-list setup 60: 60: This run will generate roughly 0 Mb of data 60: [ OK ] MsdModuleTest.trestartLessThanDt (152 ms) 60: [ RUN ] MsdModuleTest.trestartGreaterThanDt 60: 60: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_trestartGreaterThanDt.mdp]: 60: For a correct single-point energy evaluation with nsteps = 0, use 60: continuation = yes to avoid constraining the input coordinates. 60: 60: Generating 1-4 interactions: fudge = 0.5 60: 60: NOTE 2 [file alanine_vsite_solvated.top, line 28]: 60: For energy conservation with LINCS, lincs_iter should be 2 or larger. 60: 60: 60: Number of degrees of freedom in T-Coupling group rest is 1818.00 60: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 60: 60: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_trestartGreaterThanDt.mdp]: 60: NVE simulation: will use the initial temperature of 288.764 K for 60: determining the Verlet buffer size 60: 60: 60: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_trestartGreaterThanDt.mdp]: 60: There are 9 non-linear virtual site constructions. Their contribution to 60: the energy error is approximated. In most cases this does not affect the 60: error significantly. 60: 60: 60: NOTE 5 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_trestartGreaterThanDt.mdp]: 60: You are using a plain Coulomb cut-off, which might produce artifacts. 60: You might want to consider using PME electrostatics. 60: 60: 60: 60: There were 5 NOTEs 60: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_trestartGreaterThanDt.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 60: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_trestartGreaterThanDt.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 60: Reading frame 0 time 0.000 Reading frame 1 time 2.000 Reading frame 2 time 4.000 Reading frame 3 time 6.000 Reading frame 4 time 8.000 Reading frame 5 time 10.000 Reading frame 6 time 12.000 Reading frame 7 time 14.000 Reading frame 8 time 16.000 Reading frame 9 time 18.000 Reading frame 10 time 20.000 Reading frame 11 time 22.000 Reading frame 12 time 24.000 Reading frame 13 time 26.000 Reading frame 14 time 28.000 Reading frame 15 time 30.000 Reading frame 16 time 32.000 Reading frame 17 time 34.000 Reading frame 18 time 36.000 Reading frame 19 time 38.000 Reading frame 20 time 40.000 Last frame 20 time 40.000 60: Analyzed 21 frames, last time 40.000 60: Setting the LD random seed to -71451489 60: 60: Generated 2145 of the 2145 non-bonded parameter combinations 60: 60: Generated 2145 of the 2145 1-4 parameter combinations 60: 60: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' 60: 60: Excluding 2 bonded neighbours molecule type 'SOL' 60: 60: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/alanine_vsite_solvated.gro' 60: 60: Cleaning up constraints and constant bonded interactions with virtual sites 60: 60: Converted 15 Bonds with virtual sites to connections, 7 left 60: 60: Removed 18 Angles with virtual sites, 21 left 60: 60: Removed 10 Proper Dih.s with virtual sites, 44 left 60: 60: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 288.764 K 60: 60: Calculated rlist for 1x1 atom pair-list as 0.910 nm, buffer size 0.060 nm 60: 60: Set rlist, assuming 4x4 atom pair-list, to 0.898 nm, buffer size 0.048 nm 60: 60: Note that mdrun will redetermine rlist based on the actual pair-list setup 60: 60: This run will generate roughly 0 Mb of data 60: [ OK ] MsdModuleTest.trestartGreaterThanDt (180 ms) 60: [ RUN ] MsdModuleTest.trestartGreaterThanDtAndNotAMultipleOfDt 60: 60: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_trestartGreaterThanDtAndNotAMultipleOfDt.mdp]: 60: For a correct single-point energy evaluation with nsteps = 0, use 60: continuation = yes to avoid constraining the input coordinates. 60: 60: Generating 1-4 interactions: fudge = 0.5 60: 60: NOTE 2 [file alanine_vsite_solvated.top, line 28]: 60: For energy conservation with LINCS, lincs_iter should be 2 or larger. 60: 60: 60: Number of degrees of freedom in T-Coupling group rest is 1818.00 60: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 60: 60: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_trestartGreaterThanDtAndNotAMultipleOfDt.mdp]: 60: NVE simulation: will use the initial temperature of 288.764 K for 60: determining the Verlet buffer size 60: 60: 60: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_trestartGreaterThanDtAndNotAMultipleOfDt.mdp]: 60: There are 9 non-linear virtual site constructions. Their contribution to 60: the energy error is approximated. In most cases this does not affect the 60: error significantly. 60: 60: 60: NOTE 5 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_trestartGreaterThanDtAndNotAMultipleOfDt.mdp]: 60: You are using a plain Coulomb cut-off, which might produce artifacts. 60: You might want to consider using PME electrostatics. 60: 60: 60: 60: There were 5 NOTEs 60: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_trestartGreaterThanDtAndNotAMultipleOfDt.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 60: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_trestartGreaterThanDtAndNotAMultipleOfDt.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 60: Reading frame 0 time 0.000 Reading frame 1 time 2.000 Setting the LD random seed to -606356231 60: 60: Generated 2145 of the 2145 non-bonded parameter combinations 60: 60: Generated 2145 of the 2145 1-4 parameter combinations 60: 60: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' 60: 60: Excluding 2 bonded neighbours molecule type 'SOL' 60: 60: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/alanine_vsite_solvated.gro' 60: 60: Cleaning up constraints and constant bonded interactions with virtual sites 60: 60: Converted 15 Bonds with virtual sites to connections, 7 left 60: 60: Removed 18 Angles with virtual sites, 21 left 60: 60: Removed 10 Proper Dih.s with virtual sites, 44 left 60: 60: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 288.764 K 60: 60: Calculated rlist for 1x1 atom pair-list as 0.910 nm, buffer size 0.060 nm 60: 60: Set rlist, assuming 4x4 atom pair-list, to 0.898 nm, buffer size 0.048 nm 60: 60: Note that mdrun will redetermine rlist based on the actual pair-list setup 60: 60: This run will generate roughly 0 Mb of data 60: [ OK ] MsdModuleTest.trestartGreaterThanDtAndNotAMultipleOfDt (152 ms) 60: [ RUN ] MsdModuleTest.molTest 60: 60: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_molTest.mdp]: 60: For a correct single-point energy evaluation with nsteps = 0, use 60: continuation = yes to avoid constraining the input coordinates. 60: 60: Generating 1-4 interactions: fudge = 0.5 60: 60: NOTE 2 [file alanine_vsite_solvated.top, line 28]: 60: For energy conservation with LINCS, lincs_iter should be 2 or larger. 60: 60: 60: Number of degrees of freedom in T-Coupling group rest is 1818.00 60: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 60: 60: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_molTest.mdp]: 60: NVE simulation: will use the initial temperature of 288.764 K for 60: determining the Verlet buffer size 60: 60: 60: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_molTest.mdp]: 60: There are 9 non-linear virtual site constructions. Their contribution to 60: the energy error is approximated. In most cases this does not affect the 60: error significantly. 60: 60: 60: NOTE 5 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_molTest.mdp]: 60: You are using a plain Coulomb cut-off, which might produce artifacts. 60: You might want to consider using PME electrostatics. 60: 60: 60: 60: There were 5 NOTEs 60: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_molTest.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 60: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_molTest.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 60: Reading frame 0 time 0.000 Reading frame 1 time 2.000 Reading frame 2 time 4.000 Reading frame 3 time 6.000 Reading frame 4 time 8.000 Reading frame 5 time 10.000 Reading frame 6 time 12.000 Reading frame 7 time 14.000 Reading frame 8 time 16.000 Reading frame 9 time 18.000 Reading frame 10 time 20.000 Reading frame 11 time 22.000 Reading frame 12 time 24.000 Reading frame 13 time 26.000 Reading frame 14 time 28.000 Reading frame 15 time 30.000 Reading frame 16 time 32.000 Reading frame 17 time 34.000 Reading frame 18 time 36.000 Reading frame 19 time 38.000 Reading frame 20 time 40.000 Last frame 20 time 40.000 60: Analyzed 21 frames, last time 40.000 60: Setting the LD random seed to 2146930683 60: 60: Generated 2145 of the 2145 non-bonded parameter combinations 60: 60: Generated 2145 of the 2145 1-4 parameter combinations 60: 60: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' 60: 60: Excluding 2 bonded neighbours molecule type 'SOL' 60: 60: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/alanine_vsite_solvated.gro' 60: 60: Cleaning up constraints and constant bonded interactions with virtual sites 60: 60: Converted 15 Bonds with virtual sites to connections, 7 left 60: 60: Removed 18 Angles with virtual sites, 21 left 60: 60: Removed 10 Proper Dih.s with virtual sites, 44 left 60: 60: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 288.764 K 60: 60: Calculated rlist for 1x1 atom pair-list as 0.910 nm, buffer size 0.060 nm 60: 60: Set rlist, assuming 4x4 atom pair-list, to 0.898 nm, buffer size 0.048 nm 60: 60: Note that mdrun will redetermine rlist based on the actual pair-list setup 60: 60: This run will generate roughly 0 Mb of data 60: [ OK ] MsdModuleTest.molTest (175 ms) 60: [ RUN ] MsdModuleTest.beginFit 60: 60: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_beginFit.mdp]: 60: For a correct single-point energy evaluation with nsteps = 0, use 60: continuation = yes to avoid constraining the input coordinates. 60: 60: Generating 1-4 interactions: fudge = 0.5 60: 60: NOTE 2 [file alanine_vsite_solvated.top, line 28]: 60: For energy conservation with LINCS, lincs_iter should be 2 or larger. 60: 60: 60: Number of degrees of freedom in T-Coupling group rest is 1818.00 60: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 60: 60: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_beginFit.mdp]: 60: NVE simulation: will use the initial temperature of 288.764 K for 60: determining the Verlet buffer size 60: 60: 60: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_beginFit.mdp]: 60: There are 9 non-linear virtual site constructions. Their contribution to 60: the energy error is approximated. In most cases this does not affect the 60: error significantly. 60: 60: 60: NOTE 5 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_beginFit.mdp]: 60: You are using a plain Coulomb cut-off, which might produce artifacts. 60: You might want to consider using PME electrostatics. 60: 60: 60: 60: There were 5 NOTEs 60: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_beginFit.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 60: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_beginFit.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 60: Reading frame 0 time 0.000 Reading frame 1 time 2.000 60: WARNING: -dt and -trestart are equal. Statistics for each tau data point will not be independent. 60: Reading frame 2 time 4.000 Reading frame 3 time 6.000 Reading frame 4 time 8.000 Reading frame 5 time 10.000 Reading frame 6 time 12.000 Reading frame 7 time 14.000 Reading frame 8 time 16.000 Reading frame 9 time 18.000 Reading frame 10 time 20.000 Reading frame 11 time 22.000 Reading frame 12 time 24.000 Reading frame 13 time 26.000 Reading frame 14 time 28.000 Reading frame 15 time 30.000 Reading frame 16 time 32.000 Reading frame 17 time 34.000 Reading frame 18 time 36.000 Reading frame 19 time 38.000 Reading frame 20 time 40.000 Last frame 20 time 40.000 60: Analyzed 21 frames, last time 40.000 60: Setting the LD random seed to -537657373 60: 60: Generated 2145 of the 2145 non-bonded parameter combinations 60: 60: Generated 2145 of the 2145 1-4 parameter combinations 60: 60: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' 60: 60: Excluding 2 bonded neighbours molecule type 'SOL' 60: 60: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/alanine_vsite_solvated.gro' 60: 60: Cleaning up constraints and constant bonded interactions with virtual sites 60: 60: Converted 15 Bonds with virtual sites to connections, 7 left 60: 60: Removed 18 Angles with virtual sites, 21 left 60: 60: Removed 10 Proper Dih.s with virtual sites, 44 left 60: 60: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 288.764 K 60: 60: Calculated rlist for 1x1 atom pair-list as 0.910 nm, buffer size 0.060 nm 60: 60: Set rlist, assuming 4x4 atom pair-list, to 0.898 nm, buffer size 0.048 nm 60: 60: Note that mdrun will redetermine rlist based on the actual pair-list setup 60: 60: This run will generate roughly 0 Mb of data 60: [ OK ] MsdModuleTest.beginFit (181 ms) 60: [ RUN ] MsdModuleTest.endFit 60: 60: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_endFit.mdp]: 60: For a correct single-point energy evaluation with nsteps = 0, use 60: continuation = yes to avoid constraining the input coordinates. 60: 60: Generating 1-4 interactions: fudge = 0.5 60: 60: NOTE 2 [file alanine_vsite_solvated.top, line 28]: 60: For energy conservation with LINCS, lincs_iter should be 2 or larger. 60: 60: 60: Number of degrees of freedom in T-Coupling group rest is 1818.00 60: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 60: 60: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_endFit.mdp]: 60: NVE simulation: will use the initial temperature of 288.764 K for 60: determining the Verlet buffer size 60: 60: 60: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_endFit.mdp]: 60: There are 9 non-linear virtual site constructions. Their contribution to 60: the energy error is approximated. In most cases this does not affect the 60: error significantly. 60: 60: 60: NOTE 5 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_endFit.mdp]: 60: You are using a plain Coulomb cut-off, which might produce artifacts. 60: You might want to consider using PME electrostatics. 60: 60: 60: 60: There were 5 NOTEs 60: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_endFit.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 60: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_endFit.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 60: Reading frame 0 time 0.000 Reading frame 1 time 2.000 60: WARNING: -dt and -trestart are equal. Statistics for each tau data point will not be independent. 60: Reading frame 2 time 4.000 Reading frame 3 time 6.000 Reading frame 4 time 8.000 Reading frame 5 time 10.000 Reading frame 6 time 12.000 Reading frame 7 time 14.000 Reading frame 8 time 16.000 Reading frame 9 time 18.000 Reading frame 10 time 20.000 Reading frame 11 time 22.000 Reading frame 12 time 24.000 Reading frame 13 time 26.000 Reading frame 14 time 28.000 Reading frame 15 time 30.000 Reading frame 16 time 32.000 Reading frame 17 time 34.000 Reading frame 18 time 36.000 Reading frame 19 time 38.000 Reading frame 20 time 40.000 Last frame 20 time 40.000 60: Analyzed 21 frames, last time 40.000 60: Setting the LD random seed to 1610227635 60: 60: Generated 2145 of the 2145 non-bonded parameter combinations 60: 60: Generated 2145 of the 2145 1-4 parameter combinations 60: 60: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' 60: 60: Excluding 2 bonded neighbours molecule type 'SOL' 60: 60: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/alanine_vsite_solvated.gro' 60: 60: Cleaning up constraints and constant bonded interactions with virtual sites 60: 60: Converted 15 Bonds with virtual sites to connections, 7 left 60: 60: Removed 18 Angles with virtual sites, 21 left 60: 60: Removed 10 Proper Dih.s with virtual sites, 44 left 60: 60: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 288.764 K 60: 60: Calculated rlist for 1x1 atom pair-list as 0.910 nm, buffer size 0.060 nm 60: 60: Set rlist, assuming 4x4 atom pair-list, to 0.898 nm, buffer size 0.048 nm 60: 60: Note that mdrun will redetermine rlist based on the actual pair-list setup 60: 60: This run will generate roughly 0 Mb of data 60: [ OK ] MsdModuleTest.endFit (182 ms) 60: [ RUN ] MsdModuleTest.notEnoughPointsForFitErrorEstimate 60: 60: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_notEnoughPointsForFitErrorEstimate.mdp]: 60: For a correct single-point energy evaluation with nsteps = 0, use 60: continuation = yes to avoid constraining the input coordinates. 60: 60: Generating 1-4 interactions: fudge = 0.5 60: 60: NOTE 2 [file alanine_vsite_solvated.top, line 28]: 60: For energy conservation with LINCS, lincs_iter should be 2 or larger. 60: 60: 60: Number of degrees of freedom in T-Coupling group rest is 1818.00 60: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 60: 60: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_notEnoughPointsForFitErrorEstimate.mdp]: 60: NVE simulation: will use the initial temperature of 288.764 K for 60: determining the Verlet buffer size 60: 60: 60: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_notEnoughPointsForFitErrorEstimate.mdp]: 60: There are 9 non-linear virtual site constructions. Their contribution to 60: the energy error is approximated. In most cases this does not affect the 60: error significantly. 60: 60: 60: NOTE 5 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_notEnoughPointsForFitErrorEstimate.mdp]: 60: You are using a plain Coulomb cut-off, which might produce artifacts. 60: You might want to consider using PME electrostatics. 60: 60: 60: 60: There were 5 NOTEs 60: NOTE: You provided an index file 60: /build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/alanine_vsite_solvated.ndx 60: (with -n), but it was not used by any selection. 60: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_notEnoughPointsForFitErrorEstimate.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 60: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_notEnoughPointsForFitErrorEstimate.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 60: Reading frame 0 time 0.000 Reading frame 1 time 2.000 60: WARNING: -dt and -trestart are equal. Statistics for each tau data point will not be independent. 60: Reading frame 2 time 4.000 Reading frame 3 time 6.000 Reading frame 4 time 8.000 Reading frame 5 time 10.000 Reading frame 6 time 12.000 Reading frame 7 time 14.000 Reading frame 8 time 16.000 Reading frame 9 time 18.000 Reading frame 10 time 20.000 Reading frame 11 time 22.000 Reading frame 12 time 24.000 Reading frame 13 time 26.000 Reading frame 14 time 28.000 Reading frame 15 time 30.000 Reading frame 16 time 32.000 Reading frame 17 time 34.000 Reading frame 18 time 36.000 Reading frame 19 time 38.000 Reading frame 20 time 40.000 Last frame 20 time 40.000 60: Analyzed 21 frames, last time 40.000 60: Setting the LD random seed to -1116770444 60: 60: Generated 2145 of the 2145 non-bonded parameter combinations 60: 60: Generated 2145 of the 2145 1-4 parameter combinations 60: 60: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' 60: 60: Excluding 2 bonded neighbours molecule type 'SOL' 60: 60: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/alanine_vsite_solvated.gro' 60: 60: Cleaning up constraints and constant bonded interactions with virtual sites 60: 60: Converted 15 Bonds with virtual sites to connections, 7 left 60: 60: Removed 18 Angles with virtual sites, 21 left 60: 60: Removed 10 Proper Dih.s with virtual sites, 44 left 60: 60: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 288.764 K 60: 60: Calculated rlist for 1x1 atom pair-list as 0.910 nm, buffer size 0.060 nm 60: 60: Set rlist, assuming 4x4 atom pair-list, to 0.898 nm, buffer size 0.048 nm 60: 60: Note that mdrun will redetermine rlist based on the actual pair-list setup 60: 60: This run will generate roughly 0 Mb of data 60: [ OK ] MsdModuleTest.notEnoughPointsForFitErrorEstimate (198 ms) 60: [----------] 13 tests from MsdModuleTest (1659 ms total) 60: 60: [----------] 9 tests from PairDistanceModuleTest 60: [ RUN ] PairDistanceModuleTest.ComputesAllDistances 60: Analyzed topology coordinates 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: [ OK ] PairDistanceModuleTest.ComputesAllDistances (12 ms) 60: [ RUN ] PairDistanceModuleTest.ComputesAllDistancesWithCutoff 60: Analyzed topology coordinates 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: [ OK ] PairDistanceModuleTest.ComputesAllDistancesWithCutoff (12 ms) 60: [ RUN ] PairDistanceModuleTest.ComputesMinDistanceWithCutoff 60: Analyzed topology coordinates 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: [ OK ] PairDistanceModuleTest.ComputesMinDistanceWithCutoff (12 ms) 60: [ RUN ] PairDistanceModuleTest.ComputesMaxDistance 60: Analyzed topology coordinates 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: [ OK ] PairDistanceModuleTest.ComputesMaxDistance (11 ms) 60: [ RUN ] PairDistanceModuleTest.ComputesMaxDistanceWithCutoff 60: Analyzed topology coordinates 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: [ OK ] PairDistanceModuleTest.ComputesMaxDistanceWithCutoff (12 ms) 60: [ RUN ] PairDistanceModuleTest.ComputesGroupedMinDistanceWithCutoff 60: Analyzed topology coordinates 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: [ OK ] PairDistanceModuleTest.ComputesGroupedMinDistanceWithCutoff (11 ms) 60: [ RUN ] PairDistanceModuleTest.ComputesGroupedMaxDistanceWithCutoff 60: Analyzed topology coordinates 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: [ OK ] PairDistanceModuleTest.ComputesGroupedMaxDistanceWithCutoff (12 ms) 60: [ RUN ] PairDistanceModuleTest.CoordinateSelectionIsNotOverwritten 60: Analyzed topology coordinates 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: [ OK ] PairDistanceModuleTest.CoordinateSelectionIsNotOverwritten (12 ms) 60: [ RUN ] PairDistanceModuleTest.CoordinateSelectionIsNotOverwrittenWithExplicitGroup 60: Analyzed topology coordinates 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: [ OK ] PairDistanceModuleTest.CoordinateSelectionIsNotOverwrittenWithExplicitGroup (12 ms) 60: [----------] 9 tests from PairDistanceModuleTest (110 ms total) 60: 60: [----------] 5 tests from RdfModuleTest 60: [ RUN ] RdfModuleTest.BasicTest 60: Analyzed topology coordinates 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: [ OK ] RdfModuleTest.BasicTest (147 ms) 60: [ RUN ] RdfModuleTest.SelectionsSolelyFromIndexFileWork 60: Reading frames from gro file '216H2O,WATJP01,SPC216,SPC-MODEL,300K,BOX(M)=1.86206NM,WFVG,MAR. 1984', 648 atoms. 60: Reading frame 0 time 0.000 Last frame 0 time 0.000 60: Analyzed 1 frames, last time 0.000 60: [ OK ] RdfModuleTest.SelectionsSolelyFromIndexFileWork (141 ms) 60: [ RUN ] RdfModuleTest.SelectionsFromBothTopologyFileAndIndexFileWork 60: Analyzed topology coordinates 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: [ OK ] RdfModuleTest.SelectionsFromBothTopologyFileAndIndexFileWork (163 ms) 60: [ RUN ] RdfModuleTest.CalculatesSurf 60: Analyzed topology coordinates 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: [ OK ] RdfModuleTest.CalculatesSurf (47 ms) 60: [ RUN ] RdfModuleTest.CalculatesXY 60: Analyzed topology coordinates 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: [ OK ] RdfModuleTest.CalculatesXY (187 ms) 60: [----------] 5 tests from RdfModuleTest (689 ms total) 60: 60: [----------] 5 tests from SasaModuleTest 60: [ RUN ] SasaModuleTest.BasicTest 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: Frank Eisenhaber, Philip Lijnzaad, Patrick Argos, Chris Sander, Michael Scharf 60: The Double Cube Lattice Method: Efficient Approaches to Numerical Integration 60: of Surface Area and Volume and to Dot Surface Contouring of Molecular 60: Assemblies 60: J. Comp. Chem. (1995) 60: DOI: 10.1002/jcc.540160303 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: NOTE: From version 5.0 trajectoryanalysis-test uses the Van der Waals radii 60: from the source below. This means the results may be different 60: compared to previous GROMACS versions. 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: A. Bondi 60: van der Waals Volumes and Radii 60: J. Phys. Chem. (1964) 60: DOI: 10.1021/j100785a001 60: -------- -------- --- Thank You --- -------- -------- 60: 60: Analyzed topology coordinates 60: [ OK ] SasaModuleTest.BasicTest (58 ms) 60: [ RUN ] SasaModuleTest.HandlesSelectedResidues 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: Frank Eisenhaber, Philip Lijnzaad, Patrick Argos, Chris Sander, Michael Scharf 60: The Double Cube Lattice Method: Efficient Approaches to Numerical Integration 60: of Surface Area and Volume and to Dot Surface Contouring of Molecular 60: Assemblies 60: J. Comp. Chem. (1995) 60: DOI: 10.1002/jcc.540160303 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: NOTE: From version 5.0 trajectoryanalysis-test uses the Van der Waals radii 60: from the source below. This means the results may be different 60: compared to previous GROMACS versions. 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: A. Bondi 60: van der Waals Volumes and Radii 60: J. Phys. Chem. (1964) 60: DOI: 10.1021/j100785a001 60: -------- -------- --- Thank You --- -------- -------- 60: 60: Analyzed topology coordinates 60: [ OK ] SasaModuleTest.HandlesSelectedResidues (29 ms) 60: [ RUN ] SasaModuleTest.WritesConnollySurfaceWithSolute 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: Frank Eisenhaber, Philip Lijnzaad, Patrick Argos, Chris Sander, Michael Scharf 60: The Double Cube Lattice Method: Efficient Approaches to Numerical Integration 60: of Surface Area and Volume and to Dot Surface Contouring of Molecular 60: Assemblies 60: J. Comp. Chem. (1995) 60: DOI: 10.1002/jcc.540160303 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: NOTE: From version 5.0 trajectoryanalysis-test uses the Van der Waals radii 60: from the source below. This means the results may be different 60: compared to previous GROMACS versions. 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: A. Bondi 60: van der Waals Volumes and Radii 60: J. Phys. Chem. (1964) 60: DOI: 10.1021/j100785a001 60: -------- -------- --- Thank You --- -------- -------- 60: 60: Analyzed topology coordinates 60: [ OK ] SasaModuleTest.WritesConnollySurfaceWithSolute (21 ms) 60: [ RUN ] SasaModuleTest.HandlesDynamicOutputGroup 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: Frank Eisenhaber, Philip Lijnzaad, Patrick Argos, Chris Sander, Michael Scharf 60: The Double Cube Lattice Method: Efficient Approaches to Numerical Integration 60: of Surface Area and Volume and to Dot Surface Contouring of Molecular 60: Assemblies 60: J. Comp. Chem. (1995) 60: DOI: 10.1002/jcc.540160303 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: NOTE: From version 5.0 trajectoryanalysis-test uses the Van der Waals radii 60: from the source below. This means the results may be different 60: compared to previous GROMACS versions. 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: A. Bondi 60: van der Waals Volumes and Radii 60: J. Phys. Chem. (1964) 60: DOI: 10.1021/j100785a001 60: -------- -------- --- Thank You --- -------- -------- 60: 60: Analyzed topology coordinates 60: [ OK ] SasaModuleTest.HandlesDynamicOutputGroup (39 ms) 60: [ RUN ] SasaModuleTest.HandlesDynamicCalculationGroup 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: Frank Eisenhaber, Philip Lijnzaad, Patrick Argos, Chris Sander, Michael Scharf 60: The Double Cube Lattice Method: Efficient Approaches to Numerical Integration 60: of Surface Area and Volume and to Dot Surface Contouring of Molecular 60: Assemblies 60: J. Comp. Chem. (1995) 60: DOI: 10.1002/jcc.540160303 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: NOTE: From version 5.0 trajectoryanalysis-test uses the Van der Waals radii 60: from the source below. This means the results may be different 60: compared to previous GROMACS versions. 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: A. Bondi 60: van der Waals Volumes and Radii 60: J. Phys. Chem. (1964) 60: DOI: 10.1021/j100785a001 60: -------- -------- --- Thank You --- -------- -------- 60: 60: Analyzed topology coordinates 60: [ OK ] SasaModuleTest.HandlesDynamicCalculationGroup (36 ms) 60: [----------] 5 tests from SasaModuleTest (195 ms total) 60: 60: [----------] 8 tests from SelectModuleTest 60: [ RUN ] SelectModuleTest.BasicTest 60: Reading frames from gro file 'Test system', 15 atoms. 60: Reading frame 0 time 0.000 Reading frame 1 time 0.000 Last frame 1 time 0.000 60: Analyzed 2 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: [ OK ] SelectModuleTest.BasicTest (22 ms) 60: [ RUN ] SelectModuleTest.HandlesPDBOutputWithNonPDBInput 60: Reading frames from gro file 'Test system', 15 atoms. 60: Reading frame 0 time 0.000 Reading frame 1 time 0.000 Last frame 1 time 0.000 60: Analyzed 2 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: [ OK ] SelectModuleTest.HandlesPDBOutputWithNonPDBInput (14 ms) 60: [ RUN ] SelectModuleTest.HandlesPDBOutputWithPDBInput 60: Reading frames from gro file 'Test system', 15 atoms. 60: Reading frame 0 time 0.000 Reading frame 1 time 0.000 Last frame 1 time 0.000 60: Analyzed 2 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: [ OK ] SelectModuleTest.HandlesPDBOutputWithPDBInput (13 ms) 60: [ RUN ] SelectModuleTest.HandlesMaxPDBOutput 60: Reading frames from gro file 'Test system', 15 atoms. 60: Reading frame 0 time 0.000 Reading frame 1 time 0.000 Last frame 1 time 0.000 60: Analyzed 2 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: [ OK ] SelectModuleTest.HandlesMaxPDBOutput (14 ms) 60: [ RUN ] SelectModuleTest.HandlesSelectedPDBOutput 60: Reading frames from gro file 'Test system', 15 atoms. 60: Reading frame 0 time 0.000 Reading frame 1 time 0.000 Last frame 1 time 0.000 60: Analyzed 2 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: [ OK ] SelectModuleTest.HandlesSelectedPDBOutput (14 ms) 60: [ RUN ] SelectModuleTest.NormalizesSizes 60: Analyzed topology coordinates 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: [ OK ] SelectModuleTest.NormalizesSizes (10 ms) 60: [ RUN ] SelectModuleTest.WritesResidueNumbers 60: Analyzed topology coordinates 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: [ OK ] SelectModuleTest.WritesResidueNumbers (9 ms) 60: [ RUN ] SelectModuleTest.WritesResidueIndices 60: Analyzed topology coordinates 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: [ OK ] SelectModuleTest.WritesResidueIndices (9 ms) 60: [----------] 8 tests from SelectModuleTest (111 ms total) 60: 60: [----------] 10 tests from SurfaceAreaTest 60: [ RUN ] SurfaceAreaTest.ComputesSinglePoint 60: [ OK ] SurfaceAreaTest.ComputesSinglePoint (0 ms) 60: [ RUN ] SurfaceAreaTest.ComputesTwoPoints 60: [ OK ] SurfaceAreaTest.ComputesTwoPoints (7 ms) 60: [ RUN ] SurfaceAreaTest.ComputesTwoPointsOfUnequalRadius 60: [ OK ] SurfaceAreaTest.ComputesTwoPointsOfUnequalRadius (7 ms) 60: [ RUN ] SurfaceAreaTest.SurfacePoints12 60: [ OK ] SurfaceAreaTest.SurfacePoints12 (1 ms) 60: [ RUN ] SurfaceAreaTest.SurfacePoints32 60: [ OK ] SurfaceAreaTest.SurfacePoints32 (1 ms) 60: [ RUN ] SurfaceAreaTest.SurfacePoints42 60: [ OK ] SurfaceAreaTest.SurfacePoints42 (2 ms) 60: [ RUN ] SurfaceAreaTest.SurfacePoints122 60: [ OK ] SurfaceAreaTest.SurfacePoints122 (5 ms) 60: [ RUN ] SurfaceAreaTest.Computes100Points 60: [ OK ] SurfaceAreaTest.Computes100Points (3 ms) 60: [ RUN ] SurfaceAreaTest.Computes100PointsWithRectangularPBC 60: [ OK ] SurfaceAreaTest.Computes100PointsWithRectangularPBC (13 ms) 60: [ RUN ] SurfaceAreaTest.Computes100PointsWithTriclinicPBC 60: [ OK ] SurfaceAreaTest.Computes100PointsWithTriclinicPBC (16 ms) 60: [----------] 10 tests from SurfaceAreaTest (61 ms total) 60: 60: [----------] 4 tests from TopologyInformation 60: [ RUN ] TopologyInformation.CantWorkWithoutReadingAFile 60: [ OK ] TopologyInformation.CantWorkWithoutReadingAFile (0 ms) 60: [ RUN ] TopologyInformation.WorksWithGroFile 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: [ OK ] TopologyInformation.WorksWithGroFile (8 ms) 60: [ RUN ] TopologyInformation.WorksWithPdbFile 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: [ OK ] TopologyInformation.WorksWithPdbFile (8 ms) 60: [ RUN ] TopologyInformation.WorksWithTprFromPdbFile 60: 60: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/TopologyInformation_WorksWithTprFromPdbFile_lysozyme.mdp]: 60: For a correct single-point energy evaluation with nsteps = 0, use 60: continuation = yes to avoid constraining the input coordinates. 60: 60: Generating 1-4 interactions: fudge = 0.5 60: 60: NOTE 2 [file lysozyme.top, line 1465]: 60: System has non-zero total charge: 2.000000 60: Total charge should normally be an integer. See 60: https://manual.gromacs.org/current/user-guide/floating-point.html 60: for discussion on how close it should be to an integer. 60: 60: 60: 60: Number of degrees of freedom in T-Coupling group rest is 465.00 60: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 60: 60: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/TopologyInformation_WorksWithTprFromPdbFile_lysozyme.mdp]: 60: NVE simulation with an initial temperature of zero: will use a Verlet 60: buffer of 10%. Check your energy drift! 60: 60: 60: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/TopologyInformation_WorksWithTprFromPdbFile_lysozyme.mdp]: 60: You are using a plain Coulomb cut-off, which might produce artifacts. 60: You might want to consider using PME electrostatics. 60: 60: 60: 60: There were 4 NOTEs 60: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/TopologyInformation_WorksWithTprFromPdbFile_lysozyme.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 60: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/TopologyInformation_WorksWithTprFromPdbFile_lysozyme.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 60: Setting the LD random seed to -67273371 60: 60: Generated 330891 of the 330891 non-bonded parameter combinations 60: 60: Generated 330891 of the 330891 1-4 parameter combinations 60: 60: Excluding 3 bonded neighbours molecule type 'Protein_chain_B' 60: 60: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/lysozyme.pdb', all velocities are zero 60: Analysing residue names: 60: There are: 10 Protein residues 60: Analysing Protein... 60: 60: This run will generate roughly 0 Mb of data 60: [ OK ] TopologyInformation.WorksWithTprFromPdbFile (6017 ms) 60: [----------] 4 tests from TopologyInformation (6035 ms total) 60: 60: [----------] 4 tests from TrajectoryModuleTest 60: [ RUN ] TrajectoryModuleTest.BasicTest 60: Reading frames from gro file 'Test system', 15 atoms. 60: Reading frame 0 time 0.000 Reading frame 1 time 0.000 Last frame 1 time 0.000 60: Analyzed 2 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: [ OK ] TrajectoryModuleTest.BasicTest (12 ms) 60: [ RUN ] TrajectoryModuleTest.PlotsXOnly 60: Reading frames from gro file 'Test system', 15 atoms. 60: Reading frame 0 time 0.000 Reading frame 1 time 0.000 Last frame 1 time 0.000 60: Analyzed 2 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: [ OK ] TrajectoryModuleTest.PlotsXOnly (11 ms) 60: [ RUN ] TrajectoryModuleTest.HandlesNoVelocities 60: Reading frames from gro file 'Test system', 15 atoms. 60: Reading frame 0 time 0.000 Reading frame 1 time 0.000 Last frame 1 time 0.000 60: Analyzed 2 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: [ OK ] TrajectoryModuleTest.HandlesNoVelocities (10 ms) 60: [ RUN ] TrajectoryModuleTest.HandlesNoForces 60: Reading frames from gro file 'Test system', 15 atoms. 60: Reading frame 0 time 0.000 Reading frame 1 time 0.000 Last frame 1 time 0.000 60: Analyzed 2 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: [ OK ] TrajectoryModuleTest.HandlesNoForces (10 ms) 60: [----------] 4 tests from TrajectoryModuleTest (46 ms total) 60: 60: [----------] 5 tests from UnionFinderTest 60: [ RUN ] UnionFinderTest.WorksEmpty 60: [ OK ] UnionFinderTest.WorksEmpty (0 ms) 60: [ RUN ] UnionFinderTest.BasicMerges 60: [ OK ] UnionFinderTest.BasicMerges (0 ms) 60: [ RUN ] UnionFinderTest.LargerMerges 60: [ OK ] UnionFinderTest.LargerMerges (0 ms) 60: [ RUN ] UnionFinderTest.LongRightMerge 60: [ OK ] UnionFinderTest.LongRightMerge (0 ms) 60: [ RUN ] UnionFinderTest.LongLeftMerge 60: [ OK ] UnionFinderTest.LongLeftMerge (0 ms) 60: [----------] 5 tests from UnionFinderTest (0 ms total) 60: 60: [----------] 1 test from MappedUnionFinderTest 60: [ RUN ] MappedUnionFinderTest.BasicMerges 60: [ OK ] MappedUnionFinderTest.BasicMerges (0 ms) 60: [----------] 1 test from MappedUnionFinderTest (0 ms total) 60: 60: [----------] 192 tests from MoleculeTests/DsspModuleTest 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/0 60: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 60: Last frame 0 time 0.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/0 (153 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/1 60: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 60: Last frame 0 time 0.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/1 (156 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/2 60: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 60: Last frame 0 time 0.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/2 (152 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/3 60: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 60: Last frame 0 time 0.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/3 (145 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/4 60: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 60: Last frame 0 time 0.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/4 (148 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/5 60: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 60: Last frame 0 time 0.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/5 (143 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/6 60: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 60: Last frame 0 time 0.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/6 (144 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/7 60: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 60: Last frame 0 time 0.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/7 (145 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/8 60: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 60: Last frame 0 time 0.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/8 (150 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/9 60: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 60: Last frame 0 time 0.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/9 (149 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/10 60: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 60: Last frame 0 time 0.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/10 (148 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/11 60: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 60: Last frame 0 time 0.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/11 (150 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/12 60: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 60: Last frame 0 time 0.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/12 (150 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/13 60: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 60: Last frame 0 time 0.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/13 (136 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/14 60: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 60: Last frame 0 time 0.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/14 (141 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/15 60: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 60: Last frame 0 time 0.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/15 (138 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/16 60: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 60: Last frame 0 time 0.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/16 (141 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/17 60: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 60: Last frame 0 time 0.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/17 (143 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/18 60: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 60: Last frame 0 time 0.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/18 (143 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/19 60: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 60: Last frame 0 time 0.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/19 (143 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/20 60: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 60: Last frame 0 time 0.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/20 (144 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/21 60: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 60: Last frame 0 time 0.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/21 (142 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/22 60: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 60: Last frame 0 time 0.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/22 (144 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/23 60: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 60: Last frame 0 time 0.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/23 (159 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/24 60: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 60: Last frame 0 time 0.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/24 (154 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/25 60: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 60: Last frame 0 time 0.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/25 (146 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/26 60: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 60: Last frame 0 time 0.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/26 (156 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/27 60: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 60: Last frame 0 time 0.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/27 (163 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/28 60: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 60: Last frame 0 time 0.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/28 (155 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/29 60: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 60: Last frame 0 time 0.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/29 (152 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/30 60: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 60: Last frame 0 time 0.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/30 (157 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/31 60: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 60: Last frame 0 time 0.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/31 (155 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/32 60: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 60: Last frame 0 time 0.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/32 (153 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/33 60: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 60: Last frame 0 time 0.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/33 (155 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/34 60: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 60: Last frame 0 time 0.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/34 (155 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/35 60: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 60: Last frame 0 time 0.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/35 (155 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/36 60: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 60: Last frame 0 time 0.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/36 (154 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/37 60: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 60: Last frame 0 time 0.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/37 (148 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/38 60: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 60: Last frame 0 time 0.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/38 (154 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/39 60: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 60: Last frame 0 time 0.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/39 (151 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/40 60: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 60: Last frame 0 time 0.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/40 (156 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/41 60: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 60: Last frame 0 time 0.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/41 (159 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/42 60: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 60: Last frame 0 time 0.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/42 (160 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/43 60: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 60: Last frame 0 time 0.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/43 (162 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/44 60: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 60: Last frame 0 time 0.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/44 (155 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/45 60: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 60: Last frame 0 time 0.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/45 (156 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/46 60: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 60: Last frame 0 time 0.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/46 (155 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/47 60: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 60: Last frame 0 time 0.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/47 (157 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/48 60: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 60: Last frame 0 time 0.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/48 (145 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/49 60: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 60: Last frame 0 time 0.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/49 (155 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/50 60: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 60: Last frame 0 time 0.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/50 (155 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/51 60: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 60: Last frame 0 time 0.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/51 (136 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/52 60: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 60: Last frame 0 time 0.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/52 (158 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/53 60: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 60: Last frame 0 time 0.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/53 (146 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/54 60: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 60: Last frame 0 time 0.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/54 (156 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/55 60: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 60: Last frame 0 time 0.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/55 (157 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/56 60: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 60: Last frame 0 time 0.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/56 (157 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/57 60: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 60: Last frame 0 time 0.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/57 (155 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/58 60: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 60: Last frame 0 time 0.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/58 (157 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/59 60: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 60: Last frame 0 time 0.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/59 (152 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/60 60: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 60: Last frame 0 time 0.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/60 (150 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/61 60: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 60: Last frame 0 time 0.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/61 (159 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/62 60: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 60: Last frame 0 time 0.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/62 (155 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/63 60: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 60: Last frame 0 time 0.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/63 (153 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/64 60: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 60: Last frame 0 time 0.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/64 (147 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/65 60: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 60: Last frame 0 time 0.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/65 (142 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/66 60: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 60: Last frame 0 time 0.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/66 (141 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/67 60: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 60: Last frame 0 time 0.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/67 (146 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/68 60: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 60: Last frame 0 time 0.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/68 (134 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/69 60: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 60: Last frame 0 time 0.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/69 (136 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/70 60: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 60: Last frame 0 time 0.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/70 (142 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/71 60: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 60: Last frame 0 time 0.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/71 (141 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/72 60: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 60: Last frame 0 time 0.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/72 (143 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/73 60: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 60: Last frame 0 time 0.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/73 (144 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/74 60: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 60: Last frame 0 time 0.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/74 (148 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/75 60: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 60: Last frame 0 time 0.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/75 (134 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/76 60: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 60: Last frame 0 time 0.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/76 (147 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/77 60: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 60: Last frame 0 time 0.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/77 (134 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/78 60: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 60: Last frame 0 time 0.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/78 (151 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/79 60: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 60: Last frame 0 time 0.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/79 (141 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/80 60: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 60: Last frame 0 time 0.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/80 (145 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/81 60: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 60: Last frame 0 time 0.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/81 (141 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/82 60: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 60: Last frame 0 time 0.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/82 (147 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/83 60: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 60: Last frame 0 time 0.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/83 (140 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/84 60: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 60: Last frame 0 time 0.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/84 (137 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/85 60: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 60: Last frame 0 time 0.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/85 (143 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/86 60: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 60: Last frame 0 time 0.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/86 (137 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/87 60: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 60: Last frame 0 time 0.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/87 (144 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/88 60: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 60: Last frame 0 time 0.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/88 (147 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/89 60: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 60: Last frame 0 time 0.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/89 (140 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/90 60: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 60: Last frame 0 time 0.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/90 (144 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/91 60: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 60: Last frame 0 time 0.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/91 (143 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/92 60: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 60: Last frame 0 time 0.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/92 (143 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/93 60: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 60: Last frame 0 time 0.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/93 (143 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/94 60: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 60: Last frame 0 time 0.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/94 (137 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/95 60: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 60: Last frame 0 time 0.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/95 (141 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/96 60: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 60: Last frame 0 time 0.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/96 (135 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/97 60: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 60: Last frame 0 time 0.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/97 (133 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/98 60: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 60: Last frame 0 time 0.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/98 (134 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/99 60: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 60: Last frame 0 time 0.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/99 (136 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/100 60: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 60: Last frame 0 time 0.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/100 (140 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/101 60: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 60: Last frame 0 time 0.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/101 (135 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/102 60: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 60: Last frame 0 time 0.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/102 (135 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/103 60: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 60: Last frame 0 time 0.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/103 (135 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/104 60: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 60: Last frame 0 time 0.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/104 (141 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/105 60: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 60: Last frame 0 time 0.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/105 (155 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/106 60: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 60: Last frame 0 time 0.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/106 (144 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/107 60: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 60: Last frame 0 time 0.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/107 (134 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/108 60: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 60: Last frame 0 time 0.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/108 (140 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/109 60: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 60: Last frame 0 time 0.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/109 (138 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/110 60: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 60: Last frame 0 time 0.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/110 (138 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/111 60: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 60: Last frame 0 time 0.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/111 (138 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/112 60: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 60: Last frame 0 time 0.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/112 (131 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/113 60: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 60: Last frame 0 time 0.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/113 (139 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/114 60: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 60: Last frame 0 time 0.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/114 (138 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/115 60: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 60: Last frame 0 time 0.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/115 (139 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/116 60: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 60: Last frame 0 time 0.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/116 (129 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/117 60: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 60: Last frame 0 time 0.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/117 (133 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/118 60: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 60: Last frame 0 time 0.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/118 (138 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/119 60: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 60: Last frame 0 time 0.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/119 (135 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/120 60: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 60: Last frame 0 time 0.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/120 (139 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/121 60: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 60: Last frame 0 time 0.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/121 (133 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/122 60: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 60: Last frame 0 time 0.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/122 (134 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/123 60: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 60: Last frame 0 time 0.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/123 (131 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/124 60: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 60: Last frame 0 time 0.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/124 (128 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/125 60: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 60: Last frame 0 time 0.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/125 (132 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/126 60: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 60: Last frame 0 time 0.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/126 (135 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/127 60: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 60: Last frame 0 time 0.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/127 (129 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/128 60: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 60: Last frame 0 time 500.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/128 (107 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/129 60: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 60: Last frame 0 time 500.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/129 (108 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/130 60: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 60: Last frame 0 time 500.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/130 (108 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/131 60: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 60: Last frame 0 time 500.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/131 (106 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/132 60: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 60: Last frame 0 time 500.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/132 (107 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/133 60: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 60: Last frame 0 time 500.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/133 (93 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/134 60: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 60: Last frame 0 time 500.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/134 (108 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/135 60: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 60: Last frame 0 time 500.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/135 (106 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/136 60: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 60: Last frame 0 time 500.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/136 (108 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/137 60: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 60: Last frame 0 time 500.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/137 (105 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/138 60: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 60: Last frame 0 time 500.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/138 (108 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/139 60: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 60: Last frame 0 time 500.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/139 (104 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/140 60: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 60: Last frame 0 time 500.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/140 (93 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/141 60: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 60: Last frame 0 time 500.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/141 (105 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/142 60: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 60: Last frame 0 time 500.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/142 (111 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/143 60: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 60: Last frame 0 time 500.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/143 (108 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/144 60: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 60: Last frame 0 time 500.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/144 (113 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/145 60: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 60: Last frame 0 time 500.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/145 (104 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/146 60: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 60: Last frame 0 time 500.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/146 (106 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/147 60: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 60: Last frame 0 time 500.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/147 (105 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/148 60: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 60: Last frame 0 time 500.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/148 (106 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/149 60: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 60: Last frame 0 time 500.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/149 (104 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/150 60: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 60: Last frame 0 time 500.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/150 (103 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/151 60: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 60: Last frame 0 time 500.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/151 (104 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/152 60: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 60: Last frame 0 time 500.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/152 (109 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/153 60: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 60: Last frame 0 time 500.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/153 (105 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/154 60: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 60: Last frame 0 time 500.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/154 (105 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/155 60: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 60: Last frame 0 time 500.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/155 (105 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/156 60: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 60: Last frame 0 time 500.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/156 (105 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/157 60: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 60: Last frame 0 time 500.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/157 (106 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/158 60: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 60: Last frame 0 time 500.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/158 (108 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/159 60: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 60: Last frame 0 time 500.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/159 (110 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/160 60: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 60: Last frame 0 time 500.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/160 (110 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/161 60: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 60: Last frame 0 time 500.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/161 (109 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/162 60: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 60: Last frame 0 time 500.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/162 (112 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/163 60: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 60: Last frame 0 time 500.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/163 (105 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/164 60: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 60: Last frame 0 time 500.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/164 (106 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/165 60: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 60: Last frame 0 time 500.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/165 (108 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/166 60: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 60: Last frame 0 time 500.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/166 (105 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/167 60: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 60: Last frame 0 time 500.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/167 (104 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/168 60: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 60: Last frame 0 time 500.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/168 (107 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/169 60: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 60: Last frame 0 time 500.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/169 (107 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/170 60: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 60: Last frame 0 time 500.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/170 (109 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/171 60: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 60: Last frame 0 time 500.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/171 (106 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/172 60: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 60: Last frame 0 time 500.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/172 (105 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/173 60: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 60: Last frame 0 time 500.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/173 (106 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/174 60: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 60: Last frame 0 time 500.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/174 (103 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/175 60: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 60: Last frame 0 time 500.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/175 (103 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/176 60: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 60: Last frame 0 time 500.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/176 (102 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/177 60: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 60: Last frame 0 time 500.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/177 (104 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/178 60: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 60: Last frame 0 time 500.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/178 (110 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/179 60: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 60: Last frame 0 time 500.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/179 (101 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/180 60: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 60: Last frame 0 time 500.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/180 (104 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/181 60: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 60: Last frame 0 time 500.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/181 (103 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/182 60: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 60: Last frame 0 time 500.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/182 (103 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/183 60: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 60: Last frame 0 time 500.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/183 (103 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/184 60: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 60: Last frame 0 time 500.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/184 (112 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/185 60: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 60: Last frame 0 time 500.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/185 (105 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/186 60: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 60: Last frame 0 time 500.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/186 (108 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/187 60: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 60: Last frame 0 time 500.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/187 (107 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/188 60: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 60: Last frame 0 time 500.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/188 (107 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/189 60: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 60: Last frame 0 time 500.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/189 (111 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/190 60: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 60: Last frame 0 time 500.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/190 (115 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/191 60: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 60: Last frame 0 time 500.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/191 (101 ms) 60: [----------] 192 tests from MoleculeTests/DsspModuleTest (25498 ms total) 60: 60: [----------] 3 tests from GyrateTests/GyrateModuleTest 60: [ RUN ] GyrateTests/GyrateModuleTest.Works/0 60: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 60: Analyzed 2 frames, last time 10.000 60: [ OK ] GyrateTests/GyrateModuleTest.Works/0 (64 ms) 60: [ RUN ] GyrateTests/GyrateModuleTest.Works/1 60: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 60: Analyzed 2 frames, last time 10.000 60: [ OK ] GyrateTests/GyrateModuleTest.Works/1 (64 ms) 60: [ RUN ] GyrateTests/GyrateModuleTest.Works/2 60: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 60: Analyzed 2 frames, last time 10.000 60: [ OK ] GyrateTests/GyrateModuleTest.Works/2 (57 ms) 60: [----------] 3 tests from GyrateTests/GyrateModuleTest (186 ms total) 60: 60: [----------] 96 tests from HBondTests/HbondModuleTest 60: [ RUN ] HBondTests/HbondModuleTest.Works/0 60: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 60: Analyzed 2 frames, last time 10.000 60: 60: Checking for overlap in atoms between Protein (304 atoms) and Protein (304 atoms) 60: Selection 'Protein' has 56 acceptors and 27 donors. 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 60: Memory Limitation 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c02087 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] HBondTests/HbondModuleTest.Works/0 (95 ms) 60: [ RUN ] HBondTests/HbondModuleTest.Works/1 60: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 60: Analyzed 2 frames, last time 10.000 60: 60: Checking for overlap in atoms between Protein (304 atoms) and Protein (304 atoms) 60: Selection 'Protein' has 29 acceptors and 27 donors. 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 60: Memory Limitation 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c02087 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] HBondTests/HbondModuleTest.Works/1 (104 ms) 60: [ RUN ] HBondTests/HbondModuleTest.Works/2 60: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 60: Analyzed 2 frames, last time 10.000 60: 60: Checking for overlap in atoms between Protein (304 atoms) and Protein (304 atoms) 60: Selection 'Protein' has 56 acceptors and 4 donors. 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 60: Memory Limitation 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c02087 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] HBondTests/HbondModuleTest.Works/2 (95 ms) 60: [ RUN ] HBondTests/HbondModuleTest.Works/3 60: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 60: Analyzed 2 frames, last time 10.000 60: 60: Checking for overlap in atoms between Protein (304 atoms) and Protein (304 atoms) 60: Selection 'Protein' has 29 acceptors and 4 donors. 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 60: Memory Limitation 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c02087 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] HBondTests/HbondModuleTest.Works/3 (89 ms) 60: [ RUN ] HBondTests/HbondModuleTest.Works/4 60: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 60: Analyzed 2 frames, last time 10.000 60: 60: Checking for overlap in atoms between Protein (304 atoms) and Protein (304 atoms) 60: Selection 'Protein' has 56 acceptors and 27 donors. 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 60: Memory Limitation 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c02087 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] HBondTests/HbondModuleTest.Works/4 (102 ms) 60: [ RUN ] HBondTests/HbondModuleTest.Works/5 60: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 60: Analyzed 2 frames, last time 10.000 60: 60: Checking for overlap in atoms between Protein (304 atoms) and Protein (304 atoms) 60: Selection 'Protein' has 29 acceptors and 27 donors. 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 60: Memory Limitation 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c02087 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] HBondTests/HbondModuleTest.Works/5 (98 ms) 60: [ RUN ] HBondTests/HbondModuleTest.Works/6 60: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 60: Analyzed 2 frames, last time 10.000 60: 60: Checking for overlap in atoms between Protein (304 atoms) and Protein (304 atoms) 60: Selection 'Protein' has 56 acceptors and 4 donors. 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 60: Memory Limitation 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c02087 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] HBondTests/HbondModuleTest.Works/6 (94 ms) 60: [ RUN ] HBondTests/HbondModuleTest.Works/7 60: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 60: Analyzed 2 frames, last time 10.000 60: 60: Checking for overlap in atoms between Protein (304 atoms) and Protein (304 atoms) 60: Selection 'Protein' has 29 acceptors and 4 donors. 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 60: Memory Limitation 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c02087 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] HBondTests/HbondModuleTest.Works/7 (89 ms) 60: [ RUN ] HBondTests/HbondModuleTest.Works/8 60: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 60: Analyzed 2 frames, last time 10.000 60: 60: Checking for overlap in atoms between Protein (304 atoms) and Protein (304 atoms) 60: Selection 'Protein' has 56 acceptors and 27 donors. 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 60: Memory Limitation 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c02087 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] HBondTests/HbondModuleTest.Works/8 (95 ms) 60: [ RUN ] HBondTests/HbondModuleTest.Works/9 60: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 60: Analyzed 2 frames, last time 10.000 60: 60: Checking for overlap in atoms between Protein (304 atoms) and Protein (304 atoms) 60: Selection 'Protein' has 29 acceptors and 27 donors. 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 60: Memory Limitation 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c02087 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] HBondTests/HbondModuleTest.Works/9 (101 ms) 60: [ RUN ] HBondTests/HbondModuleTest.Works/10 60: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 60: Analyzed 2 frames, last time 10.000 60: 60: Checking for overlap in atoms between Protein (304 atoms) and Protein (304 atoms) 60: Selection 'Protein' has 56 acceptors and 4 donors. 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 60: Memory Limitation 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c02087 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] HBondTests/HbondModuleTest.Works/10 (92 ms) 60: [ RUN ] HBondTests/HbondModuleTest.Works/11 60: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 60: Analyzed 2 frames, last time 10.000 60: 60: Checking for overlap in atoms between Protein (304 atoms) and Protein (304 atoms) 60: Selection 'Protein' has 29 acceptors and 4 donors. 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 60: Memory Limitation 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c02087 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] HBondTests/HbondModuleTest.Works/11 (96 ms) 60: [ RUN ] HBondTests/HbondModuleTest.Works/12 60: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 60: Analyzed 2 frames, last time 10.000 60: 60: Checking for overlap in atoms between Protein (304 atoms) and Protein (304 atoms) 60: Selection 'Protein' has 56 acceptors and 27 donors. 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 60: Memory Limitation 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c02087 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] HBondTests/HbondModuleTest.Works/12 (104 ms) 60: [ RUN ] HBondTests/HbondModuleTest.Works/13 60: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 60: Analyzed 2 frames, last time 10.000 60: 60: Checking for overlap in atoms between Protein (304 atoms) and Protein (304 atoms) 60: Selection 'Protein' has 29 acceptors and 27 donors. 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 60: Memory Limitation 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c02087 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] HBondTests/HbondModuleTest.Works/13 (91 ms) 60: [ RUN ] HBondTests/HbondModuleTest.Works/14 60: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 60: Analyzed 2 frames, last time 10.000 60: 60: Checking for overlap in atoms between Protein (304 atoms) and Protein (304 atoms) 60: Selection 'Protein' has 56 acceptors and 4 donors. 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 60: Memory Limitation 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c02087 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] HBondTests/HbondModuleTest.Works/14 (87 ms) 60: [ RUN ] HBondTests/HbondModuleTest.Works/15 60: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 60: Analyzed 2 frames, last time 10.000 60: 60: Checking for overlap in atoms between Protein (304 atoms) and Protein (304 atoms) 60: Selection 'Protein' has 29 acceptors and 4 donors. 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 60: Memory Limitation 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c02087 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] HBondTests/HbondModuleTest.Works/15 (90 ms) 60: [ RUN ] HBondTests/HbondModuleTest.Works/16 60: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 60: Analyzed 2 frames, last time 10.000 60: 60: Checking for overlap in atoms between Protein (304 atoms) and Protein (304 atoms) 60: Selection 'Protein' has 56 acceptors and 27 donors. 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 60: Memory Limitation 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c02087 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] HBondTests/HbondModuleTest.Works/16 (92 ms) 60: [ RUN ] HBondTests/HbondModuleTest.Works/17 60: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 60: Analyzed 2 frames, last time 10.000 60: 60: Checking for overlap in atoms between Protein (304 atoms) and Protein (304 atoms) 60: Selection 'Protein' has 29 acceptors and 27 donors. 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 60: Memory Limitation 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c02087 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] HBondTests/HbondModuleTest.Works/17 (92 ms) 60: [ RUN ] HBondTests/HbondModuleTest.Works/18 60: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 60: Analyzed 2 frames, last time 10.000 60: 60: Checking for overlap in atoms between Protein (304 atoms) and Protein (304 atoms) 60: Selection 'Protein' has 56 acceptors and 4 donors. 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 60: Memory Limitation 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c02087 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] HBondTests/HbondModuleTest.Works/18 (88 ms) 60: [ RUN ] HBondTests/HbondModuleTest.Works/19 60: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 60: Analyzed 2 frames, last time 10.000 60: 60: Checking for overlap in atoms between Protein (304 atoms) and Protein (304 atoms) 60: Selection 'Protein' has 29 acceptors and 4 donors. 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 60: Memory Limitation 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c02087 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] HBondTests/HbondModuleTest.Works/19 (88 ms) 60: [ RUN ] HBondTests/HbondModuleTest.Works/20 60: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 60: Analyzed 2 frames, last time 10.000 60: 60: Checking for overlap in atoms between Protein (304 atoms) and Protein (304 atoms) 60: Selection 'Protein' has 56 acceptors and 27 donors. 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 60: Memory Limitation 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c02087 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] HBondTests/HbondModuleTest.Works/20 (103 ms) 60: [ RUN ] HBondTests/HbondModuleTest.Works/21 60: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 60: Analyzed 2 frames, last time 10.000 60: 60: Checking for overlap in atoms between Protein (304 atoms) and Protein (304 atoms) 60: Selection 'Protein' has 29 acceptors and 27 donors. 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 60: Memory Limitation 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c02087 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] HBondTests/HbondModuleTest.Works/21 (106 ms) 60: [ RUN ] HBondTests/HbondModuleTest.Works/22 60: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 60: Analyzed 2 frames, last time 10.000 60: 60: Checking for overlap in atoms between Protein (304 atoms) and Protein (304 atoms) 60: Selection 'Protein' has 56 acceptors and 4 donors. 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 60: Memory Limitation 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c02087 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] HBondTests/HbondModuleTest.Works/22 (95 ms) 60: [ RUN ] HBondTests/HbondModuleTest.Works/23 60: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 60: Analyzed 2 frames, last time 10.000 60: 60: Checking for overlap in atoms between Protein (304 atoms) and Protein (304 atoms) 60: Selection 'Protein' has 29 acceptors and 4 donors. 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 60: Memory Limitation 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c02087 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] HBondTests/HbondModuleTest.Works/23 (89 ms) 60: [ RUN ] HBondTests/HbondModuleTest.Works/24 60: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 60: Analyzed 2 frames, last time 10.000 60: 60: Checking for overlap in atoms between Protein (304 atoms) and Protein (304 atoms) 60: Selection 'Protein' has 56 acceptors and 27 donors. 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 60: Memory Limitation 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c02087 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] HBondTests/HbondModuleTest.Works/24 (96 ms) 60: [ RUN ] HBondTests/HbondModuleTest.Works/25 60: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 60: Analyzed 2 frames, last time 10.000 60: 60: Checking for overlap in atoms between Protein (304 atoms) and Protein (304 atoms) 60: Selection 'Protein' has 29 acceptors and 27 donors. 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 60: Memory Limitation 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c02087 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] HBondTests/HbondModuleTest.Works/25 (96 ms) 60: [ RUN ] HBondTests/HbondModuleTest.Works/26 60: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 60: Analyzed 2 frames, last time 10.000 60: 60: Checking for overlap in atoms between Protein (304 atoms) and Protein (304 atoms) 60: Selection 'Protein' has 56 acceptors and 4 donors. 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 60: Memory Limitation 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c02087 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] HBondTests/HbondModuleTest.Works/26 (89 ms) 60: [ RUN ] HBondTests/HbondModuleTest.Works/27 60: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 60: Analyzed 2 frames, last time 10.000 60: 60: Checking for overlap in atoms between Protein (304 atoms) and Protein (304 atoms) 60: Selection 'Protein' has 29 acceptors and 4 donors. 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 60: Memory Limitation 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c02087 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] HBondTests/HbondModuleTest.Works/27 (93 ms) 60: [ RUN ] HBondTests/HbondModuleTest.Works/28 60: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 60: Analyzed 2 frames, last time 10.000 60: 60: Checking for overlap in atoms between Protein (304 atoms) and Protein (304 atoms) 60: Selection 'Protein' has 56 acceptors and 27 donors. 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 60: Memory Limitation 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c02087 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] HBondTests/HbondModuleTest.Works/28 (93 ms) 60: [ RUN ] HBondTests/HbondModuleTest.Works/29 60: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 60: Analyzed 2 frames, last time 10.000 60: 60: Checking for overlap in atoms between Protein (304 atoms) and Protein (304 atoms) 60: Selection 'Protein' has 29 acceptors and 27 donors. 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 60: Memory Limitation 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c02087 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] HBondTests/HbondModuleTest.Works/29 (97 ms) 60: [ RUN ] HBondTests/HbondModuleTest.Works/30 60: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 60: Analyzed 2 frames, last time 10.000 60: 60: Checking for overlap in atoms between Protein (304 atoms) and Protein (304 atoms) 60: Selection 'Protein' has 56 acceptors and 4 donors. 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 60: Memory Limitation 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c02087 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] HBondTests/HbondModuleTest.Works/30 (92 ms) 60: [ RUN ] HBondTests/HbondModuleTest.Works/31 60: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 60: Analyzed 2 frames, last time 10.000 60: 60: Checking for overlap in atoms between Protein (304 atoms) and Protein (304 atoms) 60: Selection 'Protein' has 29 acceptors and 4 donors. 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 60: Memory Limitation 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c02087 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] HBondTests/HbondModuleTest.Works/31 (90 ms) 60: [ RUN ] HBondTests/HbondModuleTest.Works/32 60: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 60: Analyzed 2 frames, last time 10.000 60: 60: Checking for overlap in atoms between Protein (304 atoms) and Water (3480 atoms) 60: Selection 'Protein' has 56 acceptors and 27 donors. 60: Selection 'Water' has 1160 acceptors and 1160 donors. 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 60: Memory Limitation 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c02087 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] HBondTests/HbondModuleTest.Works/32 (471 ms) 60: [ RUN ] HBondTests/HbondModuleTest.Works/33 60: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 60: Analyzed 2 frames, last time 10.000 60: 60: Checking for overlap in atoms between Protein (304 atoms) and Water (3480 atoms) 60: Selection 'Protein' has 29 acceptors and 27 donors. 60: Selection 'Water' has 1160 acceptors and 1160 donors. 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 60: Memory Limitation 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c02087 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] HBondTests/HbondModuleTest.Works/33 (475 ms) 60: [ RUN ] HBondTests/HbondModuleTest.Works/34 60: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 60: Analyzed 2 frames, last time 10.000 60: 60: Checking for overlap in atoms between Protein (304 atoms) and Water (3480 atoms) 60: Selection 'Protein' has 56 acceptors and 4 donors. 60: Selection 'Water' has 1160 acceptors and 1160 donors. 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 60: Memory Limitation 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c02087 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] HBondTests/HbondModuleTest.Works/34 (462 ms) 60: [ RUN ] HBondTests/HbondModuleTest.Works/35 60: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 60: Analyzed 2 frames, last time 10.000 60: 60: Checking for overlap in atoms between Protein (304 atoms) and Water (3480 atoms) 60: Selection 'Protein' has 29 acceptors and 4 donors. 60: Selection 'Water' has 1160 acceptors and 1160 donors. 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 60: Memory Limitation 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c02087 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] HBondTests/HbondModuleTest.Works/35 (451 ms) 60: [ RUN ] HBondTests/HbondModuleTest.Works/36 60: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 60: Analyzed 2 frames, last time 10.000 60: 60: Checking for overlap in atoms between Protein (304 atoms) and Water (3480 atoms) 60: Selection 'Protein' has 56 acceptors and 27 donors. 60: Selection 'Water' has 1160 acceptors and 1160 donors. 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 60: Memory Limitation 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c02087 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] HBondTests/HbondModuleTest.Works/36 (493 ms) 60: [ RUN ] HBondTests/HbondModuleTest.Works/37 60: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 60: Analyzed 2 frames, last time 10.000 60: 60: Checking for overlap in atoms between Protein (304 atoms) and Water (3480 atoms) 60: Selection 'Protein' has 29 acceptors and 27 donors. 60: Selection 'Water' has 1160 acceptors and 1160 donors. 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 60: Memory Limitation 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c02087 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] HBondTests/HbondModuleTest.Works/37 (487 ms) 60: [ RUN ] HBondTests/HbondModuleTest.Works/38 60: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 60: Analyzed 2 frames, last time 10.000 60: 60: Checking for overlap in atoms between Protein (304 atoms) and Water (3480 atoms) 60: Selection 'Protein' has 56 acceptors and 4 donors. 60: Selection 'Water' has 1160 acceptors and 1160 donors. 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 60: Memory Limitation 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c02087 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] HBondTests/HbondModuleTest.Works/38 (496 ms) 60: [ RUN ] HBondTests/HbondModuleTest.Works/39 60: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 60: Analyzed 2 frames, last time 10.000 60: 60: Checking for overlap in atoms between Protein (304 atoms) and Water (3480 atoms) 60: Selection 'Protein' has 29 acceptors and 4 donors. 60: Selection 'Water' has 1160 acceptors and 1160 donors. 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 60: Memory Limitation 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c02087 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] HBondTests/HbondModuleTest.Works/39 (470 ms) 60: [ RUN ] HBondTests/HbondModuleTest.Works/40 60: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 60: Analyzed 2 frames, last time 10.000 60: 60: Checking for overlap in atoms between Protein (304 atoms) and Water (3480 atoms) 60: Selection 'Protein' has 56 acceptors and 27 donors. 60: Selection 'Water' has 1160 acceptors and 1160 donors. 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 60: Memory Limitation 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c02087 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] HBondTests/HbondModuleTest.Works/40 (488 ms) 60: [ RUN ] HBondTests/HbondModuleTest.Works/41 60: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 60: Analyzed 2 frames, last time 10.000 60: 60: Checking for overlap in atoms between Protein (304 atoms) and Water (3480 atoms) 60: Selection 'Protein' has 29 acceptors and 27 donors. 60: Selection 'Water' has 1160 acceptors and 1160 donors. 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 60: Memory Limitation 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c02087 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] HBondTests/HbondModuleTest.Works/41 (443 ms) 60: [ RUN ] HBondTests/HbondModuleTest.Works/42 60: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 60: Analyzed 2 frames, last time 10.000 60: 60: Checking for overlap in atoms between Protein (304 atoms) and Water (3480 atoms) 60: Selection 'Protein' has 56 acceptors and 4 donors. 60: Selection 'Water' has 1160 acceptors and 1160 donors. 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 60: Memory Limitation 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c02087 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] HBondTests/HbondModuleTest.Works/42 (452 ms) 60: [ RUN ] HBondTests/HbondModuleTest.Works/43 60: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 60: Analyzed 2 frames, last time 10.000 60: 60: Checking for overlap in atoms between Protein (304 atoms) and Water (3480 atoms) 60: Selection 'Protein' has 29 acceptors and 4 donors. 60: Selection 'Water' has 1160 acceptors and 1160 donors. 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 60: Memory Limitation 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c02087 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] HBondTests/HbondModuleTest.Works/43 (459 ms) 60: [ RUN ] HBondTests/HbondModuleTest.Works/44 60: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 60: Analyzed 2 frames, last time 10.000 60: 60: Checking for overlap in atoms between Protein (304 atoms) and Water (3480 atoms) 60: Selection 'Protein' has 56 acceptors and 27 donors. 60: Selection 'Water' has 1160 acceptors and 1160 donors. 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 60: Memory Limitation 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c02087 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] HBondTests/HbondModuleTest.Works/44 (496 ms) 60: [ RUN ] HBondTests/HbondModuleTest.Works/45 60: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 60: Analyzed 2 frames, last time 10.000 60: 60: Checking for overlap in atoms between Protein (304 atoms) and Water (3480 atoms) 60: Selection 'Protein' has 29 acceptors and 27 donors. 60: Selection 'Water' has 1160 acceptors and 1160 donors. 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 60: Memory Limitation 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c02087 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] HBondTests/HbondModuleTest.Works/45 (472 ms) 60: [ RUN ] HBondTests/HbondModuleTest.Works/46 60: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 60: Analyzed 2 frames, last time 10.000 60: 60: Checking for overlap in atoms between Protein (304 atoms) and Water (3480 atoms) 60: Selection 'Protein' has 56 acceptors and 4 donors. 60: Selection 'Water' has 1160 acceptors and 1160 donors. 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 60: Memory Limitation 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c02087 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] HBondTests/HbondModuleTest.Works/46 (488 ms) 60: [ RUN ] HBondTests/HbondModuleTest.Works/47 60: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 60: Analyzed 2 frames, last time 10.000 60: 60: Checking for overlap in atoms between Protein (304 atoms) and Water (3480 atoms) 60: Selection 'Protein' has 29 acceptors and 4 donors. 60: Selection 'Water' has 1160 acceptors and 1160 donors. 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 60: Memory Limitation 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c02087 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] HBondTests/HbondModuleTest.Works/47 (478 ms) 60: [ RUN ] HBondTests/HbondModuleTest.Works/48 60: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 60: Analyzed 2 frames, last time 10.000 60: 60: Checking for overlap in atoms between Protein (304 atoms) and Water (3480 atoms) 60: Selection 'Protein' has 56 acceptors and 27 donors. 60: Selection 'Water' has 1160 acceptors and 1160 donors. 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 60: Memory Limitation 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c02087 60: -------- -------- --- Thank You --- -------- -------- 60: 60: Merging hbonds with Acceptor and Donor swapped 60: [ OK ] HBondTests/HbondModuleTest.Works/48 (503 ms) 60: [ RUN ] HBondTests/HbondModuleTest.Works/49 60: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 60: Analyzed 2 frames, last time 10.000 60: 60: Checking for overlap in atoms between Protein (304 atoms) and Water (3480 atoms) 60: Selection 'Protein' has 29 acceptors and 27 donors. 60: Selection 'Water' has 1160 acceptors and 1160 donors. 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 60: Memory Limitation 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c02087 60: -------- -------- --- Thank You --- -------- -------- 60: 60: Merging hbonds with Acceptor and Donor swapped 60: [ OK ] HBondTests/HbondModuleTest.Works/49 (487 ms) 60: [ RUN ] HBondTests/HbondModuleTest.Works/50 60: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 60: Analyzed 2 frames, last time 10.000 60: 60: Checking for overlap in atoms between Protein (304 atoms) and Water (3480 atoms) 60: Selection 'Protein' has 56 acceptors and 4 donors. 60: Selection 'Water' has 1160 acceptors and 1160 donors. 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 60: Memory Limitation 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c02087 60: -------- -------- --- Thank You --- -------- -------- 60: 60: Merging hbonds with Acceptor and Donor swapped 60: [ OK ] HBondTests/HbondModuleTest.Works/50 (498 ms) 60: [ RUN ] HBondTests/HbondModuleTest.Works/51 60: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 60: Analyzed 2 frames, last time 10.000 60: 60: Checking for overlap in atoms between Protein (304 atoms) and Water (3480 atoms) 60: Selection 'Protein' has 29 acceptors and 4 donors. 60: Selection 'Water' has 1160 acceptors and 1160 donors. 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 60: Memory Limitation 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c02087 60: -------- -------- --- Thank You --- -------- -------- 60: 60: Merging hbonds with Acceptor and Donor swapped 60: [ OK ] HBondTests/HbondModuleTest.Works/51 (479 ms) 60: [ RUN ] HBondTests/HbondModuleTest.Works/52 60: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 60: Analyzed 2 frames, last time 10.000 60: 60: Checking for overlap in atoms between Protein (304 atoms) and Water (3480 atoms) 60: Selection 'Protein' has 56 acceptors and 27 donors. 60: Selection 'Water' has 1160 acceptors and 1160 donors. 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 60: Memory Limitation 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c02087 60: -------- -------- --- Thank You --- -------- -------- 60: 60: Merging hbonds with Acceptor and Donor swapped 60: [ OK ] HBondTests/HbondModuleTest.Works/52 (501 ms) 60: [ RUN ] HBondTests/HbondModuleTest.Works/53 60: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 60: Analyzed 2 frames, last time 10.000 60: 60: Checking for overlap in atoms between Protein (304 atoms) and Water (3480 atoms) 60: Selection 'Protein' has 29 acceptors and 27 donors. 60: Selection 'Water' has 1160 acceptors and 1160 donors. 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 60: Memory Limitation 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c02087 60: -------- -------- --- Thank You --- -------- -------- 60: 60: Merging hbonds with Acceptor and Donor swapped 60: [ OK ] HBondTests/HbondModuleTest.Works/53 (484 ms) 60: [ RUN ] HBondTests/HbondModuleTest.Works/54 60: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 60: Analyzed 2 frames, last time 10.000 60: 60: Checking for overlap in atoms between Protein (304 atoms) and Water (3480 atoms) 60: Selection 'Protein' has 56 acceptors and 4 donors. 60: Selection 'Water' has 1160 acceptors and 1160 donors. 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 60: Memory Limitation 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c02087 60: -------- -------- --- Thank You --- -------- -------- 60: 60: Merging hbonds with Acceptor and Donor swapped 60: [ OK ] HBondTests/HbondModuleTest.Works/54 (486 ms) 60: [ RUN ] HBondTests/HbondModuleTest.Works/55 60: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 60: Analyzed 2 frames, last time 10.000 60: 60: Checking for overlap in atoms between Protein (304 atoms) and Water (3480 atoms) 60: Selection 'Protein' has 29 acceptors and 4 donors. 60: Selection 'Water' has 1160 acceptors and 1160 donors. 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 60: Memory Limitation 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c02087 60: -------- -------- --- Thank You --- -------- -------- 60: 60: Merging hbonds with Acceptor and Donor swapped 60: [ OK ] HBondTests/HbondModuleTest.Works/55 (483 ms) 60: [ RUN ] HBondTests/HbondModuleTest.Works/56 60: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 60: Analyzed 2 frames, last time 10.000 60: 60: Checking for overlap in atoms between Protein (304 atoms) and Water (3480 atoms) 60: Selection 'Protein' has 56 acceptors and 27 donors. 60: Selection 'Water' has 1160 acceptors and 1160 donors. 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 60: Memory Limitation 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c02087 60: -------- -------- --- Thank You --- -------- -------- 60: 60: Merging hbonds with Acceptor and Donor swapped 60: [ OK ] HBondTests/HbondModuleTest.Works/56 (505 ms) 60: [ RUN ] HBondTests/HbondModuleTest.Works/57 60: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 60: Analyzed 2 frames, last time 10.000 60: 60: Checking for overlap in atoms between Protein (304 atoms) and Water (3480 atoms) 60: Selection 'Protein' has 29 acceptors and 27 donors. 60: Selection 'Water' has 1160 acceptors and 1160 donors. 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 60: Memory Limitation 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c02087 60: -------- -------- --- Thank You --- -------- -------- 60: 60: Merging hbonds with Acceptor and Donor swapped 60: [ OK ] HBondTests/HbondModuleTest.Works/57 (490 ms) 60: [ RUN ] HBondTests/HbondModuleTest.Works/58 60: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 60: Analyzed 2 frames, last time 10.000 60: 60: Checking for overlap in atoms between Protein (304 atoms) and Water (3480 atoms) 60: Selection 'Protein' has 56 acceptors and 4 donors. 60: Selection 'Water' has 1160 acceptors and 1160 donors. 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 60: Memory Limitation 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c02087 60: -------- -------- --- Thank You --- -------- -------- 60: 60: Merging hbonds with Acceptor and Donor swapped 60: [ OK ] HBondTests/HbondModuleTest.Works/58 (499 ms) 60: [ RUN ] HBondTests/HbondModuleTest.Works/59 60: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 60: Analyzed 2 frames, last time 10.000 60: 60: Checking for overlap in atoms between Protein (304 atoms) and Water (3480 atoms) 60: Selection 'Protein' has 29 acceptors and 4 donors. 60: Selection 'Water' has 1160 acceptors and 1160 donors. 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 60: Memory Limitation 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c02087 60: -------- -------- --- Thank You --- -------- -------- 60: 60: Merging hbonds with Acceptor and Donor swapped 60: [ OK ] HBondTests/HbondModuleTest.Works/59 (463 ms) 60: [ RUN ] HBondTests/HbondModuleTest.Works/60 60: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 60: Analyzed 2 frames, last time 10.000 60: 60: Checking for overlap in atoms between Protein (304 atoms) and Water (3480 atoms) 60: Selection 'Protein' has 56 acceptors and 27 donors. 60: Selection 'Water' has 1160 acceptors and 1160 donors. 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 60: Memory Limitation 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c02087 60: -------- -------- --- Thank You --- -------- -------- 60: 60: Merging hbonds with Acceptor and Donor swapped 60: [ OK ] HBondTests/HbondModuleTest.Works/60 (498 ms) 60: [ RUN ] HBondTests/HbondModuleTest.Works/61 60: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 60: Analyzed 2 frames, last time 10.000 60: 60: Checking for overlap in atoms between Protein (304 atoms) and Water (3480 atoms) 60: Selection 'Protein' has 29 acceptors and 27 donors. 60: Selection 'Water' has 1160 acceptors and 1160 donors. 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 60: Memory Limitation 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c02087 60: -------- -------- --- Thank You --- -------- -------- 60: 60: Merging hbonds with Acceptor and Donor swapped 60: [ OK ] HBondTests/HbondModuleTest.Works/61 (489 ms) 60: [ RUN ] HBondTests/HbondModuleTest.Works/62 60: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 60: Analyzed 2 frames, last time 10.000 60: 60: Checking for overlap in atoms between Protein (304 atoms) and Water (3480 atoms) 60: Selection 'Protein' has 56 acceptors and 4 donors. 60: Selection 'Water' has 1160 acceptors and 1160 donors. 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 60: Memory Limitation 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c02087 60: -------- -------- --- Thank You --- -------- -------- 60: 60: Merging hbonds with Acceptor and Donor swapped 60: [ OK ] HBondTests/HbondModuleTest.Works/62 (490 ms) 60: [ RUN ] HBondTests/HbondModuleTest.Works/63 60: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 60: Analyzed 2 frames, last time 10.000 60: 60: Checking for overlap in atoms between Protein (304 atoms) and Water (3480 atoms) 60: Selection 'Protein' has 29 acceptors and 4 donors. 60: Selection 'Water' has 1160 acceptors and 1160 donors. 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 60: Memory Limitation 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c02087 60: -------- -------- --- Thank You --- -------- -------- 60: 60: Merging hbonds with Acceptor and Donor swapped 60: [ OK ] HBondTests/HbondModuleTest.Works/63 (476 ms) 60: [ RUN ] HBondTests/HbondModuleTest.Works/64 60: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 60: Analyzed 2 frames, last time 10.000 60: 60: Checking for overlap in atoms between Water (3480 atoms) and Water (3480 atoms) 60: Selection 'Water' has 1160 acceptors and 1160 donors. 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 60: Memory Limitation 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c02087 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] HBondTests/HbondModuleTest.Works/64 (483 ms) 60: [ RUN ] HBondTests/HbondModuleTest.Works/65 60: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 60: Analyzed 2 frames, last time 10.000 60: 60: Checking for overlap in atoms between Water (3480 atoms) and Water (3480 atoms) 60: Selection 'Water' has 1160 acceptors and 1160 donors. 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 60: Memory Limitation 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c02087 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] HBondTests/HbondModuleTest.Works/65 (474 ms) 60: [ RUN ] HBondTests/HbondModuleTest.Works/66 60: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 60: Analyzed 2 frames, last time 10.000 60: 60: Checking for overlap in atoms between Water (3480 atoms) and Water (3480 atoms) 60: Selection 'Water' has 1160 acceptors and 1160 donors. 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 60: Memory Limitation 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c02087 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] HBondTests/HbondModuleTest.Works/66 (476 ms) 60: [ RUN ] HBondTests/HbondModuleTest.Works/67 60: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 60: Analyzed 2 frames, last time 10.000 60: 60: Checking for overlap in atoms between Water (3480 atoms) and Water (3480 atoms) 60: Selection 'Water' has 1160 acceptors and 1160 donors. 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 60: Memory Limitation 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c02087 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] HBondTests/HbondModuleTest.Works/67 (485 ms) 60: [ RUN ] HBondTests/HbondModuleTest.Works/68 60: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 60: Analyzed 2 frames, last time 10.000 60: 60: Checking for overlap in atoms between Water (3480 atoms) and Water (3480 atoms) 60: Selection 'Water' has 1160 acceptors and 1160 donors. 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 60: Memory Limitation 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c02087 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] HBondTests/HbondModuleTest.Works/68 (499 ms) 60: [ RUN ] HBondTests/HbondModuleTest.Works/69 60: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 60: Analyzed 2 frames, last time 10.000 60: 60: Checking for overlap in atoms between Water (3480 atoms) and Water (3480 atoms) 60: Selection 'Water' has 1160 acceptors and 1160 donors. 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 60: Memory Limitation 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c02087 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] HBondTests/HbondModuleTest.Works/69 (493 ms) 60: [ RUN ] HBondTests/HbondModuleTest.Works/70 60: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 60: Analyzed 2 frames, last time 10.000 60: 60: Checking for overlap in atoms between Water (3480 atoms) and Water (3480 atoms) 60: Selection 'Water' has 1160 acceptors and 1160 donors. 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 60: Memory Limitation 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c02087 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] HBondTests/HbondModuleTest.Works/70 (503 ms) 60: [ RUN ] HBondTests/HbondModuleTest.Works/71 60: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 60: Analyzed 2 frames, last time 10.000 60: 60: Checking for overlap in atoms between Water (3480 atoms) and Water (3480 atoms) 60: Selection 'Water' has 1160 acceptors and 1160 donors. 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 60: Memory Limitation 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c02087 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] HBondTests/HbondModuleTest.Works/71 (496 ms) 60: [ RUN ] HBondTests/HbondModuleTest.Works/72 60: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 60: Analyzed 2 frames, last time 10.000 60: 60: Checking for overlap in atoms between Water (3480 atoms) and Water (3480 atoms) 60: Selection 'Water' has 1160 acceptors and 1160 donors. 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 60: Memory Limitation 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c02087 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] HBondTests/HbondModuleTest.Works/72 (507 ms) 60: [ RUN ] HBondTests/HbondModuleTest.Works/73 60: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 60: Analyzed 2 frames, last time 10.000 60: 60: Checking for overlap in atoms between Water (3480 atoms) and Water (3480 atoms) 60: Selection 'Water' has 1160 acceptors and 1160 donors. 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 60: Memory Limitation 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c02087 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] HBondTests/HbondModuleTest.Works/73 (522 ms) 60: [ RUN ] HBondTests/HbondModuleTest.Works/74 60: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 60: Analyzed 2 frames, last time 10.000 60: 60: Checking for overlap in atoms between Water (3480 atoms) and Water (3480 atoms) 60: Selection 'Water' has 1160 acceptors and 1160 donors. 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 60: Memory Limitation 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c02087 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] HBondTests/HbondModuleTest.Works/74 (513 ms) 60: [ RUN ] HBondTests/HbondModuleTest.Works/75 60: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 60: Analyzed 2 frames, last time 10.000 60: 60: Checking for overlap in atoms between Water (3480 atoms) and Water (3480 atoms) 60: Selection 'Water' has 1160 acceptors and 1160 donors. 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 60: Memory Limitation 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c02087 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] HBondTests/HbondModuleTest.Works/75 (514 ms) 60: [ RUN ] HBondTests/HbondModuleTest.Works/76 60: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 60: Analyzed 2 frames, last time 10.000 60: 60: Checking for overlap in atoms between Water (3480 atoms) and Water (3480 atoms) 60: Selection 'Water' has 1160 acceptors and 1160 donors. 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 60: Memory Limitation 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c02087 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] HBondTests/HbondModuleTest.Works/76 (501 ms) 60: [ RUN ] HBondTests/HbondModuleTest.Works/77 60: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 60: Analyzed 2 frames, last time 10.000 60: 60: Checking for overlap in atoms between Water (3480 atoms) and Water (3480 atoms) 60: Selection 'Water' has 1160 acceptors and 1160 donors. 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 60: Memory Limitation 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c02087 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] HBondTests/HbondModuleTest.Works/77 (490 ms) 60: [ RUN ] HBondTests/HbondModuleTest.Works/78 60: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 60: Analyzed 2 frames, last time 10.000 60: 60: Checking for overlap in atoms between Water (3480 atoms) and Water (3480 atoms) 60: Selection 'Water' has 1160 acceptors and 1160 donors. 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 60: Memory Limitation 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c02087 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] HBondTests/HbondModuleTest.Works/78 (497 ms) 60: [ RUN ] HBondTests/HbondModuleTest.Works/79 60: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 60: Analyzed 2 frames, last time 10.000 60: 60: Checking for overlap in atoms between Water (3480 atoms) and Water (3480 atoms) 60: Selection 'Water' has 1160 acceptors and 1160 donors. 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 60: Memory Limitation 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c02087 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] HBondTests/HbondModuleTest.Works/79 (517 ms) 60: [ RUN ] HBondTests/HbondModuleTest.Works/80 60: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 60: Analyzed 2 frames, last time 10.000 60: 60: Checking for overlap in atoms between Water (3480 atoms) and Water (3480 atoms) 60: Selection 'Water' has 1160 acceptors and 1160 donors. 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 60: Memory Limitation 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c02087 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] HBondTests/HbondModuleTest.Works/80 (471 ms) 60: [ RUN ] HBondTests/HbondModuleTest.Works/81 60: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 60: Analyzed 2 frames, last time 10.000 60: 60: Checking for overlap in atoms between Water (3480 atoms) and Water (3480 atoms) 60: Selection 'Water' has 1160 acceptors and 1160 donors. 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 60: Memory Limitation 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c02087 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] HBondTests/HbondModuleTest.Works/81 (477 ms) 60: [ RUN ] HBondTests/HbondModuleTest.Works/82 60: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 60: Analyzed 2 frames, last time 10.000 60: 60: Checking for overlap in atoms between Water (3480 atoms) and Water (3480 atoms) 60: Selection 'Water' has 1160 acceptors and 1160 donors. 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 60: Memory Limitation 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c02087 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] HBondTests/HbondModuleTest.Works/82 (472 ms) 60: [ RUN ] HBondTests/HbondModuleTest.Works/83 60: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 60: Analyzed 2 frames, last time 10.000 60: 60: Checking for overlap in atoms between Water (3480 atoms) and Water (3480 atoms) 60: Selection 'Water' has 1160 acceptors and 1160 donors. 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 60: Memory Limitation 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c02087 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] HBondTests/HbondModuleTest.Works/83 (455 ms) 60: [ RUN ] HBondTests/HbondModuleTest.Works/84 60: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 60: Analyzed 2 frames, last time 10.000 60: 60: Checking for overlap in atoms between Water (3480 atoms) and Water (3480 atoms) 60: Selection 'Water' has 1160 acceptors and 1160 donors. 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 60: Memory Limitation 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c02087 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] HBondTests/HbondModuleTest.Works/84 (500 ms) 60: [ RUN ] HBondTests/HbondModuleTest.Works/85 60: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 60: Analyzed 2 frames, last time 10.000 60: 60: Checking for overlap in atoms between Water (3480 atoms) and Water (3480 atoms) 60: Selection 'Water' has 1160 acceptors and 1160 donors. 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 60: Memory Limitation 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c02087 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] HBondTests/HbondModuleTest.Works/85 (490 ms) 60: [ RUN ] HBondTests/HbondModuleTest.Works/86 60: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 60: Analyzed 2 frames, last time 10.000 60: 60: Checking for overlap in atoms between Water (3480 atoms) and Water (3480 atoms) 60: Selection 'Water' has 1160 acceptors and 1160 donors. 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 60: Memory Limitation 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c02087 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] HBondTests/HbondModuleTest.Works/86 (504 ms) 60: [ RUN ] HBondTests/HbondModuleTest.Works/87 60: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 60: Analyzed 2 frames, last time 10.000 60: 60: Checking for overlap in atoms between Water (3480 atoms) and Water (3480 atoms) 60: Selection 'Water' has 1160 acceptors and 1160 donors. 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 60: Memory Limitation 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c02087 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] HBondTests/HbondModuleTest.Works/87 (509 ms) 60: [ RUN ] HBondTests/HbondModuleTest.Works/88 60: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 60: Analyzed 2 frames, last time 10.000 60: 60: Checking for overlap in atoms between Water (3480 atoms) and Water (3480 atoms) 60: Selection 'Water' has 1160 acceptors and 1160 donors. 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 60: Memory Limitation 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c02087 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] HBondTests/HbondModuleTest.Works/88 (504 ms) 60: [ RUN ] HBondTests/HbondModuleTest.Works/89 60: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 60: Analyzed 2 frames, last time 10.000 60: 60: Checking for overlap in atoms between Water (3480 atoms) and Water (3480 atoms) 60: Selection 'Water' has 1160 acceptors and 1160 donors. 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 60: Memory Limitation 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c02087 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] HBondTests/HbondModuleTest.Works/89 (526 ms) 60: [ RUN ] HBondTests/HbondModuleTest.Works/90 60: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 60: Analyzed 2 frames, last time 10.000 60: 60: Checking for overlap in atoms between Water (3480 atoms) and Water (3480 atoms) 60: Selection 'Water' has 1160 acceptors and 1160 donors. 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 60: Memory Limitation 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c02087 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] HBondTests/HbondModuleTest.Works/90 (710 ms) 60: [ RUN ] HBondTests/HbondModuleTest.Works/91 60: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 60: Analyzed 2 frames, last time 10.000 60: 60: Checking for overlap in atoms between Water (3480 atoms) and Water (3480 atoms) 60: Selection 'Water' has 1160 acceptors and 1160 donors. 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 60: Memory Limitation 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c02087 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] HBondTests/HbondModuleTest.Works/91 (590 ms) 60: [ RUN ] HBondTests/HbondModuleTest.Works/92 60: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 60: Analyzed 2 frames, last time 10.000 60: 60: Checking for overlap in atoms between Water (3480 atoms) and Water (3480 atoms) 60: Selection 'Water' has 1160 acceptors and 1160 donors. 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 60: Memory Limitation 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c02087 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] HBondTests/HbondModuleTest.Works/92 (626 ms) 60: [ RUN ] HBondTests/HbondModuleTest.Works/93 60: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 60: Analyzed 2 frames, last time 10.000 60: 60: Checking for overlap in atoms between Water (3480 atoms) and Water (3480 atoms) 60: Selection 'Water' has 1160 acceptors and 1160 donors. 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 60: Memory Limitation 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c02087 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] HBondTests/HbondModuleTest.Works/93 (566 ms) 60: [ RUN ] HBondTests/HbondModuleTest.Works/94 60: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 60: Analyzed 2 frames, last time 10.000 60: 60: Checking for overlap in atoms between Water (3480 atoms) and Water (3480 atoms) 60: Selection 'Water' has 1160 acceptors and 1160 donors. 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 60: Memory Limitation 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c02087 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] HBondTests/HbondModuleTest.Works/94 (675 ms) 60: [ RUN ] HBondTests/HbondModuleTest.Works/95 60: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 60: Analyzed 2 frames, last time 10.000 60: 60: Checking for overlap in atoms between Water (3480 atoms) and Water (3480 atoms) 60: Selection 'Water' has 1160 acceptors and 1160 donors. 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 60: Memory Limitation 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c02087 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] HBondTests/HbondModuleTest.Works/95 (633 ms) 60: [----------] 96 tests from HBondTests/HbondModuleTest (40989 ms total) 60: 60: [----------] 4 tests from MoleculeTests/ScatteringModule 60: [ RUN ] MoleculeTests/ScatteringModule.DirectMode/0 60: Reading frames from pdb file Reading frame 0 time 0.000 '', 156 atoms 60: Last frame 0 time 0.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: A. V. Shvetsov, A. E. Schmidt, D. V. Lebedev, V. V. Isaev-Ivanov 60: Method for calculating small-angle neutron scattering spectra using all-atom 60: molecular dynamics trajectories 60: Journal of Surface Investigation. X-ray, Synchrotron and Neutron Techniques (2013) 60: DOI: 10.1134/S1027451013060372 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/ScatteringModule.DirectMode/0 (167 ms) 60: [ RUN ] MoleculeTests/ScatteringModule.DirectMode/1 60: Reading frames from pdb file Reading frame 0 time 0.000 '', 156 atoms 60: Last frame 0 time 0.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: A. V. Shvetsov, A. E. Schmidt, D. V. Lebedev, V. V. Isaev-Ivanov 60: Method for calculating small-angle neutron scattering spectra using all-atom 60: molecular dynamics trajectories 60: Journal of Surface Investigation. X-ray, Synchrotron and Neutron Techniques (2013) 60: DOI: 10.1134/S1027451013060372 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: D. T. Cromer, J. B. Mann 60: X-ray scattering factors computed from numerical Hartree-Fock wave functions 60: Acta Cryst. A (1968) 60: DOI: 10.1107/S0567739468000550 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/ScatteringModule.DirectMode/1 (2434 ms) 60: [ RUN ] MoleculeTests/ScatteringModule.MCMode/0 60: Reading frames from pdb file Reading frame 0 time 0.000 '', 156 atoms 60: Last frame 0 time 0.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: A. V. Shvetsov, A. E. Schmidt, D. V. Lebedev, V. V. Isaev-Ivanov 60: Method for calculating small-angle neutron scattering spectra using all-atom 60: molecular dynamics trajectories 60: Journal of Surface Investigation. X-ray, Synchrotron and Neutron Techniques (2013) 60: DOI: 10.1134/S1027451013060372 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/ScatteringModule.MCMode/0 (81 ms) 60: [ RUN ] MoleculeTests/ScatteringModule.MCMode/1 60: Reading frames from pdb file Reading frame 0 time 0.000 '', 156 atoms 60: Last frame 0 time 0.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: A. V. Shvetsov, A. E. Schmidt, D. V. Lebedev, V. V. Isaev-Ivanov 60: Method for calculating small-angle neutron scattering spectra using all-atom 60: molecular dynamics trajectories 60: Journal of Surface Investigation. X-ray, Synchrotron and Neutron Techniques (2013) 60: DOI: 10.1134/S1027451013060372 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: D. T. Cromer, J. B. Mann 60: X-ray scattering factors computed from numerical Hartree-Fock wave functions 60: Acta Cryst. A (1968) 60: DOI: 10.1107/S0567739468000550 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/ScatteringModule.MCMode/1 (499 ms) 60: [----------] 4 tests from MoleculeTests/ScatteringModule (3204 ms total) 60: 60: [----------] Global test environment tear-down 60: [==========] 393 tests from 21 test suites ran. (80437 ms total) 60: [ PASSED ] 393 tests. 60/92 Test #60: TrajectoryAnalysisUnitTests ............... Passed 80.66 sec test 61 Start 61: EnergyAnalysisUnitTests 61: Test command: /build/reproducible-path/gromacs-2025.1/build/basic-dp/bin/energyanalysis-test "--gtest_output=xml:/build/reproducible-path/gromacs-2025.1/build/basic-dp/Testing/Temporary/EnergyAnalysisUnitTests.xml" 61: Working Directory: /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/energyanalysis/tests 61: Test timeout computed to be: 30 61: [==========] Running 12 tests from 5 test suites. 61: [----------] Global test environment set-up. 61: [----------] 2 tests from EnergyTermTest 61: [ RUN ] EnergyTermTest.ConstructWorks 61: [ OK ] EnergyTermTest.ConstructWorks (0 ms) 61: [ RUN ] EnergyTermTest.AddFrameWorks 61: [ OK ] EnergyTermTest.AddFrameWorks (0 ms) 61: [----------] 2 tests from EnergyTermTest (0 ms total) 61: 61: [----------] 1 test from DhdlTest 61: [ RUN ] DhdlTest.ExtractDhdl 61: Opened /build/reproducible-path/gromacs-2025.1/src/gromacs/energyanalysis/tests/dhdl.edr as double precision energy file 61: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/energyanalysis/tests/dhdl.tpr, VERSION 2016-dev-20160810-e3ded7f (double precision) 61: Note: file tpx version 110, software tpx version 137 61: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.010 Reading energy frame 2 time 0.020 Reading energy frame 3 time 0.030 Reading energy frame 4 time 0.040 Reading energy frame 5 time 0.050 Reading energy frame 6 time 0.060 Reading energy frame 7 time 0.070 Reading energy frame 8 time 0.080 Reading energy frame 9 time 0.090 Reading energy frame 10 time 0.100 Reading energy frame 11 time 0.110 Reading energy frame 12 time 0.120 Reading energy frame 13 time 0.130 Reading energy frame 14 time 0.140 Reading energy frame 15 time 0.150 Reading energy frame 16 time 0.160 Reading energy frame 17 time 0.170 Reading energy frame 18 time 0.180 Reading energy frame 19 time 0.190 Reading energy frame 20 time 0.200 Reading energy frame 30 time 0.300 Reading energy frame 40 time 0.400 Reading energy frame 50 time 0.500 Reading energy frame 60 time 0.600 Reading energy frame 70 time 0.700 Reading energy frame 80 time 0.800 Reading energy frame 90 time 0.900 Reading energy frame 100 time 1.000 Last energy frame read 100 time 1.000 61: 61: 61: Wrote 8 lambda values with 101 samples as 808 dH data blocks to /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/energyanalysis/tests/Testing/Temporary/DhdlTest_ExtractDhdl_dhdl.xvg 61: [ OK ] DhdlTest.ExtractDhdl (55 ms) 61: [----------] 1 test from DhdlTest (59 ms total) 61: 61: [----------] 1 test from OriresTest 61: [ RUN ] OriresTest.ExtractOrires 61: Opened /build/reproducible-path/gromacs-2025.1/src/gromacs/energyanalysis/tests/orires.edr as single precision energy file 61: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/energyanalysis/tests/orires.tpr, VERSION 2017-dev-20170725-fea8651 (single precision) 61: Note: file tpx version 111, software tpx version 137 61: Found 7 orientation restraints with 1 experimentsSelect the orientation restraint labels you want (-1 is all) 61: End your selection with 0 61: Selecting all 7 orientation restraints 61: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.002 Reading energy frame 2 time 0.004 Reading energy frame 3 time 0.006 Reading energy frame 4 time 0.008 Reading energy frame 5 time 0.010 Reading energy frame 6 time 0.012 Reading energy frame 7 time 0.014 Reading energy frame 8 time 0.016 Reading energy frame 9 time 0.018 Reading energy frame 10 time 0.020 Last energy frame read 10 time 0.020 61: [ OK ] OriresTest.ExtractOrires (82 ms) 61: [----------] 1 test from OriresTest (83 ms total) 61: 61: [----------] 5 tests from EnergyTest 61: [ RUN ] EnergyTest.ExtractEnergy 61: Opened /build/reproducible-path/gromacs-2025.1/src/gromacs/energyanalysis/tests/ener.edr as single precision energy file 61: 61: Select the terms you want from the following list by 61: selecting either (part of) the name or the number or a combination. 61: End your selection with an empty line or a zero. 61: ------------------------------------------------------------------- 61: 1 LJ-(SR) 2 Disper.-corr. 3 Coulomb-(SR) 4 Coul.-recip. 61: 5 Potential 6 Kinetic-En. 7 Total-Energy 8 Temperature 61: 9 Pres.-DC 10 Pressure 11 Box-X 12 Box-Y 61: 13 Box-Z 14 Volume 15 Density 16 pV 61: 17 Enthalpy 18 Vir-XX 19 Vir-XY 20 Vir-XZ 61: 21 Vir-YX 22 Vir-YY 23 Vir-YZ 24 Vir-ZX 61: 25 Vir-ZY 26 Vir-ZZ 27 Pres-XX 28 Pres-XY 61: 29 Pres-XZ 30 Pres-YX 31 Pres-YY 32 Pres-YZ 61: 33 Pres-ZX 34 Pres-ZY 35 Pres-ZZ 36 #Surf*SurfTen 61: 37 Box-Vel-XX 38 Box-Vel-YY 39 Box-Vel-ZZ 40 T-System 61: 61: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.200 Reading energy frame 2 time 0.400 Reading energy frame 3 time 0.600 Reading energy frame 4 time 0.800 Reading energy frame 5 time 1.000 Reading energy frame 6 time 1.200 Reading energy frame 7 time 1.400 Reading energy frame 8 time 1.600 Reading energy frame 9 time 1.800 Reading energy frame 10 time 2.000 Reading energy frame 11 time 2.200 Reading energy frame 12 time 2.400 Reading energy frame 13 time 2.600 Reading energy frame 14 time 2.800 Reading energy frame 15 time 3.000 Reading energy frame 16 time 3.200 Reading energy frame 17 time 3.400 Reading energy frame 18 time 3.600 Reading energy frame 19 time 3.800 Reading energy frame 20 time 4.000 Reading energy frame 30 time 6.000 Reading energy frame 40 time 8.000 Reading energy frame 50 time 10.000 Last energy frame read 50 time 10.000 61: 61: Statistics over 5001 steps [ 0.0000 through 10.0000 ps ], 3 data sets 61: All statistics are over 5001 points 61: 61: Energy Average Err.Est. RMSD Tot-Drift 61: ------------------------------------------------------------------------------- 61: Potential -34142.2 39 228.993 -62.8906 (kJ/mol) 61: Kinetic En. 6132.38 0.42 119.428 -0.266996 (kJ/mol) 61: Total Energy -28009.8 39 258.637 -63.1577 (kJ/mol) 61: [ OK ] EnergyTest.ExtractEnergy (14 ms) 61: [ RUN ] EnergyTest.ExtractEnergyByNumber 61: Opened /build/reproducible-path/gromacs-2025.1/src/gromacs/energyanalysis/tests/ener.edr as single precision energy file 61: 61: Select the terms you want from the following list by 61: selecting either (part of) the name or the number or a combination. 61: End your selection with an empty line or a zero. 61: ------------------------------------------------------------------- 61: 1 LJ-(SR) 2 Disper.-corr. 3 Coulomb-(SR) 4 Coul.-recip. 61: 5 Potential 6 Kinetic-En. 7 Total-Energy 8 Temperature 61: 9 Pres.-DC 10 Pressure 11 Box-X 12 Box-Y 61: 13 Box-Z 14 Volume 15 Density 16 pV 61: 17 Enthalpy 18 Vir-XX 19 Vir-XY 20 Vir-XZ 61: 21 Vir-YX 22 Vir-YY 23 Vir-YZ 24 Vir-ZX 61: 25 Vir-ZY 26 Vir-ZZ 27 Pres-XX 28 Pres-XY 61: 29 Pres-XZ 30 Pres-YX 31 Pres-YY 32 Pres-YZ 61: 33 Pres-ZX 34 Pres-ZY 35 Pres-ZZ 36 #Surf*SurfTen 61: 37 Box-Vel-XX 38 Box-Vel-YY 39 Box-Vel-ZZ 40 T-System 61: 61: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.200 Reading energy frame 2 time 0.400 Reading energy frame 3 time 0.600 Reading energy frame 4 time 0.800 Reading energy frame 5 time 1.000 Reading energy frame 6 time 1.200 Reading energy frame 7 time 1.400 Reading energy frame 8 time 1.600 Reading energy frame 9 time 1.800 Reading energy frame 10 time 2.000 Reading energy frame 11 time 2.200 Reading energy frame 12 time 2.400 Reading energy frame 13 time 2.600 Reading energy frame 14 time 2.800 Reading energy frame 15 time 3.000 Reading energy frame 16 time 3.200 Reading energy frame 17 time 3.400 Reading energy frame 18 time 3.600 Reading energy frame 19 time 3.800 Reading energy frame 20 time 4.000 Reading energy frame 30 time 6.000 Reading energy frame 40 time 8.000 Reading energy frame 50 time 10.000 Last energy frame read 50 time 10.000 61: 61: Statistics over 5001 steps [ 0.0000 through 10.0000 ps ], 3 data sets 61: All statistics are over 5001 points 61: 61: Energy Average Err.Est. RMSD Tot-Drift 61: ------------------------------------------------------------------------------- 61: Coul. recip. 302.771 2.8 17.5152 12.5403 (kJ/mol) 61: Kinetic En. 6132.38 0.42 119.428 -0.266996 (kJ/mol) 61: Pres. DC -268.49 3 8.52175 13.2804 (bar) 61: [ OK ] EnergyTest.ExtractEnergyByNumber (16 ms) 61: [ RUN ] EnergyTest.ExtractEnergyMixed 61: Opened /build/reproducible-path/gromacs-2025.1/src/gromacs/energyanalysis/tests/ener.edr as single precision energy file 61: 61: Select the terms you want from the following list by 61: selecting either (part of) the name or the number or a combination. 61: End your selection with an empty line or a zero. 61: ------------------------------------------------------------------- 61: 1 LJ-(SR) 2 Disper.-corr. 3 Coulomb-(SR) 4 Coul.-recip. 61: 5 Potential 6 Kinetic-En. 7 Total-Energy 8 Temperature 61: 9 Pres.-DC 10 Pressure 11 Box-X 12 Box-Y 61: 13 Box-Z 14 Volume 15 Density 16 pV 61: 17 Enthalpy 18 Vir-XX 19 Vir-XY 20 Vir-XZ 61: 21 Vir-YX 22 Vir-YY 23 Vir-YZ 24 Vir-ZX 61: 25 Vir-ZY 26 Vir-ZZ 27 Pres-XX 28 Pres-XY 61: 29 Pres-XZ 30 Pres-YX 31 Pres-YY 32 Pres-YZ 61: 33 Pres-ZX 34 Pres-ZY 35 Pres-ZZ 36 #Surf*SurfTen 61: 37 Box-Vel-XX 38 Box-Vel-YY 39 Box-Vel-ZZ 40 T-System 61: 61: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.200 Reading energy frame 2 time 0.400 Reading energy frame 3 time 0.600 Reading energy frame 4 time 0.800 Reading energy frame 5 time 1.000 Reading energy frame 6 time 1.200 Reading energy frame 7 time 1.400 Reading energy frame 8 time 1.600 Reading energy frame 9 time 1.800 Reading energy frame 10 time 2.000 Reading energy frame 11 time 2.200 Reading energy frame 12 time 2.400 Reading energy frame 13 time 2.600 Reading energy frame 14 time 2.800 Reading energy frame 15 time 3.000 Reading energy frame 16 time 3.200 Reading energy frame 17 time 3.400 Reading energy frame 18 time 3.600 Reading energy frame 19 time 3.800 Reading energy frame 20 time 4.000 Reading energy frame 30 time 6.000 Reading energy frame 40 time 8.000 Reading energy frame 50 time 10.000 Last energy frame read 50 time 10.000 61: 61: Statistics over 5001 steps [ 0.0000 through 10.0000 ps ], 4 data sets 61: All statistics are over 5001 points 61: 61: Energy Average Err.Est. RMSD Tot-Drift 61: ------------------------------------------------------------------------------- 61: Total Energy -28009.8 39 258.637 -63.1577 (kJ/mol) 61: Pressure 5.34371 4.1 605.307 -4.88771 (bar) 61: Box-Z 2.92457 0.0054 0.0151558 0.0234974 (nm) 61: Volume 25.0162 0.14 0.386769 0.598615 (nm^3) 61: [ OK ] EnergyTest.ExtractEnergyMixed (19 ms) 61: [ RUN ] EnergyTest.ExtractEnergyWithNumberInName 61: Opened /build/reproducible-path/gromacs-2025.1/src/gromacs/energyanalysis/tests/ener_numberInName.edr as single precision energy file 61: 61: Select the terms you want from the following list by 61: selecting either (part of) the name or the number or a combination. 61: End your selection with an empty line or a zero. 61: ------------------------------------------------------------------- 61: 1 Bond 2 Angle 3 Proper-Dih. 4 Per.-Imp.-Dih. 61: 5 LJ-14 6 Coulomb-14 7 LJ-(SR) 8 Coulomb-(SR) 61: 9 Coul.-recip. 10 Potential 11 Kinetic-En. 12 Total-Energy 61: 13 Conserved-En. 14 Temperature 15 Pressure 16 Constr.-rmsd 61: 17 Vir-XX 18 Vir-XY 19 Vir-XZ 20 Vir-YX 61: 21 Vir-YY 22 Vir-YZ 23 Vir-ZX 24 Vir-ZY 61: 25 Vir-ZZ 26 Pres-XX 27 Pres-XY 28 Pres-XZ 61: 29 Pres-YX 30 Pres-YY 31 Pres-YZ 32 Pres-ZX 61: 33 Pres-ZY 34 Pres-ZZ 35 #Surf*SurfTen 36 2CosZ*Vel-X 61: 37 1/Viscosity 38 T-System 39 Lamb-System 61: 61: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.002 Reading energy frame 2 time 0.004 Last energy frame read 2 time 0.004 61: 61: Statistics over 3 steps [ 0.0000 through 0.0040 ps ], 1 data sets 61: All statistics are over 3 points (frames) 61: 61: Energy Average Err.Est. RMSD Tot-Drift 61: ------------------------------------------------------------------------------- 61: 1/Viscosity 57767.2 -- 10666.2 -25998 (m s/kg) 61: [ OK ] EnergyTest.ExtractEnergyWithNumberInName (8 ms) 61: [ RUN ] EnergyTest.ExtractEnergyWithNumberInNameAndAlsoByNumber 61: Opened /build/reproducible-path/gromacs-2025.1/src/gromacs/energyanalysis/tests/ener_numberInName.edr as single precision energy file 61: 61: Select the terms you want from the following list by 61: selecting either (part of) the name or the number or a combination. 61: End your selection with an empty line or a zero. 61: ------------------------------------------------------------------- 61: 1 Bond 2 Angle 3 Proper-Dih. 4 Per.-Imp.-Dih. 61: 5 LJ-14 6 Coulomb-14 7 LJ-(SR) 8 Coulomb-(SR) 61: 9 Coul.-recip. 10 Potential 11 Kinetic-En. 12 Total-Energy 61: 13 Conserved-En. 14 Temperature 15 Pressure 16 Constr.-rmsd 61: 17 Vir-XX 18 Vir-XY 19 Vir-XZ 20 Vir-YX 61: 21 Vir-YY 22 Vir-YZ 23 Vir-ZX 24 Vir-ZY 61: 25 Vir-ZZ 26 Pres-XX 27 Pres-XY 28 Pres-XZ 61: 29 Pres-YX 30 Pres-YY 31 Pres-YZ 32 Pres-ZX 61: 33 Pres-ZY 34 Pres-ZZ 35 #Surf*SurfTen 36 2CosZ*Vel-X 61: 37 1/Viscosity 38 T-System 39 Lamb-System 61: 61: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.002 Reading energy frame 2 time 0.004 Last energy frame read 2 time 0.004 61: 61: Statistics over 3 steps [ 0.0000 through 0.0040 ps ], 2 data sets 61: All statistics are over 3 points (frames) 61: 61: Energy Average Err.Est. RMSD Tot-Drift 61: ------------------------------------------------------------------------------- 61: LJ (SR) -14.1095 -- 0.384124 0.932214 (kJ/mol) 61: 1/Viscosity 57767.2 -- 10666.2 -25998 (m s/kg) 61: [ OK ] EnergyTest.ExtractEnergyWithNumberInNameAndAlsoByNumber (18 ms) 61: [----------] 5 tests from EnergyTest (80 ms total) 61: 61: [----------] 3 tests from ViscosityTest 61: [ RUN ] ViscosityTest.EinsteinViscosity 61: Opened /build/reproducible-path/gromacs-2025.1/src/gromacs/energyanalysis/tests/ener.edr as single precision energy file 61: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.200 Reading energy frame 2 time 0.400 Reading energy frame 3 time 0.600 Reading energy frame 4 time 0.800 Reading energy frame 5 time 1.000 Reading energy frame 6 time 1.200 Reading energy frame 7 time 1.400 Reading energy frame 8 time 1.600 Reading energy frame 9 time 1.800 Reading energy frame 10 time 2.000 Reading energy frame 11 time 2.200 Reading energy frame 12 time 2.400 Reading energy frame 13 time 2.600 Reading energy frame 14 time 2.800 Reading energy frame 15 time 3.000 Reading energy frame 16 time 3.200 Reading energy frame 17 time 3.400 Reading energy frame 18 time 3.600 Reading energy frame 19 time 3.800 Reading energy frame 20 time 4.000 Reading energy frame 30 time 6.000 Reading energy frame 40 time 8.000 Reading energy frame 50 time 10.000 Last energy frame read 50 time 10.000 61: 61: Statistics over 5001 steps [ 0.0000 through 10.0000 ps ], 12 data sets 61: All statistics are over 5001 points 61: 61: Energy Average Err.Est. RMSD Tot-Drift 61: ------------------------------------------------------------------------------- 61: Pres-XX 20.2092 65 717.193 185.978 (bar) 61: Pres-XY -47.7351 39 372.522 207.456 (bar) 61: Pres-XZ 11.477 31 379.79 6.80818 (bar) 61: Pres-YX -47.7106 39 372.525 207.5 (bar) 61: Pres-YY 38.9241 40 803.899 -27.1505 (bar) 61: Pres-YZ -41.3534 45 401.216 114.663 (bar) 61: Pres-ZX 11.5238 31 379.804 6.91707 (bar) 61: Pres-ZY -41.3119 45 401.196 114.743 (bar) 61: Pres-ZZ -43.1021 63 748.522 -173.491 (bar) 61: Temperature 300.001 0.02 5.8425 -0.0130558 (K) 61: Volume 25.0162 0.14 0.386769 0.598615 (nm^3) 61: Pressure 5.34371 4.1 605.307 -4.88771 (bar) 61: 61: Computing shear viscosity using the Einstein relation with 6 start points separated by 0.2 ps 61: [ OK ] ViscosityTest.EinsteinViscosity (75 ms) 61: [ RUN ] ViscosityTest.EinsteinViscosityIntegral 61: Opened /build/reproducible-path/gromacs-2025.1/src/gromacs/energyanalysis/tests/ener.edr as single precision energy file 61: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.200 Reading energy frame 2 time 0.400 Reading energy frame 3 time 0.600 Reading energy frame 4 time 0.800 Reading energy frame 5 time 1.000 Reading energy frame 6 time 1.200 Reading energy frame 7 time 1.400 Reading energy frame 8 time 1.600 Reading energy frame 9 time 1.800 Reading energy frame 10 time 2.000 Reading energy frame 11 time 2.200 Reading energy frame 12 time 2.400 Reading energy frame 13 time 2.600 Reading energy frame 14 time 2.800 Reading energy frame 15 time 3.000 Reading energy frame 16 time 3.200 Reading energy frame 17 time 3.400 Reading energy frame 18 time 3.600 Reading energy frame 19 time 3.800 Reading energy frame 20 time 4.000 Reading energy frame 30 time 6.000 Reading energy frame 40 time 8.000 Reading energy frame 50 time 10.000 Last energy frame read 50 time 10.000 61: 61: Statistics over 5001 steps [ 0.0000 through 10.0000 ps ], 12 data sets 61: All statistics are over 5001 points 61: 61: Energy Average Err.Est. RMSD Tot-Drift 61: ------------------------------------------------------------------------------- 61: Pres-XX 20.2092 65 717.193 185.978 (bar) 61: Pres-XY -47.7351 39 372.522 207.456 (bar) 61: Pres-XZ 11.477 31 379.79 6.80818 (bar) 61: Pres-YX -47.7106 39 372.525 207.5 (bar) 61: Pres-YY 38.9241 40 803.899 -27.1505 (bar) 61: Pres-YZ -41.3534 45 401.216 114.663 (bar) 61: Pres-ZX 11.5238 31 379.804 6.91707 (bar) 61: Pres-ZY -41.3119 45 401.196 114.743 (bar) 61: Pres-ZZ -43.1021 63 748.522 -173.491 (bar) 61: Temperature 300.001 0.02 5.8425 -0.0130558 (K) 61: Volume 25.0162 0.14 0.386769 0.598615 (nm^3) 61: Pressure 5.34371 4.1 605.307 -4.88771 (bar) 61: 61: Computing shear viscosity using the Einstein relation with 6 start points separated by 0.2 ps 61: [ OK ] ViscosityTest.EinsteinViscosityIntegral (118 ms) 61: [ RUN ] ViscosityTest.EinsteinViscosityDefaultArguments 61: Opened /build/reproducible-path/gromacs-2025.1/src/gromacs/energyanalysis/tests/ener.edr as single precision energy file 61: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.200 Reading energy frame 2 time 0.400 Reading energy frame 3 time 0.600 Reading energy frame 4 time 0.800 Reading energy frame 5 time 1.000 Reading energy frame 6 time 1.200 Reading energy frame 7 time 1.400 Reading energy frame 8 time 1.600 Reading energy frame 9 time 1.800 Reading energy frame 10 time 2.000 Reading energy frame 11 time 2.200 Reading energy frame 12 time 2.400 Reading energy frame 13 time 2.600 Reading energy frame 14 time 2.800 Reading energy frame 15 time 3.000 Reading energy frame 16 time 3.200 Reading energy frame 17 time 3.400 Reading energy frame 18 time 3.600 Reading energy frame 19 time 3.800 Reading energy frame 20 time 4.000 Reading energy frame 30 time 6.000 Reading energy frame 40 time 8.000 Reading energy frame 50 time 10.000 Last energy frame read 50 time 10.000 61: 61: Statistics over 5001 steps [ 0.0000 through 10.0000 ps ], 12 data sets 61: All statistics are over 5001 points 61: 61: Energy Average Err.Est. RMSD Tot-Drift 61: ------------------------------------------------------------------------------- 61: Pres-XX 20.2092 65 717.193 185.978 (bar) 61: Pres-XY -47.7351 39 372.522 207.456 (bar) 61: Pres-XZ 11.477 31 379.79 6.80818 (bar) 61: Pres-YX -47.7106 39 372.525 207.5 (bar) 61: Pres-YY 38.9241 40 803.899 -27.1505 (bar) 61: Pres-YZ -41.3534 45 401.216 114.663 (bar) 61: Pres-ZX 11.5238 31 379.804 6.91707 (bar) 61: Pres-ZY -41.3119 45 401.196 114.743 (bar) 61: Pres-ZZ -43.1021 63 748.522 -173.491 (bar) 61: Temperature 300.001 0.02 5.8425 -0.0130558 (K) 61: Volume 25.0162 0.14 0.386769 0.598615 (nm^3) 61: Pressure 5.34371 4.1 605.307 -4.88771 (bar) 61: 61: Computing shear viscosity using the Einstein relation with 6 start points separated by 0.2 ps 61: [ OK ] ViscosityTest.EinsteinViscosityDefaultArguments (88 ms) 61: [----------] 3 tests from ViscosityTest (283 ms total) 61: 61: [----------] Global test environment tear-down 61: [==========] 12 tests from 5 test suites ran. (509 ms total) 61: [ PASSED ] 12 tests. 61/92 Test #61: EnergyAnalysisUnitTests ................... Passed 0.60 sec test 62 Start 62: ToolUnitTests 62: Test command: /build/reproducible-path/gromacs-2025.1/build/basic-dp/bin/tool-test "--gtest_output=xml:/build/reproducible-path/gromacs-2025.1/build/basic-dp/Testing/Temporary/ToolUnitTests.xml" 62: Working Directory: /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/tools/tests 62: Test timeout computed to be: 1920 62: [==========] Running 63 tests from 8 test suites. 62: [----------] Global test environment set-up. 62: [----------] 2 tests from DumpTest 62: 62: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/tools/tests/Testing/Temporary/DumpTest_lysozyme.mdp]: 62: For a correct single-point energy evaluation with nsteps = 0, use 62: continuation = yes to avoid constraining the input coordinates. 62: 62: Generating 1-4 interactions: fudge = 0.5 62: 62: NOTE 2 [file lysozyme.top, line 1465]: 62: System has non-zero total charge: 2.000000 62: Total charge should normally be an integer. See 62: https://manual.gromacs.org/current/user-guide/floating-point.html 62: for discussion on how close it should be to an integer. 62: 62: 62: 62: Number of degrees of freedom in T-Coupling group rest is 465.00 62: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 62: 62: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/tools/tests/Testing/Temporary/DumpTest_lysozyme.mdp]: 62: NVE simulation with an initial temperature of zero: will use a Verlet 62: buffer of 10%. Check your energy drift! 62: 62: 62: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/tools/tests/Testing/Temporary/DumpTest_lysozyme.mdp]: 62: You are using a plain Coulomb cut-off, which might produce artifacts. 62: You might want to consider using PME electrostatics. 62: 62: 62: 62: There were 4 NOTEs 62: Setting the LD random seed to 2146107199 62: 62: Generated 330891 of the 330891 non-bonded parameter combinations 62: 62: Generated 330891 of the 330891 1-4 parameter combinations 62: 62: Excluding 3 bonded neighbours molecule type 'Protein_chain_B' 62: 62: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/lysozyme.pdb', all velocities are zero 62: Analysing residue names: 62: There are: 10 Protein residues 62: Analysing Protein... 62: 62: This run will generate roughly 0 Mb of data 62: [ RUN ] DumpTest.WorksWithTpr 62: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/tools/tests/Testing/Temporary/DumpTest_lysozyme.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 62: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/tools/tests/Testing/Temporary/DumpTest_lysozyme.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 62: /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/tools/tests/Testing/Temporary/DumpTest_lysozyme.tpr: 62: inputrec: 62: integrator = md 62: tinit = 0 62: dt = 0.001 62: nsteps = 0 62: init-step = 0 62: simulation-part = 1 62: mts = false 62: mass-repartition-factor = 1 62: comm-mode = Linear 62: nstcomm = 100 62: bd-fric = 0 62: ld-seed = 2146107199 62: emtol = 10 62: emstep = 0.01 62: niter = 20 62: fcstep = 0 62: nstcgsteep = 1000 62: nbfgscorr = 10 62: rtpi = 0.05 62: nstxout = 0 62: nstvout = 0 62: nstfout = 0 62: nstlog = 1000 62: nstcalcenergy = 100 62: nstenergy = 1000 62: nstxout-compressed = 0 62: compressed-x-precision = 1000 62: cutoff-scheme = Verlet 62: nstlist = 10 62: pbc = xyz 62: periodic-molecules = false 62: verlet-buffer-tolerance = -1 62: verlet-buffer-pressure-tolerance = 0.5 62: rlist = 1.1 62: coulombtype = Cut-off 62: coulomb-modifier = Potential-shift 62: rcoulomb-switch = 0 62: rcoulomb = 1 62: epsilon-r = 1 62: epsilon-rf = inf 62: vdw-type = Cut-off 62: vdw-modifier = Potential-shift 62: rvdw-switch = 0 62: rvdw = 1 62: DispCorr = No 62: table-extension = 1 62: fourierspacing = 0.12 62: fourier-nx = 0 62: fourier-ny = 0 62: fourier-nz = 0 62: pme-order = 4 62: ewald-rtol = 1e-05 62: ewald-rtol-lj = 0.001 62: lj-pme-comb-rule = Geometric 62: ewald-geometry = 3d 62: epsilon-surface = 0 62: ensemble-temperature-setting = not available 62: tcoupl = No 62: nsttcouple = -1 62: nh-chain-length = 0 62: print-nose-hoover-chain-variables = false 62: pcoupl = No 62: refcoord-scaling = No 62: posres-com: not available 62: posres-comB: not available 62: QMMM = false 62: qm-opts: 62: ngQM = 0 62: constraint-algorithm = Lincs 62: continuation = false 62: Shake-SOR = false 62: shake-tol = 0.0001 62: lincs-order = 4 62: lincs-iter = 1 62: lincs-warnangle = 30 62: nwall = 0 62: wall-type = 9-3 62: wall-r-linpot = -1 62: wall-atomtype[0] = -1 62: wall-atomtype[1] = -1 62: wall-density[0] = 0 62: wall-density[1] = 0 62: wall-ewald-zfac = 3 62: pull = false 62: awh = false 62: rotation = false 62: interactiveMD = false 62: disre = No 62: disre-weighting = Conservative 62: disre-mixed = false 62: dr-fc = 1000 62: dr-tau = 0 62: nstdisreout = 100 62: orire-fc = 0 62: orire-tau = 0 62: nstorireout = 100 62: free-energy = no 62: cos-acceleration = 0 62: deform (3x3): 62: deform[ 0]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 62: deform[ 1]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 62: deform[ 2]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 62: simulated-tempering = false 62: swapcoords = no 62: userint1 = 0 62: userint2 = 0 62: userint3 = 0 62: userint4 = 0 62: userreal1 = 0 62: userreal2 = 0 62: userreal3 = 0 62: userreal4 = 0 62: applied-forces: 62: electric-field: 62: x: 62: E0 = 0 62: omega = 0 62: t0 = 0 62: sigma = 0 62: y: 62: E0 = 0 62: omega = 0 62: t0 = 0 62: sigma = 0 62: z: 62: E0 = 0 62: omega = 0 62: t0 = 0 62: sigma = 0 62: density-guided-simulation: 62: active = false 62: group = protein 62: similarity-measure = inner-product 62: atom-spreading-weight = unity 62: force-constant = 1e+09 62: gaussian-transform-spreading-width = 0.2 62: gaussian-transform-spreading-range-in-multiples-of-width = 4 62: reference-density-filename = reference.mrc 62: nst = 1 62: normalize-densities = true 62: adaptive-force-scaling = false 62: adaptive-force-scaling-time-constant = 4 62: shift-vector = 62: transformation-matrix = 62: qmmm-cp2k: 62: active = false 62: qmgroup = System 62: qmmethod = PBE 62: qmfilenames = 62: qmcharge = 0 62: qmmultiplicity = 1 62: colvars: 62: active = false 62: configfile = 62: seed = -1 62: nnpot: 62: active = false 62: modelfile = model.pt 62: input-group = System 62: model-input1 = 62: model-input2 = 62: model-input3 = 62: model-input4 = 62: grpopts: 62: nrdf: 465 62: ref-t: 0 62: tau-t: 0 62: annealing: No 62: annealing-npoints: 0 62: acc: 0 0 0 62: nfreeze: N N N 62: energygrp-flags[ 0]: 0 62: header: 62: bIr = present 62: bBox = present 62: bTop = present 62: bX = present 62: bV = present 62: bF = not present 62: natoms = 156 62: lambda = 0.000000e+00 62: buffer size = 57082 62: topology: 62: name="First 10 residues from 1AKI" 62: #atoms = 156 62: #molblock = 1 62: molblock (0): 62: moltype = 0 "Protein_chain_B" 62: #molecules = 1 62: #posres_xA = 0 62: #posres_xB = 0 62: bIntermolecularInteractions = false 62: ffparams: 62: atnr=10 62: ntypes=212 62: functype[0]=LJ_SR, c6= 3.35274678e-03, c12= 3.95094442e-06 62: functype[1]=LJ_SR, c6= 0.00000000e+00, c12= 0.00000000e+00 62: functype[2]=LJ_SR, c6= 2.60916961e-03, c12= 3.84022374e-06 62: functype[3]=LJ_SR, c6= 6.41072082e-04, c12= 3.43856290e-07 62: functype[4]=LJ_SR, c6= 4.04775915e-03, c12= 7.32754594e-06 62: functype[5]=LJ_SR, c6= 2.81521126e-03, c12= 2.50631820e-06 62: functype[6]=LJ_SR, c6= 2.80388560e-03, c12= 4.30621225e-06 62: functype[7]=LJ_SR, c6= 5.81477529e-04, c12= 2.82897505e-07 62: functype[8]=LJ_SR, c6= 6.03335344e-04, c12= 2.35915461e-07 62: functype[9]=LJ_SR, c6= 7.20490366e-03, c12= 1.15394674e-05 62: functype[10]=LJ_SR, c6= 0.00000000e+00, c12= 0.00000000e+00 62: functype[11]=LJ_SR, c6= 0.00000000e+00, c12= 0.00000000e+00 62: functype[12]=LJ_SR, c6= 0.00000000e+00, c12= 0.00000000e+00 62: functype[13]=LJ_SR, c6= 0.00000000e+00, c12= 0.00000000e+00 62: functype[14]=LJ_SR, c6= 0.00000000e+00, c12= 0.00000000e+00 62: functype[15]=LJ_SR, c6= 0.00000000e+00, c12= 0.00000000e+00 62: functype[16]=LJ_SR, c6= 0.00000000e+00, c12= 0.00000000e+00 62: functype[17]=LJ_SR, c6= 0.00000000e+00, c12= 0.00000000e+00 62: functype[18]=LJ_SR, c6= 0.00000000e+00, c12= 0.00000000e+00 62: functype[19]=LJ_SR, c6= 0.00000000e+00, c12= 0.00000000e+00 62: functype[20]=LJ_SR, c6= 2.60916961e-03, c12= 3.84022374e-06 62: functype[21]=LJ_SR, c6= 0.00000000e+00, c12= 0.00000000e+00 62: functype[22]=LJ_SR, c6= 2.03050409e-03, c12= 3.73260587e-06 62: functype[23]=LJ_SR, c6= 4.98894161e-04, c12= 3.34220112e-07 62: functype[24]=LJ_SR, c6= 3.15004110e-03, c12= 7.12219987e-06 62: functype[25]=LJ_SR, c6= 2.19084952e-03, c12= 2.43608151e-06 62: functype[26]=LJ_SR, c6= 2.18203568e-03, c12= 4.18553559e-06 62: functype[27]=LJ_SR, c6= 4.52516577e-04, c12= 2.74969627e-07 62: functype[28]=LJ_SR, c6= 4.69526733e-04, c12= 2.29304201e-07 62: functype[29]=LJ_SR, c6= 5.60698940e-03, c12= 1.12160870e-05 62: functype[30]=LJ_SR, c6= 6.41072082e-04, c12= 3.43856290e-07 62: functype[31]=LJ_SR, c6= 0.00000000e+00, c12= 0.00000000e+00 62: functype[32]=LJ_SR, c6= 4.98894161e-04, c12= 3.34220112e-07 62: functype[33]=LJ_SR, c6= 1.22578125e-04, c12= 2.99263000e-08 62: functype[34]=LJ_SR, c6= 7.73964023e-04, c12= 6.37726703e-07 62: functype[35]=LJ_SR, c6= 5.38290978e-04, c12= 2.18128423e-07 62: functype[36]=LJ_SR, c6= 5.36125420e-04, c12= 3.74775753e-07 62: functype[37]=LJ_SR, c6= 1.11183168e-04, c12= 2.46209706e-08 62: functype[38]=LJ_SR, c6= 1.15362558e-04, c12= 2.05320568e-08 62: functype[39]=LJ_SR, c6= 1.37763538e-03, c12= 1.00429619e-06 62: functype[40]=LJ_SR, c6= 4.04775915e-03, c12= 7.32754594e-06 62: functype[41]=LJ_SR, c6= 0.00000000e+00, c12= 0.00000000e+00 62: functype[42]=LJ_SR, c6= 3.15004110e-03, c12= 7.12219987e-06 62: functype[43]=LJ_SR, c6= 7.73964023e-04, c12= 6.37726703e-07 62: functype[44]=LJ_SR, c6= 4.88684509e-03, c12= 1.35898974e-05 62: functype[45]=LJ_SR, c6= 3.39879445e-03, c12= 4.64829665e-06 62: functype[46]=LJ_SR, c6= 3.38512102e-03, c12= 7.98643684e-06 62: functype[47]=LJ_SR, c6= 7.02015733e-04, c12= 5.24670621e-07 62: functype[48]=LJ_SR, c6= 7.28404594e-04, c12= 4.37536244e-07 62: functype[49]=LJ_SR, c6= 8.69845432e-03, c12= 2.14014596e-05 62: functype[50]=LJ_SR, c6= 2.81521126e-03, c12= 2.50631820e-06 62: functype[51]=LJ_SR, c6= 0.00000000e+00, c12= 0.00000000e+00 62: functype[52]=LJ_SR, c6= 2.19084952e-03, c12= 2.43608151e-06 62: functype[53]=LJ_SR, c6= 5.38290978e-04, c12= 2.18128423e-07 62: functype[54]=LJ_SR, c6= 3.39879445e-03, c12= 4.64829665e-06 62: functype[55]=LJ_SR, c6= 2.36385715e-03, c12= 1.58990617e-06 62: functype[56]=LJ_SR, c6= 2.35434729e-03, c12= 2.73168564e-06 62: functype[57]=LJ_SR, c6= 4.88251036e-04, c12= 1.79458653e-07 62: functype[58]=LJ_SR, c6= 5.06604455e-04, c12= 1.49655159e-07 62: functype[59]=LJ_SR, c6= 6.04976375e-03, c12= 7.32016804e-06 62: functype[60]=LJ_SR, c6= 2.80388560e-03, c12= 4.30621225e-06 62: functype[61]=LJ_SR, c6= 0.00000000e+00, c12= 0.00000000e+00 62: functype[62]=LJ_SR, c6= 2.18203568e-03, c12= 4.18553559e-06 62: functype[63]=LJ_SR, c6= 5.36125420e-04, c12= 3.74775753e-07 62: functype[64]=LJ_SR, c6= 3.38512102e-03, c12= 7.98643684e-06 62: functype[65]=LJ_SR, c6= 2.35434729e-03, c12= 2.73168564e-06 62: functype[66]=LJ_SR, c6= 2.34487570e-03, c12= 4.69342567e-06 62: functype[67]=LJ_SR, c6= 4.86286790e-04, c12= 3.08335570e-07 62: functype[68]=LJ_SR, c6= 5.04566372e-04, c12= 2.57128914e-07 62: functype[69]=LJ_SR, c6= 6.02542540e-03, c12= 1.25770931e-05 62: functype[70]=LJ_SR, c6= 5.81477529e-04, c12= 2.82897505e-07 62: functype[71]=LJ_SR, c6= 0.00000000e+00, c12= 0.00000000e+00 62: functype[72]=LJ_SR, c6= 4.52516577e-04, c12= 2.74969627e-07 62: functype[73]=LJ_SR, c6= 1.11183168e-04, c12= 2.46209706e-08 62: functype[74]=LJ_SR, c6= 7.02015733e-04, c12= 5.24670621e-07 62: functype[75]=LJ_SR, c6= 4.88251036e-04, c12= 1.79458653e-07 62: functype[76]=LJ_SR, c6= 4.86286790e-04, c12= 3.08335570e-07 62: functype[77]=LJ_SR, c6= 1.00847496e-04, c12= 2.02561691e-08 62: functype[78]=LJ_SR, c6= 1.04638366e-04, c12= 1.68921372e-08 62: functype[79]=LJ_SR, c6= 1.24956934e-03, c12= 8.26254733e-07 62: functype[80]=LJ_SR, c6= 6.03335344e-04, c12= 2.35915461e-07 62: functype[81]=LJ_SR, c6= 0.00000000e+00, c12= 0.00000000e+00 62: functype[82]=LJ_SR, c6= 4.69526733e-04, c12= 2.29304201e-07 62: functype[83]=LJ_SR, c6= 1.15362558e-04, c12= 2.05320568e-08 62: functype[84]=LJ_SR, c6= 7.28404594e-04, c12= 4.37536244e-07 62: functype[85]=LJ_SR, c6= 5.06604455e-04, c12= 1.49655159e-07 62: functype[86]=LJ_SR, c6= 5.04566372e-04, c12= 2.57128914e-07 62: functype[87]=LJ_SR, c6= 1.04638366e-04, c12= 1.68921372e-08 62: functype[88]=LJ_SR, c6= 1.08571736e-04, c12= 1.40867851e-08 62: functype[89]=LJ_SR, c6= 1.29654081e-03, c12= 6.89034944e-07 62: functype[90]=LJ_SR, c6= 7.20490366e-03, c12= 1.15394674e-05 62: functype[91]=LJ_SR, c6= 0.00000000e+00, c12= 0.00000000e+00 62: functype[92]=LJ_SR, c6= 5.60698940e-03, c12= 1.12160870e-05 62: functype[93]=LJ_SR, c6= 1.37763538e-03, c12= 1.00429619e-06 62: functype[94]=LJ_SR, c6= 8.69845432e-03, c12= 2.14014596e-05 62: functype[95]=LJ_SR, c6= 6.04976375e-03, c12= 7.32016804e-06 62: functype[96]=LJ_SR, c6= 6.02542540e-03, c12= 1.25770931e-05 62: functype[97]=LJ_SR, c6= 1.24956934e-03, c12= 8.26254733e-07 62: functype[98]=LJ_SR, c6= 1.29654081e-03, c12= 6.89034944e-07 62: functype[99]=LJ_SR, c6= 1.54830174e-02, c12= 3.37031588e-05 62: functype[100]=BONDS, b0A= 1.01000e-01, cbA= 3.63171e+05, b0B= 1.01000e-01, cbB= 3.63171e+05 62: functype[101]=BONDS, b0A= 1.47100e-01, cbA= 3.07106e+05, b0B= 1.47100e-01, cbB= 3.07106e+05 62: functype[102]=BONDS, b0A= 1.09000e-01, cbA= 2.84512e+05, b0B= 1.09000e-01, cbB= 2.84512e+05 62: functype[103]=BONDS, b0A= 1.52900e-01, cbA= 2.24262e+05, b0B= 1.52900e-01, cbB= 2.24262e+05 62: functype[104]=BONDS, b0A= 1.52200e-01, cbA= 2.65266e+05, b0B= 1.52200e-01, cbB= 2.65266e+05 62: functype[105]=BONDS, b0A= 1.22900e-01, cbA= 4.76976e+05, b0B= 1.22900e-01, cbB= 4.76976e+05 62: functype[106]=BONDS, b0A= 1.33500e-01, cbA= 4.10032e+05, b0B= 1.33500e-01, cbB= 4.10032e+05 62: functype[107]=BONDS, b0A= 1.44900e-01, cbA= 2.82002e+05, b0B= 1.44900e-01, cbB= 2.82002e+05 62: functype[108]=BONDS, b0A= 1.51000e-01, cbA= 2.65266e+05, b0B= 1.51000e-01, cbB= 2.65266e+05 62: functype[109]=BONDS, b0A= 1.40000e-01, cbA= 3.92459e+05, b0B= 1.40000e-01, cbB= 3.92459e+05 62: functype[110]=BONDS, b0A= 1.08000e-01, cbA= 3.07106e+05, b0B= 1.08000e-01, cbB= 3.07106e+05 62: functype[111]=BONDS, b0A= 1.46300e-01, cbA= 2.82002e+05, b0B= 1.46300e-01, cbB= 2.82002e+05 62: functype[112]=BONDS, b0A= 1.34000e-01, cbA= 4.02501e+05, b0B= 1.34000e-01, cbB= 4.02501e+05 62: functype[113]=BONDS, b0A= 1.81000e-01, cbA= 1.85770e+05, b0B= 1.81000e-01, cbB= 1.85770e+05 62: functype[114]=BONDS, b0A= 1.33600e-01, cbA= 2.29283e+05, b0B= 1.33600e-01, cbB= 2.29283e+05 62: functype[115]=BONDS, b0A= 1.25000e-01, cbA= 5.48941e+05, b0B= 1.25000e-01, cbB= 5.48941e+05 62: functype[116]=ANGLES, thA= 1.09500e+02, ctA= 2.92880e+02, thB= 1.09500e+02, ctB= 2.92880e+02 62: functype[117]=ANGLES, thA= 1.11200e+02, ctA= 6.69440e+02, thB= 1.11200e+02, ctB= 6.69440e+02 62: functype[118]=ANGLES, thA= 1.10700e+02, ctA= 3.13800e+02, thB= 1.10700e+02, ctB= 3.13800e+02 62: functype[119]=ANGLES, thA= 1.11100e+02, ctA= 5.27184e+02, thB= 1.11100e+02, ctB= 5.27184e+02 62: functype[120]=ANGLES, thA= 1.12700e+02, ctA= 4.88273e+02, thB= 1.12700e+02, ctB= 4.88273e+02 62: functype[121]=ANGLES, thA= 1.07800e+02, ctA= 2.76144e+02, thB= 1.07800e+02, ctB= 2.76144e+02 62: functype[122]=ANGLES, thA= 1.20400e+02, ctA= 6.69440e+02, thB= 1.20400e+02, ctB= 6.69440e+02 62: functype[123]=ANGLES, thA= 1.16600e+02, ctA= 5.85760e+02, thB= 1.16600e+02, ctB= 5.85760e+02 62: functype[124]=ANGLES, thA= 1.22900e+02, ctA= 6.69440e+02, thB= 1.22900e+02, ctB= 6.69440e+02 62: functype[125]=ANGLES, thA= 1.19800e+02, ctA= 2.92880e+02, thB= 1.19800e+02, ctB= 2.92880e+02 62: functype[126]=ANGLES, thA= 1.21900e+02, ctA= 4.18400e+02, thB= 1.21900e+02, ctB= 4.18400e+02 62: functype[127]=ANGLES, thA= 1.18400e+02, ctA= 3.17984e+02, thB= 1.18400e+02, ctB= 3.17984e+02 62: functype[128]=ANGLES, thA= 1.09700e+02, ctA= 6.69440e+02, thB= 1.09700e+02, ctB= 6.69440e+02 62: functype[129]=ANGLES, thA= 1.10100e+02, ctA= 5.27184e+02, thB= 1.10100e+02, ctB= 5.27184e+02 62: functype[130]=ANGLES, thA= 1.14000e+02, ctA= 5.27184e+02, thB= 1.14000e+02, ctB= 5.27184e+02 62: functype[131]=ANGLES, thA= 1.20000e+02, ctA= 5.85760e+02, thB= 1.20000e+02, ctB= 5.85760e+02 62: functype[132]=ANGLES, thA= 1.20000e+02, ctA= 5.27184e+02, thB= 1.20000e+02, ctB= 5.27184e+02 62: functype[133]=ANGLES, thA= 1.20000e+02, ctA= 2.92880e+02, thB= 1.20000e+02, ctB= 2.92880e+02 62: functype[134]=ANGLES, thA= 1.18400e+02, ctA= 2.92880e+02, thB= 1.18400e+02, ctB= 2.92880e+02 62: functype[135]=ANGLES, thA= 1.23200e+02, ctA= 4.18400e+02, thB= 1.23200e+02, ctB= 4.18400e+02 62: functype[136]=ANGLES, thA= 1.08600e+02, ctA= 4.18400e+02, thB= 1.08600e+02, ctB= 4.18400e+02 62: functype[137]=ANGLES, thA= 9.60000e+01, ctA= 3.68192e+02, thB= 9.60000e+01, ctB= 3.68192e+02 62: functype[138]=ANGLES, thA= 1.17000e+02, ctA= 5.85760e+02, thB= 1.17000e+02, ctB= 5.85760e+02 62: functype[139]=ANGLES, thA= 1.26000e+02, ctA= 6.69440e+02, thB= 1.26000e+02, ctB= 6.69440e+02 62: functype[140]=PDIHS, phiA= 1.80000000e+02, cpA= 4.39320000e+01, phiB= 1.80000000e+02, cpB= 4.39320000e+01, mult=2 62: functype[141]=PDIHS, phiA= 1.80000000e+02, cpA= 4.18400000e+00, phiB= 1.80000000e+02, cpB= 4.18400000e+00, mult=2 62: functype[142]=PDIHS, phiA= 1.80000000e+02, cpA= 4.60240000e+00, phiB= 1.80000000e+02, cpB= 4.60240000e+00, mult=2 62: functype[143]=RBDIHS, rbcA[0]= 5.46010000e-01, rbcA[1]= 1.63803000e+00, rbcA[2]= 0.00000000e+00, rbcA[3]=-2.18405000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 62: rbcB[0]= 5.46010000e-01, rbcB[1]= 1.63803000e+00, rbcB[2]= 0.00000000e+00, rbcB[3]=-2.18405000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 62: functype[144]=RBDIHS, rbcA[0]= 7.25920000e-01, rbcA[1]= 2.17777000e+00, rbcA[2]= 0.00000000e+00, rbcA[3]=-2.90370000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 62: rbcB[0]= 7.25920000e-01, rbcB[1]= 2.17777000e+00, rbcB[2]= 0.00000000e+00, rbcB[3]=-2.90370000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 62: functype[145]=RBDIHS, rbcA[0]= 1.27612000e+00, rbcA[1]= 1.16734000e+00, rbcA[2]= 8.95380000e-01, rbcA[3]=-3.33884000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 62: rbcB[0]= 1.27612000e+00, rbcB[1]= 1.16734000e+00, rbcB[2]= 8.95380000e-01, rbcB[3]=-3.33884000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 62: functype[146]=RBDIHS, rbcA[0]=-6.91824000e+00, rbcA[1]= 4.67562000e+00, rbcA[2]= 2.24262000e+00, rbcA[3]= 0.00000000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 62: rbcB[0]=-6.91824000e+00, rbcB[1]= 4.67562000e+00, rbcB[2]= 2.24262000e+00, rbcB[3]= 0.00000000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 62: functype[147]=RBDIHS, rbcA[0]= 9.70690000e-01, rbcA[1]= 2.91206000e+00, rbcA[2]= 0.00000000e+00, rbcA[3]=-3.88275000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 62: rbcB[0]= 9.70690000e-01, rbcB[1]= 2.91206000e+00, rbcB[2]= 0.00000000e+00, rbcB[3]=-3.88275000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 62: functype[148]=RBDIHS, rbcA[0]= 6.27600000e-01, rbcA[1]= 1.88280000e+00, rbcA[2]= 0.00000000e+00, rbcA[3]=-2.51040000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 62: rbcB[0]= 6.27600000e-01, rbcB[1]= 1.88280000e+00, rbcB[2]= 0.00000000e+00, rbcB[3]=-2.51040000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 62: functype[149]=RBDIHS, rbcA[0]=-1.58990000e-01, rbcA[1]=-4.76980000e-01, rbcA[2]= 0.00000000e+00, rbcA[3]= 6.35960000e-01, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 62: rbcB[0]=-1.58990000e-01, rbcB[1]=-4.76980000e-01, rbcB[2]= 0.00000000e+00, rbcB[3]= 6.35960000e-01, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 62: functype[150]=RBDIHS, rbcA[0]= 1.03637600e+01, rbcA[1]=-6.60654000e+00, rbcA[2]=-1.04934700e+01, rbcA[3]= 6.73624000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 62: rbcB[0]= 1.03637600e+01, rbcB[1]=-6.60654000e+00, rbcB[2]=-1.04934700e+01, rbcB[3]= 6.73624000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 62: functype[151]=RBDIHS, rbcA[0]= 5.00825000e+00, rbcA[1]=-1.69870000e+00, rbcA[2]=-3.72380000e-01, rbcA[3]=-2.93716000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 62: rbcB[0]= 5.00825000e+00, rbcB[1]=-1.69870000e+00, rbcB[2]=-3.72380000e-01, rbcB[3]=-2.93716000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 62: functype[152]=RBDIHS, rbcA[0]= 2.92880000e+00, rbcA[1]=-1.46440000e+00, rbcA[2]= 2.09200000e-01, rbcA[3]=-1.67360000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 62: rbcB[0]= 2.92880000e+00, rbcB[1]=-1.46440000e+00, rbcB[2]= 2.09200000e-01, rbcB[3]=-1.67360000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 62: functype[153]=RBDIHS, rbcA[0]= 5.77183000e+00, rbcA[1]=-2.67148000e+00, rbcA[2]= 9.58140000e-01, rbcA[3]=-4.05848000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 62: rbcB[0]= 5.77183000e+00, rbcB[1]=-2.67148000e+00, rbcB[2]= 9.58140000e-01, rbcB[3]=-4.05848000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 62: functype[154]=RBDIHS, rbcA[0]= 8.03330000e-01, rbcA[1]= 2.40999000e+00, rbcA[2]= 0.00000000e+00, rbcA[3]=-3.21331000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 62: rbcB[0]= 8.03330000e-01, rbcB[1]= 2.40999000e+00, rbcB[2]= 0.00000000e+00, rbcB[3]=-3.21331000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 62: functype[155]=RBDIHS, rbcA[0]= 2.05016000e+01, rbcA[1]= 0.00000000e+00, rbcA[2]=-2.05016000e+01, rbcA[3]= 0.00000000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 62: rbcB[0]= 2.05016000e+01, rbcB[1]= 0.00000000e+00, rbcB[2]=-2.05016000e+01, rbcB[3]= 0.00000000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 62: functype[156]=RBDIHS, rbcA[0]= 3.02879800e+01, rbcA[1]=-4.81160000e+00, rbcA[2]=-2.54763800e+01, rbcA[3]= 0.00000000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 62: rbcB[0]= 3.02879800e+01, rbcB[1]=-4.81160000e+00, rbcB[2]=-2.54763800e+01, rbcB[3]= 0.00000000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 62: functype[157]=RBDIHS, rbcA[0]= 2.54763800e+01, rbcA[1]= 0.00000000e+00, rbcA[2]=-2.54763800e+01, rbcA[3]= 0.00000000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 62: rbcB[0]= 2.54763800e+01, rbcB[1]= 0.00000000e+00, rbcB[2]=-2.54763800e+01, rbcB[3]= 0.00000000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 62: functype[158]=RBDIHS, rbcA[0]= 1.57025500e+01, rbcA[1]= 3.17565600e+01, rbcA[2]=-3.66936000e+00, rbcA[3]=-4.37897500e+01, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 62: rbcB[0]= 1.57025500e+01, rbcB[1]= 3.17565600e+01, rbcB[2]=-3.66936000e+00, rbcB[3]=-4.37897500e+01, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 62: functype[159]=RBDIHS, rbcA[0]=-1.03574900e+01, rbcA[1]=-2.95871600e+01, rbcA[2]=-1.16734000e+00, rbcA[3]= 4.11119900e+01, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 62: rbcB[0]=-1.03574900e+01, rbcB[1]=-2.95871600e+01, rbcB[2]=-1.16734000e+00, rbcB[3]= 4.11119900e+01, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 62: functype[160]=RBDIHS, rbcA[0]= 4.50199000e+00, rbcA[1]= 7.82410000e-01, rbcA[2]=-1.60247000e+00, rbcA[3]=-3.68192000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 62: rbcB[0]= 4.50199000e+00, rbcB[1]= 7.82410000e-01, rbcB[2]=-1.60247000e+00, rbcB[3]=-3.68192000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 62: functype[161]=RBDIHS, rbcA[0]= 4.22590000e-01, rbcA[1]= 2.70705000e+00, rbcA[2]=-3.12964000e+00, rbcA[3]= 0.00000000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 62: rbcB[0]= 4.22590000e-01, rbcB[1]= 2.70705000e+00, rbcB[2]=-3.12964000e+00, rbcB[3]= 0.00000000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 62: functype[162]=RBDIHS, rbcA[0]=-7.65670000e-01, rbcA[1]= 2.70705000e+00, rbcA[2]= 4.02501000e+00, rbcA[3]=-5.96639000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 62: rbcB[0]=-7.65670000e-01, rbcB[1]= 2.70705000e+00, rbcB[2]= 4.02501000e+00, rbcB[3]=-5.96639000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 62: functype[163]=RBDIHS, rbcA[0]= 9.66500000e-01, rbcA[1]= 2.89951000e+00, rbcA[2]= 0.00000000e+00, rbcA[3]=-3.86601000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 62: rbcB[0]= 9.66500000e-01, rbcB[1]= 2.89951000e+00, rbcB[2]= 0.00000000e+00, rbcB[3]=-3.86601000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 62: functype[164]=RBDIHS, rbcA[0]=-4.23421000e+00, rbcA[1]= 7.22159000e+00, rbcA[2]= 1.90790000e+00, rbcA[3]=-4.89528000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 62: rbcB[0]=-4.23421000e+00, rbcB[1]= 7.22159000e+00, rbcB[2]= 1.90790000e+00, rbcB[3]=-4.89528000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 62: functype[165]=RBDIHS, rbcA[0]= 3.03340000e+01, rbcA[1]= 0.00000000e+00, rbcA[2]=-3.03340000e+01, rbcA[3]= 0.00000000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 62: rbcB[0]= 3.03340000e+01, rbcB[1]= 0.00000000e+00, rbcB[2]=-3.03340000e+01, rbcB[3]= 0.00000000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 62: functype[166]=RBDIHS, rbcA[0]= 1.02319700e+01, rbcA[1]= 3.52083000e+00, rbcA[2]=-3.97899000e+00, rbcA[3]=-9.77382000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 62: rbcB[0]= 1.02319700e+01, rbcB[1]= 3.52083000e+00, rbcB[2]=-3.97899000e+00, rbcB[3]=-9.77382000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 62: functype[167]=RBDIHS, rbcA[0]= 5.49778000e+00, rbcA[1]= 1.41838000e+00, rbcA[2]=-6.91615000e+00, rbcA[3]= 0.00000000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 62: rbcB[0]= 5.49778000e+00, rbcB[1]= 1.41838000e+00, rbcB[2]=-6.91615000e+00, rbcB[3]= 0.00000000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 62: functype[168]=RBDIHS, rbcA[0]=-1.21755000e+00, rbcA[1]=-3.65264000e+00, rbcA[2]= 0.00000000e+00, rbcA[3]= 4.87018000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 62: rbcB[0]=-1.21755000e+00, rbcB[1]=-3.65264000e+00, rbcB[2]= 0.00000000e+00, rbcB[3]= 4.87018000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 62: functype[169]=RBDIHS, rbcA[0]=-1.26775000e+00, rbcA[1]= 3.02085000e+00, rbcA[2]= 1.74473000e+00, rbcA[3]=-3.49782000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 62: rbcB[0]=-1.26775000e+00, rbcB[1]= 3.02085000e+00, rbcB[2]= 1.74473000e+00, rbcB[3]=-3.49782000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 62: functype[170]=RBDIHS, rbcA[0]= 3.80117000e+00, rbcA[1]=-6.95172000e+00, rbcA[2]=-1.01671000e+00, rbcA[3]= 4.16726000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 62: rbcB[0]= 3.80117000e+00, rbcB[1]=-6.95172000e+00, rbcB[2]=-1.01671000e+00, rbcB[3]= 4.16726000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 62: functype[171]=RBDIHS, rbcA[0]= 3.70280000e-01, rbcA[1]= 1.11086000e+00, rbcA[2]= 0.00000000e+00, rbcA[3]=-1.48114000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 62: rbcB[0]= 3.70280000e-01, rbcB[1]= 1.11086000e+00, rbcB[2]= 0.00000000e+00, rbcB[3]=-1.48114000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 62: functype[172]=RBDIHS, rbcA[0]= 3.32042200e+01, rbcA[1]= 0.00000000e+00, rbcA[2]=-3.32042200e+01, rbcA[3]= 0.00000000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 62: rbcB[0]= 3.32042200e+01, rbcB[1]= 0.00000000e+00, rbcB[2]=-3.32042200e+01, rbcB[3]= 0.00000000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 62: functype[173]=RBDIHS, rbcA[0]= 1.63176000e+01, rbcA[1]= 0.00000000e+00, rbcA[2]=-1.63176000e+01, rbcA[3]= 0.00000000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 62: rbcB[0]= 1.63176000e+01, rbcB[1]= 0.00000000e+00, rbcB[2]=-1.63176000e+01, rbcB[3]= 0.00000000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 62: functype[174]=RBDIHS, rbcA[0]= 3.40787000e+00, rbcA[1]=-2.80537000e+00, rbcA[2]=-3.59820000e-01, rbcA[3]=-2.42670000e-01, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 62: rbcB[0]= 3.40787000e+00, rbcB[1]=-2.80537000e+00, rbcB[2]=-3.59820000e-01, rbcB[3]=-2.42670000e-01, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 62: functype[175]=RBDIHS, rbcA[0]=-1.62590200e+01, rbcA[1]= 9.08765000e+00, rbcA[2]= 7.17138000e+00, rbcA[3]= 0.00000000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 62: rbcB[0]=-1.62590200e+01, rbcB[1]= 9.08765000e+00, rbcB[2]= 7.17138000e+00, rbcB[3]= 0.00000000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 62: functype[176]=RBDIHS, rbcA[0]= 9.45590000e-01, rbcA[1]= 2.83675000e+00, rbcA[2]= 0.00000000e+00, rbcA[3]=-3.78234000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 62: rbcB[0]= 9.45590000e-01, rbcB[1]= 2.83675000e+00, rbcB[2]= 0.00000000e+00, rbcB[3]=-3.78234000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 62: functype[177]=RBDIHS, rbcA[0]=-1.50624000e+00, rbcA[1]= 5.37225000e+00, rbcA[2]= 1.17989000e+00, rbcA[3]=-5.04590000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 62: rbcB[0]=-1.50624000e+00, rbcB[1]= 5.37225000e+00, rbcB[2]= 1.17989000e+00, rbcB[3]=-5.04590000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 62: functype[178]=RBDIHS, rbcA[0]= 1.00416000e+00, rbcA[1]= 3.01248000e+00, rbcA[2]= 0.00000000e+00, rbcA[3]=-4.01664000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 62: rbcB[0]= 1.00416000e+00, rbcB[1]= 3.01248000e+00, rbcB[2]= 0.00000000e+00, rbcB[3]=-4.01664000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 62: functype[179]=RBDIHS, rbcA[0]= 8.79268000e+00, rbcA[1]=-1.18344400e+01, rbcA[2]= 1.07529000e+00, rbcA[3]= 1.96648000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 62: rbcB[0]= 8.79268000e+00, rbcB[1]=-1.18344400e+01, rbcB[2]= 1.07529000e+00, rbcB[3]= 1.96648000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 62: functype[180]=RBDIHS, rbcA[0]=-5.77392000e+00, rbcA[1]= 3.38485000e+00, rbcA[2]= 2.38906000e+00, rbcA[3]= 0.00000000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 62: rbcB[0]=-5.77392000e+00, rbcB[1]= 3.38485000e+00, rbcB[2]= 2.38906000e+00, rbcB[3]= 0.00000000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 62: functype[181]=RBDIHS, rbcA[0]=-9.08346000e+00, rbcA[1]= 9.75709000e+00, rbcA[2]= 3.45180000e+00, rbcA[3]=-4.12542000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 62: rbcB[0]=-9.08346000e+00, rbcB[1]= 9.75709000e+00, rbcB[2]= 3.45180000e+00, rbcB[3]=-4.12542000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 62: functype[182]=RBDIHS, rbcA[0]=-4.70700000e-01, rbcA[1]=-1.41210000e+00, rbcA[2]= 0.00000000e+00, rbcA[3]= 1.88280000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 62: rbcB[0]=-4.70700000e-01, rbcB[1]=-1.41210000e+00, rbcB[2]= 0.00000000e+00, rbcB[3]= 1.88280000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 62: functype[183]=RBDIHS, rbcA[0]= 3.43088000e+00, rbcA[1]= 0.00000000e+00, rbcA[2]=-3.43088000e+00, rbcA[3]= 0.00000000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 62: rbcB[0]= 3.43088000e+00, rbcB[1]= 0.00000000e+00, rbcB[2]=-3.43088000e+00, rbcB[3]= 0.00000000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 62: functype[184]=RBDIHS, rbcA[0]= 2.57316000e+00, rbcA[1]= 3.49782000e+00, rbcA[2]=-1.10039000e+00, rbcA[3]=-4.97059000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 62: rbcB[0]= 2.57316000e+00, rbcB[1]= 3.49782000e+00, rbcB[2]=-1.10039000e+00, rbcB[3]=-4.97059000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 62: functype[185]=RBDIHS, rbcA[0]=-8.22160000e-01, rbcA[1]= 1.12759000e+00, rbcA[2]=-3.05440000e-01, rbcA[3]= 0.00000000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 62: rbcB[0]=-8.22160000e-01, rbcB[1]= 1.12759000e+00, rbcB[2]=-3.05440000e-01, rbcB[3]= 0.00000000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 62: functype[186]=LJ14, c6A= 3.20536041e-04, c12A= 1.71928145e-07, c6B= 3.20536041e-04, c12B= 1.71928145e-07 62: functype[187]=LJ14, c6A= 1.30458481e-03, c12A= 1.92011187e-06, c6B= 1.30458481e-03, c12B= 1.92011187e-06 62: functype[188]=LJ14, c6A= 1.40760563e-03, c12A= 1.25315910e-06, c6B= 1.40760563e-03, c12B= 1.25315910e-06 62: functype[189]=LJ14, c6A= 1.67637339e-03, c12A= 1.97547221e-06, c6B= 1.67637339e-03, c12B= 1.97547221e-06 62: functype[190]=LJ14, c6A= 0.00000000e+00, c12A= 0.00000000e+00, c6B= 0.00000000e+00, c12B= 0.00000000e+00 62: functype[191]=LJ14, c6A= 2.49447081e-04, c12A= 1.67110056e-07, c6B= 2.49447081e-04, c12B= 1.67110056e-07 62: functype[192]=LJ14, c6A= 1.01525205e-03, c12A= 1.86630294e-06, c6B= 1.01525205e-03, c12B= 1.86630294e-06 62: functype[193]=LJ14, c6A= 6.12890625e-05, c12A= 1.49631500e-08, c6B= 6.12890625e-05, c12B= 1.49631500e-08 62: functype[194]=LJ14, c6A= 2.69145489e-04, c12A= 1.09064212e-07, c6B= 2.69145489e-04, c12B= 1.09064212e-07 62: functype[195]=LJ14, c6A= 1.09542476e-03, c12A= 1.21804075e-06, c6B= 1.09542476e-03, c12B= 1.21804075e-06 62: functype[196]=LJ14, c6A= 3.86982011e-04, c12A= 3.18863352e-07, c6B= 3.86982011e-04, c12B= 3.18863352e-07 62: functype[197]=LJ14, c6A= 1.57502055e-03, c12A= 3.56109993e-06, c6B= 1.57502055e-03, c12B= 3.56109993e-06 62: functype[198]=LJ14, c6A= 2.44342255e-03, c12A= 6.79494872e-06, c6B= 2.44342255e-03, c12B= 6.79494872e-06 62: functype[199]=LJ14, c6A= 1.40194280e-03, c12A= 2.15310613e-06, c6B= 1.40194280e-03, c12B= 2.15310613e-06 62: functype[200]=LJ14, c6A= 1.09101784e-03, c12A= 2.09276780e-06, c6B= 1.09101784e-03, c12B= 2.09276780e-06 62: functype[201]=LJ14, c6A= 2.68062710e-04, c12A= 1.87387876e-07, c6B= 2.68062710e-04, c12B= 1.87387876e-07 62: functype[202]=LJ14, c6A= 2.26258289e-04, c12A= 1.37484813e-07, c6B= 2.26258289e-04, c12B= 1.37484813e-07 62: functype[203]=LJ14, c6A= 2.43143395e-04, c12A= 1.54167785e-07, c6B= 2.43143395e-04, c12B= 1.54167785e-07 62: functype[204]=LJ14, c6A= 1.17243785e-03, c12A= 2.34671283e-06, c6B= 1.17243785e-03, c12B= 2.34671283e-06 62: functype[205]=LJ14, c6A= 1.69256051e-03, c12A= 3.99321842e-06, c6B= 1.69256051e-03, c12B= 3.99321842e-06 62: functype[206]=LJ14, c6A= 5.04237478e-05, c12A= 1.01280845e-08, c6B= 5.04237478e-05, c12B= 1.01280845e-08 62: functype[207]=LJ14, c6A= 2.34763367e-04, c12A= 1.14652101e-07, c6B= 2.34763367e-04, c12B= 1.14652101e-07 62: functype[208]=LJ14, c6A= 5.76812790e-05, c12A= 1.02660284e-08, c6B= 5.76812790e-05, c12B= 1.02660284e-08 62: functype[209]=LJ14, c6A= 3.60245183e-03, c12A= 5.76973368e-06, c6B= 3.60245183e-03, c12B= 5.76973368e-06 62: functype[210]=LJ14, c6A= 6.88817690e-04, c12A= 5.02148096e-07, c6B= 6.88817690e-04, c12B= 5.02148096e-07 62: functype[211]=LJ14, c6A= 4.34922716e-03, c12A= 1.07007298e-05, c6B= 4.34922716e-03, c12B= 1.07007298e-05 62: reppow = 12 62: fudgeQQ = 0.5 62: cmap 62: moltype (0): 62: name="Protein_chain_B" 62: atoms: 62: atom (156): 62: atom[ 0]={type= 0, typeB= 0, ptype= Atom, m= 1.40027e+01, q=-3.00000e-01, mB= 1.40027e+01, qB=-3.00000e-01, resind= 0, atomnumber= 7} 62: atom[ 1]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 3.30000e-01, mB= 1.00800e+00, qB= 3.30000e-01, resind= 0, atomnumber= 1} 62: atom[ 2]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 3.30000e-01, mB= 1.00800e+00, qB= 3.30000e-01, resind= 0, atomnumber= 1} 62: atom[ 3]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 3.30000e-01, mB= 1.00800e+00, qB= 3.30000e-01, resind= 0, atomnumber= 1} 62: atom[ 4]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q= 2.50000e-01, mB= 1.20110e+01, qB= 2.50000e-01, resind= 0, atomnumber= 6} 62: atom[ 5]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 0, atomnumber= 1} 62: atom[ 6]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q=-1.20000e-01, mB= 1.20110e+01, qB=-1.20000e-01, resind= 0, atomnumber= 6} 62: atom[ 7]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 0, atomnumber= 1} 62: atom[ 8]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 0, atomnumber= 1} 62: atom[ 9]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q=-1.20000e-01, mB= 1.20110e+01, qB=-1.20000e-01, resind= 0, atomnumber= 6} 62: atom[ 10]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 0, atomnumber= 1} 62: atom[ 11]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 0, atomnumber= 1} 62: atom[ 12]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q=-1.20000e-01, mB= 1.20110e+01, qB=-1.20000e-01, resind= 0, atomnumber= 6} 62: atom[ 13]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 0, atomnumber= 1} 62: atom[ 14]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 0, atomnumber= 1} 62: atom[ 15]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q= 1.90000e-01, mB= 1.20110e+01, qB= 1.90000e-01, resind= 0, atomnumber= 6} 62: atom[ 16]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 0, atomnumber= 1} 62: atom[ 17]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 0, atomnumber= 1} 62: atom[ 18]={type= 0, typeB= 0, ptype= Atom, m= 1.40067e+01, q=-3.00000e-01, mB= 1.40067e+01, qB=-3.00000e-01, resind= 0, atomnumber= 7} 62: atom[ 19]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 3.30000e-01, mB= 1.00800e+00, qB= 3.30000e-01, resind= 0, atomnumber= 1} 62: atom[ 20]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 3.30000e-01, mB= 1.00800e+00, qB= 3.30000e-01, resind= 0, atomnumber= 1} 62: atom[ 21]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 3.30000e-01, mB= 1.00800e+00, qB= 3.30000e-01, resind= 0, atomnumber= 1} 62: atom[ 22]={type= 4, typeB= 4, ptype= Atom, m= 1.20110e+01, q= 5.00000e-01, mB= 1.20110e+01, qB= 5.00000e-01, resind= 0, atomnumber= 6} 62: atom[ 23]={type= 5, typeB= 5, ptype= Atom, m= 1.59994e+01, q=-5.00000e-01, mB= 1.59994e+01, qB=-5.00000e-01, resind= 0, atomnumber= 8} 62: atom[ 24]={type= 0, typeB= 0, ptype= Atom, m= 1.40067e+01, q=-5.00000e-01, mB= 1.40067e+01, qB=-5.00000e-01, resind= 1, atomnumber= 7} 62: atom[ 25]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 3.00000e-01, mB= 1.00800e+00, qB= 3.00000e-01, resind= 1, atomnumber= 1} 62: atom[ 26]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q= 1.40000e-01, mB= 1.20110e+01, qB= 1.40000e-01, resind= 1, atomnumber= 6} 62: atom[ 27]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 1, atomnumber= 1} 62: atom[ 28]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q=-6.00000e-02, mB= 1.20110e+01, qB=-6.00000e-02, resind= 1, atomnumber= 6} 62: atom[ 29]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 1, atomnumber= 1} 62: atom[ 30]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q=-1.80000e-01, mB= 1.20110e+01, qB=-1.80000e-01, resind= 1, atomnumber= 6} 62: atom[ 31]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 1, atomnumber= 1} 62: atom[ 32]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 1, atomnumber= 1} 62: atom[ 33]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 1, atomnumber= 1} 62: atom[ 34]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q=-1.80000e-01, mB= 1.20110e+01, qB=-1.80000e-01, resind= 1, atomnumber= 6} 62: atom[ 35]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 1, atomnumber= 1} 62: atom[ 36]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 1, atomnumber= 1} 62: atom[ 37]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 1, atomnumber= 1} 62: atom[ 38]={type= 4, typeB= 4, ptype= Atom, m= 1.20110e+01, q= 5.00000e-01, mB= 1.20110e+01, qB= 5.00000e-01, resind= 1, atomnumber= 6} 62: atom[ 39]={type= 5, typeB= 5, ptype= Atom, m= 1.59994e+01, q=-5.00000e-01, mB= 1.59994e+01, qB=-5.00000e-01, resind= 1, atomnumber= 8} 62: atom[ 40]={type= 0, typeB= 0, ptype= Atom, m= 1.40067e+01, q=-5.00000e-01, mB= 1.40067e+01, qB=-5.00000e-01, resind= 2, atomnumber= 7} 62: atom[ 41]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 3.00000e-01, mB= 1.00800e+00, qB= 3.00000e-01, resind= 2, atomnumber= 1} 62: atom[ 42]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q= 1.40000e-01, mB= 1.20110e+01, qB= 1.40000e-01, resind= 2, atomnumber= 6} 62: atom[ 43]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 2, atomnumber= 1} 62: atom[ 44]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q=-5.00000e-03, mB= 1.20110e+01, qB=-5.00000e-03, resind= 2, atomnumber= 6} 62: atom[ 45]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 2, atomnumber= 1} 62: atom[ 46]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 2, atomnumber= 1} 62: atom[ 47]={type= 6, typeB= 6, ptype= Atom, m= 1.20110e+01, q=-1.15000e-01, mB= 1.20110e+01, qB=-1.15000e-01, resind= 2, atomnumber= 6} 62: atom[ 48]={type= 6, typeB= 6, ptype= Atom, m= 1.20110e+01, q=-1.15000e-01, mB= 1.20110e+01, qB=-1.15000e-01, resind= 2, atomnumber= 6} 62: atom[ 49]={type= 7, typeB= 7, ptype= Atom, m= 1.00800e+00, q= 1.15000e-01, mB= 1.00800e+00, qB= 1.15000e-01, resind= 2, atomnumber= 1} 62: atom[ 50]={type= 6, typeB= 6, ptype= Atom, m= 1.20110e+01, q=-1.15000e-01, mB= 1.20110e+01, qB=-1.15000e-01, resind= 2, atomnumber= 6} 62: atom[ 51]={type= 7, typeB= 7, ptype= Atom, m= 1.00800e+00, q= 1.15000e-01, mB= 1.00800e+00, qB= 1.15000e-01, resind= 2, atomnumber= 1} 62: atom[ 52]={type= 6, typeB= 6, ptype= Atom, m= 1.20110e+01, q=-1.15000e-01, mB= 1.20110e+01, qB=-1.15000e-01, resind= 2, atomnumber= 6} 62: atom[ 53]={type= 7, typeB= 7, ptype= Atom, m= 1.00800e+00, q= 1.15000e-01, mB= 1.00800e+00, qB= 1.15000e-01, resind= 2, atomnumber= 1} 62: atom[ 54]={type= 6, typeB= 6, ptype= Atom, m= 1.20110e+01, q=-1.15000e-01, mB= 1.20110e+01, qB=-1.15000e-01, resind= 2, atomnumber= 6} 62: atom[ 55]={type= 7, typeB= 7, ptype= Atom, m= 1.00800e+00, q= 1.15000e-01, mB= 1.00800e+00, qB= 1.15000e-01, resind= 2, atomnumber= 1} 62: atom[ 56]={type= 6, typeB= 6, ptype= Atom, m= 1.20110e+01, q=-1.15000e-01, mB= 1.20110e+01, qB=-1.15000e-01, resind= 2, atomnumber= 6} 62: atom[ 57]={type= 7, typeB= 7, ptype= Atom, m= 1.00800e+00, q= 1.15000e-01, mB= 1.00800e+00, qB= 1.15000e-01, resind= 2, atomnumber= 1} 62: atom[ 58]={type= 4, typeB= 4, ptype= Atom, m= 1.20110e+01, q= 5.00000e-01, mB= 1.20110e+01, qB= 5.00000e-01, resind= 2, atomnumber= 6} 62: atom[ 59]={type= 5, typeB= 5, ptype= Atom, m= 1.59994e+01, q=-5.00000e-01, mB= 1.59994e+01, qB=-5.00000e-01, resind= 2, atomnumber= 8} 62: atom[ 60]={type= 0, typeB= 0, ptype= Atom, m= 1.40067e+01, q=-5.00000e-01, mB= 1.40067e+01, qB=-5.00000e-01, resind= 3, atomnumber= 7} 62: atom[ 61]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 3.00000e-01, mB= 1.00800e+00, qB= 3.00000e-01, resind= 3, atomnumber= 1} 62: atom[ 62]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q= 8.00000e-02, mB= 1.20110e+01, qB= 8.00000e-02, resind= 3, atomnumber= 6} 62: atom[ 63]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 3, atomnumber= 1} 62: atom[ 64]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 3, atomnumber= 1} 62: atom[ 65]={type= 4, typeB= 4, ptype= Atom, m= 1.20110e+01, q= 5.00000e-01, mB= 1.20110e+01, qB= 5.00000e-01, resind= 3, atomnumber= 6} 62: atom[ 66]={type= 5, typeB= 5, ptype= Atom, m= 1.59994e+01, q=-5.00000e-01, mB= 1.59994e+01, qB=-5.00000e-01, resind= 3, atomnumber= 8} 62: atom[ 67]={type= 0, typeB= 0, ptype= Atom, m= 1.40067e+01, q=-5.00000e-01, mB= 1.40067e+01, qB=-5.00000e-01, resind= 4, atomnumber= 7} 62: atom[ 68]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 3.00000e-01, mB= 1.00800e+00, qB= 3.00000e-01, resind= 4, atomnumber= 1} 62: atom[ 69]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q= 1.40000e-01, mB= 1.20110e+01, qB= 1.40000e-01, resind= 4, atomnumber= 6} 62: atom[ 70]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 4, atomnumber= 1} 62: atom[ 71]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q=-1.20000e-01, mB= 1.20110e+01, qB=-1.20000e-01, resind= 4, atomnumber= 6} 62: atom[ 72]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 4, atomnumber= 1} 62: atom[ 73]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 4, atomnumber= 1} 62: atom[ 74]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q=-5.00000e-02, mB= 1.20110e+01, qB=-5.00000e-02, resind= 4, atomnumber= 6} 62: atom[ 75]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 4, atomnumber= 1} 62: atom[ 76]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 4, atomnumber= 1} 62: atom[ 77]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q= 1.90000e-01, mB= 1.20110e+01, qB= 1.90000e-01, resind= 4, atomnumber= 6} 62: atom[ 78]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 4, atomnumber= 1} 62: atom[ 79]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 4, atomnumber= 1} 62: atom[ 80]={type= 0, typeB= 0, ptype= Atom, m= 1.40067e+01, q=-7.00000e-01, mB= 1.40067e+01, qB=-7.00000e-01, resind= 4, atomnumber= 7} 62: atom[ 81]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 4.40000e-01, mB= 1.00800e+00, qB= 4.40000e-01, resind= 4, atomnumber= 1} 62: atom[ 82]={type= 8, typeB= 8, ptype= Atom, m= 1.20110e+01, q= 6.40000e-01, mB= 1.20110e+01, qB= 6.40000e-01, resind= 4, atomnumber= 6} 62: atom[ 83]={type= 0, typeB= 0, ptype= Atom, m= 1.40067e+01, q=-8.00000e-01, mB= 1.40067e+01, qB=-8.00000e-01, resind= 4, atomnumber= 7} 62: atom[ 84]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 4.60000e-01, mB= 1.00800e+00, qB= 4.60000e-01, resind= 4, atomnumber= 1} 62: atom[ 85]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 4.60000e-01, mB= 1.00800e+00, qB= 4.60000e-01, resind= 4, atomnumber= 1} 62: atom[ 86]={type= 0, typeB= 0, ptype= Atom, m= 1.40067e+01, q=-8.00000e-01, mB= 1.40067e+01, qB=-8.00000e-01, resind= 4, atomnumber= 7} 62: atom[ 87]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 4.60000e-01, mB= 1.00800e+00, qB= 4.60000e-01, resind= 4, atomnumber= 1} 62: atom[ 88]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 4.60000e-01, mB= 1.00800e+00, qB= 4.60000e-01, resind= 4, atomnumber= 1} 62: atom[ 89]={type= 4, typeB= 4, ptype= Atom, m= 1.20110e+01, q= 5.00000e-01, mB= 1.20110e+01, qB= 5.00000e-01, resind= 4, atomnumber= 6} 62: atom[ 90]={type= 5, typeB= 5, ptype= Atom, m= 1.59994e+01, q=-5.00000e-01, mB= 1.59994e+01, qB=-5.00000e-01, resind= 4, atomnumber= 8} 62: atom[ 91]={type= 0, typeB= 0, ptype= Atom, m= 1.40067e+01, q=-5.00000e-01, mB= 1.40067e+01, qB=-5.00000e-01, resind= 5, atomnumber= 7} 62: atom[ 92]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 3.00000e-01, mB= 1.00800e+00, qB= 3.00000e-01, resind= 5, atomnumber= 1} 62: atom[ 93]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q= 1.40000e-01, mB= 1.20110e+01, qB= 1.40000e-01, resind= 5, atomnumber= 6} 62: atom[ 94]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 5, atomnumber= 1} 62: atom[ 95]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q= 6.00000e-02, mB= 1.20110e+01, qB= 6.00000e-02, resind= 5, atomnumber= 6} 62: atom[ 96]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 5, atomnumber= 1} 62: atom[ 97]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 5, atomnumber= 1} 62: atom[ 98]={type= 9, typeB= 9, ptype= Atom, m= 3.20600e+01, q=-3.35000e-01, mB= 3.20600e+01, qB=-3.35000e-01, resind= 5, atomnumber= 16} 62: atom[ 99]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 1.55000e-01, mB= 1.00800e+00, qB= 1.55000e-01, resind= 5, atomnumber= 1} 62: atom[ 100]={type= 4, typeB= 4, ptype= Atom, m= 1.20110e+01, q= 5.00000e-01, mB= 1.20110e+01, qB= 5.00000e-01, resind= 5, atomnumber= 6} 62: atom[ 101]={type= 5, typeB= 5, ptype= Atom, m= 1.59994e+01, q=-5.00000e-01, mB= 1.59994e+01, qB=-5.00000e-01, resind= 5, atomnumber= 8} 62: atom[ 102]={type= 0, typeB= 0, ptype= Atom, m= 1.40067e+01, q=-5.00000e-01, mB= 1.40067e+01, qB=-5.00000e-01, resind= 6, atomnumber= 7} 62: atom[ 103]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 3.00000e-01, mB= 1.00800e+00, qB= 3.00000e-01, resind= 6, atomnumber= 1} 62: atom[ 104]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q= 1.40000e-01, mB= 1.20110e+01, qB= 1.40000e-01, resind= 6, atomnumber= 6} 62: atom[ 105]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 6, atomnumber= 1} 62: atom[ 106]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q=-1.20000e-01, mB= 1.20110e+01, qB=-1.20000e-01, resind= 6, atomnumber= 6} 62: atom[ 107]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 6, atomnumber= 1} 62: atom[ 108]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 6, atomnumber= 1} 62: atom[ 109]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q=-2.20000e-01, mB= 1.20110e+01, qB=-2.20000e-01, resind= 6, atomnumber= 6} 62: atom[ 110]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 6, atomnumber= 1} 62: atom[ 111]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 6, atomnumber= 1} 62: atom[ 112]={type= 4, typeB= 4, ptype= Atom, m= 1.20110e+01, q= 7.00000e-01, mB= 1.20110e+01, qB= 7.00000e-01, resind= 6, atomnumber= 6} 62: atom[ 113]={type= 5, typeB= 5, ptype= Atom, m= 1.59994e+01, q=-8.00000e-01, mB= 1.59994e+01, qB=-8.00000e-01, resind= 6, atomnumber= 8} 62: atom[ 114]={type= 5, typeB= 5, ptype= Atom, m= 1.59994e+01, q=-8.00000e-01, mB= 1.59994e+01, qB=-8.00000e-01, resind= 6, atomnumber= 8} 62: atom[ 115]={type= 4, typeB= 4, ptype= Atom, m= 1.20110e+01, q= 5.00000e-01, mB= 1.20110e+01, qB= 5.00000e-01, resind= 6, atomnumber= 6} 62: atom[ 116]={type= 5, typeB= 5, ptype= Atom, m= 1.59994e+01, q=-5.00000e-01, mB= 1.59994e+01, qB=-5.00000e-01, resind= 6, atomnumber= 8} 62: atom[ 117]={type= 0, typeB= 0, ptype= Atom, m= 1.40067e+01, q=-5.00000e-01, mB= 1.40067e+01, qB=-5.00000e-01, resind= 7, atomnumber= 7} 62: atom[ 118]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 3.00000e-01, mB= 1.00800e+00, qB= 3.00000e-01, resind= 7, atomnumber= 1} 62: atom[ 119]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q= 1.40000e-01, mB= 1.20110e+01, qB= 1.40000e-01, resind= 7, atomnumber= 6} 62: atom[ 120]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 7, atomnumber= 1} 62: atom[ 121]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q=-1.20000e-01, mB= 1.20110e+01, qB=-1.20000e-01, resind= 7, atomnumber= 6} 62: atom[ 122]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 7, atomnumber= 1} 62: atom[ 123]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 7, atomnumber= 1} 62: atom[ 124]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q=-6.00000e-02, mB= 1.20110e+01, qB=-6.00000e-02, resind= 7, atomnumber= 6} 62: atom[ 125]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 7, atomnumber= 1} 62: atom[ 126]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q=-1.80000e-01, mB= 1.20110e+01, qB=-1.80000e-01, resind= 7, atomnumber= 6} 62: atom[ 127]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 7, atomnumber= 1} 62: atom[ 128]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 7, atomnumber= 1} 62: atom[ 129]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 7, atomnumber= 1} 62: atom[ 130]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q=-1.80000e-01, mB= 1.20110e+01, qB=-1.80000e-01, resind= 7, atomnumber= 6} 62: atom[ 131]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 7, atomnumber= 1} 62: atom[ 132]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 7, atomnumber= 1} 62: atom[ 133]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 7, atomnumber= 1} 62: atom[ 134]={type= 4, typeB= 4, ptype= Atom, m= 1.20110e+01, q= 5.00000e-01, mB= 1.20110e+01, qB= 5.00000e-01, resind= 7, atomnumber= 6} 62: atom[ 135]={type= 5, typeB= 5, ptype= Atom, m= 1.59994e+01, q=-5.00000e-01, mB= 1.59994e+01, qB=-5.00000e-01, resind= 7, atomnumber= 8} 62: atom[ 136]={type= 0, typeB= 0, ptype= Atom, m= 1.40067e+01, q=-5.00000e-01, mB= 1.40067e+01, qB=-5.00000e-01, resind= 8, atomnumber= 7} 62: atom[ 137]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 3.00000e-01, mB= 1.00800e+00, qB= 3.00000e-01, resind= 8, atomnumber= 1} 62: atom[ 138]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q= 1.40000e-01, mB= 1.20110e+01, qB= 1.40000e-01, resind= 8, atomnumber= 6} 62: atom[ 139]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 8, atomnumber= 1} 62: atom[ 140]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q=-1.80000e-01, mB= 1.20110e+01, qB=-1.80000e-01, resind= 8, atomnumber= 6} 62: atom[ 141]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 8, atomnumber= 1} 62: atom[ 142]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 8, atomnumber= 1} 62: atom[ 143]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 8, atomnumber= 1} 62: atom[ 144]={type= 4, typeB= 4, ptype= Atom, m= 1.20110e+01, q= 5.00000e-01, mB= 1.20110e+01, qB= 5.00000e-01, resind= 8, atomnumber= 6} 62: atom[ 145]={type= 5, typeB= 5, ptype= Atom, m= 1.59994e+01, q=-5.00000e-01, mB= 1.59994e+01, qB=-5.00000e-01, resind= 8, atomnumber= 8} 62: atom[ 146]={type= 0, typeB= 0, ptype= Atom, m= 1.40067e+01, q=-5.00000e-01, mB= 1.40067e+01, qB=-5.00000e-01, resind= 9, atomnumber= 7} 62: atom[ 147]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 3.00000e-01, mB= 1.00800e+00, qB= 3.00000e-01, resind= 9, atomnumber= 1} 62: atom[ 148]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q= 1.40000e-01, mB= 1.20110e+01, qB= 1.40000e-01, resind= 9, atomnumber= 6} 62: atom[ 149]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 9, atomnumber= 1} 62: atom[ 150]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q=-1.80000e-01, mB= 1.20110e+01, qB=-1.80000e-01, resind= 9, atomnumber= 6} 62: atom[ 151]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 9, atomnumber= 1} 62: atom[ 152]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 9, atomnumber= 1} 62: atom[ 153]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 9, atomnumber= 1} 62: atom[ 154]={type= 4, typeB= 4, ptype= Atom, m= 1.20110e+01, q= 5.00000e-01, mB= 1.20110e+01, qB= 5.00000e-01, resind= 9, atomnumber= 6} 62: atom[ 155]={type= 5, typeB= 5, ptype= Atom, m= 1.59994e+01, q=-5.00000e-01, mB= 1.59994e+01, qB=-5.00000e-01, resind= 9, atomnumber= 8} 62: atom (156): 62: atom[0]={name="N"} 62: atom[1]={name="H1"} 62: atom[2]={name="H2"} 62: atom[3]={name="H3"} 62: atom[4]={name="CA"} 62: atom[5]={name="HA"} 62: atom[6]={name="CB"} 62: atom[7]={name="HB1"} 62: atom[8]={name="HB2"} 62: atom[9]={name="CG"} 62: atom[10]={name="HG1"} 62: atom[11]={name="HG2"} 62: atom[12]={name="CD"} 62: atom[13]={name="HD1"} 62: atom[14]={name="HD2"} 62: atom[15]={name="CE"} 62: atom[16]={name="HE1"} 62: atom[17]={name="HE2"} 62: atom[18]={name="NZ"} 62: atom[19]={name="HZ1"} 62: atom[20]={name="HZ2"} 62: atom[21]={name="HZ3"} 62: atom[22]={name="C"} 62: atom[23]={name="O"} 62: atom[24]={name="N"} 62: atom[25]={name="H"} 62: atom[26]={name="CA"} 62: atom[27]={name="HA"} 62: atom[28]={name="CB"} 62: atom[29]={name="HB"} 62: atom[30]={name="CG1"} 62: atom[31]={name="HG11"} 62: atom[32]={name="HG12"} 62: atom[33]={name="HG13"} 62: atom[34]={name="CG2"} 62: atom[35]={name="HG21"} 62: atom[36]={name="HG22"} 62: atom[37]={name="HG23"} 62: atom[38]={name="C"} 62: atom[39]={name="O"} 62: atom[40]={name="N"} 62: atom[41]={name="H"} 62: atom[42]={name="CA"} 62: atom[43]={name="HA"} 62: atom[44]={name="CB"} 62: atom[45]={name="HB1"} 62: atom[46]={name="HB2"} 62: atom[47]={name="CG"} 62: atom[48]={name="CD1"} 62: atom[49]={name="HD1"} 62: atom[50]={name="CD2"} 62: atom[51]={name="HD2"} 62: atom[52]={name="CE1"} 62: atom[53]={name="HE1"} 62: atom[54]={name="CE2"} 62: atom[55]={name="HE2"} 62: atom[56]={name="CZ"} 62: atom[57]={name="HZ"} 62: atom[58]={name="C"} 62: atom[59]={name="O"} 62: atom[60]={name="N"} 62: atom[61]={name="H"} 62: atom[62]={name="CA"} 62: atom[63]={name="HA1"} 62: atom[64]={name="HA2"} 62: atom[65]={name="C"} 62: atom[66]={name="O"} 62: atom[67]={name="N"} 62: atom[68]={name="H"} 62: atom[69]={name="CA"} 62: atom[70]={name="HA"} 62: atom[71]={name="CB"} 62: atom[72]={name="HB1"} 62: atom[73]={name="HB2"} 62: atom[74]={name="CG"} 62: atom[75]={name="HG1"} 62: atom[76]={name="HG2"} 62: atom[77]={name="CD"} 62: atom[78]={name="HD1"} 62: atom[79]={name="HD2"} 62: atom[80]={name="NE"} 62: atom[81]={name="HE"} 62: atom[82]={name="CZ"} 62: atom[83]={name="NH1"} 62: atom[84]={name="HH11"} 62: atom[85]={name="HH12"} 62: atom[86]={name="NH2"} 62: atom[87]={name="HH21"} 62: atom[88]={name="HH22"} 62: atom[89]={name="C"} 62: atom[90]={name="O"} 62: atom[91]={name="N"} 62: atom[92]={name="H"} 62: atom[93]={name="CA"} 62: atom[94]={name="HA"} 62: atom[95]={name="CB"} 62: atom[96]={name="HB1"} 62: atom[97]={name="HB2"} 62: atom[98]={name="SG"} 62: atom[99]={name="HG"} 62: atom[100]={name="C"} 62: atom[101]={name="O"} 62: atom[102]={name="N"} 62: atom[103]={name="H"} 62: atom[104]={name="CA"} 62: atom[105]={name="HA"} 62: atom[106]={name="CB"} 62: atom[107]={name="HB1"} 62: atom[108]={name="HB2"} 62: atom[109]={name="CG"} 62: atom[110]={name="HG1"} 62: atom[111]={name="HG2"} 62: atom[112]={name="CD"} 62: atom[113]={name="OE1"} 62: atom[114]={name="OE2"} 62: atom[115]={name="C"} 62: atom[116]={name="O"} 62: atom[117]={name="N"} 62: atom[118]={name="H"} 62: atom[119]={name="CA"} 62: atom[120]={name="HA"} 62: atom[121]={name="CB"} 62: atom[122]={name="HB1"} 62: atom[123]={name="HB2"} 62: atom[124]={name="CG"} 62: atom[125]={name="HG"} 62: atom[126]={name="CD1"} 62: atom[127]={name="HD11"} 62: atom[128]={name="HD12"} 62: atom[129]={name="HD13"} 62: atom[130]={name="CD2"} 62: atom[131]={name="HD21"} 62: atom[132]={name="HD22"} 62: atom[133]={name="HD23"} 62: atom[134]={name="C"} 62: atom[135]={name="O"} 62: atom[136]={name="N"} 62: atom[137]={name="H"} 62: atom[138]={name="CA"} 62: atom[139]={name="HA"} 62: atom[140]={name="CB"} 62: atom[141]={name="HB1"} 62: atom[142]={name="HB2"} 62: atom[143]={name="HB3"} 62: atom[144]={name="C"} 62: atom[145]={name="O"} 62: atom[146]={name="N"} 62: atom[147]={name="H"} 62: atom[148]={name="CA"} 62: atom[149]={name="HA"} 62: atom[150]={name="CB"} 62: atom[151]={name="HB1"} 62: atom[152]={name="HB2"} 62: atom[153]={name="HB3"} 62: atom[154]={name="C"} 62: atom[155]={name="O"} 62: type (156): 62: type[0]={name="opls_287",nameB="opls_287"} 62: type[1]={name="opls_290",nameB="opls_290"} 62: type[2]={name="opls_290",nameB="opls_290"} 62: type[3]={name="opls_290",nameB="opls_290"} 62: type[4]={name="opls_293B",nameB="opls_293B"} 62: type[5]={name="opls_140",nameB="opls_140"} 62: type[6]={name="opls_136",nameB="opls_136"} 62: type[7]={name="opls_140",nameB="opls_140"} 62: type[8]={name="opls_140",nameB="opls_140"} 62: type[9]={name="opls_136",nameB="opls_136"} 62: type[10]={name="opls_140",nameB="opls_140"} 62: type[11]={name="opls_140",nameB="opls_140"} 62: type[12]={name="opls_136",nameB="opls_136"} 62: type[13]={name="opls_140",nameB="opls_140"} 62: type[14]={name="opls_140",nameB="opls_140"} 62: type[15]={name="opls_292",nameB="opls_292"} 62: type[16]={name="opls_140",nameB="opls_140"} 62: type[17]={name="opls_140",nameB="opls_140"} 62: type[18]={name="opls_287",nameB="opls_287"} 62: type[19]={name="opls_290",nameB="opls_290"} 62: type[20]={name="opls_290",nameB="opls_290"} 62: type[21]={name="opls_290",nameB="opls_290"} 62: type[22]={name="opls_235",nameB="opls_235"} 62: type[23]={name="opls_236",nameB="opls_236"} 62: type[24]={name="opls_238",nameB="opls_238"} 62: type[25]={name="opls_241",nameB="opls_241"} 62: type[26]={name="opls_224B",nameB="opls_224B"} 62: type[27]={name="opls_140",nameB="opls_140"} 62: type[28]={name="opls_137",nameB="opls_137"} 62: type[29]={name="opls_140",nameB="opls_140"} 62: type[30]={name="opls_135",nameB="opls_135"} 62: type[31]={name="opls_140",nameB="opls_140"} 62: type[32]={name="opls_140",nameB="opls_140"} 62: type[33]={name="opls_140",nameB="opls_140"} 62: type[34]={name="opls_135",nameB="opls_135"} 62: type[35]={name="opls_140",nameB="opls_140"} 62: type[36]={name="opls_140",nameB="opls_140"} 62: type[37]={name="opls_140",nameB="opls_140"} 62: type[38]={name="opls_235",nameB="opls_235"} 62: type[39]={name="opls_236",nameB="opls_236"} 62: type[40]={name="opls_238",nameB="opls_238"} 62: type[41]={name="opls_241",nameB="opls_241"} 62: type[42]={name="opls_224B",nameB="opls_224B"} 62: type[43]={name="opls_140",nameB="opls_140"} 62: type[44]={name="opls_149",nameB="opls_149"} 62: type[45]={name="opls_140",nameB="opls_140"} 62: type[46]={name="opls_140",nameB="opls_140"} 62: type[47]={name="opls_145",nameB="opls_145"} 62: type[48]={name="opls_145",nameB="opls_145"} 62: type[49]={name="opls_146",nameB="opls_146"} 62: type[50]={name="opls_145",nameB="opls_145"} 62: type[51]={name="opls_146",nameB="opls_146"} 62: type[52]={name="opls_145",nameB="opls_145"} 62: type[53]={name="opls_146",nameB="opls_146"} 62: type[54]={name="opls_145",nameB="opls_145"} 62: type[55]={name="opls_146",nameB="opls_146"} 62: type[56]={name="opls_145",nameB="opls_145"} 62: type[57]={name="opls_146",nameB="opls_146"} 62: type[58]={name="opls_235",nameB="opls_235"} 62: type[59]={name="opls_236",nameB="opls_236"} 62: type[60]={name="opls_238",nameB="opls_238"} 62: type[61]={name="opls_241",nameB="opls_241"} 62: type[62]={name="opls_223B",nameB="opls_223B"} 62: type[63]={name="opls_140",nameB="opls_140"} 62: type[64]={name="opls_140",nameB="opls_140"} 62: type[65]={name="opls_235",nameB="opls_235"} 62: type[66]={name="opls_236",nameB="opls_236"} 62: type[67]={name="opls_238",nameB="opls_238"} 62: type[68]={name="opls_241",nameB="opls_241"} 62: type[69]={name="opls_224B",nameB="opls_224B"} 62: type[70]={name="opls_140",nameB="opls_140"} 62: type[71]={name="opls_136",nameB="opls_136"} 62: type[72]={name="opls_140",nameB="opls_140"} 62: type[73]={name="opls_140",nameB="opls_140"} 62: type[74]={name="opls_308",nameB="opls_308"} 62: type[75]={name="opls_140",nameB="opls_140"} 62: type[76]={name="opls_140",nameB="opls_140"} 62: type[77]={name="opls_307",nameB="opls_307"} 62: type[78]={name="opls_140",nameB="opls_140"} 62: type[79]={name="opls_140",nameB="opls_140"} 62: type[80]={name="opls_303",nameB="opls_303"} 62: type[81]={name="opls_304",nameB="opls_304"} 62: type[82]={name="opls_302",nameB="opls_302"} 62: type[83]={name="opls_300",nameB="opls_300"} 62: type[84]={name="opls_301",nameB="opls_301"} 62: type[85]={name="opls_301",nameB="opls_301"} 62: type[86]={name="opls_300",nameB="opls_300"} 62: type[87]={name="opls_301",nameB="opls_301"} 62: type[88]={name="opls_301",nameB="opls_301"} 62: type[89]={name="opls_235",nameB="opls_235"} 62: type[90]={name="opls_236",nameB="opls_236"} 62: type[91]={name="opls_238",nameB="opls_238"} 62: type[92]={name="opls_241",nameB="opls_241"} 62: type[93]={name="opls_224B",nameB="opls_224B"} 62: type[94]={name="opls_140",nameB="opls_140"} 62: type[95]={name="opls_206",nameB="opls_206"} 62: type[96]={name="opls_140",nameB="opls_140"} 62: type[97]={name="opls_140",nameB="opls_140"} 62: type[98]={name="opls_200",nameB="opls_200"} 62: type[99]={name="opls_204",nameB="opls_204"} 62: type[100]={name="opls_235",nameB="opls_235"} 62: type[101]={name="opls_236",nameB="opls_236"} 62: type[102]={name="opls_238",nameB="opls_238"} 62: type[103]={name="opls_241",nameB="opls_241"} 62: type[104]={name="opls_224B",nameB="opls_224B"} 62: type[105]={name="opls_140",nameB="opls_140"} 62: type[106]={name="opls_136",nameB="opls_136"} 62: type[107]={name="opls_140",nameB="opls_140"} 62: type[108]={name="opls_140",nameB="opls_140"} 62: type[109]={name="opls_274",nameB="opls_274"} 62: type[110]={name="opls_140",nameB="opls_140"} 62: type[111]={name="opls_140",nameB="opls_140"} 62: type[112]={name="opls_271",nameB="opls_271"} 62: type[113]={name="opls_272",nameB="opls_272"} 62: type[114]={name="opls_272",nameB="opls_272"} 62: type[115]={name="opls_235",nameB="opls_235"} 62: type[116]={name="opls_236",nameB="opls_236"} 62: type[117]={name="opls_238",nameB="opls_238"} 62: type[118]={name="opls_241",nameB="opls_241"} 62: type[119]={name="opls_224B",nameB="opls_224B"} 62: type[120]={name="opls_140",nameB="opls_140"} 62: type[121]={name="opls_136",nameB="opls_136"} 62: type[122]={name="opls_140",nameB="opls_140"} 62: type[123]={name="opls_140",nameB="opls_140"} 62: type[124]={name="opls_137",nameB="opls_137"} 62: type[125]={name="opls_140",nameB="opls_140"} 62: type[126]={name="opls_135",nameB="opls_135"} 62: type[127]={name="opls_140",nameB="opls_140"} 62: type[128]={name="opls_140",nameB="opls_140"} 62: type[129]={name="opls_140",nameB="opls_140"} 62: type[130]={name="opls_135",nameB="opls_135"} 62: type[131]={name="opls_140",nameB="opls_140"} 62: type[132]={name="opls_140",nameB="opls_140"} 62: type[133]={name="opls_140",nameB="opls_140"} 62: type[134]={name="opls_235",nameB="opls_235"} 62: type[135]={name="opls_236",nameB="opls_236"} 62: type[136]={name="opls_238",nameB="opls_238"} 62: type[137]={name="opls_241",nameB="opls_241"} 62: type[138]={name="opls_224B",nameB="opls_224B"} 62: type[139]={name="opls_140",nameB="opls_140"} 62: type[140]={name="opls_135",nameB="opls_135"} 62: type[141]={name="opls_140",nameB="opls_140"} 62: type[142]={name="opls_140",nameB="opls_140"} 62: type[143]={name="opls_140",nameB="opls_140"} 62: type[144]={name="opls_235",nameB="opls_235"} 62: type[145]={name="opls_236",nameB="opls_236"} 62: type[146]={name="opls_238",nameB="opls_238"} 62: type[147]={name="opls_241",nameB="opls_241"} 62: type[148]={name="opls_224B",nameB="opls_224B"} 62: type[149]={name="opls_140",nameB="opls_140"} 62: type[150]={name="opls_135",nameB="opls_135"} 62: type[151]={name="opls_140",nameB="opls_140"} 62: type[152]={name="opls_140",nameB="opls_140"} 62: type[153]={name="opls_140",nameB="opls_140"} 62: type[154]={name="opls_235",nameB="opls_235"} 62: type[155]={name="opls_236",nameB="opls_236"} 62: residue (10): 62: residue[0]={name="LYS", nr=1, ic=' '} 62: residue[1]={name="VAL", nr=2, ic=' '} 62: residue[2]={name="PHE", nr=3, ic=' '} 62: residue[3]={name="GLY", nr=4, ic=' '} 62: residue[4]={name="ARG", nr=5, ic=' '} 62: residue[5]={name="CYS", nr=6, ic=' '} 62: residue[6]={name="GLU", nr=7, ic=' '} 62: residue[7]={name="LEU", nr=8, ic=' '} 62: residue[8]={name="ALA", nr=9, ic=' '} 62: residue[9]={name="ALA", nr=10, ic=' '} 62: excls: 62: numLists=156 62: numElements=1828 62: excls[0][num=13]={0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 22, 23, 24} 62: excls[1][num=8]={0, 1, 2, 3, 4, 5, 6, 22} 62: excls[2][num=8]={0, 1, 2, 3, 4, 5, 6, 22} 62: excls[3][num=8]={0, 1, 2, 3, 4, 5, 6, 22} 62: excls[4][num=18]={0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 22, 62: 23, 24, 25, 26} 62: excls[5][num=13]={0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 22, 23, 24} 62: excls[6][num=19]={0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 62: 14, 15, 22, 23, 24} 62: excls[7][num=11]={0, 4, 5, 6, 7, 8, 9, 10, 11, 12, 22} 62: excls[8][num=11]={0, 4, 5, 6, 7, 8, 9, 10, 11, 12, 22} 62: excls[9][num=17]={0, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 62: 16, 17, 18, 22} 62: excls[10][num=11]={4, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15} 62: excls[11][num=11]={4, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15} 62: excls[12][num=17]={4, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 62: 17, 18, 19, 20, 21} 62: excls[13][num=11]={6, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18} 62: excls[14][num=11]={6, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18} 62: excls[15][num=14]={6, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 62: 20, 21} 62: excls[16][num=11]={9, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21} 62: excls[17][num=11]={9, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21} 62: excls[18][num=11]={9, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21} 62: excls[19][num=8]={12, 15, 16, 17, 18, 19, 20, 21} 62: excls[20][num=8]={12, 15, 16, 17, 18, 19, 20, 21} 62: excls[21][num=8]={12, 15, 16, 17, 18, 19, 20, 21} 62: excls[22][num=18]={0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 22, 23, 24, 25, 62: 26, 27, 28, 38} 62: excls[23][num=9]={0, 4, 5, 6, 22, 23, 24, 25, 26} 62: excls[24][num=17]={0, 4, 5, 6, 22, 23, 24, 25, 26, 27, 28, 29, 62: 30, 34, 38, 39, 40} 62: excls[25][num=9]={4, 22, 23, 24, 25, 26, 27, 28, 38} 62: excls[26][num=22]={4, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 62: 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42} 62: excls[27][num=12]={22, 24, 25, 26, 27, 28, 29, 30, 34, 38, 39, 62: 40} 62: excls[28][num=18]={22, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 62: 34, 35, 36, 37, 38, 39, 40} 62: excls[29][num=14]={24, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 62: 36, 37, 38} 62: excls[30][num=14]={24, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 62: 36, 37, 38} 62: excls[31][num=8]={26, 28, 29, 30, 31, 32, 33, 34} 62: excls[32][num=8]={26, 28, 29, 30, 31, 32, 33, 34} 62: excls[33][num=8]={26, 28, 29, 30, 31, 32, 33, 34} 62: excls[34][num=14]={24, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 62: 36, 37, 38} 62: excls[35][num=8]={26, 28, 29, 30, 34, 35, 36, 37} 62: excls[36][num=8]={26, 28, 29, 30, 34, 35, 36, 37} 62: excls[37][num=8]={26, 28, 29, 30, 34, 35, 36, 37} 62: excls[38][num=17]={22, 24, 25, 26, 27, 28, 29, 30, 34, 38, 39, 62: 40, 41, 42, 43, 44, 58} 62: excls[39][num=9]={24, 26, 27, 28, 38, 39, 40, 41, 42} 62: excls[40][num=17]={24, 26, 27, 28, 38, 39, 40, 41, 42, 43, 44, 62: 45, 46, 47, 58, 59, 60} 62: excls[41][num=9]={26, 38, 39, 40, 41, 42, 43, 44, 58} 62: excls[42][num=18]={26, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 62: 48, 50, 58, 59, 60, 61, 62} 62: excls[43][num=12]={38, 40, 41, 42, 43, 44, 45, 46, 47, 58, 59, 62: 60} 62: excls[44][num=18]={38, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 62: 50, 51, 52, 54, 58, 59, 60} 62: excls[45][num=10]={40, 42, 43, 44, 45, 46, 47, 48, 50, 58} 62: excls[46][num=10]={40, 42, 43, 44, 45, 46, 47, 48, 50, 58} 62: excls[47][num=17]={40, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 62: 52, 53, 54, 55, 56, 58} 62: excls[48][num=14]={42, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 62: 54, 56, 57} 62: excls[49][num=8]={44, 47, 48, 49, 50, 52, 53, 56} 62: excls[50][num=14]={42, 44, 45, 46, 47, 48, 49, 50, 51, 52, 54, 62: 55, 56, 57} 62: excls[51][num=8]={44, 47, 48, 50, 51, 54, 55, 56} 62: excls[52][num=11]={44, 47, 48, 49, 50, 52, 53, 54, 55, 56, 57} 62: excls[53][num=8]={47, 48, 49, 52, 53, 54, 56, 57} 62: excls[54][num=11]={44, 47, 48, 50, 51, 52, 53, 54, 55, 56, 57} 62: excls[55][num=8]={47, 50, 51, 52, 54, 55, 56, 57} 62: excls[56][num=11]={47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57} 62: excls[57][num=8]={48, 50, 52, 53, 54, 55, 56, 57} 62: excls[58][num=17]={38, 40, 41, 42, 43, 44, 45, 46, 47, 58, 59, 62: 60, 61, 62, 63, 64, 65} 62: excls[59][num=9]={40, 42, 43, 44, 58, 59, 60, 61, 62} 62: excls[60][num=14]={40, 42, 43, 44, 58, 59, 60, 61, 62, 63, 64, 62: 65, 66, 67} 62: excls[61][num=9]={42, 58, 59, 60, 61, 62, 63, 64, 65} 62: excls[62][num=13]={42, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 62: 68, 69} 62: excls[63][num=9]={58, 60, 61, 62, 63, 64, 65, 66, 67} 62: excls[64][num=9]={58, 60, 61, 62, 63, 64, 65, 66, 67} 62: excls[65][num=14]={58, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 62: 70, 71, 89} 62: excls[66][num=9]={60, 62, 63, 64, 65, 66, 67, 68, 69} 62: excls[67][num=17]={60, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 62: 72, 73, 74, 89, 90, 91} 62: excls[68][num=9]={62, 65, 66, 67, 68, 69, 70, 71, 89} 62: excls[69][num=19]={62, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 62: 75, 76, 77, 89, 90, 91, 92, 93} 62: excls[70][num=12]={65, 67, 68, 69, 70, 71, 72, 73, 74, 89, 90, 62: 91} 62: excls[71][num=18]={65, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 62: 77, 78, 79, 80, 89, 90, 91} 62: excls[72][num=11]={67, 69, 70, 71, 72, 73, 74, 75, 76, 77, 89} 62: excls[73][num=11]={67, 69, 70, 71, 72, 73, 74, 75, 76, 77, 89} 62: excls[74][num=16]={67, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 62: 79, 80, 81, 82, 89} 62: excls[75][num=11]={69, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80} 62: excls[76][num=11]={69, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80} 62: excls[77][num=15]={69, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80, 62: 81, 82, 83, 86} 62: excls[78][num=10]={71, 74, 75, 76, 77, 78, 79, 80, 81, 82} 62: excls[79][num=10]={71, 74, 75, 76, 77, 78, 79, 80, 81, 82} 62: excls[80][num=16]={71, 74, 75, 76, 77, 78, 79, 80, 81, 82, 83, 62: 84, 85, 86, 87, 88} 62: excls[81][num=9]={74, 77, 78, 79, 80, 81, 82, 83, 86} 62: excls[82][num=13]={74, 77, 78, 79, 80, 81, 82, 83, 84, 85, 86, 62: 87, 88} 62: excls[83][num=10]={77, 80, 81, 82, 83, 84, 85, 86, 87, 88} 62: excls[84][num=6]={80, 82, 83, 84, 85, 86} 62: excls[85][num=6]={80, 82, 83, 84, 85, 86} 62: excls[86][num=10]={77, 80, 81, 82, 83, 84, 85, 86, 87, 88} 62: excls[87][num=6]={80, 82, 83, 86, 87, 88} 62: excls[88][num=6]={80, 82, 83, 86, 87, 88} 62: excls[89][num=17]={65, 67, 68, 69, 70, 71, 72, 73, 74, 89, 90, 62: 91, 92, 93, 94, 95, 100} 62: excls[90][num=9]={67, 69, 70, 71, 89, 90, 91, 92, 93} 62: excls[91][num=17]={67, 69, 70, 71, 89, 90, 91, 92, 93, 94, 95, 62: 96, 97, 98, 100, 101, 102} 62: excls[92][num=9]={69, 89, 90, 91, 92, 93, 94, 95, 100} 62: excls[93][num=17]={69, 89, 90, 91, 92, 93, 94, 95, 96, 97, 98, 62: 99, 100, 101, 102, 103, 104} 62: excls[94][num=12]={89, 91, 92, 93, 94, 95, 96, 97, 98, 100, 101, 62: 102} 62: excls[95][num=13]={89, 91, 92, 93, 94, 95, 96, 97, 98, 99, 100, 62: 101, 102} 62: excls[96][num=9]={91, 93, 94, 95, 96, 97, 98, 99, 100} 62: excls[97][num=9]={91, 93, 94, 95, 96, 97, 98, 99, 100} 62: excls[98][num=9]={91, 93, 94, 95, 96, 97, 98, 99, 100} 62: excls[99][num=6]={93, 95, 96, 97, 98, 99} 62: excls[100][num=17]={89, 91, 92, 93, 94, 95, 96, 97, 98, 100, 101, 62: 102, 103, 104, 105, 106, 115} 62: excls[101][num=9]={91, 93, 94, 95, 100, 101, 102, 103, 104} 62: excls[102][num=17]={91, 93, 94, 95, 100, 101, 102, 103, 104, 105, 62: 106, 107, 108, 109, 115, 116, 117} 62: excls[103][num=9]={93, 100, 101, 102, 103, 104, 105, 106, 115} 62: excls[104][num=19]={93, 100, 101, 102, 103, 104, 105, 106, 107, 62: 108, 109, 110, 111, 112, 115, 116, 117, 118, 119} 62: excls[105][num=12]={100, 102, 103, 104, 105, 106, 107, 108, 109, 62: 115, 116, 117} 62: excls[106][num=17]={100, 102, 103, 104, 105, 106, 107, 108, 109, 62: 110, 111, 112, 113, 114, 115, 116, 117} 62: excls[107][num=11]={102, 104, 105, 106, 107, 108, 109, 110, 111, 62: 112, 115} 62: excls[108][num=11]={102, 104, 105, 106, 107, 108, 109, 110, 111, 62: 112, 115} 62: excls[109][num=13]={102, 104, 105, 106, 107, 108, 109, 110, 111, 62: 112, 113, 114, 115} 62: excls[110][num=10]={104, 106, 107, 108, 109, 110, 111, 112, 113, 62: 114} 62: excls[111][num=10]={104, 106, 107, 108, 109, 110, 111, 112, 113, 62: 114} 62: excls[112][num=10]={104, 106, 107, 108, 109, 110, 111, 112, 113, 62: 114} 62: excls[113][num=7]={106, 109, 110, 111, 112, 113, 114} 62: excls[114][num=7]={106, 109, 110, 111, 112, 113, 114} 62: excls[115][num=17]={100, 102, 103, 104, 105, 106, 107, 108, 109, 62: 115, 116, 117, 118, 119, 120, 121, 134} 62: excls[116][num=9]={102, 104, 105, 106, 115, 116, 117, 118, 119} 62: excls[117][num=17]={102, 104, 105, 106, 115, 116, 117, 118, 119, 62: 120, 121, 122, 123, 124, 134, 135, 136} 62: excls[118][num=9]={104, 115, 116, 117, 118, 119, 120, 121, 134} 62: excls[119][num=19]={104, 115, 116, 117, 118, 119, 120, 121, 122, 62: 123, 124, 125, 126, 130, 134, 135, 136, 137, 138} 62: excls[120][num=12]={115, 117, 118, 119, 120, 121, 122, 123, 124, 62: 134, 135, 136} 62: excls[121][num=21]={115, 117, 118, 119, 120, 121, 122, 123, 124, 62: 125, 126, 127, 128, 129, 130, 131, 132, 133, 134, 135, 136} 62: excls[122][num=11]={117, 119, 120, 121, 122, 123, 124, 125, 126, 62: 130, 134} 62: excls[123][num=11]={117, 119, 120, 121, 122, 123, 124, 125, 126, 62: 130, 134} 62: excls[124][num=17]={117, 119, 120, 121, 122, 123, 124, 125, 126, 62: 127, 128, 129, 130, 131, 132, 133, 134} 62: excls[125][num=14]={119, 121, 122, 123, 124, 125, 126, 127, 128, 62: 129, 130, 131, 132, 133} 62: excls[126][num=14]={119, 121, 122, 123, 124, 125, 126, 127, 128, 62: 129, 130, 131, 132, 133} 62: excls[127][num=8]={121, 124, 125, 126, 127, 128, 129, 130} 62: excls[128][num=8]={121, 124, 125, 126, 127, 128, 129, 130} 62: excls[129][num=8]={121, 124, 125, 126, 127, 128, 129, 130} 62: excls[130][num=14]={119, 121, 122, 123, 124, 125, 126, 127, 128, 62: 129, 130, 131, 132, 133} 62: excls[131][num=8]={121, 124, 125, 126, 130, 131, 132, 133} 62: excls[132][num=8]={121, 124, 125, 126, 130, 131, 132, 133} 62: excls[133][num=8]={121, 124, 125, 126, 130, 131, 132, 133} 62: excls[134][num=17]={115, 117, 118, 119, 120, 121, 122, 123, 124, 62: 134, 135, 136, 137, 138, 139, 140, 144} 62: excls[135][num=9]={117, 119, 120, 121, 134, 135, 136, 137, 138} 62: excls[136][num=17]={117, 119, 120, 121, 134, 135, 136, 137, 138, 62: 139, 140, 141, 142, 143, 144, 145, 146} 62: excls[137][num=9]={119, 134, 135, 136, 137, 138, 139, 140, 144} 62: excls[138][num=16]={119, 134, 135, 136, 137, 138, 139, 140, 141, 62: 142, 143, 144, 145, 146, 147, 148} 62: excls[139][num=12]={134, 136, 137, 138, 139, 140, 141, 142, 143, 62: 144, 145, 146} 62: excls[140][num=12]={134, 136, 137, 138, 139, 140, 141, 142, 143, 62: 144, 145, 146} 62: excls[141][num=8]={136, 138, 139, 140, 141, 142, 143, 144} 62: excls[142][num=8]={136, 138, 139, 140, 141, 142, 143, 144} 62: excls[143][num=8]={136, 138, 139, 140, 141, 142, 143, 144} 62: excls[144][num=17]={134, 136, 137, 138, 139, 140, 141, 142, 143, 62: 144, 145, 146, 147, 148, 149, 150, 154} 62: excls[145][num=9]={136, 138, 139, 140, 144, 145, 146, 147, 148} 62: excls[146][num=16]={136, 138, 139, 140, 144, 145, 146, 147, 148, 62: 149, 150, 151, 152, 153, 154, 155} 62: excls[147][num=9]={138, 144, 145, 146, 147, 148, 149, 150, 154} 62: excls[148][num=13]={138, 144, 145, 146, 147, 148, 149, 150, 151, 62: 152, 153, 154, 155} 62: excls[149][num=11]={144, 146, 147, 148, 149, 150, 151, 152, 153, 62: 154, 155} 62: excls[150][num=11]={144, 146, 147, 148, 149, 150, 151, 152, 153, 62: 154, 155} 62: excls[151][num=8]={146, 148, 149, 150, 151, 152, 153, 154} 62: excls[152][num=8]={146, 148, 149, 150, 151, 152, 153, 154} 62: excls[153][num=8]={146, 148, 149, 150, 151, 152, 153, 154} 62: excls[154][num=11]={144, 146, 147, 148, 149, 150, 151, 152, 153, 62: 154, 155} 62: excls[155][num=6]={146, 148, 149, 150, 154, 155} 62: Bond: 62: nr: 468 62: iatoms: 62: 0 type=100 (BONDS) 0 1 62: 1 type=100 (BONDS) 0 2 62: 2 type=100 (BONDS) 0 3 62: 3 type=101 (BONDS) 0 4 62: 4 type=102 (BONDS) 4 5 62: 5 type=103 (BONDS) 4 6 62: 6 type=104 (BONDS) 4 22 62: 7 type=102 (BONDS) 6 7 62: 8 type=102 (BONDS) 6 8 62: 9 type=103 (BONDS) 6 9 62: 10 type=102 (BONDS) 9 10 62: 11 type=102 (BONDS) 9 11 62: 12 type=103 (BONDS) 9 12 62: 13 type=102 (BONDS) 12 13 62: 14 type=102 (BONDS) 12 14 62: 15 type=103 (BONDS) 12 15 62: 16 type=102 (BONDS) 15 16 62: 17 type=102 (BONDS) 15 17 62: 18 type=101 (BONDS) 15 18 62: 19 type=100 (BONDS) 18 19 62: 20 type=100 (BONDS) 18 20 62: 21 type=100 (BONDS) 18 21 62: 22 type=105 (BONDS) 22 23 62: 23 type=106 (BONDS) 22 24 62: 24 type=100 (BONDS) 24 25 62: 25 type=107 (BONDS) 24 26 62: 26 type=102 (BONDS) 26 27 62: 27 type=103 (BONDS) 26 28 62: 28 type=104 (BONDS) 26 38 62: 29 type=102 (BONDS) 28 29 62: 30 type=103 (BONDS) 28 30 62: 31 type=103 (BONDS) 28 34 62: 32 type=102 (BONDS) 30 31 62: 33 type=102 (BONDS) 30 32 62: 34 type=102 (BONDS) 30 33 62: 35 type=102 (BONDS) 34 35 62: 36 type=102 (BONDS) 34 36 62: 37 type=102 (BONDS) 34 37 62: 38 type=105 (BONDS) 38 39 62: 39 type=106 (BONDS) 38 40 62: 40 type=100 (BONDS) 40 41 62: 41 type=107 (BONDS) 40 42 62: 42 type=102 (BONDS) 42 43 62: 43 type=103 (BONDS) 42 44 62: 44 type=104 (BONDS) 42 58 62: 45 type=102 (BONDS) 44 45 62: 46 type=102 (BONDS) 44 46 62: 47 type=108 (BONDS) 44 47 62: 48 type=109 (BONDS) 47 48 62: 49 type=109 (BONDS) 47 50 62: 50 type=110 (BONDS) 48 49 62: 51 type=109 (BONDS) 48 52 62: 52 type=110 (BONDS) 50 51 62: 53 type=109 (BONDS) 50 54 62: 54 type=110 (BONDS) 52 53 62: 55 type=109 (BONDS) 52 56 62: 56 type=110 (BONDS) 54 55 62: 57 type=109 (BONDS) 54 56 62: 58 type=110 (BONDS) 56 57 62: 59 type=105 (BONDS) 58 59 62: 60 type=106 (BONDS) 58 60 62: 61 type=100 (BONDS) 60 61 62: 62 type=107 (BONDS) 60 62 62: 63 type=102 (BONDS) 62 63 62: 64 type=102 (BONDS) 62 64 62: 65 type=104 (BONDS) 62 65 62: 66 type=105 (BONDS) 65 66 62: 67 type=106 (BONDS) 65 67 62: 68 type=100 (BONDS) 67 68 62: 69 type=107 (BONDS) 67 69 62: 70 type=102 (BONDS) 69 70 62: 71 type=103 (BONDS) 69 71 62: 72 type=104 (BONDS) 69 89 62: 73 type=102 (BONDS) 71 72 62: 74 type=102 (BONDS) 71 73 62: 75 type=103 (BONDS) 71 74 62: 76 type=102 (BONDS) 74 75 62: 77 type=102 (BONDS) 74 76 62: 78 type=103 (BONDS) 74 77 62: 79 type=102 (BONDS) 77 78 62: 80 type=102 (BONDS) 77 79 62: 81 type=111 (BONDS) 77 80 62: 82 type=100 (BONDS) 80 81 62: 83 type=112 (BONDS) 80 82 62: 84 type=112 (BONDS) 82 83 62: 85 type=112 (BONDS) 82 86 62: 86 type=100 (BONDS) 83 84 62: 87 type=100 (BONDS) 83 85 62: 88 type=100 (BONDS) 86 87 62: 89 type=100 (BONDS) 86 88 62: 90 type=105 (BONDS) 89 90 62: 91 type=106 (BONDS) 89 91 62: 92 type=100 (BONDS) 91 92 62: 93 type=107 (BONDS) 91 93 62: 94 type=102 (BONDS) 93 94 62: 95 type=103 (BONDS) 93 95 62: 96 type=104 (BONDS) 93 100 62: 97 type=102 (BONDS) 95 96 62: 98 type=102 (BONDS) 95 97 62: 99 type=113 (BONDS) 95 98 62: 100 type=114 (BONDS) 98 99 62: 101 type=105 (BONDS) 100 101 62: 102 type=106 (BONDS) 100 102 62: 103 type=100 (BONDS) 102 103 62: 104 type=107 (BONDS) 102 104 62: 105 type=102 (BONDS) 104 105 62: 106 type=103 (BONDS) 104 106 62: 107 type=104 (BONDS) 104 115 62: 108 type=102 (BONDS) 106 107 62: 109 type=102 (BONDS) 106 108 62: 110 type=103 (BONDS) 106 109 62: 111 type=102 (BONDS) 109 110 62: 112 type=102 (BONDS) 109 111 62: 113 type=104 (BONDS) 109 112 62: 114 type=115 (BONDS) 112 113 62: 115 type=115 (BONDS) 112 114 62: 116 type=105 (BONDS) 115 116 62: 117 type=106 (BONDS) 115 117 62: 118 type=100 (BONDS) 117 118 62: 119 type=107 (BONDS) 117 119 62: 120 type=102 (BONDS) 119 120 62: 121 type=103 (BONDS) 119 121 62: 122 type=104 (BONDS) 119 134 62: 123 type=102 (BONDS) 121 122 62: 124 type=102 (BONDS) 121 123 62: 125 type=103 (BONDS) 121 124 62: 126 type=102 (BONDS) 124 125 62: 127 type=103 (BONDS) 124 126 62: 128 type=103 (BONDS) 124 130 62: 129 type=102 (BONDS) 126 127 62: 130 type=102 (BONDS) 126 128 62: 131 type=102 (BONDS) 126 129 62: 132 type=102 (BONDS) 130 131 62: 133 type=102 (BONDS) 130 132 62: 134 type=102 (BONDS) 130 133 62: 135 type=105 (BONDS) 134 135 62: 136 type=106 (BONDS) 134 136 62: 137 type=100 (BONDS) 136 137 62: 138 type=107 (BONDS) 136 138 62: 139 type=102 (BONDS) 138 139 62: 140 type=103 (BONDS) 138 140 62: 141 type=104 (BONDS) 138 144 62: 142 type=102 (BONDS) 140 141 62: 143 type=102 (BONDS) 140 142 62: 144 type=102 (BONDS) 140 143 62: 145 type=105 (BONDS) 144 145 62: 146 type=106 (BONDS) 144 146 62: 147 type=100 (BONDS) 146 147 62: 148 type=107 (BONDS) 146 148 62: 149 type=102 (BONDS) 148 149 62: 150 type=103 (BONDS) 148 150 62: 151 type=104 (BONDS) 148 154 62: 152 type=102 (BONDS) 150 151 62: 153 type=102 (BONDS) 150 152 62: 154 type=102 (BONDS) 150 153 62: 155 type=105 (BONDS) 154 155 62: G96Bond: 62: nr: 0 62: Morse: 62: nr: 0 62: Cubic Bonds: 62: nr: 0 62: Connect Bonds: 62: nr: 0 62: Harmonic Pot.: 62: nr: 0 62: FENE Bonds: 62: nr: 0 62: Tab. Bonds: 62: nr: 0 62: Tab. Bonds NC: 62: nr: 0 62: Restraint Pot.: 62: nr: 0 62: Angle: 62: nr: 1124 62: iatoms: 62: 0 type=116 (ANGLES) 1 0 2 62: 1 type=116 (ANGLES) 1 0 3 62: 2 type=116 (ANGLES) 1 0 4 62: 3 type=116 (ANGLES) 2 0 3 62: 4 type=116 (ANGLES) 2 0 4 62: 5 type=116 (ANGLES) 3 0 4 62: 6 type=116 (ANGLES) 0 4 5 62: 7 type=117 (ANGLES) 0 4 6 62: 8 type=117 (ANGLES) 0 4 22 62: 9 type=118 (ANGLES) 5 4 6 62: 10 type=116 (ANGLES) 5 4 22 62: 11 type=119 (ANGLES) 6 4 22 62: 12 type=118 (ANGLES) 4 6 7 62: 13 type=118 (ANGLES) 4 6 8 62: 14 type=120 (ANGLES) 4 6 9 62: 15 type=121 (ANGLES) 7 6 8 62: 16 type=118 (ANGLES) 7 6 9 62: 17 type=118 (ANGLES) 8 6 9 62: 18 type=118 (ANGLES) 6 9 10 62: 19 type=118 (ANGLES) 6 9 11 62: 20 type=120 (ANGLES) 6 9 12 62: 21 type=121 (ANGLES) 10 9 11 62: 22 type=118 (ANGLES) 10 9 12 62: 23 type=118 (ANGLES) 11 9 12 62: 24 type=118 (ANGLES) 9 12 13 62: 25 type=118 (ANGLES) 9 12 14 62: 26 type=120 (ANGLES) 9 12 15 62: 27 type=121 (ANGLES) 13 12 14 62: 28 type=118 (ANGLES) 13 12 15 62: 29 type=118 (ANGLES) 14 12 15 62: 30 type=118 (ANGLES) 12 15 16 62: 31 type=118 (ANGLES) 12 15 17 62: 32 type=117 (ANGLES) 12 15 18 62: 33 type=121 (ANGLES) 16 15 17 62: 34 type=116 (ANGLES) 16 15 18 62: 35 type=116 (ANGLES) 17 15 18 62: 36 type=116 (ANGLES) 15 18 19 62: 37 type=116 (ANGLES) 15 18 20 62: 38 type=116 (ANGLES) 15 18 21 62: 39 type=116 (ANGLES) 19 18 20 62: 40 type=116 (ANGLES) 19 18 21 62: 41 type=116 (ANGLES) 20 18 21 62: 42 type=122 (ANGLES) 4 22 23 62: 43 type=123 (ANGLES) 4 22 24 62: 44 type=124 (ANGLES) 23 22 24 62: 45 type=125 (ANGLES) 22 24 25 62: 46 type=126 (ANGLES) 22 24 26 62: 47 type=127 (ANGLES) 25 24 26 62: 48 type=116 (ANGLES) 24 26 27 62: 49 type=128 (ANGLES) 24 26 28 62: 50 type=129 (ANGLES) 24 26 38 62: 51 type=118 (ANGLES) 27 26 28 62: 52 type=116 (ANGLES) 27 26 38 62: 53 type=119 (ANGLES) 28 26 38 62: 54 type=118 (ANGLES) 26 28 29 62: 55 type=120 (ANGLES) 26 28 30 62: 56 type=120 (ANGLES) 26 28 34 62: 57 type=118 (ANGLES) 29 28 30 62: 58 type=118 (ANGLES) 29 28 34 62: 59 type=120 (ANGLES) 30 28 34 62: 60 type=118 (ANGLES) 28 30 31 62: 61 type=118 (ANGLES) 28 30 32 62: 62 type=118 (ANGLES) 28 30 33 62: 63 type=121 (ANGLES) 31 30 32 62: 64 type=121 (ANGLES) 31 30 33 62: 65 type=121 (ANGLES) 32 30 33 62: 66 type=118 (ANGLES) 28 34 35 62: 67 type=118 (ANGLES) 28 34 36 62: 68 type=118 (ANGLES) 28 34 37 62: 69 type=121 (ANGLES) 35 34 36 62: 70 type=121 (ANGLES) 35 34 37 62: 71 type=121 (ANGLES) 36 34 37 62: 72 type=122 (ANGLES) 26 38 39 62: 73 type=123 (ANGLES) 26 38 40 62: 74 type=124 (ANGLES) 39 38 40 62: 75 type=125 (ANGLES) 38 40 41 62: 76 type=126 (ANGLES) 38 40 42 62: 77 type=127 (ANGLES) 41 40 42 62: 78 type=116 (ANGLES) 40 42 43 62: 79 type=128 (ANGLES) 40 42 44 62: 80 type=129 (ANGLES) 40 42 58 62: 81 type=118 (ANGLES) 43 42 44 62: 82 type=116 (ANGLES) 43 42 58 62: 83 type=119 (ANGLES) 44 42 58 62: 84 type=118 (ANGLES) 42 44 45 62: 85 type=118 (ANGLES) 42 44 46 62: 86 type=130 (ANGLES) 42 44 47 62: 87 type=121 (ANGLES) 45 44 46 62: 88 type=116 (ANGLES) 45 44 47 62: 89 type=116 (ANGLES) 46 44 47 62: 90 type=131 (ANGLES) 44 47 48 62: 91 type=131 (ANGLES) 44 47 50 62: 92 type=132 (ANGLES) 48 47 50 62: 93 type=133 (ANGLES) 47 48 49 62: 94 type=132 (ANGLES) 47 48 52 62: 95 type=133 (ANGLES) 49 48 52 62: 96 type=133 (ANGLES) 47 50 51 62: 97 type=132 (ANGLES) 47 50 54 62: 98 type=133 (ANGLES) 51 50 54 62: 99 type=133 (ANGLES) 48 52 53 62: 100 type=132 (ANGLES) 48 52 56 62: 101 type=133 (ANGLES) 53 52 56 62: 102 type=133 (ANGLES) 50 54 55 62: 103 type=132 (ANGLES) 50 54 56 62: 104 type=133 (ANGLES) 55 54 56 62: 105 type=132 (ANGLES) 52 56 54 62: 106 type=133 (ANGLES) 52 56 57 62: 107 type=133 (ANGLES) 54 56 57 62: 108 type=122 (ANGLES) 42 58 59 62: 109 type=123 (ANGLES) 42 58 60 62: 110 type=124 (ANGLES) 59 58 60 62: 111 type=125 (ANGLES) 58 60 61 62: 112 type=126 (ANGLES) 58 60 62 62: 113 type=127 (ANGLES) 61 60 62 62: 114 type=116 (ANGLES) 60 62 63 62: 115 type=116 (ANGLES) 60 62 64 62: 116 type=129 (ANGLES) 60 62 65 62: 117 type=121 (ANGLES) 63 62 64 62: 118 type=116 (ANGLES) 63 62 65 62: 119 type=116 (ANGLES) 64 62 65 62: 120 type=122 (ANGLES) 62 65 66 62: 121 type=123 (ANGLES) 62 65 67 62: 122 type=124 (ANGLES) 66 65 67 62: 123 type=125 (ANGLES) 65 67 68 62: 124 type=126 (ANGLES) 65 67 69 62: 125 type=127 (ANGLES) 68 67 69 62: 126 type=116 (ANGLES) 67 69 70 62: 127 type=128 (ANGLES) 67 69 71 62: 128 type=129 (ANGLES) 67 69 89 62: 129 type=118 (ANGLES) 70 69 71 62: 130 type=116 (ANGLES) 70 69 89 62: 131 type=119 (ANGLES) 71 69 89 62: 132 type=118 (ANGLES) 69 71 72 62: 133 type=118 (ANGLES) 69 71 73 62: 134 type=120 (ANGLES) 69 71 74 62: 135 type=121 (ANGLES) 72 71 73 62: 136 type=118 (ANGLES) 72 71 74 62: 137 type=118 (ANGLES) 73 71 74 62: 138 type=118 (ANGLES) 71 74 75 62: 139 type=118 (ANGLES) 71 74 76 62: 140 type=120 (ANGLES) 71 74 77 62: 141 type=121 (ANGLES) 75 74 76 62: 142 type=118 (ANGLES) 75 74 77 62: 143 type=118 (ANGLES) 76 74 77 62: 144 type=118 (ANGLES) 74 77 78 62: 145 type=118 (ANGLES) 74 77 79 62: 146 type=117 (ANGLES) 74 77 80 62: 147 type=121 (ANGLES) 78 77 79 62: 148 type=116 (ANGLES) 78 77 80 62: 149 type=116 (ANGLES) 79 77 80 62: 150 type=134 (ANGLES) 77 80 81 62: 151 type=135 (ANGLES) 77 80 82 62: 152 type=133 (ANGLES) 81 80 82 62: 153 type=131 (ANGLES) 80 82 83 62: 154 type=131 (ANGLES) 80 82 86 62: 155 type=131 (ANGLES) 83 82 86 62: 156 type=133 (ANGLES) 82 83 84 62: 157 type=133 (ANGLES) 82 83 85 62: 158 type=133 (ANGLES) 84 83 85 62: 159 type=133 (ANGLES) 82 86 87 62: 160 type=133 (ANGLES) 82 86 88 62: 161 type=133 (ANGLES) 87 86 88 62: 162 type=122 (ANGLES) 69 89 90 62: 163 type=123 (ANGLES) 69 89 91 62: 164 type=124 (ANGLES) 90 89 91 62: 165 type=125 (ANGLES) 89 91 92 62: 166 type=126 (ANGLES) 89 91 93 62: 167 type=127 (ANGLES) 92 91 93 62: 168 type=116 (ANGLES) 91 93 94 62: 169 type=128 (ANGLES) 91 93 95 62: 170 type=129 (ANGLES) 91 93 100 62: 171 type=118 (ANGLES) 94 93 95 62: 172 type=116 (ANGLES) 94 93 100 62: 173 type=119 (ANGLES) 95 93 100 62: 174 type=118 (ANGLES) 93 95 96 62: 175 type=118 (ANGLES) 93 95 97 62: 176 type=136 (ANGLES) 93 95 98 62: 177 type=121 (ANGLES) 96 95 97 62: 178 type=116 (ANGLES) 96 95 98 62: 179 type=116 (ANGLES) 97 95 98 62: 180 type=137 (ANGLES) 95 98 99 62: 181 type=122 (ANGLES) 93 100 101 62: 182 type=123 (ANGLES) 93 100 102 62: 183 type=124 (ANGLES) 101 100 102 62: 184 type=125 (ANGLES) 100 102 103 62: 185 type=126 (ANGLES) 100 102 104 62: 186 type=127 (ANGLES) 103 102 104 62: 187 type=116 (ANGLES) 102 104 105 62: 188 type=128 (ANGLES) 102 104 106 62: 189 type=129 (ANGLES) 102 104 115 62: 190 type=118 (ANGLES) 105 104 106 62: 191 type=116 (ANGLES) 105 104 115 62: 192 type=119 (ANGLES) 106 104 115 62: 193 type=118 (ANGLES) 104 106 107 62: 194 type=118 (ANGLES) 104 106 108 62: 195 type=120 (ANGLES) 104 106 109 62: 196 type=121 (ANGLES) 107 106 108 62: 197 type=118 (ANGLES) 107 106 109 62: 198 type=118 (ANGLES) 108 106 109 62: 199 type=118 (ANGLES) 106 109 110 62: 200 type=118 (ANGLES) 106 109 111 62: 201 type=119 (ANGLES) 106 109 112 62: 202 type=121 (ANGLES) 110 109 111 62: 203 type=116 (ANGLES) 110 109 112 62: 204 type=116 (ANGLES) 111 109 112 62: 205 type=138 (ANGLES) 109 112 113 62: 206 type=138 (ANGLES) 109 112 114 62: 207 type=139 (ANGLES) 113 112 114 62: 208 type=122 (ANGLES) 104 115 116 62: 209 type=123 (ANGLES) 104 115 117 62: 210 type=124 (ANGLES) 116 115 117 62: 211 type=125 (ANGLES) 115 117 118 62: 212 type=126 (ANGLES) 115 117 119 62: 213 type=127 (ANGLES) 118 117 119 62: 214 type=116 (ANGLES) 117 119 120 62: 215 type=128 (ANGLES) 117 119 121 62: 216 type=129 (ANGLES) 117 119 134 62: 217 type=118 (ANGLES) 120 119 121 62: 218 type=116 (ANGLES) 120 119 134 62: 219 type=119 (ANGLES) 121 119 134 62: 220 type=118 (ANGLES) 119 121 122 62: 221 type=118 (ANGLES) 119 121 123 62: 222 type=120 (ANGLES) 119 121 124 62: 223 type=121 (ANGLES) 122 121 123 62: 224 type=118 (ANGLES) 122 121 124 62: 225 type=118 (ANGLES) 123 121 124 62: 226 type=118 (ANGLES) 121 124 125 62: 227 type=120 (ANGLES) 121 124 126 62: 228 type=120 (ANGLES) 121 124 130 62: 229 type=118 (ANGLES) 125 124 126 62: 230 type=118 (ANGLES) 125 124 130 62: 231 type=120 (ANGLES) 126 124 130 62: 232 type=118 (ANGLES) 124 126 127 62: 233 type=118 (ANGLES) 124 126 128 62: 234 type=118 (ANGLES) 124 126 129 62: 235 type=121 (ANGLES) 127 126 128 62: 236 type=121 (ANGLES) 127 126 129 62: 237 type=121 (ANGLES) 128 126 129 62: 238 type=118 (ANGLES) 124 130 131 62: 239 type=118 (ANGLES) 124 130 132 62: 240 type=118 (ANGLES) 124 130 133 62: 241 type=121 (ANGLES) 131 130 132 62: 242 type=121 (ANGLES) 131 130 133 62: 243 type=121 (ANGLES) 132 130 133 62: 244 type=122 (ANGLES) 119 134 135 62: 245 type=123 (ANGLES) 119 134 136 62: 246 type=124 (ANGLES) 135 134 136 62: 247 type=125 (ANGLES) 134 136 137 62: 248 type=126 (ANGLES) 134 136 138 62: 249 type=127 (ANGLES) 137 136 138 62: 250 type=116 (ANGLES) 136 138 139 62: 251 type=128 (ANGLES) 136 138 140 62: 252 type=129 (ANGLES) 136 138 144 62: 253 type=118 (ANGLES) 139 138 140 62: 254 type=116 (ANGLES) 139 138 144 62: 255 type=119 (ANGLES) 140 138 144 62: 256 type=118 (ANGLES) 138 140 141 62: 257 type=118 (ANGLES) 138 140 142 62: 258 type=118 (ANGLES) 138 140 143 62: 259 type=121 (ANGLES) 141 140 142 62: 260 type=121 (ANGLES) 141 140 143 62: 261 type=121 (ANGLES) 142 140 143 62: 262 type=122 (ANGLES) 138 144 145 62: 263 type=123 (ANGLES) 138 144 146 62: 264 type=124 (ANGLES) 145 144 146 62: 265 type=125 (ANGLES) 144 146 147 62: 266 type=126 (ANGLES) 144 146 148 62: 267 type=127 (ANGLES) 147 146 148 62: 268 type=116 (ANGLES) 146 148 149 62: 269 type=128 (ANGLES) 146 148 150 62: 270 type=129 (ANGLES) 146 148 154 62: 271 type=118 (ANGLES) 149 148 150 62: 272 type=116 (ANGLES) 149 148 154 62: 273 type=119 (ANGLES) 150 148 154 62: 274 type=118 (ANGLES) 148 150 151 62: 275 type=118 (ANGLES) 148 150 152 62: 276 type=118 (ANGLES) 148 150 153 62: 277 type=121 (ANGLES) 151 150 152 62: 278 type=121 (ANGLES) 151 150 153 62: 279 type=121 (ANGLES) 152 150 153 62: 280 type=122 (ANGLES) 148 154 155 62: G96Angle: 62: nr: 0 62: Restr. Angles: 62: nr: 0 62: Lin. Angle: 62: nr: 0 62: Bond-Cross: 62: nr: 0 62: BA-Cross: 62: nr: 0 62: U-B: 62: nr: 0 62: Quartic Angles: 62: nr: 0 62: Tab. Angles: 62: nr: 0 62: Proper Dih.: 62: nr: 145 62: iatoms: 62: 0 type=140 (PDIHS) 4 24 22 23 62: 1 type=141 (PDIHS) 22 26 24 25 62: 2 type=140 (PDIHS) 26 40 38 39 62: 3 type=141 (PDIHS) 38 42 40 41 62: 4 type=140 (PDIHS) 42 60 58 59 62: 5 type=142 (PDIHS) 44 47 50 48 62: 6 type=142 (PDIHS) 47 52 48 49 62: 7 type=142 (PDIHS) 47 54 50 51 62: 8 type=142 (PDIHS) 48 56 52 53 62: 9 type=142 (PDIHS) 50 56 54 55 62: 10 type=142 (PDIHS) 52 54 56 57 62: 11 type=141 (PDIHS) 58 62 60 61 62: 12 type=140 (PDIHS) 62 67 65 66 62: 13 type=141 (PDIHS) 65 69 67 68 62: 14 type=140 (PDIHS) 69 91 89 90 62: 15 type=141 (PDIHS) 77 82 80 81 62: 16 type=140 (PDIHS) 80 83 82 86 62: 17 type=141 (PDIHS) 82 84 83 85 62: 18 type=141 (PDIHS) 82 87 86 88 62: 19 type=141 (PDIHS) 89 93 91 92 62: 20 type=140 (PDIHS) 93 102 100 101 62: 21 type=141 (PDIHS) 100 104 102 103 62: 22 type=140 (PDIHS) 104 117 115 116 62: 23 type=140 (PDIHS) 109 113 112 114 62: 24 type=141 (PDIHS) 115 119 117 118 62: 25 type=140 (PDIHS) 119 136 134 135 62: 26 type=141 (PDIHS) 134 138 136 137 62: 27 type=140 (PDIHS) 138 146 144 145 62: 28 type=141 (PDIHS) 144 148 146 147 62: Ryckaert-Bell.: 62: nr: 1565 62: iatoms: 62: 0 type=143 (RBDIHS) 1 0 4 5 62: 1 type=144 (RBDIHS) 1 0 4 6 62: 2 type=144 (RBDIHS) 1 0 4 22 62: 3 type=143 (RBDIHS) 2 0 4 5 62: 4 type=144 (RBDIHS) 2 0 4 6 62: 5 type=144 (RBDIHS) 2 0 4 22 62: 6 type=143 (RBDIHS) 3 0 4 5 62: 7 type=144 (RBDIHS) 3 0 4 6 62: 8 type=144 (RBDIHS) 3 0 4 22 62: 9 type=145 (RBDIHS) 0 4 6 9 62: 10 type=146 (RBDIHS) 22 4 6 9 62: 11 type=147 (RBDIHS) 0 4 6 7 62: 12 type=147 (RBDIHS) 0 4 6 8 62: 13 type=148 (RBDIHS) 5 4 6 7 62: 14 type=148 (RBDIHS) 5 4 6 8 62: 15 type=148 (RBDIHS) 5 4 6 9 62: 16 type=149 (RBDIHS) 22 4 6 7 62: 17 type=149 (RBDIHS) 22 4 6 8 62: 18 type=150 (RBDIHS) 0 4 22 24 62: 19 type=151 (RBDIHS) 6 4 22 24 62: 20 type=148 (RBDIHS) 4 6 9 10 62: 21 type=148 (RBDIHS) 4 6 9 11 62: 22 type=152 (RBDIHS) 4 6 9 12 62: 23 type=148 (RBDIHS) 7 6 9 10 62: 24 type=148 (RBDIHS) 7 6 9 11 62: 25 type=148 (RBDIHS) 7 6 9 12 62: 26 type=148 (RBDIHS) 8 6 9 10 62: 27 type=148 (RBDIHS) 8 6 9 11 62: 28 type=148 (RBDIHS) 8 6 9 12 62: 29 type=148 (RBDIHS) 6 9 12 13 62: 30 type=148 (RBDIHS) 6 9 12 14 62: 31 type=152 (RBDIHS) 6 9 12 15 62: 32 type=148 (RBDIHS) 10 9 12 13 62: 33 type=148 (RBDIHS) 10 9 12 14 62: 34 type=148 (RBDIHS) 10 9 12 15 62: 35 type=148 (RBDIHS) 11 9 12 13 62: 36 type=148 (RBDIHS) 11 9 12 14 62: 37 type=148 (RBDIHS) 11 9 12 15 62: 38 type=148 (RBDIHS) 9 12 15 16 62: 39 type=148 (RBDIHS) 9 12 15 17 62: 40 type=153 (RBDIHS) 9 12 15 18 62: 41 type=148 (RBDIHS) 13 12 15 16 62: 42 type=148 (RBDIHS) 13 12 15 17 62: 43 type=154 (RBDIHS) 13 12 15 18 62: 44 type=148 (RBDIHS) 14 12 15 16 62: 45 type=148 (RBDIHS) 14 12 15 17 62: 46 type=154 (RBDIHS) 14 12 15 18 62: 47 type=144 (RBDIHS) 12 15 18 19 62: 48 type=144 (RBDIHS) 12 15 18 20 62: 49 type=144 (RBDIHS) 12 15 18 21 62: 50 type=143 (RBDIHS) 16 15 18 19 62: 51 type=143 (RBDIHS) 16 15 18 20 62: 52 type=143 (RBDIHS) 16 15 18 21 62: 53 type=143 (RBDIHS) 17 15 18 19 62: 54 type=143 (RBDIHS) 17 15 18 20 62: 55 type=143 (RBDIHS) 17 15 18 21 62: 56 type=155 (RBDIHS) 4 22 24 25 62: 57 type=156 (RBDIHS) 4 22 24 26 62: 58 type=155 (RBDIHS) 23 22 24 25 62: 59 type=157 (RBDIHS) 23 22 24 26 62: 60 type=158 (RBDIHS) 22 24 26 28 62: 61 type=159 (RBDIHS) 22 24 26 38 62: 62 type=160 (RBDIHS) 24 26 28 30 62: 63 type=160 (RBDIHS) 24 26 28 34 62: 64 type=161 (RBDIHS) 38 26 28 30 62: 65 type=161 (RBDIHS) 38 26 28 34 62: 66 type=147 (RBDIHS) 24 26 28 29 62: 67 type=148 (RBDIHS) 27 26 28 29 62: 68 type=148 (RBDIHS) 27 26 28 30 62: 69 type=148 (RBDIHS) 27 26 28 34 62: 70 type=149 (RBDIHS) 38 26 28 29 62: 71 type=150 (RBDIHS) 24 26 38 40 62: 72 type=151 (RBDIHS) 28 26 38 40 62: 73 type=148 (RBDIHS) 26 28 30 31 62: 74 type=148 (RBDIHS) 26 28 30 32 62: 75 type=148 (RBDIHS) 26 28 30 33 62: 76 type=148 (RBDIHS) 29 28 30 31 62: 77 type=148 (RBDIHS) 29 28 30 32 62: 78 type=148 (RBDIHS) 29 28 30 33 62: 79 type=148 (RBDIHS) 34 28 30 31 62: 80 type=148 (RBDIHS) 34 28 30 32 62: 81 type=148 (RBDIHS) 34 28 30 33 62: 82 type=148 (RBDIHS) 26 28 34 35 62: 83 type=148 (RBDIHS) 26 28 34 36 62: 84 type=148 (RBDIHS) 26 28 34 37 62: 85 type=148 (RBDIHS) 29 28 34 35 62: 86 type=148 (RBDIHS) 29 28 34 36 62: 87 type=148 (RBDIHS) 29 28 34 37 62: 88 type=148 (RBDIHS) 30 28 34 35 62: 89 type=148 (RBDIHS) 30 28 34 36 62: 90 type=148 (RBDIHS) 30 28 34 37 62: 91 type=155 (RBDIHS) 26 38 40 41 62: 92 type=156 (RBDIHS) 26 38 40 42 62: 93 type=155 (RBDIHS) 39 38 40 41 62: 94 type=157 (RBDIHS) 39 38 40 42 62: 95 type=158 (RBDIHS) 38 40 42 44 62: 96 type=159 (RBDIHS) 38 40 42 58 62: 97 type=147 (RBDIHS) 40 42 44 45 62: 98 type=147 (RBDIHS) 40 42 44 46 62: 99 type=162 (RBDIHS) 40 42 44 47 62: 100 type=148 (RBDIHS) 43 42 44 45 62: 101 type=148 (RBDIHS) 43 42 44 46 62: 102 type=163 (RBDIHS) 43 42 44 47 62: 103 type=149 (RBDIHS) 58 42 44 45 62: 104 type=149 (RBDIHS) 58 42 44 46 62: 105 type=164 (RBDIHS) 58 42 44 47 62: 106 type=150 (RBDIHS) 40 42 58 60 62: 107 type=151 (RBDIHS) 44 42 58 60 62: 108 type=165 (RBDIHS) 44 47 48 49 62: 109 type=165 (RBDIHS) 44 47 48 52 62: 110 type=165 (RBDIHS) 50 47 48 49 62: 111 type=165 (RBDIHS) 50 47 48 52 62: 112 type=165 (RBDIHS) 44 47 50 51 62: 113 type=165 (RBDIHS) 44 47 50 54 62: 114 type=165 (RBDIHS) 48 47 50 51 62: 115 type=165 (RBDIHS) 48 47 50 54 62: 116 type=165 (RBDIHS) 47 48 52 53 62: 117 type=165 (RBDIHS) 47 48 52 56 62: 118 type=165 (RBDIHS) 49 48 52 53 62: 119 type=165 (RBDIHS) 49 48 52 56 62: 120 type=165 (RBDIHS) 47 50 54 55 62: 121 type=165 (RBDIHS) 47 50 54 56 62: 122 type=165 (RBDIHS) 51 50 54 55 62: 123 type=165 (RBDIHS) 51 50 54 56 62: 124 type=165 (RBDIHS) 48 52 56 54 62: 125 type=165 (RBDIHS) 48 52 56 57 62: 126 type=165 (RBDIHS) 53 52 56 54 62: 127 type=165 (RBDIHS) 53 52 56 57 62: 128 type=165 (RBDIHS) 50 54 56 52 62: 129 type=165 (RBDIHS) 50 54 56 57 62: 130 type=165 (RBDIHS) 55 54 56 52 62: 131 type=165 (RBDIHS) 55 54 56 57 62: 132 type=155 (RBDIHS) 42 58 60 61 62: 133 type=156 (RBDIHS) 42 58 60 62 62: 134 type=155 (RBDIHS) 59 58 60 61 62: 135 type=157 (RBDIHS) 59 58 60 62 62: 136 type=159 (RBDIHS) 58 60 62 65 62: 137 type=150 (RBDIHS) 60 62 65 67 62: 138 type=155 (RBDIHS) 62 65 67 68 62: 139 type=156 (RBDIHS) 62 65 67 69 62: 140 type=155 (RBDIHS) 66 65 67 68 62: 141 type=157 (RBDIHS) 66 65 67 69 62: 142 type=158 (RBDIHS) 65 67 69 71 62: 143 type=159 (RBDIHS) 65 67 69 89 62: 144 type=166 (RBDIHS) 67 69 71 74 62: 145 type=167 (RBDIHS) 89 69 71 74 62: 146 type=147 (RBDIHS) 67 69 71 72 62: 147 type=147 (RBDIHS) 67 69 71 73 62: 148 type=148 (RBDIHS) 70 69 71 72 62: 149 type=148 (RBDIHS) 70 69 71 73 62: 150 type=148 (RBDIHS) 70 69 71 74 62: 151 type=149 (RBDIHS) 89 69 71 72 62: 152 type=149 (RBDIHS) 89 69 71 73 62: 153 type=150 (RBDIHS) 67 69 89 91 62: 154 type=151 (RBDIHS) 71 69 89 91 62: 155 type=148 (RBDIHS) 69 71 74 75 62: 156 type=148 (RBDIHS) 69 71 74 76 62: 157 type=152 (RBDIHS) 69 71 74 77 62: 158 type=148 (RBDIHS) 72 71 74 75 62: 159 type=148 (RBDIHS) 72 71 74 76 62: 160 type=148 (RBDIHS) 72 71 74 77 62: 161 type=148 (RBDIHS) 73 71 74 75 62: 162 type=148 (RBDIHS) 73 71 74 76 62: 163 type=148 (RBDIHS) 73 71 74 77 62: 164 type=148 (RBDIHS) 71 74 77 78 62: 165 type=148 (RBDIHS) 71 74 77 79 62: 166 type=153 (RBDIHS) 71 74 77 80 62: 167 type=148 (RBDIHS) 75 74 77 78 62: 168 type=148 (RBDIHS) 75 74 77 79 62: 169 type=168 (RBDIHS) 75 74 77 80 62: 170 type=148 (RBDIHS) 76 74 77 78 62: 171 type=148 (RBDIHS) 76 74 77 79 62: 172 type=168 (RBDIHS) 76 74 77 80 62: 173 type=169 (RBDIHS) 74 77 80 81 62: 174 type=170 (RBDIHS) 74 77 80 82 62: 175 type=171 (RBDIHS) 78 77 80 82 62: 176 type=171 (RBDIHS) 79 77 80 82 62: 177 type=172 (RBDIHS) 77 80 82 83 62: 178 type=172 (RBDIHS) 77 80 82 86 62: 179 type=173 (RBDIHS) 81 80 82 83 62: 180 type=173 (RBDIHS) 81 80 82 86 62: 181 type=173 (RBDIHS) 80 82 83 84 62: 182 type=173 (RBDIHS) 80 82 83 85 62: 183 type=173 (RBDIHS) 86 82 83 84 62: 184 type=173 (RBDIHS) 86 82 83 85 62: 185 type=173 (RBDIHS) 80 82 86 87 62: 186 type=173 (RBDIHS) 80 82 86 88 62: 187 type=173 (RBDIHS) 83 82 86 87 62: 188 type=173 (RBDIHS) 83 82 86 88 62: 189 type=155 (RBDIHS) 69 89 91 92 62: 190 type=156 (RBDIHS) 69 89 91 93 62: 191 type=155 (RBDIHS) 90 89 91 92 62: 192 type=157 (RBDIHS) 90 89 91 93 62: 193 type=158 (RBDIHS) 89 91 93 95 62: 194 type=159 (RBDIHS) 89 91 93 100 62: 195 type=174 (RBDIHS) 91 93 95 98 62: 196 type=175 (RBDIHS) 100 93 95 98 62: 197 type=147 (RBDIHS) 91 93 95 96 62: 198 type=147 (RBDIHS) 91 93 95 97 62: 199 type=148 (RBDIHS) 94 93 95 96 62: 200 type=148 (RBDIHS) 94 93 95 97 62: 201 type=176 (RBDIHS) 94 93 95 98 62: 202 type=149 (RBDIHS) 100 93 95 96 62: 203 type=149 (RBDIHS) 100 93 95 97 62: 204 type=150 (RBDIHS) 91 93 100 102 62: 205 type=151 (RBDIHS) 95 93 100 102 62: 206 type=177 (RBDIHS) 93 95 98 99 62: 207 type=178 (RBDIHS) 96 95 98 99 62: 208 type=178 (RBDIHS) 97 95 98 99 62: 209 type=155 (RBDIHS) 93 100 102 103 62: 210 type=156 (RBDIHS) 93 100 102 104 62: 211 type=155 (RBDIHS) 101 100 102 103 62: 212 type=157 (RBDIHS) 101 100 102 104 62: 213 type=158 (RBDIHS) 100 102 104 106 62: 214 type=159 (RBDIHS) 100 102 104 115 62: 215 type=179 (RBDIHS) 102 104 106 109 62: 216 type=180 (RBDIHS) 115 104 106 109 62: 217 type=147 (RBDIHS) 102 104 106 107 62: 218 type=147 (RBDIHS) 102 104 106 108 62: 219 type=148 (RBDIHS) 105 104 106 107 62: 220 type=148 (RBDIHS) 105 104 106 108 62: 221 type=148 (RBDIHS) 105 104 106 109 62: 222 type=149 (RBDIHS) 115 104 106 107 62: 223 type=149 (RBDIHS) 115 104 106 108 62: 224 type=150 (RBDIHS) 102 104 115 117 62: 225 type=151 (RBDIHS) 106 104 115 117 62: 226 type=148 (RBDIHS) 104 106 109 110 62: 227 type=148 (RBDIHS) 104 106 109 111 62: 228 type=181 (RBDIHS) 104 106 109 112 62: 229 type=148 (RBDIHS) 107 106 109 110 62: 230 type=148 (RBDIHS) 107 106 109 111 62: 231 type=182 (RBDIHS) 107 106 109 112 62: 232 type=148 (RBDIHS) 108 106 109 110 62: 233 type=148 (RBDIHS) 108 106 109 111 62: 234 type=182 (RBDIHS) 108 106 109 112 62: 235 type=183 (RBDIHS) 106 109 112 113 62: 236 type=183 (RBDIHS) 106 109 112 114 62: 237 type=155 (RBDIHS) 104 115 117 118 62: 238 type=156 (RBDIHS) 104 115 117 119 62: 239 type=155 (RBDIHS) 116 115 117 118 62: 240 type=157 (RBDIHS) 116 115 117 119 62: 241 type=158 (RBDIHS) 115 117 119 121 62: 242 type=159 (RBDIHS) 115 117 119 134 62: 243 type=184 (RBDIHS) 117 119 121 124 62: 244 type=185 (RBDIHS) 134 119 121 124 62: 245 type=147 (RBDIHS) 117 119 121 122 62: 246 type=147 (RBDIHS) 117 119 121 123 62: 247 type=148 (RBDIHS) 120 119 121 122 62: 248 type=148 (RBDIHS) 120 119 121 123 62: 249 type=148 (RBDIHS) 120 119 121 124 62: 250 type=149 (RBDIHS) 134 119 121 122 62: 251 type=149 (RBDIHS) 134 119 121 123 62: 252 type=150 (RBDIHS) 117 119 134 136 62: 253 type=151 (RBDIHS) 121 119 134 136 62: 254 type=148 (RBDIHS) 119 121 124 125 62: 255 type=152 (RBDIHS) 119 121 124 126 62: 256 type=152 (RBDIHS) 119 121 124 130 62: 257 type=148 (RBDIHS) 122 121 124 125 62: 258 type=148 (RBDIHS) 122 121 124 126 62: 259 type=148 (RBDIHS) 122 121 124 130 62: 260 type=148 (RBDIHS) 123 121 124 125 62: 261 type=148 (RBDIHS) 123 121 124 126 62: 262 type=148 (RBDIHS) 123 121 124 130 62: 263 type=148 (RBDIHS) 121 124 126 127 62: 264 type=148 (RBDIHS) 121 124 126 128 62: 265 type=148 (RBDIHS) 121 124 126 129 62: 266 type=148 (RBDIHS) 125 124 126 127 62: 267 type=148 (RBDIHS) 125 124 126 128 62: 268 type=148 (RBDIHS) 125 124 126 129 62: 269 type=148 (RBDIHS) 130 124 126 127 62: 270 type=148 (RBDIHS) 130 124 126 128 62: 271 type=148 (RBDIHS) 130 124 126 129 62: 272 type=148 (RBDIHS) 121 124 130 131 62: 273 type=148 (RBDIHS) 121 124 130 132 62: 274 type=148 (RBDIHS) 121 124 130 133 62: 275 type=148 (RBDIHS) 125 124 130 131 62: 276 type=148 (RBDIHS) 125 124 130 132 62: 277 type=148 (RBDIHS) 125 124 130 133 62: 278 type=148 (RBDIHS) 126 124 130 131 62: 279 type=148 (RBDIHS) 126 124 130 132 62: 280 type=148 (RBDIHS) 126 124 130 133 62: 281 type=155 (RBDIHS) 119 134 136 137 62: 282 type=156 (RBDIHS) 119 134 136 138 62: 283 type=155 (RBDIHS) 135 134 136 137 62: 284 type=157 (RBDIHS) 135 134 136 138 62: 285 type=158 (RBDIHS) 134 136 138 140 62: 286 type=159 (RBDIHS) 134 136 138 144 62: 287 type=147 (RBDIHS) 136 138 140 141 62: 288 type=147 (RBDIHS) 136 138 140 142 62: 289 type=147 (RBDIHS) 136 138 140 143 62: 290 type=148 (RBDIHS) 139 138 140 141 62: 291 type=148 (RBDIHS) 139 138 140 142 62: 292 type=148 (RBDIHS) 139 138 140 143 62: 293 type=149 (RBDIHS) 144 138 140 141 62: 294 type=149 (RBDIHS) 144 138 140 142 62: 295 type=149 (RBDIHS) 144 138 140 143 62: 296 type=150 (RBDIHS) 136 138 144 146 62: 297 type=151 (RBDIHS) 140 138 144 146 62: 298 type=155 (RBDIHS) 138 144 146 147 62: 299 type=156 (RBDIHS) 138 144 146 148 62: 300 type=155 (RBDIHS) 145 144 146 147 62: 301 type=157 (RBDIHS) 145 144 146 148 62: 302 type=158 (RBDIHS) 144 146 148 150 62: 303 type=159 (RBDIHS) 144 146 148 154 62: 304 type=147 (RBDIHS) 146 148 150 151 62: 305 type=147 (RBDIHS) 146 148 150 152 62: 306 type=147 (RBDIHS) 146 148 150 153 62: 307 type=148 (RBDIHS) 149 148 150 151 62: 308 type=148 (RBDIHS) 149 148 150 152 62: 309 type=148 (RBDIHS) 149 148 150 153 62: 310 type=149 (RBDIHS) 154 148 150 151 62: 311 type=149 (RBDIHS) 154 148 150 152 62: 312 type=149 (RBDIHS) 154 148 150 153 62: Restr. Dih.: 62: nr: 0 62: CBT Dih.: 62: nr: 0 62: Fourier Dih.: 62: nr: 0 62: Improper Dih.: 62: nr: 0 62: Per. Imp. Dih.: 62: nr: 0 62: Tab. Dih.: 62: nr: 0 62: CMAP Dih.: 62: nr: 0 62: GB 1-2 Pol.: 62: nr: 0 62: GB 1-3 Pol.: 62: nr: 0 62: GB 1-4 Pol.: 62: nr: 0 62: GB Polariz.: 62: nr: 0 62: Nonpolar Sol.: 62: nr: 0 62: LJ-14: 62: nr: 1197 62: iatoms: 62: 0 type=186 (LJ14) 0 7 62: 1 type=186 (LJ14) 0 8 62: 2 type=187 (LJ14) 0 9 62: 3 type=188 (LJ14) 0 23 62: 4 type=189 (LJ14) 0 24 62: 5 type=190 (LJ14) 1 5 62: 6 type=190 (LJ14) 1 6 62: 7 type=190 (LJ14) 1 22 62: 8 type=190 (LJ14) 2 5 62: 9 type=190 (LJ14) 2 6 62: 10 type=190 (LJ14) 2 22 62: 11 type=190 (LJ14) 3 5 62: 12 type=190 (LJ14) 3 6 62: 13 type=190 (LJ14) 3 22 62: 14 type=191 (LJ14) 4 10 62: 15 type=191 (LJ14) 4 11 62: 16 type=192 (LJ14) 4 12 62: 17 type=190 (LJ14) 4 25 62: 18 type=192 (LJ14) 4 26 62: 19 type=193 (LJ14) 5 7 62: 20 type=193 (LJ14) 5 8 62: 21 type=191 (LJ14) 5 9 62: 22 type=194 (LJ14) 5 23 62: 23 type=186 (LJ14) 5 24 62: 24 type=191 (LJ14) 6 13 62: 25 type=191 (LJ14) 6 14 62: 26 type=192 (LJ14) 6 15 62: 27 type=195 (LJ14) 6 23 62: 28 type=187 (LJ14) 6 24 62: 29 type=193 (LJ14) 7 10 62: 30 type=193 (LJ14) 7 11 62: 31 type=191 (LJ14) 7 12 62: 32 type=196 (LJ14) 7 22 62: 33 type=193 (LJ14) 8 10 62: 34 type=193 (LJ14) 8 11 62: 35 type=191 (LJ14) 8 12 62: 36 type=196 (LJ14) 8 22 62: 37 type=191 (LJ14) 9 16 62: 38 type=191 (LJ14) 9 17 62: 39 type=187 (LJ14) 9 18 62: 40 type=197 (LJ14) 9 22 62: 41 type=193 (LJ14) 10 13 62: 42 type=193 (LJ14) 10 14 62: 43 type=191 (LJ14) 10 15 62: 44 type=193 (LJ14) 11 13 62: 45 type=193 (LJ14) 11 14 62: 46 type=191 (LJ14) 11 15 62: 47 type=190 (LJ14) 12 19 62: 48 type=190 (LJ14) 12 20 62: 49 type=190 (LJ14) 12 21 62: 50 type=193 (LJ14) 13 16 62: 51 type=193 (LJ14) 13 17 62: 52 type=186 (LJ14) 13 18 62: 53 type=193 (LJ14) 14 16 62: 54 type=193 (LJ14) 14 17 62: 55 type=186 (LJ14) 14 18 62: 56 type=190 (LJ14) 16 19 62: 57 type=190 (LJ14) 16 20 62: 58 type=190 (LJ14) 16 21 62: 59 type=190 (LJ14) 17 19 62: 60 type=190 (LJ14) 17 20 62: 61 type=190 (LJ14) 17 21 62: 62 type=196 (LJ14) 22 27 62: 63 type=197 (LJ14) 22 28 62: 64 type=198 (LJ14) 22 38 62: 65 type=190 (LJ14) 23 25 62: 66 type=195 (LJ14) 23 26 62: 67 type=186 (LJ14) 24 29 62: 68 type=187 (LJ14) 24 30 62: 69 type=187 (LJ14) 24 34 62: 70 type=188 (LJ14) 24 39 62: 71 type=189 (LJ14) 24 40 62: 72 type=190 (LJ14) 25 27 62: 73 type=190 (LJ14) 25 28 62: 74 type=190 (LJ14) 25 38 62: 75 type=191 (LJ14) 26 31 62: 76 type=191 (LJ14) 26 32 62: 77 type=191 (LJ14) 26 33 62: 78 type=191 (LJ14) 26 35 62: 79 type=191 (LJ14) 26 36 62: 80 type=191 (LJ14) 26 37 62: 81 type=190 (LJ14) 26 41 62: 82 type=192 (LJ14) 26 42 62: 83 type=193 (LJ14) 27 29 62: 84 type=191 (LJ14) 27 30 62: 85 type=191 (LJ14) 27 34 62: 86 type=194 (LJ14) 27 39 62: 87 type=186 (LJ14) 27 40 62: 88 type=195 (LJ14) 28 39 62: 89 type=187 (LJ14) 28 40 62: 90 type=193 (LJ14) 29 31 62: 91 type=193 (LJ14) 29 32 62: 92 type=193 (LJ14) 29 33 62: 93 type=193 (LJ14) 29 35 62: 94 type=193 (LJ14) 29 36 62: 95 type=193 (LJ14) 29 37 62: 96 type=196 (LJ14) 29 38 62: 97 type=191 (LJ14) 30 35 62: 98 type=191 (LJ14) 30 36 62: 99 type=191 (LJ14) 30 37 62: 100 type=197 (LJ14) 30 38 62: 101 type=191 (LJ14) 31 34 62: 102 type=191 (LJ14) 32 34 62: 103 type=191 (LJ14) 33 34 62: 104 type=197 (LJ14) 34 38 62: 105 type=196 (LJ14) 38 43 62: 106 type=197 (LJ14) 38 44 62: 107 type=198 (LJ14) 38 58 62: 108 type=190 (LJ14) 39 41 62: 109 type=195 (LJ14) 39 42 62: 110 type=186 (LJ14) 40 45 62: 111 type=186 (LJ14) 40 46 62: 112 type=199 (LJ14) 40 47 62: 113 type=188 (LJ14) 40 59 62: 114 type=189 (LJ14) 40 60 62: 115 type=190 (LJ14) 41 43 62: 116 type=190 (LJ14) 41 44 62: 117 type=190 (LJ14) 41 58 62: 118 type=200 (LJ14) 42 48 62: 119 type=200 (LJ14) 42 50 62: 120 type=190 (LJ14) 42 61 62: 121 type=192 (LJ14) 42 62 62: 122 type=193 (LJ14) 43 45 62: 123 type=193 (LJ14) 43 46 62: 124 type=201 (LJ14) 43 47 62: 125 type=194 (LJ14) 43 59 62: 126 type=186 (LJ14) 43 60 62: 127 type=202 (LJ14) 44 49 62: 128 type=202 (LJ14) 44 51 62: 129 type=200 (LJ14) 44 52 62: 130 type=200 (LJ14) 44 54 62: 131 type=195 (LJ14) 44 59 62: 132 type=187 (LJ14) 44 60 62: 133 type=201 (LJ14) 45 48 62: 134 type=201 (LJ14) 45 50 62: 135 type=196 (LJ14) 45 58 62: 136 type=201 (LJ14) 46 48 62: 137 type=201 (LJ14) 46 50 62: 138 type=196 (LJ14) 46 58 62: 139 type=203 (LJ14) 47 53 62: 140 type=203 (LJ14) 47 55 62: 141 type=204 (LJ14) 47 56 62: 142 type=205 (LJ14) 47 58 62: 143 type=203 (LJ14) 48 51 62: 144 type=204 (LJ14) 48 54 62: 145 type=203 (LJ14) 48 57 62: 146 type=203 (LJ14) 49 50 62: 147 type=206 (LJ14) 49 53 62: 148 type=203 (LJ14) 49 56 62: 149 type=204 (LJ14) 50 52 62: 150 type=203 (LJ14) 50 57 62: 151 type=206 (LJ14) 51 55 62: 152 type=203 (LJ14) 51 56 62: 153 type=203 (LJ14) 52 55 62: 154 type=203 (LJ14) 53 54 62: 155 type=206 (LJ14) 53 57 62: 156 type=206 (LJ14) 55 57 62: 157 type=196 (LJ14) 58 63 62: 158 type=196 (LJ14) 58 64 62: 159 type=198 (LJ14) 58 65 62: 160 type=190 (LJ14) 59 61 62: 161 type=195 (LJ14) 59 62 62: 162 type=188 (LJ14) 60 66 62: 163 type=189 (LJ14) 60 67 62: 164 type=190 (LJ14) 61 63 62: 165 type=190 (LJ14) 61 64 62: 166 type=190 (LJ14) 61 65 62: 167 type=190 (LJ14) 62 68 62: 168 type=192 (LJ14) 62 69 62: 169 type=194 (LJ14) 63 66 62: 170 type=186 (LJ14) 63 67 62: 171 type=194 (LJ14) 64 66 62: 172 type=186 (LJ14) 64 67 62: 173 type=196 (LJ14) 65 70 62: 174 type=197 (LJ14) 65 71 62: 175 type=198 (LJ14) 65 89 62: 176 type=190 (LJ14) 66 68 62: 177 type=195 (LJ14) 66 69 62: 178 type=186 (LJ14) 67 72 62: 179 type=186 (LJ14) 67 73 62: 180 type=187 (LJ14) 67 74 62: 181 type=188 (LJ14) 67 90 62: 182 type=189 (LJ14) 67 91 62: 183 type=190 (LJ14) 68 70 62: 184 type=190 (LJ14) 68 71 62: 185 type=190 (LJ14) 68 89 62: 186 type=191 (LJ14) 69 75 62: 187 type=191 (LJ14) 69 76 62: 188 type=192 (LJ14) 69 77 62: 189 type=190 (LJ14) 69 92 62: 190 type=192 (LJ14) 69 93 62: 191 type=193 (LJ14) 70 72 62: 192 type=193 (LJ14) 70 73 62: 193 type=191 (LJ14) 70 74 62: 194 type=194 (LJ14) 70 90 62: 195 type=186 (LJ14) 70 91 62: 196 type=191 (LJ14) 71 78 62: 197 type=191 (LJ14) 71 79 62: 198 type=187 (LJ14) 71 80 62: 199 type=195 (LJ14) 71 90 62: 200 type=187 (LJ14) 71 91 62: 201 type=193 (LJ14) 72 75 62: 202 type=193 (LJ14) 72 76 62: 203 type=191 (LJ14) 72 77 62: 204 type=196 (LJ14) 72 89 62: 205 type=193 (LJ14) 73 75 62: 206 type=193 (LJ14) 73 76 62: 207 type=191 (LJ14) 73 77 62: 208 type=196 (LJ14) 73 89 62: 209 type=190 (LJ14) 74 81 62: 210 type=207 (LJ14) 74 82 62: 211 type=197 (LJ14) 74 89 62: 212 type=193 (LJ14) 75 78 62: 213 type=193 (LJ14) 75 79 62: 214 type=186 (LJ14) 75 80 62: 215 type=193 (LJ14) 76 78 62: 216 type=193 (LJ14) 76 79 62: 217 type=186 (LJ14) 76 80 62: 218 type=187 (LJ14) 77 83 62: 219 type=187 (LJ14) 77 86 62: 220 type=190 (LJ14) 78 81 62: 221 type=208 (LJ14) 78 82 62: 222 type=190 (LJ14) 79 81 62: 223 type=208 (LJ14) 79 82 62: 224 type=190 (LJ14) 80 84 62: 225 type=190 (LJ14) 80 85 62: 226 type=190 (LJ14) 80 87 62: 227 type=190 (LJ14) 80 88 62: 228 type=190 (LJ14) 81 83 62: 229 type=190 (LJ14) 81 86 62: 230 type=190 (LJ14) 83 87 62: 231 type=190 (LJ14) 83 88 62: 232 type=190 (LJ14) 84 86 62: 233 type=190 (LJ14) 85 86 62: 234 type=196 (LJ14) 89 94 62: 235 type=197 (LJ14) 89 95 62: 236 type=198 (LJ14) 89 100 62: 237 type=190 (LJ14) 90 92 62: 238 type=195 (LJ14) 90 93 62: 239 type=186 (LJ14) 91 96 62: 240 type=186 (LJ14) 91 97 62: 241 type=209 (LJ14) 91 98 62: 242 type=188 (LJ14) 91 101 62: 243 type=189 (LJ14) 91 102 62: 244 type=190 (LJ14) 92 94 62: 245 type=190 (LJ14) 92 95 62: 246 type=190 (LJ14) 92 100 62: 247 type=190 (LJ14) 93 99 62: 248 type=190 (LJ14) 93 103 62: 249 type=192 (LJ14) 93 104 62: 250 type=193 (LJ14) 94 96 62: 251 type=193 (LJ14) 94 97 62: 252 type=210 (LJ14) 94 98 62: 253 type=194 (LJ14) 94 101 62: 254 type=186 (LJ14) 94 102 62: 255 type=195 (LJ14) 95 101 62: 256 type=187 (LJ14) 95 102 62: 257 type=190 (LJ14) 96 99 62: 258 type=196 (LJ14) 96 100 62: 259 type=190 (LJ14) 97 99 62: 260 type=196 (LJ14) 97 100 62: 261 type=211 (LJ14) 98 100 62: 262 type=196 (LJ14) 100 105 62: 263 type=197 (LJ14) 100 106 62: 264 type=198 (LJ14) 100 115 62: 265 type=190 (LJ14) 101 103 62: 266 type=195 (LJ14) 101 104 62: 267 type=186 (LJ14) 102 107 62: 268 type=186 (LJ14) 102 108 62: 269 type=187 (LJ14) 102 109 62: 270 type=188 (LJ14) 102 116 62: 271 type=189 (LJ14) 102 117 62: 272 type=190 (LJ14) 103 105 62: 273 type=190 (LJ14) 103 106 62: 274 type=190 (LJ14) 103 115 62: 275 type=191 (LJ14) 104 110 62: 276 type=191 (LJ14) 104 111 62: 277 type=197 (LJ14) 104 112 62: 278 type=190 (LJ14) 104 118 62: 279 type=192 (LJ14) 104 119 62: 280 type=193 (LJ14) 105 107 62: 281 type=193 (LJ14) 105 108 62: 282 type=191 (LJ14) 105 109 62: 283 type=194 (LJ14) 105 116 62: 284 type=186 (LJ14) 105 117 62: 285 type=195 (LJ14) 106 113 62: 286 type=195 (LJ14) 106 114 62: 287 type=195 (LJ14) 106 116 62: 288 type=187 (LJ14) 106 117 62: 289 type=193 (LJ14) 107 110 62: 290 type=193 (LJ14) 107 111 62: 291 type=196 (LJ14) 107 112 62: 292 type=196 (LJ14) 107 115 62: 293 type=193 (LJ14) 108 110 62: 294 type=193 (LJ14) 108 111 62: 295 type=196 (LJ14) 108 112 62: 296 type=196 (LJ14) 108 115 62: 297 type=197 (LJ14) 109 115 62: 298 type=194 (LJ14) 110 113 62: 299 type=194 (LJ14) 110 114 62: 300 type=194 (LJ14) 111 113 62: 301 type=194 (LJ14) 111 114 62: 302 type=196 (LJ14) 115 120 62: 303 type=197 (LJ14) 115 121 62: 304 type=198 (LJ14) 115 134 62: 305 type=190 (LJ14) 116 118 62: 306 type=195 (LJ14) 116 119 62: 307 type=186 (LJ14) 117 122 62: 308 type=186 (LJ14) 117 123 62: 309 type=187 (LJ14) 117 124 62: 310 type=188 (LJ14) 117 135 62: 311 type=189 (LJ14) 117 136 62: 312 type=190 (LJ14) 118 120 62: 313 type=190 (LJ14) 118 121 62: 314 type=190 (LJ14) 118 134 62: 315 type=191 (LJ14) 119 125 62: 316 type=192 (LJ14) 119 126 62: 317 type=192 (LJ14) 119 130 62: 318 type=190 (LJ14) 119 137 62: 319 type=192 (LJ14) 119 138 62: 320 type=193 (LJ14) 120 122 62: 321 type=193 (LJ14) 120 123 62: 322 type=191 (LJ14) 120 124 62: 323 type=194 (LJ14) 120 135 62: 324 type=186 (LJ14) 120 136 62: 325 type=191 (LJ14) 121 127 62: 326 type=191 (LJ14) 121 128 62: 327 type=191 (LJ14) 121 129 62: 328 type=191 (LJ14) 121 131 62: 329 type=191 (LJ14) 121 132 62: 330 type=191 (LJ14) 121 133 62: 331 type=195 (LJ14) 121 135 62: 332 type=187 (LJ14) 121 136 62: 333 type=193 (LJ14) 122 125 62: 334 type=191 (LJ14) 122 126 62: 335 type=191 (LJ14) 122 130 62: 336 type=196 (LJ14) 122 134 62: 337 type=193 (LJ14) 123 125 62: 338 type=191 (LJ14) 123 126 62: 339 type=191 (LJ14) 123 130 62: 340 type=196 (LJ14) 123 134 62: 341 type=197 (LJ14) 124 134 62: 342 type=193 (LJ14) 125 127 62: 343 type=193 (LJ14) 125 128 62: 344 type=193 (LJ14) 125 129 62: 345 type=193 (LJ14) 125 131 62: 346 type=193 (LJ14) 125 132 62: 347 type=193 (LJ14) 125 133 62: 348 type=191 (LJ14) 126 131 62: 349 type=191 (LJ14) 126 132 62: 350 type=191 (LJ14) 126 133 62: 351 type=191 (LJ14) 127 130 62: 352 type=191 (LJ14) 128 130 62: 353 type=191 (LJ14) 129 130 62: 354 type=196 (LJ14) 134 139 62: 355 type=197 (LJ14) 134 140 62: 356 type=198 (LJ14) 134 144 62: 357 type=190 (LJ14) 135 137 62: 358 type=195 (LJ14) 135 138 62: 359 type=186 (LJ14) 136 141 62: 360 type=186 (LJ14) 136 142 62: 361 type=186 (LJ14) 136 143 62: 362 type=188 (LJ14) 136 145 62: 363 type=189 (LJ14) 136 146 62: 364 type=190 (LJ14) 137 139 62: 365 type=190 (LJ14) 137 140 62: 366 type=190 (LJ14) 137 144 62: 367 type=190 (LJ14) 138 147 62: 368 type=192 (LJ14) 138 148 62: 369 type=193 (LJ14) 139 141 62: 370 type=193 (LJ14) 139 142 62: 371 type=193 (LJ14) 139 143 62: 372 type=194 (LJ14) 139 145 62: 373 type=186 (LJ14) 139 146 62: 374 type=195 (LJ14) 140 145 62: 375 type=187 (LJ14) 140 146 62: 376 type=196 (LJ14) 141 144 62: 377 type=196 (LJ14) 142 144 62: 378 type=196 (LJ14) 143 144 62: 379 type=196 (LJ14) 144 149 62: 380 type=197 (LJ14) 144 150 62: 381 type=198 (LJ14) 144 154 62: 382 type=190 (LJ14) 145 147 62: 383 type=195 (LJ14) 145 148 62: 384 type=186 (LJ14) 146 151 62: 385 type=186 (LJ14) 146 152 62: 386 type=186 (LJ14) 146 153 62: 387 type=188 (LJ14) 146 155 62: 388 type=190 (LJ14) 147 149 62: 389 type=190 (LJ14) 147 150 62: 390 type=190 (LJ14) 147 154 62: 391 type=193 (LJ14) 149 151 62: 392 type=193 (LJ14) 149 152 62: 393 type=193 (LJ14) 149 153 62: 394 type=194 (LJ14) 149 155 62: 395 type=195 (LJ14) 150 155 62: 396 type=196 (LJ14) 151 154 62: 397 type=196 (LJ14) 152 154 62: 398 type=196 (LJ14) 153 154 62: Coulomb-14: 62: nr: 0 62: LJC-14 q: 62: nr: 0 62: LJC Pairs NB: 62: nr: 0 62: LJ (SR): 62: nr: 0 62: Buck.ham (SR): 62: nr: 0 62: LJ: 62: nr: 0 62: B.ham: 62: nr: 0 62: Disper. corr.: 62: nr: 0 62: Coulomb (SR): 62: nr: 0 62: Coul: 62: nr: 0 62: RF excl.: 62: nr: 0 62: Coul. recip.: 62: nr: 0 62: LJ recip.: 62: nr: 0 62: DPD: 62: nr: 0 62: Polarization: 62: nr: 0 62: Water Pol.: 62: nr: 0 62: Thole Pol.: 62: nr: 0 62: Anharm. Pol.: 62: nr: 0 62: Position Rest.: 62: nr: 0 62: Flat-b. P-R.: 62: nr: 0 62: Dis. Rest.: 62: nr: 0 62: D.R.Viol. (nm): 62: nr: 0 62: Orient. Rest.: 62: nr: 0 62: Ori. R. RMSD: 62: nr: 0 62: Angle Rest.: 62: nr: 0 62: Angle Rest. Z: 62: nr: 0 62: Dih. Rest.: 62: nr: 0 62: Dih. Rest. Vi.: 62: nr: 0 62: Constraint: 62: nr: 0 62: Constr. No Co.: 62: nr: 0 62: Settle: 62: nr: 0 62: Virtual site 1: 62: nr: 0 62: Virtual site 2: 62: nr: 0 62: Virt. site 2fd: 62: nr: 0 62: Virtual site 3: 62: nr: 0 62: Virt. site 3fd: 62: nr: 0 62: Vir. site 3fad: 62: nr: 0 62: Vir. site 3out: 62: nr: 0 62: Virt. site 4fd: 62: nr: 0 62: Vir. site 4fdn: 62: nr: 0 62: Virtual site N: 62: nr: 0 62: COM Pull En.: 62: nr: 0 62: Dens. fitting: 62: nr: 0 62: Quantum En.: 62: nr: 0 62: NN Potential: 62: nr: 0 62: Potential: 62: nr: 0 62: Kinetic En.: 62: nr: 0 62: Total Energy: 62: nr: 0 62: Conserved En.: 62: nr: 0 62: Temperature: 62: nr: 0 62: Vir. Temp.: 62: nr: 0 62: Pres. DC: 62: nr: 0 62: Pressure: 62: nr: 0 62: dH/dl constr.: 62: nr: 0 62: dVremain/dl: 62: nr: 0 62: dEkin/dl: 62: nr: 0 62: dVcoul/dl: 62: nr: 0 62: dVvdw/dl: 62: nr: 0 62: dVbonded/dl: 62: nr: 0 62: dVrestraint/dl: 62: nr: 0 62: dVtemp/dl: 62: nr: 0 62: grp[T-Coupling ] nr=1, name=[ rest] 62: grp[Energy Mon. ] nr=1, name=[ rest] 62: grp[Acc. not used] nr=1, name=[ rest] 62: grp[Freeze ] nr=1, name=[ rest] 62: grp[User1 ] nr=1, name=[ rest] 62: grp[User2 ] nr=1, name=[ rest] 62: grp[VCM ] nr=1, name=[ rest] 62: grp[Compressed X] nr=1, name=[ rest] 62: grp[Or. Res. Fit] nr=1, name=[ rest] 62: grp[QMMM ] nr=1, name=[ rest] 62: grpname (11): 62: grpname[0]={name="System"} 62: grpname[1]={name="Protein"} 62: grpname[2]={name="Protein-H"} 62: grpname[3]={name="C-alpha"} 62: grpname[4]={name="Backbone"} 62: grpname[5]={name="MainChain"} 62: grpname[6]={name="MainChain+Cb"} 62: grpname[7]={name="MainChain+H"} 62: grpname[8]={name="SideChain"} 62: grpname[9]={name="SideChain-H"} 62: grpname[10]={name="rest"} 62: groups T-Cou Energ Acc. Freez User1 User2 VCM Compr Or. R QMMM 62: allocated 0 0 0 0 0 0 0 0 0 0 62: groupnr[ *] = 0 0 0 0 0 0 0 0 0 0 62: box (3x3): 62: box[ 0]={ 5.90620e+00, 0.00000e+00, 0.00000e+00} 62: box[ 1]={ 0.00000e+00, 6.84510e+00, 0.00000e+00} 62: box[ 2]={ 0.00000e+00, 0.00000e+00, 3.05170e+00} 62: box_rel (3x3): 62: box_rel[ 0]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 62: box_rel[ 1]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 62: box_rel[ 2]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 62: boxv (3x3): 62: boxv[ 0]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 62: boxv[ 1]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 62: boxv[ 2]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 62: pres_prev (3x3): 62: pres_prev[ 0]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 62: pres_prev[ 1]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 62: pres_prev[ 2]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 62: svir_prev (3x3): 62: svir_prev[ 0]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 62: svir_prev[ 1]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 62: svir_prev[ 2]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 62: fvir_prev (3x3): 62: fvir_prev[ 0]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 62: fvir_prev[ 1]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 62: fvir_prev[ 2]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 62: nosehoover_xi: not available 62: x (156x3): 62: x[ 0]={ 3.53600e+00, 2.23400e+00, -1.19800e+00} 62: x[ 1]={ 3.61200e+00, 2.28800e+00, -1.23600e+00} 62: x[ 2]={ 3.47000e+00, 2.21400e+00, -1.27000e+00} 62: x[ 3]={ 3.49200e+00, 2.28600e+00, -1.12500e+00} 62: x[ 4]={ 3.58900e+00, 2.10700e+00, -1.14300e+00} 62: x[ 5]={ 3.63300e+00, 2.05500e+00, -1.21600e+00} 62: x[ 6]={ 3.68700e+00, 2.14400e+00, -1.03100e+00} 62: x[ 7]={ 3.76300e+00, 2.19500e+00, -1.07000e+00} 62: x[ 8]={ 3.63900e+00, 2.20100e+00, -9.64000e-01} 62: x[ 9]={ 3.74500e+00, 2.02500e+00, -9.56000e-01} 62: x[ 10]={ 3.67600e+00, 1.98900e+00, -8.94000e-01} 62: x[ 11]={ 3.77000e+00, 1.95400e+00, -1.02300e+00} 62: x[ 12]={ 3.86900e+00, 2.06500e+00, -8.77000e-01} 62: x[ 13]={ 3.94500e+00, 2.08300e+00, -9.40000e-01} 62: x[ 14]={ 3.84900e+00, 2.14700e+00, -8.24000e-01} 62: x[ 15]={ 3.90600e+00, 1.95100e+00, -7.84000e-01} 62: x[ 16]={ 3.84100e+00, 1.94600e+00, -7.08000e-01} 62: x[ 17]={ 3.90600e+00, 1.86400e+00, -8.33000e-01} 62: x[ 18]={ 4.04200e+00, 1.97700e+00, -7.30000e-01} 62: x[ 19]={ 4.06900e+00, 1.90300e+00, -6.68000e-01} 62: x[ 20]={ 4.10800e+00, 1.98200e+00, -8.06000e-01} 62: x[ 21]={ 4.04200e+00, 2.06400e+00, -6.80000e-01} 62: x[ 22]={ 3.47400e+00, 2.02600e+00, -1.08400e+00} 62: x[ 23]={ 3.39500e+00, 2.08100e+00, -1.00800e+00} 62: x[ 24]={ 3.47400e+00, 1.89600e+00, -1.10400e+00} 62: x[ 25]={ 3.53600e+00, 1.86000e+00, -1.17400e+00} 62: x[ 26]={ 3.39000e+00, 1.80000e+00, -1.03300e+00} 62: x[ 27]={ 3.31700e+00, 1.85200e+00, -9.90000e-01} 62: x[ 28]={ 3.31400e+00, 1.70300e+00, -1.12300e+00} 62: x[ 29]={ 3.38600e+00, 1.65200e+00, -1.17000e+00} 62: x[ 30]={ 3.22500e+00, 1.60800e+00, -1.04300e+00} 62: x[ 31]={ 3.17700e+00, 1.54700e+00, -1.10600e+00} 62: x[ 32]={ 3.28200e+00, 1.55500e+00, -9.81000e-01} 62: x[ 33]={ 3.15800e+00, 1.66100e+00, -9.91000e-01} 62: x[ 34]={ 3.22900e+00, 1.77100e+00, -1.22900e+00} 62: x[ 35]={ 3.18300e+00, 1.70200e+00, -1.28400e+00} 62: x[ 36]={ 3.16200e+00, 1.83000e+00, -1.18500e+00} 62: x[ 37]={ 3.28800e+00, 1.82700e+00, -1.28800e+00} 62: x[ 38]={ 3.48000e+00, 1.73100e+00, -9.29000e-01} 62: x[ 39]={ 3.57600e+00, 1.66100e+00, -9.66000e-01} 62: x[ 40]={ 3.44900e+00, 1.75500e+00, -8.04000e-01} 62: x[ 41]={ 3.37500e+00, 1.81900e+00, -7.84000e-01} 62: x[ 42]={ 3.51900e+00, 1.69000e+00, -6.92000e-01} 62: x[ 43]={ 3.61500e+00, 1.69700e+00, -7.17000e-01} 62: x[ 44]={ 3.49700e+00, 1.76300e+00, -5.59000e-01} 62: x[ 45]={ 3.40500e+00, 1.80200e+00, -5.58000e-01} 62: x[ 46]={ 3.50600e+00, 1.69800e+00, -4.84000e-01} 62: x[ 47]={ 3.59400e+00, 1.87400e+00, -5.38000e-01} 62: x[ 48]={ 3.56700e+00, 2.00500e+00, -5.80000e-01} 62: x[ 49]={ 3.48100e+00, 2.02500e+00, -6.27000e-01} 62: x[ 50]={ 3.70000e+00, 1.85600e+00, -4.47000e-01} 62: x[ 51]={ 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0.00000e+00} 62: v[ 85]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 62: v[ 86]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 62: v[ 87]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 62: v[ 88]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 62: v[ 89]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 62: v[ 90]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 62: v[ 91]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 62: v[ 92]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 62: v[ 93]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 62: v[ 94]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 62: v[ 95]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 62: v[ 96]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 62: v[ 97]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 62: v[ 98]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 62: v[ 99]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 62: v[ 100]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 62: v[ 101]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 62: v[ 102]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 62: v[ 103]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 62: v[ 104]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 62: v[ 105]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 62: v[ 106]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 62: v[ 107]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 62: v[ 108]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 62: v[ 109]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 62: v[ 110]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 62: v[ 111]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 62: v[ 112]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 62: v[ 113]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 62: v[ 114]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 62: v[ 115]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 62: v[ 116]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 62: v[ 117]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 62: v[ 118]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 62: v[ 119]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 62: v[ 120]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 62: v[ 121]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 62: v[ 122]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 62: v[ 123]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 62: v[ 124]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 62: v[ 125]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 62: v[ 126]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 62: v[ 127]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 62: v[ 128]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 62: v[ 129]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 62: v[ 130]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 62: v[ 131]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 62: v[ 132]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 62: v[ 133]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 62: v[ 134]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 62: v[ 135]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 62: v[ 136]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 62: v[ 137]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 62: v[ 138]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 62: v[ 139]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 62: v[ 140]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 62: v[ 141]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 62: v[ 142]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 62: v[ 143]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 62: v[ 144]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 62: v[ 145]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 62: v[ 146]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 62: v[ 147]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 62: v[ 148]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 62: v[ 149]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 62: v[ 150]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 62: v[ 151]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 62: v[ 152]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 62: v[ 153]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 62: v[ 154]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 62: v[ 155]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 62: Group statistics 62: T-Coupling : 156 (total 156 atoms) 62: Energy Mon. : 156 (total 156 atoms) 62: Acc. not used: 156 (total 156 atoms) 62: Freeze : 156 (total 156 atoms) 62: User1 : 156 (total 156 atoms) 62: User2 : 156 (total 156 atoms) 62: VCM : 156 (total 156 atoms) 62: Compressed X: 156 (total 156 atoms) 62: Or. Res. Fit: 156 (total 156 atoms) 62: QMMM : 156 (total 156 atoms) 62: [ OK ] DumpTest.WorksWithTpr (84 ms) 62: [ RUN ] DumpTest.WorksWithTprAndMdpWriting 62: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/tools/tests/Testing/Temporary/DumpTest_lysozyme.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 62: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/tools/tests/Testing/Temporary/DumpTest_lysozyme.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 62: [ OK ] DumpTest.WorksWithTprAndMdpWriting (15 ms) 62: [----------] 2 tests from DumpTest (99 ms total) 62: 62: [----------] 3 tests from HelpwritingTest 62: [ RUN ] HelpwritingTest.ConvertTprWritesHelp 62: [ OK ] HelpwritingTest.ConvertTprWritesHelp (7 ms) 62: [ RUN ] HelpwritingTest.DumpWritesHelp 62: [ OK ] HelpwritingTest.DumpWritesHelp (2 ms) 62: [ RUN ] HelpwritingTest.ReportMethodsWritesHelp 62: [ OK ] HelpwritingTest.ReportMethodsWritesHelp (4 ms) 62: [----------] 3 tests from HelpwritingTest (14 ms total) 62: 62: [----------] 7 tests from GmxMakeNdx 62: [ RUN ] GmxMakeNdx.WritesDefaultProteinIndexGroups 62: 62: Reading structure file 62: Going to read 0 old index file(s) 62: Analysing residue names: 62: There are: 16 Protein residues 62: Analysing Protein... 62: 62: 0 System : 256 atoms 62: 1 Protein : 256 atoms 62: 2 Protein-H : 139 atoms 62: 3 C-alpha : 16 atoms 62: 4 Backbone : 48 atoms 62: 5 MainChain : 63 atoms 62: 6 MainChain+Cb : 78 atoms 62: 7 MainChain+H : 81 atoms 62: 8 SideChain : 175 atoms 62: 9 SideChain-H : 76 atoms 62: 62: nr : group '!': not 'name' nr name 'splitch' nr Enter: list groups 62: 'a': atom '&': and 'del' nr 'splitres' nr 'l': list residues 62: 't': atom type '|': or 'keep' nr 'splitat' nr 'h': help 62: 'r': residue 'res' nr 'chain' char 62: "name": group 'case': case sensitive 'q': save and quit 62: 'ri': residue index 62: 62: > 62: [ OK ] GmxMakeNdx.WritesDefaultProteinIndexGroups (44 ms) 62: [ RUN ] GmxMakeNdx.HandlesNoStructureInput 62: Going to read 1 old index file(s) 62: Deducing 22 atoms in the system from indices in the index file 62: 62: 0 System : 22 atoms 62: 1 Protein : 22 atoms 62: 2 Protein-H : 10 atoms 62: 3 C-alpha : 1 atoms 62: 4 Backbone : 5 atoms 62: 5 MainChain : 7 atoms 62: 6 MainChain+Cb : 8 atoms 62: 7 MainChain+H : 9 atoms 62: 8 SideChain : 13 atoms 62: 9 SideChain-H : 3 atoms 62: 10 CA : 1 atoms 62: 11 C_&_r_1 : 1 atoms 62: 12 C_&_r_2 : 1 atoms 62: 13 N_&_r_2 : 1 atoms 62: 14 N_&_r_3 : 1 atoms 62: 62: nr : group '!': not 'name' nr name 'splitch' nr Enter: list groups 62: 'a': atom '&': and 'del' nr 'splitres' nr 'l': list residues 62: 't': atom type '|': or 'keep' nr 'splitat' nr 'h': help 62: 'r': residue 'res' nr 'chain' char 62: "name": group 'case': case sensitive 'q': save and quit 62: 'ri': residue index 62: 62: > 62: Copied index group 1 'Protein' 62: Copied index group 2 'Protein-H' 62: Merged two groups with OR: 22 10 -> 22 62: 62: > 62: [ OK ] GmxMakeNdx.HandlesNoStructureInput (14 ms) 62: [ RUN ] GmxMakeNdx.HandlesNotProtein 62: Going to read 1 old index file(s) 62: Deducing 6 atoms in the system from indices in the index file 62: 62: 0 System : 6 atoms 62: 62: nr : group '!': not 'name' nr name 'splitch' nr Enter: list groups 62: 'a': atom '&': and 'del' nr 'splitres' nr 'l': list residues 62: 't': atom type '|': or 'keep' nr 'splitat' nr 'h': help 62: 'r': residue 'res' nr 'chain' char 62: "name": group 'case': case sensitive 'q': save and quit 62: 'ri': residue index 62: 62: > 62: [ OK ] GmxMakeNdx.HandlesNotProtein (20 ms) 62: [ RUN ] GmxMakeNdx.HandlesEmptyIndexResult 62: Going to read 1 old index file(s) 62: Deducing 22 atoms in the system from indices in the index file 62: 62: 0 System : 22 atoms 62: 1 Protein : 22 atoms 62: 2 Protein-H : 10 atoms 62: 3 C-alpha : 1 atoms 62: 4 Backbone : 5 atoms 62: 5 MainChain : 7 atoms 62: 6 MainChain+Cb : 8 atoms 62: 7 MainChain+H : 9 atoms 62: 8 SideChain : 13 atoms 62: 9 SideChain-H : 3 atoms 62: 10 CA : 1 atoms 62: 11 C_&_r_1 : 1 atoms 62: 12 C_&_r_2 : 1 atoms 62: 13 N_&_r_2 : 1 atoms 62: 14 N_&_r_3 : 1 atoms 62: 62: nr : group '!': not 'name' nr name 'splitch' nr Enter: list groups 62: 'a': atom '&': and 'del' nr 'splitres' nr 'l': list residues 62: 't': atom type '|': or 'keep' nr 'splitat' nr 'h': help 62: 'r': residue 'res' nr 'chain' char 62: "name": group 'case': case sensitive 'q': save and quit 62: 'ri': residue index 62: 62: > 62: Copied index group 4 'Backbone' 62: Copied index group 8 'SideChain' 62: Merged two groups with AND: 5 13 -> 0 62: Group is empty 62: 62: > 62: [ OK ] GmxMakeNdx.HandlesEmptyIndexResult (18 ms) 62: [ RUN ] GmxMakeNdx.HandlesEmptyIndexFile 62: Going to read 1 old index file(s) 62: Deducing 6 atoms in the system from indices in the index file 62: 62: 0 System : 6 atoms 62: 62: nr : group '!': not 'name' nr name 'splitch' nr Enter: list groups 62: 'a': atom '&': and 'del' nr 'splitres' nr 'l': list residues 62: 't': atom type '|': or 'keep' nr 'splitat' nr 'h': help 62: 'r': residue 'res' nr 'chain' char 62: "name": group 'case': case sensitive 'q': save and quit 62: 'ri': residue index 62: 62: > 62: Removed group 0 'System' 62: 62: > 62: [ OK ] GmxMakeNdx.HandlesEmptyIndexFile (8 ms) 62: [ RUN ] GmxMakeNdx.Splitres 62: 62: Reading structure file 62: Going to read 0 old index file(s) 62: Analysing residue names: 62: There are: 2 Water residues 62: 62: 0 System : 6 atoms 62: 1 Water : 6 atoms 62: 2 SOL : 6 atoms 62: 62: nr : group '!': not 'name' nr name 'splitch' nr Enter: list groups 62: 'a': atom '&': and 'del' nr 'splitres' nr 'l': list residues 62: 't': atom type '|': or 'keep' nr 'splitat' nr 'h': help 62: 'r': residue 'res' nr 'chain' char 62: "name": group 'case': case sensitive 'q': save and quit 62: 'ri': residue index 62: 62: > 62: Splitting group 1 'Water' into residues 62: 62: > 62: [ OK ] GmxMakeNdx.Splitres (15 ms) 62: [ RUN ] GmxMakeNdx.Splitat 62: 62: Reading structure file 62: Going to read 0 old index file(s) 62: Analysing residue names: 62: There are: 2 Water residues 62: 62: 0 System : 6 atoms 62: 1 Water : 6 atoms 62: 2 SOL : 6 atoms 62: 62: nr : group '!': not 'name' nr name 'splitch' nr Enter: list groups 62: 'a': atom '&': and 'del' nr 'splitres' nr 'l': list residues 62: 't': atom type '|': or 'keep' nr 'splitat' nr 'h': help 62: 'r': residue 'res' nr 'chain' char 62: "name": group 'case': case sensitive 'q': save and quit 62: 'ri': residue index 62: 62: > 62: Splitting group 1 'Water' into atoms 62: 62: > 62: [ OK ] GmxMakeNdx.Splitat (19 ms) 62: [----------] 7 tests from GmxMakeNdx (145 ms total) 62: 62: [----------] 4 tests from ReportMethodsTest 62: 62: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/tools/tests/Testing/Temporary/ReportMethodsTest_lysozyme.mdp]: 62: For a correct single-point energy evaluation with nsteps = 0, use 62: continuation = yes to avoid constraining the input coordinates. 62: 62: Generating 1-4 interactions: fudge = 0.5 62: 62: NOTE 2 [file lysozyme.top, line 1465]: 62: System has non-zero total charge: 2.000000 62: Total charge should normally be an integer. See 62: https://manual.gromacs.org/current/user-guide/floating-point.html 62: for discussion on how close it should be to an integer. 62: 62: 62: 62: Number of degrees of freedom in T-Coupling group rest is 465.00 62: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 62: 62: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/tools/tests/Testing/Temporary/ReportMethodsTest_lysozyme.mdp]: 62: NVE simulation with an initial temperature of zero: will use a Verlet 62: buffer of 10%. Check your energy drift! 62: 62: 62: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/tools/tests/Testing/Temporary/ReportMethodsTest_lysozyme.mdp]: 62: You are using a plain Coulomb cut-off, which might produce artifacts. 62: You might want to consider using PME electrostatics. 62: 62: 62: 62: There were 4 NOTEs 62: Setting the LD random seed to -320864417 62: 62: Generated 330891 of the 330891 non-bonded parameter combinations 62: 62: Generated 330891 of the 330891 1-4 parameter combinations 62: 62: Excluding 3 bonded neighbours molecule type 'Protein_chain_B' 62: 62: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/lysozyme.pdb', all velocities are zero 62: Analysing residue names: 62: There are: 10 Protein residues 62: Analysing Protein... 62: 62: This run will generate roughly 0 Mb of data 62: [ RUN ] ReportMethodsTest.WritesCorrectHeadersFormated 62: [ OK ] ReportMethodsTest.WritesCorrectHeadersFormated (0 ms) 62: [ RUN ] ReportMethodsTest.WritesCorrectHeadersUnformatted 62: [ OK ] ReportMethodsTest.WritesCorrectHeadersUnformatted (0 ms) 62: [ RUN ] ReportMethodsTest.WritesCorrectInformation 62: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/tools/tests/Testing/Temporary/ReportMethodsTest_lysozyme.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 62: [ OK ] ReportMethodsTest.WritesCorrectInformation (4 ms) 62: [ RUN ] ReportMethodsTest.ToolEndToEndTest 62: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/tools/tests/Testing/Temporary/ReportMethodsTest_lysozyme.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 62: section: Methods 62: subsection: Simulation system 62: A system of 1 molecules (156 atoms) was simulated. 62: 62: subsection: Simulation settings 62: A total of 0 ns were simulated with a time step of 1 fs. 62: Neighbor searching was performed every 10 steps. 62: The Cut-off algorithm was used for electrostatic interactions. 62: with a cut-off of 1 nm. 62: A single cut-off of 1.1 nm was used for Van der Waals interactions. 62: [ OK ] ReportMethodsTest.ToolEndToEndTest (22 ms) 62: [----------] 4 tests from ReportMethodsTest (27 ms total) 62: 62: [----------] 4 tests from ConvertTprTest 62: [ RUN ] ConvertTprTest.ExtendRuntimeExtensionTest 62: 62: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/tools/tests/Testing/Temporary/ConvertTprTest_ExtendRuntimeExtensionTest_lysozyme.mdp]: 62: For a correct single-point energy evaluation with nsteps = 0, use 62: continuation = yes to avoid constraining the input coordinates. 62: 62: Generating 1-4 interactions: fudge = 0.5 62: 62: NOTE 2 [file lysozyme.top, line 1465]: 62: System has non-zero total charge: 2.000000 62: Total charge should normally be an integer. See 62: https://manual.gromacs.org/current/user-guide/floating-point.html 62: for discussion on how close it should be to an integer. 62: 62: 62: 62: Number of degrees of freedom in T-Coupling group rest is 465.00 62: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 62: 62: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/tools/tests/Testing/Temporary/ConvertTprTest_ExtendRuntimeExtensionTest_lysozyme.mdp]: 62: NVE simulation with an initial temperature of zero: will use a Verlet 62: buffer of 10%. Check your energy drift! 62: 62: 62: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/tools/tests/Testing/Temporary/ConvertTprTest_ExtendRuntimeExtensionTest_lysozyme.mdp]: 62: You are using a plain Coulomb cut-off, which might produce artifacts. 62: You might want to consider using PME electrostatics. 62: 62: 62: 62: There were 4 NOTEs 62: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/tools/tests/Testing/Temporary/ConvertTprTest_ExtendRuntimeExtensionTest_lysozyme.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 62: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/tools/tests/Testing/Temporary/ConvertTprTest_ExtendRuntimeExtensionTest_lysozyme.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 62: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/tools/tests/Testing/Temporary/ConvertTprTest_ExtendRuntimeExtensionTest_extended.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 62: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/tools/tests/Testing/Temporary/ConvertTprTest_ExtendRuntimeExtensionTest_extended.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 62: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/tools/tests/Testing/Temporary/ConvertTprTest_ExtendRuntimeExtensionTest_extended_again.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 62: Setting the LD random seed to -269615129 62: 62: Generated 330891 of the 330891 non-bonded parameter combinations 62: 62: Generated 330891 of the 330891 1-4 parameter combinations 62: 62: Excluding 3 bonded neighbours molecule type 'Protein_chain_B' 62: 62: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/lysozyme.pdb', all velocities are zero 62: Analysing residue names: 62: There are: 10 Protein residues 62: Analysing Protein... 62: 62: This run will generate roughly 0 Mb of data 62: Input file: 62: Run start step 0 62: Run start time 0 ps 62: Step to be made during run 0 62: Runtime for the run 0 ps 62: Run end step 0 62: Run end time 0 ps 62: 62: Extending remaining runtime by 100 ps 62: 62: Output file: 62: Run start step 0 62: Run start time 0 ps 62: Step to be made during run 100000 62: Runtime for the run 100 ps 62: Run end step 100000 62: Run end time 100 ps 62: 62: Input file: 62: Run start step 0 62: Run start time 0 ps 62: Step to be made during run 100000 62: Runtime for the run 100 ps 62: Run end step 100000 62: Run end time 100 ps 62: 62: Extending remaining runtime by 100 ps 62: 62: Output file: 62: Run start step 0 62: Run start time 0 ps 62: Step to be made during run 200000 62: Runtime for the run 200 ps 62: Run end step 200000 62: Run end time 200 ps 62: 62: [ OK ] ConvertTprTest.ExtendRuntimeExtensionTest (6023 ms) 62: [ RUN ] ConvertTprTest.UntilRuntimeExtensionTest 62: 62: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/tools/tests/Testing/Temporary/ConvertTprTest_UntilRuntimeExtensionTest_lysozyme.mdp]: 62: For a correct single-point energy evaluation with nsteps = 0, use 62: continuation = yes to avoid constraining the input coordinates. 62: 62: Generating 1-4 interactions: fudge = 0.5 62: 62: NOTE 2 [file lysozyme.top, line 1465]: 62: System has non-zero total charge: 2.000000 62: Total charge should normally be an integer. See 62: https://manual.gromacs.org/current/user-guide/floating-point.html 62: for discussion on how close it should be to an integer. 62: 62: 62: 62: Number of degrees of freedom in T-Coupling group rest is 465.00 62: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 62: 62: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/tools/tests/Testing/Temporary/ConvertTprTest_UntilRuntimeExtensionTest_lysozyme.mdp]: 62: NVE simulation with an initial temperature of zero: will use a Verlet 62: buffer of 10%. Check your energy drift! 62: 62: 62: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/tools/tests/Testing/Temporary/ConvertTprTest_UntilRuntimeExtensionTest_lysozyme.mdp]: 62: You are using a plain Coulomb cut-off, which might produce artifacts. 62: You might want to consider using PME electrostatics. 62: 62: 62: 62: There were 4 NOTEs 62: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/tools/tests/Testing/Temporary/ConvertTprTest_UntilRuntimeExtensionTest_lysozyme.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 62: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/tools/tests/Testing/Temporary/ConvertTprTest_UntilRuntimeExtensionTest_lysozyme.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 62: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/tools/tests/Testing/Temporary/ConvertTprTest_UntilRuntimeExtensionTest_extended.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 62: Setting the LD random seed to -1616126081 62: 62: Generated 330891 of the 330891 non-bonded parameter combinations 62: 62: Generated 330891 of the 330891 1-4 parameter combinations 62: 62: Excluding 3 bonded neighbours molecule type 'Protein_chain_B' 62: 62: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/lysozyme.pdb', all velocities are zero 62: Analysing residue names: 62: There are: 10 Protein residues 62: Analysing Protein... 62: 62: This run will generate roughly 0 Mb of data 62: Input file: 62: Run start step 0 62: Run start time 0 ps 62: Step to be made during run 0 62: Runtime for the run 0 ps 62: Run end step 0 62: Run end time 0 ps 62: 62: Extending remaining runtime to 100 ps 62: 62: Output file: 62: Run start step 0 62: Run start time 0 ps 62: Step to be made during run 100000 62: Runtime for the run 100 ps 62: Run end step 100000 62: Run end time 100 ps 62: 62: [ OK ] ConvertTprTest.UntilRuntimeExtensionTest (6054 ms) 62: [ RUN ] ConvertTprTest.nstepRuntimeExtensionTest 62: 62: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/tools/tests/Testing/Temporary/ConvertTprTest_nstepRuntimeExtensionTest_lysozyme.mdp]: 62: For a correct single-point energy evaluation with nsteps = 0, use 62: continuation = yes to avoid constraining the input coordinates. 62: 62: Generating 1-4 interactions: fudge = 0.5 62: 62: NOTE 2 [file lysozyme.top, line 1465]: 62: System has non-zero total charge: 2.000000 62: Total charge should normally be an integer. See 62: https://manual.gromacs.org/current/user-guide/floating-point.html 62: for discussion on how close it should be to an integer. 62: 62: 62: 62: Number of degrees of freedom in T-Coupling group rest is 465.00 62: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 62: 62: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/tools/tests/Testing/Temporary/ConvertTprTest_nstepRuntimeExtensionTest_lysozyme.mdp]: 62: NVE simulation with an initial temperature of zero: will use a Verlet 62: buffer of 10%. Check your energy drift! 62: 62: 62: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/tools/tests/Testing/Temporary/ConvertTprTest_nstepRuntimeExtensionTest_lysozyme.mdp]: 62: You are using a plain Coulomb cut-off, which might produce artifacts. 62: You might want to consider using PME electrostatics. 62: 62: 62: 62: There were 4 NOTEs 62: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/tools/tests/Testing/Temporary/ConvertTprTest_nstepRuntimeExtensionTest_lysozyme.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 62: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/tools/tests/Testing/Temporary/ConvertTprTest_nstepRuntimeExtensionTest_lysozyme.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 62: Setting nsteps to 102 62: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/tools/tests/Testing/Temporary/ConvertTprTest_nstepRuntimeExtensionTest_extended.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 62: Setting the LD random seed to -135266827 62: 62: Generated 330891 of the 330891 non-bonded parameter combinations 62: 62: Generated 330891 of the 330891 1-4 parameter combinations 62: 62: Excluding 3 bonded neighbours molecule type 'Protein_chain_B' 62: 62: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/lysozyme.pdb', all velocities are zero 62: Analysing residue names: 62: There are: 10 Protein residues 62: Analysing Protein... 62: 62: This run will generate roughly 0 Mb of data 62: Input file: 62: Run start step 0 62: Run start time 0 ps 62: Step to be made during run 0 62: Runtime for the run 0 ps 62: Run end step 0 62: Run end time 0 ps 62: 62: 62: Output file: 62: Run start step 0 62: Run start time 0 ps 62: Step to be made during run 102 62: Runtime for the run 0.102 ps 62: Run end step 102 62: Run end time 0.102 ps 62: 62: [ OK ] ConvertTprTest.nstepRuntimeExtensionTest (6076 ms) 62: [ RUN ] ConvertTprTest.generateVelocitiesTest 62: 62: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/tools/tests/Testing/Temporary/ConvertTprTest_generateVelocitiesTest_lysozyme.mdp]: 62: For a correct single-point energy evaluation with nsteps = 0, use 62: continuation = yes to avoid constraining the input coordinates. 62: 62: Generating 1-4 interactions: fudge = 0.5 62: 62: NOTE 2 [file lysozyme.top, line 1465]: 62: System has non-zero total charge: 2.000000 62: Total charge should normally be an integer. See 62: https://manual.gromacs.org/current/user-guide/floating-point.html 62: for discussion on how close it should be to an integer. 62: 62: 62: 62: Number of degrees of freedom in T-Coupling group rest is 465.00 62: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 62: 62: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/tools/tests/Testing/Temporary/ConvertTprTest_generateVelocitiesTest_lysozyme.mdp]: 62: NVE simulation with an initial temperature of zero: will use a Verlet 62: buffer of 10%. Check your energy drift! 62: 62: 62: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/tools/tests/Testing/Temporary/ConvertTprTest_generateVelocitiesTest_lysozyme.mdp]: 62: You are using a plain Coulomb cut-off, which might produce artifacts. 62: You might want to consider using PME electrostatics. 62: 62: 62: 62: There were 4 NOTEs 62: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/tools/tests/Testing/Temporary/ConvertTprTest_generateVelocitiesTest_lysozyme.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 62: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/tools/tests/Testing/Temporary/ConvertTprTest_generateVelocitiesTest_lysozyme.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 62: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/tools/tests/Testing/Temporary/ConvertTprTest_generateVelocitiesTest_new_velocities.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 62: Setting the LD random seed to -421531653 62: 62: Generated 330891 of the 330891 non-bonded parameter combinations 62: 62: Generated 330891 of the 330891 1-4 parameter combinations 62: 62: Excluding 3 bonded neighbours molecule type 'Protein_chain_B' 62: 62: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/lysozyme.pdb', all velocities are zero 62: Analysing residue names: 62: There are: 10 Protein residues 62: Analysing Protein... 62: 62: This run will generate roughly 0 Mb of data 62: [ OK ] ConvertTprTest.generateVelocitiesTest (6113 ms) 62: [----------] 4 tests from ConvertTprTest (24270 ms total) 62: 62: [----------] 1 test from ConvertTprNoVelocityTest 62: [ RUN ] ConvertTprNoVelocityTest.refuseToGenerateVelocitiesWhenTprDidNotHaveVelocitiesInitiallyTest 62: 62: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/tools/tests/Testing/Temporary/ConvertTprNoVelocityTest_refuseToGenerateVelocitiesWhenTprDidNotHaveVelocitiesInitiallyTest_lysozyme.mdp]: 62: For a correct single-point energy evaluation with nsteps = 0, use 62: continuation = yes to avoid constraining the input coordinates. 62: 62: Generating 1-4 interactions: fudge = 0.5 62: 62: NOTE 2 [file lysozyme.top, line 1465]: 62: System has non-zero total charge: 2.000000 62: Total charge should normally be an integer. See 62: https://manual.gromacs.org/current/user-guide/floating-point.html 62: for discussion on how close it should be to an integer. 62: 62: 62: 62: 62: NOTE 3 [file lysozyme.top, line 1465]: 62: Zero-step energy minimization will alter the coordinates before 62: calculating the energy. If you just want the energy of a single point, 62: try zero-step MD (with unconstrained_start = yes). To do multiple 62: single-point energy evaluations of different configurations of the same 62: topology, use mdrun -rerun. 62: 62: Number of degrees of freedom in T-Coupling group rest is 465.00 62: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 62: 62: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/tools/tests/Testing/Temporary/ConvertTprNoVelocityTest_refuseToGenerateVelocitiesWhenTprDidNotHaveVelocitiesInitiallyTest_lysozyme.mdp]: 62: You are using a plain Coulomb cut-off, which might produce artifacts. 62: You might want to consider using PME electrostatics. 62: 62: 62: 62: There were 4 NOTEs 62: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/tools/tests/Testing/Temporary/ConvertTprNoVelocityTest_refuseToGenerateVelocitiesWhenTprDidNotHaveVelocitiesInitiallyTest_lysozyme.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 62: Setting the LD random seed to -73809 62: 62: Generated 330891 of the 330891 non-bonded parameter combinations 62: 62: Generated 330891 of the 330891 1-4 parameter combinations 62: 62: Excluding 3 bonded neighbours molecule type 'Protein_chain_B' 62: Analysing residue names: 62: There are: 10 Protein residues 62: Analysing Protein... 62: 62: This run will generate roughly 0 Mb of data 62: [ OK ] ConvertTprNoVelocityTest.refuseToGenerateVelocitiesWhenTprDidNotHaveVelocitiesInitiallyTest (6148 ms) 62: [----------] 1 test from ConvertTprNoVelocityTest (6148 ms total) 62: 62: [----------] 12 tests from Works/TrjconvWithDifferentInputFormats 62: [ RUN ] Works/TrjconvWithDifferentInputFormats.WithIndexGroupSubset/file_spc2_traj_trr 62: Will write trr: Trajectory in portable xdr format 62: Group 0 ( System) has 6 elements 62: Group 1 (FirstWaterMolecule) has 3 elements 62: Group 2 (SecondWaterMolecule) has 3 elements 62: Select a group: trr version: GMX_trn_file (single precision) 62: Reading frame 0 time 0.000 Reading frame 1 time 1.000 -> frame 0 time 0.000 Last frame 1 time 1.000 62: -> frame 1 time 1.000 62: Last written: frame 1 time 1.000 62: 62: 62: Note that major changes are planned in future for trjconv, to improve usability and utility. 62: Select group for output 62: Selected 2: 'SecondWaterMolecule' 62: [ OK ] Works/TrjconvWithDifferentInputFormats.WithIndexGroupSubset/file_spc2_traj_trr (5 ms) 62: [ RUN ] Works/TrjconvWithDifferentInputFormats.WithIndexGroupSubset/file_spc2_traj_tng 62: Will write trr: Trajectory in portable xdr format 62: Group 0 ( System) has 6 elements 62: Group 1 (FirstWaterMolecule) has 3 elements 62: Group 2 (SecondWaterMolecule) has 3 elements 62: Select a group: Reading frame 0 time 0.000 62: Precision of /build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/spc2-traj.tng is 0.001 (nm) 62: Reading frame 1 time 1.000 -> frame 0 time 0.000 Last frame 1 time 1.000 62: -> frame 1 time 1.000 62: Last written: frame 1 time 1.000 62: 62: 62: Note that major changes are planned in future for trjconv, to improve usability and utility. 62: Select group for output 62: Selected 2: 'SecondWaterMolecule' 62: [ OK ] Works/TrjconvWithDifferentInputFormats.WithIndexGroupSubset/file_spc2_traj_tng (5 ms) 62: [ RUN ] Works/TrjconvWithDifferentInputFormats.WithIndexGroupSubset/file_spc2_traj_xtc 62: Will write trr: Trajectory in portable xdr format 62: Group 0 ( System) has 6 elements 62: Group 1 (FirstWaterMolecule) has 3 elements 62: Group 2 (SecondWaterMolecule) has 3 elements 62: Select a group: Reading frame 0 time 0.000 Reading frame 1 time 1.000 -> frame 0 time 0.000 Last frame 1 time 1.000 62: -> frame 1 time 1.000 62: Last written: frame 1 time 1.000 62: 62: 62: Note that major changes are planned in future for trjconv, to improve usability and utility. 62: Select group for output 62: Selected 2: 'SecondWaterMolecule' 62: [ OK ] Works/TrjconvWithDifferentInputFormats.WithIndexGroupSubset/file_spc2_traj_xtc (4 ms) 62: [ RUN ] Works/TrjconvWithDifferentInputFormats.WithIndexGroupSubset/file_spc2_traj_gro 62: Will write trr: Trajectory in portable xdr format 62: Group 0 ( System) has 6 elements 62: Group 1 (FirstWaterMolecule) has 3 elements 62: Group 2 (SecondWaterMolecule) has 3 elements 62: Select a group: Reading frames from gro file 'Generated by trjconv t= 0.00000 step= 0', 6 atoms. 62: Reading frame 0 time 0.000 62: Precision of /build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/spc2-traj.gro is 0.001 (nm) 62: Reading frame 1 time 1.000 -> frame 0 time 0.000 Last frame 1 time 1.000 62: -> frame 1 time 1.000 62: Last written: frame 1 time 1.000 62: 62: 62: Note that major changes are planned in future for trjconv, to improve usability and utility. 62: Select group for output 62: Selected 2: 'SecondWaterMolecule' 62: [ OK ] Works/TrjconvWithDifferentInputFormats.WithIndexGroupSubset/file_spc2_traj_gro (4 ms) 62: [ RUN ] Works/TrjconvWithDifferentInputFormats.WithIndexGroupSubset/file_spc2_traj_pdb 62: Will write trr: Trajectory in portable xdr format 62: Group 0 ( System) has 6 elements 62: Group 1 (FirstWaterMolecule) has 3 elements 62: Group 2 (SecondWaterMolecule) has 3 elements 62: Select a group: Reading frames from pdb file Reading frame 0 time 0.000 62: Precision of /build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/spc2-traj.pdb is 0.0001 (nm) 62: 'Generated by trjconv t= 1.00000 step= 1', 6 atoms 62: Reading frame 1 time 1.000 -> frame 0 time 0.000 Last frame 1 time 1.000 62: -> frame 1 time 1.000 62: Last written: frame 1 time 1.000 62: 62: 62: Note that major changes are planned in future for trjconv, to improve usability and utility. 62: Select group for output 62: Selected 2: 'SecondWaterMolecule' 62: [ OK ] Works/TrjconvWithDifferentInputFormats.WithIndexGroupSubset/file_spc2_traj_pdb (5 ms) 62: [ RUN ] Works/TrjconvWithDifferentInputFormats.WithIndexGroupSubset/file_spc2_traj_g96 62: Will write trr: Trajectory in portable xdr format 62: Group 0 ( System) has 6 elements 62: Group 1 (FirstWaterMolecule) has 3 elements 62: Group 2 (SecondWaterMolecule) has 3 elements 62: Select a group: Reading frame 0 time 0.000 Reading frame 1 time 1.000 -> frame 0 time 0.000 Last frame 1 time 1.000 62: -> frame 1 time 1.000 62: Last written: frame 1 time 1.000 62: 62: 62: Note that major changes are planned in future for trjconv, to improve usability and utility. 62: Select group for output 62: Selected 2: 'SecondWaterMolecule' 62: [ OK ] Works/TrjconvWithDifferentInputFormats.WithIndexGroupSubset/file_spc2_traj_g96 (6 ms) 62: [ RUN ] Works/TrjconvWithDifferentInputFormats.WithoutTopologyFile/file_spc2_traj_trr 62: Will write trr: Trajectory in portable xdr format 62: Group 0 ( System) has 6 elements 62: Group 1 (FirstWaterMolecule) has 3 elements 62: Group 2 (SecondWaterMolecule) has 3 elements 62: Select a group: Reading frame 0 time 0.000 Reading frame 1 time 1.000 -> frame 0 time 0.000 Last frame 1 time 1.000 62: -> frame 1 time 1.000 62: Last written: frame 1 time 1.000 62: 62: 62: Note that major changes are planned in future for trjconv, to improve usability and utility. 62: Select group for output 62: Selected 2: 'SecondWaterMolecule' 62: [ OK ] Works/TrjconvWithDifferentInputFormats.WithoutTopologyFile/file_spc2_traj_trr (4 ms) 62: [ RUN ] Works/TrjconvWithDifferentInputFormats.WithoutTopologyFile/file_spc2_traj_tng 62: Will write trr: Trajectory in portable xdr format 62: Group 0 ( System) has 6 elements 62: Group 1 (FirstWaterMolecule) has 3 elements 62: Group 2 (SecondWaterMolecule) has 3 elements 62: Select a group: Reading frame 0 time 0.000 62: Precision of /build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/spc2-traj.tng is 0.001 (nm) 62: Reading frame 1 time 1.000 -> frame 0 time 0.000 Last frame 1 time 1.000 62: -> frame 1 time 1.000 62: Last written: frame 1 time 1.000 62: 62: 62: Note that major changes are planned in future for trjconv, to improve usability and utility. 62: Select group for output 62: Selected 2: 'SecondWaterMolecule' 62: [ OK ] Works/TrjconvWithDifferentInputFormats.WithoutTopologyFile/file_spc2_traj_tng (5 ms) 62: [ RUN ] Works/TrjconvWithDifferentInputFormats.WithoutTopologyFile/file_spc2_traj_xtc 62: Will write trr: Trajectory in portable xdr format 62: Group 0 ( System) has 6 elements 62: Group 1 (FirstWaterMolecule) has 3 elements 62: Group 2 (SecondWaterMolecule) has 3 elements 62: Select a group: Reading frame 0 time 0.000 Reading frame 1 time 1.000 -> frame 0 time 0.000 Last frame 1 time 1.000 62: -> frame 1 time 1.000 62: Last written: frame 1 time 1.000 62: 62: 62: Note that major changes are planned in future for trjconv, to improve usability and utility. 62: Select group for output 62: Selected 2: 'SecondWaterMolecule' 62: [ OK ] Works/TrjconvWithDifferentInputFormats.WithoutTopologyFile/file_spc2_traj_xtc (3 ms) 62: [ RUN ] Works/TrjconvWithDifferentInputFormats.WithoutTopologyFile/file_spc2_traj_gro 62: Will write trr: Trajectory in portable xdr format 62: Group 0 ( System) has 6 elements 62: Group 1 (FirstWaterMolecule) has 3 elements 62: Group 2 (SecondWaterMolecule) has 3 elements 62: Select a group: Reading frames from gro file 'Generated by trjconv t= 0.00000 step= 0', 6 atoms. 62: Reading frame 0 time 0.000 62: Precision of /build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/spc2-traj.gro is 0.001 (nm) 62: Reading frame 1 time 1.000 -> frame 0 time 0.000 Last frame 1 time 1.000 62: -> frame 1 time 1.000 62: Last written: frame 1 time 1.000 62: 62: 62: Note that major changes are planned in future for trjconv, to improve usability and utility. 62: Select group for output 62: Selected 2: 'SecondWaterMolecule' 62: [ OK ] Works/TrjconvWithDifferentInputFormats.WithoutTopologyFile/file_spc2_traj_gro (3 ms) 62: [ RUN ] Works/TrjconvWithDifferentInputFormats.WithoutTopologyFile/file_spc2_traj_pdb 62: Will write trr: Trajectory in portable xdr format 62: Group 0 ( System) has 6 elements 62: Group 1 (FirstWaterMolecule) has 3 elements 62: Group 2 (SecondWaterMolecule) has 3 elements 62: Select a group: Reading frames from pdb file Reading frame 0 time 0.000 62: Precision of /build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/spc2-traj.pdb is 0.0001 (nm) 62: 'Generated by trjconv t= 1.00000 step= 1', 6 atoms 62: Reading frame 1 time 1.000 -> frame 0 time 0.000 Last frame 1 time 1.000 62: -> frame 1 time 1.000 62: Last written: frame 1 time 1.000 62: 62: 62: Note that major changes are planned in future for trjconv, to improve usability and utility. 62: Select group for output 62: Selected 2: 'SecondWaterMolecule' 62: [ OK ] Works/TrjconvWithDifferentInputFormats.WithoutTopologyFile/file_spc2_traj_pdb (4 ms) 62: [ RUN ] Works/TrjconvWithDifferentInputFormats.WithoutTopologyFile/file_spc2_traj_g96 62: Will write trr: Trajectory in portable xdr format 62: Group 0 ( System) has 6 elements 62: Group 1 (FirstWaterMolecule) has 3 elements 62: Group 2 (SecondWaterMolecule) has 3 elements 62: Select a group: Reading frame 0 time 0.000 Reading frame 1 time 1.000 -> frame 0 time 0.000 Last frame 1 time 1.000 62: -> frame 1 time 1.000 62: Last written: frame 1 time 1.000 62: 62: 62: Note that major changes are planned in future for trjconv, to improve usability and utility. 62: Select group for output 62: Selected 2: 'SecondWaterMolecule' 62: [ OK ] Works/TrjconvWithDifferentInputFormats.WithoutTopologyFile/file_spc2_traj_g96 (4 ms) 62: [----------] 12 tests from Works/TrjconvWithDifferentInputFormats (58 ms total) 62: 62: [----------] 30 tests from Works/TrjconvDumpTest 62: [ RUN ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_trr_dump_time__1_00 62: Will write trr: Trajectory in portable xdr format 62: Reading frame 0 time 0.000 Reading frame 0 time 0.000 Reading frame 1 time 1.000 62: Dumping frame at t= 0 ps 62: -> frame 0 time 0.000 62: Last written: frame 0 time 0.000 62: 62: 62: Note that major changes are planned in future for trjconv, to improve usability and utility. 62: [ OK ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_trr_dump_time__1_00 (2 ms) 62: [ RUN ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_trr_dump_time_0_00 62: Will write trr: Trajectory in portable xdr format 62: Reading frame 0 time 0.000 Reading frame 0 time 0.000 Reading frame 1 time 1.000 62: Dumping frame at t= 0 ps 62: -> frame 0 time 0.000 62: Last written: frame 0 time 0.000 62: 62: 62: Note that major changes are planned in future for trjconv, to improve usability and utility. 62: [ OK ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_trr_dump_time_0_00 (2 ms) 62: [ RUN ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_trr_dump_time_0_30 62: Will write trr: Trajectory in portable xdr format 62: Reading frame 0 time 0.000 Reading frame 0 time 0.000 Reading frame 1 time 1.000 Last frame 1 time 1.000 62: 62: Dumping frame at t= 0 ps 62: -> frame 0 time 0.000 62: Last written: frame 0 time 0.000 62: 62: 62: Note that major changes are planned in future for trjconv, to improve usability and utility. 62: [ OK ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_trr_dump_time_0_30 (2 ms) 62: [ RUN ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_trr_dump_time_1_00 62: Will write trr: Trajectory in portable xdr format 62: Reading frame 0 time 0.000 Reading frame 0 time 0.000 Reading frame 1 time 1.000 Last frame 1 time 1.000 62: 62: Dumping frame at t= 1 ps 62: -> frame 0 time 1.000 62: Last written: frame 0 time 1.000 62: 62: 62: Note that major changes are planned in future for trjconv, to improve usability and utility. 62: [ OK ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_trr_dump_time_1_00 (2 ms) 62: [ RUN ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_trr_dump_time_999999_00 62: Will write trr: Trajectory in portable xdr format 62: Reading frame 0 time 0.000 Reading frame 0 time 0.000 Reading frame 1 time 1.000 Last frame 1 time 1.000 62: 62: Dumping frame at t= 1 ps 62: -> frame 0 time 1.000 62: Last written: frame 0 time 1.000 62: 62: 62: Note that major changes are planned in future for trjconv, to improve usability and utility. 62: [ OK ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_trr_dump_time_999999_00 (6 ms) 62: [ RUN ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_tng_dump_time__1_00 62: Will write trr: Trajectory in portable xdr format 62: Reading frame 0 time 0.000 Reading frame 0 time 0.000 62: Precision of /build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/spc2-traj.tng is 0.001 (nm) 62: Reading frame 1 time 1.000 62: Dumping frame at t= 0 ps 62: -> frame 0 time 0.000 62: Last written: frame 0 time 0.000 62: 62: 62: Note that major changes are planned in future for trjconv, to improve usability and utility. 62: [ OK ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_tng_dump_time__1_00 (5 ms) 62: [ RUN ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_tng_dump_time_0_00 62: Will write trr: Trajectory in portable xdr format 62: Reading frame 0 time 0.000 Reading frame 0 time 0.000 62: Precision of /build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/spc2-traj.tng is 0.001 (nm) 62: Reading frame 1 time 1.000 62: Dumping frame at t= 0 ps 62: -> frame 0 time 0.000 62: Last written: frame 0 time 0.000 62: 62: 62: Note that major changes are planned in future for trjconv, to improve usability and utility. 62: [ OK ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_tng_dump_time_0_00 (4 ms) 62: [ RUN ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_tng_dump_time_0_30 62: Will write trr: Trajectory in portable xdr format 62: Reading frame 0 time 0.000 Reading frame 0 time 0.000 62: Precision of /build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/spc2-traj.tng is 0.001 (nm) 62: Reading frame 1 time 1.000 Last frame 1 time 1.000 62: 62: Dumping frame at t= 0 ps 62: -> frame 0 time 0.000 62: Last written: frame 0 time 0.000 62: 62: 62: Note that major changes are planned in future for trjconv, to improve usability and utility. 62: [ OK ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_tng_dump_time_0_30 (4 ms) 62: [ RUN ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_tng_dump_time_1_00 62: Will write trr: Trajectory in portable xdr format 62: Reading frame 0 time 0.000 Reading frame 0 time 0.000 62: Precision of /build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/spc2-traj.tng is 0.001 (nm) 62: Reading frame 1 time 1.000 Last frame 1 time 1.000 62: 62: Dumping frame at t= 1 ps 62: -> frame 0 time 1.000 62: Last written: frame 0 time 1.000 62: 62: 62: Note that major changes are planned in future for trjconv, to improve usability and utility. 62: [ OK ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_tng_dump_time_1_00 (5 ms) 62: [ RUN ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_tng_dump_time_999999_00 62: Will write trr: Trajectory in portable xdr format 62: Reading frame 0 time 0.000 Reading frame 0 time 0.000 62: Precision of /build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/spc2-traj.tng is 0.001 (nm) 62: Reading frame 1 time 1.000 Last frame 1 time 1.000 62: 62: Dumping frame at t= 1 ps 62: -> frame 0 time 1.000 62: Last written: frame 0 time 1.000 62: 62: 62: Note that major changes are planned in future for trjconv, to improve usability and utility. 62: [ OK ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_tng_dump_time_999999_00 (4 ms) 62: [ RUN ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_xtc_dump_time__1_00 62: Will write trr: Trajectory in portable xdr format 62: Reading frame 0 time 0.000 Reading frame 0 time 0.000 Reading frame 1 time 1.000 62: Dumping frame at t= 0 ps 62: -> frame 0 time 0.000 62: Last written: frame 0 time 0.000 62: 62: 62: Note that major changes are planned in future for trjconv, to improve usability and utility. 62: [ OK ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_xtc_dump_time__1_00 (2 ms) 62: [ RUN ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_xtc_dump_time_0_00 62: Will write trr: Trajectory in portable xdr format 62: Reading frame 0 time 0.000 Reading frame 0 time 0.000 Reading frame 1 time 1.000 62: Dumping frame at t= 0 ps 62: -> frame 0 time 0.000 62: Last written: frame 0 time 0.000 62: 62: 62: Note that major changes are planned in future for trjconv, to improve usability and utility. 62: [ OK ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_xtc_dump_time_0_00 (2 ms) 62: [ RUN ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_xtc_dump_time_0_30 62: Will write trr: Trajectory in portable xdr format 62: Reading frame 0 time 0.000 Reading frame 0 time 0.000 Reading frame 1 time 1.000 Last frame 1 time 1.000 62: 62: Dumping frame at t= 0 ps 62: -> frame 0 time 0.000 62: Last written: frame 0 time 0.000 62: 62: 62: Note that major changes are planned in future for trjconv, to improve usability and utility. 62: [ OK ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_xtc_dump_time_0_30 (4 ms) 62: [ RUN ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_xtc_dump_time_1_00 62: Will write trr: Trajectory in portable xdr format 62: Reading frame 0 time 0.000 Reading frame 0 time 0.000 Reading frame 1 time 1.000 Last frame 1 time 1.000 62: 62: Dumping frame at t= 1 ps 62: -> frame 0 time 1.000 62: Last written: frame 0 time 1.000 62: 62: 62: Note that major changes are planned in future for trjconv, to improve usability and utility. 62: [ OK ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_xtc_dump_time_1_00 (2 ms) 62: [ RUN ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_xtc_dump_time_999999_00 62: Will write trr: Trajectory in portable xdr format 62: Reading frame 0 time 0.000 Reading frame 0 time 0.000 Reading frame 1 time 1.000 Last frame 1 time 1.000 62: 62: Dumping frame at t= 1 ps 62: -> frame 0 time 1.000 62: Last written: frame 0 time 1.000 62: 62: 62: Note that major changes are planned in future for trjconv, to improve usability and utility. 62: [ OK ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_xtc_dump_time_999999_00 (2 ms) 62: [ RUN ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_gro_dump_time__1_00 62: Will write trr: Trajectory in portable xdr format 62: Reading frames from gro file 'Generated by trjconv t= 0.00000 step= 0', 6 atoms. 62: Reading frame 0 time 0.000 Reading frames from gro file 'Generated by trjconv t= 0.00000 step= 0', 6 atoms. 62: Reading frame 0 time 0.000 62: Precision of /build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/spc2-traj.gro is 0.001 (nm) 62: Reading frame 1 time 1.000 62: Dumping frame at t= 0 ps 62: -> frame 0 time 0.000 62: Last written: frame 0 time 0.000 62: 62: 62: Note that major changes are planned in future for trjconv, to improve usability and utility. 62: [ OK ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_gro_dump_time__1_00 (2 ms) 62: [ RUN ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_gro_dump_time_0_00 62: Will write trr: Trajectory in portable xdr format 62: Reading frames from gro file 'Generated by trjconv t= 0.00000 step= 0', 6 atoms. 62: Reading frame 0 time 0.000 Reading frames from gro file 'Generated by trjconv t= 0.00000 step= 0', 6 atoms. 62: Reading frame 0 time 0.000 62: Precision of /build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/spc2-traj.gro is 0.001 (nm) 62: Reading frame 1 time 1.000 62: Dumping frame at t= 0 ps 62: -> frame 0 time 0.000 62: Last written: frame 0 time 0.000 62: 62: 62: Note that major changes are planned in future for trjconv, to improve usability and utility. 62: [ OK ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_gro_dump_time_0_00 (3 ms) 62: [ RUN ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_gro_dump_time_0_30 62: Will write trr: Trajectory in portable xdr format 62: Reading frames from gro file 'Generated by trjconv t= 0.00000 step= 0', 6 atoms. 62: Reading frame 0 time 0.000 Reading frames from gro file 'Generated by trjconv t= 0.00000 step= 0', 6 atoms. 62: Reading frame 0 time 0.000 62: Precision of /build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/spc2-traj.gro is 0.001 (nm) 62: Reading frame 1 time 1.000 Last frame 1 time 1.000 62: 62: Dumping frame at t= 0 ps 62: -> frame 0 time 0.000 62: Last written: frame 0 time 0.000 62: 62: 62: Note that major changes are planned in future for trjconv, to improve usability and utility. 62: [ OK ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_gro_dump_time_0_30 (7 ms) 62: [ RUN ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_gro_dump_time_1_00 62: Will write trr: Trajectory in portable xdr format 62: Reading frames from gro file 'Generated by trjconv t= 0.00000 step= 0', 6 atoms. 62: Reading frame 0 time 0.000 Reading frames from gro file 'Generated by trjconv t= 0.00000 step= 0', 6 atoms. 62: Reading frame 0 time 0.000 62: Precision of /build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/spc2-traj.gro is 0.001 (nm) 62: Reading frame 1 time 1.000 Last frame 1 time 1.000 62: 62: Dumping frame at t= 1 ps 62: -> frame 0 time 1.000 62: Last written: frame 0 time 1.000 62: 62: 62: Note that major changes are planned in future for trjconv, to improve usability and utility. 62: [ OK ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_gro_dump_time_1_00 (4 ms) 62: [ RUN ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_gro_dump_time_999999_00 62: Will write trr: Trajectory in portable xdr format 62: Reading frames from gro file 'Generated by trjconv t= 0.00000 step= 0', 6 atoms. 62: Reading frame 0 time 0.000 Reading frames from gro file 'Generated by trjconv t= 0.00000 step= 0', 6 atoms. 62: Reading frame 0 time 0.000 62: Precision of /build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/spc2-traj.gro is 0.001 (nm) 62: Reading frame 1 time 1.000 Last frame 1 time 1.000 62: 62: Dumping frame at t= 1 ps 62: -> frame 0 time 1.000 62: Last written: frame 0 time 1.000 62: 62: 62: Note that major changes are planned in future for trjconv, to improve usability and utility. 62: [ OK ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_gro_dump_time_999999_00 (3 ms) 62: [ RUN ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_pdb_dump_time__1_00 62: Will write trr: Trajectory in portable xdr format 62: Reading frames from pdb file Reading frame 0 time 0.000 Reading frames from pdb file Reading frame 0 time 0.000 62: Precision of /build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/spc2-traj.pdb is 0.0001 (nm) 62: 'Generated by trjconv t= 1.00000 step= 1', 6 atoms 62: Reading frame 1 time 1.000 62: Dumping frame at t= 0 ps 62: -> frame 0 time 0.000 62: Last written: frame 0 time 0.000 62: 62: 62: Note that major changes are planned in future for trjconv, to improve usability and utility. 62: [ OK ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_pdb_dump_time__1_00 (2 ms) 62: [ RUN ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_pdb_dump_time_0_00 62: Will write trr: Trajectory in portable xdr format 62: Reading frames from pdb file Reading frame 0 time 0.000 Reading frames from pdb file Reading frame 0 time 0.000 62: Precision of /build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/spc2-traj.pdb is 0.0001 (nm) 62: 'Generated by trjconv t= 1.00000 step= 1', 6 atoms 62: Reading frame 1 time 1.000 62: Dumping frame at t= 0 ps 62: -> frame 0 time 0.000 62: Last written: frame 0 time 0.000 62: 62: 62: Note that major changes are planned in future for trjconv, to improve usability and utility. 62: [ OK ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_pdb_dump_time_0_00 (2 ms) 62: [ RUN ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_pdb_dump_time_0_30 62: Will write trr: Trajectory in portable xdr format 62: Reading frames from pdb file Reading frame 0 time 0.000 Reading frames from pdb file Reading frame 0 time 0.000 62: Precision of /build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/spc2-traj.pdb is 0.0001 (nm) 62: 'Generated by trjconv t= 1.00000 step= 1', 6 atoms 62: Reading frame 1 time 1.000 Last frame 1 time 1.000 62: 62: Dumping frame at t= 0 ps 62: -> frame 0 time 0.000 62: Last written: frame 0 time 0.000 62: 62: 62: Note that major changes are planned in future for trjconv, to improve usability and utility. 62: [ OK ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_pdb_dump_time_0_30 (2 ms) 62: [ RUN ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_pdb_dump_time_1_00 62: Will write trr: Trajectory in portable xdr format 62: Reading frames from pdb file Reading frame 0 time 0.000 Reading frames from pdb file Reading frame 0 time 0.000 62: Precision of /build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/spc2-traj.pdb is 0.0001 (nm) 62: 'Generated by trjconv t= 1.00000 step= 1', 6 atoms 62: Reading frame 1 time 1.000 Last frame 1 time 1.000 62: 62: Dumping frame at t= 1 ps 62: -> frame 0 time 1.000 62: Last written: frame 0 time 1.000 62: 62: 62: Note that major changes are planned in future for trjconv, to improve usability and utility. 62: [ OK ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_pdb_dump_time_1_00 (2 ms) 62: [ RUN ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_pdb_dump_time_999999_00 62: Will write trr: Trajectory in portable xdr format 62: Reading frames from pdb file Reading frame 0 time 0.000 Reading frames from pdb file Reading frame 0 time 0.000 62: Precision of /build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/spc2-traj.pdb is 0.0001 (nm) 62: 'Generated by trjconv t= 1.00000 step= 1', 6 atoms 62: Reading frame 1 time 1.000 Last frame 1 time 1.000 62: 62: Dumping frame at t= 1 ps 62: -> frame 0 time 1.000 62: Last written: frame 0 time 1.000 62: 62: 62: Note that major changes are planned in future for trjconv, to improve usability and utility. 62: [ OK ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_pdb_dump_time_999999_00 (3 ms) 62: [ RUN ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_g96_dump_time__1_00 62: Will write trr: Trajectory in portable xdr format 62: Reading frame 0 time 0.000 Reading frame 0 time 0.000 Reading frame 1 time 1.000 62: Dumping frame at t= 0 ps 62: -> frame 0 time 0.000 62: Last written: frame 0 time 0.000 62: 62: 62: Note that major changes are planned in future for trjconv, to improve usability and utility. 62: [ OK ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_g96_dump_time__1_00 (3 ms) 62: [ RUN ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_g96_dump_time_0_00 62: Will write trr: Trajectory in portable xdr format 62: Reading frame 0 time 0.000 Reading frame 0 time 0.000 Reading frame 1 time 1.000 62: Dumping frame at t= 0 ps 62: -> frame 0 time 0.000 62: Last written: frame 0 time 0.000 62: 62: 62: Note that major changes are planned in future for trjconv, to improve usability and utility. 62: [ OK ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_g96_dump_time_0_00 (4 ms) 62: [ RUN ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_g96_dump_time_0_30 62: Will write trr: Trajectory in portable xdr format 62: Reading frame 0 time 0.000 Reading frame 0 time 0.000 Reading frame 1 time 1.000 Last frame 1 time 1.000 62: 62: Dumping frame at t= 0 ps 62: -> frame 0 time 0.000 62: Last written: frame 0 time 0.000 62: 62: 62: Note that major changes are planned in future for trjconv, to improve usability and utility. 62: [ OK ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_g96_dump_time_0_30 (3 ms) 62: [ RUN ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_g96_dump_time_1_00 62: Will write trr: Trajectory in portable xdr format 62: Reading frame 0 time 0.000 Reading frame 0 time 0.000 Reading frame 1 time 1.000 Last frame 1 time 1.000 62: 62: Dumping frame at t= 1 ps 62: -> frame 0 time 1.000 62: Last written: frame 0 time 1.000 62: 62: 62: Note that major changes are planned in future for trjconv, to improve usability and utility. 62: [ OK ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_g96_dump_time_1_00 (3 ms) 62: [ RUN ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_g96_dump_time_999999_00 62: Will write trr: Trajectory in portable xdr format 62: Reading frame 0 time 0.000 Reading frame 0 time 0.000 Reading frame 1 time 1.000 Last frame 1 time 1.000 62: 62: Dumping frame at t= 1 ps 62: -> frame 0 time 1.000 62: Last written: frame 0 time 1.000 62: 62: 62: Note that major changes are planned in future for trjconv, to improve usability and utility. 62: [ OK ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_g96_dump_time_999999_00 (4 ms) 62: [----------] 30 tests from Works/TrjconvDumpTest (114 ms total) 62: 62: [----------] Global test environment tear-down 62: [==========] 63 tests from 8 test suites ran. (45026 ms total) 62: [ PASSED ] 63 tests. 62/92 Test #62: ToolUnitTests ............................. Passed 45.12 sec test 63 Start 63: ToolWithLeaksUnitTests 63: Test command: /build/reproducible-path/gromacs-2025.1/build/basic-dp/bin/tool-test-with-leaks "--gtest_output=xml:/build/reproducible-path/gromacs-2025.1/build/basic-dp/Testing/Temporary/ToolWithLeaksUnitTests.xml" 63: Working Directory: /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/tools/tests 63: Test timeout computed to be: 1920 63: [==========] Running 2 tests from 2 test suites. 63: [----------] Global test environment set-up. 63: [----------] 1 test from ConvertTprTest 63: [ RUN ] ConvertTprTest.selectIndexTest 63: 63: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/tools/tests/Testing/Temporary/ConvertTprTest_selectIndexTest_lysozyme.mdp]: 63: For a correct single-point energy evaluation with nsteps = 0, use 63: continuation = yes to avoid constraining the input coordinates. 63: 63: Generating 1-4 interactions: fudge = 0.5 63: 63: NOTE 2 [file lysozyme.top, line 1465]: 63: System has non-zero total charge: 2.000000 63: Total charge should normally be an integer. See 63: https://manual.gromacs.org/current/user-guide/floating-point.html 63: for discussion on how close it should be to an integer. 63: 63: 63: 63: Number of degrees of freedom in T-Coupling group rest is 465.00 63: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 63: 63: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/tools/tests/Testing/Temporary/ConvertTprTest_selectIndexTest_lysozyme.mdp]: 63: NVE simulation with an initial temperature of zero: will use a Verlet 63: buffer of 10%. Check your energy drift! 63: 63: 63: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/tools/tests/Testing/Temporary/ConvertTprTest_selectIndexTest_lysozyme.mdp]: 63: You are using a plain Coulomb cut-off, which might produce artifacts. 63: You might want to consider using PME electrostatics. 63: 63: 63: 63: There were 4 NOTEs 63: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/tools/tests/Testing/Temporary/ConvertTprTest_selectIndexTest_lysozyme.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 63: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/tools/tests/Testing/Temporary/ConvertTprTest_selectIndexTest_lysozyme.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 63: Group 0 ( System) has 156 elements 63: Group 1 ( Protein) has 156 elements 63: Group 2 ( Protein-H) has 75 elements 63: Group 3 ( C-alpha) has 10 elements 63: Group 4 ( Backbone) has 30 elements 63: Group 5 ( MainChain) has 40 elements 63: Group 6 ( MainChain+Cb) has 49 elements 63: Group 7 ( MainChain+H) has 52 elements 63: Group 8 ( SideChain) has 104 elements 63: Group 9 ( SideChain-H) has 35 elements 63: Select a group: Will write subset Protein-H of original tpx containing 75 atoms 63: Reduced ilist BONDS from 156 to 75 entries 63: Reduced ilist ANGLES from 281 to 98 entries 63: Reduced ilist PDIHS from 29 to 12 entries 63: Reduced ilist RBDIHS from 313 to 89 entries 63: Reduced ilist LJ14 from 399 to 107 entries 63: Reduced block excls from 156 to 75 index-, 1828 to 635 a-entries 63: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/tools/tests/Testing/Temporary/ConvertTprTest_selectIndexTest_extended.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 63: Setting the LD random seed to -25829489 63: 63: Generated 330891 of the 330891 non-bonded parameter combinations 63: 63: Generated 330891 of the 330891 1-4 parameter combinations 63: 63: Excluding 3 bonded neighbours molecule type 'Protein_chain_B' 63: 63: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/lysozyme.pdb', all velocities are zero 63: Analysing residue names: 63: There are: 10 Protein residues 63: Analysing Protein... 63: 63: This run will generate roughly 0 Mb of data 63: Selected 2: 'Protein-H' 63: [ OK ] ConvertTprTest.selectIndexTest (5950 ms) 63: [----------] 1 test from ConvertTprTest (5950 ms total) 63: 63: [----------] 1 test from ConvertTprNoVelocityTest 63: [ RUN ] ConvertTprNoVelocityTest.selectIndexTestWithoutVelocity 63: 63: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/tools/tests/Testing/Temporary/ConvertTprNoVelocityTest_selectIndexTestWithoutVelocity_lysozyme.mdp]: 63: For a correct single-point energy evaluation with nsteps = 0, use 63: continuation = yes to avoid constraining the input coordinates. 63: 63: Generating 1-4 interactions: fudge = 0.5 63: 63: NOTE 2 [file lysozyme.top, line 1465]: 63: System has non-zero total charge: 2.000000 63: Total charge should normally be an integer. See 63: https://manual.gromacs.org/current/user-guide/floating-point.html 63: for discussion on how close it should be to an integer. 63: 63: 63: 63: 63: NOTE 3 [file lysozyme.top, line 1465]: 63: Zero-step energy minimization will alter the coordinates before 63: calculating the energy. If you just want the energy of a single point, 63: try zero-step MD (with unconstrained_start = yes). To do multiple 63: single-point energy evaluations of different configurations of the same 63: topology, use mdrun -rerun. 63: 63: Number of degrees of freedom in T-Coupling group rest is 465.00 63: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 63: 63: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/tools/tests/Testing/Temporary/ConvertTprNoVelocityTest_selectIndexTestWithoutVelocity_lysozyme.mdp]: 63: You are using a plain Coulomb cut-off, which might produce artifacts. 63: You might want to consider using PME electrostatics. 63: 63: 63: 63: There were 4 NOTEs 63: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/tools/tests/Testing/Temporary/ConvertTprNoVelocityTest_selectIndexTestWithoutVelocity_lysozyme.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 63: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/tools/tests/Testing/Temporary/ConvertTprNoVelocityTest_selectIndexTestWithoutVelocity_lysozyme.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 63: Group 0 ( System) has 156 elements 63: Group 1 ( Protein) has 156 elements 63: Group 2 ( Protein-H) has 75 elements 63: Group 3 ( C-alpha) has 10 elements 63: Group 4 ( Backbone) has 30 elements 63: Group 5 ( MainChain) has 40 elements 63: Group 6 ( MainChain+Cb) has 49 elements 63: Group 7 ( MainChain+H) has 52 elements 63: Group 8 ( SideChain) has 104 elements 63: Group 9 ( SideChain-H) has 35 elements 63: Select a group: Will write subset Protein-H of original tpx containing 75 atoms 63: Reduced ilist BONDS from 156 to 75 entries 63: Reduced ilist ANGLES from 281 to 98 entries 63: Reduced ilist PDIHS from 29 to 12 entries 63: Reduced ilist RBDIHS from 313 to 89 entries 63: Reduced ilist LJ14 from 399 to 107 entries 63: Reduced block excls from 156 to 75 index-, 1828 to 635 a-entries 63: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/tools/tests/Testing/Temporary/ConvertTprNoVelocityTest_selectIndexTestWithoutVelocity_extended.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 63: Setting the LD random seed to 1648360175 63: 63: Generated 330891 of the 330891 non-bonded parameter combinations 63: 63: Generated 330891 of the 330891 1-4 parameter combinations 63: 63: Excluding 3 bonded neighbours molecule type 'Protein_chain_B' 63: Analysing residue names: 63: There are: 10 Protein residues 63: Analysing Protein... 63: 63: This run will generate roughly 0 Mb of data 63: Selected 2: 'Protein-H' 63: [ OK ] ConvertTprNoVelocityTest.selectIndexTestWithoutVelocity (5795 ms) 63: [----------] 1 test from ConvertTprNoVelocityTest (5795 ms total) 63: 63: [----------] Global test environment tear-down 63: [==========] 2 tests from 2 test suites ran. (11746 ms total) 63: [ PASSED ] 2 tests. 63/92 Test #63: ToolWithLeaksUnitTests .................... Passed 11.84 sec test 64 Start 64: FileIOTests 64: Test command: /build/reproducible-path/gromacs-2025.1/build/basic-dp/bin/fileio-test "--gtest_output=xml:/build/reproducible-path/gromacs-2025.1/build/basic-dp/Testing/Temporary/FileIOTests.xml" 64: Working Directory: /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/fileio/tests 64: Test timeout computed to be: 30 64: [==========] Running 421 tests from 17 test suites. 64: [----------] Global test environment set-up. 64: [----------] 4 tests from Checkpoint 64: [ RUN ] Checkpoint.ReadingThrowsWhenValueNotPresent 64: [ OK ] Checkpoint.ReadingThrowsWhenValueNotPresent (0 ms) 64: [ RUN ] Checkpoint.ReadingDoesNotThrowWhenValuePresent 64: [ OK ] Checkpoint.ReadingDoesNotThrowWhenValuePresent (0 ms) 64: [ RUN ] Checkpoint.KvtRoundTripInt64 64: [ OK ] Checkpoint.KvtRoundTripInt64 (0 ms) 64: [ RUN ] Checkpoint.KvtRoundTripReal 64: [ OK ] Checkpoint.KvtRoundTripReal (0 ms) 64: [----------] 4 tests from Checkpoint (0 ms total) 64: 64: [----------] 1 test from StructureIOTest 64: [ RUN ] StructureIOTest.ReadTpsConfRetainsChainids 64: [ OK ] StructureIOTest.ReadTpsConfRetainsChainids (3 ms) 64: [----------] 1 test from StructureIOTest (3 ms total) 64: 64: [----------] 2 tests from FileMD5Test 64: [ RUN ] FileMD5Test.CanComputeMD5 64: [ OK ] FileMD5Test.CanComputeMD5 (6 ms) 64: [ RUN ] FileMD5Test.ReturnsErrorIfFileModeIsWrong 64: [ OK ] FileMD5Test.ReturnsErrorIfFileModeIsWrong (0 ms) 64: [----------] 2 tests from FileMD5Test (7 ms total) 64: 64: [----------] 4 tests from FileTypeTest 64: [ RUN ] FileTypeTest.CorrectValueForEmptyString 64: [ OK ] FileTypeTest.CorrectValueForEmptyString (0 ms) 64: [ RUN ] FileTypeTest.CorrectValueForNoExtension 64: [ OK ] FileTypeTest.CorrectValueForNoExtension (0 ms) 64: [ RUN ] FileTypeTest.CorrectValueForEmptyExtension 64: [ OK ] FileTypeTest.CorrectValueForEmptyExtension (0 ms) 64: [ RUN ] FileTypeTest.CorrectValueForLongExtensionWithStrangeCharacters 64: [ OK ] FileTypeTest.CorrectValueForLongExtensionWithStrangeCharacters (0 ms) 64: [----------] 4 tests from FileTypeTest (0 ms total) 64: 64: [----------] 4 tests from ColorMapTest 64: [ RUN ] ColorMapTest.CanReadFromFile 64: [ OK ] ColorMapTest.CanReadFromFile (0 ms) 64: [ RUN ] ColorMapTest.CanWriteToFile 64: [ OK ] ColorMapTest.CanWriteToFile (1 ms) 64: [ RUN ] ColorMapTest.RoundTrip 64: [ OK ] ColorMapTest.RoundTrip (1 ms) 64: [ RUN ] ColorMapTest.SearchWorks 64: [ OK ] ColorMapTest.SearchWorks (0 ms) 64: [----------] 4 tests from ColorMapTest (3 ms total) 64: 64: [----------] 4 tests from MatioTest 64: [ RUN ] MatioTest.CanWriteToFile 64: 33% 66%100%[ OK ] MatioTest.CanWriteToFile (0 ms) 64: [ RUN ] MatioTest.CanConvertToExistingRealMatrix 64: Converted a 4x3 matrix with 4 levels to reals 64: [ OK ] MatioTest.CanConvertToExistingRealMatrix (0 ms) 64: [ RUN ] MatioTest.CanConvertToNewRealMatrix 64: Converted a 4x3 matrix with 4 levels to reals 64: [ OK ] MatioTest.CanConvertToNewRealMatrix (0 ms) 64: [ RUN ] MatioTest.CanReadSingleMatrixAfterWriting 64: 33% 66%100% 33% 66%100%[ OK ] MatioTest.CanReadSingleMatrixAfterWriting (23 ms) 64: [----------] 4 tests from MatioTest (24 ms total) 64: 64: [----------] 3 tests from MrcSerializer 64: [ RUN ] MrcSerializer.DefaultHeaderValuesAreSet 64: [ OK ] MrcSerializer.DefaultHeaderValuesAreSet (0 ms) 64: [ RUN ] MrcSerializer.DefaultHeaderHasRightSerialSize 64: [ OK ] MrcSerializer.DefaultHeaderHasRightSerialSize (0 ms) 64: [ RUN ] MrcSerializer.DefaultHeaderIdenticalAfterRoundTrip 64: [ OK ] MrcSerializer.DefaultHeaderIdenticalAfterRoundTrip (0 ms) 64: [----------] 3 tests from MrcSerializer (0 ms total) 64: 64: [----------] 4 tests from MrcDensityMap 64: [ RUN ] MrcDensityMap.RoundTripIsIdempotent 64: [ OK ] MrcDensityMap.RoundTripIsIdempotent (0 ms) 64: [ RUN ] MrcDensityMap.ThrowsFileIOErrorWhenFileNotPresent 64: [ OK ] MrcDensityMap.ThrowsFileIOErrorWhenFileNotPresent (0 ms) 64: [ RUN ] MrcDensityMap.ReadsCoordinateTransformationFromFile 64: [ OK ] MrcDensityMap.ReadsCoordinateTransformationFromFile (0 ms) 64: [ RUN ] MrcDensityMap.ReadsDensityDataFromFile 64: [ OK ] MrcDensityMap.ReadsDensityDataFromFile (7 ms) 64: [----------] 4 tests from MrcDensityMap (10 ms total) 64: 64: [----------] 8 tests from MrcDensityMapHeaderTest 64: [ RUN ] MrcDensityMapHeaderTest.DataSizeIsZeroForDefaultHeader 64: [ OK ] MrcDensityMapHeaderTest.DataSizeIsZeroForDefaultHeader (0 ms) 64: [ RUN ] MrcDensityMapHeaderTest.DataSizeIsCorrect 64: [ OK ] MrcDensityMapHeaderTest.DataSizeIsCorrect (0 ms) 64: [ RUN ] MrcDensityMapHeaderTest.DataSizeThrowsWhenInvalid 64: [ OK ] MrcDensityMapHeaderTest.DataSizeThrowsWhenInvalid (0 ms) 64: [ RUN ] MrcDensityMapHeaderTest.GetsCorrectCoordinateTransformNoOriginGiven 64: [ OK ] MrcDensityMapHeaderTest.GetsCorrectCoordinateTransformNoOriginGiven (0 ms) 64: [ RUN ] MrcDensityMapHeaderTest.GetsCorrectCoordinateTransformWithOriginDefined 64: [ OK ] MrcDensityMapHeaderTest.GetsCorrectCoordinateTransformWithOriginDefined (0 ms) 64: [ RUN ] MrcDensityMapHeaderTest.GetsCorrectCoordinateTransformWithStartValues 64: [ OK ] MrcDensityMapHeaderTest.GetsCorrectCoordinateTransformWithStartValues (0 ms) 64: [ RUN ] MrcDensityMapHeaderTest.GetsCorrectExtents 64: [ OK ] MrcDensityMapHeaderTest.GetsCorrectExtents (0 ms) 64: [ RUN ] MrcDensityMapHeaderTest.IsSane 64: [ OK ] MrcDensityMapHeaderTest.IsSane (0 ms) 64: [----------] 8 tests from MrcDensityMapHeaderTest (0 ms total) 64: 64: [----------] 10 tests from ReadTest 64: [ RUN ] ReadTest.get_eint_ReadsInteger 64: [ OK ] ReadTest.get_eint_ReadsInteger (0 ms) 64: [ RUN ] ReadTest.get_eint_WarnsAboutFloat 64: 64: ERROR 1 [file unknown]: 64: Right hand side '0.8' for parameter 'test' in parameter file is not an 64: integer value 64: 64: 64: [ OK ] ReadTest.get_eint_WarnsAboutFloat (0 ms) 64: [ RUN ] ReadTest.get_eint_WarnsAboutString 64: 64: ERROR 1 [file unknown]: 64: Right hand side 'hello' for parameter 'test' in parameter file is not an 64: integer value 64: 64: 64: [ OK ] ReadTest.get_eint_WarnsAboutString (0 ms) 64: [ RUN ] ReadTest.get_eint64_ReadsInteger 64: [ OK ] ReadTest.get_eint64_ReadsInteger (0 ms) 64: [ RUN ] ReadTest.get_eint64_WarnsAboutFloat 64: 64: ERROR 1 [file unknown]: 64: Right hand side '0.8' for parameter 'test' in parameter file is not an 64: integer value 64: 64: 64: [ OK ] ReadTest.get_eint64_WarnsAboutFloat (0 ms) 64: [ RUN ] ReadTest.get_eint64_WarnsAboutString 64: 64: ERROR 1 [file unknown]: 64: Right hand side 'hello' for parameter 'test' in parameter file is not an 64: integer value 64: 64: 64: [ OK ] ReadTest.get_eint64_WarnsAboutString (0 ms) 64: [ RUN ] ReadTest.get_ereal_ReadsInteger 64: [ OK ] ReadTest.get_ereal_ReadsInteger (0 ms) 64: [ RUN ] ReadTest.get_ereal_ReadsFloat 64: [ OK ] ReadTest.get_ereal_ReadsFloat (0 ms) 64: [ RUN ] ReadTest.get_ereal_WarnsAboutString 64: 64: ERROR 1 [file unknown]: 64: Right hand side 'hello' for parameter 'test' in parameter file is not a 64: real value 64: 64: 64: [ OK ] ReadTest.get_ereal_WarnsAboutString (0 ms) 64: [ RUN ] ReadTest.setStringEntry_ReturnsCorrectString 64: [ OK ] ReadTest.setStringEntry_ReturnsCorrectString (0 ms) 64: [----------] 10 tests from ReadTest (0 ms total) 64: 64: [----------] 3 tests from TimeControlTest 64: [ RUN ] TimeControlTest.UnSetHasNoValue 64: [ OK ] TimeControlTest.UnSetHasNoValue (0 ms) 64: [ RUN ] TimeControlTest.CanSetValue 64: [ OK ] TimeControlTest.CanSetValue (0 ms) 64: [ RUN ] TimeControlTest.CanUnsetValueAgain 64: [ OK ] TimeControlTest.CanUnsetValueAgain (0 ms) 64: [----------] 3 tests from TimeControlTest (0 ms total) 64: 64: [----------] 1 test from FileIOXdrSerializerTest 64: [ RUN ] FileIOXdrSerializerTest.SizeIsCorrect 64: [ OK ] FileIOXdrSerializerTest.SizeIsCorrect (1 ms) 64: [----------] 1 test from FileIOXdrSerializerTest (1 ms total) 64: 64: [----------] 1 test from TngTest 64: [ RUN ] TngTest.CloseBeforeOpenIsNotFatal 64: [ OK ] TngTest.CloseBeforeOpenIsNotFatal (0 ms) 64: [----------] 1 test from TngTest (0 ms total) 64: 64: [----------] 4 tests from XvgioTest 64: [ RUN ] XvgioTest.readXvgIntWorks 64: [ OK ] XvgioTest.readXvgIntWorks (0 ms) 64: [ RUN ] XvgioTest.readXvgRealWorks 64: [ OK ] XvgioTest.readXvgRealWorks (0 ms) 64: [ RUN ] XvgioTest.readXvgIgnoreCommentLineWorks 64: [ OK ] XvgioTest.readXvgIgnoreCommentLineWorks (0 ms) 64: [ RUN ] XvgioTest.readXvgDeprecatedWorks 64: [ OK ] XvgioTest.readXvgDeprecatedWorks (0 ms) 64: [----------] 4 tests from XvgioTest (3 ms total) 64: 64: [----------] 4 tests from WithDifferentFormats/StructureIORoundtripTest 64: [ RUN ] WithDifferentFormats/StructureIORoundtripTest.ReadWriteTpsConf/0 64: [ OK ] WithDifferentFormats/StructureIORoundtripTest.ReadWriteTpsConf/0 (1 ms) 64: [ RUN ] WithDifferentFormats/StructureIORoundtripTest.ReadWriteTpsConf/1 64: [ OK ] WithDifferentFormats/StructureIORoundtripTest.ReadWriteTpsConf/1 (2 ms) 64: [ RUN ] WithDifferentFormats/StructureIORoundtripTest.ReadWriteTpsConf/2 64: [ OK ] WithDifferentFormats/StructureIORoundtripTest.ReadWriteTpsConf/2 (2 ms) 64: [ RUN ] WithDifferentFormats/StructureIORoundtripTest.ReadWriteTpsConf/3 64: [ OK ] WithDifferentFormats/StructureIORoundtripTest.ReadWriteTpsConf/3 (1 ms) 64: [----------] 4 tests from WithDifferentFormats/StructureIORoundtripTest (8 ms total) 64: 64: [----------] 360 tests from FileTypeMatch/FileTypeTest 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/0 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/0 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/1 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/1 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/2 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/2 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/3 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/3 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/4 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/4 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/5 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/5 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/6 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/6 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/7 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/7 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/8 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/8 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/9 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/9 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/10 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/10 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/11 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/11 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/12 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/12 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/13 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/13 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/14 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/14 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/15 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/15 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/16 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/16 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/17 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/17 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/18 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/18 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/19 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/19 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/20 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/20 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/21 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/21 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/22 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/22 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/23 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/23 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/24 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/24 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/25 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/25 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/26 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/26 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/27 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/27 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/28 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/28 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/29 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/29 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/30 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/30 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/31 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/31 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/32 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/32 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/33 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/33 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/34 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/34 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/35 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/35 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/36 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/36 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/37 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/37 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/38 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/38 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/39 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/39 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/40 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/40 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/41 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/41 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/42 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/42 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/43 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/43 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/44 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/44 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/45 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/45 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/46 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/46 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/47 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/47 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/48 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/48 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/49 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/49 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/50 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/50 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/51 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/51 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/52 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/52 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/53 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/53 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/54 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/54 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/55 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/55 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/56 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/56 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/57 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/57 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/58 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/58 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/59 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/59 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/60 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/60 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/61 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/61 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/62 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/62 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/63 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/63 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/64 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/64 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/65 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/65 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/66 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/66 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/67 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/67 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/68 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/68 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/69 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/69 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/70 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/70 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/71 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/71 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/72 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/72 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/73 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/73 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/74 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/74 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/75 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/75 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/76 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/76 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/77 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/77 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/78 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/78 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/79 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/79 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/80 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/80 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/81 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/81 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/82 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/82 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/83 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/83 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/84 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/84 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/85 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/85 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/86 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/86 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/87 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/87 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/88 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/88 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/89 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/89 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/90 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/90 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/91 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/91 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/92 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/92 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/93 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/93 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/94 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/94 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/95 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/95 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/96 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/96 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/97 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/97 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/98 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/98 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/99 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/99 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/100 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/100 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/101 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/101 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/102 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/102 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/103 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/103 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/104 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/104 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/105 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/105 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/106 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/106 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/107 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/107 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/108 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/108 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/109 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/109 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/110 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/110 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/111 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/111 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/112 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/112 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/113 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/113 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/114 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/114 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/115 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/115 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/116 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/116 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/117 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/117 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/118 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/118 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/119 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/119 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/120 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/120 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/121 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/121 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/122 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/122 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/123 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/123 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/124 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/124 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/125 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/125 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/126 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/126 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/127 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/127 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/128 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/128 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/129 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/129 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/130 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/130 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/131 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/131 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/132 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/132 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/133 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/133 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/134 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/134 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/135 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/135 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/136 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/136 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/137 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/137 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/138 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/138 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/139 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/139 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/140 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/140 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/141 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/141 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/142 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/142 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/143 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/143 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/144 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/144 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/145 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/145 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/146 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/146 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/147 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/147 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/148 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/148 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/149 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/149 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/150 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/150 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/151 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/151 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/152 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/152 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/153 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/153 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/154 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/154 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/155 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/155 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/156 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/156 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/157 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/157 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/158 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/158 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/159 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/159 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/160 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/160 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/161 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/161 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/162 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/162 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/163 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/163 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/164 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/164 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/165 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/165 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/166 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/166 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/167 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/167 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/168 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/168 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/169 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/169 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/170 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/170 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/171 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/171 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/172 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/172 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/173 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/173 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/174 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/174 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/175 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/175 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/176 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/176 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/177 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/177 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/178 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/178 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/179 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/179 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/0 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/0 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/1 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/1 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/2 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/2 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/3 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/3 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/4 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/4 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/5 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/5 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/6 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/6 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/7 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/7 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/8 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/8 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/9 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/9 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/10 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/10 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/11 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/11 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/12 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/12 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/13 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/13 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/14 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/14 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/15 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/15 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/16 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/16 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/17 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/17 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/18 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/18 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/19 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/19 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/20 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/20 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/21 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/21 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/22 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/22 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/23 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/23 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/24 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/24 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/25 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/25 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/26 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/26 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/27 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/27 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/28 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/28 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/29 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/29 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/30 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/30 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/31 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/31 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/32 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/32 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/33 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/33 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/34 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/34 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/35 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/35 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/36 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/36 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/37 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/37 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/38 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/38 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/39 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/39 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/40 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/40 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/41 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/41 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/42 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/42 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/43 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/43 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/44 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/44 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/45 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/45 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/46 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/46 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/47 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/47 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/48 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/48 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/49 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/49 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/50 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/50 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/51 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/51 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/52 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/52 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/53 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/53 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/54 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/54 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/55 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/55 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/56 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/56 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/57 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/57 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/58 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/58 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/59 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/59 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/60 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/60 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/61 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/61 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/62 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/62 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/63 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/63 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/64 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/64 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/65 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/65 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/66 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/66 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/67 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/67 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/68 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/68 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/69 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/69 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/70 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/70 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/71 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/71 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/72 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/72 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/73 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/73 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/74 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/74 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/75 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/75 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/76 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/76 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/77 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/77 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/78 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/78 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/79 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/79 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/80 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/80 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/81 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/81 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/82 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/82 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/83 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/83 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/84 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/84 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/85 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/85 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/86 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/86 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/87 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/87 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/88 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/88 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/89 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/89 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/90 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/90 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/91 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/91 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/92 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/92 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/93 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/93 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/94 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/94 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/95 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/95 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/96 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/96 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/97 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/97 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/98 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/98 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/99 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/99 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/100 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/100 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/101 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/101 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/102 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/102 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/103 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/103 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/104 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/104 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/105 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/105 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/106 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/106 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/107 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/107 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/108 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/108 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/109 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/109 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/110 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/110 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/111 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/111 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/112 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/112 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/113 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/113 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/114 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/114 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/115 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/115 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/116 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/116 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/117 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/117 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/118 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/118 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/119 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/119 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/120 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/120 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/121 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/121 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/122 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/122 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/123 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/123 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/124 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/124 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/125 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/125 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/126 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/126 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/127 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/127 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/128 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/128 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/129 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/129 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/130 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/130 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/131 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/131 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/132 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/132 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/133 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/133 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/134 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/134 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/135 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/135 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/136 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/136 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/137 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/137 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/138 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/138 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/139 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/139 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/140 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/140 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/141 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/141 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/142 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/142 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/143 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/143 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/144 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/144 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/145 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/145 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/146 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/146 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/147 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/147 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/148 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/148 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/149 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/149 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/150 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/150 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/151 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/151 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/152 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/152 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/153 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/153 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/154 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/154 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/155 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/155 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/156 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/156 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/157 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/157 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/158 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/158 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/159 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/159 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/160 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/160 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/161 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/161 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/162 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/162 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/163 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/163 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/164 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/164 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/165 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/165 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/166 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/166 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/167 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/167 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/168 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/168 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/169 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/169 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/170 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/170 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/171 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/171 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/172 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/172 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/173 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/173 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/174 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/174 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/175 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/175 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/176 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/176 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/177 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/177 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/178 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/178 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/179 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/179 (0 ms) 64: [----------] 360 tests from FileTypeMatch/FileTypeTest (12 ms total) 64: 64: [----------] 4 tests from XvgReadTimeSeries/XvgioTest 64: [ RUN ] XvgReadTimeSeries/XvgioTest.readXvgTimeSeriesWorks/0 64: [ OK ] XvgReadTimeSeries/XvgioTest.readXvgTimeSeriesWorks/0 (6 ms) 64: [ RUN ] XvgReadTimeSeries/XvgioTest.readXvgTimeSeriesWorks/1 64: [ OK ] XvgReadTimeSeries/XvgioTest.readXvgTimeSeriesWorks/1 (7 ms) 64: [ RUN ] XvgReadTimeSeries/XvgioTest.readXvgTimeSeriesWorks/2 64: [ OK ] XvgReadTimeSeries/XvgioTest.readXvgTimeSeriesWorks/2 (1 ms) 64: [ RUN ] XvgReadTimeSeries/XvgioTest.readXvgTimeSeriesWorks/3 64: [ OK ] XvgReadTimeSeries/XvgioTest.readXvgTimeSeriesWorks/3 (1 ms) 64: [----------] 4 tests from XvgReadTimeSeries/XvgioTest (18 ms total) 64: 64: [----------] Global test environment tear-down 64: [==========] 421 tests from 17 test suites ran. (96 ms total) 64: [ PASSED ] 421 tests. 64/92 Test #64: FileIOTests ............................... Passed 0.24 sec test 65 Start 65: SelectionUnitTests 65: Test command: /build/reproducible-path/gromacs-2025.1/build/basic-dp/bin/selection-test "--gtest_output=xml:/build/reproducible-path/gromacs-2025.1/build/basic-dp/Testing/Temporary/SelectionUnitTests.xml" 65: Working Directory: /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/selection/tests 65: Test timeout computed to be: 30 65: [==========] Running 201 tests from 11 test suites. 65: [----------] Global test environment set-up. 65: [----------] 1 test from IndexGroupTest 65: [ RUN ] IndexGroupTest.RemovesDuplicates 65: [ OK ] IndexGroupTest.RemovesDuplicates (0 ms) 65: [----------] 1 test from IndexGroupTest (0 ms total) 65: 65: [----------] 15 tests from IndexBlockTest 65: [ RUN ] IndexBlockTest.CreatesUnknownBlock 65: [ OK ] IndexBlockTest.CreatesUnknownBlock (0 ms) 65: [ RUN ] IndexBlockTest.CreatesAtomBlock 65: [ OK ] IndexBlockTest.CreatesAtomBlock (0 ms) 65: [ RUN ] IndexBlockTest.CreatesResidueBlocksForSimpleTopology 65: [ OK ] IndexBlockTest.CreatesResidueBlocksForSimpleTopology (0 ms) 65: [ RUN ] IndexBlockTest.CreatesResidueBlocksForComplexTopology 65: [ OK ] IndexBlockTest.CreatesResidueBlocksForComplexTopology (2 ms) 65: [ RUN ] IndexBlockTest.CreatesMoleculeBlocksForSimpleTopology 65: [ OK ] IndexBlockTest.CreatesMoleculeBlocksForSimpleTopology (0 ms) 65: [ RUN ] IndexBlockTest.CreatesMoleculeBlocksForComplexTopology 65: [ OK ] IndexBlockTest.CreatesMoleculeBlocksForComplexTopology (0 ms) 65: [ RUN ] IndexBlockTest.CreatesSingleBlock 65: [ OK ] IndexBlockTest.CreatesSingleBlock (0 ms) 65: [ RUN ] IndexBlockTest.ChecksGroupForFullBlocksPositive 65: [ OK ] IndexBlockTest.ChecksGroupForFullBlocksPositive (0 ms) 65: [ RUN ] IndexBlockTest.ChecksOutOfOrderGroupForFullBlocksPositive 65: [ OK ] IndexBlockTest.ChecksOutOfOrderGroupForFullBlocksPositive (0 ms) 65: [ RUN ] IndexBlockTest.ChecksGroupForFullBlocksNegative 65: [ OK ] IndexBlockTest.ChecksGroupForFullBlocksNegative (0 ms) 65: [ RUN ] IndexBlockTest.ChecksGroupForCompleteElementsTrivial 65: [ OK ] IndexBlockTest.ChecksGroupForCompleteElementsTrivial (0 ms) 65: [ RUN ] IndexBlockTest.ChecksGroupForCompleteResiduesPositive 65: [ OK ] IndexBlockTest.ChecksGroupForCompleteResiduesPositive (0 ms) 65: [ RUN ] IndexBlockTest.ChecksGroupForCompleteResiduesNegative 65: [ OK ] IndexBlockTest.ChecksGroupForCompleteResiduesNegative (0 ms) 65: [ RUN ] IndexBlockTest.ChecksGroupForCompleteMoleculesPositive 65: [ OK ] IndexBlockTest.ChecksGroupForCompleteMoleculesPositive (0 ms) 65: [ RUN ] IndexBlockTest.ChecksGroupForCompleteMoleculesNegative 65: [ OK ] IndexBlockTest.ChecksGroupForCompleteMoleculesNegative (0 ms) 65: [----------] 15 tests from IndexBlockTest (9 ms total) 65: 65: [----------] 11 tests from IndexMapTest 65: [ RUN ] IndexMapTest.InitializesAtomBlock 65: [ OK ] IndexMapTest.InitializesAtomBlock (0 ms) 65: [ RUN ] IndexMapTest.InitializesOrgIdGroupAtom 65: [ OK ] IndexMapTest.InitializesOrgIdGroupAtom (0 ms) 65: [ RUN ] IndexMapTest.InitializesOrgIdGroupSingle 65: [ OK ] IndexMapTest.InitializesOrgIdGroupSingle (0 ms) 65: [ RUN ] IndexMapTest.InitializesOrgIdGroupResidue 65: [ OK ] IndexMapTest.InitializesOrgIdGroupResidue (0 ms) 65: [ RUN ] IndexMapTest.InitializesOrgIdGroupMolecule 65: [ OK ] IndexMapTest.InitializesOrgIdGroupMolecule (0 ms) 65: [ RUN ] IndexMapTest.InitializesOrgIdGroupAll 65: [ OK ] IndexMapTest.InitializesOrgIdGroupAll (0 ms) 65: [ RUN ] IndexMapTest.InitializesMoleculeBlock 65: [ OK ] IndexMapTest.InitializesMoleculeBlock (1 ms) 65: [ RUN ] IndexMapTest.MapsSingleBlock 65: [ OK ] IndexMapTest.MapsSingleBlock (0 ms) 65: [ RUN ] IndexMapTest.MapsResidueBlocks 65: [ OK ] IndexMapTest.MapsResidueBlocks (1 ms) 65: [ RUN ] IndexMapTest.MapsResidueBlocksWithMask 65: [ OK ] IndexMapTest.MapsResidueBlocksWithMask (1 ms) 65: [ RUN ] IndexMapTest.HandlesMultipleRequests 65: [ OK ] IndexMapTest.HandlesMultipleRequests (2 ms) 65: [----------] 11 tests from IndexMapTest (13 ms total) 65: 65: [----------] 3 tests from IndexGroupsAndNamesTest 65: [ RUN ] IndexGroupsAndNamesTest.containsNames 65: [ OK ] IndexGroupsAndNamesTest.containsNames (0 ms) 65: [ RUN ] IndexGroupsAndNamesTest.throwsWhenNameMissing 65: [ OK ] IndexGroupsAndNamesTest.throwsWhenNameMissing (1 ms) 65: [ RUN ] IndexGroupsAndNamesTest.groupIndicesCorrect 65: [ OK ] IndexGroupsAndNamesTest.groupIndicesCorrect (0 ms) 65: [----------] 3 tests from IndexGroupsAndNamesTest (1 ms total) 65: 65: [----------] 15 tests from NeighborhoodSearchTest 65: [ RUN ] NeighborhoodSearchTest.SimpleSearch 65: [ OK ] NeighborhoodSearchTest.SimpleSearch (82 ms) 65: [ RUN ] NeighborhoodSearchTest.SimpleSearchXY 65: [ OK ] NeighborhoodSearchTest.SimpleSearchXY (77 ms) 65: [ RUN ] NeighborhoodSearchTest.GridSearchBox 65: [ OK ] NeighborhoodSearchTest.GridSearchBox (12 ms) 65: [ RUN ] NeighborhoodSearchTest.GridSearchTriclinic 65: [ OK ] NeighborhoodSearchTest.GridSearchTriclinic (44 ms) 65: [ RUN ] NeighborhoodSearchTest.GridSearch2DPBC 65: [ OK ] NeighborhoodSearchTest.GridSearch2DPBC (23 ms) 65: [ RUN ] NeighborhoodSearchTest.GridSearchNoPBC 65: [ OK ] NeighborhoodSearchTest.GridSearchNoPBC (12 ms) 65: [ RUN ] NeighborhoodSearchTest.GridSearchXYBox 65: [ OK ] NeighborhoodSearchTest.GridSearchXYBox (12 ms) 65: [ RUN ] NeighborhoodSearchTest.SimpleSelfPairsSearch 65: [ OK ] NeighborhoodSearchTest.SimpleSelfPairsSearch (0 ms) 65: [ RUN ] NeighborhoodSearchTest.GridSelfPairsSearch 65: [ OK ] NeighborhoodSearchTest.GridSelfPairsSearch (223 ms) 65: [ RUN ] NeighborhoodSearchTest.HandlesConcurrentSearches 65: [ OK ] NeighborhoodSearchTest.HandlesConcurrentSearches (0 ms) 65: [ RUN ] NeighborhoodSearchTest.HandlesNoPBC 65: [ OK ] NeighborhoodSearchTest.HandlesNoPBC (0 ms) 65: [ RUN ] NeighborhoodSearchTest.HandlesNullPBC 65: [ OK ] NeighborhoodSearchTest.HandlesNullPBC (0 ms) 65: [ RUN ] NeighborhoodSearchTest.HandlesSkippingPairs 65: [ OK ] NeighborhoodSearchTest.HandlesSkippingPairs (0 ms) 65: [ RUN ] NeighborhoodSearchTest.SimpleSearchExclusions 65: [ OK ] NeighborhoodSearchTest.SimpleSearchExclusions (16 ms) 65: [ RUN ] NeighborhoodSearchTest.GridSearchExclusions 65: [ OK ] NeighborhoodSearchTest.GridSearchExclusions (3 ms) 65: [----------] 15 tests from NeighborhoodSearchTest (511 ms total) 65: 65: [----------] 13 tests from PositionCalculationTest 65: [ RUN ] PositionCalculationTest.ComputesAtomPositions 65: [ OK ] PositionCalculationTest.ComputesAtomPositions (1 ms) 65: [ RUN ] PositionCalculationTest.ComputesAtomPositionsWithRepeatedIndex 65: [ OK ] PositionCalculationTest.ComputesAtomPositionsWithRepeatedIndex (1 ms) 65: [ RUN ] PositionCalculationTest.ComputesResidueCOGPositions 65: [ OK ] PositionCalculationTest.ComputesResidueCOGPositions (1 ms) 65: [ RUN ] PositionCalculationTest.ComputesResidueCOMPositions 65: [ OK ] PositionCalculationTest.ComputesResidueCOMPositions (1 ms) 65: [ RUN ] PositionCalculationTest.ComputesGroupCOGPositions 65: [ OK ] PositionCalculationTest.ComputesGroupCOGPositions (0 ms) 65: [ RUN ] PositionCalculationTest.ComputesGroupCOMPositions 65: [ OK ] PositionCalculationTest.ComputesGroupCOMPositions (0 ms) 65: [ RUN ] PositionCalculationTest.ComputesPositionsWithCompleteWhole 65: [ OK ] PositionCalculationTest.ComputesPositionsWithCompleteWhole (0 ms) 65: [ RUN ] PositionCalculationTest.ComputesPositionsWithCompleteMax 65: [ OK ] PositionCalculationTest.ComputesPositionsWithCompleteMax (0 ms) 65: [ RUN ] PositionCalculationTest.ComputesPositionMask 65: [ OK ] PositionCalculationTest.ComputesPositionMask (1 ms) 65: [ RUN ] PositionCalculationTest.HandlesFramesWithLessAtoms 65: [ OK ] PositionCalculationTest.HandlesFramesWithLessAtoms (1 ms) 65: [ RUN ] PositionCalculationTest.HandlesFramesWithLessAtoms2 65: [ OK ] PositionCalculationTest.HandlesFramesWithLessAtoms2 (0 ms) 65: [ RUN ] PositionCalculationTest.HandlesIdenticalStaticCalculations 65: [ OK ] PositionCalculationTest.HandlesIdenticalStaticCalculations (1 ms) 65: [ RUN ] PositionCalculationTest.HandlesOverlappingStaticCalculations 65: [ OK ] PositionCalculationTest.HandlesOverlappingStaticCalculations (1 ms) 65: [----------] 13 tests from PositionCalculationTest (17 ms total) 65: 65: [----------] 33 tests from SelectionCollectionTest 65: [ RUN ] SelectionCollectionTest.HandlesNoSelections 65: [ OK ] SelectionCollectionTest.HandlesNoSelections (1 ms) 65: [ RUN ] SelectionCollectionTest.HandlesNoSelectionsWithDefaultPositionType 65: [ OK ] SelectionCollectionTest.HandlesNoSelectionsWithDefaultPositionType (2 ms) 65: [ RUN ] SelectionCollectionTest.HandlesVelocityAndForceRequests 65: [ OK ] SelectionCollectionTest.HandlesVelocityAndForceRequests (1 ms) 65: [ RUN ] SelectionCollectionTest.HandlesForceRequestForCenterOfGeometry 65: [ OK ] SelectionCollectionTest.HandlesForceRequestForCenterOfGeometry (2 ms) 65: [ RUN ] SelectionCollectionTest.ParsesSelectionsFromFile 65: [ OK ] SelectionCollectionTest.ParsesSelectionsFromFile (1 ms) 65: [ RUN ] SelectionCollectionTest.HandlesAtypicalWhitespace 65: [ OK ] SelectionCollectionTest.HandlesAtypicalWhitespace (1 ms) 65: [ RUN ] SelectionCollectionTest.HandlesInvalidRegularExpressions 65: [ OK ] SelectionCollectionTest.HandlesInvalidRegularExpressions (2 ms) 65: [ RUN ] SelectionCollectionTest.HandlesMissingMethodParamValue 65: [ OK ] SelectionCollectionTest.HandlesMissingMethodParamValue (2 ms) 65: [ RUN ] SelectionCollectionTest.HandlesMissingMethodParamValue2 65: [ OK ] SelectionCollectionTest.HandlesMissingMethodParamValue2 (2 ms) 65: [ RUN ] SelectionCollectionTest.HandlesMissingMethodParamValue3 65: [ OK ] SelectionCollectionTest.HandlesMissingMethodParamValue3 (2 ms) 65: [ RUN ] SelectionCollectionTest.HandlesUnknownGroupReferenceParser1 65: [ OK ] SelectionCollectionTest.HandlesUnknownGroupReferenceParser1 (2 ms) 65: [ RUN ] SelectionCollectionTest.HandlesUnknownGroupReferenceParser2 65: [ OK ] SelectionCollectionTest.HandlesUnknownGroupReferenceParser2 (2 ms) 65: [ RUN ] SelectionCollectionTest.HandlesUnknownGroupReferenceDelayed1 65: [ OK ] SelectionCollectionTest.HandlesUnknownGroupReferenceDelayed1 (1 ms) 65: [ RUN ] SelectionCollectionTest.HandlesUnknownGroupReferenceDelayed2 65: [ OK ] SelectionCollectionTest.HandlesUnknownGroupReferenceDelayed2 (2 ms) 65: [ RUN ] SelectionCollectionTest.HandlesUnsortedGroupReference 65: [ OK ] SelectionCollectionTest.HandlesUnsortedGroupReference (3 ms) 65: [ RUN ] SelectionCollectionTest.HandlesUnsortedGroupReferenceDelayed 65: [ OK ] SelectionCollectionTest.HandlesUnsortedGroupReferenceDelayed (2 ms) 65: [ RUN ] SelectionCollectionTest.HandlesOutOfRangeAtomIndexInGroup 65: [ OK ] SelectionCollectionTest.HandlesOutOfRangeAtomIndexInGroup (2 ms) 65: [ RUN ] SelectionCollectionTest.HandlesOutOfRangeAtomIndexInGroupDelayed 65: [ OK ] SelectionCollectionTest.HandlesOutOfRangeAtomIndexInGroupDelayed (2 ms) 65: [ RUN ] SelectionCollectionTest.HandlesOutOfRangeAtomIndexInGroupDelayed2 65: [ OK ] SelectionCollectionTest.HandlesOutOfRangeAtomIndexInGroupDelayed2 (2 ms) 65: [ RUN ] SelectionCollectionTest.RecoversFromMissingMoleculeInfo 65: [ OK ] SelectionCollectionTest.RecoversFromMissingMoleculeInfo (2 ms) 65: [ RUN ] SelectionCollectionTest.RecoversFromMissingAtomTypes 65: [ OK ] SelectionCollectionTest.RecoversFromMissingAtomTypes (2 ms) 65: [ RUN ] SelectionCollectionTest.RecoversFromMissingPDBInfo 65: [ OK ] SelectionCollectionTest.RecoversFromMissingPDBInfo (2 ms) 65: [ RUN ] SelectionCollectionTest.RecoversFromInvalidPermutation 65: [ OK ] SelectionCollectionTest.RecoversFromInvalidPermutation (2 ms) 65: [ RUN ] SelectionCollectionTest.RecoversFromInvalidPermutation2 65: [ OK ] SelectionCollectionTest.RecoversFromInvalidPermutation2 (1 ms) 65: [ RUN ] SelectionCollectionTest.RecoversFromInvalidPermutation3 65: [ OK ] SelectionCollectionTest.RecoversFromInvalidPermutation3 (2 ms) 65: [ RUN ] SelectionCollectionTest.HandlesFramesWithTooSmallAtomSubsets 65: [ OK ] SelectionCollectionTest.HandlesFramesWithTooSmallAtomSubsets (2 ms) 65: [ RUN ] SelectionCollectionTest.HandlesFramesWithTooSmallAtomSubsets2 65: [ OK ] SelectionCollectionTest.HandlesFramesWithTooSmallAtomSubsets2 (2 ms) 65: [ RUN ] SelectionCollectionTest.HandlesFramesWithTooSmallAtomSubsets3 65: [ OK ] SelectionCollectionTest.HandlesFramesWithTooSmallAtomSubsets3 (2 ms) 65: [ RUN ] SelectionCollectionTest.HandlesFramesWithTooSmallAtomSubsets4 65: [ OK ] SelectionCollectionTest.HandlesFramesWithTooSmallAtomSubsets4 (2 ms) 65: [ RUN ] SelectionCollectionTest.RetrieveValidSelection 65: [ OK ] SelectionCollectionTest.RetrieveValidSelection (1 ms) 65: [ RUN ] SelectionCollectionTest.RetrieveInvalidSelection 65: [ OK ] SelectionCollectionTest.RetrieveInvalidSelection (1 ms) 65: [ RUN ] SelectionCollectionTest.CanCopyEmptyCollection 65: [ OK ] SelectionCollectionTest.CanCopyEmptyCollection (3 ms) 65: [ RUN ] SelectionCollectionTest.CopiedSelectionListsAreHandledSeparately 65: [ OK ] SelectionCollectionTest.CopiedSelectionListsAreHandledSeparately (3 ms) 65: [----------] 33 tests from SelectionCollectionTest (79 ms total) 65: 65: [----------] 14 tests from SelectionCollectionInteractiveTest 65: [ RUN ] SelectionCollectionInteractiveTest.HandlesBasicInput 65: [ OK ] SelectionCollectionInteractiveTest.HandlesBasicInput (3 ms) 65: [ RUN ] SelectionCollectionInteractiveTest.HandlesContinuation 65: [ OK ] SelectionCollectionInteractiveTest.HandlesContinuation (2 ms) 65: [ RUN ] SelectionCollectionInteractiveTest.HandlesSingleSelectionInput 65: [ OK ] SelectionCollectionInteractiveTest.HandlesSingleSelectionInput (2 ms) 65: [ RUN ] SelectionCollectionInteractiveTest.HandlesTwoSelectionInput 65: [ OK ] SelectionCollectionInteractiveTest.HandlesTwoSelectionInput (2 ms) 65: [ RUN ] SelectionCollectionInteractiveTest.HandlesStatusWithGroups 65: [ OK ] SelectionCollectionInteractiveTest.HandlesStatusWithGroups (2 ms) 65: [ RUN ] SelectionCollectionInteractiveTest.HandlesStatusWithExistingSelections 65: [ OK ] SelectionCollectionInteractiveTest.HandlesStatusWithExistingSelections (2 ms) 65: [ RUN ] SelectionCollectionInteractiveTest.HandlesSingleSelectionInputStatus 65: [ OK ] SelectionCollectionInteractiveTest.HandlesSingleSelectionInputStatus (2 ms) 65: [ RUN ] SelectionCollectionInteractiveTest.HandlesTwoSelectionInputStatus 65: [ OK ] SelectionCollectionInteractiveTest.HandlesTwoSelectionInputStatus (2 ms) 65: [ RUN ] SelectionCollectionInteractiveTest.HandlesMultiSelectionInputStatus 65: [ OK ] SelectionCollectionInteractiveTest.HandlesMultiSelectionInputStatus (2 ms) 65: [ RUN ] SelectionCollectionInteractiveTest.HandlesNoFinalNewline 65: [ OK ] SelectionCollectionInteractiveTest.HandlesNoFinalNewline (2 ms) 65: [ RUN ] SelectionCollectionInteractiveTest.HandlesEmptySelections 65: [ OK ] SelectionCollectionInteractiveTest.HandlesEmptySelections (2 ms) 65: [ RUN ] SelectionCollectionInteractiveTest.HandlesMultipleSelectionsOnLine 65: [ OK ] SelectionCollectionInteractiveTest.HandlesMultipleSelectionsOnLine (2 ms) 65: [ RUN ] SelectionCollectionInteractiveTest.HandlesNoninteractiveInput 65: [ OK ] SelectionCollectionInteractiveTest.HandlesNoninteractiveInput (2 ms) 65: [ RUN ] SelectionCollectionInteractiveTest.HandlesSingleSelectionInputNoninteractively 65: [ OK ] SelectionCollectionInteractiveTest.HandlesSingleSelectionInputNoninteractively (2 ms) 65: [----------] 14 tests from SelectionCollectionInteractiveTest (36 ms total) 65: 65: [----------] 70 tests from SelectionCollectionDataTest 65: [ RUN ] SelectionCollectionDataTest.HandlesAllNone 65: [ OK ] SelectionCollectionDataTest.HandlesAllNone (2 ms) 65: [ RUN ] SelectionCollectionDataTest.HandlesAtomnr 65: [ OK ] SelectionCollectionDataTest.HandlesAtomnr (2 ms) 65: [ RUN ] SelectionCollectionDataTest.HandlesResnr 65: [ OK ] SelectionCollectionDataTest.HandlesResnr (3 ms) 65: [ RUN ] SelectionCollectionDataTest.HandlesResIndex 65: [ OK ] SelectionCollectionDataTest.HandlesResIndex (3 ms) 65: [ RUN ] SelectionCollectionDataTest.HandlesMolIndex 65: [ OK ] SelectionCollectionDataTest.HandlesMolIndex (3 ms) 65: [ RUN ] SelectionCollectionDataTest.HandlesAtomname 65: [ OK ] SelectionCollectionDataTest.HandlesAtomname (3 ms) 65: [ RUN ] SelectionCollectionDataTest.HandlesPdbAtomname 65: [ OK ] SelectionCollectionDataTest.HandlesPdbAtomname (3 ms) 65: [ RUN ] SelectionCollectionDataTest.HandlesAtomtype 65: [ OK ] SelectionCollectionDataTest.HandlesAtomtype (2 ms) 65: [ RUN ] SelectionCollectionDataTest.HandlesChain 65: [ OK ] SelectionCollectionDataTest.HandlesChain (3 ms) 65: [ RUN ] SelectionCollectionDataTest.HandlesMass 65: [ OK ] SelectionCollectionDataTest.HandlesMass (3 ms) 65: [ RUN ] SelectionCollectionDataTest.HandlesCharge 65: [ OK ] SelectionCollectionDataTest.HandlesCharge (3 ms) 65: [ RUN ] SelectionCollectionDataTest.HandlesAltLoc 65: [ OK ] SelectionCollectionDataTest.HandlesAltLoc (3 ms) 65: [ RUN ] SelectionCollectionDataTest.HandlesInsertCode 65: [ OK ] SelectionCollectionDataTest.HandlesInsertCode (3 ms) 65: [ RUN ] SelectionCollectionDataTest.HandlesOccupancy 65: [ OK ] SelectionCollectionDataTest.HandlesOccupancy (4 ms) 65: [ RUN ] SelectionCollectionDataTest.HandlesBeta 65: [ OK ] SelectionCollectionDataTest.HandlesBeta (4 ms) 65: [ RUN ] SelectionCollectionDataTest.HandlesResname 65: [ OK ] SelectionCollectionDataTest.HandlesResname (3 ms) 65: [ RUN ] SelectionCollectionDataTest.HandlesCoordinateKeywords 65: [ OK ] SelectionCollectionDataTest.HandlesCoordinateKeywords (6 ms) 65: [ RUN ] SelectionCollectionDataTest.HandlesSameResidue 65: [ OK ] SelectionCollectionDataTest.HandlesSameResidue (3 ms) 65: [ RUN ] SelectionCollectionDataTest.HandlesSameResidueName 65: [ OK ] SelectionCollectionDataTest.HandlesSameResidueName (3 ms) 65: [ RUN ] SelectionCollectionDataTest.HandlesPositionKeywords 65: [ OK ] SelectionCollectionDataTest.HandlesPositionKeywords (8 ms) 65: [ RUN ] SelectionCollectionDataTest.HandlesDistanceKeyword 65: [ OK ] SelectionCollectionDataTest.HandlesDistanceKeyword (4 ms) 65: [ RUN ] SelectionCollectionDataTest.HandlesMinDistanceKeyword 65: [ OK ] SelectionCollectionDataTest.HandlesMinDistanceKeyword (4 ms) 65: [ RUN ] SelectionCollectionDataTest.HandlesWithinKeyword 65: [ OK ] SelectionCollectionDataTest.HandlesWithinKeyword (4 ms) 65: [ RUN ] SelectionCollectionDataTest.HandlesInSolidAngleKeyword 65: [ OK ] SelectionCollectionDataTest.HandlesInSolidAngleKeyword (16 ms) 65: [ RUN ] SelectionCollectionDataTest.HandlesPermuteModifier 65: [ OK ] SelectionCollectionDataTest.HandlesPermuteModifier (10 ms) 65: [ RUN ] SelectionCollectionDataTest.HandlesPlusModifier 65: [ OK ] SelectionCollectionDataTest.HandlesPlusModifier (10 ms) 65: [ RUN ] SelectionCollectionDataTest.HandlesMergeModifier 65: [ OK ] SelectionCollectionDataTest.HandlesMergeModifier (10 ms) 65: [ RUN ] SelectionCollectionDataTest.ComputesMassesAndCharges 65: [ OK ] SelectionCollectionDataTest.ComputesMassesAndCharges (7 ms) 65: [ RUN ] SelectionCollectionDataTest.ComputesMassesAndChargesWithoutTopology 65: [ OK ] SelectionCollectionDataTest.ComputesMassesAndChargesWithoutTopology (4 ms) 65: [ RUN ] SelectionCollectionDataTest.HandlesFramesWithAtomSubsets 65: [ OK ] SelectionCollectionDataTest.HandlesFramesWithAtomSubsets (5 ms) 65: [ RUN ] SelectionCollectionDataTest.HandlesSelectionNames 65: [ OK ] SelectionCollectionDataTest.HandlesSelectionNames (3 ms) 65: [ RUN ] SelectionCollectionDataTest.HandlesIndexGroupsInSelections 65: [ OK ] SelectionCollectionDataTest.HandlesIndexGroupsInSelections (5 ms) 65: [ RUN ] SelectionCollectionDataTest.HandlesIndexGroupsInSelectionsDelayed 65: [ OK ] SelectionCollectionDataTest.HandlesIndexGroupsInSelectionsDelayed (3 ms) 65: [ RUN ] SelectionCollectionDataTest.HandlesUnsortedIndexGroupsInSelections 65: [ OK ] SelectionCollectionDataTest.HandlesUnsortedIndexGroupsInSelections (7 ms) 65: [ RUN ] SelectionCollectionDataTest.HandlesUnsortedIndexGroupsInSelectionsDelayed 65: [ OK ] SelectionCollectionDataTest.HandlesUnsortedIndexGroupsInSelectionsDelayed (4 ms) 65: [ RUN ] SelectionCollectionDataTest.HandlesConstantPositions 65: [ OK ] SelectionCollectionDataTest.HandlesConstantPositions (2 ms) 65: [ RUN ] SelectionCollectionDataTest.HandlesConstantPositionsWithModifiers 65: [ OK ] SelectionCollectionDataTest.HandlesConstantPositionsWithModifiers (3 ms) 65: [ RUN ] SelectionCollectionDataTest.HandlesWithinConstantPositions 65: [ OK ] SelectionCollectionDataTest.HandlesWithinConstantPositions (3 ms) 65: [ RUN ] SelectionCollectionDataTest.HandlesOverlappingIntegerRanges 65: [ OK ] SelectionCollectionDataTest.HandlesOverlappingIntegerRanges (2 ms) 65: [ RUN ] SelectionCollectionDataTest.HandlesOverlappingRealRanges 65: [ OK ] SelectionCollectionDataTest.HandlesOverlappingRealRanges (3 ms) 65: [ RUN ] SelectionCollectionDataTest.HandlesForcedStringMatchingMode 65: [ OK ] SelectionCollectionDataTest.HandlesForcedStringMatchingMode (3 ms) 65: [ RUN ] SelectionCollectionDataTest.HandlesWildcardMatching 65: [ OK ] SelectionCollectionDataTest.HandlesWildcardMatching (3 ms) 65: [ RUN ] SelectionCollectionDataTest.HandlesRegexMatching 65: [ OK ] SelectionCollectionDataTest.HandlesRegexMatching (4 ms) 65: [ RUN ] SelectionCollectionDataTest.HandlesBasicBoolean 65: [ OK ] SelectionCollectionDataTest.HandlesBasicBoolean (4 ms) 65: [ RUN ] SelectionCollectionDataTest.HandlesDynamicAtomValuedParameters 65: [ OK ] SelectionCollectionDataTest.HandlesDynamicAtomValuedParameters (4 ms) 65: [ RUN ] SelectionCollectionDataTest.HandlesEmptySelectionWithUnevaluatedExpressions 65: [ OK ] SelectionCollectionDataTest.HandlesEmptySelectionWithUnevaluatedExpressions (3 ms) 65: [ RUN ] SelectionCollectionDataTest.HandlesEmptyReferenceForSame 65: [ OK ] SelectionCollectionDataTest.HandlesEmptyReferenceForSame (3 ms) 65: [ RUN ] SelectionCollectionDataTest.HandlesPositionModifiersForKeywords 65: [ OK ] SelectionCollectionDataTest.HandlesPositionModifiersForKeywords (3 ms) 65: [ RUN ] SelectionCollectionDataTest.HandlesPositionModifiersForMethods 65: [ OK ] SelectionCollectionDataTest.HandlesPositionModifiersForMethods (4 ms) 65: [ RUN ] SelectionCollectionDataTest.HandlesKeywordOfPositions 65: [ OK ] SelectionCollectionDataTest.HandlesKeywordOfPositions (3 ms) 65: [ RUN ] SelectionCollectionDataTest.HandlesKeywordOfPositionsInArithmetic 65: [ OK ] SelectionCollectionDataTest.HandlesKeywordOfPositionsInArithmetic (3 ms) 65: [ RUN ] SelectionCollectionDataTest.HandlesNumericComparisons 65: [ OK ] SelectionCollectionDataTest.HandlesNumericComparisons (6 ms) 65: [ RUN ] SelectionCollectionDataTest.HandlesArithmeticExpressions 65: [ OK ] SelectionCollectionDataTest.HandlesArithmeticExpressions (6 ms) 65: [ RUN ] SelectionCollectionDataTest.HandlesNumericVariables 65: [ OK ] SelectionCollectionDataTest.HandlesNumericVariables (4 ms) 65: [ RUN ] SelectionCollectionDataTest.HandlesComplexNumericVariables 65: [ OK ] SelectionCollectionDataTest.HandlesComplexNumericVariables (5 ms) 65: [ RUN ] SelectionCollectionDataTest.HandlesPositionVariables 65: [ OK ] SelectionCollectionDataTest.HandlesPositionVariables (5 ms) 65: [ RUN ] SelectionCollectionDataTest.HandlesPositionVariableInModifier 65: [ OK ] SelectionCollectionDataTest.HandlesPositionVariableInModifier (4 ms) 65: [ RUN ] SelectionCollectionDataTest.HandlesConstantPositionInVariable 65: [ OK ] SelectionCollectionDataTest.HandlesConstantPositionInVariable (5 ms) 65: [ RUN ] SelectionCollectionDataTest.HandlesNumericConstantsInVariables 65: [ OK ] SelectionCollectionDataTest.HandlesNumericConstantsInVariables (4 ms) 65: [ RUN ] SelectionCollectionDataTest.HandlesBooleanStaticAnalysis 65: [ OK ] SelectionCollectionDataTest.HandlesBooleanStaticAnalysis (4 ms) 65: [ RUN ] SelectionCollectionDataTest.HandlesBooleanStaticAnalysisWithVariables 65: [ OK ] SelectionCollectionDataTest.HandlesBooleanStaticAnalysisWithVariables (3 ms) 65: [ RUN ] SelectionCollectionDataTest.HandlesBooleanStaticAnalysisWithMoreVariables 65: [ OK ] SelectionCollectionDataTest.HandlesBooleanStaticAnalysisWithMoreVariables (3 ms) 65: [ RUN ] SelectionCollectionDataTest.HandlesUnusedVariables 65: [ OK ] SelectionCollectionDataTest.HandlesUnusedVariables (2 ms) 65: [ RUN ] SelectionCollectionDataTest.HandlesVariablesWithStaticEvaluationGroups 65: [ OK ] SelectionCollectionDataTest.HandlesVariablesWithStaticEvaluationGroups (2 ms) 65: [ RUN ] SelectionCollectionDataTest.HandlesVariablesWithMixedEvaluationGroups 65: [ OK ] SelectionCollectionDataTest.HandlesVariablesWithMixedEvaluationGroups (3 ms) 65: [ RUN ] SelectionCollectionDataTest.HandlesVariablesWithMixedEvaluationGroups2 65: [ OK ] SelectionCollectionDataTest.HandlesVariablesWithMixedEvaluationGroups2 (4 ms) 65: [ RUN ] SelectionCollectionDataTest.CopiedSelectionWorksPreCompilation 65: [ OK ] SelectionCollectionDataTest.CopiedSelectionWorksPreCompilation (10 ms) 65: [ RUN ] SelectionCollectionDataTest.CopiedSelectionWorksPostCompilation 65: [ OK ] SelectionCollectionDataTest.CopiedSelectionWorksPostCompilation (11 ms) 65: [ RUN ] SelectionCollectionDataTest.CopiedSelectionsAreIndependent 65: [ OK ] SelectionCollectionDataTest.CopiedSelectionsAreIndependent (9 ms) 65: [ RUN ] SelectionCollectionDataTest.CopiedSelectionWithIndexPostCompilation 65: [ OK ] SelectionCollectionDataTest.CopiedSelectionWithIndexPostCompilation (11 ms) 65: [----------] 70 tests from SelectionCollectionDataTest (368 ms total) 65: 65: [----------] 17 tests from SelectionOptionTest 65: [ RUN ] SelectionOptionTest.ParsesSimpleSelection 65: [ OK ] SelectionOptionTest.ParsesSimpleSelection (1 ms) 65: [ RUN ] SelectionOptionTest.HandlesDynamicSelectionWhenStaticRequired 65: [ OK ] SelectionOptionTest.HandlesDynamicSelectionWhenStaticRequired (2 ms) 65: [ RUN ] SelectionOptionTest.HandlesNonAtomicSelectionWhenAtomsRequired 65: [ OK ] SelectionOptionTest.HandlesNonAtomicSelectionWhenAtomsRequired (2 ms) 65: [ RUN ] SelectionOptionTest.ChecksForSortedAtomsWhenRequired 65: [ OK ] SelectionOptionTest.ChecksForSortedAtomsWhenRequired (2 ms) 65: [ RUN ] SelectionOptionTest.ChecksEmptySelections 65: [ OK ] SelectionOptionTest.ChecksEmptySelections (1 ms) 65: [ RUN ] SelectionOptionTest.ChecksEmptyDelayedSelections 65: [ OK ] SelectionOptionTest.ChecksEmptyDelayedSelections (1 ms) 65: [ RUN ] SelectionOptionTest.HandlesTooManySelections 65: [ OK ] SelectionOptionTest.HandlesTooManySelections (2 ms) 65: [ RUN ] SelectionOptionTest.HandlesTooFewSelections 65: [ OK ] SelectionOptionTest.HandlesTooFewSelections (1 ms) 65: [ RUN ] SelectionOptionTest.HandlesDefaultSelectionText 65: [ OK ] SelectionOptionTest.HandlesDefaultSelectionText (1 ms) 65: [ RUN ] SelectionOptionTest.HandlesAdjuster 65: [ OK ] SelectionOptionTest.HandlesAdjuster (1 ms) 65: [ RUN ] SelectionOptionTest.HandlesDynamicWhenStaticRequiredWithAdjuster 65: [ OK ] SelectionOptionTest.HandlesDynamicWhenStaticRequiredWithAdjuster (1 ms) 65: [ RUN ] SelectionOptionTest.HandlesTooManySelectionsWithAdjuster 65: [ OK ] SelectionOptionTest.HandlesTooManySelectionsWithAdjuster (1 ms) 65: [ RUN ] SelectionOptionTest.HandlesTooFewSelectionsWithAdjuster 65: [ OK ] SelectionOptionTest.HandlesTooFewSelectionsWithAdjuster (1 ms) 65: [ RUN ] SelectionOptionTest.HandlesDelayedRequiredSelection 65: [ OK ] SelectionOptionTest.HandlesDelayedRequiredSelection (1 ms) 65: [ RUN ] SelectionOptionTest.HandlesTooFewDelayedRequiredSelections 65: [ OK ] SelectionOptionTest.HandlesTooFewDelayedRequiredSelections (1 ms) 65: [ RUN ] SelectionOptionTest.HandlesDelayedOptionalSelection 65: [ OK ] SelectionOptionTest.HandlesDelayedOptionalSelection (1 ms) 65: [ RUN ] SelectionOptionTest.HandlesDelayedSelectionWithAdjuster 65: [ OK ] SelectionOptionTest.HandlesDelayedSelectionWithAdjuster (1 ms) 65: [----------] 17 tests from SelectionOptionTest (34 ms total) 65: 65: [----------] 9 tests from SelectionFileOptionTest 65: [ RUN ] SelectionFileOptionTest.HandlesSingleSelectionOptionFromFile 65: [ OK ] SelectionFileOptionTest.HandlesSingleSelectionOptionFromFile (2 ms) 65: [ RUN ] SelectionFileOptionTest.HandlesTwoSeparateSelectionOptions 65: [ OK ] SelectionFileOptionTest.HandlesTwoSeparateSelectionOptions (2 ms) 65: [ RUN ] SelectionFileOptionTest.HandlesTwoSelectionOptionsFromSingleFile 65: [ OK ] SelectionFileOptionTest.HandlesTwoSelectionOptionsFromSingleFile (2 ms) 65: [ RUN ] SelectionFileOptionTest.HandlesRequiredOptionFromFile 65: [ OK ] SelectionFileOptionTest.HandlesRequiredOptionFromFile (2 ms) 65: [ RUN ] SelectionFileOptionTest.HandlesRequiredOptionFromFileWithOtherOptionSet 65: [ OK ] SelectionFileOptionTest.HandlesRequiredOptionFromFileWithOtherOptionSet (2 ms) 65: [ RUN ] SelectionFileOptionTest.HandlesTwoRequiredOptionsFromSingleFile 65: [ OK ] SelectionFileOptionTest.HandlesTwoRequiredOptionsFromSingleFile (2 ms) 65: [ RUN ] SelectionFileOptionTest.GivesErrorWithNoFile 65: [ OK ] SelectionFileOptionTest.GivesErrorWithNoFile (1 ms) 65: [ RUN ] SelectionFileOptionTest.GivesErrorWithNonExistentFile 65: [ OK ] SelectionFileOptionTest.GivesErrorWithNonExistentFile (2 ms) 65: [ RUN ] SelectionFileOptionTest.GivesErrorWithMultipleFiles 65: [ OK ] SelectionFileOptionTest.GivesErrorWithMultipleFiles (2 ms) 65: [----------] 9 tests from SelectionFileOptionTest (19 ms total) 65: 65: [----------] Global test environment tear-down 65: [==========] 201 tests from 11 test suites ran. (1093 ms total) 65: [ PASSED ] 201 tests. 65/92 Test #65: SelectionUnitTests ........................ Passed 1.20 sec test 66 Start 66: MdrunOutputTests 66: Test command: /build/reproducible-path/gromacs-2025.1/build/basic-dp/bin/mdrun-output-test "-ntomp" "2" "--gtest_output=xml:/build/reproducible-path/gromacs-2025.1/build/basic-dp/Testing/Temporary/MdrunOutputTests.xml" 66: Working Directory: /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests 66: Test timeout computed to be: 600 66: [==========] Running 12 tests from 5 test suites. 66: [----------] Global test environment set-up. 66: [----------] 1 test from MdrunTest 66: [ RUN ] MdrunTest.WritesHelp 66: [ OK ] MdrunTest.WritesHelp (56 ms) 66: [----------] 1 test from MdrunTest (56 ms total) 66: 66: [----------] 3 tests from WithDifferentOutputGroupSettings/MdrunCompressedXOutput 66: [ RUN ] WithDifferentOutputGroupSettings/MdrunCompressedXOutput.ExitsNormally/0 66: Generating 1-4 interactions: fudge = 0.5 66: Number of degrees of freedom in T-Coupling group rest is 9.00 66: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 66: 66: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/WithDifferentOutputGroupSettings_MdrunCompressedXOutput_ExitsNormally_0_input.mdp]: 66: NVE simulation: will use the initial temperature of 2573.591 K for 66: determining the Verlet buffer size 66: 66: 66: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/WithDifferentOutputGroupSettings_MdrunCompressedXOutput_ExitsNormally_0_input.mdp]: 66: You are using a plain Coulomb cut-off, which might produce artifacts. 66: You might want to consider using PME electrostatics. 66: 66: 66: 66: There were 2 NOTEs 66: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/WithDifferentOutputGroupSettings_MdrunCompressedXOutput_ExitsNormally_0.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 66: Can not increase nstlist because an NVE ensemble is used 66: Using 1 MPI thread 66: Using 2 OpenMP threads 66: 66: 66: NOTE: The number of threads is not equal to the number of (logical) cpus 66: and the -pin option is set to auto: will not pin threads to cpus. 66: This can lead to significant performance degradation. 66: Consider using -pin on (and -pinoffset in case you run multiple jobs). 66: starting mdrun 'spc2' 66: 1 steps, 0.0 ps. 66: Setting the LD random seed to -1346528551 66: 66: Generated 3 of the 3 non-bonded parameter combinations 66: 66: Generated 3 of the 3 1-4 parameter combinations 66: 66: Excluding 2 bonded neighbours molecule type 'SOL' 66: 66: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/spc2.gro' 66: 66: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 2573.59 K 66: 66: Calculated rlist for 1x1 atom pair-list as 1.153 nm, buffer size 0.153 nm 66: 66: Set rlist, assuming 4x4 atom pair-list, to 1.127 nm, buffer size 0.127 nm 66: 66: Note that mdrun will redetermine rlist based on the actual pair-list setup 66: 66: This run will generate roughly 0 Mb of data 66: 66: Writing final coordinates. 66: 66: Core t (s) Wall t (s) (%) 66: Time: 0.047 0.024 197.6 66: (ns/day) (hour/ns) 66: Performance: 7.213 3.327 66: Reading frame 0 time 0.000 66: # Atoms 6 66: Reading frame 1 time 0.001 Last frame 1 time 0.001 66: 66: 66: Item #frames Timestep (ps) 66: Step 2 0.001 66: Time 2 0.001 66: Lambda 0 66: Coords 2 0.001 66: Velocities 0 66: Forces 0 66: Box 2 0.001 66: Checking file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/WithDifferentOutputGroupSettings_MdrunCompressedXOutput_ExitsNormally_0.xtc 66: [ OK ] WithDifferentOutputGroupSettings/MdrunCompressedXOutput.ExitsNormally/0 (71 ms) 66: [ RUN ] WithDifferentOutputGroupSettings/MdrunCompressedXOutput.ExitsNormally/1 66: Generating 1-4 interactions: fudge = 0.5 66: Number of degrees of freedom in T-Coupling group rest is 9.00 66: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 66: 66: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/WithDifferentOutputGroupSettings_MdrunCompressedXOutput_ExitsNormally_1_input.mdp]: 66: NVE simulation: will use the initial temperature of 2573.591 K for 66: determining the Verlet buffer size 66: 66: 66: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/WithDifferentOutputGroupSettings_MdrunCompressedXOutput_ExitsNormally_1_input.mdp]: 66: You are using a plain Coulomb cut-off, which might produce artifacts. 66: You might want to consider using PME electrostatics. 66: 66: 66: 66: There were 2 NOTEs 66: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/WithDifferentOutputGroupSettings_MdrunCompressedXOutput_ExitsNormally_1.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 66: Can not increase nstlist because an NVE ensemble is used 66: Using 1 MPI thread 66: Using 2 OpenMP threads 66: 66: 66: NOTE: The number of threads is not equal to the number of (logical) cpus 66: and the -pin option is set to auto: will not pin threads to cpus. 66: This can lead to significant performance degradation. 66: Consider using -pin on (and -pinoffset in case you run multiple jobs). 66: starting mdrun 'spc2' 66: 1 steps, 0.0 ps. 66: Setting the LD random seed to -2162883 66: 66: Generated 3 of the 3 non-bonded parameter combinations 66: 66: Generated 3 of the 3 1-4 parameter combinations 66: 66: Excluding 2 bonded neighbours molecule type 'SOL' 66: 66: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/spc2.gro' 66: 66: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 2573.59 K 66: 66: Calculated rlist for 1x1 atom pair-list as 1.153 nm, buffer size 0.153 nm 66: 66: Set rlist, assuming 4x4 atom pair-list, to 1.127 nm, buffer size 0.127 nm 66: 66: Note that mdrun will redetermine rlist based on the actual pair-list setup 66: 66: This run will generate roughly 0 Mb of data 66: 66: Writing final coordinates. 66: 66: Core t (s) Wall t (s) (%) 66: Time: 0.040 0.020 197.2 66: (ns/day) (hour/ns) 66: Performance: 8.539 2.811 66: Reading frame 0 time 0.000 66: # Atoms 6 66: Reading frame 1 time 0.001 Last frame 1 time 0.001 66: 66: 66: Item #frames Timestep (ps) 66: Step 2 0.001 66: Time 2 0.001 66: Lambda 0 66: Coords 2 0.001 66: Velocities 0 66: Forces 0 66: Box 2 0.001 66: Checking file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/WithDifferentOutputGroupSettings_MdrunCompressedXOutput_ExitsNormally_1.xtc 66: [ OK ] WithDifferentOutputGroupSettings/MdrunCompressedXOutput.ExitsNormally/1 (64 ms) 66: [ RUN ] WithDifferentOutputGroupSettings/MdrunCompressedXOutput.ExitsNormally/2 66: Generating 1-4 interactions: fudge = 0.5 66: Number of degrees of freedom in T-Coupling group rest is 9.00 66: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 66: 66: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/WithDifferentOutputGroupSettings_MdrunCompressedXOutput_ExitsNormally_2_input.mdp]: 66: NVE simulation: will use the initial temperature of 2573.591 K for 66: determining the Verlet buffer size 66: 66: 66: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/WithDifferentOutputGroupSettings_MdrunCompressedXOutput_ExitsNormally_2_input.mdp]: 66: You are using a plain Coulomb cut-off, which might produce artifacts. 66: You might want to consider using PME electrostatics. 66: 66: 66: 66: There were 2 NOTEs 66: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/WithDifferentOutputGroupSettings_MdrunCompressedXOutput_ExitsNormally_2.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 66: Can not increase nstlist because an NVE ensemble is used 66: Using 1 MPI thread 66: Using 2 OpenMP threads 66: 66: 66: NOTE: The number of threads is not equal to the number of (logical) cpus 66: and the -pin option is set to auto: will not pin threads to cpus. 66: This can lead to significant performance degradation. 66: Consider using -pin on (and -pinoffset in case you run multiple jobs). 66: starting mdrun 'spc2' 66: 1 steps, 0.0 ps. 66: Setting the LD random seed to -875563053 66: 66: Generated 3 of the 3 non-bonded parameter combinations 66: 66: Generated 3 of the 3 1-4 parameter combinations 66: 66: Excluding 2 bonded neighbours molecule type 'SOL' 66: 66: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/spc2.gro' 66: 66: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 2573.59 K 66: 66: Calculated rlist for 1x1 atom pair-list as 1.153 nm, buffer size 0.153 nm 66: 66: Set rlist, assuming 4x4 atom pair-list, to 1.127 nm, buffer size 0.127 nm 66: 66: Note that mdrun will redetermine rlist based on the actual pair-list setup 66: 66: This run will generate roughly 0 Mb of data 66: 66: Writing final coordinates. 66: 66: Core t (s) Wall t (s) (%) 66: Time: 0.031 0.016 196.5 66: (ns/day) (hour/ns) 66: Performance: 10.934 2.195 66: Reading frame 0 time 0.000 66: # Atoms 3 66: Reading frame 1 time 0.001 Last frame 1 time 0.001 66: 66: 66: Item #frames Timestep (ps) 66: Step 2 0.001 66: Time 2 0.001 66: Lambda 0 66: Coords 2 0.001 66: Velocities 0 66: Forces 0 66: Box 2 0.001 66: Checking file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/WithDifferentOutputGroupSettings_MdrunCompressedXOutput_ExitsNormally_2.xtc 66: [ OK ] WithDifferentOutputGroupSettings/MdrunCompressedXOutput.ExitsNormally/2 (58 ms) 66: [----------] 3 tests from WithDifferentOutputGroupSettings/MdrunCompressedXOutput (194 ms total) 66: 66: [----------] 2 tests from Argon12/OutputFiles 66: [ RUN ] Argon12/OutputFiles.FilesArePresent/0 66: 66: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Argon12_OutputFiles_FilesArePresent_0_input.mdp]: 66: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 66: that with the Verlet scheme, nstlist has no effect on the accuracy of 66: your simulation. 66: 66: 66: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Argon12_OutputFiles_FilesArePresent_0_input.mdp]: 66: Setting nstcalcenergy (100) equal to nstenergy (4) 66: 66: Number of degrees of freedom in T-Coupling group System is 33.00 66: 66: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Argon12_OutputFiles_FilesArePresent_0_input.mdp]: 66: NVE simulation: will use the initial temperature of 68.810 K for 66: determining the Verlet buffer size 66: 66: 66: There were 3 NOTEs 66: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Argon12_OutputFiles_FilesArePresent_0.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 66: Can not increase nstlist because an NVE ensemble is used 66: Using 1 MPI thread 66: Using 2 OpenMP threads 66: 66: 66: NOTE: The number of threads is not equal to the number of (logical) cpus 66: and the -pin option is set to auto: will not pin threads to cpus. 66: This can lead to significant performance degradation. 66: Consider using -pin on (and -pinoffset in case you run multiple jobs). 66: starting mdrun 'Argon' 66: 16 steps, 0.0 ps. 66: Generated 1 of the 1 non-bonded parameter combinations 66: 66: Excluding 1 bonded neighbours molecule type 'Argon' 66: 66: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 66: 66: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 66: 66: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 66: 66: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 66: 66: Note that mdrun will redetermine rlist based on the actual pair-list setup 66: 66: This run will generate roughly 0 Mb of data 66: 66: Writing final coordinates. 66: 66: Core t (s) Wall t (s) (%) 66: Time: 0.038 0.019 197.1 66: (ns/day) (hour/ns) 66: Performance: 76.716 0.313 66: [ OK ] Argon12/OutputFiles.FilesArePresent/0 (63 ms) 66: [ RUN ] Argon12/OutputFiles.FilesArePresent/1 66: 66: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Argon12_OutputFiles_FilesArePresent_1_input.mdp]: 66: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 66: that with the Verlet scheme, nstlist has no effect on the accuracy of 66: your simulation. 66: 66: 66: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Argon12_OutputFiles_FilesArePresent_1_input.mdp]: 66: Setting nstcalcenergy (100) equal to nstenergy (4) 66: 66: Number of degrees of freedom in T-Coupling group System is 33.00 66: 66: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Argon12_OutputFiles_FilesArePresent_1_input.mdp]: 66: NVE simulation: will use the initial temperature of 68.810 K for 66: determining the Verlet buffer size 66: 66: 66: There were 3 NOTEs 66: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Argon12_OutputFiles_FilesArePresent_1.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 66: Can not increase nstlist because an NVE ensemble is used 66: Using 1 MPI thread 66: Using 2 OpenMP threads 66: 66: 66: NOTE: The number of threads is not equal to the number of (logical) cpus 66: and the -pin option is set to auto: will not pin threads to cpus. 66: This can lead to significant performance degradation. 66: Consider using -pin on (and -pinoffset in case you run multiple jobs). 66: starting mdrun 'Argon' 66: 16 steps, 0.0 ps. 66: Generated 1 of the 1 non-bonded parameter combinations 66: 66: Excluding 1 bonded neighbours molecule type 'Argon' 66: 66: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 66: 66: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 66: 66: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 66: 66: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 66: 66: Note that mdrun will redetermine rlist based on the actual pair-list setup 66: 66: This run will generate roughly 0 Mb of data 66: 66: Writing final coordinates. 66: 66: Core t (s) Wall t (s) (%) 66: Time: 0.050 0.025 197.5 66: (ns/day) (hour/ns) 66: Performance: 57.838 0.415 66: [ OK ] Argon12/OutputFiles.FilesArePresent/1 (69 ms) 66: [----------] 2 tests from Argon12/OutputFiles (133 ms total) 66: 66: [----------] 3 tests from MdrunCanWrite/Trajectories 66: [ RUN ] MdrunCanWrite/Trajectories.ThatDifferInNstxout/0 66: Number of degrees of freedom in T-Coupling group System is 12.00 66: 66: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunCanWrite_Trajectories_ThatDifferInNstxout_0_input.mdp]: 66: You are using a plain Coulomb cut-off, which might produce artifacts. 66: You might want to consider using PME electrostatics. 66: 66: 66: 66: There was 1 NOTE 66: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunCanWrite_Trajectories_ThatDifferInNstxout_0.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 66: Changing nstlist from 10 to 40, rlist from 1.031 to 1.172 66: 66: Using 1 MPI thread 66: Using 2 OpenMP threads 66: 66: 66: NOTE: The number of threads is not equal to the number of (logical) cpus 66: and the -pin option is set to auto: will not pin threads to cpus. 66: This can lead to significant performance degradation. 66: Consider using -pin on (and -pinoffset in case you run multiple jobs). 66: starting mdrun 'spc-and-methanol' 66: 6 steps, 0.0 ps. 66: Setting the LD random seed to -851576257 66: 66: Generated 8 of the 10 non-bonded parameter combinations 66: 66: Excluding 2 bonded neighbours molecule type 'Methanol' 66: 66: Excluding 2 bonded neighbours molecule type 'SOL' 66: 66: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/spc-and-methanol.gro' 66: 66: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 66: 66: Calculated rlist for 1x1 atom pair-list as 1.040 nm, buffer size 0.040 nm 66: 66: Set rlist, assuming 4x4 atom pair-list, to 1.031 nm, buffer size 0.031 nm 66: 66: Note that mdrun will redetermine rlist based on the actual pair-list setup 66: 66: This run will generate roughly 0 Mb of data 66: 66: Writing final coordinates. 66: 66: Core t (s) Wall t (s) (%) 66: Time: 0.138 0.069 199.3 66: (ns/day) (hour/ns) 66: Performance: 8.764 2.738 66: [ OK ] MdrunCanWrite/Trajectories.ThatDifferInNstxout/0 (129 ms) 66: [ RUN ] MdrunCanWrite/Trajectories.ThatDifferInNstxout/1 66: Number of degrees of freedom in T-Coupling group System is 12.00 66: 66: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunCanWrite_Trajectories_ThatDifferInNstxout_1_input.mdp]: 66: You are using a plain Coulomb cut-off, which might produce artifacts. 66: You might want to consider using PME electrostatics. 66: 66: 66: 66: There was 1 NOTE 66: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunCanWrite_Trajectories_ThatDifferInNstxout_1.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 66: Changing nstlist from 10 to 40, rlist from 1.031 to 1.172 66: 66: Using 1 MPI thread 66: Using 2 OpenMP threads 66: 66: 66: NOTE: The number of threads is not equal to the number of (logical) cpus 66: and the -pin option is set to auto: will not pin threads to cpus. 66: This can lead to significant performance degradation. 66: Consider using -pin on (and -pinoffset in case you run multiple jobs). 66: starting mdrun 'spc-and-methanol' 66: 6 steps, 0.0 ps. 66: Setting the LD random seed to 402044405 66: 66: Generated 8 of the 10 non-bonded parameter combinations 66: 66: Excluding 2 bonded neighbours molecule type 'Methanol' 66: 66: Excluding 2 bonded neighbours molecule type 'SOL' 66: 66: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/spc-and-methanol.gro' 66: 66: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 66: 66: Calculated rlist for 1x1 atom pair-list as 1.040 nm, buffer size 0.040 nm 66: 66: Set rlist, assuming 4x4 atom pair-list, to 1.031 nm, buffer size 0.031 nm 66: 66: Note that mdrun will redetermine rlist based on the actual pair-list setup 66: 66: This run will generate roughly 0 Mb of data 66: 66: Writing final coordinates. 66: 66: Core t (s) Wall t (s) (%) 66: Time: 0.127 0.064 199.2 66: (ns/day) (hour/ns) 66: Performance: 9.494 2.528 66: [ OK ] MdrunCanWrite/Trajectories.ThatDifferInNstxout/1 (122 ms) 66: [ RUN ] MdrunCanWrite/Trajectories.ThatDifferInNstxout/2 66: Number of degrees of freedom in T-Coupling group System is 12.00 66: 66: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunCanWrite_Trajectories_ThatDifferInNstxout_2_input.mdp]: 66: You are using a plain Coulomb cut-off, which might produce artifacts. 66: You might want to consider using PME electrostatics. 66: 66: 66: 66: There was 1 NOTE 66: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunCanWrite_Trajectories_ThatDifferInNstxout_2.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 66: Changing nstlist from 10 to 40, rlist from 1.031 to 1.172 66: 66: Using 1 MPI thread 66: Using 2 OpenMP threads 66: 66: 66: NOTE: The number of threads is not equal to the number of (logical) cpus 66: and the -pin option is set to auto: will not pin threads to cpus. 66: This can lead to significant performance degradation. 66: Consider using -pin on (and -pinoffset in case you run multiple jobs). 66: starting mdrun 'spc-and-methanol' 66: 6 steps, 0.0 ps. 66: Setting the LD random seed to -1090541585 66: 66: Generated 8 of the 10 non-bonded parameter combinations 66: 66: Excluding 2 bonded neighbours molecule type 'Methanol' 66: 66: Excluding 2 bonded neighbours molecule type 'SOL' 66: 66: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/spc-and-methanol.gro' 66: 66: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 66: 66: Calculated rlist for 1x1 atom pair-list as 1.040 nm, buffer size 0.040 nm 66: 66: Set rlist, assuming 4x4 atom pair-list, to 1.031 nm, buffer size 0.031 nm 66: 66: Note that mdrun will redetermine rlist based on the actual pair-list setup 66: 66: This run will generate roughly 0 Mb of data 66: 66: Writing final coordinates. 66: 66: Core t (s) Wall t (s) (%) 66: Time: 0.047 0.024 197.7 66: (ns/day) (hour/ns) 66: Performance: 25.311 0.948 66: [ OK ] MdrunCanWrite/Trajectories.ThatDifferInNstxout/2 (81 ms) 66: [----------] 3 tests from MdrunCanWrite/Trajectories (333 ms total) 66: 66: [----------] 3 tests from MdrunCanWrite/NptTrajectories 66: [ RUN ] MdrunCanWrite/NptTrajectories.WithDifferentPcoupl/0 66: Number of degrees of freedom in T-Coupling group System is 12.00 66: 66: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunCanWrite_NptTrajectories_WithDifferentPcoupl_0_input.mdp]: 66: You are using a plain Coulomb cut-off, which might produce artifacts. 66: You might want to consider using PME electrostatics. 66: 66: 66: 66: There was 1 NOTE 66: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunCanWrite_NptTrajectories_WithDifferentPcoupl_0.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 66: Changing nstlist from 10 to 40, rlist from 1.031 to 1.172 66: 66: Using 1 MPI thread 66: Using 2 OpenMP threads 66: 66: 66: NOTE: The number of threads is not equal to the number of (logical) cpus 66: and the -pin option is set to auto: will not pin threads to cpus. 66: This can lead to significant performance degradation. 66: Consider using -pin on (and -pinoffset in case you run multiple jobs). 66: starting mdrun 'spc-and-methanol' 66: 2 steps, 0.0 ps. 66: Setting the LD random seed to 2055724951 66: 66: Generated 8 of the 10 non-bonded parameter combinations 66: 66: Excluding 2 bonded neighbours molecule type 'Methanol' 66: 66: Excluding 2 bonded neighbours molecule type 'SOL' 66: 66: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/spc-and-methanol.gro' 66: 66: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 66: 66: Calculated rlist for 1x1 atom pair-list as 1.040 nm, buffer size 0.040 nm 66: 66: Set rlist, assuming 4x4 atom pair-list, to 1.031 nm, buffer size 0.031 nm 66: 66: Note that mdrun will redetermine rlist based on the actual pair-list setup 66: 66: This run will generate roughly 0 Mb of data 66: 66: Writing final coordinates. 66: 66: Core t (s) Wall t (s) (%) 66: Time: 0.031 0.016 196.9 66: (ns/day) (hour/ns) 66: Performance: 16.362 1.467 66: [ OK ] MdrunCanWrite/NptTrajectories.WithDifferentPcoupl/0 (74 ms) 66: [ RUN ] MdrunCanWrite/NptTrajectories.WithDifferentPcoupl/1 66: 66: WARNING 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunCanWrite_NptTrajectories_WithDifferentPcoupl_1_input.mdp]: 66: The Berendsen barostat does not generate any strictly correct ensemble, 66: and should not be used for new production simulations (in our opinion). 66: We recommend using the C-rescale barostat instead. 66: 66: Number of degrees of freedom in T-Coupling group System is 12.00 66: 66: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunCanWrite_NptTrajectories_WithDifferentPcoupl_1_input.mdp]: 66: You are using a plain Coulomb cut-off, which might produce artifacts. 66: You might want to consider using PME electrostatics. 66: 66: 66: 66: There was 1 NOTE 66: 66: There was 1 WARNING 66: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunCanWrite_NptTrajectories_WithDifferentPcoupl_1.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 66: Changing nstlist from 10 to 40, rlist from 1.031 to 1.172 66: 66: Using 1 MPI thread 66: Using 2 OpenMP threads 66: 66: 66: NOTE: The number of threads is not equal to the number of (logical) cpus 66: and the -pin option is set to auto: will not pin threads to cpus. 66: This can lead to significant performance degradation. 66: Consider using -pin on (and -pinoffset in case you run multiple jobs). 66: starting mdrun 'spc-and-methanol' 66: 2 steps, 0.0 ps. 66: Setting the LD random seed to -1144030213 66: 66: Generated 8 of the 10 non-bonded parameter combinations 66: 66: Excluding 2 bonded neighbours molecule type 'Methanol' 66: 66: Excluding 2 bonded neighbours molecule type 'SOL' 66: 66: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/spc-and-methanol.gro' 66: 66: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 66: 66: Calculated rlist for 1x1 atom pair-list as 1.040 nm, buffer size 0.040 nm 66: 66: Set rlist, assuming 4x4 atom pair-list, to 1.031 nm, buffer size 0.031 nm 66: 66: Note that mdrun will redetermine rlist based on the actual pair-list setup 66: 66: This run will generate roughly 0 Mb of data 66: 66: Writing final coordinates. 66: 66: Core t (s) Wall t (s) (%) 66: Time: 0.030 0.015 195.3 66: (ns/day) (hour/ns) 66: Performance: 17.038 1.409 66: [ OK ] MdrunCanWrite/NptTrajectories.WithDifferentPcoupl/1 (73 ms) 66: [ RUN ] MdrunCanWrite/NptTrajectories.WithDifferentPcoupl/2 66: Number of degrees of freedom in T-Coupling group System is 12.00 66: 66: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunCanWrite_NptTrajectories_WithDifferentPcoupl_2_input.mdp]: 66: You are using a plain Coulomb cut-off, which might produce artifacts. 66: You might want to consider using PME electrostatics. 66: 66: 66: 66: There was 1 NOTE 66: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunCanWrite_NptTrajectories_WithDifferentPcoupl_2.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 66: Changing nstlist from 10 to 40, rlist from 1.031 to 1.172 66: 66: Using 1 MPI thread 66: Using 2 OpenMP threads 66: 66: 66: NOTE: The number of threads is not equal to the number of (logical) cpus 66: and the -pin option is set to auto: will not pin threads to cpus. 66: This can lead to significant performance degradation. 66: Consider using -pin on (and -pinoffset in case you run multiple jobs). 66: starting mdrun 'spc-and-methanol' 66: 2 steps, 0.0 ps. 66: Setting the LD random seed to -137101318 66: 66: Generated 8 of the 10 non-bonded parameter combinations 66: 66: Excluding 2 bonded neighbours molecule type 'Methanol' 66: 66: Excluding 2 bonded neighbours molecule type 'SOL' 66: 66: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/spc-and-methanol.gro' 66: 66: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 66: 66: Calculated rlist for 1x1 atom pair-list as 1.040 nm, buffer size 0.040 nm 66: 66: Set rlist, assuming 4x4 atom pair-list, to 1.031 nm, buffer size 0.031 nm 66: 66: Note that mdrun will redetermine rlist based on the actual pair-list setup 66: 66: This run will generate roughly 0 Mb of data 66: 66: Writing final coordinates. 66: 66: Core t (s) Wall t (s) (%) 66: Time: 0.030 0.015 196.3 66: (ns/day) (hour/ns) 66: Performance: 16.903 1.420 66: [ OK ] MdrunCanWrite/NptTrajectories.WithDifferentPcoupl/2 (72 ms) 66: [----------] 3 tests from MdrunCanWrite/NptTrajectories (220 ms total) 66: 66: [----------] Global test environment tear-down 66: [==========] 12 tests from 5 test suites ran. (1115 ms total) 66: [ PASSED ] 12 tests. 66/92 Test #66: MdrunOutputTests .......................... Passed 1.19 sec test 67 Start 67: MdrunModulesTests 67: Test command: /build/reproducible-path/gromacs-2025.1/build/basic-dp/bin/mdrun-modules-test "-ntomp" "2" "--gtest_output=xml:/build/reproducible-path/gromacs-2025.1/build/basic-dp/Testing/Temporary/MdrunModulesTests.xml" 67: Working Directory: /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests 67: Test timeout computed to be: 600 67: [==========] Running 15 tests from 3 test suites. 67: [----------] Global test environment set-up. 67: [----------] 9 tests from DensityFittingTest 67: [ RUN ] DensityFittingTest.EnergyMinimizationEnergyCorrectInnerProduct 67: Number of degrees of freedom in T-Coupling group rest is 33.00 67: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 67: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/DensityFittingTest_EnergyMinimizationEnergyCorrectInnerProduct.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 67: Using 1 MPI thread 67: Using 2 OpenMP threads 67: 67: 67: NOTE: The number of threads is not equal to the number of (logical) cpus 67: and the -pin option is set to auto: will not pin threads to cpus. 67: This can lead to significant performance degradation. 67: Consider using -pin on (and -pinoffset in case you run multiple jobs). 67: 67: Steepest Descents: 67: Tolerance (Fmax) = 1.00000e+01 67: Number of steps = 2 67: 67: Energy minimization reached the maximum number of steps before the forces 67: reached the requested precision Fmax < 10. 67: 67: writing lowest energy coordinates. 67: 67: Steepest Descents did not converge to Fmax < 10 in 3 steps. 67: Potential Energy = -3.85652608067156e+03 67: Maximum force = 4.50998690851897e+03 on atom 3 67: Norm of force = 1.68168494163492e+03 67: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/DensityFittingTest_EnergyMinimizationEnergyCorrectInnerProduct.edr as double precision energy file 67: Reading energy frame 0 time 0.000 Reading energy frame 1 time 1.000 Reading energy frame 2 time 2.000 Last energy frame read 2 time 2.000 Setting the LD random seed to -67375539 67: 67: Generated 1 of the 1 non-bonded parameter combinations 67: 67: Excluding 1 bonded neighbours molecule type 'Argon' 67: 67: This run will generate roughly 0 Mb of data 67: [ OK ] DensityFittingTest.EnergyMinimizationEnergyCorrectInnerProduct (53 ms) 67: [ RUN ] DensityFittingTest.EnergyMinimizationEnergyCorrectInnerProductTranslation 67: Number of degrees of freedom in T-Coupling group rest is 33.00 67: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 67: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/DensityFittingTest_EnergyMinimizationEnergyCorrectInnerProductTranslation.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 67: Using 1 MPI thread 67: Using 2 OpenMP threads 67: 67: 67: NOTE: The number of threads is not equal to the number of (logical) cpus 67: and the -pin option is set to auto: will not pin threads to cpus. 67: This can lead to significant performance degradation. 67: Consider using -pin on (and -pinoffset in case you run multiple jobs). 67: 67: Steepest Descents: 67: Tolerance (Fmax) = 1.00000e+01 67: Number of steps = 2 67: 67: Energy minimization reached the maximum number of steps before the forces 67: reached the requested precision Fmax < 10. 67: 67: writing lowest energy coordinates. 67: 67: Steepest Descents did not converge to Fmax < 10 in 3 steps. 67: Potential Energy = -9.82077921283928e+03 67: Maximum force = 7.39548334240075e+03 on atom 2 67: Norm of force = 2.78250777177324e+03 67: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/DensityFittingTest_EnergyMinimizationEnergyCorrectInnerProductTranslation.edr as double precision energy file 67: Reading energy frame 0 time 0.000 Reading energy frame 1 time 1.000 Reading energy frame 2 time 2.000 Last energy frame read 2 time 2.000 Setting the LD random seed to -308089362 67: 67: Generated 1 of the 1 non-bonded parameter combinations 67: 67: Excluding 1 bonded neighbours molecule type 'Argon' 67: 67: This run will generate roughly 0 Mb of data 67: [ OK ] DensityFittingTest.EnergyMinimizationEnergyCorrectInnerProductTranslation (50 ms) 67: [ RUN ] DensityFittingTest.EnergyMinimizationEnergyTranslationParametersOff 67: 67: [WARNING] ./src/external/googletest/googletest/src/gtest-death-test.cc:1108:: Death tests use fork(), which is unsafe particularly in a threaded context. For this test, Google Test detected 2 threads. See https://github.com/google/googletest/blob/main/docs/advanced.md#death-tests-and-threads for more explanation and suggested solutions, especially if this is the last message you see before your test times out. 67: [ OK ] DensityFittingTest.EnergyMinimizationEnergyTranslationParametersOff (42 ms) 67: [ RUN ] DensityFittingTest.EnergyMinimizationEnergyCorrectInnerProductTranslationAndTransformationMatrix 67: Number of degrees of freedom in T-Coupling group rest is 33.00 67: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 67: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/DensityFittingTest_EnergyMinimizationEnergyCorrectInnerProductTranslationAndTransformationMatrix.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 67: Overriding nsteps with value passed on the command line: 4 steps 67: 67: Using 1 MPI thread 67: Using 2 OpenMP threads 67: 67: 67: NOTE: The number of threads is not equal to the number of (logical) cpus 67: and the -pin option is set to auto: will not pin threads to cpus. 67: This can lead to significant performance degradation. 67: Consider using -pin on (and -pinoffset in case you run multiple jobs). 67: 67: Steepest Descents: 67: Tolerance (Fmax) = 1.00000e+01 67: Number of steps = 4 67: 67: Energy minimization reached the maximum number of steps before the forces 67: reached the requested precision Fmax < 10. 67: 67: writing lowest energy coordinates. 67: 67: Steepest Descents did not converge to Fmax < 10 in 5 steps. 67: Potential Energy = -5.47393359520241e+03 67: Maximum force = 6.13219949575544e+03 on atom 2 67: Norm of force = 1.77021426574818e+03 67: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/DensityFittingTest_EnergyMinimizationEnergyCorrectInnerProductTranslationAndTransformationMatrix.edr as double precision energy file 67: Reading energy frame 0 time 0.000 Reading energy frame 1 time 1.000 Reading energy frame 2 time 2.000 Reading energy frame 3 time 3.000 Reading energy frame 4 time 4.000 Last energy frame read 4 time 4.000 Setting the LD random seed to 2000617181 67: 67: Generated 1 of the 1 non-bonded parameter combinations 67: 67: Excluding 1 bonded neighbours molecule type 'Argon' 67: 67: This run will generate roughly 0 Mb of data 67: [ OK ] DensityFittingTest.EnergyMinimizationEnergyCorrectInnerProductTranslationAndTransformationMatrix (51 ms) 67: [ RUN ] DensityFittingTest.EnergyMinimizationEnergyMatrixTransfromationOff 67: 67: [WARNING] ./src/external/googletest/googletest/src/gtest-death-test.cc:1108:: Death tests use fork(), which is unsafe particularly in a threaded context. For this test, Google Test detected 2 threads. See https://github.com/google/googletest/blob/main/docs/advanced.md#death-tests-and-threads for more explanation and suggested solutions, especially if this is the last message you see before your test times out. 67: [ OK ] DensityFittingTest.EnergyMinimizationEnergyMatrixTransfromationOff (42 ms) 67: [ RUN ] DensityFittingTest.EnergyMinimizationEnergyCorrectInnerProductIdentityMatrix 67: Number of degrees of freedom in T-Coupling group rest is 33.00 67: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 67: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/DensityFittingTest_EnergyMinimizationEnergyCorrectInnerProductIdentityMatrix.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 67: Using 1 MPI thread 67: Using 2 OpenMP threads 67: 67: 67: NOTE: The number of threads is not equal to the number of (logical) cpus 67: and the -pin option is set to auto: will not pin threads to cpus. 67: This can lead to significant performance degradation. 67: Consider using -pin on (and -pinoffset in case you run multiple jobs). 67: 67: Steepest Descents: 67: Tolerance (Fmax) = 1.00000e+01 67: Number of steps = 2 67: 67: Energy minimization reached the maximum number of steps before the forces 67: reached the requested precision Fmax < 10. 67: 67: writing lowest energy coordinates. 67: 67: Steepest Descents did not converge to Fmax < 10 in 3 steps. 67: Potential Energy = -3.85652608067156e+03 67: Maximum force = 4.50998690851897e+03 on atom 3 67: Norm of force = 1.68168494163492e+03 67: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/DensityFittingTest_EnergyMinimizationEnergyCorrectInnerProductIdentityMatrix.edr as double precision energy file 67: Reading energy frame 0 time 0.000 Reading energy frame 1 time 1.000 Reading energy frame 2 time 2.000 Last energy frame read 2 time 2.000 Setting the LD random seed to -415534723 67: 67: Generated 1 of the 1 non-bonded parameter combinations 67: 67: Excluding 1 bonded neighbours molecule type 'Argon' 67: 67: This run will generate roughly 0 Mb of data 67: [ OK ] DensityFittingTest.EnergyMinimizationEnergyCorrectInnerProductIdentityMatrix (48 ms) 67: [ RUN ] DensityFittingTest.EnergyMinimizationEnergyCorrectForRelativeEntropy 67: Number of degrees of freedom in T-Coupling group rest is 33.00 67: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 67: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/DensityFittingTest_EnergyMinimizationEnergyCorrectForRelativeEntropy.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 67: Using 1 MPI thread 67: Using 2 OpenMP threads 67: 67: 67: NOTE: The number of threads is not equal to the number of (logical) cpus 67: and the -pin option is set to auto: will not pin threads to cpus. 67: This can lead to significant performance degradation. 67: Consider using -pin on (and -pinoffset in case you run multiple jobs). 67: 67: Steepest Descents: 67: Tolerance (Fmax) = 1.00000e+01 67: Number of steps = 2 67: 67: Energy minimization reached the maximum number of steps before the forces 67: reached the requested precision Fmax < 10. 67: 67: writing lowest energy coordinates. 67: 67: Steepest Descents did not converge to Fmax < 10 in 3 steps. 67: Potential Energy = -2.71386626041483e+04 67: Maximum force = 6.78276506555709e+03 on atom 2 67: Norm of force = 1.96088641457984e+03 67: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/DensityFittingTest_EnergyMinimizationEnergyCorrectForRelativeEntropy.edr as double precision energy file 67: Reading energy frame 0 time 0.000 Reading energy frame 1 time 1.000 Reading energy frame 2 time 2.000 Last energy frame read 2 time 2.000 Setting the LD random seed to -538452242 67: 67: Generated 1 of the 1 non-bonded parameter combinations 67: 67: Excluding 1 bonded neighbours molecule type 'Argon' 67: 67: This run will generate roughly 0 Mb of data 67: [ OK ] DensityFittingTest.EnergyMinimizationEnergyCorrectForRelativeEntropy (46 ms) 67: [ RUN ] DensityFittingTest.GromppErrorWhenEnergyEvaluationFrequencyMismatch 67: 67: [WARNING] ./src/external/googletest/googletest/src/gtest-death-test.cc:1108:: Death tests use fork(), which is unsafe particularly in a threaded context. For this test, Google Test detected 2 threads. See https://github.com/google/googletest/blob/main/docs/advanced.md#death-tests-and-threads for more explanation and suggested solutions, especially if this is the last message you see before your test times out. 67: Setting the LD random seed to -6361610 67: 67: Generated 1 of the 1 non-bonded parameter combinations 67: 67: Excluding 1 bonded neighbours molecule type 'Argon' 67: 67: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 67: [ OK ] DensityFittingTest.GromppErrorWhenEnergyEvaluationFrequencyMismatch (43 ms) 67: [ RUN ] DensityFittingTest.CheckpointWorks 67: 67: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/DensityFittingTest_CheckpointWorks_input.mdp]: 67: Setting nstcalcenergy (100) equal to nstenergy (2) 67: 67: Number of degrees of freedom in T-Coupling group rest is 33.00 67: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 67: 67: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/DensityFittingTest_CheckpointWorks_input.mdp]: 67: NVE simulation: will use the initial temperature of 68.810 K for 67: determining the Verlet buffer size 67: 67: 67: There were 2 NOTEs 67: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/DensityFittingTest_CheckpointWorks.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 67: Can not increase nstlist because an NVE ensemble is used 67: Using 1 MPI thread 67: Using 2 OpenMP threads 67: 67: 67: NOTE: The number of threads is not equal to the number of (logical) cpus 67: and the -pin option is set to auto: will not pin threads to cpus. 67: This can lead to significant performance degradation. 67: Consider using -pin on (and -pinoffset in case you run multiple jobs). 67: starting mdrun 'Argon' 67: 2 steps, 0.0 ps. 67: Setting the LD random seed to -9961505 67: 67: Generated 1 of the 1 non-bonded parameter combinations 67: 67: Excluding 1 bonded neighbours molecule type 'Argon' 67: 67: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 67: 67: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 68.8096 K 67: 67: Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm 67: 67: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm 67: 67: Note that mdrun will redetermine rlist based on the actual pair-list setup 67: 67: This run will generate roughly 0 Mb of data 67: 67: Writing final coordinates. 67: 67: Core t (s) Wall t (s) (%) 67: Time: 0.037 0.019 197.1 67: (ns/day) (hour/ns) 67: Performance: 13.680 1.754 67: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/DensityFittingTest_CheckpointWorks.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 67: Overriding nsteps with value passed on the command line: 4 steps, 0.004 ps 67: Can not increase nstlist because an NVE ensemble is used 67: 67: Using 1 MPI thread 67: Using 2 OpenMP threads 67: 67: 67: NOTE: The number of threads is not equal to the number of (logical) cpus 67: and the -pin option is set to auto: will not pin threads to cpus. 67: This can lead to significant performance degradation. 67: Consider using -pin on (and -pinoffset in case you run multiple jobs). 67: starting mdrun 'Argon' 67: 6 steps, 0.0 ps (continuing from step 2, 0.0 ps). 67: 67: Writing final coordinates. 67: 67: Core t (s) Wall t (s) (%) 67: Time: 0.028 0.014 196.2 67: (ns/day) (hour/ns) 67: Performance: 30.780 0.780 67: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/DensityFittingTest_CheckpointWorks.edr as double precision energy file 67: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.002 Last energy frame read 1 time 0.002 [ OK ] DensityFittingTest.CheckpointWorks (93 ms) 67: [----------] 9 tests from DensityFittingTest (474 ms total) 67: 67: [----------] 4 tests from MimicTest 67: [ RUN ] MimicTest.OneQuantumMol 67: 67: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MimicTest_OneQuantumMol_input.mdp]: 67: For a correct single-point energy evaluation with nsteps = 0, use 67: continuation = yes to avoid constraining the input coordinates. 67: 67: Generating 1-4 interactions: fudge = 0.5 67: Number of degrees of freedom in T-Coupling group rest is 21.00 67: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 67: 67: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MimicTest_OneQuantumMol_input.mdp]: 67: NVE simulation with an initial temperature of zero: will use a Verlet 67: buffer of 10%. Check your energy drift! 67: 67: 67: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MimicTest_OneQuantumMol_input.mdp]: 67: You are using a plain Coulomb cut-off, which might produce artifacts. 67: You might want to consider using PME electrostatics. 67: 67: 67: 67: There were 3 NOTEs 67: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MimicTest_OneQuantumMol.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 67: Can not increase nstlist because an NVE ensemble is used 67: Using 1 MPI thread 67: Using 2 OpenMP threads 67: 67: 67: NOTE: The number of threads is not equal to the number of (logical) cpus 67: and the -pin option is set to auto: will not pin threads to cpus. 67: This can lead to significant performance degradation. 67: Consider using -pin on (and -pinoffset in case you run multiple jobs). 67: starting md rerun 'Generated by gmx solvate', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/4water.gro' 67: 67: Reading frames from gro file 'Generated by gmx solvate', 12 atoms. 67: Reading frame 0 time 0.000 Last frame 0 time 0.000 67: 67: Core t (s) Wall t (s) (%) 67: Time: 0.009 0.004 195.1 67: (ns/day) (hour/ns) 67: Performance: 19.407 1.237 67: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MimicTest_OneQuantumMol.edr as double precision energy file 67: Reading energy frame 0 time 0.000 Last energy frame read 0 time 0.000 Setting the LD random seed to -134918981 67: 67: Generated 10 of the 10 non-bonded parameter combinations 67: 67: Generated 10 of the 10 1-4 parameter combinations 67: 67: Excluding 2 bonded neighbours molecule type 'SOL' 67: 67: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/4water.gro', all velocities are zero 67: 67: This run will generate roughly 0 Mb of data 67: [ OK ] MimicTest.OneQuantumMol (46 ms) 67: [ RUN ] MimicTest.AllQuantumMol 67: 67: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MimicTest_AllQuantumMol_input.mdp]: 67: For a correct single-point energy evaluation with nsteps = 0, use 67: continuation = yes to avoid constraining the input coordinates. 67: 67: Generating 1-4 interactions: fudge = 0.5 67: Number of degrees of freedom in T-Coupling group rest is 21.00 67: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 67: 67: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MimicTest_AllQuantumMol_input.mdp]: 67: NVE simulation with an initial temperature of zero: will use a Verlet 67: buffer of 10%. Check your energy drift! 67: 67: 67: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MimicTest_AllQuantumMol_input.mdp]: 67: You are using a plain Coulomb cut-off, which might produce artifacts. 67: You might want to consider using PME electrostatics. 67: 67: 67: 67: There were 3 NOTEs 67: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MimicTest_AllQuantumMol.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 67: Can not increase nstlist because an NVE ensemble is used 67: Using 1 MPI thread 67: Using 2 OpenMP threads 67: 67: 67: NOTE: The number of threads is not equal to the number of (logical) cpus 67: and the -pin option is set to auto: will not pin threads to cpus. 67: This can lead to significant performance degradation. 67: Consider using -pin on (and -pinoffset in case you run multiple jobs). 67: starting md rerun 'Generated by gmx solvate', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/4water.gro' 67: 67: Reading frames from gro file 'Generated by gmx solvate', 12 atoms. 67: Reading frame 0 time 0.000 Last frame 0 time 0.000 67: 67: NOTE: 11 % of the run time was spent in pair search, 67: you might want to increase nstlist (this has no effect on accuracy) 67: 67: Core t (s) Wall t (s) (%) 67: Time: 0.003 0.002 188.7 67: (ns/day) (hour/ns) 67: Performance: 48.081 0.499 67: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MimicTest_AllQuantumMol.edr as double precision energy file 67: Reading energy frame 0 time 0.000 Last energy frame read 0 time 0.000 Setting the LD random seed to -537003081 67: 67: Generated 10 of the 10 non-bonded parameter combinations 67: 67: Generated 10 of the 10 1-4 parameter combinations 67: 67: Excluding 2 bonded neighbours molecule type 'SOL' 67: 67: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/4water.gro', all velocities are zero 67: 67: This run will generate roughly 0 Mb of data 67: [ OK ] MimicTest.AllQuantumMol (45 ms) 67: [ RUN ] MimicTest.TwoQuantumMol 67: 67: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MimicTest_TwoQuantumMol_input.mdp]: 67: For a correct single-point energy evaluation with nsteps = 0, use 67: continuation = yes to avoid constraining the input coordinates. 67: 67: Generating 1-4 interactions: fudge = 0.5 67: Number of degrees of freedom in T-Coupling group rest is 21.00 67: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 67: 67: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MimicTest_TwoQuantumMol_input.mdp]: 67: NVE simulation with an initial temperature of zero: will use a Verlet 67: buffer of 10%. Check your energy drift! 67: 67: 67: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MimicTest_TwoQuantumMol_input.mdp]: 67: You are using a plain Coulomb cut-off, which might produce artifacts. 67: You might want to consider using PME electrostatics. 67: 67: 67: 67: There were 3 NOTEs 67: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MimicTest_TwoQuantumMol.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 67: Can not increase nstlist because an NVE ensemble is used 67: Using 1 MPI thread 67: Using 2 OpenMP threads 67: 67: 67: NOTE: The number of threads is not equal to the number of (logical) cpus 67: and the -pin option is set to auto: will not pin threads to cpus. 67: This can lead to significant performance degradation. 67: Consider using -pin on (and -pinoffset in case you run multiple jobs). 67: starting md rerun 'Generated by gmx solvate', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/4water.gro' 67: 67: Reading frames from gro file 'Generated by gmx solvate', 12 atoms. 67: Reading frame 0 time 0.000 Last frame 0 time 0.000 67: 67: NOTE: 14 % of the run time was spent in pair search, 67: you might want to increase nstlist (this has no effect on accuracy) 67: 67: Core t (s) Wall t (s) (%) 67: Time: 0.002 0.001 184.2 67: (ns/day) (hour/ns) 67: Performance: 69.171 0.347 67: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MimicTest_TwoQuantumMol.edr as double precision energy file 67: Reading energy frame 0 time 0.000 Last energy frame read 0 time 0.000 Setting the LD random seed to -1410696257 67: 67: Generated 10 of the 10 non-bonded parameter combinations 67: 67: Generated 10 of the 10 1-4 parameter combinations 67: 67: Excluding 2 bonded neighbours molecule type 'SOL' 67: 67: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/4water.gro', all velocities are zero 67: 67: This run will generate roughly 0 Mb of data 67: [ OK ] MimicTest.TwoQuantumMol (42 ms) 67: [ RUN ] MimicTest.BondCuts 67: 67: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MimicTest_BondCuts_input.mdp]: 67: For a correct single-point energy evaluation with nsteps = 0, use 67: continuation = yes to avoid constraining the input coordinates. 67: 67: Generating 1-4 interactions: fudge = 0.5 67: Number of degrees of freedom in T-Coupling group rest is 66.00 67: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 67: 67: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MimicTest_BondCuts_input.mdp]: 67: NVE simulation: will use the initial temperature of 300.368 K for 67: determining the Verlet buffer size 67: 67: 67: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MimicTest_BondCuts_input.mdp]: 67: You are using a plain Coulomb cut-off, which might produce artifacts. 67: You might want to consider using PME electrostatics. 67: 67: 67: 67: There were 3 NOTEs 67: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MimicTest_BondCuts.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 67: Can not increase nstlist because an NVE ensemble is used 67: Using 1 MPI thread 67: Using 2 OpenMP threads 67: 67: 67: NOTE: The number of threads is not equal to the number of (logical) cpus 67: and the -pin option is set to auto: will not pin threads to cpus. 67: This can lead to significant performance degradation. 67: Consider using -pin on (and -pinoffset in case you run multiple jobs). 67: starting md rerun 'UNNAMED in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/ala.gro' 67: 67: Reading frames from gro file 'Alanine dipeptide in water', 23 atoms. 67: Reading frame 0 time 0.000 Last frame 0 time 0.000 67: 67: Core t (s) Wall t (s) (%) 67: Time: 0.008 0.004 194.8 67: (ns/day) (hour/ns) 67: Performance: 21.578 1.112 67: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MimicTest_BondCuts.edr as double precision energy file 67: Reading energy frame 0 time 0.000 Last energy frame read 0 time 0.000 Setting the LD random seed to -1351098380 67: 67: Generated 2211 of the 2211 non-bonded parameter combinations 67: 67: Generated 2211 of the 2211 1-4 parameter combinations 67: 67: Excluding 3 bonded neighbours molecule type 'Protein_chain_A' 67: 67: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/ala.gro' 67: 67: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 300.368 K 67: 67: Calculated rlist for 1x1 atom pair-list as 1.048 nm, buffer size 0.048 nm 67: 67: Set rlist, assuming 4x4 atom pair-list, to 1.036 nm, buffer size 0.036 nm 67: 67: Note that mdrun will redetermine rlist based on the actual pair-list setup 67: 67: This run will generate roughly 0 Mb of data 67: [ OK ] MimicTest.BondCuts (150 ms) 67: [----------] 4 tests from MimicTest (285 ms total) 67: 67: [----------] 2 tests from WithIntegrator/ImdTest 67: [ RUN ] WithIntegrator/ImdTest.ImdCanRun/0 67: Generating 1-4 interactions: fudge = 1 67: 67: NOTE 1 [file glycine_vacuo.top, line 12]: 67: The bond in molecule-type Glycine between atoms 1 N and 2 H1 has an 67: estimated oscillational period of 1.0e-02 ps, which is less than 10 times 67: the time step of 2.0e-03 ps. 67: Maybe you forgot to change the constraints mdp option. 67: 67: Group 'Heavy_Atoms' with 5 atoms can be activated for interactive molecular dynamics (IMD). 67: Number of degrees of freedom in T-Coupling group System is 27.00 67: 67: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/WithIntegrator_ImdTest_ImdCanRun_0_input.mdp]: 67: You are using a plain Coulomb cut-off, which might produce artifacts. 67: You might want to consider using PME electrostatics. 67: 67: 67: 67: There were 2 NOTEs 67: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/WithIntegrator_ImdTest_ImdCanRun_0.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 67: Changing nstlist from 10 to 25, rlist from 1.071 to 1.232 67: 67: Using 1 MPI thread 67: Using 2 OpenMP threads 67: 67: 67: NOTE: The number of threads is not equal to the number of (logical) cpus 67: and the -pin option is set to auto: will not pin threads to cpus. 67: This can lead to significant performance degradation. 67: Consider using -pin on (and -pinoffset in case you run multiple jobs). 67: 67: IMD: Enabled. This simulation will accept incoming IMD connections. 67: IMD: Pulling from IMD remote is enabled (-imdpull). 67: IMD: Setting port for connection requests to 0. 67: IMD: Setting up incoming socket. 67: IMD: Listening for IMD connection on port 46355. 67: IMD: -imdwait not set, starting simulation. 67: starting mdrun 'Glycine' 67: 2 steps, 0.0 ps. 67: Setting the LD random seed to 1543438198 67: 67: Generated 20503 of the 20503 non-bonded parameter combinations 67: 67: Generated 17396 of the 20503 1-4 parameter combinations 67: 67: Excluding 3 bonded neighbours molecule type 'Glycine' 67: 67: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/glycine_vacuo.gro', all velocities are zero 67: 67: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 300 K 67: 67: Calculated rlist for 1x1 atom pair-list as 1.093 nm, buffer size 0.093 nm 67: 67: Set rlist, assuming 4x4 atom pair-list, to 1.071 nm, buffer size 0.071 nm 67: 67: Note that mdrun will redetermine rlist based on the actual pair-list setup 67: 67: This run will generate roughly 0 Mb of data 67: 67: Writing final coordinates. 67: 67: Core t (s) Wall t (s) (%) 67: Time: 0.036 0.018 196.9 67: (ns/day) (hour/ns) 67: Performance: 28.288 0.848 67: [ OK ] WithIntegrator/ImdTest.ImdCanRun/0 (923 ms) 67: [ RUN ] WithIntegrator/ImdTest.ImdCanRun/1 67: 67: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/WithIntegrator_ImdTest_ImdCanRun_1_input.mdp]: 67: Setting tcoupl from 'V-rescale' to 'no'. Temperature coupling does not 67: apply to steep. 67: 67: Generating 1-4 interactions: fudge = 1 67: Group 'Heavy_Atoms' with 5 atoms can be activated for interactive molecular dynamics (IMD). 67: Number of degrees of freedom in T-Coupling group System is 27.00 67: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 67: 67: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/WithIntegrator_ImdTest_ImdCanRun_1_input.mdp]: 67: You are using a plain Coulomb cut-off, which might produce artifacts. 67: You might want to consider using PME electrostatics. 67: 67: 67: 67: There were 2 NOTEs 67: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/WithIntegrator_ImdTest_ImdCanRun_1.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 67: Using 1 MPI thread 67: Using 2 OpenMP threads 67: 67: 67: NOTE: The number of threads is not equal to the number of (logical) cpus 67: and the -pin option is set to auto: will not pin threads to cpus. 67: This can lead to significant performance degradation. 67: Consider using -pin on (and -pinoffset in case you run multiple jobs). 67: 67: IMD: Enabled. This simulation will accept incoming IMD connections. 67: IMD: Pulling from IMD remote is enabled (-imdpull). 67: IMD: Setting port for connection requests to 0. 67: IMD: Setting up incoming socket. 67: IMD: Listening for IMD connection on port 44627. 67: IMD: -imdwait not set, starting simulation. 67: 67: Steepest Descents: 67: Tolerance (Fmax) = 1.00000e+01 67: Number of steps = 2 67: 67: Energy minimization reached the maximum number of steps before the forces 67: reached the requested precision Fmax < 10. 67: 67: writing lowest energy coordinates. 67: 67: Steepest Descents did not converge to Fmax < 10 in 3 steps. 67: Potential Energy = 1.19770464690297e+03 67: Maximum force = 1.77948604657896e+04 on atom 9 67: Norm of force = 7.87328617833980e+03 67: Setting the LD random seed to -1704003721 67: 67: Generated 20503 of the 20503 non-bonded parameter combinations 67: 67: Generated 17396 of the 20503 1-4 parameter combinations 67: 67: Excluding 3 bonded neighbours molecule type 'Glycine' 67: 67: This run will generate roughly 0 Mb of data 67: [ OK ] WithIntegrator/ImdTest.ImdCanRun/1 (881 ms) 67: [----------] 2 tests from WithIntegrator/ImdTest (1805 ms total) 67: 67: [----------] Global test environment tear-down 67: [==========] 15 tests from 3 test suites ran. (2703 ms total) 67: [ PASSED ] 15 tests. 67/92 Test #67: MdrunModulesTests ......................... Passed 2.78 sec test 68 Start 68: MdrunIOTests 68: Test command: /build/reproducible-path/gromacs-2025.1/build/basic-dp/bin/mdrun-io-test "-ntomp" "2" "--gtest_output=xml:/build/reproducible-path/gromacs-2025.1/build/basic-dp/Testing/Temporary/MdrunIOTests.xml" 68: Working Directory: /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests 68: Test timeout computed to be: 600 68: [==========] Running 76 tests from 13 test suites. 68: [----------] Global test environment set-up. 68: [----------] 9 tests from GromppTest 68: [ RUN ] GromppTest.EmptyMdpFileWorks 68: 68: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/GromppTest_EmptyMdpFileWorks_input.mdp]: 68: For a correct single-point energy evaluation with nsteps = 0, use 68: continuation = yes to avoid constraining the input coordinates. 68: 68: Number of degrees of freedom in T-Coupling group rest is 12.00 68: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 68: 68: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/GromppTest_EmptyMdpFileWorks_input.mdp]: 68: NVE simulation: will use the initial temperature of 1046.791 K for 68: determining the Verlet buffer size 68: 68: 68: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/GromppTest_EmptyMdpFileWorks_input.mdp]: 68: You are using a plain Coulomb cut-off, which might produce artifacts. 68: You might want to consider using PME electrostatics. 68: 68: 68: 68: There were 3 NOTEs 68: Setting the LD random seed to -12585473 68: 68: Generated 8 of the 10 non-bonded parameter combinations 68: 68: Excluding 2 bonded neighbours molecule type 'Methanol' 68: 68: Excluding 2 bonded neighbours molecule type 'SOL' 68: 68: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/spc-and-methanol.gro' 68: 68: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 1046.79 K 68: 68: Calculated rlist for 1x1 atom pair-list as 1.089 nm, buffer size 0.089 nm 68: 68: Set rlist, assuming 4x4 atom pair-list, to 1.072 nm, buffer size 0.072 nm 68: 68: Note that mdrun will redetermine rlist based on the actual pair-list setup 68: 68: This run will generate roughly 0 Mb of data 68: [ OK ] GromppTest.EmptyMdpFileWorks (30 ms) 68: [ RUN ] GromppTest.SimulatedAnnealingWorks 68: 68: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/GromppTest_SimulatedAnnealingWorks_input.mdp]: 68: For a correct single-point energy evaluation with nsteps = 0, use 68: continuation = yes to avoid constraining the input coordinates. 68: 68: Simulated annealing for group rest: Periodic, 4 timepoints 68: Time (ps) Temperature (K) 68: 0.0 298.0 68: 2.0 320.0 68: 4.0 320.0 68: 6.0 298.0 68: Number of degrees of freedom in T-Coupling group rest is 12.00 68: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 68: 68: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/GromppTest_SimulatedAnnealingWorks_input.mdp]: 68: NVE simulation: will use the initial temperature of 1046.791 K for 68: determining the Verlet buffer size 68: 68: 68: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/GromppTest_SimulatedAnnealingWorks_input.mdp]: 68: You are using a plain Coulomb cut-off, which might produce artifacts. 68: You might want to consider using PME electrostatics. 68: 68: 68: 68: There were 3 NOTEs 68: Setting the LD random seed to -176226565 68: 68: Generated 8 of the 10 non-bonded parameter combinations 68: 68: Excluding 2 bonded neighbours molecule type 'Methanol' 68: 68: Excluding 2 bonded neighbours molecule type 'SOL' 68: 68: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/spc-and-methanol.gro' 68: 68: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 1046.79 K 68: 68: Calculated rlist for 1x1 atom pair-list as 1.089 nm, buffer size 0.089 nm 68: 68: Set rlist, assuming 4x4 atom pair-list, to 1.072 nm, buffer size 0.072 nm 68: 68: Note that mdrun will redetermine rlist based on the actual pair-list setup 68: 68: This run will generate roughly 0 Mb of data 68: [ OK ] GromppTest.SimulatedAnnealingWorks (29 ms) 68: [ RUN ] GromppTest.SimulatedAnnealingWorksWithMultipleGroups 68: 68: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/GromppTest_SimulatedAnnealingWorksWithMultipleGroups_input.mdp]: 68: For a correct single-point energy evaluation with nsteps = 0, use 68: continuation = yes to avoid constraining the input coordinates. 68: 68: Simulated annealing for group Methanol: Single, 3 timepoints 68: Time (ps) Temperature (K) 68: 0.0 298.0 68: 3.0 280.0 68: 6.0- 270.0 68: Simulated annealing for group SOL: Periodic, 4 timepoints 68: Time (ps) Temperature (K) 68: 0.0 298.0 68: 2.0 320.0 68: 4.0 320.0 68: 6.0 298.0 68: Number of degrees of freedom in T-Coupling group Methanol is 7.20 68: Number of degrees of freedom in T-Coupling group SOL is 4.80 68: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 68: 68: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/GromppTest_SimulatedAnnealingWorksWithMultipleGroups_input.mdp]: 68: NVE simulation: will use the initial temperature of 1046.791 K for 68: determining the Verlet buffer size 68: 68: 68: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/GromppTest_SimulatedAnnealingWorksWithMultipleGroups_input.mdp]: 68: You are using a plain Coulomb cut-off, which might produce artifacts. 68: You might want to consider using PME electrostatics. 68: 68: 68: 68: There were 3 NOTEs 68: Setting the LD random seed to -138428452 68: 68: Generated 8 of the 10 non-bonded parameter combinations 68: 68: Excluding 2 bonded neighbours molecule type 'Methanol' 68: 68: Excluding 2 bonded neighbours molecule type 'SOL' 68: 68: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/spc-and-methanol.gro' 68: 68: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 1046.79 K 68: 68: Calculated rlist for 1x1 atom pair-list as 1.089 nm, buffer size 0.089 nm 68: 68: Set rlist, assuming 4x4 atom pair-list, to 1.072 nm, buffer size 0.072 nm 68: 68: Note that mdrun will redetermine rlist based on the actual pair-list setup 68: 68: This run will generate roughly 0 Mb of data 68: [ OK ] GromppTest.SimulatedAnnealingWorksWithMultipleGroups (29 ms) 68: [ RUN ] GromppTest.DeathTestHandlesNoMaxwarnError 68: Setting the LD random seed to -675865 68: 68: Generated 8 of the 10 non-bonded parameter combinations 68: 68: Excluding 2 bonded neighbours molecule type 'Methanol' 68: 68: Excluding 2 bonded neighbours molecule type 'SOL' 68: 68: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/spc-and-methanol.gro' 68: 68: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 68: 68: Calculated rlist for 1x1 atom pair-list as 1.040 nm, buffer size 0.040 nm 68: 68: Set rlist, assuming 4x4 atom pair-list, to 1.031 nm, buffer size 0.031 nm 68: 68: Note that mdrun will redetermine rlist based on the actual pair-list setup 68: 68: This run will generate roughly 0 Mb of data 68: [ OK ] GromppTest.DeathTestHandlesNoMaxwarnError (51 ms) 68: [ RUN ] GromppTest.HandlesMaxwarn 68: 68: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/GromppTest_HandlesMaxwarn_input.mdp]: 68: For a correct single-point energy evaluation with nsteps = 0, use 68: continuation = yes to avoid constraining the input coordinates. 68: 68: 68: WARNING 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/GromppTest_HandlesMaxwarn_input.mdp]: 68: The Berendsen thermostat does not generate the correct kinetic energy 68: distribution, and should not be used for new production simulations (in 68: our opinion). We would recommend the V-rescale thermostat. 68: 68: Number of degrees of freedom in T-Coupling group System is 12.00 68: 68: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/GromppTest_HandlesMaxwarn_input.mdp]: 68: You are using a plain Coulomb cut-off, which might produce artifacts. 68: You might want to consider using PME electrostatics. 68: 68: 68: 68: There were 2 NOTEs 68: 68: There was 1 WARNING 68: Setting the LD random seed to 2146422271 68: 68: Generated 8 of the 10 non-bonded parameter combinations 68: 68: Excluding 2 bonded neighbours molecule type 'Methanol' 68: 68: Excluding 2 bonded neighbours molecule type 'SOL' 68: 68: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/spc-and-methanol.gro' 68: 68: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 68: 68: Calculated rlist for 1x1 atom pair-list as 1.040 nm, buffer size 0.040 nm 68: 68: Set rlist, assuming 4x4 atom pair-list, to 1.031 nm, buffer size 0.031 nm 68: 68: Note that mdrun will redetermine rlist based on the actual pair-list setup 68: 68: This run will generate roughly 0 Mb of data 68: [ OK ] GromppTest.HandlesMaxwarn (29 ms) 68: [ RUN ] GromppTest.MaxwarnShouldBePositive 68: [ OK ] GromppTest.MaxwarnShouldBePositive (4 ms) 68: [ RUN ] GromppTest.ValidTransformationCoord 68: 68: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/GromppTest_ValidTransformationCoord_input.mdp]: 68: For a correct single-point energy evaluation with nsteps = 0, use 68: continuation = yes to avoid constraining the input coordinates. 68: 68: Pull group 1 'SOL' has 3 atoms 68: Pull group 2 'Methanol' has 3 atoms 68: Number of degrees of freedom in T-Coupling group rest is 12.00 68: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 68: 68: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/GromppTest_ValidTransformationCoord_input.mdp]: 68: NVE simulation: will use the initial temperature of 1046.791 K for 68: determining the Verlet buffer size 68: 68: 68: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/GromppTest_ValidTransformationCoord_input.mdp]: 68: You are using a plain Coulomb cut-off, which might produce artifacts. 68: You might want to consider using PME electrostatics. 68: 68: 68: Pull group natoms pbc atom distance at start reference at t=0 68: 1 3 5 68: 2 3 2 0.613 nm 0.000 nm 68: 1 3 5 68: 2 3 2 0.613 nm 0.000 nm 68: 68: There were 3 NOTEs 68: Setting the LD random seed to -1074793032 68: 68: Generated 8 of the 10 non-bonded parameter combinations 68: 68: Excluding 2 bonded neighbours molecule type 'Methanol' 68: 68: Excluding 2 bonded neighbours molecule type 'SOL' 68: 68: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/spc-and-methanol.gro' 68: 68: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 1046.79 K 68: 68: Calculated rlist for 1x1 atom pair-list as 1.089 nm, buffer size 0.089 nm 68: 68: Set rlist, assuming 4x4 atom pair-list, to 1.072 nm, buffer size 0.072 nm 68: 68: Note that mdrun will redetermine rlist based on the actual pair-list setup 68: 68: This run will generate roughly 0 Mb of data 68: [ OK ] GromppTest.ValidTransformationCoord (38 ms) 68: [ RUN ] GromppTest.InvalidTransformationCoord 68: 68: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/GromppTest_InvalidTransformationCoord_input.mdp]: 68: For a correct single-point energy evaluation with nsteps = 0, use 68: continuation = yes to avoid constraining the input coordinates. 68: 68: Pull group 1 'SOL' has 3 atoms 68: Pull group 2 'Methanol' has 3 atoms 68: Number of degrees of freedom in T-Coupling group rest is 12.00 68: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 68: 68: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/GromppTest_InvalidTransformationCoord_input.mdp]: 68: NVE simulation: will use the initial temperature of 1046.791 K for 68: determining the Verlet buffer size 68: 68: 68: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/GromppTest_InvalidTransformationCoord_input.mdp]: 68: You are using a plain Coulomb cut-off, which might produce artifacts. 68: You might want to consider using PME electrostatics. 68: 68: 68: Pull group natoms pbc atom distance at start reference at t=0 68: 1 3 5 68: 2 3 2 0.613 nm 0.000 nm 68: 1 3 5 68: 2 3 2 Setting the LD random seed to 359594865 68: 68: Generated 8 of the 10 non-bonded parameter combinations 68: 68: Excluding 2 bonded neighbours molecule type 'Methanol' 68: 68: Excluding 2 bonded neighbours molecule type 'SOL' 68: 68: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/spc-and-methanol.gro' 68: 68: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 1046.79 K 68: 68: Calculated rlist for 1x1 atom pair-list as 1.089 nm, buffer size 0.089 nm 68: 68: Set rlist, assuming 4x4 atom pair-list, to 1.072 nm, buffer size 0.072 nm 68: 68: Note that mdrun will redetermine rlist based on the actual pair-list setup 68: [ OK ] GromppTest.InvalidTransformationCoord (40 ms) 68: [ RUN ] GromppTest.RejectCRescaleAndAnisotropic 68: Setting the LD random seed to -323519265 68: 68: Generated 8 of the 10 non-bonded parameter combinations 68: 68: Excluding 2 bonded neighbours molecule type 'Methanol' 68: 68: Excluding 2 bonded neighbours molecule type 'SOL' 68: 68: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/spc-and-methanol.gro' 68: [ OK ] GromppTest.RejectCRescaleAndAnisotropic (44 ms) 68: [----------] 9 tests from GromppTest (298 ms total) 68: 68: [----------] 6 tests from MdrunTerminationTest 68: [ RUN ] MdrunTerminationTest.CheckpointRestartAppendsByDefault 68: Generating 1-4 interactions: fudge = 0.5 68: Number of degrees of freedom in T-Coupling group System is 9.00 68: 68: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartAppendsByDefault_input.mdp]: 68: You are using a plain Coulomb cut-off, which might produce artifacts. 68: You might want to consider using PME electrostatics. 68: 68: 68: 68: There was 1 NOTE 68: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartAppendsByDefault.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 68: Changing nstlist from 10 to 50, rlist from 1.032 to 1.21 68: 68: Using 1 MPI thread 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'spc2' 68: 2 steps, 0.0 ps. 68: Setting the LD random seed to -375293961 68: 68: Generated 3 of the 3 non-bonded parameter combinations 68: 68: Generated 3 of the 3 1-4 parameter combinations 68: 68: Excluding 2 bonded neighbours molecule type 'SOL' 68: 68: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/spc2.gro' 68: 68: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 68: 68: Calculated rlist for 1x1 atom pair-list as 1.041 nm, buffer size 0.041 nm 68: 68: Set rlist, assuming 4x4 atom pair-list, to 1.032 nm, buffer size 0.032 nm 68: 68: Note that mdrun will redetermine rlist based on the actual pair-list setup 68: 68: This run will generate roughly 0 Mb of data 68: 68: Writing final coordinates. 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.036 0.018 197.4 68: (ns/day) (hour/ns) 68: Performance: 14.050 1.708 68: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartAppendsByDefault.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 68: Setting nsteps to 4 68: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartAppendsByDefault.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 68: Changing nstlist from 10 to 50, rlist from 1.032 to 1.21 68: 68: Using 1 MPI thread 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'spc2' 68: 4 steps, 0.0 ps (continuing from step 2, 0.0 ps). 68: Input file: 68: Run start step 0 68: Run start time 0 ps 68: Step to be made during run 2 68: Runtime for the run 0.002 ps 68: Run end step 2 68: Run end time 0.002 ps 68: 68: 68: Output file: 68: Run start step 0 68: Run start time 0 ps 68: Step to be made during run 4 68: Runtime for the run 0.004 ps 68: Run end step 4 68: Run end time 0.004 ps 68: 68: 68: Writing final coordinates. 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.035 0.018 197.4 68: (ns/day) (hour/ns) 68: Performance: 14.661 1.637 68: [ OK ] MdrunTerminationTest.CheckpointRestartAppendsByDefault (114 ms) 68: [ RUN ] MdrunTerminationTest.WritesCheckpointAfterMaxhTerminationAndThenRestarts 68: Generating 1-4 interactions: fudge = 0.5 68: Number of degrees of freedom in T-Coupling group System is 9.00 68: 68: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_WritesCheckpointAfterMaxhTerminationAndThenRestarts_input.mdp]: 68: You are using a plain Coulomb cut-off, which might produce artifacts. 68: You might want to consider using PME electrostatics. 68: 68: 68: 68: There was 1 NOTE 68: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_WritesCheckpointAfterMaxhTerminationAndThenRestarts.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 68: Changing nstlist from 10 to 1, rlist from 1.032 to 1 68: 68: Using 1 MPI thread 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'spc2' 68: 100 steps, 0.1 ps. 68: 68: Step 0: Run time exceeded 0.000 hours, will terminate the run within 200 steps 68: Setting the LD random seed to -161482373 68: 68: Generated 3 of the 3 non-bonded parameter combinations 68: 68: Generated 3 of the 3 1-4 parameter combinations 68: 68: Excluding 2 bonded neighbours molecule type 'SOL' 68: 68: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/spc2.gro' 68: 68: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 68: 68: Calculated rlist for 1x1 atom pair-list as 1.041 nm, buffer size 0.041 nm 68: 68: Set rlist, assuming 4x4 atom pair-list, to 1.032 nm, buffer size 0.032 nm 68: 68: Note that mdrun will redetermine rlist based on the actual pair-list setup 68: 68: This run will generate roughly 0 Mb of data 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.034 0.017 196.9 68: (ns/day) (hour/ns) 68: Performance: 10.012 2.397 68: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_WritesCheckpointAfterMaxhTerminationAndThenRestarts.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 68: Setting nsteps to 102 68: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_WritesCheckpointAfterMaxhTerminationAndThenRestarts.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 68: Changing nstlist from 10 to 50, rlist from 1.032 to 1.21 68: 68: Using 1 MPI thread 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'spc2' 68: 102 steps, 0.1 ps (continuing from step 1, 0.0 ps). 68: Input file: 68: Run start step 0 68: Run start time 0 ps 68: Step to be made during run 100 68: Runtime for the run 0.1 ps 68: Run end step 100 68: Run end time 0.1 ps 68: 68: 68: Output file: 68: Run start step 0 68: Run start time 0 ps 68: Step to be made during run 102 68: Runtime for the run 0.102 ps 68: Run end step 102 68: Run end time 0.102 ps 68: 68: 68: Writing final coordinates. 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.051 0.026 198.1 68: (ns/day) (hour/ns) 68: Performance: 342.642 0.070 68: [ OK ] MdrunTerminationTest.WritesCheckpointAfterMaxhTerminationAndThenRestarts (111 ms) 68: [ RUN ] MdrunTerminationTest.CheckpointRestartWithNoAppendWorksAndCannotLaterAppend 68: Generating 1-4 interactions: fudge = 0.5 68: Number of degrees of freedom in T-Coupling group System is 9.00 68: 68: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartWithNoAppendWorksAndCannotLaterAppend_input.mdp]: 68: You are using a plain Coulomb cut-off, which might produce artifacts. 68: You might want to consider using PME electrostatics. 68: 68: 68: 68: There was 1 NOTE 68: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartWithNoAppendWorksAndCannotLaterAppend.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 68: Changing nstlist from 10 to 50, rlist from 1.032 to 1.21 68: 68: Using 1 MPI thread 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'spc2' 68: 2 steps, 0.0 ps. 68: Setting the LD random seed to -411238403 68: 68: Generated 3 of the 3 non-bonded parameter combinations 68: 68: Generated 3 of the 3 1-4 parameter combinations 68: 68: Excluding 2 bonded neighbours molecule type 'SOL' 68: 68: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/spc2.gro' 68: 68: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 68: 68: Calculated rlist for 1x1 atom pair-list as 1.041 nm, buffer size 0.041 nm 68: 68: Set rlist, assuming 4x4 atom pair-list, to 1.032 nm, buffer size 0.032 nm 68: 68: Note that mdrun will redetermine rlist based on the actual pair-list setup 68: 68: This run will generate roughly 0 Mb of data 68: 68: Writing final coordinates. 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.027 0.014 196.6 68: (ns/day) (hour/ns) 68: Performance: 18.581 1.292 68: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartWithNoAppendWorksAndCannotLaterAppend.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 68: Setting nsteps to 4 68: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartWithNoAppendWorksAndCannotLaterAppend.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 68: Changing nstlist from 10 to 50, rlist from 1.032 to 1.21 68: 68: Using 1 MPI thread 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'spc2' 68: 4 steps, 0.0 ps (continuing from step 2, 0.0 ps). 68: Input file: 68: Run start step 0 68: Run start time 0 ps 68: Step to be made during run 2 68: Runtime for the run 0.002 ps 68: Run end step 2 68: Run end time 0.002 ps 68: 68: 68: Output file: 68: Run start step 0 68: Run start time 0 ps 68: Step to be made during run 4 68: Runtime for the run 0.004 ps 68: Run end step 4 68: Run end time 0.004 ps 68: 68: 68: Writing final coordinates. 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.034 0.017 198.1 68: (ns/day) (hour/ns) 68: Performance: 15.228 1.576 68: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartWithNoAppendWorksAndCannotLaterAppend.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 68: Setting nsteps to 6 68: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartWithNoAppendWorksAndCannotLaterAppend.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 68: Changing nstlist from 10 to 50, rlist from 1.032 to 1.21 68: 68: Using 1 MPI thread 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'spc2' 68: 6 steps, 0.0 ps (continuing from step 4, 0.0 ps). 68: Input file: 68: Run start step 0 68: Run start time 0 ps 68: Step to be made during run 4 68: Runtime for the run 0.004 ps 68: Run end step 4 68: Run end time 0.004 ps 68: 68: 68: Output file: 68: Run start step 0 68: Run start time 0 ps 68: Step to be made during run 6 68: Runtime for the run 0.006 ps 68: Run end step 6 68: Run end time 0.006 ps 68: 68: 68: Writing final coordinates. 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.035 0.018 198.3 68: (ns/day) (hour/ns) 68: Performance: 14.762 1.626 68: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartWithNoAppendWorksAndCannotLaterAppend.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 68: Setting nsteps to 8 68: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartWithNoAppendWorksAndCannotLaterAppend.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 68: Changing nstlist from 10 to 50, rlist from 1.032 to 1.21 68: 68: Using 1 MPI thread 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'spc2' 68: 8 steps, 0.0 ps (continuing from step 6, 0.0 ps). 68: Input file: 68: Run start step 0 68: Run start time 0 ps 68: Step to be made during run 6 68: Runtime for the run 0.006 ps 68: Run end step 6 68: Run end time 0.006 ps 68: 68: 68: Output file: 68: Run start step 0 68: Run start time 0 ps 68: Step to be made during run 8 68: Runtime for the run 0.008 ps 68: Run end step 8 68: Run end time 0.008 ps 68: 68: 68: Writing final coordinates. 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.036 0.018 198.2 68: (ns/day) (hour/ns) 68: Performance: 14.322 1.676 68: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartWithNoAppendWorksAndCannotLaterAppend.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 68: Changing nstlist from 10 to 50, rlist from 1.032 to 1.21 68: 68: Using 1 MPI thread 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'spc2' 68: 8 steps, 0.0 ps (continuing from step 8, 0.0 ps). 68: 68: NOTE: 20 % of the run time was spent in pair search, 68: you might want to increase nstlist (this has no effect on accuracy) 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.001 0.001 169.6 68: (ns/day) (hour/ns) 68: Performance: 101.766 0.236 68: [ OK ] MdrunTerminationTest.CheckpointRestartWithNoAppendWorksAndCannotLaterAppend (222 ms) 68: [ RUN ] MdrunTerminationTest.CheckpointRestartWorksEvenWithMissingCheckpointFile 68: Generating 1-4 interactions: fudge = 0.5 68: Number of degrees of freedom in T-Coupling group System is 9.00 68: 68: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartWorksEvenWithMissingCheckpointFile_input.mdp]: 68: You are using a plain Coulomb cut-off, which might produce artifacts. 68: You might want to consider using PME electrostatics. 68: 68: 68: 68: There was 1 NOTE 68: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartWorksEvenWithMissingCheckpointFile.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 68: Changing nstlist from 10 to 50, rlist from 1.032 to 1.21 68: 68: Using 1 MPI thread 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'spc2' 68: 2 steps, 0.0 ps. 68: Setting the LD random seed to -1716228 68: 68: Generated 3 of the 3 non-bonded parameter combinations 68: 68: Generated 3 of the 3 1-4 parameter combinations 68: 68: Excluding 2 bonded neighbours molecule type 'SOL' 68: 68: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/spc2.gro' 68: 68: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 68: 68: Calculated rlist for 1x1 atom pair-list as 1.041 nm, buffer size 0.041 nm 68: 68: Set rlist, assuming 4x4 atom pair-list, to 1.032 nm, buffer size 0.032 nm 68: 68: Note that mdrun will redetermine rlist based on the actual pair-list setup 68: 68: This run will generate roughly 0 Mb of data 68: 68: Writing final coordinates. 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.036 0.018 196.6 68: (ns/day) (hour/ns) 68: Performance: 14.261 1.683 68: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartWorksEvenWithMissingCheckpointFile.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 68: Setting nsteps to 4 68: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartWorksEvenWithMissingCheckpointFile.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 68: Changing nstlist from 10 to 50, rlist from 1.032 to 1.21 68: 68: Using 1 MPI thread 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'spc2' 68: 4 steps, 0.0 ps. 68: Input file: 68: Run start step 0 68: Run start time 0 ps 68: Step to be made during run 2 68: Runtime for the run 0.002 ps 68: Run end step 2 68: Run end time 0.002 ps 68: 68: 68: Output file: 68: Run start step 0 68: Run start time 0 ps 68: Step to be made during run 4 68: Runtime for the run 0.004 ps 68: Run end step 4 68: Run end time 0.004 ps 68: 68: 68: Writing final coordinates. 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.061 0.031 198.2 68: (ns/day) (hour/ns) 68: Performance: 14.020 1.712 68: [ OK ] MdrunTerminationTest.CheckpointRestartWorksEvenWithMissingCheckpointFile (141 ms) 68: [ RUN ] MdrunTerminationTest.CheckpointRestartWorksEvenWithAppendAndMissingCheckpointFile 68: Generating 1-4 interactions: fudge = 0.5 68: Number of degrees of freedom in T-Coupling group System is 9.00 68: 68: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartWorksEvenWithAppendAndMissingCheckpointFile_input.mdp]: 68: You are using a plain Coulomb cut-off, which might produce artifacts. 68: You might want to consider using PME electrostatics. 68: 68: 68: 68: There was 1 NOTE 68: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartWorksEvenWithAppendAndMissingCheckpointFile.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 68: Changing nstlist from 10 to 50, rlist from 1.032 to 1.21 68: 68: Using 1 MPI thread 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'spc2' 68: 2 steps, 0.0 ps. 68: Setting the LD random seed to -6673 68: 68: Generated 3 of the 3 non-bonded parameter combinations 68: 68: Generated 3 of the 3 1-4 parameter combinations 68: 68: Excluding 2 bonded neighbours molecule type 'SOL' 68: 68: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/spc2.gro' 68: 68: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 68: 68: Calculated rlist for 1x1 atom pair-list as 1.041 nm, buffer size 0.041 nm 68: 68: Set rlist, assuming 4x4 atom pair-list, to 1.032 nm, buffer size 0.032 nm 68: 68: Note that mdrun will redetermine rlist based on the actual pair-list setup 68: 68: This run will generate roughly 0 Mb of data 68: 68: Writing final coordinates. 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.036 0.018 197.2 68: (ns/day) (hour/ns) 68: Performance: 14.395 1.667 68: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartWorksEvenWithAppendAndMissingCheckpointFile.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 68: Setting nsteps to 4 68: Input file: 68: Run start step 0 68: Run start time 0 ps 68: Step to be made during run 2 68: Runtime for the run 0.002 ps 68: Run end step 2 68: Run end time 0.002 ps 68: 68: 68: Output file: 68: Run start step 0 68: Run start time 0 ps 68: Step to be made during run 4 68: Runtime for the run 0.004 ps 68: Run end step 4 68: Run end time 0.004 ps 68: 68: [ OK ] MdrunTerminationTest.CheckpointRestartWorksEvenWithAppendAndMissingCheckpointFile (126 ms) 68: [ RUN ] MdrunTerminationTest.RunWithNoAppendCreatesPartFiles 68: Generating 1-4 interactions: fudge = 0.5 68: Number of degrees of freedom in T-Coupling group System is 9.00 68: 68: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_RunWithNoAppendCreatesPartFiles_input.mdp]: 68: You are using a plain Coulomb cut-off, which might produce artifacts. 68: You might want to consider using PME electrostatics. 68: 68: 68: 68: There was 1 NOTE 68: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_RunWithNoAppendCreatesPartFiles.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 68: Changing nstlist from 10 to 50, rlist from 1.032 to 1.21 68: 68: Using 1 MPI thread 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'spc2' 68: 2 steps, 0.0 ps. 68: Setting the LD random seed to -2179121 68: 68: Generated 3 of the 3 non-bonded parameter combinations 68: 68: Generated 3 of the 3 1-4 parameter combinations 68: 68: Excluding 2 bonded neighbours molecule type 'SOL' 68: 68: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/spc2.gro' 68: 68: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 68: 68: Calculated rlist for 1x1 atom pair-list as 1.041 nm, buffer size 0.041 nm 68: 68: Set rlist, assuming 4x4 atom pair-list, to 1.032 nm, buffer size 0.032 nm 68: 68: Note that mdrun will redetermine rlist based on the actual pair-list setup 68: 68: This run will generate roughly 0 Mb of data 68: 68: Writing final coordinates. 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.052 0.026 197.8 68: (ns/day) (hour/ns) 68: Performance: 9.896 2.425 68: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_RunWithNoAppendCreatesPartFiles.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 68: Setting nsteps to 4 68: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_RunWithNoAppendCreatesPartFiles.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 68: Changing nstlist from 10 to 50, rlist from 1.032 to 1.21 68: 68: Using 1 MPI thread 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'spc2' 68: 4 steps, 0.0 ps (continuing from step 2, 0.0 ps). 68: Input file: 68: Run start step 0 68: Run start time 0 ps 68: Step to be made during run 2 68: Runtime for the run 0.002 ps 68: Run end step 2 68: Run end time 0.002 ps 68: 68: 68: Output file: 68: Run start step 0 68: Run start time 0 ps 68: Step to be made during run 4 68: Runtime for the run 0.004 ps 68: Run end step 4 68: Run end time 0.004 ps 68: 68: 68: Writing final coordinates. 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.065 0.033 198.7 68: (ns/day) (hour/ns) 68: Performance: 7.878 3.047 68: [ OK ] MdrunTerminationTest.RunWithNoAppendCreatesPartFiles (201 ms) 68: [----------] 6 tests from MdrunTerminationTest (919 ms total) 68: 68: [----------] 2 tests from CheckpointCoordinatesAreSane/CheckpointCoordinatesSanityChecks 68: [ RUN ] CheckpointCoordinatesAreSane/CheckpointCoordinatesSanityChecks.WithinTolerances/0 68: 68: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/CheckpointCoordinatesAreSane_CheckpointCoordinatesSanityChecks_WithinTolerances_0_input.mdp]: 68: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 68: that with the Verlet scheme, nstlist has no effect on the accuracy of 68: your simulation. 68: 68: 68: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/CheckpointCoordinatesAreSane_CheckpointCoordinatesSanityChecks_WithinTolerances_0_input.mdp]: 68: Setting nstcalcenergy (100) equal to nstenergy (4) 68: 68: Generating 1-4 interactions: fudge = 0.5 68: Number of degrees of freedom in T-Coupling group System is 9.00 68: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 68: 68: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/CheckpointCoordinatesAreSane_CheckpointCoordinatesSanityChecks_WithinTolerances_0_input.mdp]: 68: NVE simulation: will use the initial temperature of 2573.591 K for 68: determining the Verlet buffer size 68: 68: 68: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/CheckpointCoordinatesAreSane_CheckpointCoordinatesSanityChecks_WithinTolerances_0_input.mdp]: 68: You are using a plain Coulomb cut-off, which might produce artifacts. 68: You might want to consider using PME electrostatics. 68: 68: 68: 68: There were 4 NOTEs 68: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/CheckpointCoordinatesAreSane_CheckpointCoordinatesSanityChecks_WithinTolerances_0.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 68: Can not increase nstlist because an NVE ensemble is used 68: Using 1 MPI thread 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'spc2' 68: 16 steps, 0.0 ps. 68: Generated 3 of the 3 non-bonded parameter combinations 68: 68: Generated 3 of the 3 1-4 parameter combinations 68: 68: Excluding 2 bonded neighbours molecule type 'SOL' 68: 68: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/spc2.gro' 68: 68: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 2573.59 K 68: 68: Calculated rlist for 1x1 atom pair-list as 0.906 nm, buffer size 0.206 nm 68: 68: Set rlist, assuming 4x4 atom pair-list, to 0.892 nm, buffer size 0.192 nm 68: 68: Note that mdrun will redetermine rlist based on the actual pair-list setup 68: 68: This run will generate roughly 0 Mb of data 68: 68: Writing final coordinates. 68: 68: NOTE: 28 % of the run time was spent in pair search, 68: you might want to increase nstlist (this has no effect on accuracy) 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.086 0.043 198.6 68: (ns/day) (hour/ns) 68: Performance: 34.017 0.706 68: trr version: GMX_trn_file (double precision) 68: 68: 68: [ OK ] CheckpointCoordinatesAreSane/CheckpointCoordinatesSanityChecks.WithinTolerances/0 (114 ms) 68: [ RUN ] CheckpointCoordinatesAreSane/CheckpointCoordinatesSanityChecks.WithinTolerances/1 68: 68: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/CheckpointCoordinatesAreSane_CheckpointCoordinatesSanityChecks_WithinTolerances_1_input.mdp]: 68: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 68: that with the Verlet scheme, nstlist has no effect on the accuracy of 68: your simulation. 68: 68: 68: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/CheckpointCoordinatesAreSane_CheckpointCoordinatesSanityChecks_WithinTolerances_1_input.mdp]: 68: Setting nstcalcenergy (100) equal to nstenergy (4) 68: 68: Generating 1-4 interactions: fudge = 0.5 68: Number of degrees of freedom in T-Coupling group System is 9.00 68: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 68: 68: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/CheckpointCoordinatesAreSane_CheckpointCoordinatesSanityChecks_WithinTolerances_1_input.mdp]: 68: NVE simulation: will use the initial temperature of 2573.591 K for 68: determining the Verlet buffer size 68: 68: 68: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/CheckpointCoordinatesAreSane_CheckpointCoordinatesSanityChecks_WithinTolerances_1_input.mdp]: 68: You are using a plain Coulomb cut-off, which might produce artifacts. 68: You might want to consider using PME electrostatics. 68: 68: 68: 68: There were 4 NOTEs 68: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/CheckpointCoordinatesAreSane_CheckpointCoordinatesSanityChecks_WithinTolerances_1.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 68: Can not increase nstlist because an NVE ensemble is used 68: Using 1 MPI thread 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'spc2' 68: 16 steps, 0.0 ps. 68: Generated 3 of the 3 non-bonded parameter combinations 68: 68: Generated 3 of the 3 1-4 parameter combinations 68: 68: Excluding 2 bonded neighbours molecule type 'SOL' 68: 68: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/spc2.gro' 68: 68: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 2573.59 K 68: 68: Calculated rlist for 1x1 atom pair-list as 0.906 nm, buffer size 0.206 nm 68: 68: Set rlist, assuming 4x4 atom pair-list, to 0.892 nm, buffer size 0.192 nm 68: 68: Note that mdrun will redetermine rlist based on the actual pair-list setup 68: 68: This run will generate roughly 0 Mb of data 68: 68: Writing final coordinates. 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.043 0.022 198.5 68: (ns/day) (hour/ns) 68: Performance: 68.230 0.352 68: 68: 68: [ OK ] CheckpointCoordinatesAreSane/CheckpointCoordinatesSanityChecks.WithinTolerances/1 (68 ms) 68: [----------] 2 tests from CheckpointCoordinatesAreSane/CheckpointCoordinatesSanityChecks (182 ms total) 68: 68: [----------] 24 tests from NormalIntegrators/MdrunNoAppendContinuationIsExact 68: [ RUN ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/0 68: 68: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 68: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 68: that with the Verlet scheme, nstlist has no effect on the accuracy of 68: your simulation. 68: 68: 68: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 68: Setting nstcalcenergy (100) equal to nstenergy (4) 68: 68: Number of degrees of freedom in T-Coupling group System is 33.00 68: 68: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 68: NVE simulation: will use the initial temperature of 68.810 K for 68: determining the Verlet buffer size 68: 68: 68: There were 3 NOTEs 68: 68: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 68: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 68: that with the Verlet scheme, nstlist has no effect on the accuracy of 68: your simulation. 68: 68: 68: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 68: Setting nstcalcenergy (100) equal to nstenergy (4) 68: 68: Number of degrees of freedom in T-Coupling group System is 33.00 68: 68: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 68: NVE simulation: will use the initial temperature of 68.810 K for 68: determining the Verlet buffer size 68: 68: 68: There were 3 NOTEs 68: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 68: Can not increase nstlist because an NVE ensemble is used 68: Using 1 MPI thread 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'Argon' 68: 16 steps, 0.0 ps. 68: Generated 1 of the 1 non-bonded parameter combinations 68: 68: Excluding 1 bonded neighbours molecule type 'Argon' 68: 68: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 68: 68: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 68: 68: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 68: 68: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 68: 68: Note that mdrun will redetermine rlist based on the actual pair-list setup 68: 68: This run will generate roughly 0 Mb of data 68: Generated 1 of the 1 non-bonded parameter combinations 68: 68: Excluding 1 bonded neighbours molecule type 'Argon' 68: 68: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 68: 68: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 68: 68: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 68: 68: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 68: 68: Note that mdrun will redetermine rlist based on the actual pair-list setup 68: 68: This run will generate roughly 0 Mb of data 68: 68: Writing final coordinates. 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.056 0.029 197.4 68: (ns/day) (hour/ns) 68: Performance: 51.378 0.467 68: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_0_firstpart.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 68: Can not increase nstlist because an NVE ensemble is used 68: Using 1 MPI thread 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'Argon' 68: 8 steps, 0.0 ps. 68: 68: Writing final coordinates. 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.063 0.032 197.8 68: (ns/day) (hour/ns) 68: Performance: 24.506 0.979 68: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 68: Can not increase nstlist because an NVE ensemble is used 68: Using 1 MPI thread 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'Argon' 68: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 68: 68: Writing final coordinates. 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.055 0.028 197.7 68: (ns/day) (hour/ns) 68: Performance: 27.856 0.862 68: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.edr as double precision energy file 68: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_0_firstpart.edr as double precision energy file 68: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_0_secondpart.part0002.edr as double precision energy file 68: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/0 (194 ms) 68: [ RUN ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/1 68: 68: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 68: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 68: that with the Verlet scheme, nstlist has no effect on the accuracy of 68: your simulation. 68: 68: 68: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 68: Setting nstcalcenergy (100) equal to nstenergy (4) 68: 68: Number of degrees of freedom in T-Coupling group System is 33.00 68: 68: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 68: NVE simulation: will use the initial temperature of 68.810 K for 68: determining the Verlet buffer size 68: 68: 68: There were 3 NOTEs 68: 68: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 68: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 68: that with the Verlet scheme, nstlist has no effect on the accuracy of 68: your simulation. 68: 68: 68: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 68: Setting nstcalcenergy (100) equal to nstenergy (4) 68: 68: Number of degrees of freedom in T-Coupling group System is 33.00 68: 68: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 68: NVE simulation: will use the initial temperature of 68.810 K for 68: determining the Verlet buffer size 68: 68: 68: There were 3 NOTEs 68: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_1_full.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 68: Can not increase nstlist because an NVE ensemble is used 68: Using 1 MPI thread 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'Argon' 68: 16 steps, 0.0 ps. 68: Generated 1 of the 1 non-bonded parameter combinations 68: 68: Excluding 1 bonded neighbours molecule type 'Argon' 68: 68: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 68: 68: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 68.8096 K 68: 68: Calculated rlist for 1x1 atom pair-list as 0.702 nm, buffer size 0.002 nm 68: 68: Set rlist, assuming 4x4 atom pair-list, to 0.702 nm, buffer size 0.002 nm 68: 68: Note that mdrun will redetermine rlist based on the actual pair-list setup 68: 68: This run will generate roughly 0 Mb of data 68: Generated 1 of the 1 non-bonded parameter combinations 68: 68: Excluding 1 bonded neighbours molecule type 'Argon' 68: 68: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 68: 68: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 68.8096 K 68: 68: Calculated rlist for 1x1 atom pair-list as 0.702 nm, buffer size 0.002 nm 68: 68: Set rlist, assuming 4x4 atom pair-list, to 0.702 nm, buffer size 0.002 nm 68: 68: Note that mdrun will redetermine rlist based on the actual pair-list setup 68: 68: This run will generate roughly 0 Mb of data 68: 68: Writing final coordinates. 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.064 0.032 198.1 68: (ns/day) (hour/ns) 68: Performance: 45.230 0.531 68: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_1_firstpart.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 68: Can not increase nstlist because an NVE ensemble is used 68: Using 1 MPI thread 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'Argon' 68: 8 steps, 0.0 ps. 68: 68: Writing final coordinates. 68: 68: NOTE: 33 % of the run time was spent in pair search, 68: you might want to increase nstlist (this has no effect on accuracy) 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.063 0.032 198.1 68: (ns/day) (hour/ns) 68: Performance: 24.537 0.978 68: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_1_full.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 68: Can not increase nstlist because an NVE ensemble is used 68: Using 1 MPI thread 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'Argon' 68: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 68: 68: Writing final coordinates. 68: 68: NOTE: 12 % of the run time was spent in pair search, 68: you might want to increase nstlist (this has no effect on accuracy) 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.199 0.100 199.4 68: (ns/day) (hour/ns) 68: Performance: 7.782 3.084 68: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_1_full.edr as double precision energy file 68: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_1_firstpart.edr as double precision energy file 68: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_1_secondpart.part0002.edr as double precision energy file 68: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/1 (322 ms) 68: [ RUN ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/2 68: 68: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]: 68: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 68: that with the Verlet scheme, nstlist has no effect on the accuracy of 68: your simulation. 68: 68: 68: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]: 68: Setting nstcalcenergy (100) equal to nstenergy (4) 68: 68: Number of degrees of freedom in T-Coupling group System is 33.00 68: 68: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]: 68: NVE simulation: will use the initial temperature of 68.810 K for 68: determining the Verlet buffer size 68: 68: 68: There were 3 NOTEs 68: 68: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]: 68: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 68: that with the Verlet scheme, nstlist has no effect on the accuracy of 68: your simulation. 68: 68: 68: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]: 68: Setting nstcalcenergy (100) equal to nstenergy (4) 68: 68: Number of degrees of freedom in T-Coupling group System is 33.00 68: 68: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]: 68: NVE simulation: will use the initial temperature of 68.810 K for 68: determining the Verlet buffer size 68: 68: 68: There were 3 NOTEs 68: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_2_full.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 68: Can not increase nstlist because an NVE ensemble is used 68: Using 1 MPI thread 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'Argon' 68: 16 steps, 0.0 ps. 68: Generated 1 of the 1 non-bonded parameter combinations 68: 68: Excluding 1 bonded neighbours molecule type 'Argon' 68: 68: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 68: 68: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 68: 68: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 68: 68: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 68: 68: Note that mdrun will redetermine rlist based on the actual pair-list setup 68: 68: This run will generate roughly 0 Mb of data 68: Generated 1 of the 1 non-bonded parameter combinations 68: 68: Excluding 1 bonded neighbours molecule type 'Argon' 68: 68: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 68: 68: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 68: 68: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 68: 68: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 68: 68: Note that mdrun will redetermine rlist based on the actual pair-list setup 68: 68: This run will generate roughly 0 Mb of data 68: 68: Writing final coordinates. 68: 68: NOTE: 18 % of the run time was spent in pair search, 68: you might want to increase nstlist (this has no effect on accuracy) 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.071 0.036 199.1 68: (ns/day) (hour/ns) 68: Performance: 41.088 0.584 68: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_2_firstpart.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 68: Can not increase nstlist because an NVE ensemble is used 68: Using 1 MPI thread 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'Argon' 68: 8 steps, 0.0 ps. 68: 68: Writing final coordinates. 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.054 0.027 198.8 68: (ns/day) (hour/ns) 68: Performance: 28.527 0.841 68: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_2_full.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 68: Can not increase nstlist because an NVE ensemble is used 68: Using 1 MPI thread 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'Argon' 68: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 68: 68: Writing final coordinates. 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.049 0.025 197.7 68: (ns/day) (hour/ns) 68: Performance: 31.327 0.766 68: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_2_full.edr as double precision energy file 68: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_2_firstpart.edr as double precision energy file 68: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_2_secondpart.part0002.edr as double precision energy file 68: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/2 (199 ms) 68: [ RUN ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/3 68: 68: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]: 68: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 68: that with the Verlet scheme, nstlist has no effect on the accuracy of 68: your simulation. 68: 68: 68: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]: 68: Setting nstcalcenergy (100) equal to nstenergy (4) 68: 68: Number of degrees of freedom in T-Coupling group System is 33.00 68: 68: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]: 68: NVE simulation: will use the initial temperature of 68.810 K for 68: determining the Verlet buffer size 68: 68: 68: There were 3 NOTEs 68: 68: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]: 68: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 68: that with the Verlet scheme, nstlist has no effect on the accuracy of 68: your simulation. 68: 68: 68: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]: 68: Setting nstcalcenergy (100) equal to nstenergy (4) 68: 68: Number of degrees of freedom in T-Coupling group System is 33.00 68: 68: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]: 68: NVE simulation: will use the initial temperature of 68.810 K for 68: determining the Verlet buffer size 68: 68: 68: There were 3 NOTEs 68: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_3_full.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 68: Can not increase nstlist because an NVE ensemble is used 68: Using 1 MPI thread 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'Argon' 68: 16 steps, 0.0 ps. 68: Generated 1 of the 1 non-bonded parameter combinations 68: 68: Excluding 1 bonded neighbours molecule type 'Argon' 68: 68: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 68: 68: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 68.8096 K 68: 68: Calculated rlist for 1x1 atom pair-list as 0.702 nm, buffer size 0.002 nm 68: 68: Set rlist, assuming 4x4 atom pair-list, to 0.702 nm, buffer size 0.002 nm 68: 68: Note that mdrun will redetermine rlist based on the actual pair-list setup 68: 68: This run will generate roughly 0 Mb of data 68: Generated 1 of the 1 non-bonded parameter combinations 68: 68: Excluding 1 bonded neighbours molecule type 'Argon' 68: 68: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 68: 68: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 68.8096 K 68: 68: Calculated rlist for 1x1 atom pair-list as 0.702 nm, buffer size 0.002 nm 68: 68: Set rlist, assuming 4x4 atom pair-list, to 0.702 nm, buffer size 0.002 nm 68: 68: Note that mdrun will redetermine rlist based on the actual pair-list setup 68: 68: This run will generate roughly 0 Mb of data 68: 68: Writing final coordinates. 68: 68: NOTE: 39 % of the run time was spent in pair search, 68: you might want to increase nstlist (this has no effect on accuracy) 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.087 0.044 199.3 68: (ns/day) (hour/ns) 68: Performance: 33.633 0.714 68: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_3_firstpart.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 68: Can not increase nstlist because an NVE ensemble is used 68: Using 1 MPI thread 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'Argon' 68: 8 steps, 0.0 ps. 68: 68: Writing final coordinates. 68: 68: NOTE: 21 % of the run time was spent in pair search, 68: you might want to increase nstlist (this has no effect on accuracy) 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.115 0.058 199.4 68: (ns/day) (hour/ns) 68: Performance: 13.472 1.782 68: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_3_full.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 68: Can not increase nstlist because an NVE ensemble is used 68: Using 1 MPI thread 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'Argon' 68: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 68: 68: Writing final coordinates. 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.061 0.031 198.0 68: (ns/day) (hour/ns) 68: Performance: 25.421 0.944 68: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_3_full.edr as double precision energy file 68: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_3_firstpart.edr as double precision energy file 68: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_3_secondpart.part0002.edr as double precision energy file 68: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/3 (253 ms) 68: [ RUN ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/4 68: 68: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_4_input.mdp]: 68: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 68: that with the Verlet scheme, nstlist has no effect on the accuracy of 68: your simulation. 68: 68: 68: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_4_input.mdp]: 68: Setting nstcalcenergy (100) equal to nstenergy (4) 68: 68: Number of degrees of freedom in T-Coupling group System is 33.00 68: 68: There were 2 NOTEs 68: 68: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_4_input.mdp]: 68: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 68: that with the Verlet scheme, nstlist has no effect on the accuracy of 68: your simulation. 68: 68: 68: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_4_input.mdp]: 68: Setting nstcalcenergy (100) equal to nstenergy (4) 68: 68: Number of degrees of freedom in T-Coupling group System is 33.00 68: 68: There were 2 NOTEs 68: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_4_full.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 68: Using 1 MPI thread 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'Argon' 68: 16 steps, 0.0 ps. 68: Generated 1 of the 1 non-bonded parameter combinations 68: 68: Excluding 1 bonded neighbours molecule type 'Argon' 68: 68: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 68: 68: Calculated rlist for 1x1 atom pair-list as 0.713 nm, buffer size 0.013 nm 68: 68: Set rlist, assuming 4x4 atom pair-list, to 0.712 nm, buffer size 0.012 nm 68: 68: Note that mdrun will redetermine rlist based on the actual pair-list setup 68: 68: This run will generate roughly 0 Mb of data 68: Generated 1 of the 1 non-bonded parameter combinations 68: 68: Excluding 1 bonded neighbours molecule type 'Argon' 68: 68: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 68: 68: Calculated rlist for 1x1 atom pair-list as 0.713 nm, buffer size 0.013 nm 68: 68: Set rlist, assuming 4x4 atom pair-list, to 0.712 nm, buffer size 0.012 nm 68: 68: Note that mdrun will redetermine rlist based on the actual pair-list setup 68: 68: This run will generate roughly 0 Mb of data 68: 68: Writing final coordinates. 68: 68: NOTE: 26 % of the run time was spent in pair search, 68: you might want to increase nstlist (this has no effect on accuracy) 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.089 0.045 198.2 68: (ns/day) (hour/ns) 68: Performance: 32.628 0.736 68: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_4_firstpart.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 68: Using 1 MPI thread 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'Argon' 68: 8 steps, 0.0 ps. 68: 68: Writing final coordinates. 68: 68: NOTE: 25 % of the run time was spent in pair search, 68: you might want to increase nstlist (this has no effect on accuracy) 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.092 0.046 198.8 68: (ns/day) (hour/ns) 68: Performance: 16.791 1.429 68: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_4_full.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 68: Using 1 MPI thread 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'Argon' 68: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 68: 68: Writing final coordinates. 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.048 0.024 197.7 68: (ns/day) (hour/ns) 68: Performance: 31.946 0.751 68: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_4_full.edr as double precision energy file 68: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_4_firstpart.edr as double precision energy file 68: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_4_secondpart.part0002.edr as double precision energy file 68: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/4 (266 ms) 68: [ RUN ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/5 68: 68: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_5_input.mdp]: 68: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 68: that with the Verlet scheme, nstlist has no effect on the accuracy of 68: your simulation. 68: 68: 68: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_5_input.mdp]: 68: Setting nstcalcenergy (100) equal to nstenergy (4) 68: 68: Number of degrees of freedom in T-Coupling group System is 33.00 68: 68: There were 2 NOTEs 68: 68: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_5_input.mdp]: 68: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 68: that with the Verlet scheme, nstlist has no effect on the accuracy of 68: your simulation. 68: 68: 68: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_5_input.mdp]: 68: Setting nstcalcenergy (100) equal to nstenergy (4) 68: 68: Number of degrees of freedom in T-Coupling group System is 33.00 68: 68: There were 2 NOTEs 68: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_5_full.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 68: Changing nstlist from 8 to 100, rlist from 0.709 to 0.733 68: 68: Using 1 MPI thread 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'Argon' 68: 16 steps, 0.0 ps. 68: Generated 1 of the 1 non-bonded parameter combinations 68: 68: Excluding 1 bonded neighbours molecule type 'Argon' 68: 68: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 80 K 68: 68: Calculated rlist for 1x1 atom pair-list as 0.711 nm, buffer size 0.011 nm 68: 68: Set rlist, assuming 4x4 atom pair-list, to 0.709 nm, buffer size 0.009 nm 68: 68: Note that mdrun will redetermine rlist based on the actual pair-list setup 68: 68: This run will generate roughly 0 Mb of data 68: Generated 1 of the 1 non-bonded parameter combinations 68: 68: Excluding 1 bonded neighbours molecule type 'Argon' 68: 68: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 80 K 68: 68: Calculated rlist for 1x1 atom pair-list as 0.711 nm, buffer size 0.011 nm 68: 68: Set rlist, assuming 4x4 atom pair-list, to 0.709 nm, buffer size 0.009 nm 68: 68: Note that mdrun will redetermine rlist based on the actual pair-list setup 68: 68: This run will generate roughly 0 Mb of data 68: 68: Writing final coordinates. 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.072 0.036 198.3 68: (ns/day) (hour/ns) 68: Performance: 40.720 0.589 68: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_5_firstpart.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 68: Changing nstlist from 8 to 100, rlist from 0.709 to 0.733 68: 68: Using 1 MPI thread 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'Argon' 68: 8 steps, 0.0 ps. 68: 68: Writing final coordinates. 68: 68: NOTE: 24 % of the run time was spent in pair search, 68: you might want to increase nstlist (this has no effect on accuracy) 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.094 0.047 198.9 68: (ns/day) (hour/ns) 68: Performance: 16.430 1.461 68: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_5_full.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 68: Changing nstlist from 8 to 100, rlist from 0.709 to 0.733 68: 68: Using 1 MPI thread 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'Argon' 68: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 68: 68: Writing final coordinates. 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.051 0.026 197.8 68: (ns/day) (hour/ns) 68: Performance: 30.009 0.800 68: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_5_full.edr as double precision energy file 68: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_5_firstpart.edr as double precision energy file 68: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_5_secondpart.part0002.edr as double precision energy file 68: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/5 (264 ms) 68: [ RUN ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/6 68: 68: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_6_input.mdp]: 68: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 68: that with the Verlet scheme, nstlist has no effect on the accuracy of 68: your simulation. 68: 68: 68: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_6_input.mdp]: 68: Setting nstcalcenergy (100) equal to nstenergy (4) 68: 68: Number of degrees of freedom in T-Coupling group System is 33.00 68: 68: There were 2 NOTEs 68: 68: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_6_input.mdp]: 68: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 68: that with the Verlet scheme, nstlist has no effect on the accuracy of 68: your simulation. 68: 68: 68: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_6_input.mdp]: 68: Setting nstcalcenergy (100) equal to nstenergy (4) 68: 68: Number of degrees of freedom in T-Coupling group System is 33.00 68: 68: There were 2 NOTEs 68: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_6_full.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 68: Using 1 MPI thread 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'Argon' 68: 16 steps, 0.0 ps. 68: Generated 1 of the 1 non-bonded parameter combinations 68: 68: Excluding 1 bonded neighbours molecule type 'Argon' 68: 68: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 68: 68: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 68: 68: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 68: 68: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 68: 68: Note that mdrun will redetermine rlist based on the actual pair-list setup 68: 68: This run will generate roughly 0 Mb of data 68: Generated 1 of the 1 non-bonded parameter combinations 68: 68: Excluding 1 bonded neighbours molecule type 'Argon' 68: 68: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 68: 68: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 68: 68: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 68: 68: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 68: 68: Note that mdrun will redetermine rlist based on the actual pair-list setup 68: 68: This run will generate roughly 0 Mb of data 68: 68: Writing final coordinates. 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.041 0.021 197.4 68: (ns/day) (hour/ns) 68: Performance: 71.115 0.337 68: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_6_firstpart.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 68: Using 1 MPI thread 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'Argon' 68: 8 steps, 0.0 ps. 68: 68: Writing final coordinates. 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.037 0.019 197.1 68: (ns/day) (hour/ns) 68: Performance: 41.004 0.585 68: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_6_full.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 68: Using 1 MPI thread 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'Argon' 68: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 68: 68: Writing final coordinates. 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.080 0.041 198.2 68: (ns/day) (hour/ns) 68: Performance: 19.159 1.253 68: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_6_full.edr as double precision energy file 68: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_6_firstpart.edr as double precision energy file 68: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_6_secondpart.part0002.edr as double precision energy file 68: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/6 (199 ms) 68: [ RUN ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/7 68: 68: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_7_input.mdp]: 68: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 68: that with the Verlet scheme, nstlist has no effect on the accuracy of 68: your simulation. 68: 68: 68: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_7_input.mdp]: 68: Setting nstcalcenergy (100) equal to nstenergy (4) 68: 68: Number of degrees of freedom in T-Coupling group System is 33.00 68: 68: There were 2 NOTEs 68: 68: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_7_input.mdp]: 68: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 68: that with the Verlet scheme, nstlist has no effect on the accuracy of 68: your simulation. 68: 68: 68: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_7_input.mdp]: 68: Setting nstcalcenergy (100) equal to nstenergy (4) 68: 68: Number of degrees of freedom in T-Coupling group System is 33.00 68: 68: There were 2 NOTEs 68: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_7_full.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 68: Changing nstlist from 8 to 100, rlist from 0.702 to 0.738 68: 68: Using 1 MPI thread 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'Argon' 68: 16 steps, 0.0 ps. 68: Generated 1 of the 1 non-bonded parameter combinations 68: 68: Excluding 1 bonded neighbours molecule type 'Argon' 68: 68: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 68: 68: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 80 K 68: 68: Calculated rlist for 1x1 atom pair-list as 0.702 nm, buffer size 0.002 nm 68: 68: Set rlist, assuming 4x4 atom pair-list, to 0.702 nm, buffer size 0.002 nm 68: 68: Note that mdrun will redetermine rlist based on the actual pair-list setup 68: 68: This run will generate roughly 0 Mb of data 68: Generated 1 of the 1 non-bonded parameter combinations 68: 68: Excluding 1 bonded neighbours molecule type 'Argon' 68: 68: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 68: 68: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 80 K 68: 68: Calculated rlist for 1x1 atom pair-list as 0.702 nm, buffer size 0.002 nm 68: 68: Set rlist, assuming 4x4 atom pair-list, to 0.702 nm, buffer size 0.002 nm 68: 68: Note that mdrun will redetermine rlist based on the actual pair-list setup 68: 68: This run will generate roughly 0 Mb of data 68: 68: Writing final coordinates. 68: 68: NOTE: 20 % of the run time was spent in pair search, 68: you might want to increase nstlist (this has no effect on accuracy) 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.062 0.031 198.5 68: (ns/day) (hour/ns) 68: Performance: 46.925 0.511 68: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_7_firstpart.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 68: Changing nstlist from 8 to 100, rlist from 0.702 to 0.738 68: 68: Using 1 MPI thread 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'Argon' 68: 8 steps, 0.0 ps. 68: 68: Writing final coordinates. 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.043 0.022 197.8 68: (ns/day) (hour/ns) 68: Performance: 35.644 0.673 68: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_7_full.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 68: Changing nstlist from 8 to 100, rlist from 0.702 to 0.738 68: 68: Using 1 MPI thread 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'Argon' 68: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 68: 68: Writing final coordinates. 68: 68: NOTE: 17 % of the run time was spent in pair search, 68: you might want to increase nstlist (this has no effect on accuracy) 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.103 0.052 199.2 68: (ns/day) (hour/ns) 68: Performance: 14.991 1.601 68: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_7_full.edr as double precision energy file 68: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_7_firstpart.edr as double precision energy file 68: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_7_secondpart.part0002.edr as double precision energy file 68: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/7 (243 ms) 68: [ RUN ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/8 68: 68: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_8_input.mdp]: 68: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 68: that with the Verlet scheme, nstlist has no effect on the accuracy of 68: your simulation. 68: 68: 68: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_8_input.mdp]: 68: Setting nstcalcenergy (100) equal to nstenergy (4) 68: 68: Generating 1-4 interactions: fudge = 0.5 68: Number of degrees of freedom in T-Coupling group System is 9.00 68: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 68: 68: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_8_input.mdp]: 68: NVE simulation: will use the initial temperature of 2573.591 K for 68: determining the Verlet buffer size 68: 68: 68: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_8_input.mdp]: 68: You are using a plain Coulomb cut-off, which might produce artifacts. 68: You might want to consider using PME electrostatics. 68: 68: 68: 68: There were 4 NOTEs 68: 68: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_8_input.mdp]: 68: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 68: that with the Verlet scheme, nstlist has no effect on the accuracy of 68: your simulation. 68: 68: 68: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_8_input.mdp]: 68: Setting nstcalcenergy (100) equal to nstenergy (4) 68: 68: Generating 1-4 interactions: fudge = 0.5 68: Number of degrees of freedom in T-Coupling group System is 9.00 68: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 68: 68: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_8_input.mdp]: 68: NVE simulation: will use the initial temperature of 2573.591 K for 68: determining the Verlet buffer size 68: 68: 68: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_8_input.mdp]: 68: You are using a plain Coulomb cut-off, which might produce artifacts. 68: You might want to consider using PME electrostatics. 68: 68: 68: 68: There were 4 NOTEs 68: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_8_full.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 68: Can not increase nstlist because an NVE ensemble is used 68: Using 1 MPI thread 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'spc2' 68: 16 steps, 0.0 ps. 68: Generated 3 of the 3 non-bonded parameter combinations 68: 68: Generated 3 of the 3 1-4 parameter combinations 68: 68: Excluding 2 bonded neighbours molecule type 'SOL' 68: 68: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/spc2.gro' 68: 68: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 2573.59 K 68: 68: Calculated rlist for 1x1 atom pair-list as 0.906 nm, buffer size 0.206 nm 68: 68: Set rlist, assuming 4x4 atom pair-list, to 0.892 nm, buffer size 0.192 nm 68: 68: Note that mdrun will redetermine rlist based on the actual pair-list setup 68: 68: This run will generate roughly 0 Mb of data 68: Generated 3 of the 3 non-bonded parameter combinations 68: 68: Generated 3 of the 3 1-4 parameter combinations 68: 68: Excluding 2 bonded neighbours molecule type 'SOL' 68: 68: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/spc2.gro' 68: 68: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 2573.59 K 68: 68: Calculated rlist for 1x1 atom pair-list as 0.906 nm, buffer size 0.206 nm 68: 68: Set rlist, assuming 4x4 atom pair-list, to 0.892 nm, buffer size 0.192 nm 68: 68: Note that mdrun will redetermine rlist based on the actual pair-list setup 68: 68: This run will generate roughly 0 Mb of data 68: 68: Writing final coordinates. 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.052 0.026 197.7 68: (ns/day) (hour/ns) 68: Performance: 56.174 0.427 68: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_8_firstpart.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 68: Can not increase nstlist because an NVE ensemble is used 68: Using 1 MPI thread 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'spc2' 68: 8 steps, 0.0 ps. 68: 68: Writing final coordinates. 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.037 0.019 195.9 68: (ns/day) (hour/ns) 68: Performance: 40.920 0.587 68: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_8_full.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 68: Can not increase nstlist because an NVE ensemble is used 68: Using 1 MPI thread 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'spc2' 68: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 68: 68: Writing final coordinates. 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.154 0.078 199.0 68: (ns/day) (hour/ns) 68: Performance: 10.027 2.394 68: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_8_full.edr as double precision energy file 68: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_8_firstpart.edr as double precision energy file 68: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_8_secondpart.part0002.edr as double precision energy file 68: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/8 (235 ms) 68: [ RUN ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/9 68: 68: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_9_input.mdp]: 68: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 68: that with the Verlet scheme, nstlist has no effect on the accuracy of 68: your simulation. 68: 68: 68: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_9_input.mdp]: 68: Setting nstcalcenergy (100) equal to nstenergy (4) 68: 68: Generating 1-4 interactions: fudge = 0.5 68: Number of degrees of freedom in T-Coupling group System is 9.00 68: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 68: 68: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_9_input.mdp]: 68: NVE simulation: will use the initial temperature of 2573.591 K for 68: determining the Verlet buffer size 68: 68: 68: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_9_input.mdp]: 68: You are using a plain Coulomb cut-off, which might produce artifacts. 68: You might want to consider using PME electrostatics. 68: 68: 68: 68: There were 4 NOTEs 68: 68: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_9_input.mdp]: 68: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 68: that with the Verlet scheme, nstlist has no effect on the accuracy of 68: your simulation. 68: 68: 68: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_9_input.mdp]: 68: Setting nstcalcenergy (100) equal to nstenergy (4) 68: 68: Generating 1-4 interactions: fudge = 0.5 68: Number of degrees of freedom in T-Coupling group System is 9.00 68: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 68: 68: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_9_input.mdp]: 68: NVE simulation: will use the initial temperature of 2573.591 K for 68: determining the Verlet buffer size 68: 68: 68: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_9_input.mdp]: 68: You are using a plain Coulomb cut-off, which might produce artifacts. 68: You might want to consider using PME electrostatics. 68: 68: 68: 68: There were 4 NOTEs 68: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_9_full.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 68: Can not increase nstlist because an NVE ensemble is used 68: Using 1 MPI thread 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'spc2' 68: 16 steps, 0.0 ps. 68: Generated 3 of the 3 non-bonded parameter combinations 68: 68: Generated 3 of the 3 1-4 parameter combinations 68: 68: Excluding 2 bonded neighbours molecule type 'SOL' 68: 68: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/spc2.gro' 68: 68: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 2573.59 K 68: 68: Calculated rlist for 1x1 atom pair-list as 0.886 nm, buffer size 0.186 nm 68: 68: Set rlist, assuming 4x4 atom pair-list, to 0.872 nm, buffer size 0.172 nm 68: 68: Note that mdrun will redetermine rlist based on the actual pair-list setup 68: 68: This run will generate roughly 0 Mb of data 68: Generated 3 of the 3 non-bonded parameter combinations 68: 68: Generated 3 of the 3 1-4 parameter combinations 68: 68: Excluding 2 bonded neighbours molecule type 'SOL' 68: 68: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/spc2.gro' 68: 68: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 2573.59 K 68: 68: Calculated rlist for 1x1 atom pair-list as 0.886 nm, buffer size 0.186 nm 68: 68: Set rlist, assuming 4x4 atom pair-list, to 0.872 nm, buffer size 0.172 nm 68: 68: Note that mdrun will redetermine rlist based on the actual pair-list setup 68: 68: This run will generate roughly 0 Mb of data 68: 68: Writing final coordinates. 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.075 0.038 198.4 68: (ns/day) (hour/ns) 68: Performance: 38.843 0.618 68: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_9_firstpart.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 68: Can not increase nstlist because an NVE ensemble is used 68: Using 1 MPI thread 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'spc2' 68: 8 steps, 0.0 ps. 68: 68: Writing final coordinates. 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.041 0.021 196.9 68: (ns/day) (hour/ns) 68: Performance: 37.660 0.637 68: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_9_full.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 68: Can not increase nstlist because an NVE ensemble is used 68: Using 1 MPI thread 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'spc2' 68: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 68: 68: Writing final coordinates. 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.043 0.022 197.2 68: (ns/day) (hour/ns) 68: Performance: 35.326 0.679 68: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_9_full.edr as double precision energy file 68: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_9_firstpart.edr as double precision energy file 68: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_9_secondpart.part0002.edr as double precision energy file 68: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/9 (221 ms) 68: [ RUN ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/10 68: 68: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_10_input.mdp]: 68: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 68: that with the Verlet scheme, nstlist has no effect on the accuracy of 68: your simulation. 68: 68: 68: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_10_input.mdp]: 68: Setting nstcalcenergy (100) equal to nstenergy (4) 68: 68: Generating 1-4 interactions: fudge = 0.5 68: Number of degrees of freedom in T-Coupling group System is 9.00 68: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 68: 68: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_10_input.mdp]: 68: NVE simulation: will use the initial temperature of 2573.591 K for 68: determining the Verlet buffer size 68: 68: 68: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_10_input.mdp]: 68: You are using a plain Coulomb cut-off, which might produce artifacts. 68: You might want to consider using PME electrostatics. 68: 68: 68: 68: There were 4 NOTEs 68: 68: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_10_input.mdp]: 68: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 68: that with the Verlet scheme, nstlist has no effect on the accuracy of 68: your simulation. 68: 68: 68: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_10_input.mdp]: 68: Setting nstcalcenergy (100) equal to nstenergy (4) 68: 68: Generating 1-4 interactions: fudge = 0.5 68: Number of degrees of freedom in T-Coupling group System is 9.00 68: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 68: 68: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_10_input.mdp]: 68: NVE simulation: will use the initial temperature of 2573.591 K for 68: determining the Verlet buffer size 68: 68: 68: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_10_input.mdp]: 68: You are using a plain Coulomb cut-off, which might produce artifacts. 68: You might want to consider using PME electrostatics. 68: 68: 68: 68: There were 4 NOTEs 68: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_10_full.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 68: Can not increase nstlist because an NVE ensemble is used 68: Using 1 MPI thread 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'spc2' 68: 16 steps, 0.0 ps. 68: Generated 3 of the 3 non-bonded parameter combinations 68: 68: Generated 3 of the 3 1-4 parameter combinations 68: 68: Excluding 2 bonded neighbours molecule type 'SOL' 68: 68: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/spc2.gro' 68: 68: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 2573.59 K 68: 68: Calculated rlist for 1x1 atom pair-list as 0.906 nm, buffer size 0.206 nm 68: 68: Set rlist, assuming 4x4 atom pair-list, to 0.892 nm, buffer size 0.192 nm 68: 68: Note that mdrun will redetermine rlist based on the actual pair-list setup 68: 68: This run will generate roughly 0 Mb of data 68: Generated 3 of the 3 non-bonded parameter combinations 68: 68: Generated 3 of the 3 1-4 parameter combinations 68: 68: Excluding 2 bonded neighbours molecule type 'SOL' 68: 68: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/spc2.gro' 68: 68: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 2573.59 K 68: 68: Calculated rlist for 1x1 atom pair-list as 0.906 nm, buffer size 0.206 nm 68: 68: Set rlist, assuming 4x4 atom pair-list, to 0.892 nm, buffer size 0.192 nm 68: 68: Note that mdrun will redetermine rlist based on the actual pair-list setup 68: 68: This run will generate roughly 0 Mb of data 68: 68: Writing final coordinates. 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.072 0.036 199.0 68: (ns/day) (hour/ns) 68: Performance: 40.432 0.594 68: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_10_firstpart.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 68: Can not increase nstlist because an NVE ensemble is used 68: Using 1 MPI thread 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'spc2' 68: 8 steps, 0.0 ps. 68: 68: Writing final coordinates. 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.047 0.024 198.5 68: (ns/day) (hour/ns) 68: Performance: 32.983 0.728 68: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_10_full.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 68: Can not increase nstlist because an NVE ensemble is used 68: Using 1 MPI thread 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'spc2' 68: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 68: 68: Writing final coordinates. 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.094 0.047 198.9 68: (ns/day) (hour/ns) 68: Performance: 16.469 1.457 68: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_10_full.edr as double precision energy file 68: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_10_firstpart.edr as double precision energy file 68: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_10_secondpart.part0002.edr as double precision energy file 68: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/10 (221 ms) 68: [ RUN ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/11 68: 68: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_11_input.mdp]: 68: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 68: that with the Verlet scheme, nstlist has no effect on the accuracy of 68: your simulation. 68: 68: 68: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_11_input.mdp]: 68: Setting nstcalcenergy (100) equal to nstenergy (4) 68: 68: Generating 1-4 interactions: fudge = 0.5 68: Number of degrees of freedom in T-Coupling group System is 9.00 68: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 68: 68: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_11_input.mdp]: 68: NVE simulation: will use the initial temperature of 2573.591 K for 68: determining the Verlet buffer size 68: 68: 68: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_11_input.mdp]: 68: You are using a plain Coulomb cut-off, which might produce artifacts. 68: You might want to consider using PME electrostatics. 68: 68: 68: 68: There were 4 NOTEs 68: 68: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_11_input.mdp]: 68: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 68: that with the Verlet scheme, nstlist has no effect on the accuracy of 68: your simulation. 68: 68: 68: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_11_input.mdp]: 68: Setting nstcalcenergy (100) equal to nstenergy (4) 68: 68: Generating 1-4 interactions: fudge = 0.5 68: Number of degrees of freedom in T-Coupling group System is 9.00 68: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 68: 68: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_11_input.mdp]: 68: NVE simulation: will use the initial temperature of 2573.591 K for 68: determining the Verlet buffer size 68: 68: 68: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_11_input.mdp]: 68: You are using a plain Coulomb cut-off, which might produce artifacts. 68: You might want to consider using PME electrostatics. 68: 68: 68: 68: There were 4 NOTEs 68: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_11_full.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 68: Can not increase nstlist because an NVE ensemble is used 68: Using 1 MPI thread 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'spc2' 68: 16 steps, 0.0 ps. 68: Generated 3 of the 3 non-bonded parameter combinations 68: 68: Generated 3 of the 3 1-4 parameter combinations 68: 68: Excluding 2 bonded neighbours molecule type 'SOL' 68: 68: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/spc2.gro' 68: 68: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 2573.59 K 68: 68: Calculated rlist for 1x1 atom pair-list as 0.886 nm, buffer size 0.186 nm 68: 68: Set rlist, assuming 4x4 atom pair-list, to 0.872 nm, buffer size 0.172 nm 68: 68: Note that mdrun will redetermine rlist based on the actual pair-list setup 68: 68: This run will generate roughly 0 Mb of data 68: Generated 3 of the 3 non-bonded parameter combinations 68: 68: Generated 3 of the 3 1-4 parameter combinations 68: 68: Excluding 2 bonded neighbours molecule type 'SOL' 68: 68: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/spc2.gro' 68: 68: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 2573.59 K 68: 68: Calculated rlist for 1x1 atom pair-list as 0.886 nm, buffer size 0.186 nm 68: 68: Set rlist, assuming 4x4 atom pair-list, to 0.872 nm, buffer size 0.172 nm 68: 68: Note that mdrun will redetermine rlist based on the actual pair-list setup 68: 68: This run will generate roughly 0 Mb of data 68: 68: Writing final coordinates. 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.068 0.034 199.0 68: (ns/day) (hour/ns) 68: Performance: 42.906 0.559 68: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_11_firstpart.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 68: Can not increase nstlist because an NVE ensemble is used 68: Using 1 MPI thread 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'spc2' 68: 8 steps, 0.0 ps. 68: 68: Writing final coordinates. 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.052 0.026 198.7 68: (ns/day) (hour/ns) 68: Performance: 29.593 0.811 68: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_11_full.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 68: Can not increase nstlist because an NVE ensemble is used 68: Using 1 MPI thread 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'spc2' 68: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 68: 68: Writing final coordinates. 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.055 0.028 198.1 68: (ns/day) (hour/ns) 68: Performance: 27.946 0.859 68: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_11_full.edr as double precision energy file 68: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_11_firstpart.edr as double precision energy file 68: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_11_secondpart.part0002.edr as double precision energy file 68: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/11 (223 ms) 68: [ RUN ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/12 68: 68: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_12_input.mdp]: 68: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 68: that with the Verlet scheme, nstlist has no effect on the accuracy of 68: your simulation. 68: 68: 68: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_12_input.mdp]: 68: Setting nstcalcenergy (100) equal to nstenergy (4) 68: 68: Generating 1-4 interactions: fudge = 0.5 68: Number of degrees of freedom in T-Coupling group System is 9.00 68: 68: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_12_input.mdp]: 68: You are using a plain Coulomb cut-off, which might produce artifacts. 68: You might want to consider using PME electrostatics. 68: 68: 68: 68: There were 3 NOTEs 68: 68: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_12_input.mdp]: 68: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 68: that with the Verlet scheme, nstlist has no effect on the accuracy of 68: your simulation. 68: 68: 68: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_12_input.mdp]: 68: Setting nstcalcenergy (100) equal to nstenergy (4) 68: 68: Generating 1-4 interactions: fudge = 0.5 68: Number of degrees of freedom in T-Coupling group System is 9.00 68: 68: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_12_input.mdp]: 68: You are using a plain Coulomb cut-off, which might produce artifacts. 68: You might want to consider using PME electrostatics. 68: 68: 68: 68: There were 3 NOTEs 68: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_12_full.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 68: Using 1 MPI thread 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'spc2' 68: 16 steps, 0.0 ps. 68: Generated 3 of the 3 non-bonded parameter combinations 68: 68: Generated 3 of the 3 1-4 parameter combinations 68: 68: Excluding 2 bonded neighbours molecule type 'SOL' 68: 68: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 68: 68: Calculated rlist for 1x1 atom pair-list as 0.736 nm, buffer size 0.036 nm 68: 68: Set rlist, assuming 4x4 atom pair-list, to 0.734 nm, buffer size 0.034 nm 68: 68: Note that mdrun will redetermine rlist based on the actual pair-list setup 68: 68: This run will generate roughly 0 Mb of data 68: Generated 3 of the 3 non-bonded parameter combinations 68: 68: Generated 3 of the 3 1-4 parameter combinations 68: 68: Excluding 2 bonded neighbours molecule type 'SOL' 68: 68: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 68: 68: Calculated rlist for 1x1 atom pair-list as 0.736 nm, buffer size 0.036 nm 68: 68: Set rlist, assuming 4x4 atom pair-list, to 0.734 nm, buffer size 0.034 nm 68: 68: Note that mdrun will redetermine rlist based on the actual pair-list setup 68: 68: This run will generate roughly 0 Mb of data 68: 68: Writing final coordinates. 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.043 0.022 197.5 68: (ns/day) (hour/ns) 68: Performance: 67.924 0.353 68: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_12_firstpart.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 68: Using 1 MPI thread 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'spc2' 68: 8 steps, 0.0 ps. 68: 68: Writing final coordinates. 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.036 0.018 196.8 68: (ns/day) (hour/ns) 68: Performance: 42.318 0.567 68: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_12_full.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 68: Using 1 MPI thread 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'spc2' 68: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 68: 68: Writing final coordinates. 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.041 0.021 197.5 68: (ns/day) (hour/ns) 68: Performance: 37.117 0.647 68: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_12_full.edr as double precision energy file 68: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_12_firstpart.edr as double precision energy file 68: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_12_secondpart.part0002.edr as double precision energy file 68: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/12 (203 ms) 68: [ RUN ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/13 68: 68: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_13_input.mdp]: 68: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 68: that with the Verlet scheme, nstlist has no effect on the accuracy of 68: your simulation. 68: 68: 68: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_13_input.mdp]: 68: Setting nstcalcenergy (100) equal to nstenergy (4) 68: 68: Generating 1-4 interactions: fudge = 0.5 68: Number of degrees of freedom in T-Coupling group System is 9.00 68: 68: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_13_input.mdp]: 68: You are using a plain Coulomb cut-off, which might produce artifacts. 68: You might want to consider using PME electrostatics. 68: 68: 68: 68: There were 3 NOTEs 68: 68: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_13_input.mdp]: 68: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 68: that with the Verlet scheme, nstlist has no effect on the accuracy of 68: your simulation. 68: 68: 68: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_13_input.mdp]: 68: Setting nstcalcenergy (100) equal to nstenergy (4) 68: 68: Generating 1-4 interactions: fudge = 0.5 68: Number of degrees of freedom in T-Coupling group System is 9.00 68: 68: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_13_input.mdp]: 68: You are using a plain Coulomb cut-off, which might produce artifacts. 68: You might want to consider using PME electrostatics. 68: 68: 68: 68: There were 3 NOTEs 68: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_13_full.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 68: Changing nstlist from 8 to 100, rlist from 0.73 to 0.811 68: 68: Using 1 MPI thread 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'spc2' 68: 16 steps, 0.0 ps. 68: Generated 3 of the 3 non-bonded parameter combinations 68: 68: Generated 3 of the 3 1-4 parameter combinations 68: 68: Excluding 2 bonded neighbours molecule type 'SOL' 68: 68: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 298 K 68: 68: Calculated rlist for 1x1 atom pair-list as 0.732 nm, buffer size 0.032 nm 68: 68: Set rlist, assuming 4x4 atom pair-list, to 0.730 nm, buffer size 0.030 nm 68: 68: Note that mdrun will redetermine rlist based on the actual pair-list setup 68: 68: This run will generate roughly 0 Mb of data 68: Generated 3 of the 3 non-bonded parameter combinations 68: 68: Generated 3 of the 3 1-4 parameter combinations 68: 68: Excluding 2 bonded neighbours molecule type 'SOL' 68: 68: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 298 K 68: 68: Calculated rlist for 1x1 atom pair-list as 0.732 nm, buffer size 0.032 nm 68: 68: Set rlist, assuming 4x4 atom pair-list, to 0.730 nm, buffer size 0.030 nm 68: 68: Note that mdrun will redetermine rlist based on the actual pair-list setup 68: 68: This run will generate roughly 0 Mb of data 68: 68: Writing final coordinates. 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.045 0.023 197.9 68: (ns/day) (hour/ns) 68: Performance: 64.711 0.371 68: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_13_firstpart.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 68: Changing nstlist from 8 to 100, rlist from 0.73 to 0.811 68: 68: Using 1 MPI thread 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'spc2' 68: 8 steps, 0.0 ps. 68: 68: Writing final coordinates. 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.045 0.023 197.8 68: (ns/day) (hour/ns) 68: Performance: 34.155 0.703 68: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_13_full.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 68: Changing nstlist from 8 to 100, rlist from 0.73 to 0.811 68: 68: Using 1 MPI thread 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'spc2' 68: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 68: 68: Writing final coordinates. 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.039 0.020 197.6 68: (ns/day) (hour/ns) 68: Performance: 39.396 0.609 68: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_13_full.edr as double precision energy file 68: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_13_firstpart.edr as double precision energy file 68: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_13_secondpart.part0002.edr as double precision energy file 68: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/13 (223 ms) 68: [ RUN ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/14 68: 68: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_14_input.mdp]: 68: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 68: that with the Verlet scheme, nstlist has no effect on the accuracy of 68: your simulation. 68: 68: 68: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_14_input.mdp]: 68: Setting nstcalcenergy (100) equal to nstenergy (4) 68: 68: Generating 1-4 interactions: fudge = 0.5 68: Number of degrees of freedom in T-Coupling group System is 9.00 68: 68: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_14_input.mdp]: 68: You are using a plain Coulomb cut-off, which might produce artifacts. 68: You might want to consider using PME electrostatics. 68: 68: 68: 68: There were 3 NOTEs 68: 68: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_14_input.mdp]: 68: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 68: that with the Verlet scheme, nstlist has no effect on the accuracy of 68: your simulation. 68: 68: 68: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_14_input.mdp]: 68: Setting nstcalcenergy (100) equal to nstenergy (4) 68: 68: Generating 1-4 interactions: fudge = 0.5 68: Number of degrees of freedom in T-Coupling group System is 9.00 68: 68: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_14_input.mdp]: 68: You are using a plain Coulomb cut-off, which might produce artifacts. 68: You might want to consider using PME electrostatics. 68: 68: 68: 68: There were 3 NOTEs 68: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_14_full.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 68: Using 1 MPI thread 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'spc2' 68: 16 steps, 0.0 ps. 68: Generated 3 of the 3 non-bonded parameter combinations 68: 68: Generated 3 of the 3 1-4 parameter combinations 68: 68: Excluding 2 bonded neighbours molecule type 'SOL' 68: 68: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/spc2.gro' 68: 68: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 68: 68: Calculated rlist for 1x1 atom pair-list as 0.764 nm, buffer size 0.064 nm 68: 68: Set rlist, assuming 4x4 atom pair-list, to 0.760 nm, buffer size 0.060 nm 68: 68: Note that mdrun will redetermine rlist based on the actual pair-list setup 68: 68: This run will generate roughly 0 Mb of data 68: Generated 3 of the 3 non-bonded parameter combinations 68: 68: Generated 3 of the 3 1-4 parameter combinations 68: 68: Excluding 2 bonded neighbours molecule type 'SOL' 68: 68: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/spc2.gro' 68: 68: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 68: 68: Calculated rlist for 1x1 atom pair-list as 0.764 nm, buffer size 0.064 nm 68: 68: Set rlist, assuming 4x4 atom pair-list, to 0.760 nm, buffer size 0.060 nm 68: 68: Note that mdrun will redetermine rlist based on the actual pair-list setup 68: 68: This run will generate roughly 0 Mb of data 68: 68: Writing final coordinates. 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.047 0.024 198.1 68: (ns/day) (hour/ns) 68: Performance: 61.756 0.389 68: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_14_firstpart.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 68: Using 1 MPI thread 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'spc2' 68: 8 steps, 0.0 ps. 68: 68: Writing final coordinates. 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.037 0.019 197.6 68: (ns/day) (hour/ns) 68: Performance: 41.368 0.580 68: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_14_full.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 68: Using 1 MPI thread 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'spc2' 68: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 68: 68: Writing final coordinates. 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.039 0.020 195.5 68: (ns/day) (hour/ns) 68: Performance: 39.064 0.614 68: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_14_full.edr as double precision energy file 68: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_14_firstpart.edr as double precision energy file 68: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_14_secondpart.part0002.edr as double precision energy file 68: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/14 (178 ms) 68: [ RUN ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/15 68: 68: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_15_input.mdp]: 68: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 68: that with the Verlet scheme, nstlist has no effect on the accuracy of 68: your simulation. 68: 68: 68: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_15_input.mdp]: 68: Setting nstcalcenergy (100) equal to nstenergy (4) 68: 68: Generating 1-4 interactions: fudge = 0.5 68: Number of degrees of freedom in T-Coupling group System is 9.00 68: 68: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_15_input.mdp]: 68: You are using a plain Coulomb cut-off, which might produce artifacts. 68: You might want to consider using PME electrostatics. 68: 68: 68: 68: There were 3 NOTEs 68: 68: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_15_input.mdp]: 68: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 68: that with the Verlet scheme, nstlist has no effect on the accuracy of 68: your simulation. 68: 68: 68: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_15_input.mdp]: 68: Setting nstcalcenergy (100) equal to nstenergy (4) 68: 68: Generating 1-4 interactions: fudge = 0.5 68: Number of degrees of freedom in T-Coupling group System is 9.00 68: 68: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_15_input.mdp]: 68: You are using a plain Coulomb cut-off, which might produce artifacts. 68: You might want to consider using PME electrostatics. 68: 68: 68: 68: There were 3 NOTEs 68: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_15_full.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 68: Changing nstlist from 8 to 25, rlist from 0.752 to 0.89 68: 68: Using 1 MPI thread 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'spc2' 68: 16 steps, 0.0 ps. 68: Generated 3 of the 3 non-bonded parameter combinations 68: 68: Generated 3 of the 3 1-4 parameter combinations 68: 68: Excluding 2 bonded neighbours molecule type 'SOL' 68: 68: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/spc2.gro' 68: 68: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 298 K 68: 68: Calculated rlist for 1x1 atom pair-list as 0.757 nm, buffer size 0.057 nm 68: 68: Set rlist, assuming 4x4 atom pair-list, to 0.752 nm, buffer size 0.052 nm 68: 68: Note that mdrun will redetermine rlist based on the actual pair-list setup 68: 68: This run will generate roughly 0 Mb of data 68: Generated 3 of the 3 non-bonded parameter combinations 68: 68: Generated 3 of the 3 1-4 parameter combinations 68: 68: Excluding 2 bonded neighbours molecule type 'SOL' 68: 68: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/spc2.gro' 68: 68: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 298 K 68: 68: Calculated rlist for 1x1 atom pair-list as 0.757 nm, buffer size 0.057 nm 68: 68: Set rlist, assuming 4x4 atom pair-list, to 0.752 nm, buffer size 0.052 nm 68: 68: Note that mdrun will redetermine rlist based on the actual pair-list setup 68: 68: This run will generate roughly 0 Mb of data 68: 68: Writing final coordinates. 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.048 0.024 198.0 68: (ns/day) (hour/ns) 68: Performance: 60.775 0.395 68: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_15_firstpart.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 68: Changing nstlist from 8 to 25, rlist from 0.752 to 0.89 68: 68: Using 1 MPI thread 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'spc2' 68: 8 steps, 0.0 ps. 68: 68: Writing final coordinates. 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.040 0.020 197.7 68: (ns/day) (hour/ns) 68: Performance: 38.556 0.622 68: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_15_full.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 68: Changing nstlist from 8 to 25, rlist from 0.752 to 0.89 68: 68: Using 1 MPI thread 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'spc2' 68: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 68: 68: Writing final coordinates. 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.045 0.023 197.9 68: (ns/day) (hour/ns) 68: Performance: 34.442 0.697 68: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_15_full.edr as double precision energy file 68: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_15_firstpart.edr as double precision energy file 68: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_15_secondpart.part0002.edr as double precision energy file 68: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/15 (189 ms) 68: [ RUN ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/16 68: 68: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_16_input.mdp]: 68: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 68: that with the Verlet scheme, nstlist has no effect on the accuracy of 68: your simulation. 68: 68: 68: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_16_input.mdp]: 68: Setting nstcalcenergy (100) equal to nstenergy (4) 68: 68: Generating 1-4 interactions: fudge = 0.5 68: 68: NOTE 3 [file unknown]: 68: You are using constraints on all bonds, whereas the forcefield has been 68: parametrized only with constraints involving hydrogen atoms. We suggest 68: using constraints = h-bonds instead, this will also improve performance. 68: 68: Number of degrees of freedom in T-Coupling group System is 23.00 68: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 68: 68: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_16_input.mdp]: 68: NVE simulation: will use the initial temperature of 456.887 K for 68: determining the Verlet buffer size 68: 68: 68: NOTE 5 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_16_input.mdp]: 68: There are 9 non-linear virtual site constructions. Their contribution to 68: the energy error is approximated. In most cases this does not affect the 68: error significantly. 68: 68: 68: NOTE 6 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_16_input.mdp]: 68: You are using a plain Coulomb cut-off, which might produce artifacts. 68: You might want to consider using PME electrostatics. 68: 68: 68: 68: There were 6 NOTEs 68: 68: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_16_input.mdp]: 68: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 68: that with the Verlet scheme, nstlist has no effect on the accuracy of 68: your simulation. 68: 68: 68: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_16_input.mdp]: 68: Setting nstcalcenergy (100) equal to nstenergy (4) 68: 68: Generating 1-4 interactions: fudge = 0.5 68: 68: NOTE 3 [file unknown]: 68: You are using constraints on all bonds, whereas the forcefield has been 68: parametrized only with constraints involving hydrogen atoms. We suggest 68: using constraints = h-bonds instead, this will also improve performance. 68: 68: Number of degrees of freedom in T-Coupling group System is 23.00 68: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 68: 68: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_16_input.mdp]: 68: NVE simulation: will use the initial temperature of 456.887 K for 68: determining the Verlet buffer size 68: 68: 68: NOTE 5 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_16_input.mdp]: 68: There are 9 non-linear virtual site constructions. Their contribution to 68: the energy error is approximated. In most cases this does not affect the 68: error significantly. 68: 68: 68: NOTE 6 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_16_input.mdp]: 68: You are using a plain Coulomb cut-off, which might produce artifacts. 68: You might want to consider using PME electrostatics. 68: 68: 68: 68: There were 6 NOTEs 68: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_16_full.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 68: Can not increase nstlist because an NVE ensemble is used 68: Update groups can not be used for this system because an incompatible virtual site type is used 68: 68: Using 1 MPI thread 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'Alanine dipeptide in vacuo' 68: 16 steps, 0.0 ps. 68: Generated 2145 of the 2145 non-bonded parameter combinations 68: 68: Generated 2145 of the 2145 1-4 parameter combinations 68: 68: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' 68: 68: turning all bonds into constraints... 68: 68: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/alanine_vsite_vacuo.gro' 68: 68: Cleaning up constraints and constant bonded interactions with virtual sites 68: 68: Removed 18 Angles with virtual sites, 21 left 68: 68: Removed 10 Proper Dih.s with virtual sites, 44 left 68: 68: Converted 15 Constraints with virtual sites to connections, 7 left 68: 68: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 456.887 K 68: 68: Calculated rlist for 1x1 atom pair-list as 0.742 nm, buffer size 0.042 nm 68: 68: Set rlist, assuming 4x4 atom pair-list, to 0.737 nm, buffer size 0.037 nm 68: 68: Note that mdrun will redetermine rlist based on the actual pair-list setup 68: 68: This run will generate roughly 0 Mb of data 68: Generated 2145 of the 2145 non-bonded parameter combinations 68: 68: Generated 2145 of the 2145 1-4 parameter combinations 68: 68: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' 68: 68: turning all bonds into constraints... 68: 68: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/alanine_vsite_vacuo.gro' 68: 68: Cleaning up constraints and constant bonded interactions with virtual sites 68: 68: Removed 18 Angles with virtual sites, 21 left 68: 68: Removed 10 Proper Dih.s with virtual sites, 44 left 68: 68: Converted 15 Constraints with virtual sites to connections, 7 left 68: 68: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 456.887 K 68: 68: Calculated rlist for 1x1 atom pair-list as 0.742 nm, buffer size 0.042 nm 68: 68: Set rlist, assuming 4x4 atom pair-list, to 0.737 nm, buffer size 0.037 nm 68: 68: Note that mdrun will redetermine rlist based on the actual pair-list setup 68: 68: This run will generate roughly 0 Mb of data 68: 68: Writing final coordinates. 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.067 0.034 198.0 68: (ns/day) (hour/ns) 68: Performance: 43.250 0.555 68: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_16_firstpart.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 68: Can not increase nstlist because an NVE ensemble is used 68: Update groups can not be used for this system because an incompatible virtual site type is used 68: 68: Using 1 MPI thread 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'Alanine dipeptide in vacuo' 68: 8 steps, 0.0 ps. 68: 68: Writing final coordinates. 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.056 0.028 197.8 68: (ns/day) (hour/ns) 68: Performance: 27.299 0.879 68: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_16_full.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 68: Can not increase nstlist because an NVE ensemble is used 68: Update groups can not be used for this system because an incompatible virtual site type is used 68: 68: Using 1 MPI thread 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'Alanine dipeptide in vacuo' 68: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 68: 68: Writing final coordinates. 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.056 0.028 197.7 68: (ns/day) (hour/ns) 68: Performance: 27.545 0.871 68: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_16_full.edr as double precision energy file 68: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_16_firstpart.edr as double precision energy file 68: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_16_secondpart.part0002.edr as double precision energy file 68: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/16 (452 ms) 68: [ RUN ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/17 68: 68: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_17_input.mdp]: 68: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 68: that with the Verlet scheme, nstlist has no effect on the accuracy of 68: your simulation. 68: 68: 68: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_17_input.mdp]: 68: Setting nstcalcenergy (100) equal to nstenergy (4) 68: 68: Generating 1-4 interactions: fudge = 0.5 68: 68: NOTE 3 [file unknown]: 68: You are using constraints on all bonds, whereas the forcefield has been 68: parametrized only with constraints involving hydrogen atoms. We suggest 68: using constraints = h-bonds instead, this will also improve performance. 68: 68: Number of degrees of freedom in T-Coupling group System is 23.00 68: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 68: 68: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_17_input.mdp]: 68: NVE simulation: will use the initial temperature of 456.887 K for 68: determining the Verlet buffer size 68: 68: 68: NOTE 5 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_17_input.mdp]: 68: There are 9 non-linear virtual site constructions. Their contribution to 68: the energy error is approximated. In most cases this does not affect the 68: error significantly. 68: 68: 68: NOTE 6 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_17_input.mdp]: 68: You are using a plain Coulomb cut-off, which might produce artifacts. 68: You might want to consider using PME electrostatics. 68: 68: 68: 68: There were 6 NOTEs 68: 68: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_17_input.mdp]: 68: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 68: that with the Verlet scheme, nstlist has no effect on the accuracy of 68: your simulation. 68: 68: 68: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_17_input.mdp]: 68: Setting nstcalcenergy (100) equal to nstenergy (4) 68: 68: Generating 1-4 interactions: fudge = 0.5 68: 68: NOTE 3 [file unknown]: 68: You are using constraints on all bonds, whereas the forcefield has been 68: parametrized only with constraints involving hydrogen atoms. We suggest 68: using constraints = h-bonds instead, this will also improve performance. 68: 68: Number of degrees of freedom in T-Coupling group System is 23.00 68: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 68: 68: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_17_input.mdp]: 68: NVE simulation: will use the initial temperature of 456.887 K for 68: determining the Verlet buffer size 68: 68: 68: NOTE 5 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_17_input.mdp]: 68: There are 9 non-linear virtual site constructions. Their contribution to 68: the energy error is approximated. In most cases this does not affect the 68: error significantly. 68: 68: 68: NOTE 6 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_17_input.mdp]: 68: You are using a plain Coulomb cut-off, which might produce artifacts. 68: You might want to consider using PME electrostatics. 68: 68: 68: 68: There were 6 NOTEs 68: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_17_full.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 68: Can not increase nstlist because an NVE ensemble is used 68: Update groups can not be used for this system because an incompatible virtual site type is used 68: 68: Using 1 MPI thread 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'Alanine dipeptide in vacuo' 68: 16 steps, 0.0 ps. 68: Generated 2145 of the 2145 non-bonded parameter combinations 68: 68: Generated 2145 of the 2145 1-4 parameter combinations 68: 68: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' 68: 68: turning all bonds into constraints... 68: 68: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/alanine_vsite_vacuo.gro' 68: 68: Cleaning up constraints and constant bonded interactions with virtual sites 68: 68: Removed 18 Angles with virtual sites, 21 left 68: 68: Removed 10 Proper Dih.s with virtual sites, 44 left 68: 68: Converted 15 Constraints with virtual sites to connections, 7 left 68: 68: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 456.887 K 68: 68: Calculated rlist for 1x1 atom pair-list as 0.736 nm, buffer size 0.036 nm 68: 68: Set rlist, assuming 4x4 atom pair-list, to 0.731 nm, buffer size 0.031 nm 68: 68: Note that mdrun will redetermine rlist based on the actual pair-list setup 68: 68: This run will generate roughly 0 Mb of data 68: Generated 2145 of the 2145 non-bonded parameter combinations 68: 68: Generated 2145 of the 2145 1-4 parameter combinations 68: 68: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' 68: 68: turning all bonds into constraints... 68: 68: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/alanine_vsite_vacuo.gro' 68: 68: Cleaning up constraints and constant bonded interactions with virtual sites 68: 68: Removed 18 Angles with virtual sites, 21 left 68: 68: Removed 10 Proper Dih.s with virtual sites, 44 left 68: 68: Converted 15 Constraints with virtual sites to connections, 7 left 68: 68: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 456.887 K 68: 68: Calculated rlist for 1x1 atom pair-list as 0.736 nm, buffer size 0.036 nm 68: 68: Set rlist, assuming 4x4 atom pair-list, to 0.731 nm, buffer size 0.031 nm 68: 68: Note that mdrun will redetermine rlist based on the actual pair-list setup 68: 68: This run will generate roughly 0 Mb of data 68: 68: Writing final coordinates. 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.067 0.034 198.1 68: (ns/day) (hour/ns) 68: Performance: 43.342 0.554 68: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_17_firstpart.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 68: Can not increase nstlist because an NVE ensemble is used 68: Update groups can not be used for this system because an incompatible virtual site type is used 68: 68: Using 1 MPI thread 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'Alanine dipeptide in vacuo' 68: 8 steps, 0.0 ps. 68: 68: Writing final coordinates. 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.051 0.026 197.5 68: (ns/day) (hour/ns) 68: Performance: 30.170 0.796 68: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_17_full.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 68: Can not increase nstlist because an NVE ensemble is used 68: Update groups can not be used for this system because an incompatible virtual site type is used 68: 68: Using 1 MPI thread 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'Alanine dipeptide in vacuo' 68: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 68: 68: Writing final coordinates. 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.057 0.029 197.4 68: (ns/day) (hour/ns) 68: Performance: 26.992 0.889 68: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_17_full.edr as double precision energy file 68: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_17_firstpart.edr as double precision energy file 68: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_17_secondpart.part0002.edr as double precision energy file 68: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/17 (426 ms) 68: [ RUN ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/18 68: 68: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_18_input.mdp]: 68: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 68: that with the Verlet scheme, nstlist has no effect on the accuracy of 68: your simulation. 68: 68: 68: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_18_input.mdp]: 68: Setting nstcalcenergy (100) equal to nstenergy (4) 68: 68: Generating 1-4 interactions: fudge = 0.5 68: 68: NOTE 3 [file unknown]: 68: You are using constraints on all bonds, whereas the forcefield has been 68: parametrized only with constraints involving hydrogen atoms. We suggest 68: using constraints = h-bonds instead, this will also improve performance. 68: 68: Number of degrees of freedom in T-Coupling group System is 23.00 68: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 68: 68: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_18_input.mdp]: 68: NVE simulation: will use the initial temperature of 456.887 K for 68: determining the Verlet buffer size 68: 68: 68: NOTE 5 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_18_input.mdp]: 68: There are 9 non-linear virtual site constructions. Their contribution to 68: the energy error is approximated. In most cases this does not affect the 68: error significantly. 68: 68: 68: NOTE 6 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_18_input.mdp]: 68: You are using a plain Coulomb cut-off, which might produce artifacts. 68: You might want to consider using PME electrostatics. 68: 68: 68: 68: There were 6 NOTEs 68: 68: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_18_input.mdp]: 68: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 68: that with the Verlet scheme, nstlist has no effect on the accuracy of 68: your simulation. 68: 68: 68: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_18_input.mdp]: 68: Setting nstcalcenergy (100) equal to nstenergy (4) 68: 68: Generating 1-4 interactions: fudge = 0.5 68: 68: NOTE 3 [file unknown]: 68: You are using constraints on all bonds, whereas the forcefield has been 68: parametrized only with constraints involving hydrogen atoms. We suggest 68: using constraints = h-bonds instead, this will also improve performance. 68: 68: Number of degrees of freedom in T-Coupling group System is 23.00 68: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 68: 68: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_18_input.mdp]: 68: NVE simulation: will use the initial temperature of 456.887 K for 68: determining the Verlet buffer size 68: 68: 68: NOTE 5 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_18_input.mdp]: 68: There are 9 non-linear virtual site constructions. Their contribution to 68: the energy error is approximated. In most cases this does not affect the 68: error significantly. 68: 68: 68: NOTE 6 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_18_input.mdp]: 68: You are using a plain Coulomb cut-off, which might produce artifacts. 68: You might want to consider using PME electrostatics. 68: 68: 68: 68: There were 6 NOTEs 68: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_18_full.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 68: Can not increase nstlist because an NVE ensemble is used 68: Update groups can not be used for this system because an incompatible virtual site type is used 68: 68: Using 1 MPI thread 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'Alanine dipeptide in vacuo' 68: 16 steps, 0.0 ps. 68: Generated 2145 of the 2145 non-bonded parameter combinations 68: 68: Generated 2145 of the 2145 1-4 parameter combinations 68: 68: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' 68: 68: turning all bonds into constraints... 68: 68: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/alanine_vsite_vacuo.gro' 68: 68: Cleaning up constraints and constant bonded interactions with virtual sites 68: 68: Removed 18 Angles with virtual sites, 21 left 68: 68: Removed 10 Proper Dih.s with virtual sites, 44 left 68: 68: Converted 15 Constraints with virtual sites to connections, 7 left 68: 68: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 456.887 K 68: 68: Calculated rlist for 1x1 atom pair-list as 0.742 nm, buffer size 0.042 nm 68: 68: Set rlist, assuming 4x4 atom pair-list, to 0.737 nm, buffer size 0.037 nm 68: 68: Note that mdrun will redetermine rlist based on the actual pair-list setup 68: 68: This run will generate roughly 0 Mb of data 68: Generated 2145 of the 2145 non-bonded parameter combinations 68: 68: Generated 2145 of the 2145 1-4 parameter combinations 68: 68: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' 68: 68: turning all bonds into constraints... 68: 68: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/alanine_vsite_vacuo.gro' 68: 68: Cleaning up constraints and constant bonded interactions with virtual sites 68: 68: Removed 18 Angles with virtual sites, 21 left 68: 68: Removed 10 Proper Dih.s with virtual sites, 44 left 68: 68: Converted 15 Constraints with virtual sites to connections, 7 left 68: 68: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 456.887 K 68: 68: Calculated rlist for 1x1 atom pair-list as 0.742 nm, buffer size 0.042 nm 68: 68: Set rlist, assuming 4x4 atom pair-list, to 0.737 nm, buffer size 0.037 nm 68: 68: Note that mdrun will redetermine rlist based on the actual pair-list setup 68: 68: This run will generate roughly 0 Mb of data 68: 68: Writing final coordinates. 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.068 0.034 198.0 68: (ns/day) (hour/ns) 68: Performance: 42.931 0.559 68: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_18_firstpart.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 68: Can not increase nstlist because an NVE ensemble is used 68: Update groups can not be used for this system because an incompatible virtual site type is used 68: 68: Using 1 MPI thread 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'Alanine dipeptide in vacuo' 68: 8 steps, 0.0 ps. 68: 68: Writing final coordinates. 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.057 0.029 197.8 68: (ns/day) (hour/ns) 68: Performance: 27.195 0.883 68: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_18_full.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 68: Can not increase nstlist because an NVE ensemble is used 68: Update groups can not be used for this system because an incompatible virtual site type is used 68: 68: Using 1 MPI thread 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'Alanine dipeptide in vacuo' 68: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 68: 68: Writing final coordinates. 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.059 0.030 197.9 68: (ns/day) (hour/ns) 68: Performance: 26.145 0.918 68: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_18_full.edr as double precision energy file 68: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_18_firstpart.edr as double precision energy file 68: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_18_secondpart.part0002.edr as double precision energy file 68: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/18 (434 ms) 68: [ RUN ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/19 68: 68: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_19_input.mdp]: 68: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 68: that with the Verlet scheme, nstlist has no effect on the accuracy of 68: your simulation. 68: 68: 68: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_19_input.mdp]: 68: Setting nstcalcenergy (100) equal to nstenergy (4) 68: 68: Generating 1-4 interactions: fudge = 0.5 68: 68: NOTE 3 [file unknown]: 68: You are using constraints on all bonds, whereas the forcefield has been 68: parametrized only with constraints involving hydrogen atoms. We suggest 68: using constraints = h-bonds instead, this will also improve performance. 68: 68: Number of degrees of freedom in T-Coupling group System is 23.00 68: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 68: 68: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_19_input.mdp]: 68: NVE simulation: will use the initial temperature of 456.887 K for 68: determining the Verlet buffer size 68: 68: 68: NOTE 5 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_19_input.mdp]: 68: There are 9 non-linear virtual site constructions. Their contribution to 68: the energy error is approximated. In most cases this does not affect the 68: error significantly. 68: 68: 68: NOTE 6 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_19_input.mdp]: 68: You are using a plain Coulomb cut-off, which might produce artifacts. 68: You might want to consider using PME electrostatics. 68: 68: 68: 68: There were 6 NOTEs 68: 68: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_19_input.mdp]: 68: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 68: that with the Verlet scheme, nstlist has no effect on the accuracy of 68: your simulation. 68: 68: 68: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_19_input.mdp]: 68: Setting nstcalcenergy (100) equal to nstenergy (4) 68: 68: Generating 1-4 interactions: fudge = 0.5 68: 68: NOTE 3 [file unknown]: 68: You are using constraints on all bonds, whereas the forcefield has been 68: parametrized only with constraints involving hydrogen atoms. We suggest 68: using constraints = h-bonds instead, this will also improve performance. 68: 68: Number of degrees of freedom in T-Coupling group System is 23.00 68: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 68: 68: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_19_input.mdp]: 68: NVE simulation: will use the initial temperature of 456.887 K for 68: determining the Verlet buffer size 68: 68: 68: NOTE 5 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_19_input.mdp]: 68: There are 9 non-linear virtual site constructions. Their contribution to 68: the energy error is approximated. In most cases this does not affect the 68: error significantly. 68: 68: 68: NOTE 6 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_19_input.mdp]: 68: You are using a plain Coulomb cut-off, which might produce artifacts. 68: You might want to consider using PME electrostatics. 68: 68: 68: 68: There were 6 NOTEs 68: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_19_full.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 68: Can not increase nstlist because an NVE ensemble is used 68: Update groups can not be used for this system because an incompatible virtual site type is used 68: 68: Using 1 MPI thread 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'Alanine dipeptide in vacuo' 68: 16 steps, 0.0 ps. 68: Generated 2145 of the 2145 non-bonded parameter combinations 68: 68: Generated 2145 of the 2145 1-4 parameter combinations 68: 68: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' 68: 68: turning all bonds into constraints... 68: 68: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/alanine_vsite_vacuo.gro' 68: 68: Cleaning up constraints and constant bonded interactions with virtual sites 68: 68: Removed 18 Angles with virtual sites, 21 left 68: 68: Removed 10 Proper Dih.s with virtual sites, 44 left 68: 68: Converted 15 Constraints with virtual sites to connections, 7 left 68: 68: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 456.887 K 68: 68: Calculated rlist for 1x1 atom pair-list as 0.736 nm, buffer size 0.036 nm 68: 68: Set rlist, assuming 4x4 atom pair-list, to 0.731 nm, buffer size 0.031 nm 68: 68: Note that mdrun will redetermine rlist based on the actual pair-list setup 68: 68: This run will generate roughly 0 Mb of data 68: Generated 2145 of the 2145 non-bonded parameter combinations 68: 68: Generated 2145 of the 2145 1-4 parameter combinations 68: 68: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' 68: 68: turning all bonds into constraints... 68: 68: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/alanine_vsite_vacuo.gro' 68: 68: Cleaning up constraints and constant bonded interactions with virtual sites 68: 68: Removed 18 Angles with virtual sites, 21 left 68: 68: Removed 10 Proper Dih.s with virtual sites, 44 left 68: 68: Converted 15 Constraints with virtual sites to connections, 7 left 68: 68: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 456.887 K 68: 68: Calculated rlist for 1x1 atom pair-list as 0.736 nm, buffer size 0.036 nm 68: 68: Set rlist, assuming 4x4 atom pair-list, to 0.731 nm, buffer size 0.031 nm 68: 68: Note that mdrun will redetermine rlist based on the actual pair-list setup 68: 68: This run will generate roughly 0 Mb of data 68: 68: Writing final coordinates. 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.064 0.032 198.0 68: (ns/day) (hour/ns) 68: Performance: 45.219 0.531 68: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_19_firstpart.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 68: Can not increase nstlist because an NVE ensemble is used 68: Update groups can not be used for this system because an incompatible virtual site type is used 68: 68: Using 1 MPI thread 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'Alanine dipeptide in vacuo' 68: 8 steps, 0.0 ps. 68: 68: Writing final coordinates. 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.056 0.028 197.7 68: (ns/day) (hour/ns) 68: Performance: 27.527 0.872 68: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_19_full.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 68: Can not increase nstlist because an NVE ensemble is used 68: Update groups can not be used for this system because an incompatible virtual site type is used 68: 68: Using 1 MPI thread 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'Alanine dipeptide in vacuo' 68: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 68: 68: Writing final coordinates. 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.057 0.029 197.7 68: (ns/day) (hour/ns) 68: Performance: 26.915 0.892 68: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_19_full.edr as double precision energy file 68: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_19_firstpart.edr as double precision energy file 68: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_19_secondpart.part0002.edr as double precision energy file 68: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/19 (435 ms) 68: [ RUN ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/20 68: 68: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_20_input.mdp]: 68: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 68: that with the Verlet scheme, nstlist has no effect on the accuracy of 68: your simulation. 68: 68: 68: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_20_input.mdp]: 68: Setting nstcalcenergy (100) equal to nstenergy (4) 68: 68: Generating 1-4 interactions: fudge = 0.5 68: 68: NOTE 3 [file unknown]: 68: You are using constraints on all bonds, whereas the forcefield has been 68: parametrized only with constraints involving hydrogen atoms. We suggest 68: using constraints = h-bonds instead, this will also improve performance. 68: 68: Number of degrees of freedom in T-Coupling group System is 23.00 68: 68: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_20_input.mdp]: 68: There are 9 non-linear virtual site constructions. Their contribution to 68: the energy error is approximated. In most cases this does not affect the 68: error significantly. 68: 68: 68: NOTE 5 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_20_input.mdp]: 68: You are using a plain Coulomb cut-off, which might produce artifacts. 68: You might want to consider using PME electrostatics. 68: 68: 68: 68: There were 5 NOTEs 68: 68: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_20_input.mdp]: 68: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 68: that with the Verlet scheme, nstlist has no effect on the accuracy of 68: your simulation. 68: 68: 68: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_20_input.mdp]: 68: Setting nstcalcenergy (100) equal to nstenergy (4) 68: 68: Generating 1-4 interactions: fudge = 0.5 68: 68: NOTE 3 [file unknown]: 68: You are using constraints on all bonds, whereas the forcefield has been 68: parametrized only with constraints involving hydrogen atoms. We suggest 68: using constraints = h-bonds instead, this will also improve performance. 68: 68: Number of degrees of freedom in T-Coupling group System is 23.00 68: 68: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_20_input.mdp]: 68: There are 9 non-linear virtual site constructions. Their contribution to 68: the energy error is approximated. In most cases this does not affect the 68: error significantly. 68: 68: 68: NOTE 5 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_20_input.mdp]: 68: You are using a plain Coulomb cut-off, which might produce artifacts. 68: You might want to consider using PME electrostatics. 68: 68: 68: 68: There were 5 NOTEs 68: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_20_full.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 68: Update groups can not be used for this system because an incompatible virtual site type is used 68: 68: Using 1 MPI thread 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'Alanine dipeptide in vacuo' 68: 16 steps, 0.0 ps. 68: Generated 2145 of the 2145 non-bonded parameter combinations 68: 68: Generated 2145 of the 2145 1-4 parameter combinations 68: 68: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' 68: 68: turning all bonds into constraints... 68: 68: Cleaning up constraints and constant bonded interactions with virtual sites 68: 68: Removed 18 Angles with virtual sites, 21 left 68: 68: Removed 10 Proper Dih.s with virtual sites, 44 left 68: 68: Converted 15 Constraints with virtual sites to connections, 7 left 68: 68: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 68: 68: Calculated rlist for 1x1 atom pair-list as 0.754 nm, buffer size 0.054 nm 68: 68: Set rlist, assuming 4x4 atom pair-list, to 0.748 nm, buffer size 0.048 nm 68: 68: Note that mdrun will redetermine rlist based on the actual pair-list setup 68: 68: This run will generate roughly 0 Mb of data 68: Generated 2145 of the 2145 non-bonded parameter combinations 68: 68: Generated 2145 of the 2145 1-4 parameter combinations 68: 68: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' 68: 68: turning all bonds into constraints... 68: 68: Cleaning up constraints and constant bonded interactions with virtual sites 68: 68: Removed 18 Angles with virtual sites, 21 left 68: 68: Removed 10 Proper Dih.s with virtual sites, 44 left 68: 68: Converted 15 Constraints with virtual sites to connections, 7 left 68: 68: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 68: 68: Calculated rlist for 1x1 atom pair-list as 0.754 nm, buffer size 0.054 nm 68: 68: Set rlist, assuming 4x4 atom pair-list, to 0.748 nm, buffer size 0.048 nm 68: 68: Note that mdrun will redetermine rlist based on the actual pair-list setup 68: 68: This run will generate roughly 0 Mb of data 68: 68: Writing final coordinates. 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.079 0.040 198.4 68: (ns/day) (hour/ns) 68: Performance: 36.713 0.654 68: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_20_firstpart.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 68: Update groups can not be used for this system because an incompatible virtual site type is used 68: 68: Using 1 MPI thread 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'Alanine dipeptide in vacuo' 68: 8 steps, 0.0 ps. 68: 68: Writing final coordinates. 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.055 0.028 197.9 68: (ns/day) (hour/ns) 68: Performance: 28.136 0.853 68: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_20_full.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 68: Update groups can not be used for this system because an incompatible virtual site type is used 68: 68: Using 1 MPI thread 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'Alanine dipeptide in vacuo' 68: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 68: 68: Writing final coordinates. 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.055 0.028 197.8 68: (ns/day) (hour/ns) 68: Performance: 27.821 0.863 68: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_20_full.edr as double precision energy file 68: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_20_firstpart.edr as double precision energy file 68: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_20_secondpart.part0002.edr as double precision energy file 68: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/20 (811 ms) 68: [ RUN ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/21 68: 68: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_21_input.mdp]: 68: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 68: that with the Verlet scheme, nstlist has no effect on the accuracy of 68: your simulation. 68: 68: 68: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_21_input.mdp]: 68: Setting nstcalcenergy (100) equal to nstenergy (4) 68: 68: Generating 1-4 interactions: fudge = 0.5 68: 68: NOTE 3 [file unknown]: 68: You are using constraints on all bonds, whereas the forcefield has been 68: parametrized only with constraints involving hydrogen atoms. We suggest 68: using constraints = h-bonds instead, this will also improve performance. 68: 68: Number of degrees of freedom in T-Coupling group System is 23.00 68: 68: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_21_input.mdp]: 68: There are 9 non-linear virtual site constructions. Their contribution to 68: the energy error is approximated. In most cases this does not affect the 68: error significantly. 68: 68: 68: NOTE 5 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_21_input.mdp]: 68: You are using a plain Coulomb cut-off, which might produce artifacts. 68: You might want to consider using PME electrostatics. 68: 68: 68: 68: There were 5 NOTEs 68: 68: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_21_input.mdp]: 68: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 68: that with the Verlet scheme, nstlist has no effect on the accuracy of 68: your simulation. 68: 68: 68: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_21_input.mdp]: 68: Setting nstcalcenergy (100) equal to nstenergy (4) 68: 68: Generating 1-4 interactions: fudge = 0.5 68: 68: NOTE 3 [file unknown]: 68: You are using constraints on all bonds, whereas the forcefield has been 68: parametrized only with constraints involving hydrogen atoms. We suggest 68: using constraints = h-bonds instead, this will also improve performance. 68: 68: Number of degrees of freedom in T-Coupling group System is 23.00 68: 68: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_21_input.mdp]: 68: There are 9 non-linear virtual site constructions. Their contribution to 68: the energy error is approximated. In most cases this does not affect the 68: error significantly. 68: 68: 68: NOTE 5 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_21_input.mdp]: 68: You are using a plain Coulomb cut-off, which might produce artifacts. 68: You might want to consider using PME electrostatics. 68: 68: 68: 68: There were 5 NOTEs 68: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_21_full.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 68: Changing nstlist from 8 to 80, rlist from 0.741 to 0.841 68: 68: Update groups can not be used for this system because an incompatible virtual site type is used 68: 68: Using 1 MPI thread 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'Alanine dipeptide in vacuo' 68: 16 steps, 0.0 ps. 68: Generated 2145 of the 2145 non-bonded parameter combinations 68: 68: Generated 2145 of the 2145 1-4 parameter combinations 68: 68: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' 68: 68: turning all bonds into constraints... 68: 68: Cleaning up constraints and constant bonded interactions with virtual sites 68: 68: Removed 18 Angles with virtual sites, 21 left 68: 68: Removed 10 Proper Dih.s with virtual sites, 44 left 68: 68: Converted 15 Constraints with virtual sites to connections, 7 left 68: 68: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 298 K 68: 68: Calculated rlist for 1x1 atom pair-list as 0.747 nm, buffer size 0.047 nm 68: 68: Set rlist, assuming 4x4 atom pair-list, to 0.741 nm, buffer size 0.041 nm 68: 68: Note that mdrun will redetermine rlist based on the actual pair-list setup 68: 68: This run will generate roughly 0 Mb of data 68: Generated 2145 of the 2145 non-bonded parameter combinations 68: 68: Generated 2145 of the 2145 1-4 parameter combinations 68: 68: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' 68: 68: turning all bonds into constraints... 68: 68: Cleaning up constraints and constant bonded interactions with virtual sites 68: 68: Removed 18 Angles with virtual sites, 21 left 68: 68: Removed 10 Proper Dih.s with virtual sites, 44 left 68: 68: Converted 15 Constraints with virtual sites to connections, 7 left 68: 68: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 298 K 68: 68: Calculated rlist for 1x1 atom pair-list as 0.747 nm, buffer size 0.047 nm 68: 68: Set rlist, assuming 4x4 atom pair-list, to 0.741 nm, buffer size 0.041 nm 68: 68: Note that mdrun will redetermine rlist based on the actual pair-list setup 68: 68: This run will generate roughly 0 Mb of data 68: 68: Writing final coordinates. 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.063 0.032 198.1 68: (ns/day) (hour/ns) 68: Performance: 45.846 0.523 68: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_21_firstpart.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 68: Changing nstlist from 8 to 80, rlist from 0.741 to 0.841 68: 68: Update groups can not be used for this system because an incompatible virtual site type is used 68: 68: Using 1 MPI thread 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'Alanine dipeptide in vacuo' 68: 8 steps, 0.0 ps. 68: 68: Writing final coordinates. 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.057 0.029 197.9 68: (ns/day) (hour/ns) 68: Performance: 27.012 0.888 68: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_21_full.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 68: Changing nstlist from 8 to 80, rlist from 0.741 to 0.841 68: 68: Update groups can not be used for this system because an incompatible virtual site type is used 68: 68: Using 1 MPI thread 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'Alanine dipeptide in vacuo' 68: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 68: 68: Writing final coordinates. 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.050 0.025 197.8 68: (ns/day) (hour/ns) 68: Performance: 30.813 0.779 68: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_21_full.edr as double precision energy file 68: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_21_firstpart.edr as double precision energy file 68: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_21_secondpart.part0002.edr as double precision energy file 68: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/21 (2021 ms) 68: [ RUN ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/22 68: 68: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_22_input.mdp]: 68: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 68: that with the Verlet scheme, nstlist has no effect on the accuracy of 68: your simulation. 68: 68: 68: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_22_input.mdp]: 68: Setting nstcalcenergy (100) equal to nstenergy (4) 68: 68: Generating 1-4 interactions: fudge = 0.5 68: 68: NOTE 3 [file unknown]: 68: You are using constraints on all bonds, whereas the forcefield has been 68: parametrized only with constraints involving hydrogen atoms. We suggest 68: using constraints = h-bonds instead, this will also improve performance. 68: 68: Number of degrees of freedom in T-Coupling group System is 23.00 68: 68: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_22_input.mdp]: 68: There are 9 non-linear virtual site constructions. Their contribution to 68: the energy error is approximated. In most cases this does not affect the 68: error significantly. 68: 68: 68: NOTE 5 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_22_input.mdp]: 68: You are using a plain Coulomb cut-off, which might produce artifacts. 68: You might want to consider using PME electrostatics. 68: 68: 68: 68: There were 5 NOTEs 68: 68: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_22_input.mdp]: 68: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 68: that with the Verlet scheme, nstlist has no effect on the accuracy of 68: your simulation. 68: 68: 68: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_22_input.mdp]: 68: Setting nstcalcenergy (100) equal to nstenergy (4) 68: 68: Generating 1-4 interactions: fudge = 0.5 68: 68: NOTE 3 [file unknown]: 68: You are using constraints on all bonds, whereas the forcefield has been 68: parametrized only with constraints involving hydrogen atoms. We suggest 68: using constraints = h-bonds instead, this will also improve performance. 68: 68: Number of degrees of freedom in T-Coupling group System is 23.00 68: 68: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_22_input.mdp]: 68: There are 9 non-linear virtual site constructions. Their contribution to 68: the energy error is approximated. In most cases this does not affect the 68: error significantly. 68: 68: 68: NOTE 5 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_22_input.mdp]: 68: You are using a plain Coulomb cut-off, which might produce artifacts. 68: You might want to consider using PME electrostatics. 68: 68: 68: 68: There were 5 NOTEs 68: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_22_full.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 68: Update groups can not be used for this system because an incompatible virtual site type is used 68: 68: Using 1 MPI thread 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'Alanine dipeptide in vacuo' 68: 16 steps, 0.0 ps. 68: Generated 2145 of the 2145 non-bonded parameter combinations 68: 68: Generated 2145 of the 2145 1-4 parameter combinations 68: 68: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' 68: 68: turning all bonds into constraints... 68: 68: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/alanine_vsite_vacuo.gro' 68: 68: Cleaning up constraints and constant bonded interactions with virtual sites 68: 68: Removed 18 Angles with virtual sites, 21 left 68: 68: Removed 10 Proper Dih.s with virtual sites, 44 left 68: 68: Converted 15 Constraints with virtual sites to connections, 7 left 68: 68: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 68: 68: Calculated rlist for 1x1 atom pair-list as 0.733 nm, buffer size 0.033 nm 68: 68: Set rlist, assuming 4x4 atom pair-list, to 0.729 nm, buffer size 0.029 nm 68: 68: Note that mdrun will redetermine rlist based on the actual pair-list setup 68: 68: This run will generate roughly 0 Mb of data 68: Generated 2145 of the 2145 non-bonded parameter combinations 68: 68: Generated 2145 of the 2145 1-4 parameter combinations 68: 68: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' 68: 68: turning all bonds into constraints... 68: 68: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/alanine_vsite_vacuo.gro' 68: 68: Cleaning up constraints and constant bonded interactions with virtual sites 68: 68: Removed 18 Angles with virtual sites, 21 left 68: 68: Removed 10 Proper Dih.s with virtual sites, 44 left 68: 68: Converted 15 Constraints with virtual sites to connections, 7 left 68: 68: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 68: 68: Calculated rlist for 1x1 atom pair-list as 0.733 nm, buffer size 0.033 nm 68: 68: Set rlist, assuming 4x4 atom pair-list, to 0.729 nm, buffer size 0.029 nm 68: 68: Note that mdrun will redetermine rlist based on the actual pair-list setup 68: 68: This run will generate roughly 0 Mb of data 68: 68: Writing final coordinates. 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.139 0.070 199.0 68: (ns/day) (hour/ns) 68: Performance: 21.039 1.141 68: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_22_firstpart.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 68: Update groups can not be used for this system because an incompatible virtual site type is used 68: 68: Using 1 MPI thread 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'Alanine dipeptide in vacuo' 68: 8 steps, 0.0 ps. 68: 68: Writing final coordinates. 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.064 0.032 198.2 68: (ns/day) (hour/ns) 68: Performance: 23.971 1.001 68: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_22_full.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 68: Update groups can not be used for this system because an incompatible virtual site type is used 68: 68: Using 1 MPI thread 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'Alanine dipeptide in vacuo' 68: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 68: 68: Writing final coordinates. 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.056 0.028 198.0 68: (ns/day) (hour/ns) 68: Performance: 27.365 0.877 68: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_22_full.edr as double precision energy file 68: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_22_firstpart.edr as double precision energy file 68: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_22_secondpart.part0002.edr as double precision energy file 68: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/22 (761 ms) 68: [ RUN ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/23 68: 68: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_23_input.mdp]: 68: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 68: that with the Verlet scheme, nstlist has no effect on the accuracy of 68: your simulation. 68: 68: 68: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_23_input.mdp]: 68: Setting nstcalcenergy (100) equal to nstenergy (4) 68: 68: Generating 1-4 interactions: fudge = 0.5 68: 68: NOTE 3 [file unknown]: 68: You are using constraints on all bonds, whereas the forcefield has been 68: parametrized only with constraints involving hydrogen atoms. We suggest 68: using constraints = h-bonds instead, this will also improve performance. 68: 68: Number of degrees of freedom in T-Coupling group System is 23.00 68: 68: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_23_input.mdp]: 68: There are 9 non-linear virtual site constructions. Their contribution to 68: the energy error is approximated. In most cases this does not affect the 68: error significantly. 68: 68: 68: NOTE 5 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_23_input.mdp]: 68: You are using a plain Coulomb cut-off, which might produce artifacts. 68: You might want to consider using PME electrostatics. 68: 68: 68: 68: There were 5 NOTEs 68: 68: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_23_input.mdp]: 68: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 68: that with the Verlet scheme, nstlist has no effect on the accuracy of 68: your simulation. 68: 68: 68: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_23_input.mdp]: 68: Setting nstcalcenergy (100) equal to nstenergy (4) 68: 68: Generating 1-4 interactions: fudge = 0.5 68: 68: NOTE 3 [file unknown]: 68: You are using constraints on all bonds, whereas the forcefield has been 68: parametrized only with constraints involving hydrogen atoms. We suggest 68: using constraints = h-bonds instead, this will also improve performance. 68: 68: Number of degrees of freedom in T-Coupling group System is 23.00 68: 68: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_23_input.mdp]: 68: There are 9 non-linear virtual site constructions. Their contribution to 68: the energy error is approximated. In most cases this does not affect the 68: error significantly. 68: 68: 68: NOTE 5 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_23_input.mdp]: 68: You are using a plain Coulomb cut-off, which might produce artifacts. 68: You might want to consider using PME electrostatics. 68: 68: 68: 68: There were 5 NOTEs 68: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_23_full.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 68: Changing nstlist from 8 to 25, rlist from 0.724 to 0.793 68: 68: Update groups can not be used for this system because an incompatible virtual site type is used 68: 68: Using 1 MPI thread 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'Alanine dipeptide in vacuo' 68: 16 steps, 0.0 ps. 68: Generated 2145 of the 2145 non-bonded parameter combinations 68: 68: Generated 2145 of the 2145 1-4 parameter combinations 68: 68: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' 68: 68: turning all bonds into constraints... 68: 68: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/alanine_vsite_vacuo.gro' 68: 68: Cleaning up constraints and constant bonded interactions with virtual sites 68: 68: Removed 18 Angles with virtual sites, 21 left 68: 68: Removed 10 Proper Dih.s with virtual sites, 44 left 68: 68: Converted 15 Constraints with virtual sites to connections, 7 left 68: 68: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 298 K 68: 68: Calculated rlist for 1x1 atom pair-list as 0.728 nm, buffer size 0.028 nm 68: 68: Set rlist, assuming 4x4 atom pair-list, to 0.724 nm, buffer size 0.024 nm 68: 68: Note that mdrun will redetermine rlist based on the actual pair-list setup 68: 68: This run will generate roughly 0 Mb of data 68: Generated 2145 of the 2145 non-bonded parameter combinations 68: 68: Generated 2145 of the 2145 1-4 parameter combinations 68: 68: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' 68: 68: turning all bonds into constraints... 68: 68: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/alanine_vsite_vacuo.gro' 68: 68: Cleaning up constraints and constant bonded interactions with virtual sites 68: 68: Removed 18 Angles with virtual sites, 21 left 68: 68: Removed 10 Proper Dih.s with virtual sites, 44 left 68: 68: Converted 15 Constraints with virtual sites to connections, 7 left 68: 68: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 298 K 68: 68: Calculated rlist for 1x1 atom pair-list as 0.728 nm, buffer size 0.028 nm 68: 68: Set rlist, assuming 4x4 atom pair-list, to 0.724 nm, buffer size 0.024 nm 68: 68: Note that mdrun will redetermine rlist based on the actual pair-list setup 68: 68: This run will generate roughly 0 Mb of data 68: 68: Writing final coordinates. 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.069 0.035 198.3 68: (ns/day) (hour/ns) 68: Performance: 42.089 0.570 68: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_23_firstpart.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 68: Changing nstlist from 8 to 25, rlist from 0.724 to 0.793 68: 68: Update groups can not be used for this system because an incompatible virtual site type is used 68: 68: Using 1 MPI thread 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'Alanine dipeptide in vacuo' 68: 8 steps, 0.0 ps. 68: 68: Writing final coordinates. 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.049 0.025 197.8 68: (ns/day) (hour/ns) 68: Performance: 31.570 0.760 68: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_23_full.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 68: Changing nstlist from 8 to 25, rlist from 0.724 to 0.793 68: 68: Update groups can not be used for this system because an incompatible virtual site type is used 68: 68: Using 1 MPI thread 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'Alanine dipeptide in vacuo' 68: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 68: 68: Writing final coordinates. 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.051 0.026 197.6 68: (ns/day) (hour/ns) 68: Performance: 30.303 0.792 68: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_23_full.edr as double precision energy file 68: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_23_firstpart.edr as double precision energy file 68: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_23_secondpart.part0002.edr as double precision energy file 68: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/23 (1012 ms) 68: [----------] 24 tests from NormalIntegrators/MdrunNoAppendContinuationIsExact (10000 ms total) 68: 68: [----------] 8 tests from NormalIntegratorsWithFEP/MdrunNoAppendContinuationIsExact 68: [ RUN ] NormalIntegratorsWithFEP/MdrunNoAppendContinuationIsExact.WithinTolerances/0 68: 68: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 68: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 68: that with the Verlet scheme, nstlist has no effect on the accuracy of 68: your simulation. 68: 68: 68: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 68: Setting nstcalcenergy (100) equal to nstenergy (4) 68: 68: Generating 1-4 interactions: fudge = 0.5 68: Number of degrees of freedom in T-Coupling group System is 79.00 68: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 68: 68: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 68: NVE simulation: will use the initial temperature of 294.908 K for 68: determining the Verlet buffer size 68: 68: 68: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 68: You are using a plain Coulomb cut-off, which might produce artifacts. 68: You might want to consider using PME electrostatics. 68: 68: 68: 68: There were 4 NOTEs 68: 68: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 68: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 68: that with the Verlet scheme, nstlist has no effect on the accuracy of 68: your simulation. 68: 68: 68: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 68: Setting nstcalcenergy (100) equal to nstenergy (4) 68: 68: Generating 1-4 interactions: fudge = 0.5 68: Number of degrees of freedom in T-Coupling group System is 79.00 68: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 68: 68: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 68: NVE simulation: will use the initial temperature of 294.908 K for 68: determining the Verlet buffer size 68: 68: 68: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 68: You are using a plain Coulomb cut-off, which might produce artifacts. 68: You might want to consider using PME electrostatics. 68: 68: 68: 68: There were 4 NOTEs 68: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 68: Can not increase nstlist because an NVE ensemble is used 68: Using 1 MPI thread 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun '30 atom system in water' 68: 16 steps, 0.0 ps. 68: Generated 2485 of the 2485 non-bonded parameter combinations 68: 68: Generated 2485 of the 2485 1-4 parameter combinations 68: 68: Excluding 3 bonded neighbours molecule type 'nonanol' 68: 68: turning H bonds into constraints... 68: 68: Excluding 2 bonded neighbours molecule type 'SOL' 68: 68: turning H bonds into constraints... 68: 68: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/nonanol_vacuo.gro' 68: 68: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 294.908 K 68: 68: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 68: 68: Set rlist, assuming 4x4 atom pair-list, to 0.757 nm, buffer size 0.057 nm 68: 68: Note that mdrun will redetermine rlist based on the actual pair-list setup 68: 68: This run will generate roughly 0 Mb of data 68: Generated 2485 of the 2485 non-bonded parameter combinations 68: 68: Generated 2485 of the 2485 1-4 parameter combinations 68: 68: Excluding 3 bonded neighbours molecule type 'nonanol' 68: 68: turning H bonds into constraints... 68: 68: Excluding 2 bonded neighbours molecule type 'SOL' 68: 68: turning H bonds into constraints... 68: 68: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/nonanol_vacuo.gro' 68: 68: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 294.908 K 68: 68: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 68: 68: Set rlist, assuming 4x4 atom pair-list, to 0.757 nm, buffer size 0.057 nm 68: 68: Note that mdrun will redetermine rlist based on the actual pair-list setup 68: 68: This run will generate roughly 0 Mb of data 68: 68: Writing final coordinates. 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.065 0.033 197.5 68: (ns/day) (hour/ns) 68: Performance: 44.680 0.537 68: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_0_firstpart.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 68: Can not increase nstlist because an NVE ensemble is used 68: Using 1 MPI thread 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun '30 atom system in water' 68: 8 steps, 0.0 ps. 68: 68: Writing final coordinates. 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.054 0.028 194.8 68: (ns/day) (hour/ns) 68: Performance: 28.012 0.857 68: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 68: Can not increase nstlist because an NVE ensemble is used 68: Using 1 MPI thread 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun '30 atom system in water' 68: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 68: 68: Writing final coordinates. 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.054 0.027 196.5 68: (ns/day) (hour/ns) 68: Performance: 28.556 0.840 68: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.edr as double precision energy file 68: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_0_firstpart.edr as double precision energy file 68: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_0_secondpart.part0002.edr as double precision energy file 68: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NormalIntegratorsWithFEP/MdrunNoAppendContinuationIsExact.WithinTolerances/0 (436 ms) 68: [ RUN ] NormalIntegratorsWithFEP/MdrunNoAppendContinuationIsExact.WithinTolerances/1 68: 68: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 68: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 68: that with the Verlet scheme, nstlist has no effect on the accuracy of 68: your simulation. 68: 68: 68: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 68: Setting nstcalcenergy (100) equal to nstenergy (4) 68: 68: Generating 1-4 interactions: fudge = 0.5 68: Number of degrees of freedom in T-Coupling group System is 79.00 68: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 68: 68: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 68: NVE simulation: will use the initial temperature of 294.908 K for 68: determining the Verlet buffer size 68: 68: 68: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 68: You are using a plain Coulomb cut-off, which might produce artifacts. 68: You might want to consider using PME electrostatics. 68: 68: 68: 68: There were 4 NOTEs 68: 68: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 68: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 68: that with the Verlet scheme, nstlist has no effect on the accuracy of 68: your simulation. 68: 68: 68: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 68: Setting nstcalcenergy (100) equal to nstenergy (4) 68: 68: Generating 1-4 interactions: fudge = 0.5 68: Number of degrees of freedom in T-Coupling group System is 79.00 68: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 68: 68: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 68: NVE simulation: will use the initial temperature of 294.908 K for 68: determining the Verlet buffer size 68: 68: 68: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 68: You are using a plain Coulomb cut-off, which might produce artifacts. 68: You might want to consider using PME electrostatics. 68: 68: 68: 68: There were 4 NOTEs 68: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_1_full.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 68: Can not increase nstlist because an NVE ensemble is used 68: Using 1 MPI thread 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun '30 atom system in water' 68: 16 steps, 0.0 ps. 68: Generated 2485 of the 2485 non-bonded parameter combinations 68: 68: Generated 2485 of the 2485 1-4 parameter combinations 68: 68: Excluding 3 bonded neighbours molecule type 'nonanol' 68: 68: turning H bonds into constraints... 68: 68: Excluding 2 bonded neighbours molecule type 'SOL' 68: 68: turning H bonds into constraints... 68: 68: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/nonanol_vacuo.gro' 68: 68: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 294.908 K 68: 68: Calculated rlist for 1x1 atom pair-list as 0.756 nm, buffer size 0.056 nm 68: 68: Set rlist, assuming 4x4 atom pair-list, to 0.749 nm, buffer size 0.049 nm 68: 68: Note that mdrun will redetermine rlist based on the actual pair-list setup 68: 68: This run will generate roughly 0 Mb of data 68: Generated 2485 of the 2485 non-bonded parameter combinations 68: 68: Generated 2485 of the 2485 1-4 parameter combinations 68: 68: Excluding 3 bonded neighbours molecule type 'nonanol' 68: 68: turning H bonds into constraints... 68: 68: Excluding 2 bonded neighbours molecule type 'SOL' 68: 68: turning H bonds into constraints... 68: 68: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/nonanol_vacuo.gro' 68: 68: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 294.908 K 68: 68: Calculated rlist for 1x1 atom pair-list as 0.756 nm, buffer size 0.056 nm 68: 68: Set rlist, assuming 4x4 atom pair-list, to 0.749 nm, buffer size 0.049 nm 68: 68: Note that mdrun will redetermine rlist based on the actual pair-list setup 68: 68: This run will generate roughly 0 Mb of data 68: 68: Writing final coordinates. 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.063 0.032 197.4 68: (ns/day) (hour/ns) 68: Performance: 46.142 0.520 68: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_1_firstpart.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 68: Can not increase nstlist because an NVE ensemble is used 68: Using 1 MPI thread 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun '30 atom system in water' 68: 8 steps, 0.0 ps. 68: 68: Writing final coordinates. 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.050 0.025 194.9 68: (ns/day) (hour/ns) 68: Performance: 30.599 0.784 68: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_1_full.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 68: Can not increase nstlist because an NVE ensemble is used 68: Using 1 MPI thread 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun '30 atom system in water' 68: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 68: 68: Writing final coordinates. 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.052 0.026 196.8 68: (ns/day) (hour/ns) 68: Performance: 29.463 0.815 68: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_1_full.edr as double precision energy file 68: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_1_firstpart.edr as double precision energy file 68: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_1_secondpart.part0002.edr as double precision energy file 68: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NormalIntegratorsWithFEP/MdrunNoAppendContinuationIsExact.WithinTolerances/1 (413 ms) 68: [ RUN ] NormalIntegratorsWithFEP/MdrunNoAppendContinuationIsExact.WithinTolerances/2 68: 68: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]: 68: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 68: that with the Verlet scheme, nstlist has no effect on the accuracy of 68: your simulation. 68: 68: 68: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]: 68: Setting nstcalcenergy (100) equal to nstenergy (4) 68: 68: Generating 1-4 interactions: fudge = 0.5 68: Number of degrees of freedom in T-Coupling group System is 79.00 68: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 68: 68: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]: 68: NVE simulation: will use the initial temperature of 294.908 K for 68: determining the Verlet buffer size 68: 68: 68: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]: 68: You are using a plain Coulomb cut-off, which might produce artifacts. 68: You might want to consider using PME electrostatics. 68: 68: 68: 68: There were 4 NOTEs 68: 68: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]: 68: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 68: that with the Verlet scheme, nstlist has no effect on the accuracy of 68: your simulation. 68: 68: 68: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]: 68: Setting nstcalcenergy (100) equal to nstenergy (4) 68: 68: Generating 1-4 interactions: fudge = 0.5 68: Number of degrees of freedom in T-Coupling group System is 79.00 68: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 68: 68: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]: 68: NVE simulation: will use the initial temperature of 294.908 K for 68: determining the Verlet buffer size 68: 68: 68: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]: 68: You are using a plain Coulomb cut-off, which might produce artifacts. 68: You might want to consider using PME electrostatics. 68: 68: 68: 68: There were 4 NOTEs 68: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_2_full.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 68: Can not increase nstlist because an NVE ensemble is used 68: Using 1 MPI thread 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun '30 atom system in water' 68: 16 steps, 0.0 ps. 68: Generated 2485 of the 2485 non-bonded parameter combinations 68: 68: Generated 2485 of the 2485 1-4 parameter combinations 68: 68: Excluding 3 bonded neighbours molecule type 'nonanol' 68: 68: turning H bonds into constraints... 68: 68: Excluding 2 bonded neighbours molecule type 'SOL' 68: 68: turning H bonds into constraints... 68: 68: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/nonanol_vacuo.gro' 68: 68: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 294.908 K 68: 68: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 68: 68: Set rlist, assuming 4x4 atom pair-list, to 0.757 nm, buffer size 0.057 nm 68: 68: Note that mdrun will redetermine rlist based on the actual pair-list setup 68: 68: This run will generate roughly 0 Mb of data 68: Generated 2485 of the 2485 non-bonded parameter combinations 68: 68: Generated 2485 of the 2485 1-4 parameter combinations 68: 68: Excluding 3 bonded neighbours molecule type 'nonanol' 68: 68: turning H bonds into constraints... 68: 68: Excluding 2 bonded neighbours molecule type 'SOL' 68: 68: turning H bonds into constraints... 68: 68: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/nonanol_vacuo.gro' 68: 68: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 294.908 K 68: 68: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 68: 68: Set rlist, assuming 4x4 atom pair-list, to 0.757 nm, buffer size 0.057 nm 68: 68: Note that mdrun will redetermine rlist based on the actual pair-list setup 68: 68: This run will generate roughly 0 Mb of data 68: 68: Writing final coordinates. 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.078 0.039 199.0 68: (ns/day) (hour/ns) 68: Performance: 37.719 0.636 68: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_2_firstpart.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 68: Can not increase nstlist because an NVE ensemble is used 68: Using 1 MPI thread 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun '30 atom system in water' 68: 8 steps, 0.0 ps. 68: 68: Writing final coordinates. 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.064 0.032 198.7 68: (ns/day) (hour/ns) 68: Performance: 24.273 0.989 68: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_2_full.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 68: Can not increase nstlist because an NVE ensemble is used 68: Using 1 MPI thread 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun '30 atom system in water' 68: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 68: 68: Writing final coordinates. 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.067 0.034 197.1 68: (ns/day) (hour/ns) 68: Performance: 23.023 1.042 68: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_2_full.edr as double precision energy file 68: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_2_firstpart.edr as double precision energy file 68: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_2_secondpart.part0002.edr as double precision energy file 68: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NormalIntegratorsWithFEP/MdrunNoAppendContinuationIsExact.WithinTolerances/2 (431 ms) 68: [ RUN ] NormalIntegratorsWithFEP/MdrunNoAppendContinuationIsExact.WithinTolerances/3 68: 68: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]: 68: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 68: that with the Verlet scheme, nstlist has no effect on the accuracy of 68: your simulation. 68: 68: 68: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]: 68: Setting nstcalcenergy (100) equal to nstenergy (4) 68: 68: Generating 1-4 interactions: fudge = 0.5 68: Number of degrees of freedom in T-Coupling group System is 79.00 68: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 68: 68: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]: 68: NVE simulation: will use the initial temperature of 294.908 K for 68: determining the Verlet buffer size 68: 68: 68: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]: 68: You are using a plain Coulomb cut-off, which might produce artifacts. 68: You might want to consider using PME electrostatics. 68: 68: 68: 68: There were 4 NOTEs 68: 68: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]: 68: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 68: that with the Verlet scheme, nstlist has no effect on the accuracy of 68: your simulation. 68: 68: 68: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]: 68: Setting nstcalcenergy (100) equal to nstenergy (4) 68: 68: Generating 1-4 interactions: fudge = 0.5 68: Number of degrees of freedom in T-Coupling group System is 79.00 68: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 68: 68: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]: 68: NVE simulation: will use the initial temperature of 294.908 K for 68: determining the Verlet buffer size 68: 68: 68: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]: 68: You are using a plain Coulomb cut-off, which might produce artifacts. 68: You might want to consider using PME electrostatics. 68: 68: 68: 68: There were 4 NOTEs 68: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_3_full.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 68: Can not increase nstlist because an NVE ensemble is used 68: Using 1 MPI thread 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun '30 atom system in water' 68: 16 steps, 0.0 ps. 68: Generated 2485 of the 2485 non-bonded parameter combinations 68: 68: Generated 2485 of the 2485 1-4 parameter combinations 68: 68: Excluding 3 bonded neighbours molecule type 'nonanol' 68: 68: turning H bonds into constraints... 68: 68: Excluding 2 bonded neighbours molecule type 'SOL' 68: 68: turning H bonds into constraints... 68: 68: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/nonanol_vacuo.gro' 68: 68: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 294.908 K 68: 68: Calculated rlist for 1x1 atom pair-list as 0.756 nm, buffer size 0.056 nm 68: 68: Set rlist, assuming 4x4 atom pair-list, to 0.749 nm, buffer size 0.049 nm 68: 68: Note that mdrun will redetermine rlist based on the actual pair-list setup 68: 68: This run will generate roughly 0 Mb of data 68: Generated 2485 of the 2485 non-bonded parameter combinations 68: 68: Generated 2485 of the 2485 1-4 parameter combinations 68: 68: Excluding 3 bonded neighbours molecule type 'nonanol' 68: 68: turning H bonds into constraints... 68: 68: Excluding 2 bonded neighbours molecule type 'SOL' 68: 68: turning H bonds into constraints... 68: 68: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/nonanol_vacuo.gro' 68: 68: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 294.908 K 68: 68: Calculated rlist for 1x1 atom pair-list as 0.756 nm, buffer size 0.056 nm 68: 68: Set rlist, assuming 4x4 atom pair-list, to 0.749 nm, buffer size 0.049 nm 68: 68: Note that mdrun will redetermine rlist based on the actual pair-list setup 68: 68: This run will generate roughly 0 Mb of data 68: 68: Writing final coordinates. 68: 68: NOTE: 23 % of the run time was spent in pair search, 68: you might want to increase nstlist (this has no effect on accuracy) 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.114 0.057 199.3 68: (ns/day) (hour/ns) 68: Performance: 25.608 0.937 68: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_3_firstpart.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 68: Can not increase nstlist because an NVE ensemble is used 68: Using 1 MPI thread 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun '30 atom system in water' 68: 8 steps, 0.0 ps. 68: 68: Writing final coordinates. 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.073 0.037 198.9 68: (ns/day) (hour/ns) 68: Performance: 21.196 1.132 68: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_3_full.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 68: Can not increase nstlist because an NVE ensemble is used 68: Using 1 MPI thread 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun '30 atom system in water' 68: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 68: 68: Writing final coordinates. 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.069 0.035 197.3 68: (ns/day) (hour/ns) 68: Performance: 22.291 1.077 68: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_3_full.edr as double precision energy file 68: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_3_firstpart.edr as double precision energy file 68: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_3_secondpart.part0002.edr as double precision energy file 68: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NormalIntegratorsWithFEP/MdrunNoAppendContinuationIsExact.WithinTolerances/3 (468 ms) 68: [ RUN ] NormalIntegratorsWithFEP/MdrunNoAppendContinuationIsExact.WithinTolerances/4 68: 68: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_4_input.mdp]: 68: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 68: that with the Verlet scheme, nstlist has no effect on the accuracy of 68: your simulation. 68: 68: 68: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_4_input.mdp]: 68: Setting nstcalcenergy (100) equal to nstenergy (4) 68: 68: Generating 1-4 interactions: fudge = 0.5 68: Number of degrees of freedom in T-Coupling group System is 79.00 68: 68: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_4_input.mdp]: 68: You are using a plain Coulomb cut-off, which might produce artifacts. 68: You might want to consider using PME electrostatics. 68: 68: 68: 68: There were 3 NOTEs 68: 68: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_4_input.mdp]: 68: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 68: that with the Verlet scheme, nstlist has no effect on the accuracy of 68: your simulation. 68: 68: 68: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_4_input.mdp]: 68: Setting nstcalcenergy (100) equal to nstenergy (4) 68: 68: Generating 1-4 interactions: fudge = 0.5 68: Number of degrees of freedom in T-Coupling group System is 79.00 68: 68: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_4_input.mdp]: 68: You are using a plain Coulomb cut-off, which might produce artifacts. 68: You might want to consider using PME electrostatics. 68: 68: 68: 68: There were 3 NOTEs 68: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_4_full.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 68: Using 1 MPI thread 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun '30 atom system in water' 68: 16 steps, 0.0 ps. 68: Generated 2485 of the 2485 non-bonded parameter combinations 68: 68: Generated 2485 of the 2485 1-4 parameter combinations 68: 68: Excluding 3 bonded neighbours molecule type 'nonanol' 68: 68: turning H bonds into constraints... 68: 68: Excluding 2 bonded neighbours molecule type 'SOL' 68: 68: turning H bonds into constraints... 68: 68: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 68: 68: Calculated rlist for 1x1 atom pair-list as 0.736 nm, buffer size 0.036 nm 68: 68: Set rlist, assuming 4x4 atom pair-list, to 0.732 nm, buffer size 0.032 nm 68: 68: Note that mdrun will redetermine rlist based on the actual pair-list setup 68: 68: This run will generate roughly 0 Mb of data 68: Generated 2485 of the 2485 non-bonded parameter combinations 68: 68: Generated 2485 of the 2485 1-4 parameter combinations 68: 68: Excluding 3 bonded neighbours molecule type 'nonanol' 68: 68: turning H bonds into constraints... 68: 68: Excluding 2 bonded neighbours molecule type 'SOL' 68: 68: turning H bonds into constraints... 68: 68: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 68: 68: Calculated rlist for 1x1 atom pair-list as 0.736 nm, buffer size 0.036 nm 68: 68: Set rlist, assuming 4x4 atom pair-list, to 0.732 nm, buffer size 0.032 nm 68: 68: Note that mdrun will redetermine rlist based on the actual pair-list setup 68: 68: This run will generate roughly 0 Mb of data 68: 68: Writing final coordinates. 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.068 0.035 197.6 68: (ns/day) (hour/ns) 68: Performance: 42.536 0.564 68: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_4_firstpart.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 68: Using 1 MPI thread 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun '30 atom system in water' 68: 8 steps, 0.0 ps. 68: 68: Writing final coordinates. 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.054 0.028 193.9 68: (ns/day) (hour/ns) 68: Performance: 27.795 0.863 68: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_4_full.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 68: Using 1 MPI thread 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun '30 atom system in water' 68: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 68: 68: Writing final coordinates. 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.057 0.029 197.1 68: (ns/day) (hour/ns) 68: Performance: 26.804 0.895 68: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_4_full.edr as double precision energy file 68: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_4_firstpart.edr as double precision energy file 68: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_4_secondpart.part0002.edr as double precision energy file 68: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NormalIntegratorsWithFEP/MdrunNoAppendContinuationIsExact.WithinTolerances/4 (700 ms) 68: [ RUN ] NormalIntegratorsWithFEP/MdrunNoAppendContinuationIsExact.WithinTolerances/5 68: 68: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_5_input.mdp]: 68: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 68: that with the Verlet scheme, nstlist has no effect on the accuracy of 68: your simulation. 68: 68: 68: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_5_input.mdp]: 68: Setting nstcalcenergy (100) equal to nstenergy (4) 68: 68: Generating 1-4 interactions: fudge = 0.5 68: Number of degrees of freedom in T-Coupling group System is 79.00 68: 68: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_5_input.mdp]: 68: You are using a plain Coulomb cut-off, which might produce artifacts. 68: You might want to consider using PME electrostatics. 68: 68: 68: 68: There were 3 NOTEs 68: 68: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_5_input.mdp]: 68: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 68: that with the Verlet scheme, nstlist has no effect on the accuracy of 68: your simulation. 68: 68: 68: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_5_input.mdp]: 68: Setting nstcalcenergy (100) equal to nstenergy (4) 68: 68: Generating 1-4 interactions: fudge = 0.5 68: Number of degrees of freedom in T-Coupling group System is 79.00 68: 68: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_5_input.mdp]: 68: You are using a plain Coulomb cut-off, which might produce artifacts. 68: You might want to consider using PME electrostatics. 68: 68: 68: 68: There were 3 NOTEs 68: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_5_full.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 68: Changing nstlist from 8 to 100, rlist from 0.728 to 0.806 68: 68: Using 1 MPI thread 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun '30 atom system in water' 68: 16 steps, 0.0 ps. 68: Generated 2485 of the 2485 non-bonded parameter combinations 68: 68: Generated 2485 of the 2485 1-4 parameter combinations 68: 68: Excluding 3 bonded neighbours molecule type 'nonanol' 68: 68: turning H bonds into constraints... 68: 68: Excluding 2 bonded neighbours molecule type 'SOL' 68: 68: turning H bonds into constraints... 68: 68: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 298 K 68: 68: Calculated rlist for 1x1 atom pair-list as 0.732 nm, buffer size 0.032 nm 68: 68: Set rlist, assuming 4x4 atom pair-list, to 0.728 nm, buffer size 0.028 nm 68: 68: Note that mdrun will redetermine rlist based on the actual pair-list setup 68: 68: This run will generate roughly 0 Mb of data 68: Generated 2485 of the 2485 non-bonded parameter combinations 68: 68: Generated 2485 of the 2485 1-4 parameter combinations 68: 68: Excluding 3 bonded neighbours molecule type 'nonanol' 68: 68: turning H bonds into constraints... 68: 68: Excluding 2 bonded neighbours molecule type 'SOL' 68: 68: turning H bonds into constraints... 68: 68: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 298 K 68: 68: Calculated rlist for 1x1 atom pair-list as 0.732 nm, buffer size 0.032 nm 68: 68: Set rlist, assuming 4x4 atom pair-list, to 0.728 nm, buffer size 0.028 nm 68: 68: Note that mdrun will redetermine rlist based on the actual pair-list setup 68: 68: This run will generate roughly 0 Mb of data 68: 68: Writing final coordinates. 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.070 0.036 197.6 68: (ns/day) (hour/ns) 68: Performance: 41.235 0.582 68: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_5_firstpart.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 68: Changing nstlist from 8 to 100, rlist from 0.728 to 0.806 68: 68: Using 1 MPI thread 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun '30 atom system in water' 68: 8 steps, 0.0 ps. 68: 68: Writing final coordinates. 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.062 0.031 195.6 68: (ns/day) (hour/ns) 68: Performance: 24.724 0.971 68: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_5_full.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 68: Changing nstlist from 8 to 100, rlist from 0.728 to 0.806 68: 68: Using 1 MPI thread 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun '30 atom system in water' 68: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 68: 68: Writing final coordinates. 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.057 0.029 197.2 68: (ns/day) (hour/ns) 68: Performance: 27.017 0.888 68: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_5_full.edr as double precision energy file 68: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_5_firstpart.edr as double precision energy file 68: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_5_secondpart.part0002.edr as double precision energy file 68: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NormalIntegratorsWithFEP/MdrunNoAppendContinuationIsExact.WithinTolerances/5 (2215 ms) 68: [ RUN ] NormalIntegratorsWithFEP/MdrunNoAppendContinuationIsExact.WithinTolerances/6 68: 68: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_6_input.mdp]: 68: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 68: that with the Verlet scheme, nstlist has no effect on the accuracy of 68: your simulation. 68: 68: 68: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_6_input.mdp]: 68: Setting nstcalcenergy (100) equal to nstenergy (4) 68: 68: Generating 1-4 interactions: fudge = 0.5 68: Number of degrees of freedom in T-Coupling group System is 79.00 68: 68: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_6_input.mdp]: 68: You are using a plain Coulomb cut-off, which might produce artifacts. 68: You might want to consider using PME electrostatics. 68: 68: 68: 68: There were 3 NOTEs 68: 68: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_6_input.mdp]: 68: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 68: that with the Verlet scheme, nstlist has no effect on the accuracy of 68: your simulation. 68: 68: 68: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_6_input.mdp]: 68: Setting nstcalcenergy (100) equal to nstenergy (4) 68: 68: Generating 1-4 interactions: fudge = 0.5 68: Number of degrees of freedom in T-Coupling group System is 79.00 68: 68: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_6_input.mdp]: 68: You are using a plain Coulomb cut-off, which might produce artifacts. 68: You might want to consider using PME electrostatics. 68: 68: 68: 68: There were 3 NOTEs 68: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_6_full.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 68: Using 1 MPI thread 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun '30 atom system in water' 68: 16 steps, 0.0 ps. 68: Generated 2485 of the 2485 non-bonded parameter combinations 68: 68: Generated 2485 of the 2485 1-4 parameter combinations 68: 68: Excluding 3 bonded neighbours molecule type 'nonanol' 68: 68: turning H bonds into constraints... 68: 68: Excluding 2 bonded neighbours molecule type 'SOL' 68: 68: turning H bonds into constraints... 68: 68: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/nonanol_vacuo.gro' 68: 68: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 68: 68: Calculated rlist for 1x1 atom pair-list as 0.764 nm, buffer size 0.064 nm 68: 68: Set rlist, assuming 4x4 atom pair-list, to 0.757 nm, buffer size 0.057 nm 68: 68: Note that mdrun will redetermine rlist based on the actual pair-list setup 68: 68: This run will generate roughly 0 Mb of data 68: Generated 2485 of the 2485 non-bonded parameter combinations 68: 68: Generated 2485 of the 2485 1-4 parameter combinations 68: 68: Excluding 3 bonded neighbours molecule type 'nonanol' 68: 68: turning H bonds into constraints... 68: 68: Excluding 2 bonded neighbours molecule type 'SOL' 68: 68: turning H bonds into constraints... 68: 68: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/nonanol_vacuo.gro' 68: 68: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 68: 68: Calculated rlist for 1x1 atom pair-list as 0.764 nm, buffer size 0.064 nm 68: 68: Set rlist, assuming 4x4 atom pair-list, to 0.757 nm, buffer size 0.057 nm 68: 68: Note that mdrun will redetermine rlist based on the actual pair-list setup 68: 68: This run will generate roughly 0 Mb of data 68: 68: Writing final coordinates. 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.075 0.038 197.7 68: (ns/day) (hour/ns) 68: Performance: 38.606 0.622 68: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_6_firstpart.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 68: Using 1 MPI thread 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun '30 atom system in water' 68: 8 steps, 0.0 ps. 68: 68: Writing final coordinates. 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.064 0.033 194.3 68: (ns/day) (hour/ns) 68: Performance: 23.511 1.021 68: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_6_full.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 68: Using 1 MPI thread 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun '30 atom system in water' 68: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 68: 68: Writing final coordinates. 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.071 0.036 197.5 68: (ns/day) (hour/ns) 68: Performance: 21.569 1.113 68: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_6_full.edr as double precision energy file 68: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_6_firstpart.edr as double precision energy file 68: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_6_secondpart.part0002.edr as double precision energy file 68: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NormalIntegratorsWithFEP/MdrunNoAppendContinuationIsExact.WithinTolerances/6 (668 ms) 68: [ RUN ] NormalIntegratorsWithFEP/MdrunNoAppendContinuationIsExact.WithinTolerances/7 68: 68: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_7_input.mdp]: 68: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 68: that with the Verlet scheme, nstlist has no effect on the accuracy of 68: your simulation. 68: 68: 68: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_7_input.mdp]: 68: Setting nstcalcenergy (100) equal to nstenergy (4) 68: 68: Generating 1-4 interactions: fudge = 0.5 68: Number of degrees of freedom in T-Coupling group System is 79.00 68: 68: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_7_input.mdp]: 68: You are using a plain Coulomb cut-off, which might produce artifacts. 68: You might want to consider using PME electrostatics. 68: 68: 68: 68: There were 3 NOTEs 68: 68: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_7_input.mdp]: 68: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 68: that with the Verlet scheme, nstlist has no effect on the accuracy of 68: your simulation. 68: 68: 68: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_7_input.mdp]: 68: Setting nstcalcenergy (100) equal to nstenergy (4) 68: 68: Generating 1-4 interactions: fudge = 0.5 68: Number of degrees of freedom in T-Coupling group System is 79.00 68: 68: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_7_input.mdp]: 68: You are using a plain Coulomb cut-off, which might produce artifacts. 68: You might want to consider using PME electrostatics. 68: 68: 68: 68: There were 3 NOTEs 68: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_7_full.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 68: Changing nstlist from 8 to 20, rlist from 0.749 to 0.842 68: 68: Using 1 MPI thread 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun '30 atom system in water' 68: 16 steps, 0.0 ps. 68: Generated 2485 of the 2485 non-bonded parameter combinations 68: 68: Generated 2485 of the 2485 1-4 parameter combinations 68: 68: Excluding 3 bonded neighbours molecule type 'nonanol' 68: 68: turning H bonds into constraints... 68: 68: Excluding 2 bonded neighbours molecule type 'SOL' 68: 68: turning H bonds into constraints... 68: 68: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/nonanol_vacuo.gro' 68: 68: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 298 K 68: 68: Calculated rlist for 1x1 atom pair-list as 0.756 nm, buffer size 0.056 nm 68: 68: Set rlist, assuming 4x4 atom pair-list, to 0.749 nm, buffer size 0.049 nm 68: 68: Note that mdrun will redetermine rlist based on the actual pair-list setup 68: 68: This run will generate roughly 0 Mb of data 68: Generated 2485 of the 2485 non-bonded parameter combinations 68: 68: Generated 2485 of the 2485 1-4 parameter combinations 68: 68: Excluding 3 bonded neighbours molecule type 'nonanol' 68: 68: turning H bonds into constraints... 68: 68: Excluding 2 bonded neighbours molecule type 'SOL' 68: 68: turning H bonds into constraints... 68: 68: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/nonanol_vacuo.gro' 68: 68: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 298 K 68: 68: Calculated rlist for 1x1 atom pair-list as 0.756 nm, buffer size 0.056 nm 68: 68: Set rlist, assuming 4x4 atom pair-list, to 0.749 nm, buffer size 0.049 nm 68: 68: Note that mdrun will redetermine rlist based on the actual pair-list setup 68: 68: This run will generate roughly 0 Mb of data 68: 68: Writing final coordinates. 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.068 0.034 197.9 68: (ns/day) (hour/ns) 68: Performance: 42.922 0.559 68: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_7_firstpart.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 68: Changing nstlist from 8 to 20, rlist from 0.749 to 0.842 68: 68: Using 1 MPI thread 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun '30 atom system in water' 68: 8 steps, 0.0 ps. 68: 68: Writing final coordinates. 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.058 0.030 195.8 68: (ns/day) (hour/ns) 68: Performance: 26.042 0.922 68: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_7_full.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 68: Changing nstlist from 8 to 20, rlist from 0.749 to 0.843 68: 68: Using 1 MPI thread 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun '30 atom system in water' 68: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 68: 68: Writing final coordinates. 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.060 0.030 197.1 68: (ns/day) (hour/ns) 68: Performance: 25.741 0.932 68: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_7_full.edr as double precision energy file 68: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_7_firstpart.edr as double precision energy file 68: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_7_secondpart.part0002.edr as double precision energy file 68: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NormalIntegratorsWithFEP/MdrunNoAppendContinuationIsExact.WithinTolerances/7 (737 ms) 68: [----------] 8 tests from NormalIntegratorsWithFEP/MdrunNoAppendContinuationIsExact (6072 ms total) 68: 68: [----------] 8 tests from NVT/MdrunNoAppendContinuationIsExact 68: [ RUN ] NVT/MdrunNoAppendContinuationIsExact.WithinTolerances/0 68: 68: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 68: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 68: that with the Verlet scheme, nstlist has no effect on the accuracy of 68: your simulation. 68: 68: 68: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 68: Setting nstcalcenergy (100) equal to nstenergy (4) 68: 68: Number of degrees of freedom in T-Coupling group System is 33.00 68: 68: There were 2 NOTEs 68: 68: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 68: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 68: that with the Verlet scheme, nstlist has no effect on the accuracy of 68: your simulation. 68: 68: 68: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 68: Setting nstcalcenergy (100) equal to nstenergy (4) 68: 68: Number of degrees of freedom in T-Coupling group System is 33.00 68: 68: There were 2 NOTEs 68: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 68: Using 1 MPI thread 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'Argon' 68: 16 steps, 0.0 ps. 68: Generated 1 of the 1 non-bonded parameter combinations 68: 68: Excluding 1 bonded neighbours molecule type 'Argon' 68: 68: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 68: 68: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 68: 68: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 68: 68: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 68: 68: Note that mdrun will redetermine rlist based on the actual pair-list setup 68: 68: This run will generate roughly 0 Mb of data 68: Generated 1 of the 1 non-bonded parameter combinations 68: 68: Excluding 1 bonded neighbours molecule type 'Argon' 68: 68: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 68: 68: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 68: 68: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 68: 68: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 68: 68: Note that mdrun will redetermine rlist based on the actual pair-list setup 68: 68: This run will generate roughly 0 Mb of data 68: 68: Writing final coordinates. 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.053 0.027 197.7 68: (ns/day) (hour/ns) 68: Performance: 54.996 0.436 68: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_firstpart.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 68: Using 1 MPI thread 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'Argon' 68: 8 steps, 0.0 ps. 68: 68: Writing final coordinates. 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.039 0.020 196.1 68: (ns/day) (hour/ns) 68: Performance: 39.024 0.615 68: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 68: Using 1 MPI thread 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'Argon' 68: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 68: 68: Writing final coordinates. 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.041 0.021 197.5 68: (ns/day) (hour/ns) 68: Performance: 37.059 0.648 68: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.edr as double precision energy file 68: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_firstpart.edr as double precision energy file 68: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_secondpart.part0002.edr as double precision energy file 68: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NVT/MdrunNoAppendContinuationIsExact.WithinTolerances/0 (175 ms) 68: [ RUN ] NVT/MdrunNoAppendContinuationIsExact.WithinTolerances/1 68: 68: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 68: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 68: that with the Verlet scheme, nstlist has no effect on the accuracy of 68: your simulation. 68: 68: 68: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 68: Setting nstcalcenergy (100) equal to nstenergy (4) 68: 68: Number of degrees of freedom in T-Coupling group System is 33.00 68: 68: There were 2 NOTEs 68: 68: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 68: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 68: that with the Verlet scheme, nstlist has no effect on the accuracy of 68: your simulation. 68: 68: 68: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 68: Setting nstcalcenergy (100) equal to nstenergy (4) 68: 68: Number of degrees of freedom in T-Coupling group System is 33.00 68: 68: There were 2 NOTEs 68: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_full.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 68: Changing nstlist from 8 to 100, rlist from 0.702 to 0.738 68: 68: Using 1 MPI thread 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'Argon' 68: 16 steps, 0.0 ps. 68: Generated 1 of the 1 non-bonded parameter combinations 68: 68: Excluding 1 bonded neighbours molecule type 'Argon' 68: 68: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 68: 68: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 80 K 68: 68: Calculated rlist for 1x1 atom pair-list as 0.702 nm, buffer size 0.002 nm 68: 68: Set rlist, assuming 4x4 atom pair-list, to 0.702 nm, buffer size 0.002 nm 68: 68: Note that mdrun will redetermine rlist based on the actual pair-list setup 68: 68: This run will generate roughly 0 Mb of data 68: Generated 1 of the 1 non-bonded parameter combinations 68: 68: Excluding 1 bonded neighbours molecule type 'Argon' 68: 68: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 68: 68: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 80 K 68: 68: Calculated rlist for 1x1 atom pair-list as 0.702 nm, buffer size 0.002 nm 68: 68: Set rlist, assuming 4x4 atom pair-list, to 0.702 nm, buffer size 0.002 nm 68: 68: Note that mdrun will redetermine rlist based on the actual pair-list setup 68: 68: This run will generate roughly 0 Mb of data 68: 68: Writing final coordinates. 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.040 0.020 197.6 68: (ns/day) (hour/ns) 68: Performance: 72.127 0.333 68: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_firstpart.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 68: Changing nstlist from 8 to 100, rlist from 0.702 to 0.738 68: 68: Using 1 MPI thread 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'Argon' 68: 8 steps, 0.0 ps. 68: 68: Writing final coordinates. 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.039 0.020 197.5 68: (ns/day) (hour/ns) 68: Performance: 39.828 0.603 68: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_full.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 68: Changing nstlist from 8 to 100, rlist from 0.702 to 0.738 68: 68: Using 1 MPI thread 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'Argon' 68: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 68: 68: Writing final coordinates. 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.041 0.021 197.6 68: (ns/day) (hour/ns) 68: Performance: 37.900 0.633 68: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_full.edr as double precision energy file 68: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_firstpart.edr as double precision energy file 68: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_secondpart.part0002.edr as double precision energy file 68: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NVT/MdrunNoAppendContinuationIsExact.WithinTolerances/1 (178 ms) 68: [ RUN ] NVT/MdrunNoAppendContinuationIsExact.WithinTolerances/2 68: 68: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]: 68: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 68: that with the Verlet scheme, nstlist has no effect on the accuracy of 68: your simulation. 68: 68: 68: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]: 68: Setting nstcalcenergy (100) equal to nstenergy (4) 68: 68: 68: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]: 68: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 68: 1 68: 68: Number of degrees of freedom in T-Coupling group System is 33.00 68: 68: There were 3 NOTEs 68: 68: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]: 68: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 68: that with the Verlet scheme, nstlist has no effect on the accuracy of 68: your simulation. 68: 68: 68: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]: 68: Setting nstcalcenergy (100) equal to nstenergy (4) 68: 68: 68: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]: 68: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 68: 1 68: 68: Number of degrees of freedom in T-Coupling group System is 33.00 68: 68: There were 3 NOTEs 68: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_full.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 68: Using 1 MPI thread 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'Argon' 68: 16 steps, 0.0 ps. 68: Generated 1 of the 1 non-bonded parameter combinations 68: 68: Excluding 1 bonded neighbours molecule type 'Argon' 68: 68: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 68: 68: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 68: 68: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 68: 68: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 68: 68: Note that mdrun will redetermine rlist based on the actual pair-list setup 68: 68: This run will generate roughly 0 Mb of data 68: Generated 1 of the 1 non-bonded parameter combinations 68: 68: Excluding 1 bonded neighbours molecule type 'Argon' 68: 68: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 68: 68: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 68: 68: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 68: 68: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 68: 68: Note that mdrun will redetermine rlist based on the actual pair-list setup 68: 68: This run will generate roughly 0 Mb of data 68: 68: Writing final coordinates. 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.041 0.021 197.2 68: (ns/day) (hour/ns) 68: Performance: 71.387 0.336 68: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_firstpart.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 68: Using 1 MPI thread 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'Argon' 68: 8 steps, 0.0 ps. 68: 68: Writing final coordinates. 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.039 0.020 197.1 68: (ns/day) (hour/ns) 68: Performance: 39.744 0.604 68: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_full.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 68: Using 1 MPI thread 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'Argon' 68: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 68: 68: Writing final coordinates. 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.041 0.021 197.3 68: (ns/day) (hour/ns) 68: Performance: 37.747 0.636 68: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_full.edr as double precision energy file 68: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_firstpart.edr as double precision energy file 68: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_secondpart.part0002.edr as double precision energy file 68: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NVT/MdrunNoAppendContinuationIsExact.WithinTolerances/2 (169 ms) 68: [ RUN ] NVT/MdrunNoAppendContinuationIsExact.WithinTolerances/3 68: 68: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]: 68: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 68: that with the Verlet scheme, nstlist has no effect on the accuracy of 68: your simulation. 68: 68: 68: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]: 68: Setting nstcalcenergy (100) equal to nstenergy (4) 68: 68: 68: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]: 68: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 68: 1 68: 68: Number of degrees of freedom in T-Coupling group System is 33.00 68: 68: There were 3 NOTEs 68: 68: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]: 68: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 68: that with the Verlet scheme, nstlist has no effect on the accuracy of 68: your simulation. 68: 68: 68: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]: 68: Setting nstcalcenergy (100) equal to nstenergy (4) 68: 68: 68: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]: 68: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 68: 1 68: 68: Number of degrees of freedom in T-Coupling group System is 33.00 68: 68: There were 3 NOTEs 68: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_full.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 68: Changing nstlist from 8 to 100, rlist from 0.702 to 0.738 68: 68: Using 1 MPI thread 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'Argon' 68: 16 steps, 0.0 ps. 68: Generated 1 of the 1 non-bonded parameter combinations 68: 68: Excluding 1 bonded neighbours molecule type 'Argon' 68: 68: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 68: 68: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 80 K 68: 68: Calculated rlist for 1x1 atom pair-list as 0.702 nm, buffer size 0.002 nm 68: 68: Set rlist, assuming 4x4 atom pair-list, to 0.702 nm, buffer size 0.002 nm 68: 68: Note that mdrun will redetermine rlist based on the actual pair-list setup 68: 68: This run will generate roughly 0 Mb of data 68: Generated 1 of the 1 non-bonded parameter combinations 68: 68: Excluding 1 bonded neighbours molecule type 'Argon' 68: 68: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 68: 68: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 80 K 68: 68: Calculated rlist for 1x1 atom pair-list as 0.702 nm, buffer size 0.002 nm 68: 68: Set rlist, assuming 4x4 atom pair-list, to 0.702 nm, buffer size 0.002 nm 68: 68: Note that mdrun will redetermine rlist based on the actual pair-list setup 68: 68: This run will generate roughly 0 Mb of data 68: 68: Writing final coordinates. 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.041 0.021 196.8 68: (ns/day) (hour/ns) 68: Performance: 70.998 0.338 68: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_firstpart.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 68: Changing nstlist from 8 to 100, rlist from 0.702 to 0.738 68: 68: Using 1 MPI thread 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'Argon' 68: 8 steps, 0.0 ps. 68: 68: Writing final coordinates. 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.037 0.019 196.9 68: (ns/day) (hour/ns) 68: Performance: 41.104 0.584 68: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_full.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 68: Changing nstlist from 8 to 100, rlist from 0.702 to 0.738 68: 68: Using 1 MPI thread 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'Argon' 68: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 68: 68: Writing final coordinates. 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.040 0.020 197.2 68: (ns/day) (hour/ns) 68: Performance: 38.134 0.629 68: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_full.edr as double precision energy file 68: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_firstpart.edr as double precision energy file 68: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_secondpart.part0002.edr as double precision energy file 68: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NVT/MdrunNoAppendContinuationIsExact.WithinTolerances/3 (177 ms) 68: [ RUN ] NVT/MdrunNoAppendContinuationIsExact.WithinTolerances/4 68: 68: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_input.mdp]: 68: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 68: that with the Verlet scheme, nstlist has no effect on the accuracy of 68: your simulation. 68: 68: 68: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_input.mdp]: 68: Setting nstcalcenergy (100) equal to nstenergy (4) 68: 68: Number of degrees of freedom in T-Coupling group System is 33.00 68: 68: There were 2 NOTEs 68: 68: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_input.mdp]: 68: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 68: that with the Verlet scheme, nstlist has no effect on the accuracy of 68: your simulation. 68: 68: 68: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_input.mdp]: 68: Setting nstcalcenergy (100) equal to nstenergy (4) 68: 68: Number of degrees of freedom in T-Coupling group System is 33.00 68: 68: There were 2 NOTEs 68: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_full.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 68: Using 1 MPI thread 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'Argon' 68: 16 steps, 0.0 ps. 68: Generated 1 of the 1 non-bonded parameter combinations 68: 68: Excluding 1 bonded neighbours molecule type 'Argon' 68: 68: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 68: 68: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 68: 68: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 68: 68: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 68: 68: Note that mdrun will redetermine rlist based on the actual pair-list setup 68: 68: This run will generate roughly 0 Mb of data 68: Generated 1 of the 1 non-bonded parameter combinations 68: 68: Excluding 1 bonded neighbours molecule type 'Argon' 68: 68: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 68: 68: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 68: 68: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 68: 68: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 68: 68: Note that mdrun will redetermine rlist based on the actual pair-list setup 68: 68: This run will generate roughly 0 Mb of data 68: 68: Writing final coordinates. 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.070 0.035 198.9 68: (ns/day) (hour/ns) 68: Performance: 41.695 0.576 68: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_firstpart.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 68: Using 1 MPI thread 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'Argon' 68: 8 steps, 0.0 ps. 68: 68: Writing final coordinates. 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.051 0.026 198.5 68: (ns/day) (hour/ns) 68: Performance: 30.457 0.788 68: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_full.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 68: Using 1 MPI thread 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'Argon' 68: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 68: 68: Writing final coordinates. 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.049 0.025 197.3 68: (ns/day) (hour/ns) 68: Performance: 31.469 0.763 68: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_full.edr as double precision energy file 68: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_firstpart.edr as double precision energy file 68: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_secondpart.part0002.edr as double precision energy file 68: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NVT/MdrunNoAppendContinuationIsExact.WithinTolerances/4 (190 ms) 68: [ RUN ] NVT/MdrunNoAppendContinuationIsExact.WithinTolerances/5 68: 68: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_5_input.mdp]: 68: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 68: that with the Verlet scheme, nstlist has no effect on the accuracy of 68: your simulation. 68: 68: 68: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_5_input.mdp]: 68: Setting nstcalcenergy (100) equal to nstenergy (4) 68: 68: Number of degrees of freedom in T-Coupling group System is 33.00 68: 68: There were 2 NOTEs 68: 68: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_5_input.mdp]: 68: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 68: that with the Verlet scheme, nstlist has no effect on the accuracy of 68: your simulation. 68: 68: 68: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_5_input.mdp]: 68: Setting nstcalcenergy (100) equal to nstenergy (4) 68: 68: Number of degrees of freedom in T-Coupling group System is 33.00 68: 68: There were 2 NOTEs 68: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_5_full.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 68: Changing nstlist from 8 to 100, rlist from 0.702 to 0.738 68: 68: Using 1 MPI thread 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'Argon' 68: 16 steps, 0.0 ps. 68: Generated 1 of the 1 non-bonded parameter combinations 68: 68: Excluding 1 bonded neighbours molecule type 'Argon' 68: 68: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 68: 68: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 80 K 68: 68: Calculated rlist for 1x1 atom pair-list as 0.702 nm, buffer size 0.002 nm 68: 68: Set rlist, assuming 4x4 atom pair-list, to 0.702 nm, buffer size 0.002 nm 68: 68: Note that mdrun will redetermine rlist based on the actual pair-list setup 68: 68: This run will generate roughly 0 Mb of data 68: Generated 1 of the 1 non-bonded parameter combinations 68: 68: Excluding 1 bonded neighbours molecule type 'Argon' 68: 68: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 68: 68: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 80 K 68: 68: Calculated rlist for 1x1 atom pair-list as 0.702 nm, buffer size 0.002 nm 68: 68: Set rlist, assuming 4x4 atom pair-list, to 0.702 nm, buffer size 0.002 nm 68: 68: Note that mdrun will redetermine rlist based on the actual pair-list setup 68: 68: This run will generate roughly 0 Mb of data 68: 68: Writing final coordinates. 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.046 0.023 198.0 68: (ns/day) (hour/ns) 68: Performance: 63.461 0.378 68: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_5_firstpart.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 68: Changing nstlist from 8 to 100, rlist from 0.702 to 0.738 68: 68: Using 1 MPI thread 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'Argon' 68: 8 steps, 0.0 ps. 68: 68: Writing final coordinates. 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.043 0.022 198.1 68: (ns/day) (hour/ns) 68: Performance: 35.699 0.672 68: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_5_full.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 68: Changing nstlist from 8 to 100, rlist from 0.702 to 0.738 68: 68: Using 1 MPI thread 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'Argon' 68: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 68: 68: Writing final coordinates. 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.054 0.028 197.4 68: (ns/day) (hour/ns) 68: Performance: 28.260 0.849 68: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_5_full.edr as double precision energy file 68: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_5_firstpart.edr as double precision energy file 68: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_5_secondpart.part0002.edr as double precision energy file 68: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NVT/MdrunNoAppendContinuationIsExact.WithinTolerances/5 (183 ms) 68: [ RUN ] NVT/MdrunNoAppendContinuationIsExact.WithinTolerances/6 68: 68: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_6_input.mdp]: 68: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 68: that with the Verlet scheme, nstlist has no effect on the accuracy of 68: your simulation. 68: 68: 68: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_6_input.mdp]: 68: Setting nstcalcenergy (100) equal to nstenergy (4) 68: 68: Number of degrees of freedom in T-Coupling group System is 33.00 68: 68: There were 2 NOTEs 68: 68: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_6_input.mdp]: 68: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 68: that with the Verlet scheme, nstlist has no effect on the accuracy of 68: your simulation. 68: 68: 68: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_6_input.mdp]: 68: Setting nstcalcenergy (100) equal to nstenergy (4) 68: 68: Number of degrees of freedom in T-Coupling group System is 33.00 68: 68: There were 2 NOTEs 68: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_6_full.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 68: Using 1 MPI thread 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'Argon' 68: 16 steps, 0.0 ps. 68: Generated 1 of the 1 non-bonded parameter combinations 68: 68: Excluding 1 bonded neighbours molecule type 'Argon' 68: 68: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 68: 68: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 68: 68: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 68: 68: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 68: 68: Note that mdrun will redetermine rlist based on the actual pair-list setup 68: 68: This run will generate roughly 0 Mb of data 68: Generated 1 of the 1 non-bonded parameter combinations 68: 68: Excluding 1 bonded neighbours molecule type 'Argon' 68: 68: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 68: 68: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 68: 68: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 68: 68: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 68: 68: Note that mdrun will redetermine rlist based on the actual pair-list setup 68: 68: This run will generate roughly 0 Mb of data 68: 68: Writing final coordinates. 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.058 0.029 198.7 68: (ns/day) (hour/ns) 68: Performance: 50.732 0.473 68: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_6_firstpart.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 68: Using 1 MPI thread 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'Argon' 68: 8 steps, 0.0 ps. 68: 68: Writing final coordinates. 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.063 0.033 194.7 68: (ns/day) (hour/ns) 68: Performance: 23.915 1.004 68: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_6_full.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 68: Using 1 MPI thread 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'Argon' 68: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 68: 68: Writing final coordinates. 68: 68: NOTE: 21 % of the run time was spent in pair search, 68: you might want to increase nstlist (this has no effect on accuracy) 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.057 0.029 197.8 68: (ns/day) (hour/ns) 68: Performance: 27.212 0.882 68: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_6_full.edr as double precision energy file 68: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_6_firstpart.edr as double precision energy file 68: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_6_secondpart.part0002.edr as double precision energy file 68: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NVT/MdrunNoAppendContinuationIsExact.WithinTolerances/6 (199 ms) 68: [ RUN ] NVT/MdrunNoAppendContinuationIsExact.WithinTolerances/7 68: 68: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_7_input.mdp]: 68: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 68: that with the Verlet scheme, nstlist has no effect on the accuracy of 68: your simulation. 68: 68: 68: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_7_input.mdp]: 68: Setting nstcalcenergy (100) equal to nstenergy (4) 68: 68: Number of degrees of freedom in T-Coupling group System is 33.00 68: 68: There were 2 NOTEs 68: 68: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_7_input.mdp]: 68: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 68: that with the Verlet scheme, nstlist has no effect on the accuracy of 68: your simulation. 68: 68: 68: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_7_input.mdp]: 68: Setting nstcalcenergy (100) equal to nstenergy (4) 68: 68: Number of degrees of freedom in T-Coupling group System is 33.00 68: 68: There were 2 NOTEs 68: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_7_full.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 68: Changing nstlist from 8 to 100, rlist from 0.702 to 0.738 68: 68: Using 1 MPI thread 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'Argon' 68: 16 steps, 0.0 ps. 68: Generated 1 of the 1 non-bonded parameter combinations 68: 68: Excluding 1 bonded neighbours molecule type 'Argon' 68: 68: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 68: 68: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 80 K 68: 68: Calculated rlist for 1x1 atom pair-list as 0.702 nm, buffer size 0.002 nm 68: 68: Set rlist, assuming 4x4 atom pair-list, to 0.702 nm, buffer size 0.002 nm 68: 68: Note that mdrun will redetermine rlist based on the actual pair-list setup 68: 68: This run will generate roughly 0 Mb of data 68: Generated 1 of the 1 non-bonded parameter combinations 68: 68: Excluding 1 bonded neighbours molecule type 'Argon' 68: 68: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 68: 68: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 80 K 68: 68: Calculated rlist for 1x1 atom pair-list as 0.702 nm, buffer size 0.002 nm 68: 68: Set rlist, assuming 4x4 atom pair-list, to 0.702 nm, buffer size 0.002 nm 68: 68: Note that mdrun will redetermine rlist based on the actual pair-list setup 68: 68: This run will generate roughly 0 Mb of data 68: 68: Writing final coordinates. 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.057 0.029 198.4 68: (ns/day) (hour/ns) 68: Performance: 50.979 0.471 68: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_7_firstpart.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 68: Changing nstlist from 8 to 100, rlist from 0.702 to 0.738 68: 68: Using 1 MPI thread 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'Argon' 68: 8 steps, 0.0 ps. 68: 68: Writing final coordinates. 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.047 0.024 197.9 68: (ns/day) (hour/ns) 68: Performance: 33.042 0.726 68: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_7_full.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 68: Changing nstlist from 8 to 100, rlist from 0.702 to 0.738 68: 68: Using 1 MPI thread 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'Argon' 68: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 68: 68: Writing final coordinates. 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.051 0.026 195.6 68: (ns/day) (hour/ns) 68: Performance: 29.577 0.811 68: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_7_full.edr as double precision energy file 68: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_7_firstpart.edr as double precision energy file 68: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_7_secondpart.part0002.edr as double precision energy file 68: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NVT/MdrunNoAppendContinuationIsExact.WithinTolerances/7 (194 ms) 68: [----------] 8 tests from NVT/MdrunNoAppendContinuationIsExact (1468 ms total) 68: 68: [----------] 2 tests from NPH/MdrunNoAppendContinuationIsExact 68: [ RUN ] NPH/MdrunNoAppendContinuationIsExact.WithinTolerances/0 68: 68: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 68: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 68: that with the Verlet scheme, nstlist has no effect on the accuracy of 68: your simulation. 68: 68: 68: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 68: Setting nstcalcenergy (100) equal to nstenergy (4) 68: 68: Number of degrees of freedom in T-Coupling group System is 33.00 68: 68: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 68: NVE simulation: will use the initial temperature of 68.810 K for 68: determining the Verlet buffer size 68: 68: 68: There were 3 NOTEs 68: 68: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 68: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 68: that with the Verlet scheme, nstlist has no effect on the accuracy of 68: your simulation. 68: 68: 68: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 68: Setting nstcalcenergy (100) equal to nstenergy (4) 68: 68: Number of degrees of freedom in T-Coupling group System is 33.00 68: 68: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 68: NVE simulation: will use the initial temperature of 68.810 K for 68: determining the Verlet buffer size 68: 68: 68: There were 3 NOTEs 68: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 68: Can not increase nstlist because an NVE ensemble is used 68: Using 1 MPI thread 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'Argon' 68: 16 steps, 0.0 ps. 68: Generated 1 of the 1 non-bonded parameter combinations 68: 68: Excluding 1 bonded neighbours molecule type 'Argon' 68: 68: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 68: 68: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 68: 68: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 68: 68: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 68: 68: Note that mdrun will redetermine rlist based on the actual pair-list setup 68: 68: This run will generate roughly 0 Mb of data 68: Generated 1 of the 1 non-bonded parameter combinations 68: 68: Excluding 1 bonded neighbours molecule type 'Argon' 68: 68: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 68: 68: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 68: 68: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 68: 68: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 68: 68: Note that mdrun will redetermine rlist based on the actual pair-list setup 68: 68: This run will generate roughly 0 Mb of data 68: 68: Writing final coordinates. 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.044 0.022 197.6 68: (ns/day) (hour/ns) 68: Performance: 65.353 0.367 68: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_0_firstpart.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 68: Can not increase nstlist because an NVE ensemble is used 68: Using 1 MPI thread 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'Argon' 68: 8 steps, 0.0 ps. 68: 68: Writing final coordinates. 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.038 0.020 197.3 68: (ns/day) (hour/ns) 68: Performance: 39.865 0.602 68: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 68: Can not increase nstlist because an NVE ensemble is used 68: Using 1 MPI thread 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'Argon' 68: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 68: 68: Writing final coordinates. 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.040 0.020 197.4 68: (ns/day) (hour/ns) 68: Performance: 38.038 0.631 68: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.edr as double precision energy file 68: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_0_firstpart.edr as double precision energy file 68: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_0_secondpart.part0002.edr as double precision energy file 68: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NPH/MdrunNoAppendContinuationIsExact.WithinTolerances/0 (178 ms) 68: [ RUN ] NPH/MdrunNoAppendContinuationIsExact.WithinTolerances/1 68: 68: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 68: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 68: that with the Verlet scheme, nstlist has no effect on the accuracy of 68: your simulation. 68: 68: 68: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 68: Setting nstcalcenergy (100) equal to nstenergy (4) 68: 68: Number of degrees of freedom in T-Coupling group System is 33.00 68: 68: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 68: NVE simulation: will use the initial temperature of 68.810 K for 68: determining the Verlet buffer size 68: 68: 68: There were 3 NOTEs 68: 68: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 68: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 68: that with the Verlet scheme, nstlist has no effect on the accuracy of 68: your simulation. 68: 68: 68: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 68: Setting nstcalcenergy (100) equal to nstenergy (4) 68: 68: Number of degrees of freedom in T-Coupling group System is 33.00 68: 68: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 68: NVE simulation: will use the initial temperature of 68.810 K for 68: determining the Verlet buffer size 68: 68: 68: There were 3 NOTEs 68: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_1_full.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 68: Can not increase nstlist because an NVE ensemble is used 68: Using 1 MPI thread 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'Argon' 68: 16 steps, 0.0 ps. 68: Generated 1 of the 1 non-bonded parameter combinations 68: 68: Excluding 1 bonded neighbours molecule type 'Argon' 68: 68: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 68: 68: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 68: 68: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 68: 68: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 68: 68: Note that mdrun will redetermine rlist based on the actual pair-list setup 68: 68: This run will generate roughly 0 Mb of data 68: Generated 1 of the 1 non-bonded parameter combinations 68: 68: Excluding 1 bonded neighbours molecule type 'Argon' 68: 68: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 68: 68: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 68: 68: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 68: 68: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 68: 68: Note that mdrun will redetermine rlist based on the actual pair-list setup 68: 68: This run will generate roughly 0 Mb of data 68: 68: Writing final coordinates. 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.073 0.037 199.0 68: (ns/day) (hour/ns) 68: Performance: 40.098 0.599 68: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_1_firstpart.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 68: Can not increase nstlist because an NVE ensemble is used 68: Using 1 MPI thread 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'Argon' 68: 8 steps, 0.0 ps. 68: 68: Writing final coordinates. 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.063 0.031 198.9 68: (ns/day) (hour/ns) 68: Performance: 24.731 0.970 68: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_1_full.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 68: Can not increase nstlist because an NVE ensemble is used 68: Using 1 MPI thread 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'Argon' 68: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 68: 68: Writing final coordinates. 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.058 0.029 197.7 68: (ns/day) (hour/ns) 68: Performance: 26.367 0.910 68: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_1_full.edr as double precision energy file 68: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_1_firstpart.edr as double precision energy file 68: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_1_secondpart.part0002.edr as double precision energy file 68: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NPH/MdrunNoAppendContinuationIsExact.WithinTolerances/1 (211 ms) 68: [----------] 2 tests from NPH/MdrunNoAppendContinuationIsExact (389 ms total) 68: 68: [----------] 8 tests from NPT/MdrunNoAppendContinuationIsExact 68: [ RUN ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/0 68: 68: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 68: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 68: that with the Verlet scheme, nstlist has no effect on the accuracy of 68: your simulation. 68: 68: 68: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 68: Setting nstcalcenergy (100) equal to nstenergy (4) 68: 68: Number of degrees of freedom in T-Coupling group System is 33.00 68: 68: There were 2 NOTEs 68: 68: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 68: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 68: that with the Verlet scheme, nstlist has no effect on the accuracy of 68: your simulation. 68: 68: 68: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 68: Setting nstcalcenergy (100) equal to nstenergy (4) 68: 68: Number of degrees of freedom in T-Coupling group System is 33.00 68: 68: There were 2 NOTEs 68: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 68: Using 1 MPI thread 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'Argon' 68: 16 steps, 0.0 ps. 68: Generated 1 of the 1 non-bonded parameter combinations 68: 68: Excluding 1 bonded neighbours molecule type 'Argon' 68: 68: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 68: 68: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 68: 68: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 68: 68: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 68: 68: Note that mdrun will redetermine rlist based on the actual pair-list setup 68: 68: This run will generate roughly 0 Mb of data 68: Generated 1 of the 1 non-bonded parameter combinations 68: 68: Excluding 1 bonded neighbours molecule type 'Argon' 68: 68: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 68: 68: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 68: 68: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 68: 68: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 68: 68: Note that mdrun will redetermine rlist based on the actual pair-list setup 68: 68: This run will generate roughly 0 Mb of data 68: 68: Writing final coordinates. 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.056 0.028 198.0 68: (ns/day) (hour/ns) 68: Performance: 51.678 0.464 68: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_firstpart.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 68: Using 1 MPI thread 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'Argon' 68: 8 steps, 0.0 ps. 68: 68: Writing final coordinates. 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.037 0.019 197.3 68: (ns/day) (hour/ns) 68: Performance: 41.034 0.585 68: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 68: Using 1 MPI thread 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'Argon' 68: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 68: 68: Writing final coordinates. 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.042 0.021 197.3 68: (ns/day) (hour/ns) 68: Performance: 36.206 0.663 68: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.edr as double precision energy file 68: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_firstpart.edr as double precision energy file 68: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_secondpart.part0002.edr as double precision energy file 68: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/0 (176 ms) 68: [ RUN ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/1 68: 68: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 68: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 68: that with the Verlet scheme, nstlist has no effect on the accuracy of 68: your simulation. 68: 68: 68: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 68: Setting nstcalcenergy (100) equal to nstenergy (4) 68: 68: Number of degrees of freedom in T-Coupling group System is 33.00 68: 68: There were 2 NOTEs 68: 68: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 68: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 68: that with the Verlet scheme, nstlist has no effect on the accuracy of 68: your simulation. 68: 68: 68: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 68: Setting nstcalcenergy (100) equal to nstenergy (4) 68: 68: Number of degrees of freedom in T-Coupling group System is 33.00 68: 68: There were 2 NOTEs 68: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_full.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 68: Using 1 MPI thread 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'Argon' 68: 16 steps, 0.0 ps. 68: Generated 1 of the 1 non-bonded parameter combinations 68: 68: Excluding 1 bonded neighbours molecule type 'Argon' 68: 68: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 68: 68: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 68: 68: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 68: 68: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 68: 68: Note that mdrun will redetermine rlist based on the actual pair-list setup 68: 68: This run will generate roughly 0 Mb of data 68: Generated 1 of the 1 non-bonded parameter combinations 68: 68: Excluding 1 bonded neighbours molecule type 'Argon' 68: 68: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 68: 68: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 68: 68: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 68: 68: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 68: 68: Note that mdrun will redetermine rlist based on the actual pair-list setup 68: 68: This run will generate roughly 0 Mb of data 68: 68: Writing final coordinates. 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.043 0.022 197.6 68: (ns/day) (hour/ns) 68: Performance: 67.431 0.356 68: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_firstpart.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 68: Using 1 MPI thread 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'Argon' 68: 8 steps, 0.0 ps. 68: 68: Writing final coordinates. 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.037 0.019 197.1 68: (ns/day) (hour/ns) 68: Performance: 41.739 0.575 68: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_full.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 68: Using 1 MPI thread 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'Argon' 68: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 68: 68: Writing final coordinates. 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.037 0.019 197.3 68: (ns/day) (hour/ns) 68: Performance: 41.217 0.582 68: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_full.edr as double precision energy file 68: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_firstpart.edr as double precision energy file 68: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_secondpart.part0002.edr as double precision energy file 68: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/1 (183 ms) 68: [ RUN ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/2 68: 68: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]: 68: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 68: that with the Verlet scheme, nstlist has no effect on the accuracy of 68: your simulation. 68: 68: 68: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]: 68: Setting nstcalcenergy (100) equal to nstenergy (4) 68: 68: 68: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]: 68: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 68: 1 68: 68: Number of degrees of freedom in T-Coupling group System is 33.00 68: 68: There were 3 NOTEs 68: 68: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]: 68: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 68: that with the Verlet scheme, nstlist has no effect on the accuracy of 68: your simulation. 68: 68: 68: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]: 68: Setting nstcalcenergy (100) equal to nstenergy (4) 68: 68: 68: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]: 68: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 68: 1 68: 68: Number of degrees of freedom in T-Coupling group System is 33.00 68: 68: There were 3 NOTEs 68: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_full.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 68: Using 1 MPI thread 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'Argon' 68: 16 steps, 0.0 ps. 68: Generated 1 of the 1 non-bonded parameter combinations 68: 68: Excluding 1 bonded neighbours molecule type 'Argon' 68: 68: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 68: 68: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 68: 68: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 68: 68: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 68: 68: Note that mdrun will redetermine rlist based on the actual pair-list setup 68: 68: This run will generate roughly 0 Mb of data 68: Generated 1 of the 1 non-bonded parameter combinations 68: 68: Excluding 1 bonded neighbours molecule type 'Argon' 68: 68: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 68: 68: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 68: 68: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 68: 68: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 68: 68: Note that mdrun will redetermine rlist based on the actual pair-list setup 68: 68: This run will generate roughly 0 Mb of data 68: 68: Writing final coordinates. 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.044 0.022 197.5 68: (ns/day) (hour/ns) 68: Performance: 66.437 0.361 68: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_firstpart.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 68: Using 1 MPI thread 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'Argon' 68: 8 steps, 0.0 ps. 68: 68: Writing final coordinates. 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.038 0.019 197.1 68: (ns/day) (hour/ns) 68: Performance: 40.597 0.591 68: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_full.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 68: Using 1 MPI thread 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'Argon' 68: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 68: 68: Writing final coordinates. 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.039 0.020 195.3 68: (ns/day) (hour/ns) 68: Performance: 39.125 0.613 68: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_full.edr as double precision energy file 68: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_firstpart.edr as double precision energy file 68: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_secondpart.part0002.edr as double precision energy file 68: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/2 (177 ms) 68: [ RUN ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/3 68: 68: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]: 68: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 68: that with the Verlet scheme, nstlist has no effect on the accuracy of 68: your simulation. 68: 68: 68: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]: 68: Setting nstcalcenergy (100) equal to nstenergy (4) 68: 68: 68: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]: 68: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 68: 1 68: 68: Number of degrees of freedom in T-Coupling group System is 33.00 68: 68: There were 3 NOTEs 68: 68: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]: 68: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 68: that with the Verlet scheme, nstlist has no effect on the accuracy of 68: your simulation. 68: 68: 68: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]: 68: Setting nstcalcenergy (100) equal to nstenergy (4) 68: 68: 68: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]: 68: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 68: 1 68: 68: Number of degrees of freedom in T-Coupling group System is 33.00 68: 68: There were 3 NOTEs 68: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_full.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 68: Using 1 MPI thread 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'Argon' 68: 16 steps, 0.0 ps. 68: Generated 1 of the 1 non-bonded parameter combinations 68: 68: Excluding 1 bonded neighbours molecule type 'Argon' 68: 68: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 68: 68: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 68: 68: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 68: 68: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 68: 68: Note that mdrun will redetermine rlist based on the actual pair-list setup 68: 68: This run will generate roughly 0 Mb of data 68: Generated 1 of the 1 non-bonded parameter combinations 68: 68: Excluding 1 bonded neighbours molecule type 'Argon' 68: 68: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 68: 68: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 68: 68: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 68: 68: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 68: 68: Note that mdrun will redetermine rlist based on the actual pair-list setup 68: 68: This run will generate roughly 0 Mb of data 68: 68: Writing final coordinates. 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.053 0.027 197.8 68: (ns/day) (hour/ns) 68: Performance: 54.980 0.437 68: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_firstpart.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 68: Using 1 MPI thread 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'Argon' 68: 8 steps, 0.0 ps. 68: 68: Writing final coordinates. 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.038 0.019 197.1 68: (ns/day) (hour/ns) 68: Performance: 40.525 0.592 68: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_full.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 68: Using 1 MPI thread 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'Argon' 68: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 68: 68: Writing final coordinates. 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.040 0.021 197.3 68: (ns/day) (hour/ns) 68: Performance: 37.913 0.633 68: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_full.edr as double precision energy file 68: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_firstpart.edr as double precision energy file 68: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_secondpart.part0002.edr as double precision energy file 68: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/3 (177 ms) 68: [ RUN ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/4 68: 68: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_input.mdp]: 68: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 68: that with the Verlet scheme, nstlist has no effect on the accuracy of 68: your simulation. 68: 68: 68: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_input.mdp]: 68: Setting nstcalcenergy (100) equal to nstenergy (4) 68: 68: Number of degrees of freedom in T-Coupling group System is 33.00 68: 68: There were 2 NOTEs 68: 68: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_input.mdp]: 68: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 68: that with the Verlet scheme, nstlist has no effect on the accuracy of 68: your simulation. 68: 68: 68: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_input.mdp]: 68: Setting nstcalcenergy (100) equal to nstenergy (4) 68: 68: Number of degrees of freedom in T-Coupling group System is 33.00 68: 68: There were 2 NOTEs 68: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_full.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 68: Using 1 MPI thread 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'Argon' 68: 16 steps, 0.0 ps. 68: Generated 1 of the 1 non-bonded parameter combinations 68: 68: Excluding 1 bonded neighbours molecule type 'Argon' 68: 68: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 68: 68: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 68: 68: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 68: 68: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 68: 68: Note that mdrun will redetermine rlist based on the actual pair-list setup 68: 68: This run will generate roughly 0 Mb of data 68: Generated 1 of the 1 non-bonded parameter combinations 68: 68: Excluding 1 bonded neighbours molecule type 'Argon' 68: 68: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 68: 68: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 68: 68: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 68: 68: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 68: 68: Note that mdrun will redetermine rlist based on the actual pair-list setup 68: 68: This run will generate roughly 0 Mb of data 68: 68: Writing final coordinates. 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.054 0.027 198.5 68: (ns/day) (hour/ns) 68: Performance: 53.842 0.446 68: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_firstpart.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 68: Using 1 MPI thread 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'Argon' 68: 8 steps, 0.0 ps. 68: 68: Writing final coordinates. 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.048 0.024 198.4 68: (ns/day) (hour/ns) 68: Performance: 32.262 0.744 68: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_full.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 68: Using 1 MPI thread 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'Argon' 68: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 68: 68: Writing final coordinates. 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.051 0.026 197.2 68: (ns/day) (hour/ns) 68: Performance: 29.944 0.801 68: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_full.edr as double precision energy file 68: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_firstpart.edr as double precision energy file 68: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_secondpart.part0002.edr as double precision energy file 68: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/4 (190 ms) 68: [ RUN ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/5 68: 68: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_5_input.mdp]: 68: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 68: that with the Verlet scheme, nstlist has no effect on the accuracy of 68: your simulation. 68: 68: 68: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_5_input.mdp]: 68: Setting nstcalcenergy (100) equal to nstenergy (4) 68: 68: Number of degrees of freedom in T-Coupling group System is 33.00 68: 68: There were 2 NOTEs 68: 68: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_5_input.mdp]: 68: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 68: that with the Verlet scheme, nstlist has no effect on the accuracy of 68: your simulation. 68: 68: 68: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_5_input.mdp]: 68: Setting nstcalcenergy (100) equal to nstenergy (4) 68: 68: Number of degrees of freedom in T-Coupling group System is 33.00 68: 68: There were 2 NOTEs 68: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_5_full.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 68: Using 1 MPI thread 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'Argon' 68: 16 steps, 0.0 ps. 68: Generated 1 of the 1 non-bonded parameter combinations 68: 68: Excluding 1 bonded neighbours molecule type 'Argon' 68: 68: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 68: 68: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 68: 68: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 68: 68: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 68: 68: Note that mdrun will redetermine rlist based on the actual pair-list setup 68: 68: This run will generate roughly 0 Mb of data 68: Generated 1 of the 1 non-bonded parameter combinations 68: 68: Excluding 1 bonded neighbours molecule type 'Argon' 68: 68: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 68: 68: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 68: 68: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 68: 68: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 68: 68: Note that mdrun will redetermine rlist based on the actual pair-list setup 68: 68: This run will generate roughly 0 Mb of data 68: 68: Writing final coordinates. 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.052 0.026 198.6 68: (ns/day) (hour/ns) 68: Performance: 56.520 0.425 68: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_5_firstpart.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 68: Using 1 MPI thread 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'Argon' 68: 8 steps, 0.0 ps. 68: 68: Writing final coordinates. 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.049 0.025 198.5 68: (ns/day) (hour/ns) 68: Performance: 31.613 0.759 68: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_5_full.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 68: Using 1 MPI thread 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'Argon' 68: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 68: 68: Writing final coordinates. 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.054 0.027 197.4 68: (ns/day) (hour/ns) 68: Performance: 28.430 0.844 68: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_5_full.edr as double precision energy file 68: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_5_firstpart.edr as double precision energy file 68: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_5_secondpart.part0002.edr as double precision energy file 68: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/5 (186 ms) 68: [ RUN ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/6 68: [ OK ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/6 (0 ms) 68: [ RUN ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/7 68: 68: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_7_input.mdp]: 68: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 68: that with the Verlet scheme, nstlist has no effect on the accuracy of 68: your simulation. 68: 68: 68: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_7_input.mdp]: 68: Setting nstcalcenergy (100) equal to nstenergy (4) 68: 68: Number of degrees of freedom in T-Coupling group System is 33.00 68: 68: There were 2 NOTEs 68: 68: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_7_input.mdp]: 68: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 68: that with the Verlet scheme, nstlist has no effect on the accuracy of 68: your simulation. 68: 68: 68: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_7_input.mdp]: 68: Setting nstcalcenergy (100) equal to nstenergy (4) 68: 68: Number of degrees of freedom in T-Coupling group System is 33.00 68: 68: There were 2 NOTEs 68: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_7_full.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 68: Using 1 MPI thread 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'Argon' 68: 16 steps, 0.0 ps. 68: Generated 1 of the 1 non-bonded parameter combinations 68: 68: Excluding 1 bonded neighbours molecule type 'Argon' 68: 68: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 68: 68: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 68: 68: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 68: 68: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 68: 68: Note that mdrun will redetermine rlist based on the actual pair-list setup 68: 68: This run will generate roughly 0 Mb of data 68: Generated 1 of the 1 non-bonded parameter combinations 68: 68: Excluding 1 bonded neighbours molecule type 'Argon' 68: 68: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 68: 68: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 68: 68: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 68: 68: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 68: 68: Note that mdrun will redetermine rlist based on the actual pair-list setup 68: 68: This run will generate roughly 0 Mb of data 68: 68: Writing final coordinates. 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.056 0.028 198.6 68: (ns/day) (hour/ns) 68: Performance: 51.964 0.462 68: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_7_firstpart.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 68: Using 1 MPI thread 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'Argon' 68: 8 steps, 0.0 ps. 68: 68: Writing final coordinates. 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.049 0.025 198.4 68: (ns/day) (hour/ns) 68: Performance: 31.394 0.764 68: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_7_full.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 68: Using 1 MPI thread 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'Argon' 68: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 68: 68: Writing final coordinates. 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.050 0.026 197.1 68: (ns/day) (hour/ns) 68: Performance: 30.386 0.790 68: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_7_full.edr as double precision energy file 68: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_7_firstpart.edr as double precision energy file 68: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_7_secondpart.part0002.edr as double precision energy file 68: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/7 (190 ms) 68: [----------] 8 tests from NPT/MdrunNoAppendContinuationIsExact (1284 ms total) 68: 68: [----------] 1 test from MTTK/MdrunNoAppendContinuationIsExact 68: [ RUN ] MTTK/MdrunNoAppendContinuationIsExact.WithinTolerances/0 68: 68: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MTTK_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 68: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 68: that with the Verlet scheme, nstlist has no effect on the accuracy of 68: your simulation. 68: 68: 68: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MTTK_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 68: Setting nstcalcenergy (100) equal to nstenergy (4) 68: 68: 68: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MTTK_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 68: MTTK coupling is deprecated and will soon be removed 68: 68: Number of degrees of freedom in T-Coupling group System is 33.00 68: 68: There were 3 NOTEs 68: 68: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MTTK_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 68: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 68: that with the Verlet scheme, nstlist has no effect on the accuracy of 68: your simulation. 68: 68: 68: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MTTK_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 68: Setting nstcalcenergy (100) equal to nstenergy (4) 68: 68: 68: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MTTK_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 68: MTTK coupling is deprecated and will soon be removed 68: 68: Number of degrees of freedom in T-Coupling group System is 33.00 68: 68: There were 3 NOTEs 68: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MTTK_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 68: Using 1 MPI thread 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'Argon' 68: 16 steps, 0.0 ps. 68: Generated 1 of the 1 non-bonded parameter combinations 68: 68: Excluding 1 bonded neighbours molecule type 'Argon' 68: 68: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 68: 68: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 68: 68: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 68: 68: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 68: 68: Note that mdrun will redetermine rlist based on the actual pair-list setup 68: 68: This run will generate roughly 0 Mb of data 68: Generated 1 of the 1 non-bonded parameter combinations 68: 68: Excluding 1 bonded neighbours molecule type 'Argon' 68: 68: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 68: 68: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 68: 68: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 68: 68: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 68: 68: Note that mdrun will redetermine rlist based on the actual pair-list setup 68: 68: This run will generate roughly 0 Mb of data 68: 68: Writing final coordinates. 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.063 0.032 198.4 68: (ns/day) (hour/ns) 68: Performance: 46.626 0.515 68: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MTTK_MdrunNoAppendContinuationIsExact_WithinTolerances_0_firstpart.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 68: Using 1 MPI thread 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'Argon' 68: 8 steps, 0.0 ps. 68: 68: Writing final coordinates. 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.051 0.026 198.0 68: (ns/day) (hour/ns) 68: Performance: 30.061 0.798 68: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MTTK_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 68: Using 1 MPI thread 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'Argon' 68: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 68: 68: Writing final coordinates. 68: 68: NOTE: 18 % of the run time was spent in pair search, 68: you might want to increase nstlist (this has no effect on accuracy) 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.070 0.035 197.7 68: (ns/day) (hour/ns) 68: Performance: 21.982 1.092 68: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MTTK_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.edr as double precision energy file 68: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MTTK_MdrunNoAppendContinuationIsExact_WithinTolerances_0_firstpart.edr as double precision energy file 68: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MTTK_MdrunNoAppendContinuationIsExact_WithinTolerances_0_secondpart.part0002.edr as double precision energy file 68: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] MTTK/MdrunNoAppendContinuationIsExact.WithinTolerances/0 (200 ms) 68: [----------] 1 test from MTTK/MdrunNoAppendContinuationIsExact (200 ms total) 68: 68: [----------] 2 tests from Pull/MdrunNoAppendContinuationIsExact 68: [ RUN ] Pull/MdrunNoAppendContinuationIsExact.WithinTolerances/0 68: 68: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Pull_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 68: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 68: that with the Verlet scheme, nstlist has no effect on the accuracy of 68: your simulation. 68: 68: 68: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Pull_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 68: Setting nstcalcenergy (100) equal to nstenergy (4) 68: 68: Generating 1-4 interactions: fudge = 0.5 68: Pull group 1 'FirstWaterMolecule' has 3 atoms 68: Pull group 2 'SecondWaterMolecule' has 3 atoms 68: Number of degrees of freedom in T-Coupling group System is 9.00 68: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 68: 68: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Pull_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 68: NVE simulation: will use the initial temperature of 2573.591 K for 68: determining the Verlet buffer size 68: 68: Pull group natoms pbc atom distance at start reference at t=0 68: 1 3 2 68: 2 3 5 1.112 nm 1.000 nm 68: 68: There were 3 NOTEs 68: 68: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Pull_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 68: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 68: that with the Verlet scheme, nstlist has no effect on the accuracy of 68: your simulation. 68: 68: 68: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Pull_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 68: Setting nstcalcenergy (100) equal to nstenergy (4) 68: 68: Generating 1-4 interactions: fudge = 0.5 68: Pull group 1 'FirstWaterMolecule' has 3 atoms 68: Pull group 2 'SecondWaterMolecule' has 3 atoms 68: Number of degrees of freedom in T-Coupling group System is 9.00 68: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 68: 68: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Pull_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 68: NVE simulation: will use the initial temperature of 2573.591 K for 68: determining the Verlet buffer size 68: 68: Pull group natoms pbc atom distance at start reference at t=0 68: 1 3 2 68: 2 3 5 1.112 nm 1.000 nm 68: 68: There were 3 NOTEs 68: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Pull_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 68: Can not increase nstlist because an NVE ensemble is used 68: Using 1 MPI thread 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'spc2' 68: 16 steps, 0.0 ps. 68: Generated 3 of the 3 non-bonded parameter combinations 68: 68: Generated 3 of the 3 1-4 parameter combinations 68: 68: Excluding 2 bonded neighbours molecule type 'SOL' 68: 68: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/spc2.gro' 68: 68: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 2573.59 K 68: 68: Calculated rlist for 1x1 atom pair-list as 0.877 nm, buffer size 0.177 nm 68: 68: Set rlist, assuming 4x4 atom pair-list, to 0.862 nm, buffer size 0.162 nm 68: 68: Note that mdrun will redetermine rlist based on the actual pair-list setup 68: 68: This run will generate roughly 0 Mb of data 68: Generated 3 of the 3 non-bonded parameter combinations 68: 68: Generated 3 of the 3 1-4 parameter combinations 68: 68: Excluding 2 bonded neighbours molecule type 'SOL' 68: 68: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/spc2.gro' 68: 68: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 2573.59 K 68: 68: Calculated rlist for 1x1 atom pair-list as 0.877 nm, buffer size 0.177 nm 68: 68: Set rlist, assuming 4x4 atom pair-list, to 0.862 nm, buffer size 0.162 nm 68: 68: Note that mdrun will redetermine rlist based on the actual pair-list setup 68: 68: This run will generate roughly 0 Mb of data 68: 68: Writing final coordinates. 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.055 0.028 197.6 68: (ns/day) (hour/ns) 68: Performance: 53.135 0.452 68: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Pull_MdrunNoAppendContinuationIsExact_WithinTolerances_0_firstpart.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 68: Can not increase nstlist because an NVE ensemble is used 68: Using 1 MPI thread 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'spc2' 68: 8 steps, 0.0 ps. 68: 68: Writing final coordinates. 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.059 0.030 197.7 68: (ns/day) (hour/ns) 68: Performance: 25.960 0.925 68: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Pull_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 68: Can not increase nstlist because an NVE ensemble is used 68: Using 1 MPI thread 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'spc2' 68: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 68: 68: Writing final coordinates. 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.059 0.030 197.7 68: (ns/day) (hour/ns) 68: Performance: 26.242 0.915 68: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Pull_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.edr as double precision energy file 68: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Pull_MdrunNoAppendContinuationIsExact_WithinTolerances_0_firstpart.edr as double precision energy file 68: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Pull_MdrunNoAppendContinuationIsExact_WithinTolerances_0_secondpart.part0002.edr as double precision energy file 68: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] Pull/MdrunNoAppendContinuationIsExact.WithinTolerances/0 (217 ms) 68: [ RUN ] Pull/MdrunNoAppendContinuationIsExact.WithinTolerances/1 68: 68: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Pull_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 68: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 68: that with the Verlet scheme, nstlist has no effect on the accuracy of 68: your simulation. 68: 68: 68: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Pull_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 68: Setting nstcalcenergy (100) equal to nstenergy (4) 68: 68: Generating 1-4 interactions: fudge = 0.5 68: Pull group 1 'FirstWaterMolecule' has 3 atoms 68: Pull group 2 'SecondWaterMolecule' has 3 atoms 68: Number of degrees of freedom in T-Coupling group System is 9.00 68: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 68: 68: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Pull_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 68: NVE simulation: will use the initial temperature of 2573.591 K for 68: determining the Verlet buffer size 68: 68: Pull group natoms pbc atom distance at start reference at t=0 68: 1 3 2 68: 2 3 5 1.112 nm 1.000 nm 68: 68: There were 3 NOTEs 68: 68: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Pull_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 68: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 68: that with the Verlet scheme, nstlist has no effect on the accuracy of 68: your simulation. 68: 68: 68: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Pull_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 68: Setting nstcalcenergy (100) equal to nstenergy (4) 68: 68: Generating 1-4 interactions: fudge = 0.5 68: Pull group 1 'FirstWaterMolecule' has 3 atoms 68: Pull group 2 'SecondWaterMolecule' has 3 atoms 68: Number of degrees of freedom in T-Coupling group System is 9.00 68: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 68: 68: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Pull_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 68: NVE simulation: will use the initial temperature of 2573.591 K for 68: determining the Verlet buffer size 68: 68: Pull group natoms pbc atom distance at start reference at t=0 68: 1 3 2 68: 2 3 5 1.112 nm 1.000 nm 68: 68: There were 3 NOTEs 68: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Pull_MdrunNoAppendContinuationIsExact_WithinTolerances_1_full.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 68: Can not increase nstlist because an NVE ensemble is used 68: Using 1 MPI thread 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'spc2' 68: 16 steps, 0.0 ps. 68: Generated 3 of the 3 non-bonded parameter combinations 68: 68: Generated 3 of the 3 1-4 parameter combinations 68: 68: Excluding 2 bonded neighbours molecule type 'SOL' 68: 68: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/spc2.gro' 68: 68: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 2573.59 K 68: 68: Calculated rlist for 1x1 atom pair-list as 0.877 nm, buffer size 0.177 nm 68: 68: Set rlist, assuming 4x4 atom pair-list, to 0.862 nm, buffer size 0.162 nm 68: 68: Note that mdrun will redetermine rlist based on the actual pair-list setup 68: 68: This run will generate roughly 0 Mb of data 68: Generated 3 of the 3 non-bonded parameter combinations 68: 68: Generated 3 of the 3 1-4 parameter combinations 68: 68: Excluding 2 bonded neighbours molecule type 'SOL' 68: 68: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/spc2.gro' 68: 68: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 2573.59 K 68: 68: Calculated rlist for 1x1 atom pair-list as 0.877 nm, buffer size 0.177 nm 68: 68: Set rlist, assuming 4x4 atom pair-list, to 0.862 nm, buffer size 0.162 nm 68: 68: Note that mdrun will redetermine rlist based on the actual pair-list setup 68: 68: This run will generate roughly 0 Mb of data 68: 68: Writing final coordinates. 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.096 0.048 199.0 68: (ns/day) (hour/ns) 68: Performance: 30.296 0.792 68: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Pull_MdrunNoAppendContinuationIsExact_WithinTolerances_1_firstpart.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 68: Can not increase nstlist because an NVE ensemble is used 68: Using 1 MPI thread 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'spc2' 68: 8 steps, 0.0 ps. 68: 68: Writing final coordinates. 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.059 0.030 198.4 68: (ns/day) (hour/ns) 68: Performance: 26.170 0.917 68: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Pull_MdrunNoAppendContinuationIsExact_WithinTolerances_1_full.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 68: Can not increase nstlist because an NVE ensemble is used 68: Using 1 MPI thread 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'spc2' 68: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 68: 68: Writing final coordinates. 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.058 0.029 197.5 68: (ns/day) (hour/ns) 68: Performance: 26.529 0.905 68: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Pull_MdrunNoAppendContinuationIsExact_WithinTolerances_1_full.edr as double precision energy file 68: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Pull_MdrunNoAppendContinuationIsExact_WithinTolerances_1_firstpart.edr as double precision energy file 68: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Pull_MdrunNoAppendContinuationIsExact_WithinTolerances_1_secondpart.part0002.edr as double precision energy file 68: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] Pull/MdrunNoAppendContinuationIsExact.WithinTolerances/1 (245 ms) 68: [----------] 2 tests from Pull/MdrunNoAppendContinuationIsExact (462 ms total) 68: 68: [----------] 2 tests from Awh/MdrunNoAppendContinuationIsExact 68: [ RUN ] Awh/MdrunNoAppendContinuationIsExact.WithinTolerances/0 68: Setting the AWH bias MC random seed to -40985729 68: 68: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Awh_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 68: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 68: that with the Verlet scheme, nstlist has no effect on the accuracy of 68: your simulation. 68: 68: 68: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Awh_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 68: Setting nstcalcenergy (100) equal to nstenergy (4) 68: 68: Generating 1-4 interactions: fudge = 0.5 68: Pull group 1 'C_&_r_1' has 1 atoms 68: Pull group 2 'N_&_r_2' has 1 atoms 68: Pull group 3 'CA' has 1 atoms 68: Pull group 4 'C_&_r_2' has 1 atoms 68: Pull group 5 'N_&_r_3' has 1 atoms 68: Number of degrees of freedom in T-Coupling group System is 51.00 68: 68: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Awh_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 68: You are using a plain Coulomb cut-off, which might produce artifacts. 68: You might want to consider using PME electrostatics. 68: 68: 68: Pull group natoms pbc atom distance at start reference at t=0 68: 1 1 0 68: 2 1 0 179.098 deg 0.000 deg 68: 2 1 0 68: 3 1 0 158.667 deg 0.000 deg 68: 68: There were 3 NOTEs 68: Setting the AWH bias MC random seed to -675284641 68: 68: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Awh_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 68: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 68: that with the Verlet scheme, nstlist has no effect on the accuracy of 68: your simulation. 68: 68: 68: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Awh_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 68: Setting nstcalcenergy (100) equal to nstenergy (4) 68: 68: Generating 1-4 interactions: fudge = 0.5 68: Pull group 1 'C_&_r_1' has 1 atoms 68: Pull group 2 'N_&_r_2' has 1 atoms 68: Pull group 3 'CA' has 1 atoms 68: Pull group 4 'C_&_r_2' has 1 atoms 68: Pull group 5 'N_&_r_3' has 1 atoms 68: Number of degrees of freedom in T-Coupling group System is 51.00 68: 68: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Awh_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 68: You are using a plain Coulomb cut-off, which might produce artifacts. 68: You might want to consider using PME electrostatics. 68: 68: 68: Pull group natoms pbc atom distance at start reference at t=0 68: 1 1 0 68: 2 1 0 179.098 deg 0.000 deg 68: 2 1 0 68: 3 1 0 158.667 deg 0.000 deg 68: 68: There were 3 NOTEs 68: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Awh_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 68: Using 1 MPI thread 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'Alanine-dipeptide' 68: 16 steps, 0.0 ps. 68: Generated 2145 of the 2145 non-bonded parameter combinations 68: 68: Generated 2145 of the 2145 1-4 parameter combinations 68: 68: Excluding 3 bonded neighbours molecule type 'ALANINEDIPEPTIDE' 68: 68: turning H bonds into constraints... 68: 68: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/alanine_vacuo.gro' 68: 68: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 68: 68: Calculated rlist for 1x1 atom pair-list as 0.761 nm, buffer size 0.061 nm 68: 68: Set rlist, assuming 4x4 atom pair-list, to 0.754 nm, buffer size 0.054 nm 68: 68: Note that mdrun will redetermine rlist based on the actual pair-list setup 68: 68: This run will generate roughly 0 Mb of data 68: Generated 2145 of the 2145 non-bonded parameter combinations 68: 68: Generated 2145 of the 2145 1-4 parameter combinations 68: 68: Excluding 3 bonded neighbours molecule type 'ALANINEDIPEPTIDE' 68: 68: turning H bonds into constraints... 68: 68: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/alanine_vacuo.gro' 68: 68: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 68: 68: Calculated rlist for 1x1 atom pair-list as 0.761 nm, buffer size 0.061 nm 68: 68: Set rlist, assuming 4x4 atom pair-list, to 0.754 nm, buffer size 0.054 nm 68: 68: Note that mdrun will redetermine rlist based on the actual pair-list setup 68: 68: This run will generate roughly 0 Mb of data 68: 68: Writing final coordinates. 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.082 0.042 197.3 68: (ns/day) (hour/ns) 68: Performance: 35.130 0.683 68: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Awh_MdrunNoAppendContinuationIsExact_WithinTolerances_0_firstpart.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 68: Using 1 MPI thread 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'Alanine-dipeptide' 68: 8 steps, 0.0 ps. 68: 68: Writing final coordinates. 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.069 0.035 194.7 68: (ns/day) (hour/ns) 68: Performance: 21.965 1.093 68: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Awh_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 68: Using 1 MPI thread 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'Alanine-dipeptide' 68: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 68: 68: Writing final coordinates. 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.077 0.039 197.1 68: (ns/day) (hour/ns) 68: Performance: 19.818 1.211 68: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Awh_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.edr as double precision energy file 68: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Awh_MdrunNoAppendContinuationIsExact_WithinTolerances_0_firstpart.edr as double precision energy file 68: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Awh_MdrunNoAppendContinuationIsExact_WithinTolerances_0_secondpart.part0002.edr as double precision energy file 68: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] Awh/MdrunNoAppendContinuationIsExact.WithinTolerances/0 (565 ms) 68: [ RUN ] Awh/MdrunNoAppendContinuationIsExact.WithinTolerances/1 68: Setting the AWH bias MC random seed to -344195374 68: 68: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Awh_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 68: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 68: that with the Verlet scheme, nstlist has no effect on the accuracy of 68: your simulation. 68: 68: 68: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Awh_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 68: Setting nstcalcenergy (100) equal to nstenergy (4) 68: 68: Generating 1-4 interactions: fudge = 0.5 68: Pull group 1 'C_&_r_1' has 1 atoms 68: Pull group 2 'N_&_r_2' has 1 atoms 68: Pull group 3 'CA' has 1 atoms 68: Pull group 4 'C_&_r_2' has 1 atoms 68: Pull group 5 'N_&_r_3' has 1 atoms 68: Number of degrees of freedom in T-Coupling group System is 51.00 68: 68: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Awh_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 68: You are using a plain Coulomb cut-off, which might produce artifacts. 68: You might want to consider using PME electrostatics. 68: 68: 68: Pull group natoms pbc atom distance at start reference at t=0 68: 1 1 0 68: 2 1 0 179.098 deg 0.000 deg 68: 2 1 0 68: 3 1 0 158.667 deg 0.000 deg 68: 68: There were 3 NOTEs 68: Setting the AWH bias MC random seed to -1096698645 68: 68: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Awh_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 68: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 68: that with the Verlet scheme, nstlist has no effect on the accuracy of 68: your simulation. 68: 68: 68: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Awh_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 68: Setting nstcalcenergy (100) equal to nstenergy (4) 68: 68: Generating 1-4 interactions: fudge = 0.5 68: Pull group 1 'C_&_r_1' has 1 atoms 68: Pull group 2 'N_&_r_2' has 1 atoms 68: Pull group 3 'CA' has 1 atoms 68: Pull group 4 'C_&_r_2' has 1 atoms 68: Pull group 5 'N_&_r_3' has 1 atoms 68: Number of degrees of freedom in T-Coupling group System is 51.00 68: 68: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Awh_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 68: You are using a plain Coulomb cut-off, which might produce artifacts. 68: You might want to consider using PME electrostatics. 68: 68: 68: Pull group natoms pbc atom distance at start reference at t=0 68: 1 1 0 68: 2 1 0 179.098 deg 0.000 deg 68: 2 1 0 68: 3 1 0 158.667 deg 0.000 deg 68: 68: There were 3 NOTEs 68: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Awh_MdrunNoAppendContinuationIsExact_WithinTolerances_1_full.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 68: Using 1 MPI thread 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'Alanine-dipeptide' 68: 16 steps, 0.0 ps. 68: Generated 2145 of the 2145 non-bonded parameter combinations 68: 68: Generated 2145 of the 2145 1-4 parameter combinations 68: 68: Excluding 3 bonded neighbours molecule type 'ALANINEDIPEPTIDE' 68: 68: turning H bonds into constraints... 68: 68: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/alanine_vacuo.gro' 68: 68: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 68: 68: Calculated rlist for 1x1 atom pair-list as 0.761 nm, buffer size 0.061 nm 68: 68: Set rlist, assuming 4x4 atom pair-list, to 0.754 nm, buffer size 0.054 nm 68: 68: Note that mdrun will redetermine rlist based on the actual pair-list setup 68: 68: This run will generate roughly 0 Mb of data 68: Generated 2145 of the 2145 non-bonded parameter combinations 68: 68: Generated 2145 of the 2145 1-4 parameter combinations 68: 68: Excluding 3 bonded neighbours molecule type 'ALANINEDIPEPTIDE' 68: 68: turning H bonds into constraints... 68: 68: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/alanine_vacuo.gro' 68: 68: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 68: 68: Calculated rlist for 1x1 atom pair-list as 0.761 nm, buffer size 0.061 nm 68: 68: Set rlist, assuming 4x4 atom pair-list, to 0.754 nm, buffer size 0.054 nm 68: 68: Note that mdrun will redetermine rlist based on the actual pair-list setup 68: 68: This run will generate roughly 0 Mb of data 68: 68: Writing final coordinates. 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.100 0.051 197.6 68: (ns/day) (hour/ns) 68: Performance: 29.058 0.826 68: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Awh_MdrunNoAppendContinuationIsExact_WithinTolerances_1_firstpart.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 68: Using 1 MPI thread 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'Alanine-dipeptide' 68: 8 steps, 0.0 ps. 68: 68: Writing final coordinates. 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.074 0.038 194.8 68: (ns/day) (hour/ns) 68: Performance: 20.562 1.167 68: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Awh_MdrunNoAppendContinuationIsExact_WithinTolerances_1_full.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 68: Using 1 MPI thread 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'Alanine-dipeptide' 68: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 68: 68: Writing final coordinates. 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.076 0.039 196.6 68: (ns/day) (hour/ns) 68: Performance: 20.154 1.191 68: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Awh_MdrunNoAppendContinuationIsExact_WithinTolerances_1_full.edr as double precision energy file 68: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Awh_MdrunNoAppendContinuationIsExact_WithinTolerances_1_firstpart.edr as double precision energy file 68: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Awh_MdrunNoAppendContinuationIsExact_WithinTolerances_1_secondpart.part0002.edr as double precision energy file 68: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] Awh/MdrunNoAppendContinuationIsExact.WithinTolerances/1 (580 ms) 68: [----------] 2 tests from Awh/MdrunNoAppendContinuationIsExact (1146 ms total) 68: 68: [----------] 1 test from ExpandedEnsemble/MdrunNoAppendContinuationIsExact 68: [ RUN ] ExpandedEnsemble/MdrunNoAppendContinuationIsExact.WithinTolerances/0 68: 68: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/ExpandedEnsemble_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 68: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 68: that with the Verlet scheme, nstlist has no effect on the accuracy of 68: your simulation. 68: 68: Generating 1-4 interactions: fudge = 0.5 68: Number of degrees of freedom in T-Coupling group System is 79.00 68: 68: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/ExpandedEnsemble_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 68: You are using a plain Coulomb cut-off, which might produce artifacts. 68: You might want to consider using PME electrostatics. 68: 68: 68: 68: There were 2 NOTEs 68: 68: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/ExpandedEnsemble_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 68: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 68: that with the Verlet scheme, nstlist has no effect on the accuracy of 68: your simulation. 68: 68: Generating 1-4 interactions: fudge = 0.5 68: Number of degrees of freedom in T-Coupling group System is 79.00 68: 68: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/ExpandedEnsemble_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 68: You are using a plain Coulomb cut-off, which might produce artifacts. 68: You might want to consider using PME electrostatics. 68: 68: 68: 68: There were 2 NOTEs 68: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/ExpandedEnsemble_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 68: Using 1 MPI thread 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun '30 atom system in water' 68: 16 steps, 0.0 ps. 68: Generated 2485 of the 2485 non-bonded parameter combinations 68: 68: Generated 2485 of the 2485 1-4 parameter combinations 68: 68: Excluding 3 bonded neighbours molecule type 'nonanol' 68: 68: turning H bonds into constraints... 68: 68: Excluding 2 bonded neighbours molecule type 'SOL' 68: 68: turning H bonds into constraints... 68: 68: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/nonanol_vacuo.gro' 68: 68: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 68: 68: Calculated rlist for 1x1 atom pair-list as 0.764 nm, buffer size 0.064 nm 68: 68: Set rlist, assuming 4x4 atom pair-list, to 0.757 nm, buffer size 0.057 nm 68: 68: Note that mdrun will redetermine rlist based on the actual pair-list setup 68: 68: This run will generate roughly 0 Mb of data 68: Generated 2485 of the 2485 non-bonded parameter combinations 68: 68: Generated 2485 of the 2485 1-4 parameter combinations 68: 68: Excluding 3 bonded neighbours molecule type 'nonanol' 68: 68: turning H bonds into constraints... 68: 68: Excluding 2 bonded neighbours molecule type 'SOL' 68: 68: turning H bonds into constraints... 68: 68: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/nonanol_vacuo.gro' 68: 68: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 68: 68: Calculated rlist for 1x1 atom pair-list as 0.764 nm, buffer size 0.064 nm 68: 68: Set rlist, assuming 4x4 atom pair-list, to 0.757 nm, buffer size 0.057 nm 68: 68: Note that mdrun will redetermine rlist based on the actual pair-list setup 68: 68: This run will generate roughly 0 Mb of data 68: 68: Writing final coordinates. 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.121 0.061 199.2 68: (ns/day) (hour/ns) 68: Performance: 24.165 0.993 68: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/ExpandedEnsemble_MdrunNoAppendContinuationIsExact_WithinTolerances_0_firstpart.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 68: Using 1 MPI thread 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun '30 atom system in water' 68: 8 steps, 0.0 ps. 68: 68: Writing final coordinates. 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.131 0.066 199.3 68: (ns/day) (hour/ns) 68: Performance: 11.802 2.033 68: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/ExpandedEnsemble_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 68: Using 1 MPI thread 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun '30 atom system in water' 68: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 68: 68: Writing final coordinates. 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.091 0.046 197.1 68: (ns/day) (hour/ns) 68: Performance: 16.762 1.432 68: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/ExpandedEnsemble_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.edr as double precision energy file 68: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/ExpandedEnsemble_MdrunNoAppendContinuationIsExact_WithinTolerances_0_firstpart.edr as double precision energy file 68: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/ExpandedEnsemble_MdrunNoAppendContinuationIsExact_WithinTolerances_0_secondpart.part0002.edr as double precision energy file 68: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] ExpandedEnsemble/MdrunNoAppendContinuationIsExact.WithinTolerances/0 (720 ms) 68: [----------] 1 test from ExpandedEnsemble/MdrunNoAppendContinuationIsExact (720 ms total) 68: 68: [----------] 3 tests from Checking/InitialConstraintsTest 68: [ RUN ] Checking/InitialConstraintsTest.Works/0 68: Number of degrees of freedom in T-Coupling group rest is 11.00 68: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 68: 68: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Checking_InitialConstraintsTest_Works_0_input.mdp]: 68: NVE simulation: will use the initial temperature of 1141.954 K for 68: determining the Verlet buffer size 68: 68: 68: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Checking_InitialConstraintsTest_Works_0_input.mdp]: 68: You are using a plain Coulomb cut-off, which might produce artifacts. 68: You might want to consider using PME electrostatics. 68: 68: 68: 68: There were 2 NOTEs 68: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Checking_InitialConstraintsTest_Works_0.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 68: Can not increase nstlist because an NVE ensemble is used 68: Using 1 MPI thread 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'spc-and-methanol' 68: 1 steps, 0.0 ps. 68: Setting the LD random seed to -168133269 68: 68: Generated 8 of the 10 non-bonded parameter combinations 68: 68: Excluding 2 bonded neighbours molecule type 'Methanol' 68: 68: turning H bonds into constraints... 68: 68: Excluding 2 bonded neighbours molecule type 'SOL' 68: 68: turning H bonds into constraints... 68: 68: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/spc-and-methanol.gro' 68: 68: Determining Verlet buffer for a tolerance of 0.0001 kJ/mol/ps at 1141.95 K 68: 68: Calculated rlist for 1x1 atom pair-list as 1.126 nm, buffer size 0.126 nm 68: 68: Set rlist, assuming 4x4 atom pair-list, to 1.110 nm, buffer size 0.110 nm 68: 68: Note that mdrun will redetermine rlist based on the actual pair-list setup 68: 68: This run will generate roughly 0 Mb of data 68: 68: Writing final coordinates. 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.029 0.015 196.3 68: (ns/day) (hour/ns) 68: Performance: 11.602 2.069 68: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Checking_InitialConstraintsTest_Works_0_spc-and-methanol.edr as double precision energy file 68: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 [ OK ] Checking/InitialConstraintsTest.Works/0 (62 ms) 68: [ RUN ] Checking/InitialConstraintsTest.Works/1 68: Number of degrees of freedom in T-Coupling group rest is 11.00 68: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 68: 68: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Checking_InitialConstraintsTest_Works_1_input.mdp]: 68: NVE simulation: will use the initial temperature of 1141.954 K for 68: determining the Verlet buffer size 68: 68: 68: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Checking_InitialConstraintsTest_Works_1_input.mdp]: 68: You are using a plain Coulomb cut-off, which might produce artifacts. 68: You might want to consider using PME electrostatics. 68: 68: 68: 68: There were 2 NOTEs 68: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Checking_InitialConstraintsTest_Works_1.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 68: Can not increase nstlist because an NVE ensemble is used 68: Using 1 MPI thread 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'spc-and-methanol' 68: 1 steps, 0.0 ps. 68: Setting the LD random seed to -134251285 68: 68: Generated 8 of the 10 non-bonded parameter combinations 68: 68: Excluding 2 bonded neighbours molecule type 'Methanol' 68: 68: turning H bonds into constraints... 68: 68: Excluding 2 bonded neighbours molecule type 'SOL' 68: 68: turning H bonds into constraints... 68: 68: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/spc-and-methanol.gro' 68: 68: Determining Verlet buffer for a tolerance of 0.0001 kJ/mol/ps at 1141.95 K 68: 68: Calculated rlist for 1x1 atom pair-list as 1.126 nm, buffer size 0.126 nm 68: 68: Set rlist, assuming 4x4 atom pair-list, to 1.110 nm, buffer size 0.110 nm 68: 68: Note that mdrun will redetermine rlist based on the actual pair-list setup 68: 68: This run will generate roughly 0 Mb of data 68: 68: Writing final coordinates. 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.036 0.018 197.8 68: (ns/day) (hour/ns) 68: Performance: 9.403 2.552 68: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Checking_InitialConstraintsTest_Works_1_spc-and-methanol.edr as double precision energy file 68: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 [ OK ] Checking/InitialConstraintsTest.Works/1 (67 ms) 68: [ RUN ] Checking/InitialConstraintsTest.Works/2 68: 68: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Checking_InitialConstraintsTest_Works_2_input.mdp]: 68: Integrator method md-vv-avek is implemented primarily for validation 68: purposes; for molecular dynamics, you should probably be using md or 68: md-vv 68: 68: Number of degrees of freedom in T-Coupling group rest is 11.00 68: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 68: 68: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Checking_InitialConstraintsTest_Works_2_input.mdp]: 68: NVE simulation: will use the initial temperature of 1141.954 K for 68: determining the Verlet buffer size 68: 68: 68: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Checking_InitialConstraintsTest_Works_2_input.mdp]: 68: You are using a plain Coulomb cut-off, which might produce artifacts. 68: You might want to consider using PME electrostatics. 68: 68: 68: 68: There were 3 NOTEs 68: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Checking_InitialConstraintsTest_Works_2.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 68: Can not increase nstlist because an NVE ensemble is used 68: Using 1 MPI thread 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'spc-and-methanol' 68: 1 steps, 0.0 ps. 68: Setting the LD random seed to -1218449443 68: 68: Generated 8 of the 10 non-bonded parameter combinations 68: 68: Excluding 2 bonded neighbours molecule type 'Methanol' 68: 68: turning H bonds into constraints... 68: 68: Excluding 2 bonded neighbours molecule type 'SOL' 68: 68: turning H bonds into constraints... 68: 68: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/spc-and-methanol.gro' 68: 68: Determining Verlet buffer for a tolerance of 0.0001 kJ/mol/ps at 1141.95 K 68: 68: Calculated rlist for 1x1 atom pair-list as 1.126 nm, buffer size 0.126 nm 68: 68: Set rlist, assuming 4x4 atom pair-list, to 1.110 nm, buffer size 0.110 nm 68: 68: Note that mdrun will redetermine rlist based on the actual pair-list setup 68: 68: This run will generate roughly 0 Mb of data 68: 68: Writing final coordinates. 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.029 0.015 196.2 68: (ns/day) (hour/ns) 68: Performance: 11.835 2.028 68: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Checking_InitialConstraintsTest_Works_2_spc-and-methanol.edr as double precision energy file 68: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 [ OK ] Checking/InitialConstraintsTest.Works/2 (64 ms) 68: [----------] 3 tests from Checking/InitialConstraintsTest (194 ms total) 68: 68: [----------] Global test environment tear-down 68: [==========] 76 tests from 13 test suites ran. (23962 ms total) 68: [ PASSED ] 76 tests. 68/92 Test #68: MdrunIOTests .............................. Passed 24.06 sec test 69 Start 69: MdrunTestsOneRank 69: Test command: /build/reproducible-path/gromacs-2025.1/build/basic-dp/bin/mdrun-test "-ntomp" "2" "-ntmpi" "1" "--gtest_output=xml:/build/reproducible-path/gromacs-2025.1/build/basic-dp/Testing/Temporary/MdrunTestsOneRank.xml" 69: Working Directory: /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests 69: Test timeout computed to be: 600 69: [==========] Running 29 tests from 8 test suites. 69: [----------] Global test environment set-up. 69: [----------] 1 test from CompelTest 69: [ RUN ] CompelTest.SwapCanRun 69: Generating 1-4 interactions: fudge = 0.5 69: Split0 group 'Ch0' contains 83 atoms. 69: Split1 group 'Ch1' contains 83 atoms. 69: Solvent group 'SOL' contains 11931 atoms. 69: Swap group 'NA+' contains 19 atoms. 69: Swap group 'CL-' contains 19 atoms. 69: Number of degrees of freedom in T-Coupling group System is 27869.00 69: 69: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/CompelTest_SwapCanRun_input.mdp]: 69: Removing center of mass motion in the presence of position restraints 69: might cause artifacts. When you are using position restraints to 69: equilibrate a macro-molecule, the artifacts are usually negligible. 69: 69: 69: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/CompelTest_SwapCanRun_input.mdp]: 69: You are using a plain Coulomb cut-off, which might produce artifacts. 69: You might want to consider using PME electrostatics. 69: 69: 69: 69: There were 2 NOTEs 69: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/CompelTest_SwapCanRun.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 69: Update groups can not be used for this system because there are three or more consecutively coupled constraints 69: 69: Using 1 MPI thread 69: Using 2 OpenMP threads 69: 69: 69: NOTE: The number of threads is not equal to the number of (logical) cpus 69: and the -pin option is set to auto: will not pin threads to cpus. 69: This can lead to significant performance degradation. 69: Consider using -pin on (and -pinoffset in case you run multiple jobs). 69: SWAP: Determining initial numbers of ions per compartment. 69: SWAP: Setting pointers for checkpoint writing 69: SWAP: Channel 0 flux history for ion type NA+ (charge 1): 0 molecules 69: SWAP: Channel 1 flux history for ion type NA+ (charge 1): 0 molecules 69: SWAP: Channel 0 flux history for ion type CL- (charge -1): 0 molecules 69: SWAP: Channel 1 flux history for ion type CL- (charge -1): 0 molecules 69: starting mdrun 'Channel_coco in octane membrane' 69: 2 steps, 0.0 ps. 69: Setting the LD random seed to -105547849 69: 69: Generated 330891 of the 330891 non-bonded parameter combinations 69: 69: Generated 330891 of the 330891 1-4 parameter combinations 69: 69: Excluding 3 bonded neighbours molecule type 'Protein' 69: 69: turning all bonds into constraints... 69: 69: Excluding 3 bonded neighbours molecule type 'OCT' 69: 69: turning all bonds into constraints... 69: 69: Excluding 1 bonded neighbours molecule type 'NA' 69: 69: turning all bonds into constraints... 69: 69: Excluding 1 bonded neighbours molecule type 'CL' 69: 69: turning all bonds into constraints... 69: 69: Excluding 3 bonded neighbours molecule type 'Protein' 69: 69: Excluding 3 bonded neighbours molecule type 'OCT' 69: 69: Excluding 2 bonded neighbours molecule type 'SOL' 69: 69: turning all bonds into constraints... 69: 69: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/OctaneSandwich.gro' 69: 69: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 300 K 69: 69: Calculated rlist for 1x1 atom pair-list as 1.316 nm, buffer size 0.316 nm 69: 69: Set rlist, assuming 4x4 atom pair-list, to 1.262 nm, buffer size 0.262 nm 69: 69: Note that mdrun will redetermine rlist based on the actual pair-list setup 69: 69: This run will generate roughly 1 Mb of data 69: 69: Writing final coordinates. 69: 69: NOTE: 12 % of the run time was spent in pair search, 69: you might want to increase nstlist (this has no effect on accuracy) 69: 69: Core t (s) Wall t (s) (%) 69: Time: 5.929 2.965 200.0 69: (ns/day) (hour/ns) 69: Performance: 0.437 54.903 69: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/CompelTest_SwapCanRun.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 69: Overriding nsteps with value passed on the command line: 2 steps, 0.01 ps 69: 69: Update groups can not be used for this system because there are three or more consecutively coupled constraints 69: 69: Using 1 MPI thread 69: Using 2 OpenMP threads 69: 69: 69: NOTE: The number of threads is not equal to the number of (logical) cpus 69: and the -pin option is set to auto: will not pin threads to cpus. 69: This can lead to significant performance degradation. 69: Consider using -pin on (and -pinoffset in case you run multiple jobs). 69: SWAP: Setting pointers for checkpoint writing 69: SWAP: Copying channel fluxes from checkpoint file data 69: SWAP: Channel 0 flux history for ion type NA+ (charge 1): 0 molecules 69: SWAP: Channel 1 flux history for ion type NA+ (charge 1): 0 molecules 69: SWAP: Channel 0 flux history for ion type CL- (charge -1): 0 molecules 69: SWAP: Channel 1 flux history for ion type CL- (charge -1): 0 molecules 69: starting mdrun 'Channel_coco in octane membrane' 69: 4 steps, 0.0 ps (continuing from step 2, 0.0 ps). 69: 69: Writing final coordinates. 69: 69: Core t (s) Wall t (s) (%) 69: Time: 5.267 2.634 200.0 69: (ns/day) (hour/ns) 69: Performance: 0.492 48.771 69: [ OK ] CompelTest.SwapCanRun (12536 ms) 69: [----------] 1 test from CompelTest (12536 ms total) 69: 69: [----------] 6 tests from BondedInteractionsTest 69: [ RUN ] BondedInteractionsTest.NormalBondWorks 69: 69: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_NormalBondWorks_input.mdp]: 69: For a correct single-point energy evaluation with nsteps = 0, use 69: continuation = yes to avoid constraining the input coordinates. 69: 69: 69: NOTE 2 [file BondedInteractionsTest_NormalBondWorks_butane1.top, line 31]: 69: In moleculetype 'butane' 2 atoms are not bound by a potential or 69: constraint to any other atom in the same moleculetype. Although 69: technically this might not cause issues in a simulation, this often means 69: that the user forgot to add a bond/potential/constraint or put multiple 69: molecules in the same moleculetype definition by mistake. Run with -v to 69: get information for each atom. 69: 69: Number of degrees of freedom in T-Coupling group rest is 9.00 69: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 69: 69: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_NormalBondWorks_input.mdp]: 69: NVE simulation with an initial temperature of zero: will use a Verlet 69: buffer of 10%. Check your energy drift! 69: 69: 69: There were 3 NOTEs 69: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_NormalBondWorks.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 69: Can not increase nstlist because an NVE ensemble is used 69: Using 1 MPI thread 69: Using 2 OpenMP threads 69: 69: 69: NOTE: The number of threads is not equal to the number of (logical) cpus 69: and the -pin option is set to auto: will not pin threads to cpus. 69: This can lead to significant performance degradation. 69: Consider using -pin on (and -pinoffset in case you run multiple jobs). 69: starting md rerun 'A single butane', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/butane1.gro' 69: 69: Reading frames from gro file 'A single butane', 4 atoms. 69: Reading frame 0 time 0.000 Last frame 0 time 0.000 69: 69: NOTE: 14 % of the run time was spent in pair search, 69: you might want to increase nstlist (this has no effect on accuracy) 69: 69: Core t (s) Wall t (s) (%) 69: Time: 0.002 0.001 183.5 69: (ns/day) (hour/ns) 69: Performance: 77.500 0.310 69: Setting the LD random seed to -536943686 69: 69: Generated 3 of the 3 non-bonded parameter combinations 69: 69: Excluding 3 bonded neighbours molecule type 'butane' 69: 69: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/butane1.gro', all velocities are zero 69: 69: This run will generate roughly 0 Mb of data 69: [ OK ] BondedInteractionsTest.NormalBondWorks (45 ms) 69: [ RUN ] BondedInteractionsTest.TabulatedBondWorks 69: 69: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_TabulatedBondWorks_input.mdp]: 69: For a correct single-point energy evaluation with nsteps = 0, use 69: continuation = yes to avoid constraining the input coordinates. 69: 69: 69: NOTE 2 [file BondedInteractionsTest_TabulatedBondWorks_butane1.top, line 31]: 69: In moleculetype 'butane' 2 atoms are not bound by a potential or 69: constraint to any other atom in the same moleculetype. Although 69: technically this might not cause issues in a simulation, this often means 69: that the user forgot to add a bond/potential/constraint or put multiple 69: molecules in the same moleculetype definition by mistake. Run with -v to 69: get information for each atom. 69: 69: Number of degrees of freedom in T-Coupling group rest is 9.00 69: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 69: 69: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_TabulatedBondWorks_input.mdp]: 69: NVE simulation with an initial temperature of zero: will use a Verlet 69: buffer of 10%. Check your energy drift! 69: 69: 69: There were 3 NOTEs 69: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_TabulatedBondWorks.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 69: Can not increase nstlist because an NVE ensemble is used 69: Using 1 MPI thread 69: Using 2 OpenMP threads 69: 69: 69: NOTE: The number of threads is not equal to the number of (logical) cpus 69: and the -pin option is set to auto: will not pin threads to cpus. 69: This can lead to significant performance degradation. 69: Consider using -pin on (and -pinoffset in case you run multiple jobs). 69: starting md rerun 'A single butane', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/butane1.gro' 69: 69: Reading frames from gro file 'A single butane', 4 atoms. 69: Reading frame 0 time 0.000 Last frame 0 time 0.000 69: 69: NOTE: 12 % of the run time was spent in pair search, 69: you might want to increase nstlist (this has no effect on accuracy) 69: 69: Core t (s) Wall t (s) (%) 69: Time: 0.002 0.001 184.1 69: (ns/day) (hour/ns) 69: Performance: 63.722 0.377 69: Setting the LD random seed to 2130440131 69: 69: Generated 3 of the 3 non-bonded parameter combinations 69: 69: Excluding 3 bonded neighbours molecule type 'butane' 69: 69: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/butane1.gro', all velocities are zero 69: 69: This run will generate roughly 0 Mb of data 69: [ OK ] BondedInteractionsTest.TabulatedBondWorks (49 ms) 69: [ RUN ] BondedInteractionsTest.NormalAngleWorks 69: 69: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_NormalAngleWorks_input.mdp]: 69: For a correct single-point energy evaluation with nsteps = 0, use 69: continuation = yes to avoid constraining the input coordinates. 69: 69: 69: NOTE 2 [file BondedInteractionsTest_NormalAngleWorks_butane1.top, line 31]: 69: In moleculetype 'butane' 4 atoms are not bound by a potential or 69: constraint to any other atom in the same moleculetype. Although 69: technically this might not cause issues in a simulation, this often means 69: that the user forgot to add a bond/potential/constraint or put multiple 69: molecules in the same moleculetype definition by mistake. Run with -v to 69: get information for each atom. 69: 69: Number of degrees of freedom in T-Coupling group rest is 9.00 69: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 69: 69: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_NormalAngleWorks_input.mdp]: 69: NVE simulation with an initial temperature of zero: will use a Verlet 69: buffer of 10%. Check your energy drift! 69: 69: 69: There were 3 NOTEs 69: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_NormalAngleWorks.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 69: Can not increase nstlist because an NVE ensemble is used 69: Using 1 MPI thread 69: Using 2 OpenMP threads 69: 69: 69: NOTE: The number of threads is not equal to the number of (logical) cpus 69: and the -pin option is set to auto: will not pin threads to cpus. 69: This can lead to significant performance degradation. 69: Consider using -pin on (and -pinoffset in case you run multiple jobs). 69: starting md rerun 'A single butane', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/butane1.gro' 69: 69: Reading frames from gro file 'A single butane', 4 atoms. 69: Reading frame 0 time 0.000 Last frame 0 time 0.000 69: 69: NOTE: 12 % of the run time was spent in pair search, 69: you might want to increase nstlist (this has no effect on accuracy) 69: 69: Core t (s) Wall t (s) (%) 69: Time: 0.003 0.001 183.3 69: (ns/day) (hour/ns) 69: Performance: 59.633 0.402 69: Setting the LD random seed to -299941921 69: 69: Generated 3 of the 3 non-bonded parameter combinations 69: 69: Excluding 3 bonded neighbours molecule type 'butane' 69: 69: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/butane1.gro', all velocities are zero 69: 69: This run will generate roughly 0 Mb of data 69: [ OK ] BondedInteractionsTest.NormalAngleWorks (47 ms) 69: [ RUN ] BondedInteractionsTest.TabulatedAngleWorks 69: 69: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_TabulatedAngleWorks_input.mdp]: 69: For a correct single-point energy evaluation with nsteps = 0, use 69: continuation = yes to avoid constraining the input coordinates. 69: 69: 69: NOTE 2 [file BondedInteractionsTest_TabulatedAngleWorks_butane1.top, line 31]: 69: In moleculetype 'butane' 4 atoms are not bound by a potential or 69: constraint to any other atom in the same moleculetype. Although 69: technically this might not cause issues in a simulation, this often means 69: that the user forgot to add a bond/potential/constraint or put multiple 69: molecules in the same moleculetype definition by mistake. Run with -v to 69: get information for each atom. 69: 69: Number of degrees of freedom in T-Coupling group rest is 9.00 69: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 69: 69: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_TabulatedAngleWorks_input.mdp]: 69: NVE simulation with an initial temperature of zero: will use a Verlet 69: buffer of 10%. Check your energy drift! 69: 69: 69: There were 3 NOTEs 69: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_TabulatedAngleWorks.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 69: Can not increase nstlist because an NVE ensemble is used 69: Using 1 MPI thread 69: Using 2 OpenMP threads 69: 69: 69: NOTE: The number of threads is not equal to the number of (logical) cpus 69: and the -pin option is set to auto: will not pin threads to cpus. 69: This can lead to significant performance degradation. 69: Consider using -pin on (and -pinoffset in case you run multiple jobs). 69: starting md rerun 'A single butane', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/butane1.gro' 69: 69: Reading frames from gro file 'A single butane', 4 atoms. 69: Reading frame 0 time 0.000 Last frame 0 time 0.000 69: 69: NOTE: 13 % of the run time was spent in pair search, 69: you might want to increase nstlist (this has no effect on accuracy) 69: 69: Core t (s) Wall t (s) (%) 69: Time: 0.002 0.001 184.5 69: (ns/day) (hour/ns) 69: Performance: 67.134 0.357 69: Setting the LD random seed to 771153638 69: 69: Generated 3 of the 3 non-bonded parameter combinations 69: 69: Excluding 3 bonded neighbours molecule type 'butane' 69: 69: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/butane1.gro', all velocities are zero 69: 69: This run will generate roughly 0 Mb of data 69: [ OK ] BondedInteractionsTest.TabulatedAngleWorks (46 ms) 69: [ RUN ] BondedInteractionsTest.NormalDihedralWorks 69: 69: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_NormalDihedralWorks_input.mdp]: 69: For a correct single-point energy evaluation with nsteps = 0, use 69: continuation = yes to avoid constraining the input coordinates. 69: 69: 69: NOTE 2 [file BondedInteractionsTest_NormalDihedralWorks_butane1.top, line 31]: 69: In moleculetype 'butane' 4 atoms are not bound by a potential or 69: constraint to any other atom in the same moleculetype. Although 69: technically this might not cause issues in a simulation, this often means 69: that the user forgot to add a bond/potential/constraint or put multiple 69: molecules in the same moleculetype definition by mistake. Run with -v to 69: get information for each atom. 69: 69: Number of degrees of freedom in T-Coupling group rest is 9.00 69: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 69: 69: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_NormalDihedralWorks_input.mdp]: 69: NVE simulation with an initial temperature of zero: will use a Verlet 69: buffer of 10%. Check your energy drift! 69: 69: 69: There were 3 NOTEs 69: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_NormalDihedralWorks.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 69: Can not increase nstlist because an NVE ensemble is used 69: Using 1 MPI thread 69: Using 2 OpenMP threads 69: 69: 69: NOTE: The number of threads is not equal to the number of (logical) cpus 69: and the -pin option is set to auto: will not pin threads to cpus. 69: This can lead to significant performance degradation. 69: Consider using -pin on (and -pinoffset in case you run multiple jobs). 69: starting md rerun 'A single butane', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/butane1.gro' 69: 69: Reading frames from gro file 'A single butane', 4 atoms. 69: Reading frame 0 time 0.000 Last frame 0 time 0.000 69: 69: NOTE: 13 % of the run time was spent in pair search, 69: you might want to increase nstlist (this has no effect on accuracy) 69: 69: Core t (s) Wall t (s) (%) 69: Time: 0.002 0.001 173.2 69: (ns/day) (hour/ns) 69: Performance: 68.686 0.349 69: Setting the LD random seed to -77856817 69: 69: Generated 3 of the 3 non-bonded parameter combinations 69: 69: Excluding 3 bonded neighbours molecule type 'butane' 69: 69: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/butane1.gro', all velocities are zero 69: 69: This run will generate roughly 0 Mb of data 69: [ OK ] BondedInteractionsTest.NormalDihedralWorks (42 ms) 69: [ RUN ] BondedInteractionsTest.TabulatedDihedralWorks 69: 69: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_TabulatedDihedralWorks_input.mdp]: 69: For a correct single-point energy evaluation with nsteps = 0, use 69: continuation = yes to avoid constraining the input coordinates. 69: 69: 69: NOTE 2 [file BondedInteractionsTest_TabulatedDihedralWorks_butane1.top, line 31]: 69: In moleculetype 'butane' 4 atoms are not bound by a potential or 69: constraint to any other atom in the same moleculetype. Although 69: technically this might not cause issues in a simulation, this often means 69: that the user forgot to add a bond/potential/constraint or put multiple 69: molecules in the same moleculetype definition by mistake. Run with -v to 69: get information for each atom. 69: 69: Number of degrees of freedom in T-Coupling group rest is 9.00 69: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 69: 69: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_TabulatedDihedralWorks_input.mdp]: 69: NVE simulation with an initial temperature of zero: will use a Verlet 69: buffer of 10%. Check your energy drift! 69: 69: 69: There were 3 NOTEs 69: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_TabulatedDihedralWorks.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 69: Can not increase nstlist because an NVE ensemble is used 69: Using 1 MPI thread 69: Using 2 OpenMP threads 69: 69: 69: NOTE: The number of threads is not equal to the number of (logical) cpus 69: and the -pin option is set to auto: will not pin threads to cpus. 69: This can lead to significant performance degradation. 69: Consider using -pin on (and -pinoffset in case you run multiple jobs). 69: starting md rerun 'A single butane', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/butane1.gro' 69: 69: Reading frames from gro file 'A single butane', 4 atoms. 69: Reading frame 0 time 0.000 Last frame 0 time 0.000 69: 69: NOTE: 14 % of the run time was spent in pair search, 69: you might want to increase nstlist (this has no effect on accuracy) 69: 69: Core t (s) Wall t (s) (%) 69: Time: 0.002 0.001 185.4 69: (ns/day) (hour/ns) 69: Performance: 69.959 0.343 69: Setting the LD random seed to -541148053 69: 69: Generated 3 of the 3 non-bonded parameter combinations 69: 69: Excluding 3 bonded neighbours molecule type 'butane' 69: 69: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/butane1.gro', all velocities are zero 69: 69: This run will generate roughly 0 Mb of data 69: [ OK ] BondedInteractionsTest.TabulatedDihedralWorks (46 ms) 69: [----------] 6 tests from BondedInteractionsTest (277 ms total) 69: 69: [----------] 2 tests from BoxDeformationTest 69: [ RUN ] BoxDeformationTest.flowDoesNotAffectEkin 69: 69: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BoxDeformationTest_flowDoesNotAffectEkin_input.mdp]: 69: verlet-buffer-pressure-tolerance is ignored when verlet-buffer-tolerance 69: < 0 69: 69: 69: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BoxDeformationTest_flowDoesNotAffectEkin_input.mdp]: 69: Setting nstcalcenergy (100) equal to nstenergy (10) 69: 69: 69: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BoxDeformationTest_flowDoesNotAffectEkin_input.mdp]: 69: For a correct single-point energy evaluation with nsteps = 0, use 69: continuation = yes to avoid constraining the input coordinates. 69: 69: Number of degrees of freedom in T-Coupling group rest is 33.00 69: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 69: 69: There were 3 NOTEs 69: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BoxDeformationTest_flowDoesNotAffectEkin.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 69: Can not increase nstlist because an NVE ensemble is used 69: Using 1 MPI thread 69: Using 2 OpenMP threads 69: 69: 69: NOTE: The number of threads is not equal to the number of (logical) cpus 69: and the -pin option is set to auto: will not pin threads to cpus. 69: This can lead to significant performance degradation. 69: Consider using -pin on (and -pinoffset in case you run multiple jobs). 69: starting mdrun 'Argon' 69: 0 steps, 0.0 ps. 69: 69: NOTE: 26 % of the run time was spent in pair search, 69: you might want to increase nstlist (this has no effect on accuracy) 69: 69: Core t (s) Wall t (s) (%) 69: Time: 0.002 0.001 161.1 69: (ns/day) (hour/ns) 69: Performance: 150.275 0.160 69: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BoxDeformationTest_flowDoesNotAffectEkin.edr as double precision energy file 69: Reading energy frame 0 time 0.000 Last energy frame read 0 time 0.000 Setting the LD random seed to 1609215359 69: 69: Generated 1 of the 1 non-bonded parameter combinations 69: 69: Excluding 1 bonded neighbours molecule type 'Argon' 69: 69: Setting gen_seed to -42099841 69: 69: Velocities were taken from a Maxwell distribution at 0 K 69: 69: This run will generate roughly 0 Mb of data 69: [ OK ] BoxDeformationTest.flowDoesNotAffectEkin (47 ms) 69: [ RUN ] BoxDeformationTest.EnergiesWithinTolerances 69: 69: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BoxDeformationTest_EnergiesWithinTolerances_input.mdp]: 69: verlet-buffer-pressure-tolerance is ignored when verlet-buffer-tolerance 69: < 0 69: 69: 69: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BoxDeformationTest_EnergiesWithinTolerances_input.mdp]: 69: Setting nstcalcenergy (100) equal to nstenergy (10) 69: 69: Generating 1-4 interactions: fudge = 0.5 69: Number of degrees of freedom in T-Coupling group rest is 1293.00 69: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 69: 69: There were 2 NOTEs 69: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BoxDeformationTest_EnergiesWithinTolerances.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 69: Can not increase nstlist because an NVE ensemble is used 69: Using 1 MPI thread 69: Using 2 OpenMP threads 69: 69: 69: NOTE: The number of threads is not equal to the number of (logical) cpus 69: and the -pin option is set to auto: will not pin threads to cpus. 69: This can lead to significant performance degradation. 69: Consider using -pin on (and -pinoffset in case you run multiple jobs). 69: starting mdrun 'spc2' 69: 20 steps, 0.0 ps. 69: Setting the LD random seed to -587204771 69: 69: Generated 330891 of the 330891 non-bonded parameter combinations 69: 69: Generated 330891 of the 330891 1-4 parameter combinations 69: 69: Excluding 2 bonded neighbours molecule type 'SOL' 69: 69: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/spc216.gro' 69: 69: The largest distance between excluded atoms is 0.152 nm between atom 41 and 42 69: Calculating fourier grid dimensions for X Y Z 69: Using a fourier grid of 16x16x16, spacing 0.116 0.116 0.116 69: 69: Estimate for the relative computational load of the PME mesh part: 0.09 69: 69: This run will generate roughly 0 Mb of data 69: 69: Writing final coordinates. 69: 69: Core t (s) Wall t (s) (%) 69: Time: 1.391 0.696 199.9 69: (ns/day) (hour/ns) 69: Performance: 5.215 4.602 69: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BoxDeformationTest_EnergiesWithinTolerances.edr as double precision energy file 69: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.020 Reading energy frame 2 time 0.040 Last energy frame read 2 time 0.040 [ OK ] BoxDeformationTest.EnergiesWithinTolerances (6420 ms) 69: [----------] 2 tests from BoxDeformationTest (6468 ms total) 69: 69: [----------] 1 test from PositionRestraintCommTest 69: [ RUN ] PositionRestraintCommTest.PositionRestraintsTwoCOMs 69: 69: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PositionRestraintCommTest_PositionRestraintsTwoCOMs_input.mdp]: 69: You have set rlist larger than the interaction cut-off, but you also have 69: verlet-buffer-tolerance > 0. Will set rlist using 69: verlet-buffer-tolerance. 69: 69: 69: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PositionRestraintCommTest_PositionRestraintsTwoCOMs_input.mdp]: 69: Setting nstcalcenergy (100) equal to nstenergy (10) 69: 69: Generating 1-4 interactions: fudge = 0.5 69: 69: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PositionRestraintCommTest_PositionRestraintsTwoCOMs_input.mdp]: 69: 13489 atoms are not part of any of the VCM groups 69: 69: 69: WARNING 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PositionRestraintCommTest_PositionRestraintsTwoCOMs_input.mdp]: 69: 13489 atoms are not part of any center of mass motion removal group. 69: This may lead to artifacts. 69: In most cases one should use one group for the whole system. 69: 69: Number of degrees of freedom in T-Coupling group System is 29527.73 69: 69: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PositionRestraintCommTest_PositionRestraintsTwoCOMs_input.mdp]: 69: Removing center of mass motion in the presence of position restraints 69: might cause artifacts. When you are using position restraints to 69: equilibrate a macro-molecule, the artifacts are usually negligible. 69: 69: 69: There were 4 NOTEs 69: 69: There was 1 WARNING 69: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PositionRestraintCommTest_PositionRestraintsTwoCOMs.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 69: Changing nstlist from 10 to 20, rlist from 0.965 to 1.066 69: 69: Using 1 MPI thread 69: Using 2 OpenMP threads 69: 69: 69: NOTE: The number of threads is not equal to the number of (logical) cpus 69: and the -pin option is set to auto: will not pin threads to cpus. 69: This can lead to significant performance degradation. 69: Consider using -pin on (and -pinoffset in case you run multiple jobs). 69: starting mdrun 'Channel_coco in octane membrane' 69: 10 steps, 0.0 ps. 69: Setting the LD random seed to -1114676817 69: 69: Generated 330891 of the 330891 non-bonded parameter combinations 69: 69: Generated 330891 of the 330891 1-4 parameter combinations 69: 69: Excluding 3 bonded neighbours molecule type 'Protein' 69: 69: Excluding 3 bonded neighbours molecule type 'OCT' 69: 69: Excluding 1 bonded neighbours molecule type 'NA' 69: 69: Excluding 1 bonded neighbours molecule type 'CL' 69: 69: Excluding 3 bonded neighbours molecule type 'Protein' 69: 69: Excluding 3 bonded neighbours molecule type 'OCT' 69: 69: Excluding 2 bonded neighbours molecule type 'SOL' 69: 69: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/OctaneSandwich.gro' 69: 69: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 69: 69: Calculated rlist for 1x1 atom pair-list as 0.990 nm, buffer size 0.090 nm 69: 69: Set rlist, assuming 4x4 atom pair-list, to 0.965 nm, buffer size 0.065 nm 69: 69: Note that mdrun will redetermine rlist based on the actual pair-list setup 69: 69: Chain0: 2.207 2.168 7.330 69: Chain1: 2.228 2.186 2.401 69: Chain0: 2.207 2.168 7.330 69: Chain1: 2.228 2.186 2.401 69: 69: This run will generate roughly 1 Mb of data 69: 69: Writing final coordinates. 69: 69: Core t (s) Wall t (s) (%) 69: Time: 10.155 5.078 200.0 69: (ns/day) (hour/ns) 69: Performance: 0.374 64.115 69: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PositionRestraintCommTest_PositionRestraintsTwoCOMs.edr as double precision energy file 69: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.020 Last energy frame read 1 time 0.020 [ OK ] PositionRestraintCommTest.PositionRestraintsTwoCOMs (11532 ms) 69: [----------] 1 test from PositionRestraintCommTest (11533 ms total) 69: 69: [----------] 2 tests from MultipleTimeSteppingIsNearSingleTimeStepping/MtsComparisonTest 69: [ RUN ] MultipleTimeSteppingIsNearSingleTimeStepping/MtsComparisonTest.WithinTolerances/0 69: 69: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_0_input.mdp]: 69: verlet-buffer-pressure-tolerance is ignored when verlet-buffer-tolerance 69: < 0 69: 69: Generating 1-4 interactions: fudge = 0.5 69: 69: NOTE 2 [file ala.top, line 256]: 69: For energy conservation with LINCS, lincs_iter should be 2 or larger. 69: 69: 69: Number of degrees of freedom in T-Coupling group rest is 54.00 69: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 69: 69: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_0_input.mdp]: 69: The optimal PME mesh load for parallel simulations is below 0.5 69: and for highly parallel simulations between 0.25 and 0.33, 69: for higher performance, increase the cut-off and the PME grid spacing. 69: 69: 69: 69: There were 3 NOTEs 69: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_0_sim.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 69: Can not increase nstlist because an NVE ensemble is used 69: Using 1 MPI thread 69: Using 2 OpenMP threads 69: 69: 69: NOTE: The number of threads is not equal to the number of (logical) cpus 69: and the -pin option is set to auto: will not pin threads to cpus. 69: This can lead to significant performance degradation. 69: Consider using -pin on (and -pinoffset in case you run multiple jobs). 69: starting mdrun 'UNNAMED in water' 69: 4 steps, 0.0 ps. 69: Setting the LD random seed to -834699361 69: 69: Generated 2211 of the 2211 non-bonded parameter combinations 69: 69: Generated 2211 of the 2211 1-4 parameter combinations 69: 69: Excluding 3 bonded neighbours molecule type 'Protein_chain_A' 69: 69: turning H bonds into constraints... 69: 69: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/ala.gro' 69: 69: The largest distance between excluded atoms is 0.384 nm between atom 5 and 15 69: Calculating fourier grid dimensions for X Y Z 69: Using a fourier grid of 24x24x24, spacing 0.104 0.104 0.104 69: 69: Estimate for the relative computational load of the PME mesh part: 0.93 69: 69: This run will generate roughly 0 Mb of data 69: 69: Writing final coordinates. 69: 69: Core t (s) Wall t (s) (%) 69: Time: 0.085 0.043 198.2 69: (ns/day) (hour/ns) 69: Performance: 10.064 2.385 69: 69: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_0_input.mdp]: 69: verlet-buffer-pressure-tolerance is ignored when verlet-buffer-tolerance 69: < 0 69: 69: Generating 1-4 interactions: fudge = 0.5 69: 69: NOTE 2 [file ala.top, line 256]: 69: For energy conservation with LINCS, lincs_iter should be 2 or larger. 69: 69: 69: Number of degrees of freedom in T-Coupling group rest is 54.00 69: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 69: 69: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_0_input.mdp]: 69: The optimal PME mesh load for parallel simulations is below 0.5 69: and for highly parallel simulations between 0.25 and 0.33, 69: for higher performance, increase the cut-off and the PME grid spacing. 69: 69: 69: 69: There were 3 NOTEs 69: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_0_sim.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 69: Can not increase nstlist because an NVE ensemble is used 69: Using 1 MPI thread 69: Using 2 OpenMP threads 69: 69: 69: NOTE: The number of threads is not equal to the number of (logical) cpus 69: and the -pin option is set to auto: will not pin threads to cpus. 69: This can lead to significant performance degradation. 69: Consider using -pin on (and -pinoffset in case you run multiple jobs). 69: starting mdrun 'UNNAMED in water' 69: 4 steps, 0.0 ps. 69: Setting the LD random seed to -1210515521 69: 69: Generated 2211 of the 2211 non-bonded parameter combinations 69: 69: Generated 2211 of the 2211 1-4 parameter combinations 69: 69: Excluding 3 bonded neighbours molecule type 'Protein_chain_A' 69: 69: turning H bonds into constraints... 69: 69: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/ala.gro' 69: 69: The largest distance between excluded atoms is 0.384 nm between atom 5 and 15 69: Calculating fourier grid dimensions for X Y Z 69: Using a fourier grid of 24x24x24, spacing 0.104 0.104 0.104 69: 69: Estimate for the relative computational load of the PME mesh part: 0.93 69: 69: This run will generate roughly 0 Mb of data 69: 69: Writing final coordinates. 69: 69: Core t (s) Wall t (s) (%) 69: Time: 0.070 0.035 197.8 69: (ns/day) (hour/ns) 69: Performance: 12.188 1.969 69: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_0_sim1.edr as double precision energy file 69: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_0_sim2.edr as double precision energy file 69: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Last energy frame read 1 time 0.004 Last energy frame read 1 time 0.004 trr version: GMX_trn_file (double precision) 69: 69: 69: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_0_sim1.edr as double precision energy file 69: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_0_sim2.edr as double precision energy file 69: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Last energy frame read 1 time 0.004 Last energy frame read 1 time 0.004 [ OK ] MultipleTimeSteppingIsNearSingleTimeStepping/MtsComparisonTest.WithinTolerances/0 (405 ms) 69: [ RUN ] MultipleTimeSteppingIsNearSingleTimeStepping/MtsComparisonTest.WithinTolerances/1 69: 69: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_1_input.mdp]: 69: verlet-buffer-pressure-tolerance is ignored when verlet-buffer-tolerance 69: < 0 69: 69: Generating 1-4 interactions: fudge = 0.5 69: 69: NOTE 2 [file ala.top, line 256]: 69: For energy conservation with LINCS, lincs_iter should be 2 or larger. 69: 69: 69: Number of degrees of freedom in T-Coupling group rest is 54.00 69: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 69: 69: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_1_input.mdp]: 69: The optimal PME mesh load for parallel simulations is below 0.5 69: and for highly parallel simulations between 0.25 and 0.33, 69: for higher performance, increase the cut-off and the PME grid spacing. 69: 69: 69: 69: There were 3 NOTEs 69: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_1_sim.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 69: Can not increase nstlist because an NVE ensemble is used 69: Using 1 MPI thread 69: Using 2 OpenMP threads 69: 69: 69: NOTE: The number of threads is not equal to the number of (logical) cpus 69: and the -pin option is set to auto: will not pin threads to cpus. 69: This can lead to significant performance degradation. 69: Consider using -pin on (and -pinoffset in case you run multiple jobs). 69: starting mdrun 'UNNAMED in water' 69: 4 steps, 0.0 ps. 69: Setting the LD random seed to -1627389972 69: 69: Generated 2211 of the 2211 non-bonded parameter combinations 69: 69: Generated 2211 of the 2211 1-4 parameter combinations 69: 69: Excluding 3 bonded neighbours molecule type 'Protein_chain_A' 69: 69: turning H bonds into constraints... 69: 69: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/ala.gro' 69: 69: The largest distance between excluded atoms is 0.384 nm between atom 5 and 15 69: Calculating fourier grid dimensions for X Y Z 69: Using a fourier grid of 24x24x24, spacing 0.104 0.104 0.104 69: 69: Estimate for the relative computational load of the PME mesh part: 0.93 69: 69: This run will generate roughly 0 Mb of data 69: 69: Writing final coordinates. 69: 69: Core t (s) Wall t (s) (%) 69: Time: 0.089 0.045 198.3 69: (ns/day) (hour/ns) 69: Performance: 9.661 2.484 69: 69: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_1_input.mdp]: 69: verlet-buffer-pressure-tolerance is ignored when verlet-buffer-tolerance 69: < 0 69: 69: Generating 1-4 interactions: fudge = 0.5 69: 69: NOTE 2 [file ala.top, line 256]: 69: For energy conservation with LINCS, lincs_iter should be 2 or larger. 69: 69: 69: Number of degrees of freedom in T-Coupling group rest is 54.00 69: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 69: 69: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_1_input.mdp]: 69: The optimal PME mesh load for parallel simulations is below 0.5 69: and for highly parallel simulations between 0.25 and 0.33, 69: for higher performance, increase the cut-off and the PME grid spacing. 69: 69: 69: 69: There were 3 NOTEs 69: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_1_sim.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 69: Multiple time stepping is only supported with GPUs when MTS is only applied to longrange-nonbonded forces. 69: Can not increase nstlist because an NVE ensemble is used 69: 69: Using 1 MPI thread 69: Using 2 OpenMP threads 69: 69: 69: NOTE: The number of threads is not equal to the number of (logical) cpus 69: and the -pin option is set to auto: will not pin threads to cpus. 69: This can lead to significant performance degradation. 69: Consider using -pin on (and -pinoffset in case you run multiple jobs). 69: starting mdrun 'UNNAMED in water' 69: 4 steps, 0.0 ps. 69: Setting the LD random seed to -13631750 69: 69: Generated 2211 of the 2211 non-bonded parameter combinations 69: 69: Generated 2211 of the 2211 1-4 parameter combinations 69: 69: Excluding 3 bonded neighbours molecule type 'Protein_chain_A' 69: 69: turning H bonds into constraints... 69: 69: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/ala.gro' 69: 69: The largest distance between excluded atoms is 0.384 nm between atom 5 and 15 69: Calculating fourier grid dimensions for X Y Z 69: Using a fourier grid of 24x24x24, spacing 0.104 0.104 0.104 69: 69: Estimate for the relative computational load of the PME mesh part: 0.93 69: 69: This run will generate roughly 0 Mb of data 69: 69: Writing final coordinates. 69: 69: Core t (s) Wall t (s) (%) 69: Time: 0.069 0.035 197.8 69: (ns/day) (hour/ns) 69: Performance: 12.418 1.933 69: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_1_sim1.edr as double precision energy file 69: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_1_sim2.edr as double precision energy file 69: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Last energy frame read 1 time 0.004 Last energy frame read 1 time 0.004 69: 69: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_1_sim1.edr as double precision energy file 69: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_1_sim2.edr as double precision energy file 69: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Last energy frame read 1 time 0.004 Last energy frame read 1 time 0.004 [ OK ] MultipleTimeSteppingIsNearSingleTimeStepping/MtsComparisonTest.WithinTolerances/1 (363 ms) 69: [----------] 2 tests from MultipleTimeSteppingIsNearSingleTimeStepping/MtsComparisonTest (769 ms total) 69: 69: [----------] 1 test from MultipleTimeSteppingIsNearSingleTimeSteppingPull/MtsComparisonTest 69: [ RUN ] MultipleTimeSteppingIsNearSingleTimeSteppingPull/MtsComparisonTest.WithinTolerances/0 69: 69: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeSteppingPull_MtsComparisonTest_WithinTolerances_0_input.mdp]: 69: verlet-buffer-pressure-tolerance is ignored when verlet-buffer-tolerance 69: < 0 69: 69: Generating 1-4 interactions: fudge = 0.5 69: Pull group 1 'FirstWaterMolecule' has 3 atoms 69: Pull group 2 'SecondWaterMolecule' has 3 atoms 69: Number of degrees of freedom in T-Coupling group rest is 9.00 69: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 69: Pull group natoms pbc atom distance at start reference at t=0 69: 1 3 2 69: 2 3 5 1.112 nm 1.000 nm 69: 69: There was 1 NOTE 69: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeSteppingPull_MtsComparisonTest_WithinTolerances_0_sim.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 69: Can not increase nstlist because an NVE ensemble is used 69: Using 1 MPI thread 69: Using 2 OpenMP threads 69: 69: 69: NOTE: The number of threads is not equal to the number of (logical) cpus 69: and the -pin option is set to auto: will not pin threads to cpus. 69: This can lead to significant performance degradation. 69: Consider using -pin on (and -pinoffset in case you run multiple jobs). 69: starting mdrun 'spc2' 69: 4 steps, 0.0 ps. 69: Setting the LD random seed to -1166114837 69: 69: Generated 3 of the 3 non-bonded parameter combinations 69: 69: Generated 3 of the 3 1-4 parameter combinations 69: 69: Excluding 2 bonded neighbours molecule type 'SOL' 69: 69: turning H bonds into constraints... 69: 69: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/spc2.gro' 69: 69: This run will generate roughly 0 Mb of data 69: 69: Writing final coordinates. 69: 69: Core t (s) Wall t (s) (%) 69: Time: 0.051 0.026 197.4 69: (ns/day) (hour/ns) 69: Performance: 16.684 1.439 69: 69: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeSteppingPull_MtsComparisonTest_WithinTolerances_0_input.mdp]: 69: verlet-buffer-pressure-tolerance is ignored when verlet-buffer-tolerance 69: < 0 69: 69: Generating 1-4 interactions: fudge = 0.5 69: Pull group 1 'FirstWaterMolecule' has 3 atoms 69: Pull group 2 'SecondWaterMolecule' has 3 atoms 69: Number of degrees of freedom in T-Coupling group rest is 9.00 69: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 69: Pull group natoms pbc atom distance at start reference at t=0 69: 1 3 2 69: 2 3 5 1.112 nm 1.000 nm 69: 69: There was 1 NOTE 69: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeSteppingPull_MtsComparisonTest_WithinTolerances_0_sim.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 69: Multiple time stepping is only supported with GPUs when MTS is only applied to longrange-nonbonded forces. 69: Can not increase nstlist because an NVE ensemble is used 69: 69: Using 1 MPI thread 69: Using 2 OpenMP threads 69: 69: 69: NOTE: The number of threads is not equal to the number of (logical) cpus 69: and the -pin option is set to auto: will not pin threads to cpus. 69: This can lead to significant performance degradation. 69: Consider using -pin on (and -pinoffset in case you run multiple jobs). 69: starting mdrun 'spc2' 69: 4 steps, 0.0 ps. 69: Setting the LD random seed to -338137 69: 69: Generated 3 of the 3 non-bonded parameter combinations 69: 69: Generated 3 of the 3 1-4 parameter combinations 69: 69: Excluding 2 bonded neighbours molecule type 'SOL' 69: 69: turning H bonds into constraints... 69: 69: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/spc2.gro' 69: 69: This run will generate roughly 0 Mb of data 69: 69: Writing final coordinates. 69: 69: Core t (s) Wall t (s) (%) 69: Time: 0.053 0.027 197.6 69: (ns/day) (hour/ns) 69: Performance: 16.222 1.479 69: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeSteppingPull_MtsComparisonTest_WithinTolerances_0_sim1.edr as double precision energy file 69: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeSteppingPull_MtsComparisonTest_WithinTolerances_0_sim2.edr as double precision energy file 69: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Last energy frame read 1 time 0.004 Last energy frame read 1 time 0.004 69: 69: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeSteppingPull_MtsComparisonTest_WithinTolerances_0_sim1.edr as double precision energy file 69: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeSteppingPull_MtsComparisonTest_WithinTolerances_0_sim2.edr as double precision energy file 69: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Last energy frame read 1 time 0.004 Last energy frame read 1 time 0.004 [ OK ] MultipleTimeSteppingIsNearSingleTimeSteppingPull/MtsComparisonTest.WithinTolerances/0 (157 ms) 69: [----------] 1 test from MultipleTimeSteppingIsNearSingleTimeSteppingPull/MtsComparisonTest (157 ms total) 69: 69: [----------] 12 tests from FreezeWorks/FreezeGroupTest 69: [ RUN ] FreezeWorks/FreezeGroupTest.WithinTolerances/0 69: 69: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_0_input.mdp]: 69: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 69: that with the Verlet scheme, nstlist has no effect on the accuracy of 69: your simulation. 69: 69: 69: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_0_input.mdp]: 69: Setting nstcalcenergy (100) equal to nstenergy (4) 69: 69: Generating 1-4 interactions: fudge = 0.5 69: 69: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_0_input.mdp]: 69: There are 5 atoms that are fully frozen and part of COMM removal 69: group(s), removing these atoms from the COMM removal group(s) 69: 69: 69: WARNING 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_0_input.mdp]: 69: There are 3 atoms that are frozen along less then 3 dimensions and part 69: of COMM removal group(s), due to limitations in the code these still 69: contribute to the mass of the COM along frozen dimensions and therefore 69: the COMM correction will be too small. 69: 69: Number of degrees of freedom in T-Coupling group System is 33.00 69: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 69: 69: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_0_input.mdp]: 69: NVE simulation: will use the initial temperature of 246.451 K for 69: determining the Verlet buffer size 69: 69: 69: NOTE 5 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_0_input.mdp]: 69: You are using a plain Coulomb cut-off, which might produce artifacts. 69: You might want to consider using PME electrostatics. 69: 69: 69: 69: There were 5 NOTEs 69: 69: There was 1 WARNING 69: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_0.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 69: Can not increase nstlist because an NVE ensemble is used 69: Using 1 MPI thread 69: Using 2 OpenMP threads 69: 69: 69: NOTE: The number of threads is not equal to the number of (logical) cpus 69: and the -pin option is set to auto: will not pin threads to cpus. 69: This can lead to significant performance degradation. 69: Consider using -pin on (and -pinoffset in case you run multiple jobs). 69: starting mdrun 'Alanine-dipeptide' 69: 8 steps, 0.0 ps. 69: Generated 2145 of the 2145 non-bonded parameter combinations 69: 69: Generated 2145 of the 2145 1-4 parameter combinations 69: 69: Excluding 3 bonded neighbours molecule type 'ALANINEDIPEPTIDE' 69: 69: turning H bonds into constraints... 69: 69: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/alanine_vacuo.gro' 69: 69: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 246.451 K 69: 69: Calculated rlist for 1x1 atom pair-list as 0.755 nm, buffer size 0.055 nm 69: 69: Set rlist, assuming 4x4 atom pair-list, to 0.749 nm, buffer size 0.049 nm 69: 69: Note that mdrun will redetermine rlist based on the actual pair-list setup 69: 69: This run will generate roughly 0 Mb of data 69: 69: Writing final coordinates. 69: 69: Core t (s) Wall t (s) (%) 69: Time: 0.045 0.023 197.3 69: (ns/day) (hour/ns) 69: Performance: 33.835 0.709 69: 69: 69: [ OK ] FreezeWorks/FreezeGroupTest.WithinTolerances/0 (166 ms) 69: [ RUN ] FreezeWorks/FreezeGroupTest.WithinTolerances/1 69: 69: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_1_input.mdp]: 69: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 69: that with the Verlet scheme, nstlist has no effect on the accuracy of 69: your simulation. 69: 69: 69: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_1_input.mdp]: 69: Setting nstcalcenergy (100) equal to nstenergy (4) 69: 69: Generating 1-4 interactions: fudge = 0.5 69: 69: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_1_input.mdp]: 69: There are 5 atoms that are fully frozen and part of COMM removal 69: group(s), removing these atoms from the COMM removal group(s) 69: 69: 69: WARNING 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_1_input.mdp]: 69: There are 3 atoms that are frozen along less then 3 dimensions and part 69: of COMM removal group(s), due to limitations in the code these still 69: contribute to the mass of the COM along frozen dimensions and therefore 69: the COMM correction will be too small. 69: 69: Number of degrees of freedom in T-Coupling group System is 33.00 69: 69: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_1_input.mdp]: 69: NVE simulation: will use the initial temperature of 246.451 K for 69: determining the Verlet buffer size 69: 69: 69: NOTE 5 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_1_input.mdp]: 69: You are using a plain Coulomb cut-off, which might produce artifacts. 69: You might want to consider using PME electrostatics. 69: 69: 69: 69: There were 5 NOTEs 69: 69: There was 1 WARNING 69: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_1.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 69: Can not increase nstlist because an NVE ensemble is used 69: Using 1 MPI thread 69: Using 2 OpenMP threads 69: 69: 69: NOTE: The number of threads is not equal to the number of (logical) cpus 69: and the -pin option is set to auto: will not pin threads to cpus. 69: This can lead to significant performance degradation. 69: Consider using -pin on (and -pinoffset in case you run multiple jobs). 69: starting mdrun 'Alanine-dipeptide' 69: 8 steps, 0.0 ps. 69: Generated 2145 of the 2145 non-bonded parameter combinations 69: 69: Generated 2145 of the 2145 1-4 parameter combinations 69: 69: Excluding 3 bonded neighbours molecule type 'ALANINEDIPEPTIDE' 69: 69: turning H bonds into constraints... 69: 69: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/alanine_vacuo.gro' 69: 69: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 246.451 K 69: 69: Calculated rlist for 1x1 atom pair-list as 0.755 nm, buffer size 0.055 nm 69: 69: Set rlist, assuming 4x4 atom pair-list, to 0.749 nm, buffer size 0.049 nm 69: 69: Note that mdrun will redetermine rlist based on the actual pair-list setup 69: 69: This run will generate roughly 0 Mb of data 69: 69: Writing final coordinates. 69: 69: Core t (s) Wall t (s) (%) 69: Time: 0.042 0.021 196.9 69: (ns/day) (hour/ns) 69: Performance: 36.586 0.656 69: 69: 69: [ OK ] FreezeWorks/FreezeGroupTest.WithinTolerances/1 (162 ms) 69: [ RUN ] FreezeWorks/FreezeGroupTest.WithinTolerances/2 69: 69: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_2_input.mdp]: 69: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 69: that with the Verlet scheme, nstlist has no effect on the accuracy of 69: your simulation. 69: 69: 69: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_2_input.mdp]: 69: Setting nstcalcenergy (100) equal to nstenergy (4) 69: 69: Generating 1-4 interactions: fudge = 0.5 69: 69: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_2_input.mdp]: 69: There are 5 atoms that are fully frozen and part of COMM removal 69: group(s), removing these atoms from the COMM removal group(s) 69: 69: 69: WARNING 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_2_input.mdp]: 69: There are 3 atoms that are frozen along less then 3 dimensions and part 69: of COMM removal group(s), due to limitations in the code these still 69: contribute to the mass of the COM along frozen dimensions and therefore 69: the COMM correction will be too small. 69: 69: Number of degrees of freedom in T-Coupling group System is 33.00 69: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 69: 69: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_2_input.mdp]: 69: NVE simulation: will use the initial temperature of 246.451 K for 69: determining the Verlet buffer size 69: 69: 69: NOTE 5 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_2_input.mdp]: 69: You are using a plain Coulomb cut-off, which might produce artifacts. 69: You might want to consider using PME electrostatics. 69: 69: 69: 69: There were 5 NOTEs 69: 69: There was 1 WARNING 69: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_2.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 69: Can not increase nstlist because an NVE ensemble is used 69: Using 1 MPI thread 69: Using 2 OpenMP threads 69: 69: 69: NOTE: The number of threads is not equal to the number of (logical) cpus 69: and the -pin option is set to auto: will not pin threads to cpus. 69: This can lead to significant performance degradation. 69: Consider using -pin on (and -pinoffset in case you run multiple jobs). 69: starting mdrun 'Alanine-dipeptide' 69: 8 steps, 0.0 ps. 69: Generated 2145 of the 2145 non-bonded parameter combinations 69: 69: Generated 2145 of the 2145 1-4 parameter combinations 69: 69: Excluding 3 bonded neighbours molecule type 'ALANINEDIPEPTIDE' 69: 69: turning H bonds into constraints... 69: 69: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/alanine_vacuo.gro' 69: 69: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 246.451 K 69: 69: Calculated rlist for 1x1 atom pair-list as 0.755 nm, buffer size 0.055 nm 69: 69: Set rlist, assuming 4x4 atom pair-list, to 0.749 nm, buffer size 0.049 nm 69: 69: Note that mdrun will redetermine rlist based on the actual pair-list setup 69: 69: This run will generate roughly 0 Mb of data 69: 69: Writing final coordinates. 69: 69: Core t (s) Wall t (s) (%) 69: Time: 0.045 0.023 197.1 69: (ns/day) (hour/ns) 69: Performance: 34.375 0.698 69: 69: 69: [ OK ] FreezeWorks/FreezeGroupTest.WithinTolerances/2 (159 ms) 69: [ RUN ] FreezeWorks/FreezeGroupTest.WithinTolerances/3 69: 69: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_3_input.mdp]: 69: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 69: that with the Verlet scheme, nstlist has no effect on the accuracy of 69: your simulation. 69: 69: 69: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_3_input.mdp]: 69: Setting nstcalcenergy (100) equal to nstenergy (4) 69: 69: Generating 1-4 interactions: fudge = 0.5 69: 69: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_3_input.mdp]: 69: There are 5 atoms that are fully frozen and part of COMM removal 69: group(s), removing these atoms from the COMM removal group(s) 69: 69: 69: WARNING 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_3_input.mdp]: 69: There are 3 atoms that are frozen along less then 3 dimensions and part 69: of COMM removal group(s), due to limitations in the code these still 69: contribute to the mass of the COM along frozen dimensions and therefore 69: the COMM correction will be too small. 69: 69: Number of degrees of freedom in T-Coupling group System is 33.00 69: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 69: 69: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_3_input.mdp]: 69: NVE simulation: will use the initial temperature of 246.451 K for 69: determining the Verlet buffer size 69: 69: 69: NOTE 5 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_3_input.mdp]: 69: You are using a plain Coulomb cut-off, which might produce artifacts. 69: You might want to consider using PME electrostatics. 69: 69: 69: 69: There were 5 NOTEs 69: 69: There was 1 WARNING 69: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_3.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 69: Can not increase nstlist because an NVE ensemble is used 69: Using 1 MPI thread 69: Using 2 OpenMP threads 69: 69: 69: NOTE: The number of threads is not equal to the number of (logical) cpus 69: and the -pin option is set to auto: will not pin threads to cpus. 69: This can lead to significant performance degradation. 69: Consider using -pin on (and -pinoffset in case you run multiple jobs). 69: starting mdrun 'Alanine-dipeptide' 69: 8 steps, 0.0 ps. 69: Generated 2145 of the 2145 non-bonded parameter combinations 69: 69: Generated 2145 of the 2145 1-4 parameter combinations 69: 69: Excluding 3 bonded neighbours molecule type 'ALANINEDIPEPTIDE' 69: 69: turning H bonds into constraints... 69: 69: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/alanine_vacuo.gro' 69: 69: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 246.451 K 69: 69: Calculated rlist for 1x1 atom pair-list as 0.755 nm, buffer size 0.055 nm 69: 69: Set rlist, assuming 4x4 atom pair-list, to 0.749 nm, buffer size 0.049 nm 69: 69: Note that mdrun will redetermine rlist based on the actual pair-list setup 69: 69: This run will generate roughly 0 Mb of data 69: 69: Writing final coordinates. 69: 69: Core t (s) Wall t (s) (%) 69: Time: 0.050 0.026 195.7 69: (ns/day) (hour/ns) 69: Performance: 30.143 0.796 69: 69: 69: [ OK ] FreezeWorks/FreezeGroupTest.WithinTolerances/3 (175 ms) 69: [ RUN ] FreezeWorks/FreezeGroupTest.WithinTolerances/4 69: 69: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_4_input.mdp]: 69: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 69: that with the Verlet scheme, nstlist has no effect on the accuracy of 69: your simulation. 69: 69: 69: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_4_input.mdp]: 69: Setting nstcalcenergy (100) equal to nstenergy (4) 69: 69: Generating 1-4 interactions: fudge = 0.5 69: 69: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_4_input.mdp]: 69: There are 5 atoms that are fully frozen and part of COMM removal 69: group(s), removing these atoms from the COMM removal group(s) 69: 69: 69: WARNING 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_4_input.mdp]: 69: There are 3 atoms that are frozen along less then 3 dimensions and part 69: of COMM removal group(s), due to limitations in the code these still 69: contribute to the mass of the COM along frozen dimensions and therefore 69: the COMM correction will be too small. 69: 69: Number of degrees of freedom in T-Coupling group System is 33.00 69: 69: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_4_input.mdp]: 69: NVE simulation: will use the initial temperature of 246.451 K for 69: determining the Verlet buffer size 69: 69: 69: NOTE 5 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_4_input.mdp]: 69: You are using a plain Coulomb cut-off, which might produce artifacts. 69: You might want to consider using PME electrostatics. 69: 69: 69: 69: There were 5 NOTEs 69: 69: There was 1 WARNING 69: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_4.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 69: Can not increase nstlist because an NVE ensemble is used 69: Using 1 MPI thread 69: Using 2 OpenMP threads 69: 69: 69: NOTE: The number of threads is not equal to the number of (logical) cpus 69: and the -pin option is set to auto: will not pin threads to cpus. 69: This can lead to significant performance degradation. 69: Consider using -pin on (and -pinoffset in case you run multiple jobs). 69: starting mdrun 'Alanine-dipeptide' 69: 8 steps, 0.0 ps. 69: Generated 2145 of the 2145 non-bonded parameter combinations 69: 69: Generated 2145 of the 2145 1-4 parameter combinations 69: 69: Excluding 3 bonded neighbours molecule type 'ALANINEDIPEPTIDE' 69: 69: turning H bonds into constraints... 69: 69: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/alanine_vacuo.gro' 69: 69: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 246.451 K 69: 69: Calculated rlist for 1x1 atom pair-list as 0.755 nm, buffer size 0.055 nm 69: 69: Set rlist, assuming 4x4 atom pair-list, to 0.749 nm, buffer size 0.049 nm 69: 69: Note that mdrun will redetermine rlist based on the actual pair-list setup 69: 69: This run will generate roughly 0 Mb of data 69: 69: Writing final coordinates. 69: 69: Core t (s) Wall t (s) (%) 69: Time: 0.059 0.030 197.8 69: (ns/day) (hour/ns) 69: Performance: 25.854 0.928 69: 69: 69: [ OK ] FreezeWorks/FreezeGroupTest.WithinTolerances/4 (184 ms) 69: [ RUN ] FreezeWorks/FreezeGroupTest.WithinTolerances/5 69: ./src/programs/mdrun/tests/freezegroups.cpp:209: Skipped 69: Parrinello-Rahman is not implemented in md-vv. 69: [ SKIPPED ] FreezeWorks/FreezeGroupTest.WithinTolerances/5 (1 ms) 69: [ RUN ] FreezeWorks/FreezeGroupTest.WithinTolerances/6 69: 69: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_6_input.mdp]: 69: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 69: that with the Verlet scheme, nstlist has no effect on the accuracy of 69: your simulation. 69: 69: 69: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_6_input.mdp]: 69: Setting nstcalcenergy (100) equal to nstenergy (4) 69: 69: Generating 1-4 interactions: fudge = 0.5 69: 69: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_6_input.mdp]: 69: There are 5 atoms that are fully frozen and part of COMM removal 69: group(s), removing these atoms from the COMM removal group(s) 69: 69: 69: WARNING 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_6_input.mdp]: 69: There are 3 atoms that are frozen along less then 3 dimensions and part 69: of COMM removal group(s), due to limitations in the code these still 69: contribute to the mass of the COM along frozen dimensions and therefore 69: the COMM correction will be too small. 69: 69: Number of degrees of freedom in T-Coupling group System is 33.00 69: 69: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_6_input.mdp]: 69: You are using a plain Coulomb cut-off, which might produce artifacts. 69: You might want to consider using PME electrostatics. 69: 69: 69: 69: There were 4 NOTEs 69: 69: There was 1 WARNING 69: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_6.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 69: Changing nstlist from 8 to 20, rlist from 0.754 to 0.856 69: 69: Using 1 MPI thread 69: Using 2 OpenMP threads 69: 69: 69: NOTE: The number of threads is not equal to the number of (logical) cpus 69: and the -pin option is set to auto: will not pin threads to cpus. 69: This can lead to significant performance degradation. 69: Consider using -pin on (and -pinoffset in case you run multiple jobs). 69: starting mdrun 'Alanine-dipeptide' 69: 8 steps, 0.0 ps. 69: Generated 2145 of the 2145 non-bonded parameter combinations 69: 69: Generated 2145 of the 2145 1-4 parameter combinations 69: 69: Excluding 3 bonded neighbours molecule type 'ALANINEDIPEPTIDE' 69: 69: turning H bonds into constraints... 69: 69: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/alanine_vacuo.gro' 69: 69: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 69: 69: Calculated rlist for 1x1 atom pair-list as 0.761 nm, buffer size 0.061 nm 69: 69: Set rlist, assuming 4x4 atom pair-list, to 0.754 nm, buffer size 0.054 nm 69: 69: Note that mdrun will redetermine rlist based on the actual pair-list setup 69: 69: This run will generate roughly 0 Mb of data 69: 69: Writing final coordinates. 69: 69: Core t (s) Wall t (s) (%) 69: Time: 0.039 0.020 197.2 69: (ns/day) (hour/ns) 69: Performance: 39.275 0.611 69: 69: 69: [ OK ] FreezeWorks/FreezeGroupTest.WithinTolerances/6 (235 ms) 69: [ RUN ] FreezeWorks/FreezeGroupTest.WithinTolerances/7 69: 69: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_7_input.mdp]: 69: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 69: that with the Verlet scheme, nstlist has no effect on the accuracy of 69: your simulation. 69: 69: 69: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_7_input.mdp]: 69: Setting nstcalcenergy (100) equal to nstenergy (4) 69: 69: Generating 1-4 interactions: fudge = 0.5 69: 69: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_7_input.mdp]: 69: There are 5 atoms that are fully frozen and part of COMM removal 69: group(s), removing these atoms from the COMM removal group(s) 69: 69: 69: WARNING 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_7_input.mdp]: 69: There are 3 atoms that are frozen along less then 3 dimensions and part 69: of COMM removal group(s), due to limitations in the code these still 69: contribute to the mass of the COM along frozen dimensions and therefore 69: the COMM correction will be too small. 69: 69: Number of degrees of freedom in T-Coupling group System is 33.00 69: 69: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_7_input.mdp]: 69: You are using a plain Coulomb cut-off, which might produce artifacts. 69: You might want to consider using PME electrostatics. 69: 69: 69: 69: There were 4 NOTEs 69: 69: There was 1 WARNING 69: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_7.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 69: Changing nstlist from 8 to 20, rlist from 0.754 to 0.856 69: 69: Using 1 MPI thread 69: Using 2 OpenMP threads 69: 69: 69: NOTE: The number of threads is not equal to the number of (logical) cpus 69: and the -pin option is set to auto: will not pin threads to cpus. 69: This can lead to significant performance degradation. 69: Consider using -pin on (and -pinoffset in case you run multiple jobs). 69: starting mdrun 'Alanine-dipeptide' 69: 8 steps, 0.0 ps. 69: Generated 2145 of the 2145 non-bonded parameter combinations 69: 69: Generated 2145 of the 2145 1-4 parameter combinations 69: 69: Excluding 3 bonded neighbours molecule type 'ALANINEDIPEPTIDE' 69: 69: turning H bonds into constraints... 69: 69: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/alanine_vacuo.gro' 69: 69: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 69: 69: Calculated rlist for 1x1 atom pair-list as 0.761 nm, buffer size 0.061 nm 69: 69: Set rlist, assuming 4x4 atom pair-list, to 0.754 nm, buffer size 0.054 nm 69: 69: Note that mdrun will redetermine rlist based on the actual pair-list setup 69: 69: This run will generate roughly 0 Mb of data 69: 69: Writing final coordinates. 69: 69: Core t (s) Wall t (s) (%) 69: Time: 0.038 0.020 196.9 69: (ns/day) (hour/ns) 69: Performance: 39.842 0.602 69: 69: 69: [ OK ] FreezeWorks/FreezeGroupTest.WithinTolerances/7 (197 ms) 69: [ RUN ] FreezeWorks/FreezeGroupTest.WithinTolerances/8 69: 69: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_8_input.mdp]: 69: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 69: that with the Verlet scheme, nstlist has no effect on the accuracy of 69: your simulation. 69: 69: 69: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_8_input.mdp]: 69: Setting nstcalcenergy (100) equal to nstenergy (4) 69: 69: Generating 1-4 interactions: fudge = 0.5 69: 69: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_8_input.mdp]: 69: There are 5 atoms that are fully frozen and part of COMM removal 69: group(s), removing these atoms from the COMM removal group(s) 69: 69: 69: WARNING 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_8_input.mdp]: 69: There are 3 atoms that are frozen along less then 3 dimensions and part 69: of COMM removal group(s), due to limitations in the code these still 69: contribute to the mass of the COM along frozen dimensions and therefore 69: the COMM correction will be too small. 69: 69: Number of degrees of freedom in T-Coupling group System is 33.00 69: 69: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_8_input.mdp]: 69: You are using a plain Coulomb cut-off, which might produce artifacts. 69: You might want to consider using PME electrostatics. 69: 69: 69: 69: There were 4 NOTEs 69: 69: There was 1 WARNING 69: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_8.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 69: Changing nstlist from 8 to 20, rlist from 0.754 to 0.856 69: 69: Using 1 MPI thread 69: Using 2 OpenMP threads 69: 69: 69: NOTE: The number of threads is not equal to the number of (logical) cpus 69: and the -pin option is set to auto: will not pin threads to cpus. 69: This can lead to significant performance degradation. 69: Consider using -pin on (and -pinoffset in case you run multiple jobs). 69: starting mdrun 'Alanine-dipeptide' 69: 8 steps, 0.0 ps. 69: Generated 2145 of the 2145 non-bonded parameter combinations 69: 69: Generated 2145 of the 2145 1-4 parameter combinations 69: 69: Excluding 3 bonded neighbours molecule type 'ALANINEDIPEPTIDE' 69: 69: turning H bonds into constraints... 69: 69: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/alanine_vacuo.gro' 69: 69: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 69: 69: Calculated rlist for 1x1 atom pair-list as 0.761 nm, buffer size 0.061 nm 69: 69: Set rlist, assuming 4x4 atom pair-list, to 0.754 nm, buffer size 0.054 nm 69: 69: Note that mdrun will redetermine rlist based on the actual pair-list setup 69: 69: This run will generate roughly 0 Mb of data 69: 69: Writing final coordinates. 69: 69: Core t (s) Wall t (s) (%) 69: Time: 0.042 0.022 197.1 69: (ns/day) (hour/ns) 69: Performance: 36.142 0.664 69: 69: 69: [ OK ] FreezeWorks/FreezeGroupTest.WithinTolerances/8 (198 ms) 69: [ RUN ] FreezeWorks/FreezeGroupTest.WithinTolerances/9 69: 69: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_9_input.mdp]: 69: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 69: that with the Verlet scheme, nstlist has no effect on the accuracy of 69: your simulation. 69: 69: 69: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_9_input.mdp]: 69: Setting nstcalcenergy (100) equal to nstenergy (4) 69: 69: Generating 1-4 interactions: fudge = 0.5 69: 69: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_9_input.mdp]: 69: There are 5 atoms that are fully frozen and part of COMM removal 69: group(s), removing these atoms from the COMM removal group(s) 69: 69: 69: WARNING 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_9_input.mdp]: 69: There are 3 atoms that are frozen along less then 3 dimensions and part 69: of COMM removal group(s), due to limitations in the code these still 69: contribute to the mass of the COM along frozen dimensions and therefore 69: the COMM correction will be too small. 69: 69: Number of degrees of freedom in T-Coupling group System is 33.00 69: 69: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_9_input.mdp]: 69: You are using a plain Coulomb cut-off, which might produce artifacts. 69: You might want to consider using PME electrostatics. 69: 69: 69: 69: There were 4 NOTEs 69: 69: There was 1 WARNING 69: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_9.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 69: Changing nstlist from 8 to 100, rlist from 0.734 to 0.829 69: 69: Using 1 MPI thread 69: Using 2 OpenMP threads 69: 69: 69: NOTE: The number of threads is not equal to the number of (logical) cpus 69: and the -pin option is set to auto: will not pin threads to cpus. 69: This can lead to significant performance degradation. 69: Consider using -pin on (and -pinoffset in case you run multiple jobs). 69: starting mdrun 'Alanine-dipeptide' 69: 8 steps, 0.0 ps. 69: Generated 2145 of the 2145 non-bonded parameter combinations 69: 69: Generated 2145 of the 2145 1-4 parameter combinations 69: 69: Excluding 3 bonded neighbours molecule type 'ALANINEDIPEPTIDE' 69: 69: turning H bonds into constraints... 69: 69: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 69: 69: Calculated rlist for 1x1 atom pair-list as 0.737 nm, buffer size 0.037 nm 69: 69: Set rlist, assuming 4x4 atom pair-list, to 0.734 nm, buffer size 0.034 nm 69: 69: Note that mdrun will redetermine rlist based on the actual pair-list setup 69: 69: This run will generate roughly 0 Mb of data 69: 69: Writing final coordinates. 69: 69: Core t (s) Wall t (s) (%) 69: Time: 0.037 0.019 197.0 69: (ns/day) (hour/ns) 69: Performance: 40.993 0.585 69: 69: 69: [ OK ] FreezeWorks/FreezeGroupTest.WithinTolerances/9 (489 ms) 69: [ RUN ] FreezeWorks/FreezeGroupTest.WithinTolerances/10 69: 69: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_10_input.mdp]: 69: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 69: that with the Verlet scheme, nstlist has no effect on the accuracy of 69: your simulation. 69: 69: 69: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_10_input.mdp]: 69: Setting nstcalcenergy (100) equal to nstenergy (4) 69: 69: Generating 1-4 interactions: fudge = 0.5 69: 69: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_10_input.mdp]: 69: There are 5 atoms that are fully frozen and part of COMM removal 69: group(s), removing these atoms from the COMM removal group(s) 69: 69: 69: WARNING 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_10_input.mdp]: 69: There are 3 atoms that are frozen along less then 3 dimensions and part 69: of COMM removal group(s), due to limitations in the code these still 69: contribute to the mass of the COM along frozen dimensions and therefore 69: the COMM correction will be too small. 69: 69: Number of degrees of freedom in T-Coupling group System is 33.00 69: 69: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_10_input.mdp]: 69: You are using a plain Coulomb cut-off, which might produce artifacts. 69: You might want to consider using PME electrostatics. 69: 69: 69: 69: There were 4 NOTEs 69: 69: There was 1 WARNING 69: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_10.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 69: Changing nstlist from 8 to 100, rlist from 0.734 to 0.829 69: 69: Using 1 MPI thread 69: Using 2 OpenMP threads 69: 69: 69: NOTE: The number of threads is not equal to the number of (logical) cpus 69: and the -pin option is set to auto: will not pin threads to cpus. 69: This can lead to significant performance degradation. 69: Consider using -pin on (and -pinoffset in case you run multiple jobs). 69: starting mdrun 'Alanine-dipeptide' 69: 8 steps, 0.0 ps. 69: Generated 2145 of the 2145 non-bonded parameter combinations 69: 69: Generated 2145 of the 2145 1-4 parameter combinations 69: 69: Excluding 3 bonded neighbours molecule type 'ALANINEDIPEPTIDE' 69: 69: turning H bonds into constraints... 69: 69: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 69: 69: Calculated rlist for 1x1 atom pair-list as 0.737 nm, buffer size 0.037 nm 69: 69: Set rlist, assuming 4x4 atom pair-list, to 0.734 nm, buffer size 0.034 nm 69: 69: Note that mdrun will redetermine rlist based on the actual pair-list setup 69: 69: This run will generate roughly 0 Mb of data 69: 69: Writing final coordinates. 69: 69: Core t (s) Wall t (s) (%) 69: Time: 0.047 0.024 197.5 69: (ns/day) (hour/ns) 69: Performance: 32.446 0.740 69: 69: 69: [ OK ] FreezeWorks/FreezeGroupTest.WithinTolerances/10 (496 ms) 69: [ RUN ] FreezeWorks/FreezeGroupTest.WithinTolerances/11 69: 69: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_11_input.mdp]: 69: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 69: that with the Verlet scheme, nstlist has no effect on the accuracy of 69: your simulation. 69: 69: 69: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_11_input.mdp]: 69: Setting nstcalcenergy (100) equal to nstenergy (4) 69: 69: Generating 1-4 interactions: fudge = 0.5 69: 69: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_11_input.mdp]: 69: There are 5 atoms that are fully frozen and part of COMM removal 69: group(s), removing these atoms from the COMM removal group(s) 69: 69: 69: WARNING 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_11_input.mdp]: 69: There are 3 atoms that are frozen along less then 3 dimensions and part 69: of COMM removal group(s), due to limitations in the code these still 69: contribute to the mass of the COM along frozen dimensions and therefore 69: the COMM correction will be too small. 69: 69: Number of degrees of freedom in T-Coupling group System is 33.00 69: 69: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_11_input.mdp]: 69: You are using a plain Coulomb cut-off, which might produce artifacts. 69: You might want to consider using PME electrostatics. 69: 69: 69: 69: There were 4 NOTEs 69: 69: There was 1 WARNING 69: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_11.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 69: Changing nstlist from 8 to 100, rlist from 0.734 to 0.829 69: 69: Using 1 MPI thread 69: Using 2 OpenMP threads 69: 69: 69: NOTE: The number of threads is not equal to the number of (logical) cpus 69: and the -pin option is set to auto: will not pin threads to cpus. 69: This can lead to significant performance degradation. 69: Consider using -pin on (and -pinoffset in case you run multiple jobs). 69: starting mdrun 'Alanine-dipeptide' 69: 8 steps, 0.0 ps. 69: Generated 2145 of the 2145 non-bonded parameter combinations 69: 69: Generated 2145 of the 2145 1-4 parameter combinations 69: 69: Excluding 3 bonded neighbours molecule type 'ALANINEDIPEPTIDE' 69: 69: turning H bonds into constraints... 69: 69: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 69: 69: Calculated rlist for 1x1 atom pair-list as 0.737 nm, buffer size 0.037 nm 69: 69: Set rlist, assuming 4x4 atom pair-list, to 0.734 nm, buffer size 0.034 nm 69: 69: Note that mdrun will redetermine rlist based on the actual pair-list setup 69: 69: This run will generate roughly 0 Mb of data 69: 69: Writing final coordinates. 69: 69: Core t (s) Wall t (s) (%) 69: Time: 0.039 0.020 197.2 69: (ns/day) (hour/ns) 69: Performance: 39.702 0.605 69: 69: 69: [ OK ] FreezeWorks/FreezeGroupTest.WithinTolerances/11 (495 ms) 69: [----------] 12 tests from FreezeWorks/FreezeGroupTest (2964 ms total) 69: 69: [----------] 4 tests from AccelerationWorks/AccelerationGroupTest 69: [ RUN ] AccelerationWorks/AccelerationGroupTest.WithinTolerances/0 69: 69: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/AccelerationWorks_AccelerationGroupTest_WithinTolerances_0_input.mdp]: 69: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 69: that with the Verlet scheme, nstlist has no effect on the accuracy of 69: your simulation. 69: 69: 69: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/AccelerationWorks_AccelerationGroupTest_WithinTolerances_0_input.mdp]: 69: verlet-buffer-pressure-tolerance is ignored when verlet-buffer-tolerance 69: < 0 69: 69: 69: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/AccelerationWorks_AccelerationGroupTest_WithinTolerances_0_input.mdp]: 69: Setting nstcalcenergy (100) equal to nstenergy (4) 69: 69: Generating 1-4 interactions: fudge = 0.5 69: Number of degrees of freedom in T-Coupling group FirstWaterMolecule is 6.00 69: Number of degrees of freedom in T-Coupling group SecondWaterMolecule is 6.00 69: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 69: Net Acceleration in X direction, will not be corrected 69: Net Acceleration in Y direction, will not be corrected 69: Net Acceleration in Z direction, will not be corrected 69: 69: There were 3 NOTEs 69: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/AccelerationWorks_AccelerationGroupTest_WithinTolerances_0.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 69: Can not increase nstlist because an NVE ensemble is used 69: Using 1 MPI thread 69: Using 2 OpenMP threads 69: 69: 69: NOTE: The number of threads is not equal to the number of (logical) cpus 69: and the -pin option is set to auto: will not pin threads to cpus. 69: This can lead to significant performance degradation. 69: Consider using -pin on (and -pinoffset in case you run multiple jobs). 69: starting mdrun 'spc2' 69: 8 steps, 0.0 ps. 69: Generated 3 of the 3 non-bonded parameter combinations 69: 69: Generated 3 of the 3 1-4 parameter combinations 69: 69: Excluding 2 bonded neighbours molecule type 'SOL' 69: 69: Setting gen_seed to 1807572979 69: 69: Velocities were taken from a Maxwell distribution at 0 K 69: 69: This run will generate roughly 0 Mb of data 69: 69: Writing final coordinates. 69: 69: Core t (s) Wall t (s) (%) 69: Time: 0.031 0.016 196.1 69: (ns/day) (hour/ns) 69: Performance: 98.448 0.244 69: 69: [ OK ] AccelerationWorks/AccelerationGroupTest.WithinTolerances/0 (60 ms) 69: [ RUN ] AccelerationWorks/AccelerationGroupTest.WithinTolerances/1 69: 69: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/AccelerationWorks_AccelerationGroupTest_WithinTolerances_1_input.mdp]: 69: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 69: that with the Verlet scheme, nstlist has no effect on the accuracy of 69: your simulation. 69: 69: 69: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/AccelerationWorks_AccelerationGroupTest_WithinTolerances_1_input.mdp]: 69: verlet-buffer-pressure-tolerance is ignored when verlet-buffer-tolerance 69: < 0 69: 69: 69: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/AccelerationWorks_AccelerationGroupTest_WithinTolerances_1_input.mdp]: 69: Setting nstcalcenergy (100) equal to nstenergy (4) 69: 69: Generating 1-4 interactions: fudge = 0.5 69: Number of degrees of freedom in T-Coupling group FirstWaterMolecule is 6.00 69: Number of degrees of freedom in T-Coupling group SecondWaterMolecule is 6.00 69: Net Acceleration in X direction, will not be corrected 69: Net Acceleration in Y direction, will not be corrected 69: Net Acceleration in Z direction, will not be corrected 69: 69: There were 3 NOTEs 69: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/AccelerationWorks_AccelerationGroupTest_WithinTolerances_1.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 69: Can not increase nstlist because verlet-buffer-tolerance is not set or used 69: Using 1 MPI thread 69: Using 2 OpenMP threads 69: 69: 69: NOTE: The number of threads is not equal to the number of (logical) cpus 69: and the -pin option is set to auto: will not pin threads to cpus. 69: This can lead to significant performance degradation. 69: Consider using -pin on (and -pinoffset in case you run multiple jobs). 69: starting mdrun 'spc2' 69: 8 steps, 0.0 ps. 69: Generated 3 of the 3 non-bonded parameter combinations 69: 69: Generated 3 of the 3 1-4 parameter combinations 69: 69: Excluding 2 bonded neighbours molecule type 'SOL' 69: 69: Setting gen_seed to 365163921 69: 69: Velocities were taken from a Maxwell distribution at 0 K 69: 69: This run will generate roughly 0 Mb of data 69: 69: Writing final coordinates. 69: 69: Core t (s) Wall t (s) (%) 69: Time: 0.032 0.016 196.7 69: (ns/day) (hour/ns) 69: Performance: 95.172 0.252 69: 69: [ OK ] AccelerationWorks/AccelerationGroupTest.WithinTolerances/1 (60 ms) 69: [ RUN ] AccelerationWorks/AccelerationGroupTest.WithinTolerances/2 69: 69: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/AccelerationWorks_AccelerationGroupTest_WithinTolerances_2_input.mdp]: 69: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 69: that with the Verlet scheme, nstlist has no effect on the accuracy of 69: your simulation. 69: 69: 69: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/AccelerationWorks_AccelerationGroupTest_WithinTolerances_2_input.mdp]: 69: verlet-buffer-pressure-tolerance is ignored when verlet-buffer-tolerance 69: < 0 69: 69: 69: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/AccelerationWorks_AccelerationGroupTest_WithinTolerances_2_input.mdp]: 69: Setting nstcalcenergy (100) equal to nstenergy (4) 69: 69: Generating 1-4 interactions: fudge = 0.5 69: Number of degrees of freedom in T-Coupling group FirstWaterMolecule is 6.00 69: Number of degrees of freedom in T-Coupling group SecondWaterMolecule is 6.00 69: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 69: Net Acceleration in X direction, will not be corrected 69: Net Acceleration in Y direction, will not be corrected 69: Net Acceleration in Z direction, will not be corrected 69: 69: There were 3 NOTEs 69: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/AccelerationWorks_AccelerationGroupTest_WithinTolerances_2.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 69: Can not increase nstlist because an NVE ensemble is used 69: Using 1 MPI thread 69: Using 2 OpenMP threads 69: 69: 69: NOTE: The number of threads is not equal to the number of (logical) cpus 69: and the -pin option is set to auto: will not pin threads to cpus. 69: This can lead to significant performance degradation. 69: Consider using -pin on (and -pinoffset in case you run multiple jobs). 69: starting mdrun 'spc2' 69: 8 steps, 0.0 ps. 69: Generated 3 of the 3 non-bonded parameter combinations 69: 69: Generated 3 of the 3 1-4 parameter combinations 69: 69: Excluding 2 bonded neighbours molecule type 'SOL' 69: 69: Setting gen_seed to -1348931714 69: 69: Velocities were taken from a Maxwell distribution at 0 K 69: 69: This run will generate roughly 0 Mb of data 69: 69: Writing final coordinates. 69: 69: Core t (s) Wall t (s) (%) 69: Time: 0.038 0.019 196.8 69: (ns/day) (hour/ns) 69: Performance: 80.239 0.299 69: 69: [ OK ] AccelerationWorks/AccelerationGroupTest.WithinTolerances/2 (66 ms) 69: [ RUN ] AccelerationWorks/AccelerationGroupTest.WithinTolerances/3 69: 69: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/AccelerationWorks_AccelerationGroupTest_WithinTolerances_3_input.mdp]: 69: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 69: that with the Verlet scheme, nstlist has no effect on the accuracy of 69: your simulation. 69: 69: 69: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/AccelerationWorks_AccelerationGroupTest_WithinTolerances_3_input.mdp]: 69: verlet-buffer-pressure-tolerance is ignored when verlet-buffer-tolerance 69: < 0 69: 69: 69: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/AccelerationWorks_AccelerationGroupTest_WithinTolerances_3_input.mdp]: 69: Setting nstcalcenergy (100) equal to nstenergy (4) 69: 69: Generating 1-4 interactions: fudge = 0.5 69: Number of degrees of freedom in T-Coupling group FirstWaterMolecule is 6.00 69: Number of degrees of freedom in T-Coupling group SecondWaterMolecule is 6.00 69: Net Acceleration in X direction, will not be corrected 69: Net Acceleration in Y direction, will not be corrected 69: Net Acceleration in Z direction, will not be corrected 69: 69: There were 3 NOTEs 69: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/AccelerationWorks_AccelerationGroupTest_WithinTolerances_3.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 69: Can not increase nstlist because verlet-buffer-tolerance is not set or used 69: Using 1 MPI thread 69: Using 2 OpenMP threads 69: 69: 69: NOTE: The number of threads is not equal to the number of (logical) cpus 69: and the -pin option is set to auto: will not pin threads to cpus. 69: This can lead to significant performance degradation. 69: Consider using -pin on (and -pinoffset in case you run multiple jobs). 69: starting mdrun 'spc2' 69: 8 steps, 0.0 ps. 69: Generated 3 of the 3 non-bonded parameter combinations 69: 69: Generated 3 of the 3 1-4 parameter combinations 69: 69: Excluding 2 bonded neighbours molecule type 'SOL' 69: 69: Setting gen_seed to -608174081 69: 69: Velocities were taken from a Maxwell distribution at 0 K 69: 69: This run will generate roughly 0 Mb of data 69: 69: Writing final coordinates. 69: 69: Core t (s) Wall t (s) (%) 69: Time: 0.039 0.020 197.4 69: (ns/day) (hour/ns) 69: Performance: 78.849 0.304 69: 69: [ OK ] AccelerationWorks/AccelerationGroupTest.WithinTolerances/3 (66 ms) 69: [----------] 4 tests from AccelerationWorks/AccelerationGroupTest (253 ms total) 69: 69: [----------] Global test environment tear-down 69: [==========] 29 tests from 8 test suites ran. (35349 ms total) 69: [ PASSED ] 28 tests. 69: [ SKIPPED ] 1 test, listed below: 69: [ SKIPPED ] FreezeWorks/FreezeGroupTest.WithinTolerances/5 69/92 Test #69: MdrunTestsOneRank ......................... Passed 35.46 sec test 70 Start 70: MdrunTestsTwoRanks 70: Test command: /build/reproducible-path/gromacs-2025.1/build/basic-dp/bin/mdrun-test "-ntomp" "2" "-ntmpi" "2" "--gtest_output=xml:/build/reproducible-path/gromacs-2025.1/build/basic-dp/Testing/Temporary/MdrunTestsTwoRanks.xml" 70: Working Directory: /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests 70: Test timeout computed to be: 600 70: [==========] Running 29 tests from 8 test suites. 70: [----------] Global test environment set-up. 70: [----------] 1 test from CompelTest 70: [ RUN ] CompelTest.SwapCanRun 70: Generating 1-4 interactions: fudge = 0.5 70: Split0 group 'Ch0' contains 83 atoms. 70: Split1 group 'Ch1' contains 83 atoms. 70: Solvent group 'SOL' contains 11931 atoms. 70: Swap group 'NA+' contains 19 atoms. 70: Swap group 'CL-' contains 19 atoms. 70: Number of degrees of freedom in T-Coupling group System is 27869.00 70: 70: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/CompelTest_SwapCanRun_input.mdp]: 70: Removing center of mass motion in the presence of position restraints 70: might cause artifacts. When you are using position restraints to 70: equilibrate a macro-molecule, the artifacts are usually negligible. 70: 70: 70: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/CompelTest_SwapCanRun_input.mdp]: 70: You are using a plain Coulomb cut-off, which might produce artifacts. 70: You might want to consider using PME electrostatics. 70: 70: 70: 70: There were 2 NOTEs 70: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/CompelTest_SwapCanRun.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 70: Update groups can not be used for this system because there are three or more consecutively coupled constraints 70: 70: Using 2 MPI threads 70: Using 2 OpenMP threads per tMPI thread 70: 70: SWAP: Determining initial numbers of ions per compartment. 70: SWAP: Setting pointers for checkpoint writing 70: SWAP: Channel 0 flux history for ion type NA+ (charge 1): 0 molecules 70: SWAP: Channel 1 flux history for ion type NA+ (charge 1): 0 molecules 70: SWAP: Channel 0 flux history for ion type CL- (charge -1): 0 molecules 70: SWAP: Channel 1 flux history for ion type CL- (charge -1): 0 molecules 70: starting mdrun 'Channel_coco in octane membrane' 70: 2 steps, 0.0 ps. 70: Setting the LD random seed to -138414115 70: 70: Generated 330891 of the 330891 non-bonded parameter combinations 70: 70: Generated 330891 of the 330891 1-4 parameter combinations 70: 70: Excluding 3 bonded neighbours molecule type 'Protein' 70: 70: turning all bonds into constraints... 70: 70: Excluding 3 bonded neighbours molecule type 'OCT' 70: 70: turning all bonds into constraints... 70: 70: Excluding 1 bonded neighbours molecule type 'NA' 70: 70: turning all bonds into constraints... 70: 70: Excluding 1 bonded neighbours molecule type 'CL' 70: 70: turning all bonds into constraints... 70: 70: Excluding 3 bonded neighbours molecule type 'Protein' 70: 70: Excluding 3 bonded neighbours molecule type 'OCT' 70: 70: Excluding 2 bonded neighbours molecule type 'SOL' 70: 70: turning all bonds into constraints... 70: 70: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/OctaneSandwich.gro' 70: 70: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 300 K 70: 70: Calculated rlist for 1x1 atom pair-list as 1.316 nm, buffer size 0.316 nm 70: 70: Set rlist, assuming 4x4 atom pair-list, to 1.262 nm, buffer size 0.262 nm 70: 70: Note that mdrun will redetermine rlist based on the actual pair-list setup 70: 70: This run will generate roughly 1 Mb of data 70: 70: Writing final coordinates. 70: 70: 70: Dynamic load balancing report: 70: DLB was off during the run due to low measured imbalance. 70: Average load imbalance: 0.4%. 70: The balanceable part of the MD step is 56%, load imbalance is computed from this. 70: Part of the total run time spent waiting due to load imbalance: 0.2%. 70: 70: 70: Core t (s) Wall t (s) (%) 70: Time: 10.402 2.601 399.9 70: (ns/day) (hour/ns) 70: Performance: 0.498 48.169 70: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/CompelTest_SwapCanRun.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 70: Overriding nsteps with value passed on the command line: 2 steps, 0.01 ps 70: 70: Update groups can not be used for this system because there are three or more consecutively coupled constraints 70: 70: Using 2 MPI threads 70: 70: Non-default thread affinity set, disabling internal thread affinity 70: 70: Using 2 OpenMP threads per tMPI thread 70: 70: SWAP: Setting pointers for checkpoint writing 70: SWAP: Copying channel fluxes from checkpoint file data 70: SWAP: Channel 0 flux history for ion type NA+ (charge 1): 0 molecules 70: SWAP: Channel 1 flux history for ion type NA+ (charge 1): 0 molecules 70: SWAP: Channel 0 flux history for ion type CL- (charge -1): 0 molecules 70: SWAP: Channel 1 flux history for ion type CL- (charge -1): 0 molecules 70: starting mdrun 'Channel_coco in octane membrane' 70: 4 steps, 0.0 ps (continuing from step 2, 0.0 ps). 70: 70: Writing final coordinates. 70: 70: Core t (s) Wall t (s) (%) 70: Time: 18.289 4.588 398.6 70: (ns/day) (hour/ns) 70: Performance: 0.282 84.961 70: [ OK ] CompelTest.SwapCanRun (15263 ms) 70: [----------] 1 test from CompelTest (15264 ms total) 70: 70: [----------] 6 tests from BondedInteractionsTest 70: [ RUN ] BondedInteractionsTest.NormalBondWorks 70: 70: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_NormalBondWorks_input.mdp]: 70: For a correct single-point energy evaluation with nsteps = 0, use 70: continuation = yes to avoid constraining the input coordinates. 70: 70: 70: NOTE 2 [file BondedInteractionsTest_NormalBondWorks_butane1.top, line 31]: 70: In moleculetype 'butane' 2 atoms are not bound by a potential or 70: constraint to any other atom in the same moleculetype. Although 70: technically this might not cause issues in a simulation, this often means 70: that the user forgot to add a bond/potential/constraint or put multiple 70: molecules in the same moleculetype definition by mistake. Run with -v to 70: get information for each atom. 70: 70: Number of degrees of freedom in T-Coupling group rest is 9.00 70: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 70: 70: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_NormalBondWorks_input.mdp]: 70: NVE simulation with an initial temperature of zero: will use a Verlet 70: buffer of 10%. Check your energy drift! 70: 70: 70: There were 3 NOTEs 70: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_NormalBondWorks.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 70: Can not increase nstlist because an NVE ensemble is used 70: Using 2 MPI threads 70: 70: Non-default thread affinity set, disabling internal thread affinity 70: 70: Using 2 OpenMP threads per tMPI thread 70: 70: starting md rerun 'A single butane', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/butane1.gro' 70: 70: Reading frames from gro file 'A single butane', 4 atoms. 70: Reading frame 0 time 0.000 Last frame 0 time 0.000 70: 70: NOTE: 73 % of the run time was spent in domain decomposition, 70: 5 % of the run time was spent in pair search, 70: you might want to increase nstlist (this has no effect on accuracy) 70: 70: Core t (s) Wall t (s) (%) 70: Time: 1.161 0.302 384.3 70: (ns/day) (hour/ns) 70: Performance: 0.286 83.937 70: Setting the LD random seed to -269484558 70: 70: Generated 3 of the 3 non-bonded parameter combinations 70: 70: Excluding 3 bonded neighbours molecule type 'butane' 70: 70: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/butane1.gro', all velocities are zero 70: 70: This run will generate roughly 0 Mb of data 70: [ OK ] BondedInteractionsTest.NormalBondWorks (971 ms) 70: [ RUN ] BondedInteractionsTest.TabulatedBondWorks 70: 70: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_TabulatedBondWorks_input.mdp]: 70: For a correct single-point energy evaluation with nsteps = 0, use 70: continuation = yes to avoid constraining the input coordinates. 70: 70: 70: NOTE 2 [file BondedInteractionsTest_TabulatedBondWorks_butane1.top, line 31]: 70: In moleculetype 'butane' 2 atoms are not bound by a potential or 70: constraint to any other atom in the same moleculetype. Although 70: technically this might not cause issues in a simulation, this often means 70: that the user forgot to add a bond/potential/constraint or put multiple 70: molecules in the same moleculetype definition by mistake. Run with -v to 70: get information for each atom. 70: 70: Number of degrees of freedom in T-Coupling group rest is 9.00 70: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 70: 70: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_TabulatedBondWorks_input.mdp]: 70: NVE simulation with an initial temperature of zero: will use a Verlet 70: buffer of 10%. Check your energy drift! 70: 70: 70: There were 3 NOTEs 70: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_TabulatedBondWorks.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 70: Can not increase nstlist because an NVE ensemble is used 70: Using 2 MPI threads 70: 70: Non-default thread affinity set, disabling internal thread affinity 70: 70: Using 2 OpenMP threads per tMPI thread 70: 70: starting md rerun 'A single butane', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/butane1.gro' 70: 70: Reading frames from gro file 'A single butane', 4 atoms. 70: Reading frame 0 time 0.000 Last frame 0 time 0.000 70: 70: NOTE: 72 % of the run time was spent in domain decomposition, 70: 5 % of the run time was spent in pair search, 70: you might want to increase nstlist (this has no effect on accuracy) 70: 70: Core t (s) Wall t (s) (%) 70: Time: 1.173 0.305 384.3 70: (ns/day) (hour/ns) 70: Performance: 0.283 84.804 70: Setting the LD random seed to -26236737 70: 70: Generated 3 of the 3 non-bonded parameter combinations 70: 70: Excluding 3 bonded neighbours molecule type 'butane' 70: 70: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/butane1.gro', all velocities are zero 70: 70: This run will generate roughly 0 Mb of data 70: [ OK ] BondedInteractionsTest.TabulatedBondWorks (939 ms) 70: [ RUN ] BondedInteractionsTest.NormalAngleWorks 70: 70: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_NormalAngleWorks_input.mdp]: 70: For a correct single-point energy evaluation with nsteps = 0, use 70: continuation = yes to avoid constraining the input coordinates. 70: 70: 70: NOTE 2 [file BondedInteractionsTest_NormalAngleWorks_butane1.top, line 31]: 70: In moleculetype 'butane' 4 atoms are not bound by a potential or 70: constraint to any other atom in the same moleculetype. Although 70: technically this might not cause issues in a simulation, this often means 70: that the user forgot to add a bond/potential/constraint or put multiple 70: molecules in the same moleculetype definition by mistake. Run with -v to 70: get information for each atom. 70: 70: Number of degrees of freedom in T-Coupling group rest is 9.00 70: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 70: 70: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_NormalAngleWorks_input.mdp]: 70: NVE simulation with an initial temperature of zero: will use a Verlet 70: buffer of 10%. Check your energy drift! 70: 70: 70: There were 3 NOTEs 70: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_NormalAngleWorks.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 70: Can not increase nstlist because an NVE ensemble is used 70: Using 2 MPI threads 70: 70: Non-default thread affinity set, disabling internal thread affinity 70: 70: Using 2 OpenMP threads per tMPI thread 70: 70: starting md rerun 'A single butane', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/butane1.gro' 70: 70: Reading frames from gro file 'A single butane', 4 atoms. 70: Reading frame 0 time 0.000 Last frame 0 time 0.000 70: 70: NOTE: 73 % of the run time was spent in domain decomposition, 70: 6 % of the run time was spent in pair search, 70: you might want to increase nstlist (this has no effect on accuracy) 70: 70: Core t (s) Wall t (s) (%) 70: Time: 1.157 0.301 384.1 70: (ns/day) (hour/ns) 70: Performance: 0.287 83.697 70: Setting the LD random seed to -743456929 70: 70: Generated 3 of the 3 non-bonded parameter combinations 70: 70: Excluding 3 bonded neighbours molecule type 'butane' 70: 70: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/butane1.gro', all velocities are zero 70: 70: This run will generate roughly 0 Mb of data 70: [ OK ] BondedInteractionsTest.NormalAngleWorks (935 ms) 70: [ RUN ] BondedInteractionsTest.TabulatedAngleWorks 70: 70: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_TabulatedAngleWorks_input.mdp]: 70: For a correct single-point energy evaluation with nsteps = 0, use 70: continuation = yes to avoid constraining the input coordinates. 70: 70: 70: NOTE 2 [file BondedInteractionsTest_TabulatedAngleWorks_butane1.top, line 31]: 70: In moleculetype 'butane' 4 atoms are not bound by a potential or 70: constraint to any other atom in the same moleculetype. Although 70: technically this might not cause issues in a simulation, this often means 70: that the user forgot to add a bond/potential/constraint or put multiple 70: molecules in the same moleculetype definition by mistake. Run with -v to 70: get information for each atom. 70: 70: Number of degrees of freedom in T-Coupling group rest is 9.00 70: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 70: 70: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_TabulatedAngleWorks_input.mdp]: 70: NVE simulation with an initial temperature of zero: will use a Verlet 70: buffer of 10%. Check your energy drift! 70: 70: 70: There were 3 NOTEs 70: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_TabulatedAngleWorks.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 70: Can not increase nstlist because an NVE ensemble is used 70: Using 2 MPI threads 70: 70: Non-default thread affinity set, disabling internal thread affinity 70: 70: Using 2 OpenMP threads per tMPI thread 70: 70: starting md rerun 'A single butane', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/butane1.gro' 70: 70: Reading frames from gro file 'A single butane', 4 atoms. 70: Reading frame 0 time 0.000 Last frame 0 time 0.000 70: 70: NOTE: 72 % of the run time was spent in domain decomposition, 70: 5 % of the run time was spent in pair search, 70: you might want to increase nstlist (this has no effect on accuracy) 70: 70: Core t (s) Wall t (s) (%) 70: Time: 1.209 0.314 385.5 70: (ns/day) (hour/ns) 70: Performance: 0.275 87.137 70: Setting the LD random seed to 1668284158 70: 70: Generated 3 of the 3 non-bonded parameter combinations 70: 70: Excluding 3 bonded neighbours molecule type 'butane' 70: 70: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/butane1.gro', all velocities are zero 70: 70: This run will generate roughly 0 Mb of data 70: [ OK ] BondedInteractionsTest.TabulatedAngleWorks (981 ms) 70: [ RUN ] BondedInteractionsTest.NormalDihedralWorks 70: 70: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_NormalDihedralWorks_input.mdp]: 70: For a correct single-point energy evaluation with nsteps = 0, use 70: continuation = yes to avoid constraining the input coordinates. 70: 70: 70: NOTE 2 [file BondedInteractionsTest_NormalDihedralWorks_butane1.top, line 31]: 70: In moleculetype 'butane' 4 atoms are not bound by a potential or 70: constraint to any other atom in the same moleculetype. Although 70: technically this might not cause issues in a simulation, this often means 70: that the user forgot to add a bond/potential/constraint or put multiple 70: molecules in the same moleculetype definition by mistake. Run with -v to 70: get information for each atom. 70: 70: Number of degrees of freedom in T-Coupling group rest is 9.00 70: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 70: 70: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_NormalDihedralWorks_input.mdp]: 70: NVE simulation with an initial temperature of zero: will use a Verlet 70: buffer of 10%. Check your energy drift! 70: 70: 70: There were 3 NOTEs 70: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_NormalDihedralWorks.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 70: Can not increase nstlist because an NVE ensemble is used 70: Using 2 MPI threads 70: 70: Non-default thread affinity set, disabling internal thread affinity 70: 70: Using 2 OpenMP threads per tMPI thread 70: 70: starting md rerun 'A single butane', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/butane1.gro' 70: 70: Reading frames from gro file 'A single butane', 4 atoms. 70: Reading frame 0 time 0.000 Last frame 0 time 0.000 70: 70: NOTE: 71 % of the run time was spent in domain decomposition, 70: 6 % of the run time was spent in pair search, 70: you might want to increase nstlist (this has no effect on accuracy) 70: 70: Core t (s) Wall t (s) (%) 70: Time: 1.158 0.301 384.1 70: (ns/day) (hour/ns) 70: Performance: 0.287 83.710 70: Setting the LD random seed to 2096365471 70: 70: Generated 3 of the 3 non-bonded parameter combinations 70: 70: Excluding 3 bonded neighbours molecule type 'butane' 70: 70: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/butane1.gro', all velocities are zero 70: 70: This run will generate roughly 0 Mb of data 70: [ OK ] BondedInteractionsTest.NormalDihedralWorks (950 ms) 70: [ RUN ] BondedInteractionsTest.TabulatedDihedralWorks 70: 70: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_TabulatedDihedralWorks_input.mdp]: 70: For a correct single-point energy evaluation with nsteps = 0, use 70: continuation = yes to avoid constraining the input coordinates. 70: 70: 70: NOTE 2 [file BondedInteractionsTest_TabulatedDihedralWorks_butane1.top, line 31]: 70: In moleculetype 'butane' 4 atoms are not bound by a potential or 70: constraint to any other atom in the same moleculetype. Although 70: technically this might not cause issues in a simulation, this often means 70: that the user forgot to add a bond/potential/constraint or put multiple 70: molecules in the same moleculetype definition by mistake. Run with -v to 70: get information for each atom. 70: 70: Number of degrees of freedom in T-Coupling group rest is 9.00 70: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 70: 70: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_TabulatedDihedralWorks_input.mdp]: 70: NVE simulation with an initial temperature of zero: will use a Verlet 70: buffer of 10%. Check your energy drift! 70: 70: 70: There were 3 NOTEs 70: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_TabulatedDihedralWorks.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 70: Can not increase nstlist because an NVE ensemble is used 70: Using 2 MPI threads 70: 70: Non-default thread affinity set, disabling internal thread affinity 70: 70: Using 2 OpenMP threads per tMPI thread 70: 70: starting md rerun 'A single butane', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/butane1.gro' 70: 70: Reading frames from gro file 'A single butane', 4 atoms. 70: Reading frame 0 time 0.000 Last frame 0 time 0.000 70: 70: NOTE: 73 % of the run time was spent in domain decomposition, 70: 6 % of the run time was spent in pair search, 70: you might want to increase nstlist (this has no effect on accuracy) 70: 70: Core t (s) Wall t (s) (%) 70: Time: 1.127 0.294 383.7 70: (ns/day) (hour/ns) 70: Performance: 0.294 81.614 70: Setting the LD random seed to -721747983 70: 70: Generated 3 of the 3 non-bonded parameter combinations 70: 70: Excluding 3 bonded neighbours molecule type 'butane' 70: 70: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/butane1.gro', all velocities are zero 70: 70: This run will generate roughly 0 Mb of data 70: [ OK ] BondedInteractionsTest.TabulatedDihedralWorks (959 ms) 70: [----------] 6 tests from BondedInteractionsTest (5739 ms total) 70: 70: [----------] 2 tests from BoxDeformationTest 70: [ RUN ] BoxDeformationTest.flowDoesNotAffectEkin 70: 70: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BoxDeformationTest_flowDoesNotAffectEkin_input.mdp]: 70: verlet-buffer-pressure-tolerance is ignored when verlet-buffer-tolerance 70: < 0 70: 70: 70: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BoxDeformationTest_flowDoesNotAffectEkin_input.mdp]: 70: Setting nstcalcenergy (100) equal to nstenergy (10) 70: 70: 70: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BoxDeformationTest_flowDoesNotAffectEkin_input.mdp]: 70: For a correct single-point energy evaluation with nsteps = 0, use 70: continuation = yes to avoid constraining the input coordinates. 70: 70: Number of degrees of freedom in T-Coupling group rest is 33.00 70: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 70: 70: There were 3 NOTEs 70: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BoxDeformationTest_flowDoesNotAffectEkin.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 70: Can not increase nstlist because an NVE ensemble is used 70: Using 2 MPI threads 70: 70: Non-default thread affinity set, disabling internal thread affinity 70: 70: Using 2 OpenMP threads per tMPI thread 70: 70: starting mdrun 'Argon' 70: 0 steps, 0.0 ps. 70: 70: NOTE: 46 % of the run time was spent in domain decomposition, 70: 12 % of the run time was spent in pair search, 70: you might want to increase nstlist (this has no effect on accuracy) 70: 70: NOTE: 13 % of the run time was spent communicating energies, 70: you might want to increase some nst* mdp options 70: 70: Core t (s) Wall t (s) (%) 70: Time: 0.564 0.156 361.9 70: (ns/day) (hour/ns) 70: Performance: 1.108 21.658 70: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BoxDeformationTest_flowDoesNotAffectEkin.edr as double precision energy file 70: Reading energy frame 0 time 0.000 Last energy frame read 0 time 0.000 Setting the LD random seed to 1978662891 70: 70: Generated 1 of the 1 non-bonded parameter combinations 70: 70: Excluding 1 bonded neighbours molecule type 'Argon' 70: 70: Setting gen_seed to -537030690 70: 70: Velocities were taken from a Maxwell distribution at 0 K 70: 70: This run will generate roughly 0 Mb of data 70: [ OK ] BoxDeformationTest.flowDoesNotAffectEkin (834 ms) 70: [ RUN ] BoxDeformationTest.EnergiesWithinTolerances 70: 70: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BoxDeformationTest_EnergiesWithinTolerances_input.mdp]: 70: verlet-buffer-pressure-tolerance is ignored when verlet-buffer-tolerance 70: < 0 70: 70: 70: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BoxDeformationTest_EnergiesWithinTolerances_input.mdp]: 70: Setting nstcalcenergy (100) equal to nstenergy (10) 70: 70: Generating 1-4 interactions: fudge = 0.5 70: Number of degrees of freedom in T-Coupling group rest is 1293.00 70: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 70: 70: There were 2 NOTEs 70: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BoxDeformationTest_EnergiesWithinTolerances.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 70: Can not increase nstlist because an NVE ensemble is used 70: Using 2 MPI threads 70: 70: Non-default thread affinity set, disabling internal thread affinity 70: 70: Using 2 OpenMP threads per tMPI thread 70: 70: starting mdrun 'spc2' 70: 20 steps, 0.0 ps. 70: Setting the LD random seed to 1524035443 70: 70: Generated 330891 of the 330891 non-bonded parameter combinations 70: 70: Generated 330891 of the 330891 1-4 parameter combinations 70: 70: Excluding 2 bonded neighbours molecule type 'SOL' 70: 70: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/spc216.gro' 70: 70: The largest distance between excluded atoms is 0.152 nm between atom 41 and 42 70: Calculating fourier grid dimensions for X Y Z 70: Using a fourier grid of 16x16x16, spacing 0.116 0.116 0.116 70: 70: Estimate for the relative computational load of the PME mesh part: 0.09 70: 70: This run will generate roughly 0 Mb of data 70: 70: Writing final coordinates. 70: 70: 70: Dynamic load balancing report: 70: DLB got disabled because it was unsuitable to use. 70: Average load imbalance: 9.4%. 70: The balanceable part of the MD step is 26%, load imbalance is computed from this. 70: Part of the total run time spent waiting due to load imbalance: 2.5%. 70: 70: 70: Core t (s) Wall t (s) (%) 70: Time: 18.913 4.744 398.7 70: (ns/day) (hour/ns) 70: Performance: 0.765 31.375 70: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BoxDeformationTest_EnergiesWithinTolerances.edr as double precision energy file 70: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.020 Reading energy frame 2 time 0.040 Last energy frame read 2 time 0.040 [ OK ] BoxDeformationTest.EnergiesWithinTolerances (11475 ms) 70: [----------] 2 tests from BoxDeformationTest (12310 ms total) 70: 70: [----------] 1 test from PositionRestraintCommTest 70: [ RUN ] PositionRestraintCommTest.PositionRestraintsTwoCOMs 70: 70: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PositionRestraintCommTest_PositionRestraintsTwoCOMs_input.mdp]: 70: You have set rlist larger than the interaction cut-off, but you also have 70: verlet-buffer-tolerance > 0. Will set rlist using 70: verlet-buffer-tolerance. 70: 70: 70: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PositionRestraintCommTest_PositionRestraintsTwoCOMs_input.mdp]: 70: Setting nstcalcenergy (100) equal to nstenergy (10) 70: 70: Generating 1-4 interactions: fudge = 0.5 70: 70: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PositionRestraintCommTest_PositionRestraintsTwoCOMs_input.mdp]: 70: 13489 atoms are not part of any of the VCM groups 70: 70: 70: WARNING 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PositionRestraintCommTest_PositionRestraintsTwoCOMs_input.mdp]: 70: 13489 atoms are not part of any center of mass motion removal group. 70: This may lead to artifacts. 70: In most cases one should use one group for the whole system. 70: 70: Number of degrees of freedom in T-Coupling group System is 29527.73 70: 70: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PositionRestraintCommTest_PositionRestraintsTwoCOMs_input.mdp]: 70: Removing center of mass motion in the presence of position restraints 70: might cause artifacts. When you are using position restraints to 70: equilibrate a macro-molecule, the artifacts are usually negligible. 70: 70: 70: There were 4 NOTEs 70: 70: There was 1 WARNING 70: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PositionRestraintCommTest_PositionRestraintsTwoCOMs.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 70: Changing nstlist from 10 to 20, rlist from 0.965 to 1.066 70: 70: Using 2 MPI threads 70: 70: Non-default thread affinity set, disabling internal thread affinity 70: 70: Using 2 OpenMP threads per tMPI thread 70: 70: starting mdrun 'Channel_coco in octane membrane' 70: 10 steps, 0.0 ps. 70: Setting the LD random seed to -1636319266 70: 70: Generated 330891 of the 330891 non-bonded parameter combinations 70: 70: Generated 330891 of the 330891 1-4 parameter combinations 70: 70: Excluding 3 bonded neighbours molecule type 'Protein' 70: 70: Excluding 3 bonded neighbours molecule type 'OCT' 70: 70: Excluding 1 bonded neighbours molecule type 'NA' 70: 70: Excluding 1 bonded neighbours molecule type 'CL' 70: 70: Excluding 3 bonded neighbours molecule type 'Protein' 70: 70: Excluding 3 bonded neighbours molecule type 'OCT' 70: 70: Excluding 2 bonded neighbours molecule type 'SOL' 70: 70: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/OctaneSandwich.gro' 70: 70: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 70: 70: Calculated rlist for 1x1 atom pair-list as 0.990 nm, buffer size 0.090 nm 70: 70: Set rlist, assuming 4x4 atom pair-list, to 0.965 nm, buffer size 0.065 nm 70: 70: Note that mdrun will redetermine rlist based on the actual pair-list setup 70: 70: Chain0: 2.207 2.168 7.330 70: Chain1: 2.228 2.186 2.401 70: Chain0: 2.207 2.168 7.330 70: Chain1: 2.228 2.186 2.401 70: 70: This run will generate roughly 1 Mb of data 70: 70: Writing final coordinates. 70: 70: Core t (s) Wall t (s) (%) 70: Time: 33.619 8.420 399.3 70: (ns/day) (hour/ns) 70: Performance: 0.226 106.319 70: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PositionRestraintCommTest_PositionRestraintsTwoCOMs.edr as double precision energy file 70: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.020 Last energy frame read 1 time 0.020 [ OK ] PositionRestraintCommTest.PositionRestraintsTwoCOMs (15604 ms) 70: [----------] 1 test from PositionRestraintCommTest (15604 ms total) 70: 70: [----------] 2 tests from MultipleTimeSteppingIsNearSingleTimeStepping/MtsComparisonTest 70: [ RUN ] MultipleTimeSteppingIsNearSingleTimeStepping/MtsComparisonTest.WithinTolerances/0 70: 70: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_0_input.mdp]: 70: verlet-buffer-pressure-tolerance is ignored when verlet-buffer-tolerance 70: < 0 70: 70: Generating 1-4 interactions: fudge = 0.5 70: 70: NOTE 2 [file ala.top, line 256]: 70: For energy conservation with LINCS, lincs_iter should be 2 or larger. 70: 70: 70: Number of degrees of freedom in T-Coupling group rest is 54.00 70: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 70: 70: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_0_input.mdp]: 70: The optimal PME mesh load for parallel simulations is below 0.5 70: and for highly parallel simulations between 0.25 and 0.33, 70: for higher performance, increase the cut-off and the PME grid spacing. 70: 70: 70: 70: There were 3 NOTEs 70: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_0_sim.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 70: Can not increase nstlist because an NVE ensemble is used 70: Using 2 MPI threads 70: 70: Non-default thread affinity set, disabling internal thread affinity 70: 70: Using 2 OpenMP threads per tMPI thread 70: 70: starting mdrun 'UNNAMED in water' 70: 4 steps, 0.0 ps. 70: Setting the LD random seed to -72950334 70: 70: Generated 2211 of the 2211 non-bonded parameter combinations 70: 70: Generated 2211 of the 2211 1-4 parameter combinations 70: 70: Excluding 3 bonded neighbours molecule type 'Protein_chain_A' 70: 70: turning H bonds into constraints... 70: 70: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/ala.gro' 70: 70: The largest distance between excluded atoms is 0.384 nm between atom 5 and 15 70: Calculating fourier grid dimensions for X Y Z 70: Using a fourier grid of 24x24x24, spacing 0.104 0.104 0.104 70: 70: Estimate for the relative computational load of the PME mesh part: 0.93 70: 70: This run will generate roughly 0 Mb of data 70: 70: Writing final coordinates. 70: 70: NOTE: 10 % of the run time was spent in domain decomposition, 70: 2 % of the run time was spent in pair search, 70: you might want to increase nstlist (this has no effect on accuracy) 70: 70: NOTE: 7 % of the run time was spent communicating energies, 70: you might want to increase some nst* mdp options 70: 70: Core t (s) Wall t (s) (%) 70: Time: 3.585 0.912 393.1 70: (ns/day) (hour/ns) 70: Performance: 0.474 50.660 70: 70: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_0_input.mdp]: 70: verlet-buffer-pressure-tolerance is ignored when verlet-buffer-tolerance 70: < 0 70: 70: Generating 1-4 interactions: fudge = 0.5 70: 70: NOTE 2 [file ala.top, line 256]: 70: For energy conservation with LINCS, lincs_iter should be 2 or larger. 70: 70: 70: Number of degrees of freedom in T-Coupling group rest is 54.00 70: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 70: 70: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_0_input.mdp]: 70: The optimal PME mesh load for parallel simulations is below 0.5 70: and for highly parallel simulations between 0.25 and 0.33, 70: for higher performance, increase the cut-off and the PME grid spacing. 70: 70: 70: 70: There were 3 NOTEs 70: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_0_sim.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 70: Can not increase nstlist because an NVE ensemble is used 70: Using 2 MPI threads 70: 70: Non-default thread affinity set, disabling internal thread affinity 70: 70: Using 2 OpenMP threads per tMPI thread 70: 70: starting mdrun 'UNNAMED in water' 70: 4 steps, 0.0 ps. 70: Setting the LD random seed to -33696769 70: 70: Generated 2211 of the 2211 non-bonded parameter combinations 70: 70: Generated 2211 of the 2211 1-4 parameter combinations 70: 70: Excluding 3 bonded neighbours molecule type 'Protein_chain_A' 70: 70: turning H bonds into constraints... 70: 70: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/ala.gro' 70: 70: The largest distance between excluded atoms is 0.384 nm between atom 5 and 15 70: Calculating fourier grid dimensions for X Y Z 70: Using a fourier grid of 24x24x24, spacing 0.104 0.104 0.104 70: 70: Estimate for the relative computational load of the PME mesh part: 0.93 70: 70: This run will generate roughly 0 Mb of data 70: 70: Writing final coordinates. 70: 70: NOTE: 12 % of the run time was spent in domain decomposition, 70: 2 % of the run time was spent in pair search, 70: you might want to increase nstlist (this has no effect on accuracy) 70: 70: NOTE: 6 % of the run time was spent communicating energies, 70: you might want to increase some nst* mdp options 70: 70: Core t (s) Wall t (s) (%) 70: Time: 3.526 0.897 392.9 70: (ns/day) (hour/ns) 70: Performance: 0.481 49.847 70: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_0_sim1.edr as double precision energy file 70: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_0_sim2.edr as double precision energy file 70: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Last energy frame read 1 time 0.004 Last energy frame read 1 time 0.004 trr version: GMX_trn_file (double precision) 70: 70: 70: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_0_sim1.edr as double precision energy file 70: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_0_sim2.edr as double precision energy file 70: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Last energy frame read 1 time 0.004 Last energy frame read 1 time 0.004 [ OK ] MultipleTimeSteppingIsNearSingleTimeStepping/MtsComparisonTest.WithinTolerances/0 (3663 ms) 70: [ RUN ] MultipleTimeSteppingIsNearSingleTimeStepping/MtsComparisonTest.WithinTolerances/1 70: 70: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_1_input.mdp]: 70: verlet-buffer-pressure-tolerance is ignored when verlet-buffer-tolerance 70: < 0 70: 70: Generating 1-4 interactions: fudge = 0.5 70: 70: NOTE 2 [file ala.top, line 256]: 70: For energy conservation with LINCS, lincs_iter should be 2 or larger. 70: 70: 70: Number of degrees of freedom in T-Coupling group rest is 54.00 70: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 70: 70: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_1_input.mdp]: 70: The optimal PME mesh load for parallel simulations is below 0.5 70: and for highly parallel simulations between 0.25 and 0.33, 70: for higher performance, increase the cut-off and the PME grid spacing. 70: 70: 70: 70: There were 3 NOTEs 70: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_1_sim.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 70: Can not increase nstlist because an NVE ensemble is used 70: Using 2 MPI threads 70: 70: Non-default thread affinity set, disabling internal thread affinity 70: 70: Using 2 OpenMP threads per tMPI thread 70: 70: starting mdrun 'UNNAMED in water' 70: 4 steps, 0.0 ps. 70: Setting the LD random seed to 2147388223 70: 70: Generated 2211 of the 2211 non-bonded parameter combinations 70: 70: Generated 2211 of the 2211 1-4 parameter combinations 70: 70: Excluding 3 bonded neighbours molecule type 'Protein_chain_A' 70: 70: turning H bonds into constraints... 70: 70: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/ala.gro' 70: 70: The largest distance between excluded atoms is 0.384 nm between atom 5 and 15 70: Calculating fourier grid dimensions for X Y Z 70: Using a fourier grid of 24x24x24, spacing 0.104 0.104 0.104 70: 70: Estimate for the relative computational load of the PME mesh part: 0.93 70: 70: This run will generate roughly 0 Mb of data 70: 70: Writing final coordinates. 70: 70: NOTE: 11 % of the run time was spent in domain decomposition, 70: 2 % of the run time was spent in pair search, 70: you might want to increase nstlist (this has no effect on accuracy) 70: 70: NOTE: 6 % of the run time was spent communicating energies, 70: you might want to increase some nst* mdp options 70: 70: Core t (s) Wall t (s) (%) 70: Time: 3.760 0.956 393.4 70: (ns/day) (hour/ns) 70: Performance: 0.452 53.106 70: 70: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_1_input.mdp]: 70: verlet-buffer-pressure-tolerance is ignored when verlet-buffer-tolerance 70: < 0 70: 70: Generating 1-4 interactions: fudge = 0.5 70: 70: NOTE 2 [file ala.top, line 256]: 70: For energy conservation with LINCS, lincs_iter should be 2 or larger. 70: 70: 70: Number of degrees of freedom in T-Coupling group rest is 54.00 70: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 70: 70: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_1_input.mdp]: 70: The optimal PME mesh load for parallel simulations is below 0.5 70: and for highly parallel simulations between 0.25 and 0.33, 70: for higher performance, increase the cut-off and the PME grid spacing. 70: 70: 70: 70: There were 3 NOTEs 70: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_1_sim.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 70: Multiple time stepping is only supported with GPUs when MTS is only applied to longrange-nonbonded forces. 70: Can not increase nstlist because an NVE ensemble is used 70: 70: Using 2 MPI threads 70: 70: Non-default thread affinity set, disabling internal thread affinity 70: 70: Using 2 OpenMP threads per tMPI thread 70: 70: starting mdrun 'UNNAMED in water' 70: 4 steps, 0.0 ps. 70: Setting the LD random seed to 1979449326 70: 70: Generated 2211 of the 2211 non-bonded parameter combinations 70: 70: Generated 2211 of the 2211 1-4 parameter combinations 70: 70: Excluding 3 bonded neighbours molecule type 'Protein_chain_A' 70: 70: turning H bonds into constraints... 70: 70: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/ala.gro' 70: 70: The largest distance between excluded atoms is 0.384 nm between atom 5 and 15 70: Calculating fourier grid dimensions for X Y Z 70: Using a fourier grid of 24x24x24, spacing 0.104 0.104 0.104 70: 70: Estimate for the relative computational load of the PME mesh part: 0.93 70: 70: This run will generate roughly 0 Mb of data 70: 70: Writing final coordinates. 70: 70: NOTE: 11 % of the run time was spent in domain decomposition, 70: 3 % of the run time was spent in pair search, 70: you might want to increase nstlist (this has no effect on accuracy) 70: 70: NOTE: 9 % of the run time was spent communicating energies, 70: you might want to increase some nst* mdp options 70: 70: Core t (s) Wall t (s) (%) 70: Time: 3.028 0.773 391.8 70: (ns/day) (hour/ns) 70: Performance: 0.559 42.934 70: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_1_sim1.edr as double precision energy file 70: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_1_sim2.edr as double precision energy file 70: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Last energy frame read 1 time 0.004 Last energy frame read 1 time 0.004 70: 70: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_1_sim1.edr as double precision energy file 70: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_1_sim2.edr as double precision energy file 70: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Last energy frame read 1 time 0.004 Last energy frame read 1 time 0.004 [ OK ] MultipleTimeSteppingIsNearSingleTimeStepping/MtsComparisonTest.WithinTolerances/1 (3549 ms) 70: [----------] 2 tests from MultipleTimeSteppingIsNearSingleTimeStepping/MtsComparisonTest (7212 ms total) 70: 70: [----------] 1 test from MultipleTimeSteppingIsNearSingleTimeSteppingPull/MtsComparisonTest 70: [ RUN ] MultipleTimeSteppingIsNearSingleTimeSteppingPull/MtsComparisonTest.WithinTolerances/0 70: 70: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeSteppingPull_MtsComparisonTest_WithinTolerances_0_input.mdp]: 70: verlet-buffer-pressure-tolerance is ignored when verlet-buffer-tolerance 70: < 0 70: 70: Generating 1-4 interactions: fudge = 0.5 70: Pull group 1 'FirstWaterMolecule' has 3 atoms 70: Pull group 2 'SecondWaterMolecule' has 3 atoms 70: Number of degrees of freedom in T-Coupling group rest is 9.00 70: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 70: Pull group natoms pbc atom distance at start reference at t=0 70: 1 3 2 70: 2 3 5 1.112 nm 1.000 nm 70: 70: There was 1 NOTE 70: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeSteppingPull_MtsComparisonTest_WithinTolerances_0_sim.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 70: Can not increase nstlist because an NVE ensemble is used 70: Using 2 MPI threads 70: 70: Non-default thread affinity set, disabling internal thread affinity 70: 70: Using 2 OpenMP threads per tMPI thread 70: 70: starting mdrun 'spc2' 70: 4 steps, 0.0 ps. 70: Setting the LD random seed to -824445445 70: 70: Generated 3 of the 3 non-bonded parameter combinations 70: 70: Generated 3 of the 3 1-4 parameter combinations 70: 70: Excluding 2 bonded neighbours molecule type 'SOL' 70: 70: turning H bonds into constraints... 70: 70: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/spc2.gro' 70: 70: This run will generate roughly 0 Mb of data 70: 70: Writing final coordinates. 70: 70: NOTE: 13 % of the run time was spent in domain decomposition, 70: 3 % of the run time was spent in pair search, 70: you might want to increase nstlist (this has no effect on accuracy) 70: 70: NOTE: 12 % of the run time was spent communicating energies, 70: you might want to increase some nst* mdp options 70: 70: Core t (s) Wall t (s) (%) 70: Time: 2.144 0.552 388.6 70: (ns/day) (hour/ns) 70: Performance: 0.783 30.661 70: 70: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeSteppingPull_MtsComparisonTest_WithinTolerances_0_input.mdp]: 70: verlet-buffer-pressure-tolerance is ignored when verlet-buffer-tolerance 70: < 0 70: 70: Generating 1-4 interactions: fudge = 0.5 70: Pull group 1 'FirstWaterMolecule' has 3 atoms 70: Pull group 2 'SecondWaterMolecule' has 3 atoms 70: Number of degrees of freedom in T-Coupling group rest is 9.00 70: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 70: Pull group natoms pbc atom distance at start reference at t=0 70: 1 3 2 70: 2 3 5 1.112 nm 1.000 nm 70: 70: There was 1 NOTE 70: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeSteppingPull_MtsComparisonTest_WithinTolerances_0_sim.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 70: Multiple time stepping is only supported with GPUs when MTS is only applied to longrange-nonbonded forces. 70: Can not increase nstlist because an NVE ensemble is used 70: 70: Using 2 MPI threads 70: 70: Non-default thread affinity set, disabling internal thread affinity 70: 70: Using 2 OpenMP threads per tMPI thread 70: 70: starting mdrun 'spc2' 70: 4 steps, 0.0 ps. 70: Setting the LD random seed to -335728941 70: 70: Generated 3 of the 3 non-bonded parameter combinations 70: 70: Generated 3 of the 3 1-4 parameter combinations 70: 70: Excluding 2 bonded neighbours molecule type 'SOL' 70: 70: turning H bonds into constraints... 70: 70: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/spc2.gro' 70: 70: This run will generate roughly 0 Mb of data 70: 70: Writing final coordinates. 70: 70: NOTE: 12 % of the run time was spent in domain decomposition, 70: 3 % of the run time was spent in pair search, 70: you might want to increase nstlist (this has no effect on accuracy) 70: 70: NOTE: 12 % of the run time was spent communicating energies, 70: you might want to increase some nst* mdp options 70: 70: Core t (s) Wall t (s) (%) 70: Time: 2.224 0.572 389.0 70: (ns/day) (hour/ns) 70: Performance: 0.755 31.772 70: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeSteppingPull_MtsComparisonTest_WithinTolerances_0_sim1.edr as double precision energy file 70: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeSteppingPull_MtsComparisonTest_WithinTolerances_0_sim2.edr as double precision energy file 70: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Last energy frame read 1 time 0.004 Last energy frame read 1 time 0.004 70: 70: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeSteppingPull_MtsComparisonTest_WithinTolerances_0_sim1.edr as double precision energy file 70: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeSteppingPull_MtsComparisonTest_WithinTolerances_0_sim2.edr as double precision energy file 70: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Last energy frame read 1 time 0.004 Last energy frame read 1 time 0.004 [ OK ] MultipleTimeSteppingIsNearSingleTimeSteppingPull/MtsComparisonTest.WithinTolerances/0 (2583 ms) 70: [----------] 1 test from MultipleTimeSteppingIsNearSingleTimeSteppingPull/MtsComparisonTest (2584 ms total) 70: 70: [----------] 12 tests from FreezeWorks/FreezeGroupTest 70: [ RUN ] FreezeWorks/FreezeGroupTest.WithinTolerances/0 70: 70: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_0_input.mdp]: 70: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 70: that with the Verlet scheme, nstlist has no effect on the accuracy of 70: your simulation. 70: 70: 70: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_0_input.mdp]: 70: Setting nstcalcenergy (100) equal to nstenergy (4) 70: 70: Generating 1-4 interactions: fudge = 0.5 70: 70: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_0_input.mdp]: 70: There are 5 atoms that are fully frozen and part of COMM removal 70: group(s), removing these atoms from the COMM removal group(s) 70: 70: 70: WARNING 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_0_input.mdp]: 70: There are 3 atoms that are frozen along less then 3 dimensions and part 70: of COMM removal group(s), due to limitations in the code these still 70: contribute to the mass of the COM along frozen dimensions and therefore 70: the COMM correction will be too small. 70: 70: Number of degrees of freedom in T-Coupling group System is 33.00 70: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 70: 70: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_0_input.mdp]: 70: NVE simulation: will use the initial temperature of 246.451 K for 70: determining the Verlet buffer size 70: 70: 70: NOTE 5 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_0_input.mdp]: 70: You are using a plain Coulomb cut-off, which might produce artifacts. 70: You might want to consider using PME electrostatics. 70: 70: 70: 70: There were 5 NOTEs 70: 70: There was 1 WARNING 70: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_0.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 70: Can not increase nstlist because an NVE ensemble is used 70: Using 2 MPI threads 70: 70: Non-default thread affinity set, disabling internal thread affinity 70: 70: Using 2 OpenMP threads per tMPI thread 70: 70: starting mdrun 'Alanine-dipeptide' 70: 8 steps, 0.0 ps. 70: Generated 2145 of the 2145 non-bonded parameter combinations 70: 70: Generated 2145 of the 2145 1-4 parameter combinations 70: 70: Excluding 3 bonded neighbours molecule type 'ALANINEDIPEPTIDE' 70: 70: turning H bonds into constraints... 70: 70: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/alanine_vacuo.gro' 70: 70: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 246.451 K 70: 70: Calculated rlist for 1x1 atom pair-list as 0.755 nm, buffer size 0.055 nm 70: 70: Set rlist, assuming 4x4 atom pair-list, to 0.749 nm, buffer size 0.049 nm 70: 70: Note that mdrun will redetermine rlist based on the actual pair-list setup 70: 70: This run will generate roughly 0 Mb of data 70: 70: Writing final coordinates. 70: 70: 70: Dynamic load balancing report: 70: DLB was off during the run due to low measured imbalance. 70: Average load imbalance: 37.8%. 70: The balanceable part of the MD step is 40%, load imbalance is computed from this. 70: Part of the total run time spent waiting due to load imbalance: 15.3%. 70: 70: NOTE: 15.3 % of the available CPU time was lost due to load imbalance 70: in the domain decomposition. 70: Dynamic load balancing was automatically disabled, but it might be beneficial to manually turn it on (option -dlb yes.) 70: You can also consider manually changing the decomposition (option -dd); 70: e.g. by using fewer domains along the box dimension in which there is 70: considerable inhomogeneity in the simulated system. 70: 70: NOTE: 21 % of the run time was spent in domain decomposition, 70: 4 % of the run time was spent in pair search, 70: you might want to increase nstlist (this has no effect on accuracy) 70: 70: NOTE: 11 % of the run time was spent communicating energies, 70: you might want to increase some nst* mdp options 70: 70: Core t (s) Wall t (s) (%) 70: Time: 3.396 0.870 390.4 70: (ns/day) (hour/ns) 70: Performance: 0.894 26.849 70: 70: 70: [ OK ] FreezeWorks/FreezeGroupTest.WithinTolerances/0 (1761 ms) 70: [ RUN ] FreezeWorks/FreezeGroupTest.WithinTolerances/1 70: 70: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_1_input.mdp]: 70: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 70: that with the Verlet scheme, nstlist has no effect on the accuracy of 70: your simulation. 70: 70: 70: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_1_input.mdp]: 70: Setting nstcalcenergy (100) equal to nstenergy (4) 70: 70: Generating 1-4 interactions: fudge = 0.5 70: 70: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_1_input.mdp]: 70: There are 5 atoms that are fully frozen and part of COMM removal 70: group(s), removing these atoms from the COMM removal group(s) 70: 70: 70: WARNING 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_1_input.mdp]: 70: There are 3 atoms that are frozen along less then 3 dimensions and part 70: of COMM removal group(s), due to limitations in the code these still 70: contribute to the mass of the COM along frozen dimensions and therefore 70: the COMM correction will be too small. 70: 70: Number of degrees of freedom in T-Coupling group System is 33.00 70: 70: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_1_input.mdp]: 70: NVE simulation: will use the initial temperature of 246.451 K for 70: determining the Verlet buffer size 70: 70: 70: NOTE 5 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_1_input.mdp]: 70: You are using a plain Coulomb cut-off, which might produce artifacts. 70: You might want to consider using PME electrostatics. 70: 70: 70: 70: There were 5 NOTEs 70: 70: There was 1 WARNING 70: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_1.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 70: Can not increase nstlist because an NVE ensemble is used 70: Using 2 MPI threads 70: 70: Non-default thread affinity set, disabling internal thread affinity 70: 70: Using 2 OpenMP threads per tMPI thread 70: 70: starting mdrun 'Alanine-dipeptide' 70: 8 steps, 0.0 ps. 70: Generated 2145 of the 2145 non-bonded parameter combinations 70: 70: Generated 2145 of the 2145 1-4 parameter combinations 70: 70: Excluding 3 bonded neighbours molecule type 'ALANINEDIPEPTIDE' 70: 70: turning H bonds into constraints... 70: 70: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/alanine_vacuo.gro' 70: 70: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 246.451 K 70: 70: Calculated rlist for 1x1 atom pair-list as 0.755 nm, buffer size 0.055 nm 70: 70: Set rlist, assuming 4x4 atom pair-list, to 0.749 nm, buffer size 0.049 nm 70: 70: Note that mdrun will redetermine rlist based on the actual pair-list setup 70: 70: This run will generate roughly 0 Mb of data 70: 70: Writing final coordinates. 70: 70: 70: Dynamic load balancing report: 70: DLB was off during the run due to low measured imbalance. 70: Average load imbalance: 39.7%. 70: The balanceable part of the MD step is 35%, load imbalance is computed from this. 70: Part of the total run time spent waiting due to load imbalance: 14.0%. 70: 70: NOTE: 14.0 % of the available CPU time was lost due to load imbalance 70: in the domain decomposition. 70: Dynamic load balancing was automatically disabled, but it might be beneficial to manually turn it on (option -dlb yes.) 70: You can also consider manually changing the decomposition (option -dd); 70: e.g. by using fewer domains along the box dimension in which there is 70: considerable inhomogeneity in the simulated system. 70: 70: NOTE: 27 % of the run time was spent in domain decomposition, 70: 4 % of the run time was spent in pair search, 70: you might want to increase nstlist (this has no effect on accuracy) 70: 70: NOTE: 8 % of the run time was spent communicating energies, 70: you might want to increase some nst* mdp options 70: 70: Core t (s) Wall t (s) (%) 70: Time: 3.537 0.900 393.0 70: (ns/day) (hour/ns) 70: Performance: 0.864 27.774 70: 70: 70: [ OK ] FreezeWorks/FreezeGroupTest.WithinTolerances/1 (1751 ms) 70: [ RUN ] FreezeWorks/FreezeGroupTest.WithinTolerances/2 70: 70: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_2_input.mdp]: 70: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 70: that with the Verlet scheme, nstlist has no effect on the accuracy of 70: your simulation. 70: 70: 70: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_2_input.mdp]: 70: Setting nstcalcenergy (100) equal to nstenergy (4) 70: 70: Generating 1-4 interactions: fudge = 0.5 70: 70: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_2_input.mdp]: 70: There are 5 atoms that are fully frozen and part of COMM removal 70: group(s), removing these atoms from the COMM removal group(s) 70: 70: 70: WARNING 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_2_input.mdp]: 70: There are 3 atoms that are frozen along less then 3 dimensions and part 70: of COMM removal group(s), due to limitations in the code these still 70: contribute to the mass of the COM along frozen dimensions and therefore 70: the COMM correction will be too small. 70: 70: Number of degrees of freedom in T-Coupling group System is 33.00 70: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 70: 70: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_2_input.mdp]: 70: NVE simulation: will use the initial temperature of 246.451 K for 70: determining the Verlet buffer size 70: 70: 70: NOTE 5 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_2_input.mdp]: 70: You are using a plain Coulomb cut-off, which might produce artifacts. 70: You might want to consider using PME electrostatics. 70: 70: 70: 70: There were 5 NOTEs 70: 70: There was 1 WARNING 70: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_2.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 70: Can not increase nstlist because an NVE ensemble is used 70: Using 2 MPI threads 70: 70: Non-default thread affinity set, disabling internal thread affinity 70: 70: Using 2 OpenMP threads per tMPI thread 70: 70: starting mdrun 'Alanine-dipeptide' 70: 8 steps, 0.0 ps. 70: Generated 2145 of the 2145 non-bonded parameter combinations 70: 70: Generated 2145 of the 2145 1-4 parameter combinations 70: 70: Excluding 3 bonded neighbours molecule type 'ALANINEDIPEPTIDE' 70: 70: turning H bonds into constraints... 70: 70: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/alanine_vacuo.gro' 70: 70: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 246.451 K 70: 70: Calculated rlist for 1x1 atom pair-list as 0.755 nm, buffer size 0.055 nm 70: 70: Set rlist, assuming 4x4 atom pair-list, to 0.749 nm, buffer size 0.049 nm 70: 70: Note that mdrun will redetermine rlist based on the actual pair-list setup 70: 70: This run will generate roughly 0 Mb of data 70: 70: Writing final coordinates. 70: 70: 70: Dynamic load balancing report: 70: DLB was off during the run due to low measured imbalance. 70: Average load imbalance: 22.8%. 70: The balanceable part of the MD step is 43%, load imbalance is computed from this. 70: Part of the total run time spent waiting due to load imbalance: 9.8%. 70: 70: NOTE: 9.8 % of the available CPU time was lost due to load imbalance 70: in the domain decomposition. 70: Dynamic load balancing was automatically disabled, but it might be beneficial to manually turn it on (option -dlb yes.) 70: You can also consider manually changing the decomposition (option -dd); 70: e.g. by using fewer domains along the box dimension in which there is 70: considerable inhomogeneity in the simulated system. 70: 70: NOTE: 20 % of the run time was spent in domain decomposition, 70: 4 % of the run time was spent in pair search, 70: you might want to increase nstlist (this has no effect on accuracy) 70: 70: NOTE: 10 % of the run time was spent communicating energies, 70: you might want to increase some nst* mdp options 70: 70: Core t (s) Wall t (s) (%) 70: Time: 3.387 0.857 395.3 70: (ns/day) (hour/ns) 70: Performance: 0.908 26.443 70: 70: 70: [ OK ] FreezeWorks/FreezeGroupTest.WithinTolerances/2 (1710 ms) 70: [ RUN ] FreezeWorks/FreezeGroupTest.WithinTolerances/3 70: 70: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_3_input.mdp]: 70: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 70: that with the Verlet scheme, nstlist has no effect on the accuracy of 70: your simulation. 70: 70: 70: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_3_input.mdp]: 70: Setting nstcalcenergy (100) equal to nstenergy (4) 70: 70: Generating 1-4 interactions: fudge = 0.5 70: 70: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_3_input.mdp]: 70: There are 5 atoms that are fully frozen and part of COMM removal 70: group(s), removing these atoms from the COMM removal group(s) 70: 70: 70: WARNING 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_3_input.mdp]: 70: There are 3 atoms that are frozen along less then 3 dimensions and part 70: of COMM removal group(s), due to limitations in the code these still 70: contribute to the mass of the COM along frozen dimensions and therefore 70: the COMM correction will be too small. 70: 70: Number of degrees of freedom in T-Coupling group System is 33.00 70: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 70: 70: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_3_input.mdp]: 70: NVE simulation: will use the initial temperature of 246.451 K for 70: determining the Verlet buffer size 70: 70: 70: NOTE 5 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_3_input.mdp]: 70: You are using a plain Coulomb cut-off, which might produce artifacts. 70: You might want to consider using PME electrostatics. 70: 70: 70: 70: There were 5 NOTEs 70: 70: There was 1 WARNING 70: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_3.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 70: Can not increase nstlist because an NVE ensemble is used 70: Using 2 MPI threads 70: 70: Non-default thread affinity set, disabling internal thread affinity 70: 70: Using 2 OpenMP threads per tMPI thread 70: 70: starting mdrun 'Alanine-dipeptide' 70: 8 steps, 0.0 ps. 70: Generated 2145 of the 2145 non-bonded parameter combinations 70: 70: Generated 2145 of the 2145 1-4 parameter combinations 70: 70: Excluding 3 bonded neighbours molecule type 'ALANINEDIPEPTIDE' 70: 70: turning H bonds into constraints... 70: 70: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/alanine_vacuo.gro' 70: 70: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 246.451 K 70: 70: Calculated rlist for 1x1 atom pair-list as 0.755 nm, buffer size 0.055 nm 70: 70: Set rlist, assuming 4x4 atom pair-list, to 0.749 nm, buffer size 0.049 nm 70: 70: Note that mdrun will redetermine rlist based on the actual pair-list setup 70: 70: This run will generate roughly 0 Mb of data 70: 70: Writing final coordinates. 70: 70: 70: Dynamic load balancing report: 70: DLB was off during the run due to low measured imbalance. 70: Average load imbalance: 26.8%. 70: The balanceable part of the MD step is 47%, load imbalance is computed from this. 70: Part of the total run time spent waiting due to load imbalance: 12.7%. 70: 70: NOTE: 12.7 % of the available CPU time was lost due to load imbalance 70: in the domain decomposition. 70: Dynamic load balancing was automatically disabled, but it might be beneficial to manually turn it on (option -dlb yes.) 70: You can also consider manually changing the decomposition (option -dd); 70: e.g. by using fewer domains along the box dimension in which there is 70: considerable inhomogeneity in the simulated system. 70: 70: NOTE: 17 % of the run time was spent in domain decomposition, 70: 3 % of the run time was spent in pair search, 70: you might want to increase nstlist (this has no effect on accuracy) 70: 70: NOTE: 14 % of the run time was spent communicating energies, 70: you might want to increase some nst* mdp options 70: 70: Core t (s) Wall t (s) (%) 70: Time: 4.024 1.028 391.5 70: (ns/day) (hour/ns) 70: Performance: 0.757 31.723 70: 70: 70: [ OK ] FreezeWorks/FreezeGroupTest.WithinTolerances/3 (1898 ms) 70: [ RUN ] FreezeWorks/FreezeGroupTest.WithinTolerances/4 70: 70: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_4_input.mdp]: 70: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 70: that with the Verlet scheme, nstlist has no effect on the accuracy of 70: your simulation. 70: 70: 70: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_4_input.mdp]: 70: Setting nstcalcenergy (100) equal to nstenergy (4) 70: 70: Generating 1-4 interactions: fudge = 0.5 70: 70: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_4_input.mdp]: 70: There are 5 atoms that are fully frozen and part of COMM removal 70: group(s), removing these atoms from the COMM removal group(s) 70: 70: 70: WARNING 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_4_input.mdp]: 70: There are 3 atoms that are frozen along less then 3 dimensions and part 70: of COMM removal group(s), due to limitations in the code these still 70: contribute to the mass of the COM along frozen dimensions and therefore 70: the COMM correction will be too small. 70: 70: Number of degrees of freedom in T-Coupling group System is 33.00 70: 70: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_4_input.mdp]: 70: NVE simulation: will use the initial temperature of 246.451 K for 70: determining the Verlet buffer size 70: 70: 70: NOTE 5 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_4_input.mdp]: 70: You are using a plain Coulomb cut-off, which might produce artifacts. 70: You might want to consider using PME electrostatics. 70: 70: 70: 70: There were 5 NOTEs 70: 70: There was 1 WARNING 70: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_4.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 70: Can not increase nstlist because an NVE ensemble is used 70: Using 2 MPI threads 70: 70: Non-default thread affinity set, disabling internal thread affinity 70: 70: Using 2 OpenMP threads per tMPI thread 70: 70: starting mdrun 'Alanine-dipeptide' 70: 8 steps, 0.0 ps. 70: Generated 2145 of the 2145 non-bonded parameter combinations 70: 70: Generated 2145 of the 2145 1-4 parameter combinations 70: 70: Excluding 3 bonded neighbours molecule type 'ALANINEDIPEPTIDE' 70: 70: turning H bonds into constraints... 70: 70: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/alanine_vacuo.gro' 70: 70: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 246.451 K 70: 70: Calculated rlist for 1x1 atom pair-list as 0.755 nm, buffer size 0.055 nm 70: 70: Set rlist, assuming 4x4 atom pair-list, to 0.749 nm, buffer size 0.049 nm 70: 70: Note that mdrun will redetermine rlist based on the actual pair-list setup 70: 70: This run will generate roughly 0 Mb of data 70: 70: Writing final coordinates. 70: 70: 70: Dynamic load balancing report: 70: DLB was off during the run due to low measured imbalance. 70: Average load imbalance: 25.7%. 70: The balanceable part of the MD step is 48%, load imbalance is computed from this. 70: Part of the total run time spent waiting due to load imbalance: 12.2%. 70: 70: NOTE: 12.2 % of the available CPU time was lost due to load imbalance 70: in the domain decomposition. 70: Dynamic load balancing was automatically disabled, but it might be beneficial to manually turn it on (option -dlb yes.) 70: You can also consider manually changing the decomposition (option -dd); 70: e.g. by using fewer domains along the box dimension in which there is 70: considerable inhomogeneity in the simulated system. 70: 70: NOTE: 19 % of the run time was spent in domain decomposition, 70: 3 % of the run time was spent in pair search, 70: you might want to increase nstlist (this has no effect on accuracy) 70: 70: NOTE: 18 % of the run time was spent communicating energies, 70: you might want to increase some nst* mdp options 70: 70: Core t (s) Wall t (s) (%) 70: Time: 4.170 1.057 394.4 70: (ns/day) (hour/ns) 70: Performance: 0.735 32.632 70: 70: 70: [ OK ] FreezeWorks/FreezeGroupTest.WithinTolerances/4 (1967 ms) 70: [ RUN ] FreezeWorks/FreezeGroupTest.WithinTolerances/5 70: ./src/programs/mdrun/tests/freezegroups.cpp:209: Skipped 70: Parrinello-Rahman is not implemented in md-vv. 70: [ SKIPPED ] FreezeWorks/FreezeGroupTest.WithinTolerances/5 (0 ms) 70: [ RUN ] FreezeWorks/FreezeGroupTest.WithinTolerances/6 70: 70: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_6_input.mdp]: 70: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 70: that with the Verlet scheme, nstlist has no effect on the accuracy of 70: your simulation. 70: 70: 70: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_6_input.mdp]: 70: Setting nstcalcenergy (100) equal to nstenergy (4) 70: 70: Generating 1-4 interactions: fudge = 0.5 70: 70: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_6_input.mdp]: 70: There are 5 atoms that are fully frozen and part of COMM removal 70: group(s), removing these atoms from the COMM removal group(s) 70: 70: 70: WARNING 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_6_input.mdp]: 70: There are 3 atoms that are frozen along less then 3 dimensions and part 70: of COMM removal group(s), due to limitations in the code these still 70: contribute to the mass of the COM along frozen dimensions and therefore 70: the COMM correction will be too small. 70: 70: Number of degrees of freedom in T-Coupling group System is 33.00 70: 70: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_6_input.mdp]: 70: You are using a plain Coulomb cut-off, which might produce artifacts. 70: You might want to consider using PME electrostatics. 70: 70: 70: 70: There were 4 NOTEs 70: 70: There was 1 WARNING 70: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_6.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 70: Changing nstlist from 8 to 20, rlist from 0.754 to 0.856 70: 70: Using 2 MPI threads 70: 70: Non-default thread affinity set, disabling internal thread affinity 70: 70: Using 2 OpenMP threads per tMPI thread 70: 70: starting mdrun 'Alanine-dipeptide' 70: 8 steps, 0.0 ps. 70: Generated 2145 of the 2145 non-bonded parameter combinations 70: 70: Generated 2145 of the 2145 1-4 parameter combinations 70: 70: Excluding 3 bonded neighbours molecule type 'ALANINEDIPEPTIDE' 70: 70: turning H bonds into constraints... 70: 70: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/alanine_vacuo.gro' 70: 70: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 70: 70: Calculated rlist for 1x1 atom pair-list as 0.761 nm, buffer size 0.061 nm 70: 70: Set rlist, assuming 4x4 atom pair-list, to 0.754 nm, buffer size 0.054 nm 70: 70: Note that mdrun will redetermine rlist based on the actual pair-list setup 70: 70: This run will generate roughly 0 Mb of data 70: 70: Writing final coordinates. 70: 70: NOTE: 11 % of the run time was spent in domain decomposition, 70: 2 % of the run time was spent in pair search, 70: you might want to increase nstlist (this has no effect on accuracy) 70: 70: NOTE: 11 % of the run time was spent communicating energies, 70: you might want to increase some nst* mdp options 70: 70: Core t (s) Wall t (s) (%) 70: Time: 3.018 0.769 392.3 70: (ns/day) (hour/ns) 70: Performance: 1.011 23.741 70: 70: 70: [ OK ] FreezeWorks/FreezeGroupTest.WithinTolerances/6 (1799 ms) 70: [ RUN ] FreezeWorks/FreezeGroupTest.WithinTolerances/7 70: 70: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_7_input.mdp]: 70: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 70: that with the Verlet scheme, nstlist has no effect on the accuracy of 70: your simulation. 70: 70: 70: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_7_input.mdp]: 70: Setting nstcalcenergy (100) equal to nstenergy (4) 70: 70: Generating 1-4 interactions: fudge = 0.5 70: 70: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_7_input.mdp]: 70: There are 5 atoms that are fully frozen and part of COMM removal 70: group(s), removing these atoms from the COMM removal group(s) 70: 70: 70: WARNING 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_7_input.mdp]: 70: There are 3 atoms that are frozen along less then 3 dimensions and part 70: of COMM removal group(s), due to limitations in the code these still 70: contribute to the mass of the COM along frozen dimensions and therefore 70: the COMM correction will be too small. 70: 70: Number of degrees of freedom in T-Coupling group System is 33.00 70: 70: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_7_input.mdp]: 70: You are using a plain Coulomb cut-off, which might produce artifacts. 70: You might want to consider using PME electrostatics. 70: 70: 70: 70: There were 4 NOTEs 70: 70: There was 1 WARNING 70: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_7.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 70: Changing nstlist from 8 to 20, rlist from 0.754 to 0.856 70: 70: Using 2 MPI threads 70: 70: Non-default thread affinity set, disabling internal thread affinity 70: 70: Using 2 OpenMP threads per tMPI thread 70: 70: starting mdrun 'Alanine-dipeptide' 70: 8 steps, 0.0 ps. 70: Generated 2145 of the 2145 non-bonded parameter combinations 70: 70: Generated 2145 of the 2145 1-4 parameter combinations 70: 70: Excluding 3 bonded neighbours molecule type 'ALANINEDIPEPTIDE' 70: 70: turning H bonds into constraints... 70: 70: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/alanine_vacuo.gro' 70: 70: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 70: 70: Calculated rlist for 1x1 atom pair-list as 0.761 nm, buffer size 0.061 nm 70: 70: Set rlist, assuming 4x4 atom pair-list, to 0.754 nm, buffer size 0.054 nm 70: 70: Note that mdrun will redetermine rlist based on the actual pair-list setup 70: 70: This run will generate roughly 0 Mb of data 70: 70: Writing final coordinates. 70: 70: NOTE: 10 % of the run time was spent in domain decomposition, 70: 2 % of the run time was spent in pair search, 70: you might want to increase nstlist (this has no effect on accuracy) 70: 70: NOTE: 10 % of the run time was spent communicating energies, 70: you might want to increase some nst* mdp options 70: 70: Core t (s) Wall t (s) (%) 70: Time: 3.213 0.821 391.2 70: (ns/day) (hour/ns) 70: Performance: 0.947 25.346 70: 70: 70: [ OK ] FreezeWorks/FreezeGroupTest.WithinTolerances/7 (1800 ms) 70: [ RUN ] FreezeWorks/FreezeGroupTest.WithinTolerances/8 70: 70: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_8_input.mdp]: 70: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 70: that with the Verlet scheme, nstlist has no effect on the accuracy of 70: your simulation. 70: 70: 70: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_8_input.mdp]: 70: Setting nstcalcenergy (100) equal to nstenergy (4) 70: 70: Generating 1-4 interactions: fudge = 0.5 70: 70: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_8_input.mdp]: 70: There are 5 atoms that are fully frozen and part of COMM removal 70: group(s), removing these atoms from the COMM removal group(s) 70: 70: 70: WARNING 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_8_input.mdp]: 70: There are 3 atoms that are frozen along less then 3 dimensions and part 70: of COMM removal group(s), due to limitations in the code these still 70: contribute to the mass of the COM along frozen dimensions and therefore 70: the COMM correction will be too small. 70: 70: Number of degrees of freedom in T-Coupling group System is 33.00 70: 70: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_8_input.mdp]: 70: You are using a plain Coulomb cut-off, which might produce artifacts. 70: You might want to consider using PME electrostatics. 70: 70: 70: 70: There were 4 NOTEs 70: 70: There was 1 WARNING 70: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_8.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 70: Changing nstlist from 8 to 20, rlist from 0.754 to 0.856 70: 70: Using 2 MPI threads 70: 70: Non-default thread affinity set, disabling internal thread affinity 70: 70: Using 2 OpenMP threads per tMPI thread 70: 70: starting mdrun 'Alanine-dipeptide' 70: 8 steps, 0.0 ps. 70: Generated 2145 of the 2145 non-bonded parameter combinations 70: 70: Generated 2145 of the 2145 1-4 parameter combinations 70: 70: Excluding 3 bonded neighbours molecule type 'ALANINEDIPEPTIDE' 70: 70: turning H bonds into constraints... 70: 70: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/alanine_vacuo.gro' 70: 70: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 70: 70: Calculated rlist for 1x1 atom pair-list as 0.761 nm, buffer size 0.061 nm 70: 70: Set rlist, assuming 4x4 atom pair-list, to 0.754 nm, buffer size 0.054 nm 70: 70: Note that mdrun will redetermine rlist based on the actual pair-list setup 70: 70: This run will generate roughly 0 Mb of data 70: 70: Writing final coordinates. 70: 70: NOTE: 11 % of the run time was spent in domain decomposition, 70: 2 % of the run time was spent in pair search, 70: you might want to increase nstlist (this has no effect on accuracy) 70: 70: NOTE: 11 % of the run time was spent communicating energies, 70: you might want to increase some nst* mdp options 70: 70: Core t (s) Wall t (s) (%) 70: Time: 3.127 0.792 394.9 70: (ns/day) (hour/ns) 70: Performance: 0.982 24.441 70: 70: 70: [ OK ] FreezeWorks/FreezeGroupTest.WithinTolerances/8 (1711 ms) 70: [ RUN ] FreezeWorks/FreezeGroupTest.WithinTolerances/9 70: 70: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_9_input.mdp]: 70: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 70: that with the Verlet scheme, nstlist has no effect on the accuracy of 70: your simulation. 70: 70: 70: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_9_input.mdp]: 70: Setting nstcalcenergy (100) equal to nstenergy (4) 70: 70: Generating 1-4 interactions: fudge = 0.5 70: 70: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_9_input.mdp]: 70: There are 5 atoms that are fully frozen and part of COMM removal 70: group(s), removing these atoms from the COMM removal group(s) 70: 70: 70: WARNING 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_9_input.mdp]: 70: There are 3 atoms that are frozen along less then 3 dimensions and part 70: of COMM removal group(s), due to limitations in the code these still 70: contribute to the mass of the COM along frozen dimensions and therefore 70: the COMM correction will be too small. 70: 70: Number of degrees of freedom in T-Coupling group System is 33.00 70: 70: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_9_input.mdp]: 70: You are using a plain Coulomb cut-off, which might produce artifacts. 70: You might want to consider using PME electrostatics. 70: 70: 70: 70: There were 4 NOTEs 70: 70: There was 1 WARNING 70: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_9.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 70: Changing nstlist from 8 to 100, rlist from 0.734 to 0.829 70: 70: Using 2 MPI threads 70: 70: Non-default thread affinity set, disabling internal thread affinity 70: 70: Using 2 OpenMP threads per tMPI thread 70: 70: starting mdrun 'Alanine-dipeptide' 70: 8 steps, 0.0 ps. 70: Generated 2145 of the 2145 non-bonded parameter combinations 70: 70: Generated 2145 of the 2145 1-4 parameter combinations 70: 70: Excluding 3 bonded neighbours molecule type 'ALANINEDIPEPTIDE' 70: 70: turning H bonds into constraints... 70: 70: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 70: 70: Calculated rlist for 1x1 atom pair-list as 0.737 nm, buffer size 0.037 nm 70: 70: Set rlist, assuming 4x4 atom pair-list, to 0.734 nm, buffer size 0.034 nm 70: 70: Note that mdrun will redetermine rlist based on the actual pair-list setup 70: 70: This run will generate roughly 0 Mb of data 70: 70: Writing final coordinates. 70: 70: NOTE: 11 % of the run time was spent in domain decomposition, 70: 2 % of the run time was spent in pair search, 70: you might want to increase nstlist (this has no effect on accuracy) 70: 70: NOTE: 11 % of the run time was spent communicating energies, 70: you might want to increase some nst* mdp options 70: 70: Core t (s) Wall t (s) (%) 70: Time: 2.776 0.717 387.3 70: (ns/day) (hour/ns) 70: Performance: 1.085 22.121 70: 70: 70: [ OK ] FreezeWorks/FreezeGroupTest.WithinTolerances/9 (2352 ms) 70: [ RUN ] FreezeWorks/FreezeGroupTest.WithinTolerances/10 70: 70: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_10_input.mdp]: 70: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 70: that with the Verlet scheme, nstlist has no effect on the accuracy of 70: your simulation. 70: 70: 70: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_10_input.mdp]: 70: Setting nstcalcenergy (100) equal to nstenergy (4) 70: 70: Generating 1-4 interactions: fudge = 0.5 70: 70: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_10_input.mdp]: 70: There are 5 atoms that are fully frozen and part of COMM removal 70: group(s), removing these atoms from the COMM removal group(s) 70: 70: 70: WARNING 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_10_input.mdp]: 70: There are 3 atoms that are frozen along less then 3 dimensions and part 70: of COMM removal group(s), due to limitations in the code these still 70: contribute to the mass of the COM along frozen dimensions and therefore 70: the COMM correction will be too small. 70: 70: Number of degrees of freedom in T-Coupling group System is 33.00 70: 70: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_10_input.mdp]: 70: You are using a plain Coulomb cut-off, which might produce artifacts. 70: You might want to consider using PME electrostatics. 70: 70: 70: 70: There were 4 NOTEs 70: 70: There was 1 WARNING 70: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_10.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 70: Changing nstlist from 8 to 100, rlist from 0.734 to 0.829 70: 70: Using 2 MPI threads 70: 70: Non-default thread affinity set, disabling internal thread affinity 70: 70: Using 2 OpenMP threads per tMPI thread 70: 70: starting mdrun 'Alanine-dipeptide' 70: 8 steps, 0.0 ps. 70: Generated 2145 of the 2145 non-bonded parameter combinations 70: 70: Generated 2145 of the 2145 1-4 parameter combinations 70: 70: Excluding 3 bonded neighbours molecule type 'ALANINEDIPEPTIDE' 70: 70: turning H bonds into constraints... 70: 70: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 70: 70: Calculated rlist for 1x1 atom pair-list as 0.737 nm, buffer size 0.037 nm 70: 70: Set rlist, assuming 4x4 atom pair-list, to 0.734 nm, buffer size 0.034 nm 70: 70: Note that mdrun will redetermine rlist based on the actual pair-list setup 70: 70: This run will generate roughly 0 Mb of data 70: 70: Writing final coordinates. 70: 70: NOTE: 13 % of the run time was spent in domain decomposition, 70: 2 % of the run time was spent in pair search, 70: you might want to increase nstlist (this has no effect on accuracy) 70: 70: NOTE: 11 % of the run time was spent communicating energies, 70: you might want to increase some nst* mdp options 70: 70: Core t (s) Wall t (s) (%) 70: Time: 2.973 0.761 390.5 70: (ns/day) (hour/ns) 70: Performance: 1.021 23.497 70: 70: 70: [ OK ] FreezeWorks/FreezeGroupTest.WithinTolerances/10 (2431 ms) 70: [ RUN ] FreezeWorks/FreezeGroupTest.WithinTolerances/11 70: 70: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_11_input.mdp]: 70: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 70: that with the Verlet scheme, nstlist has no effect on the accuracy of 70: your simulation. 70: 70: 70: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_11_input.mdp]: 70: Setting nstcalcenergy (100) equal to nstenergy (4) 70: 70: Generating 1-4 interactions: fudge = 0.5 70: 70: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_11_input.mdp]: 70: There are 5 atoms that are fully frozen and part of COMM removal 70: group(s), removing these atoms from the COMM removal group(s) 70: 70: 70: WARNING 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_11_input.mdp]: 70: There are 3 atoms that are frozen along less then 3 dimensions and part 70: of COMM removal group(s), due to limitations in the code these still 70: contribute to the mass of the COM along frozen dimensions and therefore 70: the COMM correction will be too small. 70: 70: Number of degrees of freedom in T-Coupling group System is 33.00 70: 70: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_11_input.mdp]: 70: You are using a plain Coulomb cut-off, which might produce artifacts. 70: You might want to consider using PME electrostatics. 70: 70: 70: 70: There were 4 NOTEs 70: 70: There was 1 WARNING 70: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_11.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 70: Changing nstlist from 8 to 100, rlist from 0.734 to 0.829 70: 70: Using 2 MPI threads 70: 70: Non-default thread affinity set, disabling internal thread affinity 70: 70: Using 2 OpenMP threads per tMPI thread 70: 70: starting mdrun 'Alanine-dipeptide' 70: 8 steps, 0.0 ps. 70: Generated 2145 of the 2145 non-bonded parameter combinations 70: 70: Generated 2145 of the 2145 1-4 parameter combinations 70: 70: Excluding 3 bonded neighbours molecule type 'ALANINEDIPEPTIDE' 70: 70: turning H bonds into constraints... 70: 70: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 70: 70: Calculated rlist for 1x1 atom pair-list as 0.737 nm, buffer size 0.037 nm 70: 70: Set rlist, assuming 4x4 atom pair-list, to 0.734 nm, buffer size 0.034 nm 70: 70: Note that mdrun will redetermine rlist based on the actual pair-list setup 70: 70: This run will generate roughly 0 Mb of data 70: 70: Writing final coordinates. 70: 70: NOTE: 12 % of the run time was spent in domain decomposition, 70: 2 % of the run time was spent in pair search, 70: you might want to increase nstlist (this has no effect on accuracy) 70: 70: NOTE: 10 % of the run time was spent communicating energies, 70: you might want to increase some nst* mdp options 70: 70: Core t (s) Wall t (s) (%) 70: Time: 2.809 0.725 387.4 70: (ns/day) (hour/ns) 70: Performance: 1.072 22.384 70: 70: 70: [ OK ] FreezeWorks/FreezeGroupTest.WithinTolerances/11 (2287 ms) 70: [----------] 12 tests from FreezeWorks/FreezeGroupTest (21473 ms total) 70: 70: [----------] 4 tests from AccelerationWorks/AccelerationGroupTest 70: [ RUN ] AccelerationWorks/AccelerationGroupTest.WithinTolerances/0 70: 70: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/AccelerationWorks_AccelerationGroupTest_WithinTolerances_0_input.mdp]: 70: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 70: that with the Verlet scheme, nstlist has no effect on the accuracy of 70: your simulation. 70: 70: 70: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/AccelerationWorks_AccelerationGroupTest_WithinTolerances_0_input.mdp]: 70: verlet-buffer-pressure-tolerance is ignored when verlet-buffer-tolerance 70: < 0 70: 70: 70: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/AccelerationWorks_AccelerationGroupTest_WithinTolerances_0_input.mdp]: 70: Setting nstcalcenergy (100) equal to nstenergy (4) 70: 70: Generating 1-4 interactions: fudge = 0.5 70: Number of degrees of freedom in T-Coupling group FirstWaterMolecule is 6.00 70: Number of degrees of freedom in T-Coupling group SecondWaterMolecule is 6.00 70: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 70: Net Acceleration in X direction, will not be corrected 70: Net Acceleration in Y direction, will not be corrected 70: Net Acceleration in Z direction, will not be corrected 70: 70: There were 3 NOTEs 70: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/AccelerationWorks_AccelerationGroupTest_WithinTolerances_0.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 70: Can not increase nstlist because an NVE ensemble is used 70: Using 2 MPI threads 70: 70: Non-default thread affinity set, disabling internal thread affinity 70: 70: Using 2 OpenMP threads per tMPI thread 70: 70: starting mdrun 'spc2' 70: 8 steps, 0.0 ps. 70: Generated 3 of the 3 non-bonded parameter combinations 70: 70: Generated 3 of the 3 1-4 parameter combinations 70: 70: Excluding 2 bonded neighbours molecule type 'SOL' 70: 70: Setting gen_seed to 446537385 70: 70: Velocities were taken from a Maxwell distribution at 0 K 70: 70: This run will generate roughly 0 Mb of data 70: 70: Writing final coordinates. 70: 70: 70: Dynamic load balancing report: 70: DLB was off during the run due to low measured imbalance. 70: Average load imbalance: 21.9%. 70: The balanceable part of the MD step is 40%, load imbalance is computed from this. 70: Part of the total run time spent waiting due to load imbalance: 8.7%. 70: 70: NOTE: 8.7 % of the available CPU time was lost due to load imbalance 70: in the domain decomposition. 70: Dynamic load balancing was automatically disabled, but it might be beneficial to manually turn it on (option -dlb yes.) 70: You can also consider manually changing the decomposition (option -dd); 70: e.g. by using fewer domains along the box dimension in which there is 70: considerable inhomogeneity in the simulated system. 70: 70: NOTE: 20 % of the run time was spent in domain decomposition, 70: 4 % of the run time was spent in pair search, 70: you might want to increase nstlist (this has no effect on accuracy) 70: 70: NOTE: 10 % of the run time was spent communicating energies, 70: you might want to increase some nst* mdp options 70: 70: Core t (s) Wall t (s) (%) 70: Time: 2.976 0.760 391.7 70: (ns/day) (hour/ns) 70: Performance: 2.047 11.726 70: 70: [ OK ] AccelerationWorks/AccelerationGroupTest.WithinTolerances/0 (1461 ms) 70: [ RUN ] AccelerationWorks/AccelerationGroupTest.WithinTolerances/1 70: 70: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/AccelerationWorks_AccelerationGroupTest_WithinTolerances_1_input.mdp]: 70: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 70: that with the Verlet scheme, nstlist has no effect on the accuracy of 70: your simulation. 70: 70: 70: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/AccelerationWorks_AccelerationGroupTest_WithinTolerances_1_input.mdp]: 70: verlet-buffer-pressure-tolerance is ignored when verlet-buffer-tolerance 70: < 0 70: 70: 70: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/AccelerationWorks_AccelerationGroupTest_WithinTolerances_1_input.mdp]: 70: Setting nstcalcenergy (100) equal to nstenergy (4) 70: 70: Generating 1-4 interactions: fudge = 0.5 70: Number of degrees of freedom in T-Coupling group FirstWaterMolecule is 6.00 70: Number of degrees of freedom in T-Coupling group SecondWaterMolecule is 6.00 70: Net Acceleration in X direction, will not be corrected 70: Net Acceleration in Y direction, will not be corrected 70: Net Acceleration in Z direction, will not be corrected 70: 70: There were 3 NOTEs 70: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/AccelerationWorks_AccelerationGroupTest_WithinTolerances_1.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 70: Can not increase nstlist because verlet-buffer-tolerance is not set or used 70: Using 2 MPI threads 70: 70: Non-default thread affinity set, disabling internal thread affinity 70: 70: Using 2 OpenMP threads per tMPI thread 70: 70: starting mdrun 'spc2' 70: 8 steps, 0.0 ps. 70: Generated 3 of the 3 non-bonded parameter combinations 70: 70: Generated 3 of the 3 1-4 parameter combinations 70: 70: Excluding 2 bonded neighbours molecule type 'SOL' 70: 70: Setting gen_seed to -1088594082 70: 70: Velocities were taken from a Maxwell distribution at 0 K 70: 70: This run will generate roughly 0 Mb of data 70: 70: Writing final coordinates. 70: 70: 70: Dynamic load balancing report: 70: DLB was off during the run due to low measured imbalance. 70: Average load imbalance: 16.9%. 70: The balanceable part of the MD step is 40%, load imbalance is computed from this. 70: Part of the total run time spent waiting due to load imbalance: 6.8%. 70: 70: NOTE: 6.8 % of the available CPU time was lost due to load imbalance 70: in the domain decomposition. 70: Dynamic load balancing was automatically disabled, but it might be beneficial to manually turn it on (option -dlb yes.) 70: You can also consider manually changing the decomposition (option -dd); 70: e.g. by using fewer domains along the box dimension in which there is 70: considerable inhomogeneity in the simulated system. 70: 70: NOTE: 20 % of the run time was spent in domain decomposition, 70: 5 % of the run time was spent in pair search, 70: you might want to increase nstlist (this has no effect on accuracy) 70: 70: NOTE: 10 % of the run time was spent communicating energies, 70: you might want to increase some nst* mdp options 70: 70: Core t (s) Wall t (s) (%) 70: Time: 2.864 0.732 391.4 70: (ns/day) (hour/ns) 70: Performance: 2.125 11.295 70: 70: [ OK ] AccelerationWorks/AccelerationGroupTest.WithinTolerances/1 (1456 ms) 70: [ RUN ] AccelerationWorks/AccelerationGroupTest.WithinTolerances/2 70: 70: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/AccelerationWorks_AccelerationGroupTest_WithinTolerances_2_input.mdp]: 70: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 70: that with the Verlet scheme, nstlist has no effect on the accuracy of 70: your simulation. 70: 70: 70: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/AccelerationWorks_AccelerationGroupTest_WithinTolerances_2_input.mdp]: 70: verlet-buffer-pressure-tolerance is ignored when verlet-buffer-tolerance 70: < 0 70: 70: 70: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/AccelerationWorks_AccelerationGroupTest_WithinTolerances_2_input.mdp]: 70: Setting nstcalcenergy (100) equal to nstenergy (4) 70: 70: Generating 1-4 interactions: fudge = 0.5 70: Number of degrees of freedom in T-Coupling group FirstWaterMolecule is 6.00 70: Number of degrees of freedom in T-Coupling group SecondWaterMolecule is 6.00 70: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 70: Net Acceleration in X direction, will not be corrected 70: Net Acceleration in Y direction, will not be corrected 70: Net Acceleration in Z direction, will not be corrected 70: 70: There were 3 NOTEs 70: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/AccelerationWorks_AccelerationGroupTest_WithinTolerances_2.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 70: Can not increase nstlist because an NVE ensemble is used 70: Using 2 MPI threads 70: 70: Non-default thread affinity set, disabling internal thread affinity 70: 70: Using 2 OpenMP threads per tMPI thread 70: 70: starting mdrun 'spc2' 70: 8 steps, 0.0 ps. 70: Generated 3 of the 3 non-bonded parameter combinations 70: 70: Generated 3 of the 3 1-4 parameter combinations 70: 70: Excluding 2 bonded neighbours molecule type 'SOL' 70: 70: Setting gen_seed to 2113929018 70: 70: Velocities were taken from a Maxwell distribution at 0 K 70: 70: This run will generate roughly 0 Mb of data 70: 70: Writing final coordinates. 70: 70: 70: Dynamic load balancing report: 70: DLB was off during the run due to low measured imbalance. 70: Average load imbalance: 16.2%. 70: The balanceable part of the MD step is 46%, load imbalance is computed from this. 70: Part of the total run time spent waiting due to load imbalance: 7.4%. 70: 70: NOTE: 7.4 % of the available CPU time was lost due to load imbalance 70: in the domain decomposition. 70: Dynamic load balancing was automatically disabled, but it might be beneficial to manually turn it on (option -dlb yes.) 70: You can also consider manually changing the decomposition (option -dd); 70: e.g. by using fewer domains along the box dimension in which there is 70: considerable inhomogeneity in the simulated system. 70: 70: NOTE: 17 % of the run time was spent in domain decomposition, 70: 4 % of the run time was spent in pair search, 70: you might want to increase nstlist (this has no effect on accuracy) 70: 70: NOTE: 16 % of the run time was spent communicating energies, 70: you might want to increase some nst* mdp options 70: 70: Core t (s) Wall t (s) (%) 70: Time: 3.348 0.853 392.6 70: (ns/day) (hour/ns) 70: Performance: 1.824 13.160 70: 70: [ OK ] AccelerationWorks/AccelerationGroupTest.WithinTolerances/2 (1563 ms) 70: [ RUN ] AccelerationWorks/AccelerationGroupTest.WithinTolerances/3 70: 70: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/AccelerationWorks_AccelerationGroupTest_WithinTolerances_3_input.mdp]: 70: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 70: that with the Verlet scheme, nstlist has no effect on the accuracy of 70: your simulation. 70: 70: 70: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/AccelerationWorks_AccelerationGroupTest_WithinTolerances_3_input.mdp]: 70: verlet-buffer-pressure-tolerance is ignored when verlet-buffer-tolerance 70: < 0 70: 70: 70: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/AccelerationWorks_AccelerationGroupTest_WithinTolerances_3_input.mdp]: 70: Setting nstcalcenergy (100) equal to nstenergy (4) 70: 70: Generating 1-4 interactions: fudge = 0.5 70: Number of degrees of freedom in T-Coupling group FirstWaterMolecule is 6.00 70: Number of degrees of freedom in T-Coupling group SecondWaterMolecule is 6.00 70: Net Acceleration in X direction, will not be corrected 70: Net Acceleration in Y direction, will not be corrected 70: Net Acceleration in Z direction, will not be corrected 70: 70: There were 3 NOTEs 70: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/AccelerationWorks_AccelerationGroupTest_WithinTolerances_3.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 70: Can not increase nstlist because verlet-buffer-tolerance is not set or used 70: Using 2 MPI threads 70: 70: Non-default thread affinity set, disabling internal thread affinity 70: 70: Using 2 OpenMP threads per tMPI thread 70: 70: starting mdrun 'spc2' 70: 8 steps, 0.0 ps. 70: Generated 3 of the 3 non-bonded parameter combinations 70: 70: Generated 3 of the 3 1-4 parameter combinations 70: 70: Excluding 2 bonded neighbours molecule type 'SOL' 70: 70: Setting gen_seed to -536879394 70: 70: Velocities were taken from a Maxwell distribution at 0 K 70: 70: This run will generate roughly 0 Mb of data 70: 70: Writing final coordinates. 70: 70: 70: Dynamic load balancing report: 70: DLB was off during the run due to low measured imbalance. 70: Average load imbalance: 16.6%. 70: The balanceable part of the MD step is 46%, load imbalance is computed from this. 70: Part of the total run time spent waiting due to load imbalance: 7.7%. 70: 70: NOTE: 7.7 % of the available CPU time was lost due to load imbalance 70: in the domain decomposition. 70: Dynamic load balancing was automatically disabled, but it might be beneficial to manually turn it on (option -dlb yes.) 70: You can also consider manually changing the decomposition (option -dd); 70: e.g. by using fewer domains along the box dimension in which there is 70: considerable inhomogeneity in the simulated system. 70: 70: NOTE: 17 % of the run time was spent in domain decomposition, 70: 4 % of the run time was spent in pair search, 70: you might want to increase nstlist (this has no effect on accuracy) 70: 70: NOTE: 17 % of the run time was spent communicating energies, 70: you might want to increase some nst* mdp options 70: 70: Core t (s) Wall t (s) (%) 70: Time: 3.520 0.896 392.9 70: (ns/day) (hour/ns) 70: Performance: 1.736 13.826 70: 70: [ OK ] AccelerationWorks/AccelerationGroupTest.WithinTolerances/3 (1603 ms) 70: [----------] 4 tests from AccelerationWorks/AccelerationGroupTest (6085 ms total) 70: 70: [----------] Global test environment tear-down 70: [==========] 29 tests from 8 test suites ran. (86676 ms total) 70: [ PASSED ] 28 tests. 70: [ SKIPPED ] 1 test, listed below: 70: [ SKIPPED ] FreezeWorks/FreezeGroupTest.WithinTolerances/5 70/92 Test #70: MdrunTestsTwoRanks ........................ Passed 86.80 sec test 71 Start 71: MdrunSingleRankAlgorithmsTests 71: Test command: /build/reproducible-path/gromacs-2025.1/build/basic-dp/bin/mdrun-single-rank-algorithms-test "-ntomp" "2" "--gtest_output=xml:/build/reproducible-path/gromacs-2025.1/build/basic-dp/Testing/Temporary/MdrunSingleRankAlgorithmsTests.xml" 71: Working Directory: /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests 71: Test timeout computed to be: 600 71: [==========] Running 5 tests from 3 test suites. 71: [----------] Global test environment set-up. 71: [----------] 1 test from DispersionCorrectionTest 71: [ RUN ] DispersionCorrectionTest.DispersionCorrectionCanRun 71: Generating 1-4 interactions: fudge = 0.5 71: Number of degrees of freedom in T-Coupling group System is 30.00 71: 71: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/DispersionCorrectionTest_DispersionCorrectionCanRun_input.mdp]: 71: There are 9 non-linear virtual site constructions. Their contribution to 71: the energy error is approximated. In most cases this does not affect the 71: error significantly. 71: 71: 71: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/DispersionCorrectionTest_DispersionCorrectionCanRun_input.mdp]: 71: You are using a plain Coulomb cut-off, which might produce artifacts. 71: You might want to consider using PME electrostatics. 71: 71: 71: 71: There were 2 NOTEs 71: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/DispersionCorrectionTest_DispersionCorrectionCanRun.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 71: Changing nstlist from 10 to 40, rlist from 1.023 to 1.158 71: 71: Update groups can not be used for this system because an incompatible virtual site type is used 71: 71: Using 1 MPI thread 71: Using 2 OpenMP threads 71: 71: 71: NOTE: The number of threads is not equal to the number of (logical) cpus 71: and the -pin option is set to auto: will not pin threads to cpus. 71: This can lead to significant performance degradation. 71: Consider using -pin on (and -pinoffset in case you run multiple jobs). 71: starting mdrun 'Alanine dipeptide in vacuo' 71: 200 steps, 0.4 ps. 71: Setting the LD random seed to -197710 71: 71: Generated 2145 of the 2145 non-bonded parameter combinations 71: 71: Generated 2145 of the 2145 1-4 parameter combinations 71: 71: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' 71: 71: turning H bonds into constraints... 71: 71: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/alanine_vsite_vacuo.gro' 71: 71: Cleaning up constraints and constant bonded interactions with virtual sites 71: 71: Converted 3 Bonds with virtual sites to connections, 7 left 71: 71: Removed 18 Angles with virtual sites, 21 left 71: 71: Removed 10 Proper Dih.s with virtual sites, 44 left 71: 71: Converted 12 Constraints with virtual sites to connections, 0 left 71: 71: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 300 K 71: 71: Calculated rlist for 1x1 atom pair-list as 1.038 nm, buffer size 0.038 nm 71: 71: Set rlist, assuming 4x4 atom pair-list, to 1.023 nm, buffer size 0.023 nm 71: 71: Note that mdrun will redetermine rlist based on the actual pair-list setup 71: 71: This run will generate roughly 0 Mb of data 71: 71: Writing final coordinates. 71: 71: Core t (s) Wall t (s) (%) 71: Time: 0.182 0.092 199.1 71: (ns/day) (hour/ns) 71: Performance: 379.465 0.063 71: [ OK ] DispersionCorrectionTest.DispersionCorrectionCanRun (491 ms) 71: [----------] 1 test from DispersionCorrectionTest (491 ms total) 71: 71: [----------] 1 test from OriresTest 71: [ RUN ] OriresTest.OriresCanRun 71: Generating 1-4 interactions: fudge = 0.5 71: Number of degrees of freedom in T-Coupling group System is 518.00 71: 71: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/OriresTest_OriresCanRun_input.mdp]: 71: You are using a plain Coulomb cut-off, which might produce artifacts. 71: You might want to consider using PME electrostatics. 71: 71: 71: 71: There was 1 NOTE 71: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/OriresTest_OriresCanRun.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 71: Orientation restraints only supports a single rank. Choosing to use only a single thread-MPI rank. 71: Changing nstlist from 10 to 25, rlist from 1.07 to 1.203 71: 71: 71: Using 1 MPI thread 71: Using 2 OpenMP threads 71: 71: 71: NOTE: The number of threads is not equal to the number of (logical) cpus 71: and the -pin option is set to auto: will not pin threads to cpus. 71: This can lead to significant performance degradation. 71: Consider using -pin on (and -pinoffset in case you run multiple jobs). 71: starting mdrun 'GUANINE NUCLEOTIDE-BINDING PROTEIN G(T), ALPHA-1' 71: 10 steps, 0.0 ps. 71: Setting the LD random seed to -84235265 71: 71: Generated 2145 of the 2145 non-bonded parameter combinations 71: 71: Generated 2145 of the 2145 1-4 parameter combinations 71: 71: Excluding 3 bonded neighbours molecule type 'Protein_chain_A' 71: 71: turning H bonds into constraints... 71: 71: Excluding 2 bonded neighbours molecule type 'SOL' 71: 71: turning H bonds into constraints... 71: 71: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/orires_1lvz.gro' 71: 71: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 300 K 71: 71: Calculated rlist for 1x1 atom pair-list as 1.093 nm, buffer size 0.093 nm 71: 71: Set rlist, assuming 4x4 atom pair-list, to 1.070 nm, buffer size 0.070 nm 71: 71: Note that mdrun will redetermine rlist based on the actual pair-list setup 71: 71: This run will generate roughly 0 Mb of data 71: 71: Writing final coordinates. 71: 71: Core t (s) Wall t (s) (%) 71: Time: 0.123 0.062 198.9 71: (ns/day) (hour/ns) 71: Performance: 30.682 0.782 71: [ OK ] OriresTest.OriresCanRun (5264 ms) 71: [----------] 1 test from OriresTest (5264 ms total) 71: 71: [----------] 3 tests from EwaldSurfaceTerm/EwaldSurfaceTermTest 71: [ RUN ] EwaldSurfaceTerm/EwaldSurfaceTermTest.WithinTolerances/0 71: Number of degrees of freedom in T-Coupling group rest is 10.00 71: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 71: 71: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/EwaldSurfaceTerm_EwaldSurfaceTermTest_WithinTolerances_0_input.mdp]: 71: NVE simulation with an initial temperature of zero: will use a Verlet 71: buffer of 10%. Check your energy drift! 71: 71: 71: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/EwaldSurfaceTerm_EwaldSurfaceTermTest_WithinTolerances_0_input.mdp]: 71: The optimal PME mesh load for parallel simulations is below 0.5 71: and for highly parallel simulations between 0.25 and 0.33, 71: for higher performance, increase the cut-off and the PME grid spacing. 71: 71: 71: 71: There were 2 NOTEs 71: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/EwaldSurfaceTerm_EwaldSurfaceTermTest_WithinTolerances_0.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 71: Can not increase nstlist because an NVE ensemble is used 71: Using 1 MPI thread 71: Using 2 OpenMP threads 71: 71: 71: NOTE: The number of threads is not equal to the number of (logical) cpus 71: and the -pin option is set to auto: will not pin threads to cpus. 71: This can lead to significant performance degradation. 71: Consider using -pin on (and -pinoffset in case you run multiple jobs). 71: starting mdrun 'Dipoles' 71: 20 steps, 0.1 ps. 71: Setting the LD random seed to -1681268737 71: 71: Generated 1 of the 1 non-bonded parameter combinations 71: 71: Excluding 1 bonded neighbours molecule type 'Dipole' 71: 71: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/dipoles.gro', all velocities are zero 71: 71: Searching the wall atom type(s) 71: 71: The largest distance between excluded atoms is 0.344 nm between atom 1 and 2 71: Calculating fourier grid dimensions for X Y Z 71: Using a fourier grid of 20x20x40, spacing 0.200 0.200 0.200 71: 71: Estimate for the relative computational load of the PME mesh part: 1.00 71: 71: This run will generate roughly 0 Mb of data 71: 71: Writing final coordinates. 71: 71: Core t (s) Wall t (s) (%) 71: Time: 0.255 0.128 199.5 71: (ns/day) (hour/ns) 71: Performance: 35.507 0.676 71: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/EwaldSurfaceTerm_EwaldSurfaceTermTest_WithinTolerances_0.edr as double precision energy file 71: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.010 Reading energy frame 2 time 0.020 Reading energy frame 3 time 0.030 Reading energy frame 4 time 0.040 Reading energy frame 5 time 0.050 Last energy frame read 5 time 0.050 trr version: GMX_trn_file (double precision) 71: 71: [ OK ] EwaldSurfaceTerm/EwaldSurfaceTermTest.WithinTolerances/0 (268 ms) 71: [ RUN ] EwaldSurfaceTerm/EwaldSurfaceTermTest.WithinTolerances/1 71: Test system 'epsilon-surface-constraint' cannot run with 1 ranks. 71: The supported numbers are > 1. 71: [ OK ] EwaldSurfaceTerm/EwaldSurfaceTermTest.WithinTolerances/1 (0 ms) 71: [ RUN ] EwaldSurfaceTerm/EwaldSurfaceTermTest.WithinTolerances/2 71: 71: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/EwaldSurfaceTerm_EwaldSurfaceTermTest_WithinTolerances_2_input.mdp]: 71: With epsilon_surface > 0 all molecules should be neutral. 71: 71: 71: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/EwaldSurfaceTerm_EwaldSurfaceTermTest_WithinTolerances_2_input.mdp]: 71: With epsilon_surface > 0 you can only use domain decomposition when there 71: are only small molecules with all bonds constrained (mdrun will check for 71: this). 71: 71: Number of degrees of freedom in T-Coupling group rest is 9.00 71: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 71: 71: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/EwaldSurfaceTerm_EwaldSurfaceTermTest_WithinTolerances_2_input.mdp]: 71: NVE simulation with an initial temperature of zero: will use a Verlet 71: buffer of 10%. Check your energy drift! 71: 71: 71: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/EwaldSurfaceTerm_EwaldSurfaceTermTest_WithinTolerances_2_input.mdp]: 71: The optimal PME mesh load for parallel simulations is below 0.5 71: and for highly parallel simulations between 0.25 and 0.33, 71: for higher performance, increase the cut-off and the PME grid spacing. 71: 71: 71: 71: There were 4 NOTEs 71: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/EwaldSurfaceTerm_EwaldSurfaceTermTest_WithinTolerances_2.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 71: Can not increase nstlist because an NVE ensemble is used 71: Using 1 MPI thread 71: Using 2 OpenMP threads 71: 71: 71: NOTE: The number of threads is not equal to the number of (logical) cpus 71: and the -pin option is set to auto: will not pin threads to cpus. 71: This can lead to significant performance degradation. 71: Consider using -pin on (and -pinoffset in case you run multiple jobs). 71: starting mdrun 'Dipoles' 71: 20 steps, 0.1 ps. 71: Setting the LD random seed to -422625317 71: 71: Generated 1 of the 1 non-bonded parameter combinations 71: 71: Excluding 1 bonded neighbours molecule type 'Dipole' 71: 71: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/dipoles.gro', all velocities are zero 71: 71: The largest distance between excluded atoms is 0.344 nm between atom 1 and 2 71: Calculating fourier grid dimensions for X Y Z 71: Using a fourier grid of 20x20x20, spacing 0.200 0.200 0.200 71: 71: Estimate for the relative computational load of the PME mesh part: 1.00 71: 71: This run will generate roughly 0 Mb of data 71: 71: Writing final coordinates. 71: 71: Core t (s) Wall t (s) (%) 71: Time: 0.149 0.075 199.3 71: (ns/day) (hour/ns) 71: Performance: 60.614 0.396 71: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/EwaldSurfaceTerm_EwaldSurfaceTermTest_WithinTolerances_2.edr as double precision energy file 71: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.010 Reading energy frame 2 time 0.020 Reading energy frame 3 time 0.030 Reading energy frame 4 time 0.040 Reading energy frame 5 time 0.050 Last energy frame read 5 time 0.050 71: [ OK ] EwaldSurfaceTerm/EwaldSurfaceTermTest.WithinTolerances/2 (159 ms) 71: [----------] 3 tests from EwaldSurfaceTerm/EwaldSurfaceTermTest (429 ms total) 71: 71: [----------] Global test environment tear-down 71: [==========] 5 tests from 3 test suites ran. (6340 ms total) 71: [ PASSED ] 5 tests. 71/92 Test #71: MdrunSingleRankAlgorithmsTests ............ Passed 6.42 sec test 72 Start 72: Minimize1RankTests 72: Test command: /build/reproducible-path/gromacs-2025.1/build/basic-dp/bin/minimize-test "-ntomp" "2" "-ntmpi" "1" "--gtest_output=xml:/build/reproducible-path/gromacs-2025.1/build/basic-dp/Testing/Temporary/Minimize1RankTests.xml" 72: Working Directory: /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests 72: Test timeout computed to be: 600 72: [==========] Running 12 tests from 2 test suites. 72: [----------] Global test environment set-up. 72: [----------] 6 tests from MinimizersWorkWithConstraints/EnergyMinimizationTest 72: [ RUN ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/0 72: 72: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_0_input.mdp]: 72: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 72: that with the Verlet scheme, nstlist has no effect on the accuracy of 72: your simulation. 72: 72: 72: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_0_input.mdp]: 72: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 72: setting nstcomm equal to nstcalcenergy for less overhead 72: 72: Generating 1-4 interactions: fudge = 0.5 72: Number of degrees of freedom in T-Coupling group System is 27.00 72: 72: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_0_input.mdp]: 72: You are using a plain Coulomb cut-off, which might produce artifacts. 72: You might want to consider using PME electrostatics. 72: 72: 72: 72: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_0_input.mdp]: 72: COM removal frequency is set to (4). 72: Other settings require a global communication frequency of 100. 72: Note that this will require additional global communication steps, 72: which will reduce performance when using multiple ranks. 72: Consider setting nstcomm to a multiple of 100. 72: 72: 72: There were 4 NOTEs 72: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_0.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 72: Using 1 MPI thread 72: Using 2 OpenMP threads 72: 72: 72: NOTE: The number of threads is not equal to the number of (logical) cpus 72: and the -pin option is set to auto: will not pin threads to cpus. 72: This can lead to significant performance degradation. 72: Consider using -pin on (and -pinoffset in case you run multiple jobs). 72: 72: Steepest Descents: 72: Tolerance (Fmax) = 1.00000e+01 72: Number of steps = 4 72: 72: Energy minimization reached the maximum number of steps before the forces 72: reached the requested precision Fmax < 10. 72: 72: writing lowest energy coordinates. 72: 72: Steepest Descents did not converge to Fmax < 10 in 5 steps. 72: Potential Energy = -4.79910463671072e+01 72: Maximum force = 1.86297359432219e+02 on atom 13 72: Norm of force = 8.77219865482162e+01 72: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_0_minimize.edr as double precision energy file 72: Reading energy frame 0 time 0.000 Reading energy frame 1 time 1.000 Reading energy frame 2 time 2.000 Reading energy frame 3 time 3.000 Reading energy frame 4 time 4.000 Last energy frame read 4 time 4.000 Generated 330891 of the 330891 non-bonded parameter combinations 72: 72: Generated 330891 of the 330891 1-4 parameter combinations 72: 72: Excluding 2 bonded neighbours molecule type 'SOL' 72: 72: This run will generate roughly 0 Mb of data 72: [ OK ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/0 (5855 ms) 72: [ RUN ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/1 72: 72: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_1_input.mdp]: 72: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 72: that with the Verlet scheme, nstlist has no effect on the accuracy of 72: your simulation. 72: 72: 72: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_1_input.mdp]: 72: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 72: setting nstcomm equal to nstcalcenergy for less overhead 72: 72: Generating 1-4 interactions: fudge = 0.5 72: Number of degrees of freedom in T-Coupling group System is 27.00 72: 72: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_1_input.mdp]: 72: You are using a plain Coulomb cut-off, which might produce artifacts. 72: You might want to consider using PME electrostatics. 72: 72: 72: 72: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_1_input.mdp]: 72: COM removal frequency is set to (4). 72: Other settings require a global communication frequency of 100. 72: Note that this will require additional global communication steps, 72: which will reduce performance when using multiple ranks. 72: Consider setting nstcomm to a multiple of 100. 72: 72: 72: There were 4 NOTEs 72: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_1.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 72: Using 1 MPI thread 72: Using 2 OpenMP threads 72: 72: 72: NOTE: The number of threads is not equal to the number of (logical) cpus 72: and the -pin option is set to auto: will not pin threads to cpus. 72: This can lead to significant performance degradation. 72: Consider using -pin on (and -pinoffset in case you run multiple jobs). 72: 72: Polak-Ribiere Conjugate Gradients: 72: Tolerance (Fmax) = 1.00000e+01 72: Number of steps = 4 72: F-max = 3.02331e+02 on atom 3 72: F-Norm = 1.18024e+02 72: 72: 72: Energy minimization reached the maximum number of steps before the forces 72: reached the requested precision Fmax < 10. 72: 72: writing lowest energy coordinates. 72: 72: Polak-Ribiere Conjugate Gradients did not converge to Fmax < 10 in 5 steps. 72: Potential Energy = -5.58622538633294e+01 72: Maximum force = 4.27274822366508e+02 on atom 13 72: Norm of force = 1.84530029253822e+02 72: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_1_minimize.edr as double precision energy file 72: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.000 Reading energy frame 2 time 4.000 Last energy frame read 2 time 4.000 Generated 330891 of the 330891 non-bonded parameter combinations 72: 72: Generated 330891 of the 330891 1-4 parameter combinations 72: 72: Excluding 2 bonded neighbours molecule type 'SOL' 72: 72: This run will generate roughly 0 Mb of data 72: [ OK ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/1 (5762 ms) 72: [ RUN ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/2 72: 72: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_2_input.mdp]: 72: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 72: that with the Verlet scheme, nstlist has no effect on the accuracy of 72: your simulation. 72: 72: 72: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_2_input.mdp]: 72: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 72: setting nstcomm equal to nstcalcenergy for less overhead 72: 72: Generating 1-4 interactions: fudge = 1 72: Number of degrees of freedom in T-Coupling group System is 22.00 72: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 72: 72: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_2_input.mdp]: 72: You are using a plain Coulomb cut-off, which might produce artifacts. 72: You might want to consider using PME electrostatics. 72: 72: 72: 72: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_2_input.mdp]: 72: COM removal frequency is set to (4). 72: Other settings require a global communication frequency of 100. 72: Note that this will require additional global communication steps, 72: which will reduce performance when using multiple ranks. 72: Consider setting nstcomm to a multiple of 100. 72: 72: 72: There were 4 NOTEs 72: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_2.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 72: Using 1 MPI thread 72: Using 2 OpenMP threads 72: 72: 72: NOTE: The number of threads is not equal to the number of (logical) cpus 72: and the -pin option is set to auto: will not pin threads to cpus. 72: This can lead to significant performance degradation. 72: Consider using -pin on (and -pinoffset in case you run multiple jobs). 72: 72: Steepest Descents: 72: Tolerance (Fmax) = 1.00000e+01 72: Number of steps = 4 72: 72: Energy minimization reached the maximum number of steps before the forces 72: reached the requested precision Fmax < 10. 72: 72: writing lowest energy coordinates. 72: 72: Steepest Descents did not converge to Fmax < 10 in 5 steps. 72: Potential Energy = 3.19376899751521e+02 72: Maximum force = 9.99884921009767e+03 on atom 9 72: Norm of force = 4.61669565054298e+03 72: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_2_minimize.edr as double precision energy file 72: Reading energy frame 0 time 0.000 Reading energy frame 1 time 1.000 Reading energy frame 2 time 2.000 Reading energy frame 3 time 3.000 Reading energy frame 4 time 4.000 Last energy frame read 4 time 4.000 Generated 20503 of the 20503 non-bonded parameter combinations 72: 72: Generated 17396 of the 20503 1-4 parameter combinations 72: 72: Excluding 3 bonded neighbours molecule type 'Glycine' 72: 72: turning H bonds into constraints... 72: 72: This run will generate roughly 0 Mb of data 72: [ OK ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/2 (967 ms) 72: [ RUN ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/3 72: 72: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_3_input.mdp]: 72: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 72: that with the Verlet scheme, nstlist has no effect on the accuracy of 72: your simulation. 72: 72: 72: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_3_input.mdp]: 72: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 72: setting nstcomm equal to nstcalcenergy for less overhead 72: 72: Generating 1-4 interactions: fudge = 1 72: 72: NOTE 3 [file glycine_vacuo.top, line 12]: 72: For accurate cg with LINCS constraints, lincs-order should be 8 or more. 72: 72: Number of degrees of freedom in T-Coupling group System is 22.00 72: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 72: 72: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_3_input.mdp]: 72: You are using a plain Coulomb cut-off, which might produce artifacts. 72: You might want to consider using PME electrostatics. 72: 72: 72: 72: NOTE 5 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_3_input.mdp]: 72: COM removal frequency is set to (4). 72: Other settings require a global communication frequency of 100. 72: Note that this will require additional global communication steps, 72: which will reduce performance when using multiple ranks. 72: Consider setting nstcomm to a multiple of 100. 72: 72: 72: There were 5 NOTEs 72: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_3.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 72: Using 1 MPI thread 72: Using 2 OpenMP threads 72: 72: 72: NOTE: The number of threads is not equal to the number of (logical) cpus 72: and the -pin option is set to auto: will not pin threads to cpus. 72: This can lead to significant performance degradation. 72: Consider using -pin on (and -pinoffset in case you run multiple jobs). 72: 72: Polak-Ribiere Conjugate Gradients: 72: Tolerance (Fmax) = 1.00000e+01 72: Number of steps = 4 72: F-max = 2.41575e+04 on atom 10 72: F-Norm = 1.18451e+04 72: 72: 72: Energy minimization reached the maximum number of steps before the forces 72: reached the requested precision Fmax < 10. 72: 72: writing lowest energy coordinates. 72: 72: Polak-Ribiere Conjugate Gradients did not converge to Fmax < 10 in 5 steps. 72: Potential Energy = 1.51743018140924e+02 72: Maximum force = 7.42089573409110e+03 on atom 9 72: Norm of force = 3.56929298615738e+03 72: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_3_minimize.edr as double precision energy file 72: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.000 Reading energy frame 2 time 4.000 Last energy frame read 2 time 4.000 Generated 20503 of the 20503 non-bonded parameter combinations 72: 72: Generated 17396 of the 20503 1-4 parameter combinations 72: 72: Excluding 3 bonded neighbours molecule type 'Glycine' 72: 72: turning H bonds into constraints... 72: 72: This run will generate roughly 0 Mb of data 72: [ OK ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/3 (811 ms) 72: [ RUN ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/4 72: 72: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_4_input.mdp]: 72: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 72: that with the Verlet scheme, nstlist has no effect on the accuracy of 72: your simulation. 72: 72: 72: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_4_input.mdp]: 72: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 72: setting nstcomm equal to nstcalcenergy for less overhead 72: 72: Generating 1-4 interactions: fudge = 0.5 72: 72: NOTE 3 [file unknown]: 72: You are using constraints on all bonds, whereas the forcefield has been 72: parametrized only with constraints involving hydrogen atoms. We suggest 72: using constraints = h-bonds instead, this will also improve performance. 72: 72: Number of degrees of freedom in T-Coupling group System is 23.00 72: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 72: 72: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_4_input.mdp]: 72: You are using a plain Coulomb cut-off, which might produce artifacts. 72: You might want to consider using PME electrostatics. 72: 72: 72: 72: NOTE 5 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_4_input.mdp]: 72: COM removal frequency is set to (4). 72: Other settings require a global communication frequency of 100. 72: Note that this will require additional global communication steps, 72: which will reduce performance when using multiple ranks. 72: Consider setting nstcomm to a multiple of 100. 72: 72: 72: There were 5 NOTEs 72: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_4.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 72: Update groups can not be used for this system because an incompatible virtual site type is used 72: 72: Using 1 MPI thread 72: Using 2 OpenMP threads 72: 72: 72: NOTE: The number of threads is not equal to the number of (logical) cpus 72: and the -pin option is set to auto: will not pin threads to cpus. 72: This can lead to significant performance degradation. 72: Consider using -pin on (and -pinoffset in case you run multiple jobs). 72: 72: Steepest Descents: 72: Tolerance (Fmax) = 1.00000e+01 72: Number of steps = 4 72: 72: Energy minimization reached the maximum number of steps before the forces 72: reached the requested precision Fmax < 10. 72: 72: writing lowest energy coordinates. 72: 72: Steepest Descents did not converge to Fmax < 10 in 5 steps. 72: Potential Energy = -1.56984193848276e+02 72: Maximum force = 4.56923624626405e+02 on atom 17 72: Norm of force = 1.83258377168346e+02 72: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_4_minimize.edr as double precision energy file 72: Reading energy frame 0 time 0.000 Reading energy frame 1 time 1.000 Reading energy frame 2 time 3.000 Last energy frame read 2 time 3.000 Generated 2145 of the 2145 non-bonded parameter combinations 72: 72: Generated 2145 of the 2145 1-4 parameter combinations 72: 72: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' 72: 72: turning all bonds into constraints... 72: 72: Cleaning up constraints and constant bonded interactions with virtual sites 72: 72: Removed 18 Angles with virtual sites, 21 left 72: 72: Removed 10 Proper Dih.s with virtual sites, 44 left 72: 72: Converted 15 Constraints with virtual sites to connections, 7 left 72: 72: This run will generate roughly 0 Mb of data 72: [ OK ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/4 (125 ms) 72: [ RUN ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/5 72: 72: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_5_input.mdp]: 72: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 72: that with the Verlet scheme, nstlist has no effect on the accuracy of 72: your simulation. 72: 72: 72: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_5_input.mdp]: 72: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 72: setting nstcomm equal to nstcalcenergy for less overhead 72: 72: Generating 1-4 interactions: fudge = 0.5 72: 72: NOTE 3 [file unknown]: 72: You are using constraints on all bonds, whereas the forcefield has been 72: parametrized only with constraints involving hydrogen atoms. We suggest 72: using constraints = h-bonds instead, this will also improve performance. 72: 72: 72: NOTE 4 [file unknown]: 72: For accurate cg with LINCS constraints, lincs-order should be 8 or more. 72: 72: Number of degrees of freedom in T-Coupling group System is 23.00 72: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 72: 72: NOTE 5 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_5_input.mdp]: 72: You are using a plain Coulomb cut-off, which might produce artifacts. 72: You might want to consider using PME electrostatics. 72: 72: 72: 72: NOTE 6 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_5_input.mdp]: 72: COM removal frequency is set to (4). 72: Other settings require a global communication frequency of 100. 72: Note that this will require additional global communication steps, 72: which will reduce performance when using multiple ranks. 72: Consider setting nstcomm to a multiple of 100. 72: 72: 72: There were 6 NOTEs 72: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_5.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 72: Update groups can not be used for this system because an incompatible virtual site type is used 72: 72: Using 1 MPI thread 72: Using 2 OpenMP threads 72: 72: 72: NOTE: The number of threads is not equal to the number of (logical) cpus 72: and the -pin option is set to auto: will not pin threads to cpus. 72: This can lead to significant performance degradation. 72: Consider using -pin on (and -pinoffset in case you run multiple jobs). 72: 72: Polak-Ribiere Conjugate Gradients: 72: Tolerance (Fmax) = 1.00000e+01 72: Number of steps = 4 72: F-max = 1.06800e+03 on atom 28 72: F-Norm = 4.26922e+02 72: 72: 72: Energy minimization reached the maximum number of steps before the forces 72: reached the requested precision Fmax < 10. 72: 72: writing lowest energy coordinates. 72: 72: Polak-Ribiere Conjugate Gradients did not converge to Fmax < 10 in 5 steps. 72: Potential Energy = -1.69410778678185e+02 72: Maximum force = 2.18225948474010e+02 on atom 17 72: Norm of force = 7.92068036537787e+01 72: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_5_minimize.edr as double precision energy file 72: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.000 Reading energy frame 2 time 4.000 Last energy frame read 2 time 4.000 Generated 2145 of the 2145 non-bonded parameter combinations 72: 72: Generated 2145 of the 2145 1-4 parameter combinations 72: 72: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' 72: 72: turning all bonds into constraints... 72: 72: Cleaning up constraints and constant bonded interactions with virtual sites 72: 72: Removed 18 Angles with virtual sites, 21 left 72: 72: Removed 10 Proper Dih.s with virtual sites, 44 left 72: 72: Converted 15 Constraints with virtual sites to connections, 7 left 72: 72: This run will generate roughly 0 Mb of data 72: [ OK ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/5 (135 ms) 72: [----------] 6 tests from MinimizersWorkWithConstraints/EnergyMinimizationTest (13658 ms total) 72: 72: [----------] 6 tests from MinimizersWork/EnergyMinimizationTest 72: [ RUN ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/0 72: 72: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_0_input.mdp]: 72: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 72: that with the Verlet scheme, nstlist has no effect on the accuracy of 72: your simulation. 72: 72: 72: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_0_input.mdp]: 72: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 72: setting nstcomm equal to nstcalcenergy for less overhead 72: 72: Number of degrees of freedom in T-Coupling group System is 33.00 72: 72: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_0_input.mdp]: 72: COM removal frequency is set to (4). 72: Other settings require a global communication frequency of 100. 72: Note that this will require additional global communication steps, 72: which will reduce performance when using multiple ranks. 72: Consider setting nstcomm to a multiple of 100. 72: 72: 72: There were 3 NOTEs 72: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_0.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 72: Using 1 MPI thread 72: Using 2 OpenMP threads 72: 72: 72: NOTE: The number of threads is not equal to the number of (logical) cpus 72: and the -pin option is set to auto: will not pin threads to cpus. 72: This can lead to significant performance degradation. 72: Consider using -pin on (and -pinoffset in case you run multiple jobs). 72: 72: Steepest Descents: 72: Tolerance (Fmax) = 1.00000e+01 72: Number of steps = 4 72: 72: writing lowest energy coordinates. 72: 72: Steepest Descents converged to Fmax < 10 in 1 steps 72: Potential Energy = -9.74257075835450e-01 72: Maximum force = 4.01322929015108e+00 on atom 1 72: Norm of force = 1.63839399694368e+00 72: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_0_minimize.edr as double precision energy file 72: Reading energy frame 0 time 0.000 Last energy frame read 0 time 0.000 Generated 1 of the 1 non-bonded parameter combinations 72: 72: Excluding 1 bonded neighbours molecule type 'Argon' 72: 72: This run will generate roughly 0 Mb of data 72: [ OK ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/0 (52 ms) 72: [ RUN ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/1 72: 72: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_1_input.mdp]: 72: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 72: that with the Verlet scheme, nstlist has no effect on the accuracy of 72: your simulation. 72: 72: 72: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_1_input.mdp]: 72: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 72: setting nstcomm equal to nstcalcenergy for less overhead 72: 72: Number of degrees of freedom in T-Coupling group System is 33.00 72: 72: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_1_input.mdp]: 72: COM removal frequency is set to (4). 72: Other settings require a global communication frequency of 100. 72: Note that this will require additional global communication steps, 72: which will reduce performance when using multiple ranks. 72: Consider setting nstcomm to a multiple of 100. 72: 72: 72: There were 3 NOTEs 72: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_1.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 72: Using 1 MPI thread 72: Using 2 OpenMP threads 72: 72: 72: NOTE: The number of threads is not equal to the number of (logical) cpus 72: and the -pin option is set to auto: will not pin threads to cpus. 72: This can lead to significant performance degradation. 72: Consider using -pin on (and -pinoffset in case you run multiple jobs). 72: 72: Polak-Ribiere Conjugate Gradients: 72: Tolerance (Fmax) = 1.00000e+01 72: Number of steps = 4 72: F-max = 4.01323e+00 on atom 1 72: F-Norm = 1.63839e+00 72: 72: 72: writing lowest energy coordinates. 72: 72: Polak-Ribiere Conjugate Gradients converged to Fmax < 10 in 0 steps 72: Potential Energy = -9.90642313893957e-01 72: Maximum force = 2.57812909491105e+00 on atom 1 72: Norm of force = 1.05251679559258e+00 72: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_1_minimize.edr as double precision energy file 72: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.000 Last energy frame read 1 time 0.000 Generated 1 of the 1 non-bonded parameter combinations 72: 72: Excluding 1 bonded neighbours molecule type 'Argon' 72: 72: This run will generate roughly 0 Mb of data 72: [ OK ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/1 (50 ms) 72: [ RUN ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/2 72: 72: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_2_input.mdp]: 72: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 72: that with the Verlet scheme, nstlist has no effect on the accuracy of 72: your simulation. 72: 72: 72: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_2_input.mdp]: 72: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 72: setting nstcomm equal to nstcalcenergy for less overhead 72: 72: 72: WARNING 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_2_input.mdp]: 72: For efficient BFGS minimization, use switch/shift/pme instead of cut-off. 72: 72: Number of degrees of freedom in T-Coupling group System is 33.00 72: 72: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_2_input.mdp]: 72: COM removal frequency is set to (4). 72: Other settings require a global communication frequency of 100. 72: Note that this will require additional global communication steps, 72: which will reduce performance when using multiple ranks. 72: Consider setting nstcomm to a multiple of 100. 72: 72: 72: There were 3 NOTEs 72: 72: There was 1 WARNING 72: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_2.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 72: L-BFGS minimization only supports a single rank. Choosing to use only a single thread-MPI rank. 72: 72: Using 1 MPI thread 72: Using 2 OpenMP threads 72: 72: 72: NOTE: The number of threads is not equal to the number of (logical) cpus 72: and the -pin option is set to auto: will not pin threads to cpus. 72: This can lead to significant performance degradation. 72: Consider using -pin on (and -pinoffset in case you run multiple jobs). 72: 72: Low-Memory BFGS Minimizer: 72: Tolerance (Fmax) = 1.00000e+01 72: Number of steps = 4 72: Using 10 BFGS correction steps. 72: 72: F-max = 4.01323e+00 on atom 1 72: F-Norm = 1.63839e+00 72: 72: 72: writing lowest energy coordinates. 72: 72: Low-Memory BFGS Minimizer converged to Fmax < 10 in -1 steps 72: Potential Energy = -9.90642313893957e-01 72: Maximum force = 2.57812909491105e+00 on atom 1 72: Norm of force = 1.05251679559258e+00 72: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_2_minimize.edr as double precision energy file 72: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.000 Last energy frame read 1 time 0.000 Generated 1 of the 1 non-bonded parameter combinations 72: 72: Excluding 1 bonded neighbours molecule type 'Argon' 72: 72: This run will generate roughly 0 Mb of data 72: [ OK ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/2 (45 ms) 72: [ RUN ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/3 72: 72: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_3_input.mdp]: 72: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 72: that with the Verlet scheme, nstlist has no effect on the accuracy of 72: your simulation. 72: 72: 72: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_3_input.mdp]: 72: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 72: setting nstcomm equal to nstcalcenergy for less overhead 72: 72: Generating 1-4 interactions: fudge = 1 72: Number of degrees of freedom in T-Coupling group System is 27.00 72: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 72: 72: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_3_input.mdp]: 72: You are using a plain Coulomb cut-off, which might produce artifacts. 72: You might want to consider using PME electrostatics. 72: 72: 72: 72: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_3_input.mdp]: 72: COM removal frequency is set to (4). 72: Other settings require a global communication frequency of 100. 72: Note that this will require additional global communication steps, 72: which will reduce performance when using multiple ranks. 72: Consider setting nstcomm to a multiple of 100. 72: 72: 72: There were 4 NOTEs 72: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_3.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 72: Using 1 MPI thread 72: Using 2 OpenMP threads 72: 72: 72: NOTE: The number of threads is not equal to the number of (logical) cpus 72: and the -pin option is set to auto: will not pin threads to cpus. 72: This can lead to significant performance degradation. 72: Consider using -pin on (and -pinoffset in case you run multiple jobs). 72: 72: Steepest Descents: 72: Tolerance (Fmax) = 1.00000e+01 72: Number of steps = 4 72: 72: Energy minimization reached the maximum number of steps before the forces 72: reached the requested precision Fmax < 10. 72: 72: writing lowest energy coordinates. 72: 72: Steepest Descents did not converge to Fmax < 10 in 5 steps. 72: Potential Energy = 3.19395484891518e+02 72: Maximum force = 9.97041707197911e+03 on atom 9 72: Norm of force = 4.62274878665467e+03 72: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_3_minimize.edr as double precision energy file 72: Reading energy frame 0 time 0.000 Reading energy frame 1 time 1.000 Reading energy frame 2 time 2.000 Reading energy frame 3 time 3.000 Reading energy frame 4 time 4.000 Last energy frame read 4 time 4.000 Generated 20503 of the 20503 non-bonded parameter combinations 72: 72: Generated 17396 of the 20503 1-4 parameter combinations 72: 72: Excluding 3 bonded neighbours molecule type 'Glycine' 72: 72: This run will generate roughly 0 Mb of data 72: [ OK ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/3 (812 ms) 72: [ RUN ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/4 72: 72: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_4_input.mdp]: 72: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 72: that with the Verlet scheme, nstlist has no effect on the accuracy of 72: your simulation. 72: 72: 72: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_4_input.mdp]: 72: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 72: setting nstcomm equal to nstcalcenergy for less overhead 72: 72: Generating 1-4 interactions: fudge = 1 72: Number of degrees of freedom in T-Coupling group System is 27.00 72: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 72: 72: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_4_input.mdp]: 72: You are using a plain Coulomb cut-off, which might produce artifacts. 72: You might want to consider using PME electrostatics. 72: 72: 72: 72: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_4_input.mdp]: 72: COM removal frequency is set to (4). 72: Other settings require a global communication frequency of 100. 72: Note that this will require additional global communication steps, 72: which will reduce performance when using multiple ranks. 72: Consider setting nstcomm to a multiple of 100. 72: 72: 72: There were 4 NOTEs 72: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_4.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 72: Using 1 MPI thread 72: Using 2 OpenMP threads 72: 72: 72: NOTE: The number of threads is not equal to the number of (logical) cpus 72: and the -pin option is set to auto: will not pin threads to cpus. 72: This can lead to significant performance degradation. 72: Consider using -pin on (and -pinoffset in case you run multiple jobs). 72: 72: Polak-Ribiere Conjugate Gradients: 72: Tolerance (Fmax) = 1.00000e+01 72: Number of steps = 4 72: F-max = 2.41672e+04 on atom 10 72: F-Norm = 1.19357e+04 72: 72: 72: Energy minimization reached the maximum number of steps before the forces 72: reached the requested precision Fmax < 10. 72: 72: writing lowest energy coordinates. 72: 72: Polak-Ribiere Conjugate Gradients did not converge to Fmax < 10 in 5 steps. 72: Potential Energy = 1.56258793899479e+02 72: Maximum force = 7.50181017480397e+03 on atom 9 72: Norm of force = 3.61390332564874e+03 72: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_4_minimize.edr as double precision energy file 72: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.000 Reading energy frame 2 time 4.000 Last energy frame read 2 time 4.000 Generated 20503 of the 20503 non-bonded parameter combinations 72: 72: Generated 17396 of the 20503 1-4 parameter combinations 72: 72: Excluding 3 bonded neighbours molecule type 'Glycine' 72: 72: This run will generate roughly 0 Mb of data 72: [ OK ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/4 (809 ms) 72: [ RUN ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/5 72: 72: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_5_input.mdp]: 72: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 72: that with the Verlet scheme, nstlist has no effect on the accuracy of 72: your simulation. 72: 72: 72: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_5_input.mdp]: 72: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 72: setting nstcomm equal to nstcalcenergy for less overhead 72: 72: 72: WARNING 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_5_input.mdp]: 72: For efficient BFGS minimization, use switch/shift/pme instead of cut-off. 72: 72: Generating 1-4 interactions: fudge = 1 72: Number of degrees of freedom in T-Coupling group System is 27.00 72: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 72: 72: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_5_input.mdp]: 72: You are using a plain Coulomb cut-off, which might produce artifacts. 72: You might want to consider using PME electrostatics. 72: 72: 72: 72: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_5_input.mdp]: 72: COM removal frequency is set to (4). 72: Other settings require a global communication frequency of 100. 72: Note that this will require additional global communication steps, 72: which will reduce performance when using multiple ranks. 72: Consider setting nstcomm to a multiple of 100. 72: 72: 72: There were 4 NOTEs 72: 72: There was 1 WARNING 72: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_5.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 72: L-BFGS minimization only supports a single rank. Choosing to use only a single thread-MPI rank. 72: 72: Using 1 MPI thread 72: Using 2 OpenMP threads 72: 72: 72: NOTE: The number of threads is not equal to the number of (logical) cpus 72: and the -pin option is set to auto: will not pin threads to cpus. 72: This can lead to significant performance degradation. 72: Consider using -pin on (and -pinoffset in case you run multiple jobs). 72: 72: Low-Memory BFGS Minimizer: 72: Tolerance (Fmax) = 1.00000e+01 72: Number of steps = 4 72: Using 10 BFGS correction steps. 72: 72: F-max = 2.41672e+04 on atom 10 72: F-Norm = 1.19357e+04 72: 72: 72: Energy minimization has stopped, but the forces have not converged to the 72: requested precision Fmax < 10 (which may not be possible for your system). It 72: stopped because the algorithm tried to make a new step whose size was too 72: small, or there was no change in the energy since last step. Either way, we 72: regard the minimization as converged to within the available machine 72: precision, given your starting configuration and EM parameters. 72: 72: writing lowest energy coordinates. 72: 72: Low-Memory BFGS Minimizer converged to machine precision in 0 steps, 72: but did not reach the requested Fmax < 10. 72: Potential Energy = 5.61116097794204e+02 72: Maximum force = 1.26854826291223e+04 on atom 10 72: Norm of force = 6.06436286976271e+03 72: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_5_minimize.edr as double precision energy file 72: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.000 Reading energy frame 2 time 4.000 Last energy frame read 2 time 4.000 Generated 20503 of the 20503 non-bonded parameter combinations 72: 72: Generated 17396 of the 20503 1-4 parameter combinations 72: 72: Excluding 3 bonded neighbours molecule type 'Glycine' 72: 72: This run will generate roughly 0 Mb of data 72: [ OK ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/5 (799 ms) 72: [----------] 6 tests from MinimizersWork/EnergyMinimizationTest (2571 ms total) 72: 72: [----------] Global test environment tear-down 72: [==========] 12 tests from 2 test suites ran. (16329 ms total) 72: [ PASSED ] 12 tests. 72/92 Test #72: Minimize1RankTests ........................ Passed 16.43 sec test 73 Start 73: Minimize2RankTests 73: Test command: /build/reproducible-path/gromacs-2025.1/build/basic-dp/bin/minimize-test "-ntomp" "2" "-ntmpi" "2" "--gtest_output=xml:/build/reproducible-path/gromacs-2025.1/build/basic-dp/Testing/Temporary/Minimize2RankTests.xml" 73: Working Directory: /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests 73: Test timeout computed to be: 600 73: [==========] Running 12 tests from 2 test suites. 73: [----------] Global test environment set-up. 73: [----------] 6 tests from MinimizersWorkWithConstraints/EnergyMinimizationTest 73: [ RUN ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/0 73: 73: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_0_input.mdp]: 73: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 73: that with the Verlet scheme, nstlist has no effect on the accuracy of 73: your simulation. 73: 73: 73: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_0_input.mdp]: 73: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 73: setting nstcomm equal to nstcalcenergy for less overhead 73: 73: Generating 1-4 interactions: fudge = 0.5 73: Number of degrees of freedom in T-Coupling group System is 27.00 73: 73: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_0_input.mdp]: 73: You are using a plain Coulomb cut-off, which might produce artifacts. 73: You might want to consider using PME electrostatics. 73: 73: 73: 73: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_0_input.mdp]: 73: COM removal frequency is set to (4). 73: Other settings require a global communication frequency of 100. 73: Note that this will require additional global communication steps, 73: which will reduce performance when using multiple ranks. 73: Consider setting nstcomm to a multiple of 100. 73: 73: 73: There were 4 NOTEs 73: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_0.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 73: Using 2 MPI threads 73: Using 2 OpenMP threads per tMPI thread 73: 73: 73: Steepest Descents: 73: Tolerance (Fmax) = 1.00000e+01 73: Number of steps = 4 73: 73: Energy minimization reached the maximum number of steps before the forces 73: reached the requested precision Fmax < 10. 73: 73: writing lowest energy coordinates. 73: 73: Steepest Descents did not converge to Fmax < 10 in 5 steps. 73: Potential Energy = -4.79910463671071e+01 73: Maximum force = 1.86297359432220e+02 on atom 13 73: Norm of force = 8.77219865482162e+01 73: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_0_minimize.edr as double precision energy file 73: Reading energy frame 0 time 0.000 Reading energy frame 1 time 1.000 Reading energy frame 2 time 2.000 Reading energy frame 3 time 3.000 Reading energy frame 4 time 4.000 Last energy frame read 4 time 4.000 Generated 330891 of the 330891 non-bonded parameter combinations 73: 73: Generated 330891 of the 330891 1-4 parameter combinations 73: 73: Excluding 2 bonded neighbours molecule type 'SOL' 73: 73: This run will generate roughly 0 Mb of data 73: [ OK ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/0 (5888 ms) 73: [ RUN ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/1 73: 73: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_1_input.mdp]: 73: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 73: that with the Verlet scheme, nstlist has no effect on the accuracy of 73: your simulation. 73: 73: 73: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_1_input.mdp]: 73: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 73: setting nstcomm equal to nstcalcenergy for less overhead 73: 73: Generating 1-4 interactions: fudge = 0.5 73: Number of degrees of freedom in T-Coupling group System is 27.00 73: 73: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_1_input.mdp]: 73: You are using a plain Coulomb cut-off, which might produce artifacts. 73: You might want to consider using PME electrostatics. 73: 73: 73: 73: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_1_input.mdp]: 73: COM removal frequency is set to (4). 73: Other settings require a global communication frequency of 100. 73: Note that this will require additional global communication steps, 73: which will reduce performance when using multiple ranks. 73: Consider setting nstcomm to a multiple of 100. 73: 73: 73: There were 4 NOTEs 73: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_1.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 73: Using 2 MPI threads 73: 73: Non-default thread affinity set, disabling internal thread affinity 73: 73: Using 2 OpenMP threads per tMPI thread 73: 73: 73: Polak-Ribiere Conjugate Gradients: 73: Tolerance (Fmax) = 1.00000e+01 73: Number of steps = 4 73: F-max = 3.02331e+02 on atom 3 73: F-Norm = 1.18024e+02 73: 73: 73: Energy minimization reached the maximum number of steps before the forces 73: reached the requested precision Fmax < 10. 73: 73: writing lowest energy coordinates. 73: 73: Polak-Ribiere Conjugate Gradients did not converge to Fmax < 10 in 5 steps. 73: Potential Energy = -5.58622538633295e+01 73: Maximum force = 4.27274822366505e+02 on atom 13 73: Norm of force = 1.84530029253821e+02 73: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_1_minimize.edr as double precision energy file 73: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.000 Reading energy frame 2 time 4.000 Last energy frame read 2 time 4.000 Generated 330891 of the 330891 non-bonded parameter combinations 73: 73: Generated 330891 of the 330891 1-4 parameter combinations 73: 73: Excluding 2 bonded neighbours molecule type 'SOL' 73: 73: This run will generate roughly 0 Mb of data 73: [ OK ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/1 (8041 ms) 73: [ RUN ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/2 73: 73: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_2_input.mdp]: 73: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 73: that with the Verlet scheme, nstlist has no effect on the accuracy of 73: your simulation. 73: 73: 73: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_2_input.mdp]: 73: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 73: setting nstcomm equal to nstcalcenergy for less overhead 73: 73: Generating 1-4 interactions: fudge = 1 73: Number of degrees of freedom in T-Coupling group System is 22.00 73: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 73: 73: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_2_input.mdp]: 73: You are using a plain Coulomb cut-off, which might produce artifacts. 73: You might want to consider using PME electrostatics. 73: 73: 73: 73: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_2_input.mdp]: 73: COM removal frequency is set to (4). 73: Other settings require a global communication frequency of 100. 73: Note that this will require additional global communication steps, 73: which will reduce performance when using multiple ranks. 73: Consider setting nstcomm to a multiple of 100. 73: 73: 73: There were 4 NOTEs 73: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_2.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 73: Using 2 MPI threads 73: 73: Non-default thread affinity set, disabling internal thread affinity 73: 73: Using 2 OpenMP threads per tMPI thread 73: 73: 73: Steepest Descents: 73: Tolerance (Fmax) = 1.00000e+01 73: Number of steps = 4 73: 73: Energy minimization reached the maximum number of steps before the forces 73: reached the requested precision Fmax < 10. 73: 73: writing lowest energy coordinates. 73: 73: Steepest Descents did not converge to Fmax < 10 in 5 steps. 73: Potential Energy = 3.19376899751521e+02 73: Maximum force = 9.99884921009767e+03 on atom 9 73: Norm of force = 4.61669565054298e+03 73: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_2_minimize.edr as double precision energy file 73: Reading energy frame 0 time 0.000 Reading energy frame 1 time 1.000 Reading energy frame 2 time 2.000 Reading energy frame 3 time 3.000 Reading energy frame 4 time 4.000 Last energy frame read 4 time 4.000 Generated 20503 of the 20503 non-bonded parameter combinations 73: 73: Generated 17396 of the 20503 1-4 parameter combinations 73: 73: Excluding 3 bonded neighbours molecule type 'Glycine' 73: 73: turning H bonds into constraints... 73: 73: This run will generate roughly 0 Mb of data 73: [ OK ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/2 (2344 ms) 73: [ RUN ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/3 73: 73: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_3_input.mdp]: 73: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 73: that with the Verlet scheme, nstlist has no effect on the accuracy of 73: your simulation. 73: 73: 73: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_3_input.mdp]: 73: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 73: setting nstcomm equal to nstcalcenergy for less overhead 73: 73: Generating 1-4 interactions: fudge = 1 73: 73: NOTE 3 [file glycine_vacuo.top, line 12]: 73: For accurate cg with LINCS constraints, lincs-order should be 8 or more. 73: 73: Number of degrees of freedom in T-Coupling group System is 22.00 73: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 73: 73: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_3_input.mdp]: 73: You are using a plain Coulomb cut-off, which might produce artifacts. 73: You might want to consider using PME electrostatics. 73: 73: 73: 73: NOTE 5 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_3_input.mdp]: 73: COM removal frequency is set to (4). 73: Other settings require a global communication frequency of 100. 73: Note that this will require additional global communication steps, 73: which will reduce performance when using multiple ranks. 73: Consider setting nstcomm to a multiple of 100. 73: 73: 73: There were 5 NOTEs 73: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_3.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 73: Using 2 MPI threads 73: 73: Non-default thread affinity set, disabling internal thread affinity 73: 73: Using 2 OpenMP threads per tMPI thread 73: 73: 73: Polak-Ribiere Conjugate Gradients: 73: Tolerance (Fmax) = 1.00000e+01 73: Number of steps = 4 73: F-max = 2.41575e+04 on atom 10 73: F-Norm = 1.18451e+04 73: 73: 73: Energy minimization reached the maximum number of steps before the forces 73: reached the requested precision Fmax < 10. 73: 73: writing lowest energy coordinates. 73: 73: Polak-Ribiere Conjugate Gradients did not converge to Fmax < 10 in 5 steps. 73: Potential Energy = 1.51743018140925e+02 73: Maximum force = 7.42089573409110e+03 on atom 9 73: Norm of force = 3.56929298615738e+03 73: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_3_minimize.edr as double precision energy file 73: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.000 Reading energy frame 2 time 4.000 Last energy frame read 2 time 4.000 Generated 20503 of the 20503 non-bonded parameter combinations 73: 73: Generated 17396 of the 20503 1-4 parameter combinations 73: 73: Excluding 3 bonded neighbours molecule type 'Glycine' 73: 73: turning H bonds into constraints... 73: 73: This run will generate roughly 0 Mb of data 73: [ OK ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/3 (2915 ms) 73: [ RUN ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/4 73: 73: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_4_input.mdp]: 73: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 73: that with the Verlet scheme, nstlist has no effect on the accuracy of 73: your simulation. 73: 73: 73: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_4_input.mdp]: 73: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 73: setting nstcomm equal to nstcalcenergy for less overhead 73: 73: Generating 1-4 interactions: fudge = 0.5 73: 73: NOTE 3 [file unknown]: 73: You are using constraints on all bonds, whereas the forcefield has been 73: parametrized only with constraints involving hydrogen atoms. We suggest 73: using constraints = h-bonds instead, this will also improve performance. 73: 73: Number of degrees of freedom in T-Coupling group System is 23.00 73: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 73: 73: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_4_input.mdp]: 73: You are using a plain Coulomb cut-off, which might produce artifacts. 73: You might want to consider using PME electrostatics. 73: 73: 73: 73: NOTE 5 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_4_input.mdp]: 73: COM removal frequency is set to (4). 73: Other settings require a global communication frequency of 100. 73: Note that this will require additional global communication steps, 73: which will reduce performance when using multiple ranks. 73: Consider setting nstcomm to a multiple of 100. 73: 73: 73: There were 5 NOTEs 73: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_4.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 73: Update groups can not be used for this system because an incompatible virtual site type is used 73: 73: Using 2 MPI threads 73: 73: Non-default thread affinity set, disabling internal thread affinity 73: 73: Using 2 OpenMP threads per tMPI thread 73: 73: 73: Steepest Descents: 73: Tolerance (Fmax) = 1.00000e+01 73: Number of steps = 4 73: 73: Energy minimization reached the maximum number of steps before the forces 73: reached the requested precision Fmax < 10. 73: 73: writing lowest energy coordinates. 73: 73: Steepest Descents did not converge to Fmax < 10 in 5 steps. 73: Potential Energy = -1.56984193848276e+02 73: Maximum force = 4.56923624626405e+02 on atom 17 73: Norm of force = 1.83258377168346e+02 73: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_4_minimize.edr as double precision energy file 73: Reading energy frame 0 time 0.000 Reading energy frame 1 time 1.000 Reading energy frame 2 time 3.000 Last energy frame read 2 time 3.000 Generated 2145 of the 2145 non-bonded parameter combinations 73: 73: Generated 2145 of the 2145 1-4 parameter combinations 73: 73: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' 73: 73: turning all bonds into constraints... 73: 73: Cleaning up constraints and constant bonded interactions with virtual sites 73: 73: Removed 18 Angles with virtual sites, 21 left 73: 73: Removed 10 Proper Dih.s with virtual sites, 44 left 73: 73: Converted 15 Constraints with virtual sites to connections, 7 left 73: 73: This run will generate roughly 0 Mb of data 73: [ OK ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/4 (1752 ms) 73: [ RUN ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/5 73: 73: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_5_input.mdp]: 73: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 73: that with the Verlet scheme, nstlist has no effect on the accuracy of 73: your simulation. 73: 73: 73: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_5_input.mdp]: 73: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 73: setting nstcomm equal to nstcalcenergy for less overhead 73: 73: Generating 1-4 interactions: fudge = 0.5 73: 73: NOTE 3 [file unknown]: 73: You are using constraints on all bonds, whereas the forcefield has been 73: parametrized only with constraints involving hydrogen atoms. We suggest 73: using constraints = h-bonds instead, this will also improve performance. 73: 73: 73: NOTE 4 [file unknown]: 73: For accurate cg with LINCS constraints, lincs-order should be 8 or more. 73: 73: Number of degrees of freedom in T-Coupling group System is 23.00 73: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 73: 73: NOTE 5 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_5_input.mdp]: 73: You are using a plain Coulomb cut-off, which might produce artifacts. 73: You might want to consider using PME electrostatics. 73: 73: 73: 73: NOTE 6 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_5_input.mdp]: 73: COM removal frequency is set to (4). 73: Other settings require a global communication frequency of 100. 73: Note that this will require additional global communication steps, 73: which will reduce performance when using multiple ranks. 73: Consider setting nstcomm to a multiple of 100. 73: 73: 73: There were 6 NOTEs 73: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_5.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 73: Update groups can not be used for this system because an incompatible virtual site type is used 73: 73: Using 2 MPI threads 73: 73: Non-default thread affinity set, disabling internal thread affinity 73: 73: Using 2 OpenMP threads per tMPI thread 73: 73: 73: Polak-Ribiere Conjugate Gradients: 73: Tolerance (Fmax) = 1.00000e+01 73: Number of steps = 4 73: F-max = 1.06800e+03 on atom 28 73: F-Norm = 4.26922e+02 73: 73: 73: Energy minimization reached the maximum number of steps before the forces 73: reached the requested precision Fmax < 10. 73: 73: writing lowest energy coordinates. 73: 73: Polak-Ribiere Conjugate Gradients did not converge to Fmax < 10 in 5 steps. 73: Potential Energy = -1.69410778678187e+02 73: Maximum force = 2.18225948474252e+02 on atom 17 73: Norm of force = 7.92068036538114e+01 73: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_5_minimize.edr as double precision energy file 73: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.000 Reading energy frame 2 time 4.000 Last energy frame read 2 time 4.000 Generated 2145 of the 2145 non-bonded parameter combinations 73: 73: Generated 2145 of the 2145 1-4 parameter combinations 73: 73: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' 73: 73: turning all bonds into constraints... 73: 73: Cleaning up constraints and constant bonded interactions with virtual sites 73: 73: Removed 18 Angles with virtual sites, 21 left 73: 73: Removed 10 Proper Dih.s with virtual sites, 44 left 73: 73: Converted 15 Constraints with virtual sites to connections, 7 left 73: 73: This run will generate roughly 0 Mb of data 73: [ OK ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/5 (3231 ms) 73: [----------] 6 tests from MinimizersWorkWithConstraints/EnergyMinimizationTest (24175 ms total) 73: 73: [----------] 6 tests from MinimizersWork/EnergyMinimizationTest 73: [ RUN ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/0 73: 73: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_0_input.mdp]: 73: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 73: that with the Verlet scheme, nstlist has no effect on the accuracy of 73: your simulation. 73: 73: 73: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_0_input.mdp]: 73: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 73: setting nstcomm equal to nstcalcenergy for less overhead 73: 73: Number of degrees of freedom in T-Coupling group System is 33.00 73: 73: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_0_input.mdp]: 73: COM removal frequency is set to (4). 73: Other settings require a global communication frequency of 100. 73: Note that this will require additional global communication steps, 73: which will reduce performance when using multiple ranks. 73: Consider setting nstcomm to a multiple of 100. 73: 73: 73: There were 3 NOTEs 73: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_0.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 73: Using 2 MPI threads 73: 73: Non-default thread affinity set, disabling internal thread affinity 73: 73: Using 2 OpenMP threads per tMPI thread 73: 73: 73: Steepest Descents: 73: Tolerance (Fmax) = 1.00000e+01 73: Number of steps = 4 73: 73: writing lowest energy coordinates. 73: 73: Steepest Descents converged to Fmax < 10 in 1 steps 73: Potential Energy = -9.74257075835450e-01 73: Maximum force = 4.01322929015108e+00 on atom 3 73: Norm of force = 1.63839399694368e+00 73: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_0_minimize.edr as double precision energy file 73: Reading energy frame 0 time 0.000 Last energy frame read 0 time 0.000 Generated 1 of the 1 non-bonded parameter combinations 73: 73: Excluding 1 bonded neighbours molecule type 'Argon' 73: 73: This run will generate roughly 0 Mb of data 73: [ OK ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/0 (867 ms) 73: [ RUN ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/1 73: 73: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_1_input.mdp]: 73: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 73: that with the Verlet scheme, nstlist has no effect on the accuracy of 73: your simulation. 73: 73: 73: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_1_input.mdp]: 73: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 73: setting nstcomm equal to nstcalcenergy for less overhead 73: 73: Number of degrees of freedom in T-Coupling group System is 33.00 73: 73: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_1_input.mdp]: 73: COM removal frequency is set to (4). 73: Other settings require a global communication frequency of 100. 73: Note that this will require additional global communication steps, 73: which will reduce performance when using multiple ranks. 73: Consider setting nstcomm to a multiple of 100. 73: 73: 73: There were 3 NOTEs 73: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_1.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 73: Using 2 MPI threads 73: 73: Non-default thread affinity set, disabling internal thread affinity 73: 73: Using 2 OpenMP threads per tMPI thread 73: 73: 73: Polak-Ribiere Conjugate Gradients: 73: Tolerance (Fmax) = 1.00000e+01 73: Number of steps = 4 73: F-max = 4.01323e+00 on atom 3 73: F-Norm = 1.63839e+00 73: 73: 73: writing lowest energy coordinates. 73: 73: Polak-Ribiere Conjugate Gradients converged to Fmax < 10 in 0 steps 73: Potential Energy = -9.90642313893957e-01 73: Maximum force = 2.57812909491105e+00 on atom 3 73: Norm of force = 1.05251679559258e+00 73: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_1_minimize.edr as double precision energy file 73: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.000 Last energy frame read 1 time 0.000 Generated 1 of the 1 non-bonded parameter combinations 73: 73: Excluding 1 bonded neighbours molecule type 'Argon' 73: 73: This run will generate roughly 0 Mb of data 73: [ OK ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/1 (964 ms) 73: [ RUN ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/2 73: 73: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_2_input.mdp]: 73: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 73: that with the Verlet scheme, nstlist has no effect on the accuracy of 73: your simulation. 73: 73: 73: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_2_input.mdp]: 73: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 73: setting nstcomm equal to nstcalcenergy for less overhead 73: 73: 73: WARNING 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_2_input.mdp]: 73: For efficient BFGS minimization, use switch/shift/pme instead of cut-off. 73: 73: Number of degrees of freedom in T-Coupling group System is 33.00 73: 73: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_2_input.mdp]: 73: COM removal frequency is set to (4). 73: Other settings require a global communication frequency of 100. 73: Note that this will require additional global communication steps, 73: which will reduce performance when using multiple ranks. 73: Consider setting nstcomm to a multiple of 100. 73: 73: 73: There were 3 NOTEs 73: 73: There was 1 WARNING 73: Generated 1 of the 1 non-bonded parameter combinations 73: 73: Excluding 1 bonded neighbours molecule type 'Argon' 73: 73: This run will generate roughly 0 Mb of data 73: [ OK ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/2 (26 ms) 73: [ RUN ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/3 73: 73: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_3_input.mdp]: 73: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 73: that with the Verlet scheme, nstlist has no effect on the accuracy of 73: your simulation. 73: 73: 73: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_3_input.mdp]: 73: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 73: setting nstcomm equal to nstcalcenergy for less overhead 73: 73: Generating 1-4 interactions: fudge = 1 73: Number of degrees of freedom in T-Coupling group System is 27.00 73: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 73: 73: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_3_input.mdp]: 73: You are using a plain Coulomb cut-off, which might produce artifacts. 73: You might want to consider using PME electrostatics. 73: 73: 73: 73: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_3_input.mdp]: 73: COM removal frequency is set to (4). 73: Other settings require a global communication frequency of 100. 73: Note that this will require additional global communication steps, 73: which will reduce performance when using multiple ranks. 73: Consider setting nstcomm to a multiple of 100. 73: 73: 73: There were 4 NOTEs 73: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_3.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 73: Using 2 MPI threads 73: 73: Non-default thread affinity set, disabling internal thread affinity 73: 73: Using 2 OpenMP threads per tMPI thread 73: 73: 73: Steepest Descents: 73: Tolerance (Fmax) = 1.00000e+01 73: Number of steps = 4 73: 73: Energy minimization reached the maximum number of steps before the forces 73: reached the requested precision Fmax < 10. 73: 73: writing lowest energy coordinates. 73: 73: Steepest Descents did not converge to Fmax < 10 in 5 steps. 73: Potential Energy = 3.19395484891518e+02 73: Maximum force = 9.97041707197911e+03 on atom 9 73: Norm of force = 4.62274878665467e+03 73: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_3_minimize.edr as double precision energy file 73: Reading energy frame 0 time 0.000 Reading energy frame 1 time 1.000 Reading energy frame 2 time 2.000 Reading energy frame 3 time 3.000 Reading energy frame 4 time 4.000 Last energy frame read 4 time 4.000 Generated 20503 of the 20503 non-bonded parameter combinations 73: 73: Generated 17396 of the 20503 1-4 parameter combinations 73: 73: Excluding 3 bonded neighbours molecule type 'Glycine' 73: 73: This run will generate roughly 0 Mb of data 73: [ OK ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/3 (2149 ms) 73: [ RUN ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/4 73: 73: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_4_input.mdp]: 73: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 73: that with the Verlet scheme, nstlist has no effect on the accuracy of 73: your simulation. 73: 73: 73: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_4_input.mdp]: 73: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 73: setting nstcomm equal to nstcalcenergy for less overhead 73: 73: Generating 1-4 interactions: fudge = 1 73: Number of degrees of freedom in T-Coupling group System is 27.00 73: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 73: 73: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_4_input.mdp]: 73: You are using a plain Coulomb cut-off, which might produce artifacts. 73: You might want to consider using PME electrostatics. 73: 73: 73: 73: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_4_input.mdp]: 73: COM removal frequency is set to (4). 73: Other settings require a global communication frequency of 100. 73: Note that this will require additional global communication steps, 73: which will reduce performance when using multiple ranks. 73: Consider setting nstcomm to a multiple of 100. 73: 73: 73: There were 4 NOTEs 73: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_4.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 73: Using 2 MPI threads 73: 73: Non-default thread affinity set, disabling internal thread affinity 73: 73: Using 2 OpenMP threads per tMPI thread 73: 73: 73: Polak-Ribiere Conjugate Gradients: 73: Tolerance (Fmax) = 1.00000e+01 73: Number of steps = 4 73: F-max = 2.41672e+04 on atom 10 73: F-Norm = 1.19357e+04 73: 73: 73: Energy minimization reached the maximum number of steps before the forces 73: reached the requested precision Fmax < 10. 73: 73: writing lowest energy coordinates. 73: 73: Polak-Ribiere Conjugate Gradients did not converge to Fmax < 10 in 5 steps. 73: Potential Energy = 1.56258793899479e+02 73: Maximum force = 7.50181017480397e+03 on atom 9 73: Norm of force = 3.61390332564874e+03 73: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_4_minimize.edr as double precision energy file 73: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.000 Reading energy frame 2 time 4.000 Last energy frame read 2 time 4.000 Generated 20503 of the 20503 non-bonded parameter combinations 73: 73: Generated 17396 of the 20503 1-4 parameter combinations 73: 73: Excluding 3 bonded neighbours molecule type 'Glycine' 73: 73: This run will generate roughly 0 Mb of data 73: [ OK ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/4 (2655 ms) 73: [ RUN ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/5 73: 73: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_5_input.mdp]: 73: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 73: that with the Verlet scheme, nstlist has no effect on the accuracy of 73: your simulation. 73: 73: 73: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_5_input.mdp]: 73: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 73: setting nstcomm equal to nstcalcenergy for less overhead 73: 73: 73: WARNING 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_5_input.mdp]: 73: For efficient BFGS minimization, use switch/shift/pme instead of cut-off. 73: 73: Generating 1-4 interactions: fudge = 1 73: Number of degrees of freedom in T-Coupling group System is 27.00 73: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 73: 73: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_5_input.mdp]: 73: You are using a plain Coulomb cut-off, which might produce artifacts. 73: You might want to consider using PME electrostatics. 73: 73: 73: 73: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_5_input.mdp]: 73: COM removal frequency is set to (4). 73: Other settings require a global communication frequency of 100. 73: Note that this will require additional global communication steps, 73: which will reduce performance when using multiple ranks. 73: Consider setting nstcomm to a multiple of 100. 73: 73: 73: There were 4 NOTEs 73: 73: There was 1 WARNING 73: Generated 20503 of the 20503 non-bonded parameter combinations 73: 73: Generated 17396 of the 20503 1-4 parameter combinations 73: 73: Excluding 3 bonded neighbours molecule type 'Glycine' 73: 73: This run will generate roughly 0 Mb of data 73: [ OK ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/5 (712 ms) 73: [----------] 6 tests from MinimizersWork/EnergyMinimizationTest (7376 ms total) 73: 73: [----------] Global test environment tear-down 73: [==========] 12 tests from 2 test suites ran. (31651 ms total) 73: [ PASSED ] 12 tests. 73/92 Test #73: Minimize2RankTests ........................ Passed 31.74 sec test 74 Start 74: MdrunNonIntegratorTests 74: Test command: /build/reproducible-path/gromacs-2025.1/build/basic-dp/bin/mdrun-non-integrator-test "-ntomp" "2" "--gtest_output=xml:/build/reproducible-path/gromacs-2025.1/build/basic-dp/Testing/Temporary/MdrunNonIntegratorTests.xml" 74: Working Directory: /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests 74: Test timeout computed to be: 600 74: [==========] Running 53 tests from 5 test suites. 74: [----------] Global test environment set-up. 74: [----------] 1 test from NonbondedBenchTest 74: [ RUN ] NonbondedBenchTest.BasicEndToEndTest 74: System size: 3000 atoms 74: Cut-off radius: 1 nm 74: Number of threads: 1 74: Number of iterations: 1 74: Compute energies: no 74: Ewald excl. corr.: analytical 74: 74: Coulomb LJ comb. SIMD Mcycles Mcycles/it. pairs/cycle 74: total useful 74: Ewald all geom. no 0.280 0.2798 4.2540 2.2505 74: [ OK ] NonbondedBenchTest.BasicEndToEndTest (610 ms) 74: [----------] 1 test from NonbondedBenchTest (610 ms total) 74: 74: [----------] 5 tests from NormalModesWorks/NormalModesTest 74: [ RUN ] NormalModesWorks/NormalModesTest.WithinTolerances/0 74: 74: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalModesWorks_NormalModesTest_WithinTolerances_0_input.mdp]: 74: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 74: that with the Verlet scheme, nstlist has no effect on the accuracy of 74: your simulation. 74: 74: 74: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalModesWorks_NormalModesTest_WithinTolerances_0_input.mdp]: 74: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 74: setting nstcomm equal to nstcalcenergy for less overhead 74: 74: Generating 1-4 interactions: fudge = 0.5 74: Number of degrees of freedom in T-Coupling group System is 15.00 74: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 74: 74: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalModesWorks_NormalModesTest_WithinTolerances_0_input.mdp]: 74: You are using a plain Coulomb cut-off, which might produce artifacts. 74: You might want to consider using PME electrostatics. 74: 74: 74: 74: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalModesWorks_NormalModesTest_WithinTolerances_0_input.mdp]: 74: COM removal frequency is set to (4). 74: Other settings require a global communication frequency of 100. 74: Note that this will require additional global communication steps, 74: which will reduce performance when using multiple ranks. 74: Consider setting nstcomm to a multiple of 100. 74: 74: 74: There were 4 NOTEs 74: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalModesWorks_NormalModesTest_WithinTolerances_0.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 74: Using 1 MPI thread 74: Using 2 OpenMP threads 74: 74: 74: NOTE: The number of threads is not equal to the number of (logical) cpus 74: and the -pin option is set to auto: will not pin threads to cpus. 74: This can lead to significant performance degradation. 74: Consider using -pin on (and -pinoffset in case you run multiple jobs). 74: 74: Small system size (N=6), using full Hessian format. 74: Allocating Hessian memory... 74: 74: starting normal mode calculation '2 scaled waters' 74: 12 steps. 74: 74: Maximum force: 9.96989e-06 74: 74: 74: Writing Hessian... 74: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalModesWorks_NormalModesTest_WithinTolerances_0.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 74: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalModesWorks_NormalModesTest_WithinTolerances_0.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 74: Reading double precision matrix generated by GROMACS 2025.1-Debian_2025.1_1 74: 74: Diagonalizing to find vectors 7 through 18... 74: Writing eigenvalues... 74: 74: Writing average structure & eigenvectors 7--18 to eigenvec.trr 74: Generated 3 of the 3 non-bonded parameter combinations 74: 74: Generated 3 of the 3 1-4 parameter combinations 74: 74: Excluding 2 bonded neighbours molecule type 'SOL' 74: 74: This run will generate roughly 0 Mb of data 74: There are: 6 Atoms 74: Using begin = 7 and end = 18 74: Full matrix storage format, nrow=18, ncols=18 74: Writing eigenfrequencies - negative eigenvalues will be set to zero. 74: Cannot compute entropy when -first = 7 74: [ OK ] NormalModesWorks/NormalModesTest.WithinTolerances/0 (65 ms) 74: [ RUN ] NormalModesWorks/NormalModesTest.WithinTolerances/1 74: 74: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalModesWorks_NormalModesTest_WithinTolerances_1_input.mdp]: 74: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 74: that with the Verlet scheme, nstlist has no effect on the accuracy of 74: your simulation. 74: 74: 74: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalModesWorks_NormalModesTest_WithinTolerances_1_input.mdp]: 74: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 74: setting nstcomm equal to nstcalcenergy for less overhead 74: 74: Generating 1-4 interactions: fudge = 1 74: 74: NOTE 3 [file villin.top, line 2452]: 74: System has non-zero total charge: -2.000000 74: Total charge should normally be an integer. See 74: https://manual.gromacs.org/current/user-guide/floating-point.html 74: for discussion on how close it should be to an integer. 74: 74: 74: 74: Number of degrees of freedom in T-Coupling group System is 765.00 74: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 74: 74: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalModesWorks_NormalModesTest_WithinTolerances_1_input.mdp]: 74: You are using a plain Coulomb cut-off, which might produce artifacts. 74: You might want to consider using PME electrostatics. 74: 74: 74: 74: NOTE 5 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalModesWorks_NormalModesTest_WithinTolerances_1_input.mdp]: 74: COM removal frequency is set to (4). 74: Other settings require a global communication frequency of 100. 74: Note that this will require additional global communication steps, 74: which will reduce performance when using multiple ranks. 74: Consider setting nstcomm to a multiple of 100. 74: 74: 74: There were 5 NOTEs 74: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalModesWorks_NormalModesTest_WithinTolerances_1.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 74: Using 1 MPI thread 74: Using 2 OpenMP threads 74: 74: 74: NOTE: The number of threads is not equal to the number of (logical) cpus 74: and the -pin option is set to auto: will not pin threads to cpus. 74: This can lead to significant performance degradation. 74: Consider using -pin on (and -pinoffset in case you run multiple jobs). 74: 74: Small system size (N=256), using full Hessian format. 74: Allocating Hessian memory... 74: 74: starting normal mode calculation 'AMYLOID BETA A4 PROTEIN' 74: 512 steps. 74: 74: Maximum force: 6.97568e-04 74: 74: 74: Writing Hessian... 74: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalModesWorks_NormalModesTest_WithinTolerances_1.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 74: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalModesWorks_NormalModesTest_WithinTolerances_1.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 74: Reading double precision matrix generated by GROMACS 2025.1-Debian_2025.1_1 74: 74: Diagonalizing to find vectors 7 through 50... 74: Writing eigenvalues... 74: 74: Writing average structure & eigenvectors 7--50 to eigenvec.trr 74: Generated 20503 of the 20503 non-bonded parameter combinations 74: 74: Generated 17396 of the 20503 1-4 parameter combinations 74: 74: Excluding 3 bonded neighbours molecule type 'Protein_chain_A' 74: 74: This run will generate roughly 0 Mb of data 74: There are: 256 Atoms 74: Using begin = 7 and end = 50 74: Full matrix storage format, nrow=768, ncols=768 74: Writing eigenfrequencies - negative eigenvalues will be set to zero. 74: Cannot compute entropy when -first = 7 74: [ OK ] NormalModesWorks/NormalModesTest.WithinTolerances/1 (19157 ms) 74: [ RUN ] NormalModesWorks/NormalModesTest.WithinTolerances/2 74: 74: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalModesWorks_NormalModesTest_WithinTolerances_2_input.mdp]: 74: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 74: that with the Verlet scheme, nstlist has no effect on the accuracy of 74: your simulation. 74: 74: 74: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalModesWorks_NormalModesTest_WithinTolerances_2_input.mdp]: 74: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 74: setting nstcomm equal to nstcalcenergy for less overhead 74: 74: Generating 1-4 interactions: fudge = 0.5 74: Number of degrees of freedom in T-Coupling group System is 15.00 74: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 74: 74: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalModesWorks_NormalModesTest_WithinTolerances_2_input.mdp]: 74: You are using a plain Coulomb cut-off, which might produce artifacts. 74: You might want to consider using PME electrostatics. 74: 74: 74: 74: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalModesWorks_NormalModesTest_WithinTolerances_2_input.mdp]: 74: COM removal frequency is set to (4). 74: Other settings require a global communication frequency of 100. 74: Note that this will require additional global communication steps, 74: which will reduce performance when using multiple ranks. 74: Consider setting nstcomm to a multiple of 100. 74: 74: 74: There were 4 NOTEs 74: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalModesWorks_NormalModesTest_WithinTolerances_2.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 74: Using 1 MPI thread 74: Using 2 OpenMP threads 74: 74: 74: NOTE: The number of threads is not equal to the number of (logical) cpus 74: and the -pin option is set to auto: will not pin threads to cpus. 74: This can lead to significant performance degradation. 74: Consider using -pin on (and -pinoffset in case you run multiple jobs). 74: 74: Small system size (N=6), using full Hessian format. 74: Allocating Hessian memory... 74: 74: starting normal mode calculation 'flex spc dimer' 74: 12 steps. 74: 74: Maximum force: 3.36401e-04 74: 74: 74: Writing Hessian... 74: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalModesWorks_NormalModesTest_WithinTolerances_2.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 74: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalModesWorks_NormalModesTest_WithinTolerances_2.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 74: Reading double precision matrix generated by GROMACS 2025.1-Debian_2025.1_1 74: 74: Diagonalizing to find vectors 7 through 18... 74: Writing eigenvalues... 74: 74: Writing average structure & eigenvectors 7--18 to eigenvec.trr 74: Generated 330891 of the 330891 non-bonded parameter combinations 74: 74: Generated 330891 of the 330891 1-4 parameter combinations 74: 74: Excluding 2 bonded neighbours molecule type 'SOL' 74: 74: This run will generate roughly 0 Mb of data 74: There are: 6 Atoms 74: Using begin = 7 and end = 18 74: Full matrix storage format, nrow=18, ncols=18 74: Writing eigenfrequencies - negative eigenvalues will be set to zero. 74: Cannot compute entropy when -first = 7 74: [ OK ] NormalModesWorks/NormalModesTest.WithinTolerances/2 (5869 ms) 74: [ RUN ] NormalModesWorks/NormalModesTest.WithinTolerances/3 74: 74: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalModesWorks_NormalModesTest_WithinTolerances_3_input.mdp]: 74: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 74: that with the Verlet scheme, nstlist has no effect on the accuracy of 74: your simulation. 74: 74: 74: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalModesWorks_NormalModesTest_WithinTolerances_3_input.mdp]: 74: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 74: setting nstcomm equal to nstcalcenergy for less overhead 74: 74: Generating 1-4 interactions: fudge = 0.5 74: Number of degrees of freedom in T-Coupling group System is 6.00 74: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 74: 74: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalModesWorks_NormalModesTest_WithinTolerances_3_input.mdp]: 74: You are using a plain Coulomb cut-off, which might produce artifacts. 74: You might want to consider using PME electrostatics. 74: 74: 74: 74: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalModesWorks_NormalModesTest_WithinTolerances_3_input.mdp]: 74: COM removal frequency is set to (4). 74: Other settings require a global communication frequency of 100. 74: Note that this will require additional global communication steps, 74: which will reduce performance when using multiple ranks. 74: Consider setting nstcomm to a multiple of 100. 74: 74: 74: There were 4 NOTEs 74: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalModesWorks_NormalModesTest_WithinTolerances_3.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 74: Update groups can not be used for this system because an incompatible virtual site type is used 74: 74: Using 1 MPI thread 74: Using 2 OpenMP threads 74: 74: 74: NOTE: The number of threads is not equal to the number of (logical) cpus 74: and the -pin option is set to auto: will not pin threads to cpus. 74: This can lead to significant performance degradation. 74: Consider using -pin on (and -pinoffset in case you run multiple jobs). 74: 74: Small system size (N=3), using full Hessian format. 74: Allocating Hessian memory... 74: 74: starting normal mode calculation '1 TIP5P' 74: 6 steps. 74: 74: Maximum force: 2.42882e-04 74: 74: 74: Writing Hessian... 74: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalModesWorks_NormalModesTest_WithinTolerances_3.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 74: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalModesWorks_NormalModesTest_WithinTolerances_3.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 74: Reading double precision matrix generated by GROMACS 2025.1-Debian_2025.1_1 74: 74: Diagonalizing to find vectors 7 through 9... 74: Writing eigenvalues... 74: 74: Writing average structure & eigenvectors 7--9 to eigenvec.trr 74: Generated 330891 of the 330891 non-bonded parameter combinations 74: 74: Generated 330891 of the 330891 1-4 parameter combinations 74: 74: Excluding 2 bonded neighbours molecule type 'SOL' 74: 74: Cleaning up constraints and constant bonded interactions with virtual sites 74: 74: This run will generate roughly 0 Mb of data 74: There are: 3 Atoms 74: There are: 2 VSites 74: Using begin = 7 and end = 9 74: Full matrix storage format, nrow=9, ncols=9 74: Writing eigenfrequencies - negative eigenvalues will be set to zero. 74: Cannot compute entropy when -first = 7 74: [ OK ] NormalModesWorks/NormalModesTest.WithinTolerances/3 (5865 ms) 74: [ RUN ] NormalModesWorks/NormalModesTest.WithinTolerances/4 74: 74: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalModesWorks_NormalModesTest_WithinTolerances_4_input.mdp]: 74: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 74: that with the Verlet scheme, nstlist has no effect on the accuracy of 74: your simulation. 74: 74: Number of degrees of freedom in T-Coupling group System is 15.00 74: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 74: 74: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalModesWorks_NormalModesTest_WithinTolerances_4_input.mdp]: 74: You are using a plain Coulomb cut-off, which might produce artifacts. 74: You might want to consider using PME electrostatics. 74: 74: 74: 74: There were 2 NOTEs 74: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalModesWorks_NormalModesTest_WithinTolerances_4.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 74: Update groups can not be used for this system because the construction atoms of a virtual site are only partly with a group of constrained atoms 74: 74: Using 1 MPI thread 74: Using 2 OpenMP threads 74: 74: 74: NOTE: The number of threads is not equal to the number of (logical) cpus 74: and the -pin option is set to auto: will not pin threads to cpus. 74: This can lead to significant performance degradation. 74: Consider using -pin on (and -pinoffset in case you run multiple jobs). 74: 74: Small system size (N=6), using full Hessian format. 74: Allocating Hessian memory... 74: 74: starting normal mode calculation 'sw dimer' 74: 12 steps. 74: 74: Maximum force: 1.07599e-03 74: The force is probably not small enough to ensure that you are at a minimum. 74: Be aware that negative eigenvalues may occur 74: when the resulting matrix is diagonalized. 74: 74: 74: Writing Hessian... 74: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalModesWorks_NormalModesTest_WithinTolerances_4.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 74: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalModesWorks_NormalModesTest_WithinTolerances_4.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 74: Reading double precision matrix generated by GROMACS 2025.1-Debian_2025.1_1 74: 74: Diagonalizing to find vectors 7 through 18... 74: Writing eigenvalues... 74: 74: Writing average structure & eigenvectors 7--18 to eigenvec.trr 74: Generated 6 of the 10 non-bonded parameter combinations 74: 74: Excluding 2 bonded neighbours molecule type 'SW' 74: 74: Cleaning up constraints and constant bonded interactions with virtual sites 74: 74: This run will generate roughly 0 Mb of data 74: There are: 6 Atoms 74: There are: 2 Shells 74: There are: 2 VSites 74: 74: NOTE: in the current version shell prediction during the crun is disabled 74: 74: Using begin = 7 and end = 18 74: Full matrix storage format, nrow=18, ncols=18 74: Writing eigenfrequencies - negative eigenvalues will be set to zero. 74: Cannot compute entropy when -first = 7 74: [ OK ] NormalModesWorks/NormalModesTest.WithinTolerances/4 (61 ms) 74: [----------] 5 tests from NormalModesWorks/NormalModesTest (31022 ms total) 74: 74: [----------] 12 tests from NormalMdrunIsReproduced/MdrunRerunTest 74: [ RUN ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/0 74: 74: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_0_input.mdp]: 74: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 74: that with the Verlet scheme, nstlist has no effect on the accuracy of 74: your simulation. 74: 74: 74: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_0_input.mdp]: 74: Setting nstcalcenergy (100) equal to nstenergy (4) 74: 74: Number of degrees of freedom in T-Coupling group System is 33.00 74: 74: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_0_input.mdp]: 74: NVE simulation: will use the initial temperature of 68.810 K for 74: determining the Verlet buffer size 74: 74: 74: There were 3 NOTEs 74: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_0_sim.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 74: Can not increase nstlist because an NVE ensemble is used 74: Using 1 MPI thread 74: Using 2 OpenMP threads 74: 74: 74: NOTE: The number of threads is not equal to the number of (logical) cpus 74: and the -pin option is set to auto: will not pin threads to cpus. 74: This can lead to significant performance degradation. 74: Consider using -pin on (and -pinoffset in case you run multiple jobs). 74: starting mdrun 'Argon' 74: 16 steps, 0.0 ps. 74: Generated 1 of the 1 non-bonded parameter combinations 74: 74: Excluding 1 bonded neighbours molecule type 'Argon' 74: 74: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 74: 74: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 74: 74: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 74: 74: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 74: 74: Note that mdrun will redetermine rlist based on the actual pair-list setup 74: 74: This run will generate roughly 0 Mb of data 74: 74: Writing final coordinates. 74: 74: Core t (s) Wall t (s) (%) 74: Time: 0.039 0.020 197.1 74: (ns/day) (hour/ns) 74: Performance: 74.136 0.324 74: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_0_sim.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 74: Can not increase nstlist because an NVE ensemble is used 74: Using 1 MPI thread 74: Using 2 OpenMP threads 74: 74: 74: NOTE: The number of threads is not equal to the number of (logical) cpus 74: and the -pin option is set to auto: will not pin threads to cpus. 74: This can lead to significant performance degradation. 74: Consider using -pin on (and -pinoffset in case you run multiple jobs). 74: starting md rerun 'Argon', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_0_sim1.trr' 74: 74: trr version: GMX_trn_file (double precision) 74: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 74: 74: NOTE: 14 % of the run time was spent in pair search, 74: you might want to increase nstlist (this has no effect on accuracy) 74: 74: Core t (s) Wall t (s) (%) 74: Time: 0.006 0.003 192.7 74: (ns/day) (hour/ns) 74: Performance: 465.266 0.052 74: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_0_sim1.edr as double precision energy file 74: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_0_sim2.edr as double precision energy file 74: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 74: 74: [ OK ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/0 (84 ms) 74: [ RUN ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/1 74: 74: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_1_input.mdp]: 74: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 74: that with the Verlet scheme, nstlist has no effect on the accuracy of 74: your simulation. 74: 74: 74: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_1_input.mdp]: 74: Setting nstcalcenergy (100) equal to nstenergy (4) 74: 74: Number of degrees of freedom in T-Coupling group System is 33.00 74: 74: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_1_input.mdp]: 74: NVE simulation: will use the initial temperature of 68.810 K for 74: determining the Verlet buffer size 74: 74: 74: There were 3 NOTEs 74: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_1_sim.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 74: Can not increase nstlist because an NVE ensemble is used 74: Using 1 MPI thread 74: Using 2 OpenMP threads 74: 74: 74: NOTE: The number of threads is not equal to the number of (logical) cpus 74: and the -pin option is set to auto: will not pin threads to cpus. 74: This can lead to significant performance degradation. 74: Consider using -pin on (and -pinoffset in case you run multiple jobs). 74: starting mdrun 'Argon' 74: 16 steps, 0.0 ps. 74: Generated 1 of the 1 non-bonded parameter combinations 74: 74: Excluding 1 bonded neighbours molecule type 'Argon' 74: 74: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 74: 74: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 74: 74: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 74: 74: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 74: 74: Note that mdrun will redetermine rlist based on the actual pair-list setup 74: 74: This run will generate roughly 0 Mb of data 74: 74: Writing final coordinates. 74: 74: Core t (s) Wall t (s) (%) 74: Time: 0.072 0.036 199.1 74: (ns/day) (hour/ns) 74: Performance: 40.738 0.589 74: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_1_sim.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 74: Can not increase nstlist because an NVE ensemble is used 74: Using 1 MPI thread 74: Using 2 OpenMP threads 74: 74: 74: NOTE: The number of threads is not equal to the number of (logical) cpus 74: and the -pin option is set to auto: will not pin threads to cpus. 74: This can lead to significant performance degradation. 74: Consider using -pin on (and -pinoffset in case you run multiple jobs). 74: starting md rerun 'Argon', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_1_sim1.trr' 74: 74: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 74: 74: NOTE: 14 % of the run time was spent in pair search, 74: you might want to increase nstlist (this has no effect on accuracy) 74: 74: Core t (s) Wall t (s) (%) 74: Time: 0.006 0.003 192.7 74: (ns/day) (hour/ns) 74: Performance: 448.076 0.054 74: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_1_sim1.edr as double precision energy file 74: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_1_sim2.edr as double precision energy file 74: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 74: 74: [ OK ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/1 (104 ms) 74: [ RUN ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/2 74: 74: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_2_input.mdp]: 74: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 74: that with the Verlet scheme, nstlist has no effect on the accuracy of 74: your simulation. 74: 74: 74: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_2_input.mdp]: 74: Setting nstcalcenergy (100) equal to nstenergy (4) 74: 74: Number of degrees of freedom in T-Coupling group System is 33.00 74: 74: There were 2 NOTEs 74: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_2_sim.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 74: Changing nstlist from 8 to 100, rlist from 0.712 to 0.744 74: 74: Using 1 MPI thread 74: Using 2 OpenMP threads 74: 74: 74: NOTE: The number of threads is not equal to the number of (logical) cpus 74: and the -pin option is set to auto: will not pin threads to cpus. 74: This can lead to significant performance degradation. 74: Consider using -pin on (and -pinoffset in case you run multiple jobs). 74: starting mdrun 'Argon' 74: 16 steps, 0.0 ps. 74: Generated 1 of the 1 non-bonded parameter combinations 74: 74: Excluding 1 bonded neighbours molecule type 'Argon' 74: 74: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 74: 74: Calculated rlist for 1x1 atom pair-list as 0.713 nm, buffer size 0.013 nm 74: 74: Set rlist, assuming 4x4 atom pair-list, to 0.712 nm, buffer size 0.012 nm 74: 74: Note that mdrun will redetermine rlist based on the actual pair-list setup 74: 74: This run will generate roughly 0 Mb of data 74: 74: Writing final coordinates. 74: 74: Core t (s) Wall t (s) (%) 74: Time: 0.048 0.024 197.5 74: (ns/day) (hour/ns) 74: Performance: 60.338 0.398 74: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_2_sim.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 74: Changing nstlist from 8 to 100, rlist from 0.712 to 0.744 74: 74: Using 1 MPI thread 74: Using 2 OpenMP threads 74: 74: 74: NOTE: The number of threads is not equal to the number of (logical) cpus 74: and the -pin option is set to auto: will not pin threads to cpus. 74: This can lead to significant performance degradation. 74: Consider using -pin on (and -pinoffset in case you run multiple jobs). 74: starting md rerun 'Argon', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_2_sim1.trr' 74: 74: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 74: 74: NOTE: 13 % of the run time was spent in pair search, 74: you might want to increase nstlist (this has no effect on accuracy) 74: 74: Core t (s) Wall t (s) (%) 74: Time: 0.006 0.003 192.6 74: (ns/day) (hour/ns) 74: Performance: 463.656 0.052 74: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_2_sim1.edr as double precision energy file 74: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_2_sim2.edr as double precision energy file 74: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 74: 74: [ OK ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/2 (108 ms) 74: [ RUN ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/3 74: 74: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_3_input.mdp]: 74: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 74: that with the Verlet scheme, nstlist has no effect on the accuracy of 74: your simulation. 74: 74: 74: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_3_input.mdp]: 74: Setting nstcalcenergy (100) equal to nstenergy (4) 74: 74: Number of degrees of freedom in T-Coupling group System is 33.00 74: 74: There were 2 NOTEs 74: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_3_sim.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 74: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 74: 74: Using 1 MPI thread 74: Using 2 OpenMP threads 74: 74: 74: NOTE: The number of threads is not equal to the number of (logical) cpus 74: and the -pin option is set to auto: will not pin threads to cpus. 74: This can lead to significant performance degradation. 74: Consider using -pin on (and -pinoffset in case you run multiple jobs). 74: starting mdrun 'Argon' 74: 16 steps, 0.0 ps. 74: Generated 1 of the 1 non-bonded parameter combinations 74: 74: Excluding 1 bonded neighbours molecule type 'Argon' 74: 74: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 74: 74: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 74: 74: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 74: 74: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 74: 74: Note that mdrun will redetermine rlist based on the actual pair-list setup 74: 74: This run will generate roughly 0 Mb of data 74: 74: Writing final coordinates. 74: 74: Core t (s) Wall t (s) (%) 74: Time: 0.054 0.027 198.3 74: (ns/day) (hour/ns) 74: Performance: 54.275 0.442 74: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_3_sim.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 74: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 74: 74: Using 1 MPI thread 74: Using 2 OpenMP threads 74: 74: 74: NOTE: The number of threads is not equal to the number of (logical) cpus 74: and the -pin option is set to auto: will not pin threads to cpus. 74: This can lead to significant performance degradation. 74: Consider using -pin on (and -pinoffset in case you run multiple jobs). 74: starting md rerun 'Argon', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_3_sim1.trr' 74: 74: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 74: 74: Core t (s) Wall t (s) (%) 74: Time: 0.010 0.005 194.4 74: (ns/day) (hour/ns) 74: Performance: 281.049 0.085 74: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_3_sim1.edr as double precision energy file 74: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_3_sim2.edr as double precision energy file 74: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 74: 74: [ OK ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/3 (101 ms) 74: [ RUN ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/4 74: 74: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_4_input.mdp]: 74: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 74: that with the Verlet scheme, nstlist has no effect on the accuracy of 74: your simulation. 74: 74: 74: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_4_input.mdp]: 74: Setting nstcalcenergy (100) equal to nstenergy (4) 74: 74: Generating 1-4 interactions: fudge = 0.5 74: Number of degrees of freedom in T-Coupling group System is 27.00 74: 74: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_4_input.mdp]: 74: NVE simulation: will use the initial temperature of 398.997 K for 74: determining the Verlet buffer size 74: 74: 74: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_4_input.mdp]: 74: You are using a plain Coulomb cut-off, which might produce artifacts. 74: You might want to consider using PME electrostatics. 74: 74: 74: 74: There were 4 NOTEs 74: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_4_sim.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 74: Can not increase nstlist because an NVE ensemble is used 74: Using 1 MPI thread 74: Using 2 OpenMP threads 74: 74: 74: NOTE: The number of threads is not equal to the number of (logical) cpus 74: and the -pin option is set to auto: will not pin threads to cpus. 74: This can lead to significant performance degradation. 74: Consider using -pin on (and -pinoffset in case you run multiple jobs). 74: starting mdrun 'spc2' 74: 16 steps, 0.0 ps. 74: Generated 330891 of the 330891 non-bonded parameter combinations 74: 74: Generated 330891 of the 330891 1-4 parameter combinations 74: 74: Excluding 2 bonded neighbours molecule type 'SOL' 74: 74: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/tip3p5.gro' 74: 74: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 74: 74: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 74: 74: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 74: 74: Note that mdrun will redetermine rlist based on the actual pair-list setup 74: 74: This run will generate roughly 0 Mb of data 74: 74: Writing final coordinates. 74: 74: Core t (s) Wall t (s) (%) 74: Time: 0.069 0.035 197.9 74: (ns/day) (hour/ns) 74: Performance: 42.323 0.567 74: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_4_sim.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 74: Can not increase nstlist because an NVE ensemble is used 74: Using 1 MPI thread 74: Using 2 OpenMP threads 74: 74: 74: NOTE: The number of threads is not equal to the number of (logical) cpus 74: and the -pin option is set to auto: will not pin threads to cpus. 74: This can lead to significant performance degradation. 74: Consider using -pin on (and -pinoffset in case you run multiple jobs). 74: starting md rerun 'spc2', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_4_sim1.trr' 74: 74: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 74: 74: NOTE: 38 % of the run time was spent in pair search, 74: you might want to increase nstlist (this has no effect on accuracy) 74: 74: Core t (s) Wall t (s) (%) 74: Time: 0.027 0.013 197.9 74: (ns/day) (hour/ns) 74: Performance: 109.035 0.220 74: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_4_sim1.edr as double precision energy file 74: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_4_sim2.edr as double precision energy file 74: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 74: 74: [ OK ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/4 (5869 ms) 74: [ RUN ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/5 74: 74: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_5_input.mdp]: 74: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 74: that with the Verlet scheme, nstlist has no effect on the accuracy of 74: your simulation. 74: 74: 74: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_5_input.mdp]: 74: Setting nstcalcenergy (100) equal to nstenergy (4) 74: 74: Generating 1-4 interactions: fudge = 0.5 74: Number of degrees of freedom in T-Coupling group System is 27.00 74: 74: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_5_input.mdp]: 74: NVE simulation: will use the initial temperature of 398.997 K for 74: determining the Verlet buffer size 74: 74: 74: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_5_input.mdp]: 74: You are using a plain Coulomb cut-off, which might produce artifacts. 74: You might want to consider using PME electrostatics. 74: 74: 74: 74: There were 4 NOTEs 74: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_5_sim.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 74: Can not increase nstlist because an NVE ensemble is used 74: Using 1 MPI thread 74: Using 2 OpenMP threads 74: 74: 74: NOTE: The number of threads is not equal to the number of (logical) cpus 74: and the -pin option is set to auto: will not pin threads to cpus. 74: This can lead to significant performance degradation. 74: Consider using -pin on (and -pinoffset in case you run multiple jobs). 74: starting mdrun 'spc2' 74: 16 steps, 0.0 ps. 74: Generated 330891 of the 330891 non-bonded parameter combinations 74: 74: Generated 330891 of the 330891 1-4 parameter combinations 74: 74: Excluding 2 bonded neighbours molecule type 'SOL' 74: 74: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/tip3p5.gro' 74: 74: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 74: 74: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 74: 74: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 74: 74: Note that mdrun will redetermine rlist based on the actual pair-list setup 74: 74: This run will generate roughly 0 Mb of data 74: 74: Writing final coordinates. 74: 74: Core t (s) Wall t (s) (%) 74: Time: 0.120 0.060 199.4 74: (ns/day) (hour/ns) 74: Performance: 24.358 0.985 74: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_5_sim.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 74: Can not increase nstlist because an NVE ensemble is used 74: Using 1 MPI thread 74: Using 2 OpenMP threads 74: 74: 74: NOTE: The number of threads is not equal to the number of (logical) cpus 74: and the -pin option is set to auto: will not pin threads to cpus. 74: This can lead to significant performance degradation. 74: Consider using -pin on (and -pinoffset in case you run multiple jobs). 74: starting md rerun 'spc2', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_5_sim1.trr' 74: 74: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 74: 74: Core t (s) Wall t (s) (%) 74: Time: 0.020 0.010 197.1 74: (ns/day) (hour/ns) 74: Performance: 147.471 0.163 74: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_5_sim1.edr as double precision energy file 74: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_5_sim2.edr as double precision energy file 74: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 74: 74: [ OK ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/5 (5920 ms) 74: [ RUN ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/6 74: 74: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_6_input.mdp]: 74: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 74: that with the Verlet scheme, nstlist has no effect on the accuracy of 74: your simulation. 74: 74: 74: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_6_input.mdp]: 74: Setting nstcalcenergy (100) equal to nstenergy (4) 74: 74: Generating 1-4 interactions: fudge = 0.5 74: Number of degrees of freedom in T-Coupling group System is 27.00 74: 74: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_6_input.mdp]: 74: You are using a plain Coulomb cut-off, which might produce artifacts. 74: You might want to consider using PME electrostatics. 74: 74: 74: 74: There were 3 NOTEs 74: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_6_sim.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 74: Changing nstlist from 8 to 100, rlist from 0.735 to 0.831 74: 74: Using 1 MPI thread 74: Using 2 OpenMP threads 74: 74: 74: NOTE: The number of threads is not equal to the number of (logical) cpus 74: and the -pin option is set to auto: will not pin threads to cpus. 74: This can lead to significant performance degradation. 74: Consider using -pin on (and -pinoffset in case you run multiple jobs). 74: starting mdrun 'spc2' 74: 16 steps, 0.0 ps. 74: Generated 330891 of the 330891 non-bonded parameter combinations 74: 74: Generated 330891 of the 330891 1-4 parameter combinations 74: 74: Excluding 2 bonded neighbours molecule type 'SOL' 74: 74: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 74: 74: Calculated rlist for 1x1 atom pair-list as 0.738 nm, buffer size 0.038 nm 74: 74: Set rlist, assuming 4x4 atom pair-list, to 0.735 nm, buffer size 0.035 nm 74: 74: Note that mdrun will redetermine rlist based on the actual pair-list setup 74: 74: This run will generate roughly 0 Mb of data 74: 74: Writing final coordinates. 74: 74: Core t (s) Wall t (s) (%) 74: Time: 0.083 0.042 198.7 74: (ns/day) (hour/ns) 74: Performance: 35.222 0.681 74: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_6_sim.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 74: Changing nstlist from 8 to 100, rlist from 0.735 to 0.831 74: 74: Using 1 MPI thread 74: Using 2 OpenMP threads 74: 74: 74: NOTE: The number of threads is not equal to the number of (logical) cpus 74: and the -pin option is set to auto: will not pin threads to cpus. 74: This can lead to significant performance degradation. 74: Consider using -pin on (and -pinoffset in case you run multiple jobs). 74: starting md rerun 'spc2', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_6_sim1.trr' 74: 74: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 74: 74: NOTE: 15 % of the run time was spent in pair search, 74: you might want to increase nstlist (this has no effect on accuracy) 74: 74: Core t (s) Wall t (s) (%) 74: Time: 0.007 0.004 193.1 74: (ns/day) (hour/ns) 74: Performance: 406.640 0.059 74: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_6_sim1.edr as double precision energy file 74: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_6_sim2.edr as double precision energy file 74: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 74: 74: [ OK ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/6 (5928 ms) 74: [ RUN ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/7 74: 74: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_7_input.mdp]: 74: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 74: that with the Verlet scheme, nstlist has no effect on the accuracy of 74: your simulation. 74: 74: 74: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_7_input.mdp]: 74: Setting nstcalcenergy (100) equal to nstenergy (4) 74: 74: Generating 1-4 interactions: fudge = 0.5 74: Number of degrees of freedom in T-Coupling group System is 27.00 74: 74: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_7_input.mdp]: 74: You are using a plain Coulomb cut-off, which might produce artifacts. 74: You might want to consider using PME electrostatics. 74: 74: 74: 74: There were 3 NOTEs 74: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_7_sim.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 74: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 74: 74: Using 1 MPI thread 74: Using 2 OpenMP threads 74: 74: 74: NOTE: The number of threads is not equal to the number of (logical) cpus 74: and the -pin option is set to auto: will not pin threads to cpus. 74: This can lead to significant performance degradation. 74: Consider using -pin on (and -pinoffset in case you run multiple jobs). 74: starting mdrun 'spc2' 74: 16 steps, 0.0 ps. 74: Generated 330891 of the 330891 non-bonded parameter combinations 74: 74: Generated 330891 of the 330891 1-4 parameter combinations 74: 74: Excluding 2 bonded neighbours molecule type 'SOL' 74: 74: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/tip3p5.gro' 74: 74: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 74: 74: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 74: 74: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 74: 74: Note that mdrun will redetermine rlist based on the actual pair-list setup 74: 74: This run will generate roughly 0 Mb of data 74: 74: Writing final coordinates. 74: 74: Core t (s) Wall t (s) (%) 74: Time: 0.070 0.035 198.6 74: (ns/day) (hour/ns) 74: Performance: 41.771 0.575 74: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_7_sim.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 74: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 74: 74: Using 1 MPI thread 74: Using 2 OpenMP threads 74: 74: 74: NOTE: The number of threads is not equal to the number of (logical) cpus 74: and the -pin option is set to auto: will not pin threads to cpus. 74: This can lead to significant performance degradation. 74: Consider using -pin on (and -pinoffset in case you run multiple jobs). 74: starting md rerun 'spc2', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_7_sim1.trr' 74: 74: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 74: 74: Core t (s) Wall t (s) (%) 74: Time: 0.012 0.006 195.6 74: (ns/day) (hour/ns) 74: Performance: 237.092 0.101 74: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_7_sim1.edr as double precision energy file 74: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_7_sim2.edr as double precision energy file 74: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 74: 74: [ OK ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/7 (5902 ms) 74: [ RUN ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/8 74: 74: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_8_input.mdp]: 74: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 74: that with the Verlet scheme, nstlist has no effect on the accuracy of 74: your simulation. 74: 74: 74: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_8_input.mdp]: 74: Setting nstcalcenergy (100) equal to nstenergy (4) 74: 74: Generating 1-4 interactions: fudge = 0.5 74: 74: NOTE 3 [file unknown]: 74: You are using constraints on all bonds, whereas the forcefield has been 74: parametrized only with constraints involving hydrogen atoms. We suggest 74: using constraints = h-bonds instead, this will also improve performance. 74: 74: Number of degrees of freedom in T-Coupling group System is 23.00 74: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 74: 74: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_8_input.mdp]: 74: NVE simulation: will use the initial temperature of 456.887 K for 74: determining the Verlet buffer size 74: 74: 74: NOTE 5 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_8_input.mdp]: 74: There are 9 non-linear virtual site constructions. Their contribution to 74: the energy error is approximated. In most cases this does not affect the 74: error significantly. 74: 74: 74: NOTE 6 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_8_input.mdp]: 74: You are using a plain Coulomb cut-off, which might produce artifacts. 74: You might want to consider using PME electrostatics. 74: 74: 74: 74: There were 6 NOTEs 74: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_8_sim.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 74: Can not increase nstlist because an NVE ensemble is used 74: Update groups can not be used for this system because an incompatible virtual site type is used 74: 74: Using 1 MPI thread 74: Using 2 OpenMP threads 74: 74: 74: NOTE: The number of threads is not equal to the number of (logical) cpus 74: and the -pin option is set to auto: will not pin threads to cpus. 74: This can lead to significant performance degradation. 74: Consider using -pin on (and -pinoffset in case you run multiple jobs). 74: starting mdrun 'Alanine dipeptide in vacuo' 74: 16 steps, 0.0 ps. 74: Generated 2145 of the 2145 non-bonded parameter combinations 74: 74: Generated 2145 of the 2145 1-4 parameter combinations 74: 74: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' 74: 74: turning all bonds into constraints... 74: 74: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/alanine_vsite_vacuo.gro' 74: 74: Cleaning up constraints and constant bonded interactions with virtual sites 74: 74: Removed 18 Angles with virtual sites, 21 left 74: 74: Removed 10 Proper Dih.s with virtual sites, 44 left 74: 74: Converted 15 Constraints with virtual sites to connections, 7 left 74: 74: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 456.887 K 74: 74: Calculated rlist for 1x1 atom pair-list as 0.742 nm, buffer size 0.042 nm 74: 74: Set rlist, assuming 4x4 atom pair-list, to 0.737 nm, buffer size 0.037 nm 74: 74: Note that mdrun will redetermine rlist based on the actual pair-list setup 74: 74: This run will generate roughly 0 Mb of data 74: 74: Writing final coordinates. 74: 74: Core t (s) Wall t (s) (%) 74: Time: 0.056 0.028 197.9 74: (ns/day) (hour/ns) 74: Performance: 51.899 0.462 74: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_8_sim.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 74: Can not increase nstlist because an NVE ensemble is used 74: Update groups can not be used for this system because an incompatible virtual site type is used 74: 74: Using 1 MPI thread 74: Using 2 OpenMP threads 74: 74: 74: NOTE: The number of threads is not equal to the number of (logical) cpus 74: and the -pin option is set to auto: will not pin threads to cpus. 74: This can lead to significant performance degradation. 74: Consider using -pin on (and -pinoffset in case you run multiple jobs). 74: starting md rerun 'Alanine dipeptide in vacuo', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_8_sim1.trr' 74: 74: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 74: 74: NOTE: 10 % of the run time was spent in pair search, 74: you might want to increase nstlist (this has no effect on accuracy) 74: 74: Core t (s) Wall t (s) (%) 74: Time: 0.013 0.006 195.7 74: (ns/day) (hour/ns) 74: Performance: 228.610 0.105 74: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_8_sim1.edr as double precision energy file 74: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_8_sim2.edr as double precision energy file 74: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 74: 74: [ OK ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/8 (231 ms) 74: [ RUN ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/9 74: 74: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_9_input.mdp]: 74: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 74: that with the Verlet scheme, nstlist has no effect on the accuracy of 74: your simulation. 74: 74: 74: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_9_input.mdp]: 74: Setting nstcalcenergy (100) equal to nstenergy (4) 74: 74: Generating 1-4 interactions: fudge = 0.5 74: 74: NOTE 3 [file unknown]: 74: You are using constraints on all bonds, whereas the forcefield has been 74: parametrized only with constraints involving hydrogen atoms. We suggest 74: using constraints = h-bonds instead, this will also improve performance. 74: 74: Number of degrees of freedom in T-Coupling group System is 23.00 74: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 74: 74: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_9_input.mdp]: 74: NVE simulation: will use the initial temperature of 456.887 K for 74: determining the Verlet buffer size 74: 74: 74: NOTE 5 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_9_input.mdp]: 74: There are 9 non-linear virtual site constructions. Their contribution to 74: the energy error is approximated. In most cases this does not affect the 74: error significantly. 74: 74: 74: NOTE 6 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_9_input.mdp]: 74: You are using a plain Coulomb cut-off, which might produce artifacts. 74: You might want to consider using PME electrostatics. 74: 74: 74: 74: There were 6 NOTEs 74: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_9_sim.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 74: Can not increase nstlist because an NVE ensemble is used 74: Update groups can not be used for this system because an incompatible virtual site type is used 74: 74: Using 1 MPI thread 74: Using 2 OpenMP threads 74: 74: 74: NOTE: The number of threads is not equal to the number of (logical) cpus 74: and the -pin option is set to auto: will not pin threads to cpus. 74: This can lead to significant performance degradation. 74: Consider using -pin on (and -pinoffset in case you run multiple jobs). 74: starting mdrun 'Alanine dipeptide in vacuo' 74: 16 steps, 0.0 ps. 74: Generated 2145 of the 2145 non-bonded parameter combinations 74: 74: Generated 2145 of the 2145 1-4 parameter combinations 74: 74: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' 74: 74: turning all bonds into constraints... 74: 74: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/alanine_vsite_vacuo.gro' 74: 74: Cleaning up constraints and constant bonded interactions with virtual sites 74: 74: Removed 18 Angles with virtual sites, 21 left 74: 74: Removed 10 Proper Dih.s with virtual sites, 44 left 74: 74: Converted 15 Constraints with virtual sites to connections, 7 left 74: 74: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 456.887 K 74: 74: Calculated rlist for 1x1 atom pair-list as 0.742 nm, buffer size 0.042 nm 74: 74: Set rlist, assuming 4x4 atom pair-list, to 0.737 nm, buffer size 0.037 nm 74: 74: Note that mdrun will redetermine rlist based on the actual pair-list setup 74: 74: This run will generate roughly 0 Mb of data 74: 74: Writing final coordinates. 74: 74: Core t (s) Wall t (s) (%) 74: Time: 0.068 0.034 198.2 74: (ns/day) (hour/ns) 74: Performance: 42.902 0.559 74: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_9_sim.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 74: Can not increase nstlist because an NVE ensemble is used 74: Update groups can not be used for this system because an incompatible virtual site type is used 74: 74: Using 1 MPI thread 74: Using 2 OpenMP threads 74: 74: 74: NOTE: The number of threads is not equal to the number of (logical) cpus 74: and the -pin option is set to auto: will not pin threads to cpus. 74: This can lead to significant performance degradation. 74: Consider using -pin on (and -pinoffset in case you run multiple jobs). 74: starting md rerun 'Alanine dipeptide in vacuo', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_9_sim1.trr' 74: 74: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 74: 74: NOTE: 11 % of the run time was spent in pair search, 74: you might want to increase nstlist (this has no effect on accuracy) 74: 74: Core t (s) Wall t (s) (%) 74: Time: 0.012 0.006 194.8 74: (ns/day) (hour/ns) 74: Performance: 243.820 0.098 74: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_9_sim1.edr as double precision energy file 74: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_9_sim2.edr as double precision energy file 74: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 74: 74: [ OK ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/9 (242 ms) 74: [ RUN ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/10 74: 74: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_10_input.mdp]: 74: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 74: that with the Verlet scheme, nstlist has no effect on the accuracy of 74: your simulation. 74: 74: 74: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_10_input.mdp]: 74: Setting nstcalcenergy (100) equal to nstenergy (4) 74: 74: Generating 1-4 interactions: fudge = 0.5 74: 74: NOTE 3 [file unknown]: 74: You are using constraints on all bonds, whereas the forcefield has been 74: parametrized only with constraints involving hydrogen atoms. We suggest 74: using constraints = h-bonds instead, this will also improve performance. 74: 74: Number of degrees of freedom in T-Coupling group System is 23.00 74: 74: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_10_input.mdp]: 74: There are 9 non-linear virtual site constructions. Their contribution to 74: the energy error is approximated. In most cases this does not affect the 74: error significantly. 74: 74: 74: NOTE 5 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_10_input.mdp]: 74: You are using a plain Coulomb cut-off, which might produce artifacts. 74: You might want to consider using PME electrostatics. 74: 74: 74: 74: There were 5 NOTEs 74: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_10_sim.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 74: Changing nstlist from 8 to 80, rlist from 0.748 to 0.865 74: 74: Update groups can not be used for this system because an incompatible virtual site type is used 74: 74: Using 1 MPI thread 74: Using 2 OpenMP threads 74: 74: 74: NOTE: The number of threads is not equal to the number of (logical) cpus 74: and the -pin option is set to auto: will not pin threads to cpus. 74: This can lead to significant performance degradation. 74: Consider using -pin on (and -pinoffset in case you run multiple jobs). 74: starting mdrun 'Alanine dipeptide in vacuo' 74: 16 steps, 0.0 ps. 74: Generated 2145 of the 2145 non-bonded parameter combinations 74: 74: Generated 2145 of the 2145 1-4 parameter combinations 74: 74: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' 74: 74: turning all bonds into constraints... 74: 74: Cleaning up constraints and constant bonded interactions with virtual sites 74: 74: Removed 18 Angles with virtual sites, 21 left 74: 74: Removed 10 Proper Dih.s with virtual sites, 44 left 74: 74: Converted 15 Constraints with virtual sites to connections, 7 left 74: 74: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 74: 74: Calculated rlist for 1x1 atom pair-list as 0.754 nm, buffer size 0.054 nm 74: 74: Set rlist, assuming 4x4 atom pair-list, to 0.748 nm, buffer size 0.048 nm 74: 74: Note that mdrun will redetermine rlist based on the actual pair-list setup 74: 74: This run will generate roughly 0 Mb of data 74: 74: Writing final coordinates. 74: 74: Core t (s) Wall t (s) (%) 74: Time: 0.075 0.038 198.4 74: (ns/day) (hour/ns) 74: Performance: 39.034 0.615 74: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_10_sim.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 74: Changing nstlist from 8 to 80, rlist from 0.748 to 0.865 74: 74: Update groups can not be used for this system because an incompatible virtual site type is used 74: 74: Using 1 MPI thread 74: Using 2 OpenMP threads 74: 74: 74: NOTE: The number of threads is not equal to the number of (logical) cpus 74: and the -pin option is set to auto: will not pin threads to cpus. 74: This can lead to significant performance degradation. 74: Consider using -pin on (and -pinoffset in case you run multiple jobs). 74: starting md rerun 'Alanine dipeptide in vacuo', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_10_sim1.trr' 74: 74: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 74: 74: Core t (s) Wall t (s) (%) 74: Time: 0.019 0.010 196.4 74: (ns/day) (hour/ns) 74: Performance: 151.799 0.158 74: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_10_sim1.edr as double precision energy file 74: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_10_sim2.edr as double precision energy file 74: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 74: 74: [ OK ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/10 (1281 ms) 74: [ RUN ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/11 74: 74: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_11_input.mdp]: 74: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 74: that with the Verlet scheme, nstlist has no effect on the accuracy of 74: your simulation. 74: 74: 74: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_11_input.mdp]: 74: Setting nstcalcenergy (100) equal to nstenergy (4) 74: 74: Generating 1-4 interactions: fudge = 0.5 74: 74: NOTE 3 [file unknown]: 74: You are using constraints on all bonds, whereas the forcefield has been 74: parametrized only with constraints involving hydrogen atoms. We suggest 74: using constraints = h-bonds instead, this will also improve performance. 74: 74: Number of degrees of freedom in T-Coupling group System is 23.00 74: 74: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_11_input.mdp]: 74: There are 9 non-linear virtual site constructions. Their contribution to 74: the energy error is approximated. In most cases this does not affect the 74: error significantly. 74: 74: 74: NOTE 5 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_11_input.mdp]: 74: You are using a plain Coulomb cut-off, which might produce artifacts. 74: You might want to consider using PME electrostatics. 74: 74: 74: 74: There were 5 NOTEs 74: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_11_sim.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 74: Changing nstlist from 8 to 25, rlist from 0.729 to 0.81 74: 74: Update groups can not be used for this system because an incompatible virtual site type is used 74: 74: Using 1 MPI thread 74: Using 2 OpenMP threads 74: 74: 74: NOTE: The number of threads is not equal to the number of (logical) cpus 74: and the -pin option is set to auto: will not pin threads to cpus. 74: This can lead to significant performance degradation. 74: Consider using -pin on (and -pinoffset in case you run multiple jobs). 74: starting mdrun 'Alanine dipeptide in vacuo' 74: 16 steps, 0.0 ps. 74: Generated 2145 of the 2145 non-bonded parameter combinations 74: 74: Generated 2145 of the 2145 1-4 parameter combinations 74: 74: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' 74: 74: turning all bonds into constraints... 74: 74: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/alanine_vsite_vacuo.gro' 74: 74: Cleaning up constraints and constant bonded interactions with virtual sites 74: 74: Removed 18 Angles with virtual sites, 21 left 74: 74: Removed 10 Proper Dih.s with virtual sites, 44 left 74: 74: Converted 15 Constraints with virtual sites to connections, 7 left 74: 74: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 74: 74: Calculated rlist for 1x1 atom pair-list as 0.733 nm, buffer size 0.033 nm 74: 74: Set rlist, assuming 4x4 atom pair-list, to 0.729 nm, buffer size 0.029 nm 74: 74: Note that mdrun will redetermine rlist based on the actual pair-list setup 74: 74: This run will generate roughly 0 Mb of data 74: 74: Writing final coordinates. 74: 74: Core t (s) Wall t (s) (%) 74: Time: 0.088 0.044 198.6 74: (ns/day) (hour/ns) 74: Performance: 33.322 0.720 74: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_11_sim.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 74: Changing nstlist from 8 to 25, rlist from 0.729 to 0.81 74: 74: Update groups can not be used for this system because an incompatible virtual site type is used 74: 74: Using 1 MPI thread 74: Using 2 OpenMP threads 74: 74: 74: NOTE: The number of threads is not equal to the number of (logical) cpus 74: and the -pin option is set to auto: will not pin threads to cpus. 74: This can lead to significant performance degradation. 74: Consider using -pin on (and -pinoffset in case you run multiple jobs). 74: starting md rerun 'Alanine dipeptide in vacuo', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_11_sim1.trr' 74: 74: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 74: 74: NOTE: 22 % of the run time was spent in pair search, 74: you might want to increase nstlist (this has no effect on accuracy) 74: 74: Core t (s) Wall t (s) (%) 74: Time: 0.019 0.010 196.9 74: (ns/day) (hour/ns) 74: Performance: 153.558 0.156 74: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_11_sim1.edr as double precision energy file 74: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_11_sim2.edr as double precision energy file 74: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 74: 74: [ OK ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/11 (635 ms) 74: [----------] 12 tests from NormalMdrunIsReproduced/MdrunRerunTest (26413 ms total) 74: 74: [----------] 33 tests from MdrunIsReproduced/MdrunRerunFreeEnergyTest 74: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/0 74: 74: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_0_input.mdp]: 74: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 74: that with the Verlet scheme, nstlist has no effect on the accuracy of 74: your simulation. 74: 74: 74: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_0_input.mdp]: 74: Setting nstcalcenergy (100) equal to nstenergy (4) 74: 74: Generating 1-4 interactions: fudge = 0.5 74: Number of degrees of freedom in T-Coupling group System is 79.00 74: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 74: 74: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_0_input.mdp]: 74: NVE simulation: will use the initial temperature of 294.908 K for 74: determining the Verlet buffer size 74: 74: 74: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_0_input.mdp]: 74: You are using a plain Coulomb cut-off, which might produce artifacts. 74: You might want to consider using PME electrostatics. 74: 74: 74: 74: There were 4 NOTEs 74: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_0_sim.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 74: Can not increase nstlist because an NVE ensemble is used 74: Using 1 MPI thread 74: Using 2 OpenMP threads 74: 74: 74: NOTE: The number of threads is not equal to the number of (logical) cpus 74: and the -pin option is set to auto: will not pin threads to cpus. 74: This can lead to significant performance degradation. 74: Consider using -pin on (and -pinoffset in case you run multiple jobs). 74: starting mdrun '30 atom system in water' 74: 16 steps, 0.0 ps. 74: Generated 2485 of the 2485 non-bonded parameter combinations 74: 74: Generated 2485 of the 2485 1-4 parameter combinations 74: 74: Excluding 3 bonded neighbours molecule type 'nonanol' 74: 74: turning H bonds into constraints... 74: 74: Excluding 2 bonded neighbours molecule type 'SOL' 74: 74: turning H bonds into constraints... 74: 74: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/nonanol_vacuo.gro' 74: 74: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 294.908 K 74: 74: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 74: 74: Set rlist, assuming 4x4 atom pair-list, to 0.757 nm, buffer size 0.057 nm 74: 74: Note that mdrun will redetermine rlist based on the actual pair-list setup 74: 74: This run will generate roughly 0 Mb of data 74: 74: Writing final coordinates. 74: 74: Core t (s) Wall t (s) (%) 74: Time: 0.067 0.034 197.4 74: (ns/day) (hour/ns) 74: Performance: 43.138 0.556 74: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_0_sim.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 74: Can not increase nstlist because an NVE ensemble is used 74: Using 1 MPI thread 74: Using 2 OpenMP threads 74: 74: 74: NOTE: The number of threads is not equal to the number of (logical) cpus 74: and the -pin option is set to auto: will not pin threads to cpus. 74: This can lead to significant performance degradation. 74: Consider using -pin on (and -pinoffset in case you run multiple jobs). 74: starting md rerun '30 atom system in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_0_sim1.trr' 74: 74: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 74: 74: Core t (s) Wall t (s) (%) 74: Time: 0.018 0.010 187.6 74: (ns/day) (hour/ns) 74: Performance: 149.663 0.160 74: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_0_sim1.edr as double precision energy file 74: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_0_sim2.edr as double precision energy file 74: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 74: 74: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/0 (244 ms) 74: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/1 74: 74: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_1_input.mdp]: 74: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 74: that with the Verlet scheme, nstlist has no effect on the accuracy of 74: your simulation. 74: 74: 74: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_1_input.mdp]: 74: Setting nstcalcenergy (100) equal to nstenergy (4) 74: 74: Generating 1-4 interactions: fudge = 0.5 74: Number of degrees of freedom in T-Coupling group System is 79.00 74: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 74: 74: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_1_input.mdp]: 74: NVE simulation: will use the initial temperature of 294.908 K for 74: determining the Verlet buffer size 74: 74: 74: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_1_input.mdp]: 74: You are using a plain Coulomb cut-off, which might produce artifacts. 74: You might want to consider using PME electrostatics. 74: 74: 74: 74: There were 4 NOTEs 74: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_1_sim.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 74: Can not increase nstlist because an NVE ensemble is used 74: Using 1 MPI thread 74: Using 2 OpenMP threads 74: 74: 74: NOTE: The number of threads is not equal to the number of (logical) cpus 74: and the -pin option is set to auto: will not pin threads to cpus. 74: This can lead to significant performance degradation. 74: Consider using -pin on (and -pinoffset in case you run multiple jobs). 74: starting mdrun '30 atom system in water' 74: 16 steps, 0.0 ps. 74: Generated 2485 of the 2485 non-bonded parameter combinations 74: 74: Generated 2485 of the 2485 1-4 parameter combinations 74: 74: Excluding 3 bonded neighbours molecule type 'nonanol' 74: 74: turning H bonds into constraints... 74: 74: Excluding 2 bonded neighbours molecule type 'SOL' 74: 74: turning H bonds into constraints... 74: 74: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/nonanol_vacuo.gro' 74: 74: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 294.908 K 74: 74: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 74: 74: Set rlist, assuming 4x4 atom pair-list, to 0.757 nm, buffer size 0.057 nm 74: 74: Note that mdrun will redetermine rlist based on the actual pair-list setup 74: 74: This run will generate roughly 0 Mb of data 74: 74: Writing final coordinates. 74: 74: Core t (s) Wall t (s) (%) 74: Time: 0.080 0.040 197.6 74: (ns/day) (hour/ns) 74: Performance: 36.328 0.661 74: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_1_sim.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 74: Can not increase nstlist because an NVE ensemble is used 74: Using 1 MPI thread 74: Using 2 OpenMP threads 74: 74: 74: NOTE: The number of threads is not equal to the number of (logical) cpus 74: and the -pin option is set to auto: will not pin threads to cpus. 74: This can lead to significant performance degradation. 74: Consider using -pin on (and -pinoffset in case you run multiple jobs). 74: starting md rerun '30 atom system in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_1_sim1.trr' 74: 74: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 74: 74: Core t (s) Wall t (s) (%) 74: Time: 0.029 0.016 189.4 74: (ns/day) (hour/ns) 74: Performance: 94.323 0.254 74: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_1_sim1.edr as double precision energy file 74: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_1_sim2.edr as double precision energy file 74: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 74: 74: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/1 (255 ms) 74: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/2 74: 74: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_2_input.mdp]: 74: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 74: that with the Verlet scheme, nstlist has no effect on the accuracy of 74: your simulation. 74: 74: 74: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_2_input.mdp]: 74: Setting nstcalcenergy (100) equal to nstenergy (4) 74: 74: Generating 1-4 interactions: fudge = 0.5 74: Number of degrees of freedom in T-Coupling group System is 79.00 74: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 74: 74: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_2_input.mdp]: 74: NVE simulation: will use the initial temperature of 294.908 K for 74: determining the Verlet buffer size 74: 74: 74: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_2_input.mdp]: 74: You are using a plain Coulomb cut-off, which might produce artifacts. 74: You might want to consider using PME electrostatics. 74: 74: 74: 74: There were 4 NOTEs 74: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_2_sim.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 74: Can not increase nstlist because an NVE ensemble is used 74: Using 1 MPI thread 74: Using 2 OpenMP threads 74: 74: 74: NOTE: The number of threads is not equal to the number of (logical) cpus 74: and the -pin option is set to auto: will not pin threads to cpus. 74: This can lead to significant performance degradation. 74: Consider using -pin on (and -pinoffset in case you run multiple jobs). 74: starting mdrun '30 atom system in water' 74: 16 steps, 0.0 ps. 74: Generated 2485 of the 2485 non-bonded parameter combinations 74: 74: Generated 2485 of the 2485 1-4 parameter combinations 74: 74: Excluding 3 bonded neighbours molecule type 'nonanol' 74: 74: turning H bonds into constraints... 74: 74: Excluding 2 bonded neighbours molecule type 'SOL' 74: 74: turning H bonds into constraints... 74: 74: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/nonanol_vacuo.gro' 74: 74: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 294.908 K 74: 74: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 74: 74: Set rlist, assuming 4x4 atom pair-list, to 0.757 nm, buffer size 0.057 nm 74: 74: Note that mdrun will redetermine rlist based on the actual pair-list setup 74: 74: This run will generate roughly 0 Mb of data 74: 74: Writing final coordinates. 74: 74: Core t (s) Wall t (s) (%) 74: Time: 0.085 0.043 197.9 74: (ns/day) (hour/ns) 74: Performance: 34.001 0.706 74: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_2_sim.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 74: Can not increase nstlist because an NVE ensemble is used 74: Using 1 MPI thread 74: Using 2 OpenMP threads 74: 74: 74: NOTE: The number of threads is not equal to the number of (logical) cpus 74: and the -pin option is set to auto: will not pin threads to cpus. 74: This can lead to significant performance degradation. 74: Consider using -pin on (and -pinoffset in case you run multiple jobs). 74: starting md rerun '30 atom system in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_2_sim1.trr' 74: 74: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 74: 74: Core t (s) Wall t (s) (%) 74: Time: 0.019 0.010 186.7 74: (ns/day) (hour/ns) 74: Performance: 141.000 0.170 74: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_2_sim1.edr as double precision energy file 74: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_2_sim2.edr as double precision energy file 74: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 74: 74: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/2 (255 ms) 74: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/3 74: 74: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_3_input.mdp]: 74: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 74: that with the Verlet scheme, nstlist has no effect on the accuracy of 74: your simulation. 74: 74: 74: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_3_input.mdp]: 74: Setting nstcalcenergy (100) equal to nstenergy (4) 74: 74: Generating 1-4 interactions: fudge = 0.5 74: Number of degrees of freedom in T-Coupling group System is 79.00 74: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 74: 74: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_3_input.mdp]: 74: NVE simulation: will use the initial temperature of 294.908 K for 74: determining the Verlet buffer size 74: 74: 74: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_3_input.mdp]: 74: You are using a plain Coulomb cut-off, which might produce artifacts. 74: You might want to consider using PME electrostatics. 74: 74: 74: 74: There were 4 NOTEs 74: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_3_sim.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 74: Can not increase nstlist because an NVE ensemble is used 74: Using 1 MPI thread 74: Using 2 OpenMP threads 74: 74: 74: NOTE: The number of threads is not equal to the number of (logical) cpus 74: and the -pin option is set to auto: will not pin threads to cpus. 74: This can lead to significant performance degradation. 74: Consider using -pin on (and -pinoffset in case you run multiple jobs). 74: starting mdrun '30 atom system in water' 74: 16 steps, 0.0 ps. 74: Generated 2485 of the 2485 non-bonded parameter combinations 74: 74: Generated 2485 of the 2485 1-4 parameter combinations 74: 74: Excluding 3 bonded neighbours molecule type 'nonanol' 74: 74: turning H bonds into constraints... 74: 74: Excluding 2 bonded neighbours molecule type 'SOL' 74: 74: turning H bonds into constraints... 74: 74: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/nonanol_vacuo.gro' 74: 74: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 294.908 K 74: 74: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 74: 74: Set rlist, assuming 4x4 atom pair-list, to 0.757 nm, buffer size 0.057 nm 74: 74: Note that mdrun will redetermine rlist based on the actual pair-list setup 74: 74: This run will generate roughly 0 Mb of data 74: 74: Writing final coordinates. 74: 74: Core t (s) Wall t (s) (%) 74: Time: 0.064 0.032 197.1 74: (ns/day) (hour/ns) 74: Performance: 45.587 0.526 74: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_3_sim.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 74: Can not increase nstlist because an NVE ensemble is used 74: Using 1 MPI thread 74: Using 2 OpenMP threads 74: 74: 74: NOTE: The number of threads is not equal to the number of (logical) cpus 74: and the -pin option is set to auto: will not pin threads to cpus. 74: This can lead to significant performance degradation. 74: Consider using -pin on (and -pinoffset in case you run multiple jobs). 74: starting md rerun '30 atom system in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_3_sim1.trr' 74: 74: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 74: 74: Core t (s) Wall t (s) (%) 74: Time: 0.036 0.019 192.2 74: (ns/day) (hour/ns) 74: Performance: 78.675 0.305 74: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_3_sim1.edr as double precision energy file 74: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_3_sim2.edr as double precision energy file 74: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 74: 74: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/3 (251 ms) 74: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/4 74: 74: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_4_input.mdp]: 74: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 74: that with the Verlet scheme, nstlist has no effect on the accuracy of 74: your simulation. 74: 74: 74: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_4_input.mdp]: 74: Setting nstcalcenergy (100) equal to nstenergy (4) 74: 74: Generating 1-4 interactions: fudge = 0.5 74: Number of degrees of freedom in T-Coupling group System is 79.00 74: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 74: 74: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_4_input.mdp]: 74: NVE simulation: will use the initial temperature of 294.908 K for 74: determining the Verlet buffer size 74: 74: 74: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_4_input.mdp]: 74: You are using a plain Coulomb cut-off, which might produce artifacts. 74: You might want to consider using PME electrostatics. 74: 74: 74: 74: There were 4 NOTEs 74: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_4_sim.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 74: Can not increase nstlist because an NVE ensemble is used 74: Using 1 MPI thread 74: Using 2 OpenMP threads 74: 74: 74: NOTE: The number of threads is not equal to the number of (logical) cpus 74: and the -pin option is set to auto: will not pin threads to cpus. 74: This can lead to significant performance degradation. 74: Consider using -pin on (and -pinoffset in case you run multiple jobs). 74: starting mdrun '30 atom system in water' 74: 16 steps, 0.0 ps. 74: Generated 2485 of the 2485 non-bonded parameter combinations 74: 74: Generated 2485 of the 2485 1-4 parameter combinations 74: 74: Excluding 3 bonded neighbours molecule type 'nonanol' 74: 74: turning H bonds into constraints... 74: 74: Excluding 2 bonded neighbours molecule type 'SOL' 74: 74: turning H bonds into constraints... 74: 74: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/nonanol_vacuo.gro' 74: 74: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 294.908 K 74: 74: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 74: 74: Set rlist, assuming 4x4 atom pair-list, to 0.757 nm, buffer size 0.057 nm 74: 74: Note that mdrun will redetermine rlist based on the actual pair-list setup 74: 74: This run will generate roughly 0 Mb of data 74: 74: Writing final coordinates. 74: 74: Core t (s) Wall t (s) (%) 74: Time: 0.083 0.042 197.8 74: (ns/day) (hour/ns) 74: Performance: 34.879 0.688 74: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_4_sim.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 74: Can not increase nstlist because an NVE ensemble is used 74: Using 1 MPI thread 74: Using 2 OpenMP threads 74: 74: 74: NOTE: The number of threads is not equal to the number of (logical) cpus 74: and the -pin option is set to auto: will not pin threads to cpus. 74: This can lead to significant performance degradation. 74: Consider using -pin on (and -pinoffset in case you run multiple jobs). 74: starting md rerun '30 atom system in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_4_sim1.trr' 74: 74: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 74: 74: Core t (s) Wall t (s) (%) 74: Time: 0.022 0.012 187.5 74: (ns/day) (hour/ns) 74: Performance: 126.488 0.190 74: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_4_sim1.edr as double precision energy file 74: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_4_sim2.edr as double precision energy file 74: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 74: 74: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/4 (251 ms) 74: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/5 74: 74: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_5_input.mdp]: 74: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 74: that with the Verlet scheme, nstlist has no effect on the accuracy of 74: your simulation. 74: 74: 74: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_5_input.mdp]: 74: Setting nstcalcenergy (100) equal to nstenergy (4) 74: 74: Generating 1-4 interactions: fudge = 0.5 74: Number of degrees of freedom in T-Coupling group System is 79.00 74: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 74: 74: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_5_input.mdp]: 74: NVE simulation: will use the initial temperature of 294.908 K for 74: determining the Verlet buffer size 74: 74: 74: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_5_input.mdp]: 74: You are using a plain Coulomb cut-off, which might produce artifacts. 74: You might want to consider using PME electrostatics. 74: 74: 74: 74: There were 4 NOTEs 74: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_5_sim.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 74: Can not increase nstlist because an NVE ensemble is used 74: Using 1 MPI thread 74: Using 2 OpenMP threads 74: 74: 74: NOTE: The number of threads is not equal to the number of (logical) cpus 74: and the -pin option is set to auto: will not pin threads to cpus. 74: This can lead to significant performance degradation. 74: Consider using -pin on (and -pinoffset in case you run multiple jobs). 74: starting mdrun '30 atom system in water' 74: 16 steps, 0.0 ps. 74: Generated 2485 of the 2485 non-bonded parameter combinations 74: 74: Generated 2485 of the 2485 1-4 parameter combinations 74: 74: Excluding 3 bonded neighbours molecule type 'nonanol' 74: 74: turning H bonds into constraints... 74: 74: Excluding 2 bonded neighbours molecule type 'SOL' 74: 74: turning H bonds into constraints... 74: 74: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/nonanol_vacuo.gro' 74: 74: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 294.908 K 74: 74: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 74: 74: Set rlist, assuming 4x4 atom pair-list, to 0.757 nm, buffer size 0.057 nm 74: 74: Note that mdrun will redetermine rlist based on the actual pair-list setup 74: 74: This run will generate roughly 0 Mb of data 74: 74: Writing final coordinates. 74: 74: Core t (s) Wall t (s) (%) 74: Time: 0.077 0.039 197.8 74: (ns/day) (hour/ns) 74: Performance: 37.701 0.637 74: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_5_sim.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 74: Can not increase nstlist because an NVE ensemble is used 74: Using 1 MPI thread 74: Using 2 OpenMP threads 74: 74: 74: NOTE: The number of threads is not equal to the number of (logical) cpus 74: and the -pin option is set to auto: will not pin threads to cpus. 74: This can lead to significant performance degradation. 74: Consider using -pin on (and -pinoffset in case you run multiple jobs). 74: starting md rerun '30 atom system in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_5_sim1.trr' 74: 74: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 74: 74: Core t (s) Wall t (s) (%) 74: Time: 0.024 0.013 188.7 74: (ns/day) (hour/ns) 74: Performance: 116.431 0.206 74: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_5_sim1.edr as double precision energy file 74: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_5_sim2.edr as double precision energy file 74: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 74: 74: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/5 (248 ms) 74: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/6 74: 74: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_6_input.mdp]: 74: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 74: that with the Verlet scheme, nstlist has no effect on the accuracy of 74: your simulation. 74: 74: 74: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_6_input.mdp]: 74: Setting nstcalcenergy (100) equal to nstenergy (4) 74: 74: Generating 1-4 interactions: fudge = 0.5 74: Number of degrees of freedom in T-Coupling group System is 79.00 74: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 74: 74: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_6_input.mdp]: 74: NVE simulation: will use the initial temperature of 294.908 K for 74: determining the Verlet buffer size 74: 74: 74: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_6_input.mdp]: 74: You are using a plain Coulomb cut-off, which might produce artifacts. 74: You might want to consider using PME electrostatics. 74: 74: 74: 74: There were 4 NOTEs 74: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_6_sim.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 74: Can not increase nstlist because an NVE ensemble is used 74: Using 1 MPI thread 74: Using 2 OpenMP threads 74: 74: 74: NOTE: The number of threads is not equal to the number of (logical) cpus 74: and the -pin option is set to auto: will not pin threads to cpus. 74: This can lead to significant performance degradation. 74: Consider using -pin on (and -pinoffset in case you run multiple jobs). 74: starting mdrun '30 atom system in water' 74: 16 steps, 0.0 ps. 74: Generated 2485 of the 2485 non-bonded parameter combinations 74: 74: Generated 2485 of the 2485 1-4 parameter combinations 74: 74: Excluding 3 bonded neighbours molecule type 'nonanol' 74: 74: turning H bonds into constraints... 74: 74: Excluding 2 bonded neighbours molecule type 'SOL' 74: 74: turning H bonds into constraints... 74: 74: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/nonanol_vacuo.gro' 74: 74: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 294.908 K 74: 74: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 74: 74: Set rlist, assuming 4x4 atom pair-list, to 0.757 nm, buffer size 0.057 nm 74: 74: Note that mdrun will redetermine rlist based on the actual pair-list setup 74: 74: This run will generate roughly 0 Mb of data 74: 74: Writing final coordinates. 74: 74: Core t (s) Wall t (s) (%) 74: Time: 0.080 0.040 197.5 74: (ns/day) (hour/ns) 74: Performance: 36.434 0.659 74: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_6_sim.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 74: Can not increase nstlist because an NVE ensemble is used 74: Using 1 MPI thread 74: Using 2 OpenMP threads 74: 74: 74: NOTE: The number of threads is not equal to the number of (logical) cpus 74: and the -pin option is set to auto: will not pin threads to cpus. 74: This can lead to significant performance degradation. 74: Consider using -pin on (and -pinoffset in case you run multiple jobs). 74: starting md rerun '30 atom system in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_6_sim1.trr' 74: 74: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 74: 74: Core t (s) Wall t (s) (%) 74: Time: 0.016 0.009 184.1 74: (ns/day) (hour/ns) 74: Performance: 168.557 0.142 74: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_6_sim1.edr as double precision energy file 74: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_6_sim2.edr as double precision energy file 74: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 74: 74: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/6 (240 ms) 74: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/7 74: 74: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_7_input.mdp]: 74: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 74: that with the Verlet scheme, nstlist has no effect on the accuracy of 74: your simulation. 74: 74: 74: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_7_input.mdp]: 74: Setting nstcalcenergy (100) equal to nstenergy (4) 74: 74: Generating 1-4 interactions: fudge = 0.5 74: Number of degrees of freedom in T-Coupling group System is 79.00 74: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 74: 74: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_7_input.mdp]: 74: NVE simulation: will use the initial temperature of 294.908 K for 74: determining the Verlet buffer size 74: 74: 74: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_7_input.mdp]: 74: You are using a plain Coulomb cut-off, which might produce artifacts. 74: You might want to consider using PME electrostatics. 74: 74: 74: 74: There were 4 NOTEs 74: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_7_sim.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 74: Can not increase nstlist because an NVE ensemble is used 74: Using 1 MPI thread 74: Using 2 OpenMP threads 74: 74: 74: NOTE: The number of threads is not equal to the number of (logical) cpus 74: and the -pin option is set to auto: will not pin threads to cpus. 74: This can lead to significant performance degradation. 74: Consider using -pin on (and -pinoffset in case you run multiple jobs). 74: starting mdrun '30 atom system in water' 74: 16 steps, 0.0 ps. 74: Generated 2485 of the 2485 non-bonded parameter combinations 74: 74: Generated 2485 of the 2485 1-4 parameter combinations 74: 74: Excluding 3 bonded neighbours molecule type 'nonanol' 74: 74: turning H bonds into constraints... 74: 74: Excluding 2 bonded neighbours molecule type 'SOL' 74: 74: turning H bonds into constraints... 74: 74: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/nonanol_vacuo.gro' 74: 74: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 294.908 K 74: 74: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 74: 74: Set rlist, assuming 4x4 atom pair-list, to 0.757 nm, buffer size 0.057 nm 74: 74: Note that mdrun will redetermine rlist based on the actual pair-list setup 74: 74: This run will generate roughly 0 Mb of data 74: 74: Writing final coordinates. 74: 74: Core t (s) Wall t (s) (%) 74: Time: 0.087 0.044 198.1 74: (ns/day) (hour/ns) 74: Performance: 33.257 0.722 74: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_7_sim.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 74: Can not increase nstlist because an NVE ensemble is used 74: Using 1 MPI thread 74: Using 2 OpenMP threads 74: 74: 74: NOTE: The number of threads is not equal to the number of (logical) cpus 74: and the -pin option is set to auto: will not pin threads to cpus. 74: This can lead to significant performance degradation. 74: Consider using -pin on (and -pinoffset in case you run multiple jobs). 74: starting md rerun '30 atom system in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_7_sim1.trr' 74: 74: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 74: 74: Core t (s) Wall t (s) (%) 74: Time: 0.027 0.014 191.6 74: (ns/day) (hour/ns) 74: Performance: 102.434 0.234 74: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_7_sim1.edr as double precision energy file 74: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_7_sim2.edr as double precision energy file 74: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 74: 74: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/7 (245 ms) 74: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/8 74: 74: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_8_input.mdp]: 74: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 74: that with the Verlet scheme, nstlist has no effect on the accuracy of 74: your simulation. 74: 74: 74: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_8_input.mdp]: 74: Setting nstcalcenergy (100) equal to nstenergy (4) 74: 74: Generating 1-4 interactions: fudge = 0.5 74: Number of degrees of freedom in T-Coupling group System is 79.00 74: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 74: 74: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_8_input.mdp]: 74: NVE simulation: will use the initial temperature of 294.908 K for 74: determining the Verlet buffer size 74: 74: 74: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_8_input.mdp]: 74: You are using a plain Coulomb cut-off, which might produce artifacts. 74: You might want to consider using PME electrostatics. 74: 74: 74: 74: There were 4 NOTEs 74: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_8_sim.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 74: Can not increase nstlist because an NVE ensemble is used 74: Using 1 MPI thread 74: Using 2 OpenMP threads 74: 74: 74: NOTE: The number of threads is not equal to the number of (logical) cpus 74: and the -pin option is set to auto: will not pin threads to cpus. 74: This can lead to significant performance degradation. 74: Consider using -pin on (and -pinoffset in case you run multiple jobs). 74: starting mdrun '30 atom system in water' 74: 16 steps, 0.0 ps. 74: Generated 2485 of the 2485 non-bonded parameter combinations 74: 74: Generated 2485 of the 2485 1-4 parameter combinations 74: 74: Excluding 3 bonded neighbours molecule type 'nonanol' 74: 74: turning H bonds into constraints... 74: 74: Excluding 2 bonded neighbours molecule type 'SOL' 74: 74: turning H bonds into constraints... 74: 74: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/nonanol_vacuo.gro' 74: 74: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 294.908 K 74: 74: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 74: 74: Set rlist, assuming 4x4 atom pair-list, to 0.757 nm, buffer size 0.057 nm 74: 74: Note that mdrun will redetermine rlist based on the actual pair-list setup 74: 74: This run will generate roughly 0 Mb of data 74: 74: Writing final coordinates. 74: 74: Core t (s) Wall t (s) (%) 74: Time: 0.082 0.042 197.9 74: (ns/day) (hour/ns) 74: Performance: 35.278 0.680 74: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_8_sim.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 74: Can not increase nstlist because an NVE ensemble is used 74: Using 1 MPI thread 74: Using 2 OpenMP threads 74: 74: 74: NOTE: The number of threads is not equal to the number of (logical) cpus 74: and the -pin option is set to auto: will not pin threads to cpus. 74: This can lead to significant performance degradation. 74: Consider using -pin on (and -pinoffset in case you run multiple jobs). 74: starting md rerun '30 atom system in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_8_sim1.trr' 74: 74: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 74: 74: Core t (s) Wall t (s) (%) 74: Time: 0.022 0.012 187.6 74: (ns/day) (hour/ns) 74: Performance: 125.529 0.191 74: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_8_sim1.edr as double precision energy file 74: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_8_sim2.edr as double precision energy file 74: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 74: 74: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/8 (233 ms) 74: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/9 74: 74: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_9_input.mdp]: 74: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 74: that with the Verlet scheme, nstlist has no effect on the accuracy of 74: your simulation. 74: 74: 74: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_9_input.mdp]: 74: Setting nstcalcenergy (100) equal to nstenergy (4) 74: 74: Generating 1-4 interactions: fudge = 0.5 74: Number of degrees of freedom in T-Coupling group System is 79.00 74: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 74: 74: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_9_input.mdp]: 74: NVE simulation: will use the initial temperature of 294.908 K for 74: determining the Verlet buffer size 74: 74: 74: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_9_input.mdp]: 74: You are using a plain Coulomb cut-off, which might produce artifacts. 74: You might want to consider using PME electrostatics. 74: 74: 74: 74: There were 4 NOTEs 74: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_9_sim.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 74: Can not increase nstlist because an NVE ensemble is used 74: Using 1 MPI thread 74: Using 2 OpenMP threads 74: 74: 74: NOTE: The number of threads is not equal to the number of (logical) cpus 74: and the -pin option is set to auto: will not pin threads to cpus. 74: This can lead to significant performance degradation. 74: Consider using -pin on (and -pinoffset in case you run multiple jobs). 74: starting mdrun '30 atom system in water' 74: 16 steps, 0.0 ps. 74: Generated 2485 of the 2485 non-bonded parameter combinations 74: 74: Generated 2485 of the 2485 1-4 parameter combinations 74: 74: Excluding 3 bonded neighbours molecule type 'nonanol' 74: 74: turning H bonds into constraints... 74: 74: Excluding 2 bonded neighbours molecule type 'SOL' 74: 74: turning H bonds into constraints... 74: 74: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/nonanol_vacuo.gro' 74: 74: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 294.908 K 74: 74: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 74: 74: Set rlist, assuming 4x4 atom pair-list, to 0.757 nm, buffer size 0.057 nm 74: 74: Note that mdrun will redetermine rlist based on the actual pair-list setup 74: 74: This run will generate roughly 0 Mb of data 74: 74: Writing final coordinates. 74: 74: Core t (s) Wall t (s) (%) 74: Time: 0.072 0.036 197.3 74: (ns/day) (hour/ns) 74: Performance: 40.435 0.594 74: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_9_sim.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 74: Can not increase nstlist because an NVE ensemble is used 74: Using 1 MPI thread 74: Using 2 OpenMP threads 74: 74: 74: NOTE: The number of threads is not equal to the number of (logical) cpus 74: and the -pin option is set to auto: will not pin threads to cpus. 74: This can lead to significant performance degradation. 74: Consider using -pin on (and -pinoffset in case you run multiple jobs). 74: starting md rerun '30 atom system in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_9_sim1.trr' 74: 74: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 74: 74: Core t (s) Wall t (s) (%) 74: Time: 0.018 0.010 184.9 74: (ns/day) (hour/ns) 74: Performance: 154.254 0.156 74: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_9_sim1.edr as double precision energy file 74: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_9_sim2.edr as double precision energy file 74: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 74: 74: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/9 (229 ms) 74: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/10 74: 74: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_10_input.mdp]: 74: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 74: that with the Verlet scheme, nstlist has no effect on the accuracy of 74: your simulation. 74: 74: 74: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_10_input.mdp]: 74: Setting nstcalcenergy (100) equal to nstenergy (4) 74: 74: Generating 1-4 interactions: fudge = 0.5 74: Number of degrees of freedom in T-Coupling group System is 79.00 74: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 74: 74: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_10_input.mdp]: 74: NVE simulation: will use the initial temperature of 294.908 K for 74: determining the Verlet buffer size 74: 74: 74: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_10_input.mdp]: 74: You are using a plain Coulomb cut-off, which might produce artifacts. 74: You might want to consider using PME electrostatics. 74: 74: 74: 74: There were 4 NOTEs 74: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_10_sim.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 74: Can not increase nstlist because an NVE ensemble is used 74: Using 1 MPI thread 74: Using 2 OpenMP threads 74: 74: 74: NOTE: The number of threads is not equal to the number of (logical) cpus 74: and the -pin option is set to auto: will not pin threads to cpus. 74: This can lead to significant performance degradation. 74: Consider using -pin on (and -pinoffset in case you run multiple jobs). 74: starting mdrun '30 atom system in water' 74: 16 steps, 0.0 ps. 74: Generated 2485 of the 2485 non-bonded parameter combinations 74: 74: Generated 2485 of the 2485 1-4 parameter combinations 74: 74: Excluding 3 bonded neighbours molecule type 'nonanol' 74: 74: turning H bonds into constraints... 74: 74: Excluding 2 bonded neighbours molecule type 'SOL' 74: 74: turning H bonds into constraints... 74: 74: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/nonanol_vacuo.gro' 74: 74: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 294.908 K 74: 74: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 74: 74: Set rlist, assuming 4x4 atom pair-list, to 0.757 nm, buffer size 0.057 nm 74: 74: Note that mdrun will redetermine rlist based on the actual pair-list setup 74: 74: This run will generate roughly 0 Mb of data 74: 74: Writing final coordinates. 74: 74: Core t (s) Wall t (s) (%) 74: Time: 0.073 0.037 197.5 74: (ns/day) (hour/ns) 74: Performance: 39.863 0.602 74: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_10_sim.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 74: Can not increase nstlist because an NVE ensemble is used 74: Using 1 MPI thread 74: Using 2 OpenMP threads 74: 74: 74: NOTE: The number of threads is not equal to the number of (logical) cpus 74: and the -pin option is set to auto: will not pin threads to cpus. 74: This can lead to significant performance degradation. 74: Consider using -pin on (and -pinoffset in case you run multiple jobs). 74: starting md rerun '30 atom system in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_10_sim1.trr' 74: 74: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 74: 74: Core t (s) Wall t (s) (%) 74: Time: 0.019 0.010 186.6 74: (ns/day) (hour/ns) 74: Performance: 143.283 0.168 74: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_10_sim1.edr as double precision energy file 74: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_10_sim2.edr as double precision energy file 74: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 74: 74: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/10 (232 ms) 74: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/11 74: 74: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_11_input.mdp]: 74: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 74: that with the Verlet scheme, nstlist has no effect on the accuracy of 74: your simulation. 74: 74: 74: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_11_input.mdp]: 74: Setting nstcalcenergy (100) equal to nstenergy (4) 74: 74: Generating 1-4 interactions: fudge = 0.5 74: Number of degrees of freedom in T-Coupling group System is 79.00 74: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 74: 74: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_11_input.mdp]: 74: NVE simulation: will use the initial temperature of 294.908 K for 74: determining the Verlet buffer size 74: 74: 74: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_11_input.mdp]: 74: You are using a plain Coulomb cut-off, which might produce artifacts. 74: You might want to consider using PME electrostatics. 74: 74: 74: 74: There were 4 NOTEs 74: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_11_sim.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 74: Can not increase nstlist because an NVE ensemble is used 74: Using 1 MPI thread 74: Using 2 OpenMP threads 74: 74: 74: NOTE: The number of threads is not equal to the number of (logical) cpus 74: and the -pin option is set to auto: will not pin threads to cpus. 74: This can lead to significant performance degradation. 74: Consider using -pin on (and -pinoffset in case you run multiple jobs). 74: starting mdrun '30 atom system in water' 74: 16 steps, 0.0 ps. 74: Generated 2485 of the 2485 non-bonded parameter combinations 74: 74: Generated 2485 of the 2485 1-4 parameter combinations 74: 74: Excluding 3 bonded neighbours molecule type 'nonanol' 74: 74: turning H bonds into constraints... 74: 74: Excluding 2 bonded neighbours molecule type 'SOL' 74: 74: turning H bonds into constraints... 74: 74: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/nonanol_vacuo.gro' 74: 74: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 294.908 K 74: 74: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 74: 74: Set rlist, assuming 4x4 atom pair-list, to 0.757 nm, buffer size 0.057 nm 74: 74: Note that mdrun will redetermine rlist based on the actual pair-list setup 74: 74: This run will generate roughly 0 Mb of data 74: 74: Writing final coordinates. 74: 74: Core t (s) Wall t (s) (%) 74: Time: 0.088 0.044 199.1 74: (ns/day) (hour/ns) 74: Performance: 33.205 0.723 74: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_11_sim.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 74: Can not increase nstlist because an NVE ensemble is used 74: Using 1 MPI thread 74: Using 2 OpenMP threads 74: 74: 74: NOTE: The number of threads is not equal to the number of (logical) cpus 74: and the -pin option is set to auto: will not pin threads to cpus. 74: This can lead to significant performance degradation. 74: Consider using -pin on (and -pinoffset in case you run multiple jobs). 74: starting md rerun '30 atom system in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_11_sim1.trr' 74: 74: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 74: 74: NOTE: 12 % of the run time was spent in pair search, 74: you might want to increase nstlist (this has no effect on accuracy) 74: 74: Core t (s) Wall t (s) (%) 74: Time: 0.021 0.011 187.5 74: (ns/day) (hour/ns) 74: Performance: 129.229 0.186 74: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_11_sim1.edr as double precision energy file 74: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_11_sim2.edr as double precision energy file 74: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 74: 74: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/11 (240 ms) 74: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/12 74: 74: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_12_input.mdp]: 74: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 74: that with the Verlet scheme, nstlist has no effect on the accuracy of 74: your simulation. 74: 74: 74: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_12_input.mdp]: 74: Setting nstcalcenergy (100) equal to nstenergy (4) 74: 74: Generating 1-4 interactions: fudge = 0.5 74: Number of degrees of freedom in T-Coupling group System is 79.00 74: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 74: 74: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_12_input.mdp]: 74: NVE simulation: will use the initial temperature of 294.908 K for 74: determining the Verlet buffer size 74: 74: 74: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_12_input.mdp]: 74: You are using a plain Coulomb cut-off, which might produce artifacts. 74: You might want to consider using PME electrostatics. 74: 74: 74: 74: There were 4 NOTEs 74: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_12_sim.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 74: Can not increase nstlist because an NVE ensemble is used 74: Using 1 MPI thread 74: Using 2 OpenMP threads 74: 74: 74: NOTE: The number of threads is not equal to the number of (logical) cpus 74: and the -pin option is set to auto: will not pin threads to cpus. 74: This can lead to significant performance degradation. 74: Consider using -pin on (and -pinoffset in case you run multiple jobs). 74: starting mdrun '30 atom system in water' 74: 16 steps, 0.0 ps. 74: Generated 2485 of the 2485 non-bonded parameter combinations 74: 74: Generated 2485 of the 2485 1-4 parameter combinations 74: 74: Excluding 3 bonded neighbours molecule type 'nonanol' 74: 74: turning H bonds into constraints... 74: 74: Excluding 2 bonded neighbours molecule type 'SOL' 74: 74: turning H bonds into constraints... 74: 74: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/nonanol_vacuo.gro' 74: 74: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 294.908 K 74: 74: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 74: 74: Set rlist, assuming 4x4 atom pair-list, to 0.757 nm, buffer size 0.057 nm 74: 74: Note that mdrun will redetermine rlist based on the actual pair-list setup 74: 74: This run will generate roughly 0 Mb of data 74: 74: Writing final coordinates. 74: 74: Core t (s) Wall t (s) (%) 74: Time: 0.092 0.046 199.1 74: (ns/day) (hour/ns) 74: Performance: 31.733 0.756 74: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_12_sim.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 74: Can not increase nstlist because an NVE ensemble is used 74: Using 1 MPI thread 74: Using 2 OpenMP threads 74: 74: 74: NOTE: The number of threads is not equal to the number of (logical) cpus 74: and the -pin option is set to auto: will not pin threads to cpus. 74: This can lead to significant performance degradation. 74: Consider using -pin on (and -pinoffset in case you run multiple jobs). 74: starting md rerun '30 atom system in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_12_sim1.trr' 74: 74: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 74: 74: Core t (s) Wall t (s) (%) 74: Time: 0.025 0.013 189.4 74: (ns/day) (hour/ns) 74: Performance: 111.637 0.215 74: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_12_sim1.edr as double precision energy file 74: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_12_sim2.edr as double precision energy file 74: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 74: 74: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/12 (244 ms) 74: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/13 74: 74: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_13_input.mdp]: 74: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 74: that with the Verlet scheme, nstlist has no effect on the accuracy of 74: your simulation. 74: 74: 74: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_13_input.mdp]: 74: Setting nstcalcenergy (100) equal to nstenergy (4) 74: 74: Generating 1-4 interactions: fudge = 0.5 74: Number of degrees of freedom in T-Coupling group System is 79.00 74: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 74: 74: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_13_input.mdp]: 74: NVE simulation: will use the initial temperature of 294.908 K for 74: determining the Verlet buffer size 74: 74: 74: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_13_input.mdp]: 74: You are using a plain Coulomb cut-off, which might produce artifacts. 74: You might want to consider using PME electrostatics. 74: 74: 74: 74: There were 4 NOTEs 74: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_13_sim.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 74: Can not increase nstlist because an NVE ensemble is used 74: Using 1 MPI thread 74: Using 2 OpenMP threads 74: 74: 74: NOTE: The number of threads is not equal to the number of (logical) cpus 74: and the -pin option is set to auto: will not pin threads to cpus. 74: This can lead to significant performance degradation. 74: Consider using -pin on (and -pinoffset in case you run multiple jobs). 74: starting mdrun '30 atom system in water' 74: 16 steps, 0.0 ps. 74: Generated 2485 of the 2485 non-bonded parameter combinations 74: 74: Generated 2485 of the 2485 1-4 parameter combinations 74: 74: Excluding 3 bonded neighbours molecule type 'nonanol' 74: 74: turning H bonds into constraints... 74: 74: Excluding 2 bonded neighbours molecule type 'SOL' 74: 74: turning H bonds into constraints... 74: 74: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/nonanol_vacuo.gro' 74: 74: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 294.908 K 74: 74: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 74: 74: Set rlist, assuming 4x4 atom pair-list, to 0.757 nm, buffer size 0.057 nm 74: 74: Note that mdrun will redetermine rlist based on the actual pair-list setup 74: 74: This run will generate roughly 0 Mb of data 74: 74: Writing final coordinates. 74: 74: Core t (s) Wall t (s) (%) 74: Time: 0.126 0.063 199.1 74: (ns/day) (hour/ns) 74: Performance: 23.185 1.035 74: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_13_sim.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 74: Can not increase nstlist because an NVE ensemble is used 74: Using 1 MPI thread 74: Using 2 OpenMP threads 74: 74: 74: NOTE: The number of threads is not equal to the number of (logical) cpus 74: and the -pin option is set to auto: will not pin threads to cpus. 74: This can lead to significant performance degradation. 74: Consider using -pin on (and -pinoffset in case you run multiple jobs). 74: starting md rerun '30 atom system in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_13_sim1.trr' 74: 74: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 74: 74: NOTE: 26 % of the run time was spent in pair search, 74: you might want to increase nstlist (this has no effect on accuracy) 74: 74: Core t (s) Wall t (s) (%) 74: Time: 0.023 0.012 190.0 74: (ns/day) (hour/ns) 74: Performance: 119.057 0.202 74: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_13_sim1.edr as double precision energy file 74: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_13_sim2.edr as double precision energy file 74: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 74: 74: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/13 (264 ms) 74: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/14 74: 74: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_14_input.mdp]: 74: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 74: that with the Verlet scheme, nstlist has no effect on the accuracy of 74: your simulation. 74: 74: 74: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_14_input.mdp]: 74: Setting nstcalcenergy (100) equal to nstenergy (4) 74: 74: Generating 1-4 interactions: fudge = 0.5 74: Number of degrees of freedom in T-Coupling group System is 79.00 74: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 74: 74: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_14_input.mdp]: 74: NVE simulation: will use the initial temperature of 294.908 K for 74: determining the Verlet buffer size 74: 74: 74: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_14_input.mdp]: 74: You are using a plain Coulomb cut-off, which might produce artifacts. 74: You might want to consider using PME electrostatics. 74: 74: 74: 74: There were 4 NOTEs 74: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_14_sim.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 74: Can not increase nstlist because an NVE ensemble is used 74: Using 1 MPI thread 74: Using 2 OpenMP threads 74: 74: 74: NOTE: The number of threads is not equal to the number of (logical) cpus 74: and the -pin option is set to auto: will not pin threads to cpus. 74: This can lead to significant performance degradation. 74: Consider using -pin on (and -pinoffset in case you run multiple jobs). 74: starting mdrun '30 atom system in water' 74: 16 steps, 0.0 ps. 74: Generated 2485 of the 2485 non-bonded parameter combinations 74: 74: Generated 2485 of the 2485 1-4 parameter combinations 74: 74: Excluding 3 bonded neighbours molecule type 'nonanol' 74: 74: turning H bonds into constraints... 74: 74: Excluding 2 bonded neighbours molecule type 'SOL' 74: 74: turning H bonds into constraints... 74: 74: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/nonanol_vacuo.gro' 74: 74: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 294.908 K 74: 74: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 74: 74: Set rlist, assuming 4x4 atom pair-list, to 0.757 nm, buffer size 0.057 nm 74: 74: Note that mdrun will redetermine rlist based on the actual pair-list setup 74: 74: This run will generate roughly 0 Mb of data 74: 74: Writing final coordinates. 74: 74: Core t (s) Wall t (s) (%) 74: Time: 0.093 0.047 199.1 74: (ns/day) (hour/ns) 74: Performance: 31.433 0.764 74: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_14_sim.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 74: Can not increase nstlist because an NVE ensemble is used 74: Using 1 MPI thread 74: Using 2 OpenMP threads 74: 74: 74: NOTE: The number of threads is not equal to the number of (logical) cpus 74: and the -pin option is set to auto: will not pin threads to cpus. 74: This can lead to significant performance degradation. 74: Consider using -pin on (and -pinoffset in case you run multiple jobs). 74: starting md rerun '30 atom system in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_14_sim1.trr' 74: 74: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 74: 74: Core t (s) Wall t (s) (%) 74: Time: 0.020 0.011 186.4 74: (ns/day) (hour/ns) 74: Performance: 139.487 0.172 74: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_14_sim1.edr as double precision energy file 74: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_14_sim2.edr as double precision energy file 74: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 74: 74: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/14 (241 ms) 74: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/15 74: 74: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_15_input.mdp]: 74: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 74: that with the Verlet scheme, nstlist has no effect on the accuracy of 74: your simulation. 74: 74: 74: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_15_input.mdp]: 74: Setting nstcalcenergy (100) equal to nstenergy (4) 74: 74: Generating 1-4 interactions: fudge = 0.5 74: Number of degrees of freedom in T-Coupling group System is 79.00 74: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 74: 74: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_15_input.mdp]: 74: NVE simulation: will use the initial temperature of 294.908 K for 74: determining the Verlet buffer size 74: 74: 74: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_15_input.mdp]: 74: You are using a plain Coulomb cut-off, which might produce artifacts. 74: You might want to consider using PME electrostatics. 74: 74: 74: 74: There were 4 NOTEs 74: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_15_sim.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 74: Can not increase nstlist because an NVE ensemble is used 74: Using 1 MPI thread 74: Using 2 OpenMP threads 74: 74: 74: NOTE: The number of threads is not equal to the number of (logical) cpus 74: and the -pin option is set to auto: will not pin threads to cpus. 74: This can lead to significant performance degradation. 74: Consider using -pin on (and -pinoffset in case you run multiple jobs). 74: starting mdrun '30 atom system in water' 74: 16 steps, 0.0 ps. 74: Generated 2485 of the 2485 non-bonded parameter combinations 74: 74: Generated 2485 of the 2485 1-4 parameter combinations 74: 74: Excluding 3 bonded neighbours molecule type 'nonanol' 74: 74: turning H bonds into constraints... 74: 74: Excluding 2 bonded neighbours molecule type 'SOL' 74: 74: turning H bonds into constraints... 74: 74: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/nonanol_vacuo.gro' 74: 74: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 294.908 K 74: 74: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 74: 74: Set rlist, assuming 4x4 atom pair-list, to 0.757 nm, buffer size 0.057 nm 74: 74: Note that mdrun will redetermine rlist based on the actual pair-list setup 74: 74: This run will generate roughly 0 Mb of data 74: 74: Writing final coordinates. 74: 74: Core t (s) Wall t (s) (%) 74: Time: 0.096 0.048 198.7 74: (ns/day) (hour/ns) 74: Performance: 30.358 0.791 74: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_15_sim.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 74: Can not increase nstlist because an NVE ensemble is used 74: Using 1 MPI thread 74: Using 2 OpenMP threads 74: 74: 74: NOTE: The number of threads is not equal to the number of (logical) cpus 74: and the -pin option is set to auto: will not pin threads to cpus. 74: This can lead to significant performance degradation. 74: Consider using -pin on (and -pinoffset in case you run multiple jobs). 74: starting md rerun '30 atom system in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_15_sim1.trr' 74: 74: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 74: 74: Core t (s) Wall t (s) (%) 74: Time: 0.022 0.012 184.8 74: (ns/day) (hour/ns) 74: Performance: 122.440 0.196 74: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_15_sim1.edr as double precision energy file 74: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_15_sim2.edr as double precision energy file 74: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 74: 74: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/15 (249 ms) 74: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/16 74: 74: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_16_input.mdp]: 74: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 74: that with the Verlet scheme, nstlist has no effect on the accuracy of 74: your simulation. 74: 74: 74: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_16_input.mdp]: 74: Setting nstcalcenergy (100) equal to nstenergy (4) 74: 74: Generating 1-4 interactions: fudge = 0.5 74: Number of degrees of freedom in T-Coupling group System is 79.00 74: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 74: 74: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_16_input.mdp]: 74: NVE simulation: will use the initial temperature of 294.908 K for 74: determining the Verlet buffer size 74: 74: 74: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_16_input.mdp]: 74: You are using a plain Coulomb cut-off, which might produce artifacts. 74: You might want to consider using PME electrostatics. 74: 74: 74: 74: There were 4 NOTEs 74: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_16_sim.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 74: Can not increase nstlist because an NVE ensemble is used 74: Using 1 MPI thread 74: Using 2 OpenMP threads 74: 74: 74: NOTE: The number of threads is not equal to the number of (logical) cpus 74: and the -pin option is set to auto: will not pin threads to cpus. 74: This can lead to significant performance degradation. 74: Consider using -pin on (and -pinoffset in case you run multiple jobs). 74: starting mdrun '30 atom system in water' 74: 16 steps, 0.0 ps. 74: Generated 2485 of the 2485 non-bonded parameter combinations 74: 74: Generated 2485 of the 2485 1-4 parameter combinations 74: 74: Excluding 3 bonded neighbours molecule type 'nonanol' 74: 74: turning H bonds into constraints... 74: 74: Excluding 2 bonded neighbours molecule type 'SOL' 74: 74: turning H bonds into constraints... 74: 74: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/nonanol_vacuo.gro' 74: 74: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 294.908 K 74: 74: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 74: 74: Set rlist, assuming 4x4 atom pair-list, to 0.757 nm, buffer size 0.057 nm 74: 74: Note that mdrun will redetermine rlist based on the actual pair-list setup 74: 74: This run will generate roughly 0 Mb of data 74: 74: Writing final coordinates. 74: 74: Core t (s) Wall t (s) (%) 74: Time: 0.112 0.056 199.3 74: (ns/day) (hour/ns) 74: Performance: 26.134 0.918 74: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_16_sim.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 74: Can not increase nstlist because an NVE ensemble is used 74: Using 1 MPI thread 74: Using 2 OpenMP threads 74: 74: 74: NOTE: The number of threads is not equal to the number of (logical) cpus 74: and the -pin option is set to auto: will not pin threads to cpus. 74: This can lead to significant performance degradation. 74: Consider using -pin on (and -pinoffset in case you run multiple jobs). 74: starting md rerun '30 atom system in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_16_sim1.trr' 74: 74: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 74: 74: Core t (s) Wall t (s) (%) 74: Time: 0.022 0.012 186.8 74: (ns/day) (hour/ns) 74: Performance: 125.968 0.191 74: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_16_sim1.edr as double precision energy file 74: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_16_sim2.edr as double precision energy file 74: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 74: 74: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/16 (260 ms) 74: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/17 74: 74: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_17_input.mdp]: 74: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 74: that with the Verlet scheme, nstlist has no effect on the accuracy of 74: your simulation. 74: 74: 74: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_17_input.mdp]: 74: Setting nstcalcenergy (100) equal to nstenergy (4) 74: 74: Generating 1-4 interactions: fudge = 0.5 74: Number of degrees of freedom in T-Coupling group System is 79.00 74: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 74: 74: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_17_input.mdp]: 74: NVE simulation: will use the initial temperature of 294.908 K for 74: determining the Verlet buffer size 74: 74: 74: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_17_input.mdp]: 74: You are using a plain Coulomb cut-off, which might produce artifacts. 74: You might want to consider using PME electrostatics. 74: 74: 74: 74: There were 4 NOTEs 74: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_17_sim.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 74: Can not increase nstlist because an NVE ensemble is used 74: Using 1 MPI thread 74: Using 2 OpenMP threads 74: 74: 74: NOTE: The number of threads is not equal to the number of (logical) cpus 74: and the -pin option is set to auto: will not pin threads to cpus. 74: This can lead to significant performance degradation. 74: Consider using -pin on (and -pinoffset in case you run multiple jobs). 74: starting mdrun '30 atom system in water' 74: 16 steps, 0.0 ps. 74: Generated 2485 of the 2485 non-bonded parameter combinations 74: 74: Generated 2485 of the 2485 1-4 parameter combinations 74: 74: Excluding 3 bonded neighbours molecule type 'nonanol' 74: 74: turning H bonds into constraints... 74: 74: Excluding 2 bonded neighbours molecule type 'SOL' 74: 74: turning H bonds into constraints... 74: 74: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/nonanol_vacuo.gro' 74: 74: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 294.908 K 74: 74: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 74: 74: Set rlist, assuming 4x4 atom pair-list, to 0.757 nm, buffer size 0.057 nm 74: 74: Note that mdrun will redetermine rlist based on the actual pair-list setup 74: 74: This run will generate roughly 0 Mb of data 74: 74: Writing final coordinates. 74: 74: Core t (s) Wall t (s) (%) 74: Time: 0.085 0.043 199.0 74: (ns/day) (hour/ns) 74: Performance: 34.201 0.702 74: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_17_sim.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 74: Can not increase nstlist because an NVE ensemble is used 74: Using 1 MPI thread 74: Using 2 OpenMP threads 74: 74: 74: NOTE: The number of threads is not equal to the number of (logical) cpus 74: and the -pin option is set to auto: will not pin threads to cpus. 74: This can lead to significant performance degradation. 74: Consider using -pin on (and -pinoffset in case you run multiple jobs). 74: starting md rerun '30 atom system in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_17_sim1.trr' 74: 74: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 74: 74: Core t (s) Wall t (s) (%) 74: Time: 0.019 0.010 187.8 74: (ns/day) (hour/ns) 74: Performance: 146.719 0.164 74: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_17_sim1.edr as double precision energy file 74: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_17_sim2.edr as double precision energy file 74: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 74: 74: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/17 (239 ms) 74: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/18 74: 74: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_18_input.mdp]: 74: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 74: that with the Verlet scheme, nstlist has no effect on the accuracy of 74: your simulation. 74: 74: 74: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_18_input.mdp]: 74: Setting nstcalcenergy (100) equal to nstenergy (4) 74: 74: Generating 1-4 interactions: fudge = 0.5 74: Number of degrees of freedom in T-Coupling group System is 79.00 74: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 74: 74: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_18_input.mdp]: 74: NVE simulation: will use the initial temperature of 294.908 K for 74: determining the Verlet buffer size 74: 74: 74: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_18_input.mdp]: 74: You are using a plain Coulomb cut-off, which might produce artifacts. 74: You might want to consider using PME electrostatics. 74: 74: 74: 74: There were 4 NOTEs 74: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_18_sim.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 74: Can not increase nstlist because an NVE ensemble is used 74: Using 1 MPI thread 74: Using 2 OpenMP threads 74: 74: 74: NOTE: The number of threads is not equal to the number of (logical) cpus 74: and the -pin option is set to auto: will not pin threads to cpus. 74: This can lead to significant performance degradation. 74: Consider using -pin on (and -pinoffset in case you run multiple jobs). 74: starting mdrun '30 atom system in water' 74: 16 steps, 0.0 ps. 74: Generated 2485 of the 2485 non-bonded parameter combinations 74: 74: Generated 2485 of the 2485 1-4 parameter combinations 74: 74: Excluding 3 bonded neighbours molecule type 'nonanol' 74: 74: turning H bonds into constraints... 74: 74: Excluding 2 bonded neighbours molecule type 'SOL' 74: 74: turning H bonds into constraints... 74: 74: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/nonanol_vacuo.gro' 74: 74: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 294.908 K 74: 74: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 74: 74: Set rlist, assuming 4x4 atom pair-list, to 0.757 nm, buffer size 0.057 nm 74: 74: Note that mdrun will redetermine rlist based on the actual pair-list setup 74: 74: This run will generate roughly 0 Mb of data 74: 74: Writing final coordinates. 74: 74: Core t (s) Wall t (s) (%) 74: Time: 0.093 0.047 199.1 74: (ns/day) (hour/ns) 74: Performance: 31.355 0.765 74: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_18_sim.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 74: Can not increase nstlist because an NVE ensemble is used 74: Using 1 MPI thread 74: Using 2 OpenMP threads 74: 74: 74: NOTE: The number of threads is not equal to the number of (logical) cpus 74: and the -pin option is set to auto: will not pin threads to cpus. 74: This can lead to significant performance degradation. 74: Consider using -pin on (and -pinoffset in case you run multiple jobs). 74: starting md rerun '30 atom system in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_18_sim1.trr' 74: 74: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 74: 74: Core t (s) Wall t (s) (%) 74: Time: 0.015 0.008 183.0 74: (ns/day) (hour/ns) 74: Performance: 177.477 0.135 74: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_18_sim1.edr as double precision energy file 74: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_18_sim2.edr as double precision energy file 74: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 74: 74: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/18 (240 ms) 74: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/19 74: 74: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_19_input.mdp]: 74: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 74: that with the Verlet scheme, nstlist has no effect on the accuracy of 74: your simulation. 74: 74: 74: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_19_input.mdp]: 74: Setting nstcalcenergy (100) equal to nstenergy (4) 74: 74: Generating 1-4 interactions: fudge = 0.5 74: Number of degrees of freedom in T-Coupling group System is 79.00 74: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 74: 74: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_19_input.mdp]: 74: NVE simulation: will use the initial temperature of 294.908 K for 74: determining the Verlet buffer size 74: 74: 74: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_19_input.mdp]: 74: You are using a plain Coulomb cut-off, which might produce artifacts. 74: You might want to consider using PME electrostatics. 74: 74: 74: 74: There were 4 NOTEs 74: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_19_sim.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 74: Can not increase nstlist because an NVE ensemble is used 74: Using 1 MPI thread 74: Using 2 OpenMP threads 74: 74: 74: NOTE: The number of threads is not equal to the number of (logical) cpus 74: and the -pin option is set to auto: will not pin threads to cpus. 74: This can lead to significant performance degradation. 74: Consider using -pin on (and -pinoffset in case you run multiple jobs). 74: starting mdrun '30 atom system in water' 74: 16 steps, 0.0 ps. 74: Generated 2485 of the 2485 non-bonded parameter combinations 74: 74: Generated 2485 of the 2485 1-4 parameter combinations 74: 74: Excluding 3 bonded neighbours molecule type 'nonanol' 74: 74: turning H bonds into constraints... 74: 74: Excluding 2 bonded neighbours molecule type 'SOL' 74: 74: turning H bonds into constraints... 74: 74: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/nonanol_vacuo.gro' 74: 74: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 294.908 K 74: 74: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 74: 74: Set rlist, assuming 4x4 atom pair-list, to 0.757 nm, buffer size 0.057 nm 74: 74: Note that mdrun will redetermine rlist based on the actual pair-list setup 74: 74: This run will generate roughly 0 Mb of data 74: 74: Writing final coordinates. 74: 74: Core t (s) Wall t (s) (%) 74: Time: 0.078 0.039 199.0 74: (ns/day) (hour/ns) 74: Performance: 37.615 0.638 74: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_19_sim.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 74: Can not increase nstlist because an NVE ensemble is used 74: Using 1 MPI thread 74: Using 2 OpenMP threads 74: 74: 74: NOTE: The number of threads is not equal to the number of (logical) cpus 74: and the -pin option is set to auto: will not pin threads to cpus. 74: This can lead to significant performance degradation. 74: Consider using -pin on (and -pinoffset in case you run multiple jobs). 74: starting md rerun '30 atom system in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_19_sim1.trr' 74: 74: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 74: 74: Core t (s) Wall t (s) (%) 74: Time: 0.021 0.011 187.7 74: (ns/day) (hour/ns) 74: Performance: 129.411 0.185 74: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_19_sim1.edr as double precision energy file 74: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_19_sim2.edr as double precision energy file 74: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 74: 74: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/19 (235 ms) 74: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/20 74: 74: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_20_input.mdp]: 74: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 74: that with the Verlet scheme, nstlist has no effect on the accuracy of 74: your simulation. 74: 74: 74: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_20_input.mdp]: 74: Setting nstcalcenergy (100) equal to nstenergy (4) 74: 74: Generating 1-4 interactions: fudge = 0.5 74: Number of degrees of freedom in T-Coupling group System is 79.00 74: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 74: 74: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_20_input.mdp]: 74: NVE simulation: will use the initial temperature of 294.908 K for 74: determining the Verlet buffer size 74: 74: 74: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_20_input.mdp]: 74: You are using a plain Coulomb cut-off, which might produce artifacts. 74: You might want to consider using PME electrostatics. 74: 74: 74: 74: There were 4 NOTEs 74: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_20_sim.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 74: Can not increase nstlist because an NVE ensemble is used 74: Using 1 MPI thread 74: Using 2 OpenMP threads 74: 74: 74: NOTE: The number of threads is not equal to the number of (logical) cpus 74: and the -pin option is set to auto: will not pin threads to cpus. 74: This can lead to significant performance degradation. 74: Consider using -pin on (and -pinoffset in case you run multiple jobs). 74: starting mdrun '30 atom system in water' 74: 16 steps, 0.0 ps. 74: Generated 2485 of the 2485 non-bonded parameter combinations 74: 74: Generated 2485 of the 2485 1-4 parameter combinations 74: 74: Excluding 3 bonded neighbours molecule type 'nonanol' 74: 74: turning H bonds into constraints... 74: 74: Excluding 2 bonded neighbours molecule type 'SOL' 74: 74: turning H bonds into constraints... 74: 74: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/nonanol_vacuo.gro' 74: 74: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 294.908 K 74: 74: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 74: 74: Set rlist, assuming 4x4 atom pair-list, to 0.757 nm, buffer size 0.057 nm 74: 74: Note that mdrun will redetermine rlist based on the actual pair-list setup 74: 74: This run will generate roughly 0 Mb of data 74: 74: Writing final coordinates. 74: 74: Core t (s) Wall t (s) (%) 74: Time: 0.084 0.042 199.1 74: (ns/day) (hour/ns) 74: Performance: 34.902 0.688 74: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_20_sim.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 74: Can not increase nstlist because an NVE ensemble is used 74: Using 1 MPI thread 74: Using 2 OpenMP threads 74: 74: 74: NOTE: The number of threads is not equal to the number of (logical) cpus 74: and the -pin option is set to auto: will not pin threads to cpus. 74: This can lead to significant performance degradation. 74: Consider using -pin on (and -pinoffset in case you run multiple jobs). 74: starting md rerun '30 atom system in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_20_sim1.trr' 74: 74: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 74: 74: Core t (s) Wall t (s) (%) 74: Time: 0.020 0.011 187.4 74: (ns/day) (hour/ns) 74: Performance: 135.062 0.178 74: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_20_sim1.edr as double precision energy file 74: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_20_sim2.edr as double precision energy file 74: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 74: 74: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/20 (235 ms) 74: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/21 74: 74: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_21_input.mdp]: 74: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 74: that with the Verlet scheme, nstlist has no effect on the accuracy of 74: your simulation. 74: 74: 74: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_21_input.mdp]: 74: Setting nstcalcenergy (100) equal to nstenergy (4) 74: 74: Generating 1-4 interactions: fudge = 0.5 74: Number of degrees of freedom in T-Coupling group System is 79.00 74: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 74: 74: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_21_input.mdp]: 74: NVE simulation: will use the initial temperature of 294.908 K for 74: determining the Verlet buffer size 74: 74: 74: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_21_input.mdp]: 74: You are using a plain Coulomb cut-off, which might produce artifacts. 74: You might want to consider using PME electrostatics. 74: 74: 74: 74: There were 4 NOTEs 74: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_21_sim.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 74: Can not increase nstlist because an NVE ensemble is used 74: Using 1 MPI thread 74: Using 2 OpenMP threads 74: 74: 74: NOTE: The number of threads is not equal to the number of (logical) cpus 74: and the -pin option is set to auto: will not pin threads to cpus. 74: This can lead to significant performance degradation. 74: Consider using -pin on (and -pinoffset in case you run multiple jobs). 74: starting mdrun '30 atom system in water' 74: 16 steps, 0.0 ps. 74: Generated 2485 of the 2485 non-bonded parameter combinations 74: 74: Generated 2485 of the 2485 1-4 parameter combinations 74: 74: Excluding 3 bonded neighbours molecule type 'nonanol' 74: 74: turning H bonds into constraints... 74: 74: Excluding 2 bonded neighbours molecule type 'SOL' 74: 74: turning H bonds into constraints... 74: 74: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/nonanol_vacuo.gro' 74: 74: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 294.908 K 74: 74: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 74: 74: Set rlist, assuming 4x4 atom pair-list, to 0.757 nm, buffer size 0.057 nm 74: 74: Note that mdrun will redetermine rlist based on the actual pair-list setup 74: 74: This run will generate roughly 0 Mb of data 74: 74: Writing final coordinates. 74: 74: Core t (s) Wall t (s) (%) 74: Time: 0.081 0.041 199.0 74: (ns/day) (hour/ns) 74: Performance: 35.914 0.668 74: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_21_sim.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 74: Can not increase nstlist because an NVE ensemble is used 74: Using 1 MPI thread 74: Using 2 OpenMP threads 74: 74: 74: NOTE: The number of threads is not equal to the number of (logical) cpus 74: and the -pin option is set to auto: will not pin threads to cpus. 74: This can lead to significant performance degradation. 74: Consider using -pin on (and -pinoffset in case you run multiple jobs). 74: starting md rerun '30 atom system in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_21_sim1.trr' 74: 74: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 74: 74: Core t (s) Wall t (s) (%) 74: Time: 0.019 0.010 185.7 74: (ns/day) (hour/ns) 74: Performance: 144.822 0.166 74: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_21_sim1.edr as double precision energy file 74: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_21_sim2.edr as double precision energy file 74: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 74: 74: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/21 (246 ms) 74: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/22 74: 74: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_22_input.mdp]: 74: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 74: that with the Verlet scheme, nstlist has no effect on the accuracy of 74: your simulation. 74: 74: 74: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_22_input.mdp]: 74: Setting nstcalcenergy (100) equal to nstenergy (4) 74: 74: Generating 1-4 interactions: fudge = 0.5 74: Number of degrees of freedom in T-Coupling group System is 79.00 74: 74: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_22_input.mdp]: 74: You are using a plain Coulomb cut-off, which might produce artifacts. 74: You might want to consider using PME electrostatics. 74: 74: 74: 74: There were 3 NOTEs 74: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_22_sim.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 74: Changing nstlist from 8 to 20, rlist from 0.757 to 0.863 74: 74: Using 1 MPI thread 74: Using 2 OpenMP threads 74: 74: 74: NOTE: The number of threads is not equal to the number of (logical) cpus 74: and the -pin option is set to auto: will not pin threads to cpus. 74: This can lead to significant performance degradation. 74: Consider using -pin on (and -pinoffset in case you run multiple jobs). 74: starting mdrun '30 atom system in water' 74: 16 steps, 0.0 ps. 74: Generated 2485 of the 2485 non-bonded parameter combinations 74: 74: Generated 2485 of the 2485 1-4 parameter combinations 74: 74: Excluding 3 bonded neighbours molecule type 'nonanol' 74: 74: turning H bonds into constraints... 74: 74: Excluding 2 bonded neighbours molecule type 'SOL' 74: 74: turning H bonds into constraints... 74: 74: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/nonanol_vacuo.gro' 74: 74: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 74: 74: Calculated rlist for 1x1 atom pair-list as 0.764 nm, buffer size 0.064 nm 74: 74: Set rlist, assuming 4x4 atom pair-list, to 0.757 nm, buffer size 0.057 nm 74: 74: Note that mdrun will redetermine rlist based on the actual pair-list setup 74: 74: This run will generate roughly 0 Mb of data 74: 74: Writing final coordinates. 74: 74: Core t (s) Wall t (s) (%) 74: Time: 0.089 0.045 198.2 74: (ns/day) (hour/ns) 74: Performance: 32.533 0.738 74: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_22_sim.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 74: Changing nstlist from 8 to 20, rlist from 0.757 to 0.863 74: 74: Using 1 MPI thread 74: Using 2 OpenMP threads 74: 74: 74: NOTE: The number of threads is not equal to the number of (logical) cpus 74: and the -pin option is set to auto: will not pin threads to cpus. 74: This can lead to significant performance degradation. 74: Consider using -pin on (and -pinoffset in case you run multiple jobs). 74: starting md rerun '30 atom system in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_22_sim1.trr' 74: 74: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 74: 74: Core t (s) Wall t (s) (%) 74: Time: 0.020 0.010 189.9 74: (ns/day) (hour/ns) 74: Performance: 142.090 0.169 74: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_22_sim1.edr as double precision energy file 74: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_22_sim2.edr as double precision energy file 74: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 74: 74: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/22 (388 ms) 74: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/23 74: 74: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_23_input.mdp]: 74: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 74: that with the Verlet scheme, nstlist has no effect on the accuracy of 74: your simulation. 74: 74: 74: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_23_input.mdp]: 74: Setting nstcalcenergy (100) equal to nstenergy (4) 74: 74: Generating 1-4 interactions: fudge = 0.5 74: Number of degrees of freedom in T-Coupling group System is 79.00 74: 74: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_23_input.mdp]: 74: You are using a plain Coulomb cut-off, which might produce artifacts. 74: You might want to consider using PME electrostatics. 74: 74: 74: 74: There were 3 NOTEs 74: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_23_sim.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 74: Changing nstlist from 8 to 20, rlist from 0.757 to 0.863 74: 74: Using 1 MPI thread 74: Using 2 OpenMP threads 74: 74: 74: NOTE: The number of threads is not equal to the number of (logical) cpus 74: and the -pin option is set to auto: will not pin threads to cpus. 74: This can lead to significant performance degradation. 74: Consider using -pin on (and -pinoffset in case you run multiple jobs). 74: starting mdrun '30 atom system in water' 74: 16 steps, 0.0 ps. 74: Generated 2485 of the 2485 non-bonded parameter combinations 74: 74: Generated 2485 of the 2485 1-4 parameter combinations 74: 74: Excluding 3 bonded neighbours molecule type 'nonanol' 74: 74: turning H bonds into constraints... 74: 74: Excluding 2 bonded neighbours molecule type 'SOL' 74: 74: turning H bonds into constraints... 74: 74: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/nonanol_vacuo.gro' 74: 74: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 74: 74: Calculated rlist for 1x1 atom pair-list as 0.764 nm, buffer size 0.064 nm 74: 74: Set rlist, assuming 4x4 atom pair-list, to 0.757 nm, buffer size 0.057 nm 74: 74: Note that mdrun will redetermine rlist based on the actual pair-list setup 74: 74: This run will generate roughly 0 Mb of data 74: 74: Writing final coordinates. 74: 74: Core t (s) Wall t (s) (%) 74: Time: 0.097 0.049 198.3 74: (ns/day) (hour/ns) 74: Performance: 30.142 0.796 74: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_23_sim.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 74: Changing nstlist from 8 to 20, rlist from 0.757 to 0.863 74: 74: Using 1 MPI thread 74: Using 2 OpenMP threads 74: 74: 74: NOTE: The number of threads is not equal to the number of (logical) cpus 74: and the -pin option is set to auto: will not pin threads to cpus. 74: This can lead to significant performance degradation. 74: Consider using -pin on (and -pinoffset in case you run multiple jobs). 74: starting md rerun '30 atom system in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_23_sim1.trr' 74: 74: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 74: 74: Core t (s) Wall t (s) (%) 74: Time: 0.020 0.011 189.7 74: (ns/day) (hour/ns) 74: Performance: 138.909 0.173 74: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_23_sim1.edr as double precision energy file 74: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_23_sim2.edr as double precision energy file 74: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 74: 74: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/23 (396 ms) 74: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/24 74: 74: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_24_input.mdp]: 74: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 74: that with the Verlet scheme, nstlist has no effect on the accuracy of 74: your simulation. 74: 74: 74: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_24_input.mdp]: 74: Setting nstcalcenergy (100) equal to nstenergy (4) 74: 74: Generating 1-4 interactions: fudge = 0.5 74: Number of degrees of freedom in T-Coupling group System is 79.00 74: 74: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_24_input.mdp]: 74: You are using a plain Coulomb cut-off, which might produce artifacts. 74: You might want to consider using PME electrostatics. 74: 74: 74: 74: There were 3 NOTEs 74: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_24_sim.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 74: Changing nstlist from 8 to 20, rlist from 0.757 to 0.863 74: 74: Using 1 MPI thread 74: Using 2 OpenMP threads 74: 74: 74: NOTE: The number of threads is not equal to the number of (logical) cpus 74: and the -pin option is set to auto: will not pin threads to cpus. 74: This can lead to significant performance degradation. 74: Consider using -pin on (and -pinoffset in case you run multiple jobs). 74: starting mdrun '30 atom system in water' 74: 16 steps, 0.0 ps. 74: Generated 2485 of the 2485 non-bonded parameter combinations 74: 74: Generated 2485 of the 2485 1-4 parameter combinations 74: 74: Excluding 3 bonded neighbours molecule type 'nonanol' 74: 74: turning H bonds into constraints... 74: 74: Excluding 2 bonded neighbours molecule type 'SOL' 74: 74: turning H bonds into constraints... 74: 74: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/nonanol_vacuo.gro' 74: 74: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 74: 74: Calculated rlist for 1x1 atom pair-list as 0.764 nm, buffer size 0.064 nm 74: 74: Set rlist, assuming 4x4 atom pair-list, to 0.757 nm, buffer size 0.057 nm 74: 74: Note that mdrun will redetermine rlist based on the actual pair-list setup 74: 74: This run will generate roughly 0 Mb of data 74: 74: Writing final coordinates. 74: 74: Core t (s) Wall t (s) (%) 74: Time: 0.069 0.035 197.7 74: (ns/day) (hour/ns) 74: Performance: 42.387 0.566 74: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_24_sim.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 74: Changing nstlist from 8 to 20, rlist from 0.757 to 0.863 74: 74: Using 1 MPI thread 74: Using 2 OpenMP threads 74: 74: 74: NOTE: The number of threads is not equal to the number of (logical) cpus 74: and the -pin option is set to auto: will not pin threads to cpus. 74: This can lead to significant performance degradation. 74: Consider using -pin on (and -pinoffset in case you run multiple jobs). 74: starting md rerun '30 atom system in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_24_sim1.trr' 74: 74: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 74: 74: Core t (s) Wall t (s) (%) 74: Time: 0.023 0.012 191.3 74: (ns/day) (hour/ns) 74: Performance: 123.377 0.195 74: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_24_sim1.edr as double precision energy file 74: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_24_sim2.edr as double precision energy file 74: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 74: 74: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/24 (386 ms) 74: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/25 74: 74: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_25_input.mdp]: 74: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 74: that with the Verlet scheme, nstlist has no effect on the accuracy of 74: your simulation. 74: 74: 74: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_25_input.mdp]: 74: Setting nstcalcenergy (100) equal to nstenergy (4) 74: 74: Generating 1-4 interactions: fudge = 0.5 74: Number of degrees of freedom in T-Coupling group System is 79.00 74: 74: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_25_input.mdp]: 74: You are using a plain Coulomb cut-off, which might produce artifacts. 74: You might want to consider using PME electrostatics. 74: 74: 74: 74: There were 3 NOTEs 74: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_25_sim.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 74: Changing nstlist from 8 to 20, rlist from 0.757 to 0.863 74: 74: Using 1 MPI thread 74: Using 2 OpenMP threads 74: 74: 74: NOTE: The number of threads is not equal to the number of (logical) cpus 74: and the -pin option is set to auto: will not pin threads to cpus. 74: This can lead to significant performance degradation. 74: Consider using -pin on (and -pinoffset in case you run multiple jobs). 74: starting mdrun '30 atom system in water' 74: 16 steps, 0.0 ps. 74: Generated 2485 of the 2485 non-bonded parameter combinations 74: 74: Generated 2485 of the 2485 1-4 parameter combinations 74: 74: Excluding 3 bonded neighbours molecule type 'nonanol' 74: 74: turning H bonds into constraints... 74: 74: Excluding 2 bonded neighbours molecule type 'SOL' 74: 74: turning H bonds into constraints... 74: 74: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/nonanol_vacuo.gro' 74: 74: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 74: 74: Calculated rlist for 1x1 atom pair-list as 0.764 nm, buffer size 0.064 nm 74: 74: Set rlist, assuming 4x4 atom pair-list, to 0.757 nm, buffer size 0.057 nm 74: 74: Note that mdrun will redetermine rlist based on the actual pair-list setup 74: 74: This run will generate roughly 0 Mb of data 74: 74: Writing final coordinates. 74: 74: Core t (s) Wall t (s) (%) 74: Time: 0.113 0.057 198.7 74: (ns/day) (hour/ns) 74: Performance: 25.751 0.932 74: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_25_sim.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 74: Changing nstlist from 8 to 20, rlist from 0.757 to 0.863 74: 74: Using 1 MPI thread 74: Using 2 OpenMP threads 74: 74: 74: NOTE: The number of threads is not equal to the number of (logical) cpus 74: and the -pin option is set to auto: will not pin threads to cpus. 74: This can lead to significant performance degradation. 74: Consider using -pin on (and -pinoffset in case you run multiple jobs). 74: starting md rerun '30 atom system in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_25_sim1.trr' 74: 74: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 74: 74: Core t (s) Wall t (s) (%) 74: Time: 0.019 0.010 189.1 74: (ns/day) (hour/ns) 74: Performance: 148.166 0.162 74: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_25_sim1.edr as double precision energy file 74: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_25_sim2.edr as double precision energy file 74: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 74: 74: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/25 (405 ms) 74: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/26 74: 74: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_26_input.mdp]: 74: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 74: that with the Verlet scheme, nstlist has no effect on the accuracy of 74: your simulation. 74: 74: 74: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_26_input.mdp]: 74: Setting nstcalcenergy (100) equal to nstenergy (4) 74: 74: Generating 1-4 interactions: fudge = 0.5 74: Number of degrees of freedom in T-Coupling group System is 79.00 74: 74: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_26_input.mdp]: 74: You are using a plain Coulomb cut-off, which might produce artifacts. 74: You might want to consider using PME electrostatics. 74: 74: 74: 74: There were 3 NOTEs 74: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_26_sim.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 74: Changing nstlist from 8 to 20, rlist from 0.757 to 0.863 74: 74: Using 1 MPI thread 74: Using 2 OpenMP threads 74: 74: 74: NOTE: The number of threads is not equal to the number of (logical) cpus 74: and the -pin option is set to auto: will not pin threads to cpus. 74: This can lead to significant performance degradation. 74: Consider using -pin on (and -pinoffset in case you run multiple jobs). 74: starting mdrun '30 atom system in water' 74: 16 steps, 0.0 ps. 74: Generated 2485 of the 2485 non-bonded parameter combinations 74: 74: Generated 2485 of the 2485 1-4 parameter combinations 74: 74: Excluding 3 bonded neighbours molecule type 'nonanol' 74: 74: turning H bonds into constraints... 74: 74: Excluding 2 bonded neighbours molecule type 'SOL' 74: 74: turning H bonds into constraints... 74: 74: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/nonanol_vacuo.gro' 74: 74: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 74: 74: Calculated rlist for 1x1 atom pair-list as 0.764 nm, buffer size 0.064 nm 74: 74: Set rlist, assuming 4x4 atom pair-list, to 0.757 nm, buffer size 0.057 nm 74: 74: Note that mdrun will redetermine rlist based on the actual pair-list setup 74: 74: This run will generate roughly 0 Mb of data 74: 74: Writing final coordinates. 74: 74: Core t (s) Wall t (s) (%) 74: Time: 0.071 0.036 198.0 74: (ns/day) (hour/ns) 74: Performance: 40.809 0.588 74: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_26_sim.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 74: Changing nstlist from 8 to 20, rlist from 0.757 to 0.863 74: 74: Using 1 MPI thread 74: Using 2 OpenMP threads 74: 74: 74: NOTE: The number of threads is not equal to the number of (logical) cpus 74: and the -pin option is set to auto: will not pin threads to cpus. 74: This can lead to significant performance degradation. 74: Consider using -pin on (and -pinoffset in case you run multiple jobs). 74: starting md rerun '30 atom system in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_26_sim1.trr' 74: 74: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 74: 74: Core t (s) Wall t (s) (%) 74: Time: 0.033 0.017 193.9 74: (ns/day) (hour/ns) 74: Performance: 85.098 0.282 74: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_26_sim1.edr as double precision energy file 74: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_26_sim2.edr as double precision energy file 74: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 74: 74: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/26 (385 ms) 74: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/27 74: 74: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_27_input.mdp]: 74: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 74: that with the Verlet scheme, nstlist has no effect on the accuracy of 74: your simulation. 74: 74: 74: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_27_input.mdp]: 74: Setting nstcalcenergy (100) equal to nstenergy (4) 74: 74: Generating 1-4 interactions: fudge = 0.5 74: Number of degrees of freedom in T-Coupling group System is 79.00 74: 74: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_27_input.mdp]: 74: You are using a plain Coulomb cut-off, which might produce artifacts. 74: You might want to consider using PME electrostatics. 74: 74: 74: 74: There were 3 NOTEs 74: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_27_sim.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 74: Changing nstlist from 8 to 20, rlist from 0.757 to 0.863 74: 74: Using 1 MPI thread 74: Using 2 OpenMP threads 74: 74: 74: NOTE: The number of threads is not equal to the number of (logical) cpus 74: and the -pin option is set to auto: will not pin threads to cpus. 74: This can lead to significant performance degradation. 74: Consider using -pin on (and -pinoffset in case you run multiple jobs). 74: starting mdrun '30 atom system in water' 74: 16 steps, 0.0 ps. 74: Generated 2485 of the 2485 non-bonded parameter combinations 74: 74: Generated 2485 of the 2485 1-4 parameter combinations 74: 74: Excluding 3 bonded neighbours molecule type 'nonanol' 74: 74: turning H bonds into constraints... 74: 74: Excluding 2 bonded neighbours molecule type 'SOL' 74: 74: turning H bonds into constraints... 74: 74: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/nonanol_vacuo.gro' 74: 74: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 74: 74: Calculated rlist for 1x1 atom pair-list as 0.764 nm, buffer size 0.064 nm 74: 74: Set rlist, assuming 4x4 atom pair-list, to 0.757 nm, buffer size 0.057 nm 74: 74: Note that mdrun will redetermine rlist based on the actual pair-list setup 74: 74: This run will generate roughly 0 Mb of data 74: 74: Writing final coordinates. 74: 74: Core t (s) Wall t (s) (%) 74: Time: 0.104 0.052 198.4 74: (ns/day) (hour/ns) 74: Performance: 28.024 0.856 74: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_27_sim.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 74: Changing nstlist from 8 to 20, rlist from 0.757 to 0.863 74: 74: Using 1 MPI thread 74: Using 2 OpenMP threads 74: 74: 74: NOTE: The number of threads is not equal to the number of (logical) cpus 74: and the -pin option is set to auto: will not pin threads to cpus. 74: This can lead to significant performance degradation. 74: Consider using -pin on (and -pinoffset in case you run multiple jobs). 74: starting md rerun '30 atom system in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_27_sim1.trr' 74: 74: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 74: 74: Core t (s) Wall t (s) (%) 74: Time: 0.041 0.021 194.7 74: (ns/day) (hour/ns) 74: Performance: 69.830 0.344 74: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_27_sim1.edr as double precision energy file 74: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_27_sim2.edr as double precision energy file 74: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 74: 74: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/27 (408 ms) 74: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/28 74: 74: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_28_input.mdp]: 74: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 74: that with the Verlet scheme, nstlist has no effect on the accuracy of 74: your simulation. 74: 74: 74: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_28_input.mdp]: 74: Setting nstcalcenergy (100) equal to nstenergy (4) 74: 74: Generating 1-4 interactions: fudge = 0.5 74: Number of degrees of freedom in T-Coupling group System is 79.00 74: 74: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_28_input.mdp]: 74: You are using a plain Coulomb cut-off, which might produce artifacts. 74: You might want to consider using PME electrostatics. 74: 74: 74: 74: There were 3 NOTEs 74: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_28_sim.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 74: Changing nstlist from 8 to 20, rlist from 0.757 to 0.863 74: 74: Using 1 MPI thread 74: Using 2 OpenMP threads 74: 74: 74: NOTE: The number of threads is not equal to the number of (logical) cpus 74: and the -pin option is set to auto: will not pin threads to cpus. 74: This can lead to significant performance degradation. 74: Consider using -pin on (and -pinoffset in case you run multiple jobs). 74: starting mdrun '30 atom system in water' 74: 16 steps, 0.0 ps. 74: Generated 2485 of the 2485 non-bonded parameter combinations 74: 74: Generated 2485 of the 2485 1-4 parameter combinations 74: 74: Excluding 3 bonded neighbours molecule type 'nonanol' 74: 74: turning H bonds into constraints... 74: 74: Excluding 2 bonded neighbours molecule type 'SOL' 74: 74: turning H bonds into constraints... 74: 74: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/nonanol_vacuo.gro' 74: 74: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 74: 74: Calculated rlist for 1x1 atom pair-list as 0.764 nm, buffer size 0.064 nm 74: 74: Set rlist, assuming 4x4 atom pair-list, to 0.757 nm, buffer size 0.057 nm 74: 74: Note that mdrun will redetermine rlist based on the actual pair-list setup 74: 74: This run will generate roughly 0 Mb of data 74: 74: Writing final coordinates. 74: 74: Core t (s) Wall t (s) (%) 74: Time: 0.078 0.039 198.1 74: (ns/day) (hour/ns) 74: Performance: 37.381 0.642 74: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_28_sim.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 74: Changing nstlist from 8 to 20, rlist from 0.757 to 0.863 74: 74: Using 1 MPI thread 74: Using 2 OpenMP threads 74: 74: 74: NOTE: The number of threads is not equal to the number of (logical) cpus 74: and the -pin option is set to auto: will not pin threads to cpus. 74: This can lead to significant performance degradation. 74: Consider using -pin on (and -pinoffset in case you run multiple jobs). 74: starting md rerun '30 atom system in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_28_sim1.trr' 74: 74: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 74: 74: Core t (s) Wall t (s) (%) 74: Time: 0.017 0.009 184.4 74: (ns/day) (hour/ns) 74: Performance: 161.087 0.149 74: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_28_sim1.edr as double precision energy file 74: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_28_sim2.edr as double precision energy file 74: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 74: 74: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/28 (380 ms) 74: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/29 74: 74: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_29_input.mdp]: 74: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 74: that with the Verlet scheme, nstlist has no effect on the accuracy of 74: your simulation. 74: 74: 74: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_29_input.mdp]: 74: Setting nstcalcenergy (100) equal to nstenergy (4) 74: 74: Generating 1-4 interactions: fudge = 0.5 74: Number of degrees of freedom in T-Coupling group System is 79.00 74: 74: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_29_input.mdp]: 74: You are using a plain Coulomb cut-off, which might produce artifacts. 74: You might want to consider using PME electrostatics. 74: 74: 74: 74: There were 3 NOTEs 74: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_29_sim.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 74: Changing nstlist from 8 to 20, rlist from 0.757 to 0.863 74: 74: Using 1 MPI thread 74: Using 2 OpenMP threads 74: 74: 74: NOTE: The number of threads is not equal to the number of (logical) cpus 74: and the -pin option is set to auto: will not pin threads to cpus. 74: This can lead to significant performance degradation. 74: Consider using -pin on (and -pinoffset in case you run multiple jobs). 74: starting mdrun '30 atom system in water' 74: 16 steps, 0.0 ps. 74: Generated 2485 of the 2485 non-bonded parameter combinations 74: 74: Generated 2485 of the 2485 1-4 parameter combinations 74: 74: Excluding 3 bonded neighbours molecule type 'nonanol' 74: 74: turning H bonds into constraints... 74: 74: Excluding 2 bonded neighbours molecule type 'SOL' 74: 74: turning H bonds into constraints... 74: 74: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/nonanol_vacuo.gro' 74: 74: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 74: 74: Calculated rlist for 1x1 atom pair-list as 0.764 nm, buffer size 0.064 nm 74: 74: Set rlist, assuming 4x4 atom pair-list, to 0.757 nm, buffer size 0.057 nm 74: 74: Note that mdrun will redetermine rlist based on the actual pair-list setup 74: 74: This run will generate roughly 0 Mb of data 74: 74: Writing final coordinates. 74: 74: Core t (s) Wall t (s) (%) 74: Time: 0.076 0.038 198.0 74: (ns/day) (hour/ns) 74: Performance: 38.499 0.623 74: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_29_sim.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 74: Changing nstlist from 8 to 20, rlist from 0.757 to 0.863 74: 74: Using 1 MPI thread 74: Using 2 OpenMP threads 74: 74: 74: NOTE: The number of threads is not equal to the number of (logical) cpus 74: and the -pin option is set to auto: will not pin threads to cpus. 74: This can lead to significant performance degradation. 74: Consider using -pin on (and -pinoffset in case you run multiple jobs). 74: starting md rerun '30 atom system in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_29_sim1.trr' 74: 74: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 74: 74: Core t (s) Wall t (s) (%) 74: Time: 0.019 0.010 189.7 74: (ns/day) (hour/ns) 74: Performance: 148.077 0.162 74: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_29_sim1.edr as double precision energy file 74: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_29_sim2.edr as double precision energy file 74: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 74: 74: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/29 (379 ms) 74: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/30 74: 74: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_30_input.mdp]: 74: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 74: that with the Verlet scheme, nstlist has no effect on the accuracy of 74: your simulation. 74: 74: 74: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_30_input.mdp]: 74: Setting nstcalcenergy (100) equal to nstenergy (4) 74: 74: Generating 1-4 interactions: fudge = 0.5 74: Number of degrees of freedom in T-Coupling group System is 79.00 74: 74: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_30_input.mdp]: 74: You are using a plain Coulomb cut-off, which might produce artifacts. 74: You might want to consider using PME electrostatics. 74: 74: 74: 74: There were 3 NOTEs 74: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_30_sim.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 74: Changing nstlist from 8 to 20, rlist from 0.757 to 0.863 74: 74: Using 1 MPI thread 74: Using 2 OpenMP threads 74: 74: 74: NOTE: The number of threads is not equal to the number of (logical) cpus 74: and the -pin option is set to auto: will not pin threads to cpus. 74: This can lead to significant performance degradation. 74: Consider using -pin on (and -pinoffset in case you run multiple jobs). 74: starting mdrun '30 atom system in water' 74: 16 steps, 0.0 ps. 74: Generated 2485 of the 2485 non-bonded parameter combinations 74: 74: Generated 2485 of the 2485 1-4 parameter combinations 74: 74: Excluding 3 bonded neighbours molecule type 'nonanol' 74: 74: turning H bonds into constraints... 74: 74: Excluding 2 bonded neighbours molecule type 'SOL' 74: 74: turning H bonds into constraints... 74: 74: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/nonanol_vacuo.gro' 74: 74: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 74: 74: Calculated rlist for 1x1 atom pair-list as 0.764 nm, buffer size 0.064 nm 74: 74: Set rlist, assuming 4x4 atom pair-list, to 0.757 nm, buffer size 0.057 nm 74: 74: Note that mdrun will redetermine rlist based on the actual pair-list setup 74: 74: This run will generate roughly 0 Mb of data 74: 74: Writing final coordinates. 74: 74: Core t (s) Wall t (s) (%) 74: Time: 0.089 0.045 198.4 74: (ns/day) (hour/ns) 74: Performance: 32.693 0.734 74: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_30_sim.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 74: Changing nstlist from 8 to 20, rlist from 0.757 to 0.863 74: 74: Using 1 MPI thread 74: Using 2 OpenMP threads 74: 74: 74: NOTE: The number of threads is not equal to the number of (logical) cpus 74: and the -pin option is set to auto: will not pin threads to cpus. 74: This can lead to significant performance degradation. 74: Consider using -pin on (and -pinoffset in case you run multiple jobs). 74: starting md rerun '30 atom system in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_30_sim1.trr' 74: 74: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 74: 74: Core t (s) Wall t (s) (%) 74: Time: 0.015 0.008 187.4 74: (ns/day) (hour/ns) 74: Performance: 183.302 0.131 74: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_30_sim1.edr as double precision energy file 74: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_30_sim2.edr as double precision energy file 74: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 74: 74: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/30 (403 ms) 74: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/31 74: 74: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_31_input.mdp]: 74: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 74: that with the Verlet scheme, nstlist has no effect on the accuracy of 74: your simulation. 74: 74: 74: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_31_input.mdp]: 74: Setting nstcalcenergy (100) equal to nstenergy (4) 74: 74: Generating 1-4 interactions: fudge = 0.5 74: Number of degrees of freedom in T-Coupling group System is 79.00 74: 74: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_31_input.mdp]: 74: You are using a plain Coulomb cut-off, which might produce artifacts. 74: You might want to consider using PME electrostatics. 74: 74: 74: 74: There were 3 NOTEs 74: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_31_sim.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 74: Changing nstlist from 8 to 20, rlist from 0.757 to 0.863 74: 74: Using 1 MPI thread 74: Using 2 OpenMP threads 74: 74: 74: NOTE: The number of threads is not equal to the number of (logical) cpus 74: and the -pin option is set to auto: will not pin threads to cpus. 74: This can lead to significant performance degradation. 74: Consider using -pin on (and -pinoffset in case you run multiple jobs). 74: starting mdrun '30 atom system in water' 74: 16 steps, 0.0 ps. 74: Generated 2485 of the 2485 non-bonded parameter combinations 74: 74: Generated 2485 of the 2485 1-4 parameter combinations 74: 74: Excluding 3 bonded neighbours molecule type 'nonanol' 74: 74: turning H bonds into constraints... 74: 74: Excluding 2 bonded neighbours molecule type 'SOL' 74: 74: turning H bonds into constraints... 74: 74: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/nonanol_vacuo.gro' 74: 74: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 74: 74: Calculated rlist for 1x1 atom pair-list as 0.764 nm, buffer size 0.064 nm 74: 74: Set rlist, assuming 4x4 atom pair-list, to 0.757 nm, buffer size 0.057 nm 74: 74: Note that mdrun will redetermine rlist based on the actual pair-list setup 74: 74: This run will generate roughly 0 Mb of data 74: 74: Writing final coordinates. 74: 74: Core t (s) Wall t (s) (%) 74: Time: 0.068 0.034 197.8 74: (ns/day) (hour/ns) 74: Performance: 42.730 0.562 74: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_31_sim.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 74: Changing nstlist from 8 to 20, rlist from 0.757 to 0.863 74: 74: Using 1 MPI thread 74: Using 2 OpenMP threads 74: 74: 74: NOTE: The number of threads is not equal to the number of (logical) cpus 74: and the -pin option is set to auto: will not pin threads to cpus. 74: This can lead to significant performance degradation. 74: Consider using -pin on (and -pinoffset in case you run multiple jobs). 74: starting md rerun '30 atom system in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_31_sim1.trr' 74: 74: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 74: 74: Core t (s) Wall t (s) (%) 74: Time: 0.018 0.010 185.8 74: (ns/day) (hour/ns) 74: Performance: 152.350 0.158 74: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_31_sim1.edr as double precision energy file 74: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_31_sim2.edr as double precision energy file 74: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 74: 74: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/31 (368 ms) 74: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/32 74: 74: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_32_input.mdp]: 74: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 74: that with the Verlet scheme, nstlist has no effect on the accuracy of 74: your simulation. 74: 74: 74: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_32_input.mdp]: 74: Setting nstcalcenergy (100) equal to nstenergy (4) 74: 74: Generating 1-4 interactions: fudge = 0.5 74: Number of degrees of freedom in T-Coupling group System is 79.00 74: 74: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_32_input.mdp]: 74: You are using a plain Coulomb cut-off, which might produce artifacts. 74: You might want to consider using PME electrostatics. 74: 74: 74: 74: There were 3 NOTEs 74: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_32_sim.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 74: Changing nstlist from 8 to 20, rlist from 0.757 to 0.863 74: 74: Using 1 MPI thread 74: Using 2 OpenMP threads 74: 74: 74: NOTE: The number of threads is not equal to the number of (logical) cpus 74: and the -pin option is set to auto: will not pin threads to cpus. 74: This can lead to significant performance degradation. 74: Consider using -pin on (and -pinoffset in case you run multiple jobs). 74: starting mdrun '30 atom system in water' 74: 16 steps, 0.0 ps. 74: Generated 2485 of the 2485 non-bonded parameter combinations 74: 74: Generated 2485 of the 2485 1-4 parameter combinations 74: 74: Excluding 3 bonded neighbours molecule type 'nonanol' 74: 74: turning H bonds into constraints... 74: 74: Excluding 2 bonded neighbours molecule type 'SOL' 74: 74: turning H bonds into constraints... 74: 74: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/nonanol_vacuo.gro' 74: 74: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 74: 74: Calculated rlist for 1x1 atom pair-list as 0.764 nm, buffer size 0.064 nm 74: 74: Set rlist, assuming 4x4 atom pair-list, to 0.757 nm, buffer size 0.057 nm 74: 74: Note that mdrun will redetermine rlist based on the actual pair-list setup 74: 74: This run will generate roughly 0 Mb of data 74: 74: Writing final coordinates. 74: 74: Core t (s) Wall t (s) (%) 74: Time: 0.078 0.039 198.1 74: (ns/day) (hour/ns) 74: Performance: 37.194 0.645 74: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_32_sim.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 74: Changing nstlist from 8 to 20, rlist from 0.757 to 0.863 74: 74: Using 1 MPI thread 74: Using 2 OpenMP threads 74: 74: 74: NOTE: The number of threads is not equal to the number of (logical) cpus 74: and the -pin option is set to auto: will not pin threads to cpus. 74: This can lead to significant performance degradation. 74: Consider using -pin on (and -pinoffset in case you run multiple jobs). 74: starting md rerun '30 atom system in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_32_sim1.trr' 74: 74: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 74: 74: Core t (s) Wall t (s) (%) 74: Time: 0.021 0.011 190.5 74: (ns/day) (hour/ns) 74: Performance: 130.386 0.184 74: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_32_sim1.edr as double precision energy file 74: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_32_sim2.edr as double precision energy file 74: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 74: 74: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/32 (379 ms) 74: [----------] 33 tests from MdrunIsReproduced/MdrunRerunFreeEnergyTest (9673 ms total) 74: 74: [----------] 2 tests from Angles1/SimpleMdrunTest 74: [ RUN ] Angles1/SimpleMdrunTest.WithinTolerances/0 74: 74: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Angles1_SimpleMdrunTest_WithinTolerances_0_input.mdp]: 74: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 74: that with the Verlet scheme, nstlist has no effect on the accuracy of 74: your simulation. 74: 74: 74: NOTE 2 [file angles1.top, line 72]: 74: In moleculetype 'butane' 4 atoms are not bound by a potential or 74: constraint to any other atom in the same moleculetype. Although 74: technically this might not cause issues in a simulation, this often means 74: that the user forgot to add a bond/potential/constraint or put multiple 74: molecules in the same moleculetype definition by mistake. Run with -v to 74: get information for each atom. 74: 74: Number of degrees of freedom in T-Coupling group System is 9.00 74: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 74: 74: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Angles1_SimpleMdrunTest_WithinTolerances_0_input.mdp]: 74: NVE simulation: will use the initial temperature of 238.919 K for 74: determining the Verlet buffer size 74: 74: 74: There were 3 NOTEs 74: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Angles1_SimpleMdrunTest_WithinTolerances_0.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 74: Can not increase nstlist because an NVE ensemble is used 74: Using 1 MPI thread 74: Using 2 OpenMP threads 74: 74: 74: NOTE: The number of threads is not equal to the number of (logical) cpus 74: and the -pin option is set to auto: will not pin threads to cpus. 74: This can lead to significant performance degradation. 74: Consider using -pin on (and -pinoffset in case you run multiple jobs). 74: starting mdrun 'This_incredible_box_of_butane' 74: 50 steps, 0.1 ps. 74: Generated 3 of the 3 non-bonded parameter combinations 74: 74: Excluding 3 bonded neighbours molecule type 'butane' 74: 74: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/angles1.gro' 74: 74: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 238.919 K 74: 74: Calculated rlist for 1x1 atom pair-list as 0.700 nm, buffer size 0.000 nm 74: 74: Set rlist, assuming 4x4 atom pair-list, to 0.700 nm, buffer size 0.000 nm 74: 74: Note that mdrun will redetermine rlist based on the actual pair-list setup 74: 74: This run will generate roughly 0 Mb of data 74: 74: Writing final coordinates. 74: 74: Core t (s) Wall t (s) (%) 74: Time: 0.072 0.036 198.1 74: (ns/day) (hour/ns) 74: Performance: 121.906 0.197 74: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Angles1_SimpleMdrunTest_WithinTolerances_0.edr as double precision energy file 74: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 5 time 0.020 Reading energy frame 6 time 0.024 Reading energy frame 7 time 0.028 Reading energy frame 8 time 0.032 Reading energy frame 9 time 0.036 Reading energy frame 10 time 0.040 Reading energy frame 11 time 0.044 Reading energy frame 12 time 0.048 Reading energy frame 13 time 0.050 Last energy frame read 13 time 0.050 74: [ OK ] Angles1/SimpleMdrunTest.WithinTolerances/0 (92 ms) 74: [ RUN ] Angles1/SimpleMdrunTest.WithinTolerances/1 74: 74: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Angles1_SimpleMdrunTest_WithinTolerances_1_input.mdp]: 74: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 74: that with the Verlet scheme, nstlist has no effect on the accuracy of 74: your simulation. 74: 74: 74: NOTE 2 [file angles1.top, line 72]: 74: In moleculetype 'butane' 4 atoms are not bound by a potential or 74: constraint to any other atom in the same moleculetype. Although 74: technically this might not cause issues in a simulation, this often means 74: that the user forgot to add a bond/potential/constraint or put multiple 74: molecules in the same moleculetype definition by mistake. Run with -v to 74: get information for each atom. 74: 74: Number of degrees of freedom in T-Coupling group System is 9.00 74: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 74: 74: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Angles1_SimpleMdrunTest_WithinTolerances_1_input.mdp]: 74: NVE simulation: will use the initial temperature of 238.919 K for 74: determining the Verlet buffer size 74: 74: 74: There were 3 NOTEs 74: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Angles1_SimpleMdrunTest_WithinTolerances_1.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 74: Can not increase nstlist because an NVE ensemble is used 74: Using 1 MPI thread 74: Using 2 OpenMP threads 74: 74: 74: NOTE: The number of threads is not equal to the number of (logical) cpus 74: and the -pin option is set to auto: will not pin threads to cpus. 74: This can lead to significant performance degradation. 74: Consider using -pin on (and -pinoffset in case you run multiple jobs). 74: starting mdrun 'This_incredible_box_of_butane' 74: 50 steps, 0.1 ps. 74: Generated 3 of the 3 non-bonded parameter combinations 74: 74: Excluding 3 bonded neighbours molecule type 'butane' 74: 74: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/angles1.gro' 74: 74: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 238.919 K 74: 74: Calculated rlist for 1x1 atom pair-list as 0.700 nm, buffer size 0.000 nm 74: 74: Set rlist, assuming 4x4 atom pair-list, to 0.700 nm, buffer size 0.000 nm 74: 74: Note that mdrun will redetermine rlist based on the actual pair-list setup 74: 74: This run will generate roughly 0 Mb of data 74: 74: Writing final coordinates. 74: 74: Core t (s) Wall t (s) (%) 74: Time: 0.059 0.030 198.8 74: (ns/day) (hour/ns) 74: Performance: 149.254 0.161 74: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Angles1_SimpleMdrunTest_WithinTolerances_1.edr as double precision energy file 74: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 5 time 0.020 Reading energy frame 6 time 0.024 Reading energy frame 7 time 0.028 Reading energy frame 8 time 0.032 Reading energy frame 9 time 0.036 Reading energy frame 10 time 0.040 Reading energy frame 11 time 0.044 Reading energy frame 12 time 0.048 Reading energy frame 13 time 0.050 Last energy frame read 13 time 0.050 74: [ OK ] Angles1/SimpleMdrunTest.WithinTolerances/1 (82 ms) 74: [----------] 2 tests from Angles1/SimpleMdrunTest (176 ms total) 74: 74: [----------] Global test environment tear-down 74: [==========] 53 tests from 5 test suites ran. (68084 ms total) 74: [ PASSED ] 53 tests. 74/92 Test #74: MdrunNonIntegratorTests ................... Passed 68.19 sec test 75 Start 75: MdrunTpiTests 75: Test command: /build/reproducible-path/gromacs-2025.1/build/basic-dp/bin/mdrun-tpi-test "--gtest_output=xml:/build/reproducible-path/gromacs-2025.1/build/basic-dp/Testing/Temporary/MdrunTpiTests.xml" 75: Working Directory: /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests 75: Test timeout computed to be: 600 75: [==========] Running 3 tests from 1 test suite. 75: [----------] Global test environment set-up. 75: [----------] 3 tests from Simple/TpiTest 75: [ RUN ] Simple/TpiTest.ReproducesOutput/0 75: Generating 1-4 interactions: fudge = 0.5 75: Number of degrees of freedom in T-Coupling group System is 1308.00 75: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Simple_TpiTest_ReproducesOutput_0.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 75: TPI is not implemented for GPUs. 75: 75: Using 1 MPI thread 75: Using 1 OpenMP thread 75: 75: 75: NOTE: Thread affinity was not set. 75: Reading frames from gro file '216 water molecules', 648 atoms. 75: Reading frame 0 time 0.000 mu 6.291e+01 6.291e+01 75: Last frame 0 time 0.000 75: Generated 331705 of the 331705 non-bonded parameter combinations 75: 75: Generated 331705 of the 331705 1-4 parameter combinations 75: 75: Excluding 2 bonded neighbours molecule type 'SOL' 75: 75: Excluding 3 bonded neighbours molecule type 'methane' 75: Analysing residue names: 75: There are: 216 Water residues 75: There are: 1 Other residues 75: Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups... 75: 75: This run will generate roughly 0 Mb of data 75: [ OK ] Simple/TpiTest.ReproducesOutput/0 (6334 ms) 75: [ RUN ] Simple/TpiTest.ReproducesOutput/1 75: Generating 1-4 interactions: fudge = 0.5 75: Number of degrees of freedom in T-Coupling group System is 1308.00 75: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Simple_TpiTest_ReproducesOutput_1.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 75: TPI is not implemented for GPUs. 75: 75: Using 1 MPI thread 75: Using 1 OpenMP thread 75: 75: 75: NOTE: Thread affinity was not set. 75: Reading frames from gro file '216 water molecules', 648 atoms. 75: Reading frame 0 time 0.000 mu 4.535e+01 4.535e+01 75: Last frame 0 time 0.000 75: Generated 331705 of the 331705 non-bonded parameter combinations 75: 75: Generated 331705 of the 331705 1-4 parameter combinations 75: 75: Excluding 2 bonded neighbours molecule type 'SOL' 75: 75: Excluding 3 bonded neighbours molecule type 'methane' 75: Analysing residue names: 75: There are: 216 Water residues 75: There are: 1 Other residues 75: Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups... 75: 75: This run will generate roughly 0 Mb of data 75: [ OK ] Simple/TpiTest.ReproducesOutput/1 (6452 ms) 75: [ RUN ] Simple/TpiTest.ReproducesOutput/2 75: Generating 1-4 interactions: fudge = 0.5 75: Number of degrees of freedom in T-Coupling group System is 1308.00 75: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Simple_TpiTest_ReproducesOutput_2.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 75: TPI is not implemented for GPUs. 75: 75: Using 1 MPI thread 75: Using 1 OpenMP thread 75: 75: 75: NOTE: Thread affinity was not set. 75: Reading frames from gro file '216 water molecules', 648 atoms. 75: Reading frame 0 time 0.000 mu 6.203e+01 6.203e+01 75: Last frame 0 time 0.000 75: Generated 331705 of the 331705 non-bonded parameter combinations 75: 75: Generated 331705 of the 331705 1-4 parameter combinations 75: 75: Excluding 2 bonded neighbours molecule type 'SOL' 75: 75: Excluding 3 bonded neighbours molecule type 'methane' 75: Analysing residue names: 75: There are: 216 Water residues 75: There are: 1 Other residues 75: Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups... 75: 75: This run will generate roughly 0 Mb of data 75: [ OK ] Simple/TpiTest.ReproducesOutput/2 (6150 ms) 75: [----------] 3 tests from Simple/TpiTest (18937 ms total) 75: 75: [----------] Global test environment tear-down 75: [==========] 3 tests from 1 test suite ran. (18986 ms total) 75: [ PASSED ] 3 tests. 75/92 Test #75: MdrunTpiTests ............................. Passed 19.08 sec test 76 Start 76: MdrunMpiTests 76: Test command: /build/reproducible-path/gromacs-2025.1/build/basic-dp/bin/mdrun-mpi-test "-ntomp" "2" "-ntmpi" "2" "--gtest_output=xml:/build/reproducible-path/gromacs-2025.1/build/basic-dp/Testing/Temporary/MdrunMpiTests.xml" 76: Working Directory: /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests 76: Test timeout computed to be: 600 76: [==========] Running 16 tests from 2 test suites. 76: [----------] Global test environment set-up. 76: [----------] 4 tests from MimicTest 76: [ RUN ] MimicTest.OneQuantumMol 76: 76: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MimicTest_OneQuantumMol_input.mdp]: 76: For a correct single-point energy evaluation with nsteps = 0, use 76: continuation = yes to avoid constraining the input coordinates. 76: 76: Generating 1-4 interactions: fudge = 0.5 76: Number of degrees of freedom in T-Coupling group rest is 21.00 76: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 76: 76: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MimicTest_OneQuantumMol_input.mdp]: 76: NVE simulation with an initial temperature of zero: will use a Verlet 76: buffer of 10%. Check your energy drift! 76: 76: 76: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MimicTest_OneQuantumMol_input.mdp]: 76: You are using a plain Coulomb cut-off, which might produce artifacts. 76: You might want to consider using PME electrostatics. 76: 76: 76: 76: There were 3 NOTEs 76: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MimicTest_OneQuantumMol.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 76: Can not increase nstlist because an NVE ensemble is used 76: Using 2 MPI threads 76: Using 2 OpenMP threads per tMPI thread 76: 76: starting md rerun 'Generated by gmx solvate', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/4water.gro' 76: 76: Reading frames from gro file 'Generated by gmx solvate', 12 atoms. 76: Reading frame 0 time 0.000 Last frame 0 time 0.000 76: 76: Core t (s) Wall t (s) (%) 76: Time: 0.029 0.007 395.2 76: (ns/day) (hour/ns) 76: Performance: 11.732 2.046 76: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MimicTest_OneQuantumMol.edr as double precision energy file 76: Reading energy frame 0 time 0.000 Last energy frame read 0 time 0.000 Setting the LD random seed to -537271265 76: 76: Generated 10 of the 10 non-bonded parameter combinations 76: 76: Generated 10 of the 10 1-4 parameter combinations 76: 76: Excluding 2 bonded neighbours molecule type 'SOL' 76: 76: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/4water.gro', all velocities are zero 76: 76: This run will generate roughly 0 Mb of data 76: [ OK ] MimicTest.OneQuantumMol (58 ms) 76: [ RUN ] MimicTest.AllQuantumMol 76: 76: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MimicTest_AllQuantumMol_input.mdp]: 76: For a correct single-point energy evaluation with nsteps = 0, use 76: continuation = yes to avoid constraining the input coordinates. 76: 76: Generating 1-4 interactions: fudge = 0.5 76: Number of degrees of freedom in T-Coupling group rest is 21.00 76: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 76: 76: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MimicTest_AllQuantumMol_input.mdp]: 76: NVE simulation with an initial temperature of zero: will use a Verlet 76: buffer of 10%. Check your energy drift! 76: 76: 76: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MimicTest_AllQuantumMol_input.mdp]: 76: You are using a plain Coulomb cut-off, which might produce artifacts. 76: You might want to consider using PME electrostatics. 76: 76: 76: 76: There were 3 NOTEs 76: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MimicTest_AllQuantumMol.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 76: Can not increase nstlist because an NVE ensemble is used 76: Using 2 MPI threads 76: 76: Non-default thread affinity set, disabling internal thread affinity 76: 76: Using 2 OpenMP threads per tMPI thread 76: 76: starting md rerun 'Generated by gmx solvate', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/4water.gro' 76: 76: Reading frames from gro file 'Generated by gmx solvate', 12 atoms. 76: Reading frame 0 time 0.000 Last frame 0 time 0.000 76: 76: NOTE: 76 % of the run time was spent in domain decomposition, 76: 5 % of the run time was spent in pair search, 76: you might want to increase nstlist (this has no effect on accuracy) 76: 76: Core t (s) Wall t (s) (%) 76: Time: 1.299 0.337 385.8 76: (ns/day) (hour/ns) 76: Performance: 0.257 93.507 76: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MimicTest_AllQuantumMol.edr as double precision energy file 76: Reading energy frame 0 time 0.000 Last energy frame read 0 time 0.000 Setting the LD random seed to -27791561 76: 76: Generated 10 of the 10 non-bonded parameter combinations 76: 76: Generated 10 of the 10 1-4 parameter combinations 76: 76: Excluding 2 bonded neighbours molecule type 'SOL' 76: 76: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/4water.gro', all velocities are zero 76: 76: This run will generate roughly 0 Mb of data 76: [ OK ] MimicTest.AllQuantumMol (1006 ms) 76: [ RUN ] MimicTest.TwoQuantumMol 76: 76: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MimicTest_TwoQuantumMol_input.mdp]: 76: For a correct single-point energy evaluation with nsteps = 0, use 76: continuation = yes to avoid constraining the input coordinates. 76: 76: Generating 1-4 interactions: fudge = 0.5 76: Number of degrees of freedom in T-Coupling group rest is 21.00 76: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 76: 76: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MimicTest_TwoQuantumMol_input.mdp]: 76: NVE simulation with an initial temperature of zero: will use a Verlet 76: buffer of 10%. Check your energy drift! 76: 76: 76: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MimicTest_TwoQuantumMol_input.mdp]: 76: You are using a plain Coulomb cut-off, which might produce artifacts. 76: You might want to consider using PME electrostatics. 76: 76: 76: 76: There were 3 NOTEs 76: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MimicTest_TwoQuantumMol.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 76: Can not increase nstlist because an NVE ensemble is used 76: Using 2 MPI threads 76: 76: Non-default thread affinity set, disabling internal thread affinity 76: 76: Using 2 OpenMP threads per tMPI thread 76: 76: starting md rerun 'Generated by gmx solvate', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/4water.gro' 76: 76: Reading frames from gro file 'Generated by gmx solvate', 12 atoms. 76: Reading frame 0 time 0.000 Last frame 0 time 0.000 76: 76: NOTE: 77 % of the run time was spent in domain decomposition, 76: 5 % of the run time was spent in pair search, 76: you might want to increase nstlist (this has no effect on accuracy) 76: 76: NOTE: 6 % of the run time was spent communicating energies, 76: you might want to increase some nst* mdp options 76: 76: Core t (s) Wall t (s) (%) 76: Time: 1.180 0.307 384.6 76: (ns/day) (hour/ns) 76: Performance: 0.282 85.236 76: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MimicTest_TwoQuantumMol.edr as double precision energy file 76: Reading energy frame 0 time 0.000 Last energy frame read 0 time 0.000 Setting the LD random seed to -142837906 76: 76: Generated 10 of the 10 non-bonded parameter combinations 76: 76: Generated 10 of the 10 1-4 parameter combinations 76: 76: Excluding 2 bonded neighbours molecule type 'SOL' 76: 76: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/4water.gro', all velocities are zero 76: 76: This run will generate roughly 0 Mb of data 76: [ OK ] MimicTest.TwoQuantumMol (964 ms) 76: [ RUN ] MimicTest.BondCuts 76: 76: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MimicTest_BondCuts_input.mdp]: 76: For a correct single-point energy evaluation with nsteps = 0, use 76: continuation = yes to avoid constraining the input coordinates. 76: 76: Generating 1-4 interactions: fudge = 0.5 76: Number of degrees of freedom in T-Coupling group rest is 66.00 76: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 76: 76: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MimicTest_BondCuts_input.mdp]: 76: NVE simulation: will use the initial temperature of 300.368 K for 76: determining the Verlet buffer size 76: 76: 76: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MimicTest_BondCuts_input.mdp]: 76: You are using a plain Coulomb cut-off, which might produce artifacts. 76: You might want to consider using PME electrostatics. 76: 76: 76: 76: There were 3 NOTEs 76: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MimicTest_BondCuts.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 76: Can not increase nstlist because an NVE ensemble is used 76: Using 2 MPI threads 76: 76: Non-default thread affinity set, disabling internal thread affinity 76: 76: Using 2 OpenMP threads per tMPI thread 76: 76: starting md rerun 'UNNAMED in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/ala.gro' 76: 76: Reading frames from gro file 'Alanine dipeptide in water', 23 atoms. 76: Reading frame 0 time 0.000 Last frame 0 time 0.000 76: 76: NOTE: 73 % of the run time was spent in domain decomposition, 76: 6 % of the run time was spent in pair search, 76: you might want to increase nstlist (this has no effect on accuracy) 76: 76: NOTE: 6 % of the run time was spent communicating energies, 76: you might want to increase some nst* mdp options 76: 76: Core t (s) Wall t (s) (%) 76: Time: 1.149 0.299 384.0 76: (ns/day) (hour/ns) 76: Performance: 0.289 83.106 76: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MimicTest_BondCuts.edr as double precision energy file 76: Reading energy frame 0 time 0.000 Last energy frame read 0 time 0.000 Setting the LD random seed to -207912961 76: 76: Generated 2211 of the 2211 non-bonded parameter combinations 76: 76: Generated 2211 of the 2211 1-4 parameter combinations 76: 76: Excluding 3 bonded neighbours molecule type 'Protein_chain_A' 76: 76: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/ala.gro' 76: 76: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 300.368 K 76: 76: Calculated rlist for 1x1 atom pair-list as 1.048 nm, buffer size 0.048 nm 76: 76: Set rlist, assuming 4x4 atom pair-list, to 1.036 nm, buffer size 0.036 nm 76: 76: Note that mdrun will redetermine rlist based on the actual pair-list setup 76: 76: This run will generate roughly 0 Mb of data 76: [ OK ] MimicTest.BondCuts (1097 ms) 76: [----------] 4 tests from MimicTest (3127 ms total) 76: 76: [----------] 12 tests from DomainDecomposition/DomDecSpecialCasesTest 76: Generating 1-4 interactions: fudge = 0.5 76: Number of degrees of freedom in T-Coupling group rest is 9.00 76: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 76: 76: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/DomainDecomposition_DomDecSpecialCasesTest_input.mdp]: 76: NVE simulation with an initial temperature of zero: will use a Verlet 76: buffer of 10%. Check your energy drift! 76: 76: 76: There was 1 NOTE 76: Generating 1-4 interactions: fudge = 0.5 76: Number of degrees of freedom in T-Coupling group System is 9.00 76: Generating 1-4 interactions: fudge = 0.5 76: Number of degrees of freedom in T-Coupling group rest is 9.00 76: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 76: 76: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/DomainDecomposition_DomDecSpecialCasesTest_input.mdp]: 76: NVE simulation with an initial temperature of zero: will use a Verlet 76: buffer of 10%. Check your energy drift! 76: 76: 76: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/DomainDecomposition_DomDecSpecialCasesTest_input.mdp]: 76: The optimal PME mesh load for parallel simulations is below 0.5 76: and for highly parallel simulations between 0.25 and 0.33, 76: for higher performance, increase the cut-off and the PME grid spacing. 76: 76: 76: 76: There were 2 NOTEs 76: Generating 1-4 interactions: fudge = 0.5 76: Number of degrees of freedom in T-Coupling group System is 9.00 76: 76: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/DomainDecomposition_DomDecSpecialCasesTest_input.mdp]: 76: The optimal PME mesh load for parallel simulations is below 0.5 76: and for highly parallel simulations between 0.25 and 0.33, 76: for higher performance, increase the cut-off and the PME grid spacing. 76: 76: 76: 76: There was 1 NOTE 76: Setting the LD random seed to -545802330 76: 76: Generated 3 of the 3 non-bonded parameter combinations 76: 76: Generated 3 of the 3 1-4 parameter combinations 76: 76: Excluding 2 bonded neighbours molecule type 'SOL' 76: 76: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/spc2_and_vacuum.gro', all velocities are zero 76: 76: This run will generate roughly 0 Mb of data 76: Setting the LD random seed to 2069999597 76: 76: Generated 3 of the 3 non-bonded parameter combinations 76: 76: Generated 3 of the 3 1-4 parameter combinations 76: 76: Excluding 2 bonded neighbours molecule type 'SOL' 76: 76: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/spc2_and_vacuum.gro', all velocities are zero 76: 76: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 76: 76: Calculated rlist for 1x1 atom pair-list as 1.017 nm, buffer size 0.017 nm 76: 76: Set rlist, assuming 4x4 atom pair-list, to 1.005 nm, buffer size 0.005 nm 76: 76: Note that mdrun will redetermine rlist based on the actual pair-list setup 76: 76: This run will generate roughly 0 Mb of data 76: Setting the LD random seed to -672769 76: 76: Generated 3 of the 3 non-bonded parameter combinations 76: 76: Generated 3 of the 3 1-4 parameter combinations 76: 76: Excluding 2 bonded neighbours molecule type 'SOL' 76: 76: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/spc2_and_vacuum.gro', all velocities are zero 76: 76: The largest distance between excluded atoms is 0.164 nm between atom 2 and 3 76: Calculating fourier grid dimensions for X Y Z 76: Using a fourier grid of 28x28x28, spacing 0.107 0.107 0.107 76: 76: Estimate for the relative computational load of the PME mesh part: 1.00 76: 76: This run will generate roughly 0 Mb of data 76: Setting the LD random seed to 1056849343 76: 76: Generated 3 of the 3 non-bonded parameter combinations 76: 76: Generated 3 of the 3 1-4 parameter combinations 76: 76: Excluding 2 bonded neighbours molecule type 'SOL' 76: 76: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/spc2_and_vacuum.gro', all velocities are zero 76: 76: The largest distance between excluded atoms is 0.164 nm between atom 2 and 3 76: 76: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 76: 76: Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm 76: 76: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm 76: 76: Note that mdrun will redetermine rlist based on the actual pair-list setup 76: Calculating fourier grid dimensions for X Y Z 76: Using a fourier grid of 28x28x28, spacing 0.107 0.107 0.107 76: 76: Estimate for the relative computational load of the PME mesh part: 1.00 76: 76: This run will generate roughly 0 Mb of data 76: [ RUN ] DomainDecomposition/DomDecSpecialCasesTest.EmptyDomain/RF_No_coupling_nbcpu_pmecpu_updatecpu_npme0 76: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/DomainDecomposition_DomDecSpecialCasesTest_RF_No.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 76: Can not increase nstlist because an NVE ensemble is used 76: Using 2 MPI threads 76: 76: Non-default thread affinity set, disabling internal thread affinity 76: 76: Using 2 OpenMP threads per tMPI thread 76: 76: starting mdrun 'spc2' 76: 20 steps, 0.0 ps. 76: 76: Writing final coordinates. 76: 76: 76: Dynamic load balancing report: 76: DLB was turned on during the run due to measured imbalance. 76: Average load imbalance: 10.3%. 76: The balanceable part of the MD step is 40%, load imbalance is computed from this. 76: Part of the total run time spent waiting due to load imbalance: 4.1%. 76: Steps where the load balancing was limited by -rdd, -rcon and/or -dds: X 0 % 76: 76: 76: NOTE: 19 % of the run time was spent in domain decomposition, 76: 4 % of the run time was spent in pair search, 76: you might want to increase nstlist (this has no effect on accuracy) 76: 76: NOTE: 10 % of the run time was spent communicating energies, 76: you might want to increase some nst* mdp options 76: 76: Core t (s) Wall t (s) (%) 76: Time: 4.519 1.140 396.4 76: (ns/day) (hour/ns) 76: Performance: 1.592 15.078 76: [ OK ] DomainDecomposition/DomDecSpecialCasesTest.EmptyDomain/RF_No_coupling_nbcpu_pmecpu_updatecpu_npme0 (1827 ms) 76: [ RUN ] DomainDecomposition/DomDecSpecialCasesTest.EmptyDomain/RF_No_coupling_nbcpu_pmecpu_updatecpu_npme1 76: ./src/programs/mdrun/tests/domain_decomposition.cpp:385: Skipped 76: Test configuration is invalid: 76: Cannot have separate PME ranks when PME is not used 76: 76: [ SKIPPED ] DomainDecomposition/DomDecSpecialCasesTest.EmptyDomain/RF_No_coupling_nbcpu_pmecpu_updatecpu_npme1 (0 ms) 76: [ RUN ] DomainDecomposition/DomDecSpecialCasesTest.EmptyDomain/RF_No_coupling_nbcpu_pmecpu_updatecpu_npme2 76: ./src/programs/mdrun/tests/domain_decomposition.cpp:385: Skipped 76: Test configuration is invalid: 76: Cannot have separate PME ranks when PME is not used 76: Cannot use two separate PME ranks when there are less than four ranks total 76: 76: [ SKIPPED ] DomainDecomposition/DomDecSpecialCasesTest.EmptyDomain/RF_No_coupling_nbcpu_pmecpu_updatecpu_npme2 (0 ms) 76: [ RUN ] DomainDecomposition/DomDecSpecialCasesTest.EmptyDomain/RF_TemperatureAndPressure_coupling_nbcpu_pmecpu_updatecpu_npme0 76: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/DomainDecomposition_DomDecSpecialCasesTest_RF_TemperatureAndPressure.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 76: Changing nstlist from 10 to 50, rlist from 1.005 to 1.136 76: 76: Using 2 MPI threads 76: 76: Non-default thread affinity set, disabling internal thread affinity 76: 76: Using 2 OpenMP threads per tMPI thread 76: 76: starting mdrun 'spc2' 76: 20 steps, 0.0 ps. 76: 76: Writing final coordinates. 76: 76: NOTE: 10 % of the run time was spent communicating energies, 76: you might want to increase some nst* mdp options 76: 76: Core t (s) Wall t (s) (%) 76: Time: 4.204 1.061 396.2 76: (ns/day) (hour/ns) 76: Performance: 1.710 14.036 76: [ OK ] DomainDecomposition/DomDecSpecialCasesTest.EmptyDomain/RF_TemperatureAndPressure_coupling_nbcpu_pmecpu_updatecpu_npme0 (1742 ms) 76: [ RUN ] DomainDecomposition/DomDecSpecialCasesTest.EmptyDomain/RF_TemperatureAndPressure_coupling_nbcpu_pmecpu_updatecpu_npme1 76: ./src/programs/mdrun/tests/domain_decomposition.cpp:385: Skipped 76: Test configuration is invalid: 76: Cannot have separate PME ranks when PME is not used 76: 76: [ SKIPPED ] DomainDecomposition/DomDecSpecialCasesTest.EmptyDomain/RF_TemperatureAndPressure_coupling_nbcpu_pmecpu_updatecpu_npme1 (0 ms) 76: [ RUN ] DomainDecomposition/DomDecSpecialCasesTest.EmptyDomain/RF_TemperatureAndPressure_coupling_nbcpu_pmecpu_updatecpu_npme2 76: ./src/programs/mdrun/tests/domain_decomposition.cpp:385: Skipped 76: Test configuration is invalid: 76: Cannot have separate PME ranks when PME is not used 76: Cannot use two separate PME ranks when there are less than four ranks total 76: 76: [ SKIPPED ] DomainDecomposition/DomDecSpecialCasesTest.EmptyDomain/RF_TemperatureAndPressure_coupling_nbcpu_pmecpu_updatecpu_npme2 (0 ms) 76: [ RUN ] DomainDecomposition/DomDecSpecialCasesTest.EmptyDomain/PME_No_coupling_nbcpu_pmecpu_updatecpu_npme0 76: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/DomainDecomposition_DomDecSpecialCasesTest_PME_No.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 76: Can not increase nstlist because an NVE ensemble is used 76: Using 2 MPI threads 76: 76: Non-default thread affinity set, disabling internal thread affinity 76: 76: Using 2 OpenMP threads per tMPI thread 76: 76: starting mdrun 'spc2' 76: 20 steps, 0.0 ps. 76: 76: Writing final coordinates. 76: 76: 76: Dynamic load balancing report: 76: DLB was off during the run due to low measured imbalance. 76: Average load imbalance: 6.3%. 76: The balanceable part of the MD step is 14%, load imbalance is computed from this. 76: Part of the total run time spent waiting due to load imbalance: 0.9%. 76: 76: 76: Core t (s) Wall t (s) (%) 76: Time: 12.052 3.032 397.5 76: (ns/day) (hour/ns) 76: Performance: 0.598 40.104 76: [ OK ] DomainDecomposition/DomDecSpecialCasesTest.EmptyDomain/PME_No_coupling_nbcpu_pmecpu_updatecpu_npme0 (3798 ms) 76: [ RUN ] DomainDecomposition/DomDecSpecialCasesTest.EmptyDomain/PME_No_coupling_nbcpu_pmecpu_updatecpu_npme1 76: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/DomainDecomposition_DomDecSpecialCasesTest_PME_No.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 76: Can not increase nstlist because an NVE ensemble is used 76: Using 2 MPI threads 76: 76: Non-default thread affinity set, disabling internal thread affinity 76: 76: Using 2 OpenMP threads per tMPI thread 76: 76: starting mdrun 'spc2' 76: 20 steps, 0.0 ps. 76: 76: Writing final coordinates. 76: 76: Core t (s) Wall t (s) (%) 76: Time: 6.029 1.526 395.2 76: (ns/day) (hour/ns) 76: Performance: 1.189 20.181 76: [ OK ] DomainDecomposition/DomDecSpecialCasesTest.EmptyDomain/PME_No_coupling_nbcpu_pmecpu_updatecpu_npme1 (1986 ms) 76: [ RUN ] DomainDecomposition/DomDecSpecialCasesTest.EmptyDomain/PME_No_coupling_nbcpu_pmecpu_updatecpu_npme2 76: ./src/programs/mdrun/tests/domain_decomposition.cpp:385: Skipped 76: Test configuration is invalid: 76: Cannot use two separate PME ranks when there are less than four ranks total 76: 76: [ SKIPPED ] DomainDecomposition/DomDecSpecialCasesTest.EmptyDomain/PME_No_coupling_nbcpu_pmecpu_updatecpu_npme2 (0 ms) 76: [ RUN ] DomainDecomposition/DomDecSpecialCasesTest.EmptyDomain/PME_TemperatureAndPressure_coupling_nbcpu_pmecpu_updatecpu_npme0 76: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/DomainDecomposition_DomDecSpecialCasesTest_PME_TemperatureAndPressure.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 76: Changing nstlist from 10 to 100, rlist from 1 to 1 76: 76: Using 2 MPI threads 76: 76: Non-default thread affinity set, disabling internal thread affinity 76: 76: Using 2 OpenMP threads per tMPI thread 76: 76: starting mdrun 'spc2' 76: 20 steps, 0.0 ps. 76: 76: Writing final coordinates. 76: 76: Core t (s) Wall t (s) (%) 76: Time: 10.877 2.733 397.9 76: (ns/day) (hour/ns) 76: Performance: 0.664 36.156 76: [ OK ] DomainDecomposition/DomDecSpecialCasesTest.EmptyDomain/PME_TemperatureAndPressure_coupling_nbcpu_pmecpu_updatecpu_npme0 (3728 ms) 76: [ RUN ] DomainDecomposition/DomDecSpecialCasesTest.EmptyDomain/PME_TemperatureAndPressure_coupling_nbcpu_pmecpu_updatecpu_npme1 76: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/DomainDecomposition_DomDecSpecialCasesTest_PME_TemperatureAndPressure.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 76: Changing nstlist from 10 to 100, rlist from 1 to 1 76: 76: Using 2 MPI threads 76: 76: Non-default thread affinity set, disabling internal thread affinity 76: 76: Using 2 OpenMP threads per tMPI thread 76: 76: starting mdrun 'spc2' 76: 20 steps, 0.0 ps. 76: 76: Writing final coordinates. 76: 76: Core t (s) Wall t (s) (%) 76: Time: 6.908 1.744 396.2 76: (ns/day) (hour/ns) 76: Performance: 1.041 23.063 76: [ OK ] DomainDecomposition/DomDecSpecialCasesTest.EmptyDomain/PME_TemperatureAndPressure_coupling_nbcpu_pmecpu_updatecpu_npme1 (2442 ms) 76: [ RUN ] DomainDecomposition/DomDecSpecialCasesTest.EmptyDomain/PME_TemperatureAndPressure_coupling_nbcpu_pmecpu_updatecpu_npme2 76: ./src/programs/mdrun/tests/domain_decomposition.cpp:385: Skipped 76: Test configuration is invalid: 76: Cannot use two separate PME ranks when there are less than four ranks total 76: 76: [ SKIPPED ] DomainDecomposition/DomDecSpecialCasesTest.EmptyDomain/PME_TemperatureAndPressure_coupling_nbcpu_pmecpu_updatecpu_npme2 (1 ms) 76: [----------] 12 tests from DomainDecomposition/DomDecSpecialCasesTest (15532 ms total) 76: 76: [----------] Global test environment tear-down 76: [==========] 16 tests from 2 test suites ran. (18859 ms total) 76: [ PASSED ] 10 tests. 76: [ SKIPPED ] 6 tests, listed below: 76: [ SKIPPED ] DomainDecomposition/DomDecSpecialCasesTest.EmptyDomain/RF_No_coupling_nbcpu_pmecpu_updatecpu_npme1 76: [ SKIPPED ] DomainDecomposition/DomDecSpecialCasesTest.EmptyDomain/RF_No_coupling_nbcpu_pmecpu_updatecpu_npme2 76: [ SKIPPED ] DomainDecomposition/DomDecSpecialCasesTest.EmptyDomain/RF_TemperatureAndPressure_coupling_nbcpu_pmecpu_updatecpu_npme1 76: [ SKIPPED ] DomainDecomposition/DomDecSpecialCasesTest.EmptyDomain/RF_TemperatureAndPressure_coupling_nbcpu_pmecpu_updatecpu_npme2 76: [ SKIPPED ] DomainDecomposition/DomDecSpecialCasesTest.EmptyDomain/PME_No_coupling_nbcpu_pmecpu_updatecpu_npme2 76: [ SKIPPED ] DomainDecomposition/DomDecSpecialCasesTest.EmptyDomain/PME_TemperatureAndPressure_coupling_nbcpu_pmecpu_updatecpu_npme2 76/92 Test #76: MdrunMpiTests ............................. Passed 18.95 sec test 77 Start 77: MdrunMultiSimTests 77: Test command: /build/reproducible-path/gromacs-2025.1/build/basic-dp/bin/mdrun-multisim-test "-ntmpi" "4" "--gtest_output=xml:/build/reproducible-path/gromacs-2025.1/build/basic-dp/Testing/Temporary/MdrunMultiSimTests.xml" 77: Working Directory: /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests 77: Test timeout computed to be: 600 77: [==========] Running 2 tests from 1 test suite. 77: [----------] Global test environment set-up. 77: [----------] 2 tests from InNvt/MultiSimTerminationTest 77: [ RUN ] InNvt/MultiSimTerminationTest.WritesCheckpointAfterMaxhTerminationAndThenRestarts/0 77: [ OK ] InNvt/MultiSimTerminationTest.WritesCheckpointAfterMaxhTerminationAndThenRestarts/0 (0 ms) 77: [ RUN ] InNvt/MultiSimTerminationTest.WritesCheckpointAfterMaxhTerminationAndThenRestarts/1 77: [ OK ] InNvt/MultiSimTerminationTest.WritesCheckpointAfterMaxhTerminationAndThenRestarts/1 (0 ms) 77: [----------] 2 tests from InNvt/MultiSimTerminationTest (1 ms total) 77: 77: [----------] Global test environment tear-down 77: [==========] 2 tests from 1 test suite ran. (113 ms total) 77: [ PASSED ] 2 tests. 77: 77: YOU HAVE 4 DISABLED TESTS 77: 77/92 Test #77: MdrunMultiSimTests ........................ Passed 0.29 sec test 78 Start 78: MdrunMultiSimReplexTests 78: Test command: /build/reproducible-path/gromacs-2025.1/build/basic-dp/bin/mdrun-multisim-replex-test "-ntmpi" "4" "--gtest_output=xml:/build/reproducible-path/gromacs-2025.1/build/basic-dp/Testing/Temporary/MdrunMultiSimReplexTests.xml" 78: Working Directory: /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests 78: Test timeout computed to be: 600 78: [==========] Running 1 test from 1 test suite. 78: [----------] Global test environment set-up. 78: [----------] 1 test from InNvt/ReplicaExchangeTerminationTest 78: [ RUN ] InNvt/ReplicaExchangeTerminationTest.WritesCheckpointAfterMaxhTerminationAndThenRestarts/0 78: [ OK ] InNvt/ReplicaExchangeTerminationTest.WritesCheckpointAfterMaxhTerminationAndThenRestarts/0 (0 ms) 78: [----------] 1 test from InNvt/ReplicaExchangeTerminationTest (0 ms total) 78: 78: [----------] Global test environment tear-down 78: [==========] 1 test from 1 test suite ran. (113 ms total) 78: [ PASSED ] 1 test. 78: 78: YOU HAVE 4 DISABLED TESTS 78: 78/92 Test #78: MdrunMultiSimReplexTests .................. Passed 0.26 sec test 79 Start 79: MdrunMultiSimReplexEquivalenceTests 79: Test command: /build/reproducible-path/gromacs-2025.1/build/basic-dp/bin/mdrun-multisim-replex-equivalence-test "-ntmpi" "4" "--gtest_output=xml:/build/reproducible-path/gromacs-2025.1/build/basic-dp/Testing/Temporary/MdrunMultiSimReplexEquivalenceTests.xml" 79: Working Directory: /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests 79: Test timeout computed to be: 600 79: [==========] Running 0 tests from 0 test suites. 79: [==========] 0 tests from 0 test suites ran. (0 ms total) 79: [ PASSED ] 0 tests. 79: 79: YOU HAVE 10 DISABLED TESTS 79: 79/92 Test #79: MdrunMultiSimReplexEquivalenceTests ....... Passed 0.11 sec test 80 Start 80: MdrunMpi1RankPmeTests 80: Test command: /build/reproducible-path/gromacs-2025.1/build/basic-dp/bin/mdrun-mpi-pme-test "-ntomp" "2" "-ntmpi" "1" "--gtest_output=xml:/build/reproducible-path/gromacs-2025.1/build/basic-dp/Testing/Temporary/MdrunMpi1RankPmeTests.xml" 80: Working Directory: /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests 80: Test timeout computed to be: 600 80: [==========] Running 19 tests from 1 test suite. 80: [----------] Global test environment set-up. 80: [----------] 19 tests from ReproducesEnergies/PmeTest 80: Number of degrees of freedom in T-Coupling group rest is 12.00 80: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 80: 80: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_input.mdp]: 80: NVE simulation: will use the initial temperature of 1046.791 K for 80: determining the Verlet buffer size 80: 80: 80: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_input.mdp]: 80: The optimal PME mesh load for parallel simulations is below 0.5 80: and for highly parallel simulations between 0.25 and 0.33, 80: for higher performance, increase the cut-off and the PME grid spacing. 80: 80: 80: 80: There were 2 NOTEs 80: 80: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_input.mdp]: 80: For a correct single-point energy evaluation with nsteps = 0, use 80: continuation = yes to avoid constraining the input coordinates. 80: 80: Number of degrees of freedom in T-Coupling group rest is 13.00 80: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 80: 80: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_input.mdp]: 80: NVE simulation: will use the initial temperature of 966.268 K for 80: determining the Verlet buffer size 80: 80: 80: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_input.mdp]: 80: The optimal PME mesh load for parallel simulations is below 0.5 80: and for highly parallel simulations between 0.25 and 0.33, 80: for higher performance, increase the cut-off and the PME grid spacing. 80: 80: 80: 80: There were 3 NOTEs 80: Setting the LD random seed to -973078665 80: 80: Generated 8 of the 10 non-bonded parameter combinations 80: 80: Excluding 2 bonded neighbours molecule type 'Methanol' 80: 80: Excluding 2 bonded neighbours molecule type 'SOL' 80: 80: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/spc-and-methanol.gro' 80: 80: The largest distance between excluded atoms is 0.190 nm between atom 1 and 3 80: 80: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 1046.79 K 80: 80: Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm 80: 80: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm 80: 80: Note that mdrun will redetermine rlist based on the actual pair-list setup 80: Calculating fourier grid dimensions for X Y Z 80: Using a fourier grid of 28x28x28, spacing 0.107 0.107 0.107 80: 80: Estimate for the relative computational load of the PME mesh part: 1.00 80: 80: This run will generate roughly 0 Mb of data 80: Setting the LD random seed to -1779696145 80: 80: Generated 8 of the 10 non-bonded parameter combinations 80: 80: Excluding 2 bonded neighbours molecule type 'Methanol' 80: 80: Excluding 2 bonded neighbours molecule type 'SOL' 80: 80: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/spc-and-methanol.gro' 80: 80: Searching the wall atom type(s) 80: 80: The largest distance between excluded atoms is 0.190 nm between atom 1 and 3 80: 80: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 966.268 K 80: 80: Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm 80: 80: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm 80: 80: Note that mdrun will redetermine rlist based on the actual pair-list setup 80: Calculating fourier grid dimensions for X Y Z 80: Using a fourier grid of 28x28x128, spacing 0.107 0.107 0.118 80: 80: Estimate for the relative computational load of the PME mesh part: 1.00 80: 80: This run will generate roughly 0 Mb of data 80: [ RUN ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_0__pme_cpu 80: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_basic.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 80: Can not increase nstlist because an NVE ensemble is used 80: Using 1 MPI thread 80: Using 2 OpenMP threads 80: 80: 80: NOTE: The number of threads is not equal to the number of (logical) cpus 80: and the -pin option is set to auto: will not pin threads to cpus. 80: This can lead to significant performance degradation. 80: Consider using -pin on (and -pinoffset in case you run multiple jobs). 80: starting mdrun 'spc-and-methanol' 80: 20 steps, 0.0 ps. 80: 80: Writing final coordinates. 80: 80: Core t (s) Wall t (s) (%) 80: Time: 2.482 1.241 200.0 80: (ns/day) (hour/ns) 80: Performance: 1.462 16.420 80: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_Runs_basic__notunepme__npme_0__pme_cpu.edr as double precision energy file 80: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 17 time 0.017 Reading energy frame 18 time 0.018 Reading energy frame 19 time 0.019 Reading energy frame 20 time 0.020 Last energy frame read 20 time 0.020 [ OK ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_0__pme_cpu (1434 ms) 80: [ RUN ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_0__pme_auto 80: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_basic.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 80: Can not increase nstlist because an NVE ensemble is used 80: Using 1 MPI thread 80: Using 2 OpenMP threads 80: 80: 80: NOTE: The number of threads is not equal to the number of (logical) cpus 80: and the -pin option is set to auto: will not pin threads to cpus. 80: This can lead to significant performance degradation. 80: Consider using -pin on (and -pinoffset in case you run multiple jobs). 80: starting mdrun 'spc-and-methanol' 80: 20 steps, 0.0 ps. 80: 80: Writing final coordinates. 80: 80: Core t (s) Wall t (s) (%) 80: Time: 1.844 0.922 199.9 80: (ns/day) (hour/ns) 80: Performance: 1.967 12.199 80: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_Runs_basic__notunepme__npme_0__pme_auto.edr as double precision energy file 80: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 17 time 0.017 Reading energy frame 18 time 0.018 Reading energy frame 19 time 0.019 Reading energy frame 20 time 0.020 Last energy frame read 20 time 0.020 [ OK ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_0__pme_auto (1030 ms) 80: [ RUN ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_0__pme_gpu__pmefft_cpu 80: ./src/programs/mdrun/tests/pmetest.cpp:309: Skipped 80: Test is being skipped because: 80: it targets GPU execution, but no compatible devices were detected 80: PME GPU does not support: 80: Double-precision build of GROMACS. 80: Non-GPU build of GROMACS. 80: 80: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_0__pme_gpu__pmefft_cpu (0 ms) 80: [ RUN ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_0__pme_gpu__pmefft_gpu 80: ./src/programs/mdrun/tests/pmetest.cpp:309: Skipped 80: Test is being skipped because: 80: it targets GPU execution, but no compatible devices were detected 80: PME GPU does not support: 80: Double-precision build of GROMACS. 80: Non-GPU build of GROMACS. 80: 80: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_0__pme_gpu__pmefft_gpu (0 ms) 80: [ RUN ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_0__pme_gpu__pmefft_auto 80: ./src/programs/mdrun/tests/pmetest.cpp:309: Skipped 80: Test is being skipped because: 80: it targets GPU execution, but no compatible devices were detected 80: PME GPU does not support: 80: Double-precision build of GROMACS. 80: Non-GPU build of GROMACS. 80: 80: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_0__pme_gpu__pmefft_auto (0 ms) 80: [ RUN ] ReproducesEnergies/PmeTest.Runs/with_walls__notunepme__npme_0__pme_cpu 80: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_with_walls.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 80: Can not increase nstlist because an NVE ensemble is used 80: Using 1 MPI thread 80: Using 2 OpenMP threads 80: 80: 80: NOTE: The number of threads is not equal to the number of (logical) cpus 80: and the -pin option is set to auto: will not pin threads to cpus. 80: This can lead to significant performance degradation. 80: Consider using -pin on (and -pinoffset in case you run multiple jobs). 80: starting mdrun 'spc-and-methanol' 80: 0 steps, 0.0 ps. 80: 80: Core t (s) Wall t (s) (%) 80: Time: 0.432 0.216 199.7 80: (ns/day) (hour/ns) 80: Performance: 0.399 60.082 80: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_Runs_with_walls__notunepme__npme_0__pme_cpu.edr as double precision energy file 80: Reading energy frame 0 time 0.000 Last energy frame read 0 time 0.000 [ OK ] ReproducesEnergies/PmeTest.Runs/with_walls__notunepme__npme_0__pme_cpu (512 ms) 80: [ RUN ] ReproducesEnergies/PmeTest.Runs/with_walls__notunepme__npme_0__pme_gpu__pmefft_cpu 80: ./src/programs/mdrun/tests/pmetest.cpp:309: Skipped 80: Test is being skipped because: 80: it targets GPU execution, but no compatible devices were detected 80: PME GPU does not support: 80: Double-precision build of GROMACS. 80: Non-GPU build of GROMACS. 80: 80: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/with_walls__notunepme__npme_0__pme_gpu__pmefft_cpu (5 ms) 80: [ RUN ] ReproducesEnergies/PmeTest.Runs/with_walls__notunepme__npme_0__pme_gpu__pmefft_gpu 80: ./src/programs/mdrun/tests/pmetest.cpp:309: Skipped 80: Test is being skipped because: 80: it targets GPU execution, but no compatible devices were detected 80: PME GPU does not support: 80: Double-precision build of GROMACS. 80: Non-GPU build of GROMACS. 80: 80: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/with_walls__notunepme__npme_0__pme_gpu__pmefft_gpu (0 ms) 80: [ RUN ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_1__pme_cpu 80: ./src/programs/mdrun/tests/pmetest.cpp:309: Skipped 80: Test is being skipped because: 80: it targets using PME rank(s) but the simulation is using only one rank 80: 80: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_1__pme_cpu (0 ms) 80: [ RUN ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_1__pme_auto 80: ./src/programs/mdrun/tests/pmetest.cpp:309: Skipped 80: Test is being skipped because: 80: it targets using PME rank(s) but the simulation is using only one rank 80: 80: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_1__pme_auto (0 ms) 80: [ RUN ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_1__pme_gpu__pmefft_cpu 80: ./src/programs/mdrun/tests/pmetest.cpp:309: Skipped 80: Test is being skipped because: 80: it targets using PME rank(s) but the simulation is using only one rank 80: it targets GPU execution, but no compatible devices were detected 80: PME GPU does not support: 80: Double-precision build of GROMACS. 80: Non-GPU build of GROMACS. 80: 80: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_1__pme_gpu__pmefft_cpu (0 ms) 80: [ RUN ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_1__pme_gpu__pmefft_gpu 80: ./src/programs/mdrun/tests/pmetest.cpp:309: Skipped 80: Test is being skipped because: 80: it targets using PME rank(s) but the simulation is using only one rank 80: it targets GPU execution, but no compatible devices were detected 80: PME GPU does not support: 80: Double-precision build of GROMACS. 80: Non-GPU build of GROMACS. 80: 80: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_1__pme_gpu__pmefft_gpu (5 ms) 80: [ RUN ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_1__pme_gpu__pmefft_auto 80: ./src/programs/mdrun/tests/pmetest.cpp:309: Skipped 80: Test is being skipped because: 80: it targets using PME rank(s) but the simulation is using only one rank 80: it targets GPU execution, but no compatible devices were detected 80: PME GPU does not support: 80: Double-precision build of GROMACS. 80: Non-GPU build of GROMACS. 80: 80: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_1__pme_gpu__pmefft_auto (0 ms) 80: [ RUN ] ReproducesEnergies/PmeTest.Runs/with_walls__notunepme__npme_1__pme_cpu 80: ./src/programs/mdrun/tests/pmetest.cpp:309: Skipped 80: Test is being skipped because: 80: it targets using PME rank(s) but the simulation is using only one rank 80: 80: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/with_walls__notunepme__npme_1__pme_cpu (0 ms) 80: [ RUN ] ReproducesEnergies/PmeTest.Runs/with_walls__notunepme__npme_1__pme_gpu__pmefft_cpu 80: ./src/programs/mdrun/tests/pmetest.cpp:309: Skipped 80: Test is being skipped because: 80: it targets using PME rank(s) but the simulation is using only one rank 80: it targets GPU execution, but no compatible devices were detected 80: PME GPU does not support: 80: Double-precision build of GROMACS. 80: Non-GPU build of GROMACS. 80: 80: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/with_walls__notunepme__npme_1__pme_gpu__pmefft_cpu (0 ms) 80: [ RUN ] ReproducesEnergies/PmeTest.Runs/with_walls__notunepme__npme_1__pme_gpu__pmefft_gpu 80: ./src/programs/mdrun/tests/pmetest.cpp:309: Skipped 80: Test is being skipped because: 80: it targets using PME rank(s) but the simulation is using only one rank 80: it targets GPU execution, but no compatible devices were detected 80: PME GPU does not support: 80: Double-precision build of GROMACS. 80: Non-GPU build of GROMACS. 80: 80: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/with_walls__notunepme__npme_1__pme_gpu__pmefft_gpu (0 ms) 80: [ RUN ] ReproducesEnergies/PmeTest.Runs/basic__tunepme__npme_0__pme_cpu 80: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_basic.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 80: Can not increase nstlist because an NVE ensemble is used 80: Using 1 MPI thread 80: Using 2 OpenMP threads 80: 80: 80: NOTE: The number of threads is not equal to the number of (logical) cpus 80: and the -pin option is set to auto: will not pin threads to cpus. 80: This can lead to significant performance degradation. 80: Consider using -pin on (and -pinoffset in case you run multiple jobs). 80: starting mdrun 'spc-and-methanol' 80: 20 steps, 0.0 ps. 80: 80: Writing final coordinates. 80: 80: Core t (s) Wall t (s) (%) 80: Time: 1.384 0.692 199.9 80: (ns/day) (hour/ns) 80: Performance: 2.622 9.154 80: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_Runs_basic__tunepme__npme_0__pme_cpu.edr as double precision energy file 80: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 17 time 0.017 Reading energy frame 18 time 0.018 Reading energy frame 19 time 0.019 Reading energy frame 20 time 0.020 Last energy frame read 20 time 0.020 [ OK ] ReproducesEnergies/PmeTest.Runs/basic__tunepme__npme_0__pme_cpu (780 ms) 80: [ RUN ] ReproducesEnergies/PmeTest.Runs/basic__tunepme__npme_0__pme_gpu__pmefft_cpu 80: ./src/programs/mdrun/tests/pmetest.cpp:309: Skipped 80: Test is being skipped because: 80: it targets GPU execution, but no compatible devices were detected 80: PME GPU does not support: 80: Double-precision build of GROMACS. 80: Non-GPU build of GROMACS. 80: 80: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic__tunepme__npme_0__pme_gpu__pmefft_cpu (0 ms) 80: [ RUN ] ReproducesEnergies/PmeTest.Runs/basic__tunepme__npme_0__pme_gpu__pmefft_gpu 80: ./src/programs/mdrun/tests/pmetest.cpp:309: Skipped 80: Test is being skipped because: 80: it targets GPU execution, but no compatible devices were detected 80: PME GPU does not support: 80: Double-precision build of GROMACS. 80: Non-GPU build of GROMACS. 80: 80: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic__tunepme__npme_0__pme_gpu__pmefft_gpu (0 ms) 80: [----------] 19 tests from ReproducesEnergies/PmeTest (3779 ms total) 80: 80: [----------] Global test environment tear-down 80: [==========] 19 tests from 1 test suite ran. (3914 ms total) 80: [ PASSED ] 4 tests. 80: [ SKIPPED ] 15 tests, listed below: 80: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_0__pme_gpu__pmefft_cpu 80: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_0__pme_gpu__pmefft_gpu 80: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_0__pme_gpu__pmefft_auto 80: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/with_walls__notunepme__npme_0__pme_gpu__pmefft_cpu 80: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/with_walls__notunepme__npme_0__pme_gpu__pmefft_gpu 80: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_1__pme_cpu 80: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_1__pme_auto 80: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_1__pme_gpu__pmefft_cpu 80: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_1__pme_gpu__pmefft_gpu 80: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_1__pme_gpu__pmefft_auto 80: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/with_walls__notunepme__npme_1__pme_cpu 80: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/with_walls__notunepme__npme_1__pme_gpu__pmefft_cpu 80: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/with_walls__notunepme__npme_1__pme_gpu__pmefft_gpu 80: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic__tunepme__npme_0__pme_gpu__pmefft_cpu 80: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic__tunepme__npme_0__pme_gpu__pmefft_gpu 80/92 Test #80: MdrunMpi1RankPmeTests ..................... Passed 4.02 sec test 81 Start 81: MdrunMpi2RankPmeTests 81: Test command: /build/reproducible-path/gromacs-2025.1/build/basic-dp/bin/mdrun-mpi-pme-test "-ntomp" "2" "-ntmpi" "2" "--gtest_output=xml:/build/reproducible-path/gromacs-2025.1/build/basic-dp/Testing/Temporary/MdrunMpi2RankPmeTests.xml" 81: Working Directory: /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests 81: Test timeout computed to be: 600 81: [==========] Running 19 tests from 1 test suite. 81: [----------] Global test environment set-up. 81: [----------] 19 tests from ReproducesEnergies/PmeTest 81: Number of degrees of freedom in T-Coupling group rest is 12.00 81: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 81: 81: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_input.mdp]: 81: NVE simulation: will use the initial temperature of 1046.791 K for 81: determining the Verlet buffer size 81: 81: 81: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_input.mdp]: 81: The optimal PME mesh load for parallel simulations is below 0.5 81: and for highly parallel simulations between 0.25 and 0.33, 81: for higher performance, increase the cut-off and the PME grid spacing. 81: 81: 81: 81: There were 2 NOTEs 81: 81: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_input.mdp]: 81: For a correct single-point energy evaluation with nsteps = 0, use 81: continuation = yes to avoid constraining the input coordinates. 81: 81: Number of degrees of freedom in T-Coupling group rest is 13.00 81: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 81: 81: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_input.mdp]: 81: NVE simulation: will use the initial temperature of 966.268 K for 81: determining the Verlet buffer size 81: 81: 81: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_input.mdp]: 81: The optimal PME mesh load for parallel simulations is below 0.5 81: and for highly parallel simulations between 0.25 and 0.33, 81: for higher performance, increase the cut-off and the PME grid spacing. 81: 81: 81: 81: There were 3 NOTEs 81: Setting the LD random seed to 1869307719 81: 81: Generated 8 of the 10 non-bonded parameter combinations 81: 81: Excluding 2 bonded neighbours molecule type 'Methanol' 81: 81: Excluding 2 bonded neighbours molecule type 'SOL' 81: 81: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/spc-and-methanol.gro' 81: 81: The largest distance between excluded atoms is 0.190 nm between atom 1 and 3 81: 81: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 1046.79 K 81: 81: Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm 81: 81: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm 81: 81: Note that mdrun will redetermine rlist based on the actual pair-list setup 81: Calculating fourier grid dimensions for X Y Z 81: Using a fourier grid of 28x28x28, spacing 0.107 0.107 0.107 81: 81: Estimate for the relative computational load of the PME mesh part: 1.00 81: 81: This run will generate roughly 0 Mb of data 81: Setting the LD random seed to 2011036351 81: 81: Generated 8 of the 10 non-bonded parameter combinations 81: 81: Excluding 2 bonded neighbours molecule type 'Methanol' 81: 81: Excluding 2 bonded neighbours molecule type 'SOL' 81: 81: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/spc-and-methanol.gro' 81: 81: Searching the wall atom type(s) 81: 81: The largest distance between excluded atoms is 0.190 nm between atom 1 and 3 81: 81: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 966.268 K 81: 81: Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm 81: 81: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm 81: 81: Note that mdrun will redetermine rlist based on the actual pair-list setup 81: Calculating fourier grid dimensions for X Y Z 81: Using a fourier grid of 28x28x128, spacing 0.107 0.107 0.118 81: 81: Estimate for the relative computational load of the PME mesh part: 1.00 81: 81: This run will generate roughly 0 Mb of data 81: [ RUN ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_0__pme_cpu 81: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_basic.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 81: Can not increase nstlist because an NVE ensemble is used 81: Using 2 MPI threads 81: Using 2 OpenMP threads per tMPI thread 81: 81: starting mdrun 'spc-and-methanol' 81: 20 steps, 0.0 ps. 81: 81: Writing final coordinates. 81: 81: 81: Dynamic load balancing report: 81: DLB was off during the run due to low measured imbalance. 81: Average load imbalance: 6.0%. 81: The balanceable part of the MD step is 25%, load imbalance is computed from this. 81: Part of the total run time spent waiting due to load imbalance: 1.5%. 81: 81: 81: NOTE: 10 % of the run time was spent in domain decomposition, 81: 0 % of the run time was spent in pair search, 81: you might want to increase nstlist (this has no effect on accuracy) 81: 81: NOTE: 5 % of the run time was spent communicating energies, 81: you might want to increase some nst* mdp options 81: 81: Core t (s) Wall t (s) (%) 81: Time: 11.440 2.860 399.9 81: (ns/day) (hour/ns) 81: Performance: 0.634 37.834 81: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_Runs_basic__notunepme__npme_0__pme_cpu.edr as double precision energy file 81: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 17 time 0.017 Reading energy frame 18 time 0.018 Reading energy frame 19 time 0.019 Reading energy frame 20 time 0.020 Last energy frame read 20 time 0.020 [ OK ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_0__pme_cpu (3248 ms) 81: [ RUN ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_0__pme_auto 81: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_basic.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 81: Can not increase nstlist because an NVE ensemble is used 81: Using 2 MPI threads 81: 81: Non-default thread affinity set, disabling internal thread affinity 81: 81: Using 2 OpenMP threads per tMPI thread 81: 81: starting mdrun 'spc-and-methanol' 81: 20 steps, 0.0 ps. 81: 81: Writing final coordinates. 81: 81: 81: Dynamic load balancing report: 81: DLB was turned on during the run due to measured imbalance. 81: Average load imbalance: 26.9%. 81: The balanceable part of the MD step is 20%, load imbalance is computed from this. 81: Part of the total run time spent waiting due to load imbalance: 5.3%. 81: Steps where the load balancing was limited by -rdd, -rcon and/or -dds: X 0 % 81: 81: NOTE: 5.3 % of the available CPU time was lost due to load imbalance 81: in the domain decomposition. 81: You can consider manually changing the decomposition (option -dd); 81: e.g. by using fewer domains along the box dimension in which there is 81: considerable inhomogeneity in the simulated system. 81: 81: NOTE: 10 % of the run time was spent communicating energies, 81: you might want to increase some nst* mdp options 81: 81: Core t (s) Wall t (s) (%) 81: Time: 17.860 4.481 398.6 81: (ns/day) (hour/ns) 81: Performance: 0.405 59.270 81: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_Runs_basic__notunepme__npme_0__pme_auto.edr as double precision energy file 81: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 17 time 0.017 Reading energy frame 18 time 0.018 Reading energy frame 19 time 0.019 Reading energy frame 20 time 0.020 Last energy frame read 20 time 0.020 [ OK ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_0__pme_auto (5296 ms) 81: [ RUN ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_0__pme_gpu__pmefft_cpu 81: ./src/programs/mdrun/tests/pmetest.cpp:309: Skipped 81: Test is being skipped because: 81: it targets GPU execution, but no compatible devices were detected 81: it targets PME decomposition, but that is not supported 81: PME GPU does not support: 81: Double-precision build of GROMACS. 81: Non-GPU build of GROMACS. 81: 81: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_0__pme_gpu__pmefft_cpu (0 ms) 81: [ RUN ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_0__pme_gpu__pmefft_gpu 81: ./src/programs/mdrun/tests/pmetest.cpp:309: Skipped 81: Test is being skipped because: 81: it targets GPU execution, but no compatible devices were detected 81: it targets PME decomposition, but that is not supported 81: PME GPU does not support: 81: Double-precision build of GROMACS. 81: Non-GPU build of GROMACS. 81: 81: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_0__pme_gpu__pmefft_gpu (0 ms) 81: [ RUN ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_0__pme_gpu__pmefft_auto 81: ./src/programs/mdrun/tests/pmetest.cpp:309: Skipped 81: Test is being skipped because: 81: it targets GPU execution, but no compatible devices were detected 81: it targets PME decomposition, but that is not supported 81: PME GPU does not support: 81: Double-precision build of GROMACS. 81: Non-GPU build of GROMACS. 81: 81: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_0__pme_gpu__pmefft_auto (3 ms) 81: [ RUN ] ReproducesEnergies/PmeTest.Runs/with_walls__notunepme__npme_0__pme_cpu 81: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_with_walls.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 81: Can not increase nstlist because an NVE ensemble is used 81: Using 2 MPI threads 81: 81: Non-default thread affinity set, disabling internal thread affinity 81: 81: Using 2 OpenMP threads per tMPI thread 81: 81: starting mdrun 'spc-and-methanol' 81: 0 steps, 0.0 ps. 81: 81: NOTE: 22 % of the run time was spent in domain decomposition, 81: 4 % of the run time was spent in pair search, 81: you might want to increase nstlist (this has no effect on accuracy) 81: 81: NOTE: 6 % of the run time was spent communicating energies, 81: you might want to increase some nst* mdp options 81: 81: Core t (s) Wall t (s) (%) 81: Time: 1.371 0.353 388.6 81: (ns/day) (hour/ns) 81: Performance: 0.245 97.991 81: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_Runs_with_walls__notunepme__npme_0__pme_cpu.edr as double precision energy file 81: Reading energy frame 0 time 0.000 Last energy frame read 0 time 0.000 [ OK ] ReproducesEnergies/PmeTest.Runs/with_walls__notunepme__npme_0__pme_cpu (1261 ms) 81: [ RUN ] ReproducesEnergies/PmeTest.Runs/with_walls__notunepme__npme_0__pme_gpu__pmefft_cpu 81: ./src/programs/mdrun/tests/pmetest.cpp:309: Skipped 81: Test is being skipped because: 81: it targets GPU execution, but no compatible devices were detected 81: it targets PME decomposition, but that is not supported 81: PME GPU does not support: 81: Double-precision build of GROMACS. 81: Non-GPU build of GROMACS. 81: 81: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/with_walls__notunepme__npme_0__pme_gpu__pmefft_cpu (0 ms) 81: [ RUN ] ReproducesEnergies/PmeTest.Runs/with_walls__notunepme__npme_0__pme_gpu__pmefft_gpu 81: ./src/programs/mdrun/tests/pmetest.cpp:309: Skipped 81: Test is being skipped because: 81: it targets GPU execution, but no compatible devices were detected 81: it targets PME decomposition, but that is not supported 81: PME GPU does not support: 81: Double-precision build of GROMACS. 81: Non-GPU build of GROMACS. 81: 81: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/with_walls__notunepme__npme_0__pme_gpu__pmefft_gpu (0 ms) 81: [ RUN ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_1__pme_cpu 81: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_basic.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 81: Can not increase nstlist because an NVE ensemble is used 81: Using 2 MPI threads 81: 81: Non-default thread affinity set, disabling internal thread affinity 81: 81: Using 2 OpenMP threads per tMPI thread 81: 81: starting mdrun 'spc-and-methanol' 81: 20 steps, 0.0 ps. 81: 81: Writing final coordinates. 81: 81: Core t (s) Wall t (s) (%) 81: Time: 7.554 1.910 395.5 81: (ns/day) (hour/ns) 81: Performance: 0.950 25.263 81: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_Runs_basic__notunepme__npme_1__pme_cpu.edr as double precision energy file 81: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 17 time 0.017 Reading energy frame 18 time 0.018 Reading energy frame 19 time 0.019 Reading energy frame 20 time 0.020 Last energy frame read 20 time 0.020 [ OK ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_1__pme_cpu (2463 ms) 81: [ RUN ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_1__pme_auto 81: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_basic.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 81: Can not increase nstlist because an NVE ensemble is used 81: Using 2 MPI threads 81: 81: Non-default thread affinity set, disabling internal thread affinity 81: 81: Using 2 OpenMP threads per tMPI thread 81: 81: starting mdrun 'spc-and-methanol' 81: 20 steps, 0.0 ps. 81: 81: Writing final coordinates. 81: 81: Core t (s) Wall t (s) (%) 81: Time: 7.682 1.938 396.4 81: (ns/day) (hour/ns) 81: Performance: 0.936 25.633 81: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_Runs_basic__notunepme__npme_1__pme_auto.edr as double precision energy file 81: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 17 time 0.017 Reading energy frame 18 time 0.018 Reading energy frame 19 time 0.019 Reading energy frame 20 time 0.020 Last energy frame read 20 time 0.020 [ OK ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_1__pme_auto (2487 ms) 81: [ RUN ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_1__pme_gpu__pmefft_cpu 81: ./src/programs/mdrun/tests/pmetest.cpp:309: Skipped 81: Test is being skipped because: 81: it targets GPU execution, but no compatible devices were detected 81: PME GPU does not support: 81: Double-precision build of GROMACS. 81: Non-GPU build of GROMACS. 81: 81: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_1__pme_gpu__pmefft_cpu (0 ms) 81: [ RUN ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_1__pme_gpu__pmefft_gpu 81: ./src/programs/mdrun/tests/pmetest.cpp:309: Skipped 81: Test is being skipped because: 81: it targets GPU execution, but no compatible devices were detected 81: PME GPU does not support: 81: Double-precision build of GROMACS. 81: Non-GPU build of GROMACS. 81: 81: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_1__pme_gpu__pmefft_gpu (0 ms) 81: [ RUN ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_1__pme_gpu__pmefft_auto 81: ./src/programs/mdrun/tests/pmetest.cpp:309: Skipped 81: Test is being skipped because: 81: it targets GPU execution, but no compatible devices were detected 81: PME GPU does not support: 81: Double-precision build of GROMACS. 81: Non-GPU build of GROMACS. 81: 81: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_1__pme_gpu__pmefft_auto (0 ms) 81: [ RUN ] ReproducesEnergies/PmeTest.Runs/with_walls__notunepme__npme_1__pme_cpu 81: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_with_walls.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 81: Can not increase nstlist because an NVE ensemble is used 81: Using 2 MPI threads 81: 81: Non-default thread affinity set, disabling internal thread affinity 81: 81: Using 2 OpenMP threads per tMPI thread 81: 81: starting mdrun 'spc-and-methanol' 81: 0 steps, 0.0 ps. 81: 81: NOTE: 12 % of the run time was spent in domain decomposition, 81: 0 % of the run time was spent in pair search, 81: you might want to increase nstlist (this has no effect on accuracy) 81: 81: Core t (s) Wall t (s) (%) 81: Time: 1.124 0.302 372.4 81: (ns/day) (hour/ns) 81: Performance: 0.286 83.836 81: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_Runs_with_walls__notunepme__npme_1__pme_cpu.edr as double precision energy file 81: Reading energy frame 0 time 0.000 Last energy frame read 0 time 0.000 [ OK ] ReproducesEnergies/PmeTest.Runs/with_walls__notunepme__npme_1__pme_cpu (950 ms) 81: [ RUN ] ReproducesEnergies/PmeTest.Runs/with_walls__notunepme__npme_1__pme_gpu__pmefft_cpu 81: ./src/programs/mdrun/tests/pmetest.cpp:309: Skipped 81: Test is being skipped because: 81: it targets GPU execution, but no compatible devices were detected 81: PME GPU does not support: 81: Double-precision build of GROMACS. 81: Non-GPU build of GROMACS. 81: 81: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/with_walls__notunepme__npme_1__pme_gpu__pmefft_cpu (0 ms) 81: [ RUN ] ReproducesEnergies/PmeTest.Runs/with_walls__notunepme__npme_1__pme_gpu__pmefft_gpu 81: ./src/programs/mdrun/tests/pmetest.cpp:309: Skipped 81: Test is being skipped because: 81: it targets GPU execution, but no compatible devices were detected 81: PME GPU does not support: 81: Double-precision build of GROMACS. 81: Non-GPU build of GROMACS. 81: 81: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/with_walls__notunepme__npme_1__pme_gpu__pmefft_gpu (0 ms) 81: [ RUN ] ReproducesEnergies/PmeTest.Runs/basic__tunepme__npme_0__pme_cpu 81: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_basic.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 81: Can not increase nstlist because an NVE ensemble is used 81: Using 2 MPI threads 81: 81: Non-default thread affinity set, disabling internal thread affinity 81: 81: Using 2 OpenMP threads per tMPI thread 81: 81: starting mdrun 'spc-and-methanol' 81: 20 steps, 0.0 ps. 81: 81: Writing final coordinates. 81: 81: 81: Dynamic load balancing report: 81: DLB was turned on during the run due to measured imbalance. 81: Average load imbalance: 23.4%. 81: The balanceable part of the MD step is 20%, load imbalance is computed from this. 81: Part of the total run time spent waiting due to load imbalance: 4.6%. 81: Steps where the load balancing was limited by -rdd, -rcon and/or -dds: X 0 % 81: 81: 81: NOTE: 11 % of the run time was spent communicating energies, 81: you might want to increase some nst* mdp options 81: 81: Core t (s) Wall t (s) (%) 81: Time: 16.168 4.058 398.4 81: (ns/day) (hour/ns) 81: Performance: 0.447 53.676 81: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_Runs_basic__tunepme__npme_0__pme_cpu.edr as double precision energy file 81: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 17 time 0.017 Reading energy frame 18 time 0.018 Reading energy frame 19 time 0.019 Reading energy frame 20 time 0.020 Last energy frame read 20 time 0.020 [ OK ] ReproducesEnergies/PmeTest.Runs/basic__tunepme__npme_0__pme_cpu (4840 ms) 81: [ RUN ] ReproducesEnergies/PmeTest.Runs/basic__tunepme__npme_0__pme_gpu__pmefft_cpu 81: ./src/programs/mdrun/tests/pmetest.cpp:309: Skipped 81: Test is being skipped because: 81: it targets GPU execution, but no compatible devices were detected 81: it targets PME decomposition, but that is not supported 81: PME GPU does not support: 81: Double-precision build of GROMACS. 81: Non-GPU build of GROMACS. 81: 81: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic__tunepme__npme_0__pme_gpu__pmefft_cpu (0 ms) 81: [ RUN ] ReproducesEnergies/PmeTest.Runs/basic__tunepme__npme_0__pme_gpu__pmefft_gpu 81: ./src/programs/mdrun/tests/pmetest.cpp:309: Skipped 81: Test is being skipped because: 81: it targets GPU execution, but no compatible devices were detected 81: it targets PME decomposition, but that is not supported 81: PME GPU does not support: 81: Double-precision build of GROMACS. 81: Non-GPU build of GROMACS. 81: 81: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic__tunepme__npme_0__pme_gpu__pmefft_gpu (0 ms) 81: [----------] 19 tests from ReproducesEnergies/PmeTest (20561 ms total) 81: 81: [----------] Global test environment tear-down 81: [==========] 19 tests from 1 test suite ran. (20687 ms total) 81: [ PASSED ] 7 tests. 81: [ SKIPPED ] 12 tests, listed below: 81: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_0__pme_gpu__pmefft_cpu 81: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_0__pme_gpu__pmefft_gpu 81: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_0__pme_gpu__pmefft_auto 81: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/with_walls__notunepme__npme_0__pme_gpu__pmefft_cpu 81: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/with_walls__notunepme__npme_0__pme_gpu__pmefft_gpu 81: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_1__pme_gpu__pmefft_cpu 81: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_1__pme_gpu__pmefft_gpu 81: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_1__pme_gpu__pmefft_auto 81: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/with_walls__notunepme__npme_1__pme_gpu__pmefft_cpu 81: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/with_walls__notunepme__npme_1__pme_gpu__pmefft_gpu 81: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic__tunepme__npme_0__pme_gpu__pmefft_cpu 81: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic__tunepme__npme_0__pme_gpu__pmefft_gpu 81/92 Test #81: MdrunMpi2RankPmeTests ..................... Passed 20.80 sec test 82 Start 82: MdrunCoordinationBasicTests1Rank 82: Test command: /build/reproducible-path/gromacs-2025.1/build/basic-dp/bin/mdrun-coordination-basic-test "-ntmpi" "1" "--gtest_output=xml:/build/reproducible-path/gromacs-2025.1/build/basic-dp/Testing/Temporary/MdrunCoordinationBasicTests1Rank.xml" 82: Working Directory: /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests 82: Test timeout computed to be: 1920 82: [==========] Running 1 test from 1 test suite. 82: [----------] Global test environment set-up. 82: [----------] 1 test from BasicPropagators/PeriodicActionsTest 82: [ RUN ] BasicPropagators/PeriodicActionsTest.PeriodicActionsAgreeWithReference/0 82: 82: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 82: Setting nstcalcenergy (100) equal to nstenergy (1) 82: 82: Number of degrees of freedom in T-Coupling group System is 33.00 82: 82: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 82: NVE simulation: will use the initial temperature of 68.810 K for 82: determining the Verlet buffer size 82: 82: 82: There were 3 NOTEs 82: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 82: Can not increase nstlist because an NVE ensemble is used 82: Using 1 MPI thread 82: Using 1 OpenMP thread 82: 82: 82: NOTE: Thread affinity was not set. 82: starting mdrun 'Argon' 82: 16 steps, 0.0 ps. 82: Generated 1 of the 1 non-bonded parameter combinations 82: 82: Excluding 1 bonded neighbours molecule type 'Argon' 82: 82: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: Writing final coordinates. 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.025 0.026 99.1 82: (ns/day) (hour/ns) 82: Performance: 57.299 0.419 82: 82: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 82: Setting nstcalcenergy (100) equal to nstenergy (1) 82: 82: Number of degrees of freedom in T-Coupling group System is 33.00 82: 82: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 82: NVE simulation: will use the initial temperature of 68.810 K for 82: determining the Verlet buffer size 82: 82: 82: There were 3 NOTEs 82: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 82: Can not increase nstlist because an NVE ensemble is used 82: Using 1 MPI thread 82: Using 1 OpenMP thread 82: 82: 82: NOTE: Thread affinity was not set. 82: starting mdrun 'Argon' 82: 16 steps, 0.0 ps. 82: Generated 1 of the 1 non-bonded parameter combinations 82: 82: Excluding 1 bonded neighbours molecule type 'Argon' 82: 82: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: Writing final coordinates. 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.018 0.018 98.6 82: (ns/day) (hour/ns) 82: Performance: 80.496 0.298 82: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as double precision energy file 82: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as double precision energy file 82: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 82: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 82: Setting nstcalcenergy (100) equal to nstenergy (4) 82: 82: 82: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 82: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 82: setting nstcomm equal to nstcalcenergy for less overhead 82: 82: Number of degrees of freedom in T-Coupling group System is 33.00 82: 82: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 82: NVE simulation: will use the initial temperature of 68.810 K for 82: determining the Verlet buffer size 82: 82: 82: NOTE 5 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 82: COM removal frequency is set to (1). 82: Other settings require a global communication frequency of 4. 82: Note that this will require additional global communication steps, 82: which will reduce performance when using multiple ranks. 82: Consider setting nstcomm to a multiple of 4. 82: 82: 82: There were 5 NOTEs 82: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 82: Can not increase nstlist because an NVE ensemble is used 82: Using 1 MPI thread 82: Using 1 OpenMP thread 82: 82: 82: NOTE: Thread affinity was not set. 82: starting mdrun 'Argon' 82: 16 steps, 0.0 ps. 82: Generated 1 of the 1 non-bonded parameter combinations 82: 82: Excluding 1 bonded neighbours molecule type 'Argon' 82: 82: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: Writing final coordinates. 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.018 0.018 98.6 82: (ns/day) (hour/ns) 82: Performance: 81.586 0.294 82: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as double precision energy file 82: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as double precision energy file 82: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 82: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 82: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 82: setting nstcomm equal to nstcalcenergy for less overhead 82: 82: Number of degrees of freedom in T-Coupling group System is 33.00 82: 82: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 82: NVE simulation: will use the initial temperature of 68.810 K for 82: determining the Verlet buffer size 82: 82: 82: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 82: COM removal frequency is set to (1). 82: Other settings require a global communication frequency of 100. 82: Note that this will require additional global communication steps, 82: which will reduce performance when using multiple ranks. 82: Consider setting nstcomm to a multiple of 100. 82: 82: 82: There were 4 NOTEs 82: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 82: Can not increase nstlist because an NVE ensemble is used 82: Using 1 MPI thread 82: Using 1 OpenMP thread 82: 82: 82: NOTE: Thread affinity was not set. 82: starting mdrun 'Argon' 82: 16 steps, 0.0 ps. 82: Generated 1 of the 1 non-bonded parameter combinations 82: 82: Excluding 1 bonded neighbours molecule type 'Argon' 82: 82: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: Writing final coordinates. 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.021 0.021 98.8 82: (ns/day) (hour/ns) 82: Performance: 69.270 0.346 82: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as double precision energy file 82: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as double precision energy file 82: 82: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 82: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 82: setting nstcomm equal to nstcalcenergy for less overhead 82: 82: Number of degrees of freedom in T-Coupling group System is 33.00 82: 82: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 82: NVE simulation: will use the initial temperature of 68.810 K for 82: determining the Verlet buffer size 82: 82: 82: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 82: COM removal frequency is set to (1). 82: Other settings require a global communication frequency of 100. 82: Note that this will require additional global communication steps, 82: which will reduce performance when using multiple ranks. 82: Consider setting nstcomm to a multiple of 100. 82: 82: 82: There were 4 NOTEs 82: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 82: Can not increase nstlist because an NVE ensemble is used 82: Using 1 MPI thread 82: Using 1 OpenMP thread 82: 82: 82: NOTE: Thread affinity was not set. 82: starting mdrun 'Argon' 82: 16 steps, 0.0 ps. 82: Generated 1 of the 1 non-bonded parameter combinations 82: 82: Excluding 1 bonded neighbours molecule type 'Argon' 82: 82: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: Writing final coordinates. 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.020 0.020 98.7 82: (ns/day) (hour/ns) 82: Performance: 71.793 0.334 82: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as double precision energy file 82: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as double precision energy file 82: 82: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 82: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 82: setting nstcomm equal to nstcalcenergy for less overhead 82: 82: Number of degrees of freedom in T-Coupling group System is 33.00 82: 82: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 82: NVE simulation: will use the initial temperature of 68.810 K for 82: determining the Verlet buffer size 82: 82: 82: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 82: COM removal frequency is set to (1). 82: Other settings require a global communication frequency of 100. 82: Note that this will require additional global communication steps, 82: which will reduce performance when using multiple ranks. 82: Consider setting nstcomm to a multiple of 100. 82: 82: 82: There were 4 NOTEs 82: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 82: Can not increase nstlist because an NVE ensemble is used 82: Using 1 MPI thread 82: Using 1 OpenMP thread 82: 82: 82: NOTE: Thread affinity was not set. 82: starting mdrun 'Argon' 82: 16 steps, 0.0 ps. 82: Generated 1 of the 1 non-bonded parameter combinations 82: 82: Excluding 1 bonded neighbours molecule type 'Argon' 82: 82: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: Writing final coordinates. 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.022 0.023 98.8 82: (ns/day) (hour/ns) 82: Performance: 64.839 0.370 82: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as double precision energy file 82: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as double precision energy file 82: [ OK ] BasicPropagators/PeriodicActionsTest.PeriodicActionsAgreeWithReference/0 (386 ms) 82: [----------] 1 test from BasicPropagators/PeriodicActionsTest (386 ms total) 82: 82: [----------] Global test environment tear-down 82: [==========] 1 test from 1 test suite ran. (435 ms total) 82: [ PASSED ] 1 test. 82/92 Test #82: MdrunCoordinationBasicTests1Rank .......... Passed 0.51 sec test 83 Start 83: MdrunCoordinationBasicTests2Ranks 83: Test command: /build/reproducible-path/gromacs-2025.1/build/basic-dp/bin/mdrun-coordination-basic-test "-ntmpi" "2" "--gtest_output=xml:/build/reproducible-path/gromacs-2025.1/build/basic-dp/Testing/Temporary/MdrunCoordinationBasicTests2Ranks.xml" 83: Working Directory: /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests 83: Test timeout computed to be: 1920 83: [==========] Running 1 test from 1 test suite. 83: [----------] Global test environment set-up. 83: [----------] 1 test from BasicPropagators/PeriodicActionsTest 83: [ RUN ] BasicPropagators/PeriodicActionsTest.PeriodicActionsAgreeWithReference/0 83: 83: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 83: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 83: that with the Verlet scheme, nstlist has no effect on the accuracy of 83: your simulation. 83: 83: 83: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 83: Setting nstcalcenergy (100) equal to nstenergy (1) 83: 83: Number of degrees of freedom in T-Coupling group System is 33.00 83: 83: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 83: NVE simulation: will use the initial temperature of 68.810 K for 83: determining the Verlet buffer size 83: 83: 83: There were 3 NOTEs 83: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 83: Can not increase nstlist because an NVE ensemble is used 83: Using 2 MPI threads 83: Using 1 OpenMP thread per tMPI thread 83: 83: 83: NOTE: The number of threads is not equal to the number of (logical) cpus 83: and the -pin option is set to auto: will not pin threads to cpus. 83: This can lead to significant performance degradation. 83: Consider using -pin on (and -pinoffset in case you run multiple jobs). 83: starting mdrun 'Argon' 83: 16 steps, 0.0 ps. 83: Generated 1 of the 1 non-bonded parameter combinations 83: 83: Excluding 1 bonded neighbours molecule type 'Argon' 83: 83: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 83: 83: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 83: 83: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 83: 83: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 83: 83: Note that mdrun will redetermine rlist based on the actual pair-list setup 83: 83: This run will generate roughly 0 Mb of data 83: 83: Writing final coordinates. 83: 83: 83: Dynamic load balancing report: 83: DLB was off during the run due to low measured imbalance. 83: Average load imbalance: 0.9%. 83: The balanceable part of the MD step is 36%, load imbalance is computed from this. 83: Part of the total run time spent waiting due to load imbalance: 0.3%. 83: 83: 83: NOTE: 45 % of the run time was spent communicating energies, 83: you might want to increase some nst* mdp options 83: 83: Core t (s) Wall t (s) (%) 83: Time: 0.072 0.036 198.1 83: (ns/day) (hour/ns) 83: Performance: 40.550 0.592 83: 83: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 83: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 83: that with the Verlet scheme, nstlist has no effect on the accuracy of 83: your simulation. 83: 83: 83: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 83: Setting nstcalcenergy (100) equal to nstenergy (1) 83: 83: Number of degrees of freedom in T-Coupling group System is 33.00 83: 83: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 83: NVE simulation: will use the initial temperature of 68.810 K for 83: determining the Verlet buffer size 83: 83: 83: There were 3 NOTEs 83: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 83: Can not increase nstlist because an NVE ensemble is used 83: Using 2 MPI threads 83: Using 1 OpenMP thread per tMPI thread 83: 83: 83: NOTE: The number of threads is not equal to the number of (logical) cpus 83: and the -pin option is set to auto: will not pin threads to cpus. 83: This can lead to significant performance degradation. 83: Consider using -pin on (and -pinoffset in case you run multiple jobs). 83: starting mdrun 'Argon' 83: 16 steps, 0.0 ps. 83: Generated 1 of the 1 non-bonded parameter combinations 83: 83: Excluding 1 bonded neighbours molecule type 'Argon' 83: 83: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 83: 83: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 83: 83: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 83: 83: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 83: 83: Note that mdrun will redetermine rlist based on the actual pair-list setup 83: 83: This run will generate roughly 0 Mb of data 83: 83: Writing final coordinates. 83: 83: 83: Dynamic load balancing report: 83: DLB was turned on during the run due to measured imbalance. 83: Average load imbalance: 4.9%. 83: The balanceable part of the MD step is 42%, load imbalance is computed from this. 83: Part of the total run time spent waiting due to load imbalance: 2.1%. 83: Steps where the load balancing was limited by -rdd, -rcon and/or -dds: X 0 % 83: 83: 83: NOTE: 30 % of the run time was spent communicating energies, 83: you might want to increase some nst* mdp options 83: 83: Core t (s) Wall t (s) (%) 83: Time: 0.045 0.023 193.0 83: (ns/day) (hour/ns) 83: Performance: 63.196 0.380 83: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as double precision energy file 83: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as double precision energy file 83: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 83: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 83: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 83: that with the Verlet scheme, nstlist has no effect on the accuracy of 83: your simulation. 83: 83: 83: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 83: Setting nstcalcenergy (100) equal to nstenergy (4) 83: 83: 83: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 83: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 83: setting nstcomm equal to nstcalcenergy for less overhead 83: 83: Number of degrees of freedom in T-Coupling group System is 33.00 83: 83: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 83: NVE simulation: will use the initial temperature of 68.810 K for 83: determining the Verlet buffer size 83: 83: 83: NOTE 5 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 83: COM removal frequency is set to (1). 83: Other settings require a global communication frequency of 4. 83: Note that this will require additional global communication steps, 83: which will reduce performance when using multiple ranks. 83: Consider setting nstcomm to a multiple of 4. 83: 83: 83: There were 5 NOTEs 83: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 83: Can not increase nstlist because an NVE ensemble is used 83: Using 2 MPI threads 83: Using 1 OpenMP thread per tMPI thread 83: 83: 83: NOTE: The number of threads is not equal to the number of (logical) cpus 83: and the -pin option is set to auto: will not pin threads to cpus. 83: This can lead to significant performance degradation. 83: Consider using -pin on (and -pinoffset in case you run multiple jobs). 83: starting mdrun 'Argon' 83: 16 steps, 0.0 ps. 83: Generated 1 of the 1 non-bonded parameter combinations 83: 83: Excluding 1 bonded neighbours molecule type 'Argon' 83: 83: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 83: 83: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 83: 83: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 83: 83: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 83: 83: Note that mdrun will redetermine rlist based on the actual pair-list setup 83: 83: This run will generate roughly 0 Mb of data 83: 83: Writing final coordinates. 83: 83: 83: Dynamic load balancing report: 83: DLB was off during the run due to low measured imbalance. 83: Average load imbalance: 3.4%. 83: The balanceable part of the MD step is 21%, load imbalance is computed from this. 83: Part of the total run time spent waiting due to load imbalance: 0.7%. 83: 83: 83: NOTE: 34 % of the run time was spent communicating energies, 83: you might want to increase some nst* mdp options 83: 83: Core t (s) Wall t (s) (%) 83: Time: 0.076 0.038 198.4 83: (ns/day) (hour/ns) 83: Performance: 38.330 0.626 83: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as double precision energy file 83: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as double precision energy file 83: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 83: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 83: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 83: that with the Verlet scheme, nstlist has no effect on the accuracy of 83: your simulation. 83: 83: 83: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 83: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 83: setting nstcomm equal to nstcalcenergy for less overhead 83: 83: Number of degrees of freedom in T-Coupling group System is 33.00 83: 83: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 83: NVE simulation: will use the initial temperature of 68.810 K for 83: determining the Verlet buffer size 83: 83: 83: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 83: COM removal frequency is set to (1). 83: Other settings require a global communication frequency of 100. 83: Note that this will require additional global communication steps, 83: which will reduce performance when using multiple ranks. 83: Consider setting nstcomm to a multiple of 100. 83: 83: 83: There were 4 NOTEs 83: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 83: Can not increase nstlist because an NVE ensemble is used 83: Using 2 MPI threads 83: Using 1 OpenMP thread per tMPI thread 83: 83: 83: NOTE: The number of threads is not equal to the number of (logical) cpus 83: and the -pin option is set to auto: will not pin threads to cpus. 83: This can lead to significant performance degradation. 83: Consider using -pin on (and -pinoffset in case you run multiple jobs). 83: starting mdrun 'Argon' 83: 16 steps, 0.0 ps. 83: Generated 1 of the 1 non-bonded parameter combinations 83: 83: Excluding 1 bonded neighbours molecule type 'Argon' 83: 83: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 83: 83: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 83: 83: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 83: 83: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 83: 83: Note that mdrun will redetermine rlist based on the actual pair-list setup 83: 83: This run will generate roughly 0 Mb of data 83: 83: Writing final coordinates. 83: 83: 83: Dynamic load balancing report: 83: DLB was turned on during the run due to measured imbalance. 83: Average load imbalance: 5.5%. 83: The balanceable part of the MD step is 41%, load imbalance is computed from this. 83: Part of the total run time spent waiting due to load imbalance: 2.2%. 83: Steps where the load balancing was limited by -rdd, -rcon and/or -dds: X 0 % 83: 83: 83: NOTE: 43 % of the run time was spent communicating energies, 83: you might want to increase some nst* mdp options 83: 83: Core t (s) Wall t (s) (%) 83: Time: 0.060 0.030 198.0 83: (ns/day) (hour/ns) 83: Performance: 48.337 0.497 83: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as double precision energy file 83: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as double precision energy file 83: 83: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 83: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 83: that with the Verlet scheme, nstlist has no effect on the accuracy of 83: your simulation. 83: 83: 83: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 83: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 83: setting nstcomm equal to nstcalcenergy for less overhead 83: 83: Number of degrees of freedom in T-Coupling group System is 33.00 83: 83: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 83: NVE simulation: will use the initial temperature of 68.810 K for 83: determining the Verlet buffer size 83: 83: 83: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 83: COM removal frequency is set to (1). 83: Other settings require a global communication frequency of 100. 83: Note that this will require additional global communication steps, 83: which will reduce performance when using multiple ranks. 83: Consider setting nstcomm to a multiple of 100. 83: 83: 83: There were 4 NOTEs 83: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 83: Can not increase nstlist because an NVE ensemble is used 83: Using 2 MPI threads 83: Using 1 OpenMP thread per tMPI thread 83: 83: 83: NOTE: The number of threads is not equal to the number of (logical) cpus 83: and the -pin option is set to auto: will not pin threads to cpus. 83: This can lead to significant performance degradation. 83: Consider using -pin on (and -pinoffset in case you run multiple jobs). 83: starting mdrun 'Argon' 83: 16 steps, 0.0 ps. 83: Generated 1 of the 1 non-bonded parameter combinations 83: 83: Excluding 1 bonded neighbours molecule type 'Argon' 83: 83: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 83: 83: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 83: 83: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 83: 83: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 83: 83: Note that mdrun will redetermine rlist based on the actual pair-list setup 83: 83: This run will generate roughly 0 Mb of data 83: 83: Writing final coordinates. 83: 83: 83: Dynamic load balancing report: 83: DLB was off during the run due to low measured imbalance. 83: Average load imbalance: 1.6%. 83: The balanceable part of the MD step is 54%, load imbalance is computed from this. 83: Part of the total run time spent waiting due to load imbalance: 0.8%. 83: 83: 83: NOTE: 42 % of the run time was spent communicating energies, 83: you might want to increase some nst* mdp options 83: 83: Core t (s) Wall t (s) (%) 83: Time: 0.040 0.020 197.1 83: (ns/day) (hour/ns) 83: Performance: 72.108 0.333 83: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as double precision energy file 83: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as double precision energy file 83: 83: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 83: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 83: that with the Verlet scheme, nstlist has no effect on the accuracy of 83: your simulation. 83: 83: 83: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 83: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 83: setting nstcomm equal to nstcalcenergy for less overhead 83: 83: Number of degrees of freedom in T-Coupling group System is 33.00 83: 83: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 83: NVE simulation: will use the initial temperature of 68.810 K for 83: determining the Verlet buffer size 83: 83: 83: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 83: COM removal frequency is set to (1). 83: Other settings require a global communication frequency of 100. 83: Note that this will require additional global communication steps, 83: which will reduce performance when using multiple ranks. 83: Consider setting nstcomm to a multiple of 100. 83: 83: 83: There were 4 NOTEs 83: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 83: Can not increase nstlist because an NVE ensemble is used 83: Using 2 MPI threads 83: Using 1 OpenMP thread per tMPI thread 83: 83: 83: NOTE: The number of threads is not equal to the number of (logical) cpus 83: and the -pin option is set to auto: will not pin threads to cpus. 83: This can lead to significant performance degradation. 83: Consider using -pin on (and -pinoffset in case you run multiple jobs). 83: starting mdrun 'Argon' 83: 16 steps, 0.0 ps. 83: Generated 1 of the 1 non-bonded parameter combinations 83: 83: Excluding 1 bonded neighbours molecule type 'Argon' 83: 83: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 83: 83: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 83: 83: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 83: 83: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 83: 83: Note that mdrun will redetermine rlist based on the actual pair-list setup 83: 83: This run will generate roughly 0 Mb of data 83: 83: Writing final coordinates. 83: 83: 83: Dynamic load balancing report: 83: DLB was off during the run due to low measured imbalance. 83: Average load imbalance: 0.9%. 83: The balanceable part of the MD step is 17%, load imbalance is computed from this. 83: Part of the total run time spent waiting due to load imbalance: 0.2%. 83: 83: 83: NOTE: 32 % of the run time was spent communicating energies, 83: you might want to increase some nst* mdp options 83: 83: Core t (s) Wall t (s) (%) 83: Time: 0.056 0.028 197.9 83: (ns/day) (hour/ns) 83: Performance: 52.253 0.459 83: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as double precision energy file 83: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as double precision energy file 83: [ OK ] BasicPropagators/PeriodicActionsTest.PeriodicActionsAgreeWithReference/0 (509 ms) 83: [----------] 1 test from BasicPropagators/PeriodicActionsTest (509 ms total) 83: 83: [----------] Global test environment tear-down 83: [==========] 1 test from 1 test suite ran. (557 ms total) 83: [ PASSED ] 1 test. 83/92 Test #83: MdrunCoordinationBasicTests2Ranks ......... Passed 0.63 sec test 84 Start 84: MdrunCoordinationCouplingTests1Rank 84: Test command: /build/reproducible-path/gromacs-2025.1/build/basic-dp/bin/mdrun-coordination-coupling-test "-ntmpi" "1" "--gtest_output=xml:/build/reproducible-path/gromacs-2025.1/build/basic-dp/Testing/Temporary/MdrunCoordinationCouplingTests1Rank.xml" 84: Working Directory: /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests 84: Test timeout computed to be: 1920 84: [==========] Running 25 tests from 1 test suite. 84: [----------] Global test environment set-up. 84: [----------] 25 tests from PropagatorsWithCoupling/PeriodicActionsTest 84: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/0 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 84: Setting nstcalcenergy (100) equal to nstenergy (1) 84: 84: Number of degrees of freedom in T-Coupling group System is 33.00 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 84: NVE simulation: will use the initial temperature of 68.810 K for 84: determining the Verlet buffer size 84: 84: 84: There were 3 NOTEs 84: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 84: Can not increase nstlist because an NVE ensemble is used 84: Using 1 MPI thread 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'Argon' 84: 16 steps, 0.0 ps. 84: Generated 1 of the 1 non-bonded parameter combinations 84: 84: Excluding 1 bonded neighbours molecule type 'Argon' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.028 0.028 99.2 84: (ns/day) (hour/ns) 84: Performance: 51.610 0.465 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 84: Setting nstcalcenergy (100) equal to nstenergy (1) 84: 84: Number of degrees of freedom in T-Coupling group System is 33.00 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 84: NVE simulation: will use the initial temperature of 68.810 K for 84: determining the Verlet buffer size 84: 84: 84: There were 3 NOTEs 84: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 84: Can not increase nstlist because an NVE ensemble is used 84: Using 1 MPI thread 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'Argon' 84: 16 steps, 0.0 ps. 84: Generated 1 of the 1 non-bonded parameter combinations 84: 84: Excluding 1 bonded neighbours molecule type 'Argon' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.020 0.020 98.8 84: (ns/day) (hour/ns) 84: Performance: 71.718 0.335 84: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as double precision energy file 84: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as double precision energy file 84: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 84: Setting nstcalcenergy (100) equal to nstenergy (4) 84: 84: Number of degrees of freedom in T-Coupling group System is 33.00 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 84: NVE simulation: will use the initial temperature of 68.810 K for 84: determining the Verlet buffer size 84: 84: 84: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 84: COM removal frequency is set to (5). 84: Other settings require a global communication frequency of 4. 84: Note that this will require additional global communication steps, 84: which will reduce performance when using multiple ranks. 84: Consider setting nstcomm to a multiple of 4. 84: 84: 84: There were 4 NOTEs 84: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 84: Can not increase nstlist because an NVE ensemble is used 84: Using 1 MPI thread 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'Argon' 84: 16 steps, 0.0 ps. 84: Generated 1 of the 1 non-bonded parameter combinations 84: 84: Excluding 1 bonded neighbours molecule type 'Argon' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.021 0.021 98.7 84: (ns/day) (hour/ns) 84: Performance: 69.740 0.344 84: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as double precision energy file 84: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as double precision energy file 84: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 84: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 84: setting nstcomm equal to nstcalcenergy for less overhead 84: 84: Number of degrees of freedom in T-Coupling group System is 33.00 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 84: NVE simulation: will use the initial temperature of 68.810 K for 84: determining the Verlet buffer size 84: 84: 84: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 84: COM removal frequency is set to (5). 84: Other settings require a global communication frequency of 100. 84: Note that this will require additional global communication steps, 84: which will reduce performance when using multiple ranks. 84: Consider setting nstcomm to a multiple of 100. 84: 84: 84: There were 4 NOTEs 84: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 84: Can not increase nstlist because an NVE ensemble is used 84: Using 1 MPI thread 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'Argon' 84: 16 steps, 0.0 ps. 84: Generated 1 of the 1 non-bonded parameter combinations 84: 84: Excluding 1 bonded neighbours molecule type 'Argon' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.020 0.020 98.6 84: (ns/day) (hour/ns) 84: Performance: 72.255 0.332 84: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as double precision energy file 84: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as double precision energy file 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 84: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 84: setting nstcomm equal to nstcalcenergy for less overhead 84: 84: Number of degrees of freedom in T-Coupling group System is 33.00 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 84: NVE simulation: will use the initial temperature of 68.810 K for 84: determining the Verlet buffer size 84: 84: 84: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 84: COM removal frequency is set to (5). 84: Other settings require a global communication frequency of 100. 84: Note that this will require additional global communication steps, 84: which will reduce performance when using multiple ranks. 84: Consider setting nstcomm to a multiple of 100. 84: 84: 84: There were 4 NOTEs 84: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 84: Can not increase nstlist because an NVE ensemble is used 84: Using 1 MPI thread 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'Argon' 84: 16 steps, 0.0 ps. 84: Generated 1 of the 1 non-bonded parameter combinations 84: 84: Excluding 1 bonded neighbours molecule type 'Argon' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.022 0.022 98.7 84: (ns/day) (hour/ns) 84: Performance: 67.053 0.358 84: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as double precision energy file 84: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as double precision energy file 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 84: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 84: setting nstcomm equal to nstcalcenergy for less overhead 84: 84: Number of degrees of freedom in T-Coupling group System is 33.00 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 84: NVE simulation: will use the initial temperature of 68.810 K for 84: determining the Verlet buffer size 84: 84: 84: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 84: COM removal frequency is set to (5). 84: Other settings require a global communication frequency of 100. 84: Note that this will require additional global communication steps, 84: which will reduce performance when using multiple ranks. 84: Consider setting nstcomm to a multiple of 100. 84: 84: 84: There were 4 NOTEs 84: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 84: Can not increase nstlist because an NVE ensemble is used 84: Using 1 MPI thread 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'Argon' 84: 16 steps, 0.0 ps. 84: Generated 1 of the 1 non-bonded parameter combinations 84: 84: Excluding 1 bonded neighbours molecule type 'Argon' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.019 0.019 98.5 84: (ns/day) (hour/ns) 84: Performance: 77.966 0.308 84: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as double precision energy file 84: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as double precision energy file 84: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/0 (390 ms) 84: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/1 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 84: Setting nstcalcenergy (100) equal to nstenergy (1) 84: 84: 84: WARNING 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 84: The Berendsen barostat does not generate any strictly correct ensemble, 84: and should not be used for new production simulations (in our opinion). 84: We recommend using the C-rescale barostat instead. 84: 84: Number of degrees of freedom in T-Coupling group System is 33.00 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 84: NVE simulation: will use the initial temperature of 68.810 K for 84: determining the Verlet buffer size 84: 84: 84: There were 3 NOTEs 84: 84: There was 1 WARNING 84: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 84: Can not increase nstlist because an NVE ensemble is used 84: Using 1 MPI thread 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'Argon' 84: 16 steps, 0.0 ps. 84: Generated 1 of the 1 non-bonded parameter combinations 84: 84: Excluding 1 bonded neighbours molecule type 'Argon' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.020 0.021 98.8 84: (ns/day) (hour/ns) 84: Performance: 71.159 0.337 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 84: Setting nstcalcenergy (100) equal to nstenergy (1) 84: 84: 84: WARNING 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 84: The Berendsen barostat does not generate any strictly correct ensemble, 84: and should not be used for new production simulations (in our opinion). 84: We recommend using the C-rescale barostat instead. 84: 84: Number of degrees of freedom in T-Coupling group System is 33.00 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 84: NVE simulation: will use the initial temperature of 68.810 K for 84: determining the Verlet buffer size 84: 84: 84: There were 3 NOTEs 84: 84: There was 1 WARNING 84: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 84: Can not increase nstlist because an NVE ensemble is used 84: Using 1 MPI thread 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'Argon' 84: 16 steps, 0.0 ps. 84: Generated 1 of the 1 non-bonded parameter combinations 84: 84: Excluding 1 bonded neighbours molecule type 'Argon' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.017 0.018 98.4 84: (ns/day) (hour/ns) 84: Performance: 82.908 0.289 84: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as double precision energy file 84: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as double precision energy file 84: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 84: Setting nstcalcenergy (100) equal to nstenergy (4) 84: 84: 84: WARNING 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 84: The Berendsen barostat does not generate any strictly correct ensemble, 84: and should not be used for new production simulations (in our opinion). 84: We recommend using the C-rescale barostat instead. 84: 84: Number of degrees of freedom in T-Coupling group System is 33.00 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 84: NVE simulation: will use the initial temperature of 68.810 K for 84: determining the Verlet buffer size 84: 84: 84: There were 3 NOTEs 84: 84: There was 1 WARNING 84: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 84: Can not increase nstlist because an NVE ensemble is used 84: Using 1 MPI thread 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'Argon' 84: 16 steps, 0.0 ps. 84: Generated 1 of the 1 non-bonded parameter combinations 84: 84: Excluding 1 bonded neighbours molecule type 'Argon' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.020 0.021 98.7 84: (ns/day) (hour/ns) 84: Performance: 71.565 0.335 84: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as double precision energy file 84: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as double precision energy file 84: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 84: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 84: setting nstcomm equal to nstcalcenergy for less overhead 84: 84: 84: WARNING 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 84: The Berendsen barostat does not generate any strictly correct ensemble, 84: and should not be used for new production simulations (in our opinion). 84: We recommend using the C-rescale barostat instead. 84: 84: Number of degrees of freedom in T-Coupling group System is 33.00 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 84: NVE simulation: will use the initial temperature of 68.810 K for 84: determining the Verlet buffer size 84: 84: 84: There were 3 NOTEs 84: 84: There was 1 WARNING 84: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 84: Can not increase nstlist because an NVE ensemble is used 84: Using 1 MPI thread 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'Argon' 84: 16 steps, 0.0 ps. 84: Generated 1 of the 1 non-bonded parameter combinations 84: 84: Excluding 1 bonded neighbours molecule type 'Argon' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.022 0.022 98.7 84: (ns/day) (hour/ns) 84: Performance: 65.335 0.367 84: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as double precision energy file 84: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as double precision energy file 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 84: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 84: setting nstcomm equal to nstcalcenergy for less overhead 84: 84: 84: WARNING 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 84: The Berendsen barostat does not generate any strictly correct ensemble, 84: and should not be used for new production simulations (in our opinion). 84: We recommend using the C-rescale barostat instead. 84: 84: Number of degrees of freedom in T-Coupling group System is 33.00 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 84: NVE simulation: will use the initial temperature of 68.810 K for 84: determining the Verlet buffer size 84: 84: 84: There were 3 NOTEs 84: 84: There was 1 WARNING 84: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 84: Can not increase nstlist because an NVE ensemble is used 84: Using 1 MPI thread 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'Argon' 84: 16 steps, 0.0 ps. 84: Generated 1 of the 1 non-bonded parameter combinations 84: 84: Excluding 1 bonded neighbours molecule type 'Argon' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.020 0.021 98.6 84: (ns/day) (hour/ns) 84: Performance: 70.693 0.339 84: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as double precision energy file 84: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as double precision energy file 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 84: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 84: setting nstcomm equal to nstcalcenergy for less overhead 84: 84: 84: WARNING 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 84: The Berendsen barostat does not generate any strictly correct ensemble, 84: and should not be used for new production simulations (in our opinion). 84: We recommend using the C-rescale barostat instead. 84: 84: Number of degrees of freedom in T-Coupling group System is 33.00 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 84: NVE simulation: will use the initial temperature of 68.810 K for 84: determining the Verlet buffer size 84: 84: 84: There were 3 NOTEs 84: 84: There was 1 WARNING 84: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 84: Can not increase nstlist because an NVE ensemble is used 84: Using 1 MPI thread 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'Argon' 84: 16 steps, 0.0 ps. 84: Generated 1 of the 1 non-bonded parameter combinations 84: 84: Excluding 1 bonded neighbours molecule type 'Argon' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.023 0.024 98.6 84: (ns/day) (hour/ns) 84: Performance: 62.367 0.385 84: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as double precision energy file 84: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as double precision energy file 84: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/1 (384 ms) 84: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/2 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 84: Setting nstcalcenergy (100) equal to nstenergy (1) 84: 84: Number of degrees of freedom in T-Coupling group System is 33.00 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 84: NVE simulation: will use the initial temperature of 68.810 K for 84: determining the Verlet buffer size 84: 84: 84: There were 3 NOTEs 84: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 84: Can not increase nstlist because an NVE ensemble is used 84: Using 1 MPI thread 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'Argon' 84: 16 steps, 0.0 ps. 84: Generated 1 of the 1 non-bonded parameter combinations 84: 84: Excluding 1 bonded neighbours molecule type 'Argon' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.022 0.023 98.9 84: (ns/day) (hour/ns) 84: Performance: 65.037 0.369 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 84: Setting nstcalcenergy (100) equal to nstenergy (1) 84: 84: Number of degrees of freedom in T-Coupling group System is 33.00 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 84: NVE simulation: will use the initial temperature of 68.810 K for 84: determining the Verlet buffer size 84: 84: 84: There were 3 NOTEs 84: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 84: Can not increase nstlist because an NVE ensemble is used 84: Using 1 MPI thread 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'Argon' 84: 16 steps, 0.0 ps. 84: Generated 1 of the 1 non-bonded parameter combinations 84: 84: Excluding 1 bonded neighbours molecule type 'Argon' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.017 0.017 98.4 84: (ns/day) (hour/ns) 84: Performance: 84.327 0.285 84: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as double precision energy file 84: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as double precision energy file 84: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 84: Setting nstcalcenergy (100) equal to nstenergy (4) 84: 84: Number of degrees of freedom in T-Coupling group System is 33.00 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 84: NVE simulation: will use the initial temperature of 68.810 K for 84: determining the Verlet buffer size 84: 84: 84: There were 3 NOTEs 84: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 84: Can not increase nstlist because an NVE ensemble is used 84: Using 1 MPI thread 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'Argon' 84: 16 steps, 0.0 ps. 84: Generated 1 of the 1 non-bonded parameter combinations 84: 84: Excluding 1 bonded neighbours molecule type 'Argon' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.019 0.019 98.5 84: (ns/day) (hour/ns) 84: Performance: 75.864 0.316 84: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as double precision energy file 84: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as double precision energy file 84: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 84: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 84: setting nstcomm equal to nstcalcenergy for less overhead 84: 84: Number of degrees of freedom in T-Coupling group System is 33.00 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 84: NVE simulation: will use the initial temperature of 68.810 K for 84: determining the Verlet buffer size 84: 84: 84: There were 3 NOTEs 84: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 84: Can not increase nstlist because an NVE ensemble is used 84: Using 1 MPI thread 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'Argon' 84: 16 steps, 0.0 ps. 84: Generated 1 of the 1 non-bonded parameter combinations 84: 84: Excluding 1 bonded neighbours molecule type 'Argon' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.020 0.021 98.5 84: (ns/day) (hour/ns) 84: Performance: 70.629 0.340 84: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as double precision energy file 84: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as double precision energy file 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 84: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 84: setting nstcomm equal to nstcalcenergy for less overhead 84: 84: Number of degrees of freedom in T-Coupling group System is 33.00 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 84: NVE simulation: will use the initial temperature of 68.810 K for 84: determining the Verlet buffer size 84: 84: 84: There were 3 NOTEs 84: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 84: Can not increase nstlist because an NVE ensemble is used 84: Using 1 MPI thread 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'Argon' 84: 16 steps, 0.0 ps. 84: Generated 1 of the 1 non-bonded parameter combinations 84: 84: Excluding 1 bonded neighbours molecule type 'Argon' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.019 0.020 98.5 84: (ns/day) (hour/ns) 84: Performance: 74.820 0.321 84: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as double precision energy file 84: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as double precision energy file 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 84: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 84: setting nstcomm equal to nstcalcenergy for less overhead 84: 84: Number of degrees of freedom in T-Coupling group System is 33.00 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 84: NVE simulation: will use the initial temperature of 68.810 K for 84: determining the Verlet buffer size 84: 84: 84: There were 3 NOTEs 84: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 84: Can not increase nstlist because an NVE ensemble is used 84: Using 1 MPI thread 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'Argon' 84: 16 steps, 0.0 ps. 84: Generated 1 of the 1 non-bonded parameter combinations 84: 84: Excluding 1 bonded neighbours molecule type 'Argon' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.019 0.019 98.4 84: (ns/day) (hour/ns) 84: Performance: 75.739 0.317 84: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as double precision energy file 84: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as double precision energy file 84: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/2 (377 ms) 84: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/3 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 84: Setting nstcalcenergy (100) equal to nstenergy (1) 84: 84: Number of degrees of freedom in T-Coupling group System is 33.00 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 84: NVE simulation: will use the initial temperature of 68.810 K for 84: determining the Verlet buffer size 84: 84: 84: There were 3 NOTEs 84: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 84: Can not increase nstlist because an NVE ensemble is used 84: Using 1 MPI thread 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'Argon' 84: 16 steps, 0.0 ps. 84: Generated 1 of the 1 non-bonded parameter combinations 84: 84: Excluding 1 bonded neighbours molecule type 'Argon' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.022 0.022 98.8 84: (ns/day) (hour/ns) 84: Performance: 66.919 0.359 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 84: Setting nstcalcenergy (100) equal to nstenergy (1) 84: 84: Number of degrees of freedom in T-Coupling group System is 33.00 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 84: NVE simulation: will use the initial temperature of 68.810 K for 84: determining the Verlet buffer size 84: 84: 84: There were 3 NOTEs 84: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 84: Can not increase nstlist because an NVE ensemble is used 84: Using 1 MPI thread 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'Argon' 84: 16 steps, 0.0 ps. 84: Generated 1 of the 1 non-bonded parameter combinations 84: 84: Excluding 1 bonded neighbours molecule type 'Argon' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.016 0.016 98.6 84: (ns/day) (hour/ns) 84: Performance: 89.262 0.269 84: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as double precision energy file 84: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as double precision energy file 84: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 84: Setting nstcalcenergy (100) equal to nstenergy (4) 84: 84: Number of degrees of freedom in T-Coupling group System is 33.00 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 84: NVE simulation: will use the initial temperature of 68.810 K for 84: determining the Verlet buffer size 84: 84: 84: There were 3 NOTEs 84: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 84: Can not increase nstlist because an NVE ensemble is used 84: Using 1 MPI thread 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'Argon' 84: 16 steps, 0.0 ps. 84: Generated 1 of the 1 non-bonded parameter combinations 84: 84: Excluding 1 bonded neighbours molecule type 'Argon' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.016 0.016 98.7 84: (ns/day) (hour/ns) 84: Performance: 89.644 0.268 84: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as double precision energy file 84: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as double precision energy file 84: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 84: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 84: setting nstcomm equal to nstcalcenergy for less overhead 84: 84: Number of degrees of freedom in T-Coupling group System is 33.00 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 84: NVE simulation: will use the initial temperature of 68.810 K for 84: determining the Verlet buffer size 84: 84: 84: There were 3 NOTEs 84: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 84: Can not increase nstlist because an NVE ensemble is used 84: Using 1 MPI thread 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'Argon' 84: 16 steps, 0.0 ps. 84: Generated 1 of the 1 non-bonded parameter combinations 84: 84: Excluding 1 bonded neighbours molecule type 'Argon' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.020 0.021 98.9 84: (ns/day) (hour/ns) 84: Performance: 70.977 0.338 84: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as double precision energy file 84: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as double precision energy file 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 84: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 84: setting nstcomm equal to nstcalcenergy for less overhead 84: 84: Number of degrees of freedom in T-Coupling group System is 33.00 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 84: NVE simulation: will use the initial temperature of 68.810 K for 84: determining the Verlet buffer size 84: 84: 84: There were 3 NOTEs 84: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 84: Can not increase nstlist because an NVE ensemble is used 84: Using 1 MPI thread 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'Argon' 84: 16 steps, 0.0 ps. 84: Generated 1 of the 1 non-bonded parameter combinations 84: 84: Excluding 1 bonded neighbours molecule type 'Argon' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.020 0.020 98.8 84: (ns/day) (hour/ns) 84: Performance: 74.362 0.323 84: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as double precision energy file 84: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as double precision energy file 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 84: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 84: setting nstcomm equal to nstcalcenergy for less overhead 84: 84: Number of degrees of freedom in T-Coupling group System is 33.00 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 84: NVE simulation: will use the initial temperature of 68.810 K for 84: determining the Verlet buffer size 84: 84: 84: There were 3 NOTEs 84: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 84: Can not increase nstlist because an NVE ensemble is used 84: Using 1 MPI thread 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'Argon' 84: 16 steps, 0.0 ps. 84: Generated 1 of the 1 non-bonded parameter combinations 84: 84: Excluding 1 bonded neighbours molecule type 'Argon' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.019 0.020 97.6 84: (ns/day) (hour/ns) 84: Performance: 74.411 0.323 84: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as double precision energy file 84: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as double precision energy file 84: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/3 (354 ms) 84: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/4 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 84: Setting nstcalcenergy (100) equal to nstenergy (1) 84: 84: Number of degrees of freedom in T-Coupling group System is 33.00 84: 84: There were 2 NOTEs 84: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 84: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 84: 84: Using 1 MPI thread 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'Argon' 84: 16 steps, 0.0 ps. 84: Generated 1 of the 1 non-bonded parameter combinations 84: 84: Excluding 1 bonded neighbours molecule type 'Argon' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.020 0.020 98.8 84: (ns/day) (hour/ns) 84: Performance: 71.760 0.334 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 84: Setting nstcalcenergy (100) equal to nstenergy (1) 84: 84: Number of degrees of freedom in T-Coupling group System is 33.00 84: 84: There were 2 NOTEs 84: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 84: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 84: 84: Using 1 MPI thread 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'Argon' 84: 16 steps, 0.0 ps. 84: Generated 1 of the 1 non-bonded parameter combinations 84: 84: Excluding 1 bonded neighbours molecule type 'Argon' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.016 0.017 98.4 84: (ns/day) (hour/ns) 84: Performance: 88.237 0.272 84: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as double precision energy file 84: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as double precision energy file 84: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 84: Setting nstcalcenergy (100) equal to nstenergy (4) 84: 84: Number of degrees of freedom in T-Coupling group System is 33.00 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 84: COM removal frequency is set to (5). 84: Other settings require a global communication frequency of 2. 84: Note that this will require additional global communication steps, 84: which will reduce performance when using multiple ranks. 84: Consider setting nstcomm to a multiple of 2. 84: 84: 84: There were 3 NOTEs 84: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 84: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 84: 84: Using 1 MPI thread 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'Argon' 84: 16 steps, 0.0 ps. 84: Generated 1 of the 1 non-bonded parameter combinations 84: 84: Excluding 1 bonded neighbours molecule type 'Argon' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.015 0.016 98.4 84: (ns/day) (hour/ns) 84: Performance: 93.770 0.256 84: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as double precision energy file 84: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as double precision energy file 84: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 84: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 84: setting nstcomm equal to nstcalcenergy for less overhead 84: 84: Number of degrees of freedom in T-Coupling group System is 33.00 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 84: COM removal frequency is set to (5). 84: Other settings require a global communication frequency of 2. 84: Note that this will require additional global communication steps, 84: which will reduce performance when using multiple ranks. 84: Consider setting nstcomm to a multiple of 2. 84: 84: 84: There were 3 NOTEs 84: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 84: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 84: 84: Using 1 MPI thread 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'Argon' 84: 16 steps, 0.0 ps. 84: Generated 1 of the 1 non-bonded parameter combinations 84: 84: Excluding 1 bonded neighbours molecule type 'Argon' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.020 0.020 98.6 84: (ns/day) (hour/ns) 84: Performance: 72.508 0.331 84: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as double precision energy file 84: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as double precision energy file 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 84: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 84: setting nstcomm equal to nstcalcenergy for less overhead 84: 84: Number of degrees of freedom in T-Coupling group System is 33.00 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 84: COM removal frequency is set to (5). 84: Other settings require a global communication frequency of 2. 84: Note that this will require additional global communication steps, 84: which will reduce performance when using multiple ranks. 84: Consider setting nstcomm to a multiple of 2. 84: 84: 84: There were 3 NOTEs 84: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 84: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 84: 84: Using 1 MPI thread 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'Argon' 84: 16 steps, 0.0 ps. 84: Generated 1 of the 1 non-bonded parameter combinations 84: 84: Excluding 1 bonded neighbours molecule type 'Argon' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.019 0.020 98.6 84: (ns/day) (hour/ns) 84: Performance: 74.280 0.323 84: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as double precision energy file 84: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as double precision energy file 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 84: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 84: setting nstcomm equal to nstcalcenergy for less overhead 84: 84: Number of degrees of freedom in T-Coupling group System is 33.00 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 84: COM removal frequency is set to (5). 84: Other settings require a global communication frequency of 2. 84: Note that this will require additional global communication steps, 84: which will reduce performance when using multiple ranks. 84: Consider setting nstcomm to a multiple of 2. 84: 84: 84: There were 3 NOTEs 84: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 84: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 84: 84: Using 1 MPI thread 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'Argon' 84: 16 steps, 0.0 ps. 84: Generated 1 of the 1 non-bonded parameter combinations 84: 84: Excluding 1 bonded neighbours molecule type 'Argon' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.018 0.019 97.2 84: (ns/day) (hour/ns) 84: Performance: 78.224 0.307 84: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as double precision energy file 84: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as double precision energy file 84: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/4 (371 ms) 84: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/5 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 84: Setting nstcalcenergy (100) equal to nstenergy (1) 84: 84: 84: WARNING 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 84: The Berendsen barostat does not generate any strictly correct ensemble, 84: and should not be used for new production simulations (in our opinion). 84: We recommend using the C-rescale barostat instead. 84: 84: Number of degrees of freedom in T-Coupling group System is 33.00 84: 84: There were 2 NOTEs 84: 84: There was 1 WARNING 84: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 84: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 84: 84: Using 1 MPI thread 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'Argon' 84: 16 steps, 0.0 ps. 84: Generated 1 of the 1 non-bonded parameter combinations 84: 84: Excluding 1 bonded neighbours molecule type 'Argon' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.020 0.020 98.8 84: (ns/day) (hour/ns) 84: Performance: 71.971 0.333 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 84: Setting nstcalcenergy (100) equal to nstenergy (1) 84: 84: 84: WARNING 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 84: The Berendsen barostat does not generate any strictly correct ensemble, 84: and should not be used for new production simulations (in our opinion). 84: We recommend using the C-rescale barostat instead. 84: 84: Number of degrees of freedom in T-Coupling group System is 33.00 84: 84: There were 2 NOTEs 84: 84: There was 1 WARNING 84: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 84: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 84: 84: Using 1 MPI thread 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'Argon' 84: 16 steps, 0.0 ps. 84: Generated 1 of the 1 non-bonded parameter combinations 84: 84: Excluding 1 bonded neighbours molecule type 'Argon' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.018 0.018 98.7 84: (ns/day) (hour/ns) 84: Performance: 81.288 0.295 84: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as double precision energy file 84: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as double precision energy file 84: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 84: Setting nstcalcenergy (100) equal to nstenergy (4) 84: 84: 84: WARNING 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 84: The Berendsen barostat does not generate any strictly correct ensemble, 84: and should not be used for new production simulations (in our opinion). 84: We recommend using the C-rescale barostat instead. 84: 84: Number of degrees of freedom in T-Coupling group System is 33.00 84: 84: There were 2 NOTEs 84: 84: There was 1 WARNING 84: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 84: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 84: 84: Using 1 MPI thread 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'Argon' 84: 16 steps, 0.0 ps. 84: Generated 1 of the 1 non-bonded parameter combinations 84: 84: Excluding 1 bonded neighbours molecule type 'Argon' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.016 0.016 98.6 84: (ns/day) (hour/ns) 84: Performance: 92.933 0.258 84: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as double precision energy file 84: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as double precision energy file 84: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 84: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 84: setting nstcomm equal to nstcalcenergy for less overhead 84: 84: 84: WARNING 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 84: The Berendsen barostat does not generate any strictly correct ensemble, 84: and should not be used for new production simulations (in our opinion). 84: We recommend using the C-rescale barostat instead. 84: 84: Number of degrees of freedom in T-Coupling group System is 33.00 84: 84: There were 2 NOTEs 84: 84: There was 1 WARNING 84: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 84: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 84: 84: Using 1 MPI thread 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'Argon' 84: 16 steps, 0.0 ps. 84: Generated 1 of the 1 non-bonded parameter combinations 84: 84: Excluding 1 bonded neighbours molecule type 'Argon' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.021 0.022 98.4 84: (ns/day) (hour/ns) 84: Performance: 67.959 0.353 84: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as double precision energy file 84: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as double precision energy file 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 84: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 84: setting nstcomm equal to nstcalcenergy for less overhead 84: 84: 84: WARNING 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 84: The Berendsen barostat does not generate any strictly correct ensemble, 84: and should not be used for new production simulations (in our opinion). 84: We recommend using the C-rescale barostat instead. 84: 84: Number of degrees of freedom in T-Coupling group System is 33.00 84: 84: There were 2 NOTEs 84: 84: There was 1 WARNING 84: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 84: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 84: 84: Using 1 MPI thread 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'Argon' 84: 16 steps, 0.0 ps. 84: Generated 1 of the 1 non-bonded parameter combinations 84: 84: Excluding 1 bonded neighbours molecule type 'Argon' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.021 0.021 98.8 84: (ns/day) (hour/ns) 84: Performance: 68.767 0.349 84: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as double precision energy file 84: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as double precision energy file 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 84: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 84: setting nstcomm equal to nstcalcenergy for less overhead 84: 84: 84: WARNING 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 84: The Berendsen barostat does not generate any strictly correct ensemble, 84: and should not be used for new production simulations (in our opinion). 84: We recommend using the C-rescale barostat instead. 84: 84: Number of degrees of freedom in T-Coupling group System is 33.00 84: 84: There were 2 NOTEs 84: 84: There was 1 WARNING 84: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 84: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 84: 84: Using 1 MPI thread 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'Argon' 84: 16 steps, 0.0 ps. 84: Generated 1 of the 1 non-bonded parameter combinations 84: 84: Excluding 1 bonded neighbours molecule type 'Argon' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.020 0.020 98.8 84: (ns/day) (hour/ns) 84: Performance: 72.405 0.331 84: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as double precision energy file 84: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as double precision energy file 84: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/5 (387 ms) 84: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/6 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 84: Setting nstcalcenergy (100) equal to nstenergy (1) 84: 84: Number of degrees of freedom in T-Coupling group System is 33.00 84: 84: There were 2 NOTEs 84: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 84: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 84: 84: Using 1 MPI thread 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'Argon' 84: 16 steps, 0.0 ps. 84: Generated 1 of the 1 non-bonded parameter combinations 84: 84: Excluding 1 bonded neighbours molecule type 'Argon' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.025 0.025 98.9 84: (ns/day) (hour/ns) 84: Performance: 59.004 0.407 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 84: Setting nstcalcenergy (100) equal to nstenergy (1) 84: 84: Number of degrees of freedom in T-Coupling group System is 33.00 84: 84: There were 2 NOTEs 84: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 84: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 84: 84: Using 1 MPI thread 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'Argon' 84: 16 steps, 0.0 ps. 84: Generated 1 of the 1 non-bonded parameter combinations 84: 84: Excluding 1 bonded neighbours molecule type 'Argon' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.033 0.033 98.7 84: (ns/day) (hour/ns) 84: Performance: 44.154 0.544 84: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as double precision energy file 84: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as double precision energy file 84: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 84: Setting nstcalcenergy (100) equal to nstenergy (4) 84: 84: Number of degrees of freedom in T-Coupling group System is 33.00 84: 84: There were 2 NOTEs 84: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 84: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 84: 84: Using 1 MPI thread 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'Argon' 84: 16 steps, 0.0 ps. 84: Generated 1 of the 1 non-bonded parameter combinations 84: 84: Excluding 1 bonded neighbours molecule type 'Argon' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.015 0.016 98.7 84: (ns/day) (hour/ns) 84: Performance: 93.793 0.256 84: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as double precision energy file 84: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as double precision energy file 84: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 84: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 84: setting nstcomm equal to nstcalcenergy for less overhead 84: 84: Number of degrees of freedom in T-Coupling group System is 33.00 84: 84: There were 2 NOTEs 84: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 84: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 84: 84: Using 1 MPI thread 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'Argon' 84: 16 steps, 0.0 ps. 84: Generated 1 of the 1 non-bonded parameter combinations 84: 84: Excluding 1 bonded neighbours molecule type 'Argon' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.019 0.019 98.8 84: (ns/day) (hour/ns) 84: Performance: 76.069 0.316 84: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as double precision energy file 84: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as double precision energy file 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 84: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 84: setting nstcomm equal to nstcalcenergy for less overhead 84: 84: Number of degrees of freedom in T-Coupling group System is 33.00 84: 84: There were 2 NOTEs 84: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 84: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 84: 84: Using 1 MPI thread 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'Argon' 84: 16 steps, 0.0 ps. 84: Generated 1 of the 1 non-bonded parameter combinations 84: 84: Excluding 1 bonded neighbours molecule type 'Argon' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.020 0.020 98.8 84: (ns/day) (hour/ns) 84: Performance: 73.616 0.326 84: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as double precision energy file 84: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as double precision energy file 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 84: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 84: setting nstcomm equal to nstcalcenergy for less overhead 84: 84: Number of degrees of freedom in T-Coupling group System is 33.00 84: 84: There were 2 NOTEs 84: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 84: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 84: 84: Using 1 MPI thread 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'Argon' 84: 16 steps, 0.0 ps. 84: Generated 1 of the 1 non-bonded parameter combinations 84: 84: Excluding 1 bonded neighbours molecule type 'Argon' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.019 0.019 98.7 84: (ns/day) (hour/ns) 84: Performance: 77.925 0.308 84: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as double precision energy file 84: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as double precision energy file 84: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/6 (391 ms) 84: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/7 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 84: Setting nstcalcenergy (100) equal to nstenergy (1) 84: 84: Number of degrees of freedom in T-Coupling group System is 33.00 84: 84: There were 2 NOTEs 84: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 84: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 84: 84: Using 1 MPI thread 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'Argon' 84: 16 steps, 0.0 ps. 84: Generated 1 of the 1 non-bonded parameter combinations 84: 84: Excluding 1 bonded neighbours molecule type 'Argon' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.020 0.020 98.8 84: (ns/day) (hour/ns) 84: Performance: 71.898 0.334 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 84: Setting nstcalcenergy (100) equal to nstenergy (1) 84: 84: Number of degrees of freedom in T-Coupling group System is 33.00 84: 84: There were 2 NOTEs 84: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 84: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 84: 84: Using 1 MPI thread 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'Argon' 84: 16 steps, 0.0 ps. 84: Generated 1 of the 1 non-bonded parameter combinations 84: 84: Excluding 1 bonded neighbours molecule type 'Argon' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.017 0.018 98.7 84: (ns/day) (hour/ns) 84: Performance: 83.864 0.286 84: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as double precision energy file 84: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as double precision energy file 84: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 84: Setting nstcalcenergy (100) equal to nstenergy (4) 84: 84: Number of degrees of freedom in T-Coupling group System is 33.00 84: 84: There were 2 NOTEs 84: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 84: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 84: 84: Using 1 MPI thread 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'Argon' 84: 16 steps, 0.0 ps. 84: Generated 1 of the 1 non-bonded parameter combinations 84: 84: Excluding 1 bonded neighbours molecule type 'Argon' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.016 0.016 98.6 84: (ns/day) (hour/ns) 84: Performance: 91.531 0.262 84: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as double precision energy file 84: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as double precision energy file 84: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 84: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 84: setting nstcomm equal to nstcalcenergy for less overhead 84: 84: Number of degrees of freedom in T-Coupling group System is 33.00 84: 84: There were 2 NOTEs 84: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 84: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 84: 84: Using 1 MPI thread 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'Argon' 84: 16 steps, 0.0 ps. 84: Generated 1 of the 1 non-bonded parameter combinations 84: 84: Excluding 1 bonded neighbours molecule type 'Argon' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.018 0.018 98.7 84: (ns/day) (hour/ns) 84: Performance: 79.744 0.301 84: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as double precision energy file 84: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as double precision energy file 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 84: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 84: setting nstcomm equal to nstcalcenergy for less overhead 84: 84: Number of degrees of freedom in T-Coupling group System is 33.00 84: 84: There were 2 NOTEs 84: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 84: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 84: 84: Using 1 MPI thread 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'Argon' 84: 16 steps, 0.0 ps. 84: Generated 1 of the 1 non-bonded parameter combinations 84: 84: Excluding 1 bonded neighbours molecule type 'Argon' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.022 0.022 98.9 84: (ns/day) (hour/ns) 84: Performance: 66.654 0.360 84: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as double precision energy file 84: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as double precision energy file 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 84: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 84: setting nstcomm equal to nstcalcenergy for less overhead 84: 84: Number of degrees of freedom in T-Coupling group System is 33.00 84: 84: There were 2 NOTEs 84: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 84: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 84: 84: Using 1 MPI thread 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'Argon' 84: 16 steps, 0.0 ps. 84: Generated 1 of the 1 non-bonded parameter combinations 84: 84: Excluding 1 bonded neighbours molecule type 'Argon' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.019 0.019 98.8 84: (ns/day) (hour/ns) 84: Performance: 76.632 0.313 84: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as double precision energy file 84: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as double precision energy file 84: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/7 (371 ms) 84: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/8 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 84: Setting nstcalcenergy (100) equal to nstenergy (1) 84: 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 84: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 84: 1 84: 84: Number of degrees of freedom in T-Coupling group System is 33.00 84: 84: There were 3 NOTEs 84: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 84: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 84: 84: Using 1 MPI thread 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'Argon' 84: 16 steps, 0.0 ps. 84: Generated 1 of the 1 non-bonded parameter combinations 84: 84: Excluding 1 bonded neighbours molecule type 'Argon' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.021 0.021 98.8 84: (ns/day) (hour/ns) 84: Performance: 69.055 0.348 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 84: Setting nstcalcenergy (100) equal to nstenergy (1) 84: 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 84: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 84: 1 84: 84: Number of degrees of freedom in T-Coupling group System is 33.00 84: 84: There were 3 NOTEs 84: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 84: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 84: 84: Using 1 MPI thread 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'Argon' 84: 16 steps, 0.0 ps. 84: Generated 1 of the 1 non-bonded parameter combinations 84: 84: Excluding 1 bonded neighbours molecule type 'Argon' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.016 0.017 98.3 84: (ns/day) (hour/ns) 84: Performance: 88.621 0.271 84: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_reference.edr as double precision energy file 84: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.edr as double precision energy file 84: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 84: Setting nstcalcenergy (100) equal to nstenergy (4) 84: 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 84: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 84: 1 84: 84: Number of degrees of freedom in T-Coupling group System is 33.00 84: 84: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 84: COM removal frequency is set to (5). 84: Other settings require a global communication frequency of 2. 84: Note that this will require additional global communication steps, 84: which will reduce performance when using multiple ranks. 84: Consider setting nstcomm to a multiple of 2. 84: 84: 84: There were 4 NOTEs 84: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 84: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 84: 84: Using 1 MPI thread 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'Argon' 84: 16 steps, 0.0 ps. 84: Generated 1 of the 1 non-bonded parameter combinations 84: 84: Excluding 1 bonded neighbours molecule type 'Argon' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.016 0.016 98.3 84: (ns/day) (hour/ns) 84: Performance: 91.399 0.263 84: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_reference.edr as double precision energy file 84: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.edr as double precision energy file 84: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 84: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 84: setting nstcomm equal to nstcalcenergy for less overhead 84: 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 84: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 84: 1 84: 84: Number of degrees of freedom in T-Coupling group System is 33.00 84: 84: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 84: COM removal frequency is set to (5). 84: Other settings require a global communication frequency of 2. 84: Note that this will require additional global communication steps, 84: which will reduce performance when using multiple ranks. 84: Consider setting nstcomm to a multiple of 2. 84: 84: 84: There were 4 NOTEs 84: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 84: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 84: 84: Using 1 MPI thread 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'Argon' 84: 16 steps, 0.0 ps. 84: Generated 1 of the 1 non-bonded parameter combinations 84: 84: Excluding 1 bonded neighbours molecule type 'Argon' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.019 0.019 98.6 84: (ns/day) (hour/ns) 84: Performance: 75.448 0.318 84: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_reference.edr as double precision energy file 84: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.edr as double precision energy file 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 84: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 84: setting nstcomm equal to nstcalcenergy for less overhead 84: 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 84: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 84: 1 84: 84: Number of degrees of freedom in T-Coupling group System is 33.00 84: 84: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 84: COM removal frequency is set to (5). 84: Other settings require a global communication frequency of 2. 84: Note that this will require additional global communication steps, 84: which will reduce performance when using multiple ranks. 84: Consider setting nstcomm to a multiple of 2. 84: 84: 84: There were 4 NOTEs 84: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 84: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 84: 84: Using 1 MPI thread 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'Argon' 84: 16 steps, 0.0 ps. 84: Generated 1 of the 1 non-bonded parameter combinations 84: 84: Excluding 1 bonded neighbours molecule type 'Argon' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.020 0.021 98.6 84: (ns/day) (hour/ns) 84: Performance: 71.060 0.338 84: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_reference.edr as double precision energy file 84: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.edr as double precision energy file 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 84: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 84: setting nstcomm equal to nstcalcenergy for less overhead 84: 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 84: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 84: 1 84: 84: Number of degrees of freedom in T-Coupling group System is 33.00 84: 84: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 84: COM removal frequency is set to (5). 84: Other settings require a global communication frequency of 2. 84: Note that this will require additional global communication steps, 84: which will reduce performance when using multiple ranks. 84: Consider setting nstcomm to a multiple of 2. 84: 84: 84: There were 4 NOTEs 84: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 84: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 84: 84: Using 1 MPI thread 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'Argon' 84: 16 steps, 0.0 ps. 84: Generated 1 of the 1 non-bonded parameter combinations 84: 84: Excluding 1 bonded neighbours molecule type 'Argon' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.020 0.020 98.5 84: (ns/day) (hour/ns) 84: Performance: 72.337 0.332 84: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_reference.edr as double precision energy file 84: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.edr as double precision energy file 84: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/8 (379 ms) 84: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/9 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 84: Setting nstcalcenergy (100) equal to nstenergy (1) 84: 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 84: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 84: 1 84: 84: 84: WARNING 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 84: The Berendsen barostat does not generate any strictly correct ensemble, 84: and should not be used for new production simulations (in our opinion). 84: We recommend using the C-rescale barostat instead. 84: 84: Number of degrees of freedom in T-Coupling group System is 33.00 84: 84: There were 3 NOTEs 84: 84: There was 1 WARNING 84: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 84: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 84: 84: Using 1 MPI thread 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'Argon' 84: 16 steps, 0.0 ps. 84: Generated 1 of the 1 non-bonded parameter combinations 84: 84: Excluding 1 bonded neighbours molecule type 'Argon' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.023 0.023 98.8 84: (ns/day) (hour/ns) 84: Performance: 63.914 0.376 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 84: Setting nstcalcenergy (100) equal to nstenergy (1) 84: 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 84: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 84: 1 84: 84: 84: WARNING 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 84: The Berendsen barostat does not generate any strictly correct ensemble, 84: and should not be used for new production simulations (in our opinion). 84: We recommend using the C-rescale barostat instead. 84: 84: Number of degrees of freedom in T-Coupling group System is 33.00 84: 84: There were 3 NOTEs 84: 84: There was 1 WARNING 84: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 84: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 84: 84: Using 1 MPI thread 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'Argon' 84: 16 steps, 0.0 ps. 84: Generated 1 of the 1 non-bonded parameter combinations 84: 84: Excluding 1 bonded neighbours molecule type 'Argon' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.022 0.022 98.8 84: (ns/day) (hour/ns) 84: Performance: 67.166 0.357 84: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_reference.edr as double precision energy file 84: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.edr as double precision energy file 84: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 84: Setting nstcalcenergy (100) equal to nstenergy (4) 84: 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 84: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 84: 1 84: 84: 84: WARNING 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 84: The Berendsen barostat does not generate any strictly correct ensemble, 84: and should not be used for new production simulations (in our opinion). 84: We recommend using the C-rescale barostat instead. 84: 84: Number of degrees of freedom in T-Coupling group System is 33.00 84: 84: There were 3 NOTEs 84: 84: There was 1 WARNING 84: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 84: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 84: 84: Using 1 MPI thread 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'Argon' 84: 16 steps, 0.0 ps. 84: Generated 1 of the 1 non-bonded parameter combinations 84: 84: Excluding 1 bonded neighbours molecule type 'Argon' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.019 0.019 98.7 84: (ns/day) (hour/ns) 84: Performance: 78.198 0.307 84: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_reference.edr as double precision energy file 84: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.edr as double precision energy file 84: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 84: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 84: setting nstcomm equal to nstcalcenergy for less overhead 84: 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 84: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 84: 1 84: 84: 84: WARNING 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 84: The Berendsen barostat does not generate any strictly correct ensemble, 84: and should not be used for new production simulations (in our opinion). 84: We recommend using the C-rescale barostat instead. 84: 84: Number of degrees of freedom in T-Coupling group System is 33.00 84: 84: There were 3 NOTEs 84: 84: There was 1 WARNING 84: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 84: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 84: 84: Using 1 MPI thread 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'Argon' 84: 16 steps, 0.0 ps. 84: Generated 1 of the 1 non-bonded parameter combinations 84: 84: Excluding 1 bonded neighbours molecule type 'Argon' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.020 0.020 98.7 84: (ns/day) (hour/ns) 84: Performance: 72.050 0.333 84: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_reference.edr as double precision energy file 84: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.edr as double precision energy file 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 84: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 84: setting nstcomm equal to nstcalcenergy for less overhead 84: 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 84: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 84: 1 84: 84: 84: WARNING 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 84: The Berendsen barostat does not generate any strictly correct ensemble, 84: and should not be used for new production simulations (in our opinion). 84: We recommend using the C-rescale barostat instead. 84: 84: Number of degrees of freedom in T-Coupling group System is 33.00 84: 84: There were 3 NOTEs 84: 84: There was 1 WARNING 84: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 84: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 84: 84: Using 1 MPI thread 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'Argon' 84: 16 steps, 0.0 ps. 84: Generated 1 of the 1 non-bonded parameter combinations 84: 84: Excluding 1 bonded neighbours molecule type 'Argon' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.021 0.021 98.8 84: (ns/day) (hour/ns) 84: Performance: 70.368 0.341 84: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_reference.edr as double precision energy file 84: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.edr as double precision energy file 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 84: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 84: setting nstcomm equal to nstcalcenergy for less overhead 84: 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 84: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 84: 1 84: 84: 84: WARNING 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 84: The Berendsen barostat does not generate any strictly correct ensemble, 84: and should not be used for new production simulations (in our opinion). 84: We recommend using the C-rescale barostat instead. 84: 84: Number of degrees of freedom in T-Coupling group System is 33.00 84: 84: There were 3 NOTEs 84: 84: There was 1 WARNING 84: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 84: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 84: 84: Using 1 MPI thread 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'Argon' 84: 16 steps, 0.0 ps. 84: Generated 1 of the 1 non-bonded parameter combinations 84: 84: Excluding 1 bonded neighbours molecule type 'Argon' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.021 0.021 98.8 84: (ns/day) (hour/ns) 84: Performance: 69.826 0.344 84: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_reference.edr as double precision energy file 84: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.edr as double precision energy file 84: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/9 (403 ms) 84: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/10 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 84: Setting nstcalcenergy (100) equal to nstenergy (1) 84: 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 84: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 84: 1 84: 84: Number of degrees of freedom in T-Coupling group System is 33.00 84: 84: There were 3 NOTEs 84: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 84: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 84: 84: Using 1 MPI thread 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'Argon' 84: 16 steps, 0.0 ps. 84: Generated 1 of the 1 non-bonded parameter combinations 84: 84: Excluding 1 bonded neighbours molecule type 'Argon' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.021 0.021 98.8 84: (ns/day) (hour/ns) 84: Performance: 68.945 0.348 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 84: Setting nstcalcenergy (100) equal to nstenergy (1) 84: 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 84: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 84: 1 84: 84: Number of degrees of freedom in T-Coupling group System is 33.00 84: 84: There were 3 NOTEs 84: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 84: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 84: 84: Using 1 MPI thread 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'Argon' 84: 16 steps, 0.0 ps. 84: Generated 1 of the 1 non-bonded parameter combinations 84: 84: Excluding 1 bonded neighbours molecule type 'Argon' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.017 0.017 98.7 84: (ns/day) (hour/ns) 84: Performance: 85.535 0.281 84: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_reference.edr as double precision energy file 84: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.edr as double precision energy file 84: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 84: Setting nstcalcenergy (100) equal to nstenergy (4) 84: 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 84: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 84: 1 84: 84: Number of degrees of freedom in T-Coupling group System is 33.00 84: 84: There were 3 NOTEs 84: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 84: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 84: 84: Using 1 MPI thread 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'Argon' 84: 16 steps, 0.0 ps. 84: Generated 1 of the 1 non-bonded parameter combinations 84: 84: Excluding 1 bonded neighbours molecule type 'Argon' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.016 0.016 98.6 84: (ns/day) (hour/ns) 84: Performance: 89.884 0.267 84: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_reference.edr as double precision energy file 84: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.edr as double precision energy file 84: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 84: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 84: setting nstcomm equal to nstcalcenergy for less overhead 84: 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 84: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 84: 1 84: 84: Number of degrees of freedom in T-Coupling group System is 33.00 84: 84: There were 3 NOTEs 84: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 84: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 84: 84: Using 1 MPI thread 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'Argon' 84: 16 steps, 0.0 ps. 84: Generated 1 of the 1 non-bonded parameter combinations 84: 84: Excluding 1 bonded neighbours molecule type 'Argon' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.020 0.020 97.6 84: (ns/day) (hour/ns) 84: Performance: 73.546 0.326 84: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_reference.edr as double precision energy file 84: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.edr as double precision energy file 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 84: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 84: setting nstcomm equal to nstcalcenergy for less overhead 84: 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 84: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 84: 1 84: 84: Number of degrees of freedom in T-Coupling group System is 33.00 84: 84: There were 3 NOTEs 84: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 84: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 84: 84: Using 1 MPI thread 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'Argon' 84: 16 steps, 0.0 ps. 84: Generated 1 of the 1 non-bonded parameter combinations 84: 84: Excluding 1 bonded neighbours molecule type 'Argon' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.020 0.020 98.8 84: (ns/day) (hour/ns) 84: Performance: 73.477 0.327 84: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_reference.edr as double precision energy file 84: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.edr as double precision energy file 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 84: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 84: setting nstcomm equal to nstcalcenergy for less overhead 84: 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 84: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 84: 1 84: 84: Number of degrees of freedom in T-Coupling group System is 33.00 84: 84: There were 3 NOTEs 84: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 84: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 84: 84: Using 1 MPI thread 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'Argon' 84: 16 steps, 0.0 ps. 84: Generated 1 of the 1 non-bonded parameter combinations 84: 84: Excluding 1 bonded neighbours molecule type 'Argon' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.020 0.020 98.7 84: (ns/day) (hour/ns) 84: Performance: 73.906 0.325 84: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_reference.edr as double precision energy file 84: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.edr as double precision energy file 84: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/10 (375 ms) 84: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/11 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 84: Setting nstcalcenergy (100) equal to nstenergy (1) 84: 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 84: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 84: 1 84: 84: Number of degrees of freedom in T-Coupling group System is 33.00 84: 84: There were 3 NOTEs 84: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 84: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 84: 84: Using 1 MPI thread 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'Argon' 84: 16 steps, 0.0 ps. 84: Generated 1 of the 1 non-bonded parameter combinations 84: 84: Excluding 1 bonded neighbours molecule type 'Argon' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.020 0.021 98.8 84: (ns/day) (hour/ns) 84: Performance: 70.970 0.338 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 84: Setting nstcalcenergy (100) equal to nstenergy (1) 84: 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 84: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 84: 1 84: 84: Number of degrees of freedom in T-Coupling group System is 33.00 84: 84: There were 3 NOTEs 84: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 84: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 84: 84: Using 1 MPI thread 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'Argon' 84: 16 steps, 0.0 ps. 84: Generated 1 of the 1 non-bonded parameter combinations 84: 84: Excluding 1 bonded neighbours molecule type 'Argon' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.017 0.017 98.7 84: (ns/day) (hour/ns) 84: Performance: 86.212 0.278 84: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_reference.edr as double precision energy file 84: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.edr as double precision energy file 84: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 84: Setting nstcalcenergy (100) equal to nstenergy (4) 84: 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 84: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 84: 1 84: 84: Number of degrees of freedom in T-Coupling group System is 33.00 84: 84: There were 3 NOTEs 84: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 84: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 84: 84: Using 1 MPI thread 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'Argon' 84: 16 steps, 0.0 ps. 84: Generated 1 of the 1 non-bonded parameter combinations 84: 84: Excluding 1 bonded neighbours molecule type 'Argon' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.016 0.017 98.6 84: (ns/day) (hour/ns) 84: Performance: 88.648 0.271 84: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_reference.edr as double precision energy file 84: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.edr as double precision energy file 84: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 84: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 84: setting nstcomm equal to nstcalcenergy for less overhead 84: 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 84: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 84: 1 84: 84: Number of degrees of freedom in T-Coupling group System is 33.00 84: 84: There were 3 NOTEs 84: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 84: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 84: 84: Using 1 MPI thread 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'Argon' 84: 16 steps, 0.0 ps. 84: Generated 1 of the 1 non-bonded parameter combinations 84: 84: Excluding 1 bonded neighbours molecule type 'Argon' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.019 0.019 98.8 84: (ns/day) (hour/ns) 84: Performance: 75.840 0.316 84: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_reference.edr as double precision energy file 84: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.edr as double precision energy file 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 84: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 84: setting nstcomm equal to nstcalcenergy for less overhead 84: 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 84: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 84: 1 84: 84: Number of degrees of freedom in T-Coupling group System is 33.00 84: 84: There were 3 NOTEs 84: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 84: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 84: 84: Using 1 MPI thread 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'Argon' 84: 16 steps, 0.0 ps. 84: Generated 1 of the 1 non-bonded parameter combinations 84: 84: Excluding 1 bonded neighbours molecule type 'Argon' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.021 0.021 98.8 84: (ns/day) (hour/ns) 84: Performance: 69.767 0.344 84: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_reference.edr as double precision energy file 84: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.edr as double precision energy file 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 84: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 84: setting nstcomm equal to nstcalcenergy for less overhead 84: 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 84: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 84: 1 84: 84: Number of degrees of freedom in T-Coupling group System is 33.00 84: 84: There were 3 NOTEs 84: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 84: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 84: 84: Using 1 MPI thread 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'Argon' 84: 16 steps, 0.0 ps. 84: Generated 1 of the 1 non-bonded parameter combinations 84: 84: Excluding 1 bonded neighbours molecule type 'Argon' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.019 0.019 98.7 84: (ns/day) (hour/ns) 84: Performance: 76.488 0.314 84: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_reference.edr as double precision energy file 84: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.edr as double precision energy file 84: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/11 (374 ms) 84: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/12 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 84: Setting nstcalcenergy (100) equal to nstenergy (1) 84: 84: Number of degrees of freedom in T-Coupling group System is 33.00 84: 84: There were 2 NOTEs 84: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 84: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 84: 84: Using 1 MPI thread 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'Argon' 84: 16 steps, 0.0 ps. 84: Generated 1 of the 1 non-bonded parameter combinations 84: 84: Excluding 1 bonded neighbours molecule type 'Argon' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.022 0.022 99.1 84: (ns/day) (hour/ns) 84: Performance: 65.889 0.364 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 84: Setting nstcalcenergy (100) equal to nstenergy (1) 84: 84: Number of degrees of freedom in T-Coupling group System is 33.00 84: 84: There were 2 NOTEs 84: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 84: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 84: 84: Using 1 MPI thread 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'Argon' 84: 16 steps, 0.0 ps. 84: Generated 1 of the 1 non-bonded parameter combinations 84: 84: Excluding 1 bonded neighbours molecule type 'Argon' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.021 0.021 98.8 84: (ns/day) (hour/ns) 84: Performance: 69.977 0.343 84: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_reference.edr as double precision energy file 84: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.edr as double precision energy file 84: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 84: Setting nstcalcenergy (100) equal to nstenergy (4) 84: 84: Number of degrees of freedom in T-Coupling group System is 33.00 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 84: COM removal frequency is set to (5). 84: Other settings require a global communication frequency of 4. 84: Note that this will require additional global communication steps, 84: which will reduce performance when using multiple ranks. 84: Consider setting nstcomm to a multiple of 4. 84: 84: 84: There were 3 NOTEs 84: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 84: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 84: 84: Using 1 MPI thread 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'Argon' 84: 16 steps, 0.0 ps. 84: Generated 1 of the 1 non-bonded parameter combinations 84: 84: Excluding 1 bonded neighbours molecule type 'Argon' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.017 0.017 98.6 84: (ns/day) (hour/ns) 84: Performance: 86.798 0.277 84: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_reference.edr as double precision energy file 84: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.edr as double precision energy file 84: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 84: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 84: setting nstcomm equal to nstcalcenergy for less overhead 84: 84: Number of degrees of freedom in T-Coupling group System is 33.00 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 84: COM removal frequency is set to (5). 84: Other settings require a global communication frequency of 100. 84: Note that this will require additional global communication steps, 84: which will reduce performance when using multiple ranks. 84: Consider setting nstcomm to a multiple of 100. 84: 84: 84: There were 3 NOTEs 84: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 84: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 84: 84: Using 1 MPI thread 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'Argon' 84: 16 steps, 0.0 ps. 84: Generated 1 of the 1 non-bonded parameter combinations 84: 84: Excluding 1 bonded neighbours molecule type 'Argon' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.023 0.024 98.8 84: (ns/day) (hour/ns) 84: Performance: 62.174 0.386 84: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_reference.edr as double precision energy file 84: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.edr as double precision energy file 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 84: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 84: setting nstcomm equal to nstcalcenergy for less overhead 84: 84: Number of degrees of freedom in T-Coupling group System is 33.00 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 84: COM removal frequency is set to (5). 84: Other settings require a global communication frequency of 100. 84: Note that this will require additional global communication steps, 84: which will reduce performance when using multiple ranks. 84: Consider setting nstcomm to a multiple of 100. 84: 84: 84: There were 3 NOTEs 84: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 84: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 84: 84: Using 1 MPI thread 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'Argon' 84: 16 steps, 0.0 ps. 84: Generated 1 of the 1 non-bonded parameter combinations 84: 84: Excluding 1 bonded neighbours molecule type 'Argon' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.021 0.021 98.8 84: (ns/day) (hour/ns) 84: Performance: 70.703 0.339 84: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_reference.edr as double precision energy file 84: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.edr as double precision energy file 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 84: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 84: setting nstcomm equal to nstcalcenergy for less overhead 84: 84: Number of degrees of freedom in T-Coupling group System is 33.00 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 84: COM removal frequency is set to (5). 84: Other settings require a global communication frequency of 100. 84: Note that this will require additional global communication steps, 84: which will reduce performance when using multiple ranks. 84: Consider setting nstcomm to a multiple of 100. 84: 84: 84: There were 3 NOTEs 84: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 84: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 84: 84: Using 1 MPI thread 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'Argon' 84: 16 steps, 0.0 ps. 84: Generated 1 of the 1 non-bonded parameter combinations 84: 84: Excluding 1 bonded neighbours molecule type 'Argon' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.020 0.020 98.7 84: (ns/day) (hour/ns) 84: Performance: 73.769 0.325 84: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_reference.edr as double precision energy file 84: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.edr as double precision energy file 84: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/12 (394 ms) 84: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/13 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: 84: Setting nstcalcenergy (100) equal to nstenergy (1) 84: 84: 84: WARNING 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: 84: The Berendsen barostat does not generate any strictly correct ensemble, 84: and should not be used for new production simulations (in our opinion). 84: We recommend using the C-rescale barostat instead. 84: 84: Number of degrees of freedom in T-Coupling group System is 33.00 84: 84: There were 2 NOTEs 84: 84: There was 1 WARNING 84: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 84: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 84: 84: Using 1 MPI thread 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'Argon' 84: 16 steps, 0.0 ps. 84: Generated 1 of the 1 non-bonded parameter combinations 84: 84: Excluding 1 bonded neighbours molecule type 'Argon' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.025 0.025 99.1 84: (ns/day) (hour/ns) 84: Performance: 58.048 0.413 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: 84: Setting nstcalcenergy (100) equal to nstenergy (1) 84: 84: 84: WARNING 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: 84: The Berendsen barostat does not generate any strictly correct ensemble, 84: and should not be used for new production simulations (in our opinion). 84: We recommend using the C-rescale barostat instead. 84: 84: Number of degrees of freedom in T-Coupling group System is 33.00 84: 84: There were 2 NOTEs 84: 84: There was 1 WARNING 84: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 84: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 84: 84: Using 1 MPI thread 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'Argon' 84: 16 steps, 0.0 ps. 84: Generated 1 of the 1 non-bonded parameter combinations 84: 84: Excluding 1 bonded neighbours molecule type 'Argon' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.017 0.017 98.8 84: (ns/day) (hour/ns) 84: Performance: 86.405 0.278 84: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_reference.edr as double precision energy file 84: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.edr as double precision energy file 84: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: 84: Setting nstcalcenergy (100) equal to nstenergy (4) 84: 84: 84: WARNING 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: 84: The Berendsen barostat does not generate any strictly correct ensemble, 84: and should not be used for new production simulations (in our opinion). 84: We recommend using the C-rescale barostat instead. 84: 84: Number of degrees of freedom in T-Coupling group System is 33.00 84: 84: There were 2 NOTEs 84: 84: There was 1 WARNING 84: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 84: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 84: 84: Using 1 MPI thread 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'Argon' 84: 16 steps, 0.0 ps. 84: Generated 1 of the 1 non-bonded parameter combinations 84: 84: Excluding 1 bonded neighbours molecule type 'Argon' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.016 0.016 98.7 84: (ns/day) (hour/ns) 84: Performance: 93.512 0.257 84: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_reference.edr as double precision energy file 84: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.edr as double precision energy file 84: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: 84: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 84: setting nstcomm equal to nstcalcenergy for less overhead 84: 84: 84: WARNING 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: 84: The Berendsen barostat does not generate any strictly correct ensemble, 84: and should not be used for new production simulations (in our opinion). 84: We recommend using the C-rescale barostat instead. 84: 84: Number of degrees of freedom in T-Coupling group System is 33.00 84: 84: There were 2 NOTEs 84: 84: There was 1 WARNING 84: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 84: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 84: 84: Using 1 MPI thread 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'Argon' 84: 16 steps, 0.0 ps. 84: Generated 1 of the 1 non-bonded parameter combinations 84: 84: Excluding 1 bonded neighbours molecule type 'Argon' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.019 0.019 98.9 84: (ns/day) (hour/ns) 84: Performance: 78.181 0.307 84: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_reference.edr as double precision energy file 84: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.edr as double precision energy file 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: 84: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 84: setting nstcomm equal to nstcalcenergy for less overhead 84: 84: 84: WARNING 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: 84: The Berendsen barostat does not generate any strictly correct ensemble, 84: and should not be used for new production simulations (in our opinion). 84: We recommend using the C-rescale barostat instead. 84: 84: Number of degrees of freedom in T-Coupling group System is 33.00 84: 84: There were 2 NOTEs 84: 84: There was 1 WARNING 84: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 84: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 84: 84: Using 1 MPI thread 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'Argon' 84: 16 steps, 0.0 ps. 84: Generated 1 of the 1 non-bonded parameter combinations 84: 84: Excluding 1 bonded neighbours molecule type 'Argon' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.018 0.018 98.9 84: (ns/day) (hour/ns) 84: Performance: 80.245 0.299 84: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_reference.edr as double precision energy file 84: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.edr as double precision energy file 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: 84: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 84: setting nstcomm equal to nstcalcenergy for less overhead 84: 84: 84: WARNING 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: 84: The Berendsen barostat does not generate any strictly correct ensemble, 84: and should not be used for new production simulations (in our opinion). 84: We recommend using the C-rescale barostat instead. 84: 84: Number of degrees of freedom in T-Coupling group System is 33.00 84: 84: There were 2 NOTEs 84: 84: There was 1 WARNING 84: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 84: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 84: 84: Using 1 MPI thread 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'Argon' 84: 16 steps, 0.0 ps. 84: Generated 1 of the 1 non-bonded parameter combinations 84: 84: Excluding 1 bonded neighbours molecule type 'Argon' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.019 0.019 98.8 84: (ns/day) (hour/ns) 84: Performance: 78.407 0.306 84: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_reference.edr as double precision energy file 84: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.edr as double precision energy file 84: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/13 (366 ms) 84: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/14 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]: 84: Setting nstcalcenergy (100) equal to nstenergy (1) 84: 84: Number of degrees of freedom in T-Coupling group System is 33.00 84: 84: There were 2 NOTEs 84: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 84: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 84: 84: Using 1 MPI thread 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'Argon' 84: 16 steps, 0.0 ps. 84: Generated 1 of the 1 non-bonded parameter combinations 84: 84: Excluding 1 bonded neighbours molecule type 'Argon' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.021 0.021 98.9 84: (ns/day) (hour/ns) 84: Performance: 68.709 0.349 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]: 84: Setting nstcalcenergy (100) equal to nstenergy (1) 84: 84: Number of degrees of freedom in T-Coupling group System is 33.00 84: 84: There were 2 NOTEs 84: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 84: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 84: 84: Using 1 MPI thread 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'Argon' 84: 16 steps, 0.0 ps. 84: Generated 1 of the 1 non-bonded parameter combinations 84: 84: Excluding 1 bonded neighbours molecule type 'Argon' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.016 0.017 98.8 84: (ns/day) (hour/ns) 84: Performance: 88.840 0.270 84: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_reference.edr as double precision energy file 84: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.edr as double precision energy file 84: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]: 84: Setting nstcalcenergy (100) equal to nstenergy (4) 84: 84: Number of degrees of freedom in T-Coupling group System is 33.00 84: 84: There were 2 NOTEs 84: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 84: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 84: 84: Using 1 MPI thread 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'Argon' 84: 16 steps, 0.0 ps. 84: Generated 1 of the 1 non-bonded parameter combinations 84: 84: Excluding 1 bonded neighbours molecule type 'Argon' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.016 0.016 98.7 84: (ns/day) (hour/ns) 84: Performance: 92.070 0.261 84: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_reference.edr as double precision energy file 84: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.edr as double precision energy file 84: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]: 84: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 84: setting nstcomm equal to nstcalcenergy for less overhead 84: 84: Number of degrees of freedom in T-Coupling group System is 33.00 84: 84: There were 2 NOTEs 84: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 84: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 84: 84: Using 1 MPI thread 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'Argon' 84: 16 steps, 0.0 ps. 84: Generated 1 of the 1 non-bonded parameter combinations 84: 84: Excluding 1 bonded neighbours molecule type 'Argon' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.019 0.019 98.8 84: (ns/day) (hour/ns) 84: Performance: 77.550 0.309 84: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_reference.edr as double precision energy file 84: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.edr as double precision energy file 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]: 84: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 84: setting nstcomm equal to nstcalcenergy for less overhead 84: 84: Number of degrees of freedom in T-Coupling group System is 33.00 84: 84: There were 2 NOTEs 84: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 84: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 84: 84: Using 1 MPI thread 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'Argon' 84: 16 steps, 0.0 ps. 84: Generated 1 of the 1 non-bonded parameter combinations 84: 84: Excluding 1 bonded neighbours molecule type 'Argon' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.020 0.020 98.9 84: (ns/day) (hour/ns) 84: Performance: 74.336 0.323 84: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_reference.edr as double precision energy file 84: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.edr as double precision energy file 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]: 84: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 84: setting nstcomm equal to nstcalcenergy for less overhead 84: 84: Number of degrees of freedom in T-Coupling group System is 33.00 84: 84: There were 2 NOTEs 84: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 84: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 84: 84: Using 1 MPI thread 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'Argon' 84: 16 steps, 0.0 ps. 84: Generated 1 of the 1 non-bonded parameter combinations 84: 84: Excluding 1 bonded neighbours molecule type 'Argon' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.020 0.020 98.9 84: (ns/day) (hour/ns) 84: Performance: 73.165 0.328 84: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_reference.edr as double precision energy file 84: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.edr as double precision energy file 84: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/14 (367 ms) 84: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/15 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]: 84: Setting nstcalcenergy (100) equal to nstenergy (1) 84: 84: Number of degrees of freedom in T-Coupling group System is 33.00 84: 84: There were 2 NOTEs 84: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 84: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 84: 84: Using 1 MPI thread 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'Argon' 84: 16 steps, 0.0 ps. 84: Generated 1 of the 1 non-bonded parameter combinations 84: 84: Excluding 1 bonded neighbours molecule type 'Argon' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.019 0.019 98.8 84: (ns/day) (hour/ns) 84: Performance: 75.389 0.318 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]: 84: Setting nstcalcenergy (100) equal to nstenergy (1) 84: 84: Number of degrees of freedom in T-Coupling group System is 33.00 84: 84: There were 2 NOTEs 84: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 84: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 84: 84: Using 1 MPI thread 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'Argon' 84: 16 steps, 0.0 ps. 84: Generated 1 of the 1 non-bonded parameter combinations 84: 84: Excluding 1 bonded neighbours molecule type 'Argon' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.016 0.016 98.7 84: (ns/day) (hour/ns) 84: Performance: 89.023 0.270 84: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_reference.edr as double precision energy file 84: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.edr as double precision energy file 84: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]: 84: Setting nstcalcenergy (100) equal to nstenergy (4) 84: 84: Number of degrees of freedom in T-Coupling group System is 33.00 84: 84: There were 2 NOTEs 84: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 84: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 84: 84: Using 1 MPI thread 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'Argon' 84: 16 steps, 0.0 ps. 84: Generated 1 of the 1 non-bonded parameter combinations 84: 84: Excluding 1 bonded neighbours molecule type 'Argon' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.016 0.016 97.1 84: (ns/day) (hour/ns) 84: Performance: 91.016 0.264 84: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_reference.edr as double precision energy file 84: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.edr as double precision energy file 84: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]: 84: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 84: setting nstcomm equal to nstcalcenergy for less overhead 84: 84: Number of degrees of freedom in T-Coupling group System is 33.00 84: 84: There were 2 NOTEs 84: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 84: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 84: 84: Using 1 MPI thread 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'Argon' 84: 16 steps, 0.0 ps. 84: Generated 1 of the 1 non-bonded parameter combinations 84: 84: Excluding 1 bonded neighbours molecule type 'Argon' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.019 0.019 98.8 84: (ns/day) (hour/ns) 84: Performance: 77.714 0.309 84: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_reference.edr as double precision energy file 84: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.edr as double precision energy file 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]: 84: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 84: setting nstcomm equal to nstcalcenergy for less overhead 84: 84: Number of degrees of freedom in T-Coupling group System is 33.00 84: 84: There were 2 NOTEs 84: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 84: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 84: 84: Using 1 MPI thread 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'Argon' 84: 16 steps, 0.0 ps. 84: Generated 1 of the 1 non-bonded parameter combinations 84: 84: Excluding 1 bonded neighbours molecule type 'Argon' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.019 0.019 98.7 84: (ns/day) (hour/ns) 84: Performance: 77.493 0.310 84: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_reference.edr as double precision energy file 84: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.edr as double precision energy file 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]: 84: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 84: setting nstcomm equal to nstcalcenergy for less overhead 84: 84: Number of degrees of freedom in T-Coupling group System is 33.00 84: 84: There were 2 NOTEs 84: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 84: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 84: 84: Using 1 MPI thread 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'Argon' 84: 16 steps, 0.0 ps. 84: Generated 1 of the 1 non-bonded parameter combinations 84: 84: Excluding 1 bonded neighbours molecule type 'Argon' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.019 0.020 98.9 84: (ns/day) (hour/ns) 84: Performance: 74.638 0.322 84: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_reference.edr as double precision energy file 84: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.edr as double precision energy file 84: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/15 (366 ms) 84: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/16 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 84: Setting nstcalcenergy (100) equal to nstenergy (1) 84: 84: Number of degrees of freedom in T-Coupling group System is 33.00 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 84: NVE simulation: will use the initial temperature of 68.810 K for 84: determining the Verlet buffer size 84: 84: 84: There were 3 NOTEs 84: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 84: Can not increase nstlist because an NVE ensemble is used 84: Using 1 MPI thread 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'Argon' 84: 16 steps, 0.0 ps. 84: Generated 1 of the 1 non-bonded parameter combinations 84: 84: Excluding 1 bonded neighbours molecule type 'Argon' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.023 0.023 99.3 84: (ns/day) (hour/ns) 84: Performance: 63.142 0.380 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 84: Setting nstcalcenergy (100) equal to nstenergy (1) 84: 84: Number of degrees of freedom in T-Coupling group System is 33.00 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 84: NVE simulation: will use the initial temperature of 68.810 K for 84: determining the Verlet buffer size 84: 84: 84: There were 3 NOTEs 84: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 84: Can not increase nstlist because an NVE ensemble is used 84: Using 1 MPI thread 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'Argon' 84: 16 steps, 0.0 ps. 84: Generated 1 of the 1 non-bonded parameter combinations 84: 84: Excluding 1 bonded neighbours molecule type 'Argon' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.023 0.023 99.3 84: (ns/day) (hour/ns) 84: Performance: 63.658 0.377 84: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_reference.edr as double precision energy file 84: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.edr as double precision energy file 84: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 84: Setting nstcalcenergy (100) equal to nstenergy (4) 84: 84: Number of degrees of freedom in T-Coupling group System is 33.00 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 84: NVE simulation: will use the initial temperature of 68.810 K for 84: determining the Verlet buffer size 84: 84: 84: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 84: COM removal frequency is set to (5). 84: Other settings require a global communication frequency of 4. 84: Note that this will require additional global communication steps, 84: which will reduce performance when using multiple ranks. 84: Consider setting nstcomm to a multiple of 4. 84: 84: 84: There were 4 NOTEs 84: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 84: Can not increase nstlist because an NVE ensemble is used 84: Using 1 MPI thread 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'Argon' 84: 16 steps, 0.0 ps. 84: Generated 1 of the 1 non-bonded parameter combinations 84: 84: Excluding 1 bonded neighbours molecule type 'Argon' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.023 0.023 99.3 84: (ns/day) (hour/ns) 84: Performance: 63.739 0.377 84: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_reference.edr as double precision energy file 84: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.edr as double precision energy file 84: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 84: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 84: setting nstcomm equal to nstcalcenergy for less overhead 84: 84: Number of degrees of freedom in T-Coupling group System is 33.00 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 84: NVE simulation: will use the initial temperature of 68.810 K for 84: determining the Verlet buffer size 84: 84: 84: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 84: COM removal frequency is set to (5). 84: Other settings require a global communication frequency of 100. 84: Note that this will require additional global communication steps, 84: which will reduce performance when using multiple ranks. 84: Consider setting nstcomm to a multiple of 100. 84: 84: 84: There were 4 NOTEs 84: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 84: Can not increase nstlist because an NVE ensemble is used 84: Using 1 MPI thread 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'Argon' 84: 16 steps, 0.0 ps. 84: Generated 1 of the 1 non-bonded parameter combinations 84: 84: Excluding 1 bonded neighbours molecule type 'Argon' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.024 0.024 99.3 84: (ns/day) (hour/ns) 84: Performance: 61.639 0.389 84: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_reference.edr as double precision energy file 84: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.edr as double precision energy file 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 84: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 84: setting nstcomm equal to nstcalcenergy for less overhead 84: 84: Number of degrees of freedom in T-Coupling group System is 33.00 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 84: NVE simulation: will use the initial temperature of 68.810 K for 84: determining the Verlet buffer size 84: 84: 84: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 84: COM removal frequency is set to (5). 84: Other settings require a global communication frequency of 100. 84: Note that this will require additional global communication steps, 84: which will reduce performance when using multiple ranks. 84: Consider setting nstcomm to a multiple of 100. 84: 84: 84: There were 4 NOTEs 84: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 84: Can not increase nstlist because an NVE ensemble is used 84: Using 1 MPI thread 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'Argon' 84: 16 steps, 0.0 ps. 84: Generated 1 of the 1 non-bonded parameter combinations 84: 84: Excluding 1 bonded neighbours molecule type 'Argon' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.024 0.024 99.3 84: (ns/day) (hour/ns) 84: Performance: 61.912 0.388 84: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_reference.edr as double precision energy file 84: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.edr as double precision energy file 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 84: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 84: setting nstcomm equal to nstcalcenergy for less overhead 84: 84: Number of degrees of freedom in T-Coupling group System is 33.00 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 84: NVE simulation: will use the initial temperature of 68.810 K for 84: determining the Verlet buffer size 84: 84: 84: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 84: COM removal frequency is set to (5). 84: Other settings require a global communication frequency of 100. 84: Note that this will require additional global communication steps, 84: which will reduce performance when using multiple ranks. 84: Consider setting nstcomm to a multiple of 100. 84: 84: 84: There were 4 NOTEs 84: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 84: Can not increase nstlist because an NVE ensemble is used 84: Using 1 MPI thread 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'Argon' 84: 16 steps, 0.0 ps. 84: Generated 1 of the 1 non-bonded parameter combinations 84: 84: Excluding 1 bonded neighbours molecule type 'Argon' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.028 0.028 99.4 84: (ns/day) (hour/ns) 84: Performance: 51.901 0.462 84: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_reference.edr as double precision energy file 84: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.edr as double precision energy file 84: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/16 (405 ms) 84: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/17 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 84: Setting nstcalcenergy (100) equal to nstenergy (1) 84: 84: 84: WARNING 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 84: The Berendsen barostat does not generate any strictly correct ensemble, 84: and should not be used for new production simulations (in our opinion). 84: We recommend using the C-rescale barostat instead. 84: 84: Number of degrees of freedom in T-Coupling group System is 33.00 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 84: NVE simulation: will use the initial temperature of 68.810 K for 84: determining the Verlet buffer size 84: 84: 84: There were 3 NOTEs 84: 84: There was 1 WARNING 84: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 84: Can not increase nstlist because an NVE ensemble is used 84: Using 1 MPI thread 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'Argon' 84: 16 steps, 0.0 ps. 84: Generated 1 of the 1 non-bonded parameter combinations 84: 84: Excluding 1 bonded neighbours molecule type 'Argon' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.024 0.024 99.3 84: (ns/day) (hour/ns) 84: Performance: 60.487 0.397 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 84: Setting nstcalcenergy (100) equal to nstenergy (1) 84: 84: 84: WARNING 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 84: The Berendsen barostat does not generate any strictly correct ensemble, 84: and should not be used for new production simulations (in our opinion). 84: We recommend using the C-rescale barostat instead. 84: 84: Number of degrees of freedom in T-Coupling group System is 33.00 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 84: NVE simulation: will use the initial temperature of 68.810 K for 84: determining the Verlet buffer size 84: 84: 84: There were 3 NOTEs 84: 84: There was 1 WARNING 84: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 84: Can not increase nstlist because an NVE ensemble is used 84: Using 1 MPI thread 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'Argon' 84: 16 steps, 0.0 ps. 84: Generated 1 of the 1 non-bonded parameter combinations 84: 84: Excluding 1 bonded neighbours molecule type 'Argon' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.020 0.020 99.2 84: (ns/day) (hour/ns) 84: Performance: 71.936 0.334 84: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_reference.edr as double precision energy file 84: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.edr as double precision energy file 84: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 84: Setting nstcalcenergy (100) equal to nstenergy (4) 84: 84: 84: WARNING 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 84: The Berendsen barostat does not generate any strictly correct ensemble, 84: and should not be used for new production simulations (in our opinion). 84: We recommend using the C-rescale barostat instead. 84: 84: Number of degrees of freedom in T-Coupling group System is 33.00 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 84: NVE simulation: will use the initial temperature of 68.810 K for 84: determining the Verlet buffer size 84: 84: 84: There were 3 NOTEs 84: 84: There was 1 WARNING 84: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 84: Can not increase nstlist because an NVE ensemble is used 84: Using 1 MPI thread 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'Argon' 84: 16 steps, 0.0 ps. 84: Generated 1 of the 1 non-bonded parameter combinations 84: 84: Excluding 1 bonded neighbours molecule type 'Argon' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.020 0.020 99.2 84: (ns/day) (hour/ns) 84: Performance: 74.329 0.323 84: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_reference.edr as double precision energy file 84: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.edr as double precision energy file 84: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 84: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 84: setting nstcomm equal to nstcalcenergy for less overhead 84: 84: 84: WARNING 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 84: The Berendsen barostat does not generate any strictly correct ensemble, 84: and should not be used for new production simulations (in our opinion). 84: We recommend using the C-rescale barostat instead. 84: 84: Number of degrees of freedom in T-Coupling group System is 33.00 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 84: NVE simulation: will use the initial temperature of 68.810 K for 84: determining the Verlet buffer size 84: 84: 84: There were 3 NOTEs 84: 84: There was 1 WARNING 84: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 84: Can not increase nstlist because an NVE ensemble is used 84: Using 1 MPI thread 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'Argon' 84: 16 steps, 0.0 ps. 84: Generated 1 of the 1 non-bonded parameter combinations 84: 84: Excluding 1 bonded neighbours molecule type 'Argon' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.023 0.023 99.3 84: (ns/day) (hour/ns) 84: Performance: 62.582 0.383 84: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_reference.edr as double precision energy file 84: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.edr as double precision energy file 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 84: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 84: setting nstcomm equal to nstcalcenergy for less overhead 84: 84: 84: WARNING 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 84: The Berendsen barostat does not generate any strictly correct ensemble, 84: and should not be used for new production simulations (in our opinion). 84: We recommend using the C-rescale barostat instead. 84: 84: Number of degrees of freedom in T-Coupling group System is 33.00 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 84: NVE simulation: will use the initial temperature of 68.810 K for 84: determining the Verlet buffer size 84: 84: 84: There were 3 NOTEs 84: 84: There was 1 WARNING 84: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 84: Can not increase nstlist because an NVE ensemble is used 84: Using 1 MPI thread 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'Argon' 84: 16 steps, 0.0 ps. 84: Generated 1 of the 1 non-bonded parameter combinations 84: 84: Excluding 1 bonded neighbours molecule type 'Argon' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.022 0.023 98.2 84: (ns/day) (hour/ns) 84: Performance: 64.204 0.374 84: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_reference.edr as double precision energy file 84: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.edr as double precision energy file 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 84: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 84: setting nstcomm equal to nstcalcenergy for less overhead 84: 84: 84: WARNING 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 84: The Berendsen barostat does not generate any strictly correct ensemble, 84: and should not be used for new production simulations (in our opinion). 84: We recommend using the C-rescale barostat instead. 84: 84: Number of degrees of freedom in T-Coupling group System is 33.00 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 84: NVE simulation: will use the initial temperature of 68.810 K for 84: determining the Verlet buffer size 84: 84: 84: There were 3 NOTEs 84: 84: There was 1 WARNING 84: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 84: Can not increase nstlist because an NVE ensemble is used 84: Using 1 MPI thread 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'Argon' 84: 16 steps, 0.0 ps. 84: Generated 1 of the 1 non-bonded parameter combinations 84: 84: Excluding 1 bonded neighbours molecule type 'Argon' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.023 0.023 99.3 84: (ns/day) (hour/ns) 84: Performance: 64.745 0.371 84: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_reference.edr as double precision energy file 84: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.edr as double precision energy file 84: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/17 (381 ms) 84: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/18 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]: 84: Setting nstcalcenergy (100) equal to nstenergy (1) 84: 84: Number of degrees of freedom in T-Coupling group System is 33.00 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]: 84: NVE simulation: will use the initial temperature of 68.810 K for 84: determining the Verlet buffer size 84: 84: 84: There were 3 NOTEs 84: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 84: Can not increase nstlist because an NVE ensemble is used 84: Using 1 MPI thread 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'Argon' 84: 16 steps, 0.0 ps. 84: Generated 1 of the 1 non-bonded parameter combinations 84: 84: Excluding 1 bonded neighbours molecule type 'Argon' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.024 0.024 99.2 84: (ns/day) (hour/ns) 84: Performance: 60.375 0.398 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]: 84: Setting nstcalcenergy (100) equal to nstenergy (1) 84: 84: Number of degrees of freedom in T-Coupling group System is 33.00 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]: 84: NVE simulation: will use the initial temperature of 68.810 K for 84: determining the Verlet buffer size 84: 84: 84: There were 3 NOTEs 84: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 84: Can not increase nstlist because an NVE ensemble is used 84: Using 1 MPI thread 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'Argon' 84: 16 steps, 0.0 ps. 84: Generated 1 of the 1 non-bonded parameter combinations 84: 84: Excluding 1 bonded neighbours molecule type 'Argon' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.023 0.023 99.3 84: (ns/day) (hour/ns) 84: Performance: 62.505 0.384 84: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_reference.edr as double precision energy file 84: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18.edr as double precision energy file 84: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]: 84: Setting nstcalcenergy (100) equal to nstenergy (4) 84: 84: Number of degrees of freedom in T-Coupling group System is 33.00 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]: 84: NVE simulation: will use the initial temperature of 68.810 K for 84: determining the Verlet buffer size 84: 84: 84: There were 3 NOTEs 84: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 84: Can not increase nstlist because an NVE ensemble is used 84: Using 1 MPI thread 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'Argon' 84: 16 steps, 0.0 ps. 84: Generated 1 of the 1 non-bonded parameter combinations 84: 84: Excluding 1 bonded neighbours molecule type 'Argon' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.019 0.019 99.2 84: (ns/day) (hour/ns) 84: Performance: 75.630 0.317 84: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_reference.edr as double precision energy file 84: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18.edr as double precision energy file 84: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]: 84: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 84: setting nstcomm equal to nstcalcenergy for less overhead 84: 84: Number of degrees of freedom in T-Coupling group System is 33.00 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]: 84: NVE simulation: will use the initial temperature of 68.810 K for 84: determining the Verlet buffer size 84: 84: 84: There were 3 NOTEs 84: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 84: Can not increase nstlist because an NVE ensemble is used 84: Using 1 MPI thread 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'Argon' 84: 16 steps, 0.0 ps. 84: Generated 1 of the 1 non-bonded parameter combinations 84: 84: Excluding 1 bonded neighbours molecule type 'Argon' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.023 0.023 99.3 84: (ns/day) (hour/ns) 84: Performance: 64.389 0.373 84: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_reference.edr as double precision energy file 84: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18.edr as double precision energy file 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]: 84: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 84: setting nstcomm equal to nstcalcenergy for less overhead 84: 84: Number of degrees of freedom in T-Coupling group System is 33.00 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]: 84: NVE simulation: will use the initial temperature of 68.810 K for 84: determining the Verlet buffer size 84: 84: 84: There were 3 NOTEs 84: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 84: Can not increase nstlist because an NVE ensemble is used 84: Using 1 MPI thread 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'Argon' 84: 16 steps, 0.0 ps. 84: Generated 1 of the 1 non-bonded parameter combinations 84: 84: Excluding 1 bonded neighbours molecule type 'Argon' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.023 0.023 99.3 84: (ns/day) (hour/ns) 84: Performance: 64.682 0.371 84: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_reference.edr as double precision energy file 84: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18.edr as double precision energy file 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]: 84: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 84: setting nstcomm equal to nstcalcenergy for less overhead 84: 84: Number of degrees of freedom in T-Coupling group System is 33.00 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]: 84: NVE simulation: will use the initial temperature of 68.810 K for 84: determining the Verlet buffer size 84: 84: 84: There were 3 NOTEs 84: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 84: Can not increase nstlist because an NVE ensemble is used 84: Using 1 MPI thread 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'Argon' 84: 16 steps, 0.0 ps. 84: Generated 1 of the 1 non-bonded parameter combinations 84: 84: Excluding 1 bonded neighbours molecule type 'Argon' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.022 0.023 98.0 84: (ns/day) (hour/ns) 84: Performance: 64.320 0.373 84: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_reference.edr as double precision energy file 84: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18.edr as double precision energy file 84: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/18 (388 ms) 84: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/19 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_input.mdp]: 84: Setting nstcalcenergy (100) equal to nstenergy (1) 84: 84: Number of degrees of freedom in T-Coupling group System is 33.00 84: 84: There were 2 NOTEs 84: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 84: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 84: 84: Using 1 MPI thread 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'Argon' 84: 16 steps, 0.0 ps. 84: Generated 1 of the 1 non-bonded parameter combinations 84: 84: Excluding 1 bonded neighbours molecule type 'Argon' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.023 0.024 98.9 84: (ns/day) (hour/ns) 84: Performance: 62.190 0.386 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_input.mdp]: 84: Setting nstcalcenergy (100) equal to nstenergy (1) 84: 84: Number of degrees of freedom in T-Coupling group System is 33.00 84: 84: There were 2 NOTEs 84: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 84: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 84: 84: Using 1 MPI thread 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'Argon' 84: 16 steps, 0.0 ps. 84: Generated 1 of the 1 non-bonded parameter combinations 84: 84: Excluding 1 bonded neighbours molecule type 'Argon' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.020 0.020 98.7 84: (ns/day) (hour/ns) 84: Performance: 73.558 0.326 84: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_reference.edr as double precision energy file 84: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19.edr as double precision energy file 84: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_input.mdp]: 84: Setting nstcalcenergy (100) equal to nstenergy (4) 84: 84: Number of degrees of freedom in T-Coupling group System is 33.00 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_input.mdp]: 84: COM removal frequency is set to (5). 84: Other settings require a global communication frequency of 2. 84: Note that this will require additional global communication steps, 84: which will reduce performance when using multiple ranks. 84: Consider setting nstcomm to a multiple of 2. 84: 84: 84: There were 3 NOTEs 84: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 84: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 84: 84: Using 1 MPI thread 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'Argon' 84: 16 steps, 0.0 ps. 84: Generated 1 of the 1 non-bonded parameter combinations 84: 84: Excluding 1 bonded neighbours molecule type 'Argon' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.020 0.020 98.8 84: (ns/day) (hour/ns) 84: Performance: 71.767 0.334 84: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_reference.edr as double precision energy file 84: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19.edr as double precision energy file 84: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_input.mdp]: 84: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 84: setting nstcomm equal to nstcalcenergy for less overhead 84: 84: Number of degrees of freedom in T-Coupling group System is 33.00 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_input.mdp]: 84: COM removal frequency is set to (5). 84: Other settings require a global communication frequency of 2. 84: Note that this will require additional global communication steps, 84: which will reduce performance when using multiple ranks. 84: Consider setting nstcomm to a multiple of 2. 84: 84: 84: There were 3 NOTEs 84: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 84: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 84: 84: Using 1 MPI thread 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'Argon' 84: 16 steps, 0.0 ps. 84: Generated 1 of the 1 non-bonded parameter combinations 84: 84: Excluding 1 bonded neighbours molecule type 'Argon' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.035 0.035 99.4 84: (ns/day) (hour/ns) 84: Performance: 41.961 0.572 84: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_reference.edr as double precision energy file 84: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19.edr as double precision energy file 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_input.mdp]: 84: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 84: setting nstcomm equal to nstcalcenergy for less overhead 84: 84: Number of degrees of freedom in T-Coupling group System is 33.00 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_input.mdp]: 84: COM removal frequency is set to (5). 84: Other settings require a global communication frequency of 2. 84: Note that this will require additional global communication steps, 84: which will reduce performance when using multiple ranks. 84: Consider setting nstcomm to a multiple of 2. 84: 84: 84: There were 3 NOTEs 84: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 84: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 84: 84: Using 1 MPI thread 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'Argon' 84: 16 steps, 0.0 ps. 84: Generated 1 of the 1 non-bonded parameter combinations 84: 84: Excluding 1 bonded neighbours molecule type 'Argon' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.024 0.024 98.9 84: (ns/day) (hour/ns) 84: Performance: 61.433 0.391 84: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_reference.edr as double precision energy file 84: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19.edr as double precision energy file 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_input.mdp]: 84: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 84: setting nstcomm equal to nstcalcenergy for less overhead 84: 84: Number of degrees of freedom in T-Coupling group System is 33.00 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_input.mdp]: 84: COM removal frequency is set to (5). 84: Other settings require a global communication frequency of 2. 84: Note that this will require additional global communication steps, 84: which will reduce performance when using multiple ranks. 84: Consider setting nstcomm to a multiple of 2. 84: 84: 84: There were 3 NOTEs 84: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 84: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 84: 84: Using 1 MPI thread 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'Argon' 84: 16 steps, 0.0 ps. 84: Generated 1 of the 1 non-bonded parameter combinations 84: 84: Excluding 1 bonded neighbours molecule type 'Argon' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.023 0.023 98.9 84: (ns/day) (hour/ns) 84: Performance: 63.727 0.377 84: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_reference.edr as double precision energy file 84: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19.edr as double precision energy file 84: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/19 (412 ms) 84: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/20 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]: 84: Setting nstcalcenergy (100) equal to nstenergy (1) 84: 84: 84: WARNING 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]: 84: The Berendsen barostat does not generate any strictly correct ensemble, 84: and should not be used for new production simulations (in our opinion). 84: We recommend using the C-rescale barostat instead. 84: 84: Number of degrees of freedom in T-Coupling group System is 33.00 84: 84: There were 2 NOTEs 84: 84: There was 1 WARNING 84: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 84: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 84: 84: Using 1 MPI thread 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'Argon' 84: 16 steps, 0.0 ps. 84: Generated 1 of the 1 non-bonded parameter combinations 84: 84: Excluding 1 bonded neighbours molecule type 'Argon' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.027 0.027 99.0 84: (ns/day) (hour/ns) 84: Performance: 54.093 0.444 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]: 84: Setting nstcalcenergy (100) equal to nstenergy (1) 84: 84: 84: WARNING 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]: 84: The Berendsen barostat does not generate any strictly correct ensemble, 84: and should not be used for new production simulations (in our opinion). 84: We recommend using the C-rescale barostat instead. 84: 84: Number of degrees of freedom in T-Coupling group System is 33.00 84: 84: There were 2 NOTEs 84: 84: There was 1 WARNING 84: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 84: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 84: 84: Using 1 MPI thread 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'Argon' 84: 16 steps, 0.0 ps. 84: Generated 1 of the 1 non-bonded parameter combinations 84: 84: Excluding 1 bonded neighbours molecule type 'Argon' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.023 0.023 98.8 84: (ns/day) (hour/ns) 84: Performance: 63.288 0.379 84: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_reference.edr as double precision energy file 84: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20.edr as double precision energy file 84: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]: 84: Setting nstcalcenergy (100) equal to nstenergy (4) 84: 84: 84: WARNING 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]: 84: The Berendsen barostat does not generate any strictly correct ensemble, 84: and should not be used for new production simulations (in our opinion). 84: We recommend using the C-rescale barostat instead. 84: 84: Number of degrees of freedom in T-Coupling group System is 33.00 84: 84: There were 2 NOTEs 84: 84: There was 1 WARNING 84: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 84: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 84: 84: Using 1 MPI thread 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'Argon' 84: 16 steps, 0.0 ps. 84: Generated 1 of the 1 non-bonded parameter combinations 84: 84: Excluding 1 bonded neighbours molecule type 'Argon' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.029 0.029 99.0 84: (ns/day) (hour/ns) 84: Performance: 50.253 0.478 84: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_reference.edr as double precision energy file 84: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20.edr as double precision energy file 84: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]: 84: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 84: setting nstcomm equal to nstcalcenergy for less overhead 84: 84: 84: WARNING 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]: 84: The Berendsen barostat does not generate any strictly correct ensemble, 84: and should not be used for new production simulations (in our opinion). 84: We recommend using the C-rescale barostat instead. 84: 84: Number of degrees of freedom in T-Coupling group System is 33.00 84: 84: There were 2 NOTEs 84: 84: There was 1 WARNING 84: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 84: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 84: 84: Using 1 MPI thread 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'Argon' 84: 16 steps, 0.0 ps. 84: Generated 1 of the 1 non-bonded parameter combinations 84: 84: Excluding 1 bonded neighbours molecule type 'Argon' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.023 0.023 99.0 84: (ns/day) (hour/ns) 84: Performance: 63.526 0.378 84: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_reference.edr as double precision energy file 84: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20.edr as double precision energy file 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]: 84: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 84: setting nstcomm equal to nstcalcenergy for less overhead 84: 84: 84: WARNING 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]: 84: The Berendsen barostat does not generate any strictly correct ensemble, 84: and should not be used for new production simulations (in our opinion). 84: We recommend using the C-rescale barostat instead. 84: 84: Number of degrees of freedom in T-Coupling group System is 33.00 84: 84: There were 2 NOTEs 84: 84: There was 1 WARNING 84: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 84: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 84: 84: Using 1 MPI thread 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'Argon' 84: 16 steps, 0.0 ps. 84: Generated 1 of the 1 non-bonded parameter combinations 84: 84: Excluding 1 bonded neighbours molecule type 'Argon' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.022 0.023 98.9 84: (ns/day) (hour/ns) 84: Performance: 64.730 0.371 84: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_reference.edr as double precision energy file 84: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20.edr as double precision energy file 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]: 84: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 84: setting nstcomm equal to nstcalcenergy for less overhead 84: 84: 84: WARNING 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]: 84: The Berendsen barostat does not generate any strictly correct ensemble, 84: and should not be used for new production simulations (in our opinion). 84: We recommend using the C-rescale barostat instead. 84: 84: Number of degrees of freedom in T-Coupling group System is 33.00 84: 84: There were 2 NOTEs 84: 84: There was 1 WARNING 84: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 84: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 84: 84: Using 1 MPI thread 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'Argon' 84: 16 steps, 0.0 ps. 84: Generated 1 of the 1 non-bonded parameter combinations 84: 84: Excluding 1 bonded neighbours molecule type 'Argon' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.023 0.023 98.9 84: (ns/day) (hour/ns) 84: Performance: 64.142 0.374 84: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_reference.edr as double precision energy file 84: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20.edr as double precision energy file 84: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/20 (402 ms) 84: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/21 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_input.mdp]: 84: Setting nstcalcenergy (100) equal to nstenergy (1) 84: 84: Number of degrees of freedom in T-Coupling group System is 33.00 84: 84: There were 2 NOTEs 84: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 84: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 84: 84: Using 1 MPI thread 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'Argon' 84: 16 steps, 0.0 ps. 84: Generated 1 of the 1 non-bonded parameter combinations 84: 84: Excluding 1 bonded neighbours molecule type 'Argon' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.024 0.024 98.9 84: (ns/day) (hour/ns) 84: Performance: 60.656 0.396 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_input.mdp]: 84: Setting nstcalcenergy (100) equal to nstenergy (1) 84: 84: Number of degrees of freedom in T-Coupling group System is 33.00 84: 84: There were 2 NOTEs 84: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 84: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 84: 84: Using 1 MPI thread 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'Argon' 84: 16 steps, 0.0 ps. 84: Generated 1 of the 1 non-bonded parameter combinations 84: 84: Excluding 1 bonded neighbours molecule type 'Argon' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.020 0.020 98.7 84: (ns/day) (hour/ns) 84: Performance: 72.666 0.330 84: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_reference.edr as double precision energy file 84: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21.edr as double precision energy file 84: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_input.mdp]: 84: Setting nstcalcenergy (100) equal to nstenergy (4) 84: 84: Number of degrees of freedom in T-Coupling group System is 33.00 84: 84: There were 2 NOTEs 84: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 84: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 84: 84: Using 1 MPI thread 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'Argon' 84: 16 steps, 0.0 ps. 84: Generated 1 of the 1 non-bonded parameter combinations 84: 84: Excluding 1 bonded neighbours molecule type 'Argon' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.020 0.021 98.9 84: (ns/day) (hour/ns) 84: Performance: 71.039 0.338 84: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_reference.edr as double precision energy file 84: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21.edr as double precision energy file 84: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_input.mdp]: 84: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 84: setting nstcomm equal to nstcalcenergy for less overhead 84: 84: Number of degrees of freedom in T-Coupling group System is 33.00 84: 84: There were 2 NOTEs 84: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 84: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 84: 84: Using 1 MPI thread 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'Argon' 84: 16 steps, 0.0 ps. 84: Generated 1 of the 1 non-bonded parameter combinations 84: 84: Excluding 1 bonded neighbours molecule type 'Argon' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.066 0.066 99.6 84: (ns/day) (hour/ns) 84: Performance: 22.111 1.085 84: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_reference.edr as double precision energy file 84: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21.edr as double precision energy file 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_input.mdp]: 84: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 84: setting nstcomm equal to nstcalcenergy for less overhead 84: 84: Number of degrees of freedom in T-Coupling group System is 33.00 84: 84: There were 2 NOTEs 84: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 84: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 84: 84: Using 1 MPI thread 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'Argon' 84: 16 steps, 0.0 ps. 84: Generated 1 of the 1 non-bonded parameter combinations 84: 84: Excluding 1 bonded neighbours molecule type 'Argon' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.066 0.066 99.6 84: (ns/day) (hour/ns) 84: Performance: 22.105 1.086 84: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_reference.edr as double precision energy file 84: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21.edr as double precision energy file 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_input.mdp]: 84: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 84: setting nstcomm equal to nstcalcenergy for less overhead 84: 84: Number of degrees of freedom in T-Coupling group System is 33.00 84: 84: There were 2 NOTEs 84: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 84: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 84: 84: Using 1 MPI thread 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'Argon' 84: 16 steps, 0.0 ps. 84: Generated 1 of the 1 non-bonded parameter combinations 84: 84: Excluding 1 bonded neighbours molecule type 'Argon' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.060 0.060 99.5 84: (ns/day) (hour/ns) 84: Performance: 24.559 0.977 84: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_reference.edr as double precision energy file 84: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21.edr as double precision energy file 84: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/21 (608 ms) 84: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/22 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_input.mdp]: 84: Setting nstcalcenergy (100) equal to nstenergy (1) 84: 84: Number of degrees of freedom in T-Coupling group System is 33.00 84: 84: There were 2 NOTEs 84: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 84: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 84: 84: Using 1 MPI thread 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'Argon' 84: 16 steps, 0.0 ps. 84: Generated 1 of the 1 non-bonded parameter combinations 84: 84: Excluding 1 bonded neighbours molecule type 'Argon' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.049 0.049 99.5 84: (ns/day) (hour/ns) 84: Performance: 30.069 0.798 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_input.mdp]: 84: Setting nstcalcenergy (100) equal to nstenergy (1) 84: 84: Number of degrees of freedom in T-Coupling group System is 33.00 84: 84: There were 2 NOTEs 84: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 84: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 84: 84: Using 1 MPI thread 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'Argon' 84: 16 steps, 0.0 ps. 84: Generated 1 of the 1 non-bonded parameter combinations 84: 84: Excluding 1 bonded neighbours molecule type 'Argon' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.023 0.023 98.9 84: (ns/day) (hour/ns) 84: Performance: 63.725 0.377 84: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_reference.edr as double precision energy file 84: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22.edr as double precision energy file 84: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_input.mdp]: 84: Setting nstcalcenergy (100) equal to nstenergy (4) 84: 84: Number of degrees of freedom in T-Coupling group System is 33.00 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_input.mdp]: 84: COM removal frequency is set to (5). 84: Other settings require a global communication frequency of 2. 84: Note that this will require additional global communication steps, 84: which will reduce performance when using multiple ranks. 84: Consider setting nstcomm to a multiple of 2. 84: 84: 84: There were 3 NOTEs 84: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 84: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 84: 84: Using 1 MPI thread 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'Argon' 84: 16 steps, 0.0 ps. 84: Generated 1 of the 1 non-bonded parameter combinations 84: 84: Excluding 1 bonded neighbours molecule type 'Argon' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.036 0.036 99.3 84: (ns/day) (hour/ns) 84: Performance: 40.845 0.588 84: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_reference.edr as double precision energy file 84: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22.edr as double precision energy file 84: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_input.mdp]: 84: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 84: setting nstcomm equal to nstcalcenergy for less overhead 84: 84: Number of degrees of freedom in T-Coupling group System is 33.00 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_input.mdp]: 84: COM removal frequency is set to (5). 84: Other settings require a global communication frequency of 2. 84: Note that this will require additional global communication steps, 84: which will reduce performance when using multiple ranks. 84: Consider setting nstcomm to a multiple of 2. 84: 84: 84: There were 3 NOTEs 84: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 84: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 84: 84: Using 1 MPI thread 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'Argon' 84: 16 steps, 0.0 ps. 84: Generated 1 of the 1 non-bonded parameter combinations 84: 84: Excluding 1 bonded neighbours molecule type 'Argon' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.062 0.063 99.5 84: (ns/day) (hour/ns) 84: Performance: 23.495 1.022 84: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_reference.edr as double precision energy file 84: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22.edr as double precision energy file 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_input.mdp]: 84: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 84: setting nstcomm equal to nstcalcenergy for less overhead 84: 84: Number of degrees of freedom in T-Coupling group System is 33.00 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_input.mdp]: 84: COM removal frequency is set to (5). 84: Other settings require a global communication frequency of 2. 84: Note that this will require additional global communication steps, 84: which will reduce performance when using multiple ranks. 84: Consider setting nstcomm to a multiple of 2. 84: 84: 84: There were 3 NOTEs 84: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 84: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 84: 84: Using 1 MPI thread 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'Argon' 84: 16 steps, 0.0 ps. 84: Generated 1 of the 1 non-bonded parameter combinations 84: 84: Excluding 1 bonded neighbours molecule type 'Argon' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.060 0.060 99.5 84: (ns/day) (hour/ns) 84: Performance: 24.446 0.982 84: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_reference.edr as double precision energy file 84: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22.edr as double precision energy file 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_input.mdp]: 84: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 84: setting nstcomm equal to nstcalcenergy for less overhead 84: 84: Number of degrees of freedom in T-Coupling group System is 33.00 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_input.mdp]: 84: COM removal frequency is set to (5). 84: Other settings require a global communication frequency of 2. 84: Note that this will require additional global communication steps, 84: which will reduce performance when using multiple ranks. 84: Consider setting nstcomm to a multiple of 2. 84: 84: 84: There were 3 NOTEs 84: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 84: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 84: 84: Using 1 MPI thread 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'Argon' 84: 16 steps, 0.0 ps. 84: Generated 1 of the 1 non-bonded parameter combinations 84: 84: Excluding 1 bonded neighbours molecule type 'Argon' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.054 0.054 99.5 84: (ns/day) (hour/ns) 84: Performance: 26.956 0.890 84: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_reference.edr as double precision energy file 84: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22.edr as double precision energy file 84: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/22 (764 ms) 84: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/23 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 84: Setting nstcalcenergy (100) equal to nstenergy (1) 84: 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 84: MTTK coupling is deprecated and will soon be removed 84: 84: 84: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 84: for current Trotter decomposition methods with vv, nsttcouple and 84: nstpcouple must be equal. Both have been reset to 84: min(nsttcouple,nstpcouple) = 2 84: 84: Number of degrees of freedom in T-Coupling group System is 33.00 84: 84: There were 4 NOTEs 84: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 84: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 84: 84: Using 1 MPI thread 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'Argon' 84: 16 steps, 0.0 ps. 84: Generated 1 of the 1 non-bonded parameter combinations 84: 84: Excluding 1 bonded neighbours molecule type 'Argon' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.063 0.063 99.4 84: (ns/day) (hour/ns) 84: Performance: 23.175 1.036 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 84: Setting nstcalcenergy (100) equal to nstenergy (1) 84: 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 84: MTTK coupling is deprecated and will soon be removed 84: 84: 84: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 84: for current Trotter decomposition methods with vv, nsttcouple and 84: nstpcouple must be equal. Both have been reset to 84: min(nsttcouple,nstpcouple) = 2 84: 84: Number of degrees of freedom in T-Coupling group System is 33.00 84: 84: There were 4 NOTEs 84: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 84: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 84: 84: Using 1 MPI thread 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'Argon' 84: 16 steps, 0.0 ps. 84: Generated 1 of the 1 non-bonded parameter combinations 84: 84: Excluding 1 bonded neighbours molecule type 'Argon' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.028 0.029 98.6 84: (ns/day) (hour/ns) 84: Performance: 51.369 0.467 84: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_reference.edr as double precision energy file 84: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23.edr as double precision energy file 84: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 84: Setting nstcalcenergy (100) equal to nstenergy (4) 84: 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 84: MTTK coupling is deprecated and will soon be removed 84: 84: 84: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 84: for current Trotter decomposition methods with vv, nsttcouple and 84: nstpcouple must be equal. Both have been reset to 84: min(nsttcouple,nstpcouple) = 2 84: 84: Number of degrees of freedom in T-Coupling group System is 33.00 84: 84: NOTE 5 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 84: COM removal frequency is set to (5). 84: Other settings require a global communication frequency of 2. 84: Note that this will require additional global communication steps, 84: which will reduce performance when using multiple ranks. 84: Consider setting nstcomm to a multiple of 2. 84: 84: 84: There were 5 NOTEs 84: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 84: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 84: 84: Using 1 MPI thread 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'Argon' 84: 16 steps, 0.0 ps. 84: Generated 1 of the 1 non-bonded parameter combinations 84: 84: Excluding 1 bonded neighbours molecule type 'Argon' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.030 0.031 98.8 84: (ns/day) (hour/ns) 84: Performance: 48.044 0.500 84: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_reference.edr as double precision energy file 84: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23.edr as double precision energy file 84: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 84: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 84: setting nstcomm equal to nstcalcenergy for less overhead 84: 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 84: MTTK coupling is deprecated and will soon be removed 84: 84: 84: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 84: for current Trotter decomposition methods with vv, nsttcouple and 84: nstpcouple must be equal. Both have been reset to 84: min(nsttcouple,nstpcouple) = 2 84: 84: Number of degrees of freedom in T-Coupling group System is 33.00 84: 84: NOTE 5 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 84: COM removal frequency is set to (5). 84: Other settings require a global communication frequency of 2. 84: Note that this will require additional global communication steps, 84: which will reduce performance when using multiple ranks. 84: Consider setting nstcomm to a multiple of 2. 84: 84: 84: There were 5 NOTEs 84: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 84: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 84: 84: Using 1 MPI thread 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'Argon' 84: 16 steps, 0.0 ps. 84: Generated 1 of the 1 non-bonded parameter combinations 84: 84: Excluding 1 bonded neighbours molecule type 'Argon' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.057 0.057 99.4 84: (ns/day) (hour/ns) 84: Performance: 25.553 0.939 84: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_reference.edr as double precision energy file 84: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23.edr as double precision energy file 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 84: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 84: setting nstcomm equal to nstcalcenergy for less overhead 84: 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 84: MTTK coupling is deprecated and will soon be removed 84: 84: 84: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 84: for current Trotter decomposition methods with vv, nsttcouple and 84: nstpcouple must be equal. Both have been reset to 84: min(nsttcouple,nstpcouple) = 2 84: 84: Number of degrees of freedom in T-Coupling group System is 33.00 84: 84: NOTE 5 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 84: COM removal frequency is set to (5). 84: Other settings require a global communication frequency of 2. 84: Note that this will require additional global communication steps, 84: which will reduce performance when using multiple ranks. 84: Consider setting nstcomm to a multiple of 2. 84: 84: 84: There were 5 NOTEs 84: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 84: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 84: 84: Using 1 MPI thread 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'Argon' 84: 16 steps, 0.0 ps. 84: Generated 1 of the 1 non-bonded parameter combinations 84: 84: Excluding 1 bonded neighbours molecule type 'Argon' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.064 0.065 99.5 84: (ns/day) (hour/ns) 84: Performance: 22.749 1.055 84: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_reference.edr as double precision energy file 84: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23.edr as double precision energy file 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 84: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 84: setting nstcomm equal to nstcalcenergy for less overhead 84: 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 84: MTTK coupling is deprecated and will soon be removed 84: 84: 84: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 84: for current Trotter decomposition methods with vv, nsttcouple and 84: nstpcouple must be equal. Both have been reset to 84: min(nsttcouple,nstpcouple) = 2 84: 84: Number of degrees of freedom in T-Coupling group System is 33.00 84: 84: NOTE 5 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 84: COM removal frequency is set to (5). 84: Other settings require a global communication frequency of 2. 84: Note that this will require additional global communication steps, 84: which will reduce performance when using multiple ranks. 84: Consider setting nstcomm to a multiple of 2. 84: 84: 84: There were 5 NOTEs 84: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 84: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 84: 84: Using 1 MPI thread 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'Argon' 84: 16 steps, 0.0 ps. 84: Generated 1 of the 1 non-bonded parameter combinations 84: 84: Excluding 1 bonded neighbours molecule type 'Argon' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.057 0.058 99.4 84: (ns/day) (hour/ns) 84: Performance: 25.503 0.941 84: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_reference.edr as double precision energy file 84: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23.edr as double precision energy file 84: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/23 (720 ms) 84: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/24 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24_input.mdp]: 84: Setting nstcalcenergy (100) equal to nstenergy (1) 84: 84: Number of degrees of freedom in T-Coupling group System is 33.00 84: 84: There were 2 NOTEs 84: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 84: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 84: 84: Using 1 MPI thread 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'Argon' 84: 16 steps, 0.0 ps. 84: Generated 1 of the 1 non-bonded parameter combinations 84: 84: Excluding 1 bonded neighbours molecule type 'Argon' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.050 0.050 99.5 84: (ns/day) (hour/ns) 84: Performance: 29.403 0.816 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24_input.mdp]: 84: Setting nstcalcenergy (100) equal to nstenergy (1) 84: 84: Number of degrees of freedom in T-Coupling group System is 33.00 84: 84: There were 2 NOTEs 84: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 84: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 84: 84: Using 1 MPI thread 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'Argon' 84: 16 steps, 0.0 ps. 84: Generated 1 of the 1 non-bonded parameter combinations 84: 84: Excluding 1 bonded neighbours molecule type 'Argon' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.052 0.053 99.2 84: (ns/day) (hour/ns) 84: Performance: 27.844 0.862 84: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24_reference.edr as double precision energy file 84: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24.edr as double precision energy file 84: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24_input.mdp]: 84: Setting nstcalcenergy (100) equal to nstenergy (4) 84: 84: Number of degrees of freedom in T-Coupling group System is 33.00 84: 84: There were 2 NOTEs 84: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 84: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 84: 84: Using 1 MPI thread 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'Argon' 84: 16 steps, 0.0 ps. 84: Generated 1 of the 1 non-bonded parameter combinations 84: 84: Excluding 1 bonded neighbours molecule type 'Argon' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.038 0.039 99.3 84: (ns/day) (hour/ns) 84: Performance: 37.875 0.634 84: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24_reference.edr as double precision energy file 84: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24.edr as double precision energy file 84: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24_input.mdp]: 84: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 84: setting nstcomm equal to nstcalcenergy for less overhead 84: 84: Number of degrees of freedom in T-Coupling group System is 33.00 84: 84: There were 2 NOTEs 84: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 84: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 84: 84: Using 1 MPI thread 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'Argon' 84: 16 steps, 0.0 ps. 84: Generated 1 of the 1 non-bonded parameter combinations 84: 84: Excluding 1 bonded neighbours molecule type 'Argon' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.027 0.027 99.0 84: (ns/day) (hour/ns) 84: Performance: 53.751 0.447 84: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24_reference.edr as double precision energy file 84: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24.edr as double precision energy file 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24_input.mdp]: 84: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 84: setting nstcomm equal to nstcalcenergy for less overhead 84: 84: Number of degrees of freedom in T-Coupling group System is 33.00 84: 84: There were 2 NOTEs 84: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 84: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 84: 84: Using 1 MPI thread 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'Argon' 84: 16 steps, 0.0 ps. 84: Generated 1 of the 1 non-bonded parameter combinations 84: 84: Excluding 1 bonded neighbours molecule type 'Argon' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.050 0.051 99.5 84: (ns/day) (hour/ns) 84: Performance: 29.051 0.826 84: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24_reference.edr as double precision energy file 84: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24.edr as double precision energy file 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24_input.mdp]: 84: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 84: setting nstcomm equal to nstcalcenergy for less overhead 84: 84: Number of degrees of freedom in T-Coupling group System is 33.00 84: 84: There were 2 NOTEs 84: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 84: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 84: 84: Using 1 MPI thread 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'Argon' 84: 16 steps, 0.0 ps. 84: Generated 1 of the 1 non-bonded parameter combinations 84: 84: Excluding 1 bonded neighbours molecule type 'Argon' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.047 0.047 99.4 84: (ns/day) (hour/ns) 84: Performance: 31.202 0.769 84: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24_reference.edr as double precision energy file 84: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24.edr as double precision energy file 84: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/24 (692 ms) 84: [----------] 25 tests from PropagatorsWithCoupling/PeriodicActionsTest (10838 ms total) 84: 84: [----------] Global test environment tear-down 84: [==========] 25 tests from 1 test suite ran. (10886 ms total) 84: [ PASSED ] 25 tests. 84/92 Test #84: MdrunCoordinationCouplingTests1Rank ....... Passed 11.00 sec test 85 Start 85: MdrunCoordinationCouplingTests2Ranks 85: Test command: /build/reproducible-path/gromacs-2025.1/build/basic-dp/bin/mdrun-coordination-coupling-test "-ntmpi" "2" "--gtest_output=xml:/build/reproducible-path/gromacs-2025.1/build/basic-dp/Testing/Temporary/MdrunCoordinationCouplingTests2Ranks.xml" 85: Working Directory: /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests 85: Test timeout computed to be: 1920 85: [==========] Running 25 tests from 1 test suite. 85: [----------] Global test environment set-up. 85: [----------] 25 tests from PropagatorsWithCoupling/PeriodicActionsTest 85: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/0 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 85: Setting nstcalcenergy (100) equal to nstenergy (1) 85: 85: Number of degrees of freedom in T-Coupling group System is 33.00 85: 85: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 85: NVE simulation: will use the initial temperature of 68.810 K for 85: determining the Verlet buffer size 85: 85: 85: There were 3 NOTEs 85: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 85: Can not increase nstlist because an NVE ensemble is used 85: Using 2 MPI threads 85: Using 1 OpenMP thread per tMPI thread 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'Argon' 85: 16 steps, 0.0 ps. 85: Generated 1 of the 1 non-bonded parameter combinations 85: 85: Excluding 1 bonded neighbours molecule type 'Argon' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: 85: Dynamic load balancing report: 85: DLB was turned on during the run due to measured imbalance. 85: Average load imbalance: 47.9%. 85: The balanceable part of the MD step is 29%, load imbalance is computed from this. 85: Part of the total run time spent waiting due to load imbalance: 14.0%. 85: Steps where the load balancing was limited by -rdd, -rcon and/or -dds: X 0 % 85: 85: NOTE: 14.0 % of the available CPU time was lost due to load imbalance 85: in the domain decomposition. 85: You can consider manually changing the decomposition (option -dd); 85: e.g. by using fewer domains along the box dimension in which there is 85: considerable inhomogeneity in the simulated system. 85: 85: NOTE: 47 % of the run time was spent communicating energies, 85: you might want to increase some nst* mdp options 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.222 0.111 199.4 85: (ns/day) (hour/ns) 85: Performance: 13.218 1.816 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 85: Setting nstcalcenergy (100) equal to nstenergy (1) 85: 85: Number of degrees of freedom in T-Coupling group System is 33.00 85: 85: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 85: NVE simulation: will use the initial temperature of 68.810 K for 85: determining the Verlet buffer size 85: 85: 85: There were 3 NOTEs 85: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 85: Can not increase nstlist because an NVE ensemble is used 85: Using 2 MPI threads 85: Using 1 OpenMP thread per tMPI thread 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'Argon' 85: 16 steps, 0.0 ps. 85: Generated 1 of the 1 non-bonded parameter combinations 85: 85: Excluding 1 bonded neighbours molecule type 'Argon' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: 85: Dynamic load balancing report: 85: DLB was off during the run due to low measured imbalance. 85: Average load imbalance: 2.0%. 85: The balanceable part of the MD step is 55%, load imbalance is computed from this. 85: Part of the total run time spent waiting due to load imbalance: 1.1%. 85: 85: 85: NOTE: 51 % of the run time was spent communicating energies, 85: you might want to increase some nst* mdp options 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.101 0.051 198.7 85: (ns/day) (hour/ns) 85: Performance: 28.849 0.832 85: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as double precision energy file 85: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as double precision energy file 85: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 85: Setting nstcalcenergy (100) equal to nstenergy (4) 85: 85: Number of degrees of freedom in T-Coupling group System is 33.00 85: 85: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 85: NVE simulation: will use the initial temperature of 68.810 K for 85: determining the Verlet buffer size 85: 85: 85: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 85: COM removal frequency is set to (5). 85: Other settings require a global communication frequency of 4. 85: Note that this will require additional global communication steps, 85: which will reduce performance when using multiple ranks. 85: Consider setting nstcomm to a multiple of 4. 85: 85: 85: There were 4 NOTEs 85: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 85: Can not increase nstlist because an NVE ensemble is used 85: Using 2 MPI threads 85: Using 1 OpenMP thread per tMPI thread 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'Argon' 85: 16 steps, 0.0 ps. 85: Generated 1 of the 1 non-bonded parameter combinations 85: 85: Excluding 1 bonded neighbours molecule type 'Argon' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: 85: Dynamic load balancing report: 85: DLB was turned on during the run due to measured imbalance. 85: Average load imbalance: 37.2%. 85: The balanceable part of the MD step is 16%, load imbalance is computed from this. 85: Part of the total run time spent waiting due to load imbalance: 6.0%. 85: Steps where the load balancing was limited by -rdd, -rcon and/or -dds: X 0 % 85: 85: NOTE: 6.0 % of the available CPU time was lost due to load imbalance 85: in the domain decomposition. 85: You can consider manually changing the decomposition (option -dd); 85: e.g. by using fewer domains along the box dimension in which there is 85: considerable inhomogeneity in the simulated system. 85: 85: NOTE: 19 % of the run time was spent in domain decomposition, 85: 0 % of the run time was spent in pair search, 85: you might want to increase nstlist (this has no effect on accuracy) 85: 85: NOTE: 37 % of the run time was spent communicating energies, 85: you might want to increase some nst* mdp options 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.307 0.154 199.5 85: (ns/day) (hour/ns) 85: Performance: 9.547 2.514 85: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as double precision energy file 85: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as double precision energy file 85: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 85: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 85: setting nstcomm equal to nstcalcenergy for less overhead 85: 85: Number of degrees of freedom in T-Coupling group System is 33.00 85: 85: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 85: NVE simulation: will use the initial temperature of 68.810 K for 85: determining the Verlet buffer size 85: 85: 85: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 85: COM removal frequency is set to (5). 85: Other settings require a global communication frequency of 100. 85: Note that this will require additional global communication steps, 85: which will reduce performance when using multiple ranks. 85: Consider setting nstcomm to a multiple of 100. 85: 85: 85: There were 4 NOTEs 85: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 85: Can not increase nstlist because an NVE ensemble is used 85: Using 2 MPI threads 85: Using 1 OpenMP thread per tMPI thread 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'Argon' 85: 16 steps, 0.0 ps. 85: Generated 1 of the 1 non-bonded parameter combinations 85: 85: Excluding 1 bonded neighbours molecule type 'Argon' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: 85: Dynamic load balancing report: 85: DLB was off during the run due to low measured imbalance. 85: Average load imbalance: 2.9%. 85: The balanceable part of the MD step is 14%, load imbalance is computed from this. 85: Part of the total run time spent waiting due to load imbalance: 0.4%. 85: 85: 85: NOTE: 40 % of the run time was spent communicating energies, 85: you might want to increase some nst* mdp options 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.122 0.061 199.0 85: (ns/day) (hour/ns) 85: Performance: 24.012 1.000 85: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as double precision energy file 85: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as double precision energy file 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 85: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 85: setting nstcomm equal to nstcalcenergy for less overhead 85: 85: Number of degrees of freedom in T-Coupling group System is 33.00 85: 85: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 85: NVE simulation: will use the initial temperature of 68.810 K for 85: determining the Verlet buffer size 85: 85: 85: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 85: COM removal frequency is set to (5). 85: Other settings require a global communication frequency of 100. 85: Note that this will require additional global communication steps, 85: which will reduce performance when using multiple ranks. 85: Consider setting nstcomm to a multiple of 100. 85: 85: 85: There were 4 NOTEs 85: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 85: Can not increase nstlist because an NVE ensemble is used 85: Using 2 MPI threads 85: Using 1 OpenMP thread per tMPI thread 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'Argon' 85: 16 steps, 0.0 ps. 85: Generated 1 of the 1 non-bonded parameter combinations 85: 85: Excluding 1 bonded neighbours molecule type 'Argon' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: 85: Dynamic load balancing report: 85: DLB was off during the run due to low measured imbalance. 85: Average load imbalance: 2.5%. 85: The balanceable part of the MD step is 9%, load imbalance is computed from this. 85: Part of the total run time spent waiting due to load imbalance: 0.2%. 85: 85: 85: NOTE: 56 % of the run time was spent communicating energies, 85: you might want to increase some nst* mdp options 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.129 0.086 149.9 85: (ns/day) (hour/ns) 85: Performance: 17.105 1.403 85: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as double precision energy file 85: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as double precision energy file 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 85: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 85: setting nstcomm equal to nstcalcenergy for less overhead 85: 85: Number of degrees of freedom in T-Coupling group System is 33.00 85: 85: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 85: NVE simulation: will use the initial temperature of 68.810 K for 85: determining the Verlet buffer size 85: 85: 85: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 85: COM removal frequency is set to (5). 85: Other settings require a global communication frequency of 100. 85: Note that this will require additional global communication steps, 85: which will reduce performance when using multiple ranks. 85: Consider setting nstcomm to a multiple of 100. 85: 85: 85: There were 4 NOTEs 85: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 85: Can not increase nstlist because an NVE ensemble is used 85: Using 2 MPI threads 85: Using 1 OpenMP thread per tMPI thread 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'Argon' 85: 16 steps, 0.0 ps. 85: Generated 1 of the 1 non-bonded parameter combinations 85: 85: Excluding 1 bonded neighbours molecule type 'Argon' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: 85: Dynamic load balancing report: 85: DLB was turned on during the run due to measured imbalance. 85: Average load imbalance: 51.6%. 85: The balanceable part of the MD step is 11%, load imbalance is computed from this. 85: Part of the total run time spent waiting due to load imbalance: 5.6%. 85: Steps where the load balancing was limited by -rdd, -rcon and/or -dds: X 0 % 85: 85: NOTE: 5.6 % of the available CPU time was lost due to load imbalance 85: in the domain decomposition. 85: You can consider manually changing the decomposition (option -dd); 85: e.g. by using fewer domains along the box dimension in which there is 85: considerable inhomogeneity in the simulated system. 85: 85: NOTE: 30 % of the run time was spent communicating energies, 85: you might want to increase some nst* mdp options 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.135 0.068 198.9 85: (ns/day) (hour/ns) 85: Performance: 21.632 1.109 85: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as double precision energy file 85: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as double precision energy file 85: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/0 (1069 ms) 85: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/1 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 85: Setting nstcalcenergy (100) equal to nstenergy (1) 85: 85: 85: WARNING 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 85: The Berendsen barostat does not generate any strictly correct ensemble, 85: and should not be used for new production simulations (in our opinion). 85: We recommend using the C-rescale barostat instead. 85: 85: Number of degrees of freedom in T-Coupling group System is 33.00 85: 85: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 85: NVE simulation: will use the initial temperature of 68.810 K for 85: determining the Verlet buffer size 85: 85: 85: There were 3 NOTEs 85: 85: There was 1 WARNING 85: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 85: Can not increase nstlist because an NVE ensemble is used 85: Using 2 MPI threads 85: Using 1 OpenMP thread per tMPI thread 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'Argon' 85: 16 steps, 0.0 ps. 85: Generated 1 of the 1 non-bonded parameter combinations 85: 85: Excluding 1 bonded neighbours molecule type 'Argon' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: 85: Dynamic load balancing report: 85: DLB was off during the run due to low measured imbalance. 85: Average load imbalance: 1.4%. 85: The balanceable part of the MD step is 25%, load imbalance is computed from this. 85: Part of the total run time spent waiting due to load imbalance: 0.3%. 85: 85: 85: NOTE: 42 % of the run time was spent communicating energies, 85: you might want to increase some nst* mdp options 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.131 0.066 198.8 85: (ns/day) (hour/ns) 85: Performance: 22.211 1.081 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 85: Setting nstcalcenergy (100) equal to nstenergy (1) 85: 85: 85: WARNING 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 85: The Berendsen barostat does not generate any strictly correct ensemble, 85: and should not be used for new production simulations (in our opinion). 85: We recommend using the C-rescale barostat instead. 85: 85: Number of degrees of freedom in T-Coupling group System is 33.00 85: 85: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 85: NVE simulation: will use the initial temperature of 68.810 K for 85: determining the Verlet buffer size 85: 85: 85: There were 3 NOTEs 85: 85: There was 1 WARNING 85: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 85: Can not increase nstlist because an NVE ensemble is used 85: Using 2 MPI threads 85: Using 1 OpenMP thread per tMPI thread 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'Argon' 85: 16 steps, 0.0 ps. 85: Generated 1 of the 1 non-bonded parameter combinations 85: 85: Excluding 1 bonded neighbours molecule type 'Argon' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: 85: Dynamic load balancing report: 85: DLB was off during the run due to low measured imbalance. 85: Average load imbalance: 1.8%. 85: The balanceable part of the MD step is 21%, load imbalance is computed from this. 85: Part of the total run time spent waiting due to load imbalance: 0.4%. 85: 85: 85: NOTE: 36 % of the run time was spent communicating energies, 85: you might want to increase some nst* mdp options 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.093 0.047 198.6 85: (ns/day) (hour/ns) 85: Performance: 31.239 0.768 85: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as double precision energy file 85: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as double precision energy file 85: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 85: Setting nstcalcenergy (100) equal to nstenergy (4) 85: 85: 85: WARNING 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 85: The Berendsen barostat does not generate any strictly correct ensemble, 85: and should not be used for new production simulations (in our opinion). 85: We recommend using the C-rescale barostat instead. 85: 85: Number of degrees of freedom in T-Coupling group System is 33.00 85: 85: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 85: NVE simulation: will use the initial temperature of 68.810 K for 85: determining the Verlet buffer size 85: 85: 85: There were 3 NOTEs 85: 85: There was 1 WARNING 85: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 85: Can not increase nstlist because an NVE ensemble is used 85: Using 2 MPI threads 85: Using 1 OpenMP thread per tMPI thread 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'Argon' 85: 16 steps, 0.0 ps. 85: Generated 1 of the 1 non-bonded parameter combinations 85: 85: Excluding 1 bonded neighbours molecule type 'Argon' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: 85: Dynamic load balancing report: 85: DLB was off during the run due to low measured imbalance. 85: Average load imbalance: 2.3%. 85: The balanceable part of the MD step is 3%, load imbalance is computed from this. 85: Part of the total run time spent waiting due to load imbalance: 0.1%. 85: 85: 85: NOTE: 23 % of the run time was spent in domain decomposition, 85: 0 % of the run time was spent in pair search, 85: you might want to increase nstlist (this has no effect on accuracy) 85: 85: NOTE: 36 % of the run time was spent communicating energies, 85: you might want to increase some nst* mdp options 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.194 0.097 199.4 85: (ns/day) (hour/ns) 85: Performance: 15.113 1.588 85: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as double precision energy file 85: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as double precision energy file 85: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 85: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 85: setting nstcomm equal to nstcalcenergy for less overhead 85: 85: 85: WARNING 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 85: The Berendsen barostat does not generate any strictly correct ensemble, 85: and should not be used for new production simulations (in our opinion). 85: We recommend using the C-rescale barostat instead. 85: 85: Number of degrees of freedom in T-Coupling group System is 33.00 85: 85: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 85: NVE simulation: will use the initial temperature of 68.810 K for 85: determining the Verlet buffer size 85: 85: 85: There were 3 NOTEs 85: 85: There was 1 WARNING 85: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 85: Can not increase nstlist because an NVE ensemble is used 85: Using 2 MPI threads 85: Using 1 OpenMP thread per tMPI thread 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'Argon' 85: 16 steps, 0.0 ps. 85: Generated 1 of the 1 non-bonded parameter combinations 85: 85: Excluding 1 bonded neighbours molecule type 'Argon' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: 85: Dynamic load balancing report: 85: DLB was off during the run due to low measured imbalance. 85: Average load imbalance: 2.3%. 85: The balanceable part of the MD step is 12%, load imbalance is computed from this. 85: Part of the total run time spent waiting due to load imbalance: 0.3%. 85: 85: 85: NOTE: 51 % of the run time was spent communicating energies, 85: you might want to increase some nst* mdp options 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.090 0.045 198.3 85: (ns/day) (hour/ns) 85: Performance: 32.367 0.741 85: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as double precision energy file 85: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as double precision energy file 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 85: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 85: setting nstcomm equal to nstcalcenergy for less overhead 85: 85: 85: WARNING 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 85: The Berendsen barostat does not generate any strictly correct ensemble, 85: and should not be used for new production simulations (in our opinion). 85: We recommend using the C-rescale barostat instead. 85: 85: Number of degrees of freedom in T-Coupling group System is 33.00 85: 85: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 85: NVE simulation: will use the initial temperature of 68.810 K for 85: determining the Verlet buffer size 85: 85: 85: There were 3 NOTEs 85: 85: There was 1 WARNING 85: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 85: Can not increase nstlist because an NVE ensemble is used 85: Using 2 MPI threads 85: Using 1 OpenMP thread per tMPI thread 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'Argon' 85: 16 steps, 0.0 ps. 85: Generated 1 of the 1 non-bonded parameter combinations 85: 85: Excluding 1 bonded neighbours molecule type 'Argon' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: 85: Dynamic load balancing report: 85: DLB was turned on during the run due to measured imbalance. 85: Average load imbalance: 48.6%. 85: The balanceable part of the MD step is 21%, load imbalance is computed from this. 85: Part of the total run time spent waiting due to load imbalance: 10.2%. 85: Steps where the load balancing was limited by -rdd, -rcon and/or -dds: X 0 % 85: 85: NOTE: 10.2 % of the available CPU time was lost due to load imbalance 85: in the domain decomposition. 85: You can consider manually changing the decomposition (option -dd); 85: e.g. by using fewer domains along the box dimension in which there is 85: considerable inhomogeneity in the simulated system. 85: 85: NOTE: 32 % of the run time was spent communicating energies, 85: you might want to increase some nst* mdp options 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.107 0.054 198.6 85: (ns/day) (hour/ns) 85: Performance: 27.198 0.882 85: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as double precision energy file 85: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as double precision energy file 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 85: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 85: setting nstcomm equal to nstcalcenergy for less overhead 85: 85: 85: WARNING 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 85: The Berendsen barostat does not generate any strictly correct ensemble, 85: and should not be used for new production simulations (in our opinion). 85: We recommend using the C-rescale barostat instead. 85: 85: Number of degrees of freedom in T-Coupling group System is 33.00 85: 85: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 85: NVE simulation: will use the initial temperature of 68.810 K for 85: determining the Verlet buffer size 85: 85: 85: There were 3 NOTEs 85: 85: There was 1 WARNING 85: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 85: Can not increase nstlist because an NVE ensemble is used 85: Using 2 MPI threads 85: Using 1 OpenMP thread per tMPI thread 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'Argon' 85: 16 steps, 0.0 ps. 85: Generated 1 of the 1 non-bonded parameter combinations 85: 85: Excluding 1 bonded neighbours molecule type 'Argon' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: 85: Dynamic load balancing report: 85: DLB was off during the run due to low measured imbalance. 85: Average load imbalance: 2.4%. 85: The balanceable part of the MD step is 13%, load imbalance is computed from this. 85: Part of the total run time spent waiting due to load imbalance: 0.3%. 85: 85: 85: NOTE: 52 % of the run time was spent communicating energies, 85: you might want to increase some nst* mdp options 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.073 0.037 198.3 85: (ns/day) (hour/ns) 85: Performance: 40.129 0.598 85: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as double precision energy file 85: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as double precision energy file 85: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/1 (1097 ms) 85: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/2 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 85: Setting nstcalcenergy (100) equal to nstenergy (1) 85: 85: Number of degrees of freedom in T-Coupling group System is 33.00 85: 85: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 85: NVE simulation: will use the initial temperature of 68.810 K for 85: determining the Verlet buffer size 85: 85: 85: There were 3 NOTEs 85: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 85: Can not increase nstlist because an NVE ensemble is used 85: Using 2 MPI threads 85: Using 1 OpenMP thread per tMPI thread 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'Argon' 85: 16 steps, 0.0 ps. 85: Generated 1 of the 1 non-bonded parameter combinations 85: 85: Excluding 1 bonded neighbours molecule type 'Argon' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: 85: Dynamic load balancing report: 85: DLB was turned on during the run due to measured imbalance. 85: Average load imbalance: 31.7%. 85: The balanceable part of the MD step is 13%, load imbalance is computed from this. 85: Part of the total run time spent waiting due to load imbalance: 4.3%. 85: Steps where the load balancing was limited by -rdd, -rcon and/or -dds: X 0 % 85: 85: 85: NOTE: 51 % of the run time was spent communicating energies, 85: you might want to increase some nst* mdp options 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.159 0.080 199.1 85: (ns/day) (hour/ns) 85: Performance: 18.442 1.301 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 85: Setting nstcalcenergy (100) equal to nstenergy (1) 85: 85: Number of degrees of freedom in T-Coupling group System is 33.00 85: 85: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 85: NVE simulation: will use the initial temperature of 68.810 K for 85: determining the Verlet buffer size 85: 85: 85: There were 3 NOTEs 85: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 85: Can not increase nstlist because an NVE ensemble is used 85: Using 2 MPI threads 85: Using 1 OpenMP thread per tMPI thread 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'Argon' 85: 16 steps, 0.0 ps. 85: Generated 1 of the 1 non-bonded parameter combinations 85: 85: Excluding 1 bonded neighbours molecule type 'Argon' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: 85: Dynamic load balancing report: 85: DLB was turned on during the run due to measured imbalance. 85: Average load imbalance: 43.3%. 85: The balanceable part of the MD step is 29%, load imbalance is computed from this. 85: Part of the total run time spent waiting due to load imbalance: 12.5%. 85: Steps where the load balancing was limited by -rdd, -rcon and/or -dds: X 0 % 85: 85: NOTE: 12.5 % of the available CPU time was lost due to load imbalance 85: in the domain decomposition. 85: You can consider manually changing the decomposition (option -dd); 85: e.g. by using fewer domains along the box dimension in which there is 85: considerable inhomogeneity in the simulated system. 85: 85: NOTE: 45 % of the run time was spent communicating energies, 85: you might want to increase some nst* mdp options 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.097 0.049 198.7 85: (ns/day) (hour/ns) 85: Performance: 30.058 0.798 85: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as double precision energy file 85: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as double precision energy file 85: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 85: Setting nstcalcenergy (100) equal to nstenergy (4) 85: 85: Number of degrees of freedom in T-Coupling group System is 33.00 85: 85: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 85: NVE simulation: will use the initial temperature of 68.810 K for 85: determining the Verlet buffer size 85: 85: 85: There were 3 NOTEs 85: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 85: Can not increase nstlist because an NVE ensemble is used 85: Using 2 MPI threads 85: Using 1 OpenMP thread per tMPI thread 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'Argon' 85: 16 steps, 0.0 ps. 85: Generated 1 of the 1 non-bonded parameter combinations 85: 85: Excluding 1 bonded neighbours molecule type 'Argon' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: 85: Dynamic load balancing report: 85: DLB was off during the run due to low measured imbalance. 85: Average load imbalance: 1.7%. 85: The balanceable part of the MD step is 39%, load imbalance is computed from this. 85: Part of the total run time spent waiting due to load imbalance: 0.7%. 85: 85: 85: NOTE: 43 % of the run time was spent communicating energies, 85: you might want to increase some nst* mdp options 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.073 0.037 198.3 85: (ns/day) (hour/ns) 85: Performance: 39.793 0.603 85: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as double precision energy file 85: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as double precision energy file 85: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 85: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 85: setting nstcomm equal to nstcalcenergy for less overhead 85: 85: Number of degrees of freedom in T-Coupling group System is 33.00 85: 85: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 85: NVE simulation: will use the initial temperature of 68.810 K for 85: determining the Verlet buffer size 85: 85: 85: There were 3 NOTEs 85: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 85: Can not increase nstlist because an NVE ensemble is used 85: Using 2 MPI threads 85: Using 1 OpenMP thread per tMPI thread 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'Argon' 85: 16 steps, 0.0 ps. 85: Generated 1 of the 1 non-bonded parameter combinations 85: 85: Excluding 1 bonded neighbours molecule type 'Argon' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: 85: Dynamic load balancing report: 85: DLB was off during the run due to low measured imbalance. 85: Average load imbalance: 1.5%. 85: The balanceable part of the MD step is 16%, load imbalance is computed from this. 85: Part of the total run time spent waiting due to load imbalance: 0.2%. 85: 85: 85: NOTE: 49 % of the run time was spent communicating energies, 85: you might want to increase some nst* mdp options 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.154 0.078 198.9 85: (ns/day) (hour/ns) 85: Performance: 18.935 1.268 85: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as double precision energy file 85: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as double precision energy file 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 85: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 85: setting nstcomm equal to nstcalcenergy for less overhead 85: 85: Number of degrees of freedom in T-Coupling group System is 33.00 85: 85: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 85: NVE simulation: will use the initial temperature of 68.810 K for 85: determining the Verlet buffer size 85: 85: 85: There were 3 NOTEs 85: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 85: Can not increase nstlist because an NVE ensemble is used 85: Using 2 MPI threads 85: Using 1 OpenMP thread per tMPI thread 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'Argon' 85: 16 steps, 0.0 ps. 85: Generated 1 of the 1 non-bonded parameter combinations 85: 85: Excluding 1 bonded neighbours molecule type 'Argon' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: 85: Dynamic load balancing report: 85: DLB was turned on during the run due to measured imbalance. 85: Average load imbalance: 6.5%. 85: The balanceable part of the MD step is 39%, load imbalance is computed from this. 85: Part of the total run time spent waiting due to load imbalance: 2.5%. 85: Steps where the load balancing was limited by -rdd, -rcon and/or -dds: X 0 % 85: 85: 85: NOTE: 35 % of the run time was spent communicating energies, 85: you might want to increase some nst* mdp options 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.108 0.054 198.6 85: (ns/day) (hour/ns) 85: Performance: 27.065 0.887 85: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as double precision energy file 85: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as double precision energy file 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 85: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 85: setting nstcomm equal to nstcalcenergy for less overhead 85: 85: Number of degrees of freedom in T-Coupling group System is 33.00 85: 85: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 85: NVE simulation: will use the initial temperature of 68.810 K for 85: determining the Verlet buffer size 85: 85: 85: There were 3 NOTEs 85: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 85: Can not increase nstlist because an NVE ensemble is used 85: Using 2 MPI threads 85: Using 1 OpenMP thread per tMPI thread 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'Argon' 85: 16 steps, 0.0 ps. 85: Generated 1 of the 1 non-bonded parameter combinations 85: 85: Excluding 1 bonded neighbours molecule type 'Argon' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: 85: Dynamic load balancing report: 85: DLB was turned on during the run due to measured imbalance. 85: Average load imbalance: 13.0%. 85: The balanceable part of the MD step is 45%, load imbalance is computed from this. 85: Part of the total run time spent waiting due to load imbalance: 5.8%. 85: Steps where the load balancing was limited by -rdd, -rcon and/or -dds: X 0 % 85: 85: NOTE: 5.8 % of the available CPU time was lost due to load imbalance 85: in the domain decomposition. 85: You can consider manually changing the decomposition (option -dd); 85: e.g. by using fewer domains along the box dimension in which there is 85: considerable inhomogeneity in the simulated system. 85: 85: NOTE: 60 % of the run time was spent communicating energies, 85: you might want to increase some nst* mdp options 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.263 0.147 178.6 85: (ns/day) (hour/ns) 85: Performance: 9.967 2.408 85: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as double precision energy file 85: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as double precision energy file 85: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/2 (1166 ms) 85: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/3 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 85: Setting nstcalcenergy (100) equal to nstenergy (1) 85: 85: Number of degrees of freedom in T-Coupling group System is 33.00 85: 85: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 85: NVE simulation: will use the initial temperature of 68.810 K for 85: determining the Verlet buffer size 85: 85: 85: There were 3 NOTEs 85: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 85: Can not increase nstlist because an NVE ensemble is used 85: Using 2 MPI threads 85: Using 1 OpenMP thread per tMPI thread 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'Argon' 85: 16 steps, 0.0 ps. 85: Generated 1 of the 1 non-bonded parameter combinations 85: 85: Excluding 1 bonded neighbours molecule type 'Argon' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: 85: Dynamic load balancing report: 85: DLB was off during the run due to low measured imbalance. 85: Average load imbalance: 1.1%. 85: The balanceable part of the MD step is 34%, load imbalance is computed from this. 85: Part of the total run time spent waiting due to load imbalance: 0.4%. 85: 85: 85: NOTE: 46 % of the run time was spent communicating energies, 85: you might want to increase some nst* mdp options 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.074 0.038 197.9 85: (ns/day) (hour/ns) 85: Performance: 39.024 0.615 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 85: Setting nstcalcenergy (100) equal to nstenergy (1) 85: 85: Number of degrees of freedom in T-Coupling group System is 33.00 85: 85: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 85: NVE simulation: will use the initial temperature of 68.810 K for 85: determining the Verlet buffer size 85: 85: 85: There were 3 NOTEs 85: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 85: Can not increase nstlist because an NVE ensemble is used 85: Using 2 MPI threads 85: Using 1 OpenMP thread per tMPI thread 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'Argon' 85: 16 steps, 0.0 ps. 85: Generated 1 of the 1 non-bonded parameter combinations 85: 85: Excluding 1 bonded neighbours molecule type 'Argon' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: 85: Dynamic load balancing report: 85: DLB was off during the run due to low measured imbalance. 85: Average load imbalance: 2.0%. 85: The balanceable part of the MD step is 32%, load imbalance is computed from this. 85: Part of the total run time spent waiting due to load imbalance: 0.6%. 85: 85: 85: NOTE: 39 % of the run time was spent communicating energies, 85: you might want to increase some nst* mdp options 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.080 0.041 198.5 85: (ns/day) (hour/ns) 85: Performance: 36.238 0.662 85: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as double precision energy file 85: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as double precision energy file 85: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 85: Setting nstcalcenergy (100) equal to nstenergy (4) 85: 85: Number of degrees of freedom in T-Coupling group System is 33.00 85: 85: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 85: NVE simulation: will use the initial temperature of 68.810 K for 85: determining the Verlet buffer size 85: 85: 85: There were 3 NOTEs 85: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 85: Can not increase nstlist because an NVE ensemble is used 85: Using 2 MPI threads 85: Using 1 OpenMP thread per tMPI thread 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'Argon' 85: 16 steps, 0.0 ps. 85: Generated 1 of the 1 non-bonded parameter combinations 85: 85: Excluding 1 bonded neighbours molecule type 'Argon' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: 85: Dynamic load balancing report: 85: DLB was off during the run due to low measured imbalance. 85: Average load imbalance: 1.6%. 85: The balanceable part of the MD step is 54%, load imbalance is computed from this. 85: Part of the total run time spent waiting due to load imbalance: 0.9%. 85: 85: 85: NOTE: 44 % of the run time was spent communicating energies, 85: you might want to increase some nst* mdp options 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.065 0.033 198.0 85: (ns/day) (hour/ns) 85: Performance: 44.754 0.536 85: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as double precision energy file 85: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as double precision energy file 85: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 85: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 85: setting nstcomm equal to nstcalcenergy for less overhead 85: 85: Number of degrees of freedom in T-Coupling group System is 33.00 85: 85: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 85: NVE simulation: will use the initial temperature of 68.810 K for 85: determining the Verlet buffer size 85: 85: 85: There were 3 NOTEs 85: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 85: Can not increase nstlist because an NVE ensemble is used 85: Using 2 MPI threads 85: Using 1 OpenMP thread per tMPI thread 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'Argon' 85: 16 steps, 0.0 ps. 85: Generated 1 of the 1 non-bonded parameter combinations 85: 85: Excluding 1 bonded neighbours molecule type 'Argon' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: 85: Dynamic load balancing report: 85: DLB was off during the run due to low measured imbalance. 85: Average load imbalance: 1.7%. 85: The balanceable part of the MD step is 9%, load imbalance is computed from this. 85: Part of the total run time spent waiting due to load imbalance: 0.2%. 85: 85: 85: NOTE: 68 % of the run time was spent communicating energies, 85: you might want to increase some nst* mdp options 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.122 0.061 198.7 85: (ns/day) (hour/ns) 85: Performance: 23.909 1.004 85: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as double precision energy file 85: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as double precision energy file 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 85: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 85: setting nstcomm equal to nstcalcenergy for less overhead 85: 85: Number of degrees of freedom in T-Coupling group System is 33.00 85: 85: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 85: NVE simulation: will use the initial temperature of 68.810 K for 85: determining the Verlet buffer size 85: 85: 85: There were 3 NOTEs 85: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 85: Can not increase nstlist because an NVE ensemble is used 85: Using 2 MPI threads 85: Using 1 OpenMP thread per tMPI thread 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'Argon' 85: 16 steps, 0.0 ps. 85: Generated 1 of the 1 non-bonded parameter combinations 85: 85: Excluding 1 bonded neighbours molecule type 'Argon' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: 85: Dynamic load balancing report: 85: DLB was off during the run due to low measured imbalance. 85: Average load imbalance: 1.1%. 85: The balanceable part of the MD step is 11%, load imbalance is computed from this. 85: Part of the total run time spent waiting due to load imbalance: 0.1%. 85: 85: 85: NOTE: 20 % of the run time was spent in domain decomposition, 85: 1 % of the run time was spent in pair search, 85: you might want to increase nstlist (this has no effect on accuracy) 85: 85: NOTE: 38 % of the run time was spent communicating energies, 85: you might want to increase some nst* mdp options 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.113 0.057 196.5 85: (ns/day) (hour/ns) 85: Performance: 25.617 0.937 85: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as double precision energy file 85: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as double precision energy file 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 85: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 85: setting nstcomm equal to nstcalcenergy for less overhead 85: 85: Number of degrees of freedom in T-Coupling group System is 33.00 85: 85: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 85: NVE simulation: will use the initial temperature of 68.810 K for 85: determining the Verlet buffer size 85: 85: 85: There were 3 NOTEs 85: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 85: Can not increase nstlist because an NVE ensemble is used 85: Using 2 MPI threads 85: Using 1 OpenMP thread per tMPI thread 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'Argon' 85: 16 steps, 0.0 ps. 85: Generated 1 of the 1 non-bonded parameter combinations 85: 85: Excluding 1 bonded neighbours molecule type 'Argon' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: 85: Dynamic load balancing report: 85: DLB was off during the run due to low measured imbalance. 85: Average load imbalance: 0.4%. 85: The balanceable part of the MD step is 27%, load imbalance is computed from this. 85: Part of the total run time spent waiting due to load imbalance: 0.1%. 85: 85: 85: NOTE: 42 % of the run time was spent communicating energies, 85: you might want to increase some nst* mdp options 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.054 0.027 197.3 85: (ns/day) (hour/ns) 85: Performance: 54.129 0.443 85: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as double precision energy file 85: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as double precision energy file 85: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/3 (777 ms) 85: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/4 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 85: Setting nstcalcenergy (100) equal to nstenergy (1) 85: 85: Number of degrees of freedom in T-Coupling group System is 33.00 85: 85: There were 2 NOTEs 85: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 85: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 85: 85: Using 2 MPI threads 85: Using 1 OpenMP thread per tMPI thread 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'Argon' 85: 16 steps, 0.0 ps. 85: Generated 1 of the 1 non-bonded parameter combinations 85: 85: Excluding 1 bonded neighbours molecule type 'Argon' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: NOTE: 40 % of the run time was spent communicating energies, 85: you might want to increase some nst* mdp options 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.046 0.023 197.1 85: (ns/day) (hour/ns) 85: Performance: 62.769 0.382 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 85: Setting nstcalcenergy (100) equal to nstenergy (1) 85: 85: Number of degrees of freedom in T-Coupling group System is 33.00 85: 85: There were 2 NOTEs 85: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 85: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 85: 85: Using 2 MPI threads 85: Using 1 OpenMP thread per tMPI thread 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'Argon' 85: 16 steps, 0.0 ps. 85: Generated 1 of the 1 non-bonded parameter combinations 85: 85: Excluding 1 bonded neighbours molecule type 'Argon' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: NOTE: 39 % of the run time was spent communicating energies, 85: you might want to increase some nst* mdp options 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.054 0.027 197.1 85: (ns/day) (hour/ns) 85: Performance: 53.687 0.447 85: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as double precision energy file 85: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as double precision energy file 85: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 85: Setting nstcalcenergy (100) equal to nstenergy (4) 85: 85: Number of degrees of freedom in T-Coupling group System is 33.00 85: 85: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 85: COM removal frequency is set to (5). 85: Other settings require a global communication frequency of 2. 85: Note that this will require additional global communication steps, 85: which will reduce performance when using multiple ranks. 85: Consider setting nstcomm to a multiple of 2. 85: 85: 85: There were 3 NOTEs 85: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 85: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 85: 85: Using 2 MPI threads 85: Using 1 OpenMP thread per tMPI thread 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'Argon' 85: 16 steps, 0.0 ps. 85: Generated 1 of the 1 non-bonded parameter combinations 85: 85: Excluding 1 bonded neighbours molecule type 'Argon' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: NOTE: 50 % of the run time was spent communicating energies, 85: you might want to increase some nst* mdp options 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.050 0.025 197.0 85: (ns/day) (hour/ns) 85: Performance: 57.948 0.414 85: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as double precision energy file 85: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as double precision energy file 85: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 85: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 85: setting nstcomm equal to nstcalcenergy for less overhead 85: 85: Number of degrees of freedom in T-Coupling group System is 33.00 85: 85: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 85: COM removal frequency is set to (5). 85: Other settings require a global communication frequency of 2. 85: Note that this will require additional global communication steps, 85: which will reduce performance when using multiple ranks. 85: Consider setting nstcomm to a multiple of 2. 85: 85: 85: There were 3 NOTEs 85: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 85: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 85: 85: Using 2 MPI threads 85: Using 1 OpenMP thread per tMPI thread 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'Argon' 85: 16 steps, 0.0 ps. 85: Generated 1 of the 1 non-bonded parameter combinations 85: 85: Excluding 1 bonded neighbours molecule type 'Argon' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: NOTE: 48 % of the run time was spent communicating energies, 85: you might want to increase some nst* mdp options 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.089 0.045 198.3 85: (ns/day) (hour/ns) 85: Performance: 32.746 0.733 85: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as double precision energy file 85: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as double precision energy file 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 85: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 85: setting nstcomm equal to nstcalcenergy for less overhead 85: 85: Number of degrees of freedom in T-Coupling group System is 33.00 85: 85: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 85: COM removal frequency is set to (5). 85: Other settings require a global communication frequency of 2. 85: Note that this will require additional global communication steps, 85: which will reduce performance when using multiple ranks. 85: Consider setting nstcomm to a multiple of 2. 85: 85: 85: There were 3 NOTEs 85: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 85: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 85: 85: Using 2 MPI threads 85: Using 1 OpenMP thread per tMPI thread 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'Argon' 85: 16 steps, 0.0 ps. 85: Generated 1 of the 1 non-bonded parameter combinations 85: 85: Excluding 1 bonded neighbours molecule type 'Argon' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: NOTE: 52 % of the run time was spent communicating energies, 85: you might want to increase some nst* mdp options 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.098 0.050 198.5 85: (ns/day) (hour/ns) 85: Performance: 29.635 0.810 85: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as double precision energy file 85: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as double precision energy file 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 85: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 85: setting nstcomm equal to nstcalcenergy for less overhead 85: 85: Number of degrees of freedom in T-Coupling group System is 33.00 85: 85: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 85: COM removal frequency is set to (5). 85: Other settings require a global communication frequency of 2. 85: Note that this will require additional global communication steps, 85: which will reduce performance when using multiple ranks. 85: Consider setting nstcomm to a multiple of 2. 85: 85: 85: There were 3 NOTEs 85: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 85: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 85: 85: Using 2 MPI threads 85: Using 1 OpenMP thread per tMPI thread 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'Argon' 85: 16 steps, 0.0 ps. 85: Generated 1 of the 1 non-bonded parameter combinations 85: 85: Excluding 1 bonded neighbours molecule type 'Argon' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: NOTE: 44 % of the run time was spent communicating energies, 85: you might want to increase some nst* mdp options 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.046 0.023 197.4 85: (ns/day) (hour/ns) 85: Performance: 63.326 0.379 85: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as double precision energy file 85: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as double precision energy file 85: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/4 (689 ms) 85: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/5 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 85: Setting nstcalcenergy (100) equal to nstenergy (1) 85: 85: 85: WARNING 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 85: The Berendsen barostat does not generate any strictly correct ensemble, 85: and should not be used for new production simulations (in our opinion). 85: We recommend using the C-rescale barostat instead. 85: 85: Number of degrees of freedom in T-Coupling group System is 33.00 85: 85: There were 2 NOTEs 85: 85: There was 1 WARNING 85: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 85: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 85: 85: Using 2 MPI threads 85: Using 1 OpenMP thread per tMPI thread 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'Argon' 85: 16 steps, 0.0 ps. 85: Generated 1 of the 1 non-bonded parameter combinations 85: 85: Excluding 1 bonded neighbours molecule type 'Argon' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: NOTE: 33 % of the run time was spent communicating energies, 85: you might want to increase some nst* mdp options 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.071 0.036 198.0 85: (ns/day) (hour/ns) 85: Performance: 40.760 0.589 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 85: Setting nstcalcenergy (100) equal to nstenergy (1) 85: 85: 85: WARNING 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 85: The Berendsen barostat does not generate any strictly correct ensemble, 85: and should not be used for new production simulations (in our opinion). 85: We recommend using the C-rescale barostat instead. 85: 85: Number of degrees of freedom in T-Coupling group System is 33.00 85: 85: There were 2 NOTEs 85: 85: There was 1 WARNING 85: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 85: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 85: 85: Using 2 MPI threads 85: Using 1 OpenMP thread per tMPI thread 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'Argon' 85: 16 steps, 0.0 ps. 85: Generated 1 of the 1 non-bonded parameter combinations 85: 85: Excluding 1 bonded neighbours molecule type 'Argon' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: NOTE: 32 % of the run time was spent communicating energies, 85: you might want to increase some nst* mdp options 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.047 0.024 197.4 85: (ns/day) (hour/ns) 85: Performance: 62.273 0.385 85: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as double precision energy file 85: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as double precision energy file 85: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 85: Setting nstcalcenergy (100) equal to nstenergy (4) 85: 85: 85: WARNING 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 85: The Berendsen barostat does not generate any strictly correct ensemble, 85: and should not be used for new production simulations (in our opinion). 85: We recommend using the C-rescale barostat instead. 85: 85: Number of degrees of freedom in T-Coupling group System is 33.00 85: 85: There were 2 NOTEs 85: 85: There was 1 WARNING 85: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 85: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 85: 85: Using 2 MPI threads 85: Using 1 OpenMP thread per tMPI thread 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'Argon' 85: 16 steps, 0.0 ps. 85: Generated 1 of the 1 non-bonded parameter combinations 85: 85: Excluding 1 bonded neighbours molecule type 'Argon' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: NOTE: 43 % of the run time was spent communicating energies, 85: you might want to increase some nst* mdp options 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.103 0.052 198.8 85: (ns/day) (hour/ns) 85: Performance: 28.314 0.848 85: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as double precision energy file 85: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as double precision energy file 85: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 85: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 85: setting nstcomm equal to nstcalcenergy for less overhead 85: 85: 85: WARNING 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 85: The Berendsen barostat does not generate any strictly correct ensemble, 85: and should not be used for new production simulations (in our opinion). 85: We recommend using the C-rescale barostat instead. 85: 85: Number of degrees of freedom in T-Coupling group System is 33.00 85: 85: There were 2 NOTEs 85: 85: There was 1 WARNING 85: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 85: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 85: 85: Using 2 MPI threads 85: Using 1 OpenMP thread per tMPI thread 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'Argon' 85: 16 steps, 0.0 ps. 85: Generated 1 of the 1 non-bonded parameter combinations 85: 85: Excluding 1 bonded neighbours molecule type 'Argon' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: NOTE: 37 % of the run time was spent communicating energies, 85: you might want to increase some nst* mdp options 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.055 0.028 197.7 85: (ns/day) (hour/ns) 85: Performance: 53.134 0.452 85: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as double precision energy file 85: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as double precision energy file 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 85: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 85: setting nstcomm equal to nstcalcenergy for less overhead 85: 85: 85: WARNING 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 85: The Berendsen barostat does not generate any strictly correct ensemble, 85: and should not be used for new production simulations (in our opinion). 85: We recommend using the C-rescale barostat instead. 85: 85: Number of degrees of freedom in T-Coupling group System is 33.00 85: 85: There were 2 NOTEs 85: 85: There was 1 WARNING 85: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 85: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 85: 85: Using 2 MPI threads 85: Using 1 OpenMP thread per tMPI thread 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'Argon' 85: 16 steps, 0.0 ps. 85: Generated 1 of the 1 non-bonded parameter combinations 85: 85: Excluding 1 bonded neighbours molecule type 'Argon' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: NOTE: 48 % of the run time was spent communicating energies, 85: you might want to increase some nst* mdp options 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.053 0.027 197.3 85: (ns/day) (hour/ns) 85: Performance: 54.940 0.437 85: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as double precision energy file 85: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as double precision energy file 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 85: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 85: setting nstcomm equal to nstcalcenergy for less overhead 85: 85: 85: WARNING 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 85: The Berendsen barostat does not generate any strictly correct ensemble, 85: and should not be used for new production simulations (in our opinion). 85: We recommend using the C-rescale barostat instead. 85: 85: Number of degrees of freedom in T-Coupling group System is 33.00 85: 85: There were 2 NOTEs 85: 85: There was 1 WARNING 85: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 85: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 85: 85: Using 2 MPI threads 85: Using 1 OpenMP thread per tMPI thread 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'Argon' 85: 16 steps, 0.0 ps. 85: Generated 1 of the 1 non-bonded parameter combinations 85: 85: Excluding 1 bonded neighbours molecule type 'Argon' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: NOTE: 44 % of the run time was spent communicating energies, 85: you might want to increase some nst* mdp options 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.041 0.021 196.7 85: (ns/day) (hour/ns) 85: Performance: 70.910 0.338 85: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as double precision energy file 85: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as double precision energy file 85: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/5 (596 ms) 85: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/6 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 85: Setting nstcalcenergy (100) equal to nstenergy (1) 85: 85: Number of degrees of freedom in T-Coupling group System is 33.00 85: 85: There were 2 NOTEs 85: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 85: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 85: 85: Using 2 MPI threads 85: Using 1 OpenMP thread per tMPI thread 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'Argon' 85: 16 steps, 0.0 ps. 85: Generated 1 of the 1 non-bonded parameter combinations 85: 85: Excluding 1 bonded neighbours molecule type 'Argon' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: NOTE: 44 % of the run time was spent communicating energies, 85: you might want to increase some nst* mdp options 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.078 0.039 198.1 85: (ns/day) (hour/ns) 85: Performance: 37.360 0.642 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 85: Setting nstcalcenergy (100) equal to nstenergy (1) 85: 85: Number of degrees of freedom in T-Coupling group System is 33.00 85: 85: There were 2 NOTEs 85: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 85: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 85: 85: Using 2 MPI threads 85: Using 1 OpenMP thread per tMPI thread 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'Argon' 85: 16 steps, 0.0 ps. 85: Generated 1 of the 1 non-bonded parameter combinations 85: 85: Excluding 1 bonded neighbours molecule type 'Argon' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: NOTE: 52 % of the run time was spent communicating energies, 85: you might want to increase some nst* mdp options 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.056 0.028 197.5 85: (ns/day) (hour/ns) 85: Performance: 51.652 0.465 85: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as double precision energy file 85: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as double precision energy file 85: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 85: Setting nstcalcenergy (100) equal to nstenergy (4) 85: 85: Number of degrees of freedom in T-Coupling group System is 33.00 85: 85: There were 2 NOTEs 85: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 85: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 85: 85: Using 2 MPI threads 85: Using 1 OpenMP thread per tMPI thread 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'Argon' 85: 16 steps, 0.0 ps. 85: Generated 1 of the 1 non-bonded parameter combinations 85: 85: Excluding 1 bonded neighbours molecule type 'Argon' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: NOTE: 40 % of the run time was spent communicating energies, 85: you might want to increase some nst* mdp options 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.043 0.022 197.1 85: (ns/day) (hour/ns) 85: Performance: 67.376 0.356 85: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as double precision energy file 85: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as double precision energy file 85: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 85: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 85: setting nstcomm equal to nstcalcenergy for less overhead 85: 85: Number of degrees of freedom in T-Coupling group System is 33.00 85: 85: There were 2 NOTEs 85: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 85: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 85: 85: Using 2 MPI threads 85: Using 1 OpenMP thread per tMPI thread 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'Argon' 85: 16 steps, 0.0 ps. 85: Generated 1 of the 1 non-bonded parameter combinations 85: 85: Excluding 1 bonded neighbours molecule type 'Argon' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: NOTE: 44 % of the run time was spent communicating energies, 85: you might want to increase some nst* mdp options 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.041 0.021 196.9 85: (ns/day) (hour/ns) 85: Performance: 70.502 0.340 85: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as double precision energy file 85: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as double precision energy file 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 85: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 85: setting nstcomm equal to nstcalcenergy for less overhead 85: 85: Number of degrees of freedom in T-Coupling group System is 33.00 85: 85: There were 2 NOTEs 85: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 85: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 85: 85: Using 2 MPI threads 85: Using 1 OpenMP thread per tMPI thread 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'Argon' 85: 16 steps, 0.0 ps. 85: Generated 1 of the 1 non-bonded parameter combinations 85: 85: Excluding 1 bonded neighbours molecule type 'Argon' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: NOTE: 48 % of the run time was spent communicating energies, 85: you might want to increase some nst* mdp options 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.088 0.044 198.4 85: (ns/day) (hour/ns) 85: Performance: 33.111 0.725 85: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as double precision energy file 85: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as double precision energy file 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 85: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 85: setting nstcomm equal to nstcalcenergy for less overhead 85: 85: Number of degrees of freedom in T-Coupling group System is 33.00 85: 85: There were 2 NOTEs 85: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 85: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 85: 85: Using 2 MPI threads 85: Using 1 OpenMP thread per tMPI thread 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'Argon' 85: 16 steps, 0.0 ps. 85: Generated 1 of the 1 non-bonded parameter combinations 85: 85: Excluding 1 bonded neighbours molecule type 'Argon' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: NOTE: 59 % of the run time was spent communicating energies, 85: you might want to increase some nst* mdp options 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.165 0.083 199.1 85: (ns/day) (hour/ns) 85: Performance: 17.689 1.357 85: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as double precision energy file 85: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as double precision energy file 85: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/6 (637 ms) 85: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/7 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 85: Setting nstcalcenergy (100) equal to nstenergy (1) 85: 85: Number of degrees of freedom in T-Coupling group System is 33.00 85: 85: There were 2 NOTEs 85: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 85: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 85: 85: Using 2 MPI threads 85: Using 1 OpenMP thread per tMPI thread 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'Argon' 85: 16 steps, 0.0 ps. 85: Generated 1 of the 1 non-bonded parameter combinations 85: 85: Excluding 1 bonded neighbours molecule type 'Argon' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: NOTE: 36 % of the run time was spent communicating energies, 85: you might want to increase some nst* mdp options 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.091 0.046 198.4 85: (ns/day) (hour/ns) 85: Performance: 32.178 0.746 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 85: Setting nstcalcenergy (100) equal to nstenergy (1) 85: 85: Number of degrees of freedom in T-Coupling group System is 33.00 85: 85: There were 2 NOTEs 85: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 85: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 85: 85: Using 2 MPI threads 85: Using 1 OpenMP thread per tMPI thread 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'Argon' 85: 16 steps, 0.0 ps. 85: Generated 1 of the 1 non-bonded parameter combinations 85: 85: Excluding 1 bonded neighbours molecule type 'Argon' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: NOTE: 38 % of the run time was spent communicating energies, 85: you might want to increase some nst* mdp options 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.102 0.052 198.5 85: (ns/day) (hour/ns) 85: Performance: 28.504 0.842 85: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as double precision energy file 85: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as double precision energy file 85: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 85: Setting nstcalcenergy (100) equal to nstenergy (4) 85: 85: Number of degrees of freedom in T-Coupling group System is 33.00 85: 85: There were 2 NOTEs 85: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 85: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 85: 85: Using 2 MPI threads 85: Using 1 OpenMP thread per tMPI thread 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'Argon' 85: 16 steps, 0.0 ps. 85: Generated 1 of the 1 non-bonded parameter combinations 85: 85: Excluding 1 bonded neighbours molecule type 'Argon' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: NOTE: 40 % of the run time was spent communicating energies, 85: you might want to increase some nst* mdp options 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.037 0.019 194.9 85: (ns/day) (hour/ns) 85: Performance: 78.390 0.306 85: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as double precision energy file 85: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as double precision energy file 85: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 85: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 85: setting nstcomm equal to nstcalcenergy for less overhead 85: 85: Number of degrees of freedom in T-Coupling group System is 33.00 85: 85: There were 2 NOTEs 85: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 85: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 85: 85: Using 2 MPI threads 85: Using 1 OpenMP thread per tMPI thread 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'Argon' 85: 16 steps, 0.0 ps. 85: Generated 1 of the 1 non-bonded parameter combinations 85: 85: Excluding 1 bonded neighbours molecule type 'Argon' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: NOTE: 46 % of the run time was spent communicating energies, 85: you might want to increase some nst* mdp options 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.073 0.037 198.3 85: (ns/day) (hour/ns) 85: Performance: 39.997 0.600 85: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as double precision energy file 85: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as double precision energy file 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 85: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 85: setting nstcomm equal to nstcalcenergy for less overhead 85: 85: Number of degrees of freedom in T-Coupling group System is 33.00 85: 85: There were 2 NOTEs 85: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 85: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 85: 85: Using 2 MPI threads 85: Using 1 OpenMP thread per tMPI thread 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'Argon' 85: 16 steps, 0.0 ps. 85: Generated 1 of the 1 non-bonded parameter combinations 85: 85: Excluding 1 bonded neighbours molecule type 'Argon' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: NOTE: 44 % of the run time was spent communicating energies, 85: you might want to increase some nst* mdp options 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.044 0.026 168.0 85: (ns/day) (hour/ns) 85: Performance: 55.622 0.431 85: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as double precision energy file 85: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as double precision energy file 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 85: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 85: setting nstcomm equal to nstcalcenergy for less overhead 85: 85: Number of degrees of freedom in T-Coupling group System is 33.00 85: 85: There were 2 NOTEs 85: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 85: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 85: 85: Using 2 MPI threads 85: Using 1 OpenMP thread per tMPI thread 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'Argon' 85: 16 steps, 0.0 ps. 85: Generated 1 of the 1 non-bonded parameter combinations 85: 85: Excluding 1 bonded neighbours molecule type 'Argon' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: NOTE: 41 % of the run time was spent communicating energies, 85: you might want to increase some nst* mdp options 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.057 0.029 197.7 85: (ns/day) (hour/ns) 85: Performance: 51.168 0.469 85: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as double precision energy file 85: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as double precision energy file 85: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/7 (790 ms) 85: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/8 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 85: Setting nstcalcenergy (100) equal to nstenergy (1) 85: 85: 85: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 85: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 85: 1 85: 85: Number of degrees of freedom in T-Coupling group System is 33.00 85: 85: There were 3 NOTEs 85: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 85: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 85: 85: Using 2 MPI threads 85: Using 1 OpenMP thread per tMPI thread 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'Argon' 85: 16 steps, 0.0 ps. 85: Generated 1 of the 1 non-bonded parameter combinations 85: 85: Excluding 1 bonded neighbours molecule type 'Argon' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: NOTE: 41 % of the run time was spent communicating energies, 85: you might want to increase some nst* mdp options 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.058 0.029 197.7 85: (ns/day) (hour/ns) 85: Performance: 50.388 0.476 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 85: Setting nstcalcenergy (100) equal to nstenergy (1) 85: 85: 85: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 85: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 85: 1 85: 85: Number of degrees of freedom in T-Coupling group System is 33.00 85: 85: There were 3 NOTEs 85: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 85: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 85: 85: Using 2 MPI threads 85: Using 1 OpenMP thread per tMPI thread 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'Argon' 85: 16 steps, 0.0 ps. 85: Generated 1 of the 1 non-bonded parameter combinations 85: 85: Excluding 1 bonded neighbours molecule type 'Argon' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: NOTE: 54 % of the run time was spent communicating energies, 85: you might want to increase some nst* mdp options 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.046 0.023 197.4 85: (ns/day) (hour/ns) 85: Performance: 63.040 0.381 85: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_reference.edr as double precision energy file 85: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.edr as double precision energy file 85: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 85: Setting nstcalcenergy (100) equal to nstenergy (4) 85: 85: 85: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 85: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 85: 1 85: 85: Number of degrees of freedom in T-Coupling group System is 33.00 85: 85: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 85: COM removal frequency is set to (5). 85: Other settings require a global communication frequency of 2. 85: Note that this will require additional global communication steps, 85: which will reduce performance when using multiple ranks. 85: Consider setting nstcomm to a multiple of 2. 85: 85: 85: There were 4 NOTEs 85: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 85: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 85: 85: Using 2 MPI threads 85: Using 1 OpenMP thread per tMPI thread 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'Argon' 85: 16 steps, 0.0 ps. 85: Generated 1 of the 1 non-bonded parameter combinations 85: 85: Excluding 1 bonded neighbours molecule type 'Argon' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: NOTE: 39 % of the run time was spent communicating energies, 85: you might want to increase some nst* mdp options 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.033 0.017 196.6 85: (ns/day) (hour/ns) 85: Performance: 86.471 0.278 85: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_reference.edr as double precision energy file 85: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.edr as double precision energy file 85: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 85: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 85: setting nstcomm equal to nstcalcenergy for less overhead 85: 85: 85: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 85: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 85: 1 85: 85: Number of degrees of freedom in T-Coupling group System is 33.00 85: 85: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 85: COM removal frequency is set to (5). 85: Other settings require a global communication frequency of 2. 85: Note that this will require additional global communication steps, 85: which will reduce performance when using multiple ranks. 85: Consider setting nstcomm to a multiple of 2. 85: 85: 85: There were 4 NOTEs 85: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 85: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 85: 85: Using 2 MPI threads 85: Using 1 OpenMP thread per tMPI thread 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'Argon' 85: 16 steps, 0.0 ps. 85: Generated 1 of the 1 non-bonded parameter combinations 85: 85: Excluding 1 bonded neighbours molecule type 'Argon' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: NOTE: 44 % of the run time was spent communicating energies, 85: you might want to increase some nst* mdp options 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.041 0.021 197.0 85: (ns/day) (hour/ns) 85: Performance: 70.889 0.339 85: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_reference.edr as double precision energy file 85: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.edr as double precision energy file 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 85: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 85: setting nstcomm equal to nstcalcenergy for less overhead 85: 85: 85: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 85: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 85: 1 85: 85: Number of degrees of freedom in T-Coupling group System is 33.00 85: 85: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 85: COM removal frequency is set to (5). 85: Other settings require a global communication frequency of 2. 85: Note that this will require additional global communication steps, 85: which will reduce performance when using multiple ranks. 85: Consider setting nstcomm to a multiple of 2. 85: 85: 85: There were 4 NOTEs 85: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 85: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 85: 85: Using 2 MPI threads 85: Using 1 OpenMP thread per tMPI thread 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'Argon' 85: 16 steps, 0.0 ps. 85: Generated 1 of the 1 non-bonded parameter combinations 85: 85: Excluding 1 bonded neighbours molecule type 'Argon' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: NOTE: 45 % of the run time was spent communicating energies, 85: you might want to increase some nst* mdp options 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.192 0.097 199.3 85: (ns/day) (hour/ns) 85: Performance: 15.218 1.577 85: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_reference.edr as double precision energy file 85: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.edr as double precision energy file 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 85: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 85: setting nstcomm equal to nstcalcenergy for less overhead 85: 85: 85: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 85: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 85: 1 85: 85: Number of degrees of freedom in T-Coupling group System is 33.00 85: 85: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 85: COM removal frequency is set to (5). 85: Other settings require a global communication frequency of 2. 85: Note that this will require additional global communication steps, 85: which will reduce performance when using multiple ranks. 85: Consider setting nstcomm to a multiple of 2. 85: 85: 85: There were 4 NOTEs 85: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 85: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 85: 85: Using 2 MPI threads 85: Using 1 OpenMP thread per tMPI thread 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'Argon' 85: 16 steps, 0.0 ps. 85: Generated 1 of the 1 non-bonded parameter combinations 85: 85: Excluding 1 bonded neighbours molecule type 'Argon' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: NOTE: 41 % of the run time was spent communicating energies, 85: you might want to increase some nst* mdp options 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.098 0.049 198.7 85: (ns/day) (hour/ns) 85: Performance: 29.896 0.803 85: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_reference.edr as double precision energy file 85: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.edr as double precision energy file 85: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/8 (609 ms) 85: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/9 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 85: Setting nstcalcenergy (100) equal to nstenergy (1) 85: 85: 85: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 85: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 85: 1 85: 85: 85: WARNING 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 85: The Berendsen barostat does not generate any strictly correct ensemble, 85: and should not be used for new production simulations (in our opinion). 85: We recommend using the C-rescale barostat instead. 85: 85: Number of degrees of freedom in T-Coupling group System is 33.00 85: 85: There were 3 NOTEs 85: 85: There was 1 WARNING 85: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 85: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 85: 85: Using 2 MPI threads 85: Using 1 OpenMP thread per tMPI thread 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'Argon' 85: 16 steps, 0.0 ps. 85: Generated 1 of the 1 non-bonded parameter combinations 85: 85: Excluding 1 bonded neighbours molecule type 'Argon' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: NOTE: 36 % of the run time was spent communicating energies, 85: you might want to increase some nst* mdp options 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.124 0.062 198.8 85: (ns/day) (hour/ns) 85: Performance: 23.568 1.018 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 85: Setting nstcalcenergy (100) equal to nstenergy (1) 85: 85: 85: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 85: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 85: 1 85: 85: 85: WARNING 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 85: The Berendsen barostat does not generate any strictly correct ensemble, 85: and should not be used for new production simulations (in our opinion). 85: We recommend using the C-rescale barostat instead. 85: 85: Number of degrees of freedom in T-Coupling group System is 33.00 85: 85: There were 3 NOTEs 85: 85: There was 1 WARNING 85: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 85: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 85: 85: Using 2 MPI threads 85: Using 1 OpenMP thread per tMPI thread 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'Argon' 85: 16 steps, 0.0 ps. 85: Generated 1 of the 1 non-bonded parameter combinations 85: 85: Excluding 1 bonded neighbours molecule type 'Argon' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: NOTE: 42 % of the run time was spent communicating energies, 85: you might want to increase some nst* mdp options 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.111 0.056 198.6 85: (ns/day) (hour/ns) 85: Performance: 26.335 0.911 85: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_reference.edr as double precision energy file 85: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.edr as double precision energy file 85: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 85: Setting nstcalcenergy (100) equal to nstenergy (4) 85: 85: 85: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 85: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 85: 1 85: 85: 85: WARNING 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 85: The Berendsen barostat does not generate any strictly correct ensemble, 85: and should not be used for new production simulations (in our opinion). 85: We recommend using the C-rescale barostat instead. 85: 85: Number of degrees of freedom in T-Coupling group System is 33.00 85: 85: There were 3 NOTEs 85: 85: There was 1 WARNING 85: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 85: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 85: 85: Using 2 MPI threads 85: Using 1 OpenMP thread per tMPI thread 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'Argon' 85: 16 steps, 0.0 ps. 85: Generated 1 of the 1 non-bonded parameter combinations 85: 85: Excluding 1 bonded neighbours molecule type 'Argon' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: NOTE: 57 % of the run time was spent communicating energies, 85: you might want to increase some nst* mdp options 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.113 0.077 146.9 85: (ns/day) (hour/ns) 85: Performance: 19.108 1.256 85: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_reference.edr as double precision energy file 85: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.edr as double precision energy file 85: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 85: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 85: setting nstcomm equal to nstcalcenergy for less overhead 85: 85: 85: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 85: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 85: 1 85: 85: 85: WARNING 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 85: The Berendsen barostat does not generate any strictly correct ensemble, 85: and should not be used for new production simulations (in our opinion). 85: We recommend using the C-rescale barostat instead. 85: 85: Number of degrees of freedom in T-Coupling group System is 33.00 85: 85: There were 3 NOTEs 85: 85: There was 1 WARNING 85: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 85: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 85: 85: Using 2 MPI threads 85: Using 1 OpenMP thread per tMPI thread 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'Argon' 85: 16 steps, 0.0 ps. 85: Generated 1 of the 1 non-bonded parameter combinations 85: 85: Excluding 1 bonded neighbours molecule type 'Argon' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: NOTE: 44 % of the run time was spent communicating energies, 85: you might want to increase some nst* mdp options 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.096 0.048 198.4 85: (ns/day) (hour/ns) 85: Performance: 30.414 0.789 85: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_reference.edr as double precision energy file 85: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.edr as double precision energy file 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 85: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 85: setting nstcomm equal to nstcalcenergy for less overhead 85: 85: 85: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 85: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 85: 1 85: 85: 85: WARNING 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 85: The Berendsen barostat does not generate any strictly correct ensemble, 85: and should not be used for new production simulations (in our opinion). 85: We recommend using the C-rescale barostat instead. 85: 85: Number of degrees of freedom in T-Coupling group System is 33.00 85: 85: There were 3 NOTEs 85: 85: There was 1 WARNING 85: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 85: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 85: 85: Using 2 MPI threads 85: Using 1 OpenMP thread per tMPI thread 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'Argon' 85: 16 steps, 0.0 ps. 85: Generated 1 of the 1 non-bonded parameter combinations 85: 85: Excluding 1 bonded neighbours molecule type 'Argon' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: NOTE: 46 % of the run time was spent communicating energies, 85: you might want to increase some nst* mdp options 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.109 0.055 198.5 85: (ns/day) (hour/ns) 85: Performance: 26.696 0.899 85: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_reference.edr as double precision energy file 85: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.edr as double precision energy file 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 85: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 85: setting nstcomm equal to nstcalcenergy for less overhead 85: 85: 85: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 85: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 85: 1 85: 85: 85: WARNING 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 85: The Berendsen barostat does not generate any strictly correct ensemble, 85: and should not be used for new production simulations (in our opinion). 85: We recommend using the C-rescale barostat instead. 85: 85: Number of degrees of freedom in T-Coupling group System is 33.00 85: 85: There were 3 NOTEs 85: 85: There was 1 WARNING 85: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 85: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 85: 85: Using 2 MPI threads 85: Using 1 OpenMP thread per tMPI thread 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'Argon' 85: 16 steps, 0.0 ps. 85: Generated 1 of the 1 non-bonded parameter combinations 85: 85: Excluding 1 bonded neighbours molecule type 'Argon' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: NOTE: 0 % of the run time was spent in domain decomposition, 85: 11 % of the run time was spent in pair search, 85: you might want to increase nstlist (this has no effect on accuracy) 85: 85: NOTE: 42 % of the run time was spent communicating energies, 85: you might want to increase some nst* mdp options 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.082 0.042 197.7 85: (ns/day) (hour/ns) 85: Performance: 35.270 0.680 85: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_reference.edr as double precision energy file 85: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.edr as double precision energy file 85: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/9 (1392 ms) 85: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/10 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 85: Setting nstcalcenergy (100) equal to nstenergy (1) 85: 85: 85: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 85: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 85: 1 85: 85: Number of degrees of freedom in T-Coupling group System is 33.00 85: 85: There were 3 NOTEs 85: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 85: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 85: 85: Using 2 MPI threads 85: Using 1 OpenMP thread per tMPI thread 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'Argon' 85: 16 steps, 0.0 ps. 85: Generated 1 of the 1 non-bonded parameter combinations 85: 85: Excluding 1 bonded neighbours molecule type 'Argon' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: NOTE: 38 % of the run time was spent communicating energies, 85: you might want to increase some nst* mdp options 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.155 0.078 199.0 85: (ns/day) (hour/ns) 85: Performance: 18.905 1.269 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 85: Setting nstcalcenergy (100) equal to nstenergy (1) 85: 85: 85: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 85: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 85: 1 85: 85: Number of degrees of freedom in T-Coupling group System is 33.00 85: 85: There were 3 NOTEs 85: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 85: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 85: 85: Using 2 MPI threads 85: Using 1 OpenMP thread per tMPI thread 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'Argon' 85: 16 steps, 0.0 ps. 85: Generated 1 of the 1 non-bonded parameter combinations 85: 85: Excluding 1 bonded neighbours molecule type 'Argon' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: NOTE: 42 % of the run time was spent communicating energies, 85: you might want to increase some nst* mdp options 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.099 0.050 198.3 85: (ns/day) (hour/ns) 85: Performance: 29.525 0.813 85: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_reference.edr as double precision energy file 85: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.edr as double precision energy file 85: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 85: Setting nstcalcenergy (100) equal to nstenergy (4) 85: 85: 85: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 85: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 85: 1 85: 85: Number of degrees of freedom in T-Coupling group System is 33.00 85: 85: There were 3 NOTEs 85: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 85: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 85: 85: Using 2 MPI threads 85: Using 1 OpenMP thread per tMPI thread 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'Argon' 85: 16 steps, 0.0 ps. 85: Generated 1 of the 1 non-bonded parameter combinations 85: 85: Excluding 1 bonded neighbours molecule type 'Argon' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: NOTE: 29 % of the run time was spent communicating energies, 85: you might want to increase some nst* mdp options 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.070 0.035 197.6 85: (ns/day) (hour/ns) 85: Performance: 41.681 0.576 85: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_reference.edr as double precision energy file 85: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.edr as double precision energy file 85: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 85: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 85: setting nstcomm equal to nstcalcenergy for less overhead 85: 85: 85: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 85: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 85: 1 85: 85: Number of degrees of freedom in T-Coupling group System is 33.00 85: 85: There were 3 NOTEs 85: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 85: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 85: 85: Using 2 MPI threads 85: Using 1 OpenMP thread per tMPI thread 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'Argon' 85: 16 steps, 0.0 ps. 85: Generated 1 of the 1 non-bonded parameter combinations 85: 85: Excluding 1 bonded neighbours molecule type 'Argon' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: NOTE: 52 % of the run time was spent communicating energies, 85: you might want to increase some nst* mdp options 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.190 0.095 199.1 85: (ns/day) (hour/ns) 85: Performance: 15.419 1.556 85: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_reference.edr as double precision energy file 85: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.edr as double precision energy file 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 85: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 85: setting nstcomm equal to nstcalcenergy for less overhead 85: 85: 85: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 85: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 85: 1 85: 85: Number of degrees of freedom in T-Coupling group System is 33.00 85: 85: There were 3 NOTEs 85: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 85: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 85: 85: Using 2 MPI threads 85: Using 1 OpenMP thread per tMPI thread 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'Argon' 85: 16 steps, 0.0 ps. 85: Generated 1 of the 1 non-bonded parameter combinations 85: 85: Excluding 1 bonded neighbours molecule type 'Argon' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: NOTE: 54 % of the run time was spent communicating energies, 85: you might want to increase some nst* mdp options 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.080 0.040 198.0 85: (ns/day) (hour/ns) 85: Performance: 36.409 0.659 85: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_reference.edr as double precision energy file 85: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.edr as double precision energy file 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 85: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 85: setting nstcomm equal to nstcalcenergy for less overhead 85: 85: 85: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 85: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 85: 1 85: 85: Number of degrees of freedom in T-Coupling group System is 33.00 85: 85: There were 3 NOTEs 85: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 85: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 85: 85: Using 2 MPI threads 85: Using 1 OpenMP thread per tMPI thread 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'Argon' 85: 16 steps, 0.0 ps. 85: Generated 1 of the 1 non-bonded parameter combinations 85: 85: Excluding 1 bonded neighbours molecule type 'Argon' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: NOTE: 47 % of the run time was spent communicating energies, 85: you might want to increase some nst* mdp options 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.101 0.051 198.6 85: (ns/day) (hour/ns) 85: Performance: 28.892 0.831 85: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_reference.edr as double precision energy file 85: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.edr as double precision energy file 85: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/10 (1110 ms) 85: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/11 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 85: Setting nstcalcenergy (100) equal to nstenergy (1) 85: 85: 85: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 85: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 85: 1 85: 85: Number of degrees of freedom in T-Coupling group System is 33.00 85: 85: There were 3 NOTEs 85: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 85: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 85: 85: Using 2 MPI threads 85: Using 1 OpenMP thread per tMPI thread 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'Argon' 85: 16 steps, 0.0 ps. 85: Generated 1 of the 1 non-bonded parameter combinations 85: 85: Excluding 1 bonded neighbours molecule type 'Argon' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: NOTE: 40 % of the run time was spent communicating energies, 85: you might want to increase some nst* mdp options 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.134 0.067 198.6 85: (ns/day) (hour/ns) 85: Performance: 21.835 1.099 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 85: Setting nstcalcenergy (100) equal to nstenergy (1) 85: 85: 85: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 85: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 85: 1 85: 85: Number of degrees of freedom in T-Coupling group System is 33.00 85: 85: There were 3 NOTEs 85: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 85: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 85: 85: Using 2 MPI threads 85: Using 1 OpenMP thread per tMPI thread 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'Argon' 85: 16 steps, 0.0 ps. 85: Generated 1 of the 1 non-bonded parameter combinations 85: 85: Excluding 1 bonded neighbours molecule type 'Argon' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: NOTE: 36 % of the run time was spent communicating energies, 85: you might want to increase some nst* mdp options 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.086 0.043 198.4 85: (ns/day) (hour/ns) 85: Performance: 34.037 0.705 85: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_reference.edr as double precision energy file 85: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.edr as double precision energy file 85: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 85: Setting nstcalcenergy (100) equal to nstenergy (4) 85: 85: 85: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 85: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 85: 1 85: 85: Number of degrees of freedom in T-Coupling group System is 33.00 85: 85: There were 3 NOTEs 85: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 85: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 85: 85: Using 2 MPI threads 85: Using 1 OpenMP thread per tMPI thread 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'Argon' 85: 16 steps, 0.0 ps. 85: Generated 1 of the 1 non-bonded parameter combinations 85: 85: Excluding 1 bonded neighbours molecule type 'Argon' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: NOTE: 44 % of the run time was spent communicating energies, 85: you might want to increase some nst* mdp options 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.059 0.030 197.7 85: (ns/day) (hour/ns) 85: Performance: 49.066 0.489 85: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_reference.edr as double precision energy file 85: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.edr as double precision energy file 85: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 85: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 85: setting nstcomm equal to nstcalcenergy for less overhead 85: 85: 85: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 85: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 85: 1 85: 85: Number of degrees of freedom in T-Coupling group System is 33.00 85: 85: There were 3 NOTEs 85: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 85: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 85: 85: Using 2 MPI threads 85: Using 1 OpenMP thread per tMPI thread 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'Argon' 85: 16 steps, 0.0 ps. 85: Generated 1 of the 1 non-bonded parameter combinations 85: 85: Excluding 1 bonded neighbours molecule type 'Argon' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: NOTE: 51 % of the run time was spent communicating energies, 85: you might want to increase some nst* mdp options 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.104 0.052 198.5 85: (ns/day) (hour/ns) 85: Performance: 28.033 0.856 85: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_reference.edr as double precision energy file 85: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.edr as double precision energy file 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 85: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 85: setting nstcomm equal to nstcalcenergy for less overhead 85: 85: 85: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 85: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 85: 1 85: 85: Number of degrees of freedom in T-Coupling group System is 33.00 85: 85: There were 3 NOTEs 85: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 85: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 85: 85: Using 2 MPI threads 85: Using 1 OpenMP thread per tMPI thread 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'Argon' 85: 16 steps, 0.0 ps. 85: Generated 1 of the 1 non-bonded parameter combinations 85: 85: Excluding 1 bonded neighbours molecule type 'Argon' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: NOTE: 56 % of the run time was spent communicating energies, 85: you might want to increase some nst* mdp options 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.149 0.075 199.1 85: (ns/day) (hour/ns) 85: Performance: 19.647 1.222 85: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_reference.edr as double precision energy file 85: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.edr as double precision energy file 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 85: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 85: setting nstcomm equal to nstcalcenergy for less overhead 85: 85: 85: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 85: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 85: 1 85: 85: Number of degrees of freedom in T-Coupling group System is 33.00 85: 85: There were 3 NOTEs 85: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 85: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 85: 85: Using 2 MPI threads 85: Using 1 OpenMP thread per tMPI thread 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'Argon' 85: 16 steps, 0.0 ps. 85: Generated 1 of the 1 non-bonded parameter combinations 85: 85: Excluding 1 bonded neighbours molecule type 'Argon' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: NOTE: 50 % of the run time was spent communicating energies, 85: you might want to increase some nst* mdp options 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.143 0.072 199.0 85: (ns/day) (hour/ns) 85: Performance: 20.469 1.172 85: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_reference.edr as double precision energy file 85: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.edr as double precision energy file 85: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/11 (1189 ms) 85: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/12 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 85: Setting nstcalcenergy (100) equal to nstenergy (1) 85: 85: Number of degrees of freedom in T-Coupling group System is 33.00 85: 85: There were 2 NOTEs 85: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 85: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 85: 85: Using 2 MPI threads 85: Using 1 OpenMP thread per tMPI thread 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'Argon' 85: 16 steps, 0.0 ps. 85: Generated 1 of the 1 non-bonded parameter combinations 85: 85: Excluding 1 bonded neighbours molecule type 'Argon' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: NOTE: 43 % of the run time was spent communicating energies, 85: you might want to increase some nst* mdp options 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.117 0.059 199.0 85: (ns/day) (hour/ns) 85: Performance: 24.920 0.963 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 85: Setting nstcalcenergy (100) equal to nstenergy (1) 85: 85: Number of degrees of freedom in T-Coupling group System is 33.00 85: 85: There were 2 NOTEs 85: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 85: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 85: 85: Using 2 MPI threads 85: Using 1 OpenMP thread per tMPI thread 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'Argon' 85: 16 steps, 0.0 ps. 85: Generated 1 of the 1 non-bonded parameter combinations 85: 85: Excluding 1 bonded neighbours molecule type 'Argon' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: NOTE: 44 % of the run time was spent communicating energies, 85: you might want to increase some nst* mdp options 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.065 0.033 198.3 85: (ns/day) (hour/ns) 85: Performance: 44.688 0.537 85: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_reference.edr as double precision energy file 85: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.edr as double precision energy file 85: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 85: Setting nstcalcenergy (100) equal to nstenergy (4) 85: 85: Number of degrees of freedom in T-Coupling group System is 33.00 85: 85: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 85: COM removal frequency is set to (5). 85: Other settings require a global communication frequency of 4. 85: Note that this will require additional global communication steps, 85: which will reduce performance when using multiple ranks. 85: Consider setting nstcomm to a multiple of 4. 85: 85: 85: There were 3 NOTEs 85: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 85: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 85: 85: Using 2 MPI threads 85: Using 1 OpenMP thread per tMPI thread 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'Argon' 85: 16 steps, 0.0 ps. 85: Generated 1 of the 1 non-bonded parameter combinations 85: 85: Excluding 1 bonded neighbours molecule type 'Argon' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: NOTE: 34 % of the run time was spent communicating energies, 85: you might want to increase some nst* mdp options 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.096 0.048 198.6 85: (ns/day) (hour/ns) 85: Performance: 30.424 0.789 85: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_reference.edr as double precision energy file 85: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.edr as double precision energy file 85: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 85: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 85: setting nstcomm equal to nstcalcenergy for less overhead 85: 85: Number of degrees of freedom in T-Coupling group System is 33.00 85: 85: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 85: COM removal frequency is set to (5). 85: Other settings require a global communication frequency of 100. 85: Note that this will require additional global communication steps, 85: which will reduce performance when using multiple ranks. 85: Consider setting nstcomm to a multiple of 100. 85: 85: 85: There were 3 NOTEs 85: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 85: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 85: 85: Using 2 MPI threads 85: Using 1 OpenMP thread per tMPI thread 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'Argon' 85: 16 steps, 0.0 ps. 85: Generated 1 of the 1 non-bonded parameter combinations 85: 85: Excluding 1 bonded neighbours molecule type 'Argon' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: NOTE: 43 % of the run time was spent communicating energies, 85: you might want to increase some nst* mdp options 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.046 0.023 197.4 85: (ns/day) (hour/ns) 85: Performance: 63.446 0.378 85: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_reference.edr as double precision energy file 85: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.edr as double precision energy file 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 85: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 85: setting nstcomm equal to nstcalcenergy for less overhead 85: 85: Number of degrees of freedom in T-Coupling group System is 33.00 85: 85: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 85: COM removal frequency is set to (5). 85: Other settings require a global communication frequency of 100. 85: Note that this will require additional global communication steps, 85: which will reduce performance when using multiple ranks. 85: Consider setting nstcomm to a multiple of 100. 85: 85: 85: There were 3 NOTEs 85: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 85: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 85: 85: Using 2 MPI threads 85: Using 1 OpenMP thread per tMPI thread 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'Argon' 85: 16 steps, 0.0 ps. 85: Generated 1 of the 1 non-bonded parameter combinations 85: 85: Excluding 1 bonded neighbours molecule type 'Argon' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: NOTE: 60 % of the run time was spent communicating energies, 85: you might want to increase some nst* mdp options 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.111 0.059 186.8 85: (ns/day) (hour/ns) 85: Performance: 24.691 0.972 85: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_reference.edr as double precision energy file 85: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.edr as double precision energy file 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 85: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 85: setting nstcomm equal to nstcalcenergy for less overhead 85: 85: Number of degrees of freedom in T-Coupling group System is 33.00 85: 85: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 85: COM removal frequency is set to (5). 85: Other settings require a global communication frequency of 100. 85: Note that this will require additional global communication steps, 85: which will reduce performance when using multiple ranks. 85: Consider setting nstcomm to a multiple of 100. 85: 85: 85: There were 3 NOTEs 85: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 85: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 85: 85: Using 2 MPI threads 85: Using 1 OpenMP thread per tMPI thread 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'Argon' 85: 16 steps, 0.0 ps. 85: Generated 1 of the 1 non-bonded parameter combinations 85: 85: Excluding 1 bonded neighbours molecule type 'Argon' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: NOTE: 42 % of the run time was spent communicating energies, 85: you might want to increase some nst* mdp options 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.083 0.042 198.6 85: (ns/day) (hour/ns) 85: Performance: 35.073 0.684 85: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_reference.edr as double precision energy file 85: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.edr as double precision energy file 85: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/12 (901 ms) 85: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/13 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: 85: Setting nstcalcenergy (100) equal to nstenergy (1) 85: 85: 85: WARNING 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: 85: The Berendsen barostat does not generate any strictly correct ensemble, 85: and should not be used for new production simulations (in our opinion). 85: We recommend using the C-rescale barostat instead. 85: 85: Number of degrees of freedom in T-Coupling group System is 33.00 85: 85: There were 2 NOTEs 85: 85: There was 1 WARNING 85: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 85: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 85: 85: Using 2 MPI threads 85: Using 1 OpenMP thread per tMPI thread 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'Argon' 85: 16 steps, 0.0 ps. 85: Generated 1 of the 1 non-bonded parameter combinations 85: 85: Excluding 1 bonded neighbours molecule type 'Argon' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: NOTE: 44 % of the run time was spent communicating energies, 85: you might want to increase some nst* mdp options 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.086 0.043 198.3 85: (ns/day) (hour/ns) 85: Performance: 34.000 0.706 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: 85: Setting nstcalcenergy (100) equal to nstenergy (1) 85: 85: 85: WARNING 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: 85: The Berendsen barostat does not generate any strictly correct ensemble, 85: and should not be used for new production simulations (in our opinion). 85: We recommend using the C-rescale barostat instead. 85: 85: Number of degrees of freedom in T-Coupling group System is 33.00 85: 85: There were 2 NOTEs 85: 85: There was 1 WARNING 85: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 85: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 85: 85: Using 2 MPI threads 85: Using 1 OpenMP thread per tMPI thread 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'Argon' 85: 16 steps, 0.0 ps. 85: Generated 1 of the 1 non-bonded parameter combinations 85: 85: Excluding 1 bonded neighbours molecule type 'Argon' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: NOTE: 49 % of the run time was spent communicating energies, 85: you might want to increase some nst* mdp options 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.120 0.061 199.0 85: (ns/day) (hour/ns) 85: Performance: 24.265 0.989 85: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_reference.edr as double precision energy file 85: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.edr as double precision energy file 85: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: 85: Setting nstcalcenergy (100) equal to nstenergy (4) 85: 85: 85: WARNING 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: 85: The Berendsen barostat does not generate any strictly correct ensemble, 85: and should not be used for new production simulations (in our opinion). 85: We recommend using the C-rescale barostat instead. 85: 85: Number of degrees of freedom in T-Coupling group System is 33.00 85: 85: There were 2 NOTEs 85: 85: There was 1 WARNING 85: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 85: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 85: 85: Using 2 MPI threads 85: Using 1 OpenMP thread per tMPI thread 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'Argon' 85: 16 steps, 0.0 ps. 85: Generated 1 of the 1 non-bonded parameter combinations 85: 85: Excluding 1 bonded neighbours molecule type 'Argon' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: NOTE: 41 % of the run time was spent communicating energies, 85: you might want to increase some nst* mdp options 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.120 0.060 199.0 85: (ns/day) (hour/ns) 85: Performance: 24.325 0.987 85: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_reference.edr as double precision energy file 85: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.edr as double precision energy file 85: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: 85: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 85: setting nstcomm equal to nstcalcenergy for less overhead 85: 85: 85: WARNING 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: 85: The Berendsen barostat does not generate any strictly correct ensemble, 85: and should not be used for new production simulations (in our opinion). 85: We recommend using the C-rescale barostat instead. 85: 85: Number of degrees of freedom in T-Coupling group System is 33.00 85: 85: There were 2 NOTEs 85: 85: There was 1 WARNING 85: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 85: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 85: 85: Using 2 MPI threads 85: Using 1 OpenMP thread per tMPI thread 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'Argon' 85: 16 steps, 0.0 ps. 85: Generated 1 of the 1 non-bonded parameter combinations 85: 85: Excluding 1 bonded neighbours molecule type 'Argon' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: NOTE: 50 % of the run time was spent communicating energies, 85: you might want to increase some nst* mdp options 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.238 0.119 199.5 85: (ns/day) (hour/ns) 85: Performance: 12.324 1.947 85: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_reference.edr as double precision energy file 85: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.edr as double precision energy file 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: 85: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 85: setting nstcomm equal to nstcalcenergy for less overhead 85: 85: 85: WARNING 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: 85: The Berendsen barostat does not generate any strictly correct ensemble, 85: and should not be used for new production simulations (in our opinion). 85: We recommend using the C-rescale barostat instead. 85: 85: Number of degrees of freedom in T-Coupling group System is 33.00 85: 85: There were 2 NOTEs 85: 85: There was 1 WARNING 85: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 85: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 85: 85: Using 2 MPI threads 85: Using 1 OpenMP thread per tMPI thread 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'Argon' 85: 16 steps, 0.0 ps. 85: Generated 1 of the 1 non-bonded parameter combinations 85: 85: Excluding 1 bonded neighbours molecule type 'Argon' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: NOTE: 45 % of the run time was spent communicating energies, 85: you might want to increase some nst* mdp options 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.056 0.028 197.8 85: (ns/day) (hour/ns) 85: Performance: 52.281 0.459 85: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_reference.edr as double precision energy file 85: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.edr as double precision energy file 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: 85: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 85: setting nstcomm equal to nstcalcenergy for less overhead 85: 85: 85: WARNING 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: 85: The Berendsen barostat does not generate any strictly correct ensemble, 85: and should not be used for new production simulations (in our opinion). 85: We recommend using the C-rescale barostat instead. 85: 85: Number of degrees of freedom in T-Coupling group System is 33.00 85: 85: There were 2 NOTEs 85: 85: There was 1 WARNING 85: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 85: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 85: 85: Using 2 MPI threads 85: Using 1 OpenMP thread per tMPI thread 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'Argon' 85: 16 steps, 0.0 ps. 85: Generated 1 of the 1 non-bonded parameter combinations 85: 85: Excluding 1 bonded neighbours molecule type 'Argon' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: NOTE: 37 % of the run time was spent communicating energies, 85: you might want to increase some nst* mdp options 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.179 0.090 199.3 85: (ns/day) (hour/ns) 85: Performance: 16.388 1.464 85: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_reference.edr as double precision energy file 85: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.edr as double precision energy file 85: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/13 (972 ms) 85: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/14 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]: 85: Setting nstcalcenergy (100) equal to nstenergy (1) 85: 85: Number of degrees of freedom in T-Coupling group System is 33.00 85: 85: There were 2 NOTEs 85: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 85: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 85: 85: Using 2 MPI threads 85: Using 1 OpenMP thread per tMPI thread 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'Argon' 85: 16 steps, 0.0 ps. 85: Generated 1 of the 1 non-bonded parameter combinations 85: 85: Excluding 1 bonded neighbours molecule type 'Argon' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: NOTE: 56 % of the run time was spent communicating energies, 85: you might want to increase some nst* mdp options 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.095 0.048 198.3 85: (ns/day) (hour/ns) 85: Performance: 30.553 0.786 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]: 85: Setting nstcalcenergy (100) equal to nstenergy (1) 85: 85: Number of degrees of freedom in T-Coupling group System is 33.00 85: 85: There were 2 NOTEs 85: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 85: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 85: 85: Using 2 MPI threads 85: Using 1 OpenMP thread per tMPI thread 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'Argon' 85: 16 steps, 0.0 ps. 85: Generated 1 of the 1 non-bonded parameter combinations 85: 85: Excluding 1 bonded neighbours molecule type 'Argon' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: NOTE: 37 % of the run time was spent communicating energies, 85: you might want to increase some nst* mdp options 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.061 0.031 198.1 85: (ns/day) (hour/ns) 85: Performance: 48.027 0.500 85: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_reference.edr as double precision energy file 85: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.edr as double precision energy file 85: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]: 85: Setting nstcalcenergy (100) equal to nstenergy (4) 85: 85: Number of degrees of freedom in T-Coupling group System is 33.00 85: 85: There were 2 NOTEs 85: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 85: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 85: 85: Using 2 MPI threads 85: Using 1 OpenMP thread per tMPI thread 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'Argon' 85: 16 steps, 0.0 ps. 85: Generated 1 of the 1 non-bonded parameter combinations 85: 85: Excluding 1 bonded neighbours molecule type 'Argon' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: NOTE: 40 % of the run time was spent communicating energies, 85: you might want to increase some nst* mdp options 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.071 0.036 198.5 85: (ns/day) (hour/ns) 85: Performance: 41.078 0.584 85: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_reference.edr as double precision energy file 85: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.edr as double precision energy file 85: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]: 85: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 85: setting nstcomm equal to nstcalcenergy for less overhead 85: 85: Number of degrees of freedom in T-Coupling group System is 33.00 85: 85: There were 2 NOTEs 85: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 85: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 85: 85: Using 2 MPI threads 85: Using 1 OpenMP thread per tMPI thread 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'Argon' 85: 16 steps, 0.0 ps. 85: Generated 1 of the 1 non-bonded parameter combinations 85: 85: Excluding 1 bonded neighbours molecule type 'Argon' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: NOTE: 48 % of the run time was spent communicating energies, 85: you might want to increase some nst* mdp options 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.146 0.073 199.2 85: (ns/day) (hour/ns) 85: Performance: 20.076 1.195 85: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_reference.edr as double precision energy file 85: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.edr as double precision energy file 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]: 85: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 85: setting nstcomm equal to nstcalcenergy for less overhead 85: 85: Number of degrees of freedom in T-Coupling group System is 33.00 85: 85: There were 2 NOTEs 85: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 85: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 85: 85: Using 2 MPI threads 85: Using 1 OpenMP thread per tMPI thread 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'Argon' 85: 16 steps, 0.0 ps. 85: Generated 1 of the 1 non-bonded parameter combinations 85: 85: Excluding 1 bonded neighbours molecule type 'Argon' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: NOTE: 47 % of the run time was spent communicating energies, 85: you might want to increase some nst* mdp options 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.099 0.050 198.8 85: (ns/day) (hour/ns) 85: Performance: 29.369 0.817 85: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_reference.edr as double precision energy file 85: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.edr as double precision energy file 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]: 85: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 85: setting nstcomm equal to nstcalcenergy for less overhead 85: 85: Number of degrees of freedom in T-Coupling group System is 33.00 85: 85: There were 2 NOTEs 85: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 85: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 85: 85: Using 2 MPI threads 85: Using 1 OpenMP thread per tMPI thread 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'Argon' 85: 16 steps, 0.0 ps. 85: Generated 1 of the 1 non-bonded parameter combinations 85: 85: Excluding 1 bonded neighbours molecule type 'Argon' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: NOTE: 44 % of the run time was spent communicating energies, 85: you might want to increase some nst* mdp options 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.047 0.024 197.6 85: (ns/day) (hour/ns) 85: Performance: 61.538 0.390 85: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_reference.edr as double precision energy file 85: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.edr as double precision energy file 85: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/14 (719 ms) 85: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/15 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]: 85: Setting nstcalcenergy (100) equal to nstenergy (1) 85: 85: Number of degrees of freedom in T-Coupling group System is 33.00 85: 85: There were 2 NOTEs 85: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 85: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 85: 85: Using 2 MPI threads 85: Using 1 OpenMP thread per tMPI thread 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'Argon' 85: 16 steps, 0.0 ps. 85: Generated 1 of the 1 non-bonded parameter combinations 85: 85: Excluding 1 bonded neighbours molecule type 'Argon' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: NOTE: 37 % of the run time was spent communicating energies, 85: you might want to increase some nst* mdp options 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.051 0.026 197.2 85: (ns/day) (hour/ns) 85: Performance: 56.621 0.424 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]: 85: Setting nstcalcenergy (100) equal to nstenergy (1) 85: 85: Number of degrees of freedom in T-Coupling group System is 33.00 85: 85: There were 2 NOTEs 85: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 85: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 85: 85: Using 2 MPI threads 85: Using 1 OpenMP thread per tMPI thread 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'Argon' 85: 16 steps, 0.0 ps. 85: Generated 1 of the 1 non-bonded parameter combinations 85: 85: Excluding 1 bonded neighbours molecule type 'Argon' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: NOTE: 58 % of the run time was spent communicating energies, 85: you might want to increase some nst* mdp options 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.090 0.045 198.6 85: (ns/day) (hour/ns) 85: Performance: 32.535 0.738 85: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_reference.edr as double precision energy file 85: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.edr as double precision energy file 85: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]: 85: Setting nstcalcenergy (100) equal to nstenergy (4) 85: 85: Number of degrees of freedom in T-Coupling group System is 33.00 85: 85: There were 2 NOTEs 85: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 85: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 85: 85: Using 2 MPI threads 85: Using 1 OpenMP thread per tMPI thread 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'Argon' 85: 16 steps, 0.0 ps. 85: Generated 1 of the 1 non-bonded parameter combinations 85: 85: Excluding 1 bonded neighbours molecule type 'Argon' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: NOTE: 37 % of the run time was spent communicating energies, 85: you might want to increase some nst* mdp options 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.046 0.024 197.5 85: (ns/day) (hour/ns) 85: Performance: 62.434 0.384 85: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_reference.edr as double precision energy file 85: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.edr as double precision energy file 85: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]: 85: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 85: setting nstcomm equal to nstcalcenergy for less overhead 85: 85: Number of degrees of freedom in T-Coupling group System is 33.00 85: 85: There were 2 NOTEs 85: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 85: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 85: 85: Using 2 MPI threads 85: Using 1 OpenMP thread per tMPI thread 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'Argon' 85: 16 steps, 0.0 ps. 85: Generated 1 of the 1 non-bonded parameter combinations 85: 85: Excluding 1 bonded neighbours molecule type 'Argon' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: NOTE: 47 % of the run time was spent communicating energies, 85: you might want to increase some nst* mdp options 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.106 0.053 198.5 85: (ns/day) (hour/ns) 85: Performance: 27.636 0.868 85: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_reference.edr as double precision energy file 85: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.edr as double precision energy file 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]: 85: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 85: setting nstcomm equal to nstcalcenergy for less overhead 85: 85: Number of degrees of freedom in T-Coupling group System is 33.00 85: 85: There were 2 NOTEs 85: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 85: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 85: 85: Using 2 MPI threads 85: Using 1 OpenMP thread per tMPI thread 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'Argon' 85: 16 steps, 0.0 ps. 85: Generated 1 of the 1 non-bonded parameter combinations 85: 85: Excluding 1 bonded neighbours molecule type 'Argon' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: NOTE: 49 % of the run time was spent communicating energies, 85: you might want to increase some nst* mdp options 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.047 0.024 197.2 85: (ns/day) (hour/ns) 85: Performance: 61.455 0.391 85: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_reference.edr as double precision energy file 85: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.edr as double precision energy file 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]: 85: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 85: setting nstcomm equal to nstcalcenergy for less overhead 85: 85: Number of degrees of freedom in T-Coupling group System is 33.00 85: 85: There were 2 NOTEs 85: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 85: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 85: 85: Using 2 MPI threads 85: Using 1 OpenMP thread per tMPI thread 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'Argon' 85: 16 steps, 0.0 ps. 85: Generated 1 of the 1 non-bonded parameter combinations 85: 85: Excluding 1 bonded neighbours molecule type 'Argon' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: NOTE: 50 % of the run time was spent communicating energies, 85: you might want to increase some nst* mdp options 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.065 0.033 197.8 85: (ns/day) (hour/ns) 85: Performance: 44.560 0.539 85: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_reference.edr as double precision energy file 85: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.edr as double precision energy file 85: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/15 (801 ms) 85: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/16 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 85: Setting nstcalcenergy (100) equal to nstenergy (1) 85: 85: Number of degrees of freedom in T-Coupling group System is 33.00 85: 85: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 85: NVE simulation: will use the initial temperature of 68.810 K for 85: determining the Verlet buffer size 85: 85: 85: There were 3 NOTEs 85: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 85: Can not increase nstlist because an NVE ensemble is used 85: Using 2 MPI threads 85: Using 1 OpenMP thread per tMPI thread 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'Argon' 85: 16 steps, 0.0 ps. 85: Generated 1 of the 1 non-bonded parameter combinations 85: 85: Excluding 1 bonded neighbours molecule type 'Argon' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: 85: Dynamic load balancing report: 85: DLB was off during the run due to low measured imbalance. 85: Average load imbalance: 1.6%. 85: The balanceable part of the MD step is 61%, load imbalance is computed from this. 85: Part of the total run time spent waiting due to load imbalance: 0.9%. 85: 85: 85: NOTE: 16 % of the run time was spent communicating energies, 85: you might want to increase some nst* mdp options 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.079 0.040 196.7 85: (ns/day) (hour/ns) 85: Performance: 36.510 0.657 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 85: Setting nstcalcenergy (100) equal to nstenergy (1) 85: 85: Number of degrees of freedom in T-Coupling group System is 33.00 85: 85: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 85: NVE simulation: will use the initial temperature of 68.810 K for 85: determining the Verlet buffer size 85: 85: 85: There were 3 NOTEs 85: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 85: Can not increase nstlist because an NVE ensemble is used 85: Using 2 MPI threads 85: Using 1 OpenMP thread per tMPI thread 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'Argon' 85: 16 steps, 0.0 ps. 85: Generated 1 of the 1 non-bonded parameter combinations 85: 85: Excluding 1 bonded neighbours molecule type 'Argon' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: 85: Dynamic load balancing report: 85: DLB was turned on during the run due to measured imbalance. 85: Average load imbalance: 4.2%. 85: The balanceable part of the MD step is 62%, load imbalance is computed from this. 85: Part of the total run time spent waiting due to load imbalance: 2.6%. 85: Steps where the load balancing was limited by -rdd, -rcon and/or -dds: X 0 % 85: 85: 85: NOTE: 6 % of the run time was spent communicating energies, 85: you might want to increase some nst* mdp options 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.063 0.032 195.1 85: (ns/day) (hour/ns) 85: Performance: 45.550 0.527 85: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_reference.edr as double precision energy file 85: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.edr as double precision energy file 85: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 85: Setting nstcalcenergy (100) equal to nstenergy (4) 85: 85: Number of degrees of freedom in T-Coupling group System is 33.00 85: 85: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 85: NVE simulation: will use the initial temperature of 68.810 K for 85: determining the Verlet buffer size 85: 85: 85: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 85: COM removal frequency is set to (5). 85: Other settings require a global communication frequency of 4. 85: Note that this will require additional global communication steps, 85: which will reduce performance when using multiple ranks. 85: Consider setting nstcomm to a multiple of 4. 85: 85: 85: There were 4 NOTEs 85: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 85: Can not increase nstlist because an NVE ensemble is used 85: Using 2 MPI threads 85: Using 1 OpenMP thread per tMPI thread 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'Argon' 85: 16 steps, 0.0 ps. 85: Generated 1 of the 1 non-bonded parameter combinations 85: 85: Excluding 1 bonded neighbours molecule type 'Argon' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: 85: Dynamic load balancing report: 85: DLB was off during the run due to low measured imbalance. 85: Average load imbalance: 2.6%. 85: The balanceable part of the MD step is 58%, load imbalance is computed from this. 85: Part of the total run time spent waiting due to load imbalance: 1.5%. 85: 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.097 0.049 197.0 85: (ns/day) (hour/ns) 85: Performance: 29.712 0.808 85: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_reference.edr as double precision energy file 85: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.edr as double precision energy file 85: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 85: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 85: setting nstcomm equal to nstcalcenergy for less overhead 85: 85: Number of degrees of freedom in T-Coupling group System is 33.00 85: 85: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 85: NVE simulation: will use the initial temperature of 68.810 K for 85: determining the Verlet buffer size 85: 85: 85: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 85: COM removal frequency is set to (5). 85: Other settings require a global communication frequency of 100. 85: Note that this will require additional global communication steps, 85: which will reduce performance when using multiple ranks. 85: Consider setting nstcomm to a multiple of 100. 85: 85: 85: There were 4 NOTEs 85: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 85: Can not increase nstlist because an NVE ensemble is used 85: Using 2 MPI threads 85: Using 1 OpenMP thread per tMPI thread 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'Argon' 85: 16 steps, 0.0 ps. 85: Generated 1 of the 1 non-bonded parameter combinations 85: 85: Excluding 1 bonded neighbours molecule type 'Argon' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: 85: Dynamic load balancing report: 85: DLB was off during the run due to low measured imbalance. 85: Average load imbalance: 2.2%. 85: The balanceable part of the MD step is 56%, load imbalance is computed from this. 85: Part of the total run time spent waiting due to load imbalance: 1.2%. 85: 85: 85: NOTE: 7 % of the run time was spent communicating energies, 85: you might want to increase some nst* mdp options 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.055 0.028 194.8 85: (ns/day) (hour/ns) 85: Performance: 51.564 0.465 85: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_reference.edr as double precision energy file 85: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.edr as double precision energy file 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 85: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 85: setting nstcomm equal to nstcalcenergy for less overhead 85: 85: Number of degrees of freedom in T-Coupling group System is 33.00 85: 85: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 85: NVE simulation: will use the initial temperature of 68.810 K for 85: determining the Verlet buffer size 85: 85: 85: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 85: COM removal frequency is set to (5). 85: Other settings require a global communication frequency of 100. 85: Note that this will require additional global communication steps, 85: which will reduce performance when using multiple ranks. 85: Consider setting nstcomm to a multiple of 100. 85: 85: 85: There were 4 NOTEs 85: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 85: Can not increase nstlist because an NVE ensemble is used 85: Using 2 MPI threads 85: Using 1 OpenMP thread per tMPI thread 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'Argon' 85: 16 steps, 0.0 ps. 85: Generated 1 of the 1 non-bonded parameter combinations 85: 85: Excluding 1 bonded neighbours molecule type 'Argon' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: 85: Dynamic load balancing report: 85: DLB was off during the run due to low measured imbalance. 85: Average load imbalance: 1.2%. 85: The balanceable part of the MD step is 5%, load imbalance is computed from this. 85: Part of the total run time spent waiting due to load imbalance: 0.1%. 85: 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.206 0.104 197.1 85: (ns/day) (hour/ns) 85: Performance: 14.069 1.706 85: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_reference.edr as double precision energy file 85: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.edr as double precision energy file 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 85: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 85: setting nstcomm equal to nstcalcenergy for less overhead 85: 85: Number of degrees of freedom in T-Coupling group System is 33.00 85: 85: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 85: NVE simulation: will use the initial temperature of 68.810 K for 85: determining the Verlet buffer size 85: 85: 85: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 85: COM removal frequency is set to (5). 85: Other settings require a global communication frequency of 100. 85: Note that this will require additional global communication steps, 85: which will reduce performance when using multiple ranks. 85: Consider setting nstcomm to a multiple of 100. 85: 85: 85: There were 4 NOTEs 85: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 85: Can not increase nstlist because an NVE ensemble is used 85: Using 2 MPI threads 85: Using 1 OpenMP thread per tMPI thread 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'Argon' 85: 16 steps, 0.0 ps. 85: Generated 1 of the 1 non-bonded parameter combinations 85: 85: Excluding 1 bonded neighbours molecule type 'Argon' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: 85: Dynamic load balancing report: 85: DLB was off during the run due to low measured imbalance. 85: Average load imbalance: 2.1%. 85: The balanceable part of the MD step is 21%, load imbalance is computed from this. 85: Part of the total run time spent waiting due to load imbalance: 0.4%. 85: 85: 85: NOTE: 14 % of the run time was spent communicating energies, 85: you might want to increase some nst* mdp options 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.149 0.083 180.6 85: (ns/day) (hour/ns) 85: Performance: 17.748 1.352 85: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_reference.edr as double precision energy file 85: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.edr as double precision energy file 85: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/16 (773 ms) 85: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/17 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 85: Setting nstcalcenergy (100) equal to nstenergy (1) 85: 85: 85: WARNING 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 85: The Berendsen barostat does not generate any strictly correct ensemble, 85: and should not be used for new production simulations (in our opinion). 85: We recommend using the C-rescale barostat instead. 85: 85: Number of degrees of freedom in T-Coupling group System is 33.00 85: 85: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 85: NVE simulation: will use the initial temperature of 68.810 K for 85: determining the Verlet buffer size 85: 85: 85: There were 3 NOTEs 85: 85: There was 1 WARNING 85: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 85: Can not increase nstlist because an NVE ensemble is used 85: Using 2 MPI threads 85: Using 1 OpenMP thread per tMPI thread 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'Argon' 85: 16 steps, 0.0 ps. 85: Generated 1 of the 1 non-bonded parameter combinations 85: 85: Excluding 1 bonded neighbours molecule type 'Argon' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: 85: Dynamic load balancing report: 85: DLB was turned on during the run due to measured imbalance. 85: Average load imbalance: 9.4%. 85: The balanceable part of the MD step is 56%, load imbalance is computed from this. 85: Part of the total run time spent waiting due to load imbalance: 5.3%. 85: Steps where the load balancing was limited by -rdd, -rcon and/or -dds: X 0 % 85: 85: NOTE: 5.3 % of the available CPU time was lost due to load imbalance 85: in the domain decomposition. 85: You can consider manually changing the decomposition (option -dd); 85: e.g. by using fewer domains along the box dimension in which there is 85: considerable inhomogeneity in the simulated system. 85: 85: NOTE: 7 % of the run time was spent communicating energies, 85: you might want to increase some nst* mdp options 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.097 0.051 191.1 85: (ns/day) (hour/ns) 85: Performance: 28.866 0.831 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 85: Setting nstcalcenergy (100) equal to nstenergy (1) 85: 85: 85: WARNING 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 85: The Berendsen barostat does not generate any strictly correct ensemble, 85: and should not be used for new production simulations (in our opinion). 85: We recommend using the C-rescale barostat instead. 85: 85: Number of degrees of freedom in T-Coupling group System is 33.00 85: 85: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 85: NVE simulation: will use the initial temperature of 68.810 K for 85: determining the Verlet buffer size 85: 85: 85: There were 3 NOTEs 85: 85: There was 1 WARNING 85: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 85: Can not increase nstlist because an NVE ensemble is used 85: Using 2 MPI threads 85: Using 1 OpenMP thread per tMPI thread 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'Argon' 85: 16 steps, 0.0 ps. 85: Generated 1 of the 1 non-bonded parameter combinations 85: 85: Excluding 1 bonded neighbours molecule type 'Argon' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: 85: Dynamic load balancing report: 85: DLB was off during the run due to low measured imbalance. 85: Average load imbalance: 2.3%. 85: The balanceable part of the MD step is 33%, load imbalance is computed from this. 85: Part of the total run time spent waiting due to load imbalance: 0.8%. 85: 85: 85: NOTE: 9 % of the run time was spent communicating energies, 85: you might want to increase some nst* mdp options 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.112 0.057 197.2 85: (ns/day) (hour/ns) 85: Performance: 25.930 0.926 85: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_reference.edr as double precision energy file 85: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.edr as double precision energy file 85: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 85: Setting nstcalcenergy (100) equal to nstenergy (4) 85: 85: 85: WARNING 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 85: The Berendsen barostat does not generate any strictly correct ensemble, 85: and should not be used for new production simulations (in our opinion). 85: We recommend using the C-rescale barostat instead. 85: 85: Number of degrees of freedom in T-Coupling group System is 33.00 85: 85: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 85: NVE simulation: will use the initial temperature of 68.810 K for 85: determining the Verlet buffer size 85: 85: 85: There were 3 NOTEs 85: 85: There was 1 WARNING 85: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 85: Can not increase nstlist because an NVE ensemble is used 85: Using 2 MPI threads 85: Using 1 OpenMP thread per tMPI thread 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'Argon' 85: 16 steps, 0.0 ps. 85: Generated 1 of the 1 non-bonded parameter combinations 85: 85: Excluding 1 bonded neighbours molecule type 'Argon' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: 85: Dynamic load balancing report: 85: DLB was off during the run due to low measured imbalance. 85: Average load imbalance: 1.8%. 85: The balanceable part of the MD step is 57%, load imbalance is computed from this. 85: Part of the total run time spent waiting due to load imbalance: 1.0%. 85: 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.101 0.052 196.5 85: (ns/day) (hour/ns) 85: Performance: 28.485 0.843 85: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_reference.edr as double precision energy file 85: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.edr as double precision energy file 85: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 85: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 85: setting nstcomm equal to nstcalcenergy for less overhead 85: 85: 85: WARNING 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 85: The Berendsen barostat does not generate any strictly correct ensemble, 85: and should not be used for new production simulations (in our opinion). 85: We recommend using the C-rescale barostat instead. 85: 85: Number of degrees of freedom in T-Coupling group System is 33.00 85: 85: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 85: NVE simulation: will use the initial temperature of 68.810 K for 85: determining the Verlet buffer size 85: 85: 85: There were 3 NOTEs 85: 85: There was 1 WARNING 85: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 85: Can not increase nstlist because an NVE ensemble is used 85: Using 2 MPI threads 85: Using 1 OpenMP thread per tMPI thread 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'Argon' 85: 16 steps, 0.0 ps. 85: Generated 1 of the 1 non-bonded parameter combinations 85: 85: Excluding 1 bonded neighbours molecule type 'Argon' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: 85: Dynamic load balancing report: 85: DLB was off during the run due to low measured imbalance. 85: Average load imbalance: 3.1%. 85: The balanceable part of the MD step is 50%, load imbalance is computed from this. 85: Part of the total run time spent waiting due to load imbalance: 1.6%. 85: 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.079 0.040 196.3 85: (ns/day) (hour/ns) 85: Performance: 36.323 0.661 85: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_reference.edr as double precision energy file 85: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.edr as double precision energy file 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 85: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 85: setting nstcomm equal to nstcalcenergy for less overhead 85: 85: 85: WARNING 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 85: The Berendsen barostat does not generate any strictly correct ensemble, 85: and should not be used for new production simulations (in our opinion). 85: We recommend using the C-rescale barostat instead. 85: 85: Number of degrees of freedom in T-Coupling group System is 33.00 85: 85: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 85: NVE simulation: will use the initial temperature of 68.810 K for 85: determining the Verlet buffer size 85: 85: 85: There were 3 NOTEs 85: 85: There was 1 WARNING 85: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 85: Can not increase nstlist because an NVE ensemble is used 85: Using 2 MPI threads 85: Using 1 OpenMP thread per tMPI thread 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'Argon' 85: 16 steps, 0.0 ps. 85: Generated 1 of the 1 non-bonded parameter combinations 85: 85: Excluding 1 bonded neighbours molecule type 'Argon' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: 85: Dynamic load balancing report: 85: DLB was off during the run due to low measured imbalance. 85: Average load imbalance: 1.1%. 85: The balanceable part of the MD step is 26%, load imbalance is computed from this. 85: Part of the total run time spent waiting due to load imbalance: 0.3%. 85: 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.118 0.060 196.6 85: (ns/day) (hour/ns) 85: Performance: 24.498 0.980 85: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_reference.edr as double precision energy file 85: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.edr as double precision energy file 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 85: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 85: setting nstcomm equal to nstcalcenergy for less overhead 85: 85: 85: WARNING 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 85: The Berendsen barostat does not generate any strictly correct ensemble, 85: and should not be used for new production simulations (in our opinion). 85: We recommend using the C-rescale barostat instead. 85: 85: Number of degrees of freedom in T-Coupling group System is 33.00 85: 85: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 85: NVE simulation: will use the initial temperature of 68.810 K for 85: determining the Verlet buffer size 85: 85: 85: There were 3 NOTEs 85: 85: There was 1 WARNING 85: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 85: Can not increase nstlist because an NVE ensemble is used 85: Using 2 MPI threads 85: Using 1 OpenMP thread per tMPI thread 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'Argon' 85: 16 steps, 0.0 ps. 85: Generated 1 of the 1 non-bonded parameter combinations 85: 85: Excluding 1 bonded neighbours molecule type 'Argon' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: 85: Dynamic load balancing report: 85: DLB was off during the run due to low measured imbalance. 85: Average load imbalance: 1.0%. 85: The balanceable part of the MD step is 56%, load imbalance is computed from this. 85: Part of the total run time spent waiting due to load imbalance: 0.6%. 85: 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.085 0.044 194.0 85: (ns/day) (hour/ns) 85: Performance: 33.484 0.717 85: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_reference.edr as double precision energy file 85: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.edr as double precision energy file 85: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/17 (816 ms) 85: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/18 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]: 85: Setting nstcalcenergy (100) equal to nstenergy (1) 85: 85: Number of degrees of freedom in T-Coupling group System is 33.00 85: 85: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]: 85: NVE simulation: will use the initial temperature of 68.810 K for 85: determining the Verlet buffer size 85: 85: 85: There were 3 NOTEs 85: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 85: Can not increase nstlist because an NVE ensemble is used 85: Using 2 MPI threads 85: Using 1 OpenMP thread per tMPI thread 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'Argon' 85: 16 steps, 0.0 ps. 85: Generated 1 of the 1 non-bonded parameter combinations 85: 85: Excluding 1 bonded neighbours molecule type 'Argon' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: 85: Dynamic load balancing report: 85: DLB was off during the run due to low measured imbalance. 85: Average load imbalance: 1.1%. 85: The balanceable part of the MD step is 27%, load imbalance is computed from this. 85: Part of the total run time spent waiting due to load imbalance: 0.3%. 85: 85: 85: NOTE: 9 % of the run time was spent communicating energies, 85: you might want to increase some nst* mdp options 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.097 0.049 197.6 85: (ns/day) (hour/ns) 85: Performance: 29.994 0.800 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]: 85: Setting nstcalcenergy (100) equal to nstenergy (1) 85: 85: Number of degrees of freedom in T-Coupling group System is 33.00 85: 85: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]: 85: NVE simulation: will use the initial temperature of 68.810 K for 85: determining the Verlet buffer size 85: 85: 85: There were 3 NOTEs 85: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 85: Can not increase nstlist because an NVE ensemble is used 85: Using 2 MPI threads 85: Using 1 OpenMP thread per tMPI thread 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'Argon' 85: 16 steps, 0.0 ps. 85: Generated 1 of the 1 non-bonded parameter combinations 85: 85: Excluding 1 bonded neighbours molecule type 'Argon' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: 85: Dynamic load balancing report: 85: DLB was off during the run due to low measured imbalance. 85: Average load imbalance: 1.9%. 85: The balanceable part of the MD step is 60%, load imbalance is computed from this. 85: Part of the total run time spent waiting due to load imbalance: 1.2%. 85: 85: 85: NOTE: 33 % of the run time was spent in domain decomposition, 85: 1 % of the run time was spent in pair search, 85: you might want to increase nstlist (this has no effect on accuracy) 85: 85: NOTE: 10 % of the run time was spent communicating energies, 85: you might want to increase some nst* mdp options 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.149 0.075 197.6 85: (ns/day) (hour/ns) 85: Performance: 19.533 1.229 85: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_reference.edr as double precision energy file 85: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18.edr as double precision energy file 85: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]: 85: Setting nstcalcenergy (100) equal to nstenergy (4) 85: 85: Number of degrees of freedom in T-Coupling group System is 33.00 85: 85: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]: 85: NVE simulation: will use the initial temperature of 68.810 K for 85: determining the Verlet buffer size 85: 85: 85: There were 3 NOTEs 85: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 85: Can not increase nstlist because an NVE ensemble is used 85: Using 2 MPI threads 85: Using 1 OpenMP thread per tMPI thread 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'Argon' 85: 16 steps, 0.0 ps. 85: Generated 1 of the 1 non-bonded parameter combinations 85: 85: Excluding 1 bonded neighbours molecule type 'Argon' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: 85: Dynamic load balancing report: 85: DLB was off during the run due to low measured imbalance. 85: Average load imbalance: 4.5%. 85: The balanceable part of the MD step is 25%, load imbalance is computed from this. 85: Part of the total run time spent waiting due to load imbalance: 1.2%. 85: 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.093 0.047 196.9 85: (ns/day) (hour/ns) 85: Performance: 31.259 0.768 85: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_reference.edr as double precision energy file 85: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18.edr as double precision energy file 85: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]: 85: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 85: setting nstcomm equal to nstcalcenergy for less overhead 85: 85: Number of degrees of freedom in T-Coupling group System is 33.00 85: 85: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]: 85: NVE simulation: will use the initial temperature of 68.810 K for 85: determining the Verlet buffer size 85: 85: 85: There were 3 NOTEs 85: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 85: Can not increase nstlist because an NVE ensemble is used 85: Using 2 MPI threads 85: Using 1 OpenMP thread per tMPI thread 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'Argon' 85: 16 steps, 0.0 ps. 85: Generated 1 of the 1 non-bonded parameter combinations 85: 85: Excluding 1 bonded neighbours molecule type 'Argon' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: 85: Dynamic load balancing report: 85: DLB was off during the run due to low measured imbalance. 85: Average load imbalance: 2.1%. 85: The balanceable part of the MD step is 53%, load imbalance is computed from this. 85: Part of the total run time spent waiting due to load imbalance: 1.1%. 85: 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.077 0.042 183.1 85: (ns/day) (hour/ns) 85: Performance: 34.909 0.688 85: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_reference.edr as double precision energy file 85: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18.edr as double precision energy file 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]: 85: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 85: setting nstcomm equal to nstcalcenergy for less overhead 85: 85: Number of degrees of freedom in T-Coupling group System is 33.00 85: 85: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]: 85: NVE simulation: will use the initial temperature of 68.810 K for 85: determining the Verlet buffer size 85: 85: 85: There were 3 NOTEs 85: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 85: Can not increase nstlist because an NVE ensemble is used 85: Using 2 MPI threads 85: Using 1 OpenMP thread per tMPI thread 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'Argon' 85: 16 steps, 0.0 ps. 85: Generated 1 of the 1 non-bonded parameter combinations 85: 85: Excluding 1 bonded neighbours molecule type 'Argon' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: 85: Dynamic load balancing report: 85: DLB was turned on during the run due to measured imbalance. 85: Average load imbalance: 6.3%. 85: The balanceable part of the MD step is 58%, load imbalance is computed from this. 85: Part of the total run time spent waiting due to load imbalance: 3.7%. 85: Steps where the load balancing was limited by -rdd, -rcon and/or -dds: X 0 % 85: 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.080 0.041 196.2 85: (ns/day) (hour/ns) 85: Performance: 35.982 0.667 85: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_reference.edr as double precision energy file 85: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18.edr as double precision energy file 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]: 85: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 85: setting nstcomm equal to nstcalcenergy for less overhead 85: 85: Number of degrees of freedom in T-Coupling group System is 33.00 85: 85: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]: 85: NVE simulation: will use the initial temperature of 68.810 K for 85: determining the Verlet buffer size 85: 85: 85: There were 3 NOTEs 85: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 85: Can not increase nstlist because an NVE ensemble is used 85: Using 2 MPI threads 85: Using 1 OpenMP thread per tMPI thread 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'Argon' 85: 16 steps, 0.0 ps. 85: Generated 1 of the 1 non-bonded parameter combinations 85: 85: Excluding 1 bonded neighbours molecule type 'Argon' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: 85: Dynamic load balancing report: 85: DLB was off during the run due to low measured imbalance. 85: Average load imbalance: 0.7%. 85: The balanceable part of the MD step is 47%, load imbalance is computed from this. 85: Part of the total run time spent waiting due to load imbalance: 0.3%. 85: 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.128 0.065 197.9 85: (ns/day) (hour/ns) 85: Performance: 22.741 1.055 85: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_reference.edr as double precision energy file 85: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18.edr as double precision energy file 85: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/18 (794 ms) 85: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/19 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_input.mdp]: 85: Setting nstcalcenergy (100) equal to nstenergy (1) 85: 85: Number of degrees of freedom in T-Coupling group System is 33.00 85: 85: There were 2 NOTEs 85: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 85: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 85: 85: Using 2 MPI threads 85: Using 1 OpenMP thread per tMPI thread 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'Argon' 85: 16 steps, 0.0 ps. 85: Generated 1 of the 1 non-bonded parameter combinations 85: 85: Excluding 1 bonded neighbours molecule type 'Argon' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.061 0.031 195.8 85: (ns/day) (hour/ns) 85: Performance: 46.796 0.513 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_input.mdp]: 85: Setting nstcalcenergy (100) equal to nstenergy (1) 85: 85: Number of degrees of freedom in T-Coupling group System is 33.00 85: 85: There were 2 NOTEs 85: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 85: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 85: 85: Using 2 MPI threads 85: Using 1 OpenMP thread per tMPI thread 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'Argon' 85: 16 steps, 0.0 ps. 85: Generated 1 of the 1 non-bonded parameter combinations 85: 85: Excluding 1 bonded neighbours molecule type 'Argon' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.131 0.066 197.7 85: (ns/day) (hour/ns) 85: Performance: 22.094 1.086 85: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_reference.edr as double precision energy file 85: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19.edr as double precision energy file 85: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_input.mdp]: 85: Setting nstcalcenergy (100) equal to nstenergy (4) 85: 85: Number of degrees of freedom in T-Coupling group System is 33.00 85: 85: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_input.mdp]: 85: COM removal frequency is set to (5). 85: Other settings require a global communication frequency of 2. 85: Note that this will require additional global communication steps, 85: which will reduce performance when using multiple ranks. 85: Consider setting nstcomm to a multiple of 2. 85: 85: 85: There were 3 NOTEs 85: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 85: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 85: 85: Using 2 MPI threads 85: Using 1 OpenMP thread per tMPI thread 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'Argon' 85: 16 steps, 0.0 ps. 85: Generated 1 of the 1 non-bonded parameter combinations 85: 85: Excluding 1 bonded neighbours molecule type 'Argon' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.065 0.033 194.6 85: (ns/day) (hour/ns) 85: Performance: 44.146 0.544 85: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_reference.edr as double precision energy file 85: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19.edr as double precision energy file 85: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_input.mdp]: 85: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 85: setting nstcomm equal to nstcalcenergy for less overhead 85: 85: Number of degrees of freedom in T-Coupling group System is 33.00 85: 85: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_input.mdp]: 85: COM removal frequency is set to (5). 85: Other settings require a global communication frequency of 2. 85: Note that this will require additional global communication steps, 85: which will reduce performance when using multiple ranks. 85: Consider setting nstcomm to a multiple of 2. 85: 85: 85: There were 3 NOTEs 85: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 85: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 85: 85: Using 2 MPI threads 85: Using 1 OpenMP thread per tMPI thread 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'Argon' 85: 16 steps, 0.0 ps. 85: Generated 1 of the 1 non-bonded parameter combinations 85: 85: Excluding 1 bonded neighbours molecule type 'Argon' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.099 0.050 196.7 85: (ns/day) (hour/ns) 85: Performance: 29.136 0.824 85: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_reference.edr as double precision energy file 85: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19.edr as double precision energy file 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_input.mdp]: 85: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 85: setting nstcomm equal to nstcalcenergy for less overhead 85: 85: Number of degrees of freedom in T-Coupling group System is 33.00 85: 85: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_input.mdp]: 85: COM removal frequency is set to (5). 85: Other settings require a global communication frequency of 2. 85: Note that this will require additional global communication steps, 85: which will reduce performance when using multiple ranks. 85: Consider setting nstcomm to a multiple of 2. 85: 85: 85: There were 3 NOTEs 85: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 85: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 85: 85: Using 2 MPI threads 85: Using 1 OpenMP thread per tMPI thread 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'Argon' 85: 16 steps, 0.0 ps. 85: Generated 1 of the 1 non-bonded parameter combinations 85: 85: Excluding 1 bonded neighbours molecule type 'Argon' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.094 0.051 185.5 85: (ns/day) (hour/ns) 85: Performance: 28.864 0.831 85: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_reference.edr as double precision energy file 85: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19.edr as double precision energy file 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_input.mdp]: 85: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 85: setting nstcomm equal to nstcalcenergy for less overhead 85: 85: Number of degrees of freedom in T-Coupling group System is 33.00 85: 85: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_input.mdp]: 85: COM removal frequency is set to (5). 85: Other settings require a global communication frequency of 2. 85: Note that this will require additional global communication steps, 85: which will reduce performance when using multiple ranks. 85: Consider setting nstcomm to a multiple of 2. 85: 85: 85: There were 3 NOTEs 85: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 85: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 85: 85: Using 2 MPI threads 85: Using 1 OpenMP thread per tMPI thread 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'Argon' 85: 16 steps, 0.0 ps. 85: Generated 1 of the 1 non-bonded parameter combinations 85: 85: Excluding 1 bonded neighbours molecule type 'Argon' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.052 0.027 193.6 85: (ns/day) (hour/ns) 85: Performance: 54.675 0.439 85: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_reference.edr as double precision energy file 85: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19.edr as double precision energy file 85: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/19 (750 ms) 85: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/20 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]: 85: Setting nstcalcenergy (100) equal to nstenergy (1) 85: 85: 85: WARNING 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]: 85: The Berendsen barostat does not generate any strictly correct ensemble, 85: and should not be used for new production simulations (in our opinion). 85: We recommend using the C-rescale barostat instead. 85: 85: Number of degrees of freedom in T-Coupling group System is 33.00 85: 85: There were 2 NOTEs 85: 85: There was 1 WARNING 85: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 85: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 85: 85: Using 2 MPI threads 85: Using 1 OpenMP thread per tMPI thread 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'Argon' 85: 16 steps, 0.0 ps. 85: Generated 1 of the 1 non-bonded parameter combinations 85: 85: Excluding 1 bonded neighbours molecule type 'Argon' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.086 0.044 196.8 85: (ns/day) (hour/ns) 85: Performance: 33.486 0.717 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]: 85: Setting nstcalcenergy (100) equal to nstenergy (1) 85: 85: 85: WARNING 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]: 85: The Berendsen barostat does not generate any strictly correct ensemble, 85: and should not be used for new production simulations (in our opinion). 85: We recommend using the C-rescale barostat instead. 85: 85: Number of degrees of freedom in T-Coupling group System is 33.00 85: 85: There were 2 NOTEs 85: 85: There was 1 WARNING 85: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 85: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 85: 85: Using 2 MPI threads 85: Using 1 OpenMP thread per tMPI thread 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'Argon' 85: 16 steps, 0.0 ps. 85: Generated 1 of the 1 non-bonded parameter combinations 85: 85: Excluding 1 bonded neighbours molecule type 'Argon' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.056 0.029 194.5 85: (ns/day) (hour/ns) 85: Performance: 51.306 0.468 85: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_reference.edr as double precision energy file 85: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20.edr as double precision energy file 85: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]: 85: Setting nstcalcenergy (100) equal to nstenergy (4) 85: 85: 85: WARNING 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]: 85: The Berendsen barostat does not generate any strictly correct ensemble, 85: and should not be used for new production simulations (in our opinion). 85: We recommend using the C-rescale barostat instead. 85: 85: Number of degrees of freedom in T-Coupling group System is 33.00 85: 85: There were 2 NOTEs 85: 85: There was 1 WARNING 85: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 85: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 85: 85: Using 2 MPI threads 85: Using 1 OpenMP thread per tMPI thread 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'Argon' 85: 16 steps, 0.0 ps. 85: Generated 1 of the 1 non-bonded parameter combinations 85: 85: Excluding 1 bonded neighbours molecule type 'Argon' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.041 0.021 193.3 85: (ns/day) (hour/ns) 85: Performance: 68.514 0.350 85: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_reference.edr as double precision energy file 85: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20.edr as double precision energy file 85: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]: 85: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 85: setting nstcomm equal to nstcalcenergy for less overhead 85: 85: 85: WARNING 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]: 85: The Berendsen barostat does not generate any strictly correct ensemble, 85: and should not be used for new production simulations (in our opinion). 85: We recommend using the C-rescale barostat instead. 85: 85: Number of degrees of freedom in T-Coupling group System is 33.00 85: 85: There were 2 NOTEs 85: 85: There was 1 WARNING 85: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 85: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 85: 85: Using 2 MPI threads 85: Using 1 OpenMP thread per tMPI thread 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'Argon' 85: 16 steps, 0.0 ps. 85: Generated 1 of the 1 non-bonded parameter combinations 85: 85: Excluding 1 bonded neighbours molecule type 'Argon' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.055 0.028 194.4 85: (ns/day) (hour/ns) 85: Performance: 51.601 0.465 85: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_reference.edr as double precision energy file 85: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20.edr as double precision energy file 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]: 85: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 85: setting nstcomm equal to nstcalcenergy for less overhead 85: 85: 85: WARNING 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]: 85: The Berendsen barostat does not generate any strictly correct ensemble, 85: and should not be used for new production simulations (in our opinion). 85: We recommend using the C-rescale barostat instead. 85: 85: Number of degrees of freedom in T-Coupling group System is 33.00 85: 85: There were 2 NOTEs 85: 85: There was 1 WARNING 85: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 85: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 85: 85: Using 2 MPI threads 85: Using 1 OpenMP thread per tMPI thread 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'Argon' 85: 16 steps, 0.0 ps. 85: Generated 1 of the 1 non-bonded parameter combinations 85: 85: Excluding 1 bonded neighbours molecule type 'Argon' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.049 0.025 194.4 85: (ns/day) (hour/ns) 85: Performance: 58.591 0.410 85: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_reference.edr as double precision energy file 85: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20.edr as double precision energy file 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]: 85: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 85: setting nstcomm equal to nstcalcenergy for less overhead 85: 85: 85: WARNING 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]: 85: The Berendsen barostat does not generate any strictly correct ensemble, 85: and should not be used for new production simulations (in our opinion). 85: We recommend using the C-rescale barostat instead. 85: 85: Number of degrees of freedom in T-Coupling group System is 33.00 85: 85: There were 2 NOTEs 85: 85: There was 1 WARNING 85: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 85: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 85: 85: Using 2 MPI threads 85: Using 1 OpenMP thread per tMPI thread 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'Argon' 85: 16 steps, 0.0 ps. 85: Generated 1 of the 1 non-bonded parameter combinations 85: 85: Excluding 1 bonded neighbours molecule type 'Argon' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.056 0.029 194.8 85: (ns/day) (hour/ns) 85: Performance: 51.316 0.468 85: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_reference.edr as double precision energy file 85: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20.edr as double precision energy file 85: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/20 (534 ms) 85: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/21 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_input.mdp]: 85: Setting nstcalcenergy (100) equal to nstenergy (1) 85: 85: Number of degrees of freedom in T-Coupling group System is 33.00 85: 85: There were 2 NOTEs 85: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 85: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 85: 85: Using 2 MPI threads 85: Using 1 OpenMP thread per tMPI thread 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'Argon' 85: 16 steps, 0.0 ps. 85: Generated 1 of the 1 non-bonded parameter combinations 85: 85: Excluding 1 bonded neighbours molecule type 'Argon' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: NOTE: 7 % of the run time was spent communicating energies, 85: you might want to increase some nst* mdp options 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.064 0.033 196.1 85: (ns/day) (hour/ns) 85: Performance: 44.953 0.534 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_input.mdp]: 85: Setting nstcalcenergy (100) equal to nstenergy (1) 85: 85: Number of degrees of freedom in T-Coupling group System is 33.00 85: 85: There were 2 NOTEs 85: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 85: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 85: 85: Using 2 MPI threads 85: Using 1 OpenMP thread per tMPI thread 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'Argon' 85: 16 steps, 0.0 ps. 85: Generated 1 of the 1 non-bonded parameter combinations 85: 85: Excluding 1 bonded neighbours molecule type 'Argon' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: NOTE: 9 % of the run time was spent communicating energies, 85: you might want to increase some nst* mdp options 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.065 0.033 194.7 85: (ns/day) (hour/ns) 85: Performance: 44.059 0.545 85: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_reference.edr as double precision energy file 85: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21.edr as double precision energy file 85: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_input.mdp]: 85: Setting nstcalcenergy (100) equal to nstenergy (4) 85: 85: Number of degrees of freedom in T-Coupling group System is 33.00 85: 85: There were 2 NOTEs 85: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 85: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 85: 85: Using 2 MPI threads 85: Using 1 OpenMP thread per tMPI thread 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'Argon' 85: 16 steps, 0.0 ps. 85: Generated 1 of the 1 non-bonded parameter combinations 85: 85: Excluding 1 bonded neighbours molecule type 'Argon' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: NOTE: 14 % of the run time was spent in domain decomposition, 85: 0 % of the run time was spent in pair search, 85: you might want to increase nstlist (this has no effect on accuracy) 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.064 0.033 194.3 85: (ns/day) (hour/ns) 85: Performance: 44.906 0.534 85: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_reference.edr as double precision energy file 85: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21.edr as double precision energy file 85: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_input.mdp]: 85: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 85: setting nstcomm equal to nstcalcenergy for less overhead 85: 85: Number of degrees of freedom in T-Coupling group System is 33.00 85: 85: There were 2 NOTEs 85: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 85: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 85: 85: Using 2 MPI threads 85: Using 1 OpenMP thread per tMPI thread 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'Argon' 85: 16 steps, 0.0 ps. 85: Generated 1 of the 1 non-bonded parameter combinations 85: 85: Excluding 1 bonded neighbours molecule type 'Argon' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.073 0.042 175.4 85: (ns/day) (hour/ns) 85: Performance: 35.056 0.685 85: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_reference.edr as double precision energy file 85: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21.edr as double precision energy file 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_input.mdp]: 85: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 85: setting nstcomm equal to nstcalcenergy for less overhead 85: 85: Number of degrees of freedom in T-Coupling group System is 33.00 85: 85: There were 2 NOTEs 85: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 85: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 85: 85: Using 2 MPI threads 85: Using 1 OpenMP thread per tMPI thread 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'Argon' 85: 16 steps, 0.0 ps. 85: Generated 1 of the 1 non-bonded parameter combinations 85: 85: Excluding 1 bonded neighbours molecule type 'Argon' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: NOTE: 5 % of the run time was spent communicating energies, 85: you might want to increase some nst* mdp options 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.055 0.034 162.3 85: (ns/day) (hour/ns) 85: Performance: 43.708 0.549 85: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_reference.edr as double precision energy file 85: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21.edr as double precision energy file 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_input.mdp]: 85: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 85: setting nstcomm equal to nstcalcenergy for less overhead 85: 85: Number of degrees of freedom in T-Coupling group System is 33.00 85: 85: There were 2 NOTEs 85: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 85: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 85: 85: Using 2 MPI threads 85: Using 1 OpenMP thread per tMPI thread 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'Argon' 85: 16 steps, 0.0 ps. 85: Generated 1 of the 1 non-bonded parameter combinations 85: 85: Excluding 1 bonded neighbours molecule type 'Argon' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.059 0.030 194.5 85: (ns/day) (hour/ns) 85: Performance: 48.746 0.492 85: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_reference.edr as double precision energy file 85: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21.edr as double precision energy file 85: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/21 (512 ms) 85: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/22 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_input.mdp]: 85: Setting nstcalcenergy (100) equal to nstenergy (1) 85: 85: Number of degrees of freedom in T-Coupling group System is 33.00 85: 85: There were 2 NOTEs 85: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 85: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 85: 85: Using 2 MPI threads 85: Using 1 OpenMP thread per tMPI thread 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'Argon' 85: 16 steps, 0.0 ps. 85: Generated 1 of the 1 non-bonded parameter combinations 85: 85: Excluding 1 bonded neighbours molecule type 'Argon' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.081 0.042 192.1 85: (ns/day) (hour/ns) 85: Performance: 34.666 0.692 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_input.mdp]: 85: Setting nstcalcenergy (100) equal to nstenergy (1) 85: 85: Number of degrees of freedom in T-Coupling group System is 33.00 85: 85: There were 2 NOTEs 85: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 85: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 85: 85: Using 2 MPI threads 85: Using 1 OpenMP thread per tMPI thread 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'Argon' 85: 16 steps, 0.0 ps. 85: Generated 1 of the 1 non-bonded parameter combinations 85: 85: Excluding 1 bonded neighbours molecule type 'Argon' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.062 0.037 168.0 85: (ns/day) (hour/ns) 85: Performance: 39.944 0.601 85: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_reference.edr as double precision energy file 85: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22.edr as double precision energy file 85: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_input.mdp]: 85: Setting nstcalcenergy (100) equal to nstenergy (4) 85: 85: Number of degrees of freedom in T-Coupling group System is 33.00 85: 85: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_input.mdp]: 85: COM removal frequency is set to (5). 85: Other settings require a global communication frequency of 2. 85: Note that this will require additional global communication steps, 85: which will reduce performance when using multiple ranks. 85: Consider setting nstcomm to a multiple of 2. 85: 85: 85: There were 3 NOTEs 85: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 85: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 85: 85: Using 2 MPI threads 85: Using 1 OpenMP thread per tMPI thread 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'Argon' 85: 16 steps, 0.0 ps. 85: Generated 1 of the 1 non-bonded parameter combinations 85: 85: Excluding 1 bonded neighbours molecule type 'Argon' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.048 0.025 194.0 85: (ns/day) (hour/ns) 85: Performance: 58.817 0.408 85: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_reference.edr as double precision energy file 85: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22.edr as double precision energy file 85: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_input.mdp]: 85: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 85: setting nstcomm equal to nstcalcenergy for less overhead 85: 85: Number of degrees of freedom in T-Coupling group System is 33.00 85: 85: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_input.mdp]: 85: COM removal frequency is set to (5). 85: Other settings require a global communication frequency of 2. 85: Note that this will require additional global communication steps, 85: which will reduce performance when using multiple ranks. 85: Consider setting nstcomm to a multiple of 2. 85: 85: 85: There were 3 NOTEs 85: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 85: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 85: 85: Using 2 MPI threads 85: Using 1 OpenMP thread per tMPI thread 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'Argon' 85: 16 steps, 0.0 ps. 85: Generated 1 of the 1 non-bonded parameter combinations 85: 85: Excluding 1 bonded neighbours molecule type 'Argon' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.060 0.031 195.1 85: (ns/day) (hour/ns) 85: Performance: 48.052 0.499 85: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_reference.edr as double precision energy file 85: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22.edr as double precision energy file 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_input.mdp]: 85: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 85: setting nstcomm equal to nstcalcenergy for less overhead 85: 85: Number of degrees of freedom in T-Coupling group System is 33.00 85: 85: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_input.mdp]: 85: COM removal frequency is set to (5). 85: Other settings require a global communication frequency of 2. 85: Note that this will require additional global communication steps, 85: which will reduce performance when using multiple ranks. 85: Consider setting nstcomm to a multiple of 2. 85: 85: 85: There were 3 NOTEs 85: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 85: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 85: 85: Using 2 MPI threads 85: Using 1 OpenMP thread per tMPI thread 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'Argon' 85: 16 steps, 0.0 ps. 85: Generated 1 of the 1 non-bonded parameter combinations 85: 85: Excluding 1 bonded neighbours molecule type 'Argon' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.055 0.035 157.5 85: (ns/day) (hour/ns) 85: Performance: 42.003 0.571 85: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_reference.edr as double precision energy file 85: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22.edr as double precision energy file 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_input.mdp]: 85: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 85: setting nstcomm equal to nstcalcenergy for less overhead 85: 85: Number of degrees of freedom in T-Coupling group System is 33.00 85: 85: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_input.mdp]: 85: COM removal frequency is set to (5). 85: Other settings require a global communication frequency of 2. 85: Note that this will require additional global communication steps, 85: which will reduce performance when using multiple ranks. 85: Consider setting nstcomm to a multiple of 2. 85: 85: 85: There were 3 NOTEs 85: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 85: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 85: 85: Using 2 MPI threads 85: Using 1 OpenMP thread per tMPI thread 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'Argon' 85: 16 steps, 0.0 ps. 85: Generated 1 of the 1 non-bonded parameter combinations 85: 85: Excluding 1 bonded neighbours molecule type 'Argon' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.072 0.037 195.3 85: (ns/day) (hour/ns) 85: Performance: 39.965 0.601 85: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_reference.edr as double precision energy file 85: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22.edr as double precision energy file 85: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/22 (522 ms) 85: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/23 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 85: Setting nstcalcenergy (100) equal to nstenergy (1) 85: 85: 85: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 85: MTTK coupling is deprecated and will soon be removed 85: 85: 85: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 85: for current Trotter decomposition methods with vv, nsttcouple and 85: nstpcouple must be equal. Both have been reset to 85: min(nsttcouple,nstpcouple) = 2 85: 85: Number of degrees of freedom in T-Coupling group System is 33.00 85: 85: There were 4 NOTEs 85: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 85: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 85: 85: Using 2 MPI threads 85: Using 1 OpenMP thread per tMPI thread 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'Argon' 85: 16 steps, 0.0 ps. 85: Generated 1 of the 1 non-bonded parameter combinations 85: 85: Excluding 1 bonded neighbours molecule type 'Argon' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: NOTE: 7 % of the run time was spent communicating energies, 85: you might want to increase some nst* mdp options 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.069 0.041 168.5 85: (ns/day) (hour/ns) 85: Performance: 35.879 0.669 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 85: Setting nstcalcenergy (100) equal to nstenergy (1) 85: 85: 85: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 85: MTTK coupling is deprecated and will soon be removed 85: 85: 85: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 85: for current Trotter decomposition methods with vv, nsttcouple and 85: nstpcouple must be equal. Both have been reset to 85: min(nsttcouple,nstpcouple) = 2 85: 85: Number of degrees of freedom in T-Coupling group System is 33.00 85: 85: There were 4 NOTEs 85: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 85: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 85: 85: Using 2 MPI threads 85: Using 1 OpenMP thread per tMPI thread 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'Argon' 85: 16 steps, 0.0 ps. 85: Generated 1 of the 1 non-bonded parameter combinations 85: 85: Excluding 1 bonded neighbours molecule type 'Argon' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: NOTE: 7 % of the run time was spent communicating energies, 85: you might want to increase some nst* mdp options 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.070 0.036 195.0 85: (ns/day) (hour/ns) 85: Performance: 41.030 0.585 85: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_reference.edr as double precision energy file 85: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23.edr as double precision energy file 85: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 85: Setting nstcalcenergy (100) equal to nstenergy (4) 85: 85: 85: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 85: MTTK coupling is deprecated and will soon be removed 85: 85: 85: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 85: for current Trotter decomposition methods with vv, nsttcouple and 85: nstpcouple must be equal. Both have been reset to 85: min(nsttcouple,nstpcouple) = 2 85: 85: Number of degrees of freedom in T-Coupling group System is 33.00 85: 85: NOTE 5 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 85: COM removal frequency is set to (5). 85: Other settings require a global communication frequency of 2. 85: Note that this will require additional global communication steps, 85: which will reduce performance when using multiple ranks. 85: Consider setting nstcomm to a multiple of 2. 85: 85: 85: There were 5 NOTEs 85: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 85: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 85: 85: Using 2 MPI threads 85: Using 1 OpenMP thread per tMPI thread 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'Argon' 85: 16 steps, 0.0 ps. 85: Generated 1 of the 1 non-bonded parameter combinations 85: 85: Excluding 1 bonded neighbours molecule type 'Argon' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.065 0.033 194.6 85: (ns/day) (hour/ns) 85: Performance: 43.863 0.547 85: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_reference.edr as double precision energy file 85: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23.edr as double precision energy file 85: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 85: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 85: setting nstcomm equal to nstcalcenergy for less overhead 85: 85: 85: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 85: MTTK coupling is deprecated and will soon be removed 85: 85: 85: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 85: for current Trotter decomposition methods with vv, nsttcouple and 85: nstpcouple must be equal. Both have been reset to 85: min(nsttcouple,nstpcouple) = 2 85: 85: Number of degrees of freedom in T-Coupling group System is 33.00 85: 85: NOTE 5 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 85: COM removal frequency is set to (5). 85: Other settings require a global communication frequency of 2. 85: Note that this will require additional global communication steps, 85: which will reduce performance when using multiple ranks. 85: Consider setting nstcomm to a multiple of 2. 85: 85: 85: There were 5 NOTEs 85: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 85: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 85: 85: Using 2 MPI threads 85: Using 1 OpenMP thread per tMPI thread 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'Argon' 85: 16 steps, 0.0 ps. 85: Generated 1 of the 1 non-bonded parameter combinations 85: 85: Excluding 1 bonded neighbours molecule type 'Argon' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.080 0.041 195.7 85: (ns/day) (hour/ns) 85: Performance: 35.809 0.670 85: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_reference.edr as double precision energy file 85: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23.edr as double precision energy file 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 85: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 85: setting nstcomm equal to nstcalcenergy for less overhead 85: 85: 85: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 85: MTTK coupling is deprecated and will soon be removed 85: 85: 85: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 85: for current Trotter decomposition methods with vv, nsttcouple and 85: nstpcouple must be equal. Both have been reset to 85: min(nsttcouple,nstpcouple) = 2 85: 85: Number of degrees of freedom in T-Coupling group System is 33.00 85: 85: NOTE 5 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 85: COM removal frequency is set to (5). 85: Other settings require a global communication frequency of 2. 85: Note that this will require additional global communication steps, 85: which will reduce performance when using multiple ranks. 85: Consider setting nstcomm to a multiple of 2. 85: 85: 85: There were 5 NOTEs 85: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 85: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 85: 85: Using 2 MPI threads 85: Using 1 OpenMP thread per tMPI thread 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'Argon' 85: 16 steps, 0.0 ps. 85: Generated 1 of the 1 non-bonded parameter combinations 85: 85: Excluding 1 bonded neighbours molecule type 'Argon' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.061 0.031 194.9 85: (ns/day) (hour/ns) 85: Performance: 46.878 0.512 85: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_reference.edr as double precision energy file 85: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23.edr as double precision energy file 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 85: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 85: setting nstcomm equal to nstcalcenergy for less overhead 85: 85: 85: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 85: MTTK coupling is deprecated and will soon be removed 85: 85: 85: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 85: for current Trotter decomposition methods with vv, nsttcouple and 85: nstpcouple must be equal. Both have been reset to 85: min(nsttcouple,nstpcouple) = 2 85: 85: Number of degrees of freedom in T-Coupling group System is 33.00 85: 85: NOTE 5 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 85: COM removal frequency is set to (5). 85: Other settings require a global communication frequency of 2. 85: Note that this will require additional global communication steps, 85: which will reduce performance when using multiple ranks. 85: Consider setting nstcomm to a multiple of 2. 85: 85: 85: There were 5 NOTEs 85: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 85: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 85: 85: Using 2 MPI threads 85: Using 1 OpenMP thread per tMPI thread 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'Argon' 85: 16 steps, 0.0 ps. 85: Generated 1 of the 1 non-bonded parameter combinations 85: 85: Excluding 1 bonded neighbours molecule type 'Argon' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.064 0.033 194.2 85: (ns/day) (hour/ns) 85: Performance: 44.352 0.541 85: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_reference.edr as double precision energy file 85: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23.edr as double precision energy file 85: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/23 (536 ms) 85: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/24 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24_input.mdp]: 85: Setting nstcalcenergy (100) equal to nstenergy (1) 85: 85: Number of degrees of freedom in T-Coupling group System is 33.00 85: 85: There were 2 NOTEs 85: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 85: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 85: 85: Using 2 MPI threads 85: Using 1 OpenMP thread per tMPI thread 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'Argon' 85: 16 steps, 0.0 ps. 85: Generated 1 of the 1 non-bonded parameter combinations 85: 85: Excluding 1 bonded neighbours molecule type 'Argon' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.082 0.042 196.3 85: (ns/day) (hour/ns) 85: Performance: 35.105 0.684 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24_input.mdp]: 85: Setting nstcalcenergy (100) equal to nstenergy (1) 85: 85: Number of degrees of freedom in T-Coupling group System is 33.00 85: 85: There were 2 NOTEs 85: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 85: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 85: 85: Using 2 MPI threads 85: Using 1 OpenMP thread per tMPI thread 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'Argon' 85: 16 steps, 0.0 ps. 85: Generated 1 of the 1 non-bonded parameter combinations 85: 85: Excluding 1 bonded neighbours molecule type 'Argon' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: NOTE: 10 % of the run time was spent communicating energies, 85: you might want to increase some nst* mdp options 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.072 0.037 195.1 85: (ns/day) (hour/ns) 85: Performance: 39.690 0.605 85: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24_reference.edr as double precision energy file 85: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24.edr as double precision energy file 85: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24_input.mdp]: 85: Setting nstcalcenergy (100) equal to nstenergy (4) 85: 85: Number of degrees of freedom in T-Coupling group System is 33.00 85: 85: There were 2 NOTEs 85: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 85: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 85: 85: Using 2 MPI threads 85: Using 1 OpenMP thread per tMPI thread 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'Argon' 85: 16 steps, 0.0 ps. 85: Generated 1 of the 1 non-bonded parameter combinations 85: 85: Excluding 1 bonded neighbours molecule type 'Argon' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.047 0.024 193.6 85: (ns/day) (hour/ns) 85: Performance: 60.650 0.396 85: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24_reference.edr as double precision energy file 85: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24.edr as double precision energy file 85: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24_input.mdp]: 85: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 85: setting nstcomm equal to nstcalcenergy for less overhead 85: 85: Number of degrees of freedom in T-Coupling group System is 33.00 85: 85: There were 2 NOTEs 85: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 85: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 85: 85: Using 2 MPI threads 85: Using 1 OpenMP thread per tMPI thread 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'Argon' 85: 16 steps, 0.0 ps. 85: Generated 1 of the 1 non-bonded parameter combinations 85: 85: Excluding 1 bonded neighbours molecule type 'Argon' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: NOTE: 7 % of the run time was spent communicating energies, 85: you might want to increase some nst* mdp options 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.058 0.030 194.5 85: (ns/day) (hour/ns) 85: Performance: 49.643 0.483 85: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24_reference.edr as double precision energy file 85: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24.edr as double precision energy file 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24_input.mdp]: 85: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 85: setting nstcomm equal to nstcalcenergy for less overhead 85: 85: Number of degrees of freedom in T-Coupling group System is 33.00 85: 85: There were 2 NOTEs 85: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 85: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 85: 85: Using 2 MPI threads 85: Using 1 OpenMP thread per tMPI thread 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'Argon' 85: 16 steps, 0.0 ps. 85: Generated 1 of the 1 non-bonded parameter combinations 85: 85: Excluding 1 bonded neighbours molecule type 'Argon' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: NOTE: 8 % of the run time was spent communicating energies, 85: you might want to increase some nst* mdp options 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.074 0.038 194.9 85: (ns/day) (hour/ns) 85: Performance: 38.719 0.620 85: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24_reference.edr as double precision energy file 85: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24.edr as double precision energy file 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24_input.mdp]: 85: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 85: setting nstcomm equal to nstcalcenergy for less overhead 85: 85: Number of degrees of freedom in T-Coupling group System is 33.00 85: 85: There were 2 NOTEs 85: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 85: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 85: 85: Using 2 MPI threads 85: Using 1 OpenMP thread per tMPI thread 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'Argon' 85: 16 steps, 0.0 ps. 85: Generated 1 of the 1 non-bonded parameter combinations 85: 85: Excluding 1 bonded neighbours molecule type 'Argon' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.063 0.035 179.2 85: (ns/day) (hour/ns) 85: Performance: 41.696 0.576 85: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24_reference.edr as double precision energy file 85: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24.edr as double precision energy file 85: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/24 (516 ms) 85: [----------] 25 tests from PropagatorsWithCoupling/PeriodicActionsTest (20286 ms total) 85: 85: [----------] Global test environment tear-down 85: [==========] 25 tests from 1 test suite ran. (20355 ms total) 85: [ PASSED ] 25 tests. 85/92 Test #85: MdrunCoordinationCouplingTests2Ranks ...... Passed 20.52 sec test 86 Start 86: MdrunCoordinationConstraintsTests1Rank 86: Test command: /build/reproducible-path/gromacs-2025.1/build/basic-dp/bin/mdrun-coordination-constraints-test "-ntmpi" "1" "--gtest_output=xml:/build/reproducible-path/gromacs-2025.1/build/basic-dp/Testing/Temporary/MdrunCoordinationConstraintsTests1Rank.xml" 86: Working Directory: /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests 86: Test timeout computed to be: 1920 86: [==========] Running 13 tests from 1 test suite. 86: [----------] Global test environment set-up. 86: [----------] 13 tests from PropagatorsWithConstraints/PeriodicActionsTest 86: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/0 86: 86: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 86: that with the Verlet scheme, nstlist has no effect on the accuracy of 86: your simulation. 86: 86: 86: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 86: Setting nstcalcenergy (100) equal to nstenergy (1) 86: 86: Generating 1-4 interactions: fudge = 0.5 86: Number of degrees of freedom in T-Coupling group System is 27.00 86: 86: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 86: NVE simulation: will use the initial temperature of 398.997 K for 86: determining the Verlet buffer size 86: 86: 86: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 86: You are using a plain Coulomb cut-off, which might produce artifacts. 86: You might want to consider using PME electrostatics. 86: 86: 86: 86: There were 4 NOTEs 86: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 86: Can not increase nstlist because an NVE ensemble is used 86: Using 1 MPI thread 86: Using 1 OpenMP thread 86: 86: 86: NOTE: Thread affinity was not set. 86: starting mdrun 'spc2' 86: 16 steps, 0.0 ps. 86: Generated 330891 of the 330891 non-bonded parameter combinations 86: 86: Generated 330891 of the 330891 1-4 parameter combinations 86: 86: Excluding 2 bonded neighbours molecule type 'SOL' 86: 86: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/tip3p5.gro' 86: 86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 86: 86: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 86: 86: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 86: 86: Note that mdrun will redetermine rlist based on the actual pair-list setup 86: 86: This run will generate roughly 0 Mb of data 86: 86: Writing final coordinates. 86: 86: Core t (s) Wall t (s) (%) 86: Time: 0.023 0.023 98.5 86: (ns/day) (hour/ns) 86: Performance: 63.267 0.379 86: 86: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 86: that with the Verlet scheme, nstlist has no effect on the accuracy of 86: your simulation. 86: 86: 86: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 86: Setting nstcalcenergy (100) equal to nstenergy (1) 86: 86: Generating 1-4 interactions: fudge = 0.5 86: Number of degrees of freedom in T-Coupling group System is 27.00 86: 86: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 86: NVE simulation: will use the initial temperature of 398.997 K for 86: determining the Verlet buffer size 86: 86: 86: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 86: You are using a plain Coulomb cut-off, which might produce artifacts. 86: You might want to consider using PME electrostatics. 86: 86: 86: 86: There were 4 NOTEs 86: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 86: Can not increase nstlist because an NVE ensemble is used 86: Using 1 MPI thread 86: Using 1 OpenMP thread 86: 86: 86: NOTE: Thread affinity was not set. 86: starting mdrun 'spc2' 86: 16 steps, 0.0 ps. 86: Generated 330891 of the 330891 non-bonded parameter combinations 86: 86: Generated 330891 of the 330891 1-4 parameter combinations 86: 86: Excluding 2 bonded neighbours molecule type 'SOL' 86: 86: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/tip3p5.gro' 86: 86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 86: 86: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 86: 86: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 86: 86: Note that mdrun will redetermine rlist based on the actual pair-list setup 86: 86: This run will generate roughly 0 Mb of data 86: 86: Writing final coordinates. 86: 86: Core t (s) Wall t (s) (%) 86: Time: 0.020 0.020 98.6 86: (ns/day) (hour/ns) 86: Performance: 73.056 0.329 86: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as double precision energy file 86: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as double precision energy file 86: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 86: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 86: that with the Verlet scheme, nstlist has no effect on the accuracy of 86: your simulation. 86: 86: 86: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 86: Setting nstcalcenergy (100) equal to nstenergy (4) 86: 86: Generating 1-4 interactions: fudge = 0.5 86: Number of degrees of freedom in T-Coupling group System is 27.00 86: 86: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 86: NVE simulation: will use the initial temperature of 398.997 K for 86: determining the Verlet buffer size 86: 86: 86: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 86: You are using a plain Coulomb cut-off, which might produce artifacts. 86: You might want to consider using PME electrostatics. 86: 86: 86: 86: NOTE 5 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 86: COM removal frequency is set to (5). 86: Other settings require a global communication frequency of 4. 86: Note that this will require additional global communication steps, 86: which will reduce performance when using multiple ranks. 86: Consider setting nstcomm to a multiple of 4. 86: 86: 86: There were 5 NOTEs 86: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 86: Can not increase nstlist because an NVE ensemble is used 86: Using 1 MPI thread 86: Using 1 OpenMP thread 86: 86: 86: NOTE: Thread affinity was not set. 86: starting mdrun 'spc2' 86: 16 steps, 0.0 ps. 86: Generated 330891 of the 330891 non-bonded parameter combinations 86: 86: Generated 330891 of the 330891 1-4 parameter combinations 86: 86: Excluding 2 bonded neighbours molecule type 'SOL' 86: 86: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/tip3p5.gro' 86: 86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 86: 86: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 86: 86: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 86: 86: Note that mdrun will redetermine rlist based on the actual pair-list setup 86: 86: This run will generate roughly 0 Mb of data 86: 86: Writing final coordinates. 86: 86: Core t (s) Wall t (s) (%) 86: Time: 0.024 0.024 98.8 86: (ns/day) (hour/ns) 86: Performance: 61.554 0.390 86: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as double precision energy file 86: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as double precision energy file 86: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 86: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 86: that with the Verlet scheme, nstlist has no effect on the accuracy of 86: your simulation. 86: 86: 86: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 86: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 86: setting nstcomm equal to nstcalcenergy for less overhead 86: 86: Generating 1-4 interactions: fudge = 0.5 86: Number of degrees of freedom in T-Coupling group System is 27.00 86: 86: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 86: NVE simulation: will use the initial temperature of 398.997 K for 86: determining the Verlet buffer size 86: 86: 86: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 86: You are using a plain Coulomb cut-off, which might produce artifacts. 86: You might want to consider using PME electrostatics. 86: 86: 86: 86: NOTE 5 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 86: COM removal frequency is set to (5). 86: Other settings require a global communication frequency of 100. 86: Note that this will require additional global communication steps, 86: which will reduce performance when using multiple ranks. 86: Consider setting nstcomm to a multiple of 100. 86: 86: 86: There were 5 NOTEs 86: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 86: Can not increase nstlist because an NVE ensemble is used 86: Using 1 MPI thread 86: Using 1 OpenMP thread 86: 86: 86: NOTE: Thread affinity was not set. 86: starting mdrun 'spc2' 86: 16 steps, 0.0 ps. 86: Generated 330891 of the 330891 non-bonded parameter combinations 86: 86: Generated 330891 of the 330891 1-4 parameter combinations 86: 86: Excluding 2 bonded neighbours molecule type 'SOL' 86: 86: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/tip3p5.gro' 86: 86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 86: 86: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 86: 86: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 86: 86: Note that mdrun will redetermine rlist based on the actual pair-list setup 86: 86: This run will generate roughly 0 Mb of data 86: 86: Writing final coordinates. 86: 86: Core t (s) Wall t (s) (%) 86: Time: 0.023 0.024 98.8 86: (ns/day) (hour/ns) 86: Performance: 62.245 0.386 86: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as double precision energy file 86: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as double precision energy file 86: 86: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 86: that with the Verlet scheme, nstlist has no effect on the accuracy of 86: your simulation. 86: 86: 86: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 86: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 86: setting nstcomm equal to nstcalcenergy for less overhead 86: 86: Generating 1-4 interactions: fudge = 0.5 86: Number of degrees of freedom in T-Coupling group System is 27.00 86: 86: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 86: NVE simulation: will use the initial temperature of 398.997 K for 86: determining the Verlet buffer size 86: 86: 86: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 86: You are using a plain Coulomb cut-off, which might produce artifacts. 86: You might want to consider using PME electrostatics. 86: 86: 86: 86: NOTE 5 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 86: COM removal frequency is set to (5). 86: Other settings require a global communication frequency of 100. 86: Note that this will require additional global communication steps, 86: which will reduce performance when using multiple ranks. 86: Consider setting nstcomm to a multiple of 100. 86: 86: 86: There were 5 NOTEs 86: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 86: Can not increase nstlist because an NVE ensemble is used 86: Using 1 MPI thread 86: Using 1 OpenMP thread 86: 86: 86: NOTE: Thread affinity was not set. 86: starting mdrun 'spc2' 86: 16 steps, 0.0 ps. 86: Generated 330891 of the 330891 non-bonded parameter combinations 86: 86: Generated 330891 of the 330891 1-4 parameter combinations 86: 86: Excluding 2 bonded neighbours molecule type 'SOL' 86: 86: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/tip3p5.gro' 86: 86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 86: 86: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 86: 86: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 86: 86: Note that mdrun will redetermine rlist based on the actual pair-list setup 86: 86: This run will generate roughly 0 Mb of data 86: 86: Writing final coordinates. 86: 86: Core t (s) Wall t (s) (%) 86: Time: 0.022 0.022 98.6 86: (ns/day) (hour/ns) 86: Performance: 66.216 0.362 86: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as double precision energy file 86: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as double precision energy file 86: 86: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 86: that with the Verlet scheme, nstlist has no effect on the accuracy of 86: your simulation. 86: 86: 86: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 86: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 86: setting nstcomm equal to nstcalcenergy for less overhead 86: 86: Generating 1-4 interactions: fudge = 0.5 86: Number of degrees of freedom in T-Coupling group System is 27.00 86: 86: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 86: NVE simulation: will use the initial temperature of 398.997 K for 86: determining the Verlet buffer size 86: 86: 86: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 86: You are using a plain Coulomb cut-off, which might produce artifacts. 86: You might want to consider using PME electrostatics. 86: 86: 86: 86: NOTE 5 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 86: COM removal frequency is set to (5). 86: Other settings require a global communication frequency of 100. 86: Note that this will require additional global communication steps, 86: which will reduce performance when using multiple ranks. 86: Consider setting nstcomm to a multiple of 100. 86: 86: 86: There were 5 NOTEs 86: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 86: Can not increase nstlist because an NVE ensemble is used 86: Using 1 MPI thread 86: Using 1 OpenMP thread 86: 86: 86: NOTE: Thread affinity was not set. 86: starting mdrun 'spc2' 86: 16 steps, 0.0 ps. 86: Generated 330891 of the 330891 non-bonded parameter combinations 86: 86: Generated 330891 of the 330891 1-4 parameter combinations 86: 86: Excluding 2 bonded neighbours molecule type 'SOL' 86: 86: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/tip3p5.gro' 86: 86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 86: 86: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 86: 86: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 86: 86: Note that mdrun will redetermine rlist based on the actual pair-list setup 86: 86: This run will generate roughly 0 Mb of data 86: 86: Writing final coordinates. 86: 86: Core t (s) Wall t (s) (%) 86: Time: 0.023 0.023 98.8 86: (ns/day) (hour/ns) 86: Performance: 63.259 0.379 86: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as double precision energy file 86: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as double precision energy file 86: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/0 (35892 ms) 86: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/1 86: 86: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 86: that with the Verlet scheme, nstlist has no effect on the accuracy of 86: your simulation. 86: 86: 86: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 86: Setting nstcalcenergy (100) equal to nstenergy (1) 86: 86: Generating 1-4 interactions: fudge = 0.5 86: Number of degrees of freedom in T-Coupling group System is 27.00 86: 86: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 86: NVE simulation: will use the initial temperature of 398.997 K for 86: determining the Verlet buffer size 86: 86: 86: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 86: You are using a plain Coulomb cut-off, which might produce artifacts. 86: You might want to consider using PME electrostatics. 86: 86: 86: 86: There were 4 NOTEs 86: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 86: Can not increase nstlist because an NVE ensemble is used 86: Using 1 MPI thread 86: Using 1 OpenMP thread 86: 86: 86: NOTE: Thread affinity was not set. 86: starting mdrun 'spc2' 86: 16 steps, 0.0 ps. 86: Generated 330891 of the 330891 non-bonded parameter combinations 86: 86: Generated 330891 of the 330891 1-4 parameter combinations 86: 86: Excluding 2 bonded neighbours molecule type 'SOL' 86: 86: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/tip3p5.gro' 86: 86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 86: 86: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 86: 86: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 86: 86: Note that mdrun will redetermine rlist based on the actual pair-list setup 86: 86: This run will generate roughly 0 Mb of data 86: 86: Writing final coordinates. 86: 86: Core t (s) Wall t (s) (%) 86: Time: 0.048 0.049 99.4 86: (ns/day) (hour/ns) 86: Performance: 30.212 0.794 86: 86: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 86: that with the Verlet scheme, nstlist has no effect on the accuracy of 86: your simulation. 86: 86: 86: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 86: Setting nstcalcenergy (100) equal to nstenergy (1) 86: 86: Generating 1-4 interactions: fudge = 0.5 86: Number of degrees of freedom in T-Coupling group System is 27.00 86: 86: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 86: NVE simulation: will use the initial temperature of 398.997 K for 86: determining the Verlet buffer size 86: 86: 86: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 86: You are using a plain Coulomb cut-off, which might produce artifacts. 86: You might want to consider using PME electrostatics. 86: 86: 86: 86: There were 4 NOTEs 86: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 86: Can not increase nstlist because an NVE ensemble is used 86: Using 1 MPI thread 86: Using 1 OpenMP thread 86: 86: 86: NOTE: Thread affinity was not set. 86: starting mdrun 'spc2' 86: 16 steps, 0.0 ps. 86: Generated 330891 of the 330891 non-bonded parameter combinations 86: 86: Generated 330891 of the 330891 1-4 parameter combinations 86: 86: Excluding 2 bonded neighbours molecule type 'SOL' 86: 86: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/tip3p5.gro' 86: 86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 86: 86: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 86: 86: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 86: 86: Note that mdrun will redetermine rlist based on the actual pair-list setup 86: 86: This run will generate roughly 0 Mb of data 86: 86: Writing final coordinates. 86: 86: Core t (s) Wall t (s) (%) 86: Time: 0.021 0.021 98.8 86: (ns/day) (hour/ns) 86: Performance: 69.823 0.344 86: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as double precision energy file 86: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as double precision energy file 86: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 86: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 86: that with the Verlet scheme, nstlist has no effect on the accuracy of 86: your simulation. 86: 86: 86: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 86: Setting nstcalcenergy (100) equal to nstenergy (4) 86: 86: Generating 1-4 interactions: fudge = 0.5 86: Number of degrees of freedom in T-Coupling group System is 27.00 86: 86: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 86: NVE simulation: will use the initial temperature of 398.997 K for 86: determining the Verlet buffer size 86: 86: 86: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 86: You are using a plain Coulomb cut-off, which might produce artifacts. 86: You might want to consider using PME electrostatics. 86: 86: 86: 86: There were 4 NOTEs 86: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 86: Can not increase nstlist because an NVE ensemble is used 86: Using 1 MPI thread 86: Using 1 OpenMP thread 86: 86: 86: NOTE: Thread affinity was not set. 86: starting mdrun 'spc2' 86: 16 steps, 0.0 ps. 86: Generated 330891 of the 330891 non-bonded parameter combinations 86: 86: Generated 330891 of the 330891 1-4 parameter combinations 86: 86: Excluding 2 bonded neighbours molecule type 'SOL' 86: 86: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/tip3p5.gro' 86: 86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 86: 86: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 86: 86: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 86: 86: Note that mdrun will redetermine rlist based on the actual pair-list setup 86: 86: This run will generate roughly 0 Mb of data 86: 86: Writing final coordinates. 86: 86: Core t (s) Wall t (s) (%) 86: Time: 0.021 0.022 98.9 86: (ns/day) (hour/ns) 86: Performance: 67.568 0.355 86: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as double precision energy file 86: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as double precision energy file 86: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 86: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 86: that with the Verlet scheme, nstlist has no effect on the accuracy of 86: your simulation. 86: 86: 86: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 86: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 86: setting nstcomm equal to nstcalcenergy for less overhead 86: 86: Generating 1-4 interactions: fudge = 0.5 86: Number of degrees of freedom in T-Coupling group System is 27.00 86: 86: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 86: NVE simulation: will use the initial temperature of 398.997 K for 86: determining the Verlet buffer size 86: 86: 86: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 86: You are using a plain Coulomb cut-off, which might produce artifacts. 86: You might want to consider using PME electrostatics. 86: 86: 86: 86: There were 4 NOTEs 86: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 86: Can not increase nstlist because an NVE ensemble is used 86: Using 1 MPI thread 86: Using 1 OpenMP thread 86: 86: 86: NOTE: Thread affinity was not set. 86: starting mdrun 'spc2' 86: 16 steps, 0.0 ps. 86: Generated 330891 of the 330891 non-bonded parameter combinations 86: 86: Generated 330891 of the 330891 1-4 parameter combinations 86: 86: Excluding 2 bonded neighbours molecule type 'SOL' 86: 86: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/tip3p5.gro' 86: 86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 86: 86: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 86: 86: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 86: 86: Note that mdrun will redetermine rlist based on the actual pair-list setup 86: 86: This run will generate roughly 0 Mb of data 86: 86: Writing final coordinates. 86: 86: Core t (s) Wall t (s) (%) 86: Time: 0.029 0.030 99.0 86: (ns/day) (hour/ns) 86: Performance: 49.749 0.482 86: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as double precision energy file 86: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as double precision energy file 86: 86: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 86: that with the Verlet scheme, nstlist has no effect on the accuracy of 86: your simulation. 86: 86: 86: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 86: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 86: setting nstcomm equal to nstcalcenergy for less overhead 86: 86: Generating 1-4 interactions: fudge = 0.5 86: Number of degrees of freedom in T-Coupling group System is 27.00 86: 86: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 86: NVE simulation: will use the initial temperature of 398.997 K for 86: determining the Verlet buffer size 86: 86: 86: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 86: You are using a plain Coulomb cut-off, which might produce artifacts. 86: You might want to consider using PME electrostatics. 86: 86: 86: 86: There were 4 NOTEs 86: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 86: Can not increase nstlist because an NVE ensemble is used 86: Using 1 MPI thread 86: Using 1 OpenMP thread 86: 86: 86: NOTE: Thread affinity was not set. 86: starting mdrun 'spc2' 86: 16 steps, 0.0 ps. 86: Generated 330891 of the 330891 non-bonded parameter combinations 86: 86: Generated 330891 of the 330891 1-4 parameter combinations 86: 86: Excluding 2 bonded neighbours molecule type 'SOL' 86: 86: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/tip3p5.gro' 86: 86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 86: 86: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 86: 86: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 86: 86: Note that mdrun will redetermine rlist based on the actual pair-list setup 86: 86: This run will generate roughly 0 Mb of data 86: 86: Writing final coordinates. 86: 86: Core t (s) Wall t (s) (%) 86: Time: 0.025 0.025 98.8 86: (ns/day) (hour/ns) 86: Performance: 58.513 0.410 86: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as double precision energy file 86: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as double precision energy file 86: 86: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 86: that with the Verlet scheme, nstlist has no effect on the accuracy of 86: your simulation. 86: 86: 86: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 86: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 86: setting nstcomm equal to nstcalcenergy for less overhead 86: 86: Generating 1-4 interactions: fudge = 0.5 86: Number of degrees of freedom in T-Coupling group System is 27.00 86: 86: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 86: NVE simulation: will use the initial temperature of 398.997 K for 86: determining the Verlet buffer size 86: 86: 86: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 86: You are using a plain Coulomb cut-off, which might produce artifacts. 86: You might want to consider using PME electrostatics. 86: 86: 86: 86: There were 4 NOTEs 86: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 86: Can not increase nstlist because an NVE ensemble is used 86: Using 1 MPI thread 86: Using 1 OpenMP thread 86: 86: 86: NOTE: Thread affinity was not set. 86: starting mdrun 'spc2' 86: 16 steps, 0.0 ps. 86: Generated 330891 of the 330891 non-bonded parameter combinations 86: 86: Generated 330891 of the 330891 1-4 parameter combinations 86: 86: Excluding 2 bonded neighbours molecule type 'SOL' 86: 86: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/tip3p5.gro' 86: 86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 86: 86: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 86: 86: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 86: 86: Note that mdrun will redetermine rlist based on the actual pair-list setup 86: 86: This run will generate roughly 0 Mb of data 86: 86: Writing final coordinates. 86: 86: Core t (s) Wall t (s) (%) 86: Time: 0.025 0.025 99.0 86: (ns/day) (hour/ns) 86: Performance: 58.614 0.409 86: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as double precision energy file 86: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as double precision energy file 86: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/1 (35459 ms) 86: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/2 86: 86: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 86: that with the Verlet scheme, nstlist has no effect on the accuracy of 86: your simulation. 86: 86: 86: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 86: Setting nstcalcenergy (100) equal to nstenergy (1) 86: 86: Generating 1-4 interactions: fudge = 0.5 86: Number of degrees of freedom in T-Coupling group System is 27.00 86: 86: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 86: NVE simulation: will use the initial temperature of 398.997 K for 86: determining the Verlet buffer size 86: 86: 86: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 86: You are using a plain Coulomb cut-off, which might produce artifacts. 86: You might want to consider using PME electrostatics. 86: 86: 86: 86: There were 4 NOTEs 86: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 86: Can not increase nstlist because an NVE ensemble is used 86: Using 1 MPI thread 86: Using 1 OpenMP thread 86: 86: 86: NOTE: Thread affinity was not set. 86: starting mdrun 'spc2' 86: 16 steps, 0.0 ps. 86: Generated 330891 of the 330891 non-bonded parameter combinations 86: 86: Generated 330891 of the 330891 1-4 parameter combinations 86: 86: Excluding 2 bonded neighbours molecule type 'SOL' 86: 86: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/tip3p5.gro' 86: 86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 86: 86: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 86: 86: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 86: 86: Note that mdrun will redetermine rlist based on the actual pair-list setup 86: 86: This run will generate roughly 0 Mb of data 86: 86: Writing final coordinates. 86: 86: Core t (s) Wall t (s) (%) 86: Time: 0.045 0.045 99.4 86: (ns/day) (hour/ns) 86: Performance: 32.665 0.735 86: 86: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 86: that with the Verlet scheme, nstlist has no effect on the accuracy of 86: your simulation. 86: 86: 86: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 86: Setting nstcalcenergy (100) equal to nstenergy (1) 86: 86: Generating 1-4 interactions: fudge = 0.5 86: Number of degrees of freedom in T-Coupling group System is 27.00 86: 86: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 86: NVE simulation: will use the initial temperature of 398.997 K for 86: determining the Verlet buffer size 86: 86: 86: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 86: You are using a plain Coulomb cut-off, which might produce artifacts. 86: You might want to consider using PME electrostatics. 86: 86: 86: 86: There were 4 NOTEs 86: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 86: Can not increase nstlist because an NVE ensemble is used 86: Using 1 MPI thread 86: Using 1 OpenMP thread 86: 86: 86: NOTE: Thread affinity was not set. 86: starting mdrun 'spc2' 86: 16 steps, 0.0 ps. 86: Generated 330891 of the 330891 non-bonded parameter combinations 86: 86: Generated 330891 of the 330891 1-4 parameter combinations 86: 86: Excluding 2 bonded neighbours molecule type 'SOL' 86: 86: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/tip3p5.gro' 86: 86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 86: 86: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 86: 86: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 86: 86: Note that mdrun will redetermine rlist based on the actual pair-list setup 86: 86: This run will generate roughly 0 Mb of data 86: 86: Writing final coordinates. 86: 86: Core t (s) Wall t (s) (%) 86: Time: 0.020 0.021 98.7 86: (ns/day) (hour/ns) 86: Performance: 71.607 0.335 86: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as double precision energy file 86: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as double precision energy file 86: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 86: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 86: that with the Verlet scheme, nstlist has no effect on the accuracy of 86: your simulation. 86: 86: 86: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 86: Setting nstcalcenergy (100) equal to nstenergy (4) 86: 86: Generating 1-4 interactions: fudge = 0.5 86: Number of degrees of freedom in T-Coupling group System is 27.00 86: 86: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 86: NVE simulation: will use the initial temperature of 398.997 K for 86: determining the Verlet buffer size 86: 86: 86: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 86: You are using a plain Coulomb cut-off, which might produce artifacts. 86: You might want to consider using PME electrostatics. 86: 86: 86: 86: There were 4 NOTEs 86: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 86: Can not increase nstlist because an NVE ensemble is used 86: Using 1 MPI thread 86: Using 1 OpenMP thread 86: 86: 86: NOTE: Thread affinity was not set. 86: starting mdrun 'spc2' 86: 16 steps, 0.0 ps. 86: Generated 330891 of the 330891 non-bonded parameter combinations 86: 86: Generated 330891 of the 330891 1-4 parameter combinations 86: 86: Excluding 2 bonded neighbours molecule type 'SOL' 86: 86: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/tip3p5.gro' 86: 86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 86: 86: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 86: 86: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 86: 86: Note that mdrun will redetermine rlist based on the actual pair-list setup 86: 86: This run will generate roughly 0 Mb of data 86: 86: Writing final coordinates. 86: 86: Core t (s) Wall t (s) (%) 86: Time: 0.020 0.020 98.8 86: (ns/day) (hour/ns) 86: Performance: 73.016 0.329 86: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as double precision energy file 86: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as double precision energy file 86: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 86: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 86: that with the Verlet scheme, nstlist has no effect on the accuracy of 86: your simulation. 86: 86: 86: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 86: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 86: setting nstcomm equal to nstcalcenergy for less overhead 86: 86: Generating 1-4 interactions: fudge = 0.5 86: Number of degrees of freedom in T-Coupling group System is 27.00 86: 86: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 86: NVE simulation: will use the initial temperature of 398.997 K for 86: determining the Verlet buffer size 86: 86: 86: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 86: You are using a plain Coulomb cut-off, which might produce artifacts. 86: You might want to consider using PME electrostatics. 86: 86: 86: 86: There were 4 NOTEs 86: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 86: Can not increase nstlist because an NVE ensemble is used 86: Using 1 MPI thread 86: Using 1 OpenMP thread 86: 86: 86: NOTE: Thread affinity was not set. 86: starting mdrun 'spc2' 86: 16 steps, 0.0 ps. 86: Generated 330891 of the 330891 non-bonded parameter combinations 86: 86: Generated 330891 of the 330891 1-4 parameter combinations 86: 86: Excluding 2 bonded neighbours molecule type 'SOL' 86: 86: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/tip3p5.gro' 86: 86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 86: 86: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 86: 86: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 86: 86: Note that mdrun will redetermine rlist based on the actual pair-list setup 86: 86: This run will generate roughly 0 Mb of data 86: 86: Writing final coordinates. 86: 86: Core t (s) Wall t (s) (%) 86: Time: 0.022 0.022 98.8 86: (ns/day) (hour/ns) 86: Performance: 66.384 0.362 86: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as double precision energy file 86: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as double precision energy file 86: 86: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 86: that with the Verlet scheme, nstlist has no effect on the accuracy of 86: your simulation. 86: 86: 86: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 86: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 86: setting nstcomm equal to nstcalcenergy for less overhead 86: 86: Generating 1-4 interactions: fudge = 0.5 86: Number of degrees of freedom in T-Coupling group System is 27.00 86: 86: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 86: NVE simulation: will use the initial temperature of 398.997 K for 86: determining the Verlet buffer size 86: 86: 86: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 86: You are using a plain Coulomb cut-off, which might produce artifacts. 86: You might want to consider using PME electrostatics. 86: 86: 86: 86: There were 4 NOTEs 86: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 86: Can not increase nstlist because an NVE ensemble is used 86: Using 1 MPI thread 86: Using 1 OpenMP thread 86: 86: 86: NOTE: Thread affinity was not set. 86: starting mdrun 'spc2' 86: 16 steps, 0.0 ps. 86: Generated 330891 of the 330891 non-bonded parameter combinations 86: 86: Generated 330891 of the 330891 1-4 parameter combinations 86: 86: Excluding 2 bonded neighbours molecule type 'SOL' 86: 86: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/tip3p5.gro' 86: 86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 86: 86: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 86: 86: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 86: 86: Note that mdrun will redetermine rlist based on the actual pair-list setup 86: 86: This run will generate roughly 0 Mb of data 86: 86: Writing final coordinates. 86: 86: Core t (s) Wall t (s) (%) 86: Time: 0.024 0.025 99.0 86: (ns/day) (hour/ns) 86: Performance: 59.432 0.404 86: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as double precision energy file 86: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as double precision energy file 86: 86: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 86: that with the Verlet scheme, nstlist has no effect on the accuracy of 86: your simulation. 86: 86: 86: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 86: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 86: setting nstcomm equal to nstcalcenergy for less overhead 86: 86: Generating 1-4 interactions: fudge = 0.5 86: Number of degrees of freedom in T-Coupling group System is 27.00 86: 86: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 86: NVE simulation: will use the initial temperature of 398.997 K for 86: determining the Verlet buffer size 86: 86: 86: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 86: You are using a plain Coulomb cut-off, which might produce artifacts. 86: You might want to consider using PME electrostatics. 86: 86: 86: 86: There were 4 NOTEs 86: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 86: Can not increase nstlist because an NVE ensemble is used 86: Using 1 MPI thread 86: Using 1 OpenMP thread 86: 86: 86: NOTE: Thread affinity was not set. 86: starting mdrun 'spc2' 86: 16 steps, 0.0 ps. 86: Generated 330891 of the 330891 non-bonded parameter combinations 86: 86: Generated 330891 of the 330891 1-4 parameter combinations 86: 86: Excluding 2 bonded neighbours molecule type 'SOL' 86: 86: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/tip3p5.gro' 86: 86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 86: 86: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 86: 86: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 86: 86: Note that mdrun will redetermine rlist based on the actual pair-list setup 86: 86: This run will generate roughly 0 Mb of data 86: 86: Writing final coordinates. 86: 86: Core t (s) Wall t (s) (%) 86: Time: 0.022 0.022 98.8 86: (ns/day) (hour/ns) 86: Performance: 67.290 0.357 86: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as double precision energy file 86: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as double precision energy file 86: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/2 (35432 ms) 86: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/3 86: 86: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 86: that with the Verlet scheme, nstlist has no effect on the accuracy of 86: your simulation. 86: 86: 86: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 86: Setting nstcalcenergy (100) equal to nstenergy (1) 86: 86: Generating 1-4 interactions: fudge = 0.5 86: Number of degrees of freedom in T-Coupling group System is 27.00 86: 86: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 86: You are using a plain Coulomb cut-off, which might produce artifacts. 86: You might want to consider using PME electrostatics. 86: 86: 86: 86: There were 3 NOTEs 86: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 86: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 86: 86: Using 1 MPI thread 86: Using 1 OpenMP thread 86: 86: 86: NOTE: Thread affinity was not set. 86: starting mdrun 'spc2' 86: 16 steps, 0.0 ps. 86: Generated 330891 of the 330891 non-bonded parameter combinations 86: 86: Generated 330891 of the 330891 1-4 parameter combinations 86: 86: Excluding 2 bonded neighbours molecule type 'SOL' 86: 86: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/tip3p5.gro' 86: 86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 86: 86: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 86: 86: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 86: 86: Note that mdrun will redetermine rlist based on the actual pair-list setup 86: 86: This run will generate roughly 0 Mb of data 86: 86: Writing final coordinates. 86: 86: Core t (s) Wall t (s) (%) 86: Time: 0.025 0.025 99.0 86: (ns/day) (hour/ns) 86: Performance: 57.982 0.414 86: 86: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 86: that with the Verlet scheme, nstlist has no effect on the accuracy of 86: your simulation. 86: 86: 86: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 86: Setting nstcalcenergy (100) equal to nstenergy (1) 86: 86: Generating 1-4 interactions: fudge = 0.5 86: Number of degrees of freedom in T-Coupling group System is 27.00 86: 86: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 86: You are using a plain Coulomb cut-off, which might produce artifacts. 86: You might want to consider using PME electrostatics. 86: 86: 86: 86: There were 3 NOTEs 86: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 86: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 86: 86: Using 1 MPI thread 86: Using 1 OpenMP thread 86: 86: 86: NOTE: Thread affinity was not set. 86: starting mdrun 'spc2' 86: 16 steps, 0.0 ps. 86: Generated 330891 of the 330891 non-bonded parameter combinations 86: 86: Generated 330891 of the 330891 1-4 parameter combinations 86: 86: Excluding 2 bonded neighbours molecule type 'SOL' 86: 86: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/tip3p5.gro' 86: 86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 86: 86: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 86: 86: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 86: 86: Note that mdrun will redetermine rlist based on the actual pair-list setup 86: 86: This run will generate roughly 0 Mb of data 86: 86: Writing final coordinates. 86: 86: Core t (s) Wall t (s) (%) 86: Time: 0.020 0.020 98.8 86: (ns/day) (hour/ns) 86: Performance: 73.411 0.327 86: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as double precision energy file 86: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as double precision energy file 86: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 86: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 86: that with the Verlet scheme, nstlist has no effect on the accuracy of 86: your simulation. 86: 86: 86: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 86: Setting nstcalcenergy (100) equal to nstenergy (4) 86: 86: Generating 1-4 interactions: fudge = 0.5 86: Number of degrees of freedom in T-Coupling group System is 27.00 86: 86: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 86: You are using a plain Coulomb cut-off, which might produce artifacts. 86: You might want to consider using PME electrostatics. 86: 86: 86: 86: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 86: COM removal frequency is set to (5). 86: Other settings require a global communication frequency of 2. 86: Note that this will require additional global communication steps, 86: which will reduce performance when using multiple ranks. 86: Consider setting nstcomm to a multiple of 2. 86: 86: 86: There were 4 NOTEs 86: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 86: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 86: 86: Using 1 MPI thread 86: Using 1 OpenMP thread 86: 86: 86: NOTE: Thread affinity was not set. 86: starting mdrun 'spc2' 86: 16 steps, 0.0 ps. 86: Generated 330891 of the 330891 non-bonded parameter combinations 86: 86: Generated 330891 of the 330891 1-4 parameter combinations 86: 86: Excluding 2 bonded neighbours molecule type 'SOL' 86: 86: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/tip3p5.gro' 86: 86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 86: 86: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 86: 86: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 86: 86: Note that mdrun will redetermine rlist based on the actual pair-list setup 86: 86: This run will generate roughly 0 Mb of data 86: 86: Writing final coordinates. 86: 86: Core t (s) Wall t (s) (%) 86: Time: 0.021 0.022 99.0 86: (ns/day) (hour/ns) 86: Performance: 67.630 0.355 86: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as double precision energy file 86: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as double precision energy file 86: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 86: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 86: that with the Verlet scheme, nstlist has no effect on the accuracy of 86: your simulation. 86: 86: 86: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 86: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 86: setting nstcomm equal to nstcalcenergy for less overhead 86: 86: Generating 1-4 interactions: fudge = 0.5 86: Number of degrees of freedom in T-Coupling group System is 27.00 86: 86: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 86: You are using a plain Coulomb cut-off, which might produce artifacts. 86: You might want to consider using PME electrostatics. 86: 86: 86: 86: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 86: COM removal frequency is set to (5). 86: Other settings require a global communication frequency of 2. 86: Note that this will require additional global communication steps, 86: which will reduce performance when using multiple ranks. 86: Consider setting nstcomm to a multiple of 2. 86: 86: 86: There were 4 NOTEs 86: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 86: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 86: 86: Using 1 MPI thread 86: Using 1 OpenMP thread 86: 86: 86: NOTE: Thread affinity was not set. 86: starting mdrun 'spc2' 86: 16 steps, 0.0 ps. 86: Generated 330891 of the 330891 non-bonded parameter combinations 86: 86: Generated 330891 of the 330891 1-4 parameter combinations 86: 86: Excluding 2 bonded neighbours molecule type 'SOL' 86: 86: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/tip3p5.gro' 86: 86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 86: 86: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 86: 86: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 86: 86: Note that mdrun will redetermine rlist based on the actual pair-list setup 86: 86: This run will generate roughly 0 Mb of data 86: 86: Writing final coordinates. 86: 86: Core t (s) Wall t (s) (%) 86: Time: 0.024 0.024 98.9 86: (ns/day) (hour/ns) 86: Performance: 61.035 0.393 86: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as double precision energy file 86: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as double precision energy file 86: 86: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 86: that with the Verlet scheme, nstlist has no effect on the accuracy of 86: your simulation. 86: 86: 86: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 86: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 86: setting nstcomm equal to nstcalcenergy for less overhead 86: 86: Generating 1-4 interactions: fudge = 0.5 86: Number of degrees of freedom in T-Coupling group System is 27.00 86: 86: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 86: You are using a plain Coulomb cut-off, which might produce artifacts. 86: You might want to consider using PME electrostatics. 86: 86: 86: 86: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 86: COM removal frequency is set to (5). 86: Other settings require a global communication frequency of 2. 86: Note that this will require additional global communication steps, 86: which will reduce performance when using multiple ranks. 86: Consider setting nstcomm to a multiple of 2. 86: 86: 86: There were 4 NOTEs 86: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 86: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 86: 86: Using 1 MPI thread 86: Using 1 OpenMP thread 86: 86: 86: NOTE: Thread affinity was not set. 86: starting mdrun 'spc2' 86: 16 steps, 0.0 ps. 86: Generated 330891 of the 330891 non-bonded parameter combinations 86: 86: Generated 330891 of the 330891 1-4 parameter combinations 86: 86: Excluding 2 bonded neighbours molecule type 'SOL' 86: 86: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/tip3p5.gro' 86: 86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 86: 86: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 86: 86: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 86: 86: Note that mdrun will redetermine rlist based on the actual pair-list setup 86: 86: This run will generate roughly 0 Mb of data 86: 86: Writing final coordinates. 86: 86: Core t (s) Wall t (s) (%) 86: Time: 0.023 0.023 99.0 86: (ns/day) (hour/ns) 86: Performance: 64.143 0.374 86: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as double precision energy file 86: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as double precision energy file 86: 86: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 86: that with the Verlet scheme, nstlist has no effect on the accuracy of 86: your simulation. 86: 86: 86: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 86: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 86: setting nstcomm equal to nstcalcenergy for less overhead 86: 86: Generating 1-4 interactions: fudge = 0.5 86: Number of degrees of freedom in T-Coupling group System is 27.00 86: 86: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 86: You are using a plain Coulomb cut-off, which might produce artifacts. 86: You might want to consider using PME electrostatics. 86: 86: 86: 86: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 86: COM removal frequency is set to (5). 86: Other settings require a global communication frequency of 2. 86: Note that this will require additional global communication steps, 86: which will reduce performance when using multiple ranks. 86: Consider setting nstcomm to a multiple of 2. 86: 86: 86: There were 4 NOTEs 86: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 86: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 86: 86: Using 1 MPI thread 86: Using 1 OpenMP thread 86: 86: 86: NOTE: Thread affinity was not set. 86: starting mdrun 'spc2' 86: 16 steps, 0.0 ps. 86: Generated 330891 of the 330891 non-bonded parameter combinations 86: 86: Generated 330891 of the 330891 1-4 parameter combinations 86: 86: Excluding 2 bonded neighbours molecule type 'SOL' 86: 86: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/tip3p5.gro' 86: 86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 86: 86: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 86: 86: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 86: 86: Note that mdrun will redetermine rlist based on the actual pair-list setup 86: 86: This run will generate roughly 0 Mb of data 86: 86: Writing final coordinates. 86: 86: Core t (s) Wall t (s) (%) 86: Time: 0.023 0.023 98.9 86: (ns/day) (hour/ns) 86: Performance: 63.365 0.379 86: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as double precision energy file 86: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as double precision energy file 86: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/3 (35117 ms) 86: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/4 86: 86: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 86: that with the Verlet scheme, nstlist has no effect on the accuracy of 86: your simulation. 86: 86: 86: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 86: Setting nstcalcenergy (100) equal to nstenergy (1) 86: 86: Generating 1-4 interactions: fudge = 0.5 86: Number of degrees of freedom in T-Coupling group System is 27.00 86: 86: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 86: You are using a plain Coulomb cut-off, which might produce artifacts. 86: You might want to consider using PME electrostatics. 86: 86: 86: 86: There were 3 NOTEs 86: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 86: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 86: 86: Using 1 MPI thread 86: Using 1 OpenMP thread 86: 86: 86: NOTE: Thread affinity was not set. 86: starting mdrun 'spc2' 86: 16 steps, 0.0 ps. 86: Generated 330891 of the 330891 non-bonded parameter combinations 86: 86: Generated 330891 of the 330891 1-4 parameter combinations 86: 86: Excluding 2 bonded neighbours molecule type 'SOL' 86: 86: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/tip3p5.gro' 86: 86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 86: 86: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 86: 86: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 86: 86: Note that mdrun will redetermine rlist based on the actual pair-list setup 86: 86: This run will generate roughly 0 Mb of data 86: 86: Writing final coordinates. 86: 86: Core t (s) Wall t (s) (%) 86: Time: 0.044 0.045 99.4 86: (ns/day) (hour/ns) 86: Performance: 32.978 0.728 86: 86: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 86: that with the Verlet scheme, nstlist has no effect on the accuracy of 86: your simulation. 86: 86: 86: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 86: Setting nstcalcenergy (100) equal to nstenergy (1) 86: 86: Generating 1-4 interactions: fudge = 0.5 86: Number of degrees of freedom in T-Coupling group System is 27.00 86: 86: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 86: You are using a plain Coulomb cut-off, which might produce artifacts. 86: You might want to consider using PME electrostatics. 86: 86: 86: 86: There were 3 NOTEs 86: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 86: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 86: 86: Using 1 MPI thread 86: Using 1 OpenMP thread 86: 86: 86: NOTE: Thread affinity was not set. 86: starting mdrun 'spc2' 86: 16 steps, 0.0 ps. 86: Generated 330891 of the 330891 non-bonded parameter combinations 86: 86: Generated 330891 of the 330891 1-4 parameter combinations 86: 86: Excluding 2 bonded neighbours molecule type 'SOL' 86: 86: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/tip3p5.gro' 86: 86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 86: 86: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 86: 86: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 86: 86: Note that mdrun will redetermine rlist based on the actual pair-list setup 86: 86: This run will generate roughly 0 Mb of data 86: 86: Writing final coordinates. 86: 86: Core t (s) Wall t (s) (%) 86: Time: 0.019 0.019 98.7 86: (ns/day) (hour/ns) 86: Performance: 75.938 0.316 86: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as double precision energy file 86: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as double precision energy file 86: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 86: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 86: that with the Verlet scheme, nstlist has no effect on the accuracy of 86: your simulation. 86: 86: 86: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 86: Setting nstcalcenergy (100) equal to nstenergy (4) 86: 86: Generating 1-4 interactions: fudge = 0.5 86: Number of degrees of freedom in T-Coupling group System is 27.00 86: 86: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 86: You are using a plain Coulomb cut-off, which might produce artifacts. 86: You might want to consider using PME electrostatics. 86: 86: 86: 86: There were 3 NOTEs 86: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 86: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 86: 86: Using 1 MPI thread 86: Using 1 OpenMP thread 86: 86: 86: NOTE: Thread affinity was not set. 86: starting mdrun 'spc2' 86: 16 steps, 0.0 ps. 86: Generated 330891 of the 330891 non-bonded parameter combinations 86: 86: Generated 330891 of the 330891 1-4 parameter combinations 86: 86: Excluding 2 bonded neighbours molecule type 'SOL' 86: 86: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/tip3p5.gro' 86: 86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 86: 86: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 86: 86: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 86: 86: Note that mdrun will redetermine rlist based on the actual pair-list setup 86: 86: This run will generate roughly 0 Mb of data 86: 86: Writing final coordinates. 86: 86: Core t (s) Wall t (s) (%) 86: Time: 0.024 0.024 98.9 86: (ns/day) (hour/ns) 86: Performance: 60.160 0.399 86: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as double precision energy file 86: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as double precision energy file 86: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 86: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 86: that with the Verlet scheme, nstlist has no effect on the accuracy of 86: your simulation. 86: 86: 86: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 86: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 86: setting nstcomm equal to nstcalcenergy for less overhead 86: 86: Generating 1-4 interactions: fudge = 0.5 86: Number of degrees of freedom in T-Coupling group System is 27.00 86: 86: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 86: You are using a plain Coulomb cut-off, which might produce artifacts. 86: You might want to consider using PME electrostatics. 86: 86: 86: 86: There were 3 NOTEs 86: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 86: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 86: 86: Using 1 MPI thread 86: Using 1 OpenMP thread 86: 86: 86: NOTE: Thread affinity was not set. 86: starting mdrun 'spc2' 86: 16 steps, 0.0 ps. 86: Generated 330891 of the 330891 non-bonded parameter combinations 86: 86: Generated 330891 of the 330891 1-4 parameter combinations 86: 86: Excluding 2 bonded neighbours molecule type 'SOL' 86: 86: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/tip3p5.gro' 86: 86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 86: 86: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 86: 86: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 86: 86: Note that mdrun will redetermine rlist based on the actual pair-list setup 86: 86: This run will generate roughly 0 Mb of data 86: 86: Writing final coordinates. 86: 86: Core t (s) Wall t (s) (%) 86: Time: 0.026 0.026 99.0 86: (ns/day) (hour/ns) 86: Performance: 56.710 0.423 86: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as double precision energy file 86: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as double precision energy file 86: 86: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 86: that with the Verlet scheme, nstlist has no effect on the accuracy of 86: your simulation. 86: 86: 86: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 86: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 86: setting nstcomm equal to nstcalcenergy for less overhead 86: 86: Generating 1-4 interactions: fudge = 0.5 86: Number of degrees of freedom in T-Coupling group System is 27.00 86: 86: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 86: You are using a plain Coulomb cut-off, which might produce artifacts. 86: You might want to consider using PME electrostatics. 86: 86: 86: 86: There were 3 NOTEs 86: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 86: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 86: 86: Using 1 MPI thread 86: Using 1 OpenMP thread 86: 86: 86: NOTE: Thread affinity was not set. 86: starting mdrun 'spc2' 86: 16 steps, 0.0 ps. 86: Generated 330891 of the 330891 non-bonded parameter combinations 86: 86: Generated 330891 of the 330891 1-4 parameter combinations 86: 86: Excluding 2 bonded neighbours molecule type 'SOL' 86: 86: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/tip3p5.gro' 86: 86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 86: 86: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 86: 86: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 86: 86: Note that mdrun will redetermine rlist based on the actual pair-list setup 86: 86: This run will generate roughly 0 Mb of data 86: 86: Writing final coordinates. 86: 86: Core t (s) Wall t (s) (%) 86: Time: 0.023 0.023 98.9 86: (ns/day) (hour/ns) 86: Performance: 64.427 0.373 86: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as double precision energy file 86: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as double precision energy file 86: 86: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 86: that with the Verlet scheme, nstlist has no effect on the accuracy of 86: your simulation. 86: 86: 86: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 86: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 86: setting nstcomm equal to nstcalcenergy for less overhead 86: 86: Generating 1-4 interactions: fudge = 0.5 86: Number of degrees of freedom in T-Coupling group System is 27.00 86: 86: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 86: You are using a plain Coulomb cut-off, which might produce artifacts. 86: You might want to consider using PME electrostatics. 86: 86: 86: 86: There were 3 NOTEs 86: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 86: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 86: 86: Using 1 MPI thread 86: Using 1 OpenMP thread 86: 86: 86: NOTE: Thread affinity was not set. 86: starting mdrun 'spc2' 86: 16 steps, 0.0 ps. 86: Generated 330891 of the 330891 non-bonded parameter combinations 86: 86: Generated 330891 of the 330891 1-4 parameter combinations 86: 86: Excluding 2 bonded neighbours molecule type 'SOL' 86: 86: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/tip3p5.gro' 86: 86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 86: 86: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 86: 86: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 86: 86: Note that mdrun will redetermine rlist based on the actual pair-list setup 86: 86: This run will generate roughly 0 Mb of data 86: 86: Writing final coordinates. 86: 86: Core t (s) Wall t (s) (%) 86: Time: 0.026 0.026 98.9 86: (ns/day) (hour/ns) 86: Performance: 55.810 0.430 86: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as double precision energy file 86: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as double precision energy file 86: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/4 (35091 ms) 86: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/5 86: 86: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 86: that with the Verlet scheme, nstlist has no effect on the accuracy of 86: your simulation. 86: 86: 86: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 86: Setting nstcalcenergy (100) equal to nstenergy (1) 86: 86: Generating 1-4 interactions: fudge = 0.5 86: Number of degrees of freedom in T-Coupling group System is 27.00 86: 86: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 86: You are using a plain Coulomb cut-off, which might produce artifacts. 86: You might want to consider using PME electrostatics. 86: 86: 86: 86: There were 3 NOTEs 86: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 86: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 86: 86: Using 1 MPI thread 86: Using 1 OpenMP thread 86: 86: 86: NOTE: Thread affinity was not set. 86: starting mdrun 'spc2' 86: 16 steps, 0.0 ps. 86: Generated 330891 of the 330891 non-bonded parameter combinations 86: 86: Generated 330891 of the 330891 1-4 parameter combinations 86: 86: Excluding 2 bonded neighbours molecule type 'SOL' 86: 86: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/tip3p5.gro' 86: 86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 86: 86: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 86: 86: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 86: 86: Note that mdrun will redetermine rlist based on the actual pair-list setup 86: 86: This run will generate roughly 0 Mb of data 86: 86: Writing final coordinates. 86: 86: Core t (s) Wall t (s) (%) 86: Time: 0.043 0.044 99.3 86: (ns/day) (hour/ns) 86: Performance: 33.616 0.714 86: 86: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 86: that with the Verlet scheme, nstlist has no effect on the accuracy of 86: your simulation. 86: 86: 86: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 86: Setting nstcalcenergy (100) equal to nstenergy (1) 86: 86: Generating 1-4 interactions: fudge = 0.5 86: Number of degrees of freedom in T-Coupling group System is 27.00 86: 86: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 86: You are using a plain Coulomb cut-off, which might produce artifacts. 86: You might want to consider using PME electrostatics. 86: 86: 86: 86: There were 3 NOTEs 86: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 86: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 86: 86: Using 1 MPI thread 86: Using 1 OpenMP thread 86: 86: 86: NOTE: Thread affinity was not set. 86: starting mdrun 'spc2' 86: 16 steps, 0.0 ps. 86: Generated 330891 of the 330891 non-bonded parameter combinations 86: 86: Generated 330891 of the 330891 1-4 parameter combinations 86: 86: Excluding 2 bonded neighbours molecule type 'SOL' 86: 86: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/tip3p5.gro' 86: 86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 86: 86: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 86: 86: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 86: 86: Note that mdrun will redetermine rlist based on the actual pair-list setup 86: 86: This run will generate roughly 0 Mb of data 86: 86: Writing final coordinates. 86: 86: Core t (s) Wall t (s) (%) 86: Time: 0.022 0.023 98.9 86: (ns/day) (hour/ns) 86: Performance: 64.819 0.370 86: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as double precision energy file 86: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as double precision energy file 86: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 86: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 86: that with the Verlet scheme, nstlist has no effect on the accuracy of 86: your simulation. 86: 86: 86: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 86: Setting nstcalcenergy (100) equal to nstenergy (4) 86: 86: Generating 1-4 interactions: fudge = 0.5 86: Number of degrees of freedom in T-Coupling group System is 27.00 86: 86: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 86: You are using a plain Coulomb cut-off, which might produce artifacts. 86: You might want to consider using PME electrostatics. 86: 86: 86: 86: There were 3 NOTEs 86: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 86: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 86: 86: Using 1 MPI thread 86: Using 1 OpenMP thread 86: 86: 86: NOTE: Thread affinity was not set. 86: starting mdrun 'spc2' 86: 16 steps, 0.0 ps. 86: Generated 330891 of the 330891 non-bonded parameter combinations 86: 86: Generated 330891 of the 330891 1-4 parameter combinations 86: 86: Excluding 2 bonded neighbours molecule type 'SOL' 86: 86: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/tip3p5.gro' 86: 86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 86: 86: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 86: 86: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 86: 86: Note that mdrun will redetermine rlist based on the actual pair-list setup 86: 86: This run will generate roughly 0 Mb of data 86: 86: Writing final coordinates. 86: 86: Core t (s) Wall t (s) (%) 86: Time: 0.019 0.020 98.8 86: (ns/day) (hour/ns) 86: Performance: 74.889 0.320 86: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as double precision energy file 86: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as double precision energy file 86: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 86: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 86: that with the Verlet scheme, nstlist has no effect on the accuracy of 86: your simulation. 86: 86: 86: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 86: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 86: setting nstcomm equal to nstcalcenergy for less overhead 86: 86: Generating 1-4 interactions: fudge = 0.5 86: Number of degrees of freedom in T-Coupling group System is 27.00 86: 86: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 86: You are using a plain Coulomb cut-off, which might produce artifacts. 86: You might want to consider using PME electrostatics. 86: 86: 86: 86: There were 3 NOTEs 86: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 86: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 86: 86: Using 1 MPI thread 86: Using 1 OpenMP thread 86: 86: 86: NOTE: Thread affinity was not set. 86: starting mdrun 'spc2' 86: 16 steps, 0.0 ps. 86: Generated 330891 of the 330891 non-bonded parameter combinations 86: 86: Generated 330891 of the 330891 1-4 parameter combinations 86: 86: Excluding 2 bonded neighbours molecule type 'SOL' 86: 86: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/tip3p5.gro' 86: 86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 86: 86: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 86: 86: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 86: 86: Note that mdrun will redetermine rlist based on the actual pair-list setup 86: 86: This run will generate roughly 0 Mb of data 86: 86: Writing final coordinates. 86: 86: Core t (s) Wall t (s) (%) 86: Time: 0.025 0.026 99.0 86: (ns/day) (hour/ns) 86: Performance: 57.290 0.419 86: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as double precision energy file 86: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as double precision energy file 86: 86: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 86: that with the Verlet scheme, nstlist has no effect on the accuracy of 86: your simulation. 86: 86: 86: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 86: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 86: setting nstcomm equal to nstcalcenergy for less overhead 86: 86: Generating 1-4 interactions: fudge = 0.5 86: Number of degrees of freedom in T-Coupling group System is 27.00 86: 86: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 86: You are using a plain Coulomb cut-off, which might produce artifacts. 86: You might want to consider using PME electrostatics. 86: 86: 86: 86: There were 3 NOTEs 86: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 86: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 86: 86: Using 1 MPI thread 86: Using 1 OpenMP thread 86: 86: 86: NOTE: Thread affinity was not set. 86: starting mdrun 'spc2' 86: 16 steps, 0.0 ps. 86: Generated 330891 of the 330891 non-bonded parameter combinations 86: 86: Generated 330891 of the 330891 1-4 parameter combinations 86: 86: Excluding 2 bonded neighbours molecule type 'SOL' 86: 86: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/tip3p5.gro' 86: 86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 86: 86: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 86: 86: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 86: 86: Note that mdrun will redetermine rlist based on the actual pair-list setup 86: 86: This run will generate roughly 0 Mb of data 86: 86: Writing final coordinates. 86: 86: Core t (s) Wall t (s) (%) 86: Time: 0.024 0.024 99.0 86: (ns/day) (hour/ns) 86: Performance: 60.694 0.395 86: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as double precision energy file 86: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as double precision energy file 86: 86: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 86: that with the Verlet scheme, nstlist has no effect on the accuracy of 86: your simulation. 86: 86: 86: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 86: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 86: setting nstcomm equal to nstcalcenergy for less overhead 86: 86: Generating 1-4 interactions: fudge = 0.5 86: Number of degrees of freedom in T-Coupling group System is 27.00 86: 86: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 86: You are using a plain Coulomb cut-off, which might produce artifacts. 86: You might want to consider using PME electrostatics. 86: 86: 86: 86: There were 3 NOTEs 86: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 86: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 86: 86: Using 1 MPI thread 86: Using 1 OpenMP thread 86: 86: 86: NOTE: Thread affinity was not set. 86: starting mdrun 'spc2' 86: 16 steps, 0.0 ps. 86: Generated 330891 of the 330891 non-bonded parameter combinations 86: 86: Generated 330891 of the 330891 1-4 parameter combinations 86: 86: Excluding 2 bonded neighbours molecule type 'SOL' 86: 86: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/tip3p5.gro' 86: 86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 86: 86: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 86: 86: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 86: 86: Note that mdrun will redetermine rlist based on the actual pair-list setup 86: 86: This run will generate roughly 0 Mb of data 86: 86: Writing final coordinates. 86: 86: Core t (s) Wall t (s) (%) 86: Time: 0.022 0.022 98.8 86: (ns/day) (hour/ns) 86: Performance: 65.489 0.366 86: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as double precision energy file 86: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as double precision energy file 86: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/5 (35072 ms) 86: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/6 86: 86: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 86: that with the Verlet scheme, nstlist has no effect on the accuracy of 86: your simulation. 86: 86: 86: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 86: Setting nstcalcenergy (100) equal to nstenergy (1) 86: 86: Generating 1-4 interactions: fudge = 0.5 86: Number of degrees of freedom in T-Coupling group System is 27.00 86: 86: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 86: You are using a plain Coulomb cut-off, which might produce artifacts. 86: You might want to consider using PME electrostatics. 86: 86: 86: 86: There were 3 NOTEs 86: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 86: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 86: 86: Using 1 MPI thread 86: Using 1 OpenMP thread 86: 86: 86: NOTE: Thread affinity was not set. 86: starting mdrun 'spc2' 86: 16 steps, 0.0 ps. 86: Generated 330891 of the 330891 non-bonded parameter combinations 86: 86: Generated 330891 of the 330891 1-4 parameter combinations 86: 86: Excluding 2 bonded neighbours molecule type 'SOL' 86: 86: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/tip3p5.gro' 86: 86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 86: 86: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 86: 86: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 86: 86: Note that mdrun will redetermine rlist based on the actual pair-list setup 86: 86: This run will generate roughly 0 Mb of data 86: 86: Writing final coordinates. 86: 86: Core t (s) Wall t (s) (%) 86: Time: 0.048 0.048 99.5 86: (ns/day) (hour/ns) 86: Performance: 30.412 0.789 86: 86: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 86: that with the Verlet scheme, nstlist has no effect on the accuracy of 86: your simulation. 86: 86: 86: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 86: Setting nstcalcenergy (100) equal to nstenergy (1) 86: 86: Generating 1-4 interactions: fudge = 0.5 86: Number of degrees of freedom in T-Coupling group System is 27.00 86: 86: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 86: You are using a plain Coulomb cut-off, which might produce artifacts. 86: You might want to consider using PME electrostatics. 86: 86: 86: 86: There were 3 NOTEs 86: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 86: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 86: 86: Using 1 MPI thread 86: Using 1 OpenMP thread 86: 86: 86: NOTE: Thread affinity was not set. 86: starting mdrun 'spc2' 86: 16 steps, 0.0 ps. 86: Generated 330891 of the 330891 non-bonded parameter combinations 86: 86: Generated 330891 of the 330891 1-4 parameter combinations 86: 86: Excluding 2 bonded neighbours molecule type 'SOL' 86: 86: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/tip3p5.gro' 86: 86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 86: 86: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 86: 86: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 86: 86: Note that mdrun will redetermine rlist based on the actual pair-list setup 86: 86: This run will generate roughly 0 Mb of data 86: 86: Writing final coordinates. 86: 86: Core t (s) Wall t (s) (%) 86: Time: 0.020 0.020 98.9 86: (ns/day) (hour/ns) 86: Performance: 74.085 0.324 86: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as double precision energy file 86: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as double precision energy file 86: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 86: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 86: that with the Verlet scheme, nstlist has no effect on the accuracy of 86: your simulation. 86: 86: 86: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 86: Setting nstcalcenergy (100) equal to nstenergy (4) 86: 86: Generating 1-4 interactions: fudge = 0.5 86: Number of degrees of freedom in T-Coupling group System is 27.00 86: 86: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 86: You are using a plain Coulomb cut-off, which might produce artifacts. 86: You might want to consider using PME electrostatics. 86: 86: 86: 86: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 86: COM removal frequency is set to (5). 86: Other settings require a global communication frequency of 4. 86: Note that this will require additional global communication steps, 86: which will reduce performance when using multiple ranks. 86: Consider setting nstcomm to a multiple of 4. 86: 86: 86: There were 4 NOTEs 86: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 86: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 86: 86: Using 1 MPI thread 86: Using 1 OpenMP thread 86: 86: 86: NOTE: Thread affinity was not set. 86: starting mdrun 'spc2' 86: 16 steps, 0.0 ps. 86: Generated 330891 of the 330891 non-bonded parameter combinations 86: 86: Generated 330891 of the 330891 1-4 parameter combinations 86: 86: Excluding 2 bonded neighbours molecule type 'SOL' 86: 86: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/tip3p5.gro' 86: 86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 86: 86: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 86: 86: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 86: 86: Note that mdrun will redetermine rlist based on the actual pair-list setup 86: 86: This run will generate roughly 0 Mb of data 86: 86: Writing final coordinates. 86: 86: Core t (s) Wall t (s) (%) 86: Time: 0.023 0.023 99.1 86: (ns/day) (hour/ns) 86: Performance: 64.050 0.375 86: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as double precision energy file 86: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as double precision energy file 86: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 86: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 86: that with the Verlet scheme, nstlist has no effect on the accuracy of 86: your simulation. 86: 86: 86: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 86: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 86: setting nstcomm equal to nstcalcenergy for less overhead 86: 86: Generating 1-4 interactions: fudge = 0.5 86: Number of degrees of freedom in T-Coupling group System is 27.00 86: 86: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 86: You are using a plain Coulomb cut-off, which might produce artifacts. 86: You might want to consider using PME electrostatics. 86: 86: 86: 86: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 86: COM removal frequency is set to (5). 86: Other settings require a global communication frequency of 100. 86: Note that this will require additional global communication steps, 86: which will reduce performance when using multiple ranks. 86: Consider setting nstcomm to a multiple of 100. 86: 86: 86: There were 4 NOTEs 86: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 86: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 86: 86: Using 1 MPI thread 86: Using 1 OpenMP thread 86: 86: 86: NOTE: Thread affinity was not set. 86: starting mdrun 'spc2' 86: 16 steps, 0.0 ps. 86: Generated 330891 of the 330891 non-bonded parameter combinations 86: 86: Generated 330891 of the 330891 1-4 parameter combinations 86: 86: Excluding 2 bonded neighbours molecule type 'SOL' 86: 86: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/tip3p5.gro' 86: 86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 86: 86: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 86: 86: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 86: 86: Note that mdrun will redetermine rlist based on the actual pair-list setup 86: 86: This run will generate roughly 0 Mb of data 86: 86: Writing final coordinates. 86: 86: Core t (s) Wall t (s) (%) 86: Time: 0.027 0.027 99.2 86: (ns/day) (hour/ns) 86: Performance: 54.296 0.442 86: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as double precision energy file 86: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as double precision energy file 86: 86: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 86: that with the Verlet scheme, nstlist has no effect on the accuracy of 86: your simulation. 86: 86: 86: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 86: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 86: setting nstcomm equal to nstcalcenergy for less overhead 86: 86: Generating 1-4 interactions: fudge = 0.5 86: Number of degrees of freedom in T-Coupling group System is 27.00 86: 86: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 86: You are using a plain Coulomb cut-off, which might produce artifacts. 86: You might want to consider using PME electrostatics. 86: 86: 86: 86: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 86: COM removal frequency is set to (5). 86: Other settings require a global communication frequency of 100. 86: Note that this will require additional global communication steps, 86: which will reduce performance when using multiple ranks. 86: Consider setting nstcomm to a multiple of 100. 86: 86: 86: There were 4 NOTEs 86: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 86: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 86: 86: Using 1 MPI thread 86: Using 1 OpenMP thread 86: 86: 86: NOTE: Thread affinity was not set. 86: starting mdrun 'spc2' 86: 16 steps, 0.0 ps. 86: Generated 330891 of the 330891 non-bonded parameter combinations 86: 86: Generated 330891 of the 330891 1-4 parameter combinations 86: 86: Excluding 2 bonded neighbours molecule type 'SOL' 86: 86: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/tip3p5.gro' 86: 86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 86: 86: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 86: 86: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 86: 86: Note that mdrun will redetermine rlist based on the actual pair-list setup 86: 86: This run will generate roughly 0 Mb of data 86: 86: Writing final coordinates. 86: 86: Core t (s) Wall t (s) (%) 86: Time: 0.022 0.022 99.1 86: (ns/day) (hour/ns) 86: Performance: 65.318 0.367 86: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as double precision energy file 86: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as double precision energy file 86: 86: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 86: that with the Verlet scheme, nstlist has no effect on the accuracy of 86: your simulation. 86: 86: 86: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 86: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 86: setting nstcomm equal to nstcalcenergy for less overhead 86: 86: Generating 1-4 interactions: fudge = 0.5 86: Number of degrees of freedom in T-Coupling group System is 27.00 86: 86: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 86: You are using a plain Coulomb cut-off, which might produce artifacts. 86: You might want to consider using PME electrostatics. 86: 86: 86: 86: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 86: COM removal frequency is set to (5). 86: Other settings require a global communication frequency of 100. 86: Note that this will require additional global communication steps, 86: which will reduce performance when using multiple ranks. 86: Consider setting nstcomm to a multiple of 100. 86: 86: 86: There were 4 NOTEs 86: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 86: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 86: 86: Using 1 MPI thread 86: Using 1 OpenMP thread 86: 86: 86: NOTE: Thread affinity was not set. 86: starting mdrun 'spc2' 86: 16 steps, 0.0 ps. 86: Generated 330891 of the 330891 non-bonded parameter combinations 86: 86: Generated 330891 of the 330891 1-4 parameter combinations 86: 86: Excluding 2 bonded neighbours molecule type 'SOL' 86: 86: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/tip3p5.gro' 86: 86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 86: 86: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 86: 86: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 86: 86: Note that mdrun will redetermine rlist based on the actual pair-list setup 86: 86: This run will generate roughly 0 Mb of data 86: 86: Writing final coordinates. 86: 86: Core t (s) Wall t (s) (%) 86: Time: 0.024 0.025 99.1 86: (ns/day) (hour/ns) 86: Performance: 59.507 0.403 86: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as double precision energy file 86: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as double precision energy file 86: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/6 (35208 ms) 86: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/7 86: 86: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 86: that with the Verlet scheme, nstlist has no effect on the accuracy of 86: your simulation. 86: 86: 86: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 86: Setting nstcalcenergy (100) equal to nstenergy (1) 86: 86: Generating 1-4 interactions: fudge = 0.5 86: Number of degrees of freedom in T-Coupling group System is 27.00 86: 86: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 86: You are using a plain Coulomb cut-off, which might produce artifacts. 86: You might want to consider using PME electrostatics. 86: 86: 86: 86: There were 3 NOTEs 86: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 86: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 86: 86: Using 1 MPI thread 86: Using 1 OpenMP thread 86: 86: 86: NOTE: Thread affinity was not set. 86: starting mdrun 'spc2' 86: 16 steps, 0.0 ps. 86: Generated 330891 of the 330891 non-bonded parameter combinations 86: 86: Generated 330891 of the 330891 1-4 parameter combinations 86: 86: Excluding 2 bonded neighbours molecule type 'SOL' 86: 86: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/tip3p5.gro' 86: 86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 86: 86: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 86: 86: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 86: 86: Note that mdrun will redetermine rlist based on the actual pair-list setup 86: 86: This run will generate roughly 0 Mb of data 86: 86: Writing final coordinates. 86: 86: Core t (s) Wall t (s) (%) 86: Time: 0.049 0.049 99.5 86: (ns/day) (hour/ns) 86: Performance: 29.782 0.806 86: 86: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 86: that with the Verlet scheme, nstlist has no effect on the accuracy of 86: your simulation. 86: 86: 86: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 86: Setting nstcalcenergy (100) equal to nstenergy (1) 86: 86: Generating 1-4 interactions: fudge = 0.5 86: Number of degrees of freedom in T-Coupling group System is 27.00 86: 86: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 86: You are using a plain Coulomb cut-off, which might produce artifacts. 86: You might want to consider using PME electrostatics. 86: 86: 86: 86: There were 3 NOTEs 86: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 86: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 86: 86: Using 1 MPI thread 86: Using 1 OpenMP thread 86: 86: 86: NOTE: Thread affinity was not set. 86: starting mdrun 'spc2' 86: 16 steps, 0.0 ps. 86: Generated 330891 of the 330891 non-bonded parameter combinations 86: 86: Generated 330891 of the 330891 1-4 parameter combinations 86: 86: Excluding 2 bonded neighbours molecule type 'SOL' 86: 86: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/tip3p5.gro' 86: 86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 86: 86: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 86: 86: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 86: 86: Note that mdrun will redetermine rlist based on the actual pair-list setup 86: 86: This run will generate roughly 0 Mb of data 86: 86: Writing final coordinates. 86: 86: Core t (s) Wall t (s) (%) 86: Time: 0.023 0.023 99.0 86: (ns/day) (hour/ns) 86: Performance: 63.944 0.375 86: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as double precision energy file 86: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as double precision energy file 86: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 86: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 86: that with the Verlet scheme, nstlist has no effect on the accuracy of 86: your simulation. 86: 86: 86: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 86: Setting nstcalcenergy (100) equal to nstenergy (4) 86: 86: Generating 1-4 interactions: fudge = 0.5 86: Number of degrees of freedom in T-Coupling group System is 27.00 86: 86: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 86: You are using a plain Coulomb cut-off, which might produce artifacts. 86: You might want to consider using PME electrostatics. 86: 86: 86: 86: There were 3 NOTEs 86: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 86: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 86: 86: Using 1 MPI thread 86: Using 1 OpenMP thread 86: 86: 86: NOTE: Thread affinity was not set. 86: starting mdrun 'spc2' 86: 16 steps, 0.0 ps. 86: Generated 330891 of the 330891 non-bonded parameter combinations 86: 86: Generated 330891 of the 330891 1-4 parameter combinations 86: 86: Excluding 2 bonded neighbours molecule type 'SOL' 86: 86: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/tip3p5.gro' 86: 86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 86: 86: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 86: 86: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 86: 86: Note that mdrun will redetermine rlist based on the actual pair-list setup 86: 86: This run will generate roughly 0 Mb of data 86: 86: Writing final coordinates. 86: 86: Core t (s) Wall t (s) (%) 86: Time: 0.020 0.020 98.9 86: (ns/day) (hour/ns) 86: Performance: 71.915 0.334 86: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as double precision energy file 86: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as double precision energy file 86: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 86: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 86: that with the Verlet scheme, nstlist has no effect on the accuracy of 86: your simulation. 86: 86: 86: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 86: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 86: setting nstcomm equal to nstcalcenergy for less overhead 86: 86: Generating 1-4 interactions: fudge = 0.5 86: Number of degrees of freedom in T-Coupling group System is 27.00 86: 86: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 86: You are using a plain Coulomb cut-off, which might produce artifacts. 86: You might want to consider using PME electrostatics. 86: 86: 86: 86: There were 3 NOTEs 86: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 86: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 86: 86: Using 1 MPI thread 86: Using 1 OpenMP thread 86: 86: 86: NOTE: Thread affinity was not set. 86: starting mdrun 'spc2' 86: 16 steps, 0.0 ps. 86: Generated 330891 of the 330891 non-bonded parameter combinations 86: 86: Generated 330891 of the 330891 1-4 parameter combinations 86: 86: Excluding 2 bonded neighbours molecule type 'SOL' 86: 86: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/tip3p5.gro' 86: 86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 86: 86: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 86: 86: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 86: 86: Note that mdrun will redetermine rlist based on the actual pair-list setup 86: 86: This run will generate roughly 0 Mb of data 86: 86: Writing final coordinates. 86: 86: Core t (s) Wall t (s) (%) 86: Time: 0.024 0.024 99.0 86: (ns/day) (hour/ns) 86: Performance: 60.397 0.397 86: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as double precision energy file 86: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as double precision energy file 86: 86: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 86: that with the Verlet scheme, nstlist has no effect on the accuracy of 86: your simulation. 86: 86: 86: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 86: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 86: setting nstcomm equal to nstcalcenergy for less overhead 86: 86: Generating 1-4 interactions: fudge = 0.5 86: Number of degrees of freedom in T-Coupling group System is 27.00 86: 86: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 86: You are using a plain Coulomb cut-off, which might produce artifacts. 86: You might want to consider using PME electrostatics. 86: 86: 86: 86: There were 3 NOTEs 86: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 86: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 86: 86: Using 1 MPI thread 86: Using 1 OpenMP thread 86: 86: 86: NOTE: Thread affinity was not set. 86: starting mdrun 'spc2' 86: 16 steps, 0.0 ps. 86: Generated 330891 of the 330891 non-bonded parameter combinations 86: 86: Generated 330891 of the 330891 1-4 parameter combinations 86: 86: Excluding 2 bonded neighbours molecule type 'SOL' 86: 86: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/tip3p5.gro' 86: 86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 86: 86: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 86: 86: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 86: 86: Note that mdrun will redetermine rlist based on the actual pair-list setup 86: 86: This run will generate roughly 0 Mb of data 86: 86: Writing final coordinates. 86: 86: Core t (s) Wall t (s) (%) 86: Time: 0.027 0.027 99.2 86: (ns/day) (hour/ns) 86: Performance: 54.203 0.443 86: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as double precision energy file 86: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as double precision energy file 86: 86: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 86: that with the Verlet scheme, nstlist has no effect on the accuracy of 86: your simulation. 86: 86: 86: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 86: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 86: setting nstcomm equal to nstcalcenergy for less overhead 86: 86: Generating 1-4 interactions: fudge = 0.5 86: Number of degrees of freedom in T-Coupling group System is 27.00 86: 86: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 86: You are using a plain Coulomb cut-off, which might produce artifacts. 86: You might want to consider using PME electrostatics. 86: 86: 86: 86: There were 3 NOTEs 86: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 86: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 86: 86: Using 1 MPI thread 86: Using 1 OpenMP thread 86: 86: 86: NOTE: Thread affinity was not set. 86: starting mdrun 'spc2' 86: 16 steps, 0.0 ps. 86: Generated 330891 of the 330891 non-bonded parameter combinations 86: 86: Generated 330891 of the 330891 1-4 parameter combinations 86: 86: Excluding 2 bonded neighbours molecule type 'SOL' 86: 86: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/tip3p5.gro' 86: 86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 86: 86: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 86: 86: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 86: 86: Note that mdrun will redetermine rlist based on the actual pair-list setup 86: 86: This run will generate roughly 0 Mb of data 86: 86: Writing final coordinates. 86: 86: Core t (s) Wall t (s) (%) 86: Time: 0.024 0.024 99.1 86: (ns/day) (hour/ns) 86: Performance: 60.150 0.399 86: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as double precision energy file 86: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as double precision energy file 86: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/7 (35077 ms) 86: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/8 86: 86: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 86: that with the Verlet scheme, nstlist has no effect on the accuracy of 86: your simulation. 86: 86: 86: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 86: Setting nstcalcenergy (100) equal to nstenergy (1) 86: 86: Generating 1-4 interactions: fudge = 0.5 86: Number of degrees of freedom in T-Coupling group System is 27.00 86: 86: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 86: You are using a plain Coulomb cut-off, which might produce artifacts. 86: You might want to consider using PME electrostatics. 86: 86: 86: 86: There were 3 NOTEs 86: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 86: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 86: 86: Using 1 MPI thread 86: Using 1 OpenMP thread 86: 86: 86: NOTE: Thread affinity was not set. 86: starting mdrun 'spc2' 86: 16 steps, 0.0 ps. 86: Generated 330891 of the 330891 non-bonded parameter combinations 86: 86: Generated 330891 of the 330891 1-4 parameter combinations 86: 86: Excluding 2 bonded neighbours molecule type 'SOL' 86: 86: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/tip3p5.gro' 86: 86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 86: 86: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 86: 86: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 86: 86: Note that mdrun will redetermine rlist based on the actual pair-list setup 86: 86: This run will generate roughly 0 Mb of data 86: 86: Writing final coordinates. 86: 86: Core t (s) Wall t (s) (%) 86: Time: 0.049 0.049 99.2 86: (ns/day) (hour/ns) 86: Performance: 29.925 0.802 86: 86: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 86: that with the Verlet scheme, nstlist has no effect on the accuracy of 86: your simulation. 86: 86: 86: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 86: Setting nstcalcenergy (100) equal to nstenergy (1) 86: 86: Generating 1-4 interactions: fudge = 0.5 86: Number of degrees of freedom in T-Coupling group System is 27.00 86: 86: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 86: You are using a plain Coulomb cut-off, which might produce artifacts. 86: You might want to consider using PME electrostatics. 86: 86: 86: 86: There were 3 NOTEs 86: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 86: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 86: 86: Using 1 MPI thread 86: Using 1 OpenMP thread 86: 86: 86: NOTE: Thread affinity was not set. 86: starting mdrun 'spc2' 86: 16 steps, 0.0 ps. 86: Generated 330891 of the 330891 non-bonded parameter combinations 86: 86: Generated 330891 of the 330891 1-4 parameter combinations 86: 86: Excluding 2 bonded neighbours molecule type 'SOL' 86: 86: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/tip3p5.gro' 86: 86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 86: 86: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 86: 86: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 86: 86: Note that mdrun will redetermine rlist based on the actual pair-list setup 86: 86: This run will generate roughly 0 Mb of data 86: 86: Writing final coordinates. 86: 86: Core t (s) Wall t (s) (%) 86: Time: 0.021 0.021 98.9 86: (ns/day) (hour/ns) 86: Performance: 69.684 0.344 86: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_reference.edr as double precision energy file 86: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.edr as double precision energy file 86: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 86: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 86: that with the Verlet scheme, nstlist has no effect on the accuracy of 86: your simulation. 86: 86: 86: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 86: Setting nstcalcenergy (100) equal to nstenergy (4) 86: 86: Generating 1-4 interactions: fudge = 0.5 86: Number of degrees of freedom in T-Coupling group System is 27.00 86: 86: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 86: You are using a plain Coulomb cut-off, which might produce artifacts. 86: You might want to consider using PME electrostatics. 86: 86: 86: 86: There were 3 NOTEs 86: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 86: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 86: 86: Using 1 MPI thread 86: Using 1 OpenMP thread 86: 86: 86: NOTE: Thread affinity was not set. 86: starting mdrun 'spc2' 86: 16 steps, 0.0 ps. 86: Generated 330891 of the 330891 non-bonded parameter combinations 86: 86: Generated 330891 of the 330891 1-4 parameter combinations 86: 86: Excluding 2 bonded neighbours molecule type 'SOL' 86: 86: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/tip3p5.gro' 86: 86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 86: 86: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 86: 86: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 86: 86: Note that mdrun will redetermine rlist based on the actual pair-list setup 86: 86: This run will generate roughly 0 Mb of data 86: 86: Writing final coordinates. 86: 86: Core t (s) Wall t (s) (%) 86: Time: 0.022 0.022 98.9 86: (ns/day) (hour/ns) 86: Performance: 66.882 0.359 86: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_reference.edr as double precision energy file 86: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.edr as double precision energy file 86: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 86: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 86: that with the Verlet scheme, nstlist has no effect on the accuracy of 86: your simulation. 86: 86: 86: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 86: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 86: setting nstcomm equal to nstcalcenergy for less overhead 86: 86: Generating 1-4 interactions: fudge = 0.5 86: Number of degrees of freedom in T-Coupling group System is 27.00 86: 86: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 86: You are using a plain Coulomb cut-off, which might produce artifacts. 86: You might want to consider using PME electrostatics. 86: 86: 86: 86: There were 3 NOTEs 86: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 86: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 86: 86: Using 1 MPI thread 86: Using 1 OpenMP thread 86: 86: 86: NOTE: Thread affinity was not set. 86: starting mdrun 'spc2' 86: 16 steps, 0.0 ps. 86: Generated 330891 of the 330891 non-bonded parameter combinations 86: 86: Generated 330891 of the 330891 1-4 parameter combinations 86: 86: Excluding 2 bonded neighbours molecule type 'SOL' 86: 86: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/tip3p5.gro' 86: 86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 86: 86: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 86: 86: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 86: 86: Note that mdrun will redetermine rlist based on the actual pair-list setup 86: 86: This run will generate roughly 0 Mb of data 86: 86: Writing final coordinates. 86: 86: Core t (s) Wall t (s) (%) 86: Time: 0.024 0.024 99.1 86: (ns/day) (hour/ns) 86: Performance: 59.961 0.400 86: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_reference.edr as double precision energy file 86: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.edr as double precision energy file 86: 86: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 86: that with the Verlet scheme, nstlist has no effect on the accuracy of 86: your simulation. 86: 86: 86: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 86: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 86: setting nstcomm equal to nstcalcenergy for less overhead 86: 86: Generating 1-4 interactions: fudge = 0.5 86: Number of degrees of freedom in T-Coupling group System is 27.00 86: 86: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 86: You are using a plain Coulomb cut-off, which might produce artifacts. 86: You might want to consider using PME electrostatics. 86: 86: 86: 86: There were 3 NOTEs 86: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 86: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 86: 86: Using 1 MPI thread 86: Using 1 OpenMP thread 86: 86: 86: NOTE: Thread affinity was not set. 86: starting mdrun 'spc2' 86: 16 steps, 0.0 ps. 86: Generated 330891 of the 330891 non-bonded parameter combinations 86: 86: Generated 330891 of the 330891 1-4 parameter combinations 86: 86: Excluding 2 bonded neighbours molecule type 'SOL' 86: 86: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/tip3p5.gro' 86: 86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 86: 86: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 86: 86: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 86: 86: Note that mdrun will redetermine rlist based on the actual pair-list setup 86: 86: This run will generate roughly 0 Mb of data 86: 86: Writing final coordinates. 86: 86: Core t (s) Wall t (s) (%) 86: Time: 0.025 0.026 99.1 86: (ns/day) (hour/ns) 86: Performance: 57.483 0.418 86: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_reference.edr as double precision energy file 86: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.edr as double precision energy file 86: 86: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 86: that with the Verlet scheme, nstlist has no effect on the accuracy of 86: your simulation. 86: 86: 86: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 86: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 86: setting nstcomm equal to nstcalcenergy for less overhead 86: 86: Generating 1-4 interactions: fudge = 0.5 86: Number of degrees of freedom in T-Coupling group System is 27.00 86: 86: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 86: You are using a plain Coulomb cut-off, which might produce artifacts. 86: You might want to consider using PME electrostatics. 86: 86: 86: 86: There were 3 NOTEs 86: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 86: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 86: 86: Using 1 MPI thread 86: Using 1 OpenMP thread 86: 86: 86: NOTE: Thread affinity was not set. 86: starting mdrun 'spc2' 86: 16 steps, 0.0 ps. 86: Generated 330891 of the 330891 non-bonded parameter combinations 86: 86: Generated 330891 of the 330891 1-4 parameter combinations 86: 86: Excluding 2 bonded neighbours molecule type 'SOL' 86: 86: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/tip3p5.gro' 86: 86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 86: 86: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 86: 86: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 86: 86: Note that mdrun will redetermine rlist based on the actual pair-list setup 86: 86: This run will generate roughly 0 Mb of data 86: 86: Writing final coordinates. 86: 86: Core t (s) Wall t (s) (%) 86: Time: 0.027 0.027 99.2 86: (ns/day) (hour/ns) 86: Performance: 54.647 0.439 86: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_reference.edr as double precision energy file 86: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.edr as double precision energy file 86: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/8 (35285 ms) 86: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/9 86: 86: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 86: that with the Verlet scheme, nstlist has no effect on the accuracy of 86: your simulation. 86: 86: 86: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 86: Setting nstcalcenergy (100) equal to nstenergy (1) 86: 86: Generating 1-4 interactions: fudge = 0.5 86: Number of degrees of freedom in T-Coupling group System is 27.00 86: 86: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 86: NVE simulation: will use the initial temperature of 398.997 K for 86: determining the Verlet buffer size 86: 86: 86: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 86: You are using a plain Coulomb cut-off, which might produce artifacts. 86: You might want to consider using PME electrostatics. 86: 86: 86: 86: There were 4 NOTEs 86: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 86: Can not increase nstlist because an NVE ensemble is used 86: Using 1 MPI thread 86: Using 1 OpenMP thread 86: 86: 86: NOTE: Thread affinity was not set. 86: starting mdrun 'spc2' 86: 16 steps, 0.0 ps. 86: Generated 330891 of the 330891 non-bonded parameter combinations 86: 86: Generated 330891 of the 330891 1-4 parameter combinations 86: 86: Excluding 2 bonded neighbours molecule type 'SOL' 86: 86: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/tip3p5.gro' 86: 86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 86: 86: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 86: 86: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 86: 86: Note that mdrun will redetermine rlist based on the actual pair-list setup 86: 86: This run will generate roughly 0 Mb of data 86: 86: Writing final coordinates. 86: 86: Core t (s) Wall t (s) (%) 86: Time: 0.047 0.048 99.6 86: (ns/day) (hour/ns) 86: Performance: 30.915 0.776 86: 86: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 86: that with the Verlet scheme, nstlist has no effect on the accuracy of 86: your simulation. 86: 86: 86: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 86: Setting nstcalcenergy (100) equal to nstenergy (1) 86: 86: Generating 1-4 interactions: fudge = 0.5 86: Number of degrees of freedom in T-Coupling group System is 27.00 86: 86: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 86: NVE simulation: will use the initial temperature of 398.997 K for 86: determining the Verlet buffer size 86: 86: 86: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 86: You are using a plain Coulomb cut-off, which might produce artifacts. 86: You might want to consider using PME electrostatics. 86: 86: 86: 86: There were 4 NOTEs 86: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 86: Can not increase nstlist because an NVE ensemble is used 86: Using 1 MPI thread 86: Using 1 OpenMP thread 86: 86: 86: NOTE: Thread affinity was not set. 86: starting mdrun 'spc2' 86: 16 steps, 0.0 ps. 86: Generated 330891 of the 330891 non-bonded parameter combinations 86: 86: Generated 330891 of the 330891 1-4 parameter combinations 86: 86: Excluding 2 bonded neighbours molecule type 'SOL' 86: 86: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/tip3p5.gro' 86: 86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 86: 86: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 86: 86: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 86: 86: Note that mdrun will redetermine rlist based on the actual pair-list setup 86: 86: This run will generate roughly 0 Mb of data 86: 86: Writing final coordinates. 86: 86: Core t (s) Wall t (s) (%) 86: Time: 0.023 0.023 99.3 86: (ns/day) (hour/ns) 86: Performance: 63.587 0.377 86: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_reference.edr as double precision energy file 86: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.edr as double precision energy file 86: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 86: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 86: that with the Verlet scheme, nstlist has no effect on the accuracy of 86: your simulation. 86: 86: 86: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 86: Setting nstcalcenergy (100) equal to nstenergy (4) 86: 86: Generating 1-4 interactions: fudge = 0.5 86: Number of degrees of freedom in T-Coupling group System is 27.00 86: 86: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 86: NVE simulation: will use the initial temperature of 398.997 K for 86: determining the Verlet buffer size 86: 86: 86: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 86: You are using a plain Coulomb cut-off, which might produce artifacts. 86: You might want to consider using PME electrostatics. 86: 86: 86: 86: NOTE 5 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 86: COM removal frequency is set to (5). 86: Other settings require a global communication frequency of 4. 86: Note that this will require additional global communication steps, 86: which will reduce performance when using multiple ranks. 86: Consider setting nstcomm to a multiple of 4. 86: 86: 86: There were 5 NOTEs 86: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 86: Can not increase nstlist because an NVE ensemble is used 86: Using 1 MPI thread 86: Using 1 OpenMP thread 86: 86: 86: NOTE: Thread affinity was not set. 86: starting mdrun 'spc2' 86: 16 steps, 0.0 ps. 86: Generated 330891 of the 330891 non-bonded parameter combinations 86: 86: Generated 330891 of the 330891 1-4 parameter combinations 86: 86: Excluding 2 bonded neighbours molecule type 'SOL' 86: 86: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/tip3p5.gro' 86: 86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 86: 86: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 86: 86: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 86: 86: Note that mdrun will redetermine rlist based on the actual pair-list setup 86: 86: This run will generate roughly 0 Mb of data 86: 86: Writing final coordinates. 86: 86: Core t (s) Wall t (s) (%) 86: Time: 0.023 0.023 99.3 86: (ns/day) (hour/ns) 86: Performance: 63.819 0.376 86: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_reference.edr as double precision energy file 86: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.edr as double precision energy file 86: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 86: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 86: that with the Verlet scheme, nstlist has no effect on the accuracy of 86: your simulation. 86: 86: 86: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 86: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 86: setting nstcomm equal to nstcalcenergy for less overhead 86: 86: Generating 1-4 interactions: fudge = 0.5 86: Number of degrees of freedom in T-Coupling group System is 27.00 86: 86: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 86: NVE simulation: will use the initial temperature of 398.997 K for 86: determining the Verlet buffer size 86: 86: 86: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 86: You are using a plain Coulomb cut-off, which might produce artifacts. 86: You might want to consider using PME electrostatics. 86: 86: 86: 86: NOTE 5 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 86: COM removal frequency is set to (5). 86: Other settings require a global communication frequency of 100. 86: Note that this will require additional global communication steps, 86: which will reduce performance when using multiple ranks. 86: Consider setting nstcomm to a multiple of 100. 86: 86: 86: There were 5 NOTEs 86: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 86: Can not increase nstlist because an NVE ensemble is used 86: Using 1 MPI thread 86: Using 1 OpenMP thread 86: 86: 86: NOTE: Thread affinity was not set. 86: starting mdrun 'spc2' 86: 16 steps, 0.0 ps. 86: Generated 330891 of the 330891 non-bonded parameter combinations 86: 86: Generated 330891 of the 330891 1-4 parameter combinations 86: 86: Excluding 2 bonded neighbours molecule type 'SOL' 86: 86: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/tip3p5.gro' 86: 86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 86: 86: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 86: 86: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 86: 86: Note that mdrun will redetermine rlist based on the actual pair-list setup 86: 86: This run will generate roughly 0 Mb of data 86: 86: Writing final coordinates. 86: 86: Core t (s) Wall t (s) (%) 86: Time: 0.026 0.026 99.1 86: (ns/day) (hour/ns) 86: Performance: 56.756 0.423 86: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_reference.edr as double precision energy file 86: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.edr as double precision energy file 86: 86: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 86: that with the Verlet scheme, nstlist has no effect on the accuracy of 86: your simulation. 86: 86: 86: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 86: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 86: setting nstcomm equal to nstcalcenergy for less overhead 86: 86: Generating 1-4 interactions: fudge = 0.5 86: Number of degrees of freedom in T-Coupling group System is 27.00 86: 86: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 86: NVE simulation: will use the initial temperature of 398.997 K for 86: determining the Verlet buffer size 86: 86: 86: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 86: You are using a plain Coulomb cut-off, which might produce artifacts. 86: You might want to consider using PME electrostatics. 86: 86: 86: 86: NOTE 5 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 86: COM removal frequency is set to (5). 86: Other settings require a global communication frequency of 100. 86: Note that this will require additional global communication steps, 86: which will reduce performance when using multiple ranks. 86: Consider setting nstcomm to a multiple of 100. 86: 86: 86: There were 5 NOTEs 86: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 86: Can not increase nstlist because an NVE ensemble is used 86: Using 1 MPI thread 86: Using 1 OpenMP thread 86: 86: 86: NOTE: Thread affinity was not set. 86: starting mdrun 'spc2' 86: 16 steps, 0.0 ps. 86: Generated 330891 of the 330891 non-bonded parameter combinations 86: 86: Generated 330891 of the 330891 1-4 parameter combinations 86: 86: Excluding 2 bonded neighbours molecule type 'SOL' 86: 86: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/tip3p5.gro' 86: 86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 86: 86: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 86: 86: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 86: 86: Note that mdrun will redetermine rlist based on the actual pair-list setup 86: 86: This run will generate roughly 0 Mb of data 86: 86: Writing final coordinates. 86: 86: Core t (s) Wall t (s) (%) 86: Time: 0.026 0.026 99.4 86: (ns/day) (hour/ns) 86: Performance: 55.965 0.429 86: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_reference.edr as double precision energy file 86: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.edr as double precision energy file 86: 86: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 86: that with the Verlet scheme, nstlist has no effect on the accuracy of 86: your simulation. 86: 86: 86: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 86: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 86: setting nstcomm equal to nstcalcenergy for less overhead 86: 86: Generating 1-4 interactions: fudge = 0.5 86: Number of degrees of freedom in T-Coupling group System is 27.00 86: 86: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 86: NVE simulation: will use the initial temperature of 398.997 K for 86: determining the Verlet buffer size 86: 86: 86: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 86: You are using a plain Coulomb cut-off, which might produce artifacts. 86: You might want to consider using PME electrostatics. 86: 86: 86: 86: NOTE 5 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 86: COM removal frequency is set to (5). 86: Other settings require a global communication frequency of 100. 86: Note that this will require additional global communication steps, 86: which will reduce performance when using multiple ranks. 86: Consider setting nstcomm to a multiple of 100. 86: 86: 86: There were 5 NOTEs 86: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 86: Can not increase nstlist because an NVE ensemble is used 86: Using 1 MPI thread 86: Using 1 OpenMP thread 86: 86: 86: NOTE: Thread affinity was not set. 86: starting mdrun 'spc2' 86: 16 steps, 0.0 ps. 86: Generated 330891 of the 330891 non-bonded parameter combinations 86: 86: Generated 330891 of the 330891 1-4 parameter combinations 86: 86: Excluding 2 bonded neighbours molecule type 'SOL' 86: 86: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/tip3p5.gro' 86: 86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 86: 86: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 86: 86: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 86: 86: Note that mdrun will redetermine rlist based on the actual pair-list setup 86: 86: This run will generate roughly 0 Mb of data 86: 86: Writing final coordinates. 86: 86: Core t (s) Wall t (s) (%) 86: Time: 0.028 0.028 99.4 86: (ns/day) (hour/ns) 86: Performance: 53.021 0.453 86: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_reference.edr as double precision energy file 86: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.edr as double precision energy file 86: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/9 (35275 ms) 86: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/10 86: 86: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 86: that with the Verlet scheme, nstlist has no effect on the accuracy of 86: your simulation. 86: 86: 86: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 86: Setting nstcalcenergy (100) equal to nstenergy (1) 86: 86: Generating 1-4 interactions: fudge = 0.5 86: Number of degrees of freedom in T-Coupling group System is 27.00 86: 86: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 86: NVE simulation: will use the initial temperature of 398.997 K for 86: determining the Verlet buffer size 86: 86: 86: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 86: You are using a plain Coulomb cut-off, which might produce artifacts. 86: You might want to consider using PME electrostatics. 86: 86: 86: 86: There were 4 NOTEs 86: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 86: Can not increase nstlist because an NVE ensemble is used 86: Using 1 MPI thread 86: Using 1 OpenMP thread 86: 86: 86: NOTE: Thread affinity was not set. 86: starting mdrun 'spc2' 86: 16 steps, 0.0 ps. 86: Generated 330891 of the 330891 non-bonded parameter combinations 86: 86: Generated 330891 of the 330891 1-4 parameter combinations 86: 86: Excluding 2 bonded neighbours molecule type 'SOL' 86: 86: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/tip3p5.gro' 86: 86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 86: 86: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 86: 86: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 86: 86: Note that mdrun will redetermine rlist based on the actual pair-list setup 86: 86: This run will generate roughly 0 Mb of data 86: 86: Writing final coordinates. 86: 86: Core t (s) Wall t (s) (%) 86: Time: 0.052 0.053 99.6 86: (ns/day) (hour/ns) 86: Performance: 27.877 0.861 86: 86: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 86: that with the Verlet scheme, nstlist has no effect on the accuracy of 86: your simulation. 86: 86: 86: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 86: Setting nstcalcenergy (100) equal to nstenergy (1) 86: 86: Generating 1-4 interactions: fudge = 0.5 86: Number of degrees of freedom in T-Coupling group System is 27.00 86: 86: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 86: NVE simulation: will use the initial temperature of 398.997 K for 86: determining the Verlet buffer size 86: 86: 86: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 86: You are using a plain Coulomb cut-off, which might produce artifacts. 86: You might want to consider using PME electrostatics. 86: 86: 86: 86: There were 4 NOTEs 86: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 86: Can not increase nstlist because an NVE ensemble is used 86: Using 1 MPI thread 86: Using 1 OpenMP thread 86: 86: 86: NOTE: Thread affinity was not set. 86: starting mdrun 'spc2' 86: 16 steps, 0.0 ps. 86: Generated 330891 of the 330891 non-bonded parameter combinations 86: 86: Generated 330891 of the 330891 1-4 parameter combinations 86: 86: Excluding 2 bonded neighbours molecule type 'SOL' 86: 86: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/tip3p5.gro' 86: 86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 86: 86: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 86: 86: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 86: 86: Note that mdrun will redetermine rlist based on the actual pair-list setup 86: 86: This run will generate roughly 0 Mb of data 86: 86: Writing final coordinates. 86: 86: Core t (s) Wall t (s) (%) 86: Time: 0.026 0.026 99.3 86: (ns/day) (hour/ns) 86: Performance: 55.731 0.431 86: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_reference.edr as double precision energy file 86: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.edr as double precision energy file 86: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 86: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 86: that with the Verlet scheme, nstlist has no effect on the accuracy of 86: your simulation. 86: 86: 86: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 86: Setting nstcalcenergy (100) equal to nstenergy (4) 86: 86: Generating 1-4 interactions: fudge = 0.5 86: Number of degrees of freedom in T-Coupling group System is 27.00 86: 86: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 86: NVE simulation: will use the initial temperature of 398.997 K for 86: determining the Verlet buffer size 86: 86: 86: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 86: You are using a plain Coulomb cut-off, which might produce artifacts. 86: You might want to consider using PME electrostatics. 86: 86: 86: 86: There were 4 NOTEs 86: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 86: Can not increase nstlist because an NVE ensemble is used 86: Using 1 MPI thread 86: Using 1 OpenMP thread 86: 86: 86: NOTE: Thread affinity was not set. 86: starting mdrun 'spc2' 86: 16 steps, 0.0 ps. 86: Generated 330891 of the 330891 non-bonded parameter combinations 86: 86: Generated 330891 of the 330891 1-4 parameter combinations 86: 86: Excluding 2 bonded neighbours molecule type 'SOL' 86: 86: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/tip3p5.gro' 86: 86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 86: 86: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 86: 86: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 86: 86: Note that mdrun will redetermine rlist based on the actual pair-list setup 86: 86: This run will generate roughly 0 Mb of data 86: 86: Writing final coordinates. 86: 86: Core t (s) Wall t (s) (%) 86: Time: 0.023 0.023 99.2 86: (ns/day) (hour/ns) 86: Performance: 62.788 0.382 86: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_reference.edr as double precision energy file 86: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.edr as double precision energy file 86: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 86: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 86: that with the Verlet scheme, nstlist has no effect on the accuracy of 86: your simulation. 86: 86: 86: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 86: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 86: setting nstcomm equal to nstcalcenergy for less overhead 86: 86: Generating 1-4 interactions: fudge = 0.5 86: Number of degrees of freedom in T-Coupling group System is 27.00 86: 86: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 86: NVE simulation: will use the initial temperature of 398.997 K for 86: determining the Verlet buffer size 86: 86: 86: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 86: You are using a plain Coulomb cut-off, which might produce artifacts. 86: You might want to consider using PME electrostatics. 86: 86: 86: 86: There were 4 NOTEs 86: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 86: Can not increase nstlist because an NVE ensemble is used 86: Using 1 MPI thread 86: Using 1 OpenMP thread 86: 86: 86: NOTE: Thread affinity was not set. 86: starting mdrun 'spc2' 86: 16 steps, 0.0 ps. 86: Generated 330891 of the 330891 non-bonded parameter combinations 86: 86: Generated 330891 of the 330891 1-4 parameter combinations 86: 86: Excluding 2 bonded neighbours molecule type 'SOL' 86: 86: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/tip3p5.gro' 86: 86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 86: 86: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 86: 86: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 86: 86: Note that mdrun will redetermine rlist based on the actual pair-list setup 86: 86: This run will generate roughly 0 Mb of data 86: 86: Writing final coordinates. 86: 86: Core t (s) Wall t (s) (%) 86: Time: 0.028 0.028 99.4 86: (ns/day) (hour/ns) 86: Performance: 52.834 0.454 86: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_reference.edr as double precision energy file 86: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.edr as double precision energy file 86: 86: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 86: that with the Verlet scheme, nstlist has no effect on the accuracy of 86: your simulation. 86: 86: 86: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 86: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 86: setting nstcomm equal to nstcalcenergy for less overhead 86: 86: Generating 1-4 interactions: fudge = 0.5 86: Number of degrees of freedom in T-Coupling group System is 27.00 86: 86: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 86: NVE simulation: will use the initial temperature of 398.997 K for 86: determining the Verlet buffer size 86: 86: 86: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 86: You are using a plain Coulomb cut-off, which might produce artifacts. 86: You might want to consider using PME electrostatics. 86: 86: 86: 86: There were 4 NOTEs 86: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 86: Can not increase nstlist because an NVE ensemble is used 86: Using 1 MPI thread 86: Using 1 OpenMP thread 86: 86: 86: NOTE: Thread affinity was not set. 86: starting mdrun 'spc2' 86: 16 steps, 0.0 ps. 86: Generated 330891 of the 330891 non-bonded parameter combinations 86: 86: Generated 330891 of the 330891 1-4 parameter combinations 86: 86: Excluding 2 bonded neighbours molecule type 'SOL' 86: 86: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/tip3p5.gro' 86: 86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 86: 86: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 86: 86: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 86: 86: Note that mdrun will redetermine rlist based on the actual pair-list setup 86: 86: This run will generate roughly 0 Mb of data 86: 86: Writing final coordinates. 86: 86: Core t (s) Wall t (s) (%) 86: Time: 0.034 0.034 99.5 86: (ns/day) (hour/ns) 86: Performance: 43.022 0.558 86: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_reference.edr as double precision energy file 86: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.edr as double precision energy file 86: 86: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 86: that with the Verlet scheme, nstlist has no effect on the accuracy of 86: your simulation. 86: 86: 86: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 86: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 86: setting nstcomm equal to nstcalcenergy for less overhead 86: 86: Generating 1-4 interactions: fudge = 0.5 86: Number of degrees of freedom in T-Coupling group System is 27.00 86: 86: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 86: NVE simulation: will use the initial temperature of 398.997 K for 86: determining the Verlet buffer size 86: 86: 86: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 86: You are using a plain Coulomb cut-off, which might produce artifacts. 86: You might want to consider using PME electrostatics. 86: 86: 86: 86: There were 4 NOTEs 86: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 86: Can not increase nstlist because an NVE ensemble is used 86: Using 1 MPI thread 86: Using 1 OpenMP thread 86: 86: 86: NOTE: Thread affinity was not set. 86: starting mdrun 'spc2' 86: 16 steps, 0.0 ps. 86: Generated 330891 of the 330891 non-bonded parameter combinations 86: 86: Generated 330891 of the 330891 1-4 parameter combinations 86: 86: Excluding 2 bonded neighbours molecule type 'SOL' 86: 86: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/tip3p5.gro' 86: 86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 86: 86: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 86: 86: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 86: 86: Note that mdrun will redetermine rlist based on the actual pair-list setup 86: 86: This run will generate roughly 0 Mb of data 86: 86: Writing final coordinates. 86: 86: Core t (s) Wall t (s) (%) 86: Time: 0.027 0.027 99.4 86: (ns/day) (hour/ns) 86: Performance: 54.181 0.443 86: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_reference.edr as double precision energy file 86: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.edr as double precision energy file 86: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/10 (35175 ms) 86: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/11 86: 86: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 86: that with the Verlet scheme, nstlist has no effect on the accuracy of 86: your simulation. 86: 86: 86: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 86: Setting nstcalcenergy (100) equal to nstenergy (1) 86: 86: Generating 1-4 interactions: fudge = 0.5 86: Number of degrees of freedom in T-Coupling group System is 27.00 86: 86: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 86: You are using a plain Coulomb cut-off, which might produce artifacts. 86: You might want to consider using PME electrostatics. 86: 86: 86: 86: There were 3 NOTEs 86: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 86: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 86: 86: Using 1 MPI thread 86: Using 1 OpenMP thread 86: 86: 86: NOTE: Thread affinity was not set. 86: starting mdrun 'spc2' 86: 16 steps, 0.0 ps. 86: Generated 330891 of the 330891 non-bonded parameter combinations 86: 86: Generated 330891 of the 330891 1-4 parameter combinations 86: 86: Excluding 2 bonded neighbours molecule type 'SOL' 86: 86: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/tip3p5.gro' 86: 86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 86: 86: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 86: 86: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 86: 86: Note that mdrun will redetermine rlist based on the actual pair-list setup 86: 86: This run will generate roughly 0 Mb of data 86: 86: Writing final coordinates. 86: 86: Core t (s) Wall t (s) (%) 86: Time: 0.048 0.049 99.4 86: (ns/day) (hour/ns) 86: Performance: 30.277 0.793 86: 86: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 86: that with the Verlet scheme, nstlist has no effect on the accuracy of 86: your simulation. 86: 86: 86: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 86: Setting nstcalcenergy (100) equal to nstenergy (1) 86: 86: Generating 1-4 interactions: fudge = 0.5 86: Number of degrees of freedom in T-Coupling group System is 27.00 86: 86: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 86: You are using a plain Coulomb cut-off, which might produce artifacts. 86: You might want to consider using PME electrostatics. 86: 86: 86: 86: There were 3 NOTEs 86: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 86: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 86: 86: Using 1 MPI thread 86: Using 1 OpenMP thread 86: 86: 86: NOTE: Thread affinity was not set. 86: starting mdrun 'spc2' 86: 16 steps, 0.0 ps. 86: Generated 330891 of the 330891 non-bonded parameter combinations 86: 86: Generated 330891 of the 330891 1-4 parameter combinations 86: 86: Excluding 2 bonded neighbours molecule type 'SOL' 86: 86: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/tip3p5.gro' 86: 86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 86: 86: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 86: 86: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 86: 86: Note that mdrun will redetermine rlist based on the actual pair-list setup 86: 86: This run will generate roughly 0 Mb of data 86: 86: Writing final coordinates. 86: 86: Core t (s) Wall t (s) (%) 86: Time: 0.023 0.023 98.9 86: (ns/day) (hour/ns) 86: Performance: 63.725 0.377 86: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_reference.edr as double precision energy file 86: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.edr as double precision energy file 86: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 86: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 86: that with the Verlet scheme, nstlist has no effect on the accuracy of 86: your simulation. 86: 86: 86: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 86: Setting nstcalcenergy (100) equal to nstenergy (4) 86: 86: Generating 1-4 interactions: fudge = 0.5 86: Number of degrees of freedom in T-Coupling group System is 27.00 86: 86: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 86: You are using a plain Coulomb cut-off, which might produce artifacts. 86: You might want to consider using PME electrostatics. 86: 86: 86: 86: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 86: COM removal frequency is set to (5). 86: Other settings require a global communication frequency of 2. 86: Note that this will require additional global communication steps, 86: which will reduce performance when using multiple ranks. 86: Consider setting nstcomm to a multiple of 2. 86: 86: 86: There were 4 NOTEs 86: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 86: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 86: 86: Using 1 MPI thread 86: Using 1 OpenMP thread 86: 86: 86: NOTE: Thread affinity was not set. 86: starting mdrun 'spc2' 86: 16 steps, 0.0 ps. 86: Generated 330891 of the 330891 non-bonded parameter combinations 86: 86: Generated 330891 of the 330891 1-4 parameter combinations 86: 86: Excluding 2 bonded neighbours molecule type 'SOL' 86: 86: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/tip3p5.gro' 86: 86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 86: 86: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 86: 86: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 86: 86: Note that mdrun will redetermine rlist based on the actual pair-list setup 86: 86: This run will generate roughly 0 Mb of data 86: 86: Writing final coordinates. 86: 86: Core t (s) Wall t (s) (%) 86: Time: 0.022 0.022 98.9 86: (ns/day) (hour/ns) 86: Performance: 65.283 0.368 86: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_reference.edr as double precision energy file 86: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.edr as double precision energy file 86: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 86: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 86: that with the Verlet scheme, nstlist has no effect on the accuracy of 86: your simulation. 86: 86: 86: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 86: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 86: setting nstcomm equal to nstcalcenergy for less overhead 86: 86: Generating 1-4 interactions: fudge = 0.5 86: Number of degrees of freedom in T-Coupling group System is 27.00 86: 86: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 86: You are using a plain Coulomb cut-off, which might produce artifacts. 86: You might want to consider using PME electrostatics. 86: 86: 86: 86: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 86: COM removal frequency is set to (5). 86: Other settings require a global communication frequency of 2. 86: Note that this will require additional global communication steps, 86: which will reduce performance when using multiple ranks. 86: Consider setting nstcomm to a multiple of 2. 86: 86: 86: There were 4 NOTEs 86: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 86: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 86: 86: Using 1 MPI thread 86: Using 1 OpenMP thread 86: 86: 86: NOTE: Thread affinity was not set. 86: starting mdrun 'spc2' 86: 16 steps, 0.0 ps. 86: Generated 330891 of the 330891 non-bonded parameter combinations 86: 86: Generated 330891 of the 330891 1-4 parameter combinations 86: 86: Excluding 2 bonded neighbours molecule type 'SOL' 86: 86: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/tip3p5.gro' 86: 86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 86: 86: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 86: 86: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 86: 86: Note that mdrun will redetermine rlist based on the actual pair-list setup 86: 86: This run will generate roughly 0 Mb of data 86: 86: Writing final coordinates. 86: 86: Core t (s) Wall t (s) (%) 86: Time: 0.029 0.029 99.1 86: (ns/day) (hour/ns) 86: Performance: 50.603 0.474 86: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_reference.edr as double precision energy file 86: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.edr as double precision energy file 86: 86: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 86: that with the Verlet scheme, nstlist has no effect on the accuracy of 86: your simulation. 86: 86: 86: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 86: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 86: setting nstcomm equal to nstcalcenergy for less overhead 86: 86: Generating 1-4 interactions: fudge = 0.5 86: Number of degrees of freedom in T-Coupling group System is 27.00 86: 86: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 86: You are using a plain Coulomb cut-off, which might produce artifacts. 86: You might want to consider using PME electrostatics. 86: 86: 86: 86: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 86: COM removal frequency is set to (5). 86: Other settings require a global communication frequency of 2. 86: Note that this will require additional global communication steps, 86: which will reduce performance when using multiple ranks. 86: Consider setting nstcomm to a multiple of 2. 86: 86: 86: There were 4 NOTEs 86: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 86: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 86: 86: Using 1 MPI thread 86: Using 1 OpenMP thread 86: 86: 86: NOTE: Thread affinity was not set. 86: starting mdrun 'spc2' 86: 16 steps, 0.0 ps. 86: Generated 330891 of the 330891 non-bonded parameter combinations 86: 86: Generated 330891 of the 330891 1-4 parameter combinations 86: 86: Excluding 2 bonded neighbours molecule type 'SOL' 86: 86: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/tip3p5.gro' 86: 86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 86: 86: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 86: 86: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 86: 86: Note that mdrun will redetermine rlist based on the actual pair-list setup 86: 86: This run will generate roughly 0 Mb of data 86: 86: Writing final coordinates. 86: 86: Core t (s) Wall t (s) (%) 86: Time: 0.026 0.027 99.1 86: (ns/day) (hour/ns) 86: Performance: 54.982 0.437 86: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_reference.edr as double precision energy file 86: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.edr as double precision energy file 86: 86: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 86: that with the Verlet scheme, nstlist has no effect on the accuracy of 86: your simulation. 86: 86: 86: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 86: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 86: setting nstcomm equal to nstcalcenergy for less overhead 86: 86: Generating 1-4 interactions: fudge = 0.5 86: Number of degrees of freedom in T-Coupling group System is 27.00 86: 86: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 86: You are using a plain Coulomb cut-off, which might produce artifacts. 86: You might want to consider using PME electrostatics. 86: 86: 86: 86: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 86: COM removal frequency is set to (5). 86: Other settings require a global communication frequency of 2. 86: Note that this will require additional global communication steps, 86: which will reduce performance when using multiple ranks. 86: Consider setting nstcomm to a multiple of 2. 86: 86: 86: There were 4 NOTEs 86: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 86: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 86: 86: Using 1 MPI thread 86: Using 1 OpenMP thread 86: 86: 86: NOTE: Thread affinity was not set. 86: starting mdrun 'spc2' 86: 16 steps, 0.0 ps. 86: Generated 330891 of the 330891 non-bonded parameter combinations 86: 86: Generated 330891 of the 330891 1-4 parameter combinations 86: 86: Excluding 2 bonded neighbours molecule type 'SOL' 86: 86: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/tip3p5.gro' 86: 86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 86: 86: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 86: 86: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 86: 86: Note that mdrun will redetermine rlist based on the actual pair-list setup 86: 86: This run will generate roughly 0 Mb of data 86: 86: Writing final coordinates. 86: 86: Core t (s) Wall t (s) (%) 86: Time: 0.030 0.031 99.0 86: (ns/day) (hour/ns) 86: Performance: 48.047 0.500 86: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_reference.edr as double precision energy file 86: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.edr as double precision energy file 86: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/11 (35098 ms) 86: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/12 86: 86: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 86: that with the Verlet scheme, nstlist has no effect on the accuracy of 86: your simulation. 86: 86: 86: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 86: Setting nstcalcenergy (100) equal to nstenergy (1) 86: 86: Generating 1-4 interactions: fudge = 0.5 86: Number of degrees of freedom in T-Coupling group System is 27.00 86: 86: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 86: You are using a plain Coulomb cut-off, which might produce artifacts. 86: You might want to consider using PME electrostatics. 86: 86: 86: 86: There were 3 NOTEs 86: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 86: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 86: 86: Using 1 MPI thread 86: Using 1 OpenMP thread 86: 86: 86: NOTE: Thread affinity was not set. 86: starting mdrun 'spc2' 86: 16 steps, 0.0 ps. 86: Generated 330891 of the 330891 non-bonded parameter combinations 86: 86: Generated 330891 of the 330891 1-4 parameter combinations 86: 86: Excluding 2 bonded neighbours molecule type 'SOL' 86: 86: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/tip3p5.gro' 86: 86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 86: 86: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 86: 86: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 86: 86: Note that mdrun will redetermine rlist based on the actual pair-list setup 86: 86: This run will generate roughly 0 Mb of data 86: 86: Writing final coordinates. 86: 86: Core t (s) Wall t (s) (%) 86: Time: 0.051 0.052 99.5 86: (ns/day) (hour/ns) 86: Performance: 28.498 0.842 86: 86: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 86: that with the Verlet scheme, nstlist has no effect on the accuracy of 86: your simulation. 86: 86: 86: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 86: Setting nstcalcenergy (100) equal to nstenergy (1) 86: 86: Generating 1-4 interactions: fudge = 0.5 86: Number of degrees of freedom in T-Coupling group System is 27.00 86: 86: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 86: You are using a plain Coulomb cut-off, which might produce artifacts. 86: You might want to consider using PME electrostatics. 86: 86: 86: 86: There were 3 NOTEs 86: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 86: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 86: 86: Using 1 MPI thread 86: Using 1 OpenMP thread 86: 86: 86: NOTE: Thread affinity was not set. 86: starting mdrun 'spc2' 86: 16 steps, 0.0 ps. 86: Generated 330891 of the 330891 non-bonded parameter combinations 86: 86: Generated 330891 of the 330891 1-4 parameter combinations 86: 86: Excluding 2 bonded neighbours molecule type 'SOL' 86: 86: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/tip3p5.gro' 86: 86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 86: 86: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 86: 86: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 86: 86: Note that mdrun will redetermine rlist based on the actual pair-list setup 86: 86: This run will generate roughly 0 Mb of data 86: 86: Writing final coordinates. 86: 86: Core t (s) Wall t (s) (%) 86: Time: 0.024 0.024 98.8 86: (ns/day) (hour/ns) 86: Performance: 60.450 0.397 86: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_reference.edr as double precision energy file 86: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.edr as double precision energy file 86: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 86: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 86: that with the Verlet scheme, nstlist has no effect on the accuracy of 86: your simulation. 86: 86: 86: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 86: Setting nstcalcenergy (100) equal to nstenergy (4) 86: 86: Generating 1-4 interactions: fudge = 0.5 86: Number of degrees of freedom in T-Coupling group System is 27.00 86: 86: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 86: You are using a plain Coulomb cut-off, which might produce artifacts. 86: You might want to consider using PME electrostatics. 86: 86: 86: 86: There were 3 NOTEs 86: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 86: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 86: 86: Using 1 MPI thread 86: Using 1 OpenMP thread 86: 86: 86: NOTE: Thread affinity was not set. 86: starting mdrun 'spc2' 86: 16 steps, 0.0 ps. 86: Generated 330891 of the 330891 non-bonded parameter combinations 86: 86: Generated 330891 of the 330891 1-4 parameter combinations 86: 86: Excluding 2 bonded neighbours molecule type 'SOL' 86: 86: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/tip3p5.gro' 86: 86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 86: 86: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 86: 86: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 86: 86: Note that mdrun will redetermine rlist based on the actual pair-list setup 86: 86: This run will generate roughly 0 Mb of data 86: 86: Writing final coordinates. 86: 86: Core t (s) Wall t (s) (%) 86: Time: 0.025 0.025 99.0 86: (ns/day) (hour/ns) 86: Performance: 59.123 0.406 86: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_reference.edr as double precision energy file 86: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.edr as double precision energy file 86: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 86: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 86: that with the Verlet scheme, nstlist has no effect on the accuracy of 86: your simulation. 86: 86: 86: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 86: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 86: setting nstcomm equal to nstcalcenergy for less overhead 86: 86: Generating 1-4 interactions: fudge = 0.5 86: Number of degrees of freedom in T-Coupling group System is 27.00 86: 86: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 86: You are using a plain Coulomb cut-off, which might produce artifacts. 86: You might want to consider using PME electrostatics. 86: 86: 86: 86: There were 3 NOTEs 86: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 86: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 86: 86: Using 1 MPI thread 86: Using 1 OpenMP thread 86: 86: 86: NOTE: Thread affinity was not set. 86: starting mdrun 'spc2' 86: 16 steps, 0.0 ps. 86: Generated 330891 of the 330891 non-bonded parameter combinations 86: 86: Generated 330891 of the 330891 1-4 parameter combinations 86: 86: Excluding 2 bonded neighbours molecule type 'SOL' 86: 86: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/tip3p5.gro' 86: 86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 86: 86: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 86: 86: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 86: 86: Note that mdrun will redetermine rlist based on the actual pair-list setup 86: 86: This run will generate roughly 0 Mb of data 86: 86: Writing final coordinates. 86: 86: Core t (s) Wall t (s) (%) 86: Time: 0.026 0.026 99.1 86: (ns/day) (hour/ns) 86: Performance: 55.506 0.432 86: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_reference.edr as double precision energy file 86: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.edr as double precision energy file 86: 86: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 86: that with the Verlet scheme, nstlist has no effect on the accuracy of 86: your simulation. 86: 86: 86: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 86: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 86: setting nstcomm equal to nstcalcenergy for less overhead 86: 86: Generating 1-4 interactions: fudge = 0.5 86: Number of degrees of freedom in T-Coupling group System is 27.00 86: 86: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 86: You are using a plain Coulomb cut-off, which might produce artifacts. 86: You might want to consider using PME electrostatics. 86: 86: 86: 86: There were 3 NOTEs 86: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 86: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 86: 86: Using 1 MPI thread 86: Using 1 OpenMP thread 86: 86: 86: NOTE: Thread affinity was not set. 86: starting mdrun 'spc2' 86: 16 steps, 0.0 ps. 86: Generated 330891 of the 330891 non-bonded parameter combinations 86: 86: Generated 330891 of the 330891 1-4 parameter combinations 86: 86: Excluding 2 bonded neighbours molecule type 'SOL' 86: 86: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/tip3p5.gro' 86: 86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 86: 86: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 86: 86: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 86: 86: Note that mdrun will redetermine rlist based on the actual pair-list setup 86: 86: This run will generate roughly 0 Mb of data 86: 86: Writing final coordinates. 86: 86: Core t (s) Wall t (s) (%) 86: Time: 0.027 0.027 98.6 86: (ns/day) (hour/ns) 86: Performance: 54.110 0.444 86: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_reference.edr as double precision energy file 86: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.edr as double precision energy file 86: 86: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 86: that with the Verlet scheme, nstlist has no effect on the accuracy of 86: your simulation. 86: 86: 86: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 86: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 86: setting nstcomm equal to nstcalcenergy for less overhead 86: 86: Generating 1-4 interactions: fudge = 0.5 86: Number of degrees of freedom in T-Coupling group System is 27.00 86: 86: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 86: You are using a plain Coulomb cut-off, which might produce artifacts. 86: You might want to consider using PME electrostatics. 86: 86: 86: 86: There were 3 NOTEs 86: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 86: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 86: 86: Using 1 MPI thread 86: Using 1 OpenMP thread 86: 86: 86: NOTE: Thread affinity was not set. 86: starting mdrun 'spc2' 86: 16 steps, 0.0 ps. 86: Generated 330891 of the 330891 non-bonded parameter combinations 86: 86: Generated 330891 of the 330891 1-4 parameter combinations 86: 86: Excluding 2 bonded neighbours molecule type 'SOL' 86: 86: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/tip3p5.gro' 86: 86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 86: 86: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 86: 86: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 86: 86: Note that mdrun will redetermine rlist based on the actual pair-list setup 86: 86: This run will generate roughly 0 Mb of data 86: 86: Writing final coordinates. 86: 86: Core t (s) Wall t (s) (%) 86: Time: 0.028 0.028 99.1 86: (ns/day) (hour/ns) 86: Performance: 51.588 0.465 86: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_reference.edr as double precision energy file 86: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.edr as double precision energy file 86: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/12 (35004 ms) 86: [----------] 13 tests from PropagatorsWithConstraints/PeriodicActionsTest (458192 ms total) 86: 86: [----------] Global test environment tear-down 86: [==========] 13 tests from 1 test suite ran. (458243 ms total) 86: [ PASSED ] 13 tests. 86/92 Test #86: MdrunCoordinationConstraintsTests1Rank .... Passed 458.35 sec test 87 Start 87: MdrunCoordinationConstraintsTests2Ranks 87: Test command: /build/reproducible-path/gromacs-2025.1/build/basic-dp/bin/mdrun-coordination-constraints-test "-ntmpi" "2" "--gtest_output=xml:/build/reproducible-path/gromacs-2025.1/build/basic-dp/Testing/Temporary/MdrunCoordinationConstraintsTests2Ranks.xml" 87: Working Directory: /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests 87: Test timeout computed to be: 1920 87: [==========] Running 13 tests from 1 test suite. 87: [----------] Global test environment set-up. 87: [----------] 13 tests from PropagatorsWithConstraints/PeriodicActionsTest 87: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/0 87: 87: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 87: that with the Verlet scheme, nstlist has no effect on the accuracy of 87: your simulation. 87: 87: 87: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 87: Setting nstcalcenergy (100) equal to nstenergy (1) 87: 87: Generating 1-4 interactions: fudge = 0.5 87: Number of degrees of freedom in T-Coupling group System is 27.00 87: 87: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 87: NVE simulation: will use the initial temperature of 398.997 K for 87: determining the Verlet buffer size 87: 87: 87: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 87: You are using a plain Coulomb cut-off, which might produce artifacts. 87: You might want to consider using PME electrostatics. 87: 87: 87: 87: There were 4 NOTEs 87: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 87: Can not increase nstlist because an NVE ensemble is used 87: Using 2 MPI threads 87: Using 1 OpenMP thread per tMPI thread 87: 87: 87: NOTE: The number of threads is not equal to the number of (logical) cpus 87: and the -pin option is set to auto: will not pin threads to cpus. 87: This can lead to significant performance degradation. 87: Consider using -pin on (and -pinoffset in case you run multiple jobs). 87: starting mdrun 'spc2' 87: 16 steps, 0.0 ps. 87: Generated 330891 of the 330891 non-bonded parameter combinations 87: 87: Generated 330891 of the 330891 1-4 parameter combinations 87: 87: Excluding 2 bonded neighbours molecule type 'SOL' 87: 87: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/tip3p5.gro' 87: 87: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 87: 87: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 87: 87: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 87: 87: Note that mdrun will redetermine rlist based on the actual pair-list setup 87: 87: This run will generate roughly 0 Mb of data 87: 87: Writing final coordinates. 87: 87: 87: Dynamic load balancing report: 87: DLB got disabled because it was unsuitable to use. 87: Average load imbalance: 9.7%. 87: The balanceable part of the MD step is 50%, load imbalance is computed from this. 87: Part of the total run time spent waiting due to load imbalance: 4.8%. 87: 87: 87: NOTE: 40 % of the run time was spent communicating energies, 87: you might want to increase some nst* mdp options 87: 87: Core t (s) Wall t (s) (%) 87: Time: 0.073 0.037 198.1 87: (ns/day) (hour/ns) 87: Performance: 40.077 0.599 87: 87: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 87: that with the Verlet scheme, nstlist has no effect on the accuracy of 87: your simulation. 87: 87: 87: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 87: Setting nstcalcenergy (100) equal to nstenergy (1) 87: 87: Generating 1-4 interactions: fudge = 0.5 87: Number of degrees of freedom in T-Coupling group System is 27.00 87: 87: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 87: NVE simulation: will use the initial temperature of 398.997 K for 87: determining the Verlet buffer size 87: 87: 87: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 87: You are using a plain Coulomb cut-off, which might produce artifacts. 87: You might want to consider using PME electrostatics. 87: 87: 87: 87: There were 4 NOTEs 87: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 87: Can not increase nstlist because an NVE ensemble is used 87: Using 2 MPI threads 87: Using 1 OpenMP thread per tMPI thread 87: 87: 87: NOTE: The number of threads is not equal to the number of (logical) cpus 87: and the -pin option is set to auto: will not pin threads to cpus. 87: This can lead to significant performance degradation. 87: Consider using -pin on (and -pinoffset in case you run multiple jobs). 87: starting mdrun 'spc2' 87: 16 steps, 0.0 ps. 87: Generated 330891 of the 330891 non-bonded parameter combinations 87: 87: Generated 330891 of the 330891 1-4 parameter combinations 87: 87: Excluding 2 bonded neighbours molecule type 'SOL' 87: 87: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/tip3p5.gro' 87: 87: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 87: 87: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 87: 87: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 87: 87: Note that mdrun will redetermine rlist based on the actual pair-list setup 87: 87: This run will generate roughly 0 Mb of data 87: 87: Writing final coordinates. 87: 87: 87: Dynamic load balancing report: 87: DLB got disabled because it was unsuitable to use. 87: Average load imbalance: 9.0%. 87: The balanceable part of the MD step is 53%, load imbalance is computed from this. 87: Part of the total run time spent waiting due to load imbalance: 4.8%. 87: 87: 87: NOTE: 38 % of the run time was spent communicating energies, 87: you might want to increase some nst* mdp options 87: 87: Core t (s) Wall t (s) (%) 87: Time: 0.042 0.022 197.2 87: (ns/day) (hour/ns) 87: Performance: 68.265 0.352 87: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as double precision energy file 87: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as double precision energy file 87: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 87: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 87: that with the Verlet scheme, nstlist has no effect on the accuracy of 87: your simulation. 87: 87: 87: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 87: Setting nstcalcenergy (100) equal to nstenergy (4) 87: 87: Generating 1-4 interactions: fudge = 0.5 87: Number of degrees of freedom in T-Coupling group System is 27.00 87: 87: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 87: NVE simulation: will use the initial temperature of 398.997 K for 87: determining the Verlet buffer size 87: 87: 87: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 87: You are using a plain Coulomb cut-off, which might produce artifacts. 87: You might want to consider using PME electrostatics. 87: 87: 87: 87: NOTE 5 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 87: COM removal frequency is set to (5). 87: Other settings require a global communication frequency of 4. 87: Note that this will require additional global communication steps, 87: which will reduce performance when using multiple ranks. 87: Consider setting nstcomm to a multiple of 4. 87: 87: 87: There were 5 NOTEs 87: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 87: Can not increase nstlist because an NVE ensemble is used 87: Using 2 MPI threads 87: Using 1 OpenMP thread per tMPI thread 87: 87: 87: NOTE: The number of threads is not equal to the number of (logical) cpus 87: and the -pin option is set to auto: will not pin threads to cpus. 87: This can lead to significant performance degradation. 87: Consider using -pin on (and -pinoffset in case you run multiple jobs). 87: starting mdrun 'spc2' 87: 16 steps, 0.0 ps. 87: Generated 330891 of the 330891 non-bonded parameter combinations 87: 87: Generated 330891 of the 330891 1-4 parameter combinations 87: 87: Excluding 2 bonded neighbours molecule type 'SOL' 87: 87: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/tip3p5.gro' 87: 87: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 87: 87: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 87: 87: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 87: 87: Note that mdrun will redetermine rlist based on the actual pair-list setup 87: 87: This run will generate roughly 0 Mb of data 87: 87: Writing final coordinates. 87: 87: 87: Dynamic load balancing report: 87: DLB got disabled because it was unsuitable to use. 87: Average load imbalance: 17.0%. 87: The balanceable part of the MD step is 25%, load imbalance is computed from this. 87: Part of the total run time spent waiting due to load imbalance: 4.2%. 87: 87: 87: NOTE: 45 % of the run time was spent communicating energies, 87: you might want to increase some nst* mdp options 87: 87: Core t (s) Wall t (s) (%) 87: Time: 0.057 0.029 197.5 87: (ns/day) (hour/ns) 87: Performance: 51.195 0.469 87: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as double precision energy file 87: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as double precision energy file 87: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 87: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 87: that with the Verlet scheme, nstlist has no effect on the accuracy of 87: your simulation. 87: 87: 87: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 87: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 87: setting nstcomm equal to nstcalcenergy for less overhead 87: 87: Generating 1-4 interactions: fudge = 0.5 87: Number of degrees of freedom in T-Coupling group System is 27.00 87: 87: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 87: NVE simulation: will use the initial temperature of 398.997 K for 87: determining the Verlet buffer size 87: 87: 87: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 87: You are using a plain Coulomb cut-off, which might produce artifacts. 87: You might want to consider using PME electrostatics. 87: 87: 87: 87: NOTE 5 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 87: COM removal frequency is set to (5). 87: Other settings require a global communication frequency of 100. 87: Note that this will require additional global communication steps, 87: which will reduce performance when using multiple ranks. 87: Consider setting nstcomm to a multiple of 100. 87: 87: 87: There were 5 NOTEs 87: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 87: Can not increase nstlist because an NVE ensemble is used 87: Using 2 MPI threads 87: Using 1 OpenMP thread per tMPI thread 87: 87: 87: NOTE: The number of threads is not equal to the number of (logical) cpus 87: and the -pin option is set to auto: will not pin threads to cpus. 87: This can lead to significant performance degradation. 87: Consider using -pin on (and -pinoffset in case you run multiple jobs). 87: starting mdrun 'spc2' 87: 16 steps, 0.0 ps. 87: Generated 330891 of the 330891 non-bonded parameter combinations 87: 87: Generated 330891 of the 330891 1-4 parameter combinations 87: 87: Excluding 2 bonded neighbours molecule type 'SOL' 87: 87: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/tip3p5.gro' 87: 87: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 87: 87: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 87: 87: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 87: 87: Note that mdrun will redetermine rlist based on the actual pair-list setup 87: 87: This run will generate roughly 0 Mb of data 87: 87: Writing final coordinates. 87: 87: 87: Dynamic load balancing report: 87: DLB got disabled because it was unsuitable to use. 87: Average load imbalance: 13.9%. 87: The balanceable part of the MD step is 23%, load imbalance is computed from this. 87: Part of the total run time spent waiting due to load imbalance: 3.1%. 87: 87: 87: NOTE: 40 % of the run time was spent communicating energies, 87: you might want to increase some nst* mdp options 87: 87: Core t (s) Wall t (s) (%) 87: Time: 0.080 0.040 198.4 87: (ns/day) (hour/ns) 87: Performance: 36.575 0.656 87: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as double precision energy file 87: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as double precision energy file 87: 87: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 87: that with the Verlet scheme, nstlist has no effect on the accuracy of 87: your simulation. 87: 87: 87: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 87: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 87: setting nstcomm equal to nstcalcenergy for less overhead 87: 87: Generating 1-4 interactions: fudge = 0.5 87: Number of degrees of freedom in T-Coupling group System is 27.00 87: 87: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 87: NVE simulation: will use the initial temperature of 398.997 K for 87: determining the Verlet buffer size 87: 87: 87: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 87: You are using a plain Coulomb cut-off, which might produce artifacts. 87: You might want to consider using PME electrostatics. 87: 87: 87: 87: NOTE 5 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 87: COM removal frequency is set to (5). 87: Other settings require a global communication frequency of 100. 87: Note that this will require additional global communication steps, 87: which will reduce performance when using multiple ranks. 87: Consider setting nstcomm to a multiple of 100. 87: 87: 87: There were 5 NOTEs 87: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 87: Can not increase nstlist because an NVE ensemble is used 87: Using 2 MPI threads 87: Using 1 OpenMP thread per tMPI thread 87: 87: 87: NOTE: The number of threads is not equal to the number of (logical) cpus 87: and the -pin option is set to auto: will not pin threads to cpus. 87: This can lead to significant performance degradation. 87: Consider using -pin on (and -pinoffset in case you run multiple jobs). 87: starting mdrun 'spc2' 87: 16 steps, 0.0 ps. 87: Generated 330891 of the 330891 non-bonded parameter combinations 87: 87: Generated 330891 of the 330891 1-4 parameter combinations 87: 87: Excluding 2 bonded neighbours molecule type 'SOL' 87: 87: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/tip3p5.gro' 87: 87: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 87: 87: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 87: 87: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 87: 87: Note that mdrun will redetermine rlist based on the actual pair-list setup 87: 87: This run will generate roughly 0 Mb of data 87: 87: Writing final coordinates. 87: 87: 87: Dynamic load balancing report: 87: DLB got disabled because it was unsuitable to use. 87: Average load imbalance: 12.3%. 87: The balanceable part of the MD step is 42%, load imbalance is computed from this. 87: Part of the total run time spent waiting due to load imbalance: 5.2%. 87: 87: NOTE: 5.2 % of the available CPU time was lost due to load imbalance 87: in the domain decomposition. 87: You can consider manually changing the decomposition (option -dd); 87: e.g. by using fewer domains along the box dimension in which there is 87: considerable inhomogeneity in the simulated system. 87: 87: NOTE: 42 % of the run time was spent communicating energies, 87: you might want to increase some nst* mdp options 87: 87: Core t (s) Wall t (s) (%) 87: Time: 0.049 0.025 197.5 87: (ns/day) (hour/ns) 87: Performance: 58.710 0.409 87: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as double precision energy file 87: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as double precision energy file 87: 87: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 87: that with the Verlet scheme, nstlist has no effect on the accuracy of 87: your simulation. 87: 87: 87: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 87: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 87: setting nstcomm equal to nstcalcenergy for less overhead 87: 87: Generating 1-4 interactions: fudge = 0.5 87: Number of degrees of freedom in T-Coupling group System is 27.00 87: 87: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 87: NVE simulation: will use the initial temperature of 398.997 K for 87: determining the Verlet buffer size 87: 87: 87: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 87: You are using a plain Coulomb cut-off, which might produce artifacts. 87: You might want to consider using PME electrostatics. 87: 87: 87: 87: NOTE 5 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 87: COM removal frequency is set to (5). 87: Other settings require a global communication frequency of 100. 87: Note that this will require additional global communication steps, 87: which will reduce performance when using multiple ranks. 87: Consider setting nstcomm to a multiple of 100. 87: 87: 87: There were 5 NOTEs 87: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 87: Can not increase nstlist because an NVE ensemble is used 87: Using 2 MPI threads 87: Using 1 OpenMP thread per tMPI thread 87: 87: 87: NOTE: The number of threads is not equal to the number of (logical) cpus 87: and the -pin option is set to auto: will not pin threads to cpus. 87: This can lead to significant performance degradation. 87: Consider using -pin on (and -pinoffset in case you run multiple jobs). 87: starting mdrun 'spc2' 87: 16 steps, 0.0 ps. 87: Generated 330891 of the 330891 non-bonded parameter combinations 87: 87: Generated 330891 of the 330891 1-4 parameter combinations 87: 87: Excluding 2 bonded neighbours molecule type 'SOL' 87: 87: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/tip3p5.gro' 87: 87: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 87: 87: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 87: 87: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 87: 87: Note that mdrun will redetermine rlist based on the actual pair-list setup 87: 87: This run will generate roughly 0 Mb of data 87: 87: Writing final coordinates. 87: 87: 87: Dynamic load balancing report: 87: DLB got disabled because it was unsuitable to use. 87: Average load imbalance: 11.2%. 87: The balanceable part of the MD step is 40%, load imbalance is computed from this. 87: Part of the total run time spent waiting due to load imbalance: 4.5%. 87: 87: 87: NOTE: 46 % of the run time was spent communicating energies, 87: you might want to increase some nst* mdp options 87: 87: Core t (s) Wall t (s) (%) 87: Time: 0.125 0.063 198.7 87: (ns/day) (hour/ns) 87: Performance: 23.400 1.026 87: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as double precision energy file 87: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as double precision energy file 87: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/0 (35230 ms) 87: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/1 87: 87: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 87: that with the Verlet scheme, nstlist has no effect on the accuracy of 87: your simulation. 87: 87: 87: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 87: Setting nstcalcenergy (100) equal to nstenergy (1) 87: 87: Generating 1-4 interactions: fudge = 0.5 87: Number of degrees of freedom in T-Coupling group System is 27.00 87: 87: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 87: NVE simulation: will use the initial temperature of 398.997 K for 87: determining the Verlet buffer size 87: 87: 87: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 87: You are using a plain Coulomb cut-off, which might produce artifacts. 87: You might want to consider using PME electrostatics. 87: 87: 87: 87: There were 4 NOTEs 87: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 87: Can not increase nstlist because an NVE ensemble is used 87: Using 2 MPI threads 87: Using 1 OpenMP thread per tMPI thread 87: 87: 87: NOTE: The number of threads is not equal to the number of (logical) cpus 87: and the -pin option is set to auto: will not pin threads to cpus. 87: This can lead to significant performance degradation. 87: Consider using -pin on (and -pinoffset in case you run multiple jobs). 87: starting mdrun 'spc2' 87: 16 steps, 0.0 ps. 87: Generated 330891 of the 330891 non-bonded parameter combinations 87: 87: Generated 330891 of the 330891 1-4 parameter combinations 87: 87: Excluding 2 bonded neighbours molecule type 'SOL' 87: 87: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/tip3p5.gro' 87: 87: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 87: 87: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 87: 87: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 87: 87: Note that mdrun will redetermine rlist based on the actual pair-list setup 87: 87: This run will generate roughly 0 Mb of data 87: 87: Writing final coordinates. 87: 87: 87: Dynamic load balancing report: 87: DLB was off during the run due to low measured imbalance. 87: Average load imbalance: 3.6%. 87: The balanceable part of the MD step is 52%, load imbalance is computed from this. 87: Part of the total run time spent waiting due to load imbalance: 1.9%. 87: 87: 87: NOTE: 39 % of the run time was spent communicating energies, 87: you might want to increase some nst* mdp options 87: 87: Core t (s) Wall t (s) (%) 87: Time: 0.080 0.040 198.0 87: (ns/day) (hour/ns) 87: Performance: 36.454 0.658 87: 87: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 87: that with the Verlet scheme, nstlist has no effect on the accuracy of 87: your simulation. 87: 87: 87: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 87: Setting nstcalcenergy (100) equal to nstenergy (1) 87: 87: Generating 1-4 interactions: fudge = 0.5 87: Number of degrees of freedom in T-Coupling group System is 27.00 87: 87: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 87: NVE simulation: will use the initial temperature of 398.997 K for 87: determining the Verlet buffer size 87: 87: 87: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 87: You are using a plain Coulomb cut-off, which might produce artifacts. 87: You might want to consider using PME electrostatics. 87: 87: 87: 87: There were 4 NOTEs 87: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 87: Can not increase nstlist because an NVE ensemble is used 87: Using 2 MPI threads 87: Using 1 OpenMP thread per tMPI thread 87: 87: 87: NOTE: The number of threads is not equal to the number of (logical) cpus 87: and the -pin option is set to auto: will not pin threads to cpus. 87: This can lead to significant performance degradation. 87: Consider using -pin on (and -pinoffset in case you run multiple jobs). 87: starting mdrun 'spc2' 87: 16 steps, 0.0 ps. 87: Generated 330891 of the 330891 non-bonded parameter combinations 87: 87: Generated 330891 of the 330891 1-4 parameter combinations 87: 87: Excluding 2 bonded neighbours molecule type 'SOL' 87: 87: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/tip3p5.gro' 87: 87: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 87: 87: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 87: 87: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 87: 87: Note that mdrun will redetermine rlist based on the actual pair-list setup 87: 87: This run will generate roughly 0 Mb of data 87: 87: Writing final coordinates. 87: 87: 87: Dynamic load balancing report: 87: DLB got disabled because it was unsuitable to use. 87: Average load imbalance: 9.0%. 87: The balanceable part of the MD step is 48%, load imbalance is computed from this. 87: Part of the total run time spent waiting due to load imbalance: 4.3%. 87: 87: 87: NOTE: 37 % of the run time was spent communicating energies, 87: you might want to increase some nst* mdp options 87: 87: Core t (s) Wall t (s) (%) 87: Time: 0.048 0.024 197.1 87: (ns/day) (hour/ns) 87: Performance: 60.518 0.397 87: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as double precision energy file 87: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as double precision energy file 87: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 87: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 87: that with the Verlet scheme, nstlist has no effect on the accuracy of 87: your simulation. 87: 87: 87: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 87: Setting nstcalcenergy (100) equal to nstenergy (4) 87: 87: Generating 1-4 interactions: fudge = 0.5 87: Number of degrees of freedom in T-Coupling group System is 27.00 87: 87: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 87: NVE simulation: will use the initial temperature of 398.997 K for 87: determining the Verlet buffer size 87: 87: 87: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 87: You are using a plain Coulomb cut-off, which might produce artifacts. 87: You might want to consider using PME electrostatics. 87: 87: 87: 87: There were 4 NOTEs 87: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 87: Can not increase nstlist because an NVE ensemble is used 87: Using 2 MPI threads 87: Using 1 OpenMP thread per tMPI thread 87: 87: 87: NOTE: The number of threads is not equal to the number of (logical) cpus 87: and the -pin option is set to auto: will not pin threads to cpus. 87: This can lead to significant performance degradation. 87: Consider using -pin on (and -pinoffset in case you run multiple jobs). 87: starting mdrun 'spc2' 87: 16 steps, 0.0 ps. 87: Generated 330891 of the 330891 non-bonded parameter combinations 87: 87: Generated 330891 of the 330891 1-4 parameter combinations 87: 87: Excluding 2 bonded neighbours molecule type 'SOL' 87: 87: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/tip3p5.gro' 87: 87: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 87: 87: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 87: 87: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 87: 87: Note that mdrun will redetermine rlist based on the actual pair-list setup 87: 87: This run will generate roughly 0 Mb of data 87: 87: Writing final coordinates. 87: 87: 87: Dynamic load balancing report: 87: DLB got disabled because it was unsuitable to use. 87: Average load imbalance: 9.4%. 87: The balanceable part of the MD step is 22%, load imbalance is computed from this. 87: Part of the total run time spent waiting due to load imbalance: 2.0%. 87: 87: 87: NOTE: 47 % of the run time was spent communicating energies, 87: you might want to increase some nst* mdp options 87: 87: Core t (s) Wall t (s) (%) 87: Time: 0.062 0.031 197.5 87: (ns/day) (hour/ns) 87: Performance: 46.632 0.515 87: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as double precision energy file 87: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as double precision energy file 87: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 87: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 87: that with the Verlet scheme, nstlist has no effect on the accuracy of 87: your simulation. 87: 87: 87: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 87: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 87: setting nstcomm equal to nstcalcenergy for less overhead 87: 87: Generating 1-4 interactions: fudge = 0.5 87: Number of degrees of freedom in T-Coupling group System is 27.00 87: 87: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 87: NVE simulation: will use the initial temperature of 398.997 K for 87: determining the Verlet buffer size 87: 87: 87: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 87: You are using a plain Coulomb cut-off, which might produce artifacts. 87: You might want to consider using PME electrostatics. 87: 87: 87: 87: There were 4 NOTEs 87: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 87: Can not increase nstlist because an NVE ensemble is used 87: Using 2 MPI threads 87: Using 1 OpenMP thread per tMPI thread 87: 87: 87: NOTE: The number of threads is not equal to the number of (logical) cpus 87: and the -pin option is set to auto: will not pin threads to cpus. 87: This can lead to significant performance degradation. 87: Consider using -pin on (and -pinoffset in case you run multiple jobs). 87: starting mdrun 'spc2' 87: 16 steps, 0.0 ps. 87: Generated 330891 of the 330891 non-bonded parameter combinations 87: 87: Generated 330891 of the 330891 1-4 parameter combinations 87: 87: Excluding 2 bonded neighbours molecule type 'SOL' 87: 87: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/tip3p5.gro' 87: 87: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 87: 87: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 87: 87: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 87: 87: Note that mdrun will redetermine rlist based on the actual pair-list setup 87: 87: This run will generate roughly 0 Mb of data 87: 87: Writing final coordinates. 87: 87: 87: Dynamic load balancing report: 87: DLB got disabled because it was unsuitable to use. 87: Average load imbalance: 17.8%. 87: The balanceable part of the MD step is 28%, load imbalance is computed from this. 87: Part of the total run time spent waiting due to load imbalance: 5.1%. 87: 87: NOTE: 5.1 % of the available CPU time was lost due to load imbalance 87: in the domain decomposition. 87: You can consider manually changing the decomposition (option -dd); 87: e.g. by using fewer domains along the box dimension in which there is 87: considerable inhomogeneity in the simulated system. 87: 87: NOTE: 38 % of the run time was spent communicating energies, 87: you might want to increase some nst* mdp options 87: 87: Core t (s) Wall t (s) (%) 87: Time: 0.063 0.032 197.8 87: (ns/day) (hour/ns) 87: Performance: 46.230 0.519 87: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as double precision energy file 87: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as double precision energy file 87: 87: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 87: that with the Verlet scheme, nstlist has no effect on the accuracy of 87: your simulation. 87: 87: 87: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 87: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 87: setting nstcomm equal to nstcalcenergy for less overhead 87: 87: Generating 1-4 interactions: fudge = 0.5 87: Number of degrees of freedom in T-Coupling group System is 27.00 87: 87: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 87: NVE simulation: will use the initial temperature of 398.997 K for 87: determining the Verlet buffer size 87: 87: 87: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 87: You are using a plain Coulomb cut-off, which might produce artifacts. 87: You might want to consider using PME electrostatics. 87: 87: 87: 87: There were 4 NOTEs 87: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 87: Can not increase nstlist because an NVE ensemble is used 87: Using 2 MPI threads 87: Using 1 OpenMP thread per tMPI thread 87: 87: 87: NOTE: The number of threads is not equal to the number of (logical) cpus 87: and the -pin option is set to auto: will not pin threads to cpus. 87: This can lead to significant performance degradation. 87: Consider using -pin on (and -pinoffset in case you run multiple jobs). 87: starting mdrun 'spc2' 87: 16 steps, 0.0 ps. 87: Generated 330891 of the 330891 non-bonded parameter combinations 87: 87: Generated 330891 of the 330891 1-4 parameter combinations 87: 87: Excluding 2 bonded neighbours molecule type 'SOL' 87: 87: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/tip3p5.gro' 87: 87: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 87: 87: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 87: 87: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 87: 87: Note that mdrun will redetermine rlist based on the actual pair-list setup 87: 87: This run will generate roughly 0 Mb of data 87: 87: Writing final coordinates. 87: 87: 87: Dynamic load balancing report: 87: DLB got disabled because it was unsuitable to use. 87: Average load imbalance: 8.3%. 87: The balanceable part of the MD step is 28%, load imbalance is computed from this. 87: Part of the total run time spent waiting due to load imbalance: 2.3%. 87: 87: 87: NOTE: 42 % of the run time was spent communicating energies, 87: you might want to increase some nst* mdp options 87: 87: Core t (s) Wall t (s) (%) 87: Time: 0.054 0.028 197.2 87: (ns/day) (hour/ns) 87: Performance: 53.403 0.449 87: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as double precision energy file 87: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as double precision energy file 87: 87: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 87: that with the Verlet scheme, nstlist has no effect on the accuracy of 87: your simulation. 87: 87: 87: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 87: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 87: setting nstcomm equal to nstcalcenergy for less overhead 87: 87: Generating 1-4 interactions: fudge = 0.5 87: Number of degrees of freedom in T-Coupling group System is 27.00 87: 87: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 87: NVE simulation: will use the initial temperature of 398.997 K for 87: determining the Verlet buffer size 87: 87: 87: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 87: You are using a plain Coulomb cut-off, which might produce artifacts. 87: You might want to consider using PME electrostatics. 87: 87: 87: 87: There were 4 NOTEs 87: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 87: Can not increase nstlist because an NVE ensemble is used 87: Using 2 MPI threads 87: Using 1 OpenMP thread per tMPI thread 87: 87: 87: NOTE: The number of threads is not equal to the number of (logical) cpus 87: and the -pin option is set to auto: will not pin threads to cpus. 87: This can lead to significant performance degradation. 87: Consider using -pin on (and -pinoffset in case you run multiple jobs). 87: starting mdrun 'spc2' 87: 16 steps, 0.0 ps. 87: Generated 330891 of the 330891 non-bonded parameter combinations 87: 87: Generated 330891 of the 330891 1-4 parameter combinations 87: 87: Excluding 2 bonded neighbours molecule type 'SOL' 87: 87: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/tip3p5.gro' 87: 87: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 87: 87: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 87: 87: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 87: 87: Note that mdrun will redetermine rlist based on the actual pair-list setup 87: 87: This run will generate roughly 0 Mb of data 87: 87: Writing final coordinates. 87: 87: 87: Dynamic load balancing report: 87: DLB got disabled because it was unsuitable to use. 87: Average load imbalance: 8.4%. 87: The balanceable part of the MD step is 49%, load imbalance is computed from this. 87: Part of the total run time spent waiting due to load imbalance: 4.1%. 87: 87: 87: NOTE: 42 % of the run time was spent communicating energies, 87: you might want to increase some nst* mdp options 87: 87: Core t (s) Wall t (s) (%) 87: Time: 0.053 0.027 197.4 87: (ns/day) (hour/ns) 87: Performance: 54.416 0.441 87: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as double precision energy file 87: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as double precision energy file 87: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/1 (35094 ms) 87: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/2 87: 87: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 87: that with the Verlet scheme, nstlist has no effect on the accuracy of 87: your simulation. 87: 87: 87: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 87: Setting nstcalcenergy (100) equal to nstenergy (1) 87: 87: Generating 1-4 interactions: fudge = 0.5 87: Number of degrees of freedom in T-Coupling group System is 27.00 87: 87: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 87: NVE simulation: will use the initial temperature of 398.997 K for 87: determining the Verlet buffer size 87: 87: 87: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 87: You are using a plain Coulomb cut-off, which might produce artifacts. 87: You might want to consider using PME electrostatics. 87: 87: 87: 87: There were 4 NOTEs 87: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 87: Can not increase nstlist because an NVE ensemble is used 87: Using 2 MPI threads 87: Using 1 OpenMP thread per tMPI thread 87: 87: 87: NOTE: The number of threads is not equal to the number of (logical) cpus 87: and the -pin option is set to auto: will not pin threads to cpus. 87: This can lead to significant performance degradation. 87: Consider using -pin on (and -pinoffset in case you run multiple jobs). 87: starting mdrun 'spc2' 87: 16 steps, 0.0 ps. 87: Generated 330891 of the 330891 non-bonded parameter combinations 87: 87: Generated 330891 of the 330891 1-4 parameter combinations 87: 87: Excluding 2 bonded neighbours molecule type 'SOL' 87: 87: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/tip3p5.gro' 87: 87: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 87: 87: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 87: 87: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 87: 87: Note that mdrun will redetermine rlist based on the actual pair-list setup 87: 87: This run will generate roughly 0 Mb of data 87: 87: Writing final coordinates. 87: 87: 87: Dynamic load balancing report: 87: DLB was off during the run due to low measured imbalance. 87: Average load imbalance: 4.8%. 87: The balanceable part of the MD step is 34%, load imbalance is computed from this. 87: Part of the total run time spent waiting due to load imbalance: 1.6%. 87: 87: 87: NOTE: 45 % of the run time was spent communicating energies, 87: you might want to increase some nst* mdp options 87: 87: Core t (s) Wall t (s) (%) 87: Time: 0.070 0.035 197.8 87: (ns/day) (hour/ns) 87: Performance: 41.424 0.579 87: 87: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 87: that with the Verlet scheme, nstlist has no effect on the accuracy of 87: your simulation. 87: 87: 87: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 87: Setting nstcalcenergy (100) equal to nstenergy (1) 87: 87: Generating 1-4 interactions: fudge = 0.5 87: Number of degrees of freedom in T-Coupling group System is 27.00 87: 87: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 87: NVE simulation: will use the initial temperature of 398.997 K for 87: determining the Verlet buffer size 87: 87: 87: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 87: You are using a plain Coulomb cut-off, which might produce artifacts. 87: You might want to consider using PME electrostatics. 87: 87: 87: 87: There were 4 NOTEs 87: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 87: Can not increase nstlist because an NVE ensemble is used 87: Using 2 MPI threads 87: Using 1 OpenMP thread per tMPI thread 87: 87: 87: NOTE: The number of threads is not equal to the number of (logical) cpus 87: and the -pin option is set to auto: will not pin threads to cpus. 87: This can lead to significant performance degradation. 87: Consider using -pin on (and -pinoffset in case you run multiple jobs). 87: starting mdrun 'spc2' 87: 16 steps, 0.0 ps. 87: Generated 330891 of the 330891 non-bonded parameter combinations 87: 87: Generated 330891 of the 330891 1-4 parameter combinations 87: 87: Excluding 2 bonded neighbours molecule type 'SOL' 87: 87: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/tip3p5.gro' 87: 87: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 87: 87: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 87: 87: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 87: 87: Note that mdrun will redetermine rlist based on the actual pair-list setup 87: 87: This run will generate roughly 0 Mb of data 87: 87: Writing final coordinates. 87: 87: 87: Dynamic load balancing report: 87: DLB got disabled because it was unsuitable to use. 87: Average load imbalance: 7.2%. 87: The balanceable part of the MD step is 47%, load imbalance is computed from this. 87: Part of the total run time spent waiting due to load imbalance: 3.4%. 87: 87: 87: NOTE: 38 % of the run time was spent communicating energies, 87: you might want to increase some nst* mdp options 87: 87: Core t (s) Wall t (s) (%) 87: Time: 0.050 0.025 197.4 87: (ns/day) (hour/ns) 87: Performance: 58.294 0.412 87: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as double precision energy file 87: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as double precision energy file 87: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 87: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 87: that with the Verlet scheme, nstlist has no effect on the accuracy of 87: your simulation. 87: 87: 87: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 87: Setting nstcalcenergy (100) equal to nstenergy (4) 87: 87: Generating 1-4 interactions: fudge = 0.5 87: Number of degrees of freedom in T-Coupling group System is 27.00 87: 87: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 87: NVE simulation: will use the initial temperature of 398.997 K for 87: determining the Verlet buffer size 87: 87: 87: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 87: You are using a plain Coulomb cut-off, which might produce artifacts. 87: You might want to consider using PME electrostatics. 87: 87: 87: 87: There were 4 NOTEs 87: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 87: Can not increase nstlist because an NVE ensemble is used 87: Using 2 MPI threads 87: Using 1 OpenMP thread per tMPI thread 87: 87: 87: NOTE: The number of threads is not equal to the number of (logical) cpus 87: and the -pin option is set to auto: will not pin threads to cpus. 87: This can lead to significant performance degradation. 87: Consider using -pin on (and -pinoffset in case you run multiple jobs). 87: starting mdrun 'spc2' 87: 16 steps, 0.0 ps. 87: Generated 330891 of the 330891 non-bonded parameter combinations 87: 87: Generated 330891 of the 330891 1-4 parameter combinations 87: 87: Excluding 2 bonded neighbours molecule type 'SOL' 87: 87: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/tip3p5.gro' 87: 87: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 87: 87: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 87: 87: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 87: 87: Note that mdrun will redetermine rlist based on the actual pair-list setup 87: 87: This run will generate roughly 0 Mb of data 87: 87: Writing final coordinates. 87: 87: 87: Dynamic load balancing report: 87: DLB got disabled because it was unsuitable to use. 87: Average load imbalance: 7.8%. 87: The balanceable part of the MD step is 34%, load imbalance is computed from this. 87: Part of the total run time spent waiting due to load imbalance: 2.7%. 87: 87: 87: NOTE: 44 % of the run time was spent communicating energies, 87: you might want to increase some nst* mdp options 87: 87: Core t (s) Wall t (s) (%) 87: Time: 0.075 0.038 198.2 87: (ns/day) (hour/ns) 87: Performance: 38.815 0.618 87: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as double precision energy file 87: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as double precision energy file 87: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 87: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 87: that with the Verlet scheme, nstlist has no effect on the accuracy of 87: your simulation. 87: 87: 87: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 87: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 87: setting nstcomm equal to nstcalcenergy for less overhead 87: 87: Generating 1-4 interactions: fudge = 0.5 87: Number of degrees of freedom in T-Coupling group System is 27.00 87: 87: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 87: NVE simulation: will use the initial temperature of 398.997 K for 87: determining the Verlet buffer size 87: 87: 87: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 87: You are using a plain Coulomb cut-off, which might produce artifacts. 87: You might want to consider using PME electrostatics. 87: 87: 87: 87: There were 4 NOTEs 87: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 87: Can not increase nstlist because an NVE ensemble is used 87: Using 2 MPI threads 87: Using 1 OpenMP thread per tMPI thread 87: 87: 87: NOTE: The number of threads is not equal to the number of (logical) cpus 87: and the -pin option is set to auto: will not pin threads to cpus. 87: This can lead to significant performance degradation. 87: Consider using -pin on (and -pinoffset in case you run multiple jobs). 87: starting mdrun 'spc2' 87: 16 steps, 0.0 ps. 87: Generated 330891 of the 330891 non-bonded parameter combinations 87: 87: Generated 330891 of the 330891 1-4 parameter combinations 87: 87: Excluding 2 bonded neighbours molecule type 'SOL' 87: 87: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/tip3p5.gro' 87: 87: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 87: 87: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 87: 87: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 87: 87: Note that mdrun will redetermine rlist based on the actual pair-list setup 87: 87: This run will generate roughly 0 Mb of data 87: 87: Writing final coordinates. 87: 87: 87: Dynamic load balancing report: 87: DLB got disabled because it was unsuitable to use. 87: Average load imbalance: 8.3%. 87: The balanceable part of the MD step is 45%, load imbalance is computed from this. 87: Part of the total run time spent waiting due to load imbalance: 3.8%. 87: 87: 87: NOTE: 55 % of the run time was spent communicating energies, 87: you might want to increase some nst* mdp options 87: 87: Core t (s) Wall t (s) (%) 87: Time: 0.065 0.033 197.3 87: (ns/day) (hour/ns) 87: Performance: 44.295 0.542 87: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as double precision energy file 87: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as double precision energy file 87: 87: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 87: that with the Verlet scheme, nstlist has no effect on the accuracy of 87: your simulation. 87: 87: 87: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 87: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 87: setting nstcomm equal to nstcalcenergy for less overhead 87: 87: Generating 1-4 interactions: fudge = 0.5 87: Number of degrees of freedom in T-Coupling group System is 27.00 87: 87: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 87: NVE simulation: will use the initial temperature of 398.997 K for 87: determining the Verlet buffer size 87: 87: 87: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 87: You are using a plain Coulomb cut-off, which might produce artifacts. 87: You might want to consider using PME electrostatics. 87: 87: 87: 87: There were 4 NOTEs 87: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 87: Can not increase nstlist because an NVE ensemble is used 87: Using 2 MPI threads 87: Using 1 OpenMP thread per tMPI thread 87: 87: 87: NOTE: The number of threads is not equal to the number of (logical) cpus 87: and the -pin option is set to auto: will not pin threads to cpus. 87: This can lead to significant performance degradation. 87: Consider using -pin on (and -pinoffset in case you run multiple jobs). 87: starting mdrun 'spc2' 87: 16 steps, 0.0 ps. 87: Generated 330891 of the 330891 non-bonded parameter combinations 87: 87: Generated 330891 of the 330891 1-4 parameter combinations 87: 87: Excluding 2 bonded neighbours molecule type 'SOL' 87: 87: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/tip3p5.gro' 87: 87: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 87: 87: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 87: 87: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 87: 87: Note that mdrun will redetermine rlist based on the actual pair-list setup 87: 87: This run will generate roughly 0 Mb of data 87: 87: Writing final coordinates. 87: 87: 87: Dynamic load balancing report: 87: DLB was off during the run due to low measured imbalance. 87: Average load imbalance: 8.7%. 87: The balanceable part of the MD step is 22%, load imbalance is computed from this. 87: Part of the total run time spent waiting due to load imbalance: 2.0%. 87: 87: 87: NOTE: 40 % of the run time was spent communicating energies, 87: you might want to increase some nst* mdp options 87: 87: Core t (s) Wall t (s) (%) 87: Time: 0.081 0.041 198.3 87: (ns/day) (hour/ns) 87: Performance: 35.758 0.671 87: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as double precision energy file 87: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as double precision energy file 87: 87: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 87: that with the Verlet scheme, nstlist has no effect on the accuracy of 87: your simulation. 87: 87: 87: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 87: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 87: setting nstcomm equal to nstcalcenergy for less overhead 87: 87: Generating 1-4 interactions: fudge = 0.5 87: Number of degrees of freedom in T-Coupling group System is 27.00 87: 87: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 87: NVE simulation: will use the initial temperature of 398.997 K for 87: determining the Verlet buffer size 87: 87: 87: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 87: You are using a plain Coulomb cut-off, which might produce artifacts. 87: You might want to consider using PME electrostatics. 87: 87: 87: 87: There were 4 NOTEs 87: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 87: Can not increase nstlist because an NVE ensemble is used 87: Using 2 MPI threads 87: Using 1 OpenMP thread per tMPI thread 87: 87: 87: NOTE: The number of threads is not equal to the number of (logical) cpus 87: and the -pin option is set to auto: will not pin threads to cpus. 87: This can lead to significant performance degradation. 87: Consider using -pin on (and -pinoffset in case you run multiple jobs). 87: starting mdrun 'spc2' 87: 16 steps, 0.0 ps. 87: Generated 330891 of the 330891 non-bonded parameter combinations 87: 87: Generated 330891 of the 330891 1-4 parameter combinations 87: 87: Excluding 2 bonded neighbours molecule type 'SOL' 87: 87: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/tip3p5.gro' 87: 87: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 87: 87: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 87: 87: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 87: 87: Note that mdrun will redetermine rlist based on the actual pair-list setup 87: 87: This run will generate roughly 0 Mb of data 87: 87: Writing final coordinates. 87: 87: 87: Dynamic load balancing report: 87: DLB was off during the run due to low measured imbalance. 87: Average load imbalance: 9.8%. 87: The balanceable part of the MD step is 17%, load imbalance is computed from this. 87: Part of the total run time spent waiting due to load imbalance: 1.7%. 87: 87: 87: NOTE: 23 % of the run time was spent in domain decomposition, 87: 1 % of the run time was spent in pair search, 87: you might want to increase nstlist (this has no effect on accuracy) 87: 87: NOTE: 35 % of the run time was spent communicating energies, 87: you might want to increase some nst* mdp options 87: 87: Core t (s) Wall t (s) (%) 87: Time: 0.068 0.034 197.9 87: (ns/day) (hour/ns) 87: Performance: 42.631 0.563 87: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as double precision energy file 87: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as double precision energy file 87: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/2 (35154 ms) 87: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/3 87: 87: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 87: that with the Verlet scheme, nstlist has no effect on the accuracy of 87: your simulation. 87: 87: 87: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 87: Setting nstcalcenergy (100) equal to nstenergy (1) 87: 87: Generating 1-4 interactions: fudge = 0.5 87: Number of degrees of freedom in T-Coupling group System is 27.00 87: 87: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 87: You are using a plain Coulomb cut-off, which might produce artifacts. 87: You might want to consider using PME electrostatics. 87: 87: 87: 87: There were 3 NOTEs 87: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 87: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 87: 87: Using 2 MPI threads 87: Using 1 OpenMP thread per tMPI thread 87: 87: 87: NOTE: The number of threads is not equal to the number of (logical) cpus 87: and the -pin option is set to auto: will not pin threads to cpus. 87: This can lead to significant performance degradation. 87: Consider using -pin on (and -pinoffset in case you run multiple jobs). 87: starting mdrun 'spc2' 87: 16 steps, 0.0 ps. 87: Generated 330891 of the 330891 non-bonded parameter combinations 87: 87: Generated 330891 of the 330891 1-4 parameter combinations 87: 87: Excluding 2 bonded neighbours molecule type 'SOL' 87: 87: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/tip3p5.gro' 87: 87: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 87: 87: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 87: 87: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 87: 87: Note that mdrun will redetermine rlist based on the actual pair-list setup 87: 87: This run will generate roughly 0 Mb of data 87: 87: Writing final coordinates. 87: 87: Core t (s) Wall t (s) (%) 87: Time: 0.059 0.030 197.5 87: (ns/day) (hour/ns) 87: Performance: 48.765 0.492 87: 87: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 87: that with the Verlet scheme, nstlist has no effect on the accuracy of 87: your simulation. 87: 87: 87: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 87: Setting nstcalcenergy (100) equal to nstenergy (1) 87: 87: Generating 1-4 interactions: fudge = 0.5 87: Number of degrees of freedom in T-Coupling group System is 27.00 87: 87: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 87: You are using a plain Coulomb cut-off, which might produce artifacts. 87: You might want to consider using PME electrostatics. 87: 87: 87: 87: There were 3 NOTEs 87: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 87: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 87: 87: Using 2 MPI threads 87: Using 1 OpenMP thread per tMPI thread 87: 87: 87: NOTE: The number of threads is not equal to the number of (logical) cpus 87: and the -pin option is set to auto: will not pin threads to cpus. 87: This can lead to significant performance degradation. 87: Consider using -pin on (and -pinoffset in case you run multiple jobs). 87: starting mdrun 'spc2' 87: 16 steps, 0.0 ps. 87: Generated 330891 of the 330891 non-bonded parameter combinations 87: 87: Generated 330891 of the 330891 1-4 parameter combinations 87: 87: Excluding 2 bonded neighbours molecule type 'SOL' 87: 87: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/tip3p5.gro' 87: 87: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 87: 87: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 87: 87: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 87: 87: Note that mdrun will redetermine rlist based on the actual pair-list setup 87: 87: This run will generate roughly 0 Mb of data 87: 87: Writing final coordinates. 87: 87: Core t (s) Wall t (s) (%) 87: Time: 0.045 0.023 197.1 87: (ns/day) (hour/ns) 87: Performance: 64.461 0.372 87: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as double precision energy file 87: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as double precision energy file 87: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 87: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 87: that with the Verlet scheme, nstlist has no effect on the accuracy of 87: your simulation. 87: 87: 87: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 87: Setting nstcalcenergy (100) equal to nstenergy (4) 87: 87: Generating 1-4 interactions: fudge = 0.5 87: Number of degrees of freedom in T-Coupling group System is 27.00 87: 87: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 87: You are using a plain Coulomb cut-off, which might produce artifacts. 87: You might want to consider using PME electrostatics. 87: 87: 87: 87: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 87: COM removal frequency is set to (5). 87: Other settings require a global communication frequency of 2. 87: Note that this will require additional global communication steps, 87: which will reduce performance when using multiple ranks. 87: Consider setting nstcomm to a multiple of 2. 87: 87: 87: There were 4 NOTEs 87: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 87: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 87: 87: Using 2 MPI threads 87: Using 1 OpenMP thread per tMPI thread 87: 87: 87: NOTE: The number of threads is not equal to the number of (logical) cpus 87: and the -pin option is set to auto: will not pin threads to cpus. 87: This can lead to significant performance degradation. 87: Consider using -pin on (and -pinoffset in case you run multiple jobs). 87: starting mdrun 'spc2' 87: 16 steps, 0.0 ps. 87: Generated 330891 of the 330891 non-bonded parameter combinations 87: 87: Generated 330891 of the 330891 1-4 parameter combinations 87: 87: Excluding 2 bonded neighbours molecule type 'SOL' 87: 87: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/tip3p5.gro' 87: 87: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 87: 87: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 87: 87: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 87: 87: Note that mdrun will redetermine rlist based on the actual pair-list setup 87: 87: This run will generate roughly 0 Mb of data 87: 87: Writing final coordinates. 87: 87: Core t (s) Wall t (s) (%) 87: Time: 0.043 0.022 196.9 87: (ns/day) (hour/ns) 87: Performance: 68.047 0.353 87: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as double precision energy file 87: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as double precision energy file 87: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 87: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 87: that with the Verlet scheme, nstlist has no effect on the accuracy of 87: your simulation. 87: 87: 87: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 87: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 87: setting nstcomm equal to nstcalcenergy for less overhead 87: 87: Generating 1-4 interactions: fudge = 0.5 87: Number of degrees of freedom in T-Coupling group System is 27.00 87: 87: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 87: You are using a plain Coulomb cut-off, which might produce artifacts. 87: You might want to consider using PME electrostatics. 87: 87: 87: 87: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 87: COM removal frequency is set to (5). 87: Other settings require a global communication frequency of 2. 87: Note that this will require additional global communication steps, 87: which will reduce performance when using multiple ranks. 87: Consider setting nstcomm to a multiple of 2. 87: 87: 87: There were 4 NOTEs 87: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 87: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 87: 87: Using 2 MPI threads 87: Using 1 OpenMP thread per tMPI thread 87: 87: 87: NOTE: The number of threads is not equal to the number of (logical) cpus 87: and the -pin option is set to auto: will not pin threads to cpus. 87: This can lead to significant performance degradation. 87: Consider using -pin on (and -pinoffset in case you run multiple jobs). 87: starting mdrun 'spc2' 87: 16 steps, 0.0 ps. 87: Generated 330891 of the 330891 non-bonded parameter combinations 87: 87: Generated 330891 of the 330891 1-4 parameter combinations 87: 87: Excluding 2 bonded neighbours molecule type 'SOL' 87: 87: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/tip3p5.gro' 87: 87: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 87: 87: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 87: 87: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 87: 87: Note that mdrun will redetermine rlist based on the actual pair-list setup 87: 87: This run will generate roughly 0 Mb of data 87: 87: Writing final coordinates. 87: 87: Core t (s) Wall t (s) (%) 87: Time: 0.048 0.024 197.2 87: (ns/day) (hour/ns) 87: Performance: 60.792 0.395 87: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as double precision energy file 87: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as double precision energy file 87: 87: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 87: that with the Verlet scheme, nstlist has no effect on the accuracy of 87: your simulation. 87: 87: 87: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 87: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 87: setting nstcomm equal to nstcalcenergy for less overhead 87: 87: Generating 1-4 interactions: fudge = 0.5 87: Number of degrees of freedom in T-Coupling group System is 27.00 87: 87: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 87: You are using a plain Coulomb cut-off, which might produce artifacts. 87: You might want to consider using PME electrostatics. 87: 87: 87: 87: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 87: COM removal frequency is set to (5). 87: Other settings require a global communication frequency of 2. 87: Note that this will require additional global communication steps, 87: which will reduce performance when using multiple ranks. 87: Consider setting nstcomm to a multiple of 2. 87: 87: 87: There were 4 NOTEs 87: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 87: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 87: 87: Using 2 MPI threads 87: Using 1 OpenMP thread per tMPI thread 87: 87: 87: NOTE: The number of threads is not equal to the number of (logical) cpus 87: and the -pin option is set to auto: will not pin threads to cpus. 87: This can lead to significant performance degradation. 87: Consider using -pin on (and -pinoffset in case you run multiple jobs). 87: starting mdrun 'spc2' 87: 16 steps, 0.0 ps. 87: Generated 330891 of the 330891 non-bonded parameter combinations 87: 87: Generated 330891 of the 330891 1-4 parameter combinations 87: 87: Excluding 2 bonded neighbours molecule type 'SOL' 87: 87: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/tip3p5.gro' 87: 87: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 87: 87: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 87: 87: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 87: 87: Note that mdrun will redetermine rlist based on the actual pair-list setup 87: 87: This run will generate roughly 0 Mb of data 87: 87: Writing final coordinates. 87: 87: Core t (s) Wall t (s) (%) 87: Time: 0.060 0.030 197.8 87: (ns/day) (hour/ns) 87: Performance: 48.470 0.495 87: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as double precision energy file 87: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as double precision energy file 87: 87: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 87: that with the Verlet scheme, nstlist has no effect on the accuracy of 87: your simulation. 87: 87: 87: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 87: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 87: setting nstcomm equal to nstcalcenergy for less overhead 87: 87: Generating 1-4 interactions: fudge = 0.5 87: Number of degrees of freedom in T-Coupling group System is 27.00 87: 87: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 87: You are using a plain Coulomb cut-off, which might produce artifacts. 87: You might want to consider using PME electrostatics. 87: 87: 87: 87: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 87: COM removal frequency is set to (5). 87: Other settings require a global communication frequency of 2. 87: Note that this will require additional global communication steps, 87: which will reduce performance when using multiple ranks. 87: Consider setting nstcomm to a multiple of 2. 87: 87: 87: There were 4 NOTEs 87: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 87: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 87: 87: Using 2 MPI threads 87: Using 1 OpenMP thread per tMPI thread 87: 87: 87: NOTE: The number of threads is not equal to the number of (logical) cpus 87: and the -pin option is set to auto: will not pin threads to cpus. 87: This can lead to significant performance degradation. 87: Consider using -pin on (and -pinoffset in case you run multiple jobs). 87: starting mdrun 'spc2' 87: 16 steps, 0.0 ps. 87: Generated 330891 of the 330891 non-bonded parameter combinations 87: 87: Generated 330891 of the 330891 1-4 parameter combinations 87: 87: Excluding 2 bonded neighbours molecule type 'SOL' 87: 87: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/tip3p5.gro' 87: 87: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 87: 87: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 87: 87: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 87: 87: Note that mdrun will redetermine rlist based on the actual pair-list setup 87: 87: This run will generate roughly 0 Mb of data 87: 87: Writing final coordinates. 87: 87: Core t (s) Wall t (s) (%) 87: Time: 0.061 0.031 197.4 87: (ns/day) (hour/ns) 87: Performance: 47.780 0.502 87: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as double precision energy file 87: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as double precision energy file 87: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/3 (35048 ms) 87: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/4 87: 87: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 87: that with the Verlet scheme, nstlist has no effect on the accuracy of 87: your simulation. 87: 87: 87: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 87: Setting nstcalcenergy (100) equal to nstenergy (1) 87: 87: Generating 1-4 interactions: fudge = 0.5 87: Number of degrees of freedom in T-Coupling group System is 27.00 87: 87: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 87: You are using a plain Coulomb cut-off, which might produce artifacts. 87: You might want to consider using PME electrostatics. 87: 87: 87: 87: There were 3 NOTEs 87: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 87: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 87: 87: Using 2 MPI threads 87: Using 1 OpenMP thread per tMPI thread 87: 87: 87: NOTE: The number of threads is not equal to the number of (logical) cpus 87: and the -pin option is set to auto: will not pin threads to cpus. 87: This can lead to significant performance degradation. 87: Consider using -pin on (and -pinoffset in case you run multiple jobs). 87: starting mdrun 'spc2' 87: 16 steps, 0.0 ps. 87: Generated 330891 of the 330891 non-bonded parameter combinations 87: 87: Generated 330891 of the 330891 1-4 parameter combinations 87: 87: Excluding 2 bonded neighbours molecule type 'SOL' 87: 87: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/tip3p5.gro' 87: 87: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 87: 87: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 87: 87: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 87: 87: Note that mdrun will redetermine rlist based on the actual pair-list setup 87: 87: This run will generate roughly 0 Mb of data 87: 87: Writing final coordinates. 87: 87: Core t (s) Wall t (s) (%) 87: Time: 0.103 0.052 198.5 87: (ns/day) (hour/ns) 87: Performance: 28.407 0.845 87: 87: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 87: that with the Verlet scheme, nstlist has no effect on the accuracy of 87: your simulation. 87: 87: 87: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 87: Setting nstcalcenergy (100) equal to nstenergy (1) 87: 87: Generating 1-4 interactions: fudge = 0.5 87: Number of degrees of freedom in T-Coupling group System is 27.00 87: 87: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 87: You are using a plain Coulomb cut-off, which might produce artifacts. 87: You might want to consider using PME electrostatics. 87: 87: 87: 87: There were 3 NOTEs 87: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 87: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 87: 87: Using 2 MPI threads 87: Using 1 OpenMP thread per tMPI thread 87: 87: 87: NOTE: The number of threads is not equal to the number of (logical) cpus 87: and the -pin option is set to auto: will not pin threads to cpus. 87: This can lead to significant performance degradation. 87: Consider using -pin on (and -pinoffset in case you run multiple jobs). 87: starting mdrun 'spc2' 87: 16 steps, 0.0 ps. 87: Generated 330891 of the 330891 non-bonded parameter combinations 87: 87: Generated 330891 of the 330891 1-4 parameter combinations 87: 87: Excluding 2 bonded neighbours molecule type 'SOL' 87: 87: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/tip3p5.gro' 87: 87: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 87: 87: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 87: 87: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 87: 87: Note that mdrun will redetermine rlist based on the actual pair-list setup 87: 87: This run will generate roughly 0 Mb of data 87: 87: Writing final coordinates. 87: 87: NOTE: 13 % of the run time was spent in domain decomposition, 87: 1 % of the run time was spent in pair search, 87: you might want to increase nstlist (this has no effect on accuracy) 87: 87: Core t (s) Wall t (s) (%) 87: Time: 0.069 0.035 197.9 87: (ns/day) (hour/ns) 87: Performance: 42.016 0.571 87: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as double precision energy file 87: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as double precision energy file 87: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 87: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 87: that with the Verlet scheme, nstlist has no effect on the accuracy of 87: your simulation. 87: 87: 87: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 87: Setting nstcalcenergy (100) equal to nstenergy (4) 87: 87: Generating 1-4 interactions: fudge = 0.5 87: Number of degrees of freedom in T-Coupling group System is 27.00 87: 87: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 87: You are using a plain Coulomb cut-off, which might produce artifacts. 87: You might want to consider using PME electrostatics. 87: 87: 87: 87: There were 3 NOTEs 87: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 87: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 87: 87: Using 2 MPI threads 87: Using 1 OpenMP thread per tMPI thread 87: 87: 87: NOTE: The number of threads is not equal to the number of (logical) cpus 87: and the -pin option is set to auto: will not pin threads to cpus. 87: This can lead to significant performance degradation. 87: Consider using -pin on (and -pinoffset in case you run multiple jobs). 87: starting mdrun 'spc2' 87: 16 steps, 0.0 ps. 87: Generated 330891 of the 330891 non-bonded parameter combinations 87: 87: Generated 330891 of the 330891 1-4 parameter combinations 87: 87: Excluding 2 bonded neighbours molecule type 'SOL' 87: 87: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/tip3p5.gro' 87: 87: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 87: 87: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 87: 87: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 87: 87: Note that mdrun will redetermine rlist based on the actual pair-list setup 87: 87: This run will generate roughly 0 Mb of data 87: 87: Writing final coordinates. 87: 87: Core t (s) Wall t (s) (%) 87: Time: 0.049 0.025 197.2 87: (ns/day) (hour/ns) 87: Performance: 58.780 0.408 87: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as double precision energy file 87: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as double precision energy file 87: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 87: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 87: that with the Verlet scheme, nstlist has no effect on the accuracy of 87: your simulation. 87: 87: 87: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 87: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 87: setting nstcomm equal to nstcalcenergy for less overhead 87: 87: Generating 1-4 interactions: fudge = 0.5 87: Number of degrees of freedom in T-Coupling group System is 27.00 87: 87: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 87: You are using a plain Coulomb cut-off, which might produce artifacts. 87: You might want to consider using PME electrostatics. 87: 87: 87: 87: There were 3 NOTEs 87: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 87: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 87: 87: Using 2 MPI threads 87: Using 1 OpenMP thread per tMPI thread 87: 87: 87: NOTE: The number of threads is not equal to the number of (logical) cpus 87: and the -pin option is set to auto: will not pin threads to cpus. 87: This can lead to significant performance degradation. 87: Consider using -pin on (and -pinoffset in case you run multiple jobs). 87: starting mdrun 'spc2' 87: 16 steps, 0.0 ps. 87: Generated 330891 of the 330891 non-bonded parameter combinations 87: 87: Generated 330891 of the 330891 1-4 parameter combinations 87: 87: Excluding 2 bonded neighbours molecule type 'SOL' 87: 87: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/tip3p5.gro' 87: 87: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 87: 87: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 87: 87: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 87: 87: Note that mdrun will redetermine rlist based on the actual pair-list setup 87: 87: This run will generate roughly 0 Mb of data 87: 87: Writing final coordinates. 87: 87: Core t (s) Wall t (s) (%) 87: Time: 0.059 0.030 197.5 87: (ns/day) (hour/ns) 87: Performance: 49.540 0.484 87: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as double precision energy file 87: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as double precision energy file 87: 87: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 87: that with the Verlet scheme, nstlist has no effect on the accuracy of 87: your simulation. 87: 87: 87: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 87: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 87: setting nstcomm equal to nstcalcenergy for less overhead 87: 87: Generating 1-4 interactions: fudge = 0.5 87: Number of degrees of freedom in T-Coupling group System is 27.00 87: 87: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 87: You are using a plain Coulomb cut-off, which might produce artifacts. 87: You might want to consider using PME electrostatics. 87: 87: 87: 87: There were 3 NOTEs 87: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 87: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 87: 87: Using 2 MPI threads 87: Using 1 OpenMP thread per tMPI thread 87: 87: 87: NOTE: The number of threads is not equal to the number of (logical) cpus 87: and the -pin option is set to auto: will not pin threads to cpus. 87: This can lead to significant performance degradation. 87: Consider using -pin on (and -pinoffset in case you run multiple jobs). 87: starting mdrun 'spc2' 87: 16 steps, 0.0 ps. 87: Generated 330891 of the 330891 non-bonded parameter combinations 87: 87: Generated 330891 of the 330891 1-4 parameter combinations 87: 87: Excluding 2 bonded neighbours molecule type 'SOL' 87: 87: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/tip3p5.gro' 87: 87: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 87: 87: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 87: 87: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 87: 87: Note that mdrun will redetermine rlist based on the actual pair-list setup 87: 87: This run will generate roughly 0 Mb of data 87: 87: Writing final coordinates. 87: 87: NOTE: 11 % of the run time was spent communicating energies, 87: you might want to increase some nst* mdp options 87: 87: Core t (s) Wall t (s) (%) 87: Time: 0.103 0.052 198.1 87: (ns/day) (hour/ns) 87: Performance: 28.270 0.849 87: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as double precision energy file 87: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as double precision energy file 87: 87: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 87: that with the Verlet scheme, nstlist has no effect on the accuracy of 87: your simulation. 87: 87: 87: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 87: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 87: setting nstcomm equal to nstcalcenergy for less overhead 87: 87: Generating 1-4 interactions: fudge = 0.5 87: Number of degrees of freedom in T-Coupling group System is 27.00 87: 87: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 87: You are using a plain Coulomb cut-off, which might produce artifacts. 87: You might want to consider using PME electrostatics. 87: 87: 87: 87: There were 3 NOTEs 87: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 87: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 87: 87: Using 2 MPI threads 87: Using 1 OpenMP thread per tMPI thread 87: 87: 87: NOTE: The number of threads is not equal to the number of (logical) cpus 87: and the -pin option is set to auto: will not pin threads to cpus. 87: This can lead to significant performance degradation. 87: Consider using -pin on (and -pinoffset in case you run multiple jobs). 87: starting mdrun 'spc2' 87: 16 steps, 0.0 ps. 87: Generated 330891 of the 330891 non-bonded parameter combinations 87: 87: Generated 330891 of the 330891 1-4 parameter combinations 87: 87: Excluding 2 bonded neighbours molecule type 'SOL' 87: 87: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/tip3p5.gro' 87: 87: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 87: 87: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 87: 87: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 87: 87: Note that mdrun will redetermine rlist based on the actual pair-list setup 87: 87: This run will generate roughly 0 Mb of data 87: 87: Writing final coordinates. 87: 87: Core t (s) Wall t (s) (%) 87: Time: 0.065 0.033 197.6 87: (ns/day) (hour/ns) 87: Performance: 44.510 0.539 87: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as double precision energy file 87: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as double precision energy file 87: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/4 (35436 ms) 87: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/5 87: 87: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 87: that with the Verlet scheme, nstlist has no effect on the accuracy of 87: your simulation. 87: 87: 87: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 87: Setting nstcalcenergy (100) equal to nstenergy (1) 87: 87: Generating 1-4 interactions: fudge = 0.5 87: Number of degrees of freedom in T-Coupling group System is 27.00 87: 87: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 87: You are using a plain Coulomb cut-off, which might produce artifacts. 87: You might want to consider using PME electrostatics. 87: 87: 87: 87: There were 3 NOTEs 87: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 87: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 87: 87: Using 2 MPI threads 87: Using 1 OpenMP thread per tMPI thread 87: 87: 87: NOTE: The number of threads is not equal to the number of (logical) cpus 87: and the -pin option is set to auto: will not pin threads to cpus. 87: This can lead to significant performance degradation. 87: Consider using -pin on (and -pinoffset in case you run multiple jobs). 87: starting mdrun 'spc2' 87: 16 steps, 0.0 ps. 87: Generated 330891 of the 330891 non-bonded parameter combinations 87: 87: Generated 330891 of the 330891 1-4 parameter combinations 87: 87: Excluding 2 bonded neighbours molecule type 'SOL' 87: 87: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/tip3p5.gro' 87: 87: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 87: 87: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 87: 87: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 87: 87: Note that mdrun will redetermine rlist based on the actual pair-list setup 87: 87: This run will generate roughly 0 Mb of data 87: 87: Writing final coordinates. 87: 87: Core t (s) Wall t (s) (%) 87: Time: 0.104 0.053 198.3 87: (ns/day) (hour/ns) 87: Performance: 27.975 0.858 87: 87: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 87: that with the Verlet scheme, nstlist has no effect on the accuracy of 87: your simulation. 87: 87: 87: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 87: Setting nstcalcenergy (100) equal to nstenergy (1) 87: 87: Generating 1-4 interactions: fudge = 0.5 87: Number of degrees of freedom in T-Coupling group System is 27.00 87: 87: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 87: You are using a plain Coulomb cut-off, which might produce artifacts. 87: You might want to consider using PME electrostatics. 87: 87: 87: 87: There were 3 NOTEs 87: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 87: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 87: 87: Using 2 MPI threads 87: Using 1 OpenMP thread per tMPI thread 87: 87: 87: NOTE: The number of threads is not equal to the number of (logical) cpus 87: and the -pin option is set to auto: will not pin threads to cpus. 87: This can lead to significant performance degradation. 87: Consider using -pin on (and -pinoffset in case you run multiple jobs). 87: starting mdrun 'spc2' 87: 16 steps, 0.0 ps. 87: Generated 330891 of the 330891 non-bonded parameter combinations 87: 87: Generated 330891 of the 330891 1-4 parameter combinations 87: 87: Excluding 2 bonded neighbours molecule type 'SOL' 87: 87: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/tip3p5.gro' 87: 87: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 87: 87: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 87: 87: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 87: 87: Note that mdrun will redetermine rlist based on the actual pair-list setup 87: 87: This run will generate roughly 0 Mb of data 87: 87: Writing final coordinates. 87: 87: Core t (s) Wall t (s) (%) 87: Time: 0.041 0.021 196.3 87: (ns/day) (hour/ns) 87: Performance: 69.881 0.343 87: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as double precision energy file 87: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as double precision energy file 87: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 87: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 87: that with the Verlet scheme, nstlist has no effect on the accuracy of 87: your simulation. 87: 87: 87: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 87: Setting nstcalcenergy (100) equal to nstenergy (4) 87: 87: Generating 1-4 interactions: fudge = 0.5 87: Number of degrees of freedom in T-Coupling group System is 27.00 87: 87: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 87: You are using a plain Coulomb cut-off, which might produce artifacts. 87: You might want to consider using PME electrostatics. 87: 87: 87: 87: There were 3 NOTEs 87: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 87: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 87: 87: Using 2 MPI threads 87: Using 1 OpenMP thread per tMPI thread 87: 87: 87: NOTE: The number of threads is not equal to the number of (logical) cpus 87: and the -pin option is set to auto: will not pin threads to cpus. 87: This can lead to significant performance degradation. 87: Consider using -pin on (and -pinoffset in case you run multiple jobs). 87: starting mdrun 'spc2' 87: 16 steps, 0.0 ps. 87: Generated 330891 of the 330891 non-bonded parameter combinations 87: 87: Generated 330891 of the 330891 1-4 parameter combinations 87: 87: Excluding 2 bonded neighbours molecule type 'SOL' 87: 87: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/tip3p5.gro' 87: 87: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 87: 87: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 87: 87: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 87: 87: Note that mdrun will redetermine rlist based on the actual pair-list setup 87: 87: This run will generate roughly 0 Mb of data 87: 87: Writing final coordinates. 87: 87: Core t (s) Wall t (s) (%) 87: Time: 0.049 0.025 196.4 87: (ns/day) (hour/ns) 87: Performance: 59.025 0.407 87: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as double precision energy file 87: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as double precision energy file 87: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 87: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 87: that with the Verlet scheme, nstlist has no effect on the accuracy of 87: your simulation. 87: 87: 87: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 87: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 87: setting nstcomm equal to nstcalcenergy for less overhead 87: 87: Generating 1-4 interactions: fudge = 0.5 87: Number of degrees of freedom in T-Coupling group System is 27.00 87: 87: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 87: You are using a plain Coulomb cut-off, which might produce artifacts. 87: You might want to consider using PME electrostatics. 87: 87: 87: 87: There were 3 NOTEs 87: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 87: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 87: 87: Using 2 MPI threads 87: Using 1 OpenMP thread per tMPI thread 87: 87: 87: NOTE: The number of threads is not equal to the number of (logical) cpus 87: and the -pin option is set to auto: will not pin threads to cpus. 87: This can lead to significant performance degradation. 87: Consider using -pin on (and -pinoffset in case you run multiple jobs). 87: starting mdrun 'spc2' 87: 16 steps, 0.0 ps. 87: Generated 330891 of the 330891 non-bonded parameter combinations 87: 87: Generated 330891 of the 330891 1-4 parameter combinations 87: 87: Excluding 2 bonded neighbours molecule type 'SOL' 87: 87: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/tip3p5.gro' 87: 87: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 87: 87: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 87: 87: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 87: 87: Note that mdrun will redetermine rlist based on the actual pair-list setup 87: 87: This run will generate roughly 0 Mb of data 87: 87: Writing final coordinates. 87: 87: Core t (s) Wall t (s) (%) 87: Time: 0.063 0.032 197.5 87: (ns/day) (hour/ns) 87: Performance: 46.341 0.518 87: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as double precision energy file 87: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as double precision energy file 87: 87: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 87: that with the Verlet scheme, nstlist has no effect on the accuracy of 87: your simulation. 87: 87: 87: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 87: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 87: setting nstcomm equal to nstcalcenergy for less overhead 87: 87: Generating 1-4 interactions: fudge = 0.5 87: Number of degrees of freedom in T-Coupling group System is 27.00 87: 87: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 87: You are using a plain Coulomb cut-off, which might produce artifacts. 87: You might want to consider using PME electrostatics. 87: 87: 87: 87: There were 3 NOTEs 87: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 87: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 87: 87: Using 2 MPI threads 87: Using 1 OpenMP thread per tMPI thread 87: 87: 87: NOTE: The number of threads is not equal to the number of (logical) cpus 87: and the -pin option is set to auto: will not pin threads to cpus. 87: This can lead to significant performance degradation. 87: Consider using -pin on (and -pinoffset in case you run multiple jobs). 87: starting mdrun 'spc2' 87: 16 steps, 0.0 ps. 87: Generated 330891 of the 330891 non-bonded parameter combinations 87: 87: Generated 330891 of the 330891 1-4 parameter combinations 87: 87: Excluding 2 bonded neighbours molecule type 'SOL' 87: 87: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/tip3p5.gro' 87: 87: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 87: 87: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 87: 87: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 87: 87: Note that mdrun will redetermine rlist based on the actual pair-list setup 87: 87: This run will generate roughly 0 Mb of data 87: 87: Writing final coordinates. 87: 87: Core t (s) Wall t (s) (%) 87: Time: 0.091 0.046 198.0 87: (ns/day) (hour/ns) 87: Performance: 32.127 0.747 87: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as double precision energy file 87: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as double precision energy file 87: 87: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 87: that with the Verlet scheme, nstlist has no effect on the accuracy of 87: your simulation. 87: 87: 87: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 87: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 87: setting nstcomm equal to nstcalcenergy for less overhead 87: 87: Generating 1-4 interactions: fudge = 0.5 87: Number of degrees of freedom in T-Coupling group System is 27.00 87: 87: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 87: You are using a plain Coulomb cut-off, which might produce artifacts. 87: You might want to consider using PME electrostatics. 87: 87: 87: 87: There were 3 NOTEs 87: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 87: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 87: 87: Using 2 MPI threads 87: Using 1 OpenMP thread per tMPI thread 87: 87: 87: NOTE: The number of threads is not equal to the number of (logical) cpus 87: and the -pin option is set to auto: will not pin threads to cpus. 87: This can lead to significant performance degradation. 87: Consider using -pin on (and -pinoffset in case you run multiple jobs). 87: starting mdrun 'spc2' 87: 16 steps, 0.0 ps. 87: Generated 330891 of the 330891 non-bonded parameter combinations 87: 87: Generated 330891 of the 330891 1-4 parameter combinations 87: 87: Excluding 2 bonded neighbours molecule type 'SOL' 87: 87: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/tip3p5.gro' 87: 87: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 87: 87: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 87: 87: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 87: 87: Note that mdrun will redetermine rlist based on the actual pair-list setup 87: 87: This run will generate roughly 0 Mb of data 87: 87: Writing final coordinates. 87: 87: NOTE: 10 % of the run time was spent in domain decomposition, 87: 0 % of the run time was spent in pair search, 87: you might want to increase nstlist (this has no effect on accuracy) 87: 87: Core t (s) Wall t (s) (%) 87: Time: 0.079 0.040 198.0 87: (ns/day) (hour/ns) 87: Performance: 36.616 0.655 87: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as double precision energy file 87: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as double precision energy file 87: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/5 (34840 ms) 87: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/6 87: 87: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 87: that with the Verlet scheme, nstlist has no effect on the accuracy of 87: your simulation. 87: 87: 87: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 87: Setting nstcalcenergy (100) equal to nstenergy (1) 87: 87: Generating 1-4 interactions: fudge = 0.5 87: Number of degrees of freedom in T-Coupling group System is 27.00 87: 87: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 87: You are using a plain Coulomb cut-off, which might produce artifacts. 87: You might want to consider using PME electrostatics. 87: 87: 87: 87: There were 3 NOTEs 87: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 87: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 87: 87: Using 2 MPI threads 87: Using 1 OpenMP thread per tMPI thread 87: 87: 87: NOTE: The number of threads is not equal to the number of (logical) cpus 87: and the -pin option is set to auto: will not pin threads to cpus. 87: This can lead to significant performance degradation. 87: Consider using -pin on (and -pinoffset in case you run multiple jobs). 87: starting mdrun 'spc2' 87: 16 steps, 0.0 ps. 87: Generated 330891 of the 330891 non-bonded parameter combinations 87: 87: Generated 330891 of the 330891 1-4 parameter combinations 87: 87: Excluding 2 bonded neighbours molecule type 'SOL' 87: 87: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/tip3p5.gro' 87: 87: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 87: 87: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 87: 87: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 87: 87: Note that mdrun will redetermine rlist based on the actual pair-list setup 87: 87: This run will generate roughly 0 Mb of data 87: 87: Writing final coordinates. 87: 87: Core t (s) Wall t (s) (%) 87: Time: 0.108 0.054 198.7 87: (ns/day) (hour/ns) 87: Performance: 27.137 0.884 87: 87: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 87: that with the Verlet scheme, nstlist has no effect on the accuracy of 87: your simulation. 87: 87: 87: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 87: Setting nstcalcenergy (100) equal to nstenergy (1) 87: 87: Generating 1-4 interactions: fudge = 0.5 87: Number of degrees of freedom in T-Coupling group System is 27.00 87: 87: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 87: You are using a plain Coulomb cut-off, which might produce artifacts. 87: You might want to consider using PME electrostatics. 87: 87: 87: 87: There were 3 NOTEs 87: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 87: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 87: 87: Using 2 MPI threads 87: Using 1 OpenMP thread per tMPI thread 87: 87: 87: NOTE: The number of threads is not equal to the number of (logical) cpus 87: and the -pin option is set to auto: will not pin threads to cpus. 87: This can lead to significant performance degradation. 87: Consider using -pin on (and -pinoffset in case you run multiple jobs). 87: starting mdrun 'spc2' 87: 16 steps, 0.0 ps. 87: Generated 330891 of the 330891 non-bonded parameter combinations 87: 87: Generated 330891 of the 330891 1-4 parameter combinations 87: 87: Excluding 2 bonded neighbours molecule type 'SOL' 87: 87: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/tip3p5.gro' 87: 87: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 87: 87: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 87: 87: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 87: 87: Note that mdrun will redetermine rlist based on the actual pair-list setup 87: 87: This run will generate roughly 0 Mb of data 87: 87: Writing final coordinates. 87: 87: Core t (s) Wall t (s) (%) 87: Time: 0.074 0.037 198.5 87: (ns/day) (hour/ns) 87: Performance: 39.596 0.606 87: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as double precision energy file 87: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as double precision energy file 87: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 87: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 87: that with the Verlet scheme, nstlist has no effect on the accuracy of 87: your simulation. 87: 87: 87: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 87: Setting nstcalcenergy (100) equal to nstenergy (4) 87: 87: Generating 1-4 interactions: fudge = 0.5 87: Number of degrees of freedom in T-Coupling group System is 27.00 87: 87: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 87: You are using a plain Coulomb cut-off, which might produce artifacts. 87: You might want to consider using PME electrostatics. 87: 87: 87: 87: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 87: COM removal frequency is set to (5). 87: Other settings require a global communication frequency of 4. 87: Note that this will require additional global communication steps, 87: which will reduce performance when using multiple ranks. 87: Consider setting nstcomm to a multiple of 4. 87: 87: 87: There were 4 NOTEs 87: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 87: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 87: 87: Using 2 MPI threads 87: Using 1 OpenMP thread per tMPI thread 87: 87: 87: NOTE: The number of threads is not equal to the number of (logical) cpus 87: and the -pin option is set to auto: will not pin threads to cpus. 87: This can lead to significant performance degradation. 87: Consider using -pin on (and -pinoffset in case you run multiple jobs). 87: starting mdrun 'spc2' 87: 16 steps, 0.0 ps. 87: Generated 330891 of the 330891 non-bonded parameter combinations 87: 87: Generated 330891 of the 330891 1-4 parameter combinations 87: 87: Excluding 2 bonded neighbours molecule type 'SOL' 87: 87: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/tip3p5.gro' 87: 87: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 87: 87: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 87: 87: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 87: 87: Note that mdrun will redetermine rlist based on the actual pair-list setup 87: 87: This run will generate roughly 0 Mb of data 87: 87: Writing final coordinates. 87: 87: Core t (s) Wall t (s) (%) 87: Time: 0.072 0.036 198.5 87: (ns/day) (hour/ns) 87: Performance: 40.250 0.596 87: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as double precision energy file 87: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as double precision energy file 87: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 87: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 87: that with the Verlet scheme, nstlist has no effect on the accuracy of 87: your simulation. 87: 87: 87: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 87: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 87: setting nstcomm equal to nstcalcenergy for less overhead 87: 87: Generating 1-4 interactions: fudge = 0.5 87: Number of degrees of freedom in T-Coupling group System is 27.00 87: 87: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 87: You are using a plain Coulomb cut-off, which might produce artifacts. 87: You might want to consider using PME electrostatics. 87: 87: 87: 87: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 87: COM removal frequency is set to (5). 87: Other settings require a global communication frequency of 100. 87: Note that this will require additional global communication steps, 87: which will reduce performance when using multiple ranks. 87: Consider setting nstcomm to a multiple of 100. 87: 87: 87: There were 4 NOTEs 87: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 87: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 87: 87: Using 2 MPI threads 87: Using 1 OpenMP thread per tMPI thread 87: 87: 87: NOTE: The number of threads is not equal to the number of (logical) cpus 87: and the -pin option is set to auto: will not pin threads to cpus. 87: This can lead to significant performance degradation. 87: Consider using -pin on (and -pinoffset in case you run multiple jobs). 87: starting mdrun 'spc2' 87: 16 steps, 0.0 ps. 87: Generated 330891 of the 330891 non-bonded parameter combinations 87: 87: Generated 330891 of the 330891 1-4 parameter combinations 87: 87: Excluding 2 bonded neighbours molecule type 'SOL' 87: 87: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/tip3p5.gro' 87: 87: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 87: 87: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 87: 87: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 87: 87: Note that mdrun will redetermine rlist based on the actual pair-list setup 87: 87: This run will generate roughly 0 Mb of data 87: 87: Writing final coordinates. 87: 87: Core t (s) Wall t (s) (%) 87: Time: 0.054 0.027 197.8 87: (ns/day) (hour/ns) 87: Performance: 53.501 0.449 87: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as double precision energy file 87: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as double precision energy file 87: 87: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 87: that with the Verlet scheme, nstlist has no effect on the accuracy of 87: your simulation. 87: 87: 87: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 87: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 87: setting nstcomm equal to nstcalcenergy for less overhead 87: 87: Generating 1-4 interactions: fudge = 0.5 87: Number of degrees of freedom in T-Coupling group System is 27.00 87: 87: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 87: You are using a plain Coulomb cut-off, which might produce artifacts. 87: You might want to consider using PME electrostatics. 87: 87: 87: 87: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 87: COM removal frequency is set to (5). 87: Other settings require a global communication frequency of 100. 87: Note that this will require additional global communication steps, 87: which will reduce performance when using multiple ranks. 87: Consider setting nstcomm to a multiple of 100. 87: 87: 87: There were 4 NOTEs 87: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 87: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 87: 87: Using 2 MPI threads 87: Using 1 OpenMP thread per tMPI thread 87: 87: 87: NOTE: The number of threads is not equal to the number of (logical) cpus 87: and the -pin option is set to auto: will not pin threads to cpus. 87: This can lead to significant performance degradation. 87: Consider using -pin on (and -pinoffset in case you run multiple jobs). 87: starting mdrun 'spc2' 87: 16 steps, 0.0 ps. 87: Generated 330891 of the 330891 non-bonded parameter combinations 87: 87: Generated 330891 of the 330891 1-4 parameter combinations 87: 87: Excluding 2 bonded neighbours molecule type 'SOL' 87: 87: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/tip3p5.gro' 87: 87: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 87: 87: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 87: 87: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 87: 87: Note that mdrun will redetermine rlist based on the actual pair-list setup 87: 87: This run will generate roughly 0 Mb of data 87: 87: Writing final coordinates. 87: 87: Core t (s) Wall t (s) (%) 87: Time: 0.075 0.038 198.5 87: (ns/day) (hour/ns) 87: Performance: 38.775 0.619 87: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as double precision energy file 87: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as double precision energy file 87: 87: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 87: that with the Verlet scheme, nstlist has no effect on the accuracy of 87: your simulation. 87: 87: 87: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 87: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 87: setting nstcomm equal to nstcalcenergy for less overhead 87: 87: Generating 1-4 interactions: fudge = 0.5 87: Number of degrees of freedom in T-Coupling group System is 27.00 87: 87: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 87: You are using a plain Coulomb cut-off, which might produce artifacts. 87: You might want to consider using PME electrostatics. 87: 87: 87: 87: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 87: COM removal frequency is set to (5). 87: Other settings require a global communication frequency of 100. 87: Note that this will require additional global communication steps, 87: which will reduce performance when using multiple ranks. 87: Consider setting nstcomm to a multiple of 100. 87: 87: 87: There were 4 NOTEs 87: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 87: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 87: 87: Using 2 MPI threads 87: Using 1 OpenMP thread per tMPI thread 87: 87: 87: NOTE: The number of threads is not equal to the number of (logical) cpus 87: and the -pin option is set to auto: will not pin threads to cpus. 87: This can lead to significant performance degradation. 87: Consider using -pin on (and -pinoffset in case you run multiple jobs). 87: starting mdrun 'spc2' 87: 16 steps, 0.0 ps. 87: Generated 330891 of the 330891 non-bonded parameter combinations 87: 87: Generated 330891 of the 330891 1-4 parameter combinations 87: 87: Excluding 2 bonded neighbours molecule type 'SOL' 87: 87: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/tip3p5.gro' 87: 87: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 87: 87: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 87: 87: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 87: 87: Note that mdrun will redetermine rlist based on the actual pair-list setup 87: 87: This run will generate roughly 0 Mb of data 87: 87: Writing final coordinates. 87: 87: Core t (s) Wall t (s) (%) 87: Time: 0.053 0.027 197.8 87: (ns/day) (hour/ns) 87: Performance: 54.476 0.441 87: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as double precision energy file 87: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as double precision energy file 87: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/6 (35138 ms) 87: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/7 87: 87: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 87: that with the Verlet scheme, nstlist has no effect on the accuracy of 87: your simulation. 87: 87: 87: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 87: Setting nstcalcenergy (100) equal to nstenergy (1) 87: 87: Generating 1-4 interactions: fudge = 0.5 87: Number of degrees of freedom in T-Coupling group System is 27.00 87: 87: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 87: You are using a plain Coulomb cut-off, which might produce artifacts. 87: You might want to consider using PME electrostatics. 87: 87: 87: 87: There were 3 NOTEs 87: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 87: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 87: 87: Using 2 MPI threads 87: Using 1 OpenMP thread per tMPI thread 87: 87: 87: NOTE: The number of threads is not equal to the number of (logical) cpus 87: and the -pin option is set to auto: will not pin threads to cpus. 87: This can lead to significant performance degradation. 87: Consider using -pin on (and -pinoffset in case you run multiple jobs). 87: starting mdrun 'spc2' 87: 16 steps, 0.0 ps. 87: Generated 330891 of the 330891 non-bonded parameter combinations 87: 87: Generated 330891 of the 330891 1-4 parameter combinations 87: 87: Excluding 2 bonded neighbours molecule type 'SOL' 87: 87: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/tip3p5.gro' 87: 87: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 87: 87: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 87: 87: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 87: 87: Note that mdrun will redetermine rlist based on the actual pair-list setup 87: 87: This run will generate roughly 0 Mb of data 87: 87: Writing final coordinates. 87: 87: Core t (s) Wall t (s) (%) 87: Time: 0.097 0.049 198.5 87: (ns/day) (hour/ns) 87: Performance: 30.219 0.794 87: 87: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 87: that with the Verlet scheme, nstlist has no effect on the accuracy of 87: your simulation. 87: 87: 87: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 87: Setting nstcalcenergy (100) equal to nstenergy (1) 87: 87: Generating 1-4 interactions: fudge = 0.5 87: Number of degrees of freedom in T-Coupling group System is 27.00 87: 87: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 87: You are using a plain Coulomb cut-off, which might produce artifacts. 87: You might want to consider using PME electrostatics. 87: 87: 87: 87: There were 3 NOTEs 87: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 87: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 87: 87: Using 2 MPI threads 87: Using 1 OpenMP thread per tMPI thread 87: 87: 87: NOTE: The number of threads is not equal to the number of (logical) cpus 87: and the -pin option is set to auto: will not pin threads to cpus. 87: This can lead to significant performance degradation. 87: Consider using -pin on (and -pinoffset in case you run multiple jobs). 87: starting mdrun 'spc2' 87: 16 steps, 0.0 ps. 87: Generated 330891 of the 330891 non-bonded parameter combinations 87: 87: Generated 330891 of the 330891 1-4 parameter combinations 87: 87: Excluding 2 bonded neighbours molecule type 'SOL' 87: 87: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/tip3p5.gro' 87: 87: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 87: 87: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 87: 87: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 87: 87: Note that mdrun will redetermine rlist based on the actual pair-list setup 87: 87: This run will generate roughly 0 Mb of data 87: 87: Writing final coordinates. 87: 87: Core t (s) Wall t (s) (%) 87: Time: 0.052 0.026 197.7 87: (ns/day) (hour/ns) 87: Performance: 56.133 0.428 87: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as double precision energy file 87: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as double precision energy file 87: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 87: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 87: that with the Verlet scheme, nstlist has no effect on the accuracy of 87: your simulation. 87: 87: 87: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 87: Setting nstcalcenergy (100) equal to nstenergy (4) 87: 87: Generating 1-4 interactions: fudge = 0.5 87: Number of degrees of freedom in T-Coupling group System is 27.00 87: 87: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 87: You are using a plain Coulomb cut-off, which might produce artifacts. 87: You might want to consider using PME electrostatics. 87: 87: 87: 87: There were 3 NOTEs 87: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 87: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 87: 87: Using 2 MPI threads 87: Using 1 OpenMP thread per tMPI thread 87: 87: 87: NOTE: The number of threads is not equal to the number of (logical) cpus 87: and the -pin option is set to auto: will not pin threads to cpus. 87: This can lead to significant performance degradation. 87: Consider using -pin on (and -pinoffset in case you run multiple jobs). 87: starting mdrun 'spc2' 87: 16 steps, 0.0 ps. 87: Generated 330891 of the 330891 non-bonded parameter combinations 87: 87: Generated 330891 of the 330891 1-4 parameter combinations 87: 87: Excluding 2 bonded neighbours molecule type 'SOL' 87: 87: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/tip3p5.gro' 87: 87: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 87: 87: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 87: 87: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 87: 87: Note that mdrun will redetermine rlist based on the actual pair-list setup 87: 87: This run will generate roughly 0 Mb of data 87: 87: Writing final coordinates. 87: 87: Core t (s) Wall t (s) (%) 87: Time: 0.063 0.032 197.7 87: (ns/day) (hour/ns) 87: Performance: 45.752 0.525 87: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as double precision energy file 87: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as double precision energy file 87: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 87: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 87: that with the Verlet scheme, nstlist has no effect on the accuracy of 87: your simulation. 87: 87: 87: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 87: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 87: setting nstcomm equal to nstcalcenergy for less overhead 87: 87: Generating 1-4 interactions: fudge = 0.5 87: Number of degrees of freedom in T-Coupling group System is 27.00 87: 87: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 87: You are using a plain Coulomb cut-off, which might produce artifacts. 87: You might want to consider using PME electrostatics. 87: 87: 87: 87: There were 3 NOTEs 87: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 87: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 87: 87: Using 2 MPI threads 87: Using 1 OpenMP thread per tMPI thread 87: 87: 87: NOTE: The number of threads is not equal to the number of (logical) cpus 87: and the -pin option is set to auto: will not pin threads to cpus. 87: This can lead to significant performance degradation. 87: Consider using -pin on (and -pinoffset in case you run multiple jobs). 87: starting mdrun 'spc2' 87: 16 steps, 0.0 ps. 87: Generated 330891 of the 330891 non-bonded parameter combinations 87: 87: Generated 330891 of the 330891 1-4 parameter combinations 87: 87: Excluding 2 bonded neighbours molecule type 'SOL' 87: 87: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/tip3p5.gro' 87: 87: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 87: 87: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 87: 87: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 87: 87: Note that mdrun will redetermine rlist based on the actual pair-list setup 87: 87: This run will generate roughly 0 Mb of data 87: 87: Writing final coordinates. 87: 87: Core t (s) Wall t (s) (%) 87: Time: 0.058 0.029 197.8 87: (ns/day) (hour/ns) 87: Performance: 50.239 0.478 87: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as double precision energy file 87: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as double precision energy file 87: 87: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 87: that with the Verlet scheme, nstlist has no effect on the accuracy of 87: your simulation. 87: 87: 87: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 87: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 87: setting nstcomm equal to nstcalcenergy for less overhead 87: 87: Generating 1-4 interactions: fudge = 0.5 87: Number of degrees of freedom in T-Coupling group System is 27.00 87: 87: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 87: You are using a plain Coulomb cut-off, which might produce artifacts. 87: You might want to consider using PME electrostatics. 87: 87: 87: 87: There were 3 NOTEs 87: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 87: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 87: 87: Using 2 MPI threads 87: Using 1 OpenMP thread per tMPI thread 87: 87: 87: NOTE: The number of threads is not equal to the number of (logical) cpus 87: and the -pin option is set to auto: will not pin threads to cpus. 87: This can lead to significant performance degradation. 87: Consider using -pin on (and -pinoffset in case you run multiple jobs). 87: starting mdrun 'spc2' 87: 16 steps, 0.0 ps. 87: Generated 330891 of the 330891 non-bonded parameter combinations 87: 87: Generated 330891 of the 330891 1-4 parameter combinations 87: 87: Excluding 2 bonded neighbours molecule type 'SOL' 87: 87: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/tip3p5.gro' 87: 87: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 87: 87: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 87: 87: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 87: 87: Note that mdrun will redetermine rlist based on the actual pair-list setup 87: 87: This run will generate roughly 0 Mb of data 87: 87: Writing final coordinates. 87: 87: Core t (s) Wall t (s) (%) 87: Time: 0.103 0.052 198.7 87: (ns/day) (hour/ns) 87: Performance: 28.420 0.844 87: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as double precision energy file 87: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as double precision energy file 87: 87: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 87: that with the Verlet scheme, nstlist has no effect on the accuracy of 87: your simulation. 87: 87: 87: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 87: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 87: setting nstcomm equal to nstcalcenergy for less overhead 87: 87: Generating 1-4 interactions: fudge = 0.5 87: Number of degrees of freedom in T-Coupling group System is 27.00 87: 87: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 87: You are using a plain Coulomb cut-off, which might produce artifacts. 87: You might want to consider using PME electrostatics. 87: 87: 87: 87: There were 3 NOTEs 87: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 87: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 87: 87: Using 2 MPI threads 87: Using 1 OpenMP thread per tMPI thread 87: 87: 87: NOTE: The number of threads is not equal to the number of (logical) cpus 87: and the -pin option is set to auto: will not pin threads to cpus. 87: This can lead to significant performance degradation. 87: Consider using -pin on (and -pinoffset in case you run multiple jobs). 87: starting mdrun 'spc2' 87: 16 steps, 0.0 ps. 87: Generated 330891 of the 330891 non-bonded parameter combinations 87: 87: Generated 330891 of the 330891 1-4 parameter combinations 87: 87: Excluding 2 bonded neighbours molecule type 'SOL' 87: 87: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/tip3p5.gro' 87: 87: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 87: 87: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 87: 87: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 87: 87: Note that mdrun will redetermine rlist based on the actual pair-list setup 87: 87: This run will generate roughly 0 Mb of data 87: 87: Writing final coordinates. 87: 87: Core t (s) Wall t (s) (%) 87: Time: 0.061 0.031 198.0 87: (ns/day) (hour/ns) 87: Performance: 47.515 0.505 87: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as double precision energy file 87: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as double precision energy file 87: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/7 (35135 ms) 87: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/8 87: 87: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 87: that with the Verlet scheme, nstlist has no effect on the accuracy of 87: your simulation. 87: 87: 87: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 87: Setting nstcalcenergy (100) equal to nstenergy (1) 87: 87: Generating 1-4 interactions: fudge = 0.5 87: Number of degrees of freedom in T-Coupling group System is 27.00 87: 87: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 87: You are using a plain Coulomb cut-off, which might produce artifacts. 87: You might want to consider using PME electrostatics. 87: 87: 87: 87: There were 3 NOTEs 87: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 87: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 87: 87: Using 2 MPI threads 87: Using 1 OpenMP thread per tMPI thread 87: 87: 87: NOTE: The number of threads is not equal to the number of (logical) cpus 87: and the -pin option is set to auto: will not pin threads to cpus. 87: This can lead to significant performance degradation. 87: Consider using -pin on (and -pinoffset in case you run multiple jobs). 87: starting mdrun 'spc2' 87: 16 steps, 0.0 ps. 87: Generated 330891 of the 330891 non-bonded parameter combinations 87: 87: Generated 330891 of the 330891 1-4 parameter combinations 87: 87: Excluding 2 bonded neighbours molecule type 'SOL' 87: 87: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/tip3p5.gro' 87: 87: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 87: 87: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 87: 87: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 87: 87: Note that mdrun will redetermine rlist based on the actual pair-list setup 87: 87: This run will generate roughly 0 Mb of data 87: 87: Writing final coordinates. 87: 87: NOTE: 9 % of the run time was spent communicating energies, 87: you might want to increase some nst* mdp options 87: 87: Core t (s) Wall t (s) (%) 87: Time: 0.102 0.051 198.7 87: (ns/day) (hour/ns) 87: Performance: 28.560 0.840 87: 87: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 87: that with the Verlet scheme, nstlist has no effect on the accuracy of 87: your simulation. 87: 87: 87: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 87: Setting nstcalcenergy (100) equal to nstenergy (1) 87: 87: Generating 1-4 interactions: fudge = 0.5 87: Number of degrees of freedom in T-Coupling group System is 27.00 87: 87: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 87: You are using a plain Coulomb cut-off, which might produce artifacts. 87: You might want to consider using PME electrostatics. 87: 87: 87: 87: There were 3 NOTEs 87: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 87: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 87: 87: Using 2 MPI threads 87: Using 1 OpenMP thread per tMPI thread 87: 87: 87: NOTE: The number of threads is not equal to the number of (logical) cpus 87: and the -pin option is set to auto: will not pin threads to cpus. 87: This can lead to significant performance degradation. 87: Consider using -pin on (and -pinoffset in case you run multiple jobs). 87: starting mdrun 'spc2' 87: 16 steps, 0.0 ps. 87: Generated 330891 of the 330891 non-bonded parameter combinations 87: 87: Generated 330891 of the 330891 1-4 parameter combinations 87: 87: Excluding 2 bonded neighbours molecule type 'SOL' 87: 87: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/tip3p5.gro' 87: 87: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 87: 87: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 87: 87: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 87: 87: Note that mdrun will redetermine rlist based on the actual pair-list setup 87: 87: This run will generate roughly 0 Mb of data 87: 87: Writing final coordinates. 87: 87: Core t (s) Wall t (s) (%) 87: Time: 0.090 0.046 195.8 87: (ns/day) (hour/ns) 87: Performance: 31.859 0.753 87: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_reference.edr as double precision energy file 87: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.edr as double precision energy file 87: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 87: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 87: that with the Verlet scheme, nstlist has no effect on the accuracy of 87: your simulation. 87: 87: 87: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 87: Setting nstcalcenergy (100) equal to nstenergy (4) 87: 87: Generating 1-4 interactions: fudge = 0.5 87: Number of degrees of freedom in T-Coupling group System is 27.00 87: 87: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 87: You are using a plain Coulomb cut-off, which might produce artifacts. 87: You might want to consider using PME electrostatics. 87: 87: 87: 87: There were 3 NOTEs 87: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 87: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 87: 87: Using 2 MPI threads 87: Using 1 OpenMP thread per tMPI thread 87: 87: 87: NOTE: The number of threads is not equal to the number of (logical) cpus 87: and the -pin option is set to auto: will not pin threads to cpus. 87: This can lead to significant performance degradation. 87: Consider using -pin on (and -pinoffset in case you run multiple jobs). 87: starting mdrun 'spc2' 87: 16 steps, 0.0 ps. 87: Generated 330891 of the 330891 non-bonded parameter combinations 87: 87: Generated 330891 of the 330891 1-4 parameter combinations 87: 87: Excluding 2 bonded neighbours molecule type 'SOL' 87: 87: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/tip3p5.gro' 87: 87: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 87: 87: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 87: 87: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 87: 87: Note that mdrun will redetermine rlist based on the actual pair-list setup 87: 87: This run will generate roughly 0 Mb of data 87: 87: Writing final coordinates. 87: 87: Core t (s) Wall t (s) (%) 87: Time: 0.050 0.025 197.6 87: (ns/day) (hour/ns) 87: Performance: 58.113 0.413 87: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_reference.edr as double precision energy file 87: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.edr as double precision energy file 87: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 87: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 87: that with the Verlet scheme, nstlist has no effect on the accuracy of 87: your simulation. 87: 87: 87: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 87: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 87: setting nstcomm equal to nstcalcenergy for less overhead 87: 87: Generating 1-4 interactions: fudge = 0.5 87: Number of degrees of freedom in T-Coupling group System is 27.00 87: 87: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 87: You are using a plain Coulomb cut-off, which might produce artifacts. 87: You might want to consider using PME electrostatics. 87: 87: 87: 87: There were 3 NOTEs 87: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 87: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 87: 87: Using 2 MPI threads 87: Using 1 OpenMP thread per tMPI thread 87: 87: 87: NOTE: The number of threads is not equal to the number of (logical) cpus 87: and the -pin option is set to auto: will not pin threads to cpus. 87: This can lead to significant performance degradation. 87: Consider using -pin on (and -pinoffset in case you run multiple jobs). 87: starting mdrun 'spc2' 87: 16 steps, 0.0 ps. 87: Generated 330891 of the 330891 non-bonded parameter combinations 87: 87: Generated 330891 of the 330891 1-4 parameter combinations 87: 87: Excluding 2 bonded neighbours molecule type 'SOL' 87: 87: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/tip3p5.gro' 87: 87: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 87: 87: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 87: 87: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 87: 87: Note that mdrun will redetermine rlist based on the actual pair-list setup 87: 87: This run will generate roughly 0 Mb of data 87: 87: Writing final coordinates. 87: 87: Core t (s) Wall t (s) (%) 87: Time: 0.062 0.031 198.0 87: (ns/day) (hour/ns) 87: Performance: 46.983 0.511 87: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_reference.edr as double precision energy file 87: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.edr as double precision energy file 87: 87: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 87: that with the Verlet scheme, nstlist has no effect on the accuracy of 87: your simulation. 87: 87: 87: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 87: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 87: setting nstcomm equal to nstcalcenergy for less overhead 87: 87: Generating 1-4 interactions: fudge = 0.5 87: Number of degrees of freedom in T-Coupling group System is 27.00 87: 87: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 87: You are using a plain Coulomb cut-off, which might produce artifacts. 87: You might want to consider using PME electrostatics. 87: 87: 87: 87: There were 3 NOTEs 87: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 87: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 87: 87: Using 2 MPI threads 87: Using 1 OpenMP thread per tMPI thread 87: 87: 87: NOTE: The number of threads is not equal to the number of (logical) cpus 87: and the -pin option is set to auto: will not pin threads to cpus. 87: This can lead to significant performance degradation. 87: Consider using -pin on (and -pinoffset in case you run multiple jobs). 87: starting mdrun 'spc2' 87: 16 steps, 0.0 ps. 87: Generated 330891 of the 330891 non-bonded parameter combinations 87: 87: Generated 330891 of the 330891 1-4 parameter combinations 87: 87: Excluding 2 bonded neighbours molecule type 'SOL' 87: 87: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/tip3p5.gro' 87: 87: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 87: 87: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 87: 87: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 87: 87: Note that mdrun will redetermine rlist based on the actual pair-list setup 87: 87: This run will generate roughly 0 Mb of data 87: 87: Writing final coordinates. 87: 87: Core t (s) Wall t (s) (%) 87: Time: 0.058 0.029 198.0 87: (ns/day) (hour/ns) 87: Performance: 50.208 0.478 87: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_reference.edr as double precision energy file 87: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.edr as double precision energy file 87: 87: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 87: that with the Verlet scheme, nstlist has no effect on the accuracy of 87: your simulation. 87: 87: 87: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 87: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 87: setting nstcomm equal to nstcalcenergy for less overhead 87: 87: Generating 1-4 interactions: fudge = 0.5 87: Number of degrees of freedom in T-Coupling group System is 27.00 87: 87: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 87: You are using a plain Coulomb cut-off, which might produce artifacts. 87: You might want to consider using PME electrostatics. 87: 87: 87: 87: There were 3 NOTEs 87: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 87: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 87: 87: Using 2 MPI threads 87: Using 1 OpenMP thread per tMPI thread 87: 87: 87: NOTE: The number of threads is not equal to the number of (logical) cpus 87: and the -pin option is set to auto: will not pin threads to cpus. 87: This can lead to significant performance degradation. 87: Consider using -pin on (and -pinoffset in case you run multiple jobs). 87: starting mdrun 'spc2' 87: 16 steps, 0.0 ps. 87: Generated 330891 of the 330891 non-bonded parameter combinations 87: 87: Generated 330891 of the 330891 1-4 parameter combinations 87: 87: Excluding 2 bonded neighbours molecule type 'SOL' 87: 87: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/tip3p5.gro' 87: 87: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 87: 87: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 87: 87: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 87: 87: Note that mdrun will redetermine rlist based on the actual pair-list setup 87: 87: This run will generate roughly 0 Mb of data 87: 87: Writing final coordinates. 87: 87: Core t (s) Wall t (s) (%) 87: Time: 0.073 0.037 198.1 87: (ns/day) (hour/ns) 87: Performance: 39.802 0.603 87: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_reference.edr as double precision energy file 87: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.edr as double precision energy file 87: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/8 (35129 ms) 87: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/9 87: 87: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 87: that with the Verlet scheme, nstlist has no effect on the accuracy of 87: your simulation. 87: 87: 87: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 87: Setting nstcalcenergy (100) equal to nstenergy (1) 87: 87: Generating 1-4 interactions: fudge = 0.5 87: Number of degrees of freedom in T-Coupling group System is 27.00 87: 87: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 87: NVE simulation: will use the initial temperature of 398.997 K for 87: determining the Verlet buffer size 87: 87: 87: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 87: You are using a plain Coulomb cut-off, which might produce artifacts. 87: You might want to consider using PME electrostatics. 87: 87: 87: 87: There were 4 NOTEs 87: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 87: Can not increase nstlist because an NVE ensemble is used 87: Using 2 MPI threads 87: Using 1 OpenMP thread per tMPI thread 87: 87: 87: NOTE: The number of threads is not equal to the number of (logical) cpus 87: and the -pin option is set to auto: will not pin threads to cpus. 87: This can lead to significant performance degradation. 87: Consider using -pin on (and -pinoffset in case you run multiple jobs). 87: starting mdrun 'spc2' 87: 16 steps, 0.0 ps. 87: Generated 330891 of the 330891 non-bonded parameter combinations 87: 87: Generated 330891 of the 330891 1-4 parameter combinations 87: 87: Excluding 2 bonded neighbours molecule type 'SOL' 87: 87: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/tip3p5.gro' 87: 87: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 87: 87: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 87: 87: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 87: 87: Note that mdrun will redetermine rlist based on the actual pair-list setup 87: 87: This run will generate roughly 0 Mb of data 87: 87: Writing final coordinates. 87: 87: 87: Dynamic load balancing report: 87: DLB got disabled because it was unsuitable to use. 87: Average load imbalance: 17.2%. 87: The balanceable part of the MD step is 46%, load imbalance is computed from this. 87: Part of the total run time spent waiting due to load imbalance: 7.9%. 87: 87: NOTE: 7.9 % of the available CPU time was lost due to load imbalance 87: in the domain decomposition. 87: You can consider manually changing the decomposition (option -dd); 87: e.g. by using fewer domains along the box dimension in which there is 87: considerable inhomogeneity in the simulated system. 87: 87: Core t (s) Wall t (s) (%) 87: Time: 0.107 0.054 197.9 87: (ns/day) (hour/ns) 87: Performance: 27.155 0.884 87: 87: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 87: that with the Verlet scheme, nstlist has no effect on the accuracy of 87: your simulation. 87: 87: 87: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 87: Setting nstcalcenergy (100) equal to nstenergy (1) 87: 87: Generating 1-4 interactions: fudge = 0.5 87: Number of degrees of freedom in T-Coupling group System is 27.00 87: 87: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 87: NVE simulation: will use the initial temperature of 398.997 K for 87: determining the Verlet buffer size 87: 87: 87: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 87: You are using a plain Coulomb cut-off, which might produce artifacts. 87: You might want to consider using PME electrostatics. 87: 87: 87: 87: There were 4 NOTEs 87: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 87: Can not increase nstlist because an NVE ensemble is used 87: Using 2 MPI threads 87: Using 1 OpenMP thread per tMPI thread 87: 87: 87: NOTE: The number of threads is not equal to the number of (logical) cpus 87: and the -pin option is set to auto: will not pin threads to cpus. 87: This can lead to significant performance degradation. 87: Consider using -pin on (and -pinoffset in case you run multiple jobs). 87: starting mdrun 'spc2' 87: 16 steps, 0.0 ps. 87: Generated 330891 of the 330891 non-bonded parameter combinations 87: 87: Generated 330891 of the 330891 1-4 parameter combinations 87: 87: Excluding 2 bonded neighbours molecule type 'SOL' 87: 87: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/tip3p5.gro' 87: 87: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 87: 87: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 87: 87: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 87: 87: Note that mdrun will redetermine rlist based on the actual pair-list setup 87: 87: This run will generate roughly 0 Mb of data 87: 87: Writing final coordinates. 87: 87: 87: Dynamic load balancing report: 87: DLB got disabled because it was unsuitable to use. 87: Average load imbalance: 6.2%. 87: The balanceable part of the MD step is 60%, load imbalance is computed from this. 87: Part of the total run time spent waiting due to load imbalance: 3.7%. 87: 87: 87: Core t (s) Wall t (s) (%) 87: Time: 0.047 0.024 195.0 87: (ns/day) (hour/ns) 87: Performance: 60.964 0.394 87: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_reference.edr as double precision energy file 87: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.edr as double precision energy file 87: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 87: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 87: that with the Verlet scheme, nstlist has no effect on the accuracy of 87: your simulation. 87: 87: 87: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 87: Setting nstcalcenergy (100) equal to nstenergy (4) 87: 87: Generating 1-4 interactions: fudge = 0.5 87: Number of degrees of freedom in T-Coupling group System is 27.00 87: 87: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 87: NVE simulation: will use the initial temperature of 398.997 K for 87: determining the Verlet buffer size 87: 87: 87: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 87: You are using a plain Coulomb cut-off, which might produce artifacts. 87: You might want to consider using PME electrostatics. 87: 87: 87: 87: NOTE 5 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 87: COM removal frequency is set to (5). 87: Other settings require a global communication frequency of 4. 87: Note that this will require additional global communication steps, 87: which will reduce performance when using multiple ranks. 87: Consider setting nstcomm to a multiple of 4. 87: 87: 87: There were 5 NOTEs 87: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 87: Can not increase nstlist because an NVE ensemble is used 87: Using 2 MPI threads 87: Using 1 OpenMP thread per tMPI thread 87: 87: 87: NOTE: The number of threads is not equal to the number of (logical) cpus 87: and the -pin option is set to auto: will not pin threads to cpus. 87: This can lead to significant performance degradation. 87: Consider using -pin on (and -pinoffset in case you run multiple jobs). 87: starting mdrun 'spc2' 87: 16 steps, 0.0 ps. 87: Generated 330891 of the 330891 non-bonded parameter combinations 87: 87: Generated 330891 of the 330891 1-4 parameter combinations 87: 87: Excluding 2 bonded neighbours molecule type 'SOL' 87: 87: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/tip3p5.gro' 87: 87: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 87: 87: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 87: 87: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 87: 87: Note that mdrun will redetermine rlist based on the actual pair-list setup 87: 87: This run will generate roughly 0 Mb of data 87: 87: Writing final coordinates. 87: 87: 87: Dynamic load balancing report: 87: DLB got disabled because it was unsuitable to use. 87: Average load imbalance: 13.0%. 87: The balanceable part of the MD step is 45%, load imbalance is computed from this. 87: Part of the total run time spent waiting due to load imbalance: 5.8%. 87: 87: NOTE: 5.8 % of the available CPU time was lost due to load imbalance 87: in the domain decomposition. 87: You can consider manually changing the decomposition (option -dd); 87: e.g. by using fewer domains along the box dimension in which there is 87: considerable inhomogeneity in the simulated system. 87: 87: Core t (s) Wall t (s) (%) 87: Time: 0.067 0.034 193.1 87: (ns/day) (hour/ns) 87: Performance: 42.644 0.563 87: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_reference.edr as double precision energy file 87: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.edr as double precision energy file 87: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 87: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 87: that with the Verlet scheme, nstlist has no effect on the accuracy of 87: your simulation. 87: 87: 87: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 87: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 87: setting nstcomm equal to nstcalcenergy for less overhead 87: 87: Generating 1-4 interactions: fudge = 0.5 87: Number of degrees of freedom in T-Coupling group System is 27.00 87: 87: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 87: NVE simulation: will use the initial temperature of 398.997 K for 87: determining the Verlet buffer size 87: 87: 87: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 87: You are using a plain Coulomb cut-off, which might produce artifacts. 87: You might want to consider using PME electrostatics. 87: 87: 87: 87: NOTE 5 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 87: COM removal frequency is set to (5). 87: Other settings require a global communication frequency of 100. 87: Note that this will require additional global communication steps, 87: which will reduce performance when using multiple ranks. 87: Consider setting nstcomm to a multiple of 100. 87: 87: 87: There were 5 NOTEs 87: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 87: Can not increase nstlist because an NVE ensemble is used 87: Using 2 MPI threads 87: Using 1 OpenMP thread per tMPI thread 87: 87: 87: NOTE: The number of threads is not equal to the number of (logical) cpus 87: and the -pin option is set to auto: will not pin threads to cpus. 87: This can lead to significant performance degradation. 87: Consider using -pin on (and -pinoffset in case you run multiple jobs). 87: starting mdrun 'spc2' 87: 16 steps, 0.0 ps. 87: Generated 330891 of the 330891 non-bonded parameter combinations 87: 87: Generated 330891 of the 330891 1-4 parameter combinations 87: 87: Excluding 2 bonded neighbours molecule type 'SOL' 87: 87: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/tip3p5.gro' 87: 87: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 87: 87: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 87: 87: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 87: 87: Note that mdrun will redetermine rlist based on the actual pair-list setup 87: 87: This run will generate roughly 0 Mb of data 87: 87: Writing final coordinates. 87: 87: 87: Dynamic load balancing report: 87: DLB got disabled because it was unsuitable to use. 87: Average load imbalance: 9.7%. 87: The balanceable part of the MD step is 53%, load imbalance is computed from this. 87: Part of the total run time spent waiting due to load imbalance: 5.1%. 87: 87: NOTE: 5.1 % of the available CPU time was lost due to load imbalance 87: in the domain decomposition. 87: You can consider manually changing the decomposition (option -dd); 87: e.g. by using fewer domains along the box dimension in which there is 87: considerable inhomogeneity in the simulated system. 87: 87: Core t (s) Wall t (s) (%) 87: Time: 0.063 0.032 195.9 87: (ns/day) (hour/ns) 87: Performance: 45.664 0.526 87: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_reference.edr as double precision energy file 87: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.edr as double precision energy file 87: 87: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 87: that with the Verlet scheme, nstlist has no effect on the accuracy of 87: your simulation. 87: 87: 87: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 87: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 87: setting nstcomm equal to nstcalcenergy for less overhead 87: 87: Generating 1-4 interactions: fudge = 0.5 87: Number of degrees of freedom in T-Coupling group System is 27.00 87: 87: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 87: NVE simulation: will use the initial temperature of 398.997 K for 87: determining the Verlet buffer size 87: 87: 87: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 87: You are using a plain Coulomb cut-off, which might produce artifacts. 87: You might want to consider using PME electrostatics. 87: 87: 87: 87: NOTE 5 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 87: COM removal frequency is set to (5). 87: Other settings require a global communication frequency of 100. 87: Note that this will require additional global communication steps, 87: which will reduce performance when using multiple ranks. 87: Consider setting nstcomm to a multiple of 100. 87: 87: 87: There were 5 NOTEs 87: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 87: Can not increase nstlist because an NVE ensemble is used 87: Using 2 MPI threads 87: Using 1 OpenMP thread per tMPI thread 87: 87: 87: NOTE: The number of threads is not equal to the number of (logical) cpus 87: and the -pin option is set to auto: will not pin threads to cpus. 87: This can lead to significant performance degradation. 87: Consider using -pin on (and -pinoffset in case you run multiple jobs). 87: starting mdrun 'spc2' 87: 16 steps, 0.0 ps. 87: Generated 330891 of the 330891 non-bonded parameter combinations 87: 87: Generated 330891 of the 330891 1-4 parameter combinations 87: 87: Excluding 2 bonded neighbours molecule type 'SOL' 87: 87: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/tip3p5.gro' 87: 87: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 87: 87: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 87: 87: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 87: 87: Note that mdrun will redetermine rlist based on the actual pair-list setup 87: 87: This run will generate roughly 0 Mb of data 87: 87: Writing final coordinates. 87: 87: 87: Dynamic load balancing report: 87: DLB got disabled because it was unsuitable to use. 87: Average load imbalance: 13.8%. 87: The balanceable part of the MD step is 47%, load imbalance is computed from this. 87: Part of the total run time spent waiting due to load imbalance: 6.5%. 87: 87: NOTE: 6.5 % of the available CPU time was lost due to load imbalance 87: in the domain decomposition. 87: You can consider manually changing the decomposition (option -dd); 87: e.g. by using fewer domains along the box dimension in which there is 87: considerable inhomogeneity in the simulated system. 87: 87: Core t (s) Wall t (s) (%) 87: Time: 0.075 0.038 195.6 87: (ns/day) (hour/ns) 87: Performance: 38.444 0.624 87: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_reference.edr as double precision energy file 87: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.edr as double precision energy file 87: 87: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 87: that with the Verlet scheme, nstlist has no effect on the accuracy of 87: your simulation. 87: 87: 87: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 87: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 87: setting nstcomm equal to nstcalcenergy for less overhead 87: 87: Generating 1-4 interactions: fudge = 0.5 87: Number of degrees of freedom in T-Coupling group System is 27.00 87: 87: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 87: NVE simulation: will use the initial temperature of 398.997 K for 87: determining the Verlet buffer size 87: 87: 87: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 87: You are using a plain Coulomb cut-off, which might produce artifacts. 87: You might want to consider using PME electrostatics. 87: 87: 87: 87: NOTE 5 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 87: COM removal frequency is set to (5). 87: Other settings require a global communication frequency of 100. 87: Note that this will require additional global communication steps, 87: which will reduce performance when using multiple ranks. 87: Consider setting nstcomm to a multiple of 100. 87: 87: 87: There were 5 NOTEs 87: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 87: Can not increase nstlist because an NVE ensemble is used 87: Using 2 MPI threads 87: Using 1 OpenMP thread per tMPI thread 87: 87: 87: NOTE: The number of threads is not equal to the number of (logical) cpus 87: and the -pin option is set to auto: will not pin threads to cpus. 87: This can lead to significant performance degradation. 87: Consider using -pin on (and -pinoffset in case you run multiple jobs). 87: starting mdrun 'spc2' 87: 16 steps, 0.0 ps. 87: Generated 330891 of the 330891 non-bonded parameter combinations 87: 87: Generated 330891 of the 330891 1-4 parameter combinations 87: 87: Excluding 2 bonded neighbours molecule type 'SOL' 87: 87: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/tip3p5.gro' 87: 87: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 87: 87: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 87: 87: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 87: 87: Note that mdrun will redetermine rlist based on the actual pair-list setup 87: 87: This run will generate roughly 0 Mb of data 87: 87: Writing final coordinates. 87: 87: 87: Dynamic load balancing report: 87: DLB got disabled because it was unsuitable to use. 87: Average load imbalance: 9.5%. 87: The balanceable part of the MD step is 52%, load imbalance is computed from this. 87: Part of the total run time spent waiting due to load imbalance: 5.0%. 87: 87: 87: Core t (s) Wall t (s) (%) 87: Time: 0.069 0.036 193.1 87: (ns/day) (hour/ns) 87: Performance: 40.907 0.587 87: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_reference.edr as double precision energy file 87: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.edr as double precision energy file 87: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/9 (35224 ms) 87: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/10 87: 87: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 87: that with the Verlet scheme, nstlist has no effect on the accuracy of 87: your simulation. 87: 87: 87: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 87: Setting nstcalcenergy (100) equal to nstenergy (1) 87: 87: Generating 1-4 interactions: fudge = 0.5 87: Number of degrees of freedom in T-Coupling group System is 27.00 87: 87: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 87: NVE simulation: will use the initial temperature of 398.997 K for 87: determining the Verlet buffer size 87: 87: 87: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 87: You are using a plain Coulomb cut-off, which might produce artifacts. 87: You might want to consider using PME electrostatics. 87: 87: 87: 87: There were 4 NOTEs 87: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 87: Can not increase nstlist because an NVE ensemble is used 87: Using 2 MPI threads 87: Using 1 OpenMP thread per tMPI thread 87: 87: 87: NOTE: The number of threads is not equal to the number of (logical) cpus 87: and the -pin option is set to auto: will not pin threads to cpus. 87: This can lead to significant performance degradation. 87: Consider using -pin on (and -pinoffset in case you run multiple jobs). 87: starting mdrun 'spc2' 87: 16 steps, 0.0 ps. 87: Generated 330891 of the 330891 non-bonded parameter combinations 87: 87: Generated 330891 of the 330891 1-4 parameter combinations 87: 87: Excluding 2 bonded neighbours molecule type 'SOL' 87: 87: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/tip3p5.gro' 87: 87: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 87: 87: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 87: 87: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 87: 87: Note that mdrun will redetermine rlist based on the actual pair-list setup 87: 87: This run will generate roughly 0 Mb of data 87: 87: Writing final coordinates. 87: 87: 87: Dynamic load balancing report: 87: DLB was off during the run due to low measured imbalance. 87: Average load imbalance: 3.8%. 87: The balanceable part of the MD step is 51%, load imbalance is computed from this. 87: Part of the total run time spent waiting due to load imbalance: 1.9%. 87: 87: 87: Core t (s) Wall t (s) (%) 87: Time: 0.107 0.061 176.3 87: (ns/day) (hour/ns) 87: Performance: 24.176 0.993 87: 87: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 87: that with the Verlet scheme, nstlist has no effect on the accuracy of 87: your simulation. 87: 87: 87: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 87: Setting nstcalcenergy (100) equal to nstenergy (1) 87: 87: Generating 1-4 interactions: fudge = 0.5 87: Number of degrees of freedom in T-Coupling group System is 27.00 87: 87: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 87: NVE simulation: will use the initial temperature of 398.997 K for 87: determining the Verlet buffer size 87: 87: 87: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 87: You are using a plain Coulomb cut-off, which might produce artifacts. 87: You might want to consider using PME electrostatics. 87: 87: 87: 87: There were 4 NOTEs 87: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 87: Can not increase nstlist because an NVE ensemble is used 87: Using 2 MPI threads 87: Using 1 OpenMP thread per tMPI thread 87: 87: 87: NOTE: The number of threads is not equal to the number of (logical) cpus 87: and the -pin option is set to auto: will not pin threads to cpus. 87: This can lead to significant performance degradation. 87: Consider using -pin on (and -pinoffset in case you run multiple jobs). 87: starting mdrun 'spc2' 87: 16 steps, 0.0 ps. 87: Generated 330891 of the 330891 non-bonded parameter combinations 87: 87: Generated 330891 of the 330891 1-4 parameter combinations 87: 87: Excluding 2 bonded neighbours molecule type 'SOL' 87: 87: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/tip3p5.gro' 87: 87: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 87: 87: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 87: 87: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 87: 87: Note that mdrun will redetermine rlist based on the actual pair-list setup 87: 87: This run will generate roughly 0 Mb of data 87: 87: Writing final coordinates. 87: 87: 87: Dynamic load balancing report: 87: DLB was off during the run due to low measured imbalance. 87: Average load imbalance: 6.2%. 87: The balanceable part of the MD step is 31%, load imbalance is computed from this. 87: Part of the total run time spent waiting due to load imbalance: 1.9%. 87: 87: 87: NOTE: 6 % of the run time was spent communicating energies, 87: you might want to increase some nst* mdp options 87: 87: Core t (s) Wall t (s) (%) 87: Time: 0.079 0.042 190.1 87: (ns/day) (hour/ns) 87: Performance: 35.314 0.680 87: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_reference.edr as double precision energy file 87: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.edr as double precision energy file 87: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 87: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 87: that with the Verlet scheme, nstlist has no effect on the accuracy of 87: your simulation. 87: 87: 87: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 87: Setting nstcalcenergy (100) equal to nstenergy (4) 87: 87: Generating 1-4 interactions: fudge = 0.5 87: Number of degrees of freedom in T-Coupling group System is 27.00 87: 87: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 87: NVE simulation: will use the initial temperature of 398.997 K for 87: determining the Verlet buffer size 87: 87: 87: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 87: You are using a plain Coulomb cut-off, which might produce artifacts. 87: You might want to consider using PME electrostatics. 87: 87: 87: 87: There were 4 NOTEs 87: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 87: Can not increase nstlist because an NVE ensemble is used 87: Using 2 MPI threads 87: Using 1 OpenMP thread per tMPI thread 87: 87: 87: NOTE: The number of threads is not equal to the number of (logical) cpus 87: and the -pin option is set to auto: will not pin threads to cpus. 87: This can lead to significant performance degradation. 87: Consider using -pin on (and -pinoffset in case you run multiple jobs). 87: starting mdrun 'spc2' 87: 16 steps, 0.0 ps. 87: Generated 330891 of the 330891 non-bonded parameter combinations 87: 87: Generated 330891 of the 330891 1-4 parameter combinations 87: 87: Excluding 2 bonded neighbours molecule type 'SOL' 87: 87: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/tip3p5.gro' 87: 87: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 87: 87: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 87: 87: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 87: 87: Note that mdrun will redetermine rlist based on the actual pair-list setup 87: 87: This run will generate roughly 0 Mb of data 87: 87: Writing final coordinates. 87: 87: 87: Dynamic load balancing report: 87: DLB got disabled because it was unsuitable to use. 87: Average load imbalance: 9.5%. 87: The balanceable part of the MD step is 55%, load imbalance is computed from this. 87: Part of the total run time spent waiting due to load imbalance: 5.2%. 87: 87: NOTE: 5.2 % of the available CPU time was lost due to load imbalance 87: in the domain decomposition. 87: You can consider manually changing the decomposition (option -dd); 87: e.g. by using fewer domains along the box dimension in which there is 87: considerable inhomogeneity in the simulated system. 87: 87: Core t (s) Wall t (s) (%) 87: Time: 0.086 0.045 190.5 87: (ns/day) (hour/ns) 87: Performance: 32.601 0.736 87: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_reference.edr as double precision energy file 87: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.edr as double precision energy file 87: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 87: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 87: that with the Verlet scheme, nstlist has no effect on the accuracy of 87: your simulation. 87: 87: 87: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 87: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 87: setting nstcomm equal to nstcalcenergy for less overhead 87: 87: Generating 1-4 interactions: fudge = 0.5 87: Number of degrees of freedom in T-Coupling group System is 27.00 87: 87: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 87: NVE simulation: will use the initial temperature of 398.997 K for 87: determining the Verlet buffer size 87: 87: 87: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 87: You are using a plain Coulomb cut-off, which might produce artifacts. 87: You might want to consider using PME electrostatics. 87: 87: 87: 87: There were 4 NOTEs 87: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 87: Can not increase nstlist because an NVE ensemble is used 87: Using 2 MPI threads 87: Using 1 OpenMP thread per tMPI thread 87: 87: 87: NOTE: The number of threads is not equal to the number of (logical) cpus 87: and the -pin option is set to auto: will not pin threads to cpus. 87: This can lead to significant performance degradation. 87: Consider using -pin on (and -pinoffset in case you run multiple jobs). 87: starting mdrun 'spc2' 87: 16 steps, 0.0 ps. 87: Generated 330891 of the 330891 non-bonded parameter combinations 87: 87: Generated 330891 of the 330891 1-4 parameter combinations 87: 87: Excluding 2 bonded neighbours molecule type 'SOL' 87: 87: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/tip3p5.gro' 87: 87: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 87: 87: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 87: 87: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 87: 87: Note that mdrun will redetermine rlist based on the actual pair-list setup 87: 87: This run will generate roughly 0 Mb of data 87: 87: Writing final coordinates. 87: 87: 87: Dynamic load balancing report: 87: DLB got disabled because it was unsuitable to use. 87: Average load imbalance: 11.7%. 87: The balanceable part of the MD step is 27%, load imbalance is computed from this. 87: Part of the total run time spent waiting due to load imbalance: 3.2%. 87: 87: 87: Core t (s) Wall t (s) (%) 87: Time: 0.085 0.043 195.9 87: (ns/day) (hour/ns) 87: Performance: 33.824 0.710 87: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_reference.edr as double precision energy file 87: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.edr as double precision energy file 87: 87: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 87: that with the Verlet scheme, nstlist has no effect on the accuracy of 87: your simulation. 87: 87: 87: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 87: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 87: setting nstcomm equal to nstcalcenergy for less overhead 87: 87: Generating 1-4 interactions: fudge = 0.5 87: Number of degrees of freedom in T-Coupling group System is 27.00 87: 87: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 87: NVE simulation: will use the initial temperature of 398.997 K for 87: determining the Verlet buffer size 87: 87: 87: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 87: You are using a plain Coulomb cut-off, which might produce artifacts. 87: You might want to consider using PME electrostatics. 87: 87: 87: 87: There were 4 NOTEs 87: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 87: Can not increase nstlist because an NVE ensemble is used 87: Using 2 MPI threads 87: Using 1 OpenMP thread per tMPI thread 87: 87: 87: NOTE: The number of threads is not equal to the number of (logical) cpus 87: and the -pin option is set to auto: will not pin threads to cpus. 87: This can lead to significant performance degradation. 87: Consider using -pin on (and -pinoffset in case you run multiple jobs). 87: starting mdrun 'spc2' 87: 16 steps, 0.0 ps. 87: Generated 330891 of the 330891 non-bonded parameter combinations 87: 87: Generated 330891 of the 330891 1-4 parameter combinations 87: 87: Excluding 2 bonded neighbours molecule type 'SOL' 87: 87: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/tip3p5.gro' 87: 87: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 87: 87: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 87: 87: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 87: 87: Note that mdrun will redetermine rlist based on the actual pair-list setup 87: 87: This run will generate roughly 0 Mb of data 87: 87: Writing final coordinates. 87: 87: 87: Dynamic load balancing report: 87: DLB got disabled because it was unsuitable to use. 87: Average load imbalance: 6.5%. 87: The balanceable part of the MD step is 50%, load imbalance is computed from this. 87: Part of the total run time spent waiting due to load imbalance: 3.3%. 87: 87: 87: Core t (s) Wall t (s) (%) 87: Time: 0.058 0.030 194.8 87: (ns/day) (hour/ns) 87: Performance: 49.258 0.487 87: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_reference.edr as double precision energy file 87: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.edr as double precision energy file 87: 87: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 87: that with the Verlet scheme, nstlist has no effect on the accuracy of 87: your simulation. 87: 87: 87: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 87: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 87: setting nstcomm equal to nstcalcenergy for less overhead 87: 87: Generating 1-4 interactions: fudge = 0.5 87: Number of degrees of freedom in T-Coupling group System is 27.00 87: 87: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 87: NVE simulation: will use the initial temperature of 398.997 K for 87: determining the Verlet buffer size 87: 87: 87: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 87: You are using a plain Coulomb cut-off, which might produce artifacts. 87: You might want to consider using PME electrostatics. 87: 87: 87: 87: There were 4 NOTEs 87: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 87: Can not increase nstlist because an NVE ensemble is used 87: Using 2 MPI threads 87: Using 1 OpenMP thread per tMPI thread 87: 87: 87: NOTE: The number of threads is not equal to the number of (logical) cpus 87: and the -pin option is set to auto: will not pin threads to cpus. 87: This can lead to significant performance degradation. 87: Consider using -pin on (and -pinoffset in case you run multiple jobs). 87: starting mdrun 'spc2' 87: 16 steps, 0.0 ps. 87: Generated 330891 of the 330891 non-bonded parameter combinations 87: 87: Generated 330891 of the 330891 1-4 parameter combinations 87: 87: Excluding 2 bonded neighbours molecule type 'SOL' 87: 87: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/tip3p5.gro' 87: 87: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 87: 87: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 87: 87: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 87: 87: Note that mdrun will redetermine rlist based on the actual pair-list setup 87: 87: This run will generate roughly 0 Mb of data 87: 87: Writing final coordinates. 87: 87: 87: Dynamic load balancing report: 87: DLB got disabled because it was unsuitable to use. 87: Average load imbalance: 7.1%. 87: The balanceable part of the MD step is 55%, load imbalance is computed from this. 87: Part of the total run time spent waiting due to load imbalance: 3.9%. 87: 87: 87: Core t (s) Wall t (s) (%) 87: Time: 0.059 0.030 195.8 87: (ns/day) (hour/ns) 87: Performance: 48.323 0.497 87: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_reference.edr as double precision energy file 87: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.edr as double precision energy file 87: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/10 (35113 ms) 87: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/11 87: 87: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 87: that with the Verlet scheme, nstlist has no effect on the accuracy of 87: your simulation. 87: 87: 87: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 87: Setting nstcalcenergy (100) equal to nstenergy (1) 87: 87: Generating 1-4 interactions: fudge = 0.5 87: Number of degrees of freedom in T-Coupling group System is 27.00 87: 87: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 87: You are using a plain Coulomb cut-off, which might produce artifacts. 87: You might want to consider using PME electrostatics. 87: 87: 87: 87: There were 3 NOTEs 87: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 87: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 87: 87: Using 2 MPI threads 87: Using 1 OpenMP thread per tMPI thread 87: 87: 87: NOTE: The number of threads is not equal to the number of (logical) cpus 87: and the -pin option is set to auto: will not pin threads to cpus. 87: This can lead to significant performance degradation. 87: Consider using -pin on (and -pinoffset in case you run multiple jobs). 87: starting mdrun 'spc2' 87: 16 steps, 0.0 ps. 87: Generated 330891 of the 330891 non-bonded parameter combinations 87: 87: Generated 330891 of the 330891 1-4 parameter combinations 87: 87: Excluding 2 bonded neighbours molecule type 'SOL' 87: 87: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/tip3p5.gro' 87: 87: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 87: 87: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 87: 87: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 87: 87: Note that mdrun will redetermine rlist based on the actual pair-list setup 87: 87: This run will generate roughly 0 Mb of data 87: 87: Writing final coordinates. 87: 87: Core t (s) Wall t (s) (%) 87: Time: 0.105 0.053 197.3 87: (ns/day) (hour/ns) 87: Performance: 27.530 0.872 87: 87: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 87: that with the Verlet scheme, nstlist has no effect on the accuracy of 87: your simulation. 87: 87: 87: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 87: Setting nstcalcenergy (100) equal to nstenergy (1) 87: 87: Generating 1-4 interactions: fudge = 0.5 87: Number of degrees of freedom in T-Coupling group System is 27.00 87: 87: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 87: You are using a plain Coulomb cut-off, which might produce artifacts. 87: You might want to consider using PME electrostatics. 87: 87: 87: 87: There were 3 NOTEs 87: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 87: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 87: 87: Using 2 MPI threads 87: Using 1 OpenMP thread per tMPI thread 87: 87: 87: NOTE: The number of threads is not equal to the number of (logical) cpus 87: and the -pin option is set to auto: will not pin threads to cpus. 87: This can lead to significant performance degradation. 87: Consider using -pin on (and -pinoffset in case you run multiple jobs). 87: starting mdrun 'spc2' 87: 16 steps, 0.0 ps. 87: Generated 330891 of the 330891 non-bonded parameter combinations 87: 87: Generated 330891 of the 330891 1-4 parameter combinations 87: 87: Excluding 2 bonded neighbours molecule type 'SOL' 87: 87: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/tip3p5.gro' 87: 87: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 87: 87: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 87: 87: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 87: 87: Note that mdrun will redetermine rlist based on the actual pair-list setup 87: 87: This run will generate roughly 0 Mb of data 87: 87: Writing final coordinates. 87: 87: Core t (s) Wall t (s) (%) 87: Time: 0.063 0.033 191.9 87: (ns/day) (hour/ns) 87: Performance: 45.062 0.533 87: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_reference.edr as double precision energy file 87: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.edr as double precision energy file 87: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 87: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 87: that with the Verlet scheme, nstlist has no effect on the accuracy of 87: your simulation. 87: 87: 87: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 87: Setting nstcalcenergy (100) equal to nstenergy (4) 87: 87: Generating 1-4 interactions: fudge = 0.5 87: Number of degrees of freedom in T-Coupling group System is 27.00 87: 87: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 87: You are using a plain Coulomb cut-off, which might produce artifacts. 87: You might want to consider using PME electrostatics. 87: 87: 87: 87: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 87: COM removal frequency is set to (5). 87: Other settings require a global communication frequency of 2. 87: Note that this will require additional global communication steps, 87: which will reduce performance when using multiple ranks. 87: Consider setting nstcomm to a multiple of 2. 87: 87: 87: There were 4 NOTEs 87: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 87: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 87: 87: Using 2 MPI threads 87: Using 1 OpenMP thread per tMPI thread 87: 87: 87: NOTE: The number of threads is not equal to the number of (logical) cpus 87: and the -pin option is set to auto: will not pin threads to cpus. 87: This can lead to significant performance degradation. 87: Consider using -pin on (and -pinoffset in case you run multiple jobs). 87: starting mdrun 'spc2' 87: 16 steps, 0.0 ps. 87: Generated 330891 of the 330891 non-bonded parameter combinations 87: 87: Generated 330891 of the 330891 1-4 parameter combinations 87: 87: Excluding 2 bonded neighbours molecule type 'SOL' 87: 87: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/tip3p5.gro' 87: 87: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 87: 87: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 87: 87: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 87: 87: Note that mdrun will redetermine rlist based on the actual pair-list setup 87: 87: This run will generate roughly 0 Mb of data 87: 87: Writing final coordinates. 87: 87: Core t (s) Wall t (s) (%) 87: Time: 0.050 0.026 190.9 87: (ns/day) (hour/ns) 87: Performance: 56.523 0.425 87: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_reference.edr as double precision energy file 87: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.edr as double precision energy file 87: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 87: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 87: that with the Verlet scheme, nstlist has no effect on the accuracy of 87: your simulation. 87: 87: 87: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 87: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 87: setting nstcomm equal to nstcalcenergy for less overhead 87: 87: Generating 1-4 interactions: fudge = 0.5 87: Number of degrees of freedom in T-Coupling group System is 27.00 87: 87: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 87: You are using a plain Coulomb cut-off, which might produce artifacts. 87: You might want to consider using PME electrostatics. 87: 87: 87: 87: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 87: COM removal frequency is set to (5). 87: Other settings require a global communication frequency of 2. 87: Note that this will require additional global communication steps, 87: which will reduce performance when using multiple ranks. 87: Consider setting nstcomm to a multiple of 2. 87: 87: 87: There were 4 NOTEs 87: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 87: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 87: 87: Using 2 MPI threads 87: Using 1 OpenMP thread per tMPI thread 87: 87: 87: NOTE: The number of threads is not equal to the number of (logical) cpus 87: and the -pin option is set to auto: will not pin threads to cpus. 87: This can lead to significant performance degradation. 87: Consider using -pin on (and -pinoffset in case you run multiple jobs). 87: starting mdrun 'spc2' 87: 16 steps, 0.0 ps. 87: Generated 330891 of the 330891 non-bonded parameter combinations 87: 87: Generated 330891 of the 330891 1-4 parameter combinations 87: 87: Excluding 2 bonded neighbours molecule type 'SOL' 87: 87: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/tip3p5.gro' 87: 87: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 87: 87: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 87: 87: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 87: 87: Note that mdrun will redetermine rlist based on the actual pair-list setup 87: 87: This run will generate roughly 0 Mb of data 87: 87: Writing final coordinates. 87: 87: NOTE: 12 % of the run time was spent in domain decomposition, 87: 1 % of the run time was spent in pair search, 87: you might want to increase nstlist (this has no effect on accuracy) 87: 87: Core t (s) Wall t (s) (%) 87: Time: 0.073 0.039 189.6 87: (ns/day) (hour/ns) 87: Performance: 37.904 0.633 87: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_reference.edr as double precision energy file 87: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.edr as double precision energy file 87: 87: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 87: that with the Verlet scheme, nstlist has no effect on the accuracy of 87: your simulation. 87: 87: 87: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 87: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 87: setting nstcomm equal to nstcalcenergy for less overhead 87: 87: Generating 1-4 interactions: fudge = 0.5 87: Number of degrees of freedom in T-Coupling group System is 27.00 87: 87: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 87: You are using a plain Coulomb cut-off, which might produce artifacts. 87: You might want to consider using PME electrostatics. 87: 87: 87: 87: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 87: COM removal frequency is set to (5). 87: Other settings require a global communication frequency of 2. 87: Note that this will require additional global communication steps, 87: which will reduce performance when using multiple ranks. 87: Consider setting nstcomm to a multiple of 2. 87: 87: 87: There were 4 NOTEs 87: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 87: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 87: 87: Using 2 MPI threads 87: Using 1 OpenMP thread per tMPI thread 87: 87: 87: NOTE: The number of threads is not equal to the number of (logical) cpus 87: and the -pin option is set to auto: will not pin threads to cpus. 87: This can lead to significant performance degradation. 87: Consider using -pin on (and -pinoffset in case you run multiple jobs). 87: starting mdrun 'spc2' 87: 16 steps, 0.0 ps. 87: Generated 330891 of the 330891 non-bonded parameter combinations 87: 87: Generated 330891 of the 330891 1-4 parameter combinations 87: 87: Excluding 2 bonded neighbours molecule type 'SOL' 87: 87: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/tip3p5.gro' 87: 87: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 87: 87: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 87: 87: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 87: 87: Note that mdrun will redetermine rlist based on the actual pair-list setup 87: 87: This run will generate roughly 0 Mb of data 87: 87: Writing final coordinates. 87: 87: Core t (s) Wall t (s) (%) 87: Time: 0.061 0.032 190.0 87: (ns/day) (hour/ns) 87: Performance: 46.049 0.521 87: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_reference.edr as double precision energy file 87: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.edr as double precision energy file 87: 87: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 87: that with the Verlet scheme, nstlist has no effect on the accuracy of 87: your simulation. 87: 87: 87: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 87: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 87: setting nstcomm equal to nstcalcenergy for less overhead 87: 87: Generating 1-4 interactions: fudge = 0.5 87: Number of degrees of freedom in T-Coupling group System is 27.00 87: 87: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 87: You are using a plain Coulomb cut-off, which might produce artifacts. 87: You might want to consider using PME electrostatics. 87: 87: 87: 87: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 87: COM removal frequency is set to (5). 87: Other settings require a global communication frequency of 2. 87: Note that this will require additional global communication steps, 87: which will reduce performance when using multiple ranks. 87: Consider setting nstcomm to a multiple of 2. 87: 87: 87: There were 4 NOTEs 87: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 87: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 87: 87: Using 2 MPI threads 87: Using 1 OpenMP thread per tMPI thread 87: 87: 87: NOTE: The number of threads is not equal to the number of (logical) cpus 87: and the -pin option is set to auto: will not pin threads to cpus. 87: This can lead to significant performance degradation. 87: Consider using -pin on (and -pinoffset in case you run multiple jobs). 87: starting mdrun 'spc2' 87: 16 steps, 0.0 ps. 87: Generated 330891 of the 330891 non-bonded parameter combinations 87: 87: Generated 330891 of the 330891 1-4 parameter combinations 87: 87: Excluding 2 bonded neighbours molecule type 'SOL' 87: 87: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/tip3p5.gro' 87: 87: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 87: 87: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 87: 87: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 87: 87: Note that mdrun will redetermine rlist based on the actual pair-list setup 87: 87: This run will generate roughly 0 Mb of data 87: 87: Writing final coordinates. 87: 87: Core t (s) Wall t (s) (%) 87: Time: 0.077 0.040 193.3 87: (ns/day) (hour/ns) 87: Performance: 36.697 0.654 87: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_reference.edr as double precision energy file 87: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.edr as double precision energy file 87: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/11 (35137 ms) 87: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/12 87: 87: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 87: that with the Verlet scheme, nstlist has no effect on the accuracy of 87: your simulation. 87: 87: 87: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 87: Setting nstcalcenergy (100) equal to nstenergy (1) 87: 87: Generating 1-4 interactions: fudge = 0.5 87: Number of degrees of freedom in T-Coupling group System is 27.00 87: 87: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 87: You are using a plain Coulomb cut-off, which might produce artifacts. 87: You might want to consider using PME electrostatics. 87: 87: 87: 87: There were 3 NOTEs 87: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 87: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 87: 87: Using 2 MPI threads 87: Using 1 OpenMP thread per tMPI thread 87: 87: 87: NOTE: The number of threads is not equal to the number of (logical) cpus 87: and the -pin option is set to auto: will not pin threads to cpus. 87: This can lead to significant performance degradation. 87: Consider using -pin on (and -pinoffset in case you run multiple jobs). 87: starting mdrun 'spc2' 87: 16 steps, 0.0 ps. 87: Generated 330891 of the 330891 non-bonded parameter combinations 87: 87: Generated 330891 of the 330891 1-4 parameter combinations 87: 87: Excluding 2 bonded neighbours molecule type 'SOL' 87: 87: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/tip3p5.gro' 87: 87: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 87: 87: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 87: 87: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 87: 87: Note that mdrun will redetermine rlist based on the actual pair-list setup 87: 87: This run will generate roughly 0 Mb of data 87: 87: Writing final coordinates. 87: 87: Core t (s) Wall t (s) (%) 87: Time: 0.122 0.062 197.3 87: (ns/day) (hour/ns) 87: Performance: 23.829 1.007 87: 87: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 87: that with the Verlet scheme, nstlist has no effect on the accuracy of 87: your simulation. 87: 87: 87: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 87: Setting nstcalcenergy (100) equal to nstenergy (1) 87: 87: Generating 1-4 interactions: fudge = 0.5 87: Number of degrees of freedom in T-Coupling group System is 27.00 87: 87: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 87: You are using a plain Coulomb cut-off, which might produce artifacts. 87: You might want to consider using PME electrostatics. 87: 87: 87: 87: There were 3 NOTEs 87: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 87: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 87: 87: Using 2 MPI threads 87: Using 1 OpenMP thread per tMPI thread 87: 87: 87: NOTE: The number of threads is not equal to the number of (logical) cpus 87: and the -pin option is set to auto: will not pin threads to cpus. 87: This can lead to significant performance degradation. 87: Consider using -pin on (and -pinoffset in case you run multiple jobs). 87: starting mdrun 'spc2' 87: 16 steps, 0.0 ps. 87: Generated 330891 of the 330891 non-bonded parameter combinations 87: 87: Generated 330891 of the 330891 1-4 parameter combinations 87: 87: Excluding 2 bonded neighbours molecule type 'SOL' 87: 87: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/tip3p5.gro' 87: 87: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 87: 87: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 87: 87: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 87: 87: Note that mdrun will redetermine rlist based on the actual pair-list setup 87: 87: This run will generate roughly 0 Mb of data 87: 87: Writing final coordinates. 87: 87: Core t (s) Wall t (s) (%) 87: Time: 0.061 0.038 161.5 87: (ns/day) (hour/ns) 87: Performance: 39.034 0.615 87: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_reference.edr as double precision energy file 87: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.edr as double precision energy file 87: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 87: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 87: that with the Verlet scheme, nstlist has no effect on the accuracy of 87: your simulation. 87: 87: 87: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 87: Setting nstcalcenergy (100) equal to nstenergy (4) 87: 87: Generating 1-4 interactions: fudge = 0.5 87: Number of degrees of freedom in T-Coupling group System is 27.00 87: 87: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 87: You are using a plain Coulomb cut-off, which might produce artifacts. 87: You might want to consider using PME electrostatics. 87: 87: 87: 87: There were 3 NOTEs 87: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 87: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 87: 87: Using 2 MPI threads 87: Using 1 OpenMP thread per tMPI thread 87: 87: 87: NOTE: The number of threads is not equal to the number of (logical) cpus 87: and the -pin option is set to auto: will not pin threads to cpus. 87: This can lead to significant performance degradation. 87: Consider using -pin on (and -pinoffset in case you run multiple jobs). 87: starting mdrun 'spc2' 87: 16 steps, 0.0 ps. 87: Generated 330891 of the 330891 non-bonded parameter combinations 87: 87: Generated 330891 of the 330891 1-4 parameter combinations 87: 87: Excluding 2 bonded neighbours molecule type 'SOL' 87: 87: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/tip3p5.gro' 87: 87: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 87: 87: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 87: 87: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 87: 87: Note that mdrun will redetermine rlist based on the actual pair-list setup 87: 87: This run will generate roughly 0 Mb of data 87: 87: Writing final coordinates. 87: 87: Core t (s) Wall t (s) (%) 87: Time: 0.072 0.037 192.8 87: (ns/day) (hour/ns) 87: Performance: 39.576 0.606 87: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_reference.edr as double precision energy file 87: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.edr as double precision energy file 87: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 87: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 87: that with the Verlet scheme, nstlist has no effect on the accuracy of 87: your simulation. 87: 87: 87: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 87: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 87: setting nstcomm equal to nstcalcenergy for less overhead 87: 87: Generating 1-4 interactions: fudge = 0.5 87: Number of degrees of freedom in T-Coupling group System is 27.00 87: 87: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 87: You are using a plain Coulomb cut-off, which might produce artifacts. 87: You might want to consider using PME electrostatics. 87: 87: 87: 87: There were 3 NOTEs 87: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 87: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 87: 87: Using 2 MPI threads 87: Using 1 OpenMP thread per tMPI thread 87: 87: 87: NOTE: The number of threads is not equal to the number of (logical) cpus 87: and the -pin option is set to auto: will not pin threads to cpus. 87: This can lead to significant performance degradation. 87: Consider using -pin on (and -pinoffset in case you run multiple jobs). 87: starting mdrun 'spc2' 87: 16 steps, 0.0 ps. 87: Generated 330891 of the 330891 non-bonded parameter combinations 87: 87: Generated 330891 of the 330891 1-4 parameter combinations 87: 87: Excluding 2 bonded neighbours molecule type 'SOL' 87: 87: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/tip3p5.gro' 87: 87: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 87: 87: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 87: 87: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 87: 87: Note that mdrun will redetermine rlist based on the actual pair-list setup 87: 87: This run will generate roughly 0 Mb of data 87: 87: Writing final coordinates. 87: 87: Core t (s) Wall t (s) (%) 87: Time: 0.072 0.042 171.9 87: (ns/day) (hour/ns) 87: Performance: 35.016 0.685 87: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_reference.edr as double precision energy file 87: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.edr as double precision energy file 87: 87: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 87: that with the Verlet scheme, nstlist has no effect on the accuracy of 87: your simulation. 87: 87: 87: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 87: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 87: setting nstcomm equal to nstcalcenergy for less overhead 87: 87: Generating 1-4 interactions: fudge = 0.5 87: Number of degrees of freedom in T-Coupling group System is 27.00 87: 87: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 87: You are using a plain Coulomb cut-off, which might produce artifacts. 87: You might want to consider using PME electrostatics. 87: 87: 87: 87: There were 3 NOTEs 87: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 87: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 87: 87: Using 2 MPI threads 87: Using 1 OpenMP thread per tMPI thread 87: 87: 87: NOTE: The number of threads is not equal to the number of (logical) cpus 87: and the -pin option is set to auto: will not pin threads to cpus. 87: This can lead to significant performance degradation. 87: Consider using -pin on (and -pinoffset in case you run multiple jobs). 87: starting mdrun 'spc2' 87: 16 steps, 0.0 ps. 87: Generated 330891 of the 330891 non-bonded parameter combinations 87: 87: Generated 330891 of the 330891 1-4 parameter combinations 87: 87: Excluding 2 bonded neighbours molecule type 'SOL' 87: 87: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/tip3p5.gro' 87: 87: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 87: 87: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 87: 87: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 87: 87: Note that mdrun will redetermine rlist based on the actual pair-list setup 87: 87: This run will generate roughly 0 Mb of data 87: 87: Writing final coordinates. 87: 87: Core t (s) Wall t (s) (%) 87: Time: 0.070 0.039 182.1 87: (ns/day) (hour/ns) 87: Performance: 38.141 0.629 87: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_reference.edr as double precision energy file 87: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.edr as double precision energy file 87: 87: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 87: that with the Verlet scheme, nstlist has no effect on the accuracy of 87: your simulation. 87: 87: 87: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 87: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 87: setting nstcomm equal to nstcalcenergy for less overhead 87: 87: Generating 1-4 interactions: fudge = 0.5 87: Number of degrees of freedom in T-Coupling group System is 27.00 87: 87: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 87: You are using a plain Coulomb cut-off, which might produce artifacts. 87: You might want to consider using PME electrostatics. 87: 87: 87: 87: There were 3 NOTEs 87: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 87: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 87: 87: Using 2 MPI threads 87: Using 1 OpenMP thread per tMPI thread 87: 87: 87: NOTE: The number of threads is not equal to the number of (logical) cpus 87: and the -pin option is set to auto: will not pin threads to cpus. 87: This can lead to significant performance degradation. 87: Consider using -pin on (and -pinoffset in case you run multiple jobs). 87: starting mdrun 'spc2' 87: 16 steps, 0.0 ps. 87: Generated 330891 of the 330891 non-bonded parameter combinations 87: 87: Generated 330891 of the 330891 1-4 parameter combinations 87: 87: Excluding 2 bonded neighbours molecule type 'SOL' 87: 87: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/tip3p5.gro' 87: 87: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 87: 87: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 87: 87: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 87: 87: Note that mdrun will redetermine rlist based on the actual pair-list setup 87: 87: This run will generate roughly 0 Mb of data 87: 87: Writing final coordinates. 87: 87: Core t (s) Wall t (s) (%) 87: Time: 0.050 0.026 193.2 87: (ns/day) (hour/ns) 87: Performance: 56.284 0.426 87: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_reference.edr as double precision energy file 87: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.edr as double precision energy file 87: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/12 (35199 ms) 87: [----------] 13 tests from PropagatorsWithConstraints/PeriodicActionsTest (456884 ms total) 87: 87: [----------] Global test environment tear-down 87: [==========] 13 tests from 1 test suite ran. (456932 ms total) 87: [ PASSED ] 13 tests. 87/92 Test #87: MdrunCoordinationConstraintsTests2Ranks ... Passed 457.04 sec test 88 Start 88: MdrunFEPTests 88: Test command: /build/reproducible-path/gromacs-2025.1/build/basic-dp/bin/mdrun-fep-test "-ntomp" "2" "--gtest_output=xml:/build/reproducible-path/gromacs-2025.1/build/basic-dp/Testing/Temporary/MdrunFEPTests.xml" 88: Working Directory: /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests 88: Test timeout computed to be: 600 88: [==========] Running 14 tests from 2 test suites. 88: [----------] Global test environment set-up. 88: [----------] 2 tests from ExpandedEnsembleTest 88: [ RUN ] ExpandedEnsembleTest.ContinuationPreservesExpandedEnsembleState 88: 88: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/ExpandedEnsembleTest_ContinuationPreservesExpandedEnsembleState_input.mdp]: 88: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 88: that with the Verlet scheme, nstlist has no effect on the accuracy of 88: your simulation. 88: 88: Generating 1-4 interactions: fudge = 0.5 88: Number of degrees of freedom in T-Coupling group System is 79.00 88: 88: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/ExpandedEnsembleTest_ContinuationPreservesExpandedEnsembleState_input.mdp]: 88: You are using a plain Coulomb cut-off, which might produce artifacts. 88: You might want to consider using PME electrostatics. 88: 88: 88: 88: There were 2 NOTEs 88: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/ExpandedEnsembleTest_ContinuationPreservesExpandedEnsembleState.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 88: Changing nstlist from 8 to 20, rlist from 0.757 to 0.863 88: 88: Using 1 MPI thread 88: Using 2 OpenMP threads 88: 88: 88: NOTE: The number of threads is not equal to the number of (logical) cpus 88: and the -pin option is set to auto: will not pin threads to cpus. 88: This can lead to significant performance degradation. 88: Consider using -pin on (and -pinoffset in case you run multiple jobs). 88: starting mdrun '30 atom system in water' 88: 16 steps, 0.0 ps. 88: Generated 2485 of the 2485 non-bonded parameter combinations 88: 88: Generated 2485 of the 2485 1-4 parameter combinations 88: 88: Excluding 3 bonded neighbours molecule type 'nonanol' 88: 88: turning H bonds into constraints... 88: 88: Excluding 2 bonded neighbours molecule type 'SOL' 88: 88: turning H bonds into constraints... 88: 88: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/nonanol_vacuo.gro' 88: 88: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 88: 88: Calculated rlist for 1x1 atom pair-list as 0.764 nm, buffer size 0.064 nm 88: 88: Set rlist, assuming 4x4 atom pair-list, to 0.757 nm, buffer size 0.057 nm 88: 88: Note that mdrun will redetermine rlist based on the actual pair-list setup 88: 88: This run will generate roughly 0 Mb of data 88: 88: Writing final coordinates. 88: 88: Core t (s) Wall t (s) (%) 88: Time: 0.094 0.047 198.8 88: (ns/day) (hour/ns) 88: Performance: 30.927 0.776 88: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/ExpandedEnsembleTest_ContinuationPreservesExpandedEnsembleState.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 88: Overriding nsteps with value passed on the command line: 8 steps, 0.008 ps 88: Changing nstlist from 8 to 20, rlist from 0.757 to 0.863 88: 88: 88: Using 1 MPI thread 88: Using 2 OpenMP threads 88: 88: 88: NOTE: The number of threads is not equal to the number of (logical) cpus 88: and the -pin option is set to auto: will not pin threads to cpus. 88: This can lead to significant performance degradation. 88: Consider using -pin on (and -pinoffset in case you run multiple jobs). 88: starting mdrun '30 atom system in water' 88: 24 steps, 0.0 ps (continuing from step 16, 0.0 ps). 88: 88: Writing final coordinates. 88: 88: Core t (s) Wall t (s) (%) 88: Time: 0.094 0.048 197.1 88: (ns/day) (hour/ns) 88: Performance: 16.238 1.478 88: [ OK ] ExpandedEnsembleTest.ContinuationPreservesExpandedEnsembleState (461 ms) 88: [ RUN ] ExpandedEnsembleTest.WeightEquilibrationReported 88: 88: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/ExpandedEnsembleTest_WeightEquilibrationReported_input.mdp]: 88: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 88: that with the Verlet scheme, nstlist has no effect on the accuracy of 88: your simulation. 88: 88: Generating 1-4 interactions: fudge = 0.5 88: Number of degrees of freedom in T-Coupling group System is 79.00 88: 88: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/ExpandedEnsembleTest_WeightEquilibrationReported_input.mdp]: 88: You are using a plain Coulomb cut-off, which might produce artifacts. 88: You might want to consider using PME electrostatics. 88: 88: 88: 88: There were 2 NOTEs 88: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/ExpandedEnsembleTest_WeightEquilibrationReported.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 88: Changing nstlist from 8 to 20, rlist from 0.757 to 0.863 88: 88: Using 1 MPI thread 88: Using 2 OpenMP threads 88: 88: 88: NOTE: The number of threads is not equal to the number of (logical) cpus 88: and the -pin option is set to auto: will not pin threads to cpus. 88: This can lead to significant performance degradation. 88: Consider using -pin on (and -pinoffset in case you run multiple jobs). 88: starting mdrun '30 atom system in water' 88: 1 steps, 0.0 ps. 88: Generated 2485 of the 2485 non-bonded parameter combinations 88: 88: Generated 2485 of the 2485 1-4 parameter combinations 88: 88: Excluding 3 bonded neighbours molecule type 'nonanol' 88: 88: turning H bonds into constraints... 88: 88: Excluding 2 bonded neighbours molecule type 'SOL' 88: 88: turning H bonds into constraints... 88: 88: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/nonanol_vacuo.gro' 88: 88: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 88: 88: Calculated rlist for 1x1 atom pair-list as 0.764 nm, buffer size 0.064 nm 88: 88: Set rlist, assuming 4x4 atom pair-list, to 0.757 nm, buffer size 0.057 nm 88: 88: Note that mdrun will redetermine rlist based on the actual pair-list setup 88: 88: This run will generate roughly 0 Mb of data 88: 88: Writing final coordinates. 88: 88: Core t (s) Wall t (s) (%) 88: Time: 0.063 0.032 198.6 88: (ns/day) (hour/ns) 88: Performance: 5.439 4.413 88: [ OK ] ExpandedEnsembleTest.WeightEquilibrationReported (257 ms) 88: [----------] 2 tests from ExpandedEnsembleTest (718 ms total) 88: 88: [----------] 12 tests from EquivalentToReference/FreeEnergyReferenceTest 88: [ RUN ] EquivalentToReference/FreeEnergyReferenceTest.WithinTolerances/coulandvdwsequential_coul_d 88: 88: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/freeenergy/coulandvdwsequential_coul/grompp.mdp, line 149]: 88: For proper sampling of the (nearly) decoupled state, stochastic dynamics 88: should be used 88: 88: 88: WARNING 1 [file /build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/freeenergy/coulandvdwsequential_coul/grompp.mdp]: 88: The Berendsen thermostat does not generate the correct kinetic energy 88: distribution, and should not be used for new production simulations (in 88: our opinion). We would recommend the V-rescale thermostat. 88: 88: Generating 1-4 interactions: fudge = 0.5 88: Number of degrees of freedom in T-Coupling group System is 355.00 88: 88: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/freeenergy/coulandvdwsequential_coul/grompp.mdp]: 88: The optimal PME mesh load for parallel simulations is below 0.5 88: and for highly parallel simulations between 0.25 and 0.33, 88: for higher performance, increase the cut-off and the PME grid spacing. 88: 88: 88: 88: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/freeenergy/coulandvdwsequential_coul/grompp.mdp]: 88: For free energy simulations, the optimal load limit increases from 0.5 to 88: 0.667 88: 88: 88: 88: There were 3 NOTEs 88: 88: There was 1 WARNING 88: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/EquivalentToReference_FreeEnergyReferenceTest_WithinTolerances_coulandvdwsequential_coul_d_sim.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 88: Changing nstlist from 10 to 100, rlist from 1 to 1 88: 88: Using 1 MPI thread 88: Using 2 OpenMP threads 88: 88: 88: NOTE: The number of threads is not equal to the number of (logical) cpus 88: and the -pin option is set to auto: will not pin threads to cpus. 88: This can lead to significant performance degradation. 88: Consider using -pin on (and -pinoffset in case you run multiple jobs). 88: starting mdrun 'AA' 88: 20 steps, 0.0 ps. 88: Setting the LD random seed to -37290005 88: 88: Generated 153 of the 153 non-bonded parameter combinations 88: 88: Generated 153 of the 153 1-4 parameter combinations 88: 88: Excluding 3 bonded neighbours molecule type 'ASN' 88: 88: turning H bonds into constraints... 88: 88: Excluding 2 bonded neighbours molecule type 'SOL' 88: 88: turning H bonds into constraints... 88: 88: Coupling 1 copies of molecule type 'ASN' 88: 88: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/freeenergy/coulandvdwsequential_coul/conf.gro' 88: Analysing residue names: 88: There are: 1 Protein residues 88: There are: 56 Water residues 88: Analysing Protein... 88: 88: The largest distance between non-perturbed excluded atoms is 0.164 nm between atom 41 and 42 88: 88: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 88: 88: Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm 88: 88: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm 88: 88: Note that mdrun will redetermine rlist based on the actual pair-list setup 88: Calculating fourier grid dimensions for X Y Z 88: Using a fourier grid of 28x28x28, spacing 0.108 0.108 0.108 88: 88: Estimate for the relative computational load of the PME mesh part: 0.89 88: 88: This run will generate roughly 0 Mb of data 88: 88: Writing final coordinates. 88: 88: Core t (s) Wall t (s) (%) 88: Time: 1.428 0.714 199.9 88: (ns/day) (hour/ns) 88: Performance: 2.540 9.449 88: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/EquivalentToReference_FreeEnergyReferenceTest_WithinTolerances_coulandvdwsequential_coul_d_energy.edr as double precision energy file 88: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 17 time 0.017 Reading energy frame 18 time 0.018 Reading energy frame 19 time 0.019 Reading energy frame 20 time 0.020 Last energy frame read 20 time 0.020 trr version: GMX_trn_file (double precision) 88: 88: [ OK ] EquivalentToReference/FreeEnergyReferenceTest.WithinTolerances/coulandvdwsequential_coul_d (2060 ms) 88: [ RUN ] EquivalentToReference/FreeEnergyReferenceTest.WithinTolerances/coulandvdwsequential_vdw_d 88: 88: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/freeenergy/coulandvdwsequential_vdw/grompp.mdp, line 148]: 88: For proper sampling of the (nearly) decoupled state, stochastic dynamics 88: should be used 88: 88: 88: WARNING 1 [file /build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/freeenergy/coulandvdwsequential_vdw/grompp.mdp]: 88: The Berendsen thermostat does not generate the correct kinetic energy 88: distribution, and should not be used for new production simulations (in 88: our opinion). We would recommend the V-rescale thermostat. 88: 88: Generating 1-4 interactions: fudge = 0.5 88: Number of degrees of freedom in T-Coupling group System is 355.00 88: 88: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/freeenergy/coulandvdwsequential_vdw/grompp.mdp]: 88: The optimal PME mesh load for parallel simulations is below 0.5 88: and for highly parallel simulations between 0.25 and 0.33, 88: for higher performance, increase the cut-off and the PME grid spacing. 88: 88: 88: 88: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/freeenergy/coulandvdwsequential_vdw/grompp.mdp]: 88: For free energy simulations, the optimal load limit increases from 0.5 to 88: 0.667 88: 88: 88: 88: There were 3 NOTEs 88: 88: There was 1 WARNING 88: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/EquivalentToReference_FreeEnergyReferenceTest_WithinTolerances_coulandvdwsequential_vdw_d_sim.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 88: Changing nstlist from 10 to 100, rlist from 1 to 1 88: 88: Using 1 MPI thread 88: Using 2 OpenMP threads 88: 88: 88: NOTE: The number of threads is not equal to the number of (logical) cpus 88: and the -pin option is set to auto: will not pin threads to cpus. 88: This can lead to significant performance degradation. 88: Consider using -pin on (and -pinoffset in case you run multiple jobs). 88: starting mdrun 'AA' 88: 20 steps, 0.0 ps. 88: Setting the LD random seed to -304101379 88: 88: Generated 153 of the 153 non-bonded parameter combinations 88: 88: Generated 153 of the 153 1-4 parameter combinations 88: 88: Excluding 3 bonded neighbours molecule type 'ASN' 88: 88: turning H bonds into constraints... 88: 88: Excluding 2 bonded neighbours molecule type 'SOL' 88: 88: turning H bonds into constraints... 88: 88: Coupling 1 copies of molecule type 'ASN' 88: 88: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/freeenergy/coulandvdwsequential_vdw/conf.gro' 88: Analysing residue names: 88: There are: 1 Protein residues 88: There are: 56 Water residues 88: Analysing Protein... 88: 88: The largest distance between non-perturbed excluded atoms is 0.164 nm between atom 41 and 42 88: 88: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 88: 88: Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm 88: 88: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm 88: 88: Note that mdrun will redetermine rlist based on the actual pair-list setup 88: Calculating fourier grid dimensions for X Y Z 88: Using a fourier grid of 28x28x28, spacing 0.108 0.108 0.108 88: 88: Estimate for the relative computational load of the PME mesh part: 0.89 88: 88: This run will generate roughly 0 Mb of data 88: 88: Writing final coordinates. 88: 88: Core t (s) Wall t (s) (%) 88: Time: 1.319 0.660 199.9 88: (ns/day) (hour/ns) 88: Performance: 2.750 8.726 88: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/EquivalentToReference_FreeEnergyReferenceTest_WithinTolerances_coulandvdwsequential_vdw_d_energy.edr as double precision energy file 88: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 17 time 0.017 Reading energy frame 18 time 0.018 Reading energy frame 19 time 0.019 Reading energy frame 20 time 0.020 Last energy frame read 20 time 0.020 88: [ OK ] EquivalentToReference/FreeEnergyReferenceTest.WithinTolerances/coulandvdwsequential_vdw_d (1947 ms) 88: [ RUN ] EquivalentToReference/FreeEnergyReferenceTest.WithinTolerances/coulandvdwtogether_d 88: 88: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/freeenergy/coulandvdwtogether/grompp.mdp, line 147]: 88: For proper sampling of the (nearly) decoupled state, stochastic dynamics 88: should be used 88: 88: 88: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/freeenergy/coulandvdwtogether/grompp.mdp]: 88: With PME there is a minor soft core effect present at the cut-off, 88: proportional to (LJsigma/rcoulomb)^6. This could have a minor effect on 88: energy conservation, but usually other effects dominate. With a common 88: sigma value of 0.34 nm the fraction of the particle-particle potential at 88: the cut-off at lambda=0.5 is around 6.4e-05, while ewald-rtol is 1.0e-06. 88: 88: 88: WARNING 1 [file /build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/freeenergy/coulandvdwtogether/grompp.mdp]: 88: The Berendsen thermostat does not generate the correct kinetic energy 88: distribution, and should not be used for new production simulations (in 88: our opinion). We would recommend the V-rescale thermostat. 88: 88: Generating 1-4 interactions: fudge = 0.5 88: Number of degrees of freedom in T-Coupling group System is 355.00 88: 88: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/freeenergy/coulandvdwtogether/grompp.mdp]: 88: The optimal PME mesh load for parallel simulations is below 0.5 88: and for highly parallel simulations between 0.25 and 0.33, 88: for higher performance, increase the cut-off and the PME grid spacing. 88: 88: 88: 88: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/freeenergy/coulandvdwtogether/grompp.mdp]: 88: For free energy simulations, the optimal load limit increases from 0.5 to 88: 0.667 88: 88: 88: 88: There were 4 NOTEs 88: 88: There was 1 WARNING 88: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/EquivalentToReference_FreeEnergyReferenceTest_WithinTolerances_coulandvdwtogether_d_sim.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 88: Changing nstlist from 10 to 100, rlist from 1 to 1 88: 88: Using 1 MPI thread 88: Using 2 OpenMP threads 88: 88: 88: NOTE: The number of threads is not equal to the number of (logical) cpus 88: and the -pin option is set to auto: will not pin threads to cpus. 88: This can lead to significant performance degradation. 88: Consider using -pin on (and -pinoffset in case you run multiple jobs). 88: starting mdrun 'AA' 88: 20 steps, 0.0 ps. 88: Setting the LD random seed to 1734063295 88: 88: Generated 153 of the 153 non-bonded parameter combinations 88: 88: Generated 153 of the 153 1-4 parameter combinations 88: 88: Excluding 3 bonded neighbours molecule type 'ASN' 88: 88: turning H bonds into constraints... 88: 88: Excluding 2 bonded neighbours molecule type 'SOL' 88: 88: turning H bonds into constraints... 88: 88: Coupling 1 copies of molecule type 'ASN' 88: 88: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/freeenergy/coulandvdwtogether/conf.gro' 88: Analysing residue names: 88: There are: 1 Protein residues 88: There are: 56 Water residues 88: Analysing Protein... 88: 88: The largest distance between non-perturbed excluded atoms is 0.164 nm between atom 41 and 42 88: 88: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 88: 88: Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm 88: 88: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm 88: 88: Note that mdrun will redetermine rlist based on the actual pair-list setup 88: Calculating fourier grid dimensions for X Y Z 88: Using a fourier grid of 28x28x28, spacing 0.108 0.108 0.108 88: 88: Estimate for the relative computational load of the PME mesh part: 0.89 88: 88: This run will generate roughly 0 Mb of data 88: 88: Writing final coordinates. 88: 88: Core t (s) Wall t (s) (%) 88: Time: 0.976 0.488 199.9 88: (ns/day) (hour/ns) 88: Performance: 3.716 6.459 88: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/EquivalentToReference_FreeEnergyReferenceTest_WithinTolerances_coulandvdwtogether_d_energy.edr as double precision energy file 88: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 17 time 0.017 Reading energy frame 18 time 0.018 Reading energy frame 19 time 0.019 Reading energy frame 20 time 0.020 Last energy frame read 20 time 0.020 88: [ OK ] EquivalentToReference/FreeEnergyReferenceTest.WithinTolerances/coulandvdwtogether_d (1765 ms) 88: [ RUN ] EquivalentToReference/FreeEnergyReferenceTest.WithinTolerances/coulandvdwtogether_net_charge_d 88: 88: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/freeenergy/coulandvdwtogether-net-charge/grompp.mdp, line 147]: 88: For proper sampling of the (nearly) decoupled state, stochastic dynamics 88: should be used 88: 88: 88: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/freeenergy/coulandvdwtogether-net-charge/grompp.mdp]: 88: With PME there is a minor soft core effect present at the cut-off, 88: proportional to (LJsigma/rcoulomb)^6. This could have a minor effect on 88: energy conservation, but usually other effects dominate. With a common 88: sigma value of 0.34 nm the fraction of the particle-particle potential at 88: the cut-off at lambda=0.5 is around 6.4e-05, while ewald-rtol is 1.0e-06. 88: 88: 88: WARNING 1 [file /build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/freeenergy/coulandvdwtogether-net-charge/grompp.mdp]: 88: The Berendsen thermostat does not generate the correct kinetic energy 88: distribution, and should not be used for new production simulations (in 88: our opinion). We would recommend the V-rescale thermostat. 88: 88: Generating 1-4 interactions: fudge = 0.5 88: 88: NOTE 3 [file topol.top, line 155]: 88: System has non-zero total charge: 1.000000 88: Total charge should normally be an integer. See 88: https://manual.gromacs.org/current/user-guide/floating-point.html 88: for discussion on how close it should be to an integer. 88: 88: 88: 88: 88: WARNING 2 [file topol.top, line 155]: 88: You are using Ewald electrostatics in a system with net charge. This can 88: lead to severe artifacts, such as ions moving into regions with low 88: dielectric, due to the uniform background charge. We suggest to 88: neutralize your system with counter ions, possibly in combination with a 88: physiological salt concentration. 88: 88: Setting the LD random seed to 1851128815 88: 88: Generated 171 of the 171 non-bonded parameter combinations 88: 88: Generated 171 of the 171 1-4 parameter combinations 88: 88: Excluding 3 bonded neighbours molecule type 'ASN' 88: 88: turning H bonds into constraints... 88: 88: Excluding 2 bonded neighbours molecule type 'SOL' 88: 88: turning H bonds into constraints... 88: 88: Excluding 1 bonded neighbours molecule type 'NA' 88: 88: turning H bonds into constraints... 88: 88: Coupling 1 copies of molecule type 'ASN' 88: 88: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 88: J. S. Hub, B. L. de Groot, H. Grubmueller, G. Groenhof 88: Quantifying Artifacts in Ewald Simulations of Inhomogeneous Systems with a Net 88: Charge 88: J. Chem. Theory Comput. (2014) 88: DOI: 10.1021/ct400626b 88: -------- -------- --- Thank You --- -------- -------- 88: 88: Number of degrees of freedom in T-Coupling group System is 358.00 88: 88: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/freeenergy/coulandvdwtogether-net-charge/grompp.mdp]: 88: The optimal PME mesh load for parallel simulations is below 0.5 88: and for highly parallel simulations between 0.25 and 0.33, 88: for higher performance, increase the cut-off and the PME grid spacing. 88: 88: 88: 88: NOTE 5 [file /build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/freeenergy/coulandvdwtogether-net-charge/grompp.mdp]: 88: For free energy simulations, the optimal load limit increases from 0.5 to 88: 0.667 88: 88: 88: 88: There were 5 NOTEs 88: 88: There were 2 WARNINGs 88: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/EquivalentToReference_FreeEnergyReferenceTest_WithinTolerances_coulandvdwtogether_net_charge_d_sim.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 88: Changing nstlist from 10 to 50, rlist from 1.004 to 1.101 88: 88: Using 1 MPI thread 88: Using 2 OpenMP threads 88: 88: 88: NOTE: The number of threads is not equal to the number of (logical) cpus 88: and the -pin option is set to auto: will not pin threads to cpus. 88: This can lead to significant performance degradation. 88: Consider using -pin on (and -pinoffset in case you run multiple jobs). 88: starting mdrun 'AA' 88: 20 steps, 0.0 ps. 88: 88: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/freeenergy/coulandvdwtogether-net-charge/conf.gro' 88: Analysing residue names: 88: There are: 1 Protein residues 88: There are: 56 Water residues 88: There are: 1 Ion residues 88: Analysing Protein... 88: 88: The largest distance between non-perturbed excluded atoms is 0.164 nm between atom 41 and 42 88: 88: Determining Verlet buffer for a tolerance of 5e-05 kJ/mol/ps at 298 K 88: 88: Calculated rlist for 1x1 atom pair-list as 1.020 nm, buffer size 0.020 nm 88: 88: Set rlist, assuming 4x4 atom pair-list, to 1.004 nm, buffer size 0.004 nm 88: 88: Note that mdrun will redetermine rlist based on the actual pair-list setup 88: Calculating fourier grid dimensions for X Y Z 88: Using a fourier grid of 32x32x32, spacing 0.095 0.095 0.095 88: 88: Estimate for the relative computational load of the PME mesh part: 0.92 88: 88: This run will generate roughly 0 Mb of data 88: 88: Writing final coordinates. 88: 88: Core t (s) Wall t (s) (%) 88: Time: 1.214 0.608 199.9 88: (ns/day) (hour/ns) 88: Performance: 2.987 8.036 88: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/EquivalentToReference_FreeEnergyReferenceTest_WithinTolerances_coulandvdwtogether_net_charge_d_energy.edr as double precision energy file 88: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 17 time 0.017 Reading energy frame 18 time 0.018 Reading energy frame 19 time 0.019 Reading energy frame 20 time 0.020 Last energy frame read 20 time 0.020 88: [ OK ] EquivalentToReference/FreeEnergyReferenceTest.WithinTolerances/coulandvdwtogether_net_charge_d (870 ms) 88: [ RUN ] EquivalentToReference/FreeEnergyReferenceTest.WithinTolerances/coulandvdwtogether_decouple_counter_charge_d 88: 88: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/freeenergy/coulandvdwtogether-decouple-counter-charge/grompp.mdp, line 147]: 88: For proper sampling of the (nearly) decoupled state, stochastic dynamics 88: should be used 88: 88: 88: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/freeenergy/coulandvdwtogether-decouple-counter-charge/grompp.mdp]: 88: With PME there is a minor soft core effect present at the cut-off, 88: proportional to (LJsigma/rcoulomb)^6. This could have a minor effect on 88: energy conservation, but usually other effects dominate. With a common 88: sigma value of 0.34 nm the fraction of the particle-particle potential at 88: the cut-off at lambda=0.5 is around 6.4e-05, while ewald-rtol is 1.0e-06. 88: 88: 88: WARNING 1 [file /build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/freeenergy/coulandvdwtogether-decouple-counter-charge/grompp.mdp]: 88: The Berendsen thermostat does not generate the correct kinetic energy 88: distribution, and should not be used for new production simulations (in 88: our opinion). We would recommend the V-rescale thermostat. 88: 88: Generating 1-4 interactions: fudge = 0.5 88: 88: NOTE 3 [file topol.top, line 165]: 88: System has non-zero total charge: 1.000000 88: Total charge should normally be an integer. See 88: https://manual.gromacs.org/current/user-guide/floating-point.html 88: for discussion on how close it should be to an integer. 88: 88: 88: 88: 88: WARNING 2 [file topol.top, line 165]: 88: You are using Ewald electrostatics in a system with net charge. This can 88: lead to severe artifacts, such as ions moving into regions with low 88: dielectric, due to the uniform background charge. We suggest to 88: neutralize your system with counter ions, possibly in combination with a 88: physiological salt concentration. 88: 88: Setting the LD random seed to 2143132671 88: 88: Generated 190 of the 190 non-bonded parameter combinations 88: 88: Generated 190 of the 190 1-4 parameter combinations 88: 88: Excluding 3 bonded neighbours molecule type 'ASN' 88: 88: turning H bonds into constraints... 88: 88: Excluding 2 bonded neighbours molecule type 'SOL' 88: 88: turning H bonds into constraints... 88: 88: Excluding 1 bonded neighbours molecule type 'NA' 88: 88: turning H bonds into constraints... 88: 88: Excluding 1 bonded neighbours molecule type 'CL' 88: 88: turning H bonds into constraints... 88: 88: Coupling 1 copies of molecule type 'CL' 88: 88: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 88: J. S. Hub, B. L. de Groot, H. Grubmueller, G. Groenhof 88: Quantifying Artifacts in Ewald Simulations of Inhomogeneous Systems with a Net 88: Charge 88: J. Chem. Theory Comput. (2014) 88: DOI: 10.1021/ct400626b 88: -------- -------- --- Thank You --- -------- -------- 88: 88: Number of degrees of freedom in T-Coupling group System is 361.00 88: 88: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/freeenergy/coulandvdwtogether-decouple-counter-charge/grompp.mdp]: 88: The optimal PME mesh load for parallel simulations is below 0.5 88: and for highly parallel simulations between 0.25 and 0.33, 88: for higher performance, increase the cut-off and the PME grid spacing. 88: 88: 88: 88: NOTE 5 [file /build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/freeenergy/coulandvdwtogether-decouple-counter-charge/grompp.mdp]: 88: For free energy simulations, the optimal load limit increases from 0.5 to 88: 0.667 88: 88: 88: 88: There were 5 NOTEs 88: 88: There were 2 WARNINGs 88: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/EquivalentToReference_FreeEnergyReferenceTest_WithinTolerances_coulandvdwtogether_decouple_counter_charge_d_sim.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 88: Changing nstlist from 10 to 50, rlist from 1.004 to 1.102 88: 88: Using 1 MPI thread 88: Using 2 OpenMP threads 88: 88: 88: NOTE: The number of threads is not equal to the number of (logical) cpus 88: and the -pin option is set to auto: will not pin threads to cpus. 88: This can lead to significant performance degradation. 88: Consider using -pin on (and -pinoffset in case you run multiple jobs). 88: starting mdrun 'AA' 88: 20 steps, 0.0 ps. 88: 88: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/freeenergy/coulandvdwtogether-decouple-counter-charge/conf.gro' 88: Analysing residue names: 88: There are: 1 Protein residues 88: There are: 56 Water residues 88: There are: 2 Ion residues 88: Analysing Protein... 88: 88: The largest distance between non-perturbed excluded atoms is 0.331 nm between atom 1 and 9 88: 88: Determining Verlet buffer for a tolerance of 5e-05 kJ/mol/ps at 298 K 88: 88: Calculated rlist for 1x1 atom pair-list as 1.020 nm, buffer size 0.020 nm 88: 88: Set rlist, assuming 4x4 atom pair-list, to 1.004 nm, buffer size 0.004 nm 88: 88: Note that mdrun will redetermine rlist based on the actual pair-list setup 88: Calculating fourier grid dimensions for X Y Z 88: Using a fourier grid of 32x32x32, spacing 0.095 0.095 0.095 88: 88: Estimate for the relative computational load of the PME mesh part: 0.92 88: 88: This run will generate roughly 0 Mb of data 88: 88: Writing final coordinates. 88: 88: Core t (s) Wall t (s) (%) 88: Time: 1.203 0.602 199.9 88: (ns/day) (hour/ns) 88: Performance: 3.015 7.961 88: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/EquivalentToReference_FreeEnergyReferenceTest_WithinTolerances_coulandvdwtogether_decouple_counter_charge_d_energy.edr as double precision energy file 88: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 17 time 0.017 Reading energy frame 18 time 0.018 Reading energy frame 19 time 0.019 Reading energy frame 20 time 0.020 Last energy frame read 20 time 0.020 88: [ OK ] EquivalentToReference/FreeEnergyReferenceTest.WithinTolerances/coulandvdwtogether_decouple_counter_charge_d (877 ms) 88: [ RUN ] EquivalentToReference/FreeEnergyReferenceTest.WithinTolerances/expanded_d 88: 88: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/freeenergy/expanded/grompp.mdp, line 171]: 88: For proper sampling of the (nearly) decoupled state, stochastic dynamics 88: should be used 88: 88: 88: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/freeenergy/expanded/grompp.mdp]: 88: Replacing vdwtype=Shift by the equivalent combination of vdwtype=Cut-off 88: and vdw_modifier=Force-switch 88: 88: 88: WARNING 1 [file /build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/freeenergy/expanded/grompp.mdp]: 88: The Berendsen thermostat does not generate the correct kinetic energy 88: distribution, and should not be used for new production simulations (in 88: our opinion). We would recommend the V-rescale thermostat. 88: 88: Generating 1-4 interactions: fudge = 0.5 88: Number of degrees of freedom in T-Coupling group System is 355.00 88: 88: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/freeenergy/expanded/grompp.mdp]: 88: The optimal PME mesh load for parallel simulations is below 0.5 88: and for highly parallel simulations between 0.25 and 0.33, 88: for higher performance, increase the cut-off and the PME grid spacing. 88: 88: 88: 88: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/freeenergy/expanded/grompp.mdp]: 88: For free energy simulations, the optimal load limit increases from 0.5 to 88: 0.667 88: 88: 88: 88: There were 4 NOTEs 88: 88: There was 1 WARNING 88: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/EquivalentToReference_FreeEnergyReferenceTest_WithinTolerances_expanded_d_sim.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 88: Changing nstlist from 10 to 100, rlist from 1 to 1 88: 88: Using 1 MPI thread 88: Using 2 OpenMP threads 88: 88: 88: NOTE: The number of threads is not equal to the number of (logical) cpus 88: and the -pin option is set to auto: will not pin threads to cpus. 88: This can lead to significant performance degradation. 88: Consider using -pin on (and -pinoffset in case you run multiple jobs). 88: starting mdrun 'AA' 88: 100 steps, 0.1 ps. 88: Setting the LD random seed to 956292478 88: 88: Generated 153 of the 153 non-bonded parameter combinations 88: 88: Generated 153 of the 153 1-4 parameter combinations 88: 88: Excluding 3 bonded neighbours molecule type 'ASN' 88: 88: turning H bonds into constraints... 88: 88: Excluding 2 bonded neighbours molecule type 'SOL' 88: 88: turning H bonds into constraints... 88: 88: Coupling 1 copies of molecule type 'ASN' 88: 88: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/freeenergy/expanded/conf.gro' 88: Analysing residue names: 88: There are: 1 Protein residues 88: There are: 56 Water residues 88: Analysing Protein... 88: 88: The largest distance between non-perturbed excluded atoms is 0.164 nm between atom 41 and 42 88: 88: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 88: 88: Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm 88: 88: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm 88: 88: Note that mdrun will redetermine rlist based on the actual pair-list setup 88: Calculating fourier grid dimensions for X Y Z 88: Using a fourier grid of 28x28x28, spacing 0.108 0.108 0.108 88: 88: Estimate for the relative computational load of the PME mesh part: 0.89 88: 88: This run will generate roughly 0 Mb of data 88: 88: Writing final coordinates. 88: 88: Core t (s) Wall t (s) (%) 88: Time: 6.087 3.044 200.0 88: (ns/day) (hour/ns) 88: Performance: 2.867 8.371 88: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/EquivalentToReference_FreeEnergyReferenceTest_WithinTolerances_expanded_d_energy.edr as double precision energy file 88: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 17 time 0.017 Reading energy frame 18 time 0.018 Reading energy frame 19 time 0.019 Reading energy frame 20 time 0.020 Reading energy frame 30 time 0.030 Reading energy frame 40 time 0.040 Reading energy frame 50 time 0.050 Reading energy frame 60 time 0.060 Reading energy frame 70 time 0.070 Reading energy frame 80 time 0.080 Reading energy frame 90 time 0.090 Reading energy frame 100 time 0.100 Last energy frame read 100 time 0.100 [ OK ] EquivalentToReference/FreeEnergyReferenceTest.WithinTolerances/expanded_d (4347 ms) 88: [ RUN ] EquivalentToReference/FreeEnergyReferenceTest.WithinTolerances/relative_d 88: 88: WARNING 1 [file /build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/freeenergy/relative/grompp.mdp]: 88: The Berendsen thermostat does not generate the correct kinetic energy 88: distribution, and should not be used for new production simulations (in 88: our opinion). We would recommend the V-rescale thermostat. 88: 88: Generating 1-4 interactions: fudge = 0.5 88: 88: WARNING 2 [file topol.top, line 72]: 88: No default Bond types for perturbed atoms in interaction, using normal 88: values. The interaction was 88: '7 8 1'. 88: 88: 88: WARNING 3 [file topol.top, line 73]: 88: No default Bond types for perturbed atoms in interaction, using normal 88: values. The interaction was 88: '7 9 1'. 88: 88: 88: WARNING 4 [file topol.top, line 98]: 88: No default Angle types for perturbed atoms in interaction, using normal 88: values. The interaction was 88: '6 5 7 1'. 88: 88: 88: WARNING 5 [file topol.top, line 99]: 88: No default Angle types for perturbed atoms in interaction, using normal 88: values. The interaction was 88: '5 7 8 1'. 88: 88: 88: WARNING 6 [file topol.top, line 100]: 88: No default Angle types for perturbed atoms in interaction, using normal 88: values. The interaction was 88: '5 7 9 1'. 88: 88: 88: WARNING 7 [file topol.top, line 101]: 88: No default Angle types for perturbed atoms in interaction, using normal 88: values. The interaction was 88: '8 7 9 1'. 88: 88: 88: WARNING 8 [file topol.top, line 111]: 88: No default Ryckaert-Bell. types for perturbed atoms in interaction, using 88: normal values. The interaction was 88: '1 5 7 8 3'. 88: 88: 88: WARNING 9 [file topol.top, line 112]: 88: No default Ryckaert-Bell. types for perturbed atoms in interaction, using 88: normal values. The interaction was 88: '1 5 7 9 3'. 88: 88: 88: WARNING 10 [file topol.top, line 113]: 88: No default Ryckaert-Bell. types for perturbed atoms in interaction, using 88: normal values. The interaction was 88: '6 5 7 8 3'. 88: 88: 88: WARNING 11 [file topol.top, line 114]: 88: No default Ryckaert-Bell. types for perturbed atoms in interaction, using 88: normal values. The interaction was 88: '6 5 7 9 3'. 88: 88: Number of degrees of freedom in T-Coupling group System is 355.00 88: 88: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/freeenergy/relative/grompp.mdp]: 88: The optimal PME mesh load for parallel simulations is below 0.5 88: and for highly parallel simulations between 0.25 and 0.33, 88: for higher performance, increase the cut-off and the PME grid spacing. 88: 88: 88: 88: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/freeenergy/relative/grompp.mdp]: 88: For free energy simulations, the optimal load limit increases from 0.5 to 88: 0.667 88: 88: 88: 88: There were 2 NOTEs 88: 88: There were 11 WARNINGs 88: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/EquivalentToReference_FreeEnergyReferenceTest_WithinTolerances_relative_d_sim.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 88: Changing nstlist from 10 to 100, rlist from 1 to 1 88: 88: Using 1 MPI thread 88: Using 2 OpenMP threads 88: 88: 88: NOTE: The number of threads is not equal to the number of (logical) cpus 88: and the -pin option is set to auto: will not pin threads to cpus. 88: This can lead to significant performance degradation. 88: Consider using -pin on (and -pinoffset in case you run multiple jobs). 88: starting mdrun 'AA' 88: 20 steps, 0.0 ps. 88: Setting the LD random seed to -111282470 88: 88: Generated 136 of the 136 non-bonded parameter combinations 88: 88: Generated 136 of the 136 1-4 parameter combinations 88: 88: Excluding 3 bonded neighbours molecule type 'ASN' 88: 88: turning H bonds into constraints... 88: 88: Excluding 2 bonded neighbours molecule type 'SOL' 88: 88: turning H bonds into constraints... 88: 88: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/freeenergy/relative/conf.gro' 88: Analysing residue names: 88: There are: 1 Protein residues 88: There are: 56 Water residues 88: Analysing Protein... 88: 88: The largest distance between non-perturbed excluded atoms is 0.164 nm between atom 41 and 42 88: 88: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 88: 88: Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm 88: 88: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm 88: 88: Note that mdrun will redetermine rlist based on the actual pair-list setup 88: Calculating fourier grid dimensions for X Y Z 88: Using a fourier grid of 28x28x28, spacing 0.108 0.108 0.108 88: 88: Estimate for the relative computational load of the PME mesh part: 0.89 88: 88: This run will generate roughly 0 Mb of data 88: 88: Writing final coordinates. 88: 88: Core t (s) Wall t (s) (%) 88: Time: 2.067 1.034 199.9 88: (ns/day) (hour/ns) 88: Performance: 1.754 13.680 88: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/EquivalentToReference_FreeEnergyReferenceTest_WithinTolerances_relative_d_energy.edr as double precision energy file 88: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 17 time 0.017 Reading energy frame 18 time 0.018 Reading energy frame 19 time 0.019 Reading energy frame 20 time 0.020 Last energy frame read 20 time 0.020 88: [ OK ] EquivalentToReference/FreeEnergyReferenceTest.WithinTolerances/relative_d (2323 ms) 88: [ RUN ] EquivalentToReference/FreeEnergyReferenceTest.WithinTolerances/relative_position_restraints_d 88: 88: WARNING 1 [file /build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/freeenergy/relative-position-restraints/grompp.mdp]: 88: The Berendsen thermostat does not generate the correct kinetic energy 88: distribution, and should not be used for new production simulations (in 88: our opinion). We would recommend the V-rescale thermostat. 88: 88: Generating 1-4 interactions: fudge = 0.5 88: 88: WARNING 2 [file topol.top, line 72]: 88: No default Bond types for perturbed atoms in interaction, using normal 88: values. The interaction was 88: '7 8 1'. 88: 88: 88: WARNING 3 [file topol.top, line 73]: 88: No default Bond types for perturbed atoms in interaction, using normal 88: values. The interaction was 88: '7 9 1'. 88: 88: 88: WARNING 4 [file topol.top, line 98]: 88: No default Angle types for perturbed atoms in interaction, using normal 88: values. The interaction was 88: '6 5 7 1'. 88: 88: 88: WARNING 5 [file topol.top, line 99]: 88: No default Angle types for perturbed atoms in interaction, using normal 88: values. The interaction was 88: '5 7 8 1'. 88: 88: 88: WARNING 6 [file topol.top, line 100]: 88: No default Angle types for perturbed atoms in interaction, using normal 88: values. The interaction was 88: '5 7 9 1'. 88: 88: 88: WARNING 7 [file topol.top, line 101]: 88: No default Angle types for perturbed atoms in interaction, using normal 88: values. The interaction was 88: '8 7 9 1'. 88: 88: 88: WARNING 8 [file topol.top, line 111]: 88: No default Ryckaert-Bell. types for perturbed atoms in interaction, using 88: normal values. The interaction was 88: '1 5 7 8 3'. 88: 88: 88: WARNING 9 [file topol.top, line 112]: 88: No default Ryckaert-Bell. types for perturbed atoms in interaction, using 88: normal values. The interaction was 88: '1 5 7 9 3'. 88: 88: 88: WARNING 10 [file topol.top, line 113]: 88: No default Ryckaert-Bell. types for perturbed atoms in interaction, using 88: normal values. The interaction was 88: '6 5 7 8 3'. 88: 88: 88: WARNING 11 [file topol.top, line 114]: 88: No default Ryckaert-Bell. types for perturbed atoms in interaction, using 88: normal values. The interaction was 88: '6 5 7 9 3'. 88: 88: Number of degrees of freedom in T-Coupling group System is 355.00 88: 88: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/freeenergy/relative-position-restraints/grompp.mdp]: 88: Removing center of mass motion in the presence of position restraints 88: might cause artifacts. When you are using position restraints to 88: equilibrate a macro-molecule, the artifacts are usually negligible. 88: 88: 88: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/freeenergy/relative-position-restraints/grompp.mdp]: 88: The optimal PME mesh load for parallel simulations is below 0.5 88: and for highly parallel simulations between 0.25 and 0.33, 88: for higher performance, increase the cut-off and the PME grid spacing. 88: 88: 88: 88: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/freeenergy/relative-position-restraints/grompp.mdp]: 88: For free energy simulations, the optimal load limit increases from 0.5 to 88: 0.667 88: 88: 88: 88: There were 3 NOTEs 88: 88: There were 11 WARNINGs 88: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/EquivalentToReference_FreeEnergyReferenceTest_WithinTolerances_relative_position_restraints_d_sim.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 88: Changing nstlist from 10 to 100, rlist from 1 to 1 88: 88: Using 1 MPI thread 88: Using 2 OpenMP threads 88: 88: 88: NOTE: The number of threads is not equal to the number of (logical) cpus 88: and the -pin option is set to auto: will not pin threads to cpus. 88: This can lead to significant performance degradation. 88: Consider using -pin on (and -pinoffset in case you run multiple jobs). 88: starting mdrun 'AA' 88: 20 steps, 0.0 ps. 88: Setting the LD random seed to -52628786 88: 88: Generated 136 of the 136 non-bonded parameter combinations 88: 88: Generated 136 of the 136 1-4 parameter combinations 88: 88: Excluding 3 bonded neighbours molecule type 'ASN' 88: 88: turning H bonds into constraints... 88: 88: Excluding 2 bonded neighbours molecule type 'SOL' 88: 88: turning H bonds into constraints... 88: 88: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/freeenergy/relative-position-restraints/conf.gro' 88: Analysing residue names: 88: There are: 1 Protein residues 88: There are: 56 Water residues 88: Analysing Protein... 88: 88: The largest distance between non-perturbed excluded atoms is 0.164 nm between atom 41 and 42 88: 88: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 88: 88: Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm 88: 88: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm 88: 88: Note that mdrun will redetermine rlist based on the actual pair-list setup 88: Calculating fourier grid dimensions for X Y Z 88: Using a fourier grid of 28x28x28, spacing 0.108 0.108 0.108 88: 88: Estimate for the relative computational load of the PME mesh part: 0.89 88: 88: This run will generate roughly 0 Mb of data 88: 88: Writing final coordinates. 88: 88: Core t (s) Wall t (s) (%) 88: Time: 2.086 1.043 199.9 88: (ns/day) (hour/ns) 88: Performance: 1.739 13.803 88: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/EquivalentToReference_FreeEnergyReferenceTest_WithinTolerances_relative_position_restraints_d_energy.edr as double precision energy file 88: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 17 time 0.017 Reading energy frame 18 time 0.018 Reading energy frame 19 time 0.019 Reading energy frame 20 time 0.020 Last energy frame read 20 time 0.020 88: [ OK ] EquivalentToReference/FreeEnergyReferenceTest.WithinTolerances/relative_position_restraints_d (2351 ms) 88: [ RUN ] EquivalentToReference/FreeEnergyReferenceTest.WithinTolerances/restraints_d 88: 88: WARNING 1 [file /build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/freeenergy/restraints/grompp.mdp]: 88: The Berendsen thermostat does not generate the correct kinetic energy 88: distribution, and should not be used for new production simulations (in 88: our opinion). We would recommend the V-rescale thermostat. 88: 88: Generating 1-4 interactions: fudge = 0.5 88: Number of degrees of freedom in T-Coupling group System is 355.00 88: 88: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/freeenergy/restraints/grompp.mdp]: 88: The optimal PME mesh load for parallel simulations is below 0.5 88: and for highly parallel simulations between 0.25 and 0.33, 88: for higher performance, increase the cut-off and the PME grid spacing. 88: 88: 88: 88: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/freeenergy/restraints/grompp.mdp]: 88: For free energy simulations, the optimal load limit increases from 0.5 to 88: 0.667 88: 88: 88: 88: There were 2 NOTEs 88: 88: There was 1 WARNING 88: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/EquivalentToReference_FreeEnergyReferenceTest_WithinTolerances_restraints_d_sim.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 88: Changing nstlist from 10 to 100, rlist from 1 to 1 88: 88: Using 1 MPI thread 88: Using 2 OpenMP threads 88: 88: 88: NOTE: The number of threads is not equal to the number of (logical) cpus 88: and the -pin option is set to auto: will not pin threads to cpus. 88: This can lead to significant performance degradation. 88: Consider using -pin on (and -pinoffset in case you run multiple jobs). 88: starting mdrun 'AA' 88: 20 steps, 0.0 ps. 88: Setting the LD random seed to -562044981 88: 88: Generated 136 of the 136 non-bonded parameter combinations 88: 88: Generated 136 of the 136 1-4 parameter combinations 88: 88: Excluding 3 bonded neighbours molecule type 'ASN' 88: 88: turning H bonds into constraints... 88: 88: Excluding 2 bonded neighbours molecule type 'SOL' 88: 88: turning H bonds into constraints... 88: 88: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/freeenergy/restraints/conf.gro' 88: Analysing residue names: 88: There are: 1 Protein residues 88: There are: 56 Water residues 88: Analysing Protein... 88: 88: The largest distance between non-perturbed excluded atoms is 0.331 nm between atom 1 and 9 88: 88: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 88: 88: Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm 88: 88: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm 88: 88: Note that mdrun will redetermine rlist based on the actual pair-list setup 88: Calculating fourier grid dimensions for X Y Z 88: Using a fourier grid of 28x28x28, spacing 0.108 0.108 0.108 88: 88: Estimate for the relative computational load of the PME mesh part: 0.81 88: 88: This run will generate roughly 0 Mb of data 88: 88: Writing final coordinates. 88: 88: Core t (s) Wall t (s) (%) 88: Time: 0.551 0.276 199.7 88: (ns/day) (hour/ns) 88: Performance: 6.574 3.651 88: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/EquivalentToReference_FreeEnergyReferenceTest_WithinTolerances_restraints_d_energy.edr as double precision energy file 88: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 17 time 0.017 Reading energy frame 18 time 0.018 Reading energy frame 19 time 0.019 Reading energy frame 20 time 0.020 Last energy frame read 20 time 0.020 88: [ OK ] EquivalentToReference/FreeEnergyReferenceTest.WithinTolerances/restraints_d (1546 ms) 88: [ RUN ] EquivalentToReference/FreeEnergyReferenceTest.WithinTolerances/simtemp_d 88: 88: WARNING 1 [file /build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/freeenergy/simtemp/grompp.mdp]: 88: The Berendsen thermostat does not generate the correct kinetic energy 88: distribution, and should not be used for new production simulations (in 88: our opinion). We would recommend the V-rescale thermostat. 88: 88: Generating 1-4 interactions: fudge = 0.5 88: Number of degrees of freedom in T-Coupling group System is 355.00 88: 88: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/freeenergy/simtemp/grompp.mdp]: 88: The optimal PME mesh load for parallel simulations is below 0.5 88: and for highly parallel simulations between 0.25 and 0.33, 88: for higher performance, increase the cut-off and the PME grid spacing. 88: 88: 88: 88: There was 1 NOTE 88: 88: There was 1 WARNING 88: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/EquivalentToReference_FreeEnergyReferenceTest_WithinTolerances_simtemp_d_sim.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 88: Changing nstlist from 10 to 100, rlist from 1 to 1 88: 88: Using 1 MPI thread 88: Using 2 OpenMP threads 88: 88: 88: NOTE: The number of threads is not equal to the number of (logical) cpus 88: and the -pin option is set to auto: will not pin threads to cpus. 88: This can lead to significant performance degradation. 88: Consider using -pin on (and -pinoffset in case you run multiple jobs). 88: starting mdrun 'AA' 88: 20 steps, 0.0 ps. 88: 88: Writing final coordinates. 88: 88: Core t (s) Wall t (s) (%) 88: Time: 0.521 0.261 199.7 88: (ns/day) (hour/ns) 88: Performance: 6.949 3.454 88: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/EquivalentToReference_FreeEnergyReferenceTest_WithinTolerances_simtemp_d_energy.edr as double precision energy file 88: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 17 time 0.017 Reading energy frame 18 time 0.018 Reading energy frame 19 time 0.019 Reading energy frame 20 time 0.020 Last energy frame read 20 time 0.020 88: Setting the LD random seed to -1681981442 88: 88: Generated 136 of the 136 non-bonded parameter combinations 88: 88: Generated 136 of the 136 1-4 parameter combinations 88: 88: Excluding 3 bonded neighbours molecule type 'ASN' 88: 88: turning H bonds into constraints... 88: 88: Excluding 2 bonded neighbours molecule type 'SOL' 88: 88: turning H bonds into constraints... 88: 88: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/freeenergy/simtemp/conf.gro' 88: Analysing residue names: 88: There are: 1 Protein residues 88: There are: 56 Water residues 88: Analysing Protein... 88: 88: The largest distance between excluded atoms is 0.331 nm between atom 1 and 9 88: 88: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 88: 88: Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm 88: 88: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm 88: 88: Note that mdrun will redetermine rlist based on the actual pair-list setup 88: Calculating fourier grid dimensions for X Y Z 88: Using a fourier grid of 28x28x28, spacing 0.108 0.108 0.108 88: 88: Estimate for the relative computational load of the PME mesh part: 0.81 88: 88: This run will generate roughly 0 Mb of data 88: [ OK ] EquivalentToReference/FreeEnergyReferenceTest.WithinTolerances/simtemp_d (1540 ms) 88: [ RUN ] EquivalentToReference/FreeEnergyReferenceTest.WithinTolerances/transformAtoB_d 88: 88: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/freeenergy/transformAtoB/grompp.mdp]: 88: With PME there is a minor soft core effect present at the cut-off, 88: proportional to (LJsigma/rcoulomb)^6. This could have a minor effect on 88: energy conservation, but usually other effects dominate. With a common 88: sigma value of 0.34 nm the fraction of the particle-particle potential at 88: the cut-off at lambda=0.5 is around 6.4e-05, while ewald-rtol is 1.0e-06. 88: 88: 88: WARNING 1 [file /build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/freeenergy/transformAtoB/grompp.mdp]: 88: The Berendsen thermostat does not generate the correct kinetic energy 88: distribution, and should not be used for new production simulations (in 88: our opinion). We would recommend the V-rescale thermostat. 88: 88: Generating 1-4 interactions: fudge = 0.5 88: Number of degrees of freedom in T-Coupling group System is 355.00 88: 88: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/freeenergy/transformAtoB/grompp.mdp]: 88: The optimal PME mesh load for parallel simulations is below 0.5 88: and for highly parallel simulations between 0.25 and 0.33, 88: for higher performance, increase the cut-off and the PME grid spacing. 88: 88: 88: 88: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/freeenergy/transformAtoB/grompp.mdp]: 88: For free energy simulations, the optimal load limit increases from 0.5 to 88: 0.667 88: 88: 88: 88: There were 3 NOTEs 88: 88: There was 1 WARNING 88: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/EquivalentToReference_FreeEnergyReferenceTest_WithinTolerances_transformAtoB_d_sim.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 88: Changing nstlist from 10 to 100, rlist from 1 to 1 88: 88: Using 1 MPI thread 88: Using 2 OpenMP threads 88: 88: 88: NOTE: The number of threads is not equal to the number of (logical) cpus 88: and the -pin option is set to auto: will not pin threads to cpus. 88: This can lead to significant performance degradation. 88: Consider using -pin on (and -pinoffset in case you run multiple jobs). 88: starting mdrun 'AA' 88: 20 steps, 0.0 ps. 88: Setting the LD random seed to 2066740213 88: 88: Generated 136 of the 136 non-bonded parameter combinations 88: 88: Generated 136 of the 136 1-4 parameter combinations 88: 88: Excluding 3 bonded neighbours molecule type 'ASN' 88: 88: turning H bonds into constraints... 88: 88: Excluding 2 bonded neighbours molecule type 'SOL' 88: 88: turning H bonds into constraints... 88: 88: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/freeenergy/transformAtoB/conf.gro' 88: Analysing residue names: 88: There are: 1 Protein residues 88: There are: 56 Water residues 88: Analysing Protein... 88: 88: The largest distance between non-perturbed excluded atoms is 0.164 nm between atom 41 and 42 88: 88: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 88: 88: Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm 88: 88: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm 88: 88: Note that mdrun will redetermine rlist based on the actual pair-list setup 88: Calculating fourier grid dimensions for X Y Z 88: Using a fourier grid of 28x28x28, spacing 0.108 0.108 0.108 88: 88: Estimate for the relative computational load of the PME mesh part: 0.89 88: 88: This run will generate roughly 0 Mb of data 88: 88: Writing final coordinates. 88: 88: Core t (s) Wall t (s) (%) 88: Time: 1.207 0.604 199.9 88: (ns/day) (hour/ns) 88: Performance: 3.005 7.986 88: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/EquivalentToReference_FreeEnergyReferenceTest_WithinTolerances_transformAtoB_d_energy.edr as double precision energy file 88: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 17 time 0.017 Reading energy frame 18 time 0.018 Reading energy frame 19 time 0.019 Reading energy frame 20 time 0.020 Last energy frame read 20 time 0.020 88: [ OK ] EquivalentToReference/FreeEnergyReferenceTest.WithinTolerances/transformAtoB_d (1889 ms) 88: [ RUN ] EquivalentToReference/FreeEnergyReferenceTest.WithinTolerances/vdwalone_d 88: 88: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/freeenergy/vdwalone/grompp.mdp]: 88: With PME there is a minor soft core effect present at the cut-off, 88: proportional to (LJsigma/rcoulomb)^6. This could have a minor effect on 88: energy conservation, but usually other effects dominate. With a common 88: sigma value of 0.34 nm the fraction of the particle-particle potential at 88: the cut-off at lambda=0.5 is around 6.4e-05, while ewald-rtol is 1.0e-06. 88: 88: 88: WARNING 1 [file /build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/freeenergy/vdwalone/grompp.mdp]: 88: The Berendsen thermostat does not generate the correct kinetic energy 88: distribution, and should not be used for new production simulations (in 88: our opinion). We would recommend the V-rescale thermostat. 88: 88: Generating 1-4 interactions: fudge = 0.5 88: Number of degrees of freedom in T-Coupling group System is 355.00 88: 88: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/freeenergy/vdwalone/grompp.mdp]: 88: The optimal PME mesh load for parallel simulations is below 0.5 88: and for highly parallel simulations between 0.25 and 0.33, 88: for higher performance, increase the cut-off and the PME grid spacing. 88: 88: 88: 88: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/freeenergy/vdwalone/grompp.mdp]: 88: For free energy simulations, the optimal load limit increases from 0.5 to 88: 0.667 88: 88: 88: 88: There were 3 NOTEs 88: 88: There was 1 WARNING 88: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/EquivalentToReference_FreeEnergyReferenceTest_WithinTolerances_vdwalone_d_sim.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 88: Changing nstlist from 10 to 100, rlist from 1 to 1 88: 88: Using 1 MPI thread 88: Using 2 OpenMP threads 88: 88: 88: NOTE: The number of threads is not equal to the number of (logical) cpus 88: and the -pin option is set to auto: will not pin threads to cpus. 88: This can lead to significant performance degradation. 88: Consider using -pin on (and -pinoffset in case you run multiple jobs). 88: starting mdrun 'AA' 88: 20 steps, 0.0 ps. 88: Setting the LD random seed to -4282371 88: 88: Generated 136 of the 136 non-bonded parameter combinations 88: 88: Generated 136 of the 136 1-4 parameter combinations 88: 88: Excluding 3 bonded neighbours molecule type 'ASN' 88: 88: turning H bonds into constraints... 88: 88: Excluding 2 bonded neighbours molecule type 'SOL' 88: 88: turning H bonds into constraints... 88: 88: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/freeenergy/vdwalone/conf.gro' 88: Analysing residue names: 88: There are: 1 Protein residues 88: There are: 56 Water residues 88: Analysing Protein... 88: 88: The largest distance between non-perturbed excluded atoms is 0.172 nm between atom 8 and 9 88: 88: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 88: 88: Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm 88: 88: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm 88: 88: Note that mdrun will redetermine rlist based on the actual pair-list setup 88: Calculating fourier grid dimensions for X Y Z 88: Using a fourier grid of 28x28x28, spacing 0.108 0.108 0.108 88: 88: Estimate for the relative computational load of the PME mesh part: 0.81 88: 88: This run will generate roughly 0 Mb of data 88: 88: Writing final coordinates. 88: 88: Core t (s) Wall t (s) (%) 88: Time: 0.586 0.293 199.8 88: (ns/day) (hour/ns) 88: Performance: 6.187 3.879 88: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/EquivalentToReference_FreeEnergyReferenceTest_WithinTolerances_vdwalone_d_energy.edr as double precision energy file 88: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 17 time 0.017 Reading energy frame 18 time 0.018 Reading energy frame 19 time 0.019 Reading energy frame 20 time 0.020 Last energy frame read 20 time 0.020 88: [ OK ] EquivalentToReference/FreeEnergyReferenceTest.WithinTolerances/vdwalone_d (1556 ms) 88: [----------] 12 tests from EquivalentToReference/FreeEnergyReferenceTest (23129 ms total) 88: 88: [----------] Global test environment tear-down 88: [==========] 14 tests from 2 test suites ran. (23941 ms total) 88: [ PASSED ] 14 tests. 88/92 Test #88: MdrunFEPTests ............................. Passed 24.02 sec test 89 Start 89: MdrunPullTests 89: Test command: /build/reproducible-path/gromacs-2025.1/build/basic-dp/bin/mdrun-pull-test "-ntomp" "2" "--gtest_output=xml:/build/reproducible-path/gromacs-2025.1/build/basic-dp/Testing/Temporary/MdrunPullTests.xml" 89: Working Directory: /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests 89: Test timeout computed to be: 600 89: [==========] Running 4 tests from 1 test suite. 89: [----------] Global test environment set-up. 89: [----------] 4 tests from PullTest/PullIntegrationTest 89: [ RUN ] PullTest/PullIntegrationTest.WithinTolerances/0 89: Generating 1-4 interactions: fudge = 0.5 89: Pull group 1 'r_1' has 3 atoms 89: Pull group 2 'r_2' has 3 atoms 89: Number of degrees of freedom in T-Coupling group System is 1293.00 89: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 89: 89: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PullTest_PullIntegrationTest_WithinTolerances_0_input.mdp]: 89: NVE simulation: will use the initial temperature of 303.122 K for 89: determining the Verlet buffer size 89: 89: Pull group natoms pbc atom distance at start reference at t=0 89: 1 3 2 89: 2 3 5 0.575 nm 0.600 nm 89: 89: There was 1 NOTE 89: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PullTest_PullIntegrationTest_WithinTolerances_0.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 89: Can not increase nstlist because an NVE ensemble is used 89: Using 1 MPI thread 89: Using 2 OpenMP threads 89: 89: 89: NOTE: The number of threads is not equal to the number of (logical) cpus 89: and the -pin option is set to auto: will not pin threads to cpus. 89: This can lead to significant performance degradation. 89: Consider using -pin on (and -pinoffset in case you run multiple jobs). 89: starting mdrun 'spc2' 89: 20 steps, 0.0 ps. 89: Generated 330891 of the 330891 non-bonded parameter combinations 89: 89: Generated 330891 of the 330891 1-4 parameter combinations 89: 89: Excluding 2 bonded neighbours molecule type 'SOL' 89: 89: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/spc216.gro' 89: 89: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 303.122 K 89: 89: Calculated rlist for 1x1 atom pair-list as 0.781 nm, buffer size 0.081 nm 89: 89: Set rlist, assuming 4x4 atom pair-list, to 0.772 nm, buffer size 0.072 nm 89: 89: Note that mdrun will redetermine rlist based on the actual pair-list setup 89: 89: This run will generate roughly 0 Mb of data 89: 89: Writing final coordinates. 89: 89: Core t (s) Wall t (s) (%) 89: Time: 0.755 0.378 199.8 89: (ns/day) (hour/ns) 89: Performance: 4.802 4.998 89: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PullTest_PullIntegrationTest_WithinTolerances_0.edr as double precision energy file 89: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.005 Reading energy frame 2 time 0.010 Reading energy frame 3 time 0.015 Reading energy frame 4 time 0.020 Last energy frame read 4 time 0.020 [ OK ] PullTest/PullIntegrationTest.WithinTolerances/0 (6175 ms) 89: [ RUN ] PullTest/PullIntegrationTest.WithinTolerances/1 89: Generating 1-4 interactions: fudge = 0.5 89: Pull group 1 'r_1' has 3 atoms 89: Pull group 2 'r_2' has 3 atoms 89: Number of degrees of freedom in T-Coupling group System is 1293.00 89: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 89: 89: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PullTest_PullIntegrationTest_WithinTolerances_1_input.mdp]: 89: NVE simulation: will use the initial temperature of 303.122 K for 89: determining the Verlet buffer size 89: 89: Pull group natoms pbc atom distance at start reference at t=0 89: 1 3 2 89: 2 3 5 0.301 nm 0.400 nm 89: 89: There was 1 NOTE 89: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PullTest_PullIntegrationTest_WithinTolerances_1.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 89: Can not increase nstlist because an NVE ensemble is used 89: Using 1 MPI thread 89: Using 2 OpenMP threads 89: 89: 89: NOTE: The number of threads is not equal to the number of (logical) cpus 89: and the -pin option is set to auto: will not pin threads to cpus. 89: This can lead to significant performance degradation. 89: Consider using -pin on (and -pinoffset in case you run multiple jobs). 89: starting mdrun 'spc2' 89: 20 steps, 0.0 ps. 89: Generated 330891 of the 330891 non-bonded parameter combinations 89: 89: Generated 330891 of the 330891 1-4 parameter combinations 89: 89: Excluding 2 bonded neighbours molecule type 'SOL' 89: 89: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/spc216.gro' 89: 89: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 303.122 K 89: 89: Calculated rlist for 1x1 atom pair-list as 0.781 nm, buffer size 0.081 nm 89: 89: Set rlist, assuming 4x4 atom pair-list, to 0.772 nm, buffer size 0.072 nm 89: 89: Note that mdrun will redetermine rlist based on the actual pair-list setup 89: 89: This run will generate roughly 0 Mb of data 89: 89: Writing final coordinates. 89: 89: Core t (s) Wall t (s) (%) 89: Time: 0.772 0.386 199.9 89: (ns/day) (hour/ns) 89: Performance: 4.696 5.111 89: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PullTest_PullIntegrationTest_WithinTolerances_1.edr as double precision energy file 89: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.005 Reading energy frame 2 time 0.010 Reading energy frame 3 time 0.015 Reading energy frame 4 time 0.020 Last energy frame read 4 time 0.020 [ OK ] PullTest/PullIntegrationTest.WithinTolerances/1 (6073 ms) 89: [ RUN ] PullTest/PullIntegrationTest.WithinTolerances/2 89: Generating 1-4 interactions: fudge = 0.5 89: Pull group 1 'r_1' has 3 atoms 89: Pull group 2 'r_2' has 3 atoms 89: Pull group 3 'r_3' has 3 atoms 89: Number of degrees of freedom in T-Coupling group System is 1292.00 89: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 89: 89: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PullTest_PullIntegrationTest_WithinTolerances_2_input.mdp]: 89: NVE simulation: will use the initial temperature of 303.357 K for 89: determining the Verlet buffer size 89: 89: Pull group natoms pbc atom distance at start reference at t=0 89: 1 3 2 89: 2 3 5 0.575 nm 0.500 nm 89: 1 3 2 89: 3 3 8 0.331 nm 0.400 nm 89: 89: There was 1 NOTE 89: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PullTest_PullIntegrationTest_WithinTolerances_2.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 89: Can not increase nstlist because an NVE ensemble is used 89: Using 1 MPI thread 89: Using 2 OpenMP threads 89: 89: 89: NOTE: The number of threads is not equal to the number of (logical) cpus 89: and the -pin option is set to auto: will not pin threads to cpus. 89: This can lead to significant performance degradation. 89: Consider using -pin on (and -pinoffset in case you run multiple jobs). 89: starting mdrun 'spc2' 89: 20 steps, 0.0 ps. 89: Generated 330891 of the 330891 non-bonded parameter combinations 89: 89: Generated 330891 of the 330891 1-4 parameter combinations 89: 89: Excluding 2 bonded neighbours molecule type 'SOL' 89: 89: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/spc216.gro' 89: 89: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 303.357 K 89: 89: Calculated rlist for 1x1 atom pair-list as 0.781 nm, buffer size 0.081 nm 89: 89: Set rlist, assuming 4x4 atom pair-list, to 0.772 nm, buffer size 0.072 nm 89: 89: Note that mdrun will redetermine rlist based on the actual pair-list setup 89: 89: This run will generate roughly 0 Mb of data 89: 89: Writing final coordinates. 89: 89: Core t (s) Wall t (s) (%) 89: Time: 0.783 0.392 199.8 89: (ns/day) (hour/ns) 89: Performance: 4.631 5.183 89: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PullTest_PullIntegrationTest_WithinTolerances_2.edr as double precision energy file 89: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.005 Reading energy frame 2 time 0.010 Reading energy frame 3 time 0.015 Reading energy frame 4 time 0.020 Last energy frame read 4 time 0.020 [ OK ] PullTest/PullIntegrationTest.WithinTolerances/2 (6252 ms) 89: [ RUN ] PullTest/PullIntegrationTest.WithinTolerances/3 89: Generating 1-4 interactions: fudge = 0.5 89: Pull group 1 'r_1' has 3 atoms 89: Pull group 2 'r_2' has 3 atoms 89: Number of degrees of freedom in T-Coupling group System is 1293.00 89: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 89: 89: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PullTest_PullIntegrationTest_WithinTolerances_3_input.mdp]: 89: NVE simulation: will use the initial temperature of 303.122 K for 89: determining the Verlet buffer size 89: 89: Pull group natoms pbc atom distance at start reference at t=0 89: 1 3 2 89: 2 3 5 0.575 nm 0.000 nm 89: 1 3 2 89: 2 3 5 0.050 nm 0.000 nm 89: 89: There was 1 NOTE 89: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PullTest_PullIntegrationTest_WithinTolerances_3.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 89: Can not increase nstlist because an NVE ensemble is used 89: Using 1 MPI thread 89: Using 2 OpenMP threads 89: 89: 89: NOTE: The number of threads is not equal to the number of (logical) cpus 89: and the -pin option is set to auto: will not pin threads to cpus. 89: This can lead to significant performance degradation. 89: Consider using -pin on (and -pinoffset in case you run multiple jobs). 89: starting mdrun 'spc2' 89: 20 steps, 0.0 ps. 89: Generated 330891 of the 330891 non-bonded parameter combinations 89: 89: Generated 330891 of the 330891 1-4 parameter combinations 89: 89: Excluding 2 bonded neighbours molecule type 'SOL' 89: 89: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/spc216.gro' 89: 89: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 303.122 K 89: 89: Calculated rlist for 1x1 atom pair-list as 0.781 nm, buffer size 0.081 nm 89: 89: Set rlist, assuming 4x4 atom pair-list, to 0.772 nm, buffer size 0.072 nm 89: 89: Note that mdrun will redetermine rlist based on the actual pair-list setup 89: 89: This run will generate roughly 0 Mb of data 89: 89: Writing final coordinates. 89: 89: Core t (s) Wall t (s) (%) 89: Time: 0.771 0.386 199.8 89: (ns/day) (hour/ns) 89: Performance: 4.704 5.102 89: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PullTest_PullIntegrationTest_WithinTolerances_3.edr as double precision energy file 89: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.005 Reading energy frame 2 time 0.010 Reading energy frame 3 time 0.015 Reading energy frame 4 time 0.020 Last energy frame read 4 time 0.020 [ OK ] PullTest/PullIntegrationTest.WithinTolerances/3 (6161 ms) 89: [----------] 4 tests from PullTest/PullIntegrationTest (24664 ms total) 89: 89: [----------] Global test environment tear-down 89: [==========] 4 tests from 1 test suite ran. (24714 ms total) 89: [ PASSED ] 4 tests. 89/92 Test #89: MdrunPullTests ............................ Passed 24.80 sec test 90 Start 90: MdrunRotationTests 90: Test command: /build/reproducible-path/gromacs-2025.1/build/basic-dp/bin/mdrun-rotation-test "-ntomp" "2" "--gtest_output=xml:/build/reproducible-path/gromacs-2025.1/build/basic-dp/Testing/Temporary/MdrunRotationTests.xml" 90: Working Directory: /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests 90: Test timeout computed to be: 600 90: [==========] Running 12 tests from 1 test suite. 90: [----------] Global test environment set-up. 90: [----------] 12 tests from RotationWorks/RotationTest 90: [ RUN ] RotationWorks/RotationTest.CheckEnergiesForcesAndTraj/0 90: Enforced rotation: Group 0 (iso) normalized rot. vector: 0.267261 0.534522 0.801784 90: 90: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_0_input.mdp]: 90: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 90: that with the Verlet scheme, nstlist has no effect on the accuracy of 90: your simulation. 90: 90: Rotation group 0 'system' has 4 atoms 90: Number of degrees of freedom in T-Coupling group rest is 9.00 90: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 90: 90: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_0_input.mdp]: 90: NVE simulation with an initial temperature of zero: will use a Verlet 90: buffer of 10%. Check your energy drift! 90: 90: Enforced rotation: group 0 has 4 reference positions. 90: Reading them from /build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/rotref.0.trr. 90: trr version: GMX_trn_file (single precision) 90: 90: There were 2 NOTEs 90: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_0.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 90: Can not increase nstlist because an NVE ensemble is used 90: Using 1 MPI thread 90: Using 2 OpenMP threads 90: 90: 90: NOTE: The number of threads is not equal to the number of (logical) cpus 90: and the -pin option is set to auto: will not pin threads to cpus. 90: This can lead to significant performance degradation. 90: Consider using -pin on (and -pinoffset in case you run multiple jobs). 90: starting mdrun 'Good gRace! Old Maple Actually Chews Slate' 90: 25 steps, 0.1 ps. 90: Setting the LD random seed to 937352146 90: 90: Generated 1 of the 1 non-bonded parameter combinations 90: 90: Excluding 1 bonded neighbours molecule type 'ArgonA' 90: 90: Excluding 1 bonded neighbours molecule type 'ArgonB' 90: 90: Excluding 1 bonded neighbours molecule type 'ArgonC' 90: 90: Excluding 1 bonded neighbours molecule type 'ArgonD' 90: 90: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon4.gro', all velocities are zero 90: 90: This run will generate roughly 0 Mb of data 90: 90: Writing final coordinates. 90: 90: Core t (s) Wall t (s) (%) 90: Time: 0.051 0.026 197.9 90: (ns/day) (hour/ns) 90: Performance: 175.967 0.136 90: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_0.edr as double precision energy file 90: Reading energy frame 0 time 0.002 Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_0.edr as double precision energy file 90: Reading energy frame 0 time 0.002 Reading energy frame 1 time 0.012 Reading energy frame 2 time 0.022 Reading energy frame 3 time 0.032 Reading energy frame 4 time 0.042 Reading energy frame 5 time 0.052 Last energy frame read 5 time 0.052 90: [ OK ] RotationWorks/RotationTest.CheckEnergiesForcesAndTraj/0 (83 ms) 90: [ RUN ] RotationWorks/RotationTest.CheckEnergiesForcesAndTraj/1 90: Enforced rotation: Group 0 (iso-pf) normalized rot. vector: 0.267261 0.534522 0.801784 90: 90: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_1_input.mdp]: 90: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 90: that with the Verlet scheme, nstlist has no effect on the accuracy of 90: your simulation. 90: 90: Rotation group 0 'system' has 4 atoms 90: Number of degrees of freedom in T-Coupling group rest is 9.00 90: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 90: 90: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_1_input.mdp]: 90: NVE simulation with an initial temperature of zero: will use a Verlet 90: buffer of 10%. Check your energy drift! 90: 90: Enforced rotation: group 0 has 4 reference positions. 90: Reading them from /build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/rotref.0.trr. 90: 90: There were 2 NOTEs 90: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_1.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 90: Can not increase nstlist because an NVE ensemble is used 90: Using 1 MPI thread 90: Using 2 OpenMP threads 90: 90: 90: NOTE: The number of threads is not equal to the number of (logical) cpus 90: and the -pin option is set to auto: will not pin threads to cpus. 90: This can lead to significant performance degradation. 90: Consider using -pin on (and -pinoffset in case you run multiple jobs). 90: starting mdrun 'Good gRace! Old Maple Actually Chews Slate' 90: 25 steps, 0.1 ps. 90: Setting the LD random seed to -2021785781 90: 90: Generated 1 of the 1 non-bonded parameter combinations 90: 90: Excluding 1 bonded neighbours molecule type 'ArgonA' 90: 90: Excluding 1 bonded neighbours molecule type 'ArgonB' 90: 90: Excluding 1 bonded neighbours molecule type 'ArgonC' 90: 90: Excluding 1 bonded neighbours molecule type 'ArgonD' 90: 90: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon4.gro', all velocities are zero 90: 90: This run will generate roughly 0 Mb of data 90: 90: Writing final coordinates. 90: 90: Core t (s) Wall t (s) (%) 90: Time: 0.040 0.020 197.4 90: (ns/day) (hour/ns) 90: Performance: 219.547 0.109 90: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_1.edr as double precision energy file 90: Reading energy frame 0 time 0.002 Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_1.edr as double precision energy file 90: Reading energy frame 0 time 0.002 Reading energy frame 1 time 0.012 Reading energy frame 2 time 0.022 Reading energy frame 3 time 0.032 Reading energy frame 4 time 0.042 Reading energy frame 5 time 0.052 Last energy frame read 5 time 0.052 90: [ OK ] RotationWorks/RotationTest.CheckEnergiesForcesAndTraj/1 (73 ms) 90: [ RUN ] RotationWorks/RotationTest.CheckEnergiesForcesAndTraj/2 90: Enforced rotation: Group 0 (pm) normalized rot. vector: 0.267261 0.534522 0.801784 90: 90: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_2_input.mdp]: 90: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 90: that with the Verlet scheme, nstlist has no effect on the accuracy of 90: your simulation. 90: 90: Rotation group 0 'system' has 4 atoms 90: Number of degrees of freedom in T-Coupling group rest is 9.00 90: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 90: 90: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_2_input.mdp]: 90: NVE simulation with an initial temperature of zero: will use a Verlet 90: buffer of 10%. Check your energy drift! 90: 90: Enforced rotation: group 0 has 4 reference positions. 90: Reading them from /build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/rotref.0.trr. 90: 90: There were 2 NOTEs 90: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_2.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 90: Can not increase nstlist because an NVE ensemble is used 90: Using 1 MPI thread 90: Using 2 OpenMP threads 90: 90: 90: NOTE: The number of threads is not equal to the number of (logical) cpus 90: and the -pin option is set to auto: will not pin threads to cpus. 90: This can lead to significant performance degradation. 90: Consider using -pin on (and -pinoffset in case you run multiple jobs). 90: starting mdrun 'Good gRace! Old Maple Actually Chews Slate' 90: 25 steps, 0.1 ps. 90: Setting the LD random seed to 1006632891 90: 90: Generated 1 of the 1 non-bonded parameter combinations 90: 90: Excluding 1 bonded neighbours molecule type 'ArgonA' 90: 90: Excluding 1 bonded neighbours molecule type 'ArgonB' 90: 90: Excluding 1 bonded neighbours molecule type 'ArgonC' 90: 90: Excluding 1 bonded neighbours molecule type 'ArgonD' 90: 90: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon4.gro', all velocities are zero 90: 90: This run will generate roughly 0 Mb of data 90: 90: Writing final coordinates. 90: 90: Core t (s) Wall t (s) (%) 90: Time: 0.041 0.021 197.4 90: (ns/day) (hour/ns) 90: Performance: 217.527 0.110 90: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_2.edr as double precision energy file 90: Reading energy frame 0 time 0.002 Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_2.edr as double precision energy file 90: Reading energy frame 0 time 0.002 Reading energy frame 1 time 0.012 Reading energy frame 2 time 0.022 Reading energy frame 3 time 0.032 Reading energy frame 4 time 0.042 Reading energy frame 5 time 0.052 Last energy frame read 5 time 0.052 90: [ OK ] RotationWorks/RotationTest.CheckEnergiesForcesAndTraj/2 (74 ms) 90: [ RUN ] RotationWorks/RotationTest.CheckEnergiesForcesAndTraj/3 90: Enforced rotation: Group 0 (pm-pf) normalized rot. vector: 0.267261 0.534522 0.801784 90: 90: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_3_input.mdp]: 90: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 90: that with the Verlet scheme, nstlist has no effect on the accuracy of 90: your simulation. 90: 90: Rotation group 0 'system' has 4 atoms 90: Number of degrees of freedom in T-Coupling group rest is 9.00 90: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 90: 90: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_3_input.mdp]: 90: NVE simulation with an initial temperature of zero: will use a Verlet 90: buffer of 10%. Check your energy drift! 90: 90: Enforced rotation: group 0 has 4 reference positions. 90: Reading them from /build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/rotref.0.trr. 90: 90: There were 2 NOTEs 90: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_3.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 90: Can not increase nstlist because an NVE ensemble is used 90: Using 1 MPI thread 90: Using 2 OpenMP threads 90: 90: 90: NOTE: The number of threads is not equal to the number of (logical) cpus 90: and the -pin option is set to auto: will not pin threads to cpus. 90: This can lead to significant performance degradation. 90: Consider using -pin on (and -pinoffset in case you run multiple jobs). 90: starting mdrun 'Good gRace! Old Maple Actually Chews Slate' 90: 25 steps, 0.1 ps. 90: Setting the LD random seed to -25953540 90: 90: Generated 1 of the 1 non-bonded parameter combinations 90: 90: Excluding 1 bonded neighbours molecule type 'ArgonA' 90: 90: Excluding 1 bonded neighbours molecule type 'ArgonB' 90: 90: Excluding 1 bonded neighbours molecule type 'ArgonC' 90: 90: Excluding 1 bonded neighbours molecule type 'ArgonD' 90: 90: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon4.gro', all velocities are zero 90: 90: This run will generate roughly 0 Mb of data 90: 90: Writing final coordinates. 90: 90: Core t (s) Wall t (s) (%) 90: Time: 0.041 0.021 197.4 90: (ns/day) (hour/ns) 90: Performance: 217.307 0.110 90: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_3.edr as double precision energy file 90: Reading energy frame 0 time 0.002 Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_3.edr as double precision energy file 90: Reading energy frame 0 time 0.002 Reading energy frame 1 time 0.012 Reading energy frame 2 time 0.022 Reading energy frame 3 time 0.032 Reading energy frame 4 time 0.042 Reading energy frame 5 time 0.052 Last energy frame read 5 time 0.052 90: [ OK ] RotationWorks/RotationTest.CheckEnergiesForcesAndTraj/3 (75 ms) 90: [ RUN ] RotationWorks/RotationTest.CheckEnergiesForcesAndTraj/4 90: Enforced rotation: Group 0 (rm) normalized rot. vector: 0.267261 0.534522 0.801784 90: 90: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_4_input.mdp]: 90: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 90: that with the Verlet scheme, nstlist has no effect on the accuracy of 90: your simulation. 90: 90: Rotation group 0 'system' has 4 atoms 90: Number of degrees of freedom in T-Coupling group rest is 9.00 90: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 90: 90: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_4_input.mdp]: 90: NVE simulation with an initial temperature of zero: will use a Verlet 90: buffer of 10%. Check your energy drift! 90: 90: Enforced rotation: group 0 has 4 reference positions. 90: Reading them from /build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/rotref.0.trr. 90: 90: There were 2 NOTEs 90: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_4.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 90: Can not increase nstlist because an NVE ensemble is used 90: Using 1 MPI thread 90: Using 2 OpenMP threads 90: 90: 90: NOTE: The number of threads is not equal to the number of (logical) cpus 90: and the -pin option is set to auto: will not pin threads to cpus. 90: This can lead to significant performance degradation. 90: Consider using -pin on (and -pinoffset in case you run multiple jobs). 90: starting mdrun 'Good gRace! Old Maple Actually Chews Slate' 90: 25 steps, 0.1 ps. 90: Setting the LD random seed to -2098198 90: 90: Generated 1 of the 1 non-bonded parameter combinations 90: 90: Excluding 1 bonded neighbours molecule type 'ArgonA' 90: 90: Excluding 1 bonded neighbours molecule type 'ArgonB' 90: 90: Excluding 1 bonded neighbours molecule type 'ArgonC' 90: 90: Excluding 1 bonded neighbours molecule type 'ArgonD' 90: 90: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon4.gro', all velocities are zero 90: 90: This run will generate roughly 0 Mb of data 90: 90: Writing final coordinates. 90: 90: Core t (s) Wall t (s) (%) 90: Time: 0.040 0.020 197.2 90: (ns/day) (hour/ns) 90: Performance: 220.518 0.109 90: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_4.edr as double precision energy file 90: Reading energy frame 0 time 0.002 Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_4.edr as double precision energy file 90: Reading energy frame 0 time 0.002 Reading energy frame 1 time 0.012 Reading energy frame 2 time 0.022 Reading energy frame 3 time 0.032 Reading energy frame 4 time 0.042 Reading energy frame 5 time 0.052 Last energy frame read 5 time 0.052 90: [ OK ] RotationWorks/RotationTest.CheckEnergiesForcesAndTraj/4 (73 ms) 90: [ RUN ] RotationWorks/RotationTest.CheckEnergiesForcesAndTraj/5 90: Enforced rotation: Group 0 (rm-pf) normalized rot. vector: 0.267261 0.534522 0.801784 90: 90: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_5_input.mdp]: 90: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 90: that with the Verlet scheme, nstlist has no effect on the accuracy of 90: your simulation. 90: 90: Rotation group 0 'system' has 4 atoms 90: Number of degrees of freedom in T-Coupling group rest is 9.00 90: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 90: 90: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_5_input.mdp]: 90: NVE simulation with an initial temperature of zero: will use a Verlet 90: buffer of 10%. Check your energy drift! 90: 90: Enforced rotation: group 0 has 4 reference positions. 90: Reading them from /build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/rotref.0.trr. 90: 90: There were 2 NOTEs 90: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_5.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 90: Can not increase nstlist because an NVE ensemble is used 90: Using 1 MPI thread 90: Using 2 OpenMP threads 90: 90: 90: NOTE: The number of threads is not equal to the number of (logical) cpus 90: and the -pin option is set to auto: will not pin threads to cpus. 90: This can lead to significant performance degradation. 90: Consider using -pin on (and -pinoffset in case you run multiple jobs). 90: starting mdrun 'Good gRace! Old Maple Actually Chews Slate' 90: 25 steps, 0.1 ps. 90: Setting the LD random seed to -8421442 90: 90: Generated 1 of the 1 non-bonded parameter combinations 90: 90: Excluding 1 bonded neighbours molecule type 'ArgonA' 90: 90: Excluding 1 bonded neighbours molecule type 'ArgonB' 90: 90: Excluding 1 bonded neighbours molecule type 'ArgonC' 90: 90: Excluding 1 bonded neighbours molecule type 'ArgonD' 90: 90: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon4.gro', all velocities are zero 90: 90: This run will generate roughly 0 Mb of data 90: 90: Writing final coordinates. 90: 90: Core t (s) Wall t (s) (%) 90: Time: 0.041 0.021 197.3 90: (ns/day) (hour/ns) 90: Performance: 218.638 0.110 90: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_5.edr as double precision energy file 90: Reading energy frame 0 time 0.002 Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_5.edr as double precision energy file 90: Reading energy frame 0 time 0.002 Reading energy frame 1 time 0.012 Reading energy frame 2 time 0.022 Reading energy frame 3 time 0.032 Reading energy frame 4 time 0.042 Reading energy frame 5 time 0.052 Last energy frame read 5 time 0.052 90: [ OK ] RotationWorks/RotationTest.CheckEnergiesForcesAndTraj/5 (74 ms) 90: [ RUN ] RotationWorks/RotationTest.CheckEnergiesForcesAndTraj/6 90: Enforced rotation: Group 0 (rm2) normalized rot. vector: 0.267261 0.534522 0.801784 90: 90: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_6_input.mdp]: 90: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 90: that with the Verlet scheme, nstlist has no effect on the accuracy of 90: your simulation. 90: 90: Rotation group 0 'system' has 4 atoms 90: Number of degrees of freedom in T-Coupling group rest is 9.00 90: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 90: 90: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_6_input.mdp]: 90: NVE simulation with an initial temperature of zero: will use a Verlet 90: buffer of 10%. Check your energy drift! 90: 90: Enforced rotation: group 0 has 4 reference positions. 90: Reading them from /build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/rotref.0.trr. 90: 90: There were 2 NOTEs 90: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_6.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 90: Can not increase nstlist because an NVE ensemble is used 90: Using 1 MPI thread 90: Using 2 OpenMP threads 90: 90: 90: NOTE: The number of threads is not equal to the number of (logical) cpus 90: and the -pin option is set to auto: will not pin threads to cpus. 90: This can lead to significant performance degradation. 90: Consider using -pin on (and -pinoffset in case you run multiple jobs). 90: starting mdrun 'Good gRace! Old Maple Actually Chews Slate' 90: 25 steps, 0.1 ps. 90: Setting the LD random seed to 2141056828 90: 90: Generated 1 of the 1 non-bonded parameter combinations 90: 90: Excluding 1 bonded neighbours molecule type 'ArgonA' 90: 90: Excluding 1 bonded neighbours molecule type 'ArgonB' 90: 90: Excluding 1 bonded neighbours molecule type 'ArgonC' 90: 90: Excluding 1 bonded neighbours molecule type 'ArgonD' 90: 90: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon4.gro', all velocities are zero 90: 90: This run will generate roughly 0 Mb of data 90: 90: Writing final coordinates. 90: 90: Core t (s) Wall t (s) (%) 90: Time: 0.041 0.021 197.4 90: (ns/day) (hour/ns) 90: Performance: 218.554 0.110 90: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_6.edr as double precision energy file 90: Reading energy frame 0 time 0.002 Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_6.edr as double precision energy file 90: Reading energy frame 0 time 0.002 Reading energy frame 1 time 0.012 Reading energy frame 2 time 0.022 Reading energy frame 3 time 0.032 Reading energy frame 4 time 0.042 Reading energy frame 5 time 0.052 Last energy frame read 5 time 0.052 90: [ OK ] RotationWorks/RotationTest.CheckEnergiesForcesAndTraj/6 (75 ms) 90: [ RUN ] RotationWorks/RotationTest.CheckEnergiesForcesAndTraj/7 90: Enforced rotation: Group 0 (rm2-pf) normalized rot. vector: 0.267261 0.534522 0.801784 90: 90: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_7_input.mdp]: 90: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 90: that with the Verlet scheme, nstlist has no effect on the accuracy of 90: your simulation. 90: 90: Rotation group 0 'system' has 4 atoms 90: Number of degrees of freedom in T-Coupling group rest is 9.00 90: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 90: 90: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_7_input.mdp]: 90: NVE simulation with an initial temperature of zero: will use a Verlet 90: buffer of 10%. Check your energy drift! 90: 90: Enforced rotation: group 0 has 4 reference positions. 90: Reading them from /build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/rotref.0.trr. 90: 90: There were 2 NOTEs 90: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_7.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 90: Can not increase nstlist because an NVE ensemble is used 90: Using 1 MPI thread 90: Using 2 OpenMP threads 90: 90: 90: NOTE: The number of threads is not equal to the number of (logical) cpus 90: and the -pin option is set to auto: will not pin threads to cpus. 90: This can lead to significant performance degradation. 90: Consider using -pin on (and -pinoffset in case you run multiple jobs). 90: starting mdrun 'Good gRace! Old Maple Actually Chews Slate' 90: 25 steps, 0.1 ps. 90: Setting the LD random seed to -271386 90: 90: Generated 1 of the 1 non-bonded parameter combinations 90: 90: Excluding 1 bonded neighbours molecule type 'ArgonA' 90: 90: Excluding 1 bonded neighbours molecule type 'ArgonB' 90: 90: Excluding 1 bonded neighbours molecule type 'ArgonC' 90: 90: Excluding 1 bonded neighbours molecule type 'ArgonD' 90: 90: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon4.gro', all velocities are zero 90: 90: This run will generate roughly 0 Mb of data 90: 90: Writing final coordinates. 90: 90: Core t (s) Wall t (s) (%) 90: Time: 0.041 0.021 197.5 90: (ns/day) (hour/ns) 90: Performance: 216.909 0.111 90: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_7.edr as double precision energy file 90: Reading energy frame 0 time 0.002 Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_7.edr as double precision energy file 90: Reading energy frame 0 time 0.002 Reading energy frame 1 time 0.012 Reading energy frame 2 time 0.022 Reading energy frame 3 time 0.032 Reading energy frame 4 time 0.042 Reading energy frame 5 time 0.052 Last energy frame read 5 time 0.052 90: [ OK ] RotationWorks/RotationTest.CheckEnergiesForcesAndTraj/7 (74 ms) 90: [ RUN ] RotationWorks/RotationTest.CheckEnergiesForcesAndTraj/8 90: Enforced rotation: Group 0 (flex) normalized rot. vector: 0.267261 0.534522 0.801784 90: 90: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_8_input.mdp]: 90: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 90: that with the Verlet scheme, nstlist has no effect on the accuracy of 90: your simulation. 90: 90: Rotation group 0 'system' has 4 atoms 90: Number of degrees of freedom in T-Coupling group rest is 9.00 90: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 90: 90: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_8_input.mdp]: 90: NVE simulation with an initial temperature of zero: will use a Verlet 90: buffer of 10%. Check your energy drift! 90: 90: Enforced rotation: group 0 has 4 reference positions. 90: Reading them from /build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/rotref.0.trr. 90: 90: There were 2 NOTEs 90: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_8.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 90: Can not increase nstlist because an NVE ensemble is used 90: Using 1 MPI thread 90: Using 2 OpenMP threads 90: 90: 90: NOTE: The number of threads is not equal to the number of (logical) cpus 90: and the -pin option is set to auto: will not pin threads to cpus. 90: This can lead to significant performance degradation. 90: Consider using -pin on (and -pinoffset in case you run multiple jobs). 90: starting mdrun 'Good gRace! Old Maple Actually Chews Slate' 90: 25 steps, 0.1 ps. 90: Setting the LD random seed to -277610645 90: 90: Generated 1 of the 1 non-bonded parameter combinations 90: 90: Excluding 1 bonded neighbours molecule type 'ArgonA' 90: 90: Excluding 1 bonded neighbours molecule type 'ArgonB' 90: 90: Excluding 1 bonded neighbours molecule type 'ArgonC' 90: 90: Excluding 1 bonded neighbours molecule type 'ArgonD' 90: 90: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon4.gro', all velocities are zero 90: 90: This run will generate roughly 0 Mb of data 90: 90: Writing final coordinates. 90: 90: Core t (s) Wall t (s) (%) 90: Time: 0.065 0.033 198.3 90: (ns/day) (hour/ns) 90: Performance: 137.546 0.174 90: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_8.edr as double precision energy file 90: Reading energy frame 0 time 0.002 Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_8.edr as double precision energy file 90: Reading energy frame 0 time 0.002 Reading energy frame 1 time 0.012 Reading energy frame 2 time 0.022 Reading energy frame 3 time 0.032 Reading energy frame 4 time 0.042 Reading energy frame 5 time 0.052 Last energy frame read 5 time 0.052 90: [ OK ] RotationWorks/RotationTest.CheckEnergiesForcesAndTraj/8 (90 ms) 90: [ RUN ] RotationWorks/RotationTest.CheckEnergiesForcesAndTraj/9 90: Enforced rotation: Group 0 (flex-t) normalized rot. vector: 0.267261 0.534522 0.801784 90: 90: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_9_input.mdp]: 90: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 90: that with the Verlet scheme, nstlist has no effect on the accuracy of 90: your simulation. 90: 90: Rotation group 0 'system' has 4 atoms 90: Number of degrees of freedom in T-Coupling group rest is 9.00 90: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 90: 90: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_9_input.mdp]: 90: NVE simulation with an initial temperature of zero: will use a Verlet 90: buffer of 10%. Check your energy drift! 90: 90: Enforced rotation: group 0 has 4 reference positions. 90: Reading them from /build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/rotref.0.trr. 90: 90: There were 2 NOTEs 90: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_9.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 90: Can not increase nstlist because an NVE ensemble is used 90: Using 1 MPI thread 90: Using 2 OpenMP threads 90: 90: 90: NOTE: The number of threads is not equal to the number of (logical) cpus 90: and the -pin option is set to auto: will not pin threads to cpus. 90: This can lead to significant performance degradation. 90: Consider using -pin on (and -pinoffset in case you run multiple jobs). 90: starting mdrun 'Good gRace! Old Maple Actually Chews Slate' 90: 25 steps, 0.1 ps. 90: Setting the LD random seed to -1073873473 90: 90: Generated 1 of the 1 non-bonded parameter combinations 90: 90: Excluding 1 bonded neighbours molecule type 'ArgonA' 90: 90: Excluding 1 bonded neighbours molecule type 'ArgonB' 90: 90: Excluding 1 bonded neighbours molecule type 'ArgonC' 90: 90: Excluding 1 bonded neighbours molecule type 'ArgonD' 90: 90: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon4.gro', all velocities are zero 90: 90: This run will generate roughly 0 Mb of data 90: 90: Writing final coordinates. 90: 90: Core t (s) Wall t (s) (%) 90: Time: 0.065 0.033 198.3 90: (ns/day) (hour/ns) 90: Performance: 138.049 0.174 90: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_9.edr as double precision energy file 90: Reading energy frame 0 time 0.002 Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_9.edr as double precision energy file 90: Reading energy frame 0 time 0.002 Reading energy frame 1 time 0.012 Reading energy frame 2 time 0.022 Reading energy frame 3 time 0.032 Reading energy frame 4 time 0.042 Reading energy frame 5 time 0.052 Last energy frame read 5 time 0.052 90: [ OK ] RotationWorks/RotationTest.CheckEnergiesForcesAndTraj/9 (90 ms) 90: [ RUN ] RotationWorks/RotationTest.CheckEnergiesForcesAndTraj/10 90: Enforced rotation: Group 0 (flex2) normalized rot. vector: 0.267261 0.534522 0.801784 90: 90: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_10_input.mdp]: 90: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 90: that with the Verlet scheme, nstlist has no effect on the accuracy of 90: your simulation. 90: 90: Rotation group 0 'system' has 4 atoms 90: Number of degrees of freedom in T-Coupling group rest is 9.00 90: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 90: 90: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_10_input.mdp]: 90: NVE simulation with an initial temperature of zero: will use a Verlet 90: buffer of 10%. Check your energy drift! 90: 90: Enforced rotation: group 0 has 4 reference positions. 90: Reading them from /build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/rotref.0.trr. 90: 90: There were 2 NOTEs 90: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_10.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 90: Can not increase nstlist because an NVE ensemble is used 90: Using 1 MPI thread 90: Using 2 OpenMP threads 90: 90: 90: NOTE: The number of threads is not equal to the number of (logical) cpus 90: and the -pin option is set to auto: will not pin threads to cpus. 90: This can lead to significant performance degradation. 90: Consider using -pin on (and -pinoffset in case you run multiple jobs). 90: starting mdrun 'Good gRace! Old Maple Actually Chews Slate' 90: 25 steps, 0.1 ps. 90: Setting the LD random seed to -805389089 90: 90: Generated 1 of the 1 non-bonded parameter combinations 90: 90: Excluding 1 bonded neighbours molecule type 'ArgonA' 90: 90: Excluding 1 bonded neighbours molecule type 'ArgonB' 90: 90: Excluding 1 bonded neighbours molecule type 'ArgonC' 90: 90: Excluding 1 bonded neighbours molecule type 'ArgonD' 90: 90: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon4.gro', all velocities are zero 90: 90: This run will generate roughly 0 Mb of data 90: 90: Writing final coordinates. 90: 90: Core t (s) Wall t (s) (%) 90: Time: 0.062 0.031 198.3 90: (ns/day) (hour/ns) 90: Performance: 142.778 0.168 90: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_10.edr as double precision energy file 90: Reading energy frame 0 time 0.002 Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_10.edr as double precision energy file 90: Reading energy frame 0 time 0.002 Reading energy frame 1 time 0.012 Reading energy frame 2 time 0.022 Reading energy frame 3 time 0.032 Reading energy frame 4 time 0.042 Reading energy frame 5 time 0.052 Last energy frame read 5 time 0.052 90: [ OK ] RotationWorks/RotationTest.CheckEnergiesForcesAndTraj/10 (88 ms) 90: [ RUN ] RotationWorks/RotationTest.CheckEnergiesForcesAndTraj/11 90: Enforced rotation: Group 0 (flex2-t) normalized rot. vector: 0.267261 0.534522 0.801784 90: 90: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_11_input.mdp]: 90: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 90: that with the Verlet scheme, nstlist has no effect on the accuracy of 90: your simulation. 90: 90: Rotation group 0 'system' has 4 atoms 90: Number of degrees of freedom in T-Coupling group rest is 9.00 90: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 90: 90: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_11_input.mdp]: 90: NVE simulation with an initial temperature of zero: will use a Verlet 90: buffer of 10%. Check your energy drift! 90: 90: Enforced rotation: group 0 has 4 reference positions. 90: Reading them from /build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/rotref.0.trr. 90: 90: There were 2 NOTEs 90: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_11.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 90: Can not increase nstlist because an NVE ensemble is used 90: Using 1 MPI thread 90: Using 2 OpenMP threads 90: 90: 90: NOTE: The number of threads is not equal to the number of (logical) cpus 90: and the -pin option is set to auto: will not pin threads to cpus. 90: This can lead to significant performance degradation. 90: Consider using -pin on (and -pinoffset in case you run multiple jobs). 90: starting mdrun 'Good gRace! Old Maple Actually Chews Slate' 90: 25 steps, 0.1 ps. 90: Setting the LD random seed to -1208503841 90: 90: Generated 1 of the 1 non-bonded parameter combinations 90: 90: Excluding 1 bonded neighbours molecule type 'ArgonA' 90: 90: Excluding 1 bonded neighbours molecule type 'ArgonB' 90: 90: Excluding 1 bonded neighbours molecule type 'ArgonC' 90: 90: Excluding 1 bonded neighbours molecule type 'ArgonD' 90: 90: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon4.gro', all velocities are zero 90: 90: This run will generate roughly 0 Mb of data 90: 90: Writing final coordinates. 90: 90: Core t (s) Wall t (s) (%) 90: Time: 0.065 0.033 198.4 90: (ns/day) (hour/ns) 90: Performance: 137.715 0.174 90: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_11.edr as double precision energy file 90: Reading energy frame 0 time 0.002 Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_11.edr as double precision energy file 90: Reading energy frame 0 time 0.002 Reading energy frame 1 time 0.012 Reading energy frame 2 time 0.022 Reading energy frame 3 time 0.032 Reading energy frame 4 time 0.042 Reading energy frame 5 time 0.052 Last energy frame read 5 time 0.052 90: [ OK ] RotationWorks/RotationTest.CheckEnergiesForcesAndTraj/11 (91 ms) 90: [----------] 12 tests from RotationWorks/RotationTest (975 ms total) 90: 90: [----------] Global test environment tear-down 90: [==========] 12 tests from 1 test suite ran. (1022 ms total) 90: [ PASSED ] 12 tests. 90/92 Test #90: MdrunRotationTests ........................ Passed 1.10 sec test 91 Start 91: MdrunSimulatorComparison 91: Test command: /build/reproducible-path/gromacs-2025.1/build/basic-dp/bin/mdrun-simulator-comparison-test "-ntomp" "2" "--gtest_output=xml:/build/reproducible-path/gromacs-2025.1/build/basic-dp/Testing/Temporary/MdrunSimulatorComparison.xml" 91: Working Directory: /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests 91: Test timeout computed to be: 600 91: [==========] Running 94 tests from 4 test suites. 91: [----------] Global test environment set-up. 91: [----------] 60 tests from SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest 91: [ RUN ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/0 91: [ OK ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/0 (0 ms) 91: [ RUN ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/1 91: 91: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_1_input.mdp]: 91: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 91: that with the Verlet scheme, nstlist has no effect on the accuracy of 91: your simulation. 91: 91: 91: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_1_input.mdp]: 91: Setting nstcalcenergy (100) equal to nstenergy (4) 91: 91: Number of degrees of freedom in T-Coupling group System is 33.00 91: 91: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_1_input.mdp]: 91: NVE simulation: will use the initial temperature of 68.810 K for 91: determining the Verlet buffer size 91: 91: 91: There were 3 NOTEs 91: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_1_sim.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 91: Can not increase nstlist because an NVE ensemble is used 91: Using 1 MPI thread 91: Using 2 OpenMP threads 91: 91: 91: NOTE: The number of threads is not equal to the number of (logical) cpus 91: and the -pin option is set to auto: will not pin threads to cpus. 91: This can lead to significant performance degradation. 91: Consider using -pin on (and -pinoffset in case you run multiple jobs). 91: starting mdrun 'Argon' 91: 16 steps, 0.0 ps. 91: Generated 1 of the 1 non-bonded parameter combinations 91: 91: Excluding 1 bonded neighbours molecule type 'Argon' 91: 91: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 91: 91: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 91: 91: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 91: 91: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 91: 91: Note that mdrun will redetermine rlist based on the actual pair-list setup 91: 91: This run will generate roughly 0 Mb of data 91: 91: Writing final coordinates. 91: 91: Core t (s) Wall t (s) (%) 91: Time: 0.057 0.029 199.0 91: (ns/day) (hour/ns) 91: Performance: 50.995 0.471 91: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_1_sim.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 91: Can not increase nstlist because an NVE ensemble is used 91: Using 1 MPI thread 91: Using 2 OpenMP threads 91: 91: 91: NOTE: The number of threads is not equal to the number of (logical) cpus 91: and the -pin option is set to auto: will not pin threads to cpus. 91: This can lead to significant performance degradation. 91: Consider using -pin on (and -pinoffset in case you run multiple jobs). 91: starting mdrun 'Argon' 91: 16 steps, 0.0 ps. 91: 91: Writing final coordinates. 91: 91: Core t (s) Wall t (s) (%) 91: Time: 0.037 0.019 196.9 91: (ns/day) (hour/ns) 91: Performance: 79.070 0.304 91: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_1_sim1.edr as double precision energy file 91: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_1_sim2.edr as double precision energy file 91: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 trr version: GMX_trn_file (double precision) 91: 91: 91: [ OK ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/1 (105 ms) 91: [ RUN ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/2 91: 91: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_2_input.mdp]: 91: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 91: that with the Verlet scheme, nstlist has no effect on the accuracy of 91: your simulation. 91: 91: 91: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_2_input.mdp]: 91: Setting nstcalcenergy (100) equal to nstenergy (4) 91: 91: 91: WARNING 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_2_input.mdp]: 91: The Berendsen barostat does not generate any strictly correct ensemble, 91: and should not be used for new production simulations (in our opinion). 91: We recommend using the C-rescale barostat instead. 91: 91: Number of degrees of freedom in T-Coupling group System is 33.00 91: 91: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_2_input.mdp]: 91: NVE simulation: will use the initial temperature of 68.810 K for 91: determining the Verlet buffer size 91: 91: 91: There were 3 NOTEs 91: 91: There was 1 WARNING 91: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_2_sim.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 91: Can not increase nstlist because an NVE ensemble is used 91: Using 1 MPI thread 91: Using 2 OpenMP threads 91: 91: 91: NOTE: The number of threads is not equal to the number of (logical) cpus 91: and the -pin option is set to auto: will not pin threads to cpus. 91: This can lead to significant performance degradation. 91: Consider using -pin on (and -pinoffset in case you run multiple jobs). 91: starting mdrun 'Argon' 91: 16 steps, 0.0 ps. 91: Generated 1 of the 1 non-bonded parameter combinations 91: 91: Excluding 1 bonded neighbours molecule type 'Argon' 91: 91: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 91: 91: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 91: 91: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 91: 91: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 91: 91: Note that mdrun will redetermine rlist based on the actual pair-list setup 91: 91: This run will generate roughly 0 Mb of data 91: 91: Writing final coordinates. 91: 91: Core t (s) Wall t (s) (%) 91: Time: 0.043 0.021 198.6 91: (ns/day) (hour/ns) 91: Performance: 68.440 0.351 91: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_2_sim.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 91: Can not increase nstlist because an NVE ensemble is used 91: Using 1 MPI thread 91: Using 2 OpenMP threads 91: 91: 91: NOTE: The number of threads is not equal to the number of (logical) cpus 91: and the -pin option is set to auto: will not pin threads to cpus. 91: This can lead to significant performance degradation. 91: Consider using -pin on (and -pinoffset in case you run multiple jobs). 91: starting mdrun 'Argon' 91: 16 steps, 0.0 ps. 91: 91: Writing final coordinates. 91: 91: Core t (s) Wall t (s) (%) 91: Time: 0.037 0.019 197.3 91: (ns/day) (hour/ns) 91: Performance: 78.323 0.306 91: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_2_sim1.edr as double precision energy file 91: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_2_sim2.edr as double precision energy file 91: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 91: 91: [ OK ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/2 (95 ms) 91: [ RUN ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/3 91: [ OK ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/3 (0 ms) 91: [ RUN ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/4 91: [ OK ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/4 (0 ms) 91: [ RUN ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/5 91: [ OK ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/5 (0 ms) 91: [ RUN ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/6 91: 91: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_6_input.mdp]: 91: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 91: that with the Verlet scheme, nstlist has no effect on the accuracy of 91: your simulation. 91: 91: 91: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_6_input.mdp]: 91: Setting nstcalcenergy (100) equal to nstenergy (4) 91: 91: Number of degrees of freedom in T-Coupling group System is 33.00 91: 91: There were 2 NOTEs 91: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_6_sim.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 91: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 91: 91: Using 1 MPI thread 91: Using 2 OpenMP threads 91: 91: 91: NOTE: The number of threads is not equal to the number of (logical) cpus 91: and the -pin option is set to auto: will not pin threads to cpus. 91: This can lead to significant performance degradation. 91: Consider using -pin on (and -pinoffset in case you run multiple jobs). 91: starting mdrun 'Argon' 91: 16 steps, 0.0 ps. 91: Generated 1 of the 1 non-bonded parameter combinations 91: 91: Excluding 1 bonded neighbours molecule type 'Argon' 91: 91: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 91: 91: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 91: 91: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 91: 91: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 91: 91: Note that mdrun will redetermine rlist based on the actual pair-list setup 91: 91: This run will generate roughly 0 Mb of data 91: 91: Writing final coordinates. 91: 91: Core t (s) Wall t (s) (%) 91: Time: 0.042 0.021 198.0 91: (ns/day) (hour/ns) 91: Performance: 68.873 0.348 91: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_6_sim.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 91: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 91: 91: Using 1 MPI thread 91: Using 2 OpenMP threads 91: 91: 91: NOTE: The number of threads is not equal to the number of (logical) cpus 91: and the -pin option is set to auto: will not pin threads to cpus. 91: This can lead to significant performance degradation. 91: Consider using -pin on (and -pinoffset in case you run multiple jobs). 91: starting mdrun 'Argon' 91: 16 steps, 0.0 ps. 91: 91: Writing final coordinates. 91: 91: Core t (s) Wall t (s) (%) 91: Time: 0.048 0.024 197.8 91: (ns/day) (hour/ns) 91: Performance: 60.246 0.398 91: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_6_sim1.edr as double precision energy file 91: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_6_sim2.edr as double precision energy file 91: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 91: 91: [ OK ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/6 (105 ms) 91: [ RUN ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/7 91: 91: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_7_input.mdp]: 91: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 91: that with the Verlet scheme, nstlist has no effect on the accuracy of 91: your simulation. 91: 91: 91: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_7_input.mdp]: 91: Setting nstcalcenergy (100) equal to nstenergy (4) 91: 91: 91: WARNING 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_7_input.mdp]: 91: The Berendsen barostat does not generate any strictly correct ensemble, 91: and should not be used for new production simulations (in our opinion). 91: We recommend using the C-rescale barostat instead. 91: 91: Number of degrees of freedom in T-Coupling group System is 33.00 91: 91: There were 2 NOTEs 91: 91: There was 1 WARNING 91: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_7_sim.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 91: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 91: 91: Using 1 MPI thread 91: Using 2 OpenMP threads 91: 91: 91: NOTE: The number of threads is not equal to the number of (logical) cpus 91: and the -pin option is set to auto: will not pin threads to cpus. 91: This can lead to significant performance degradation. 91: Consider using -pin on (and -pinoffset in case you run multiple jobs). 91: starting mdrun 'Argon' 91: 16 steps, 0.0 ps. 91: Generated 1 of the 1 non-bonded parameter combinations 91: 91: Excluding 1 bonded neighbours molecule type 'Argon' 91: 91: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 91: 91: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 91: 91: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 91: 91: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 91: 91: Note that mdrun will redetermine rlist based on the actual pair-list setup 91: 91: This run will generate roughly 0 Mb of data 91: 91: Writing final coordinates. 91: 91: Core t (s) Wall t (s) (%) 91: Time: 0.045 0.023 197.2 91: (ns/day) (hour/ns) 91: Performance: 64.148 0.374 91: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_7_sim.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 91: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 91: 91: Using 1 MPI thread 91: Using 2 OpenMP threads 91: 91: 91: NOTE: The number of threads is not equal to the number of (logical) cpus 91: and the -pin option is set to auto: will not pin threads to cpus. 91: This can lead to significant performance degradation. 91: Consider using -pin on (and -pinoffset in case you run multiple jobs). 91: starting mdrun 'Argon' 91: 16 steps, 0.0 ps. 91: 91: Writing final coordinates. 91: 91: Core t (s) Wall t (s) (%) 91: Time: 0.036 0.018 197.2 91: (ns/day) (hour/ns) 91: Performance: 79.995 0.300 91: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_7_sim1.edr as double precision energy file 91: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_7_sim2.edr as double precision energy file 91: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 91: 91: [ OK ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/7 (107 ms) 91: [ RUN ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/8 91: 91: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_8_input.mdp]: 91: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 91: that with the Verlet scheme, nstlist has no effect on the accuracy of 91: your simulation. 91: 91: 91: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_8_input.mdp]: 91: Setting nstcalcenergy (100) equal to nstenergy (4) 91: 91: Number of degrees of freedom in T-Coupling group System is 33.00 91: 91: There were 2 NOTEs 91: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_8_sim.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 91: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 91: 91: Using 1 MPI thread 91: Using 2 OpenMP threads 91: 91: 91: NOTE: The number of threads is not equal to the number of (logical) cpus 91: and the -pin option is set to auto: will not pin threads to cpus. 91: This can lead to significant performance degradation. 91: Consider using -pin on (and -pinoffset in case you run multiple jobs). 91: starting mdrun 'Argon' 91: 16 steps, 0.0 ps. 91: Generated 1 of the 1 non-bonded parameter combinations 91: 91: Excluding 1 bonded neighbours molecule type 'Argon' 91: 91: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 91: 91: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 91: 91: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 91: 91: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 91: 91: Note that mdrun will redetermine rlist based on the actual pair-list setup 91: 91: This run will generate roughly 0 Mb of data 91: 91: Writing final coordinates. 91: 91: Core t (s) Wall t (s) (%) 91: Time: 0.043 0.022 197.9 91: (ns/day) (hour/ns) 91: Performance: 67.690 0.355 91: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_8_sim.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 91: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 91: 91: Using 1 MPI thread 91: Using 2 OpenMP threads 91: 91: 91: NOTE: The number of threads is not equal to the number of (logical) cpus 91: and the -pin option is set to auto: will not pin threads to cpus. 91: This can lead to significant performance degradation. 91: Consider using -pin on (and -pinoffset in case you run multiple jobs). 91: starting mdrun 'Argon' 91: 16 steps, 0.0 ps. 91: 91: Writing final coordinates. 91: 91: Core t (s) Wall t (s) (%) 91: Time: 0.038 0.019 197.3 91: (ns/day) (hour/ns) 91: Performance: 76.289 0.315 91: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_8_sim1.edr as double precision energy file 91: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_8_sim2.edr as double precision energy file 91: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 91: 91: [ OK ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/8 (100 ms) 91: [ RUN ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/9 91: [ OK ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/9 (0 ms) 91: [ RUN ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/10 91: [ OK ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/10 (0 ms) 91: [ RUN ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/11 91: 91: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_11_input.mdp]: 91: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 91: that with the Verlet scheme, nstlist has no effect on the accuracy of 91: your simulation. 91: 91: 91: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_11_input.mdp]: 91: Setting nstcalcenergy (100) equal to nstenergy (4) 91: 91: 91: WARNING 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_11_input.mdp]: 91: The Berendsen thermostat does not generate the correct kinetic energy 91: distribution, and should not be used for new production simulations (in 91: our opinion). We would recommend the V-rescale thermostat. 91: 91: Number of degrees of freedom in T-Coupling group System is 33.00 91: 91: There were 2 NOTEs 91: 91: There was 1 WARNING 91: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_11_sim.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 91: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 91: 91: Using 1 MPI thread 91: Using 2 OpenMP threads 91: 91: 91: NOTE: The number of threads is not equal to the number of (logical) cpus 91: and the -pin option is set to auto: will not pin threads to cpus. 91: This can lead to significant performance degradation. 91: Consider using -pin on (and -pinoffset in case you run multiple jobs). 91: starting mdrun 'Argon' 91: 16 steps, 0.0 ps. 91: Generated 1 of the 1 non-bonded parameter combinations 91: 91: Excluding 1 bonded neighbours molecule type 'Argon' 91: 91: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 91: 91: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 91: 91: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 91: 91: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 91: 91: Note that mdrun will redetermine rlist based on the actual pair-list setup 91: 91: This run will generate roughly 0 Mb of data 91: 91: Writing final coordinates. 91: 91: Core t (s) Wall t (s) (%) 91: Time: 0.041 0.021 198.0 91: (ns/day) (hour/ns) 91: Performance: 70.133 0.342 91: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_11_sim.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 91: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 91: 91: Using 1 MPI thread 91: Using 2 OpenMP threads 91: 91: 91: NOTE: The number of threads is not equal to the number of (logical) cpus 91: and the -pin option is set to auto: will not pin threads to cpus. 91: This can lead to significant performance degradation. 91: Consider using -pin on (and -pinoffset in case you run multiple jobs). 91: starting mdrun 'Argon' 91: 16 steps, 0.0 ps. 91: 91: Writing final coordinates. 91: 91: Core t (s) Wall t (s) (%) 91: Time: 0.037 0.019 197.5 91: (ns/day) (hour/ns) 91: Performance: 77.497 0.310 91: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_11_sim1.edr as double precision energy file 91: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_11_sim2.edr as double precision energy file 91: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 91: 91: [ OK ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/11 (99 ms) 91: [ RUN ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/12 91: 91: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_12_input.mdp]: 91: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 91: that with the Verlet scheme, nstlist has no effect on the accuracy of 91: your simulation. 91: 91: 91: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_12_input.mdp]: 91: Setting nstcalcenergy (100) equal to nstenergy (4) 91: 91: 91: WARNING 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_12_input.mdp]: 91: The Berendsen thermostat does not generate the correct kinetic energy 91: distribution, and should not be used for new production simulations (in 91: our opinion). We would recommend the V-rescale thermostat. 91: 91: 91: WARNING 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_12_input.mdp]: 91: The Berendsen barostat does not generate any strictly correct ensemble, 91: and should not be used for new production simulations (in our opinion). 91: We recommend using the C-rescale barostat instead. 91: 91: Number of degrees of freedom in T-Coupling group System is 33.00 91: 91: There were 2 NOTEs 91: 91: There were 2 WARNINGs 91: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_12_sim.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 91: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 91: 91: Using 1 MPI thread 91: Using 2 OpenMP threads 91: 91: 91: NOTE: The number of threads is not equal to the number of (logical) cpus 91: and the -pin option is set to auto: will not pin threads to cpus. 91: This can lead to significant performance degradation. 91: Consider using -pin on (and -pinoffset in case you run multiple jobs). 91: starting mdrun 'Argon' 91: 16 steps, 0.0 ps. 91: Generated 1 of the 1 non-bonded parameter combinations 91: 91: Excluding 1 bonded neighbours molecule type 'Argon' 91: 91: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 91: 91: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 91: 91: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 91: 91: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 91: 91: Note that mdrun will redetermine rlist based on the actual pair-list setup 91: 91: This run will generate roughly 0 Mb of data 91: 91: Writing final coordinates. 91: 91: Core t (s) Wall t (s) (%) 91: Time: 0.043 0.022 197.9 91: (ns/day) (hour/ns) 91: Performance: 68.051 0.353 91: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_12_sim.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 91: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 91: 91: Using 1 MPI thread 91: Using 2 OpenMP threads 91: 91: 91: NOTE: The number of threads is not equal to the number of (logical) cpus 91: and the -pin option is set to auto: will not pin threads to cpus. 91: This can lead to significant performance degradation. 91: Consider using -pin on (and -pinoffset in case you run multiple jobs). 91: starting mdrun 'Argon' 91: 16 steps, 0.0 ps. 91: 91: Writing final coordinates. 91: 91: Core t (s) Wall t (s) (%) 91: Time: 0.038 0.019 197.4 91: (ns/day) (hour/ns) 91: Performance: 76.836 0.312 91: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_12_sim1.edr as double precision energy file 91: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_12_sim2.edr as double precision energy file 91: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 91: 91: [ OK ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/12 (101 ms) 91: [ RUN ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/13 91: 91: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_13_input.mdp]: 91: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 91: that with the Verlet scheme, nstlist has no effect on the accuracy of 91: your simulation. 91: 91: 91: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_13_input.mdp]: 91: Setting nstcalcenergy (100) equal to nstenergy (4) 91: 91: 91: WARNING 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_13_input.mdp]: 91: The Berendsen thermostat does not generate the correct kinetic energy 91: distribution, and should not be used for new production simulations (in 91: our opinion). We would recommend the V-rescale thermostat. 91: 91: Number of degrees of freedom in T-Coupling group System is 33.00 91: 91: There were 2 NOTEs 91: 91: There was 1 WARNING 91: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_13_sim.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 91: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 91: 91: Using 1 MPI thread 91: Using 2 OpenMP threads 91: 91: 91: NOTE: The number of threads is not equal to the number of (logical) cpus 91: and the -pin option is set to auto: will not pin threads to cpus. 91: This can lead to significant performance degradation. 91: Consider using -pin on (and -pinoffset in case you run multiple jobs). 91: starting mdrun 'Argon' 91: 16 steps, 0.0 ps. 91: Generated 1 of the 1 non-bonded parameter combinations 91: 91: Excluding 1 bonded neighbours molecule type 'Argon' 91: 91: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 91: 91: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 91: 91: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 91: 91: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 91: 91: Note that mdrun will redetermine rlist based on the actual pair-list setup 91: 91: This run will generate roughly 0 Mb of data 91: 91: Writing final coordinates. 91: 91: Core t (s) Wall t (s) (%) 91: Time: 0.043 0.022 197.9 91: (ns/day) (hour/ns) 91: Performance: 68.177 0.352 91: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_13_sim.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 91: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 91: 91: Using 1 MPI thread 91: Using 2 OpenMP threads 91: 91: 91: NOTE: The number of threads is not equal to the number of (logical) cpus 91: and the -pin option is set to auto: will not pin threads to cpus. 91: This can lead to significant performance degradation. 91: Consider using -pin on (and -pinoffset in case you run multiple jobs). 91: starting mdrun 'Argon' 91: 16 steps, 0.0 ps. 91: 91: Writing final coordinates. 91: 91: Core t (s) Wall t (s) (%) 91: Time: 0.038 0.019 197.3 91: (ns/day) (hour/ns) 91: Performance: 76.804 0.312 91: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_13_sim1.edr as double precision energy file 91: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_13_sim2.edr as double precision energy file 91: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 91: 91: [ OK ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/13 (102 ms) 91: [ RUN ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/14 91: [ OK ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/14 (0 ms) 91: [ RUN ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/15 91: 91: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_15_input.mdp]: 91: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 91: that with the Verlet scheme, nstlist has no effect on the accuracy of 91: your simulation. 91: 91: 91: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_15_input.mdp]: 91: Setting nstcalcenergy (100) equal to nstenergy (4) 91: 91: 91: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_15_input.mdp]: 91: MTTK coupling is deprecated and will soon be removed 91: 91: Number of degrees of freedom in T-Coupling group System is 33.00 91: 91: There were 3 NOTEs 91: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_15_sim.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 91: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 91: 91: Using 1 MPI thread 91: Using 2 OpenMP threads 91: 91: 91: NOTE: The number of threads is not equal to the number of (logical) cpus 91: and the -pin option is set to auto: will not pin threads to cpus. 91: This can lead to significant performance degradation. 91: Consider using -pin on (and -pinoffset in case you run multiple jobs). 91: starting mdrun 'Argon' 91: 16 steps, 0.0 ps. 91: Generated 1 of the 1 non-bonded parameter combinations 91: 91: Excluding 1 bonded neighbours molecule type 'Argon' 91: 91: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 91: 91: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 91: 91: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 91: 91: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 91: 91: Note that mdrun will redetermine rlist based on the actual pair-list setup 91: 91: This run will generate roughly 0 Mb of data 91: 91: Writing final coordinates. 91: 91: Core t (s) Wall t (s) (%) 91: Time: 0.055 0.028 197.8 91: (ns/day) (hour/ns) 91: Performance: 52.542 0.457 91: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_15_sim.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 91: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 91: 91: Using 1 MPI thread 91: Using 2 OpenMP threads 91: 91: 91: NOTE: The number of threads is not equal to the number of (logical) cpus 91: and the -pin option is set to auto: will not pin threads to cpus. 91: This can lead to significant performance degradation. 91: Consider using -pin on (and -pinoffset in case you run multiple jobs). 91: starting mdrun 'Argon' 91: 16 steps, 0.0 ps. 91: 91: Writing final coordinates. 91: 91: Core t (s) Wall t (s) (%) 91: Time: 0.045 0.023 197.6 91: (ns/day) (hour/ns) 91: Performance: 63.861 0.376 91: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_15_sim1.edr as double precision energy file 91: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_15_sim2.edr as double precision energy file 91: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 91: 91: [ OK ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/15 (115 ms) 91: [ RUN ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/16 91: 91: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_16_input.mdp]: 91: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 91: that with the Verlet scheme, nstlist has no effect on the accuracy of 91: your simulation. 91: 91: 91: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_16_input.mdp]: 91: Setting nstcalcenergy (100) equal to nstenergy (4) 91: 91: Number of degrees of freedom in T-Coupling group System is 33.00 91: 91: There were 2 NOTEs 91: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_16_sim.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 91: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 91: 91: Using 1 MPI thread 91: Using 2 OpenMP threads 91: 91: 91: NOTE: The number of threads is not equal to the number of (logical) cpus 91: and the -pin option is set to auto: will not pin threads to cpus. 91: This can lead to significant performance degradation. 91: Consider using -pin on (and -pinoffset in case you run multiple jobs). 91: starting mdrun 'Argon' 91: 16 steps, 0.0 ps. 91: Generated 1 of the 1 non-bonded parameter combinations 91: 91: Excluding 1 bonded neighbours molecule type 'Argon' 91: 91: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 91: 91: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 91: 91: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 91: 91: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 91: 91: Note that mdrun will redetermine rlist based on the actual pair-list setup 91: 91: This run will generate roughly 0 Mb of data 91: 91: Writing final coordinates. 91: 91: Core t (s) Wall t (s) (%) 91: Time: 0.047 0.024 198.0 91: (ns/day) (hour/ns) 91: Performance: 61.655 0.389 91: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_16_sim.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 91: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 91: 91: Using 1 MPI thread 91: Using 2 OpenMP threads 91: 91: 91: NOTE: The number of threads is not equal to the number of (logical) cpus 91: and the -pin option is set to auto: will not pin threads to cpus. 91: This can lead to significant performance degradation. 91: Consider using -pin on (and -pinoffset in case you run multiple jobs). 91: starting mdrun 'Argon' 91: 16 steps, 0.0 ps. 91: 91: Writing final coordinates. 91: 91: Core t (s) Wall t (s) (%) 91: Time: 0.042 0.021 197.2 91: (ns/day) (hour/ns) 91: Performance: 68.434 0.351 91: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_16_sim1.edr as double precision energy file 91: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_16_sim2.edr as double precision energy file 91: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 91: 91: [ OK ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/16 (108 ms) 91: [ RUN ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/17 91: [ OK ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/17 (0 ms) 91: [ RUN ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/18 91: 91: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_18_input.mdp]: 91: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 91: that with the Verlet scheme, nstlist has no effect on the accuracy of 91: your simulation. 91: 91: 91: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_18_input.mdp]: 91: Setting nstcalcenergy (100) equal to nstenergy (4) 91: 91: Number of degrees of freedom in T-Coupling group System is 33.00 91: 91: There were 2 NOTEs 91: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_18_sim.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 91: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 91: 91: Using 1 MPI thread 91: Using 2 OpenMP threads 91: 91: 91: NOTE: The number of threads is not equal to the number of (logical) cpus 91: and the -pin option is set to auto: will not pin threads to cpus. 91: This can lead to significant performance degradation. 91: Consider using -pin on (and -pinoffset in case you run multiple jobs). 91: starting mdrun 'Argon' 91: 16 steps, 0.0 ps. 91: Generated 1 of the 1 non-bonded parameter combinations 91: 91: Excluding 1 bonded neighbours molecule type 'Argon' 91: 91: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 91: 91: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 91: 91: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 91: 91: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 91: 91: Note that mdrun will redetermine rlist based on the actual pair-list setup 91: 91: This run will generate roughly 0 Mb of data 91: 91: Writing final coordinates. 91: 91: Core t (s) Wall t (s) (%) 91: Time: 0.048 0.024 197.9 91: (ns/day) (hour/ns) 91: Performance: 60.848 0.394 91: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_18_sim.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 91: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 91: 91: Using 1 MPI thread 91: Using 2 OpenMP threads 91: 91: 91: NOTE: The number of threads is not equal to the number of (logical) cpus 91: and the -pin option is set to auto: will not pin threads to cpus. 91: This can lead to significant performance degradation. 91: Consider using -pin on (and -pinoffset in case you run multiple jobs). 91: starting mdrun 'Argon' 91: 16 steps, 0.0 ps. 91: 91: Writing final coordinates. 91: 91: Core t (s) Wall t (s) (%) 91: Time: 0.043 0.022 197.6 91: (ns/day) (hour/ns) 91: Performance: 67.179 0.357 91: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_18_sim1.edr as double precision energy file 91: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_18_sim2.edr as double precision energy file 91: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 91: 91: [ OK ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/18 (109 ms) 91: [ RUN ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/19 91: 91: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_19_input.mdp]: 91: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 91: that with the Verlet scheme, nstlist has no effect on the accuracy of 91: your simulation. 91: 91: 91: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_19_input.mdp]: 91: Setting nstcalcenergy (100) equal to nstenergy (4) 91: 91: 91: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_19_input.mdp]: 91: MTTK coupling is deprecated and will soon be removed 91: 91: Number of degrees of freedom in T-Coupling group System is 33.00 91: 91: There were 3 NOTEs 91: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_19_sim.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 91: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 91: 91: Using 1 MPI thread 91: Using 2 OpenMP threads 91: 91: 91: NOTE: The number of threads is not equal to the number of (logical) cpus 91: and the -pin option is set to auto: will not pin threads to cpus. 91: This can lead to significant performance degradation. 91: Consider using -pin on (and -pinoffset in case you run multiple jobs). 91: starting mdrun 'Argon' 91: 16 steps, 0.0 ps. 91: Generated 1 of the 1 non-bonded parameter combinations 91: 91: Excluding 1 bonded neighbours molecule type 'Argon' 91: 91: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 91: 91: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 91: 91: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 91: 91: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 91: 91: Note that mdrun will redetermine rlist based on the actual pair-list setup 91: 91: This run will generate roughly 0 Mb of data 91: 91: Writing final coordinates. 91: 91: Core t (s) Wall t (s) (%) 91: Time: 0.049 0.025 197.7 91: (ns/day) (hour/ns) 91: Performance: 59.152 0.406 91: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_19_sim.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 91: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 91: 91: Using 1 MPI thread 91: Using 2 OpenMP threads 91: 91: 91: NOTE: The number of threads is not equal to the number of (logical) cpus 91: and the -pin option is set to auto: will not pin threads to cpus. 91: This can lead to significant performance degradation. 91: Consider using -pin on (and -pinoffset in case you run multiple jobs). 91: starting mdrun 'Argon' 91: 16 steps, 0.0 ps. 91: 91: Writing final coordinates. 91: 91: Core t (s) Wall t (s) (%) 91: Time: 0.042 0.021 197.5 91: (ns/day) (hour/ns) 91: Performance: 68.809 0.349 91: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_19_sim1.edr as double precision energy file 91: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_19_sim2.edr as double precision energy file 91: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 91: 91: [ OK ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/19 (107 ms) 91: [ RUN ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/20 91: [ OK ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/20 (0 ms) 91: [ RUN ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/21 91: 91: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_21_input.mdp]: 91: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 91: that with the Verlet scheme, nstlist has no effect on the accuracy of 91: your simulation. 91: 91: 91: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_21_input.mdp]: 91: Setting nstcalcenergy (100) equal to nstenergy (4) 91: 91: 91: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_21_input.mdp]: 91: Andersen temperature control methods assume nsttcouple = 1; there is no 91: need for larger nsttcouple > 1, since no global parameters are computed. 91: nsttcouple has been reset to 1 91: 91: Number of degrees of freedom in T-Coupling group System is 33.00 91: 91: There were 3 NOTEs 91: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_21_sim.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 91: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 91: 91: Using 1 MPI thread 91: Using 2 OpenMP threads 91: 91: 91: NOTE: The number of threads is not equal to the number of (logical) cpus 91: and the -pin option is set to auto: will not pin threads to cpus. 91: This can lead to significant performance degradation. 91: Consider using -pin on (and -pinoffset in case you run multiple jobs). 91: starting mdrun 'Argon' 91: 16 steps, 0.0 ps. 91: Generated 1 of the 1 non-bonded parameter combinations 91: 91: Excluding 1 bonded neighbours molecule type 'Argon' 91: 91: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 91: 91: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 91: 91: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 91: 91: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 91: 91: Note that mdrun will redetermine rlist based on the actual pair-list setup 91: 91: This run will generate roughly 0 Mb of data 91: 91: Writing final coordinates. 91: 91: Core t (s) Wall t (s) (%) 91: Time: 0.043 0.022 198.0 91: (ns/day) (hour/ns) 91: Performance: 67.699 0.355 91: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_21_sim.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 91: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 91: 91: Using 1 MPI thread 91: Using 2 OpenMP threads 91: 91: 91: NOTE: The number of threads is not equal to the number of (logical) cpus 91: and the -pin option is set to auto: will not pin threads to cpus. 91: This can lead to significant performance degradation. 91: Consider using -pin on (and -pinoffset in case you run multiple jobs). 91: starting mdrun 'Argon' 91: 16 steps, 0.0 ps. 91: 91: Writing final coordinates. 91: 91: Core t (s) Wall t (s) (%) 91: Time: 0.038 0.019 197.0 91: (ns/day) (hour/ns) 91: Performance: 75.462 0.318 91: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_21_sim1.edr as double precision energy file 91: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_21_sim2.edr as double precision energy file 91: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 91: 91: [ OK ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/21 (101 ms) 91: [ RUN ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/22 91: 91: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_22_input.mdp]: 91: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 91: that with the Verlet scheme, nstlist has no effect on the accuracy of 91: your simulation. 91: 91: 91: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_22_input.mdp]: 91: Setting nstcalcenergy (100) equal to nstenergy (4) 91: 91: 91: WARNING 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_22_input.mdp]: 91: The Berendsen barostat does not generate any strictly correct ensemble, 91: and should not be used for new production simulations (in our opinion). 91: We recommend using the C-rescale barostat instead. 91: 91: 91: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_22_input.mdp]: 91: Andersen temperature control methods assume nsttcouple = 1; there is no 91: need for larger nsttcouple > 1, since no global parameters are computed. 91: nsttcouple has been reset to 1 91: 91: Number of degrees of freedom in T-Coupling group System is 33.00 91: 91: There were 3 NOTEs 91: 91: There was 1 WARNING 91: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_22_sim.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 91: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 91: 91: Using 1 MPI thread 91: Using 2 OpenMP threads 91: 91: 91: NOTE: The number of threads is not equal to the number of (logical) cpus 91: and the -pin option is set to auto: will not pin threads to cpus. 91: This can lead to significant performance degradation. 91: Consider using -pin on (and -pinoffset in case you run multiple jobs). 91: starting mdrun 'Argon' 91: 16 steps, 0.0 ps. 91: Generated 1 of the 1 non-bonded parameter combinations 91: 91: Excluding 1 bonded neighbours molecule type 'Argon' 91: 91: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 91: 91: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 91: 91: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 91: 91: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 91: 91: Note that mdrun will redetermine rlist based on the actual pair-list setup 91: 91: This run will generate roughly 0 Mb of data 91: 91: Writing final coordinates. 91: 91: Core t (s) Wall t (s) (%) 91: Time: 0.043 0.022 197.8 91: (ns/day) (hour/ns) 91: Performance: 68.167 0.352 91: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_22_sim.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 91: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 91: 91: Using 1 MPI thread 91: Using 2 OpenMP threads 91: 91: 91: NOTE: The number of threads is not equal to the number of (logical) cpus 91: and the -pin option is set to auto: will not pin threads to cpus. 91: This can lead to significant performance degradation. 91: Consider using -pin on (and -pinoffset in case you run multiple jobs). 91: starting mdrun 'Argon' 91: 16 steps, 0.0 ps. 91: 91: Writing final coordinates. 91: 91: Core t (s) Wall t (s) (%) 91: Time: 0.038 0.019 197.3 91: (ns/day) (hour/ns) 91: Performance: 75.455 0.318 91: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_22_sim1.edr as double precision energy file 91: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_22_sim2.edr as double precision energy file 91: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 91: 91: [ OK ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/22 (101 ms) 91: [ RUN ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/23 91: 91: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_23_input.mdp]: 91: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 91: that with the Verlet scheme, nstlist has no effect on the accuracy of 91: your simulation. 91: 91: 91: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_23_input.mdp]: 91: Setting nstcalcenergy (100) equal to nstenergy (4) 91: 91: 91: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_23_input.mdp]: 91: Andersen temperature control methods assume nsttcouple = 1; there is no 91: need for larger nsttcouple > 1, since no global parameters are computed. 91: nsttcouple has been reset to 1 91: 91: Number of degrees of freedom in T-Coupling group System is 33.00 91: 91: There were 3 NOTEs 91: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_23_sim.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 91: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 91: 91: Using 1 MPI thread 91: Using 2 OpenMP threads 91: 91: 91: NOTE: The number of threads is not equal to the number of (logical) cpus 91: and the -pin option is set to auto: will not pin threads to cpus. 91: This can lead to significant performance degradation. 91: Consider using -pin on (and -pinoffset in case you run multiple jobs). 91: starting mdrun 'Argon' 91: 16 steps, 0.0 ps. 91: Generated 1 of the 1 non-bonded parameter combinations 91: 91: Excluding 1 bonded neighbours molecule type 'Argon' 91: 91: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 91: 91: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 91: 91: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 91: 91: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 91: 91: Note that mdrun will redetermine rlist based on the actual pair-list setup 91: 91: This run will generate roughly 0 Mb of data 91: 91: Writing final coordinates. 91: 91: Core t (s) Wall t (s) (%) 91: Time: 0.043 0.022 197.8 91: (ns/day) (hour/ns) 91: Performance: 67.899 0.353 91: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_23_sim.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 91: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 91: 91: Using 1 MPI thread 91: Using 2 OpenMP threads 91: 91: 91: NOTE: The number of threads is not equal to the number of (logical) cpus 91: and the -pin option is set to auto: will not pin threads to cpus. 91: This can lead to significant performance degradation. 91: Consider using -pin on (and -pinoffset in case you run multiple jobs). 91: starting mdrun 'Argon' 91: 16 steps, 0.0 ps. 91: 91: Writing final coordinates. 91: 91: Core t (s) Wall t (s) (%) 91: Time: 0.038 0.019 197.3 91: (ns/day) (hour/ns) 91: Performance: 75.408 0.318 91: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_23_sim1.edr as double precision energy file 91: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_23_sim2.edr as double precision energy file 91: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 91: 91: [ OK ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/23 (102 ms) 91: [ RUN ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/24 91: [ OK ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/24 (0 ms) 91: [ RUN ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/25 91: [ OK ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/25 (0 ms) 91: [ RUN ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/26 91: 91: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_26_input.mdp]: 91: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 91: that with the Verlet scheme, nstlist has no effect on the accuracy of 91: your simulation. 91: 91: 91: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_26_input.mdp]: 91: Center of mass removal not necessary for Andersen. All velocities of 91: coupled groups are rerandomized periodically, so flying ice cube errors 91: will not occur. 91: 91: 91: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_26_input.mdp]: 91: Andersen temperature control methods assume nsttcouple = 1; there is no 91: need for larger nsttcouple > 1, since no global parameters are computed. 91: nsttcouple has been reset to 1 91: 91: Number of degrees of freedom in T-Coupling group System is 33.00 91: 91: There were 3 NOTEs 91: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_26_sim.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 91: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 91: 91: Using 1 MPI thread 91: Using 2 OpenMP threads 91: 91: 91: NOTE: The number of threads is not equal to the number of (logical) cpus 91: and the -pin option is set to auto: will not pin threads to cpus. 91: This can lead to significant performance degradation. 91: Consider using -pin on (and -pinoffset in case you run multiple jobs). 91: starting mdrun 'Argon' 91: 16 steps, 0.0 ps. 91: Generated 1 of the 1 non-bonded parameter combinations 91: 91: Excluding 1 bonded neighbours molecule type 'Argon' 91: 91: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 91: 91: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 91: 91: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 91: 91: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 91: 91: Note that mdrun will redetermine rlist based on the actual pair-list setup 91: 91: This run will generate roughly 0 Mb of data 91: 91: Writing final coordinates. 91: 91: Core t (s) Wall t (s) (%) 91: Time: 0.044 0.022 197.9 91: (ns/day) (hour/ns) 91: Performance: 66.339 0.362 91: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_26_sim.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 91: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 91: 91: Using 1 MPI thread 91: Using 2 OpenMP threads 91: 91: 91: NOTE: The number of threads is not equal to the number of (logical) cpus 91: and the -pin option is set to auto: will not pin threads to cpus. 91: This can lead to significant performance degradation. 91: Consider using -pin on (and -pinoffset in case you run multiple jobs). 91: starting mdrun 'Argon' 91: 16 steps, 0.0 ps. 91: 91: Writing final coordinates. 91: 91: Core t (s) Wall t (s) (%) 91: Time: 0.039 0.020 197.1 91: (ns/day) (hour/ns) 91: Performance: 73.876 0.325 91: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_26_sim1.edr as double precision energy file 91: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_26_sim2.edr as double precision energy file 91: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 91: 91: [ OK ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/26 (102 ms) 91: [ RUN ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/27 91: 91: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_27_input.mdp]: 91: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 91: that with the Verlet scheme, nstlist has no effect on the accuracy of 91: your simulation. 91: 91: 91: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_27_input.mdp]: 91: Center of mass removal not necessary for Andersen. All velocities of 91: coupled groups are rerandomized periodically, so flying ice cube errors 91: will not occur. 91: 91: 91: WARNING 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_27_input.mdp]: 91: The Berendsen barostat does not generate any strictly correct ensemble, 91: and should not be used for new production simulations (in our opinion). 91: We recommend using the C-rescale barostat instead. 91: 91: 91: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_27_input.mdp]: 91: Andersen temperature control methods assume nsttcouple = 1; there is no 91: need for larger nsttcouple > 1, since no global parameters are computed. 91: nsttcouple has been reset to 1 91: 91: Number of degrees of freedom in T-Coupling group System is 33.00 91: 91: There were 3 NOTEs 91: 91: There was 1 WARNING 91: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_27_sim.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 91: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 91: 91: Using 1 MPI thread 91: Using 2 OpenMP threads 91: 91: 91: NOTE: The number of threads is not equal to the number of (logical) cpus 91: and the -pin option is set to auto: will not pin threads to cpus. 91: This can lead to significant performance degradation. 91: Consider using -pin on (and -pinoffset in case you run multiple jobs). 91: starting mdrun 'Argon' 91: 16 steps, 0.0 ps. 91: Generated 1 of the 1 non-bonded parameter combinations 91: 91: Excluding 1 bonded neighbours molecule type 'Argon' 91: 91: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 91: 91: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 91: 91: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 91: 91: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 91: 91: Note that mdrun will redetermine rlist based on the actual pair-list setup 91: 91: This run will generate roughly 0 Mb of data 91: 91: Writing final coordinates. 91: 91: Core t (s) Wall t (s) (%) 91: Time: 0.045 0.023 197.8 91: (ns/day) (hour/ns) 91: Performance: 64.529 0.372 91: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_27_sim.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 91: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 91: 91: Using 1 MPI thread 91: Using 2 OpenMP threads 91: 91: 91: NOTE: The number of threads is not equal to the number of (logical) cpus 91: and the -pin option is set to auto: will not pin threads to cpus. 91: This can lead to significant performance degradation. 91: Consider using -pin on (and -pinoffset in case you run multiple jobs). 91: starting mdrun 'Argon' 91: 16 steps, 0.0 ps. 91: 91: Writing final coordinates. 91: 91: Core t (s) Wall t (s) (%) 91: Time: 0.040 0.020 197.5 91: (ns/day) (hour/ns) 91: Performance: 71.796 0.334 91: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_27_sim1.edr as double precision energy file 91: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_27_sim2.edr as double precision energy file 91: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 91: 91: [ OK ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/27 (104 ms) 91: [ RUN ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/28 91: 91: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_28_input.mdp]: 91: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 91: that with the Verlet scheme, nstlist has no effect on the accuracy of 91: your simulation. 91: 91: 91: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_28_input.mdp]: 91: Center of mass removal not necessary for Andersen. All velocities of 91: coupled groups are rerandomized periodically, so flying ice cube errors 91: will not occur. 91: 91: 91: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_28_input.mdp]: 91: Andersen temperature control methods assume nsttcouple = 1; there is no 91: need for larger nsttcouple > 1, since no global parameters are computed. 91: nsttcouple has been reset to 1 91: 91: Number of degrees of freedom in T-Coupling group System is 33.00 91: 91: There were 3 NOTEs 91: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_28_sim.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 91: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 91: 91: Using 1 MPI thread 91: Using 2 OpenMP threads 91: 91: 91: NOTE: The number of threads is not equal to the number of (logical) cpus 91: and the -pin option is set to auto: will not pin threads to cpus. 91: This can lead to significant performance degradation. 91: Consider using -pin on (and -pinoffset in case you run multiple jobs). 91: starting mdrun 'Argon' 91: 16 steps, 0.0 ps. 91: Generated 1 of the 1 non-bonded parameter combinations 91: 91: Excluding 1 bonded neighbours molecule type 'Argon' 91: 91: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 91: 91: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 91: 91: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 91: 91: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 91: 91: Note that mdrun will redetermine rlist based on the actual pair-list setup 91: 91: This run will generate roughly 0 Mb of data 91: 91: Writing final coordinates. 91: 91: Core t (s) Wall t (s) (%) 91: Time: 0.045 0.023 197.9 91: (ns/day) (hour/ns) 91: Performance: 64.585 0.372 91: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_28_sim.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 91: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 91: 91: Using 1 MPI thread 91: Using 2 OpenMP threads 91: 91: 91: NOTE: The number of threads is not equal to the number of (logical) cpus 91: and the -pin option is set to auto: will not pin threads to cpus. 91: This can lead to significant performance degradation. 91: Consider using -pin on (and -pinoffset in case you run multiple jobs). 91: starting mdrun 'Argon' 91: 16 steps, 0.0 ps. 91: 91: Writing final coordinates. 91: 91: Core t (s) Wall t (s) (%) 91: Time: 0.041 0.021 197.6 91: (ns/day) (hour/ns) 91: Performance: 71.587 0.335 91: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_28_sim1.edr as double precision energy file 91: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_28_sim2.edr as double precision energy file 91: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 91: 91: [ OK ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/28 (104 ms) 91: [ RUN ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/29 91: [ OK ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/29 (0 ms) 91: [ RUN ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/30 91: [ OK ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/30 (0 ms) 91: [ RUN ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/31 91: 91: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_31_input.mdp]: 91: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 91: that with the Verlet scheme, nstlist has no effect on the accuracy of 91: your simulation. 91: 91: 91: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_31_input.mdp]: 91: Setting nstcalcenergy (100) equal to nstenergy (4) 91: 91: Generating 1-4 interactions: fudge = 0.5 91: Number of degrees of freedom in T-Coupling group System is 27.00 91: 91: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_31_input.mdp]: 91: NVE simulation: will use the initial temperature of 398.997 K for 91: determining the Verlet buffer size 91: 91: 91: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_31_input.mdp]: 91: You are using a plain Coulomb cut-off, which might produce artifacts. 91: You might want to consider using PME electrostatics. 91: 91: 91: 91: There were 4 NOTEs 91: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_31_sim.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 91: Can not increase nstlist because an NVE ensemble is used 91: Using 1 MPI thread 91: Using 2 OpenMP threads 91: 91: 91: NOTE: The number of threads is not equal to the number of (logical) cpus 91: and the -pin option is set to auto: will not pin threads to cpus. 91: This can lead to significant performance degradation. 91: Consider using -pin on (and -pinoffset in case you run multiple jobs). 91: starting mdrun 'spc2' 91: 16 steps, 0.0 ps. 91: Generated 330891 of the 330891 non-bonded parameter combinations 91: 91: Generated 330891 of the 330891 1-4 parameter combinations 91: 91: Excluding 2 bonded neighbours molecule type 'SOL' 91: 91: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/tip3p5.gro' 91: 91: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 91: 91: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 91: 91: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 91: 91: Note that mdrun will redetermine rlist based on the actual pair-list setup 91: 91: This run will generate roughly 0 Mb of data 91: 91: Writing final coordinates. 91: 91: Core t (s) Wall t (s) (%) 91: Time: 0.049 0.025 198.6 91: (ns/day) (hour/ns) 91: Performance: 58.995 0.407 91: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_31_sim.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 91: Can not increase nstlist because an NVE ensemble is used 91: Using 1 MPI thread 91: Using 2 OpenMP threads 91: 91: 91: NOTE: The number of threads is not equal to the number of (logical) cpus 91: and the -pin option is set to auto: will not pin threads to cpus. 91: This can lead to significant performance degradation. 91: Consider using -pin on (and -pinoffset in case you run multiple jobs). 91: starting mdrun 'spc2' 91: 16 steps, 0.0 ps. 91: 91: Writing final coordinates. 91: 91: Core t (s) Wall t (s) (%) 91: Time: 0.052 0.026 197.6 91: (ns/day) (hour/ns) 91: Performance: 55.950 0.429 91: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_31_sim1.edr as double precision energy file 91: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_31_sim2.edr as double precision energy file 91: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 91: 91: [ OK ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/31 (5842 ms) 91: [ RUN ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/32 91: 91: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_32_input.mdp]: 91: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 91: that with the Verlet scheme, nstlist has no effect on the accuracy of 91: your simulation. 91: 91: 91: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_32_input.mdp]: 91: Setting nstcalcenergy (100) equal to nstenergy (4) 91: 91: 91: WARNING 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_32_input.mdp]: 91: The Berendsen barostat does not generate any strictly correct ensemble, 91: and should not be used for new production simulations (in our opinion). 91: We recommend using the C-rescale barostat instead. 91: 91: Generating 1-4 interactions: fudge = 0.5 91: Number of degrees of freedom in T-Coupling group System is 27.00 91: 91: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_32_input.mdp]: 91: NVE simulation: will use the initial temperature of 398.997 K for 91: determining the Verlet buffer size 91: 91: 91: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_32_input.mdp]: 91: You are using a plain Coulomb cut-off, which might produce artifacts. 91: You might want to consider using PME electrostatics. 91: 91: 91: 91: There were 4 NOTEs 91: 91: There was 1 WARNING 91: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_32_sim.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 91: Can not increase nstlist because an NVE ensemble is used 91: Using 1 MPI thread 91: Using 2 OpenMP threads 91: 91: 91: NOTE: The number of threads is not equal to the number of (logical) cpus 91: and the -pin option is set to auto: will not pin threads to cpus. 91: This can lead to significant performance degradation. 91: Consider using -pin on (and -pinoffset in case you run multiple jobs). 91: starting mdrun 'spc2' 91: 16 steps, 0.0 ps. 91: Generated 330891 of the 330891 non-bonded parameter combinations 91: 91: Generated 330891 of the 330891 1-4 parameter combinations 91: 91: Excluding 2 bonded neighbours molecule type 'SOL' 91: 91: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/tip3p5.gro' 91: 91: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 91: 91: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 91: 91: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 91: 91: Note that mdrun will redetermine rlist based on the actual pair-list setup 91: 91: This run will generate roughly 0 Mb of data 91: 91: Writing final coordinates. 91: 91: Core t (s) Wall t (s) (%) 91: Time: 0.109 0.055 199.4 91: (ns/day) (hour/ns) 91: Performance: 26.767 0.897 91: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_32_sim.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 91: Can not increase nstlist because an NVE ensemble is used 91: Using 1 MPI thread 91: Using 2 OpenMP threads 91: 91: 91: NOTE: The number of threads is not equal to the number of (logical) cpus 91: and the -pin option is set to auto: will not pin threads to cpus. 91: This can lead to significant performance degradation. 91: Consider using -pin on (and -pinoffset in case you run multiple jobs). 91: starting mdrun 'spc2' 91: 16 steps, 0.0 ps. 91: 91: Writing final coordinates. 91: 91: Core t (s) Wall t (s) (%) 91: Time: 0.040 0.021 197.2 91: (ns/day) (hour/ns) 91: Performance: 71.562 0.335 91: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_32_sim1.edr as double precision energy file 91: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_32_sim2.edr as double precision energy file 91: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 91: 91: [ OK ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/32 (5761 ms) 91: [ RUN ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/33 91: [ OK ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/33 (0 ms) 91: [ RUN ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/34 91: [ OK ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/34 (0 ms) 91: [ RUN ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/35 91: [ OK ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/35 (0 ms) 91: [ RUN ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/36 91: 91: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_36_input.mdp]: 91: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 91: that with the Verlet scheme, nstlist has no effect on the accuracy of 91: your simulation. 91: 91: 91: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_36_input.mdp]: 91: Setting nstcalcenergy (100) equal to nstenergy (4) 91: 91: Generating 1-4 interactions: fudge = 0.5 91: Number of degrees of freedom in T-Coupling group System is 27.00 91: 91: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_36_input.mdp]: 91: You are using a plain Coulomb cut-off, which might produce artifacts. 91: You might want to consider using PME electrostatics. 91: 91: 91: 91: There were 3 NOTEs 91: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_36_sim.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 91: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 91: 91: Using 1 MPI thread 91: Using 2 OpenMP threads 91: 91: 91: NOTE: The number of threads is not equal to the number of (logical) cpus 91: and the -pin option is set to auto: will not pin threads to cpus. 91: This can lead to significant performance degradation. 91: Consider using -pin on (and -pinoffset in case you run multiple jobs). 91: starting mdrun 'spc2' 91: 16 steps, 0.0 ps. 91: Generated 330891 of the 330891 non-bonded parameter combinations 91: 91: Generated 330891 of the 330891 1-4 parameter combinations 91: 91: Excluding 2 bonded neighbours molecule type 'SOL' 91: 91: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/tip3p5.gro' 91: 91: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 91: 91: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 91: 91: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 91: 91: Note that mdrun will redetermine rlist based on the actual pair-list setup 91: 91: This run will generate roughly 0 Mb of data 91: 91: Writing final coordinates. 91: 91: Core t (s) Wall t (s) (%) 91: Time: 0.100 0.050 199.0 91: (ns/day) (hour/ns) 91: Performance: 29.155 0.823 91: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_36_sim.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 91: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 91: 91: Using 1 MPI thread 91: Using 2 OpenMP threads 91: 91: 91: NOTE: The number of threads is not equal to the number of (logical) cpus 91: and the -pin option is set to auto: will not pin threads to cpus. 91: This can lead to significant performance degradation. 91: Consider using -pin on (and -pinoffset in case you run multiple jobs). 91: starting mdrun 'spc2' 91: 16 steps, 0.0 ps. 91: 91: Writing final coordinates. 91: 91: Core t (s) Wall t (s) (%) 91: Time: 0.042 0.021 196.9 91: (ns/day) (hour/ns) 91: Performance: 68.456 0.351 91: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_36_sim1.edr as double precision energy file 91: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_36_sim2.edr as double precision energy file 91: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 91: 91: [ OK ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/36 (5841 ms) 91: [ RUN ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/37 91: 91: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_37_input.mdp]: 91: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 91: that with the Verlet scheme, nstlist has no effect on the accuracy of 91: your simulation. 91: 91: 91: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_37_input.mdp]: 91: Setting nstcalcenergy (100) equal to nstenergy (4) 91: 91: 91: WARNING 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_37_input.mdp]: 91: The Berendsen barostat does not generate any strictly correct ensemble, 91: and should not be used for new production simulations (in our opinion). 91: We recommend using the C-rescale barostat instead. 91: 91: Generating 1-4 interactions: fudge = 0.5 91: Number of degrees of freedom in T-Coupling group System is 27.00 91: 91: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_37_input.mdp]: 91: You are using a plain Coulomb cut-off, which might produce artifacts. 91: You might want to consider using PME electrostatics. 91: 91: 91: 91: There were 3 NOTEs 91: 91: There was 1 WARNING 91: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_37_sim.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 91: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 91: 91: Using 1 MPI thread 91: Using 2 OpenMP threads 91: 91: 91: NOTE: The number of threads is not equal to the number of (logical) cpus 91: and the -pin option is set to auto: will not pin threads to cpus. 91: This can lead to significant performance degradation. 91: Consider using -pin on (and -pinoffset in case you run multiple jobs). 91: starting mdrun 'spc2' 91: 16 steps, 0.0 ps. 91: Generated 330891 of the 330891 non-bonded parameter combinations 91: 91: Generated 330891 of the 330891 1-4 parameter combinations 91: 91: Excluding 2 bonded neighbours molecule type 'SOL' 91: 91: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/tip3p5.gro' 91: 91: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 91: 91: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 91: 91: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 91: 91: Note that mdrun will redetermine rlist based on the actual pair-list setup 91: 91: This run will generate roughly 0 Mb of data 91: 91: Writing final coordinates. 91: 91: Core t (s) Wall t (s) (%) 91: Time: 0.096 0.048 198.9 91: (ns/day) (hour/ns) 91: Performance: 30.536 0.786 91: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_37_sim.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 91: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 91: 91: Using 1 MPI thread 91: Using 2 OpenMP threads 91: 91: 91: NOTE: The number of threads is not equal to the number of (logical) cpus 91: and the -pin option is set to auto: will not pin threads to cpus. 91: This can lead to significant performance degradation. 91: Consider using -pin on (and -pinoffset in case you run multiple jobs). 91: starting mdrun 'spc2' 91: 16 steps, 0.0 ps. 91: 91: Writing final coordinates. 91: 91: Core t (s) Wall t (s) (%) 91: Time: 0.046 0.023 197.0 91: (ns/day) (hour/ns) 91: Performance: 62.724 0.383 91: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_37_sim1.edr as double precision energy file 91: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_37_sim2.edr as double precision energy file 91: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 91: 91: [ OK ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/37 (5844 ms) 91: [ RUN ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/38 91: 91: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_38_input.mdp]: 91: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 91: that with the Verlet scheme, nstlist has no effect on the accuracy of 91: your simulation. 91: 91: 91: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_38_input.mdp]: 91: Setting nstcalcenergy (100) equal to nstenergy (4) 91: 91: Generating 1-4 interactions: fudge = 0.5 91: Number of degrees of freedom in T-Coupling group System is 27.00 91: 91: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_38_input.mdp]: 91: You are using a plain Coulomb cut-off, which might produce artifacts. 91: You might want to consider using PME electrostatics. 91: 91: 91: 91: There were 3 NOTEs 91: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_38_sim.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 91: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 91: 91: Using 1 MPI thread 91: Using 2 OpenMP threads 91: 91: 91: NOTE: The number of threads is not equal to the number of (logical) cpus 91: and the -pin option is set to auto: will not pin threads to cpus. 91: This can lead to significant performance degradation. 91: Consider using -pin on (and -pinoffset in case you run multiple jobs). 91: starting mdrun 'spc2' 91: 16 steps, 0.0 ps. 91: Generated 330891 of the 330891 non-bonded parameter combinations 91: 91: Generated 330891 of the 330891 1-4 parameter combinations 91: 91: Excluding 2 bonded neighbours molecule type 'SOL' 91: 91: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/tip3p5.gro' 91: 91: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 91: 91: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 91: 91: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 91: 91: Note that mdrun will redetermine rlist based on the actual pair-list setup 91: 91: This run will generate roughly 0 Mb of data 91: 91: Writing final coordinates. 91: 91: Core t (s) Wall t (s) (%) 91: Time: 0.098 0.049 198.9 91: (ns/day) (hour/ns) 91: Performance: 29.704 0.808 91: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_38_sim.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 91: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 91: 91: Using 1 MPI thread 91: Using 2 OpenMP threads 91: 91: 91: NOTE: The number of threads is not equal to the number of (logical) cpus 91: and the -pin option is set to auto: will not pin threads to cpus. 91: This can lead to significant performance degradation. 91: Consider using -pin on (and -pinoffset in case you run multiple jobs). 91: starting mdrun 'spc2' 91: 16 steps, 0.0 ps. 91: 91: Writing final coordinates. 91: 91: Core t (s) Wall t (s) (%) 91: Time: 0.043 0.022 197.2 91: (ns/day) (hour/ns) 91: Performance: 68.009 0.353 91: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_38_sim1.edr as double precision energy file 91: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_38_sim2.edr as double precision energy file 91: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 91: 91: [ OK ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/38 (5840 ms) 91: [ RUN ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/39 91: [ OK ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/39 (0 ms) 91: [ RUN ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/40 91: [ OK ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/40 (0 ms) 91: [ RUN ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/41 91: 91: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_41_input.mdp]: 91: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 91: that with the Verlet scheme, nstlist has no effect on the accuracy of 91: your simulation. 91: 91: 91: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_41_input.mdp]: 91: Setting nstcalcenergy (100) equal to nstenergy (4) 91: 91: 91: WARNING 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_41_input.mdp]: 91: The Berendsen thermostat does not generate the correct kinetic energy 91: distribution, and should not be used for new production simulations (in 91: our opinion). We would recommend the V-rescale thermostat. 91: 91: Generating 1-4 interactions: fudge = 0.5 91: Number of degrees of freedom in T-Coupling group System is 27.00 91: 91: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_41_input.mdp]: 91: You are using a plain Coulomb cut-off, which might produce artifacts. 91: You might want to consider using PME electrostatics. 91: 91: 91: 91: There were 3 NOTEs 91: 91: There was 1 WARNING 91: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_41_sim.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 91: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 91: 91: Using 1 MPI thread 91: Using 2 OpenMP threads 91: 91: 91: NOTE: The number of threads is not equal to the number of (logical) cpus 91: and the -pin option is set to auto: will not pin threads to cpus. 91: This can lead to significant performance degradation. 91: Consider using -pin on (and -pinoffset in case you run multiple jobs). 91: starting mdrun 'spc2' 91: 16 steps, 0.0 ps. 91: Generated 330891 of the 330891 non-bonded parameter combinations 91: 91: Generated 330891 of the 330891 1-4 parameter combinations 91: 91: Excluding 2 bonded neighbours molecule type 'SOL' 91: 91: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/tip3p5.gro' 91: 91: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 91: 91: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 91: 91: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 91: 91: Note that mdrun will redetermine rlist based on the actual pair-list setup 91: 91: This run will generate roughly 0 Mb of data 91: 91: Writing final coordinates. 91: 91: Core t (s) Wall t (s) (%) 91: Time: 0.093 0.047 199.0 91: (ns/day) (hour/ns) 91: Performance: 31.335 0.766 91: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_41_sim.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 91: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 91: 91: Using 1 MPI thread 91: Using 2 OpenMP threads 91: 91: 91: NOTE: The number of threads is not equal to the number of (logical) cpus 91: and the -pin option is set to auto: will not pin threads to cpus. 91: This can lead to significant performance degradation. 91: Consider using -pin on (and -pinoffset in case you run multiple jobs). 91: starting mdrun 'spc2' 91: 16 steps, 0.0 ps. 91: 91: Writing final coordinates. 91: 91: Core t (s) Wall t (s) (%) 91: Time: 0.042 0.021 197.4 91: (ns/day) (hour/ns) 91: Performance: 69.043 0.348 91: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_41_sim1.edr as double precision energy file 91: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_41_sim2.edr as double precision energy file 91: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 91: 91: [ OK ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/41 (5811 ms) 91: [ RUN ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/42 91: 91: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_42_input.mdp]: 91: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 91: that with the Verlet scheme, nstlist has no effect on the accuracy of 91: your simulation. 91: 91: 91: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_42_input.mdp]: 91: Setting nstcalcenergy (100) equal to nstenergy (4) 91: 91: 91: WARNING 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_42_input.mdp]: 91: The Berendsen thermostat does not generate the correct kinetic energy 91: distribution, and should not be used for new production simulations (in 91: our opinion). We would recommend the V-rescale thermostat. 91: 91: 91: WARNING 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_42_input.mdp]: 91: The Berendsen barostat does not generate any strictly correct ensemble, 91: and should not be used for new production simulations (in our opinion). 91: We recommend using the C-rescale barostat instead. 91: 91: Generating 1-4 interactions: fudge = 0.5 91: Number of degrees of freedom in T-Coupling group System is 27.00 91: 91: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_42_input.mdp]: 91: You are using a plain Coulomb cut-off, which might produce artifacts. 91: You might want to consider using PME electrostatics. 91: 91: 91: 91: There were 3 NOTEs 91: 91: There were 2 WARNINGs 91: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_42_sim.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 91: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 91: 91: Using 1 MPI thread 91: Using 2 OpenMP threads 91: 91: 91: NOTE: The number of threads is not equal to the number of (logical) cpus 91: and the -pin option is set to auto: will not pin threads to cpus. 91: This can lead to significant performance degradation. 91: Consider using -pin on (and -pinoffset in case you run multiple jobs). 91: starting mdrun 'spc2' 91: 16 steps, 0.0 ps. 91: Generated 330891 of the 330891 non-bonded parameter combinations 91: 91: Generated 330891 of the 330891 1-4 parameter combinations 91: 91: Excluding 2 bonded neighbours molecule type 'SOL' 91: 91: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/tip3p5.gro' 91: 91: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 91: 91: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 91: 91: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 91: 91: Note that mdrun will redetermine rlist based on the actual pair-list setup 91: 91: This run will generate roughly 0 Mb of data 91: 91: Writing final coordinates. 91: 91: Core t (s) Wall t (s) (%) 91: Time: 0.048 0.024 197.8 91: (ns/day) (hour/ns) 91: Performance: 60.943 0.394 91: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_42_sim.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 91: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 91: 91: Using 1 MPI thread 91: Using 2 OpenMP threads 91: 91: 91: NOTE: The number of threads is not equal to the number of (logical) cpus 91: and the -pin option is set to auto: will not pin threads to cpus. 91: This can lead to significant performance degradation. 91: Consider using -pin on (and -pinoffset in case you run multiple jobs). 91: starting mdrun 'spc2' 91: 16 steps, 0.0 ps. 91: 91: Writing final coordinates. 91: 91: Core t (s) Wall t (s) (%) 91: Time: 0.042 0.021 197.3 91: (ns/day) (hour/ns) 91: Performance: 69.446 0.346 91: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_42_sim1.edr as double precision energy file 91: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_42_sim2.edr as double precision energy file 91: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 91: 91: [ OK ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/42 (5792 ms) 91: [ RUN ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/43 91: 91: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_43_input.mdp]: 91: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 91: that with the Verlet scheme, nstlist has no effect on the accuracy of 91: your simulation. 91: 91: 91: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_43_input.mdp]: 91: Setting nstcalcenergy (100) equal to nstenergy (4) 91: 91: 91: WARNING 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_43_input.mdp]: 91: The Berendsen thermostat does not generate the correct kinetic energy 91: distribution, and should not be used for new production simulations (in 91: our opinion). We would recommend the V-rescale thermostat. 91: 91: Generating 1-4 interactions: fudge = 0.5 91: Number of degrees of freedom in T-Coupling group System is 27.00 91: 91: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_43_input.mdp]: 91: You are using a plain Coulomb cut-off, which might produce artifacts. 91: You might want to consider using PME electrostatics. 91: 91: 91: 91: There were 3 NOTEs 91: 91: There was 1 WARNING 91: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_43_sim.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 91: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 91: 91: Using 1 MPI thread 91: Using 2 OpenMP threads 91: 91: 91: NOTE: The number of threads is not equal to the number of (logical) cpus 91: and the -pin option is set to auto: will not pin threads to cpus. 91: This can lead to significant performance degradation. 91: Consider using -pin on (and -pinoffset in case you run multiple jobs). 91: starting mdrun 'spc2' 91: 16 steps, 0.0 ps. 91: Generated 330891 of the 330891 non-bonded parameter combinations 91: 91: Generated 330891 of the 330891 1-4 parameter combinations 91: 91: Excluding 2 bonded neighbours molecule type 'SOL' 91: 91: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/tip3p5.gro' 91: 91: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 91: 91: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 91: 91: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 91: 91: Note that mdrun will redetermine rlist based on the actual pair-list setup 91: 91: This run will generate roughly 0 Mb of data 91: 91: Writing final coordinates. 91: 91: Core t (s) Wall t (s) (%) 91: Time: 0.094 0.047 198.6 91: (ns/day) (hour/ns) 91: Performance: 31.073 0.772 91: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_43_sim.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 91: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 91: 91: Using 1 MPI thread 91: Using 2 OpenMP threads 91: 91: 91: NOTE: The number of threads is not equal to the number of (logical) cpus 91: and the -pin option is set to auto: will not pin threads to cpus. 91: This can lead to significant performance degradation. 91: Consider using -pin on (and -pinoffset in case you run multiple jobs). 91: starting mdrun 'spc2' 91: 16 steps, 0.0 ps. 91: 91: Writing final coordinates. 91: 91: Core t (s) Wall t (s) (%) 91: Time: 0.041 0.021 197.3 91: (ns/day) (hour/ns) 91: Performance: 71.426 0.336 91: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_43_sim1.edr as double precision energy file 91: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_43_sim2.edr as double precision energy file 91: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 91: 91: [ OK ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/43 (5810 ms) 91: [ RUN ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/44 91: [ OK ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/44 (0 ms) 91: [ RUN ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/45 91: [ OK ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/45 (0 ms) 91: [ RUN ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/46 91: 91: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_46_input.mdp]: 91: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 91: that with the Verlet scheme, nstlist has no effect on the accuracy of 91: your simulation. 91: 91: 91: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_46_input.mdp]: 91: Setting nstcalcenergy (100) equal to nstenergy (4) 91: 91: Generating 1-4 interactions: fudge = 0.5 91: Number of degrees of freedom in T-Coupling group System is 27.00 91: 91: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_46_input.mdp]: 91: You are using a plain Coulomb cut-off, which might produce artifacts. 91: You might want to consider using PME electrostatics. 91: 91: 91: 91: There were 3 NOTEs 91: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_46_sim.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 91: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 91: 91: Using 1 MPI thread 91: Using 2 OpenMP threads 91: 91: 91: NOTE: The number of threads is not equal to the number of (logical) cpus 91: and the -pin option is set to auto: will not pin threads to cpus. 91: This can lead to significant performance degradation. 91: Consider using -pin on (and -pinoffset in case you run multiple jobs). 91: starting mdrun 'spc2' 91: 16 steps, 0.0 ps. 91: Generated 330891 of the 330891 non-bonded parameter combinations 91: 91: Generated 330891 of the 330891 1-4 parameter combinations 91: 91: Excluding 2 bonded neighbours molecule type 'SOL' 91: 91: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/tip3p5.gro' 91: 91: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 91: 91: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 91: 91: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 91: 91: Note that mdrun will redetermine rlist based on the actual pair-list setup 91: 91: This run will generate roughly 0 Mb of data 91: 91: Writing final coordinates. 91: 91: Core t (s) Wall t (s) (%) 91: Time: 0.108 0.054 199.0 91: (ns/day) (hour/ns) 91: Performance: 27.111 0.885 91: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_46_sim.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 91: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 91: 91: Using 1 MPI thread 91: Using 2 OpenMP threads 91: 91: 91: NOTE: The number of threads is not equal to the number of (logical) cpus 91: and the -pin option is set to auto: will not pin threads to cpus. 91: This can lead to significant performance degradation. 91: Consider using -pin on (and -pinoffset in case you run multiple jobs). 91: starting mdrun 'spc2' 91: 16 steps, 0.0 ps. 91: 91: Writing final coordinates. 91: 91: Core t (s) Wall t (s) (%) 91: Time: 0.044 0.022 197.5 91: (ns/day) (hour/ns) 91: Performance: 66.257 0.362 91: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_46_sim1.edr as double precision energy file 91: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_46_sim2.edr as double precision energy file 91: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 91: 91: [ OK ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/46 (5855 ms) 91: [ RUN ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/47 91: [ OK ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/47 (0 ms) 91: [ RUN ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/48 91: 91: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_48_input.mdp]: 91: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 91: that with the Verlet scheme, nstlist has no effect on the accuracy of 91: your simulation. 91: 91: 91: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_48_input.mdp]: 91: Setting nstcalcenergy (100) equal to nstenergy (4) 91: 91: Generating 1-4 interactions: fudge = 0.5 91: Number of degrees of freedom in T-Coupling group System is 27.00 91: 91: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_48_input.mdp]: 91: You are using a plain Coulomb cut-off, which might produce artifacts. 91: You might want to consider using PME electrostatics. 91: 91: 91: 91: There were 3 NOTEs 91: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_48_sim.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 91: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 91: 91: Using 1 MPI thread 91: Using 2 OpenMP threads 91: 91: 91: NOTE: The number of threads is not equal to the number of (logical) cpus 91: and the -pin option is set to auto: will not pin threads to cpus. 91: This can lead to significant performance degradation. 91: Consider using -pin on (and -pinoffset in case you run multiple jobs). 91: starting mdrun 'spc2' 91: 16 steps, 0.0 ps. 91: Generated 330891 of the 330891 non-bonded parameter combinations 91: 91: Generated 330891 of the 330891 1-4 parameter combinations 91: 91: Excluding 2 bonded neighbours molecule type 'SOL' 91: 91: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/tip3p5.gro' 91: 91: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 91: 91: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 91: 91: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 91: 91: Note that mdrun will redetermine rlist based on the actual pair-list setup 91: 91: This run will generate roughly 0 Mb of data 91: 91: Writing final coordinates. 91: 91: Core t (s) Wall t (s) (%) 91: Time: 0.050 0.025 197.9 91: (ns/day) (hour/ns) 91: Performance: 58.402 0.411 91: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_48_sim.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 91: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 91: 91: Using 1 MPI thread 91: Using 2 OpenMP threads 91: 91: 91: NOTE: The number of threads is not equal to the number of (logical) cpus 91: and the -pin option is set to auto: will not pin threads to cpus. 91: This can lead to significant performance degradation. 91: Consider using -pin on (and -pinoffset in case you run multiple jobs). 91: starting mdrun 'spc2' 91: 16 steps, 0.0 ps. 91: 91: Writing final coordinates. 91: 91: Core t (s) Wall t (s) (%) 91: Time: 0.045 0.023 197.5 91: (ns/day) (hour/ns) 91: Performance: 64.782 0.370 91: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_48_sim1.edr as double precision energy file 91: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_48_sim2.edr as double precision energy file 91: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 91: 91: [ OK ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/48 (5835 ms) 91: [ RUN ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/49 91: [ OK ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/49 (0 ms) 91: [ RUN ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/50 91: [ OK ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/50 (0 ms) 91: [ RUN ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/51 91: 91: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_51_input.mdp]: 91: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 91: that with the Verlet scheme, nstlist has no effect on the accuracy of 91: your simulation. 91: 91: 91: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_51_input.mdp]: 91: Setting nstcalcenergy (100) equal to nstenergy (4) 91: 91: Generating 1-4 interactions: fudge = 0.5 91: 91: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_51_input.mdp]: 91: Andersen temperature control methods assume nsttcouple = 1; there is no 91: need for larger nsttcouple > 1, since no global parameters are computed. 91: nsttcouple has been reset to 1 91: 91: Number of degrees of freedom in T-Coupling group System is 27.00 91: 91: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_51_input.mdp]: 91: You are using a plain Coulomb cut-off, which might produce artifacts. 91: You might want to consider using PME electrostatics. 91: 91: 91: 91: There were 4 NOTEs 91: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_51_sim.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 91: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 91: 91: Using 1 MPI thread 91: Using 2 OpenMP threads 91: 91: 91: NOTE: The number of threads is not equal to the number of (logical) cpus 91: and the -pin option is set to auto: will not pin threads to cpus. 91: This can lead to significant performance degradation. 91: Consider using -pin on (and -pinoffset in case you run multiple jobs). 91: starting mdrun 'spc2' 91: 16 steps, 0.0 ps. 91: Generated 330891 of the 330891 non-bonded parameter combinations 91: 91: Generated 330891 of the 330891 1-4 parameter combinations 91: 91: Excluding 2 bonded neighbours molecule type 'SOL' 91: 91: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/tip3p5.gro' 91: 91: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 91: 91: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 91: 91: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 91: 91: Note that mdrun will redetermine rlist based on the actual pair-list setup 91: 91: This run will generate roughly 0 Mb of data 91: 91: Writing final coordinates. 91: 91: Core t (s) Wall t (s) (%) 91: Time: 0.092 0.046 198.9 91: (ns/day) (hour/ns) 91: Performance: 31.617 0.759 91: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_51_sim.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 91: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 91: 91: Using 1 MPI thread 91: Using 2 OpenMP threads 91: 91: 91: NOTE: The number of threads is not equal to the number of (logical) cpus 91: and the -pin option is set to auto: will not pin threads to cpus. 91: This can lead to significant performance degradation. 91: Consider using -pin on (and -pinoffset in case you run multiple jobs). 91: starting mdrun 'spc2' 91: 16 steps, 0.0 ps. 91: 91: Writing final coordinates. 91: 91: Core t (s) Wall t (s) (%) 91: Time: 0.041 0.021 197.4 91: (ns/day) (hour/ns) 91: Performance: 70.477 0.341 91: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_51_sim1.edr as double precision energy file 91: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_51_sim2.edr as double precision energy file 91: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 91: 91: [ OK ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/51 (5816 ms) 91: [ RUN ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/52 91: 91: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_52_input.mdp]: 91: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 91: that with the Verlet scheme, nstlist has no effect on the accuracy of 91: your simulation. 91: 91: 91: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_52_input.mdp]: 91: Setting nstcalcenergy (100) equal to nstenergy (4) 91: 91: 91: WARNING 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_52_input.mdp]: 91: The Berendsen barostat does not generate any strictly correct ensemble, 91: and should not be used for new production simulations (in our opinion). 91: We recommend using the C-rescale barostat instead. 91: 91: Generating 1-4 interactions: fudge = 0.5 91: 91: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_52_input.mdp]: 91: Andersen temperature control methods assume nsttcouple = 1; there is no 91: need for larger nsttcouple > 1, since no global parameters are computed. 91: nsttcouple has been reset to 1 91: 91: Number of degrees of freedom in T-Coupling group System is 27.00 91: 91: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_52_input.mdp]: 91: You are using a plain Coulomb cut-off, which might produce artifacts. 91: You might want to consider using PME electrostatics. 91: 91: 91: 91: There were 4 NOTEs 91: 91: There was 1 WARNING 91: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_52_sim.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 91: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 91: 91: Using 1 MPI thread 91: Using 2 OpenMP threads 91: 91: 91: NOTE: The number of threads is not equal to the number of (logical) cpus 91: and the -pin option is set to auto: will not pin threads to cpus. 91: This can lead to significant performance degradation. 91: Consider using -pin on (and -pinoffset in case you run multiple jobs). 91: starting mdrun 'spc2' 91: 16 steps, 0.0 ps. 91: Generated 330891 of the 330891 non-bonded parameter combinations 91: 91: Generated 330891 of the 330891 1-4 parameter combinations 91: 91: Excluding 2 bonded neighbours molecule type 'SOL' 91: 91: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/tip3p5.gro' 91: 91: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 91: 91: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 91: 91: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 91: 91: Note that mdrun will redetermine rlist based on the actual pair-list setup 91: 91: This run will generate roughly 0 Mb of data 91: 91: Writing final coordinates. 91: 91: Core t (s) Wall t (s) (%) 91: Time: 0.097 0.049 198.9 91: (ns/day) (hour/ns) 91: Performance: 30.116 0.797 91: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_52_sim.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 91: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 91: 91: Using 1 MPI thread 91: Using 2 OpenMP threads 91: 91: 91: NOTE: The number of threads is not equal to the number of (logical) cpus 91: and the -pin option is set to auto: will not pin threads to cpus. 91: This can lead to significant performance degradation. 91: Consider using -pin on (and -pinoffset in case you run multiple jobs). 91: starting mdrun 'spc2' 91: 16 steps, 0.0 ps. 91: 91: Writing final coordinates. 91: 91: Core t (s) Wall t (s) (%) 91: Time: 0.046 0.023 197.5 91: (ns/day) (hour/ns) 91: Performance: 63.160 0.380 91: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_52_sim1.edr as double precision energy file 91: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_52_sim2.edr as double precision energy file 91: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 91: 91: [ OK ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/52 (5796 ms) 91: [ RUN ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/53 91: 91: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_53_input.mdp]: 91: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 91: that with the Verlet scheme, nstlist has no effect on the accuracy of 91: your simulation. 91: 91: 91: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_53_input.mdp]: 91: Setting nstcalcenergy (100) equal to nstenergy (4) 91: 91: Generating 1-4 interactions: fudge = 0.5 91: 91: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_53_input.mdp]: 91: Andersen temperature control methods assume nsttcouple = 1; there is no 91: need for larger nsttcouple > 1, since no global parameters are computed. 91: nsttcouple has been reset to 1 91: 91: Number of degrees of freedom in T-Coupling group System is 27.00 91: 91: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_53_input.mdp]: 91: You are using a plain Coulomb cut-off, which might produce artifacts. 91: You might want to consider using PME electrostatics. 91: 91: 91: 91: There were 4 NOTEs 91: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_53_sim.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 91: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 91: 91: Using 1 MPI thread 91: Using 2 OpenMP threads 91: 91: 91: NOTE: The number of threads is not equal to the number of (logical) cpus 91: and the -pin option is set to auto: will not pin threads to cpus. 91: This can lead to significant performance degradation. 91: Consider using -pin on (and -pinoffset in case you run multiple jobs). 91: starting mdrun 'spc2' 91: 16 steps, 0.0 ps. 91: Generated 330891 of the 330891 non-bonded parameter combinations 91: 91: Generated 330891 of the 330891 1-4 parameter combinations 91: 91: Excluding 2 bonded neighbours molecule type 'SOL' 91: 91: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/tip3p5.gro' 91: 91: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 91: 91: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 91: 91: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 91: 91: Note that mdrun will redetermine rlist based on the actual pair-list setup 91: 91: This run will generate roughly 0 Mb of data 91: 91: Writing final coordinates. 91: 91: Core t (s) Wall t (s) (%) 91: Time: 0.095 0.048 198.9 91: (ns/day) (hour/ns) 91: Performance: 30.844 0.778 91: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_53_sim.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 91: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 91: 91: Using 1 MPI thread 91: Using 2 OpenMP threads 91: 91: 91: NOTE: The number of threads is not equal to the number of (logical) cpus 91: and the -pin option is set to auto: will not pin threads to cpus. 91: This can lead to significant performance degradation. 91: Consider using -pin on (and -pinoffset in case you run multiple jobs). 91: starting mdrun 'spc2' 91: 16 steps, 0.0 ps. 91: 91: Writing final coordinates. 91: 91: Core t (s) Wall t (s) (%) 91: Time: 0.044 0.022 197.4 91: (ns/day) (hour/ns) 91: Performance: 66.621 0.360 91: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_53_sim1.edr as double precision energy file 91: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_53_sim2.edr as double precision energy file 91: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 91: 91: [ OK ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/53 (5822 ms) 91: [ RUN ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/54 91: [ OK ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/54 (0 ms) 91: [ RUN ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/55 91: [ OK ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/55 (0 ms) 91: [ RUN ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/56 91: [ OK ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/56 (0 ms) 91: [ RUN ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/57 91: [ OK ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/57 (0 ms) 91: [ RUN ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/58 91: [ OK ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/58 (0 ms) 91: [ RUN ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/59 91: [ OK ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/59 (0 ms) 91: [----------] 60 tests from SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest (77568 ms total) 91: 91: [----------] 32 tests from SimulatorsAreEquivalentDefaultLegacy/SimulatorComparisonTest 91: [ RUN ] SimulatorsAreEquivalentDefaultLegacy/SimulatorComparisonTest.WithinTolerances/0 91: 91: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_0_input.mdp]: 91: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 91: that with the Verlet scheme, nstlist has no effect on the accuracy of 91: your simulation. 91: 91: 91: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_0_input.mdp]: 91: Setting nstcalcenergy (100) equal to nstenergy (4) 91: 91: Number of degrees of freedom in T-Coupling group System is 33.00 91: 91: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_0_input.mdp]: 91: NVE simulation: will use the initial temperature of 68.810 K for 91: determining the Verlet buffer size 91: 91: 91: There were 3 NOTEs 91: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_0_sim.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 91: Can not increase nstlist because an NVE ensemble is used 91: Using 1 MPI thread 91: Using 2 OpenMP threads 91: 91: 91: NOTE: The number of threads is not equal to the number of (logical) cpus 91: and the -pin option is set to auto: will not pin threads to cpus. 91: This can lead to significant performance degradation. 91: Consider using -pin on (and -pinoffset in case you run multiple jobs). 91: starting mdrun 'Argon' 91: 16 steps, 0.0 ps. 91: Generated 1 of the 1 non-bonded parameter combinations 91: 91: Excluding 1 bonded neighbours molecule type 'Argon' 91: 91: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 91: 91: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 91: 91: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 91: 91: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 91: 91: Note that mdrun will redetermine rlist based on the actual pair-list setup 91: 91: This run will generate roughly 0 Mb of data 91: 91: Writing final coordinates. 91: 91: Core t (s) Wall t (s) (%) 91: Time: 0.039 0.020 197.0 91: (ns/day) (hour/ns) 91: Performance: 74.227 0.323 91: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_0_sim.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 91: Can not increase nstlist because an NVE ensemble is used 91: Using 1 MPI thread 91: Using 2 OpenMP threads 91: 91: 91: NOTE: The number of threads is not equal to the number of (logical) cpus 91: and the -pin option is set to auto: will not pin threads to cpus. 91: This can lead to significant performance degradation. 91: Consider using -pin on (and -pinoffset in case you run multiple jobs). 91: starting mdrun 'Argon' 91: 16 steps, 0.0 ps. 91: 91: Writing final coordinates. 91: 91: Core t (s) Wall t (s) (%) 91: Time: 0.052 0.026 198.9 91: (ns/day) (hour/ns) 91: Performance: 56.553 0.424 91: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_0_sim1.edr as double precision energy file 91: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_0_sim2.edr as double precision energy file 91: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 91: 91: [ OK ] SimulatorsAreEquivalentDefaultLegacy/SimulatorComparisonTest.WithinTolerances/0 (105 ms) 91: [ RUN ] SimulatorsAreEquivalentDefaultLegacy/SimulatorComparisonTest.WithinTolerances/1 91: 91: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_1_input.mdp]: 91: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 91: that with the Verlet scheme, nstlist has no effect on the accuracy of 91: your simulation. 91: 91: 91: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_1_input.mdp]: 91: Setting nstcalcenergy (100) equal to nstenergy (4) 91: 91: Number of degrees of freedom in T-Coupling group System is 33.00 91: 91: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_1_input.mdp]: 91: NVE simulation: will use the initial temperature of 68.810 K for 91: determining the Verlet buffer size 91: 91: 91: There were 3 NOTEs 91: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_1_sim.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 91: Can not increase nstlist because an NVE ensemble is used 91: Using 1 MPI thread 91: Using 2 OpenMP threads 91: 91: 91: NOTE: The number of threads is not equal to the number of (logical) cpus 91: and the -pin option is set to auto: will not pin threads to cpus. 91: This can lead to significant performance degradation. 91: Consider using -pin on (and -pinoffset in case you run multiple jobs). 91: starting mdrun 'Argon' 91: 16 steps, 0.0 ps. 91: Generated 1 of the 1 non-bonded parameter combinations 91: 91: Excluding 1 bonded neighbours molecule type 'Argon' 91: 91: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 91: 91: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 91: 91: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 91: 91: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 91: 91: Note that mdrun will redetermine rlist based on the actual pair-list setup 91: 91: This run will generate roughly 0 Mb of data 91: 91: Writing final coordinates. 91: 91: Core t (s) Wall t (s) (%) 91: Time: 0.036 0.018 197.1 91: (ns/day) (hour/ns) 91: Performance: 80.907 0.297 91: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_1_sim.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 91: Can not increase nstlist because an NVE ensemble is used 91: Using 1 MPI thread 91: Using 2 OpenMP threads 91: 91: 91: NOTE: The number of threads is not equal to the number of (logical) cpus 91: and the -pin option is set to auto: will not pin threads to cpus. 91: This can lead to significant performance degradation. 91: Consider using -pin on (and -pinoffset in case you run multiple jobs). 91: starting mdrun 'Argon' 91: 16 steps, 0.0 ps. 91: 91: Writing final coordinates. 91: 91: Core t (s) Wall t (s) (%) 91: Time: 0.047 0.024 198.6 91: (ns/day) (hour/ns) 91: Performance: 62.079 0.387 91: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_1_sim1.edr as double precision energy file 91: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_1_sim2.edr as double precision energy file 91: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 91: 91: [ OK ] SimulatorsAreEquivalentDefaultLegacy/SimulatorComparisonTest.WithinTolerances/1 (108 ms) 91: [ RUN ] SimulatorsAreEquivalentDefaultLegacy/SimulatorComparisonTest.WithinTolerances/2 91: 91: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_2_input.mdp]: 91: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 91: that with the Verlet scheme, nstlist has no effect on the accuracy of 91: your simulation. 91: 91: 91: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_2_input.mdp]: 91: Setting nstcalcenergy (100) equal to nstenergy (4) 91: 91: 91: WARNING 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_2_input.mdp]: 91: The Berendsen barostat does not generate any strictly correct ensemble, 91: and should not be used for new production simulations (in our opinion). 91: We recommend using the C-rescale barostat instead. 91: 91: Number of degrees of freedom in T-Coupling group System is 33.00 91: 91: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_2_input.mdp]: 91: NVE simulation: will use the initial temperature of 68.810 K for 91: determining the Verlet buffer size 91: 91: 91: There were 3 NOTEs 91: 91: There was 1 WARNING 91: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_2_sim.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 91: Can not increase nstlist because an NVE ensemble is used 91: Using 1 MPI thread 91: Using 2 OpenMP threads 91: 91: 91: NOTE: The number of threads is not equal to the number of (logical) cpus 91: and the -pin option is set to auto: will not pin threads to cpus. 91: This can lead to significant performance degradation. 91: Consider using -pin on (and -pinoffset in case you run multiple jobs). 91: starting mdrun 'Argon' 91: 16 steps, 0.0 ps. 91: Generated 1 of the 1 non-bonded parameter combinations 91: 91: Excluding 1 bonded neighbours molecule type 'Argon' 91: 91: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 91: 91: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 91: 91: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 91: 91: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 91: 91: Note that mdrun will redetermine rlist based on the actual pair-list setup 91: 91: This run will generate roughly 0 Mb of data 91: 91: Writing final coordinates. 91: 91: Core t (s) Wall t (s) (%) 91: Time: 0.035 0.018 197.2 91: (ns/day) (hour/ns) 91: Performance: 81.868 0.293 91: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_2_sim.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 91: Can not increase nstlist because an NVE ensemble is used 91: Using 1 MPI thread 91: Using 2 OpenMP threads 91: 91: 91: NOTE: The number of threads is not equal to the number of (logical) cpus 91: and the -pin option is set to auto: will not pin threads to cpus. 91: This can lead to significant performance degradation. 91: Consider using -pin on (and -pinoffset in case you run multiple jobs). 91: starting mdrun 'Argon' 91: 16 steps, 0.0 ps. 91: 91: Writing final coordinates. 91: 91: Core t (s) Wall t (s) (%) 91: Time: 0.057 0.028 198.8 91: (ns/day) (hour/ns) 91: Performance: 51.560 0.465 91: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_2_sim1.edr as double precision energy file 91: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_2_sim2.edr as double precision energy file 91: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 91: 91: [ OK ] SimulatorsAreEquivalentDefaultLegacy/SimulatorComparisonTest.WithinTolerances/2 (106 ms) 91: [ RUN ] SimulatorsAreEquivalentDefaultLegacy/SimulatorComparisonTest.WithinTolerances/3 91: [ OK ] SimulatorsAreEquivalentDefaultLegacy/SimulatorComparisonTest.WithinTolerances/3 (0 ms) 91: [ RUN ] SimulatorsAreEquivalentDefaultLegacy/SimulatorComparisonTest.WithinTolerances/4 91: 91: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_4_input.mdp]: 91: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 91: that with the Verlet scheme, nstlist has no effect on the accuracy of 91: your simulation. 91: 91: 91: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_4_input.mdp]: 91: Setting nstcalcenergy (100) equal to nstenergy (4) 91: 91: Number of degrees of freedom in T-Coupling group System is 33.00 91: 91: There were 2 NOTEs 91: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_4_sim.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 91: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 91: 91: Using 1 MPI thread 91: Using 2 OpenMP threads 91: 91: 91: NOTE: The number of threads is not equal to the number of (logical) cpus 91: and the -pin option is set to auto: will not pin threads to cpus. 91: This can lead to significant performance degradation. 91: Consider using -pin on (and -pinoffset in case you run multiple jobs). 91: starting mdrun 'Argon' 91: 16 steps, 0.0 ps. 91: Generated 1 of the 1 non-bonded parameter combinations 91: 91: Excluding 1 bonded neighbours molecule type 'Argon' 91: 91: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 91: 91: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 91: 91: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 91: 91: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 91: 91: Note that mdrun will redetermine rlist based on the actual pair-list setup 91: 91: This run will generate roughly 0 Mb of data 91: 91: Writing final coordinates. 91: 91: Core t (s) Wall t (s) (%) 91: Time: 0.036 0.018 197.2 91: (ns/day) (hour/ns) 91: Performance: 81.441 0.295 91: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_4_sim.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 91: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 91: 91: Using 1 MPI thread 91: Using 2 OpenMP threads 91: 91: 91: NOTE: The number of threads is not equal to the number of (logical) cpus 91: and the -pin option is set to auto: will not pin threads to cpus. 91: This can lead to significant performance degradation. 91: Consider using -pin on (and -pinoffset in case you run multiple jobs). 91: starting mdrun 'Argon' 91: 16 steps, 0.0 ps. 91: 91: Writing final coordinates. 91: 91: Core t (s) Wall t (s) (%) 91: Time: 0.046 0.023 198.2 91: (ns/day) (hour/ns) 91: Performance: 63.365 0.379 91: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_4_sim1.edr as double precision energy file 91: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_4_sim2.edr as double precision energy file 91: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 91: 91: [ OK ] SimulatorsAreEquivalentDefaultLegacy/SimulatorComparisonTest.WithinTolerances/4 (106 ms) 91: [ RUN ] SimulatorsAreEquivalentDefaultLegacy/SimulatorComparisonTest.WithinTolerances/5 91: 91: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_5_input.mdp]: 91: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 91: that with the Verlet scheme, nstlist has no effect on the accuracy of 91: your simulation. 91: 91: 91: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_5_input.mdp]: 91: Setting nstcalcenergy (100) equal to nstenergy (4) 91: 91: Number of degrees of freedom in T-Coupling group System is 33.00 91: 91: There were 2 NOTEs 91: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_5_sim.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 91: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 91: 91: Using 1 MPI thread 91: Using 2 OpenMP threads 91: 91: 91: NOTE: The number of threads is not equal to the number of (logical) cpus 91: and the -pin option is set to auto: will not pin threads to cpus. 91: This can lead to significant performance degradation. 91: Consider using -pin on (and -pinoffset in case you run multiple jobs). 91: starting mdrun 'Argon' 91: 16 steps, 0.0 ps. 91: Generated 1 of the 1 non-bonded parameter combinations 91: 91: Excluding 1 bonded neighbours molecule type 'Argon' 91: 91: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 91: 91: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 91: 91: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 91: 91: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 91: 91: Note that mdrun will redetermine rlist based on the actual pair-list setup 91: 91: This run will generate roughly 0 Mb of data 91: 91: Writing final coordinates. 91: 91: Core t (s) Wall t (s) (%) 91: Time: 0.037 0.019 197.3 91: (ns/day) (hour/ns) 91: Performance: 78.458 0.306 91: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_5_sim.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 91: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 91: 91: Using 1 MPI thread 91: Using 2 OpenMP threads 91: 91: 91: NOTE: The number of threads is not equal to the number of (logical) cpus 91: and the -pin option is set to auto: will not pin threads to cpus. 91: This can lead to significant performance degradation. 91: Consider using -pin on (and -pinoffset in case you run multiple jobs). 91: starting mdrun 'Argon' 91: 16 steps, 0.0 ps. 91: 91: Writing final coordinates. 91: 91: Core t (s) Wall t (s) (%) 91: Time: 0.046 0.023 198.1 91: (ns/day) (hour/ns) 91: Performance: 62.873 0.382 91: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_5_sim1.edr as double precision energy file 91: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_5_sim2.edr as double precision energy file 91: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 91: 91: [ OK ] SimulatorsAreEquivalentDefaultLegacy/SimulatorComparisonTest.WithinTolerances/5 (108 ms) 91: [ RUN ] SimulatorsAreEquivalentDefaultLegacy/SimulatorComparisonTest.WithinTolerances/6 91: 91: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_6_input.mdp]: 91: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 91: that with the Verlet scheme, nstlist has no effect on the accuracy of 91: your simulation. 91: 91: 91: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_6_input.mdp]: 91: Setting nstcalcenergy (100) equal to nstenergy (4) 91: 91: 91: WARNING 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_6_input.mdp]: 91: The Berendsen barostat does not generate any strictly correct ensemble, 91: and should not be used for new production simulations (in our opinion). 91: We recommend using the C-rescale barostat instead. 91: 91: Number of degrees of freedom in T-Coupling group System is 33.00 91: 91: There were 2 NOTEs 91: 91: There was 1 WARNING 91: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_6_sim.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 91: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 91: 91: Using 1 MPI thread 91: Using 2 OpenMP threads 91: 91: 91: NOTE: The number of threads is not equal to the number of (logical) cpus 91: and the -pin option is set to auto: will not pin threads to cpus. 91: This can lead to significant performance degradation. 91: Consider using -pin on (and -pinoffset in case you run multiple jobs). 91: starting mdrun 'Argon' 91: 16 steps, 0.0 ps. 91: Generated 1 of the 1 non-bonded parameter combinations 91: 91: Excluding 1 bonded neighbours molecule type 'Argon' 91: 91: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 91: 91: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 91: 91: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 91: 91: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 91: 91: Note that mdrun will redetermine rlist based on the actual pair-list setup 91: 91: This run will generate roughly 0 Mb of data 91: 91: Writing final coordinates. 91: 91: Core t (s) Wall t (s) (%) 91: Time: 0.037 0.019 197.3 91: (ns/day) (hour/ns) 91: Performance: 77.461 0.310 91: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_6_sim.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 91: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 91: 91: Using 1 MPI thread 91: Using 2 OpenMP threads 91: 91: 91: NOTE: The number of threads is not equal to the number of (logical) cpus 91: and the -pin option is set to auto: will not pin threads to cpus. 91: This can lead to significant performance degradation. 91: Consider using -pin on (and -pinoffset in case you run multiple jobs). 91: starting mdrun 'Argon' 91: 16 steps, 0.0 ps. 91: 91: Writing final coordinates. 91: 91: Core t (s) Wall t (s) (%) 91: Time: 0.042 0.021 198.0 91: (ns/day) (hour/ns) 91: Performance: 69.240 0.347 91: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_6_sim1.edr as double precision energy file 91: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_6_sim2.edr as double precision energy file 91: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 91: 91: [ OK ] SimulatorsAreEquivalentDefaultLegacy/SimulatorComparisonTest.WithinTolerances/6 (107 ms) 91: [ RUN ] SimulatorsAreEquivalentDefaultLegacy/SimulatorComparisonTest.WithinTolerances/7 91: 91: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_7_input.mdp]: 91: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 91: that with the Verlet scheme, nstlist has no effect on the accuracy of 91: your simulation. 91: 91: 91: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_7_input.mdp]: 91: Setting nstcalcenergy (100) equal to nstenergy (4) 91: 91: Number of degrees of freedom in T-Coupling group System is 33.00 91: 91: There were 2 NOTEs 91: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_7_sim.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 91: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 91: 91: Using 1 MPI thread 91: Using 2 OpenMP threads 91: 91: 91: NOTE: The number of threads is not equal to the number of (logical) cpus 91: and the -pin option is set to auto: will not pin threads to cpus. 91: This can lead to significant performance degradation. 91: Consider using -pin on (and -pinoffset in case you run multiple jobs). 91: starting mdrun 'Argon' 91: 16 steps, 0.0 ps. 91: Generated 1 of the 1 non-bonded parameter combinations 91: 91: Excluding 1 bonded neighbours molecule type 'Argon' 91: 91: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 91: 91: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 91: 91: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 91: 91: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 91: 91: Note that mdrun will redetermine rlist based on the actual pair-list setup 91: 91: This run will generate roughly 0 Mb of data 91: 91: Writing final coordinates. 91: 91: Core t (s) Wall t (s) (%) 91: Time: 0.036 0.018 197.3 91: (ns/day) (hour/ns) 91: Performance: 80.967 0.296 91: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_7_sim.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 91: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 91: 91: Using 1 MPI thread 91: Using 2 OpenMP threads 91: 91: 91: NOTE: The number of threads is not equal to the number of (logical) cpus 91: and the -pin option is set to auto: will not pin threads to cpus. 91: This can lead to significant performance degradation. 91: Consider using -pin on (and -pinoffset in case you run multiple jobs). 91: starting mdrun 'Argon' 91: 16 steps, 0.0 ps. 91: 91: Writing final coordinates. 91: 91: Core t (s) Wall t (s) (%) 91: Time: 0.052 0.026 198.3 91: (ns/day) (hour/ns) 91: Performance: 56.492 0.425 91: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_7_sim1.edr as double precision energy file 91: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_7_sim2.edr as double precision energy file 91: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 91: 91: [ OK ] SimulatorsAreEquivalentDefaultLegacy/SimulatorComparisonTest.WithinTolerances/7 (110 ms) 91: [ RUN ] SimulatorsAreEquivalentDefaultLegacy/SimulatorComparisonTest.WithinTolerances/8 91: 91: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_8_input.mdp]: 91: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 91: that with the Verlet scheme, nstlist has no effect on the accuracy of 91: your simulation. 91: 91: 91: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_8_input.mdp]: 91: Setting nstcalcenergy (100) equal to nstenergy (4) 91: 91: 91: WARNING 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_8_input.mdp]: 91: The Berendsen thermostat does not generate the correct kinetic energy 91: distribution, and should not be used for new production simulations (in 91: our opinion). We would recommend the V-rescale thermostat. 91: 91: Number of degrees of freedom in T-Coupling group System is 33.00 91: 91: There were 2 NOTEs 91: 91: There was 1 WARNING 91: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_8_sim.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 91: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 91: 91: Using 1 MPI thread 91: Using 2 OpenMP threads 91: 91: 91: NOTE: The number of threads is not equal to the number of (logical) cpus 91: and the -pin option is set to auto: will not pin threads to cpus. 91: This can lead to significant performance degradation. 91: Consider using -pin on (and -pinoffset in case you run multiple jobs). 91: starting mdrun 'Argon' 91: 16 steps, 0.0 ps. 91: Generated 1 of the 1 non-bonded parameter combinations 91: 91: Excluding 1 bonded neighbours molecule type 'Argon' 91: 91: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 91: 91: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 91: 91: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 91: 91: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 91: 91: Note that mdrun will redetermine rlist based on the actual pair-list setup 91: 91: This run will generate roughly 0 Mb of data 91: 91: Writing final coordinates. 91: 91: Core t (s) Wall t (s) (%) 91: Time: 0.035 0.018 197.3 91: (ns/day) (hour/ns) 91: Performance: 82.304 0.292 91: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_8_sim.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 91: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 91: 91: Using 1 MPI thread 91: Using 2 OpenMP threads 91: 91: 91: NOTE: The number of threads is not equal to the number of (logical) cpus 91: and the -pin option is set to auto: will not pin threads to cpus. 91: This can lead to significant performance degradation. 91: Consider using -pin on (and -pinoffset in case you run multiple jobs). 91: starting mdrun 'Argon' 91: 16 steps, 0.0 ps. 91: 91: Writing final coordinates. 91: 91: Core t (s) Wall t (s) (%) 91: Time: 0.043 0.022 198.0 91: (ns/day) (hour/ns) 91: Performance: 67.035 0.358 91: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_8_sim1.edr as double precision energy file 91: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_8_sim2.edr as double precision energy file 91: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 91: 91: [ OK ] SimulatorsAreEquivalentDefaultLegacy/SimulatorComparisonTest.WithinTolerances/8 (100 ms) 91: [ RUN ] SimulatorsAreEquivalentDefaultLegacy/SimulatorComparisonTest.WithinTolerances/9 91: 91: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_9_input.mdp]: 91: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 91: that with the Verlet scheme, nstlist has no effect on the accuracy of 91: your simulation. 91: 91: 91: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_9_input.mdp]: 91: Setting nstcalcenergy (100) equal to nstenergy (4) 91: 91: 91: WARNING 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_9_input.mdp]: 91: The Berendsen thermostat does not generate the correct kinetic energy 91: distribution, and should not be used for new production simulations (in 91: our opinion). We would recommend the V-rescale thermostat. 91: 91: Number of degrees of freedom in T-Coupling group System is 33.00 91: 91: There were 2 NOTEs 91: 91: There was 1 WARNING 91: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_9_sim.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 91: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 91: 91: Using 1 MPI thread 91: Using 2 OpenMP threads 91: 91: 91: NOTE: The number of threads is not equal to the number of (logical) cpus 91: and the -pin option is set to auto: will not pin threads to cpus. 91: This can lead to significant performance degradation. 91: Consider using -pin on (and -pinoffset in case you run multiple jobs). 91: starting mdrun 'Argon' 91: 16 steps, 0.0 ps. 91: Generated 1 of the 1 non-bonded parameter combinations 91: 91: Excluding 1 bonded neighbours molecule type 'Argon' 91: 91: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 91: 91: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 91: 91: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 91: 91: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 91: 91: Note that mdrun will redetermine rlist based on the actual pair-list setup 91: 91: This run will generate roughly 0 Mb of data 91: 91: Writing final coordinates. 91: 91: Core t (s) Wall t (s) (%) 91: Time: 0.036 0.018 196.6 91: (ns/day) (hour/ns) 91: Performance: 80.180 0.299 91: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_9_sim.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 91: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 91: 91: Using 1 MPI thread 91: Using 2 OpenMP threads 91: 91: 91: NOTE: The number of threads is not equal to the number of (logical) cpus 91: and the -pin option is set to auto: will not pin threads to cpus. 91: This can lead to significant performance degradation. 91: Consider using -pin on (and -pinoffset in case you run multiple jobs). 91: starting mdrun 'Argon' 91: 16 steps, 0.0 ps. 91: 91: Writing final coordinates. 91: 91: Core t (s) Wall t (s) (%) 91: Time: 0.043 0.022 198.0 91: (ns/day) (hour/ns) 91: Performance: 67.336 0.356 91: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_9_sim1.edr as double precision energy file 91: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_9_sim2.edr as double precision energy file 91: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 91: 91: [ OK ] SimulatorsAreEquivalentDefaultLegacy/SimulatorComparisonTest.WithinTolerances/9 (99 ms) 91: [ RUN ] SimulatorsAreEquivalentDefaultLegacy/SimulatorComparisonTest.WithinTolerances/10 91: 91: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_10_input.mdp]: 91: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 91: that with the Verlet scheme, nstlist has no effect on the accuracy of 91: your simulation. 91: 91: 91: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_10_input.mdp]: 91: Setting nstcalcenergy (100) equal to nstenergy (4) 91: 91: 91: WARNING 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_10_input.mdp]: 91: The Berendsen thermostat does not generate the correct kinetic energy 91: distribution, and should not be used for new production simulations (in 91: our opinion). We would recommend the V-rescale thermostat. 91: 91: 91: WARNING 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_10_input.mdp]: 91: The Berendsen barostat does not generate any strictly correct ensemble, 91: and should not be used for new production simulations (in our opinion). 91: We recommend using the C-rescale barostat instead. 91: 91: Number of degrees of freedom in T-Coupling group System is 33.00 91: 91: There were 2 NOTEs 91: 91: There were 2 WARNINGs 91: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_10_sim.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 91: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 91: 91: Using 1 MPI thread 91: Using 2 OpenMP threads 91: 91: 91: NOTE: The number of threads is not equal to the number of (logical) cpus 91: and the -pin option is set to auto: will not pin threads to cpus. 91: This can lead to significant performance degradation. 91: Consider using -pin on (and -pinoffset in case you run multiple jobs). 91: starting mdrun 'Argon' 91: 16 steps, 0.0 ps. 91: Generated 1 of the 1 non-bonded parameter combinations 91: 91: Excluding 1 bonded neighbours molecule type 'Argon' 91: 91: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 91: 91: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 91: 91: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 91: 91: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 91: 91: Note that mdrun will redetermine rlist based on the actual pair-list setup 91: 91: This run will generate roughly 0 Mb of data 91: 91: Writing final coordinates. 91: 91: Core t (s) Wall t (s) (%) 91: Time: 0.035 0.018 197.2 91: (ns/day) (hour/ns) 91: Performance: 82.047 0.293 91: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_10_sim.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 91: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 91: 91: Using 1 MPI thread 91: Using 2 OpenMP threads 91: 91: 91: NOTE: The number of threads is not equal to the number of (logical) cpus 91: and the -pin option is set to auto: will not pin threads to cpus. 91: This can lead to significant performance degradation. 91: Consider using -pin on (and -pinoffset in case you run multiple jobs). 91: starting mdrun 'Argon' 91: 16 steps, 0.0 ps. 91: 91: Writing final coordinates. 91: 91: Core t (s) Wall t (s) (%) 91: Time: 0.043 0.022 198.0 91: (ns/day) (hour/ns) 91: Performance: 68.275 0.352 91: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_10_sim1.edr as double precision energy file 91: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_10_sim2.edr as double precision energy file 91: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 91: 91: [ OK ] SimulatorsAreEquivalentDefaultLegacy/SimulatorComparisonTest.WithinTolerances/10 (98 ms) 91: [ RUN ] SimulatorsAreEquivalentDefaultLegacy/SimulatorComparisonTest.WithinTolerances/11 91: 91: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_11_input.mdp]: 91: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 91: that with the Verlet scheme, nstlist has no effect on the accuracy of 91: your simulation. 91: 91: 91: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_11_input.mdp]: 91: Setting nstcalcenergy (100) equal to nstenergy (4) 91: 91: 91: WARNING 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_11_input.mdp]: 91: The Berendsen thermostat does not generate the correct kinetic energy 91: distribution, and should not be used for new production simulations (in 91: our opinion). We would recommend the V-rescale thermostat. 91: 91: Number of degrees of freedom in T-Coupling group System is 33.00 91: 91: There were 2 NOTEs 91: 91: There was 1 WARNING 91: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_11_sim.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 91: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 91: 91: Using 1 MPI thread 91: Using 2 OpenMP threads 91: 91: 91: NOTE: The number of threads is not equal to the number of (logical) cpus 91: and the -pin option is set to auto: will not pin threads to cpus. 91: This can lead to significant performance degradation. 91: Consider using -pin on (and -pinoffset in case you run multiple jobs). 91: starting mdrun 'Argon' 91: 16 steps, 0.0 ps. 91: Generated 1 of the 1 non-bonded parameter combinations 91: 91: Excluding 1 bonded neighbours molecule type 'Argon' 91: 91: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 91: 91: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 91: 91: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 91: 91: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 91: 91: Note that mdrun will redetermine rlist based on the actual pair-list setup 91: 91: This run will generate roughly 0 Mb of data 91: 91: Writing final coordinates. 91: 91: Core t (s) Wall t (s) (%) 91: Time: 0.036 0.018 197.3 91: (ns/day) (hour/ns) 91: Performance: 80.854 0.297 91: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_11_sim.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 91: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 91: 91: Using 1 MPI thread 91: Using 2 OpenMP threads 91: 91: 91: NOTE: The number of threads is not equal to the number of (logical) cpus 91: and the -pin option is set to auto: will not pin threads to cpus. 91: This can lead to significant performance degradation. 91: Consider using -pin on (and -pinoffset in case you run multiple jobs). 91: starting mdrun 'Argon' 91: 16 steps, 0.0 ps. 91: 91: Writing final coordinates. 91: 91: Core t (s) Wall t (s) (%) 91: Time: 0.044 0.022 198.2 91: (ns/day) (hour/ns) 91: Performance: 66.118 0.363 91: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_11_sim1.edr as double precision energy file 91: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_11_sim2.edr as double precision energy file 91: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 91: 91: [ OK ] SimulatorsAreEquivalentDefaultLegacy/SimulatorComparisonTest.WithinTolerances/11 (99 ms) 91: [ RUN ] SimulatorsAreEquivalentDefaultLegacy/SimulatorComparisonTest.WithinTolerances/12 91: 91: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_12_input.mdp]: 91: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 91: that with the Verlet scheme, nstlist has no effect on the accuracy of 91: your simulation. 91: 91: 91: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_12_input.mdp]: 91: Setting nstcalcenergy (100) equal to nstenergy (4) 91: 91: 91: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_12_input.mdp]: 91: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 91: 1 91: 91: Number of degrees of freedom in T-Coupling group System is 33.00 91: 91: There were 3 NOTEs 91: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_12_sim.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 91: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 91: 91: Using 1 MPI thread 91: Using 2 OpenMP threads 91: 91: 91: NOTE: The number of threads is not equal to the number of (logical) cpus 91: and the -pin option is set to auto: will not pin threads to cpus. 91: This can lead to significant performance degradation. 91: Consider using -pin on (and -pinoffset in case you run multiple jobs). 91: starting mdrun 'Argon' 91: 16 steps, 0.0 ps. 91: Generated 1 of the 1 non-bonded parameter combinations 91: 91: Excluding 1 bonded neighbours molecule type 'Argon' 91: 91: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 91: 91: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 91: 91: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 91: 91: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 91: 91: Note that mdrun will redetermine rlist based on the actual pair-list setup 91: 91: This run will generate roughly 0 Mb of data 91: 91: Writing final coordinates. 91: 91: Core t (s) Wall t (s) (%) 91: Time: 0.039 0.020 196.9 91: (ns/day) (hour/ns) 91: Performance: 73.798 0.325 91: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_12_sim.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 91: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 91: 91: Using 1 MPI thread 91: Using 2 OpenMP threads 91: 91: 91: NOTE: The number of threads is not equal to the number of (logical) cpus 91: and the -pin option is set to auto: will not pin threads to cpus. 91: This can lead to significant performance degradation. 91: Consider using -pin on (and -pinoffset in case you run multiple jobs). 91: starting mdrun 'Argon' 91: 16 steps, 0.0 ps. 91: 91: Writing final coordinates. 91: 91: Core t (s) Wall t (s) (%) 91: Time: 0.052 0.026 198.4 91: (ns/day) (hour/ns) 91: Performance: 55.752 0.430 91: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_12_sim1.edr as double precision energy file 91: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_12_sim2.edr as double precision energy file 91: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 91: 91: [ OK ] SimulatorsAreEquivalentDefaultLegacy/SimulatorComparisonTest.WithinTolerances/12 (107 ms) 91: [ RUN ] SimulatorsAreEquivalentDefaultLegacy/SimulatorComparisonTest.WithinTolerances/13 91: 91: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_13_input.mdp]: 91: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 91: that with the Verlet scheme, nstlist has no effect on the accuracy of 91: your simulation. 91: 91: 91: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_13_input.mdp]: 91: Setting nstcalcenergy (100) equal to nstenergy (4) 91: 91: 91: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_13_input.mdp]: 91: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 91: 1 91: 91: Number of degrees of freedom in T-Coupling group System is 33.00 91: 91: There were 3 NOTEs 91: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_13_sim.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 91: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 91: 91: Using 1 MPI thread 91: Using 2 OpenMP threads 91: 91: 91: NOTE: The number of threads is not equal to the number of (logical) cpus 91: and the -pin option is set to auto: will not pin threads to cpus. 91: This can lead to significant performance degradation. 91: Consider using -pin on (and -pinoffset in case you run multiple jobs). 91: starting mdrun 'Argon' 91: 16 steps, 0.0 ps. 91: Generated 1 of the 1 non-bonded parameter combinations 91: 91: Excluding 1 bonded neighbours molecule type 'Argon' 91: 91: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 91: 91: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 91: 91: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 91: 91: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 91: 91: Note that mdrun will redetermine rlist based on the actual pair-list setup 91: 91: This run will generate roughly 0 Mb of data 91: 91: Writing final coordinates. 91: 91: Core t (s) Wall t (s) (%) 91: Time: 0.039 0.020 197.5 91: (ns/day) (hour/ns) 91: Performance: 74.486 0.322 91: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_13_sim.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 91: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 91: 91: Using 1 MPI thread 91: Using 2 OpenMP threads 91: 91: 91: NOTE: The number of threads is not equal to the number of (logical) cpus 91: and the -pin option is set to auto: will not pin threads to cpus. 91: This can lead to significant performance degradation. 91: Consider using -pin on (and -pinoffset in case you run multiple jobs). 91: starting mdrun 'Argon' 91: 16 steps, 0.0 ps. 91: 91: Writing final coordinates. 91: 91: Core t (s) Wall t (s) (%) 91: Time: 0.048 0.024 198.2 91: (ns/day) (hour/ns) 91: Performance: 61.022 0.393 91: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_13_sim1.edr as double precision energy file 91: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_13_sim2.edr as double precision energy file 91: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 91: 91: [ OK ] SimulatorsAreEquivalentDefaultLegacy/SimulatorComparisonTest.WithinTolerances/13 (107 ms) 91: [ RUN ] SimulatorsAreEquivalentDefaultLegacy/SimulatorComparisonTest.WithinTolerances/14 91: 91: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_14_input.mdp]: 91: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 91: that with the Verlet scheme, nstlist has no effect on the accuracy of 91: your simulation. 91: 91: 91: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_14_input.mdp]: 91: Setting nstcalcenergy (100) equal to nstenergy (4) 91: 91: 91: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_14_input.mdp]: 91: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 91: 1 91: 91: 91: WARNING 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_14_input.mdp]: 91: The Berendsen barostat does not generate any strictly correct ensemble, 91: and should not be used for new production simulations (in our opinion). 91: We recommend using the C-rescale barostat instead. 91: 91: Number of degrees of freedom in T-Coupling group System is 33.00 91: 91: There were 3 NOTEs 91: 91: There was 1 WARNING 91: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_14_sim.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 91: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 91: 91: Using 1 MPI thread 91: Using 2 OpenMP threads 91: 91: 91: NOTE: The number of threads is not equal to the number of (logical) cpus 91: and the -pin option is set to auto: will not pin threads to cpus. 91: This can lead to significant performance degradation. 91: Consider using -pin on (and -pinoffset in case you run multiple jobs). 91: starting mdrun 'Argon' 91: 16 steps, 0.0 ps. 91: Generated 1 of the 1 non-bonded parameter combinations 91: 91: Excluding 1 bonded neighbours molecule type 'Argon' 91: 91: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 91: 91: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 91: 91: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 91: 91: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 91: 91: Note that mdrun will redetermine rlist based on the actual pair-list setup 91: 91: This run will generate roughly 0 Mb of data 91: 91: Writing final coordinates. 91: 91: Core t (s) Wall t (s) (%) 91: Time: 0.040 0.020 197.6 91: (ns/day) (hour/ns) 91: Performance: 72.130 0.333 91: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_14_sim.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 91: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 91: 91: Using 1 MPI thread 91: Using 2 OpenMP threads 91: 91: 91: NOTE: The number of threads is not equal to the number of (logical) cpus 91: and the -pin option is set to auto: will not pin threads to cpus. 91: This can lead to significant performance degradation. 91: Consider using -pin on (and -pinoffset in case you run multiple jobs). 91: starting mdrun 'Argon' 91: 16 steps, 0.0 ps. 91: 91: Writing final coordinates. 91: 91: Core t (s) Wall t (s) (%) 91: Time: 0.050 0.025 198.3 91: (ns/day) (hour/ns) 91: Performance: 57.779 0.415 91: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_14_sim1.edr as double precision energy file 91: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_14_sim2.edr as double precision energy file 91: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 91: 91: [ OK ] SimulatorsAreEquivalentDefaultLegacy/SimulatorComparisonTest.WithinTolerances/14 (109 ms) 91: [ RUN ] SimulatorsAreEquivalentDefaultLegacy/SimulatorComparisonTest.WithinTolerances/15 91: 91: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_15_input.mdp]: 91: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 91: that with the Verlet scheme, nstlist has no effect on the accuracy of 91: your simulation. 91: 91: 91: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_15_input.mdp]: 91: Setting nstcalcenergy (100) equal to nstenergy (4) 91: 91: 91: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_15_input.mdp]: 91: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 91: 1 91: 91: Number of degrees of freedom in T-Coupling group System is 33.00 91: 91: There were 3 NOTEs 91: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_15_sim.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 91: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 91: 91: Using 1 MPI thread 91: Using 2 OpenMP threads 91: 91: 91: NOTE: The number of threads is not equal to the number of (logical) cpus 91: and the -pin option is set to auto: will not pin threads to cpus. 91: This can lead to significant performance degradation. 91: Consider using -pin on (and -pinoffset in case you run multiple jobs). 91: starting mdrun 'Argon' 91: 16 steps, 0.0 ps. 91: Generated 1 of the 1 non-bonded parameter combinations 91: 91: Excluding 1 bonded neighbours molecule type 'Argon' 91: 91: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 91: 91: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 91: 91: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 91: 91: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 91: 91: Note that mdrun will redetermine rlist based on the actual pair-list setup 91: 91: This run will generate roughly 0 Mb of data 91: 91: Writing final coordinates. 91: 91: Core t (s) Wall t (s) (%) 91: Time: 0.037 0.019 197.2 91: (ns/day) (hour/ns) 91: Performance: 79.193 0.303 91: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_15_sim.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 91: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 91: 91: Using 1 MPI thread 91: Using 2 OpenMP threads 91: 91: 91: NOTE: The number of threads is not equal to the number of (logical) cpus 91: and the -pin option is set to auto: will not pin threads to cpus. 91: This can lead to significant performance degradation. 91: Consider using -pin on (and -pinoffset in case you run multiple jobs). 91: starting mdrun 'Argon' 91: 16 steps, 0.0 ps. 91: 91: Writing final coordinates. 91: 91: Core t (s) Wall t (s) (%) 91: Time: 0.045 0.023 197.6 91: (ns/day) (hour/ns) 91: Performance: 64.373 0.373 91: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_15_sim1.edr as double precision energy file 91: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_15_sim2.edr as double precision energy file 91: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 91: 91: [ OK ] SimulatorsAreEquivalentDefaultLegacy/SimulatorComparisonTest.WithinTolerances/15 (104 ms) 91: [ RUN ] SimulatorsAreEquivalentDefaultLegacy/SimulatorComparisonTest.WithinTolerances/16 91: 91: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_16_input.mdp]: 91: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 91: that with the Verlet scheme, nstlist has no effect on the accuracy of 91: your simulation. 91: 91: 91: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_16_input.mdp]: 91: Setting nstcalcenergy (100) equal to nstenergy (4) 91: 91: Generating 1-4 interactions: fudge = 0.5 91: Number of degrees of freedom in T-Coupling group System is 27.00 91: 91: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_16_input.mdp]: 91: NVE simulation: will use the initial temperature of 398.997 K for 91: determining the Verlet buffer size 91: 91: 91: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_16_input.mdp]: 91: You are using a plain Coulomb cut-off, which might produce artifacts. 91: You might want to consider using PME electrostatics. 91: 91: 91: 91: There were 4 NOTEs 91: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_16_sim.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 91: Can not increase nstlist because an NVE ensemble is used 91: Using 1 MPI thread 91: Using 2 OpenMP threads 91: 91: 91: NOTE: The number of threads is not equal to the number of (logical) cpus 91: and the -pin option is set to auto: will not pin threads to cpus. 91: This can lead to significant performance degradation. 91: Consider using -pin on (and -pinoffset in case you run multiple jobs). 91: starting mdrun 'spc2' 91: 16 steps, 0.0 ps. 91: Generated 330891 of the 330891 non-bonded parameter combinations 91: 91: Generated 330891 of the 330891 1-4 parameter combinations 91: 91: Excluding 2 bonded neighbours molecule type 'SOL' 91: 91: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/tip3p5.gro' 91: 91: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 91: 91: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 91: 91: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 91: 91: Note that mdrun will redetermine rlist based on the actual pair-list setup 91: 91: This run will generate roughly 0 Mb of data 91: 91: Writing final coordinates. 91: 91: Core t (s) Wall t (s) (%) 91: Time: 0.085 0.043 198.5 91: (ns/day) (hour/ns) 91: Performance: 34.194 0.702 91: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_16_sim.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 91: Can not increase nstlist because an NVE ensemble is used 91: Using 1 MPI thread 91: Using 2 OpenMP threads 91: 91: 91: NOTE: The number of threads is not equal to the number of (logical) cpus 91: and the -pin option is set to auto: will not pin threads to cpus. 91: This can lead to significant performance degradation. 91: Consider using -pin on (and -pinoffset in case you run multiple jobs). 91: starting mdrun 'spc2' 91: 16 steps, 0.0 ps. 91: 91: Writing final coordinates. 91: 91: Core t (s) Wall t (s) (%) 91: Time: 0.049 0.024 198.6 91: (ns/day) (hour/ns) 91: Performance: 60.103 0.399 91: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_16_sim1.edr as double precision energy file 91: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_16_sim2.edr as double precision energy file 91: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 91: 91: [ OK ] SimulatorsAreEquivalentDefaultLegacy/SimulatorComparisonTest.WithinTolerances/16 (5823 ms) 91: [ RUN ] SimulatorsAreEquivalentDefaultLegacy/SimulatorComparisonTest.WithinTolerances/17 91: 91: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_17_input.mdp]: 91: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 91: that with the Verlet scheme, nstlist has no effect on the accuracy of 91: your simulation. 91: 91: 91: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_17_input.mdp]: 91: Setting nstcalcenergy (100) equal to nstenergy (4) 91: 91: Generating 1-4 interactions: fudge = 0.5 91: Number of degrees of freedom in T-Coupling group System is 27.00 91: 91: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_17_input.mdp]: 91: NVE simulation: will use the initial temperature of 398.997 K for 91: determining the Verlet buffer size 91: 91: 91: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_17_input.mdp]: 91: You are using a plain Coulomb cut-off, which might produce artifacts. 91: You might want to consider using PME electrostatics. 91: 91: 91: 91: There were 4 NOTEs 91: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_17_sim.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 91: Can not increase nstlist because an NVE ensemble is used 91: Using 1 MPI thread 91: Using 2 OpenMP threads 91: 91: 91: NOTE: The number of threads is not equal to the number of (logical) cpus 91: and the -pin option is set to auto: will not pin threads to cpus. 91: This can lead to significant performance degradation. 91: Consider using -pin on (and -pinoffset in case you run multiple jobs). 91: starting mdrun 'spc2' 91: 16 steps, 0.0 ps. 91: Generated 330891 of the 330891 non-bonded parameter combinations 91: 91: Generated 330891 of the 330891 1-4 parameter combinations 91: 91: Excluding 2 bonded neighbours molecule type 'SOL' 91: 91: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/tip3p5.gro' 91: 91: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 91: 91: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 91: 91: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 91: 91: Note that mdrun will redetermine rlist based on the actual pair-list setup 91: 91: This run will generate roughly 0 Mb of data 91: 91: Writing final coordinates. 91: 91: Core t (s) Wall t (s) (%) 91: Time: 0.097 0.049 196.9 91: (ns/day) (hour/ns) 91: Performance: 29.865 0.804 91: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_17_sim.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 91: Can not increase nstlist because an NVE ensemble is used 91: Using 1 MPI thread 91: Using 2 OpenMP threads 91: 91: 91: NOTE: The number of threads is not equal to the number of (logical) cpus 91: and the -pin option is set to auto: will not pin threads to cpus. 91: This can lead to significant performance degradation. 91: Consider using -pin on (and -pinoffset in case you run multiple jobs). 91: starting mdrun 'spc2' 91: 16 steps, 0.0 ps. 91: 91: Writing final coordinates. 91: 91: Core t (s) Wall t (s) (%) 91: Time: 0.055 0.028 198.7 91: (ns/day) (hour/ns) 91: Performance: 53.075 0.452 91: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_17_sim1.edr as double precision energy file 91: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_17_sim2.edr as double precision energy file 91: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 91: 91: [ OK ] SimulatorsAreEquivalentDefaultLegacy/SimulatorComparisonTest.WithinTolerances/17 (5834 ms) 91: [ RUN ] SimulatorsAreEquivalentDefaultLegacy/SimulatorComparisonTest.WithinTolerances/18 91: 91: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_18_input.mdp]: 91: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 91: that with the Verlet scheme, nstlist has no effect on the accuracy of 91: your simulation. 91: 91: 91: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_18_input.mdp]: 91: Setting nstcalcenergy (100) equal to nstenergy (4) 91: 91: 91: WARNING 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_18_input.mdp]: 91: The Berendsen barostat does not generate any strictly correct ensemble, 91: and should not be used for new production simulations (in our opinion). 91: We recommend using the C-rescale barostat instead. 91: 91: Generating 1-4 interactions: fudge = 0.5 91: Number of degrees of freedom in T-Coupling group System is 27.00 91: 91: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_18_input.mdp]: 91: NVE simulation: will use the initial temperature of 398.997 K for 91: determining the Verlet buffer size 91: 91: 91: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_18_input.mdp]: 91: You are using a plain Coulomb cut-off, which might produce artifacts. 91: You might want to consider using PME electrostatics. 91: 91: 91: 91: There were 4 NOTEs 91: 91: There was 1 WARNING 91: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_18_sim.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 91: Can not increase nstlist because an NVE ensemble is used 91: Using 1 MPI thread 91: Using 2 OpenMP threads 91: 91: 91: NOTE: The number of threads is not equal to the number of (logical) cpus 91: and the -pin option is set to auto: will not pin threads to cpus. 91: This can lead to significant performance degradation. 91: Consider using -pin on (and -pinoffset in case you run multiple jobs). 91: starting mdrun 'spc2' 91: 16 steps, 0.0 ps. 91: Generated 330891 of the 330891 non-bonded parameter combinations 91: 91: Generated 330891 of the 330891 1-4 parameter combinations 91: 91: Excluding 2 bonded neighbours molecule type 'SOL' 91: 91: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/tip3p5.gro' 91: 91: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 91: 91: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 91: 91: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 91: 91: Note that mdrun will redetermine rlist based on the actual pair-list setup 91: 91: This run will generate roughly 0 Mb of data 91: 91: Writing final coordinates. 91: 91: Core t (s) Wall t (s) (%) 91: Time: 0.097 0.049 198.9 91: (ns/day) (hour/ns) 91: Performance: 30.022 0.799 91: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_18_sim.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 91: Can not increase nstlist because an NVE ensemble is used 91: Using 1 MPI thread 91: Using 2 OpenMP threads 91: 91: 91: NOTE: The number of threads is not equal to the number of (logical) cpus 91: and the -pin option is set to auto: will not pin threads to cpus. 91: This can lead to significant performance degradation. 91: Consider using -pin on (and -pinoffset in case you run multiple jobs). 91: starting mdrun 'spc2' 91: 16 steps, 0.0 ps. 91: 91: Writing final coordinates. 91: 91: Core t (s) Wall t (s) (%) 91: Time: 0.061 0.031 198.8 91: (ns/day) (hour/ns) 91: Performance: 47.757 0.503 91: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_18_sim1.edr as double precision energy file 91: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_18_sim2.edr as double precision energy file 91: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 91: 91: [ OK ] SimulatorsAreEquivalentDefaultLegacy/SimulatorComparisonTest.WithinTolerances/18 (5889 ms) 91: [ RUN ] SimulatorsAreEquivalentDefaultLegacy/SimulatorComparisonTest.WithinTolerances/19 91: [ OK ] SimulatorsAreEquivalentDefaultLegacy/SimulatorComparisonTest.WithinTolerances/19 (0 ms) 91: [ RUN ] SimulatorsAreEquivalentDefaultLegacy/SimulatorComparisonTest.WithinTolerances/20 91: 91: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_20_input.mdp]: 91: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 91: that with the Verlet scheme, nstlist has no effect on the accuracy of 91: your simulation. 91: 91: 91: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_20_input.mdp]: 91: Setting nstcalcenergy (100) equal to nstenergy (4) 91: 91: Generating 1-4 interactions: fudge = 0.5 91: Number of degrees of freedom in T-Coupling group System is 27.00 91: 91: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_20_input.mdp]: 91: You are using a plain Coulomb cut-off, which might produce artifacts. 91: You might want to consider using PME electrostatics. 91: 91: 91: 91: There were 3 NOTEs 91: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_20_sim.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 91: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 91: 91: Using 1 MPI thread 91: Using 2 OpenMP threads 91: 91: 91: NOTE: The number of threads is not equal to the number of (logical) cpus 91: and the -pin option is set to auto: will not pin threads to cpus. 91: This can lead to significant performance degradation. 91: Consider using -pin on (and -pinoffset in case you run multiple jobs). 91: starting mdrun 'spc2' 91: 16 steps, 0.0 ps. 91: Generated 330891 of the 330891 non-bonded parameter combinations 91: 91: Generated 330891 of the 330891 1-4 parameter combinations 91: 91: Excluding 2 bonded neighbours molecule type 'SOL' 91: 91: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/tip3p5.gro' 91: 91: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 91: 91: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 91: 91: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 91: 91: Note that mdrun will redetermine rlist based on the actual pair-list setup 91: 91: This run will generate roughly 0 Mb of data 91: 91: Writing final coordinates. 91: 91: Core t (s) Wall t (s) (%) 91: Time: 0.096 0.048 198.8 91: (ns/day) (hour/ns) 91: Performance: 30.383 0.790 91: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_20_sim.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 91: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 91: 91: Using 1 MPI thread 91: Using 2 OpenMP threads 91: 91: 91: NOTE: The number of threads is not equal to the number of (logical) cpus 91: and the -pin option is set to auto: will not pin threads to cpus. 91: This can lead to significant performance degradation. 91: Consider using -pin on (and -pinoffset in case you run multiple jobs). 91: starting mdrun 'spc2' 91: 16 steps, 0.0 ps. 91: 91: Writing final coordinates. 91: 91: Core t (s) Wall t (s) (%) 91: Time: 0.056 0.028 198.4 91: (ns/day) (hour/ns) 91: Performance: 51.941 0.462 91: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_20_sim1.edr as double precision energy file 91: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_20_sim2.edr as double precision energy file 91: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 91: 91: [ OK ] SimulatorsAreEquivalentDefaultLegacy/SimulatorComparisonTest.WithinTolerances/20 (5921 ms) 91: [ RUN ] SimulatorsAreEquivalentDefaultLegacy/SimulatorComparisonTest.WithinTolerances/21 91: 91: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_21_input.mdp]: 91: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 91: that with the Verlet scheme, nstlist has no effect on the accuracy of 91: your simulation. 91: 91: 91: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_21_input.mdp]: 91: Setting nstcalcenergy (100) equal to nstenergy (4) 91: 91: Generating 1-4 interactions: fudge = 0.5 91: Number of degrees of freedom in T-Coupling group System is 27.00 91: 91: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_21_input.mdp]: 91: You are using a plain Coulomb cut-off, which might produce artifacts. 91: You might want to consider using PME electrostatics. 91: 91: 91: 91: There were 3 NOTEs 91: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_21_sim.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 91: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 91: 91: Using 1 MPI thread 91: Using 2 OpenMP threads 91: 91: 91: NOTE: The number of threads is not equal to the number of (logical) cpus 91: and the -pin option is set to auto: will not pin threads to cpus. 91: This can lead to significant performance degradation. 91: Consider using -pin on (and -pinoffset in case you run multiple jobs). 91: starting mdrun 'spc2' 91: 16 steps, 0.0 ps. 91: Generated 330891 of the 330891 non-bonded parameter combinations 91: 91: Generated 330891 of the 330891 1-4 parameter combinations 91: 91: Excluding 2 bonded neighbours molecule type 'SOL' 91: 91: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/tip3p5.gro' 91: 91: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 91: 91: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 91: 91: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 91: 91: Note that mdrun will redetermine rlist based on the actual pair-list setup 91: 91: This run will generate roughly 0 Mb of data 91: 91: Writing final coordinates. 91: 91: Core t (s) Wall t (s) (%) 91: Time: 0.086 0.043 198.5 91: (ns/day) (hour/ns) 91: Performance: 33.957 0.707 91: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_21_sim.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 91: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 91: 91: Using 1 MPI thread 91: Using 2 OpenMP threads 91: 91: 91: NOTE: The number of threads is not equal to the number of (logical) cpus 91: and the -pin option is set to auto: will not pin threads to cpus. 91: This can lead to significant performance degradation. 91: Consider using -pin on (and -pinoffset in case you run multiple jobs). 91: starting mdrun 'spc2' 91: 16 steps, 0.0 ps. 91: 91: Writing final coordinates. 91: 91: NOTE: 13 % of the run time was spent in pair search, 91: you might want to increase nstlist (this has no effect on accuracy) 91: 91: Core t (s) Wall t (s) (%) 91: Time: 0.066 0.033 198.5 91: (ns/day) (hour/ns) 91: Performance: 44.304 0.542 91: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_21_sim1.edr as double precision energy file 91: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_21_sim2.edr as double precision energy file 91: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 91: 91: [ OK ] SimulatorsAreEquivalentDefaultLegacy/SimulatorComparisonTest.WithinTolerances/21 (5905 ms) 91: [ RUN ] SimulatorsAreEquivalentDefaultLegacy/SimulatorComparisonTest.WithinTolerances/22 91: 91: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_22_input.mdp]: 91: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 91: that with the Verlet scheme, nstlist has no effect on the accuracy of 91: your simulation. 91: 91: 91: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_22_input.mdp]: 91: Setting nstcalcenergy (100) equal to nstenergy (4) 91: 91: 91: WARNING 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_22_input.mdp]: 91: The Berendsen barostat does not generate any strictly correct ensemble, 91: and should not be used for new production simulations (in our opinion). 91: We recommend using the C-rescale barostat instead. 91: 91: Generating 1-4 interactions: fudge = 0.5 91: Number of degrees of freedom in T-Coupling group System is 27.00 91: 91: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_22_input.mdp]: 91: You are using a plain Coulomb cut-off, which might produce artifacts. 91: You might want to consider using PME electrostatics. 91: 91: 91: 91: There were 3 NOTEs 91: 91: There was 1 WARNING 91: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_22_sim.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 91: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 91: 91: Using 1 MPI thread 91: Using 2 OpenMP threads 91: 91: 91: NOTE: The number of threads is not equal to the number of (logical) cpus 91: and the -pin option is set to auto: will not pin threads to cpus. 91: This can lead to significant performance degradation. 91: Consider using -pin on (and -pinoffset in case you run multiple jobs). 91: starting mdrun 'spc2' 91: 16 steps, 0.0 ps. 91: Generated 330891 of the 330891 non-bonded parameter combinations 91: 91: Generated 330891 of the 330891 1-4 parameter combinations 91: 91: Excluding 2 bonded neighbours molecule type 'SOL' 91: 91: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/tip3p5.gro' 91: 91: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 91: 91: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 91: 91: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 91: 91: Note that mdrun will redetermine rlist based on the actual pair-list setup 91: 91: This run will generate roughly 0 Mb of data 91: 91: Writing final coordinates. 91: 91: Core t (s) Wall t (s) (%) 91: Time: 0.086 0.043 198.7 91: (ns/day) (hour/ns) 91: Performance: 34.041 0.705 91: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_22_sim.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 91: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 91: 91: Using 1 MPI thread 91: Using 2 OpenMP threads 91: 91: 91: NOTE: The number of threads is not equal to the number of (logical) cpus 91: and the -pin option is set to auto: will not pin threads to cpus. 91: This can lead to significant performance degradation. 91: Consider using -pin on (and -pinoffset in case you run multiple jobs). 91: starting mdrun 'spc2' 91: 16 steps, 0.0 ps. 91: 91: Writing final coordinates. 91: 91: Core t (s) Wall t (s) (%) 91: Time: 0.047 0.024 198.1 91: (ns/day) (hour/ns) 91: Performance: 61.712 0.389 91: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_22_sim1.edr as double precision energy file 91: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_22_sim2.edr as double precision energy file 91: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 91: 91: [ OK ] SimulatorsAreEquivalentDefaultLegacy/SimulatorComparisonTest.WithinTolerances/22 (5827 ms) 91: [ RUN ] SimulatorsAreEquivalentDefaultLegacy/SimulatorComparisonTest.WithinTolerances/23 91: 91: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_23_input.mdp]: 91: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 91: that with the Verlet scheme, nstlist has no effect on the accuracy of 91: your simulation. 91: 91: 91: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_23_input.mdp]: 91: Setting nstcalcenergy (100) equal to nstenergy (4) 91: 91: Generating 1-4 interactions: fudge = 0.5 91: Number of degrees of freedom in T-Coupling group System is 27.00 91: 91: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_23_input.mdp]: 91: You are using a plain Coulomb cut-off, which might produce artifacts. 91: You might want to consider using PME electrostatics. 91: 91: 91: 91: There were 3 NOTEs 91: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_23_sim.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 91: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 91: 91: Using 1 MPI thread 91: Using 2 OpenMP threads 91: 91: 91: NOTE: The number of threads is not equal to the number of (logical) cpus 91: and the -pin option is set to auto: will not pin threads to cpus. 91: This can lead to significant performance degradation. 91: Consider using -pin on (and -pinoffset in case you run multiple jobs). 91: starting mdrun 'spc2' 91: 16 steps, 0.0 ps. 91: Generated 330891 of the 330891 non-bonded parameter combinations 91: 91: Generated 330891 of the 330891 1-4 parameter combinations 91: 91: Excluding 2 bonded neighbours molecule type 'SOL' 91: 91: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/tip3p5.gro' 91: 91: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 91: 91: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 91: 91: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 91: 91: Note that mdrun will redetermine rlist based on the actual pair-list setup 91: 91: This run will generate roughly 0 Mb of data 91: 91: Writing final coordinates. 91: 91: Core t (s) Wall t (s) (%) 91: Time: 0.061 0.031 198.2 91: (ns/day) (hour/ns) 91: Performance: 47.498 0.505 91: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_23_sim.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 91: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 91: 91: Using 1 MPI thread 91: Using 2 OpenMP threads 91: 91: 91: NOTE: The number of threads is not equal to the number of (logical) cpus 91: and the -pin option is set to auto: will not pin threads to cpus. 91: This can lead to significant performance degradation. 91: Consider using -pin on (and -pinoffset in case you run multiple jobs). 91: starting mdrun 'spc2' 91: 16 steps, 0.0 ps. 91: 91: Writing final coordinates. 91: 91: Core t (s) Wall t (s) (%) 91: Time: 0.049 0.025 198.1 91: (ns/day) (hour/ns) 91: Performance: 59.826 0.401 91: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_23_sim1.edr as double precision energy file 91: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_23_sim2.edr as double precision energy file 91: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 91: 91: [ OK ] SimulatorsAreEquivalentDefaultLegacy/SimulatorComparisonTest.WithinTolerances/23 (5806 ms) 91: [ RUN ] SimulatorsAreEquivalentDefaultLegacy/SimulatorComparisonTest.WithinTolerances/24 91: 91: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_24_input.mdp]: 91: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 91: that with the Verlet scheme, nstlist has no effect on the accuracy of 91: your simulation. 91: 91: 91: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_24_input.mdp]: 91: Setting nstcalcenergy (100) equal to nstenergy (4) 91: 91: 91: WARNING 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_24_input.mdp]: 91: The Berendsen thermostat does not generate the correct kinetic energy 91: distribution, and should not be used for new production simulations (in 91: our opinion). We would recommend the V-rescale thermostat. 91: 91: Generating 1-4 interactions: fudge = 0.5 91: Number of degrees of freedom in T-Coupling group System is 27.00 91: 91: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_24_input.mdp]: 91: You are using a plain Coulomb cut-off, which might produce artifacts. 91: You might want to consider using PME electrostatics. 91: 91: 91: 91: There were 3 NOTEs 91: 91: There was 1 WARNING 91: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_24_sim.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 91: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 91: 91: Using 1 MPI thread 91: Using 2 OpenMP threads 91: 91: 91: NOTE: The number of threads is not equal to the number of (logical) cpus 91: and the -pin option is set to auto: will not pin threads to cpus. 91: This can lead to significant performance degradation. 91: Consider using -pin on (and -pinoffset in case you run multiple jobs). 91: starting mdrun 'spc2' 91: 16 steps, 0.0 ps. 91: Generated 330891 of the 330891 non-bonded parameter combinations 91: 91: Generated 330891 of the 330891 1-4 parameter combinations 91: 91: Excluding 2 bonded neighbours molecule type 'SOL' 91: 91: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/tip3p5.gro' 91: 91: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 91: 91: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 91: 91: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 91: 91: Note that mdrun will redetermine rlist based on the actual pair-list setup 91: 91: This run will generate roughly 0 Mb of data 91: 91: Writing final coordinates. 91: 91: Core t (s) Wall t (s) (%) 91: Time: 0.075 0.038 198.6 91: (ns/day) (hour/ns) 91: Performance: 38.879 0.617 91: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_24_sim.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 91: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 91: 91: Using 1 MPI thread 91: Using 2 OpenMP threads 91: 91: 91: NOTE: The number of threads is not equal to the number of (logical) cpus 91: and the -pin option is set to auto: will not pin threads to cpus. 91: This can lead to significant performance degradation. 91: Consider using -pin on (and -pinoffset in case you run multiple jobs). 91: starting mdrun 'spc2' 91: 16 steps, 0.0 ps. 91: 91: Writing final coordinates. 91: 91: Core t (s) Wall t (s) (%) 91: Time: 0.046 0.023 198.2 91: (ns/day) (hour/ns) 91: Performance: 63.964 0.375 91: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_24_sim1.edr as double precision energy file 91: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_24_sim2.edr as double precision energy file 91: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 91: 91: [ OK ] SimulatorsAreEquivalentDefaultLegacy/SimulatorComparisonTest.WithinTolerances/24 (5757 ms) 91: [ RUN ] SimulatorsAreEquivalentDefaultLegacy/SimulatorComparisonTest.WithinTolerances/25 91: 91: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_25_input.mdp]: 91: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 91: that with the Verlet scheme, nstlist has no effect on the accuracy of 91: your simulation. 91: 91: 91: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_25_input.mdp]: 91: Setting nstcalcenergy (100) equal to nstenergy (4) 91: 91: 91: WARNING 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_25_input.mdp]: 91: The Berendsen thermostat does not generate the correct kinetic energy 91: distribution, and should not be used for new production simulations (in 91: our opinion). We would recommend the V-rescale thermostat. 91: 91: Generating 1-4 interactions: fudge = 0.5 91: Number of degrees of freedom in T-Coupling group System is 27.00 91: 91: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_25_input.mdp]: 91: You are using a plain Coulomb cut-off, which might produce artifacts. 91: You might want to consider using PME electrostatics. 91: 91: 91: 91: There were 3 NOTEs 91: 91: There was 1 WARNING 91: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_25_sim.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 91: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 91: 91: Using 1 MPI thread 91: Using 2 OpenMP threads 91: 91: 91: NOTE: The number of threads is not equal to the number of (logical) cpus 91: and the -pin option is set to auto: will not pin threads to cpus. 91: This can lead to significant performance degradation. 91: Consider using -pin on (and -pinoffset in case you run multiple jobs). 91: starting mdrun 'spc2' 91: 16 steps, 0.0 ps. 91: Generated 330891 of the 330891 non-bonded parameter combinations 91: 91: Generated 330891 of the 330891 1-4 parameter combinations 91: 91: Excluding 2 bonded neighbours molecule type 'SOL' 91: 91: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/tip3p5.gro' 91: 91: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 91: 91: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 91: 91: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 91: 91: Note that mdrun will redetermine rlist based on the actual pair-list setup 91: 91: This run will generate roughly 0 Mb of data 91: 91: Writing final coordinates. 91: 91: Core t (s) Wall t (s) (%) 91: Time: 0.074 0.038 198.3 91: (ns/day) (hour/ns) 91: Performance: 39.119 0.614 91: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_25_sim.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 91: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 91: 91: Using 1 MPI thread 91: Using 2 OpenMP threads 91: 91: 91: NOTE: The number of threads is not equal to the number of (logical) cpus 91: and the -pin option is set to auto: will not pin threads to cpus. 91: This can lead to significant performance degradation. 91: Consider using -pin on (and -pinoffset in case you run multiple jobs). 91: starting mdrun 'spc2' 91: 16 steps, 0.0 ps. 91: 91: Writing final coordinates. 91: 91: Core t (s) Wall t (s) (%) 91: Time: 0.084 0.042 198.7 91: (ns/day) (hour/ns) 91: Performance: 34.900 0.688 91: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_25_sim1.edr as double precision energy file 91: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_25_sim2.edr as double precision energy file 91: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 91: 91: [ OK ] SimulatorsAreEquivalentDefaultLegacy/SimulatorComparisonTest.WithinTolerances/25 (5824 ms) 91: [ RUN ] SimulatorsAreEquivalentDefaultLegacy/SimulatorComparisonTest.WithinTolerances/26 91: 91: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_26_input.mdp]: 91: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 91: that with the Verlet scheme, nstlist has no effect on the accuracy of 91: your simulation. 91: 91: 91: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_26_input.mdp]: 91: Setting nstcalcenergy (100) equal to nstenergy (4) 91: 91: 91: WARNING 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_26_input.mdp]: 91: The Berendsen thermostat does not generate the correct kinetic energy 91: distribution, and should not be used for new production simulations (in 91: our opinion). We would recommend the V-rescale thermostat. 91: 91: 91: WARNING 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_26_input.mdp]: 91: The Berendsen barostat does not generate any strictly correct ensemble, 91: and should not be used for new production simulations (in our opinion). 91: We recommend using the C-rescale barostat instead. 91: 91: Generating 1-4 interactions: fudge = 0.5 91: Number of degrees of freedom in T-Coupling group System is 27.00 91: 91: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_26_input.mdp]: 91: You are using a plain Coulomb cut-off, which might produce artifacts. 91: You might want to consider using PME electrostatics. 91: 91: 91: 91: There were 3 NOTEs 91: 91: There were 2 WARNINGs 91: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_26_sim.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 91: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 91: 91: Using 1 MPI thread 91: Using 2 OpenMP threads 91: 91: 91: NOTE: The number of threads is not equal to the number of (logical) cpus 91: and the -pin option is set to auto: will not pin threads to cpus. 91: This can lead to significant performance degradation. 91: Consider using -pin on (and -pinoffset in case you run multiple jobs). 91: starting mdrun 'spc2' 91: 16 steps, 0.0 ps. 91: Generated 330891 of the 330891 non-bonded parameter combinations 91: 91: Generated 330891 of the 330891 1-4 parameter combinations 91: 91: Excluding 2 bonded neighbours molecule type 'SOL' 91: 91: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/tip3p5.gro' 91: 91: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 91: 91: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 91: 91: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 91: 91: Note that mdrun will redetermine rlist based on the actual pair-list setup 91: 91: This run will generate roughly 0 Mb of data 91: 91: Writing final coordinates. 91: 91: Core t (s) Wall t (s) (%) 91: Time: 0.054 0.027 197.9 91: (ns/day) (hour/ns) 91: Performance: 53.520 0.448 91: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_26_sim.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 91: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 91: 91: Using 1 MPI thread 91: Using 2 OpenMP threads 91: 91: 91: NOTE: The number of threads is not equal to the number of (logical) cpus 91: and the -pin option is set to auto: will not pin threads to cpus. 91: This can lead to significant performance degradation. 91: Consider using -pin on (and -pinoffset in case you run multiple jobs). 91: starting mdrun 'spc2' 91: 16 steps, 0.0 ps. 91: 91: Writing final coordinates. 91: 91: Core t (s) Wall t (s) (%) 91: Time: 0.056 0.028 198.3 91: (ns/day) (hour/ns) 91: Performance: 51.963 0.462 91: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_26_sim1.edr as double precision energy file 91: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_26_sim2.edr as double precision energy file 91: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 91: 91: [ OK ] SimulatorsAreEquivalentDefaultLegacy/SimulatorComparisonTest.WithinTolerances/26 (5822 ms) 91: [ RUN ] SimulatorsAreEquivalentDefaultLegacy/SimulatorComparisonTest.WithinTolerances/27 91: 91: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_27_input.mdp]: 91: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 91: that with the Verlet scheme, nstlist has no effect on the accuracy of 91: your simulation. 91: 91: 91: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_27_input.mdp]: 91: Setting nstcalcenergy (100) equal to nstenergy (4) 91: 91: 91: WARNING 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_27_input.mdp]: 91: The Berendsen thermostat does not generate the correct kinetic energy 91: distribution, and should not be used for new production simulations (in 91: our opinion). We would recommend the V-rescale thermostat. 91: 91: Generating 1-4 interactions: fudge = 0.5 91: Number of degrees of freedom in T-Coupling group System is 27.00 91: 91: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_27_input.mdp]: 91: You are using a plain Coulomb cut-off, which might produce artifacts. 91: You might want to consider using PME electrostatics. 91: 91: 91: 91: There were 3 NOTEs 91: 91: There was 1 WARNING 91: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_27_sim.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 91: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 91: 91: Using 1 MPI thread 91: Using 2 OpenMP threads 91: 91: 91: NOTE: The number of threads is not equal to the number of (logical) cpus 91: and the -pin option is set to auto: will not pin threads to cpus. 91: This can lead to significant performance degradation. 91: Consider using -pin on (and -pinoffset in case you run multiple jobs). 91: starting mdrun 'spc2' 91: 16 steps, 0.0 ps. 91: Generated 330891 of the 330891 non-bonded parameter combinations 91: 91: Generated 330891 of the 330891 1-4 parameter combinations 91: 91: Excluding 2 bonded neighbours molecule type 'SOL' 91: 91: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/tip3p5.gro' 91: 91: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 91: 91: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 91: 91: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 91: 91: Note that mdrun will redetermine rlist based on the actual pair-list setup 91: 91: This run will generate roughly 0 Mb of data 91: 91: Writing final coordinates. 91: 91: Core t (s) Wall t (s) (%) 91: Time: 0.089 0.045 198.6 91: (ns/day) (hour/ns) 91: Performance: 32.659 0.735 91: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_27_sim.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 91: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 91: 91: Using 1 MPI thread 91: Using 2 OpenMP threads 91: 91: 91: NOTE: The number of threads is not equal to the number of (logical) cpus 91: and the -pin option is set to auto: will not pin threads to cpus. 91: This can lead to significant performance degradation. 91: Consider using -pin on (and -pinoffset in case you run multiple jobs). 91: starting mdrun 'spc2' 91: 16 steps, 0.0 ps. 91: 91: Writing final coordinates. 91: 91: Core t (s) Wall t (s) (%) 91: Time: 0.058 0.029 198.4 91: (ns/day) (hour/ns) 91: Performance: 50.502 0.475 91: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_27_sim1.edr as double precision energy file 91: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_27_sim2.edr as double precision energy file 91: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 91: 91: [ OK ] SimulatorsAreEquivalentDefaultLegacy/SimulatorComparisonTest.WithinTolerances/27 (5788 ms) 91: [ RUN ] SimulatorsAreEquivalentDefaultLegacy/SimulatorComparisonTest.WithinTolerances/28 91: 91: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_28_input.mdp]: 91: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 91: that with the Verlet scheme, nstlist has no effect on the accuracy of 91: your simulation. 91: 91: 91: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_28_input.mdp]: 91: Setting nstcalcenergy (100) equal to nstenergy (4) 91: 91: 91: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_28_input.mdp]: 91: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 91: 1 91: 91: Generating 1-4 interactions: fudge = 0.5 91: Number of degrees of freedom in T-Coupling group System is 27.00 91: 91: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_28_input.mdp]: 91: You are using a plain Coulomb cut-off, which might produce artifacts. 91: You might want to consider using PME electrostatics. 91: 91: 91: 91: There were 4 NOTEs 91: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_28_sim.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 91: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 91: 91: Using 1 MPI thread 91: Using 2 OpenMP threads 91: 91: 91: NOTE: The number of threads is not equal to the number of (logical) cpus 91: and the -pin option is set to auto: will not pin threads to cpus. 91: This can lead to significant performance degradation. 91: Consider using -pin on (and -pinoffset in case you run multiple jobs). 91: starting mdrun 'spc2' 91: 16 steps, 0.0 ps. 91: Generated 330891 of the 330891 non-bonded parameter combinations 91: 91: Generated 330891 of the 330891 1-4 parameter combinations 91: 91: Excluding 2 bonded neighbours molecule type 'SOL' 91: 91: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/tip3p5.gro' 91: 91: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 91: 91: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 91: 91: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 91: 91: Note that mdrun will redetermine rlist based on the actual pair-list setup 91: 91: This run will generate roughly 0 Mb of data 91: 91: Writing final coordinates. 91: 91: Core t (s) Wall t (s) (%) 91: Time: 0.083 0.042 198.7 91: (ns/day) (hour/ns) 91: Performance: 35.270 0.680 91: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_28_sim.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 91: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 91: 91: Using 1 MPI thread 91: Using 2 OpenMP threads 91: 91: 91: NOTE: The number of threads is not equal to the number of (logical) cpus 91: and the -pin option is set to auto: will not pin threads to cpus. 91: This can lead to significant performance degradation. 91: Consider using -pin on (and -pinoffset in case you run multiple jobs). 91: starting mdrun 'spc2' 91: 16 steps, 0.0 ps. 91: 91: Writing final coordinates. 91: 91: Core t (s) Wall t (s) (%) 91: Time: 0.059 0.030 198.5 91: (ns/day) (hour/ns) 91: Performance: 49.014 0.490 91: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_28_sim1.edr as double precision energy file 91: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_28_sim2.edr as double precision energy file 91: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 91: 91: [ OK ] SimulatorsAreEquivalentDefaultLegacy/SimulatorComparisonTest.WithinTolerances/28 (5866 ms) 91: [ RUN ] SimulatorsAreEquivalentDefaultLegacy/SimulatorComparisonTest.WithinTolerances/29 91: 91: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_29_input.mdp]: 91: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 91: that with the Verlet scheme, nstlist has no effect on the accuracy of 91: your simulation. 91: 91: 91: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_29_input.mdp]: 91: Setting nstcalcenergy (100) equal to nstenergy (4) 91: 91: 91: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_29_input.mdp]: 91: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 91: 1 91: 91: Generating 1-4 interactions: fudge = 0.5 91: Number of degrees of freedom in T-Coupling group System is 27.00 91: 91: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_29_input.mdp]: 91: You are using a plain Coulomb cut-off, which might produce artifacts. 91: You might want to consider using PME electrostatics. 91: 91: 91: 91: There were 4 NOTEs 91: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_29_sim.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 91: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 91: 91: Using 1 MPI thread 91: Using 2 OpenMP threads 91: 91: 91: NOTE: The number of threads is not equal to the number of (logical) cpus 91: and the -pin option is set to auto: will not pin threads to cpus. 91: This can lead to significant performance degradation. 91: Consider using -pin on (and -pinoffset in case you run multiple jobs). 91: starting mdrun 'spc2' 91: 16 steps, 0.0 ps. 91: Generated 330891 of the 330891 non-bonded parameter combinations 91: 91: Generated 330891 of the 330891 1-4 parameter combinations 91: 91: Excluding 2 bonded neighbours molecule type 'SOL' 91: 91: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/tip3p5.gro' 91: 91: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 91: 91: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 91: 91: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 91: 91: Note that mdrun will redetermine rlist based on the actual pair-list setup 91: 91: This run will generate roughly 0 Mb of data 91: 91: Writing final coordinates. 91: 91: Core t (s) Wall t (s) (%) 91: Time: 0.087 0.044 198.7 91: (ns/day) (hour/ns) 91: Performance: 33.548 0.715 91: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_29_sim.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 91: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 91: 91: Using 1 MPI thread 91: Using 2 OpenMP threads 91: 91: 91: NOTE: The number of threads is not equal to the number of (logical) cpus 91: and the -pin option is set to auto: will not pin threads to cpus. 91: This can lead to significant performance degradation. 91: Consider using -pin on (and -pinoffset in case you run multiple jobs). 91: starting mdrun 'spc2' 91: 16 steps, 0.0 ps. 91: 91: Writing final coordinates. 91: 91: Core t (s) Wall t (s) (%) 91: Time: 0.058 0.029 198.4 91: (ns/day) (hour/ns) 91: Performance: 50.454 0.476 91: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_29_sim1.edr as double precision energy file 91: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_29_sim2.edr as double precision energy file 91: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 91: 91: [ OK ] SimulatorsAreEquivalentDefaultLegacy/SimulatorComparisonTest.WithinTolerances/29 (5843 ms) 91: [ RUN ] SimulatorsAreEquivalentDefaultLegacy/SimulatorComparisonTest.WithinTolerances/30 91: 91: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_30_input.mdp]: 91: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 91: that with the Verlet scheme, nstlist has no effect on the accuracy of 91: your simulation. 91: 91: 91: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_30_input.mdp]: 91: Setting nstcalcenergy (100) equal to nstenergy (4) 91: 91: 91: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_30_input.mdp]: 91: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 91: 1 91: 91: 91: WARNING 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_30_input.mdp]: 91: The Berendsen barostat does not generate any strictly correct ensemble, 91: and should not be used for new production simulations (in our opinion). 91: We recommend using the C-rescale barostat instead. 91: 91: Generating 1-4 interactions: fudge = 0.5 91: Number of degrees of freedom in T-Coupling group System is 27.00 91: 91: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_30_input.mdp]: 91: You are using a plain Coulomb cut-off, which might produce artifacts. 91: You might want to consider using PME electrostatics. 91: 91: 91: 91: There were 4 NOTEs 91: 91: There was 1 WARNING 91: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_30_sim.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 91: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 91: 91: Using 1 MPI thread 91: Using 2 OpenMP threads 91: 91: 91: NOTE: The number of threads is not equal to the number of (logical) cpus 91: and the -pin option is set to auto: will not pin threads to cpus. 91: This can lead to significant performance degradation. 91: Consider using -pin on (and -pinoffset in case you run multiple jobs). 91: starting mdrun 'spc2' 91: 16 steps, 0.0 ps. 91: Generated 330891 of the 330891 non-bonded parameter combinations 91: 91: Generated 330891 of the 330891 1-4 parameter combinations 91: 91: Excluding 2 bonded neighbours molecule type 'SOL' 91: 91: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/tip3p5.gro' 91: 91: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 91: 91: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 91: 91: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 91: 91: Note that mdrun will redetermine rlist based on the actual pair-list setup 91: 91: This run will generate roughly 0 Mb of data 91: 91: Writing final coordinates. 91: 91: Core t (s) Wall t (s) (%) 91: Time: 0.097 0.049 198.7 91: (ns/day) (hour/ns) 91: Performance: 30.227 0.794 91: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_30_sim.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 91: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 91: 91: Using 1 MPI thread 91: Using 2 OpenMP threads 91: 91: 91: NOTE: The number of threads is not equal to the number of (logical) cpus 91: and the -pin option is set to auto: will not pin threads to cpus. 91: This can lead to significant performance degradation. 91: Consider using -pin on (and -pinoffset in case you run multiple jobs). 91: starting mdrun 'spc2' 91: 16 steps, 0.0 ps. 91: 91: Writing final coordinates. 91: 91: Core t (s) Wall t (s) (%) 91: Time: 0.062 0.031 198.5 91: (ns/day) (hour/ns) 91: Performance: 46.989 0.511 91: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_30_sim1.edr as double precision energy file 91: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_30_sim2.edr as double precision energy file 91: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 91: 91: [ OK ] SimulatorsAreEquivalentDefaultLegacy/SimulatorComparisonTest.WithinTolerances/30 (5833 ms) 91: [ RUN ] SimulatorsAreEquivalentDefaultLegacy/SimulatorComparisonTest.WithinTolerances/31 91: 91: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_31_input.mdp]: 91: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 91: that with the Verlet scheme, nstlist has no effect on the accuracy of 91: your simulation. 91: 91: 91: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_31_input.mdp]: 91: Setting nstcalcenergy (100) equal to nstenergy (4) 91: 91: 91: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_31_input.mdp]: 91: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 91: 1 91: 91: Generating 1-4 interactions: fudge = 0.5 91: Number of degrees of freedom in T-Coupling group System is 27.00 91: 91: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_31_input.mdp]: 91: You are using a plain Coulomb cut-off, which might produce artifacts. 91: You might want to consider using PME electrostatics. 91: 91: 91: 91: There were 4 NOTEs 91: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_31_sim.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 91: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 91: 91: Using 1 MPI thread 91: Using 2 OpenMP threads 91: 91: 91: NOTE: The number of threads is not equal to the number of (logical) cpus 91: and the -pin option is set to auto: will not pin threads to cpus. 91: This can lead to significant performance degradation. 91: Consider using -pin on (and -pinoffset in case you run multiple jobs). 91: starting mdrun 'spc2' 91: 16 steps, 0.0 ps. 91: Generated 330891 of the 330891 non-bonded parameter combinations 91: 91: Generated 330891 of the 330891 1-4 parameter combinations 91: 91: Excluding 2 bonded neighbours molecule type 'SOL' 91: 91: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/tip3p5.gro' 91: 91: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 91: 91: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 91: 91: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 91: 91: Note that mdrun will redetermine rlist based on the actual pair-list setup 91: 91: This run will generate roughly 0 Mb of data 91: 91: Writing final coordinates. 91: 91: Core t (s) Wall t (s) (%) 91: Time: 0.104 0.052 198.9 91: (ns/day) (hour/ns) 91: Performance: 28.120 0.853 91: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_31_sim.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 91: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 91: 91: Using 1 MPI thread 91: Using 2 OpenMP threads 91: 91: 91: NOTE: The number of threads is not equal to the number of (logical) cpus 91: and the -pin option is set to auto: will not pin threads to cpus. 91: This can lead to significant performance degradation. 91: Consider using -pin on (and -pinoffset in case you run multiple jobs). 91: starting mdrun 'spc2' 91: 16 steps, 0.0 ps. 91: 91: Writing final coordinates. 91: 91: Core t (s) Wall t (s) (%) 91: Time: 0.081 0.041 198.9 91: (ns/day) (hour/ns) 91: Performance: 36.241 0.662 91: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_31_sim1.edr as double precision energy file 91: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_31_sim2.edr as double precision energy file 91: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 91: 91: [ OK ] SimulatorsAreEquivalentDefaultLegacy/SimulatorComparisonTest.WithinTolerances/31 (5855 ms) 91: [----------] 32 tests from SimulatorsAreEquivalentDefaultLegacy/SimulatorComparisonTest (89185 ms total) 91: 91: [----------] 1 test from SimulatorsAreEquivalentDefaultModularPull/SimulatorComparisonTest 91: [ RUN ] SimulatorsAreEquivalentDefaultModularPull/SimulatorComparisonTest.WithinTolerances/0 91: 91: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModularPull_SimulatorComparisonTest_WithinTolerances_0_input.mdp]: 91: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 91: that with the Verlet scheme, nstlist has no effect on the accuracy of 91: your simulation. 91: 91: 91: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModularPull_SimulatorComparisonTest_WithinTolerances_0_input.mdp]: 91: Setting nstcalcenergy (100) equal to nstenergy (4) 91: 91: Generating 1-4 interactions: fudge = 0.5 91: Pull group 1 'FirstWaterMolecule' has 3 atoms 91: Pull group 2 'SecondWaterMolecule' has 3 atoms 91: Number of degrees of freedom in T-Coupling group System is 9.00 91: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 91: 91: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModularPull_SimulatorComparisonTest_WithinTolerances_0_input.mdp]: 91: NVE simulation: will use the initial temperature of 2573.591 K for 91: determining the Verlet buffer size 91: 91: Pull group natoms pbc atom distance at start reference at t=0 91: 1 3 2 91: 2 3 5 1.112 nm 1.000 nm 91: 91: There were 3 NOTEs 91: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModularPull_SimulatorComparisonTest_WithinTolerances_0_sim.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 91: Can not increase nstlist because an NVE ensemble is used 91: Using 1 MPI thread 91: Using 2 OpenMP threads 91: 91: 91: NOTE: The number of threads is not equal to the number of (logical) cpus 91: and the -pin option is set to auto: will not pin threads to cpus. 91: This can lead to significant performance degradation. 91: Consider using -pin on (and -pinoffset in case you run multiple jobs). 91: starting mdrun 'spc2' 91: 16 steps, 0.0 ps. 91: Generated 3 of the 3 non-bonded parameter combinations 91: 91: Generated 3 of the 3 1-4 parameter combinations 91: 91: Excluding 2 bonded neighbours molecule type 'SOL' 91: 91: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/spc2.gro' 91: 91: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 2573.59 K 91: 91: Calculated rlist for 1x1 atom pair-list as 0.877 nm, buffer size 0.177 nm 91: 91: Set rlist, assuming 4x4 atom pair-list, to 0.862 nm, buffer size 0.162 nm 91: 91: Note that mdrun will redetermine rlist based on the actual pair-list setup 91: 91: This run will generate roughly 0 Mb of data 91: 91: Writing final coordinates. 91: 91: Core t (s) Wall t (s) (%) 91: Time: 0.068 0.034 198.7 91: (ns/day) (hour/ns) 91: Performance: 43.193 0.556 91: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModularPull_SimulatorComparisonTest_WithinTolerances_0_sim.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 91: Can not increase nstlist because an NVE ensemble is used 91: Using 1 MPI thread 91: Using 2 OpenMP threads 91: 91: 91: NOTE: The number of threads is not equal to the number of (logical) cpus 91: and the -pin option is set to auto: will not pin threads to cpus. 91: This can lead to significant performance degradation. 91: Consider using -pin on (and -pinoffset in case you run multiple jobs). 91: starting mdrun 'spc2' 91: 16 steps, 0.0 ps. 91: 91: Writing final coordinates. 91: 91: Core t (s) Wall t (s) (%) 91: Time: 0.053 0.027 197.5 91: (ns/day) (hour/ns) 91: Performance: 54.665 0.439 91: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModularPull_SimulatorComparisonTest_WithinTolerances_0_sim1.edr as double precision energy file 91: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModularPull_SimulatorComparisonTest_WithinTolerances_0_sim2.edr as double precision energy file 91: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 91: 91: [ OK ] SimulatorsAreEquivalentDefaultModularPull/SimulatorComparisonTest.WithinTolerances/0 (127 ms) 91: [----------] 1 test from SimulatorsAreEquivalentDefaultModularPull/SimulatorComparisonTest (127 ms total) 91: 91: [----------] 1 test from SimulatorsAreEquivalentDefaultLegacyPull/SimulatorComparisonTest 91: [ RUN ] SimulatorsAreEquivalentDefaultLegacyPull/SimulatorComparisonTest.WithinTolerances/0 91: 91: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacyPull_SimulatorComparisonTest_WithinTolerances_0_input.mdp]: 91: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 91: that with the Verlet scheme, nstlist has no effect on the accuracy of 91: your simulation. 91: 91: 91: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacyPull_SimulatorComparisonTest_WithinTolerances_0_input.mdp]: 91: Setting nstcalcenergy (100) equal to nstenergy (4) 91: 91: Generating 1-4 interactions: fudge = 0.5 91: Pull group 1 'FirstWaterMolecule' has 3 atoms 91: Pull group 2 'SecondWaterMolecule' has 3 atoms 91: Number of degrees of freedom in T-Coupling group System is 9.00 91: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 91: 91: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacyPull_SimulatorComparisonTest_WithinTolerances_0_input.mdp]: 91: NVE simulation: will use the initial temperature of 2573.591 K for 91: determining the Verlet buffer size 91: 91: Pull group natoms pbc atom distance at start reference at t=0 91: 1 3 2 91: 2 3 5 1.112 nm 1.000 nm 91: 91: There were 3 NOTEs 91: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacyPull_SimulatorComparisonTest_WithinTolerances_0_sim.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 91: Can not increase nstlist because an NVE ensemble is used 91: Using 1 MPI thread 91: Using 2 OpenMP threads 91: 91: 91: NOTE: The number of threads is not equal to the number of (logical) cpus 91: and the -pin option is set to auto: will not pin threads to cpus. 91: This can lead to significant performance degradation. 91: Consider using -pin on (and -pinoffset in case you run multiple jobs). 91: starting mdrun 'spc2' 91: 16 steps, 0.0 ps. 91: Generated 3 of the 3 non-bonded parameter combinations 91: 91: Generated 3 of the 3 1-4 parameter combinations 91: 91: Excluding 2 bonded neighbours molecule type 'SOL' 91: 91: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/spc2.gro' 91: 91: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 2573.59 K 91: 91: Calculated rlist for 1x1 atom pair-list as 0.877 nm, buffer size 0.177 nm 91: 91: Set rlist, assuming 4x4 atom pair-list, to 0.862 nm, buffer size 0.162 nm 91: 91: Note that mdrun will redetermine rlist based on the actual pair-list setup 91: 91: This run will generate roughly 0 Mb of data 91: 91: Writing final coordinates. 91: 91: Core t (s) Wall t (s) (%) 91: Time: 0.052 0.026 197.6 91: (ns/day) (hour/ns) 91: Performance: 56.134 0.428 91: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacyPull_SimulatorComparisonTest_WithinTolerances_0_sim.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 91: Can not increase nstlist because an NVE ensemble is used 91: Using 1 MPI thread 91: Using 2 OpenMP threads 91: 91: 91: NOTE: The number of threads is not equal to the number of (logical) cpus 91: and the -pin option is set to auto: will not pin threads to cpus. 91: This can lead to significant performance degradation. 91: Consider using -pin on (and -pinoffset in case you run multiple jobs). 91: starting mdrun 'spc2' 91: 16 steps, 0.0 ps. 91: 91: Writing final coordinates. 91: 91: Core t (s) Wall t (s) (%) 91: Time: 0.057 0.029 198.5 91: (ns/day) (hour/ns) 91: Performance: 51.037 0.470 91: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacyPull_SimulatorComparisonTest_WithinTolerances_0_sim1.edr as double precision energy file 91: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacyPull_SimulatorComparisonTest_WithinTolerances_0_sim2.edr as double precision energy file 91: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 91: 91: [ OK ] SimulatorsAreEquivalentDefaultLegacyPull/SimulatorComparisonTest.WithinTolerances/0 (123 ms) 91: [----------] 1 test from SimulatorsAreEquivalentDefaultLegacyPull/SimulatorComparisonTest (124 ms total) 91: 91: [----------] Global test environment tear-down 91: [==========] 94 tests from 4 test suites ran. (167186 ms total) 91: [ PASSED ] 94 tests. 91/92 Test #91: MdrunSimulatorComparison .................. Passed 167.28 sec test 92 Start 92: MdrunVirtualSiteTests 92: Test command: /build/reproducible-path/gromacs-2025.1/build/basic-dp/bin/mdrun-vsites-test "-ntmpi" "2" "--gtest_output=xml:/build/reproducible-path/gromacs-2025.1/build/basic-dp/Testing/Temporary/MdrunVirtualSiteTests.xml" 92: Working Directory: /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests 92: Test timeout computed to be: 600 92: [==========] Running 37 tests from 2 test suites. 92: [----------] Global test environment set-up. 92: [----------] 1 test from VirtualSiteVelocityTest 92: [ RUN ] VirtualSiteVelocityTest.ReferenceIsCorrect 92: [ OK ] VirtualSiteVelocityTest.ReferenceIsCorrect (0 ms) 92: [----------] 1 test from VirtualSiteVelocityTest (0 ms total) 92: 92: [----------] 36 tests from VelocitiesConformToExpectations/VirtualSiteTest 92: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/0 92: 92: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_0_input.mdp]: 92: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 92: that with the Verlet scheme, nstlist has no effect on the accuracy of 92: your simulation. 92: 92: 92: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_0_input.mdp]: 92: Setting nstcalcenergy (100) equal to nstenergy (4) 92: 92: Number of degrees of freedom in T-Coupling group System is 45.00 92: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 92: 92: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_0_input.mdp]: 92: NVE simulation with an initial temperature of zero: will use a Verlet 92: buffer of 10%. Check your energy drift! 92: 92: 92: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_0_input.mdp]: 92: You are using a plain Coulomb cut-off, which might produce artifacts. 92: You might want to consider using PME electrostatics. 92: 92: 92: 92: There were 4 NOTEs 92: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_0.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 92: Can not increase nstlist because an NVE ensemble is used 92: Update groups can not be used for this system because an incompatible virtual site type is used 92: 92: Using 2 MPI threads 92: Using 1 OpenMP thread per tMPI thread 92: 92: 92: NOTE: The number of threads is not equal to the number of (logical) cpus 92: and the -pin option is set to auto: will not pin threads to cpus. 92: This can lead to significant performance degradation. 92: Consider using -pin on (and -pinoffset in case you run multiple jobs). 92: starting mdrun 'Virtual sites test system in vacuo' 92: 8 steps, 0.0 ps. 92: Generated 3 of the 6 non-bonded parameter combinations 92: 92: Excluding 3 bonded neighbours molecule type 'VSTEST' 92: 92: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/vsite_test.gro', all velocities are zero 92: 92: Cleaning up constraints and constant bonded interactions with virtual sites 92: 92: This run will generate roughly 0 Mb of data 92: 92: Writing final coordinates. 92: 92: 92: Dynamic load balancing report: 92: DLB was off during the run due to low measured imbalance. 92: Average load imbalance: 7.0%. 92: The balanceable part of the MD step is 49%, load imbalance is computed from this. 92: Part of the total run time spent waiting due to load imbalance: 3.4%. 92: 92: 92: NOTE: 42 % of the run time was spent communicating energies, 92: you might want to increase some nst* mdp options 92: 92: Core t (s) Wall t (s) (%) 92: Time: 0.055 0.028 197.4 92: (ns/day) (hour/ns) 92: Performance: 28.041 0.856 92: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_0.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 92: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_0.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 92: trr version: GMX_trn_file (double precision) 92: 92: Reading virtual site types... 92: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/0 (114 ms) 92: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/1 92: 92: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_1_input.mdp]: 92: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 92: that with the Verlet scheme, nstlist has no effect on the accuracy of 92: your simulation. 92: 92: 92: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_1_input.mdp]: 92: Setting nstcalcenergy (100) equal to nstenergy (4) 92: 92: Number of degrees of freedom in T-Coupling group System is 45.00 92: 92: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_1_input.mdp]: 92: NVE simulation with an initial temperature of zero: will use a Verlet 92: buffer of 10%. Check your energy drift! 92: 92: 92: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_1_input.mdp]: 92: You are using a plain Coulomb cut-off, which might produce artifacts. 92: You might want to consider using PME electrostatics. 92: 92: 92: 92: There were 4 NOTEs 92: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_1.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 92: Can not increase nstlist because an NVE ensemble is used 92: Update groups can not be used for this system because an incompatible virtual site type is used 92: 92: Using 2 MPI threads 92: Using 1 OpenMP thread per tMPI thread 92: 92: 92: NOTE: The number of threads is not equal to the number of (logical) cpus 92: and the -pin option is set to auto: will not pin threads to cpus. 92: This can lead to significant performance degradation. 92: Consider using -pin on (and -pinoffset in case you run multiple jobs). 92: starting mdrun 'Virtual sites test system in vacuo' 92: 8 steps, 0.0 ps. 92: Generated 3 of the 6 non-bonded parameter combinations 92: 92: Excluding 3 bonded neighbours molecule type 'VSTEST' 92: 92: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/vsite_test.gro', all velocities are zero 92: 92: Cleaning up constraints and constant bonded interactions with virtual sites 92: 92: This run will generate roughly 0 Mb of data 92: 92: Writing final coordinates. 92: 92: 92: Dynamic load balancing report: 92: DLB was off during the run due to low measured imbalance. 92: Average load imbalance: 10.2%. 92: The balanceable part of the MD step is 42%, load imbalance is computed from this. 92: Part of the total run time spent waiting due to load imbalance: 4.3%. 92: 92: 92: NOTE: 41 % of the run time was spent communicating energies, 92: you might want to increase some nst* mdp options 92: 92: Core t (s) Wall t (s) (%) 92: Time: 0.047 0.024 196.8 92: (ns/day) (hour/ns) 92: Performance: 32.853 0.731 92: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_1.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 92: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_1.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 92: 92: Reading virtual site types... 92: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/1 (106 ms) 92: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/2 92: 92: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_2_input.mdp]: 92: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 92: that with the Verlet scheme, nstlist has no effect on the accuracy of 92: your simulation. 92: 92: 92: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_2_input.mdp]: 92: Setting nstcalcenergy (100) equal to nstenergy (4) 92: 92: Number of degrees of freedom in T-Coupling group System is 45.00 92: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 92: 92: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_2_input.mdp]: 92: NVE simulation with an initial temperature of zero: will use a Verlet 92: buffer of 10%. Check your energy drift! 92: 92: 92: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_2_input.mdp]: 92: You are using a plain Coulomb cut-off, which might produce artifacts. 92: You might want to consider using PME electrostatics. 92: 92: 92: 92: There were 4 NOTEs 92: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_2.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 92: Can not increase nstlist because an NVE ensemble is used 92: Update groups can not be used for this system because an incompatible virtual site type is used 92: 92: Using 2 MPI threads 92: Using 1 OpenMP thread per tMPI thread 92: 92: 92: NOTE: The number of threads is not equal to the number of (logical) cpus 92: and the -pin option is set to auto: will not pin threads to cpus. 92: This can lead to significant performance degradation. 92: Consider using -pin on (and -pinoffset in case you run multiple jobs). 92: starting mdrun 'Virtual sites test system in vacuo' 92: 8 steps, 0.0 ps. 92: Generated 3 of the 6 non-bonded parameter combinations 92: 92: Excluding 3 bonded neighbours molecule type 'VSTEST' 92: 92: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/vsite_test.gro', all velocities are zero 92: 92: Cleaning up constraints and constant bonded interactions with virtual sites 92: 92: This run will generate roughly 0 Mb of data 92: 92: Writing final coordinates. 92: 92: 92: Dynamic load balancing report: 92: DLB was off during the run due to low measured imbalance. 92: Average load imbalance: 14.0%. 92: The balanceable part of the MD step is 27%, load imbalance is computed from this. 92: Part of the total run time spent waiting due to load imbalance: 3.7%. 92: 92: 92: NOTE: 34 % of the run time was spent communicating energies, 92: you might want to increase some nst* mdp options 92: 92: Core t (s) Wall t (s) (%) 92: Time: 0.048 0.024 197.0 92: (ns/day) (hour/ns) 92: Performance: 31.875 0.753 92: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_2.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 92: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_2.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 92: 92: Reading virtual site types... 92: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/2 (93 ms) 92: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/3 92: 92: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_3_input.mdp]: 92: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 92: that with the Verlet scheme, nstlist has no effect on the accuracy of 92: your simulation. 92: 92: 92: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_3_input.mdp]: 92: Setting nstcalcenergy (100) equal to nstenergy (4) 92: 92: Number of degrees of freedom in T-Coupling group System is 45.00 92: 92: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_3_input.mdp]: 92: There are 6 non-linear virtual site constructions. Their contribution to 92: the energy error is approximated. In most cases this does not affect the 92: error significantly. 92: 92: 92: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_3_input.mdp]: 92: You are using a plain Coulomb cut-off, which might produce artifacts. 92: You might want to consider using PME electrostatics. 92: 92: 92: 92: There were 4 NOTEs 92: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_3.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 92: Changing nstlist from 8 to 50, rlist from 0.712 to 0.801 92: 92: Update groups can not be used for this system because an incompatible virtual site type is used 92: 92: Using 2 MPI threads 92: Using 1 OpenMP thread per tMPI thread 92: 92: 92: NOTE: The number of threads is not equal to the number of (logical) cpus 92: and the -pin option is set to auto: will not pin threads to cpus. 92: This can lead to significant performance degradation. 92: Consider using -pin on (and -pinoffset in case you run multiple jobs). 92: starting mdrun 'Virtual sites test system in vacuo' 92: 8 steps, 0.0 ps. 92: Generated 3 of the 6 non-bonded parameter combinations 92: 92: Excluding 3 bonded neighbours molecule type 'VSTEST' 92: 92: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/vsite_test.gro', all velocities are zero 92: 92: Cleaning up constraints and constant bonded interactions with virtual sites 92: 92: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 92: 92: Calculated rlist for 1x1 atom pair-list as 0.715 nm, buffer size 0.015 nm 92: 92: Set rlist, assuming 4x4 atom pair-list, to 0.712 nm, buffer size 0.012 nm 92: 92: Note that mdrun will redetermine rlist based on the actual pair-list setup 92: 92: This run will generate roughly 0 Mb of data 92: 92: Writing final coordinates. 92: 92: NOTE: 44 % of the run time was spent communicating energies, 92: you might want to increase some nst* mdp options 92: 92: Core t (s) Wall t (s) (%) 92: Time: 0.064 0.032 197.4 92: (ns/day) (hour/ns) 92: Performance: 24.035 0.999 92: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_3.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 92: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_3.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 92: 92: Reading virtual site types... 92: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/3 (187 ms) 92: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/4 92: 92: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_4_input.mdp]: 92: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 92: that with the Verlet scheme, nstlist has no effect on the accuracy of 92: your simulation. 92: 92: 92: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_4_input.mdp]: 92: Setting nstcalcenergy (100) equal to nstenergy (4) 92: 92: Number of degrees of freedom in T-Coupling group System is 45.00 92: 92: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_4_input.mdp]: 92: There are 6 non-linear virtual site constructions. Their contribution to 92: the energy error is approximated. In most cases this does not affect the 92: error significantly. 92: 92: 92: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_4_input.mdp]: 92: You are using a plain Coulomb cut-off, which might produce artifacts. 92: You might want to consider using PME electrostatics. 92: 92: 92: 92: There were 4 NOTEs 92: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_4.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 92: Changing nstlist from 8 to 50, rlist from 0.712 to 0.801 92: 92: Update groups can not be used for this system because an incompatible virtual site type is used 92: 92: Using 2 MPI threads 92: Using 1 OpenMP thread per tMPI thread 92: 92: 92: NOTE: The number of threads is not equal to the number of (logical) cpus 92: and the -pin option is set to auto: will not pin threads to cpus. 92: This can lead to significant performance degradation. 92: Consider using -pin on (and -pinoffset in case you run multiple jobs). 92: starting mdrun 'Virtual sites test system in vacuo' 92: 8 steps, 0.0 ps. 92: Generated 3 of the 6 non-bonded parameter combinations 92: 92: Excluding 3 bonded neighbours molecule type 'VSTEST' 92: 92: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/vsite_test.gro', all velocities are zero 92: 92: Cleaning up constraints and constant bonded interactions with virtual sites 92: 92: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 92: 92: Calculated rlist for 1x1 atom pair-list as 0.715 nm, buffer size 0.015 nm 92: 92: Set rlist, assuming 4x4 atom pair-list, to 0.712 nm, buffer size 0.012 nm 92: 92: Note that mdrun will redetermine rlist based on the actual pair-list setup 92: 92: This run will generate roughly 0 Mb of data 92: 92: Writing final coordinates. 92: 92: NOTE: 44 % of the run time was spent communicating energies, 92: you might want to increase some nst* mdp options 92: 92: Core t (s) Wall t (s) (%) 92: Time: 0.075 0.038 197.6 92: (ns/day) (hour/ns) 92: Performance: 20.381 1.178 92: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_4.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 92: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_4.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 92: 92: Reading virtual site types... 92: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/4 (184 ms) 92: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/5 92: 92: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_5_input.mdp]: 92: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 92: that with the Verlet scheme, nstlist has no effect on the accuracy of 92: your simulation. 92: 92: 92: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_5_input.mdp]: 92: Setting nstcalcenergy (100) equal to nstenergy (4) 92: 92: Number of degrees of freedom in T-Coupling group System is 45.00 92: 92: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_5_input.mdp]: 92: There are 6 non-linear virtual site constructions. Their contribution to 92: the energy error is approximated. In most cases this does not affect the 92: error significantly. 92: 92: 92: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_5_input.mdp]: 92: You are using a plain Coulomb cut-off, which might produce artifacts. 92: You might want to consider using PME electrostatics. 92: 92: 92: 92: There were 4 NOTEs 92: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_5.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 92: Changing nstlist from 8 to 50, rlist from 0.712 to 0.801 92: 92: Update groups can not be used for this system because an incompatible virtual site type is used 92: 92: Using 2 MPI threads 92: Using 1 OpenMP thread per tMPI thread 92: 92: 92: NOTE: The number of threads is not equal to the number of (logical) cpus 92: and the -pin option is set to auto: will not pin threads to cpus. 92: This can lead to significant performance degradation. 92: Consider using -pin on (and -pinoffset in case you run multiple jobs). 92: starting mdrun 'Virtual sites test system in vacuo' 92: 8 steps, 0.0 ps. 92: Generated 3 of the 6 non-bonded parameter combinations 92: 92: Excluding 3 bonded neighbours molecule type 'VSTEST' 92: 92: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/vsite_test.gro', all velocities are zero 92: 92: Cleaning up constraints and constant bonded interactions with virtual sites 92: 92: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 92: 92: Calculated rlist for 1x1 atom pair-list as 0.715 nm, buffer size 0.015 nm 92: 92: Set rlist, assuming 4x4 atom pair-list, to 0.712 nm, buffer size 0.012 nm 92: 92: Note that mdrun will redetermine rlist based on the actual pair-list setup 92: 92: This run will generate roughly 0 Mb of data 92: 92: Writing final coordinates. 92: 92: NOTE: 42 % of the run time was spent communicating energies, 92: you might want to increase some nst* mdp options 92: 92: Core t (s) Wall t (s) (%) 92: Time: 0.045 0.023 196.2 92: (ns/day) (hour/ns) 92: Performance: 34.105 0.704 92: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_5.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 92: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_5.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 92: 92: Reading virtual site types... 92: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/5 (166 ms) 92: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/6 92: 92: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_6_input.mdp]: 92: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 92: that with the Verlet scheme, nstlist has no effect on the accuracy of 92: your simulation. 92: 92: 92: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_6_input.mdp]: 92: Setting nstcalcenergy (100) equal to nstenergy (4) 92: 92: 92: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_6_input.mdp]: 92: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 92: 1 92: 92: Number of degrees of freedom in T-Coupling group System is 45.00 92: 92: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_6_input.mdp]: 92: There are 6 non-linear virtual site constructions. Their contribution to 92: the energy error is approximated. In most cases this does not affect the 92: error significantly. 92: 92: 92: NOTE 5 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_6_input.mdp]: 92: You are using a plain Coulomb cut-off, which might produce artifacts. 92: You might want to consider using PME electrostatics. 92: 92: 92: 92: There were 5 NOTEs 92: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_6.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 92: Changing nstlist from 8 to 50, rlist from 0.712 to 0.801 92: 92: Update groups can not be used for this system because an incompatible virtual site type is used 92: 92: Using 2 MPI threads 92: Using 1 OpenMP thread per tMPI thread 92: 92: 92: NOTE: The number of threads is not equal to the number of (logical) cpus 92: and the -pin option is set to auto: will not pin threads to cpus. 92: This can lead to significant performance degradation. 92: Consider using -pin on (and -pinoffset in case you run multiple jobs). 92: starting mdrun 'Virtual sites test system in vacuo' 92: 8 steps, 0.0 ps. 92: Generated 3 of the 6 non-bonded parameter combinations 92: 92: Excluding 3 bonded neighbours molecule type 'VSTEST' 92: 92: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/vsite_test.gro', all velocities are zero 92: 92: Cleaning up constraints and constant bonded interactions with virtual sites 92: 92: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 92: 92: Calculated rlist for 1x1 atom pair-list as 0.715 nm, buffer size 0.015 nm 92: 92: Set rlist, assuming 4x4 atom pair-list, to 0.712 nm, buffer size 0.012 nm 92: 92: Note that mdrun will redetermine rlist based on the actual pair-list setup 92: 92: This run will generate roughly 0 Mb of data 92: 92: Writing final coordinates. 92: 92: NOTE: 42 % of the run time was spent communicating energies, 92: you might want to increase some nst* mdp options 92: 92: Core t (s) Wall t (s) (%) 92: Time: 0.043 0.022 196.5 92: (ns/day) (hour/ns) 92: Performance: 35.314 0.680 92: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_6.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 92: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_6.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 92: 92: Reading virtual site types... 92: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/6 (159 ms) 92: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/7 92: 92: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_7_input.mdp]: 92: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 92: that with the Verlet scheme, nstlist has no effect on the accuracy of 92: your simulation. 92: 92: 92: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_7_input.mdp]: 92: Setting nstcalcenergy (100) equal to nstenergy (4) 92: 92: 92: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_7_input.mdp]: 92: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 92: 1 92: 92: Number of degrees of freedom in T-Coupling group System is 45.00 92: 92: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_7_input.mdp]: 92: There are 6 non-linear virtual site constructions. Their contribution to 92: the energy error is approximated. In most cases this does not affect the 92: error significantly. 92: 92: 92: NOTE 5 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_7_input.mdp]: 92: You are using a plain Coulomb cut-off, which might produce artifacts. 92: You might want to consider using PME electrostatics. 92: 92: 92: 92: There were 5 NOTEs 92: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_7.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 92: Changing nstlist from 8 to 50, rlist from 0.712 to 0.801 92: 92: Update groups can not be used for this system because an incompatible virtual site type is used 92: 92: Using 2 MPI threads 92: Using 1 OpenMP thread per tMPI thread 92: 92: 92: NOTE: The number of threads is not equal to the number of (logical) cpus 92: and the -pin option is set to auto: will not pin threads to cpus. 92: This can lead to significant performance degradation. 92: Consider using -pin on (and -pinoffset in case you run multiple jobs). 92: starting mdrun 'Virtual sites test system in vacuo' 92: 8 steps, 0.0 ps. 92: Generated 3 of the 6 non-bonded parameter combinations 92: 92: Excluding 3 bonded neighbours molecule type 'VSTEST' 92: 92: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/vsite_test.gro', all velocities are zero 92: 92: Cleaning up constraints and constant bonded interactions with virtual sites 92: 92: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 92: 92: Calculated rlist for 1x1 atom pair-list as 0.715 nm, buffer size 0.015 nm 92: 92: Set rlist, assuming 4x4 atom pair-list, to 0.712 nm, buffer size 0.012 nm 92: 92: Note that mdrun will redetermine rlist based on the actual pair-list setup 92: 92: This run will generate roughly 0 Mb of data 92: 92: Writing final coordinates. 92: 92: NOTE: 42 % of the run time was spent communicating energies, 92: you might want to increase some nst* mdp options 92: 92: Core t (s) Wall t (s) (%) 92: Time: 0.044 0.023 196.1 92: (ns/day) (hour/ns) 92: Performance: 34.491 0.696 92: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_7.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 92: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_7.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 92: 92: Reading virtual site types... 92: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/7 (159 ms) 92: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/8 92: 92: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_8_input.mdp]: 92: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 92: that with the Verlet scheme, nstlist has no effect on the accuracy of 92: your simulation. 92: 92: 92: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_8_input.mdp]: 92: Setting nstcalcenergy (100) equal to nstenergy (4) 92: 92: 92: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_8_input.mdp]: 92: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 92: 1 92: 92: Number of degrees of freedom in T-Coupling group System is 45.00 92: 92: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_8_input.mdp]: 92: There are 6 non-linear virtual site constructions. Their contribution to 92: the energy error is approximated. In most cases this does not affect the 92: error significantly. 92: 92: 92: NOTE 5 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_8_input.mdp]: 92: You are using a plain Coulomb cut-off, which might produce artifacts. 92: You might want to consider using PME electrostatics. 92: 92: 92: 92: There were 5 NOTEs 92: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_8.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 92: Changing nstlist from 8 to 50, rlist from 0.712 to 0.801 92: 92: Update groups can not be used for this system because an incompatible virtual site type is used 92: 92: Using 2 MPI threads 92: Using 1 OpenMP thread per tMPI thread 92: 92: 92: NOTE: The number of threads is not equal to the number of (logical) cpus 92: and the -pin option is set to auto: will not pin threads to cpus. 92: This can lead to significant performance degradation. 92: Consider using -pin on (and -pinoffset in case you run multiple jobs). 92: starting mdrun 'Virtual sites test system in vacuo' 92: 8 steps, 0.0 ps. 92: Generated 3 of the 6 non-bonded parameter combinations 92: 92: Excluding 3 bonded neighbours molecule type 'VSTEST' 92: 92: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/vsite_test.gro', all velocities are zero 92: 92: Cleaning up constraints and constant bonded interactions with virtual sites 92: 92: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 92: 92: Calculated rlist for 1x1 atom pair-list as 0.715 nm, buffer size 0.015 nm 92: 92: Set rlist, assuming 4x4 atom pair-list, to 0.712 nm, buffer size 0.012 nm 92: 92: Note that mdrun will redetermine rlist based on the actual pair-list setup 92: 92: This run will generate roughly 0 Mb of data 92: 92: Writing final coordinates. 92: 92: NOTE: 41 % of the run time was spent communicating energies, 92: you might want to increase some nst* mdp options 92: 92: Core t (s) Wall t (s) (%) 92: Time: 0.044 0.022 196.1 92: (ns/day) (hour/ns) 92: Performance: 34.947 0.687 92: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_8.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 92: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_8.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 92: 92: Reading virtual site types... 92: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/8 (160 ms) 92: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/9 92: 92: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_9_input.mdp]: 92: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 92: that with the Verlet scheme, nstlist has no effect on the accuracy of 92: your simulation. 92: 92: 92: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_9_input.mdp]: 92: Setting nstcalcenergy (100) equal to nstenergy (4) 92: 92: Number of degrees of freedom in T-Coupling group System is 45.00 92: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 92: 92: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_9_input.mdp]: 92: NVE simulation with an initial temperature of zero: will use a Verlet 92: buffer of 10%. Check your energy drift! 92: 92: 92: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_9_input.mdp]: 92: You are using a plain Coulomb cut-off, which might produce artifacts. 92: You might want to consider using PME electrostatics. 92: 92: 92: 92: There were 4 NOTEs 92: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_9.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 92: Can not increase nstlist because an NVE ensemble is used 92: Update groups can not be used for this system because an incompatible virtual site type is used 92: 92: Using 2 MPI threads 92: Using 1 OpenMP thread per tMPI thread 92: 92: 92: NOTE: The number of threads is not equal to the number of (logical) cpus 92: and the -pin option is set to auto: will not pin threads to cpus. 92: This can lead to significant performance degradation. 92: Consider using -pin on (and -pinoffset in case you run multiple jobs). 92: starting mdrun 'Virtual sites test system in vacuo' 92: 8 steps, 0.0 ps. 92: Generated 3 of the 6 non-bonded parameter combinations 92: 92: Excluding 3 bonded neighbours molecule type 'VSTEST' 92: 92: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/vsite_test.gro', all velocities are zero 92: 92: Cleaning up constraints and constant bonded interactions with virtual sites 92: 92: This run will generate roughly 0 Mb of data 92: 92: Writing final coordinates. 92: 92: 92: Dynamic load balancing report: 92: DLB was off during the run due to low measured imbalance. 92: Average load imbalance: 8.5%. 92: The balanceable part of the MD step is 48%, load imbalance is computed from this. 92: Part of the total run time spent waiting due to load imbalance: 4.1%. 92: 92: 92: NOTE: 45 % of the run time was spent communicating energies, 92: you might want to increase some nst* mdp options 92: 92: Core t (s) Wall t (s) (%) 92: Time: 0.048 0.025 196.5 92: (ns/day) (hour/ns) 92: Performance: 31.565 0.760 92: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_9.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 92: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_9.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 92: 92: Reading virtual site types... 92: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/9 (97 ms) 92: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/10 92: 92: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_10_input.mdp]: 92: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 92: that with the Verlet scheme, nstlist has no effect on the accuracy of 92: your simulation. 92: 92: 92: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_10_input.mdp]: 92: Setting nstcalcenergy (100) equal to nstenergy (4) 92: 92: Number of degrees of freedom in T-Coupling group System is 45.00 92: 92: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_10_input.mdp]: 92: NVE simulation with an initial temperature of zero: will use a Verlet 92: buffer of 10%. Check your energy drift! 92: 92: 92: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_10_input.mdp]: 92: You are using a plain Coulomb cut-off, which might produce artifacts. 92: You might want to consider using PME electrostatics. 92: 92: 92: 92: There were 4 NOTEs 92: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_10.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 92: Can not increase nstlist because an NVE ensemble is used 92: Update groups can not be used for this system because an incompatible virtual site type is used 92: 92: Using 2 MPI threads 92: Using 1 OpenMP thread per tMPI thread 92: 92: 92: NOTE: The number of threads is not equal to the number of (logical) cpus 92: and the -pin option is set to auto: will not pin threads to cpus. 92: This can lead to significant performance degradation. 92: Consider using -pin on (and -pinoffset in case you run multiple jobs). 92: starting mdrun 'Virtual sites test system in vacuo' 92: 8 steps, 0.0 ps. 92: Generated 3 of the 6 non-bonded parameter combinations 92: 92: Excluding 3 bonded neighbours molecule type 'VSTEST' 92: 92: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/vsite_test.gro', all velocities are zero 92: 92: Cleaning up constraints and constant bonded interactions with virtual sites 92: 92: This run will generate roughly 0 Mb of data 92: 92: Writing final coordinates. 92: 92: 92: Dynamic load balancing report: 92: DLB was off during the run due to low measured imbalance. 92: Average load imbalance: 7.3%. 92: The balanceable part of the MD step is 37%, load imbalance is computed from this. 92: Part of the total run time spent waiting due to load imbalance: 2.7%. 92: 92: 92: NOTE: 38 % of the run time was spent communicating energies, 92: you might want to increase some nst* mdp options 92: 92: Core t (s) Wall t (s) (%) 92: Time: 0.046 0.023 196.6 92: (ns/day) (hour/ns) 92: Performance: 33.315 0.720 92: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_10.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 92: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_10.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 92: 92: Reading virtual site types... 92: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/10 (92 ms) 92: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/11 92: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/11 (0 ms) 92: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/12 92: 92: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_12_input.mdp]: 92: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 92: that with the Verlet scheme, nstlist has no effect on the accuracy of 92: your simulation. 92: 92: 92: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_12_input.mdp]: 92: Setting nstcalcenergy (100) equal to nstenergy (4) 92: 92: Number of degrees of freedom in T-Coupling group System is 45.00 92: 92: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_12_input.mdp]: 92: There are 6 non-linear virtual site constructions. Their contribution to 92: the energy error is approximated. In most cases this does not affect the 92: error significantly. 92: 92: 92: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_12_input.mdp]: 92: You are using a plain Coulomb cut-off, which might produce artifacts. 92: You might want to consider using PME electrostatics. 92: 92: 92: 92: There were 4 NOTEs 92: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_12.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 92: Changing nstlist from 8 to 50, rlist from 0.712 to 0.801 92: 92: Update groups can not be used for this system because an incompatible virtual site type is used 92: 92: Using 2 MPI threads 92: Using 1 OpenMP thread per tMPI thread 92: 92: 92: NOTE: The number of threads is not equal to the number of (logical) cpus 92: and the -pin option is set to auto: will not pin threads to cpus. 92: This can lead to significant performance degradation. 92: Consider using -pin on (and -pinoffset in case you run multiple jobs). 92: starting mdrun 'Virtual sites test system in vacuo' 92: 8 steps, 0.0 ps. 92: Generated 3 of the 6 non-bonded parameter combinations 92: 92: Excluding 3 bonded neighbours molecule type 'VSTEST' 92: 92: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/vsite_test.gro', all velocities are zero 92: 92: Cleaning up constraints and constant bonded interactions with virtual sites 92: 92: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 92: 92: Calculated rlist for 1x1 atom pair-list as 0.715 nm, buffer size 0.015 nm 92: 92: Set rlist, assuming 4x4 atom pair-list, to 0.712 nm, buffer size 0.012 nm 92: 92: Note that mdrun will redetermine rlist based on the actual pair-list setup 92: 92: This run will generate roughly 0 Mb of data 92: 92: Writing final coordinates. 92: 92: NOTE: 46 % of the run time was spent communicating energies, 92: you might want to increase some nst* mdp options 92: 92: Core t (s) Wall t (s) (%) 92: Time: 0.100 0.050 198.0 92: (ns/day) (hour/ns) 92: Performance: 15.456 1.553 92: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_12.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 92: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_12.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 92: 92: Reading virtual site types... 92: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/12 (199 ms) 92: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/13 92: 92: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_13_input.mdp]: 92: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 92: that with the Verlet scheme, nstlist has no effect on the accuracy of 92: your simulation. 92: 92: 92: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_13_input.mdp]: 92: Setting nstcalcenergy (100) equal to nstenergy (4) 92: 92: Number of degrees of freedom in T-Coupling group System is 45.00 92: 92: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_13_input.mdp]: 92: There are 6 non-linear virtual site constructions. Their contribution to 92: the energy error is approximated. In most cases this does not affect the 92: error significantly. 92: 92: 92: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_13_input.mdp]: 92: You are using a plain Coulomb cut-off, which might produce artifacts. 92: You might want to consider using PME electrostatics. 92: 92: 92: 92: There were 4 NOTEs 92: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_13.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 92: Changing nstlist from 8 to 50, rlist from 0.712 to 0.801 92: 92: Update groups can not be used for this system because an incompatible virtual site type is used 92: 92: Using 2 MPI threads 92: Using 1 OpenMP thread per tMPI thread 92: 92: 92: NOTE: The number of threads is not equal to the number of (logical) cpus 92: and the -pin option is set to auto: will not pin threads to cpus. 92: This can lead to significant performance degradation. 92: Consider using -pin on (and -pinoffset in case you run multiple jobs). 92: starting mdrun 'Virtual sites test system in vacuo' 92: 8 steps, 0.0 ps. 92: Generated 3 of the 6 non-bonded parameter combinations 92: 92: Excluding 3 bonded neighbours molecule type 'VSTEST' 92: 92: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/vsite_test.gro', all velocities are zero 92: 92: Cleaning up constraints and constant bonded interactions with virtual sites 92: 92: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 92: 92: Calculated rlist for 1x1 atom pair-list as 0.715 nm, buffer size 0.015 nm 92: 92: Set rlist, assuming 4x4 atom pair-list, to 0.712 nm, buffer size 0.012 nm 92: 92: Note that mdrun will redetermine rlist based on the actual pair-list setup 92: 92: This run will generate roughly 0 Mb of data 92: 92: Writing final coordinates. 92: 92: NOTE: 42 % of the run time was spent communicating energies, 92: you might want to increase some nst* mdp options 92: 92: Core t (s) Wall t (s) (%) 92: Time: 0.055 0.028 196.7 92: (ns/day) (hour/ns) 92: Performance: 27.889 0.861 92: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_13.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 92: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_13.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 92: 92: Reading virtual site types... 92: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/13 (172 ms) 92: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/14 92: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/14 (0 ms) 92: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/15 92: 92: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_15_input.mdp]: 92: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 92: that with the Verlet scheme, nstlist has no effect on the accuracy of 92: your simulation. 92: 92: 92: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_15_input.mdp]: 92: Setting nstcalcenergy (100) equal to nstenergy (4) 92: 92: Number of degrees of freedom in T-Coupling group System is 45.00 92: 92: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_15_input.mdp]: 92: There are 6 non-linear virtual site constructions. Their contribution to 92: the energy error is approximated. In most cases this does not affect the 92: error significantly. 92: 92: 92: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_15_input.mdp]: 92: You are using a plain Coulomb cut-off, which might produce artifacts. 92: You might want to consider using PME electrostatics. 92: 92: 92: 92: There were 4 NOTEs 92: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_15.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 92: Changing nstlist from 8 to 50, rlist from 0.712 to 0.801 92: 92: Update groups can not be used for this system because an incompatible virtual site type is used 92: 92: Using 2 MPI threads 92: Using 1 OpenMP thread per tMPI thread 92: 92: 92: NOTE: The number of threads is not equal to the number of (logical) cpus 92: and the -pin option is set to auto: will not pin threads to cpus. 92: This can lead to significant performance degradation. 92: Consider using -pin on (and -pinoffset in case you run multiple jobs). 92: starting mdrun 'Virtual sites test system in vacuo' 92: 8 steps, 0.0 ps. 92: Generated 3 of the 6 non-bonded parameter combinations 92: 92: Excluding 3 bonded neighbours molecule type 'VSTEST' 92: 92: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/vsite_test.gro', all velocities are zero 92: 92: Cleaning up constraints and constant bonded interactions with virtual sites 92: 92: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 92: 92: Calculated rlist for 1x1 atom pair-list as 0.715 nm, buffer size 0.015 nm 92: 92: Set rlist, assuming 4x4 atom pair-list, to 0.712 nm, buffer size 0.012 nm 92: 92: Note that mdrun will redetermine rlist based on the actual pair-list setup 92: 92: This run will generate roughly 0 Mb of data 92: 92: Writing final coordinates. 92: 92: NOTE: 58 % of the run time was spent communicating energies, 92: you might want to increase some nst* mdp options 92: 92: Core t (s) Wall t (s) (%) 92: Time: 0.074 0.037 197.9 92: (ns/day) (hour/ns) 92: Performance: 20.757 1.156 92: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_15.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 92: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_15.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 92: 92: Reading virtual site types... 92: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/15 (183 ms) 92: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/16 92: 92: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_16_input.mdp]: 92: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 92: that with the Verlet scheme, nstlist has no effect on the accuracy of 92: your simulation. 92: 92: 92: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_16_input.mdp]: 92: Setting nstcalcenergy (100) equal to nstenergy (4) 92: 92: Number of degrees of freedom in T-Coupling group System is 45.00 92: 92: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_16_input.mdp]: 92: There are 6 non-linear virtual site constructions. Their contribution to 92: the energy error is approximated. In most cases this does not affect the 92: error significantly. 92: 92: 92: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_16_input.mdp]: 92: You are using a plain Coulomb cut-off, which might produce artifacts. 92: You might want to consider using PME electrostatics. 92: 92: 92: 92: There were 4 NOTEs 92: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_16.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 92: Changing nstlist from 8 to 50, rlist from 0.712 to 0.801 92: 92: Update groups can not be used for this system because an incompatible virtual site type is used 92: 92: Using 2 MPI threads 92: Using 1 OpenMP thread per tMPI thread 92: 92: 92: NOTE: The number of threads is not equal to the number of (logical) cpus 92: and the -pin option is set to auto: will not pin threads to cpus. 92: This can lead to significant performance degradation. 92: Consider using -pin on (and -pinoffset in case you run multiple jobs). 92: starting mdrun 'Virtual sites test system in vacuo' 92: 8 steps, 0.0 ps. 92: Generated 3 of the 6 non-bonded parameter combinations 92: 92: Excluding 3 bonded neighbours molecule type 'VSTEST' 92: 92: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/vsite_test.gro', all velocities are zero 92: 92: Cleaning up constraints and constant bonded interactions with virtual sites 92: 92: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 92: 92: Calculated rlist for 1x1 atom pair-list as 0.715 nm, buffer size 0.015 nm 92: 92: Set rlist, assuming 4x4 atom pair-list, to 0.712 nm, buffer size 0.012 nm 92: 92: Note that mdrun will redetermine rlist based on the actual pair-list setup 92: 92: This run will generate roughly 0 Mb of data 92: 92: Writing final coordinates. 92: 92: NOTE: 40 % of the run time was spent communicating energies, 92: you might want to increase some nst* mdp options 92: 92: Core t (s) Wall t (s) (%) 92: Time: 0.047 0.024 196.2 92: (ns/day) (hour/ns) 92: Performance: 32.269 0.744 92: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_16.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 92: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_16.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 92: 92: Reading virtual site types... 92: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/16 (165 ms) 92: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/17 92: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/17 (0 ms) 92: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/18 92: 92: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_18_input.mdp]: 92: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 92: that with the Verlet scheme, nstlist has no effect on the accuracy of 92: your simulation. 92: 92: 92: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_18_input.mdp]: 92: Setting nstcalcenergy (100) equal to nstenergy (4) 92: 92: Number of degrees of freedom in T-Coupling group System is 45.00 92: 92: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_18_input.mdp]: 92: There are 6 non-linear virtual site constructions. Their contribution to 92: the energy error is approximated. In most cases this does not affect the 92: error significantly. 92: 92: 92: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_18_input.mdp]: 92: You are using a plain Coulomb cut-off, which might produce artifacts. 92: You might want to consider using PME electrostatics. 92: 92: 92: 92: There were 4 NOTEs 92: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_18.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 92: Changing nstlist from 8 to 50, rlist from 0.712 to 0.801 92: 92: Update groups can not be used for this system because an incompatible virtual site type is used 92: 92: Using 2 MPI threads 92: Using 1 OpenMP thread per tMPI thread 92: 92: 92: NOTE: The number of threads is not equal to the number of (logical) cpus 92: and the -pin option is set to auto: will not pin threads to cpus. 92: This can lead to significant performance degradation. 92: Consider using -pin on (and -pinoffset in case you run multiple jobs). 92: starting mdrun 'Virtual sites test system in vacuo' 92: 8 steps, 0.0 ps. 92: Generated 3 of the 6 non-bonded parameter combinations 92: 92: Excluding 3 bonded neighbours molecule type 'VSTEST' 92: 92: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/vsite_test.gro', all velocities are zero 92: 92: Cleaning up constraints and constant bonded interactions with virtual sites 92: 92: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 92: 92: Calculated rlist for 1x1 atom pair-list as 0.715 nm, buffer size 0.015 nm 92: 92: Set rlist, assuming 4x4 atom pair-list, to 0.712 nm, buffer size 0.012 nm 92: 92: Note that mdrun will redetermine rlist based on the actual pair-list setup 92: 92: This run will generate roughly 0 Mb of data 92: 92: Writing final coordinates. 92: 92: NOTE: 41 % of the run time was spent communicating energies, 92: you might want to increase some nst* mdp options 92: 92: Core t (s) Wall t (s) (%) 92: Time: 0.039 0.020 193.5 92: (ns/day) (hour/ns) 92: Performance: 38.338 0.626 92: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_18.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 92: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_18.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 92: 92: Reading virtual site types... 92: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/18 (153 ms) 92: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/19 92: 92: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_19_input.mdp]: 92: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 92: that with the Verlet scheme, nstlist has no effect on the accuracy of 92: your simulation. 92: 92: 92: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_19_input.mdp]: 92: Setting nstcalcenergy (100) equal to nstenergy (4) 92: 92: Number of degrees of freedom in T-Coupling group System is 45.00 92: 92: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_19_input.mdp]: 92: There are 6 non-linear virtual site constructions. Their contribution to 92: the energy error is approximated. In most cases this does not affect the 92: error significantly. 92: 92: 92: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_19_input.mdp]: 92: You are using a plain Coulomb cut-off, which might produce artifacts. 92: You might want to consider using PME electrostatics. 92: 92: 92: 92: There were 4 NOTEs 92: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_19.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 92: Changing nstlist from 8 to 50, rlist from 0.712 to 0.801 92: 92: Update groups can not be used for this system because an incompatible virtual site type is used 92: 92: Using 2 MPI threads 92: Using 1 OpenMP thread per tMPI thread 92: 92: 92: NOTE: The number of threads is not equal to the number of (logical) cpus 92: and the -pin option is set to auto: will not pin threads to cpus. 92: This can lead to significant performance degradation. 92: Consider using -pin on (and -pinoffset in case you run multiple jobs). 92: starting mdrun 'Virtual sites test system in vacuo' 92: 8 steps, 0.0 ps. 92: Generated 3 of the 6 non-bonded parameter combinations 92: 92: Excluding 3 bonded neighbours molecule type 'VSTEST' 92: 92: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/vsite_test.gro', all velocities are zero 92: 92: Cleaning up constraints and constant bonded interactions with virtual sites 92: 92: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 92: 92: Calculated rlist for 1x1 atom pair-list as 0.715 nm, buffer size 0.015 nm 92: 92: Set rlist, assuming 4x4 atom pair-list, to 0.712 nm, buffer size 0.012 nm 92: 92: Note that mdrun will redetermine rlist based on the actual pair-list setup 92: 92: This run will generate roughly 0 Mb of data 92: 92: Writing final coordinates. 92: 92: NOTE: 42 % of the run time was spent communicating energies, 92: you might want to increase some nst* mdp options 92: 92: Core t (s) Wall t (s) (%) 92: Time: 0.048 0.025 196.9 92: (ns/day) (hour/ns) 92: Performance: 31.641 0.759 92: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_19.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 92: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_19.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 92: 92: Reading virtual site types... 92: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/19 (162 ms) 92: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/20 92: 92: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_20_input.mdp]: 92: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 92: that with the Verlet scheme, nstlist has no effect on the accuracy of 92: your simulation. 92: 92: 92: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_20_input.mdp]: 92: Setting nstcalcenergy (100) equal to nstenergy (4) 92: 92: Number of degrees of freedom in T-Coupling group System is 45.00 92: 92: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_20_input.mdp]: 92: There are 6 non-linear virtual site constructions. Their contribution to 92: the energy error is approximated. In most cases this does not affect the 92: error significantly. 92: 92: 92: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_20_input.mdp]: 92: You are using a plain Coulomb cut-off, which might produce artifacts. 92: You might want to consider using PME electrostatics. 92: 92: 92: 92: There were 4 NOTEs 92: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_20.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 92: Changing nstlist from 8 to 50, rlist from 0.712 to 0.801 92: 92: Update groups can not be used for this system because an incompatible virtual site type is used 92: 92: Using 2 MPI threads 92: Using 1 OpenMP thread per tMPI thread 92: 92: 92: NOTE: The number of threads is not equal to the number of (logical) cpus 92: and the -pin option is set to auto: will not pin threads to cpus. 92: This can lead to significant performance degradation. 92: Consider using -pin on (and -pinoffset in case you run multiple jobs). 92: starting mdrun 'Virtual sites test system in vacuo' 92: 8 steps, 0.0 ps. 92: Generated 3 of the 6 non-bonded parameter combinations 92: 92: Excluding 3 bonded neighbours molecule type 'VSTEST' 92: 92: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/vsite_test.gro', all velocities are zero 92: 92: Cleaning up constraints and constant bonded interactions with virtual sites 92: 92: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 92: 92: Calculated rlist for 1x1 atom pair-list as 0.715 nm, buffer size 0.015 nm 92: 92: Set rlist, assuming 4x4 atom pair-list, to 0.712 nm, buffer size 0.012 nm 92: 92: Note that mdrun will redetermine rlist based on the actual pair-list setup 92: 92: This run will generate roughly 0 Mb of data 92: 92: Writing final coordinates. 92: 92: NOTE: 41 % of the run time was spent communicating energies, 92: you might want to increase some nst* mdp options 92: 92: Core t (s) Wall t (s) (%) 92: Time: 0.044 0.022 196.4 92: (ns/day) (hour/ns) 92: Performance: 34.912 0.687 92: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_20.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 92: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_20.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 92: 92: Reading virtual site types... 92: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/20 (185 ms) 92: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/21 92: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/21 (0 ms) 92: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/22 92: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/22 (0 ms) 92: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/23 92: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/23 (0 ms) 92: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/24 92: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/24 (0 ms) 92: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/25 92: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/25 (0 ms) 92: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/26 92: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/26 (0 ms) 92: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/27 92: 92: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_27_input.mdp]: 92: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 92: that with the Verlet scheme, nstlist has no effect on the accuracy of 92: your simulation. 92: 92: 92: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_27_input.mdp]: 92: Setting nstcalcenergy (100) equal to nstenergy (4) 92: 92: Number of degrees of freedom in T-Coupling group System is 45.00 92: 92: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_27_input.mdp]: 92: There are 6 non-linear virtual site constructions. Their contribution to 92: the energy error is approximated. In most cases this does not affect the 92: error significantly. 92: 92: 92: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_27_input.mdp]: 92: You are using a plain Coulomb cut-off, which might produce artifacts. 92: You might want to consider using PME electrostatics. 92: 92: 92: 92: There were 4 NOTEs 92: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_27.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 92: Changing nstlist from 8 to 100, rlist from 0.728 to 0.805 92: 92: Update groups can not be used for this system because an incompatible virtual site type is used 92: 92: Using 2 MPI threads 92: Using 1 OpenMP thread per tMPI thread 92: 92: 92: NOTE: The number of threads is not equal to the number of (logical) cpus 92: and the -pin option is set to auto: will not pin threads to cpus. 92: This can lead to significant performance degradation. 92: Consider using -pin on (and -pinoffset in case you run multiple jobs). 92: starting mdrun 'Virtual sites test system in vacuo' 92: 8 steps, 0.0 ps. 92: Generated 3 of the 6 non-bonded parameter combinations 92: 92: Excluding 3 bonded neighbours molecule type 'VSTEST' 92: 92: Cleaning up constraints and constant bonded interactions with virtual sites 92: 92: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 92: 92: Calculated rlist for 1x1 atom pair-list as 0.732 nm, buffer size 0.032 nm 92: 92: Set rlist, assuming 4x4 atom pair-list, to 0.728 nm, buffer size 0.028 nm 92: 92: Note that mdrun will redetermine rlist based on the actual pair-list setup 92: 92: This run will generate roughly 0 Mb of data 92: 92: Writing final coordinates. 92: 92: NOTE: 43 % of the run time was spent communicating energies, 92: you might want to increase some nst* mdp options 92: 92: Core t (s) Wall t (s) (%) 92: Time: 0.047 0.024 197.0 92: (ns/day) (hour/ns) 92: Performance: 32.890 0.730 92: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_27.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 92: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_27.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 92: 92: Reading virtual site types... 92: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/27 (220 ms) 92: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/28 92: 92: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_28_input.mdp]: 92: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 92: that with the Verlet scheme, nstlist has no effect on the accuracy of 92: your simulation. 92: 92: 92: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_28_input.mdp]: 92: Setting nstcalcenergy (100) equal to nstenergy (4) 92: 92: Number of degrees of freedom in T-Coupling group System is 45.00 92: 92: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_28_input.mdp]: 92: There are 6 non-linear virtual site constructions. Their contribution to 92: the energy error is approximated. In most cases this does not affect the 92: error significantly. 92: 92: 92: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_28_input.mdp]: 92: You are using a plain Coulomb cut-off, which might produce artifacts. 92: You might want to consider using PME electrostatics. 92: 92: 92: 92: There were 4 NOTEs 92: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_28.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 92: Changing nstlist from 8 to 100, rlist from 0.728 to 0.805 92: 92: Update groups can not be used for this system because an incompatible virtual site type is used 92: 92: Using 2 MPI threads 92: Using 1 OpenMP thread per tMPI thread 92: 92: 92: NOTE: The number of threads is not equal to the number of (logical) cpus 92: and the -pin option is set to auto: will not pin threads to cpus. 92: This can lead to significant performance degradation. 92: Consider using -pin on (and -pinoffset in case you run multiple jobs). 92: starting mdrun 'Virtual sites test system in vacuo' 92: 8 steps, 0.0 ps. 92: Generated 3 of the 6 non-bonded parameter combinations 92: 92: Excluding 3 bonded neighbours molecule type 'VSTEST' 92: 92: Cleaning up constraints and constant bonded interactions with virtual sites 92: 92: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 92: 92: Calculated rlist for 1x1 atom pair-list as 0.732 nm, buffer size 0.032 nm 92: 92: Set rlist, assuming 4x4 atom pair-list, to 0.728 nm, buffer size 0.028 nm 92: 92: Note that mdrun will redetermine rlist based on the actual pair-list setup 92: 92: This run will generate roughly 0 Mb of data 92: 92: Writing final coordinates. 92: 92: NOTE: 42 % of the run time was spent communicating energies, 92: you might want to increase some nst* mdp options 92: 92: Core t (s) Wall t (s) (%) 92: Time: 0.047 0.024 196.5 92: (ns/day) (hour/ns) 92: Performance: 32.200 0.745 92: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_28.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 92: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_28.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 92: 92: Reading virtual site types... 92: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/28 (224 ms) 92: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/29 92: 92: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_29_input.mdp]: 92: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 92: that with the Verlet scheme, nstlist has no effect on the accuracy of 92: your simulation. 92: 92: 92: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_29_input.mdp]: 92: Setting nstcalcenergy (100) equal to nstenergy (4) 92: 92: Number of degrees of freedom in T-Coupling group System is 45.00 92: 92: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_29_input.mdp]: 92: There are 6 non-linear virtual site constructions. Their contribution to 92: the energy error is approximated. In most cases this does not affect the 92: error significantly. 92: 92: 92: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_29_input.mdp]: 92: You are using a plain Coulomb cut-off, which might produce artifacts. 92: You might want to consider using PME electrostatics. 92: 92: 92: 92: There were 4 NOTEs 92: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_29.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 92: Changing nstlist from 8 to 100, rlist from 0.728 to 0.805 92: 92: Update groups can not be used for this system because an incompatible virtual site type is used 92: 92: Using 2 MPI threads 92: Using 1 OpenMP thread per tMPI thread 92: 92: 92: NOTE: The number of threads is not equal to the number of (logical) cpus 92: and the -pin option is set to auto: will not pin threads to cpus. 92: This can lead to significant performance degradation. 92: Consider using -pin on (and -pinoffset in case you run multiple jobs). 92: starting mdrun 'Virtual sites test system in vacuo' 92: 8 steps, 0.0 ps. 92: Generated 3 of the 6 non-bonded parameter combinations 92: 92: Excluding 3 bonded neighbours molecule type 'VSTEST' 92: 92: Cleaning up constraints and constant bonded interactions with virtual sites 92: 92: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 92: 92: Calculated rlist for 1x1 atom pair-list as 0.732 nm, buffer size 0.032 nm 92: 92: Set rlist, assuming 4x4 atom pair-list, to 0.728 nm, buffer size 0.028 nm 92: 92: Note that mdrun will redetermine rlist based on the actual pair-list setup 92: 92: This run will generate roughly 0 Mb of data 92: 92: Writing final coordinates. 92: 92: NOTE: 50 % of the run time was spent communicating energies, 92: you might want to increase some nst* mdp options 92: 92: Core t (s) Wall t (s) (%) 92: Time: 0.057 0.029 197.0 92: (ns/day) (hour/ns) 92: Performance: 26.842 0.894 92: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_29.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 92: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_29.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 92: 92: Reading virtual site types... 92: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/29 (231 ms) 92: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/30 92: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/30 (0 ms) 92: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/31 92: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/31 (0 ms) 92: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/32 92: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/32 (0 ms) 92: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/33 92: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/33 (0 ms) 92: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/34 92: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/34 (0 ms) 92: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/35 92: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/35 (0 ms) 92: [----------] 36 tests from VelocitiesConformToExpectations/VirtualSiteTest (3431 ms total) 92: 92: [----------] Global test environment tear-down 92: [==========] 37 tests from 2 test suites ran. (3481 ms total) 92: [ PASSED ] 37 tests. 92/92 Test #92: MdrunVirtualSiteTests ..................... Passed 3.57 sec 100% tests passed, 0 tests failed out of 92 Label Time Summary: GTest = 3169.34 sec*proc (90 tests) IntegrationTest = 1519.83 sec*proc (29 tests) MpiTest = 2185.37 sec*proc (21 tests) QuickGpuTest = 427.45 sec*proc (23 tests) SlowGpuTest = 2514.21 sec*proc (14 tests) SlowTest = 1620.24 sec*proc (14 tests) UnitTest = 29.27 sec*proc (47 tests) Total Test time (real) = 1784.37 sec touch build-basic dh_testdir LD_LIBRARY_PATH=/build/reproducible-path/gromacs-2025.1/build/mpi/lib /usr/bin/make -j4 -C build/mpi make[1]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/mpi' /usr/bin/cmake -P /build/reproducible-path/gromacs-2025.1/build/mpi/CMakeFiles/VerifyGlobs.cmake /usr/bin/cmake -S/build/reproducible-path/gromacs-2025.1 -B/build/reproducible-path/gromacs-2025.1/build/mpi --check-build-system CMakeFiles/Makefile.cmake 0 /usr/bin/cmake -E cmake_progress_start /build/reproducible-path/gromacs-2025.1/build/mpi/CMakeFiles /build/reproducible-path/gromacs-2025.1/build/mpi//CMakeFiles/progress.marks /usr/bin/make -f CMakeFiles/Makefile2 all make[2]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/mpi' /usr/bin/make -f src/gromacs/selection/CMakeFiles/scanner.dir/build.make src/gromacs/selection/CMakeFiles/scanner.dir/depend /usr/bin/make -f CMakeFiles/release-version-info.dir/build.make CMakeFiles/release-version-info.dir/depend /usr/bin/make -f src/external/rpc_xdr/CMakeFiles/internal_rpc_xdr.dir/build.make src/external/rpc_xdr/CMakeFiles/internal_rpc_xdr.dir/depend make[3]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/mpi' cd /build/reproducible-path/gromacs-2025.1/build/mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.1 /build/reproducible-path/gromacs-2025.1 /build/reproducible-path/gromacs-2025.1/build/mpi /build/reproducible-path/gromacs-2025.1/build/mpi /build/reproducible-path/gromacs-2025.1/build/mpi/CMakeFiles/release-version-info.dir/DependInfo.cmake "--color=" make[3]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/mpi' cd /build/reproducible-path/gromacs-2025.1/build/mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.1 /build/reproducible-path/gromacs-2025.1/src/gromacs/selection /build/reproducible-path/gromacs-2025.1/build/mpi /build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs/selection /build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs/selection/CMakeFiles/scanner.dir/DependInfo.cmake "--color=" /usr/bin/make -f src/gromacs/CMakeFiles/thread_mpi.dir/build.make src/gromacs/CMakeFiles/thread_mpi.dir/depend make[3]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/mpi' cd /build/reproducible-path/gromacs-2025.1/build/mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.1 /build/reproducible-path/gromacs-2025.1/src/external/rpc_xdr /build/reproducible-path/gromacs-2025.1/build/mpi /build/reproducible-path/gromacs-2025.1/build/mpi/src/external/rpc_xdr /build/reproducible-path/gromacs-2025.1/build/mpi/src/external/rpc_xdr/CMakeFiles/internal_rpc_xdr.dir/DependInfo.cmake "--color=" make[3]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/mpi' cd /build/reproducible-path/gromacs-2025.1/build/mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.1 /build/reproducible-path/gromacs-2025.1/src/gromacs /build/reproducible-path/gromacs-2025.1/build/mpi /build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs /build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs/CMakeFiles/thread_mpi.dir/DependInfo.cmake "--color=" make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/mpi' /usr/bin/make -f src/gromacs/selection/CMakeFiles/scanner.dir/build.make src/gromacs/selection/CMakeFiles/scanner.dir/build make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/mpi' /usr/bin/make -f src/gromacs/CMakeFiles/thread_mpi.dir/build.make src/gromacs/CMakeFiles/thread_mpi.dir/build make[3]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/mpi' cd /build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs/selection && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/mpi/src/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -Wno-null-conversion -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -MD -MT src/gromacs/selection/CMakeFiles/scanner.dir/parser.cpp.o -MF CMakeFiles/scanner.dir/parser.cpp.o.d -o CMakeFiles/scanner.dir/parser.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/selection/parser.cpp make[3]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/mpi' cd /build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/mpi/src/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -MD -MT src/gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/errhandler.cpp.o -MF CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/errhandler.cpp.o.d -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/errhandler.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/src/errhandler.cpp make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/mpi' /usr/bin/make -f src/external/rpc_xdr/CMakeFiles/internal_rpc_xdr.dir/build.make src/external/rpc_xdr/CMakeFiles/internal_rpc_xdr.dir/build make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/mpi' /usr/bin/make -f CMakeFiles/release-version-info.dir/build.make CMakeFiles/release-version-info.dir/build make[3]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/mpi' cd /build/reproducible-path/gromacs-2025.1/build/mpi/src/external/rpc_xdr && /usr/bin/mpicxx -DGMX_DOUBLE=0 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -MD -MT src/external/rpc_xdr/CMakeFiles/internal_rpc_xdr.dir/xdr.cpp.o -MF CMakeFiles/internal_rpc_xdr.dir/xdr.cpp.o.d -o CMakeFiles/internal_rpc_xdr.dir/xdr.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/external/rpc_xdr/xdr.cpp make[3]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/mpi' cd /build/reproducible-path/gromacs-2025.1 && /usr/bin/cmake -D PYTHON_EXECUTABLE=/usr/bin/python3 -D PROJECT_VERSION=2025.1-Debian_2025.1_1 -D PROJECT_SOURCE_DIR=/build/reproducible-path/gromacs-2025.1 -D VERSION_CMAKEIN=/build/reproducible-path/gromacs-2025.1/build/mpi/VersionInfo-partial.cmake.cmakein -D VERSION_OUT=/build/reproducible-path/gromacs-2025.1/build/mpi/VersionInfo.cmake -D VERSION_STRING_OF_FORK=Debian-2025.1-1 -P /build/reproducible-path/gromacs-2025.1/cmake/gmxGenerateVersionInfoWithoutGit.cmake make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/mpi' [ 0%] Built target release-version-info /usr/bin/make -f src/gromacs/CMakeFiles/tng_io_obj.dir/build.make src/gromacs/CMakeFiles/tng_io_obj.dir/depend make[3]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/mpi' cd /build/reproducible-path/gromacs-2025.1/build/mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.1 /build/reproducible-path/gromacs-2025.1/src/gromacs /build/reproducible-path/gromacs-2025.1/build/mpi /build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs /build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs/CMakeFiles/tng_io_obj.dir/DependInfo.cmake "--color=" make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/mpi' /usr/bin/make -f src/gromacs/CMakeFiles/tng_io_obj.dir/build.make src/gromacs/CMakeFiles/tng_io_obj.dir/build make[3]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/mpi' cd /build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs && /usr/bin/mpicc -DGMX_DOUBLE=0 -I/build/reproducible-path/gromacs-2025.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.1/build/mpi/tng/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -MD -MT src/gromacs/CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/bwlzh.c.o -MF 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-I/build/reproducible-path/gromacs-2025.1/build/mpi/src/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -MD -MT src/gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/atomic.cpp.o -MF CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/atomic.cpp.o.d -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/atomic.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/src/atomic.cpp cd /build/reproducible-path/gromacs-2025.1/build/mpi/src/external/rpc_xdr && /usr/bin/mpicxx -DGMX_DOUBLE=0 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG 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CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/lock.cpp.o.d -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/lock.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/src/lock.cpp cd /build/reproducible-path/gromacs-2025.1/build/mpi/src/external/rpc_xdr && /usr/bin/mpicxx -DGMX_DOUBLE=0 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -MD -MT src/external/rpc_xdr/CMakeFiles/internal_rpc_xdr.dir/xdr_stdio.cpp.o -MF CMakeFiles/internal_rpc_xdr.dir/xdr_stdio.cpp.o.d -o CMakeFiles/internal_rpc_xdr.dir/xdr_stdio.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/external/rpc_xdr/xdr_stdio.cpp cd /build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/mpi/src/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -MD -MT src/gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/pthreads.cpp.o -MF CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/pthreads.cpp.o.d -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/pthreads.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/src/pthreads.cpp make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/mpi' [ 0%] Built target internal_rpc_xdr /usr/bin/make -f src/gromacs/CMakeFiles/lmfit_objlib.dir/build.make src/gromacs/CMakeFiles/lmfit_objlib.dir/depend make[3]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/mpi' cd /build/reproducible-path/gromacs-2025.1/build/mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.1 /build/reproducible-path/gromacs-2025.1/src/gromacs /build/reproducible-path/gromacs-2025.1/build/mpi /build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs /build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs/CMakeFiles/lmfit_objlib.dir/DependInfo.cmake "--color=" make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/mpi' /usr/bin/make -f src/gromacs/CMakeFiles/lmfit_objlib.dir/build.make src/gromacs/CMakeFiles/lmfit_objlib.dir/build make[3]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/mpi' cd /build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -MD -MT src/gromacs/CMakeFiles/lmfit_objlib.dir/__/external/lmfit/lmmin.cpp.o -MF CMakeFiles/lmfit_objlib.dir/__/external/lmfit/lmmin.cpp.o.d -o CMakeFiles/lmfit_objlib.dir/__/external/lmfit/lmmin.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/external/lmfit/lmmin.cpp make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/mpi' [ 0%] Built target thread_mpi /usr/bin/make -f src/gromacs/CMakeFiles/colvars_objlib.dir/build.make src/gromacs/CMakeFiles/colvars_objlib.dir/depend make[3]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/mpi' cd /build/reproducible-path/gromacs-2025.1/build/mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.1 /build/reproducible-path/gromacs-2025.1/src/gromacs /build/reproducible-path/gromacs-2025.1/build/mpi /build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs /build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs/CMakeFiles/colvars_objlib.dir/DependInfo.cmake "--color=" make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/mpi' /usr/bin/make -f src/gromacs/CMakeFiles/colvars_objlib.dir/build.make src/gromacs/CMakeFiles/colvars_objlib.dir/build make[3]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/mpi' cd /build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fopenmp -MD -MT src/gromacs/CMakeFiles/colvars_objlib.dir/__/external/colvars/colvar.cpp.o -MF CMakeFiles/colvars_objlib.dir/__/external/colvars/colvar.cpp.o.d -o CMakeFiles/colvars_objlib.dir/__/external/colvars/colvar.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/external/colvars/colvar.cpp cd /build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs && /usr/bin/mpicc -DGMX_DOUBLE=0 -I/build/reproducible-path/gromacs-2025.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.1/build/mpi/tng/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -MD -MT src/gromacs/CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/bwt.c.o -MF CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/bwt.c.o.d -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/bwt.c.o -c /build/reproducible-path/gromacs-2025.1/src/external/tng_io/src/compression/bwt.c cd /build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs && /usr/bin/mpicc -DGMX_DOUBLE=0 -I/build/reproducible-path/gromacs-2025.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.1/build/mpi/tng/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -MD -MT src/gromacs/CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/coder.c.o -MF CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/coder.c.o.d -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/coder.c.o -c /build/reproducible-path/gromacs-2025.1/src/external/tng_io/src/compression/coder.c cd /build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs && /usr/bin/mpicc -DGMX_DOUBLE=0 -I/build/reproducible-path/gromacs-2025.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.1/build/mpi/tng/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -MD -MT src/gromacs/CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/dict.c.o -MF CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/dict.c.o.d -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/dict.c.o -c /build/reproducible-path/gromacs-2025.1/src/external/tng_io/src/compression/dict.c cd /build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs && /usr/bin/mpicc -DGMX_DOUBLE=0 -I/build/reproducible-path/gromacs-2025.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.1/build/mpi/tng/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -MD -MT src/gromacs/CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/fixpoint.c.o -MF CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/fixpoint.c.o.d -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/fixpoint.c.o -c /build/reproducible-path/gromacs-2025.1/src/external/tng_io/src/compression/fixpoint.c cd /build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs && /usr/bin/mpicc -DGMX_DOUBLE=0 -I/build/reproducible-path/gromacs-2025.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.1/build/mpi/tng/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -MD -MT src/gromacs/CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/huffman.c.o -MF CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/huffman.c.o.d -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/huffman.c.o -c /build/reproducible-path/gromacs-2025.1/src/external/tng_io/src/compression/huffman.c make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/mpi' [ 0%] Built target lmfit_objlib /usr/bin/make -f src/gromacs/linearalgebra/CMakeFiles/linearalgebra.dir/build.make src/gromacs/linearalgebra/CMakeFiles/linearalgebra.dir/depend make[3]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/mpi' cd /build/reproducible-path/gromacs-2025.1/build/mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.1 /build/reproducible-path/gromacs-2025.1/src/gromacs/linearalgebra /build/reproducible-path/gromacs-2025.1/build/mpi 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-I/build/reproducible-path/gromacs-2025.1/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -MD -MT src/gromacs/linearalgebra/CMakeFiles/linearalgebra.dir/eigensolver.cpp.o -MF CMakeFiles/linearalgebra.dir/eigensolver.cpp.o.d -o CMakeFiles/linearalgebra.dir/eigensolver.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/linearalgebra/eigensolver.cpp cd /build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs && /usr/bin/mpicc -DGMX_DOUBLE=0 -I/build/reproducible-path/gromacs-2025.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.1/build/mpi/tng/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -MD -MT src/gromacs/CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/huffmem.c.o -MF CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/huffmem.c.o.d -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/huffmem.c.o -c /build/reproducible-path/gromacs-2025.1/src/external/tng_io/src/compression/huffmem.c cd /build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs && /usr/bin/mpicc -DGMX_DOUBLE=0 -I/build/reproducible-path/gromacs-2025.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.1/build/mpi/tng/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -MD -MT src/gromacs/CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/lz77.c.o -MF CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/lz77.c.o.d -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/lz77.c.o -c /build/reproducible-path/gromacs-2025.1/src/external/tng_io/src/compression/lz77.c cd /build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs && /usr/bin/mpicc -DGMX_DOUBLE=0 -I/build/reproducible-path/gromacs-2025.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.1/build/mpi/tng/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -MD -MT src/gromacs/CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/merge_sort.c.o -MF CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/merge_sort.c.o.d -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/merge_sort.c.o -c /build/reproducible-path/gromacs-2025.1/src/external/tng_io/src/compression/merge_sort.c cd /build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs/linearalgebra && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/reproducible-path/gromacs-2025.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/linearalgebra -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -MD -MT src/gromacs/linearalgebra/CMakeFiles/linearalgebra.dir/gmx_arpack.cpp.o -MF CMakeFiles/linearalgebra.dir/gmx_arpack.cpp.o.d -o CMakeFiles/linearalgebra.dir/gmx_arpack.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/linearalgebra/gmx_arpack.cpp cd /build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs && /usr/bin/mpicc -DGMX_DOUBLE=0 -I/build/reproducible-path/gromacs-2025.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.1/build/mpi/tng/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -MD -MT src/gromacs/CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/mtf.c.o -MF CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/mtf.c.o.d -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/mtf.c.o -c /build/reproducible-path/gromacs-2025.1/src/external/tng_io/src/compression/mtf.c cd /build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs && /usr/bin/mpicc -DGMX_DOUBLE=0 -I/build/reproducible-path/gromacs-2025.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.1/build/mpi/tng/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -MD -MT src/gromacs/CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/rle.c.o -MF CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/rle.c.o.d -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/rle.c.o -c /build/reproducible-path/gromacs-2025.1/src/external/tng_io/src/compression/rle.c cd /build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs && /usr/bin/mpicc -DGMX_DOUBLE=0 -I/build/reproducible-path/gromacs-2025.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.1/build/mpi/tng/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -Wformat -Werror=format-security 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-Wno-missing-field-initializers -MD -MT src/gromacs/CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/vals16.c.o -MF CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/vals16.c.o.d -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/vals16.c.o -c /build/reproducible-path/gromacs-2025.1/src/external/tng_io/src/compression/vals16.c cd /build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs && /usr/bin/mpicc -DGMX_DOUBLE=0 -I/build/reproducible-path/gromacs-2025.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.1/build/mpi/tng/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -MD -MT src/gromacs/CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/warnmalloc.c.o -MF 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CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/widemuldiv.c.o -c /build/reproducible-path/gromacs-2025.1/src/external/tng_io/src/compression/widemuldiv.c cd /build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs && /usr/bin/mpicc -DGMX_DOUBLE=0 -I/build/reproducible-path/gromacs-2025.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.1/build/mpi/tng/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -MD -MT src/gromacs/CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/xtc2.c.o -MF CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/xtc2.c.o.d -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/xtc2.c.o -c /build/reproducible-path/gromacs-2025.1/src/external/tng_io/src/compression/xtc2.c cd /build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs/linearalgebra && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/reproducible-path/gromacs-2025.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/linearalgebra -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -MD -MT src/gromacs/linearalgebra/CMakeFiles/linearalgebra.dir/matrix.cpp.o -MF CMakeFiles/linearalgebra.dir/matrix.cpp.o.d -o CMakeFiles/linearalgebra.dir/matrix.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/linearalgebra/matrix.cpp cd /build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs/linearalgebra && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/reproducible-path/gromacs-2025.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/linearalgebra -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -MD -MT src/gromacs/linearalgebra/CMakeFiles/linearalgebra.dir/sparsematrix.cpp.o -MF CMakeFiles/linearalgebra.dir/sparsematrix.cpp.o.d -o CMakeFiles/linearalgebra.dir/sparsematrix.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/linearalgebra/sparsematrix.cpp make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/mpi' cd /build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs/selection && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/mpi/src/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -Wno-null-conversion -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -MD -MT src/gromacs/selection/CMakeFiles/scanner.dir/scanner.cpp.o -MF CMakeFiles/scanner.dir/scanner.cpp.o.d -o CMakeFiles/scanner.dir/scanner.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/selection/scanner.cpp [ 0%] Built target linearalgebra /usr/bin/make -f src/gromacs/options/CMakeFiles/options.dir/build.make src/gromacs/options/CMakeFiles/options.dir/depend make[3]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/mpi' cd /build/reproducible-path/gromacs-2025.1/build/mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.1 /build/reproducible-path/gromacs-2025.1/src/gromacs/options /build/reproducible-path/gromacs-2025.1/build/mpi /build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs/options /build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs/options/CMakeFiles/options.dir/DependInfo.cmake "--color=" make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/mpi' /usr/bin/make -f src/gromacs/options/CMakeFiles/options.dir/build.make src/gromacs/options/CMakeFiles/options.dir/build make[3]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/mpi' cd /build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs/options && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/mpi/src/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -MD -MT src/gromacs/options/CMakeFiles/options.dir/abstractoption.cpp.o -MF CMakeFiles/options.dir/abstractoption.cpp.o.d -o CMakeFiles/options.dir/abstractoption.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/options/abstractoption.cpp cd /build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs && /usr/bin/mpicc -DGMX_DOUBLE=0 -I/build/reproducible-path/gromacs-2025.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.1/build/mpi/tng/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -MD -MT src/gromacs/CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/xtc3.c.o -MF CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/xtc3.c.o.d -o 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/build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs/options && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/mpi/src/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -MD -MT src/gromacs/options/CMakeFiles/options.dir/abstractsection.cpp.o -MF CMakeFiles/options.dir/abstractsection.cpp.o.d -o CMakeFiles/options.dir/abstractsection.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/options/abstractsection.cpp cd /build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs/options && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/mpi/src/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -MD -MT src/gromacs/options/CMakeFiles/options.dir/basicoptions.cpp.o -MF CMakeFiles/options.dir/basicoptions.cpp.o.d -o CMakeFiles/options.dir/basicoptions.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/options/basicoptions.cpp cd /build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs && /usr/bin/mpicc -DGMX_DOUBLE=0 -DUSE_STD_INTTYPES_H -I/build/reproducible-path/gromacs-2025.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.1/build/mpi/tng/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -MD -MT src/gromacs/CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/lib/tng_io.c.o -MF CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/lib/tng_io.c.o.d -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/lib/tng_io.c.o -c /build/reproducible-path/gromacs-2025.1/src/external/tng_io/src/lib/tng_io.c cd /build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fopenmp -MD -MT src/gromacs/CMakeFiles/colvars_objlib.dir/__/external/colvars/colvaratoms.cpp.o -MF CMakeFiles/colvars_objlib.dir/__/external/colvars/colvaratoms.cpp.o.d -o CMakeFiles/colvars_objlib.dir/__/external/colvars/colvaratoms.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/external/colvars/colvaratoms.cpp cd /build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fopenmp -MD -MT src/gromacs/CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarbias.cpp.o -MF CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarbias.cpp.o.d -o CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarbias.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/external/colvars/colvarbias.cpp cd /build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fopenmp -MD -MT src/gromacs/CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarbias_abf.cpp.o -MF CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarbias_abf.cpp.o.d -o CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarbias_abf.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/external/colvars/colvarbias_abf.cpp cd /build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fopenmp -MD -MT src/gromacs/CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarbias_abmd.cpp.o -MF CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarbias_abmd.cpp.o.d -o CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarbias_abmd.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/external/colvars/colvarbias_abmd.cpp cd /build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs && /usr/bin/mpicc -DGMX_DOUBLE=0 -I/build/reproducible-path/gromacs-2025.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.1/build/mpi/tng/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -MD -MT src/gromacs/CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/lib/md5.c.o -MF CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/lib/md5.c.o.d -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/lib/md5.c.o -c /build/reproducible-path/gromacs-2025.1/src/external/tng_io/src/lib/md5.c make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/mpi' [ 3%] Built target tng_io_obj /usr/bin/make -f src/gromacs/pulling/CMakeFiles/pulling.dir/build.make src/gromacs/pulling/CMakeFiles/pulling.dir/depend make[3]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/mpi' cd /build/reproducible-path/gromacs-2025.1/build/mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.1 /build/reproducible-path/gromacs-2025.1/src/gromacs/pulling /build/reproducible-path/gromacs-2025.1/build/mpi /build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs/pulling /build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs/pulling/CMakeFiles/pulling.dir/DependInfo.cmake "--color=" make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/mpi' /usr/bin/make -f src/gromacs/pulling/CMakeFiles/pulling.dir/build.make src/gromacs/pulling/CMakeFiles/pulling.dir/build make[3]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/mpi' cd /build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs/pulling && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -fopenmp -MD -MT src/gromacs/pulling/CMakeFiles/pulling.dir/output.cpp.o -MF CMakeFiles/pulling.dir/output.cpp.o.d -o CMakeFiles/pulling.dir/output.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/pulling/output.cpp cd /build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs/options && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/mpi/src/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -MD -MT src/gromacs/options/CMakeFiles/options.dir/behaviorcollection.cpp.o -MF CMakeFiles/options.dir/behaviorcollection.cpp.o.d -o CMakeFiles/options.dir/behaviorcollection.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/options/behaviorcollection.cpp cd /build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fopenmp -MD -MT src/gromacs/CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarbias_alb.cpp.o -MF CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarbias_alb.cpp.o.d -o CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarbias_alb.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/external/colvars/colvarbias_alb.cpp cd /build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs/options && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/mpi/src/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -MD -MT src/gromacs/options/CMakeFiles/options.dir/filenameoption.cpp.o -MF CMakeFiles/options.dir/filenameoption.cpp.o.d -o CMakeFiles/options.dir/filenameoption.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/options/filenameoption.cpp cd /build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs/pulling && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -fopenmp -MD -MT src/gromacs/pulling/CMakeFiles/pulling.dir/pull.cpp.o -MF CMakeFiles/pulling.dir/pull.cpp.o.d -o CMakeFiles/pulling.dir/pull.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/pulling/pull.cpp cd /build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs/pulling && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -fopenmp -MD -MT src/gromacs/pulling/CMakeFiles/pulling.dir/pull_rotation.cpp.o -MF CMakeFiles/pulling.dir/pull_rotation.cpp.o.d -o CMakeFiles/pulling.dir/pull_rotation.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/pulling/pull_rotation.cpp cd /build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs/options && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/mpi/src/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -MD -MT src/gromacs/options/CMakeFiles/options.dir/filenameoptionmanager.cpp.o -MF CMakeFiles/options.dir/filenameoptionmanager.cpp.o.d -o CMakeFiles/options.dir/filenameoptionmanager.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/options/filenameoptionmanager.cpp cd /build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs/options && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/mpi/src/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -MD -MT src/gromacs/options/CMakeFiles/options.dir/options.cpp.o -MF CMakeFiles/options.dir/options.cpp.o.d -o CMakeFiles/options.dir/options.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/options/options.cpp cd /build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs/options && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/mpi/src/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -MD -MT src/gromacs/options/CMakeFiles/options.dir/optionsassigner.cpp.o -MF CMakeFiles/options.dir/optionsassigner.cpp.o.d -o CMakeFiles/options.dir/optionsassigner.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/options/optionsassigner.cpp cd /build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs/pulling && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include 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-I/build/reproducible-path/gromacs-2025.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -fopenmp -MD -MT src/gromacs/pulling/CMakeFiles/pulling.dir/transformationcoordinate.cpp.o -MF CMakeFiles/pulling.dir/transformationcoordinate.cpp.o.d -o CMakeFiles/pulling.dir/transformationcoordinate.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/pulling/transformationcoordinate.cpp cd /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY 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'/build/reproducible-path/gromacs-2025.1/build/mpi' /usr/bin/make -f src/programs/CMakeFiles/gmx_objlib.dir/build.make src/programs/CMakeFiles/gmx_objlib.dir/build make[3]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/mpi' cd /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -MD -MT src/programs/CMakeFiles/gmx_objlib.dir/gmx.cpp.o -MF CMakeFiles/gmx_objlib.dir/gmx.cpp.o.d -o CMakeFiles/gmx_objlib.dir/gmx.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/programs/gmx.cpp make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/mpi' [ 6%] Built target options /usr/bin/make -f src/gromacs/taskassignment/CMakeFiles/taskassignment.dir/build.make src/gromacs/taskassignment/CMakeFiles/taskassignment.dir/depend make[3]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/mpi' cd /build/reproducible-path/gromacs-2025.1/build/mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.1 /build/reproducible-path/gromacs-2025.1/src/gromacs/taskassignment /build/reproducible-path/gromacs-2025.1/build/mpi /build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs/taskassignment /build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs/taskassignment/CMakeFiles/taskassignment.dir/DependInfo.cmake "--color=" make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/mpi' /usr/bin/make -f src/gromacs/taskassignment/CMakeFiles/taskassignment.dir/build.make src/gromacs/taskassignment/CMakeFiles/taskassignment.dir/build make[3]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/mpi' cd /build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs/taskassignment && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/reproducible-path/gromacs-2025.1/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/mpi/api/legacy/include 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-I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -MD -MT src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/andersentemperaturecoupling.cpp.o -MF CMakeFiles/modularsimulator.dir/andersentemperaturecoupling.cpp.o.d -o CMakeFiles/modularsimulator.dir/andersentemperaturecoupling.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/modularsimulator/andersentemperaturecoupling.cpp cd /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -MD -MT src/programs/CMakeFiles/gmx_objlib.dir/legacymodules.cpp.o -MF CMakeFiles/gmx_objlib.dir/legacymodules.cpp.o.d -o CMakeFiles/gmx_objlib.dir/legacymodules.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/programs/legacymodules.cpp make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/mpi' [ 9%] Built target gmx_objlib cd /build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fopenmp -MD -MT src/gromacs/CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarbias_opes.cpp.o -MF CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarbias_opes.cpp.o.d -o CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarbias_opes.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/external/colvars/colvarbias_opes.cpp cd 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-fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -MD -MT src/gromacs/taskassignment/CMakeFiles/taskassignment.dir/decidesimulationworkload.cpp.o -MF CMakeFiles/taskassignment.dir/decidesimulationworkload.cpp.o.d -o CMakeFiles/taskassignment.dir/decidesimulationworkload.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/taskassignment/decidesimulationworkload.cpp cd /build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs/modularsimulator && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -I/build/reproducible-path/gromacs-2025.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.1/build/mpi/tng/include 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-D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -MD -MT src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/checkpointhelper.cpp.o -MF CMakeFiles/modularsimulator.dir/checkpointhelper.cpp.o.d -o CMakeFiles/modularsimulator.dir/checkpointhelper.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/modularsimulator/checkpointhelper.cpp cd /build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs/taskassignment && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/reproducible-path/gromacs-2025.1/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -MD -MT src/gromacs/taskassignment/CMakeFiles/taskassignment.dir/findallgputasks.cpp.o -MF CMakeFiles/taskassignment.dir/findallgputasks.cpp.o.d -o CMakeFiles/taskassignment.dir/findallgputasks.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/taskassignment/findallgputasks.cpp cd /build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs/taskassignment && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/reproducible-path/gromacs-2025.1/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -MD -MT src/gromacs/taskassignment/CMakeFiles/taskassignment.dir/reportgpuusage.cpp.o -MF CMakeFiles/taskassignment.dir/reportgpuusage.cpp.o.d -o CMakeFiles/taskassignment.dir/reportgpuusage.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/taskassignment/reportgpuusage.cpp cd /build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs/taskassignment && /usr/bin/mpicxx -DGMX_DOUBLE=0 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-I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -MD -MT src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/velocityscalingtemperaturecoupling.cpp.o -MF CMakeFiles/modularsimulator.dir/velocityscalingtemperaturecoupling.cpp.o.d -o CMakeFiles/modularsimulator.dir/velocityscalingtemperaturecoupling.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/modularsimulator/velocityscalingtemperaturecoupling.cpp cd /build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fopenmp -MD -MT src/gromacs/CMakeFiles/colvars_objlib.dir/__/external/colvars/colvargrid.cpp.o -MF CMakeFiles/colvars_objlib.dir/__/external/colvars/colvargrid.cpp.o.d -o CMakeFiles/colvars_objlib.dir/__/external/colvars/colvargrid.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/external/colvars/colvargrid.cpp cd /build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fopenmp -MD -MT src/gromacs/CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarmodule.cpp.o -MF CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarmodule.cpp.o.d -o CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarmodule.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/external/colvars/colvarmodule.cpp cd /build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fopenmp -MD -MT src/gromacs/CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarparams.cpp.o -MF CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarparams.cpp.o.d -o CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarparams.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/external/colvars/colvarparams.cpp cd /build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fopenmp -MD -MT src/gromacs/CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarparse.cpp.o -MF CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarparse.cpp.o.d -o CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarparse.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/external/colvars/colvarparse.cpp make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/mpi' [ 12%] Built target modularsimulator cd /build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fopenmp -MD -MT src/gromacs/CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarproxy.cpp.o -MF CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarproxy.cpp.o.d -o CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarproxy.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/external/colvars/colvarproxy.cpp cd /build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fopenmp -MD -MT src/gromacs/CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarproxy_io.cpp.o -MF CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarproxy_io.cpp.o.d -o CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarproxy_io.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/external/colvars/colvarproxy_io.cpp cd /build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fopenmp -MD -MT src/gromacs/CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarproxy_replicas.cpp.o -MF CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarproxy_replicas.cpp.o.d -o CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarproxy_replicas.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/external/colvars/colvarproxy_replicas.cpp cd /build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fopenmp -MD -MT src/gromacs/CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarproxy_system.cpp.o -MF CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarproxy_system.cpp.o.d -o CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarproxy_system.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/external/colvars/colvarproxy_system.cpp cd /build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fopenmp -MD -MT src/gromacs/CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarproxy_tcl.cpp.o -MF CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarproxy_tcl.cpp.o.d -o CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarproxy_tcl.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/external/colvars/colvarproxy_tcl.cpp cd /build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fopenmp -MD -MT src/gromacs/CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarproxy_volmaps.cpp.o -MF CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarproxy_volmaps.cpp.o.d -o CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarproxy_volmaps.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/external/colvars/colvarproxy_volmaps.cpp cd /build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fopenmp -MD -MT src/gromacs/CMakeFiles/colvars_objlib.dir/__/external/colvars/colvars_memstream.cpp.o -MF CMakeFiles/colvars_objlib.dir/__/external/colvars/colvars_memstream.cpp.o.d -o CMakeFiles/colvars_objlib.dir/__/external/colvars/colvars_memstream.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/external/colvars/colvars_memstream.cpp cd /build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fopenmp -MD -MT src/gromacs/CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarscript.cpp.o -MF CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarscript.cpp.o.d -o CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarscript.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/external/colvars/colvarscript.cpp cd /build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fopenmp -MD -MT src/gromacs/CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarscript_commands.cpp.o -MF CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarscript_commands.cpp.o.d -o CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarscript_commands.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/external/colvars/colvarscript_commands.cpp cd /build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fopenmp -MD -MT src/gromacs/CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarscript_commands_bias.cpp.o -MF CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarscript_commands_bias.cpp.o.d -o CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarscript_commands_bias.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/external/colvars/colvarscript_commands_bias.cpp cd /build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fopenmp -MD -MT src/gromacs/CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarscript_commands_colvar.cpp.o -MF CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarscript_commands_colvar.cpp.o.d -o CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarscript_commands_colvar.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/external/colvars/colvarscript_commands_colvar.cpp cd /build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fopenmp -MD -MT src/gromacs/CMakeFiles/colvars_objlib.dir/__/external/colvars/colvartypes.cpp.o -MF CMakeFiles/colvars_objlib.dir/__/external/colvars/colvartypes.cpp.o.d -o CMakeFiles/colvars_objlib.dir/__/external/colvars/colvartypes.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/external/colvars/colvartypes.cpp cd /build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fopenmp -MD -MT src/gromacs/CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarvalue.cpp.o -MF CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarvalue.cpp.o.d -o CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarvalue.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/external/colvars/colvarvalue.cpp cd /build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fopenmp -MD -MT src/gromacs/CMakeFiles/colvars_objlib.dir/__/external/colvars/nr_jacobi.cpp.o -MF CMakeFiles/colvars_objlib.dir/__/external/colvars/nr_jacobi.cpp.o.d -o CMakeFiles/colvars_objlib.dir/__/external/colvars/nr_jacobi.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/external/colvars/nr_jacobi.cpp make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/mpi' [ 17%] Built target colvars_objlib /usr/bin/make -f src/gromacs/CMakeFiles/libgromacs.dir/build.make src/gromacs/CMakeFiles/libgromacs.dir/depend make[3]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/mpi' cd /build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs && /usr/bin/cmake -D VERSION_VARIABLES=/build/reproducible-path/gromacs-2025.1/build/mpi/VersionInfo.cmake -D VERSION_CMAKEIN=/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/baseversion-gen.cpp.cmakein -D VERSION_OUT=utility/baseversion-gen.cpp -D GMX_SOURCE_DOI= -D GMX_RELEASE_HASH= -D GMX_SOURCE_HASH= -P /build/reproducible-path/gromacs-2025.1/cmake/gmxConfigureVersionInfo.cmake cd /build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs && /usr/bin/cmake -E touch utility/baseversion-gen.cpp cd /build/reproducible-path/gromacs-2025.1/build/mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.1 /build/reproducible-path/gromacs-2025.1/src/gromacs /build/reproducible-path/gromacs-2025.1/build/mpi /build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs /build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs/CMakeFiles/libgromacs.dir/DependInfo.cmake "--color=" make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/mpi' /usr/bin/make -f src/gromacs/CMakeFiles/libgromacs.dir/build.make src/gromacs/CMakeFiles/libgromacs.dir/build make[3]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/mpi' cd 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src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombGeom_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombGeom_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombGeom_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombGeom_VgrpF.cpp cd /build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.1/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include 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-I/build/reproducible-path/gromacs-2025.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJEwCombGeom_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJEwCombGeom_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJEwCombGeom_F.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJEwCombGeom_F.cpp cd /build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.1/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJEwCombGeom_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJEwCombGeom_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJEwCombGeom_VF.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJEwCombGeom_VF.cpp cd /build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.1/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJEwCombGeom_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJEwCombGeom_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJEwCombGeom_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJEwCombGeom_VgrpF.cpp cd 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/build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJFSw_VF.cpp cd /build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.1/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include 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-I/build/reproducible-path/gromacs-2025.1/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.1/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJPSw_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJPSw_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJPSw_F.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJPSw_F.cpp cd /build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.1/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include 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-isystem /build/reproducible-path/gromacs-2025.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJPSw_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJPSw_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJPSw_VF.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJPSw_VF.cpp cd 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-I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJPSw_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJPSw_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJPSw_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJPSw_VgrpF.cpp cd /build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.1/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJ_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJ_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJ_F.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJ_F.cpp cd /build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.1/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include 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src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_VF.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_VF.cpp cd /build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.1/build/mpi/tng/include 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-I/build/reproducible-path/gromacs-2025.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJ_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJ_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJ_F.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJ_F.cpp cd /build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.1/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include 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-I/build/reproducible-path/gromacs-2025.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombGeom_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombGeom_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombGeom_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombGeom_VgrpF.cpp cd /build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.1/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include 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-I/build/reproducible-path/gromacs-2025.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.1/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJ_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJ_F.cpp.o.d -o 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-fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJ_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJ_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJ_VF.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJ_VF.cpp cd /build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.1/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJ_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJ_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJ_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJ_VgrpF.cpp cd /build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.1/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include 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-I/build/reproducible-path/gromacs-2025.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombLB_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombLB_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombLB_VF.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombLB_VF.cpp cd /build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.1/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.1/src/external/lmfit 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-I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.1/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJFSw_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJFSw_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJFSw_F.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJFSw_F.cpp cd /build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.1/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include 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-isystem /build/reproducible-path/gromacs-2025.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJFSw_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJFSw_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJFSw_VF.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJFSw_VF.cpp cd 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-I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJFSw_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJFSw_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJFSw_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJFSw_VgrpF.cpp cd /build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.1/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem 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/build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJPSw_F.cpp cd /build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.1/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time 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src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJFSw_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJFSw_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJFSw_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJFSw_VgrpF.cpp cd /build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.1/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include 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-I/build/reproducible-path/gromacs-2025.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.1/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem 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-fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombGeom_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombGeom_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombGeom_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombGeom_VgrpF.cpp cd /build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS 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src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombLB_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombLB_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombLB_F.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombLB_F.cpp cd /build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.1/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include 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/build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJEwCombGeom_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJEwCombGeom_F.cpp.o.d -o 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-I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJEwCombGeom_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJEwCombGeom_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJEwCombGeom_VF.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJEwCombGeom_VF.cpp cd /build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.1/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJEwCombGeom_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJEwCombGeom_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJEwCombGeom_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJEwCombGeom_VgrpF.cpp cd /build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.1/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJFSw_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJFSw_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJFSw_F.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJFSw_F.cpp cd 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-I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers 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-I/build/reproducible-path/gromacs-2025.1/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem 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-I/build/reproducible-path/gromacs-2025.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJPSw_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJPSw_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJPSw_F.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJPSw_F.cpp cd /build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.1/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJPSw_VF.cpp.o -MF 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-I/build/reproducible-path/gromacs-2025.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJPSw_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJPSw_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJPSw_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJPSw_VgrpF.cpp cd /build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.1/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJ_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJ_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJ_F.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJ_F.cpp cd /build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.1/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.1/src/external/lmfit 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-Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.1/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict 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-I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/gromacs/../external/rpc_xdr 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/build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombLB_F.cpp cd /build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.1/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombLB_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombLB_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombLB_VF.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombLB_VF.cpp cd /build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.1/src/include 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-I/build/reproducible-path/gromacs-2025.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombLB_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombLB_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombLB_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombLB_VgrpF.cpp cd /build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.1/build/mpi/tng/include 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-I/build/reproducible-path/gromacs-2025.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_VgrpF.cpp cd /build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.1/build/mpi/tng/include 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-D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJFSw_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJFSw_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJFSw_VF.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJFSw_VF.cpp cd /build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.1/src/include 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-I/build/reproducible-path/gromacs-2025.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJFSw_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJFSw_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJFSw_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJFSw_VgrpF.cpp cd /build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.1/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include 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-fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJ_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJ_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJ_F.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJ_F.cpp cd /build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.1/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJ_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJ_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJ_VF.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJ_VF.cpp cd /build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.1/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.1/src/external/lmfit 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-I/build/reproducible-path/gromacs-2025.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombLB_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombLB_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombLB_F.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombLB_F.cpp cd /build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.1/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include 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-I/build/reproducible-path/gromacs-2025.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJPSw_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJPSw_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJPSw_VF.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJPSw_VF.cpp cd /build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.1/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include 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-I/build/reproducible-path/gromacs-2025.1/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJ_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJ_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJ_VF.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJ_VF.cpp cd /build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.1/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJ_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJ_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJ_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJ_VgrpF.cpp cd /build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.1/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombGeom_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombGeom_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombGeom_F.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombGeom_F.cpp cd /build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.1/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombGeom_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombGeom_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombGeom_VF.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombGeom_VF.cpp cd 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-I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. 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-I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.1/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombLB_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombLB_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombLB_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombLB_VgrpF.cpp cd /build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.1/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include 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-I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.1/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJFSw_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJFSw_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJFSw_VF.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJFSw_VF.cpp cd /build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.1/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include 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-isystem /build/reproducible-path/gromacs-2025.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJFSw_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJFSw_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJFSw_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJFSw_VgrpF.cpp cd 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-I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJPSw_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJPSw_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJPSw_F.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJPSw_F.cpp cd /build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.1/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJPSw_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJPSw_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJPSw_VF.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJPSw_VF.cpp cd /build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.1/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJPSw_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJPSw_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJPSw_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJPSw_VgrpF.cpp cd /build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.1/src/include 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-I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/gromacs/../external/rpc_xdr 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